Doctorat De

Universite De L'

Marie Pierre

Epidémiologie Clinique

Blandine Denis

Directeur De

Dominique Mme

Costagliola

Mr Olivier

Lortholary Co-Directeur De Thèse

M David

W Denning

Rapporteur M Hansjakob

Furrer Rapporteur

M Willy

Rozenbaum Examinateur

Mechaï F, Revest M, Melica G, Costagliola D Guiguet M, De Castro N

Lortholary

M Guiguet

N De Castro

F Mechai

H Stitou

M Revest

G Gregoire

D Costagliola

O Lortholary

A Mahamat

THESE

Keywords: HIV, AIDS, fungal infections, Pneumocystis, Aspergillosis, incidence, outcome

The advent of combined antiretroviral therapy (cART) in 1996 resulted in a dramatic fall in the incidence of AIDS-defining illness (ADI), including Pneumocystis jirovecii pneumonia (PCP). Nevertheless, PCP was the second most frequent ADI in France in 2001-2003 and fungal infections remain a major threat for HIV-infected individuals worldwide. Epidemiological data on fungal infections in the late cART period in resource-rich settings are scarce. The purpose of our work was to study changes in the epidemiology of fungal infections among HIV-infected individuals in France in the late cART period, focusing on PCP and invasive aspergillosis (IA) in the French Hospital Database on HIV ANRS CO4 (FHDH). In the FHDH, during the 2004-2011 period, half of the 1259 PCP cases occurred among HIV-infected individuals who had waning adherence to care, and for those who had a prior ADI before PCP the 3-year mortality rate was 25%. For the second study on IA, a review committee validated IA cases among all the cases that included a diagnostic code for aspergillosis (ICD-9 or ICD-10) in the FHDH over a 20-year period. Our study demonstrated that only half of validated IA cases among HIV-infected individuals met EORTC criteria. The 3-months survival rate after IA diagnosis improved after the advent of cART and a protective role of voriconazole was observed in the period after 2001.

A ma famille, REMERCIEMENTS Je remercie, Ma directrice de thèse, Madame Dominique Costagliola, de m'avoir montré la voie de l'épidémiologie et donner l'opportunité de faire ces travaux de recherche dans son équipe.

Avec son savoir et sa rigueur scientifique, elle m'a permis d'acquérir de nouvelles compétences méthodologiques en épidémiologie et ses entretiens étaient toujours d'une grande richesse scientifique. Merci pour avoir pris le temps de suivre pas à pas l'avancement de cette thèse.

Mon co-directeur de thèse, Monsieur le Professeur Olivier Lortholary, pour sa bienveillance et la confiance qu'il me témoigne depuis toutes ses années. Tu m'as permis de découvrir le monde de la recherche grâce à un premier travail de Master puis par ce travail de thèse, tes conseils ont toujours été très précieux. Cela a toujours été un réél plaisir de travailler avec toi autant sur le plan clinique que de la recherche. Merci pour ton aide et ton écoute.

Madame Marguerite Guiguet, qui m'a suivi tout au long de cette thèse avec une grande patience et une grande pédagogie. Nos nombreux échanges m'ont été très précieux. Merci pour m'avoir tant appris, tes conseils et suggestions ont permis de mener à bien tous ces travaux.

Monsieur le

Résumé

Depuis la disponibilité des combinaisons antirétrovirales (cART) en 1996, l'incidence des infections opportunistes classantes SIDA (IO), dont la pneumocystose (PCP), a très fortement diminué. Malgré tout, chez les patients infectés par le VIH, la PCP était la 2 ème IO la plus fréquente en France en 2001-2003 et les infections fongiques, avec 1 million de nouveaux cas/an de cryptococcose, restent un problème de santé publique majeur au niveau mondial.

Cependant, depuis l'ère des cART, peu de recherches épidémiologiques sur les infections fongiques dans les pays industrialisés ont été entreprises. C'est dans ce contexte que nous avons mené une étude épidémiologique de 2 infections fongiques chez les patients infectés par le VIH en France sur la French Hospital Database on HIV ANRS CO4 (FHDH) : la pneumocystose et l'aspergillose invasive. Concernant la pneumocystose, sur la période 2004-2011, dans la base FHDH, la moitié des 1259 cas de PCP étaient survenus chez des patients qui avaient interrompus leur suivi, et, pour ceux qui avaient déjà eu une IO avant la PCP, leur mortalité était de 25% à 3 ans. Pour l'aspergillose invasive (AI), après un retour national aux dossiers des cas déclarés sur 20 ans sur la base FHDH, un comité d'experts a validé 242 cas d'AI. Les données montrent que, chez les patients infectés par le VIH, seulement la moitié des AI validées répondaient aux critères EORTC. La mortalité à 3 mois après une AI s'est améliorée après l'ère des cART et un rôle protecteur du voriconazole sur la survie à 3 mois a également été démontré pour la 1 ère fois chez les patients infectés par le VIH.

Résumé long

INFECTIONS FONGIQUES CHEZ LES PATIENTS INFECTES PAR LE VIH A L'ERE DES COMBINAISONS ANTIRETROVIRALES (cART) : ETUDE DES PNEUMOCYSTOSES ET ASPERGILLOSES INVASIVES SUR LA BASE FHDH

Les infections fongiques sont les plus fréquentes des infections opportunistes (IO) au cours de l'infection par le VIH même si leur incidence a beaucoup diminué depuis l'instauration des traitements antirétroviraux hautement actifs (cART) [START_REF] Palella | Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators[END_REF]. Elles s'observent le plus souvent chez des patients naïfs de traitement, en échec thérapeutique ou non observants et sont un bon marqueur de la sévérité du déficit immunitaire. Au début de l'épidémie du VIH, la pneumocystose pulmonaire (pneumocystose) représentait 2/3 des infections classantes SIDA (ADI) et il était estimé que 75% des patients infectés par le VIH développeraient une pneumocystose au cours de leur suivi (Hay JW JAIDS 1988, Morris A Emerg Inf Dis 2004). Même si son incidence a beaucoup diminué depuis la mise en route des prophylaxies préventives et l'accès aux cART, la pneumocystose reste l'une des infections opportunistes les plus fréquentes dans les pays industrialisés et sur la base FHDH elle était la 2 ème IO classante SIDA en [2001][2002][2003] [START_REF] Grabar | Causes of the first AIDS-defining illness and subsequent survival before and after the advent of combined antiretroviral therapy[END_REF]. Par ailleurs, la cryptococcose est un problème majeur à l'échelon mondial avec 1 million de nouveaux cas /an [START_REF] Park | Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS[END_REF], c'est la 1ère cause de méningite en Afrique du Sud et la 4ème cause de mortalité infectieuse dans le monde. Plus de 500000 décès par an en Afrique Subsaharienne en 2008 étaient liés aux cryptococcoses neuro-méningées. Malgré la fréquence et mortalité importantes des infections fongiques invasives, seulement 2-2.5% des budgets alloués par les fonds anglo-saxons aux maladies infectieuses sont destinés à la recherche sur les infections fongiques (Brown GD, Sci Transl Med 2012). Les recherches sur les infections fongiques sont insuffisantes dans les pays à ressources limitées mais également dans les pays industrialisés où peu d'études ont été publiées depuis 10 ans sur les infections fongiques chez les patients infectés par le VIH. C'est dans ce contexte que nous avons entrepris une étude épidémiologique de deux infections fongiques chez les patients infectés par le VIH en France sur la base FHDH : la pneumocystose et l'aspergillose invasive. Deux infections fongiques qui ont en commun de survenir chez des patients ayant un profond déficit immunitaire. La 1 ère est très fréquente mais il n'y avait pas de grande étude récente sur l'évolution des pneumocystoses chez les patients infectés par le VIH, la seconde portait sur l'aspergillose invasive, infection très rare mais de pronostic effroyable avant l'ère des cART avec une médiane de survie de 2-4 mois. Il n'y avait pas d'étude sur les aspergilloses invasives depuis l'accessibilité des cART. Nous voulions savoir quelle était l'évolution des aspergilloses invasives depuis 20 ans et si les critères EORTC, utilisés en onco-hématologie pour définir les aspergilloses invasives, étaient applicables à la population des patients infectés par le VIH présentant une aspergillose invasive.

La base FHDH collecte les données de patients infectés par le VIH depuis 1992, et regroupe actuellement des données de 70 hôpitaux français répartis sur 26 des 28 COREVIH (Coordination régionale de la lutte contre le VIH). Des données sur plus de 128000 patients entre 1992 et 2012 ont été recueillies et la cohorte FHDH-ANRS CO4 représente la plus grande cohorte prospective mondiale de suivi de patients infectés par le VIH. Par sa taille, la base FHDH offre la possibilité d'étudier un événement rare comme l'aspergillose invasive mais également d'avoir un bon reflet de l'épidémiologie récente des pneumocystoses en France.

Nous avons d'abord regardé sur la période 2004-2011 l'évolution de l'incidence des premières pneumocystoses déclarées sur la base FHDH, les caractéristiques des patients au diagnostic, l'évolution en terme de reconstitution immunitaire, contrôle virologique et mortalité à 3 ans après une pneumocystose. Comme sur la base FHDH 82% des patients suivis sont sous traitement antirétroviral depuis au moins 6 mois, notre première hypothèse était que la majorité des patients présentant une pneumocystose sur cette période seraient des patients diagnostiqués tardivement avec une pneumocystose inaugurale du VIH et non des patients déjà suivis sur la base FHDH.

De façon surprenante, parmi les 1259 cas de 1ères pneumocystoses durant la période 2004-2011, seulement 50% des cas avaient une pneumocystose inaugurale du VIH. L'autre moitié concernait des patients déjà suivis dans la base FHDH, avec une médiane de suivi de 8 ans par rapport à la date d'inclusion dans la base FHDH, 68% avaient déjà reçus au moins une année de cART avant le diagnostic de pneumocystose, avec dans 2/3 des cas, des CD4 > 350/mm 3 notés dans leur historique immunovirologique. Au moment du diagnostic de pneumocystose, la médiane des CD4 était de 38/mm 3 , la charge virale VIH à 5.2 log copies/ml tout comme les patients présentant une pneumocystose inaugurale du VIH (médiane des CD4 à 53/mm 3 , charge virale VIH à 5.1 log copies/ml).

Le fait que 50% des patients étaient déjà suivis dans la base FHDH et qu'ils avaient pour la majorité bénéficié de cART avec une immunité correcte avant le diagnostic de pneumocystose nous a amené à étudier l'observance chez les patients suivis dans la base FHDH. Nous avons décidé de prendre comme critère de suivi optimal d'avoir une mesure de CD4 au moins tous les 6 mois. La proportion de suivi optimal avant la pneumocystose a ainsi été estimée et comparée avec la proportion de suivi optimal chez tous les patients suivis dans la base FHDH. La médiane de proportion de suivi optimal était de 85% (IQR, 66-96) pour tous les patients suivis dans la base FHDH, alors qu'elle n'était que de 45% (IQR,1-81) dans les 2 ans précédant la pneumocystose pour les cas étudiés. Ainsi, pour certains patients, nous avons pu démontrer que l'observance diminuait au cours du temps avec le risque de développer une ADI lors de la reprise du suivi. Il nous semble donc important de travailler sur l'évolution comportementale des patients suivis pendant de nombreuses années pour une maladie chronique et de comprendre pourquoi certaines personnes sortent du suivi après de nombreuses années. La base FHDH ne recueille pas de données psychosociales permettant d'approfondir les facteurs de risques sociaux pouvant éventuellement participer à la rupture du suivi, mais nous pensons, tout comme d'autres auteurs [START_REF] Masur | Opportunistic Infections and Mortality: Still Room for Improvement[END_REF] (50.4% en 1992-1995, 48.1% en 1996-2001, et 54.4% en 2002-2011 (p=0.7)). La moitié des patients n'avait pas les critères -voriconazole (1992[START_REF] Wheat | Endemic mycoses in AIDS: a clinical review[END_REF]), post-cART et pré-voriconazole (1996-2001), et post-cART et post-voriconazole (2002-2011).

Nous avons confirmé que la médiane de survie après une aspergillose invasive aspergillosis s'est améliorée deuis l'accès des cART, passant de 1.9 mois (IQR, 0.9-3. En conclusion, nous avons démontré que les infections fongiques restaient un sujet majeur en 2016, même dans les pays industrialisés. Nous planifions maintenant de reprendre les cryptococcoses sur la base FHDH, ces infections fongiques ayant également la particularité de survenir chez des patients avec des CD4 très bas. La cryptococcose méningée est un problème de santé publique dans les pays à ressources limitées, avec une mortalité d'environ 50% dans les 2 1ères semaines dans ces pays. C'est une infection rare chez les patients suivis dans les pays industrialisés. Dans la base FHDH, l'incidence de la cryptococcose a été divisée par 10 depuis 1996, passant de (47.5 (42.5-52.5) /10 000 PA) en 1992-1995 à (4.5 (3.9-5.2) /10 000 PA) en2002-2011. Nous allons également étudier qui est à risque de nos jours, l'évolution de la mortalité au cours du temps, ainsi que le délai d'initiation entre le début du traitement de la cryptococcose.

Au-delà de nos résultats, ces etudes montrent que le screening VIH doit être améliorée, que nous devons améliorer le suivi à "très long terme" de certains patients et nous proposons qu'un suivi adequat tous les 6 mois fasse partie des indicateurs de qualité du suivi chez les patients infectés par le VIH. [START_REF] Hay | Projecting the medical costs of AIDS and ARC in the United States[END_REF][START_REF] Morris | Current epidemiology of Pneumocystis pneumonia[END_REF]. After the advent of cART, many studies showed a dramatic fall in the incidence of AIDS-defining clinical illness (ADI) and also an improvement in survival [START_REF] Palella | Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators[END_REF]. Nevertheless, PCP remains one of the most common AIDS-defining illnesses in resource-rich settings and was the second most frequent ADI in France in 2001-2003[START_REF] Grabar | Causes of the first AIDS-defining illness and subsequent survival before and after the advent of combined antiretroviral therapy[END_REF][START_REF] Kaplan | Epidemiology of human immunodeficiency virusassociated opportunistic infections in the United States in the era of highly active antiretroviral therapy[END_REF][START_REF] Morris | Current epidemiology of Pneumocystis pneumonia[END_REF].

Glossary

Fungal infections remain a major threat for HIV-infected individuals worldwide.

Approximately one million cases of cryptococcal meningitis occur globally every year, with over 500 000 related deaths in sub-Saharan Africa in 2008 [START_REF] Park | Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS[END_REF]. It has been estimated that HIV/AIDS results in nearly 10 million cases of oral thrush and 2 million cases of esophageal fungal infections annually (Brown et al., 2012a(Brown et al., , 2012b). Probably about oneand-a-half million people die from fungal infections every year, as many as from tuberculosis or malaria. Despite the high global burden of invasive mycoses, only 2-2.5% of the infectious-disease research budgets of major funders in the UK and USA are targeted at human fungal infections (Brown et al., 2012a). A meeting on AIDS-related mycoses in 2013 in Cape Town, South Africa [START_REF] Brown | Working Group from the EMBO-AIDS Related Mycoses Workshop[END_REF], fixed several urgent priorities in order to reduce morbidity and mortality due to fungal infections.

Research on fungal infections in resource-limited settings are lacking, and epidemiological data on fungal infections in the late cART period in resource-rich settings are also scarce. In this context, we examined changes in the epidemiology of fungal infections among HIVinfected individuals in France in the late cART period, focusing on PCP and invasive aspergillosis. In this era of powerful cART regimens, PCP should no longer be observed if HIV-infected individuals are diagnosed early and remain in care. We thus analyzed trends in the incidence of PCP in the French Hospital Database on HIV (ANRS CO4) from 2004 to 2011. Studies published before the cART era showed that invasive aspergillosis (IA) was rare, difficult to diagnose, occurred in patients with very low CD4 cell counts, and carried a very poor prognosis. No research has been undertaken in the late cART period, yet the situation has changed with the availability of cART and its impact on immune restoration, but also with population aging and the increase in cancer, as chemotherapy-induced neutropenia is a classical predisposing factor for IA. We retrieved all medical charts in the French Hospital Database on HIV (ANRS CO4) that included a diagnostic code for aspergillosis (ICD-9 or ICD-10). After a review committee had validated IA cases, we analyzed the incidence, diagnostic circumstances, risk factors, and trends in IA among HIV-infected individuals. Angeles were found to have biopsy-confirmed Pneumocystis jirovecii pneumonia as well as confirmed CMV disease or virus shedding within 5 months of the diagnosis of Pneumocystis pneumonia and candida mucosal infections (Centers for Disease Control (CDC), 1981a). This report in the MMWR alerted the medical and public health communities 4 months before the first peer-reviewed article was published [START_REF] Hymes | Kaposi's sarcoma in homosexual men-a report of eight cases[END_REF]. Scientists in the Parasitic Diseases division of CDC's Center for Infectious Diseases were already concerned with an increase in requests for pentamidine isethionate to treat unusual cases of PCP in New York.

One month later, a new MMWR report included 26 cases of Kaposi's sarcoma in young male homosexuals, 20 in New York and 6 in San Francisco, 7 of whom also had PCP, CMV or other opportunistic infections (OI) (Centers for Disease Control (CDC), 1981b). In July 1981, another 10 cases of PCP (without Kaposi's sarcoma) were identified. The CDC then formed a task force on Kaposi's sarcoma and opportunistic infections. Results from active surveillance in the United States rapidly established that the syndrome was new, and showed that the number of cases was increasing rapidly ("Epidemiologic aspects of the current outbreak of Kaposi's sarcoma and opportunistic infections," 1982). In England, the first case of PCP and acquired cellular immunodepression was reported in 1981 in a MSM with PCP who had been to the USA (du [START_REF] Bois | Primary Pneumocystis carinii and cytomegalovirus infections[END_REF]. In France, the first reported case was that of a MSM who was admitted to hospital in 1981 with PCP [START_REF] Rozenbaum | Multiple opportunistic infection in a male homosexual in France[END_REF]. The name "acquired immunodeficiency syndrome" (AIDS) was first used in 1982. By the end of 1982, the case distribution strongly suggested that AIDS was caused by an agent transmitted through sexual contact between men (Centers for Disease Control (CDC), 1982a;[START_REF] Jaffe | National case-control study of Kaposi's sarcoma and Pneumocystis carinii pneumonia in homosexual men: Part 1. Epidemiologic results[END_REF] and between men and women (Centers for Disease Control (CDC), 1983a;[START_REF] Harris | Immunodeficiency in female sexual partners of men with the acquired immunodeficiency syndrome[END_REF], and also through blood exposure among injecting-drug users and recipients of blood or blood products (Centers for Disease Control (CDC), 1982b, 1982c, 1982d). Cases were also identified among infants born to women with AIDS or at risk of AIDS (Centers for Disease Control (CDC), 1982e), and persistent unexplained lymphadenopathy emerged as a frequent feature (Centers for Disease Control (CDC), 1982f). To prevent transmission of AIDS, in 1983 the USA Public Health Service used epidemiological information about the condition to recommend that sexual contact be avoided with persons known or suspected to have AIDS, and that persons at increased risk for AIDS refrain from donating plasma or blood (Centers for Disease Control (CDC), 1983b, 1982d). Work was intensified toward developing safer blood products for persons with hemophilia. These recommendations were developed and published only 21 months after the first cases had been reported and before the first published report by F Barre-Sinoussi and Luc Montagnier's team identifying the causative retrovirus [START_REF] Barré-Sinoussi | Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS)[END_REF]. By 1984, the National Heart, Lung, and Blood Institute (NHLBI) had analyzed the types and frequencies of pulmonary diseases in 441 patients with AIDS and found that 373 (85%) had PCP (27). In 1986, the French and Americans agreed to call this retrovirus HIV. By the end of 1986, 38 401 cases of AIDS had been identified by WHO: 31 741 in the USA, 3858 in Europe, 2323 in Africa, 395 in Oceania, and 395 in Asia. In humans, epidemic forms of interstitial plasma cell pneumonitis were described in the 1940s, and a relationship with Pneumocystis was suggested by Van der Meer and Brug in 1942. In 1951and 1952, Vanek and Jirovec reported the association between pneumocystis and interstitial pneumonitis among premature and malnourished children. In the 1950s and 1960s, Pneumocystis spp was described as an opportunistic pathogen among children with acute leukemia or congenital immunodeficiencies that impaired T-cell function.

P. carinii was first thought to be a protozoan, but in 1988 Edman and Stringer showed that ribosomal RNA sequences of P. carinii were related to fungal RNAs and this was confirmed by phylogenetic analyses. The 18S rRNA sequences from human-derived Pneumocystis and rat-derived Pneumocystis differed by 5%. At the 2001 International Workshop on Opportunistic Protists in Cincinnati, the name Pneumocystis jirovecii was chosen for the form that infects humans and Pneumocystis carinii for 1 of the 2 forms infecting rats.

Remark: For this study, we have decided to keep the acronym "PCP" for Pneumocystis jirovecii pneumonia, as it is still used in most publications. However, PjP should be used in future.

Pneumocystis species are classified within the phylum Ascomycota. They are atypical fungal microorganisms unable to grow in vitro in fungal culture media. They respond to antiparasitic agents (cotrimoxazole, pentamidine), and their cell wall contains cholesterol rather than ergosterol. There are 2 predominant life cycle forms, the trophic form and the cyst form. In an infected host, Pneumocystis exists almost exclusively within the alveoli of the lung. Alveolar macrophages are the primary resident phagocytes that mediate the clearance of Pneumocystis Radiological presentation: on chest radiography, PCP usually manifests as bilateral diffuse reticular opacities. Chest radiography may be normal at diagnosis in more than 1/3 of cases.

Computed tomography (CT) shows ground-glass opacities with a patchy distribution, predominating in perihilar regions. Multiple and bilateral cysts are observed in 10 to 34% of cases.

Microbial diagnosis: As Pneumocystis cannot be cultured, the diagnosis continues to rely on microscopic demonstration of Pneumocystis in BAL fluid or induced sputum. Trophic forms can be stained with Papanicolaou, Giemsa or Gram-Weigert. Cysts can be stained with Gomori-methenamine silver, toluidine blue O or Calcofluor white. Fluorescein-labeled monoclonal anti-Pneumocystis antibodies are commercially available and can be used to detect both trophic forms and cysts; they now represent the gold standard method for detection. Quantitative PCR is broadly used but the cut-off between Pneumocystis carriage and PCP still needs to be determined. Serum (1-3) β D glucan is an adjunctive noninvasive marker of PCP with good negative predictive value. If clinical signs are compatible with a PCP, having a serum (1-3) β D glucan above 500 pg/ml makes PCP diagnosis highly probable. However, the number of false positives is high and this reagent cannot be used to monitor the response to therapy. The detection of serum (1-3) β D glucan and P. jirovecii DNA could be usefully combined as serum markers for the diagnosis of PCP in patients with severe diseases or other conditions precluding the BAL procedure [START_REF] Costa | Association between circulating DNA, serum (1->3)-β-D-glucan, and pulmonary fungal burden in Pneumocystis pneumonia[END_REF].

Treatment: Trimethoprim-sulfamethoxazole (TMP-SMX) is the first-line agent of choice.

Parenteral pentamidine is the most extensively studied alternative but is very poorly tolerated.

No clinical trials have compared atovaquone, clindamycin-primaquine or dapsone-TMP with TMP-SMX for the treatment of moderate to severe PCP. For patients with mild to moderate PCP, clindamycin-primaquine and dapsone-TMP exhibit comparable efficacy and toxicity to TMP-SMX, while atovaquone is less effective but better tolerated than TMP-SMX, and as effective as pentamidine.

Corticoid administration starting within the first 72 h after diagnosis improves survival among

HIV-infected patients whose arterial oxygen pressure is ≤ 70 mm Hg.

iii) PCP: epidemiological changes

During the early years of the AIDS pandemic, PCP accounted for 2/3 of AIDS-defining illnesses in patients in the USA, and an estimated 75% of HIV-infected individuals developed PCP during their lifetime [START_REF] Hay | Projecting the medical costs of AIDS and ARC in the United States[END_REF][START_REF] Morris | Current epidemiology of Pneumocystis pneumonia[END_REF]. Rates of PCP were as high as 20/100 PY among those with CD4 <200/mm 3 . The first decline in the incidence of PCP occurred after the introduction of anti-Pneumocystis prophylaxis in 1989 [START_REF] Jones | Surveillance for AIDS-defining opportunistic illnesses, 1992-1997[END_REF].

The advent of cART resulted in further declines in PCP and other opportunistic infections (figure 1). Many studies showed a dramatic fall in the incidence of AIDS-defining clinical illness (ADI) and improved survival [START_REF] Palella | Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators[END_REF]. In Europe, the Euro SIDA study [START_REF] Mocroft | AIDS across Europe, 1994-98: the EuroSIDA study[END_REF][START_REF] Weverling | Discontinuation of Pneumocystis carinii pneumonia prophylaxis after start of highly active antiretroviral therapy in HIV-1 infection. EuroSIDA Study Group[END_REF] showed a reduction in the incidence of PCP from 4.9 cases/100 PY before March 1995 to 0.3 cases/100 PY after March 1998. Yet PCP remains one of the most common AIDS-defining illnesses in resource-rich settings and was the second most frequent ADI in France in 2001-2003[START_REF] Grabar | Causes of the first AIDS-defining illness and subsequent survival before and after the advent of combined antiretroviral therapy[END_REF][START_REF] Kaplan | Epidemiology of human immunodeficiency virusassociated opportunistic infections in the United States in the era of highly active antiretroviral therapy[END_REF][START_REF] Morris | Current epidemiology of Pneumocystis pneumonia[END_REF]. One large prospective study showed that PCP survival at 3 years rose from 51% in the pre-cART era to 87% in 2001-2003 [START_REF] Grabar | Causes of the first AIDS-defining illness and subsequent survival before and after the advent of combined antiretroviral therapy[END_REF]. Another study in France showed that PCP was the second invasive fungal disease, and while PCP's incidence decreased in HIV infected individuals, PCP's incidence increased in HIVseronegative patients between 2001 and 2010 [START_REF] Bitar | Population-based analysis of invasive fungal infections, France, 2001-2010[END_REF]. CMV, cytomegalovirus; HAART, highly active antiretroviral therapy; KS, Kaposi's sarcoma; MAC, Mycobacterium avium complex; PCP, Pneumocystis pneumonia. Data are standardized to the population of AIDS cases reported nationally in the same year by age, sex, race, HIV exposure mode, country of origin, and CD4+ lymphocyte count.

b) Other fungal infections in HIV-infected individuals

This section is inspired by the chapter Fungal infections in patients with AIDS of the Oxford Textbook of Infectious Disease and Microbiology: Medical Mycology (B. Denis, F. Lanternier, O.Lortholary), to be published soon.

Invasive fungal infections (IFIs) are a major cause of HIV-related mortality globally. Despite widespread rollout of combined antiretroviral therapy, there are still up to 1 million deaths annually from IFIs, accounting for 50% of all AIDS-related deaths. Fungal infections are the most frequent opportunistic diseases occurring during the course of HIV infection. Untreated individuals living with HIV have an immune deficit that worsens with time, allowing mycotic diseases to develop [START_REF] Cunliffe | Uncommon invasive mycoses in AIDS[END_REF][START_REF] Perfect | Uncommon invasive fungal pathogens in the acquired immunodeficiency syndrome[END_REF][START_REF] Spellberg | Type 1/Type 2 immunity in infectious diseases[END_REF]. Pneumocystis jiroveci, Candida albicans and Cryptococcus neoformans are the three major fungal pathogens in patients with AIDS [START_REF] Catherinot | Pneumocystis jirovecii Pneumonia[END_REF][START_REF] Mitchell | Cryptococcosis in the era of AIDS--100 years after the discovery of Cryptococcus neoformans[END_REF]. In endemic areas, infections due to dimorphic fungi also represent an important group.

Histoplasma capsulatum, Coccidioides species and Penicillium marneffei are the most important endemic pathogens. In some AIDS patients, mycotic disease is the consequence of reactivation several years after a primary infection [START_REF] Wheat | Endemic mycoses in AIDS: a clinical review[END_REF]. Some fungal infections, such as oropharyngeal candidiasis, are relatively benign, but others such as cryptococcal meningitis and invasive aspergillosis are usually severe and carry a poor prognosis.

i) Cryptococcosis

C. neoformans var. grubii (serotype A) is responsible for most cases of cryptococcosis in AIDS patients. It will be referred to as C. neoformans in this section.

Epidemiology

While the incidence of cryptococcosis has declined dramatically among HIV-infected patients in resource-rich settings since the availability of cART [START_REF] Dromer | Epidemiology of HIV-associated cryptococcosis in France (1985-2001): comparison of the pre-and post-HAART eras[END_REF], cryptococcosis is an increasing concern in Africa and Southeast Asia. It is encountered in up to 15-20% of hospitalized AIDS patients in sub-Saharan Africa [START_REF] Jarvis | Managing cryptococcosis in the immunocompromised host[END_REF][START_REF] Micol | Prevalence, determinants of positivity, and clinical utility of cryptococcal antigenemia in Cambodian HIV-infected patients[END_REF].

Many countries in Africa and Asia have limited access to antifungal agents, and mortality rates ≥ 50% within the first 15 days have been observed in low-resource countries (Loyse et al., 2013a(Loyse et al., , 2013b)). In France, mortality remains at about 17% [START_REF] Dromer | Determinants of disease presentation and outcome during cryptococcosis: the CryptoA/D study[END_REF].

Pathogenesis

Quantitative and/or qualitative CD4 T cell deficiency is a major risk factor for cryptococcosis, and HIV infection is the most prevalent underlying disease. The median CD4 cell count at diagnosis is 20/µL [START_REF] Dromer | Determinants of disease presentation and outcome during cryptococcosis: the CryptoA/D study[END_REF]. The portal of entry is mainly pulmonary and the interaction of cryptococci with alveolar macrophages determines pulmonary infection and subsequent systemic dissemination.

Clinical manifestations

Meningoencephalitis is the most frequent clinical form of cryptococcosis in HIV-infected patients. Neurological symptoms are most often subacute. Fever and headache are common, while meningeal symptoms are not inconsistent. Cerebral imaging is abnormal in 50% of cases and MRI is more sensitive than computed tomography (CT) [START_REF] Charlier | Cryptococcal neuroradiological lesions correlate with severity during cryptococcal meningoencephalitis in HIV-positive patients in the HAART era[END_REF].

Measurement of CSF opening pressure is mandatory, as the prognosis is tightly associated with the degree of intracranial hypertension.

Pneumonia can be associated with cough and dyspnea and, less commonly, with chest pain and hemoptysis. The acute respiratory distress syndrome is associated with poor outcome.

Standard chest radiographs and CT show interstitial infiltrates, nodules, pleural effusion, mediastinal lymphadenopathy, and/or cavitary lesions. Disseminated cryptococcosis should be suspected in febrile HIV-infected patients who present with skin lesions. Urinary tract involvement is common in men but is usually asymptomatic. The prostate can serve as a sanctuary for C. neoformans.

Diagnosis

Analysis of CSF with India ink shows encapsulated yeasts in more than 80% of HIV-infected patients with cryptococcosis. Samples should be incubated for at least 4 weeks at 35-37°C, and sensitivity increases with the volume of CSF. Blood and urine culture should be done systematically.

Cryptococcal antigen (CrAg) should be sought in serum and CSF. Commercially available tests are sensitive (≥ 95%) and specific (≥ 95%). A high serum CrAg titer is associated with a higher mycological failure rate, but a lack of decrease is not predictive of worse outcome.

New CrAg detection methods such as CRAG Lateral Flow assays (LFA), particularly the kit developed by Immy, are easy to use and have improved the diagnosis of cryptococcal meningitis in Africa [START_REF] Binnicker | Comparison of four assays for the detection of cryptococcal antigen[END_REF]Boulware et al., 2014b;[START_REF] Kabanda | Point-of-care diagnosis and prognostication of cryptococcal meningitis with the cryptococcal antigen lateral flow assay on cerebrospinal fluid[END_REF]. A recent study showed that baseline CSF CrAg LFA titers predicted vital outcome at 2 and 10 weeks [START_REF] Kabanda | Point-of-care diagnosis and prognostication of cryptococcal meningitis with the cryptococcal antigen lateral flow assay on cerebrospinal fluid[END_REF]. More recently, a new LFA has been developed by Biosynex and Institut Pasteur, with the advantage of offering simultaneous diagnosis and semiquantitation. Clinical studies comparing both tests are currently ongoing both as screening and diagnostic strategies in South Africa, Cameroon and Malawi/Kenya.

Treatment

Antifungal agents used to treat cryptococcosis include amphotericin B (including a liposomal formulation), flucytosine and fluconazole. For initial therapy, a combination of amphotericin B (1 mg/kg daily) and flucytosine (100 mg/kg daily), given for at least 14 days, has been shown to be superior to monotherapy, and flucytosine use is an independent predictor of better early mycological outcome [START_REF] Day | Combination antifungal therapy for cryptococcal meningitis[END_REF][START_REF] Dromer | Determinants of disease presentation and outcome during cryptococcosis: the CryptoA/D study[END_REF][START_REF] Perfect | Clinical practice guidelines for the management of cryptococcal disease: 2010 update by the infectious diseases society of america[END_REF][START_REF] Van Der Horst | Treatment of cryptococcal meningitis associated with the acquired immunodeficiency syndrome. National Institute of Allergy and Infectious Diseases Mycoses Study Group and AIDS Clinical Trials Group[END_REF]. The largest study ever performed ACTA (MRC and ANRS) with 691 patients to be included should provide major informations regarding potential alternatives to amphotericin B and flucytosine as a first-line strategy.

If clinical outcome is favorable and CSF culture becomes negative, therapy can be switched to oral fluconazole 400 mg daily for 8-10 weeks. Maintenance therapy with fluconazole, 200 mg daily, should be given until persistent immune restoration is obtained. If the patient has renal failure, liposomal amphotericin B, 3-5 mg/kg daily, can be used.

Appropriate management of elevated CSF opening pressure (≥ 25 cmH 2 0) strongly reduces early mortality, and repeated lumbar puncture with evacuation of up to 20 cc should be performed every 1-3 days until pressure normalizes (Boulware et al., 2014a;[START_REF] Perfect | Clinical practice guidelines for the management of cryptococcal disease: 2010 update by the infectious diseases society of america[END_REF]. In case of persistently increased intracranial pressure, a ventriculo-peritoneal shunt or lumbar drain should be used. Mannitol, acetazolamide and steroids have not been shown to be helpful [START_REF] Graybill | Diagnosis and management of increased intracranial pressure in patients with AIDS and cryptococcal meningitis. The NIAID Mycoses Study Group and AIDS Cooperative Treatment Groups[END_REF].

In case of an isolated positive serum CrAg titer, an exhaustive workup should be performed to search for a site of infection; fluconazole should be initiated if none is found and if the patient has a CD4 cell count <200/µL. Maintenance therapy can be safely withdrawn in patients who have been treated for cryptococcosis for at least a year, who are on cART, and who have a CD4 cell count >100/µL, undetectable HIV viral load for at least 3 months, and a CrAg titer < 1/512 [START_REF] Lortholary | Long-term outcome of AIDS-associated cryptococcosis in the era of combination antiretroviral therapy[END_REF][START_REF] Vibhagool | Discontinuation of secondary prophylaxis for cryptococcal meningitis in human immunodeficiency virus-infected patients treated with highly active antiretroviral therapy: a prospective, multicenter, randomized study[END_REF].

Primary prophylaxis is not recommended in developed countries. WHO recommends cryptococcal antigen screening and pre-emptive therapy for patients who are CrAg-positive and have 100 CD4/mm3 in regions where there is a high prevalence of cryptococcal antigenemia. Screening and pre-emptive treatment for cryptococcal infection has been shown to reduce mortality among HIV-infected patients in Africa when combined with counseling strategy [START_REF] Mfinanga | Cryptococcal meningitis screening and community-based early adherence support in people with advanced HIV infection starting antiretroviral therapy in Tanzania and Zambia: an open-label, randomised controlled trial[END_REF].

ii) Dimorphic fungi

Among fungal infections due to dimorphic fungi, only three --histoplasmosis, coccidioidomycosis, and penicilliosis --are frequently seen in AIDS patients.

Histoplasmosis

Histoplasmosis due to H. capsulatum var. capsulatum is endemic in the United States, the Caribbean, and Central and South America. It is much less frequent in Africa and South East Asia. Among HIV-positive patients living in endemic areas in midwestern United States, the incidence of histoplasmosis has ranged from 1% to 25% historically. It is a major threat in areas such as French Guyana and Surinam [START_REF] Nacher | Disseminated histoplasmosis in HIV-infected patients in South America: a neglected killer continues on its rampage[END_REF] and more generally in South America. Outside endemic areas, it usually results from reactivation several years after the primary infection [START_REF] Warnock | Imported mycoses in Europe[END_REF]. Histoplasmosis generally occurs in patients with CD4 counts <100/µL and is an AIDS-defining illness in its disseminated form.

Clinical manifestations

In AIDS patients, histoplasmosis is usually disseminated and manifests with fever (84%), weight loss, fatigue, and night sweats. Pneumonia is present in over half of cases, and hepatomegaly (40%), splenomegaly (40%), and lymphadenopathy (63%) are common findings [START_REF] Peigne | Imported acquired immunodeficiency syndrome-related histoplasmosis in metropolitan France: a comparison of pre-highly active anti-retroviral therapy and highly active anti-retroviral therapy eras[END_REF]. Septic shock and respiratory failure are seen in about 10% of cases and are associated with a poor prognosis [START_REF] Wheat | Practice guidelines for the management of patients with histoplasmosis[END_REF]. Central nervous system involvement (meningitis or a space-occupying lesion) occurs in approximately 15% of patients [START_REF] Wheat | Disseminated histoplasmosis in the acquired immune deficiency syndrome: clinical findings, diagnosis and treatment, and review of the literature[END_REF]. Various cutaneous lesions are seen, including maculopapular rash, pustules, papules and ulcers, and mucosal ulcers are typical. Gastrointestinal involvement is fairly frequent. Mediastinal granuloma and chronic cavitary lung disease are unusual in this population. Death is associated with low CD4 counts and the absence of ARV treatment [START_REF] Nacher | Disseminated histoplasmosis in HIV-infected patients in South America: a neglected killer continues on its rampage[END_REF].

Histoplasmosis due to H. duboisii is rarely observed in AIDS patients, and usually occurs among patients living in or having traveled to Central or West Africa or Madagascar [START_REF] Loulergue | Literature review and case histories of Histoplasma capsulatum var. duboisii infections in HIV-infected patients[END_REF].

Diagnosis

Pancytopenia is common at presentation. Chest radiography demonstrates patchy infiltrates, with diffuse interstitial pneumonitis in more severe cases. Microscopic examination of biopsy specimens or body fluid aspirates is the fastest diagnostic approach but its sensitivity varies.

The highest diagnostic yield is from bone marrow and skin or mucosal lesions. The classic 2-4 µm budding yeasts are best visualized after periodic acid Schiff or methenamine silver staining. Samples suitable for culture of H. capsulatum include blood, bone marrow, bronchoalveolar lavage fluid and solid tissues. Cultures have to be handled in a P3 facility.

Histoplasma antigen detection in blood, urine or CSF is specific and sensitive in patients with disseminated disease. Antigenuria correlates well with the response to therapy and is useful for detecting relapsing histoplasmosis [START_REF] Wheat | Clinical practice guidelines for the management of patients with histoplasmosis: 2007 update by the Infectious Diseases Society of America[END_REF]. Serum galactomannan antigen can also be used for diagnosis and follow-up when Histoplasma antigen testing is negative [START_REF] Rivière | Serum Aspergillus galactomannan for the management of disseminated histoplasmosis in AIDS[END_REF]. More recently, specific PCR,targeting fungal RNA, methods have been developed.

Treatment

Amphotericin B and itraconazole are effective against both H. capsulatum and H. duboisii [START_REF] Wheat | Clinical practice guidelines for the management of patients with histoplasmosis: 2007 update by the Infectious Diseases Society of America[END_REF]. Among patients with severe disease, initial treatment should consist of liposomal amphotericin B, 3 mg/kg daily. When patients have improved, generally after several weeks, they can be switched to oral itraconazole, 400 mg daily for 12 months. Milder illness can be treated initially with itraconazole, beginning with a loading dose of 200 mg thrice daily for 3 days, then 400 mg daily for 12 months [START_REF] Wheat | Clinical practice guidelines for the management of patients with histoplasmosis: 2007 update by the Infectious Diseases Society of America[END_REF]. Monitoring of serum itraconazole levels is mandatory in AIDS patients. Fluconazole is less effective than itraconazole but can be given, at a dosage of 400-800 mg daily, if itraconazole is not tolerated. The role of newer azoles has not been established.

Itraconazole can be withdrawn in patients who have been treated for at least 12 months, have at least 2 CD4 cell counts > 150/µL in the preceding 6 months, and have received cART for at least 6 months [START_REF] Goldman | Safety of discontinuation of maintenance therapy for disseminated histoplasmosis after immunologic response to antiretroviral therapy[END_REF]. Maintenance therapy should be restarted when CD4 cells number less than 100/µL. Primary prophylaxis can be considered in areas in which the incidence of histoplasmosis is highest. An immune reconstitution inflammatory syndrome (IRI) can occur after ARV initiation [START_REF] Breton | Immune reconstitution inflammatory syndrome in HIV-infected patients with disseminated histoplasmosis[END_REF]

Coccidioidomycosis

Coccidioides immitis and Coccidioides posadasii are dimorphic fungi found in semi-arid areas of the southwestern United States, Mexico, and Central and South America. Infection can occur after inhalation of arthroconidia present in soil, and may reactivate. Extrathoracic coccidioidomycosis involving sites other than the respiratory tract is an AIDS-defining illness.

Clinical manifestations

The most common symptoms of coccidioidomycosis in AIDS patients are fever, cough, and weight loss. Chest radiography reveals a variety of abnormalities, including focal pulmonary alvelolar infiltrates, discrete nodules, hilar lymphadenopathy, and pleural effusion in more than 60% of patients. A diffuse reticulonodular infiltrate is present in 40% of patients.

Approximately 12% of patients develop meningitis. Lymphadenopathy, cutaneous lesions, and subcutaneous abscesses are common. Fungemia, thyroiditis, peritonitis, adrenal involvement, osteoarticular disease, and prostatic involvement have also been reported [START_REF] Fish | Coccidioidomycosis during human immunodeficiency virus infection. A review of 77 patients[END_REF].

Diagnosis

The CD4 cell count is usually <200/µL and often <50/µL. Definitive diagnosis relies on visualization of the typical large spherules containing numerous endospores in clinical specimens, and isolation of Coccidioides in culture. Coccidioides cannot be handled in clinical microbiology laboratories that are not equipped with a P3 facility. In case of meningitis, cerebrospinal fluid analysis typically shows leukocytic pleocytosis, with the possible presence of eosinophils, decreased glucose and increased protein values.

Coccidioides culture from CSF is often negative, but positive serology can establish the diagnosis of coccidioidal meningitis. More recently, specific PCR methods, targeting fungal RNA, have been developed.

Treatment

The drug of choice for severe or life-threatening coccidioidal infection is amphotericin B lipid formulation, 3-5 mg/kg daily [START_REF] Galgiani | Infectious Diseases Society of America[END_REF]. Once the disease is controlled, generally after 2 to 3 weeks, a switch to an oral triazole drug should be considered. Fluconazole 400 mg daily is a good alternative, particularly in patients with meningitis; itraconazole 400 mg daily has also given good results, especially in patients with skeletal disease [START_REF] Galgiani | Infectious Diseases Society of America[END_REF].

Lifelong maintenance therapy with a triazole (fluconazole 400 mg daily or itraconazole 400 mg daily) is necessary to avoid relapse in AIDS patients [START_REF] Kaplan | Guidelines for prevention and treatment of opportunistic infections in HIV-infected adults and adolescents: recommendations from CDC, the National Institutes of Health, and the HIV Medicine Association of the Infectious Diseases Society of America[END_REF].

Penicilliosis

Penicillium marneffei is a dimorphic fungus present in soil in Southeast Asia. Several imported cases of infection have occurred in Europe. Penicillium marneffei is associated with several species of bamboo rats, but contact with soil seems to be the most important risk factor for exposure to this fungus. In northern Thailand, penicilliosis used to be the third most common AIDS-defining opportunistic disease, after tuberculosis and cryptococcosis [START_REF] Supparatpinyo | Disseminated Penicillium marneffei infection in southeast Asia[END_REF]. Penicilliosis is frequent in South China, accounting for 4.8% of AIDS-related hospital admissions.

Clinical manifestations

Penicilliosis is frequently disseminated at presentation, and the CD4 cell count is usually below 50 cells/µL. In a study of 92 patients with disseminated penicilliosis seen at Chiang Mai University Hospital in Thailand, 86 (93%) of patients were HIV-infected [START_REF] Supparatpinyo | Disseminated Penicillium marneffei infection in southeast Asia[END_REF], and most were young men. Signs and symptoms included fever (93%), anemia (78%), pronounced weight loss (76%), skin lesions (68%), generalized lymphadenopathy (58%), hepatomegaly (51%), cough (49%), diarrhea (31%), splenomegaly (16%), and jaundice (8%). Skin lesions, especially a generalized papular rash, are very suggestive of penicilliosis in patients at risk. Some papules, with central umbilication, mimic lesions caused by molluscum contagiosum. Subcutaneous nodules, acne-like lesions and folliculitis may also be present. Genital ulcers and palatal papules have been reported. Chest radiography is abnormal in almost 30% of patients with disseminated penicilliosis. Penicilliosis accounted for 11% of mucocutaneous lesions in HIV-infected patients in Guangxi, China [START_REF] Han | Mucocutaneous manifestations of HIV-infected patients in the era of HAART in Guangxi Zhuang Autonomous Region, China[END_REF], and 16.5% of all positive blood cultures in Ho Chi Minh City in 2005 [START_REF] Nga | The decline of typhoid and the rise of non-typhoid salmonellae and fungal infections in a changing HIV landscape: bloodstream infection trends over 15 years in southern Vietnam[END_REF]. Cases of IRIS have been reported.

Diagnosis

Fever, with or without pancytopenia, skin and/or lung lesions may also suggest a diagnosis of leishmaniasis or disseminated histoplasmosis. For any HIV-infected individual, a history of residence in or travel to Southeast Asia or South China should evoke the possibility of penicilliosis [START_REF] Warnock | Imported mycoses in Europe[END_REF].

In the Chiang Mai series, diagnosis of penicilliosis was made by culture of the fungus from blood (76%), skin lesions (90%), bone marrow aspirate (100%), or sputum. The galactomannan test for Aspergillus antigen cross-reacts with P. marneffei [START_REF] Zheng | A Clinical Study of Acquired Immunodeficiency Syndrome Associated Penicillium Marneffei Infection from a Non-Endemic Area in China[END_REF].

A presumptive diagnosis of penicilliosis can be made from examination of sputum or biopsy material from bone marrow, skin or a lymph node.

Treatment

Itraconazole and amphotericin B are the mainstays of therapy for penicilliosis, regardless of immune status. Induction treatment with amphotericin B 0.6 mg/kg daily for approximately 2 weeks, followed by itraconazole 400 mg daily for 10 weeks, is the treatment of choice [START_REF] Sirisanthana | Amphotericin B and itraconazole for treatment of disseminated Penicillium marneffei infection in human immunodeficiency virus-infected patients[END_REF]. Voriconazole has also been shown to be effective. Suppressive therapy with itraconazole, 200 mg daily, is recommended for all patients with persistently low CD4 cell counts [START_REF] Supparatpinyo | A controlled trial of itraconazole to prevent relapse of Penicillium marneffei infection in patients infected with the human immunodeficiency virus[END_REF]. In geographic areas in which P. marneffei is endemic, primary prophylaxis with itraconazole 200 mg daily was recommended before the ART era [START_REF] Chariyalertsak | A controlled trial of itraconazole as primary prophylaxis for systemic fungal infections in patients with advanced human immunodeficiency virus infection in Thailand[END_REF] .

Other dimorphic fungi

Paracoccidioidomycosis

Paracoccidioidomycosis is not commonly reported in AIDS patients, for unexplained reasons. Lifelong maintenance therapy with trimethoprimsulfamethoxazole or itraconazole is recommended [START_REF] Paniago | Paracoccidioidomycosis in patients with human immunodeficiency virus: review of 12 cases observed in an endemic region in Brazil[END_REF].

Blastomycosis

Blastomycosis is also uncommon among HIV-infected patients. Several cases of blastomycosis have been reported in patients with AIDS, most of whom had CD4 cell counts well below 200/µL. Amphotericin B is considered to be the initial treatment of choice for patients with severe disease and for all immunosuppressed patients [START_REF] Chapman | Clinical practice guidelines for the management of blastomycosis: 2008 update by the Infectious Diseases Society of America[END_REF].

Patients who are improved after 2-4 weeks on amphotericin B may reasonably be switched to oral itraconazole 200 mg twice daily. Suppressive therapy with itraconazole should be maintained indefinitely in patients who remain severely immunodeficient.

Sporotrichosis

In a review of 16 cases of disseminated sporotrichosis in HIV-infected patients, diffuse ulcerative skin lesions were always present. Other disease sites included the CNS, joints, eyes, spleen, and bone marrow. Sporothrix schenckii fungemia was noted in two patients. The mean CD4 cell count was 73/µL.

Examination of tissue biopsies or material aspirated from skin lesions usually leads to the diagnosis when the typical cigar-shaped yeast forms are seen. Culture of tissue or body fluids at 25°C reveals the mould form of S. schenckii.

The optimal therapy for disseminated sporotrichosis in HIV-positive patients has not been determined. The most reasonable treatment would be amphotericin B for the most severe cases, followed by itraconazole. Itraconazole should be considered for long-term maintenance therapy among patients who remain immunosuppressed [START_REF] Kauffman | Clinical practice guidelines for the management of sporotrichosis: 2007 update by the Infectious Diseases Society of America[END_REF].

Emmonsiosis

Emmonsia sp. is a novel dimorphic fungi recently reported to cause disseminated infections in South African HIV-infected patients with very low CD4 cell counts (average 16/mm 3 ). All the patients had disseminated infection involving the skin and lungs in most cases. The yeasts could be seen on pathological examination. Most patients were treated with liposomal amphotericin B (71%) and the mortality rate was 48% [START_REF] Kenyon | A dimorphic fungus causing disseminated infection in South Africa[END_REF][START_REF] Schwartz | Clinical Characteristics, Diagnosis, Management, and Outcomes of Disseminated Emmonsiosis: A Retrospective Case Series[END_REF][START_REF] Van Hougenhouck-Tulleken | HIV-associated disseminated emmonsiosis, Johannesburg, South Africa[END_REF].

iii) Other opportunistic moulds: aspergillosis

Invasive aspergillosis has been reported among patients with advanced HIV disease, especially those with CD4 cell counts <50/ml [START_REF] Denning | Pulmonary aspergillosis in the acquired immunodeficiency syndrome[END_REF][START_REF] Khoo | Invasive aspergillosis in patients with AIDS[END_REF][START_REF] Lortholary | Invasive aspergillosis in patients with acquired immunodeficiency syndrome: report of 33 cases. French Cooperative Study Group on Aspergillosis in AIDS[END_REF]. The classical risk factors for invasive aspergillosis, namely neutropenia and corticosteroid therapy, were absent in many AIDS patients with Aspergillus infection. The lungs are the most common site of infection. In a study of 33 AIDS patients with invasive aspergillosis, most of whom had pulmonary disease, the predominant symptoms were fever, cough and dyspnea, while chest pain and hemoptysis were less frequent [START_REF] Lortholary | Invasive aspergillosis in patients with acquired immunodeficiency syndrome: report of 33 cases. French Cooperative Study Group on Aspergillosis in AIDS[END_REF]. Chest radiographs often show nodular lesions and cavitary infiltrates suggestive of aspergillosis. Bilateral interstitial infiltrates are also noted. Invasive necrotizing tracheobronchitis, manifested by acute dyspnea and wheezing, is a clinical form of aspergillosis also seen in AIDS patients. Bronchoscopy reveals necrotic ulceration of the trachea, with pseudomembranes [START_REF] Kemper | Ulcerative and plaque-like tracheobronchitis due to infection with Aspergillus in patients with AIDS[END_REF]. Obstructing bronchial aspergillosis with chest pain, hemoptysis and dyspnea may precede the onset of necrotizing tracheobronchitis [START_REF] Denning | Pulmonary aspergillosis in the acquired immunodeficiency syndrome[END_REF]. The majority of patients have a prior history of pulmonary infection. Preexisting cystic pulmonary lesions and bullae may be risk factors for invasive pulmonary aspergillosis in patients with AIDS. Disseminated aspergillosis often involves the CNS and myocardium. Aspergillus endocarditis and sinusitis have also been reported among patients with AIDS.

There is a good correlation between Aspergillus-positive bronchoalveolar lavage fluid Although not specifically studied in AIDS patients, voriconazole has now become the recommended therapy for invasive aspergillosis in all patient groups [START_REF] Walsh | Treatment of aspergillosis: clinical practice guidelines of the Infectious Diseases Society of America[END_REF].

Interactions with protease inhibitors and non-nucleoside reverse transcriptase inhibitors must be carefully monitored when azole agents are used. An alternative therapy is a lipid formulation of amphotericin B. The prognosis of invasive aspergillosis in AIDS patients is poor, with a mean survival time of only 2-4 months despite antifungal treatment. This opportunistic infection is very unusual among patients on effective cART.

c) Immunosuppression and fungal risk among individuals living with HIV i) Immunosuppression among individuals living with HIV

The earliest reports of AIDS showed that profound depletion of circulating CD4 T cells was central to the immune deficiency that defined the syndrome [START_REF] Gottlieb | Pneumocystis carinii pneumonia and mucosal candidiasis in previously healthy homosexual men: evidence of a new acquired cellular immunodeficiency[END_REF][START_REF] Masur | An outbreak of community-acquired Pneumocystis carinii pneumonia: initial manifestation of cellular immune dysfunction[END_REF]. The same investigators also recognized that, despite the profound immune deficiency, activation of T cells [START_REF] Gottlieb | Pneumocystis carinii pneumonia and mucosal candidiasis in previously healthy homosexual men: evidence of a new acquired cellular immunodeficiency[END_REF] and B cells [START_REF] Lane | Abnormalities of B-cell activation and immunoregulation in patients with the acquired immunodeficiency syndrome[END_REF] was also characteristic of this syndrome. The pathology of HIV disease is complex and multifaceted. In addition to high levels of systemic viral replication, HIV infection results in chronic immune activation and overall immunological dysfunction, which are closely associated with progression to AIDS.

Alteration of mucosal tissue:

HIV directly infects and depletes CD4 cells. The depletion occurs first in mucosal tissues, where large numbers of activated memory T cells expressing CCR5 chemokine receptors are present. As the majority of T cells reside within mucosal tissues, early loss of memory T cells leads to the loss of most of the body's T cells [START_REF] Brenchley | HIV infection and the gastrointestinal immune system[END_REF]. Around 90% of gut-associated lymphoid tissue (GALT) T cells are depleted within 2 weeks of simian immunodeficiency virus acquisition [START_REF] Mattapallil | Massive infection and loss of memory CD4+ T cells in multiple tissues during acute SIV infection[END_REF]. During acute HIV infection, the viral RNA is detectable in 0.01-1% of peripheral T cells, compared to 60% of mucosal memory CD4 T cells [START_REF] Brenchley | CD4+ T cell depletion during all stages of HIV disease occurs predominantly in the gastrointestinal tract[END_REF][START_REF] Mattapallil | Massive infection and loss of memory CD4+ T cells in multiple tissues during acute SIV infection[END_REF]. Slower depletion of CD4 T cells in peripheral tissues and blood ensues [START_REF] Douek | T cell dynamics in HIV-1 infection[END_REF]. While cART can in most cases restore immunity, reflected by CD4 cell recovery, T cells in the gastrointestinal tract usually fail to recover. HIV infection damages the tight epithelial barrier of the gastrointestinal tract, leading to microbial translocation, severe immunological dysfunction and chronic immune activation [START_REF] Brenchley | Microbial translocation is a cause of systemic immune activation in chronic HIV infection[END_REF][START_REF] Brenchley | HIV infection and the gastrointestinal immune system[END_REF][START_REF] Mehandru | Lack of mucosal immune reconstitution during prolonged treatment of acute and early HIV-1 infection[END_REF][START_REF] Tincati | Early initiation of highly active antiretroviral therapy fails to reverse immunovirological abnormalities in gut-associated lymphoid tissue induced by acute HIV infection[END_REF].

Altered functionality and turn-over of CD8 T cells, B cells and innate immune cells are also observed [START_REF] Paiardini | Cell-cycle dysregulation in the immunopathogenesis of AIDS[END_REF][START_REF] Ribeiro | In vivo dynamics of T cell activation, proliferation, and death in HIV-1 infection: why are CD4+ but not CD8+ T cells depleted?[END_REF]. Altered B cell function affects antibody production [START_REF] Moir | B cells in HIV infection and disease[END_REF], while altered NK cell function reduces cytokine production and increases cytotoxicity [START_REF] Alter | Increased natural killer cell activity in viremic HIV-1 infection[END_REF][START_REF] Reeves | CD16-natural killer cells: enrichment in mucosal and secondary lymphoid tissues and altered function during chronic SIV infection[END_REF]. Dendritic cells and macrophages are also dysfunctional [START_REF] Estes | Damaged intestinal epithelial integrity linked to microbial translocation in pathogenic simian immunodeficiency virus infections[END_REF][START_REF] Wallet | Microbial translocation induces persistent macrophage activation unrelated to HIV-1 levels or T-cell activation following therapy[END_REF] Alteration of naïve T cells:

Among CD4 and CD8 T cells, HIV infection leads to a loss of essential naïve and central memory cell populations, resulting in an increased frequency of short-lived effector cells [START_REF] Klatt | Microbial translocation, immune activation, and HIV disease[END_REF]. T cell maturation is also affected, with low numbers of circulating naïve CD4 and CD8 T cells [START_REF] Lederman | Immunologic failure despite suppressive antiretroviral therapy is related to activation and turnover of memory CD4 cells[END_REF]. Zeng et al explained how, in secondary lymphoid tissue, immune activation leads to fibrosis and architectural distortion of the fibroblast reticular network, limiting access to IL-7 [START_REF] Zeng | Lymphoid tissue structure and HIV-1 infection: life or death for T cells[END_REF]. This fibrosis and decreased access to IL-7 would deplete naïve T cells and limit immune reconstitution, as shown in the figure below. Impairment of thymic T cell production:

Destruction of thymic structure, thymocyte depletion and infiltration by activated T cells are observed in AIDS patients [START_REF] Haynes | The role of the thymus in immune reconstitution in aging, bone marrow transplantation, and HIV-1 infection[END_REF][START_REF] Zeng | Lymphoid tissue structure and HIV-1 infection: life or death for T cells[END_REF]. HIV-1 directly kills thymocytes and dendritic cells required for normal development, and this could be a cause of CD4 T cell depletion [START_REF] Haynes | The role of the thymus in immune reconstitution in aging, bone marrow transplantation, and HIV-1 infection[END_REF].

Immune activation and inflammation:

While the degree of CD4 T cell lymphopenia is an important predictor of HIV-related morbidity and mortality, persistent immune activation and inflammation are now recognized to be stronger and independent predictors of morbidity and mortality [START_REF] Duprez | Epidemiologic aspects of the current outbreak of Kaposi's sarcoma and opportunistic infections, 1982[END_REF][START_REF] Kuller | Inflammatory and coagulation biomarkers and mortality in patients with HIV infection[END_REF]. A number of causative factors for sustained immune activation and inflammation have been identified, and are either directly or indirectly related to HIV replication. They include the innate and adaptive immune responses against HIV and associated pathogens, translocation of bacterial products through the compromised mucosal barrier, and potential bystander stimulation of lymphocytes and macrophages by HIV gene products [START_REF] Appay | Immune activation and inflammation in HIV-1 infection: causes and consequences[END_REF]). However, the potential consequences of immune activation and its links to the CD4 T cell decline and immunodeficiency in HIV-1 infection remain a matter of debate.

ii) Immune regulation and fungi (1) Defects in CD4 T lymphocytes

The risk of opportunistic fungal infections increases with the degree of immune deficiency.

CD4+ lymphocyte defects are a primary risk factor for developing PCP, but the immune response to Pneumocystis is complex. Defects in B cells and antibody production may also predispose to PCP. CD8+ lymphocytes seem to be important in Pneumocystis clearance. A CD4 count <200 cells/µL was the leading pre-cART risk factor for PCP and is still an important risk factor in the cART era. The risk of PCP increases exponentially once the CD4 count falls below 200 cells/µL. When cART yields sustained CD4 cell recovery above 200/µL, the risk of PCP is sufficiently reduced to safely discontinue both primary and secondary prophylaxis.

(2) Other defects Phagocytic cells (neutrophils, monocytes, macrophages and dendritic cells) are essential for protection against fungal pathogens. Loss of these cells, or defects in their antifungal effector functions, therefore results in susceptibility. While an innate response mediated primarily by neutrophils and macrophages is sufficient to control infections by some fungi, full protection against most pathogens also requires an adaptive response, initiated and directed by dendritic cells (DC) with contributions from other cells such as monocytes. This ultimately generates an immune response involving several fungal-specific components, but an augmentation of the antifungal activities of phagocytes (through the actions of IFN-γ for example) is required for protection in all cases. The IL-17 pathway regulates antifungal immunity through upregulation of proinflammatory cytokines, including IL-6, neutrophil-recruiting chemokines, and antimicrobial peptides, which act to limit fungal overgrowth, and this has been well demonstrated against Candida.

Even when present at normal levels, neutrophils and peripheral blood macrophages from HIV-infected individuals exhibit impaired activity against A. fumigatus in vitro [START_REF] Pitrak | Depressed neutrophil superoxide production in human immunodeficiency virus infection[END_REF][START_REF] Roilides | Defective antifungal activity of monocyte-derived macrophages from human immunodeficiency virusinfected children against Aspergillus fumigatus[END_REF].

iii) Impact of cART on fungal infections

Chapter Fungal infections in patients with AIDS in Medical Mycology (B. Denis, et al) to be published soon

The advent of cART resulted in dramatic declines in morbidity and mortality among HIVinfected patients with advanced immune dysfunction [START_REF] Palella | Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators[END_REF] Successful cART is characterized by a marked reduction in viral load and a subsequent increase in the CD4 cell count. However, partial restoration of cell-mediated immunity and, possibly, other immune effectors may facilitate the development of an inflammatory reaction at former sites of infection, and this can mimic reactivation of the opportunistic disease itself. This "immune reconstitution inflammatory syndrome" (IRIS) has been reported in AIDS patients with cryptococcosis and histoplasmosis, PCP and penicilliosis (Boulware et al., 2014a;[START_REF] Breton | Immune reconstitution inflammatory syndrome in HIV-infected patients with disseminated histoplasmosis[END_REF][START_REF] Lortholary | Incidence and risk factors of immune reconstitution inflammatory syndrome complicating HIVassociated cryptococcosis in France[END_REF][START_REF] Shelburne | The role of immune reconstitution inflammatory syndrome in AIDS-related Cryptococcus neoformans disease in the era of highly active antiretroviral therapy[END_REF][START_REF] Sungkanuparph | Cryptococcal immune reconstitution inflammatory syndrome after antiretroviral therapy in AIDS patients with cryptococcal meningitis: a prospective multicenter study[END_REF] The symptoms and signs of IRIS pose a diagnostic challenge for the clinician, who must decide whether the patient is experiencing relapse of an initial infection, a new infection, or IRIS. When an opportunistic infection occurs at a low CD4 cell count, studies have shown that starting cART early after treatment of the opportunistic infection improves overall survival, except in the case of cryptococcal meningitis. In a recent randomized study of 500

HIV-infected individuals with cryptococcal meningitis, deferral of cART for 5 weeks after the diagnosis of cryptococcal meningitis was associated with significantly better survival than cART initiation after 1 week (Boulware et al., 2014a). CART should be introduced cautiously in patients with cryptococcal meningitis, and it is advisable to wait at least until CSF cultures have become negative (Boulware et al., 2014a;[START_REF] Kaplan | Guidelines for prevention and treatment of opportunistic infections in HIV-infected adults and adolescents: recommendations from CDC, the National Institutes of Health, and the HIV Medicine Association of the Infectious Diseases Society of America[END_REF]. If IRIS occurs, treatment with anti-inflammatory agents, including corticosteroids, may be effective, without necessitating a change in cART or in anti-infective treatment. In steroid-refractory cases, thalidomide might be indicated [START_REF] Brunel | Thalidomide for steroid-dependent immune reconstitution inflammatory syndromes during AIDS[END_REF] Chapter 2. Methods prophylaxis could be stopped when the CD4 cell count was steadily above 200/mm 3 and 15% [START_REF] Abgrall | Pneumocystis carinii pneumonia recurrence in HIV patients on highly active antiretroviral therapy: secondary prophylaxis[END_REF]. Another study from FHDH showed that PCP survival at 3 years rose from 51% in the pre-cART era to 87% in 2001-2003 [START_REF] Grabar | Causes of the first AIDS-defining illness and subsequent survival before and after the advent of combined antiretroviral therapy[END_REF].

1) The French Hospital DataBase On HIV -the ANRS CO4 cohort

Even if these opportunistic infections are now rare, the large size of the FHDH cohort allows us to continue to study their epidemiology. This is why we decided to study trends in fungal infections in the FHDH, focusing on two topics: PCP in the recent period 2004-2011, and invasive aspergillosis during the period 1992-2011. In order to obtain all available information, a specific CRF was prepared to record clinical, radiological, biological and microbiological criteria, treatments, outcomes, and causes of death. This CRF is available in the appendix.

2) Study of

Among the 515 patients with a corresponding ICD 9 or ICD10 code, 173 charts were not available for review (141 charts corresponding to 77, 44, and 20 patients, respectively, during the periods 1992-1995, 1996-2001 and 2002-2011) or had too many missing data (32 charts corresponding to 13, 14, and 5 medical records, respectively, during the periods 1992-1995, 1996-2001 and 2002-2011). 86% of the missing medical records and 84% of the incomplete medical records were for patients with an IA diagnosis in the period 1992-2001. Clinical, radiological, biological and therapeutic data relative to aspergillosis were retrieved. Finally, 342 charts were reviewed by a data review committee (DRC) which included 2 infectious diseases experts (BD and OL), in order to validate the cases.

c) Validation of IA cases and definition of "EORTC IA" and "HIV-related IA" among validated IA cases Individuals without clinico-radiological signs of IA were excluded. Each EORTC criterion was checked. We added to the EORTC host factor "fewer than 500 neutrophil cells/mm 3 for more than 10 days", the criterion "fewer than 800 neutrophil cells/mm 3 with growth factor treatment for more than 10 days". Validated IA cases meeting the EORTC criteria were classified as proven, probable or possible. Biopsy, percutaneous aspiration or autopsy was required for proven cases.

When a case did not meet the EORTC host-factor criteria, the review committee examined radiological features, the results of microscopic examination and culture of bronchoalveolar lavage fluid (BAL), the results of GM antigen testing (GM), and associations with other pathogens, as in previous studies [START_REF] Khoo | Invasive aspergillosis in patients with AIDS[END_REF].

Patients who were infected both by an Aspergillus sp. and by a major respiratory copathogen that was detected in BAL fluid and might have explained the illness, namely Mycobacterium tuberculosis, M. avium, Streptococcus pneumoniae, Histoplasma capsulatum, or Pneumocystis jirovecii, were not considered as having IA.

We also excluded patients considered to have transient Aspergillus colonization (patients without radiological abnormalities, bronchial endoscopy, or signs of necrotic tracheobronchitis on endoscopy), a typical aspergilloma, allergic bronchopulmonary aspergillosis (ABPA), or a possibly false-positive galactomannan (GM) test. This concerned seven patients, one with disseminated histoplasmosis, three with a surgically treated aspergilloma and no histological signs of surrounding invasion, one with GM positivity at 0.5 plus pan-sinusitis and an aspergilloma of the maxillary sinus, and two ICU patients with septic shock on piperacillin-tazobactam and negative fungal culture of sputum. Cases not meeting the EORTC criteria were defined as "HIV-related IA" and categorized into two groups: Group

4) Statistical methods

In both studies, statistical methods were used to calculate prevalence/incidence rates. Survival ii) Invasive aspergillosis (IA)

The estimation of IA incidence rates took into account the difficulty of retrieving medical records (particularly for diagnoses made before 2002, which accounted for 85% of unretrieved medical records), especially for deceased patients. Furthermore, the IA validation rate was significantly higher when the CD4 cell count at diagnosis was below 100/mm 3 than when it was above 100/mm 3 (82% vs 53%; p<0.0001). Thus, the number of IA cases was first corrected for non-retrieval of medical records. After stratification for the study period (1992-1995/1996-2001/2002-2011) and the CD4 cell count (CD4<100/mm 3 or CD4≥100/mm 3 ) at IA diagnosis, the rate of IA validation was applied to the 141 medical records that had not been reviewed. Incidence rates copies/ml) was included as a time-dependent variable. In the Cox model for the risk of death within 3 years after PCP onset, virological control and immune reconstitution (CD4 >200/mm 3 ) were included as time-dependent variables. In our analysis, patients previously enrolled with a prior ADI had a poorer prognosis. As there were more IV drug users in this group, and as death could have been related to other causes such as overdose, we conducted sensitivity analyses after excluding IV drug users.

ii) Invasive aspergillosis

Chapter 3. Trends in PCP among HIV-infected individuals in France in the cART era

The first part of our work consisted of an epidemiological study of HIV-infected individuals who had a first diagnosis of PCP nowadays in France. As PCP is a good marker of severe immunosuppression and as 82% of HIV-infected individuals enrolled in the FHDH cohort had been on cART for at least 6 months at the time of this study, our first hypothesis was that most PCP cases would be diagnosed among late presenters, in whom PCP revealed their HIV infection.

To our surprise, PCP revealed HIV infection in only half the 1259 patients with a first diagnosis of PCP during the period 2004-2011. The other half were previously enrolled patients (median 8 years since enrolment), 68% of whom had received more than one year of cART before PCP diagnosis, and two-thirds of whom had a history of CD4 cell counts above 350/mm 3 . At PCP diagnosis, their median CD4 cell count was 38/mm 3 and their VL was 5.2 log10 copies/ml, values similar to those of patients with inaugural PCP (53/mm 3 and 5.1 log10 copies/ml).

This led us to examine retention in care in the FHDH cohort. We defined adequate adherence to care as having a CD4 cell count at least every 6 months. The rate of adherence to care before PCP diagnosis was estimated and compared with the rate of adherence to care among all patients enrolled in the FHDH. The median proportion of time spent with adequate adherence to care was 85% (IQR, 66-96) for all FHDH enrollees, but only 45% (IQR, during the 2 years before PCP diagnosis among previously enrolled patients. Therefore, some patients' adherence had diminished over time, increasing the risk of developing an AIDSdefining clinical illness.

We found that previously enrolled patients, especially those with a prior history of AIDSdefining clinical illness, had slower immune reconstitution after PCP than patients with inaugural PCP (by comparison with patients with inaugural PCP, risk factor of achieving a CD4 cell count above 200/mm 3 : HR 0.7 (0.6-0.9) for previously enrolled patients without a prior ADI, and 0.6 (0.4-0.8) for previously enrolled patients with a prior ADI). In addition, the 3-year mortality rate after PCP diagnosis was 25% among previously enrolled patients with a prior ADI, compared to only 8% among previously enrolled patients without a prior ADI and 9% among patients with inaugural PCP. Previously enrolled patients with a prior ADI had a poorer prognosis than patients with inaugural PCP, even after adjustment for virological control and immune reconstitution (HR,2.4 [95%CI,), demonstrating persistent immune system dysfunction after an ADI that is not only reflected by the CD4 cell count.

Thus, in order to reduce the incidence of PCP and to improve its prognosis, we need to maintain patients in care in the long term, concentrating first on patients who have been in care for many years, and to design interventions to maintain adherence over time, especially among patients with a history of ADI. We are now working on indicators of adherence to care in order to help clinicians identify patients at risk. Also, as half the cases of PCP diagnosed during the study period could have been avoided by early screening for HIV, more efficient screening strategies must be developed in conjunction with the different public health stakeholders.

Chapter 4

The In that context, the evolution of the incidence of invasive aspergillosis in HIV infected individuals was unknown, and we wanted to analyze who would have an invasive aspergillosis diagnosis nowadays. We were also interested to know how these diagnoses were made, as EORTC criteria were first proposed in 2002 (and modified in 2008) for invasive aspergillosis in hemato-oncological settings. The FHDH medical records were reviewed to collect all the information needed to validate cases of invasive aspergillosis.

We used strict criteria looking if invasive aspergillosis cases corresponded to the EORTC definition (noted as "EORTC IA"), otherwise invasive aspergillosis validated on clinical, microbial and radiological factors was defined as "HIV related IA". We thus validated a total of 242 cases recorded in the FHDH cohort over a 20-year period.

The incidence of invasive aspergillosis fell over time, from 19 per 10 000 PY (95% CI, 16.0-23.0) in the period 1992-1995 to 2.2 per 10 000 PY (95% CI, 1.8-2.6) in 2002-2011.

The ratio of EORTC IA cases to all validated IA cases remained stable (50.4% in 1992-1995, 48.1% in 1996-2001, and 54.4% in 2002-2011 (p=0.7)). Surprisingly, half the voriconazole (1992[START_REF] Wheat | Endemic mycoses in AIDS: a clinical review[END_REF]), post-cART and pre-voriconazole (1996-2001), and post-cART and post-voriconazole (2002-2011). We confirmed that median survival after invasive aspergillosis improved with the advent of cART, from 1.9 months (IQR, 0.9-3. [START_REF] Grabar | Causes of the first AIDS-defining illness and subsequent survival before and after the advent of combined antiretroviral therapy[END_REF]. Furthermore, we were struck by the large number of PCP cases still declared by some FHDH participating centers.

This is why I decided to launch an epidemiologic study of fungal infections among HIVinfected individuals, using data from the FHDH cohort. I chose to study two very different diseases: PCP, a very well characterized and frequent AIDS-defining event, and invasive aspergillosis, a very rare but life-threatening fungal infection in HIV-infected individuals.

Because of its very low incidence, invasive aspergillosis was removed from the Centers for Disease Control and Prevention's list of AIDS-defining opportunistic infections in 1984.

Fungal infections are reliable markers of severe immunosuppression: PCP is extremely rare when the CD4 cell count is above 200/mm 3 (or 15%), while invasive aspergillosis (like cryptococcosis, histoplasmosis and penicilliosis) occurs at a median CD4 cell count below 50/mm 3 .

I had different objectives for the two fungal infections:

As there were no publications on PCP trends in the late cART period, I analyzed the recent incidence of PCP in HIV-infected individuals, as well as the patients' baseline characteristics and outcomes.

22 years ago my PhD co-director had published a study of 33 HIV-infected individuals with invasive aspergillosis. At that time, before the advent of cART and active antifungals, the short-term prognosis was grim. As no recent publications were available, we thought the FHDH cohort, with its very large size (data on more than 130 000 HIV-infected individuals), would yield interesting data on invasive aspergillosis among HIV-infected individuals. We decided to study incidence trends over time, how the diagnosis was made, the nature of the population at risk, how patients were treated, and how the prognosis of invasive aspergillosis changed over a 20-year period. We also wanted to see if the EORTC diagnostic criteria for IA in the hematological setting were adapted to the context of HIV infection.

In France, as special efforts have been made to increase HIV screening uptake, and as French experts have recommended cART even for patients with CD4 cell counts >350/mm 3 since 2008, most cases of PCP among HIV-infected individuals should theoretically have been related to HIV screening failure. In the FHDH, 1259 HIV-infected individuals had a first diagnosis of PCP during the period 2004-2011. Thus, PCP still exists, and, with a 3-year mortality rate of 25% among patients who developed PCP after a previous AIDS-defining event, we show that it is still a major issue, especially for patients who are not retained in care, among whom the mortality rate is particularly high.

Djawe et al [START_REF] Djawe | Mortality Risk After AIDS-Defining Opportunistic Illness Among HIV-Infected Persons--San Francisco, 1981-2012[END_REF] obtained similar results in San Francisco for HIV-infected individuals with a first diagnosis of AIDS-defining illness: the five-year mortality rate was 35% during the period 1996-2012. As H. Masur stated in his editorial relative to the previous study [START_REF] Masur | Opportunistic Infections and Mortality: Still Room for Improvement[END_REF], "we still have room for improvement".

So how could we improve the prognosis of patients with PCP?

-First of all by better diagnosis and early treatment:

PCP is easier to diagnose in a context of HIV infection. First, fungal load is higher in induced sputum and BAL fluid than in HIV-seronegative individuals. Second, when an HIV-infected individual presents with progressive dyspnea to a service used to managing HIV-related opportunistic infections, the most likely diagnosis will be PCP, and treatment with trimethoprim-sulfamethoxazole can be prescribed without delay. The diagnosis will be confirmed 48 h later on BAL fluid or induced sputum. However, all physicians, and particularly general practitioners who are not used to dealing with HIV-infected individuals, must be fully informed of opportunistic infections. Indeed, most patients have already seen a doctor before receiving the correct diagnosis, and have been prescribed various ineffective antibiotics. They finally arrive at the hospital with severe PCP revealing their HIV infection. -Another approach is to prevent PCP occurring in the first place:

-By improving HIV screening and giving PCP prophylaxis to immunosuppressed patients.

HIV screening is still inadequate in France, as reflected by the fact that half of all patients with PCP are diagnosed very late, with PCP revealing their HIV infection. A study based on the French national surveillance program showed that 30% of individuals with newly diagnosed HIV infection already had AIDS or a CD4 cell count below 200/mm 3 [START_REF] Cazein | HIV testing and new HIV diagnoses, France 2003-2010[END_REF]. CART should be introduced rapidly after HIV diagnosis in order to limit the risk of opportunistic infections, and PCP prophylaxis should be prescribed until the CD4 cell count recovers to at least 200/mm 3 .

-By maintaining patients in care:

We found that almost 50% of PCP diagnoses among HIV-infected individuals involved patients already in care who had received cART prescription but whose adherence to care was waning. A small number of patients are lost to follow-up and return to care with severe opportunistic infections. This has also been observed in other studies conducted in resourcerich settings [START_REF] Lee | Comparison of two cohorts of patients presenting with AIDS: patients with previously known HIV diagnoses and true late presenters[END_REF][START_REF] Llibre | Pneumocystis jirovecii pneumonia in HIV-1-infected patients in the late-HAART era in developed countries[END_REF]. We thus need to understand the determinants of poor long-term adherence, such as the challenge of life-long medication and interventions designed to promote adherence to cART concluded that this method could be useful and could be optimized by 1) asking the recipient to reply and 2) by not sending the messages too frequently [START_REF] Finitsis | Text message intervention designs to promote adherence to antiretroviral therapy (ART): a meta-analysis of randomized controlled trials[END_REF]. Another study showed that a reminder by a member of the clinical staff was significantly more effective than an automated system for lowering the "no-show" rate [START_REF] Parikh | The effectiveness of outpatient appointment reminder systems in reducing no-show rates[END_REF]. Various options for maintaining patients in -Third, our study illustrates the poor immune recovery among patients with PCP who had previously been diagnosed with AIDS, and their high 3-year mortality rate. Chronic immune activation certainly plays an important role, and it could be interesting to look at immunological differences between patients with PCP revealing their HIV infection and patients who develop PCP after being diagnosed with another ADI. In the first chapter, pages 50-57, we discuss immune dysregulation during HIV infection with persistent immune activation, inflammation and coagulation processes. Immune failure and inflammation are linked, and are probably the consequence of lymph node fibrosis and sustained damage to the gut. Lederman M summarized different lines of research, and the results of previous and ongoing studies [START_REF] Lederman | Residual immune dysregulation syndrome in treated HIV infection[END_REF]. They include:

-targeting residual viral replication, although most studies have shown no benefit of treatment intensification [START_REF] Dinoso | Treatment intensification does not reduce residual HIV-1 viremia in patients on highly active antiretroviral therapy[END_REF][START_REF] Gandhi | The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: a randomized controlled trial[END_REF][START_REF] Hatano | A randomized, controlled trial of raltegravir intensification in antiretroviraltreated, HIV-infected patients with a suboptimal CD4+ T cell response[END_REF][START_REF] Hunt | Response: Maraviroc intensification and microbial translocation[END_REF] -targeting chronic viral coinfections: asymptomatic CMV replication could contribute -targeting innate immune responses with drugs that have anti-inflammatory properties, but the efficacy of this approach needs to be confirmed in larger clinical trials.

Interventions to inhibit fibrosis and the disrupted stromal fibroblastic reticular cell in secondary lymphoid tissues are also interesting approaches to immune reconstitution, but currently the best route to immune reconstitution remains early diagnosis and cART initiation.

For patients with a history of ADI before developing PCP, who had slower immune reconstitution in our study, switching to integrase inhibitor-containing cART could be an option. Immune reconstitution seemed to be improved in cART-naïve patients on a regimen that included an integrase inhibitor [START_REF] Costagliola | CD4+ cell count recovery in naïve patients initiating cART, who achieved and maintained plasma HIV-RNA suppression[END_REF] and this approach could also be explored in previously treated patients.

Our second study focused on invasive aspergillosis in HIV-infected individuals. Using strict criteria, we validated 242 cases. However, half these cases did not meet the EORTC definition, confirming that it is not appropriate for the HIV/AIDS setting. As early diagnosis and treatment of invasive aspergillosis is vital, accurate diagnostic criteria are crucial.

Furthermore, as invasive aspergillosis is rare in HIV-infected individuals (2.2 cases per 10000 PY (1.8-2.6) in the 2002-2011 period of our study), this diagnosis is rarely evoked and treatment delays can therefore occur. In order to hasten diagnosis, we tried to find clinical criteria for validated cases that did not meet the EORTC definition. We found that the polynuclear cell count could not be used as a risk indicator for invasive aspergillosis in this setting. However, the median CD4 cell count was below 100/mm 3 at diagnosis of invasive aspergillosis, even in the last period studied here, and we therefore propose to add "HIVinfected individual with a CD4 cell count below 100/mm 3 " to the current EORTC definition, after validation. To further improve our case definition, we plan to review all CT scans recorded since 2002. In 2008, the term "new radiological image" used in the 2002 EORTC definition was replaced by the presence of at least one of the following three signs: dense, well-circumscribed lesions(s) with or without a halo sign, air-crescent sign, and cavity. We will see if we confirm these signs in the context of HIV infection, by comparing the radiological aspects of "EORTC IA" and "HIV-related IA". As we have seen, we cannot rely on Galactomannan antigen for the diagnosis of invasive aspergillosis. Aspergillus PCR is now better standardized for faster diagnosis. Predisposing genetic factors also need to be investigated. For example, genetic polymorphisms such as PTX3 have been shown to predispose allograft and solid organ transplant recipients to invasive aspergillosis (Cunha et al., 2014, p. 3;Wójtowicz et al., 2015).

In conclusion, we demonstrate that fungal infections among HIV-infected individuals are still a major issue in 2016, even in resource-rich settings. We are now planning to study cryptococcosis in the FHDH cohort, as this is another fungal infection occurring at very low CD4 cell counts. It is a frequent opportunistic infection in low income countries, with a ~50% mortality rate in the first 2 weeks, but it is now rare resource-rich settings. We examined trends in the incidence of cryptococcosis over time and found it was 10 times lower in the period 2002-2011 (4.5 (3.9-5.2) /10 000 PY) than in 1992-1995 (47.5 (42.5-52.5) /10 000 PY). We will examine who is most at risk nowadays, as well as changes in mortality over time, and the time interval between antifungal therapy and cART initiation.

Beyond epidemiological trends in these fungal infections, our results underline the need for more efficient HIV screening and better long-term retention in care, which should be considered as a quality indicator of patient management.

TERRAIN / AFFECTION SOUS-JACENTE DANS LES 6 MOIS PRECEDENTS L'AI

-Hématologie: Non q Oui q NSP (Ne Sait Pas) q

Si oui, préciser : Date de découverte : |___|___| |___|___| |___|___|___|___| Lymphome : Hodgkin q LNH q Leucémie : LAL q LAM q LLC q Greffé de moelle : Allogreffe q Autogreffe q Autre (myélome, aplasie médullaire, myélodysplasie) q -Pulmonaire: Non q Oui q NSP q Si oui, préciser :

BPCO r Asthme r DDB (dilatation des bronches) r -Tumeur : Non q Oui q NSP q Si oui, préciser : Date de découverte : |___|___| |___|___| |___|___|___|___| Pulmonaire q ORL q Digestif/hépatique q Kaposi q Autre q -Patient transplanté : Non q Oui q NSP q Si oui, préciser :

pulmonaire r cardiaque r hépatique r rénal r -Traitement prédisposant à l'AI: Non q Oui q NSP q Si oui, préciser :

Corticoïdes (≤2 mois avant l'AI) q Dose journalière (en mg) :……….. Type de corticoïdes : solumédrol q , cortancyl q , solupred q , soludecadron q Chimiothérapie (≤1 mois avant l'AI) q

(cure de chimio pour tumeur ou pathologie hémato)

CRITERES CLINIQUES ET RADIOLOGIQUES DE L'AI

-Infection pulmonaire Non q Oui q NSP q Si oui, préciser :

Signes cliniques : toux r douleur thoracique r dyspnée r hémoptysie r

Scanner thoracique : Fait q Non fait q

Joindre une photocopie anonymisée de la conclusion du scanner -Infection des sinus Non q Oui q NSP q Si oui, préciser :

Signes cliniques : sinusite r atteinte de la muqueuse nasale r atteinte du palais r Scanner des sinus :

Fait q Non fait q Joindre une photocopie anonymisée de la conclusion du scanner -Infection du système nerveux central Non q Oui q NSP q Si oui, préciser :

Signes cliniques : méningite r convulsions r paralysie d'1 nerf cranien r hémiparésie r

Scanner ou IRM cérébrale : Fait q Non fait q Joindre une photocopie anonymisée de la conclusion du scanner ou de l'IRM -Autres sites éventuels Non q Oui q NSP q Si oui, préciser la localisation : cutané r endocardite r infection du site opératoire r autre r :…………………..

CRITERES MYCOLOGIQUES

Remarque : Prendre les résultats positifs les plus proches de la date de l'AI.

Antigène aspergillaire : sérique (dans le sang) q LBA (Lavage BronchoAlvéolaire)q non fait q Si fait, résultats : -sérique : positif (>0,5) q négatif (<0,5) q douteux q -LBA : positif (>0,5) q négatif (<0,5) q douteux q Sérologie aspergillaire (Anticorps (=Ac) aspergillaire): fait q non fait q

Si fait, résultats : positif q négatif q Autres (pour les cas>2007):

PCR aspergillus : fait q non fait q NSP q ßD glucane : fait q non fait q NSP q Si fait : positif q négatif q Si fait: positif q négatif q Isolement d'une souche d'aspergillus : Non q Oui q NSP q Examen direct : positif (présence de filaments) q négatif q non fait q NSP q Histologie : positif (joindre photocopie) q négatif q non fait q NSP q Culture : positif (présence d'aspergillus) q négatif q non fait q NSP q Si aspergillus + en culture :

Site où l'aspergillus a été isolé : voies respiratoires q autres q préciser :……………………… Genre/espèce d'aspergillus : A.fumigatus q A.flavus q A.nidulans q Autre q Histoire de la maladie par VIH Date première sérologie VIH positive :

|___|___| |___|___| |___|___|___|___|

Traitement ARV au moment du diagnostic d'AI : Non q Oui q NSP q Traitement ARV dans le mois suivant le diagnostic d'AI : Non q Oui q NSP q Bilan biologique et immunologique :

Remarque : Prendre les résultats au plus près de la date de AI. Au maximum, des résultats datant de 3 mois avant à 2mois après l'évènement. EXERESE CHIRURGICALE (de la lésion aspergillaire): Non q Oui q NSP q CONCLUSION (à remplir par Blandine) : Aspergillose possible q probable q prouvée q exclue q Critères utilisés pour la conclusion : Hôte q Clinique q Radio q Bio q Microbio q Remarques :

Taux

EVOLUTION

Le patient est-il décédé ?

Non q Oui q NSP q Si oui :

Date

Pathologies ayant contribué au décès :

-……………………………………………… -……………………………………………… Merci de joindre une copie anonymisée du CR de décès

  Professeur David W Denning et Monsieur le Professeur Hansjakob Furrer d'avoir accepté d'être rapporteurs de ma thèse. Ils me font l'honneur de juger mon travail. Monsieur le Professeur Willy Rozembaum d'avoir accepté d'être membre du jury de ma thèse. Je remercie, Monsieur le Professeur Jean-Michel Molina, pour m'avoir permis de mener à bien ces travaux, pour sa disponibilité et son écoute. Sa rigueur scientifique et sa détermination à réaliser ses projets sont un exemple pour tous. Tous mes collègues de l'unité INSERM 1136 pour les bons moments passés en leur compagnie. L'ANRS qui m'a permis d'effectuer ce travail. Ma famille qui m'a accompagnée et soutenue pendant toutes ces années. Merci pour votre présence, votre patience et votre disponibilité sans faille. Introduction Chapter 1. State of the art: fungal infections in individuals living with HIV a) PCP and the discovery of the HIV/AIDS pandemic i) "An outbreak of community-acquired Pneumocystis carinii pneumonia: Initial manifestation of cellular immune dysfunction" ii) PCP: characteristics iii) PCP: trends over time b) Other fungal infections in HIV-infected individuals iof invasive aspergillosis (IA) in the FHDH a) Selection of patients b) Data collection: national retrieval of medical records c) Validation of IA cases 4) Statistical methods a) Estimation of prevalence and incidence in the FHDH i) PCP ii) Invasive aspergillosis (IA) b) Survival estimates for PCP and invasive aspergillosis i) PCP ii) Invasive aspergillosis c) Study of risk factors using Cox proportional hazards models i) PCP ii) Invasive aspergillosis (IA) Chapter 3. Trends in PCP among HIV-infected individuals in France in the cART era Article 1. Critical importance of long-term adherence to care in HIV infected patients in the cART era: new insights from Pneumocystis jirovecii pneumonia cases over 2004-2011 in the FHDH-ANRS CO4 cohort. Denis B, Guiguet M, de Castro N, Mechaï F, Revest M, Mahamat A, Gregoire GM, Lortholary O, Costagliola D, PLoS One. 2014 Apr 11;9(4):e94183. doi: 10.1371/journal.pone.0094183. eCollection 2014.

  , que des indicateurs de suivis devraient être intégrés dans les services prenant en charge des personnes infectées par le VIH et que ces indicateurs devraient faire parti des bonnes pratiques de suivi des patients. Nous sommes actuellement en train de travailler sur un indicateur de suivi et aimerions créer un système d'alerte dès que le patient commence à espacer son suivi. Nous devons également travailler avec les structures non hospitalières, et en 1 er lieu avec les médecins généralistes afin de fluidifier les passerelles entre la ville et l'hôpital. Le délai optimal de suivi entre 2 consultations par un spécialiste reste débattu et les médecins de proximité sont d'indispensables relais quand le patient commence à espacer son suivi. Par ailleurs, notre étude a montré que la reconstitution immunitaire étaient moins bonne chez les patients déjà suivis dans la base FHDH avec un diagnostic de pneumocystose que chez les patients présentant une pneumocystose inaugurale du VIH (HR d'avoir des CD4 >200/mm 3 après le diagnostic : 0.7 (0.6-0.9) pour les patients déjà suivis dans la base FHDH mais sans ADI avant la pneumocystose et 0.6 (0.4-0.8) chez les patients déjà suivis dans la base FHDH mais sans ADI avant la pneumocystose, reference : patients ayant une pneumocystose inaugurale du VIH). De plus, pour les patients suivis dans la base FHDH et ayant déjà eu une ADI avant la pneumocystose, la mortalité à 3 ans était élevée (25%), alors qu'elle était de 8% chez les patients suivis dans la base FHDH et sans ADI avant la pneumocystose et de 9% chez les patients ayant une pneumocystose inaugurale du VIH. En comparant les patients suivis dans la base FHDH et ayant déjà eu une ADI avant la pneumocystose avec les patients ayant une pneumocystose inaugurale du VIH, le pronostic restait péjoratif, même après ajustement sur le contrôle virologique et la reconstitution immunitaire (HR, 2.4 (IC 95%, 1.5-3.7)). Chez les patients ayant déjà présentés une ADI avant la pneumocystose, le déficit immunitaire persiste au-delà d'une remontée des CD4 sérique et il serait intéressant d'étudier plus finement les caractéristiques immunologiques de ces patients. Des alternatives thérapeutiques, notamment sur le choix de traitement antirétroviral (en privilégiant notamment les anti-intégrases) pourraient être proposées dans cette population de patients ayant déjà présentés une ADI afin d'optimiser au maximum la reconstitution des cellules CD4 naives et mémoires de l'organisme et la baisse de l'inflammation résiduelle observée chez les patients en échappement virologique. En conclusion de ce premier travail, nous avons pu démontrer que si nous voulons améliorer l'incidence et le pronostic des patients présentant une pneumocystose, nous devons réussir à optimiser le suivi à long terme, et notamment pour les patients suivis depuis de longues années qui avaient déjà fait une ADI dans le passé. Nous devons mettre en place des indicateurs de qualité de suivi et les intégrer dans les bonnes pratiques médicales de suivi de patients infectés par le VIH. Par ailleurs, comme 50 % des patients présentaient une pneumocystose inaugurale du VIH, des efforts particuliers doivent être mis en oeuvre afin de détecter les patients qui ignorent leur séropositivité et nous devons réfléchir à de nouvelles politiques de dépistage du VIH en France. Notre second travail portait sur les aspergilloses invasives (IA) chez les patients infectés par le VIH. Les publications avant l'ère des cART avaient montré que cette infection fongique était très rare chez les patients infectés par le VIH et de pronostic catastrophique, avec une médiane de survie à 3 mois. L'aspergillose invasive survenait chez des patients avec des taux de CD4 bas, et dans la moitié des cas les facteurs classiques prédisposant à l'aspergillose invasive (neutropénie, corticothérapie) étaient absents. Depuis ces publications, le nombre de diagnostic de cancers a augmenté chez les patients infectés par le VIH, avec des neutropénies post chimiothérapie et des corticothérapies prescrites, ceci pouvant potentiellement favoriser la survenue d'aspergillose invasive. Dans ce contexte, nous avons souhaité étudier l'évolution de l'incidence de l'aspergillose invasive chez les patients infectés par le VIH. Nous avons également étudié les caractéristiques des patients au diagnostic d'aspergillose invasive, les méthodes diagnostic et regardé comment la classification EORTC habituellement utilisée en hémato-oncologie pour classer les aspergilloses invasives pouvait être utilisée dans ce contexte. Un retour national sur dossiers a été entrepris afin d'avoir les données nécessaires à la validation de tous les cas déclarés en regardant plus spécifiquement les critères EORTC. Quand les cas d'aspergilloses invasives correspondaient à la définition EORTC, ils étaient classés en « EORTC IA », sinon, les cas validés après analyse des données cliniques, microbiologiques et radiologiques et ne rentrant pas dans la définition EORTC étaient classés en « HIV related IA ». Sur une période de 20 ans, 242 cas d'aspergilloses invasives ont ainsi été validés sur la base FHDH. L'incidence de l'aspergillose invasive dans la FHDH a diminuée sur la période d'étude, passant de 19/10000 PatientAnnée (PA) ((95% CI, 16.0-23.0) sur la période 1992-1995 à 2.2 /10 000 PA (95% CI, 1.8-2.6) en 2002-2011. Le ratio d'EORTC IA sur le nombre de cas d'IA validés est resté stable au cours du temps

  d'hôte correspondant à la définition EORTC. La médiane de CD4 au diagnostic d'aspergillose invasive a augmenté au cours du taux mais restait inférieure à 100/ mm 3 (médiane à 9/mm 3 (IQR, 4-26) en 1992-1995, 18/mm 3 (IQR, 9-80) en 1996-2001 et 82/mm 3 (IQR, 12-327) en 2002-2011 (p< 0.0001)), alors que la médiane de taux de polynucléaires neutrophiles était supérieure à 1500/mm 3 dans les 2 dernières périodes étudiées (1263/mm 3 (760-2535) en 1992-1995, 1500/mm 3 (700-3004) en 1996-2001, 1810/mm 3 (500-3920) en 2002-2011 (p=0.5)). Afin de faciliter le diagnostic d'aspergillose invasive chez les patients infectés par le VIH, nous proposons d'inclure le paramètre "avoir des CD4 inférieurs à 100/mm 3 " comme facteur d'hôte prédisposant, mais cette proposition devra être validée par une étude prospective. Avec une médiane de survie à 3 mois après le diagnostic d'aspergillose invasive à l'ère des pré-cART, nous avons postulé que la survie serait meilleure après la disponibilté des cART à partir de 1996. Le pronostic des patients infectés par le VIH s'est transformé après 1996, et le prognostic des patients atteints d'aspergillose invasive en oncohématologie s'est amélioré après la disponibilité de l'amphotéricine B liposomale en 1997 puis du voriconazole en 2002. Ainsi, nous avons défini 3 périodes d'étude pour le suivi évolutif des aspergilloses invasives : pré-cART et pré

  1 months) pendant la 1ère période, à 10.3 mois (IQR, 2->100 mois) et 29 mois (IQR, 2.2-98.2 mois) durant les 2 dernières périodes. Après 2002, les patients sous voriconazole ont vu leur survie s'améliorer avec une diminution importante du risque de mortalité à 3 mois (HR= 0.1 (95% CI, 0.01-0.80). Ces résultats plaident pour l'utilisation du voriconazole en 1ère intention dans l'aspergillose invasive chez les patients infectés par le VIH. L'aspergillose invasive reste de diagnostic difficile chez les patients infectés par le VIH, l'addition de la donnée "avoir des CD4 bas" comme facteur d'hôte pourrait en faciliter le diagnostic. Un taux de CD4 inférieur à 100/mm 3 semble être approprié pour une nouvelle definition des facteurs d'hôte, mais d'autres etudes seraient nécessaires pour valider cette proposition. Nous planifions également de comparer les aspects radiologiques des patients classés en EORTC IA et en HIV related IA afin d'évaluer les differences éventuelles et de les comparer aux critères radiologiques de la definition EORTC 2008.

  harmless in a context of normal host responses, but immune deficiencies, particularly in HIV-infected individuals, result in significantly increased susceptibility to many fungal infections. During the early years of the AIDS pandemic, Pneumocystis jirovecii pneumonia (PCP) accounted for two-third of AIDS-defining illnesses among patients in the USA, and an estimated 75% of HIV-infected individuals developed PCP during their lifetime

Chapter 1 .

 1 State of the art: fungal infections and HIV a. PCP and the discovery of the HIV/AIDS pandemic i. "An outbreak of community-aquired Pneumocystis carinii pneumonia: Initial manifestation of cellular immune dysfunction" The Morbidity and Mortality Report (MMWR) reported the first cases of what would become the HIV pandemic in June 1981: 5 previously healthy homosexual men (MSM) in Los

(

  Pneumocystis workshop 10 th anniversary eukaryotic cell 2009) Pneumocystis spp. are extracellular, obligate, host-specific, yeast-like parasitic fungi virtually restricted to lung tissues. The morphological forms range in size from 1 to 10 µm. Members of the fungal genus now known as Pneumocystis were first identified in 1909 by Carlos Chagas in the lungs of guinea pigs that had been experimentally infected with Trypanosoma cruzi. In 1910, Carini was studying Norway rats infected with another trypanosome, Trypanosoma lewisi, and noted the same cystic aspect. In 1912, Delanoë and Delanoë noted the presence of cysts in the lungs of Paris sewer rats free of trypanosome infection and suggested that they were due to a new parasitic species that they named Pneumocystis carinii.

  in the lung. Immune control of Pneumocystis also involves production of chemokines and inflammatory cytokines by alveolar macrophages and epithelial cells. CD4 T cells are essential for the control of Pneumocystis infection. Clinical manifestations of PCP are nonspecific. Patients classically present with a fever of several days or weeks duration, nonproductive cough, and progressive dyspnea, often with normal pulmonary auscultation. Symptoms are usually of longer duration before diagnosis in HIV-infected individuals than in other immunosuppressed patients.

Figure 1

 1 Figure 1

  All reported cases of AIDS-associated paracoccidioidomycosis have occurred in Brazil, apart from one case reported in Venezuela. Most patients had disseminated disease, with advanced AIDS and CD4 cell counts well below 200/µL.Diagnosis of paracoccidioidomycosis is usually based on direct microscopic examination and culture of clinical specimens, most commonly skin and lymph nodes. Culture of blood, bone marrow, and sputum may also be positive. Tests for P. brasiliensis antigen and PCR for P. brasiliensis DNA are promising new diagnostic tools.First-line therapeutic options include trimethoprim-sulfamethoxazole, amphotericin B, ketoconazole, and itraconazole.

  culture and histologically proven aspergillosis in immunocompromised patients, including AIDS patients. The Aspergillus species most often implicated are fumigatus, flavus, niger and terreus. Detection of galactomannan antigen in serum or bronchoalveolar lavage fluid, and/or Aspergillus PCR, may help to establish the diagnosis of invasive disease.

Figure 3 .

 3 Figure 3. Collagen deposition and damage to the FRCn in HIV infection. (a) In the T cell zone of LNs from uninfected individuals, naïve T cell survival depends on interaction with IL-7 produced and 'posted' on the surface of FRCns. (b) During the acute phase of HIV-1 infection, T cells are depleted by direct viral killing and other mechanisms such as AICD. However, immune activation also elicits a T regulatory response that activates TGFb signaling in fibroblasts, resulting in cumulative collagen deposition. Collagen deposition and depletion of the FRCn impedes access of T cells to the survival factor IL-7 on the FRCn, and reduces the production of IL-7 within LTs, thereby causing increased apoptosis of naïve T cell populations. (c) As the infection progresses, depletion of T cells decreases LTb, and this, compounded by collagen-impeded access to LTb for the FRCn, results in further loss of FRCn and IL-7. Loss of the FCRn leads to further T cell depletion, particularly in naïve T cell populations. (d) This model summarizes the 'vicious cycle' model of T cell depletion, encompassing the key pathological events described in (a-c): chronic immune activation in HIV-1 and SIV infection elicits a T regulatory response that activates TGFb1 signaling in fibroblasts, resulting in cumulative collagen deposition. Collagen deposition and loss of the FRCn together cause increased apoptosis, which, along with AICD, depletes T cells. Depletion of T cells decreases LTb, which, along with collagen-impeded access to LTb for the FRCn, results in loss of the FRCn and IL-7. This vicious cycle of survival interdependencies and collagen deposition cause progressive T cell depletion, particularly in na ïve T cell populations. HAART can prevent the loss of CD4 + T cells due to the direct effects of infection and normalize immune activation, thereby reducing losses of CD4 + T cells due to AICD. However, pre-existing collagen deposition, loss of the FRCn and T cell depletion will limit immune reconstitution by the continued cyclical mechanisms. Abbreviations: FRCn, fibroblastic reticular cell network; LNs, lymph nodes; IL, interleukin; AICD, activation-induced cell death; TGF, transforming growth factor; LTs, lymphoid tissues; SIV, simian immunodeficiency virus; HAART, highly active antiretroviral therapy.

  This part is inspired by an article from Murielle Mary Krause, Int J Epidemiol 2014. a) Creation of the FHDH -ANRS CO4 cohort (FHDH) The French Hospital Database on HIV is a multi-hospital open cohort in which inclusions have been ongoing since 1989, with the aim of collecting clinical information on HIV-infected patients managed in reference HIV treatment and information centers (CISIH: Centers d'Information et de Soins de l'Immunodeficience Humaine) created by the French Ministry of Health in 1987. Patients are eligible if they are infected by HIV-1 or HIV-2; are managed in a participating center; and give their written informed consent. The French Ministry of Health funds technical research assistants who devote half their time to clinical research and the other half to FHDH data collection in the participating centers. The data thus collected are used to describe HIV-infected patients receiving hospital care in France, as well as HIV disease outcomes and their determinants, including antiretroviral treatment (ART). The project was approved by the French computer watchdog authority (CNIL) on 27 November 1991 (Journal Officiel, 17 January 1992). Because of the need to return to the patient medical records to validate data for specific research projects, CNIL approval for a local correspondence list was obtained in 1999. The database includes data from 70 hospitals or wards distributed among 26 of the 28 COREVIH (Coordination régionale de la lute contre le VIH). Since its creation, FHDH has been supported by INSERM (French National Institute of Health and Medical Research) and the French Ministry of Health. It became an ANRS (French National Agency for Research on AIDS and Viral Hepatitis) cohort (CO4) in 1996. FHDH now includes data from 70 general or university hospitals located in 21 of the 26 French regions, including overseas departments (Aquitaine, Picardie, Poitou-Charentes, Limousin and Corse do not participate). b) Objectives The FHDH cohort is one of the largest of its type in the world, and the research projects draw on the biggest advantage of the database, namely its size. Care is taken not to encroach on other ANRS research topics. The areas of research include: -Therapeutics strategies: mid-and long-term clinical outcomes, including causal inference models of observational data -Severe AIDS and non AIDS morbidity/mortality: role of HIV infection and of exposure to antiretroviral treatments in impaired renal function, fractures, malignancies and cardiovascular diseases -Public health issues surrounding HIV infection in France -Open themes: Any participating center or researcher can submit a project to the scientific committee In addition, 2 strategic groups have been created to develop specific projects on migrants and on HCV co-infection. A scientific committee with a maximum of 40 members, regularly renewed, debates FHDH research themes and selects projects according to their feasibility and scientific pertinence. The French Hospital Database has numerous collaborations, including ART-CC, EUROCOORD (NOE FP7 2011-2015, CASCADE and COHERE) and HIV Causal. Besides research projects, the database allows the epidemiology of HIV infection in patients in hospital care in France to be analyzed (in France, ARV treatments can only be initiated or changed in hospital). The completeness of the database was around 53% in 2009, and the database is representative of patients in care in France. The database has been used to evaluate the public health impact of antiretroviral drugs, with 13 contracts involving 3 partners (INSERM, INSERM Transfert, pharmaceutical companies) either ongoing or completed. The data can also be used to estimate the cost of care for HIV-infected individuals, represented mainly by antiretroviral drugs (62%) and hospitalization (31%). c) Data collected The database includes data from 70 hospitals or wards distributed among 26 of the 28 COREVIH (Coordination régionale de la lute contre le VIH). The database includes data on over 128 000 patients aged at least 15 years and seen at least once between 1 January 1992 and 31 December 2012, with a mean follow-up of 88 months. Updates are ongoing, following a change in the software used for data collection. Since the creation of FHDH, collected baseline variables have included date of birth, gender, geographic origin, HIV transmission group, height, date of primary infection (when known) and dates of the last negative (when known) and first positive HIV tests. Variables collected at each follow-up visit include weight; standard biological markers such as the CD4 cell count and plasma HIV-RNA level; blood cell counts, lipids and liver enzymes; the date and type of AIDS and non-AIDS events, using the International Disease Classification; antiretroviral treatments and prophylaxis of opportunistic infections; and the dates and causes of death, as reported in the medical records. Since 2005, additional data have been collected on alcohol and tobacco use; serological and virological data on co-infection with hepatitis B or C virus; and liver biopsy results. Of note, FHDH linkage with the French deaths registry is not authorized. Data are collected prospectively by trained research assistants, using either dedicated software provided by the French Ministry of Health, or computerized medical records. Standardized variables are collected at each outpatient visit or hospital admission during which a new clinical manifestation is diagnosed, a new treatment is prescribed, or a change in biological markers is noted, and/or at least every 6 months. Many validation procedures are implemented before inclusion of the data into the database, as well as local audits, to ensure the quality of the data. d) Published results from FHDH Since 1992, 192 publications based on FHDH data have been published in peerreviewed journals, including 104 since 2010.Regarding mid-and long-term clinical outcomes, research based on the FHDH showed that an immunological response at 6 months was predictive of better clinical outcome, regardless of the virologic response. Studies conducted within ART-CC and HIV Causal showed that treatment initiation at a CD4 cell count above 350/mm 3 was beneficial in terms of AIDS events and mortality. This has just been confirmed by the START trial. Within COHERE, studies showed the public health benefit resulting from the arrival of new antiretroviral drugs in the period 2000-2009 among patients in whom the first three antiretroviral families had failed.In the research theme "role of HIV infection and of exposure to antiretroviral treatments", research from FHDH showed a doubling of the incidence of non AIDSdefining cancers among people living with HIV by comparison with the general population of the same age and gender, even in the era of combination antiretroviral therapy. It was also demonstrated that immunosuppression is a major risk factor both for AIDS-defining cancers (non-Hodgkin's lymphoma, Kaposi's sarcoma, cervical cancer) and for non-AIDS cancers (lung, liver, anal canal, Hodgkin's disease). More recently, research from FHDH showed that patients whose viral load is controlled by treatment and whose CD4 cell count is restored to more than 500/mm 3 for at least 2 years no longer have a higher risk of non-Hodgkin's lymphoma than the general population. A similar result was obtained for the risk of MI. A case-control study nested within the FHDH cohort showed that the risk of myocardial infarction was increased by exposure to first-generation protease inhibitors, confirming FHDH results published in 2003 (the first to show this association), and that the link to abacavir exposure could not be considered causal. HIV replication and immune status (CD4 nadir, current CD8) were also shown to influence the risk of myocardial infarction, independently of traditional risk factors and antiretroviral drug exposure.Regarding public health issues surrounding HIV infection in France, FHDH results contributed to the discovery that a large proportion of HIV-infected patients enter care late in France. This work has recently been updated to reflect the new definition of late management, namely a CD4 cell count below 350/mm 3 or AIDS status at the first hospital visit. FHDH studies showed that nearly one in two patients is managed late and that this late management increases the risk of death for up to 4 years after treatment initiation, by comparison with more timely management, even among individuals with only moderate immunosuppression (CD4 cell count between 200 and 350/mm 3 ).Since the creation of FHDH, we have been able to study epidemiological trends in opportunistic infections among HIV-infected individuals in France. For PCP, incidence rates in the FHDH were as high as 18.5/1000 in 1992, falling to 4.7/1000 PY [4.0-5.4] in 1997 and 2.7/1000 PY [2.2-3.1] in 2006 (RICE data). With the availability of cART, a study from FHDH showed that PCP/toxoplasmosis

  Pneumocystis jirovecii pneumonia (PCP) in the FHDH a) Definition of cases PCP diagnosis was considered definitive if there was histologic or cytologic evidence of P. jirovecii in bronchoalveolar lavage, sputum and/or lung biopsy specimens. The diagnosis was considered presumptive if there was a recent history of dyspnea or nonproductive cough in the absence of evidence of bacterial pneumonia, and a positive clinical response to PCP therapy.A previous study of PCP in the FHDH cohort showed that recorded diagnoses of PCP were accurate (88.5% of 455 definitive diagnoses of first episodes of PCP were confirmed[START_REF] Abgrall | Pneumocystis carinii pneumonia recurrence in HIV patients on highly active antiretroviral therapy: secondary prophylaxis[END_REF]).b) Selection of patientsIn order to study trends in PCP in France during the period 2004-2011, we selected HIV-infected individuals from the FHDH cohort who had a first diagnosis of PCP. Among 85 743 patients followed in the FHDH between 01/2004 and 12/2011, 1721 patients were diagnosed with PCP, of whom 1488 had a first episode of PCP during the study period. Furthermore, to analyze immunovirological outcomes after PCP, we excluded 169 patients with no available CD4 cell count within 3 months of PCP diagnosis, and 60 patients without available follow-up. Among the 1259 patients selected for the study, we compared baseline characteristics and outcomes between HIV-infected individuals previously enrolled in the FHDH and patients in whom PCP revealed their HIV infection. As a prior history of AIDS-defining illness (ADI) has been shown to influence the prognosis, previously enrolled patients were divided into 2 groups: those with a prior history of AIDS-defining illness (ADI) and those without a prior history of ADI. ADI was defined as a category C illness in the 1993 CDC criteria.3) Study of invasive aspergillosis (IA) in the FHDHa) Selection of patients Unlike PCP and toxoplasmosis, invasive aspergillosis is a rare and difficult diagnosis in HIV-infected individuals. Diagnosis often relies on clinical-radiological features, and specific biopsies are rarely done. Some biological data, such as the neutrophil count, are not systematically recorded in the database, and neither are specific microbial data on aspergillosis and radiological information. Thus, in order to study invasive aspergillosis in the FHDH, we first reviewed the medical charts of preselected patients. We first selected all HIV-infected individuals enrolled between 01/1992 and 12/2011, with ICD-9 or ICD-10 code B44 (aspergillosis): B440 (invasive pulmonary aspergillosis), B441 (other pulmonary aspergillosis), B442 (tonsillar aspergillosis), B447 (disseminated aspergillosis), B448 (other aspergillosis) or B449 (aspergillosis unspecified). This first selection was undertaken in 2012, when 515 patients were found to have corresponding ICD codes. Participating centers were contacted and authorization to retrieve the medical records was obtained from the heads of department. b) Data collection: national retrieval of medical records Four clinical research assistants working at INSERM UMRS 1136 retrieved medical records from the different clinical centers between May 2012 and May 2013. I first informed them of the specificities of aspergillosis, invasive aspergillosis and aspergillosis in HIV-infected individuals.

  was estimated with the Kaplan Meier method, and Cox proportional hazards models were used. Baseline characteristics of the patients at the time of fungal diagnosis were compared by using the χ2 test for categorical variables and the Kruskal-Wallis test for continuous variables. All statistical analyses used the SAS software package (version 9.3; SAS Institute, Cary, NC, USA). a) Estimation of prevalence and incidence in the FHDH: i) PCP The incidence of PCP among previously enrolled patients was calculated for each year during the study period by dividing the number of PCP cases among previously enrolled patients by the number of person-years of follow-up during the relevant year in the cohort. The frequency of inaugural PCP (revealing HIV infection) among newly enrolled patients was calculated for each year during the study period by dividing the number of PCP cases in the reference group by the number of new patients included in the cohort during the same year. Trends in the proportion of patients diagnosed with PCP during the study period among all previously enrolled patients was compared by using the Cochran Armitage test for trend.

  were then calculated for each period by dividing the estimated number of IA cases by the corresponding number of person-years (PY) of follow-up. b) Survival estimates for PCP and invasive aspergillosis: i) PCP We compared immune reconstitution and survival after PCP diagnosis across the different patient groups. We wanted to determine if previously enrolled patients, who could have been on cART before PCP onset, had the same capacity for immune reconstitution as patients with inaugural PCP. Furthermore, we analyzed survival three years after PCP onset according to baseline characteristic at PCP diagnosis, adjusting for immune reconstitution and virological control after PCP. We defined immune reconstitution as a CD4 cell count above 200/mm 3 after PCP diagnosis for patients with counts < 200/mm 3 at PCP diagnosis. We defined virological control as HIV viral load [VL] ≤50 copies/ml. The study of immune reconstitution after PCP onset involved the 1145 patients with CD4 cell counts < 200/mm 3 at PCP diagnosis. Data were censored three years after PCP diagnosis. ii) Invasive aspergillosis As survival has improved among HIV-infected individuals with the availability of cART, and among hematological patients with invasive aspergillosis (IA) with the availability of voriconazole, we studied three periods: pre-cART and pre-voriconazole (<1996), post-cART and pre-voriconazole (1996-2001), and post-cART and postvoriconazole. Kaplan-Meier estimates were used to study three-month survival rates after IA diagnosis in HIV-infected individuals, and to compare them across the three periods. Kaplan-Meier survival estimates were compared between patients with "EORTC IA" and those with "HIV-related IA". c) Study of risk factors in Cox proportional hazards models i) PCP Cox proportional hazards models were used to identify factors associated with survival or immune reconstitution, including the patient subgroup (HIV-infected individuals with inaugural PCP vs previously enrolled patients), age (<30 years, >30 to <50, and ≥ 50), region of origin (sub-Saharan Africa, others), the HIV exposure category (men who have sex with men (MSM), intravenous drug users (IDU), heterosexuals), the CD4 cell count at PCP diagnosis (CD4 <50/mm³, 50 ≤CD4< 100, 100 ≤CD4 <200, CD4≥ 200), and HIV viral load at PCP diagnosis (VL <5 log copies/ml, VL ≥5 log copies/ml). In the Cox model for immune reconstitution, virological control (VL ≤50

  second part of our work was an analysis of invasive aspergillosis (IA) among HIVinfected individuals over a 20-year period in the FHDH cohort. Work published before the advent of cART had shown that invasive aspergillosis was a rare but dreadful event in HIV-infected individuals, with a median survival time of only 3 months after diagnosis of invasive aspergillosis. Invasive aspergillosis occurred in patients with low CD4 cell counts, half of whom did not have classical predisposing host factors (neutropenia, corticosteroid use). Since these publications, cancer diagnoses have increased among HIV-infected individuals, leading to more chemotherapy-induced neutropenia and corticosteroid use, and new host-related risk factors for invasive aspergillosis.

  patients with validated IA did not have the classical predisposing host factors selected as criteria for the EORTC IA definition. The median CD4 cell count at IA diagnosis increased slightly over time but remained low (median 9/mm 3(IQR, 4-26) in 1992-1995, 18/mm 3 (IQR, 9-80) in 1996-2001 and 82/mm 3 (IQR, 12-327) in 2002-2011 (p< 0.0001)), while the median neutrophil count was above 1500/mm 3 in the last 2 periods (1263/mm 3 (760-2535) in 1992-1995, 1500/mm 3 (700-3004) in 1996-2001, 1810/mm 3 (500-3920) in 2002-2011 (p=0.5)). In order to facilitate the diagnosis of invasive aspergillosis in HIVinfected individuals, we propose to include the parameter "CD4 cell count below 100/mm 3 " as a predisposing host factor, although this should first be validated in a prospective study. With a median survival time of only 3 months after diagnosis of invasive aspergillosis in the pre-cART era, we assumed that survival would have improved after cART became available in 1996. The prognosis of HIV-infected individuals improved dramatically after 1996, while that of hematological patients with invasive aspergillosis improved with the advent of liposomal amphotericin in 1997 and voriconazole in 2002. We defined three periods to study time trends in the outcome of invasive aspergillosis: pre-cART and pre-

  care (see below) are listed in the IAPAC guidelines for optimizing the HIV care continuum (International Advisory Panel on HIV Care Continuum Optimization, 2015), and we are now also working on indicators of adherence to care in the FHDH cohort.

  to persistent immune activation in HIV-infected individuals on cART -targeting microbial translocation (ongoing studies of prebiotic interventions with prebiotic oligosaccharide mixture to improve the gut microbiota composition, rifaximin (antibiotic that is not systemically absorbed) and sevelamer (sevelamer binds bacterial lipopolysaccharide in the gut lumen)) -interventions to improve CD4 T cell recovery. Trials of IL-2 therapy failed (INSIGHT-ESPRIT Study Group et al., 2009). IL-7 could be a good candidate but provides only a transient survival benefit for naïve CD4 and CD8 T cells

  du décès : |___|___| |___|___| |___|___|___|___| Cause du décès : ..................................

  1: no EORTC-defined host factor, a new radiological lesion compatible with the clinical manifestations,

	Aspergillus sp. recovered from BAL or a bronchial aspirate, no other identified
	pathogen, and/or galactomannan antigen >0.5 in serum or BAL, and no alternative
	diagnosis; Group 2: no host factor, new radiological lesion compatible with the
	clinical features, Aspergillus sp. detected in BAL or bronchial aspirate, and
	concomitant infection by a pathogen other than M. tuberculosis, M. avium, S.
	pneumoniae, Histoplasma capsulatum or Pneumocystis jirovecii. A total of 242
	diagnoses were validated.

table 1 : Classification of validated cases of invasive aspergillosis (IA) in the pre-cART era (<1996), the post-cART, pre-voriconazole era (1996-2001), and the post-cART, post-voriconazole era (2002-2011)

 1 IA remains a difficult diagnosis in the context of HIV infection, and it might help to add "a low CD4 cell count" as a risk factor. A threshold of 100/mm 3 seems appropriate, but further studies are needed to validate this proposition. I would first like to explain why I chose this subject area. Indeed, HIV-related fungal infections are no longer a hot topic in resource-rich settings, having been superseded by cancer, long-term complications, HIV-related aging, and HIV reservoirs, etc. Many studies have shown a dramatic decline in PCP since the advent of cART, and we now have access to powerful and much better-tolerated antiretroviral regimens. More than 82% of patients enrolled in the FHDH cohort in 2011 have been on cART for at least 6 months, and 89% of them have a viral load below 50 copies/ml. However, the burden of fungal illness remains high in low-income countries. In addition, few recent studies of opportunistic infections in resource-rich settings have been published. In ("Opportunistic infections and AIDS malignancies early after initiating combination antiretroviral therapy in high-income countries," 2014), one study focused on the impact of cART on AIDS-defining events associated with IRIS, but PCP was not included, because of the low associated risk of IRIS. In

	1 months)

  Better standardization of qPCR could improve PCP diagnosis in future. The detection of serum β D glucan and P. jirovecii DNA by qPCR could usefully be combined as serum markers for the diagnosis of PCP in patients with severe diseases or other conditions where BAL fluid cannot be obtained.

	Regarding treatment, trimethoprim-sulfamethoxazole is effective and usually well tolerated,
	but treatment can still be hindered by toxicity, allergic reactions and G6PD deficiency.
	Alternatives include intravenous pentamidine (effective for severe PCP, but rather toxic) and
	atovaquone (not validated for severe PCP). Resistance to trimethoprim-sulfamethoxazole (due
	to dihydropteroate synthetase mutation) is very rare, and this treatment is cheap and effective,
	meaning that further therapeutic research on PCP is unlikely. CART should be started early
	after PCP diagnosis.
	New diagnostic tools such as qPCR and B D glucan are available, but immunofluorescence on
	BAL fluid or induced sputum remains the gold standard. It is still difficult to distinguish

colonization from infection by means of qPCR, and false-positive results are an issue with B D glucan. However, those tests have good negative predictive values. High serum B D glucan is useful for diagnosis especially when induced sputum or BAL fluid cannot be obtained.

  examinations. Efforts have mainly focused on adherence at the beginning of cART. We now need to concentrate on interventions designed to lower the risk of poor adherence among patients who have been in care for many years. Indicators are also needed to alert clinicians when patients start to attend consultations less regularly. It would certainly be interesting to study the possible role of social factors which, unfortunately, are not available in the FHDH database. Better collaboration between HIV specialists and general practitioners might help to maintain patients in care. Some French infectious diseases departments have already taken

measures. For example, in the infectious diseases department of one Paris hospital, a reminder letter is sent first if a patient does not attend a consultation. Then the patient is called by telephone, and the general practitioner is informed if they do not answer. HIV specialists now need to see HIV-infected individuals on cART less frequently, although the ideal timing between two consultations is a matter of debate. A meta-analysis of text-message

Table : Recommendations for increasing retention in care, ART adherence, and viral suppression (Journal of the International Association of Providers of AIDS Care 2015; 14 (Supplement 1))

 :

	23. Systematic monitoring of retention in HIV care is recommended for all patients. (A II)
	23a. Retention in HIV care should be considered as a quality indicator. (B III)
	23b. Measuring retention in HIV care using electronic health record and other health
	system	data	is	recommended.	(BII)
	23c. Use of clinic databases/surveillance systems for HIV clinical monitoring and
	population-level tracking is recommended. (B II)
	24. Routine ART adherence monitoring is recommended in all patients. (A II)
	24a. Viral suppression is recommended as the primary adherence monitoring metric. (B
	II)
	24b. Routine collection of self-reported adherence data from patients is recommended. (A
	II)
	24c. Pharmacy refill data are recommended for adherence monitoring. (B II)
	25. Information and communication technologies aimed at supporting patient self-care are
	recommended. (B II)
	25a. Mobile health technology using weekly interactive components (eg, 2-way SMS) is
	recommended. (B I)
	25b. Alarm devices are recommended as reminders for PLHIV with memory impairment.
	(A I)
	26. Patient education about and offering support for medication adherence and keeping clinic
	appointments are recommended. (A I)
	26a. Pillbox organizers are recommended, particularly for HIV-infected adults with
	lifestyle-related barriers to adherence. (B II)
	27. Neither directly administered nor directly observed ART is recommended for routine
	clinical	care	settings.	(A	I)
	27a. Directly administered ART is recommended for people who inject drugs and
	released prisoners at high risk of ART nonadherence. (B I)
	28. Proactive engagement and reengagement of patients who miss clinic appointments and/or
	are lost to follow-up, including intensive outreach for those not engaged in care within 1
	month of a new HIV diagnosis, is recommended. (B II)
	28a. Case management to retain PLHIV in care and to locate and reengage patients lost to
	follow-up is recommended. (B II)
	28b. Transportation support for PLHIV to attend their clinic visits is recommended. (B
	II)

  ………....................

		TRAITEMENT INITIAL DE L'ASPERGILLOSE INVASIVE
		MEDICAMENTEUX		Date de début	Date de fin
	1.	1.AMPHOTERICINE B
		DEOXYCHOLATE (AMB)		|__|__| |__|__| |__|__|__|__|	|__|__| |__|__| |__|__|__|__|
		(FUNGIZONE®)		q
		AMBISOME®		q
					|__|__| |__|__| |__|__|__|__|	|__|__| |__|__| |__|__|__|__|
		3.ABELCET ®		q
					|__|__| |__|__| |__|__|__|__|	|__|__| |__|__| |__|__|__|__|
		4.ITRACONAZOLE (SPORANOX®) q	Date	NF = Non Fait
					|__|__| |__|__| |__|__|__|__|	|__|__| |__|__| |__|__|__|__|
		CD4 5.VORICONAZOLE (VFEND®) |__|__|__|__| /mm 3 |__|__|,|__| %	q	|__|__| |__|__| |__|__|__|__| |__|__| |__|__| |__|__|__|__|	|__|__| |__|__| |__|__|__|__|
		Charge virale 6.CASPOFUNGINE (CANCIDAS®) q |__|__|__|__|__|__|__| copies/mL	|__|__| |__|__| |__|__|__|__| |__|__| |__|__| |__|__|__|__|	NF q |__|__| |__|__| |__|__|__|__|
		7.AUTRE :q Seuil en copies/ml |__|__|__|__|	|__|__| |__|__| |__|__|__|__|	|__|__| |__|__| |__|__|__|__|
		8.PAS DE TRAITEMENT	q
			Taux et unités	Date |__|__| |__|__| |__|__|__|__|	|__|__| |__|__| |__|__|__|__|
					NF
		Polynucléaires neutophiles	|__|__|__|__| /mm 3 Ou |__|__|__| 10 9 / l	|__|__| |__|__| |__|__|__|__|	q

The figure below shows key cells involved in host defenses against fungi. Key cells involved in host defenses against fungi: [START_REF] Netea | An integrated model of the recognition of Candida albicans by the innate immune system[END_REF] (

3) Immunosuppression and invasive aspergillosis

As stated above, the classical risk factors for invasive aspergillosis, namely neutropenia and corticosteroid therapy, are not always present in HIV-infected patients.

We chose a short period after IA diagnosis (3 months) to study risk factors for death after IA, because we wanted to study the direct impact of IA, as in previous studies (Herbrecht et al., 2002). We included in the Cox models the following baseline characteristics: age (<40, 40-59, or ≥60 years), the HIV transmission group (intravenous drug users vs others), CD4 cell count at diagnosis (log2 CD4), the IA classification (EORTC or HIV-related), and the period of diagnosis. We introduced voriconazole exposure as a time-dependent covariable in the Cox model in the last period, when voriconazole was available.

Furthermore, in the EORTC definition, "possible IA" does not require microbiological criteria and the diagnosis is considered less robust than for EORTC "proven" and "probable" IA. Our definition of "HIV-related IA, group 2" could include concomitant infection by a pathogen other than M. tuberculosis, M. avium, S. pneumoniae, Histoplasma capsulatum and Pneumocystis jirovecii. To substantiate our results, two sensitivity analyses were undertaken: one after excluding EORTC "possible IA", and the other after excluding both EORTC "possible" IA and "HIV-related IA, group 2".

Supplementary table 2: