Arvind Varsani
email: arvind.varsani@asu.edu

Simona Kraberger

Tanja Opriessnig

Fabrizio Maggi

Vladimir Celer

Hiroaki Okamoto

Philippe Biagini

• Fabrizio

Sead Sabanadzovic

Anelloviridae taxonomy update 2023

à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Anelloviruses have circular negative-sense single-stranded genomes ranging in size from 1.6 to 3.9 kb. In general, anelloviruses have one large open reading frame (ORF), generally referred to as ORF1 or VP1, and a few smaller ORFs [START_REF] Biagini | Classification of TTV and related viruses (anelloviruses)[END_REF][START_REF] Biagini | Family Anelloviridae[END_REF][START_REF] Kato | Gene organization of chicken anemia virus[END_REF]. There are currently 30 genera in the family Anelloviridae (Table 1) [START_REF] Kraberger | Taxonomic updates for the genus Gyrovirus (family Anelloviridae): recognition of several new members and establishment of species demarcation criteria[END_REF][START_REF] Varsani | Taxonomic update for mammalian anelloviruses (family Anelloviridae)[END_REF]. Members of the genus Gyrovirus have been identified infecting various avian species and detected in fecal samples of various mammals [START_REF] Kraberger | Taxonomic updates for the genus Gyrovirus (family Anelloviridae): recognition of several new members and establishment of species demarcation criteria[END_REF], and a report discusses their identification in reptiles [START_REF] Wu | Genetic Analysis of Avian Gyrovirus 2 Variant-Related Gyrovirus Detected in Farmed King Ratsnake (Elaphe carinata): The First Report from China[END_REF], whereas those in the remaining 29 genera have been identified in mammal species samples [START_REF] Kraberger | Taxonomic updates for the genus Gyrovirus (family Anelloviridae): recognition of several new members and establishment of species demarcation criteria[END_REF][START_REF] Varsani | Taxonomic update for mammalian anelloviruses (family Anelloviridae)[END_REF].

The ORF1/VP1 protein is the most conserved protein, a single jelly-roll capsid protein, encoded by anelloviruses, despite a size variation, which is attributed to insertions of varying length in the conserved jelly-roll domain (between β-strands H and I) [START_REF] Butkovic | Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein[END_REF]. Based on the phylogeny of this conserved ORF1/VP1, 30 genera have been established to classify various anelloviruses (Table 1, Fig. 1). Furthermore, based on the analysis of the nucleotide pairwise identities of the orf1 gene of anelloviruses, a 69% species demarcation threshold has been established [START_REF] Kraberger | Taxonomic updates for the genus Gyrovirus (family Anelloviridae): recognition of several new members and establishment of species demarcation criteria[END_REF][START_REF] Varsani | Taxonomic update for mammalian anelloviruses (family Anelloviridae)[END_REF]. Within the 30 genera in the family Anelloviridae, there are currently 155 established species (Table 1), which are listed on the International Committee on Taxonomy of Viruses (ICTV) site within the master species list (https:// ictv. global/ msl) and virus metadata resources (https:// ictv. global/ vmr) [8].

In 2021, the International Committee on Taxonomy of Viruses (ICTV) [8] proposal TaxoProp 2018.001G.R.binomial_species was ratified [START_REF] Walker | Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)[END_REF]. This requires all species names to be in binomial format comprising a "genus + epithet" with various style options for the epithets (as either freeform or Latinized; see Siddell al. [START_REF] Siddell | Binomial nomenclature for virus species: a consultation[END_REF] and Postler et al. [START_REF] Postler | Guidance for creating individual and batch latinized binomial virus species names[END_REF]). The species name is different from the name of a virus [START_REF] Zerbini | Differentiating between viruses and virus species by writing their names correctly[END_REF].

Here, we provide an update on the revised species names (using a freeform alphanumeric epithet where possible) for all species in the family Anelloviridae (Table 1). Nine species in the genus Gyrovirus have previously been named in binomial freeform alphanumeric epithet format with the five-letter epithet derived from the host species followed by a number [START_REF] Kraberger | Taxonomic updates for the genus Gyrovirus (family Anelloviridae): recognition of several new members and establishment of species demarcation criteria[END_REF]. Given that viruses in the previous species "Chicken anemia virus" (genus Gyrovirus) have been associated with disease, we have renamed this species Gyrovirus chickenanemia.

In general, we have used the first five letters of the name of the host or the source family (e.g., "phoca" for Phocidae) followed by a number such that each epithet is unique. In the case of species in the genus Betatorquevirus, we have used the epithet "homini" followed by a number to reflect "mini" from the name torque teno mini virus, e.g., the previous species "Torque teno mini virus 1" has been renamed Betatorquevirus homini1. On the other hand, in the case of the species in the genus Gammatorquevirus, we have used the epithet "homidi" followed by a number to reflect "midi" from the name torque teno midi virus, e.g., the previous species name "Torque teno midi virus 1" has been changed to Gammatorquevirus homidi1.

A summary of the changes is provided in Table 1. In addition, we provide an ORF1/VP1-protein-sequence-based phylogeny in Figure 1 showing genera and species using representative virus sequences as a reference. The ORF1/VP1 protein of the representative anellovirus sequences detailed in the virus metadata resources (https:// ictv. global/ vmr) [8] were assembled and aligned using MAFFT [START_REF] Katoh | A simple method to control overalignment in the MAFFT multiple sequence alignment program[END_REF], and the alignment was then trimmed using TrimAL [START_REF] Capella-Gutierrez | tri-mAl: a tool for automated alignment trimming in large-scale phylogenetic analyses[END_REF] with a gap setting of 0.2. This trimmed alignment was used to infer a maximum-likelihood phylogenetic tree in PHYML 3 [START_REF] Guindon | New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0[END_REF] with aLRT branch support and with VT+G+F as the best substitution model determined using ProtTest 3 [START_REF] Darriba | ProtTest 3: fast selection of best-fit models of protein evolution[END_REF]. The resulting phylogeny was visualized in iTOL 6 [START_REF] Letunic | Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation[END_REF].

As more anellovirus genomes are identified from various hosts, coupled with more insights into their genomes and coding regions, we expect to see an increased number of new species and genera and a revision of species demarcation in the near future. Further, it is likely that the family Anelloviridae, which is currently not assigned to any phylum or higher ranks would be classified in a new phylum, "Commensaviricota", in the kingdom Shotokuvirae (realm Monodnaviria), as proposed by Butkovic et al. [START_REF] Butkovic | Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein[END_REF].

Table 1

 1 et Summary of the changes to the species names in the family Anelloviridae

	New species name	Previous species name	Representative virus name Accession Host/source	Host/
					source family
	Aleptorquevirus culic1	Torque teno arthrovec	mosquito VEM Anellovi-	HQ335082 Mosquitoes (mixed spe-	Culicidae
		virus 1	rus SDBVL A	cies)
	Aleptorquevirus lepor1	Torque teno leprid virus 1 Lepus torque teno virus 1	MN994854 Lepus granatensis	Leporidae
			Lag01_EL_Anello4
	Alphatorquevirus homin31 Torque teno virus 31	torque teno virus TTV-	KJ082064 Homo sapiens	Hominidae
			Hebei-1
	Alphatorquevirus homin1 Torque teno virus 1	torque teno virus 1 VT416 AB041007 Homo sapiens	Hominidae
	Alphatorquevirus homin4 Torque teno virus 4	torque teno virus 4 Pt-	AB041957 Pan troglodytes	Hominidae
			TTV6
	Alphatorquevirus homin10 Torque teno virus 10	torque teno virus 10 JT34F AB064607 Homo sapiens	Hominidae
	Alphatorquevirus homin14 Torque teno virus 14	torque teno virus 14	AB037926 Pan troglodytes	Hominidae
			s-TTV CH65-1
	Alphatorquevirus homin19 Torque teno virus 19	torque teno virus 19 TTV	AB025946 Homo sapiens	Hominidae
			SANBAN
	Alphatorquevirus cerco6	Torque teno virus 26	torque teno virus 26 Mf-	AB041958 Macaca fuscata	Cercopithecidae
			TTV3
	Alphatorquevirus homin7 Torque teno virus 7	torque teno virus 7 PMV	AF261761 Homo sapiens	Hominidae
	Alphatorquevirus homin3 Torque teno virus 3	torque teno virus 3 HEL32 AY666122 Homo sapiens	Hominidae
	Alphatorquevirus cerco7	Torque teno virus 25	torque teno virus 25 Mf-	AB041959 Macaca fuscata	Cercopithecidae
			TTV9
	Alphatorquevirus homin6 Torque teno virus 6	torque teno virus 6 KAV	AF435014 Homo sapiens	Hominidae
	Alphatorquevirus homin15 Torque teno virus 15	torque teno virus 15	AB028668 Homo sapiens	Hominidae
			TJN01
	Alphatorquevirus homin2 Torque teno virus 2	torque teno virus 2 s-TTV	AB049608 Pan troglodytes	Hominidae
			CH71
	Alphatorquevirus cerco3	Torque teno chlorocebus	simian torque teno virus	KP296853 Chlorocebus sabaeus	Cercopithecidae
		virus 3	31 VGA00123.3
	Alphatorquevirus cerco1	Torque teno chlorocebus	simian torque teno virus	KP296857 Chlorocebus sabaeus	Cercopithecidae
		virus 1	30 VWP00522.2
	Alphatorquevirus cerco5	Torque teno chlorocebus	simian torque teno virus	KP296854 Chlorocebus sabaeus	Cercopithecidae
		virus 5	32 VGA00154.2
	Alphatorquevirus cerco2	Torque teno chlorocebus	simian torque teno virus	KP296856 Chlorocebus sabaeus	Cercopithecidae
		virus 2	34 VGA00120.1
	Alphatorquevirus homin5 Torque teno virus 5	torque teno virus 5	AF345523 Homo sapiens	Hominidae
			TCHN-C1
	Alphatorquevirus homin9 Torque teno virus 9	torque teno virus 9	DQ187006 Homo sapiens	Hominidae
			BM1C-18
	Alphatorquevirus homin13 Torque teno virus 13	torque teno virus 13	AF345526 Homo sapiens	Hominidae
			TCHN-A
	Alphatorquevirus homin20 Torque teno virus 20	torque teno virus 20	AB060594 Homo sapiens	Hominidae
			SAa-10
	Alphatorquevirus homin21 Torque teno virus 21	torque teno virus 21	AF348409 Homo sapiens	Hominidae
			TCHN-B
	Alphatorquevirus homin24 Torque teno virus 24	torque teno virus 24	AB060597 Homo sapiens	Hominidae
			SAa-01
	Alphatorquevirus homin29 Torque teno virus 29	torque teno virus 29	AB038621 Homo sapiens	Hominidae
			TTVyon-KC009
	Alphatorquevirus homin17 Torque teno virus 17	torque teno virus 17	AX025830 Homo sapiens	Hominidae
	Alphatorquevirus homin18 Torque teno virus 18	torque teno virus 18	AX025718 Homo sapiens	Hominidae
	Betatorquevirus homini13 Torque teno mini virus 13 TTV-like mini virus	KY856742 Homo sapiens	Hominidae
			zhenjiang
	Betatorquevirus homini14 Torque teno mini virus 14 torque teno mini virus 10	MH017546 Homo sapiens	Hominidae
			BNI-700620-G1-CSF

Hominidae Betatorquevirus homini35 Torque teno mini virus 35 Anelloviridae sp. ctei055 MH648966 Homo sapiens Hominidae Betatorquevirus homini36 Torque teno mini virus 36 torque teno virus Human/ Japan/KS025/2016 LC381845 Homo sapiens Hominidae Betatorquevirus homini37 Torque teno mini virus 37 Anelloviridae sp. ctbg056 MH649209 Homo sapiens Hominidae Betatorquevirus homini38 Torque teno mini virus 38 Anelloviridae sp. ctbf014 MH648982 Homo sapiens Betatorquevirus homini16 Torque teno mini virus 16 torque teno mini virus ALH8 KM259874 Homo sapiens Hominidae Betatorquevirus homini32 Torque teno mini virus 32 torque teno mini virus 18 222 KU041847 Homo sapiens Hominidae

Table 1 (

 1 continued)

	New species name	Previous species name	Representative virus name Accession Host/source	Host/
					source family
	Betatorquevirus homini10 Torque teno mini virus 10 torque teno mini virus 10	EF538880 Homo sapiens	Hominidae
			LIL-y1
	Betatorquevirus homini11 Torque teno mini virus 11 torque teno mini virus 11	EF538881 Homo sapiens	Hominidae
			LIL-y2
	Betatorquevirus homini12 Torque teno mini virus 12 torque teno mini virus 12	EF538882 Homo sapiens	Hominidae
			LIL-y3
	Chitorquevirus indri1	Torque teno indriid virus 1 torque teno indri virus 1	MF187212 Indri indri	Indriidae
			bet12.15
	Dalettorquevirus ursid6	Torque teno ursid virus 6 giant panda anellovirus	MF327539 Ailuropoda melanoleuca	Ursidae
			gpan20793
	Deltatorquevirus tupai1	Torque teno tupaia virus	torque teno tupaia virus	AB057358 Tupaia belangeri chin-	Tupaiidae
			Tbc-TTV14	ensis
	Epsilontorquevirus calli1 Torque teno tamarin virus torque teno tamarin virus	AB041960 Saguinus oedipus	Callitrichidae
			So-TTV2
	Etatorquevirus felid1	Torque teno felid virus 1	torque teno felis virus	AB076003 Felis catus	Felidae
			Fc-TTV4
	Etatorquevirus felid2	Torque teno felid virus 2	torque teno felis virus 2	EF538877 Felis catus	Felidae
			PRA1
	Etatorquevirus felid3	Torque teno felid virus 3	torque teno ocelot virus	MK069470 Leopardus pardalis	Felidae
			WF10
	Etatorquevirus felid4	Torque teno felid virus 4	torque teno felis virus-Fc-	JF304938 Felis catus	Felidae
			TTV2 VS4300008
	Etatorquevirus felid5	Torque teno felid virus 5	torque teno felis virus-Fc-	JF304937 Felis catus	Felidae
			TTV1 VS4300006
	Etatorquevirus viver3	Torque teno viverrid	Paguma larvata torque	LC387548 Paguma larvata	Viverridae
		virus 3	teno virus Pl-TTV3
	Gammatorquevirus	Torque teno midi virus 1	torque teno midi virus 1	AB290917 Homo sapiens	Hominidae
	homidi1		MD1-032
	Gammatorquevirus	Torque teno midi virus 2	torque teno midi virus 2	AB290919 Homo sapiens	Hominidae
	homidi2		MD2-013
	Gammatorquevirus	Torque teno midi virus 3	torque teno midi virus 3	EF538875 Homo sapiens	Hominidae
	homidi3		2PoSMA
	Gammatorquevirus	Torque teno midi virus 4	torque teno midi virus 4	EF538876 Homo sapiens	Hominidae
	homidi4		6PoSMA
	Gammatorquevirus	Torque teno midi virus 5	torque teno midi virus 5	AB303552 Homo sapiens	Hominidae
	homidi5		MDJHem2
	Gammatorquevirus	Torque teno midi virus 6	torque teno midi virus 6	AB303553 Homo sapiens	Hominidae
	homidi6		MDJHem3-1
	Gammatorquevirus	Torque teno midi virus 7	torque teno midi virus 7	AB303554 Homo sapiens	Hominidae
	homidi7		MDJHem3-2
	Gammatorquevirus	Torque teno midi virus 8	torque teno midi virus 8	AB303558 Homo sapiens	Hominidae
	homidi8		MDJN1
	Gammatorquevirus	Torque teno midi virus 9	torque teno midi virus 9	AB303559 Homo sapiens	Hominidae
	homidi9		MDJN2
	Gammatorquevirus	Torque teno midi virus 10 torque teno midi virus 10	AB303560 Homo sapiens	Hominidae
	homidi10		MDJN14
	Gammatorquevirus	Torque teno midi virus 11 torque teno midi virus 11	AB303561 Homo sapiens	Hominidae
	homidi11		MDJN47
	Gammatorquevirus	Torque teno midi virus 12 torque teno midi virus 12	AB303562 Homo sapiens	Hominidae
	homidi12		MDJN51
	Gammatorquevirus	Torque teno midi virus 13 torque teno midi virus 13	AB303564 Homo sapiens	Hominidae
	homidi13		MDJN69
	Gammatorquevirus	Torque teno midi virus 14 torque teno midi virus 14	AB303566 Homo sapiens	Hominidae
	homidi14		MDJN97

Table 1

 1

	(continued)
	New species name	Previous species name	Representative virus name Accession Host/source	Host/
					source family
	Gammatorquevirus	Torque teno midi virus 15 torque teno midi virus 15	AB449062 Pan troglodytes	Hominidae
	homidi15		Pt-TTMDV210
	Gimeltorquevirus ursid13 Torque teno virus 30	giant panda anellovirus	MF327544 Ailuropoda melanoleuca	Ursidae
			gpan20806
	Hetorquevirus hominid2	Torque teno hominid	Anelloviridae sp. vzttmv5 MK212032 Homo sapiens	Hominidae
		virus 2
	Iotatorquevirus suida1a	Torque teno sus virus 1a	torque teno sus virus 1	AB076001 Sus scrofa	Suidae
			Sd-TTV31
	Kappatorquevirus	Torque teno sus virus k2a torque teno sus virus k2a	AY823991 Sus scrofa	Suidae
	suidak2a		2p
	Kappatorquevirus	Torque teno sus virus k2b torque teno sus virus k2b	JQ406846 Sus scrofa	Suidae
	suidak2b		38E23
	Lambdatorquevirus phoci5 Torque teno pinniped	torque teno Leptonych-	KY246582 Leptonychotes weddellii	Phocidae
		virus 8	otes weddellii virus 1
			TTLwV-1_gt16_wsp8
	Lambdatorquevirus phoci1 Torque teno pinniped	seal anellovirus TFFN/	HQ287751 Phoca vitulina	Phocidae
		virus 1	USA/2006
	Lambdatorquevirus phoci3 Torque teno pinniped	seal anellovirus 3 12-410 KF373758 Phoca vitulina	Phocidae
		virus 3
	Lambdatorquevirus phoci2 Torque teno pinniped	seal anellovirus 2 12-410 KF373760 Phoca vitulina	Phocidae
		virus 2
	Lambdatorquevirus phoci6 Torque teno pinniped	torque teno Leptonych-	KY246547 Leptonychotes weddellii	Phocidae
		virus 9	otes weddellii virus-2
			TTLwV-2_gt3_wsp24
	Mutorquevirus equid1	Torque teno equid virus 1 torque teno equus virus 1 KR902501 Equus caballus	Equidae
	Nutorquevirus phoci4	Torque teno pinniped	seal anellovirus 5 SeAv5-	KM262782 Phoca vitulina	Phocidae
		virus 4	PV13-431
	Omegatorquevirus homi-	Torque teno hominid	gorilla anellovirus GorF	KT027939 Gorilla gorilla	Hominidae
	nid1	virus 1
	Omicrontorquevirus	Torque teno ursid virus 5 giant panda anellovirus	MF327557 Ailuropoda melanoleuca	Ursidae
	ursid5		gpan20684
	Pitorquevirus ursid11	Torque teno ursid virus 11 giant panda anellovirus	MF327548 Ailuropoda melanoleuca	Ursidae
			gpan21066
	Pitorquevirus ursid12	Torque teno ursid virus 12 giant panda anellovirus	MF327547 Ailuropoda melanoleuca	Ursidae
			gpan21031
	Pitorquevirus ursid7	Torque teno ursid virus 7 giant panda anellovirus	MF327540 Ailuropoda melanoleuca	Ursidae
			gpan21094
	Pitorquevirus ursid8	Torque teno ursid virus 8 giant panda anellovirus	MF327542 Ailuropoda melanoleuca	Ursidae
			gpan20859
	Pitorquevirus ursid9	Torque teno ursid virus 9 giant panda anellovirus	MF327550 Ailuropoda melanoleuca	Ursidae
			gpan20868
	Pitorquevirus ursid10	Torque teno ursid virus 10 giant panda anellovirus	MF327541 Ailuropoda melanoleuca	Ursidae
			gpan20688
	Psitorquevirus procy4	Torque teno procyo virus 4 Anelloviridae sp. ctcf003 MK012516 Procyon lotor	Procyonidae
	Rhotorquevirus murid1	Torque teno rodent virus 1 rodent torque teno virus 1	KJ194617 Apodemus sylvaticus	Muridae
			AS_WM1_Sp_1
	Sigmatorqueviru otari1	Torque teno pinniped	California sea lion anello-	FJ459582 Zalophus californianus	Otariidae
		virus 5	virus
	Sigmatorquevirus otari2	Torque teno pinniped	torque teno Arctocepha-	MG837569 Arctocephalus gazella	Otariidae
		virus 6	lus gazella virus 1
			ASV20_172
	Sigmatorquevirus otari3	Torque teno pinniped	torque teno Arctocepha-	MG837571 Arctocephalus gazella	Otariidae
		virus 7	lus gazella virus 2
			ASV35_197

Table 1

 1 Anelloviridae sp. ctcf003 MK012447 Procyon lotor Procyonidae Upsilontorquevirus procy2 Torque teno procyo virus 2 Anelloviridae sp. ctcf007 MK012527 Procyon lotor Procyonidae Upsilontorquevirus procy3 Torque teno procyo virus 3 Anelloviridae sp. ctdc005 MK012497 Procyon lotor Procyonidae Upsilontorquevirus procy7 Torque teno procyo virus 7 Anelloviridae sp. ctbd010 MK012464 Procyon lotor Procyonidae Upsilontorquevirus procy8 Torque teno procyo virus 8 Anelloviridae sp. ctbb008 MK012467 Procyon lotor Procyonidae Upsilontorquevirus procy9 Torque teno procyo virus 9 Anelloviridae sp. ctbb005 MK012471 Procyon lotor

	(continued)
	New species name	Previous species name	Representative virus name Accession Host/source	Host/
						source family
	Tettorquevirus felid6	Torque teno felid virus 6	feline anellovirus Felin-	KX262893 Felis catus	Felidae
			eAV621
	Thetatorquevirus ixodi1	Torque teno arthrovec	tick associated torque teno	MF173068 Dermacentor variabilis	Ixodidae
		virus 3	virus tick24_1
	Thetatorquevirus muste1	Torque teno mustilid	pine marten torque teno	JN704611 Martes americana	Mustelidae
		virus 1	virus 1 VS4700004
	Thetatorquevirus procy5	Torque teno procyo virus 5 Anelloviridae sp. ctdb009 MK012446 Procyon lotor	Procyonidae
	Thetatorquevirus procy6	Torque teno procyo virus 6 Anelloviridae sp. cthe000 MK012439 Procyon lotor	Procyonidae
	Thetatorquevirus ursid2	Torque teno ursid 2 giant panda anellovirus	MF327551 Ailuropoda melanoleuca	Ursidae
			gpan20783
	Thetatorquevirus ursid3	Torque teno ursid virus 3 giant panda anellovirus	MF327552 Ailuropoda melanoleuca	Ursidae
			gpan20682
	Thetatorquevirus ursid4	Torque teno ursid virus 4 giant panda anellovirus	MF327554 Ailuropoda melanoleuca	Ursidae
			gpan20724
	Thetatorquevirus viver4	Torque teno viverrid	Paguma larvata torque	LC387543 Paguma larvata	Viverridae
		virus 4	teno virus Pl-TTV9-2
	Thetatorquevirus canid1	Torque teno canid virus 1 torque teno canis virus	AB076002 Canis lupus familiaris	Canidae
			Cf-TTV10
	Thetatorquevirus ursid1	Torque teno ursid virus 1 lesser panda anellovirus	KX611132 Ailuropoda melanoleuca	Ursidae
			chengdu-1
	Upsilontorquevirus procy1 Torque teno procyo virus 1 Procyonidae
	Upsilontorquevirus viver2 Torque teno viverrid	Paguma larvata torque	LC387546 Paguma larvata	Viverridae
		virus 2	teno virus Pl-TTV9-1
	Wawtorquevirus crice1	Torque teno rodent virus 6 rodent torque teno virus	MF541389 Oligoryzomys nigripes	Cricetidae
			8 2252
	Wawtorquevirus culic2	Torque teno arthrovec	mosquito VEM Anellovi-	HQ335084 Mosquitoes (mixed spe-	Culicidae
		virus 2	rus SDRB A		cies)
	Wawtorquevirus murid2	Torque teno rodent virus 4 rodent torque teno virus 2	KJ194604 Apodemus sylvaticus	Muridae
			AS_WM1_Se_4
	Wawtorquevirus murid3	Torque teno rodent virus 5 rodent torque teno virus 2	KM609325 Rattus norvegicus	Muridae
			RN_8_Se11
	Wawtorquevirus crice2	Torque teno rodent virus 2 rodent torque teno virus	MF541374 Akodon montensis	Cricetidae
			3 2
	Wawtorquevirus crice3	Torque teno rodent virus 3 rodent torque teno virus	MF541388 Akodon montensis	Cricetidae
			7 15
	Xitorquevirus didel1	Torque teno didelphi	torque teno didelphis albi-	MF541378 Didelphis albiventris	Didelphidae
		virus 1	ventris virus 3470
	Xitorquevirus molos1	Torque teno chiroptera	torque teno Tadarida	KM434181 Tadarida brasiliensis	Molossidae
		virus 1	brasiliensis virus
	Zayintorquevirus viver1	Torque teno viverrid	Paguma larvata torque	LC387540 Paguma larvata	Viverridae
		virus 1	teno virus Pl-TTV5-2
	Zayintorquevirus viver5	Torque teno viverrid	Paguma larvata torque	LC387536 Paguma larvata	Viverridae
		virus 5	teno virus Pl-TTV1-1
	Zetatorquevirus aotid1	Torque teno douroucouli	torque teno douroucouli	AB041961 Aotus trivirgatus	Aotidae
		virus	virus At-TTV3
	Gyrovirus chickenanemia Chicken anemia virus	chicken anemia virus	M55918	Gallus gallus domesticus Phasianidae
			Cuxhaven-1
	Gyrovirus fulgla1	-	gyrovirus GyV8	KR137527 Fulmarus glacialis	Procellariidae

Table 1

 1 (continued) has been chosen for each species. For nine species in the genus Gyrovirus, there is no species name change because binomial species names were assigned during the establishment of these species by Kraberger et al.[START_REF] Kraberger | Taxonomic updates for the genus Gyrovirus (family Anelloviridae): recognition of several new members and establishment of species demarcation criteria[END_REF].

	New species name	Previous species name	Representative virus name Accession Host/source	Host/
					source family
	Gyrovirus galga1	-	avian gyrovirus 2	HM590588 Gallus gallus	Phasianidae
	Gyrovirus galga2	-	gyrovirus GyV7-SF	KM111536 Gallus gallus	Phasianidae
	Gyrovirus homsa1	-	gyrovirus GyV3	JQ308210 Homo sapiens	Hominidae
	Gyrovirus homsa2	-	gyrovirus Tu789	KF294862 Homo sapiens	Hominidae
	Gyrovirus homsa3	-	gyrovirus 4 D137	JX310702 Homo sapiens	Hominidae
	Gyrovirus homsa4	-	gyrovirus Tu243	KF294861 Homo sapiens	Hominidae
	Gyrovirus hydho1	-	ashy storm petrel gyrovi-	MH378452 Hydrobates homochroa	Hydrobatidae
			rus a12a1_528
	Gyrovirus myferr1	-	gyrovirus 11	MH638372 Myrmoderus ferrugineus Thamnophilidae
	A representative virus

0.5 amino acid subs / site

Funding

The authors have not disclosed any funding.

Data availability Not applicable.

Declarations

Conflict of interest The authors declare there are no conflicts of interest.

Research involving human participants and/or animals

The research did not involve human participants or animals.

Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Fig. 1 Maximum-likelihood phylogenetic tree of the representative ORF1/VP1 protein sequences of anelloviruses from each species. The accession number of the representative sequence is provided next to the binomial species name. The phylogenetic tree is rooted with gyrovirus sequences. Branch support is shown for branches with >0.6 aLRT support. ◂


Enquête sur les besoins de formation des personnels des ateliers de la donnée -2023

Une seule réponse était attendue par atelier afin de faciliter l'exploitation des résultats. Une concertation préalable au sein de l'atelier était donc nécessaire afin de répondre de manière exhaustive aux différentes questions. Ce questionnaire, administré via l'outil Limesurvey (compte institutionnel de l'université de Caen Normandie), a recueilli un total de 12 réponses sur les 15 possibles. Les ateliers répondant présentent des profils très variés, avec un nombre d'ETP impliqués allant de 1,1 à 14,2 et un nombre de membres allant de 6 à 52. Le rapport synthétique qui suit vise à montrer les principaux enseignements de cette enquête.

2

Après une première enquête sur leurs besoins de formation menée par les URFIST auprès des 5 premiers ateliers labellisés en 2022, le groupe de travail numéro 2 (Formation professionnelle des personnels des ateliers) du réseau des ateliers de la donnée a sollicité les coordinateurs des 15 ateliers labellisés ou en voie de labellisation pour une nouvelle enquête, entre avril et juin 2023.

Les ateliers de la donnée s'organisent au niveau local pour accompagner la communauté scientifique dans la gestion des données de la recherche en dispensant un premier degré d'expertise. Ils s'appuient sur des professionnels du domaine de l'appui à la recherche et dans le cadre d'une montée en compétence de cette communauté, une enquête a été commanditée pour adapter les futures formations aux besoins des enquêtés.

Celle-ci visait à répertorier de façon plus complète les pratiques de formation des personnels participant aux ateliers de la donnée et les besoins qui restent à combler en la matière. L'objectif est d'utiliser les résultats de cette enquête dans le but de co-construire une offre de formation à destination des membres des ateliers de la donnée avec les centres de ressources Recherche Data Gouv.

Formations proposées par les ateliers de la donnée

1.

Formations suivies par les personnels des ateliers de la donnée 6

La deuxième partie de l'enquête s'intéressait aux formations suivies par les personnels des ateliers de la donnée.

Dans un premier temps, les thématiques des formations suivies ont été répertoriées.

Les thématiques des 116 formations suivies sont classées dans le tableau ci-dessous par nombre d'occurrences.

Thématiques

Autoformation

Thématiques plébiscitées en autoformation

La partie IV de l'enquête, sur les besoins de formation des personnels des ateliers de la donnée, débutait par la question suivante : l'offre de formation répond-elle à vos besoins ? 10 réponses sur 11 montrent une progression attendue de cette offre.

Besoins de formation des personnels des ateliers de la donnée

L'offre de formation répond-elle à vos besoins ?

Les thématiques sont classées dans le tableau ci-dessous par nombre d'occurrences et par niveau de priorité afin de faire apparaître en haut les thématiques semblant plus prioritaires pour les répondants.

Enfin, l'enquête s'achevait par le recueil des besoins de formation des personnels des ateliers de la donnée. Seuls 11 ateliers ont répondu à cette partie de l'enquête. Au-delà des thématiques de formation, chaque répondant devait se prononcer sur le niveau de priorité de la formation, sa durée et ses modalités souhaitées.

Grandes thématiques

Cahiers de laboratoire électroniques

Stockage et partage des données

Ethique et intégrité

Généralités

  régionaux de formation aux carrières des bibliothèques Organismes formateurs des ateliers de la donnée 9 Dans un deuxième temps, les organismes formateurs des ateliers de la donnée ont été recensés. Dans le graphique ci-dessous, ils sont classés par le nombre d'occurrences de formations dispensées par organisme.Parmi les 19 organismes formateurs répertoriés, nous retrouvons des centres de ressources de Recherche Data Gouv : l'URFIST, DoRANum, l'entrepôt catalogue Recherche Data Gouv, mais également des centres de référence thématique : Huma-Num, PROGEDO et DATA TERRA. temps, l'enquête s'est intéressée aux ressources d'autoformation utilisées par les personnels des ateliers de la donnée pour se former sur les différentes thématiques touchant aux données de la recherche.

  Sans surprise, DoRANum apparaît comme la ressource la plus citée (certains ateliers l'ont citée plusieurs fois, d'où un total dépassant le nombre d'ateliers répondant). D'autres ressources sont utilisées par une bonne partie des ateliers et on constate également une longue traîne de ressources utilisées dans un seul atelier. Principales sources d'autoformation *Université de rennes 2, URFIST et MSHS. La majorité des sources d'autoformation utilisées est généraliste, viennent ensuite des besoins de connaissances sur des données disciplinaires.

  travail qui a vocation à aiguiller les centres de ressources de l'écosystème Recherche Data Gouv dans le choix des thématiques de formations, plusieurs tendances peuvent être retenues. L'enquête montre à la fois la diversité des métiers représentés au sein des ateliers de la donnée et l'hétérogénéité dans la composition de ces ateliers : pour rappel, plus d'une centaine de formateurs pour douze ateliers répondant. Malgré cela, les thématiques des formations proposées se rejoignent notamment sur la gestion des données ou bien, le stockage et le partage ou encore, le plan de gestion des données, ce qui est cohérent puisque les publics desservis sur les différents territoires auront souvent des besoins très proches.Par ailleurs, le rôle des ateliers de la donnée est bien de proposer un accompagnement généraliste de premier niveau, dont les contours n'ont à varier que marginalement d'un site à l'autre. Ainsi, les différences dans les formations proposées d'un atelier à l'autre sont souvent liées aux niveaux de maturité des différents ateliers ou à des écarts dans le nombre d'ETP investis. Ces niveaux de maturité inégaux et le fait que le réseau des ateliers se structure progressivement laissent envisager qu'une partie des besoins de formation des personnels des ateliers pourront être pris en charge par le réseau lui-même ; en particulier en ce qui concerne la gestion des données, le partage, le plan de gestion des données et les outils et traitements d'analyse qui se révèlent être les thématiques de formation les plus suivies par les enquêtés actuellement. Plusieurs ateliers se montrent déjà favorables à cette démarche. Il faudra ainsi très prochainement la formaliser au sein des ADLD.Pour les thématiques où l'autoformation semble une opportunité, l'orientation vers certaines ressources à privilégier et la construction de parcours d'autoformation pourrait aussi être envisagée en collaboration avec les centres de ressources qui ont déjà commencé ce travail dans Callisto. Enfin, les besoins de formation qui se sont exprimés dans la dernière partie de l'enquête relèvent une montée en compétences sur le droit des données, les logiciels, le code et la sécurisation des données, cela montre à la fois des besoins récurrents d'un atelier à l'autre et une très importante diversité de suggestions plus rares et où l'enquête recense des besoins relatifs aux métadonnées, à la curation, à l'archivage et au stockage.

  Le niveau de priorité a été calculé en faisant une moyenne des réponses saisies pour la grande thématique en question ; La modalité indiquée est généralement celle retenue par la totalité des répondants pour la grande thématique (avec parfois des commentaires); La durée est une moyenne des réponses apportées, quand elles étaient relativement proches et que cela avait un sens de faire ce calcul.Les thématiques sont classées dans les tableaux ci-dessous par nombre d'occurrences et par niveau de priorité afin de faire apparaître en haut les thématiques semblant plus prioritaires pour les répondants. Le niveau de priorité devait être classé de 1 à 5, avec la réponse 1 correspondant à une priorité élevée et la réponse 5 correspondant à une priorité faible.

	Grandes thématiques			Métadonnées		Archivage et préservation des données
	Détails		Aspects disciplinaires	Schémas de métadonnées	Données de la recherche VS archives de la recherche	Durée de conservation, patrimoine
	Nombre d'occurrences			5			5
	Niveau de priorité			1,2			1,5
	Modalités		4 Distanciel + 1 Autoformation	Distanciel
	Durée			Variable		150
	Grandes thématiques Détails Grandes thématiques Données de la recherche VS archives de la recherche Détails	Droit des données Perspective internationale Propriété et ouverture disciplinaires Droit et éthique Droit des logiciels Données Retours d'expérience Santé SHS (X2) Cryptage	Propriété Sécurisation Propriété intellectuelle intellectuelle et droits d'auteur Données personnelles ZRR (X2) Questions juridiques avancées
	Nombre d'occurrences Nombre d'occurrences			5		10	4
	Niveau de priorité Niveau de priorité Modalités			2,5 Variables		1	1 Distanciel
	Modalités Durée			120	6 Distanciel / 1 Présentiel	140
	Durée					Variable
	Grandes thématiques					Codes sources et logiciels
	Détails	Aspects juridiques	Dépôt et description	Forges	Gitlab + Git	Software Management Plans
	Nombre d'occurrences						10
	Niveau de priorité						2,2
	Modalités					Variables
	Durée					Variable

principales thématiques de formation ont été recensées dans les formations proposées par les ateliers de la donnée. A l'intérieur de ces grandes thématiques, on pourra parfois trouver 2 ou 3 formations aux contours différents.


Marc Leone
email: marc.leone@ap-hm.fr

Carole Bechis

Karine Baumstarck

Jean-Yves Lefrant

Jacques Albanèse

Samir Jaber

Alain Lepape

Jean-Michel Constantin

Laurent Papazian

Nicolas Bruder

Jean-Yves Lefrant

Jacques Albane

Bernard Allaouchiche

Karine Be

Antonini Julien

Á C Bechis

Á F Antonini

Á C Martin

Á L Papazian

Á J Textoris

J.-Y Lefrant

J.-M Constantin Re

Polyvalente

Ho

De-escalation versus continuation of empirical antimicrobial treatment in severe sepsis: a multicenter non-blinded randomized noninferiority trial

Keywords: Sepsis, Antibiotics, De-escalation, Empirical, Stewardship

blinded randomized noninferiority trial of patients with severe sepsis who were randomly assigned to deescalation or continuation of empirical antimicrobial treatment. Recruitment began in February 2012 and ended in April 2013 in nine intensive care units (ICUs) in France. Patients with severe sepsis were assigned to de-escalation (n = 59) or continuation of empirical antimicrobial treatment (n = 57). The primary outcome was to measure the duration of ICU stay. We defined a noninferiority margin of 2 days. If the lower boundary of the 95 % confidence interval (CI) for the difference in patients assigned to the de-escalation group was less than 2 days, as compared with that of patients assigned to the continuation group, de-escalation was considered to be noninferior to the continuation strategy. Secondary outcomes included mortality at 90 days, occurrence of organ failure, number of superinfections, and number of days with antibiotics during the ICU stay. Results: The median duration of ICU stay was 9 [interquartile range (IQR) [START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF][START_REF] Niederman | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Silva | De-escalation of antimicrobial treatment for adults with sepsis, severe sepsis or septic shock[END_REF][START_REF] Calandra | International Sepsis Forum Definition of Infection in the ICU Consensus Conference (2005) The international sepsis forum consensus conference on definitions of infection in the intensive care unit[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF][START_REF] Solomkin | Diagnosis and management of complicated intraabdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America[END_REF][START_REF] Hooton | Diagnosis, prevention, and treatment of catheterassociated urinary tract infection in adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America[END_REF][START_REF] Stevens | Practice guidelines for the diagnosis and management of skin and soft-tissue infections[END_REF][START_REF] Piaggio | Reporting of noninferiority and equivalence randomized trials: extension of the CONSORT 2010 statement[END_REF][START_REF] Renyi | On the theory of order statistics[END_REF][START_REF] Ellenberg | Selection bias in observational and experimental studies[END_REF][START_REF] Ranieri | Drotrecogin alfa (activated) in adults with septic shock[END_REF] days in the de-escalation group and 8 [IQR [START_REF] Kollef | Hospital-acquired pneumonia and de-escalation of antimicrobial treatment[END_REF][START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF][START_REF] Niederman | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Silva | De-escalation of antimicrobial treatment for adults with sepsis, severe sepsis or septic shock[END_REF][START_REF] Calandra | International Sepsis Forum Definition of Infection in the ICU Consensus Conference (2005) The international sepsis forum consensus conference on definitions of infection in the intensive care unit[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF] days in the continuation group, respectively (P = 0.71). The mean difference was 3.4 (95 %

Introduction

The increasing rate of multidrug-resistant pathogens is a major challenge in intensive care units (ICU). Because of the low number of new antibiotics available in the near future, the development of strategies preventing the emergence of resistance is critical. Hand hygiene, contact precautions, isolation of colonized patients, and surveillance are the standards of infection control policies [START_REF] Maragakis | Recognition and prevention of multidrug-resistant Gramnegative bacteria in the intensive care unit[END_REF]. Antimicrobial stewardship is another important strategy for controlling the risk of emergence of antibiotic resistance [START_REF] Dellit | Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America guidelines for developing an institutional program to enhance antimicrobial stewardship[END_REF].

With respect to antimicrobial stewardship, de-escalation of empirical antimicrobial treatment on the basis of culture results and the elimination of redundant combination therapy is a strong recommendation [START_REF] Dellit | Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America guidelines for developing an institutional program to enhance antimicrobial stewardship[END_REF][START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF]. At the bedside, de-escalation consists either in eliminating one of the antibiotics of the prescribed combination or, whenever possible, using a beta-lactam antibiotic with a narrower spectrum of activity [START_REF] Kollef | Hospital-acquired pneumonia and de-escalation of antimicrobial treatment[END_REF]. This recommendation is supported by observational studies [START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF]. De-escalation aims at reducing the use of broadspectrum antibiotics and therefore the emergence of multidrug-resistant pathogens [START_REF] Niederman | De-escalation therapy in ventilator-associated pneumonia[END_REF]. Observational studies suggested that this strategy was safe [START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF]. However, there is no adequate, direct evidence as to whether deescalation of antimicrobial agents is effective and safe for adults with sepsis, severe sepsis, or septic shock [START_REF] Silva | De-escalation of antimicrobial treatment for adults with sepsis, severe sepsis or septic shock[END_REF]. Thus, randomized clinical trials are needed for testing the safety and efficiency of de-escalation of antimicrobial therapy.

Our hypothesis was that de-escalation of empirical antimicrobial therapy in patients with severe sepsis or septic shock was noninferior to the continuation of empirical antimicrobial therapy. The first aim of the study was to demonstrate that de-escalation was noninferior to the continuation of broad-spectrum antibiotics in terms of duration of ICU stay. The secondary aims were to compare the two strategies in terms of mortality, duration of antimicrobial therapy, durations of mechanical ventilation, vasopressor use, numbers of superinfections, organ failure, and Clostridium difficile infection.

Methods

We conducted a multicenter non-blinded randomized noninferiority trial comparing de-escalation versus continuation of the appropriate empirical antimicrobial treatment. The trial was registered in ClinicalTrials.gov (NCT01626612).

Patients

Patients were enrolled from 1 February 2012 to 8 April 2013 at nine ICUs (see list of investigators in the Appendix). Eligibility criteria were (1) the presence of severe sepsis requiring an empirical antimicrobial treatment; severe sepsis was defined as systemic inflammatory response syndrome and suspected infection with at least one organ failure including hypotension, respiratory failure, coma, liver failure, thrombocytopenia, and acute renal failure [START_REF] Calandra | International Sepsis Forum Definition of Infection in the ICU Consensus Conference (2005) The international sepsis forum consensus conference on definitions of infection in the intensive care unit[END_REF]. [START_REF] Dellit | Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America guidelines for developing an institutional program to enhance antimicrobial stewardship[END_REF] The appropriateness of empirical antimicrobial therapy and positive microbiological cultures in relation to the suspected location of infection. Definitions of infections are available in Electronic Supplementary Material Table 1. The reasons for exclusion are reported in Fig. 1.

The trial was monitored by an independent data and safety monitoring board consisting of three members (Dr Nathalie Lesavre, MD; Dr Julie Brunet, PharmD; and Patrick Sudour, Senior Research Technician). They checked the quality of data and the safety of procedures during the study. They produced a report for the National Agency of Drug Safety.

Randomization was performed according to an electronic list that was under the responsibility of the Public Health and Medical Information Department (Ho ˆpital Nord, Marseille, France). The electronic list was managed and centralized by the principal investigator who checked the criteria for inclusion before randomization. The study protocol and statistical analysis plan were approved by the ethics committee of the Marseille University Hospital (Comite ´de Protection des Personnes Sud Me ´diterrane ´e no. 2011-002297-22). Written informed consent was obtained from the patients or their relatives.

Randomization

After the suspected bacteria responsible for infection was identified, the patients/relatives were invited to participate as soon as the antibiogram was available. After the written consent was signed, the eligible patients were randomly assigned (1:1) to be included in either the deescalation group or the continuation group.

De-escalation strategy

After the results of the antibiogram of the suspected causative bacteria were available, the ''pivotal'' antibiotic used for empirical treatment was switched to an antibiotic with a spectrum as narrow as possible according to the targeted pathogens [START_REF] Kollef | Hospital-acquired pneumonia and de-escalation of antimicrobial treatment[END_REF]. The companion drug (aminoglycoside or fluoroquinolone or macrolide) was stopped at day 3. The choice of antibiotics was based on international guidelines [START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF][START_REF] Solomkin | Diagnosis and management of complicated intraabdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America[END_REF][START_REF] Hooton | Diagnosis, prevention, and treatment of catheterassociated urinary tract infection in adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America[END_REF][START_REF] Stevens | Practice guidelines for the diagnosis and management of skin and soft-tissue infections[END_REF]. The empirical antibiotics directed against methicillin-resistant Staphylococcus aureus (MRSA) were stopped if MRSA was not identified in microbiological cultures. For the purpose of this study, de-escalation was considered if the pivotal antibiotic was switched for an antibiotic with a narrower spectrum than the empirical treatment, according to a ranking of molecules provided in Electronic Supplementary Material Table 2. The companion drug and the antibiotic used against MRSA were eliminated after inclusion.

Continuation strategy

After randomization, the pivotal antibiotic of the empirical treatment was continued for the entire duration of the treatment, independently of microbiological results (although the treatment should be active against the identified pathogen). For prolonged treatment ([15 days), the physician had the choice of de-escalating after 8-15 days of treatment. The companion antibiotic (aminoglycoside or fluoroquinolone or macrolide) was stopped between day 3 and day 5 [START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF][START_REF] Solomkin | Diagnosis and management of complicated intraabdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America[END_REF][START_REF] Hooton | Diagnosis, prevention, and treatment of catheterassociated urinary tract infection in adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America[END_REF][START_REF] Stevens | Practice guidelines for the diagnosis and management of skin and soft-tissue infections[END_REF]. Empirical antibiotics directed against MRSA were used according to international guidelines [START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF][START_REF] Solomkin | Diagnosis and management of complicated intraabdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America[END_REF][START_REF] Hooton | Diagnosis, prevention, and treatment of catheterassociated urinary tract infection in adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America[END_REF][START_REF] Stevens | Practice guidelines for the diagnosis and management of skin and soft-tissue infections[END_REF].

Antimicrobial treatment

The antimicrobial treatments were based on the standards of care, in agreement with international guidelines [START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF][START_REF] Solomkin | Diagnosis and management of complicated intraabdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America[END_REF][START_REF] Hooton | Diagnosis, prevention, and treatment of catheterassociated urinary tract infection in adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America[END_REF][START_REF] Stevens | Practice guidelines for the diagnosis and management of skin and soft-tissue infections[END_REF]. First, the patients with severe sepsis and septic shock received an empirical antimicrobial therapy. The choices of antibiotics were suggested according to the site of infection (Electronic Supplementary Material Table 3) [START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF][START_REF] Solomkin | Diagnosis and management of complicated intraabdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America[END_REF][START_REF] Hooton | Diagnosis, prevention, and treatment of catheterassociated urinary tract infection in adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America[END_REF][START_REF] Stevens | Practice guidelines for the diagnosis and management of skin and soft-tissue infections[END_REF]. With respect to treatment duration, the study protocol invited the co-investigators to follow international guidelines (Electronic Supplementary Material Table 4) [START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF][START_REF] Solomkin | Diagnosis and management of complicated intraabdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America[END_REF][START_REF] Hooton | Diagnosis, prevention, and treatment of catheterassociated urinary tract infection in adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America[END_REF][START_REF] Stevens | Practice guidelines for the diagnosis and management of skin and soft-tissue infections[END_REF]. The doses and routes of administration were in accordance with current medical standards. The noninfectious treatments were conducted according to international guidelines [START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF].

Data collection

Demographic characteristics, physiological variables, coexisting conditions, and medications were collected at inclusion. Risk factors for infection due to multidrugresistant bacteria were screened at inclusion, according to previous guidelines [START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF]. Briefly, they consisted of the administration of antimicrobial therapy in the preceding 90 days, current hospitalization of 5 days or more, high frequency of antibiotic resistance in the specific hospital unit, hospitalization for 2 days or more in the preceding 90 days, home infusion therapy, residence in nursing home or extended care facility, and immunosuppressive disease. The local situation of local resistance is summarized in Electronic Supplementary Material Table 5. Microbiological results, duration of antimicrobial treatments, changes in antibiotics occurring after inclusion, and superinfection episodes requiring reintroduction of antibiotics were prospectively collected. Patients were monitored during their ICU stays for signs of organ failures. Organ failure was reported as follows: circulatory failure was defined as systolic blood pressure of 90 mmHg or less or the need for vasopressor therapy. Coagulation failure was defined as a platelet count of 80,000 or less per cubic millimeter. Hepatic failure was defined as a serum bilirubin level of 2 mg/dl (34 lmol/l) or higher. Renal failure was defined as a serum creatinine level of 2 mg/dl (177 lmol/l) or higher.

Study outcomes

Primary outcome

The primary outcome was the number of days between the study inclusion and ICU discharge. For the patients who died during ICU hospitalization, the day of ICU discharge was the day of death.

Secondary outcomes

To complement the primary outcome, the duration of ICU stay was compared in the two groups after adjustment for unbalanced baseline variables. The same procedure was performed on the subgroup of patients alive at ICU discharge.

The other secondary outcomes were the number of ICU-free days (from inclusion to day 28), the day-90 mortality, the numbers of ventilator-free days (from inclusion to day 28), the number of catecholamine-free days (from inclusion to day 28), the number of antibioticfree days (from inclusion to day 28), the number of days of antibiotic treatment during the ICU stay, and the number of superinfections requiring antibiotics. During the first 8 days after inclusion, changes in SOFA score (D-SOFA) were calculated as follows: [score on day 8score on inclusion]. We also collected the number of infections due to C. difficile (positivity of toxin A or B in feces).

Post hoc outcomes

A post hoc analysis was conducted in a subgroup of patients with ventilator-associated pneumonia. From inclusion to ICU discharge, we determined the use of antibiotics directed against Pseudomonas aeruginosa, carbapenems, and antibiotics directed against MRSA. We also analyzed the number of patients in whom an escalation of treatment was required after inclusion. We conducted an analysis of outcomes in the subgroup of patients not requiring changes in antibiotics after inclusion.

Statistical analysis

Assumptions for the sample-size calculation were based on the durations of ICU stay reported in previous studies [START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF]. With respect to a mean duration of ICU stay of 10 days in the continuation group [START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF], a clinically significant noninferiority range of 2 days for 80 % statistical power with a one-sided alpha value of 2.5 %, 51 patients would be needed in each group to establish the noninferiority of de-escalation compared with the continuation of antimicrobial treatment. An additional 15 % was added for loss to follow-up, leading to a total of 120 patients. No interim analysis was planned.

Analysis was performed using SPSS software version 17.0. Statistical significance was defined as P \ 0.05. The methodology was based on the extension of Consolidated Standards of Reporting Trials Statement (CONSORT, http://www.consort-statement.org/consort-statement/) for reporting of noninferiority randomized trials [START_REF] Piaggio | Reporting of noninferiority and equivalence randomized trials: extension of the CONSORT 2010 statement[END_REF]. In view of the noninferiority hypothesis, we performed a per-protocol analysis, which excluded patients who were ineligible after randomization. Differences between groups were assessed using a Chi square test, Fisher's exact test, the Student t test, and the Mann-Whitney test, as appropriate.

Primary outcome

For each patient, we determined the duration of ICU stay. We defined a noninferiority margin of 2 days. If the lower boundary of the 95 % confidence interval (CI) for the difference in the duration of ICU stay in patients assigned to the de-escalation group was less than 2 days, as compared with the duration in patients assigned to the continuation group, we would consider de-escalation as noninferior to the continuation strategy. The duration of ICU stay was expressed as median and interquartile range (IQR) for both groups, as the mean difference and the 95 % CI (de-escalation group minus continuation group).

To complement the primary analysis on the duration of ICU stay, we performed a linear regression model after adjustment for baseline simplified acute physiology score (SAPS) II, (1) in the whole sample; (2) in the subgroup of patients alive at ICU discharge; beta standardized coefficients were presented.

Secondary outcomes

The 90-day mortality rate was compared between the two groups. The 90-day survival rate was also compared between the two groups using the Renyi test [START_REF] Renyi | On the theory of order statistics[END_REF]. Cox models were performed for adjustment on SAPS II. Modified SAPS II (SAPS II excluding the age variable) was calculated. Cox models were performed for adjustment on modified SAPS II, age, and treatment group. Hazard ratios (HR) and 95 % CI were presented. Median D-SOFA (inclusion to day 8), ventilator-free days, catecholamine-free days, antimicrobial-free days (day 1 to day 28), proportions of superinfection (defined by the occurrence of an infection with the identification of a pathogen and the need to introduce a new antimicrobial treatment) and infections due to Clostridium difficile were compared between the two groups. The follow-up was completed at day 90.

Post hoc analysis

In order to assess the effect of source of infection, we performed a multivariate linear regression including the modified unbalanced variables (SAPS II, age, chronic arterial hypertension, source of infection, and treatment group). Then, we determined the duration of ICU stay in the subgroup of patients with lung infection. Similarly, we determined the duration of ICU stay in the patients with risk factors for multidrug-resistant bacteria.

Results

Baseline characteristics

Nine ICUs enrolled 120 patients. Four patients were secondarily excluded because they were placed in the care of a guardian. Thus, the per-protocol analysis included 116 patients. Of the 116 patients, 59 and 57 were randomly assigned to the de-escalation group and the continuation group, respectively (Fig. 1). The two groups differed in age (58 ± 17 years old vs. 67 ± 15 years old, P = 0.003), SAPS II (44 ± 19 vs. 51 ± 19, P = 0.03), and proportion of prior history of hypertension (Table 1). Risk factors for multidrug-resistant bacteria were found in 93 (80 %) patients (Table 1). At inclusion, the SOFA score was 6.4 ± 3.8 (Table 2). Empirical antimicrobial treatment did not differ in either group (Table 2). Blood culture was positive in 39 (34 %) patients. Pathogens were mostly isolated in bronchial and urine samples (Electronic Supplementary Material Table 6).

Empirical treatment was based on combination of antibiotics in 52 (88 %) patients in the de-escalation group, as compared with 52 (91 %) in the continuation group (P = 0.58) (Table 2). Aminoglycosides were used in 33 (56 %) patients and 35 (61 %) patients in the deescalation group and continuation group, respectively (P = 0.55). The duration of companion antibiotics was 2.0 [2.0-3.0] days and 3.0 [2.8-3.0] days in the de-escalation group and the continuation group, respectively (P = 0.002).

Empirical antimicrobial treatment was de-escalated at a median day 3 and IQR 2-4 after the onset of treatment. The latest day for de-escalation was day 9 in one patient. Details of de-escalation are shown in Electronic Supplementary Material Table 7. After randomization, the companion drugs [i.e., aminoglycoside (n = 34), fluoroquinolones (n = 8), and macrolides (n = 3)] were stopped in all cases but one. An antibiotic directed against MRSA was empirically used in 25 (42 %) patients, respectively linezolid (n = 19) and vancomycin (n = 6). In all patients, these antibiotics were stopped after randomization.

Primary outcome

In the per-protocol population, the median duration between inclusion and ICU discharge was 9 [START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF][START_REF] Niederman | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Silva | De-escalation of antimicrobial treatment for adults with sepsis, severe sepsis or septic shock[END_REF][START_REF] Calandra | International Sepsis Forum Definition of Infection in the ICU Consensus Conference (2005) The international sepsis forum consensus conference on definitions of infection in the intensive care unit[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF][START_REF] Solomkin | Diagnosis and management of complicated intraabdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America[END_REF][START_REF] Hooton | Diagnosis, prevention, and treatment of catheterassociated urinary tract infection in adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America[END_REF][START_REF] Stevens | Practice guidelines for the diagnosis and management of skin and soft-tissue infections[END_REF][START_REF] Piaggio | Reporting of noninferiority and equivalence randomized trials: extension of the CONSORT 2010 statement[END_REF][START_REF] Renyi | On the theory of order statistics[END_REF][START_REF] Ellenberg | Selection bias in observational and experimental studies[END_REF][START_REF] Ranieri | Drotrecogin alfa (activated) in adults with septic shock[END_REF] days in the de-escalation group and 8 [START_REF] Kollef | Hospital-acquired pneumonia and de-escalation of antimicrobial treatment[END_REF][START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF][START_REF] Niederman | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Silva | De-escalation of antimicrobial treatment for adults with sepsis, severe sepsis or septic shock[END_REF][START_REF] Calandra | International Sepsis Forum Definition of Infection in the ICU Consensus Conference (2005) The international sepsis forum consensus conference on definitions of infection in the intensive care unit[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF] days in the continuation group (P = 0.71) (Table 3). The mean difference between de-escalation group and continuation group was 3.4 (95 % CI -1.7 to 8.5). After adjustment for baseline SAPS II, neither the treatment group nor the SAPS II was linked to the duration of ICU stay (b = -0.10; P = 0.28, b = -0.09; P = 0.33, respectively). The estimated marginal means and standard errors were 14.9 ± 1.8 days and 12.1 ± 1.7 days for the de-escalation group and continuation group, respectively.

Secondary prespecified outcomes

Regarding the initial episode of severe sepsis or septic shock, the duration of antibiotic treatment was similar in both groups (P = 0.94). For the patients discharged alive from the ICU, the mean duration from inclusion to discharge did not differ in either group (9 [1-79] days vs. 6 [1-60] days, P = 0.28). In the de-escalation group, severe sepsis or septic shock was diagnosed 5 [START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF][START_REF] Kollef | Hospital-acquired pneumonia and de-escalation of antimicrobial treatment[END_REF][START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF] days after ICU admission, as compared with 4 [START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF][START_REF] Kollef | Hospital-acquired pneumonia and de-escalation of antimicrobial treatment[END_REF][START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF] days in the continuation group (P = 0.24). The number of hospital days after inclusion was 24 days in the deescalation group and 20 days in the continuation group (P = 0.26). Death at 90 days was reported in 18 (31 %) patients in the de-escalation group and 13 (23 %) patients in the continuation group (P = 0.35) (Fig. 2). The 90-day mortality did not differ in either group (HR = 1.31, 95 % CI 0.64-2.67, P = 0.49). After adjustment for modified SAPS II, age, and treatment group, the Cox regression model yielded an HR for death at day 90 of 1.01 (95 % CI, 0.99-1.03, P = 0.30) for modified SAPS II, 1.02 (95 % CI 1.00-1.05, P = 0.06) for age, and 1.7 (95 % CI 0.79-3.49, P = 0.18) for treatment group.

In the 66 patients with an ICU stay of more than 7 days, the median D-SOFA score was similar in both groups (3 [0; 4] vs. 2 [-1; 3], P = 0.63). At day 28, the numbers of ventilator-free days and of catecholamine-free days did not differ significantly in either group (Table 3). Of the 86 patients discharged alive from hospital, 15 (36 %) patients in the de-escalation group and 14 (32 %) patients in the continuation group were re-admitted to hospital (P = 0.64). Globally, five patients in the deescalation group and one patient in the continuation group required ICU readmission, respectively (P = 0.1). The number of days of antimicrobial use was 9 [2-66] days in the de-escalation group and 8 days in the continuation group (P = 0.11). During ICU stay, superinfection episodes requiring antibiotics were identified in 16 (27 %) patients in the de-escalation group and six (11 %) patients in the continuation group (P = 0.03). This was related to the same bacteria in seven (44 %) of the 16 episodes in the de-escalation group and four (67 %) of the six episodes in the continuation group (P = 0.64). The locations of superinfection were lungs (n = 13), abdomen (n = 2), bloodstream (n = 2), urine (n = 2), and catheter-related infection (n = 1). No C. difficile infection was reported in the included patients.

Secondary post hoc outcomes

Because lung infection was unbalanced between groups, we performed a multivariate analysis with modified SAPS II, age, chronic arterial hypertension, and source of infection. Lung as source of infection was an independent variable linked to the duration of ICU stay. Thus, we assessed the impact of de-escalation in the 56 patients with lung infection. The durations of ICU stay were 14 days and 15 [START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF][START_REF] Niederman | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Silva | De-escalation of antimicrobial treatment for adults with sepsis, severe sepsis or septic shock[END_REF][START_REF] Calandra | International Sepsis Forum Definition of Infection in the ICU Consensus Conference (2005) The international sepsis forum consensus conference on definitions of infection in the intensive care unit[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF][START_REF] Solomkin | Diagnosis and management of complicated intraabdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America[END_REF][START_REF] Hooton | Diagnosis, prevention, and treatment of catheterassociated urinary tract infection in adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America[END_REF][START_REF] Stevens | Practice guidelines for the diagnosis and management of skin and soft-tissue infections[END_REF][START_REF] Piaggio | Reporting of noninferiority and equivalence randomized trials: extension of the CONSORT 2010 statement[END_REF][START_REF] Renyi | On the theory of order statistics[END_REF][START_REF] Ellenberg | Selection bias in observational and experimental studies[END_REF] days in the de-escalation group and the continuation group, respectively (P = 0.53). Thirteen (39 %) and five (22 %) superinfection episodes were reported in the deescalation group and continuation group (P = 0.2).

In the 93 patients with risk factors for multidrugresistant bacteria carriage, the duration of ICU stay was 10 days and 8 [START_REF] Kollef | Hospital-acquired pneumonia and de-escalation of antimicrobial treatment[END_REF][START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF][START_REF] Niederman | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Silva | De-escalation of antimicrobial treatment for adults with sepsis, severe sepsis or septic shock[END_REF][START_REF] Calandra | International Sepsis Forum Definition of Infection in the ICU Consensus Conference (2005) The international sepsis forum consensus conference on definitions of infection in the intensive care unit[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF][START_REF] Solomkin | Diagnosis and management of complicated intraabdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America[END_REF] days in the de-escalation group and continuation group, respectively (P = 0.71).

After inclusion, the antibiotics directed against P. aeruginosa were used for 12 [START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF][START_REF] Niederman | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Silva | De-escalation of antimicrobial treatment for adults with sepsis, severe sepsis or septic shock[END_REF][START_REF] Calandra | International Sepsis Forum Definition of Infection in the ICU Consensus Conference (2005) The international sepsis forum consensus conference on definitions of infection in the intensive care unit[END_REF][START_REF]Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcareassociated pneumonia[END_REF][START_REF] Solomkin | Diagnosis and management of complicated intraabdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America[END_REF][START_REF] Hooton | Diagnosis, prevention, and treatment of catheterassociated urinary tract infection in adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America[END_REF][START_REF] Stevens | Practice guidelines for the diagnosis and management of skin and soft-tissue infections[END_REF][START_REF] Piaggio | Reporting of noninferiority and equivalence randomized trials: extension of the CONSORT 2010 statement[END_REF][START_REF] Renyi | On the theory of order statistics[END_REF][START_REF] Ellenberg | Selection bias in observational and experimental studies[END_REF][START_REF] Ranieri | Drotrecogin alfa (activated) in adults with septic shock[END_REF] days in the de-escalation group and 6 [START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF][START_REF] Kollef | Hospital-acquired pneumonia and de-escalation of antimicrobial treatment[END_REF][START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF][START_REF] Niederman | De-escalation therapy in ventilator-associated pneumonia[END_REF] days in the continuation group (P = 0.03). The duration of the use of carbapenems and antibiotics directed against MRSA were similar in both groups (Table 3).

After inclusion, antimicrobial treatment was escalated in eight (14 %) patients in the de-escalation group and five (8.8 %) patients in the continuation group (P = 0.41). We assessed the duration of ICU stay, mortality rate, and number of superinfections in the 103 patients in whom the antimicrobial treatment remained unchanged after inclusion. No significant difference was reported in either group, including the number of superinfection episodes (10 (19 %) episodes vs. four (8 %) episodes, P = 0.08).

Discussion

For the first time, de-escalation of antimicrobial treatment was tested in a randomized clinical trial. In terms of duration of ICU stay we cannot conclude that the de-escalation strategy was noninferior to the continuation of an appropriate empirical treatment. De-escalation was associated with an increased number of superinfection episodes, but it did not affect the number of organ failures and mortality.

The strength of our study was to randomize de-escalation as compared to the continuation of an appropriate empirical treatment. Although guidelines recommend a strategy based on de-escalation [START_REF] Dellit | Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America guidelines for developing an institutional program to enhance antimicrobial stewardship[END_REF][START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF], such a strategy has never been tested in a randomized clinical trial [START_REF] Silva | De-escalation of antimicrobial treatment for adults with sepsis, severe sepsis or septic shock[END_REF]. The guidelines are supported by observational studies [START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF], in which several biases may affect the results [START_REF] Ellenberg | Selection bias in observational and experimental studies[END_REF]. The present randomized clinical trial did not confirm the findings of observational studies. Nevertheless, our pragmatic study protocol aimed at reflecting real-life conditions, including uncertainty about diagnosis and adequate treatment of infections. The study was performed in nine multidisciplinary ICUs. This suggests that our results can be exported to other ICUs.

In the de-escalation group, we observed an increased number of superinfections. This finding probably explains the increased use of antibiotics in this group. The duration of treatment of the initial episode was similar in both groups, suggesting that superinfection episodes were responsible for prolonged antimicrobial use in the deescalation group. Of note, in this group, new pathogens were responsible for 56 % of the superinfection episodes.

De-escalation did not affect the mortality rate. In our study, we observed a 27 % mortality rate at day 90. This rate is consistent with the selection of patients with severe sepsis [START_REF] Ranieri | Drotrecogin alfa (activated) in adults with septic shock[END_REF]. Although the study was not designed to assess this endpoint, we did not observe any difference in the 90-day mortality in either group. Our findings are in accordance with the results of several observational studies [START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF]. In contrast, an observational study concluded that de-escalation was a protective factor for mortality [START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF]. Unexpected bias can affect the findings of observational studies [START_REF] Ellenberg | Selection bias in observational and experimental studies[END_REF][START_REF] Leibovici | Non-antibiotic treatment for bacterial infections: how to validate chance findings[END_REF]. The appropriateness of antimicrobial treatment is probably critical for reducing the mortality related to severe sepsis [START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Retamar | Impact of inadequate empirical therapy on the mortality of patients with bloodstream infections: a propensity score-based analysis[END_REF][START_REF] Ibrahim | The influence of inadequate antimicrobial treatment of bloodstream infections on patient outcomes in the ICU setting[END_REF][START_REF] Kerry | Trials which randomize practices II: sample size[END_REF][START_REF] Garcin | Non-adherence to guidelines: an avoidable cause of failure of empirical antimicrobial therapy in the presence of difficult-to-treat bacteria[END_REF]. Here we found that de-escalation was not associated with a significant change in mortality.

The study was designed on a noninferiority model. This choice was based on the analysis of observational studies [START_REF] Rello | De-escalation therapy in ventilator-associated pneumonia[END_REF][START_REF] Leone | Empirical antimicrobial therapy of septic shock patients: adequacy and impact on the outcome[END_REF][START_REF] Morel | De-escalation as part of a global strategy of empiric antibiotherapy management. A retrospective study in a medico-surgical intensive care unit[END_REF][START_REF] Heenen | Antibiotic strategies in severe nosocomial sepsis: why do we not deescalate more often?[END_REF][START_REF] Shime | De-escalation of antimicrobial therapy for bacteraemia due to difficult-to-treat Gram-negative bacilli[END_REF][START_REF] Garnacho-Montero | Deescalation of empirical therapy is associated with lower mortality in patients with severe sepsis and septic shock[END_REF][START_REF] Mokart | De-escalation of antimicrobial treatment in neutropenic patients with severe sepsis: results from an observational study[END_REF]. Most of those studies did not report significant effects of de-escalation in terms of ICU duration. Importantly, this design cannot serve to state that continuing the empirical antimicrobial treatment was associated with a shorter duration of ICU stay than deescalating the empirical antimicrobial treatment.

Limitations of our study include the lack of blind treatment. The open design probably may have influenced many important variables. As we compared different strategies, it was technically difficult to conduct blind treatment. Although we designed the study to reach a power of 80 %, the number of patients remains relatively small. Mode of administration was not collected, but most treatments were given according to international guidelines [START_REF] Dellit | Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America guidelines for developing an institutional program to enhance antimicrobial stewardship[END_REF][START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF]. The inclusion of patients with severe sepsis independently of the site of infection could be viewed as a limitation. However, guidelines recommend de-escalating the empirical antimicrobial treatment in all patients with severe sepsis, wherever the source of infection [START_REF] Dellit | Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America guidelines for developing an institutional program to enhance antimicrobial stewardship[END_REF][START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF]. Of note, no significant difference was reported in the patients with lung infection. Finally, there is an arbitrary dimension in the definition of de-escalation. Future consensus is required in order to provide a definition for this process.

Our study was not designed to measure the effect of deescalation on local ecology. We collected samples from patients at inclusion and on day 8. We did not find significant differences in either groups (data not shown). In addition, no C. difficile infection was diagnosed in our patients. Larger samples of patients are probably required to explore this issue accurately [START_REF] Kerry | Trials which randomize practices II: sample size[END_REF]. Time of inclusion is another limitation. However, the time between onset of sepsis and antibiotic administration was similar in both groups. Randomization resulted in imbalances between the groups in age that could have influenced the findings. After adjustment, the differences in hospital stay and mortality were unchanged. One can note that lung as a source of infection impacted the duration of ICU stay. However, in this subgroup, the duration of ICU stay tended also to be longer in the de-escalation group than in the continuation group. In line with prior findings [START_REF] Martin-Loeches | Potentially resistant microorganisms in intubated patients with hospital-acquired pneumonia: the interaction of ecology, shock and risk factors[END_REF], a similar trend was found in the analysis of patients with risk factors of infection due to multidrug-resistance bacteria. According to guidelines [START_REF] Dellit | Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America guidelines for developing an institutional program to enhance antimicrobial stewardship[END_REF][START_REF] Dellinger | Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012[END_REF], antibiotics directed against MRSA were empirically used in our patients with severe sepsis and septic shock. However, as there is no option for deescalating linezolid or vancomycin, no patient with MRSA infection was included. Of note, in a previous study [START_REF] Leone | Routine use of Staphylococcus aureus rapid diagnostic test in patients with suspected ventilator-associated pneumonia[END_REF], we assessed the rate of patients with ventilator-associated pneumonia in three out of the nine ICUs of our present study. We noted a 1.6 % prevalence of MRSA, suggesting that this pathogen is rare in our area. In the present study, we screened two patients with MRSA infection.

In conclusion, for the first time, this multicenter trial randomly assigned de-escalation or continuation strategy. In terms of duration of ICU stays, de-escalation was inferior to continuation of the appropriate empirical treatment. De-escalation was associated with an increased number of superinfections, but it did not affect mortality.

Fig. 1

 1 Fig. 1 Flow chart of inclusion and follow-up

Fig. 2

 2 Fig. 2 Cumulative survival curves: no difference was observed in the groups

Table 1

 1 Baseline characteristics of study participants

	Characteristics	De-escalation group (n = 59) Continuation group (n = 57) P
	Age (years)	57.9 ± 17.0	66.8 ± 14.9	0.003
	Male sex (%) SAPS II a Modified SAPS II a	62.7 43.6 ± 18.5 33.9 ± 17.5	66.7 51.4 ± 18.7 38.1 ± 18.3	0.66 0.03 0.20
	Body mass index	26.8 ± 6.4	27.4 ±7.4	0.65
	Admission cause			0.56
	Medicine (%)	52.5	54.4
	Trauma (%)	8.5	15.8
	Scheduled surgery (%)	10.2	7.0
	Emergent surgery (%)	28.8	22.8
	Co-morbidities
	Chronic obstructive pulmonary disease (%)	15.3	15.8	0.94
	Diabetes (%)	18.6	28.1	0.23
	Arterial hypertension (%)	30.5	50.9	0.03
	Chronic heart failure (%)	10.2	8.8	0.80
	Prior stroke (%) Risk factors for multidrug-resistant pathogen b (%) Time between onset of empirical treatment and inclusion (days) c 3.0 ± 1.7 3.4 83.1	7.0 77.2 2.7 ± 1.4	0.38 0.43 0.25
	Time between sepsis and inclusion (days) c	3.0 [2.0-4.0] 3.2 ± 1.6	2.0 [2.0-3.5] 2.7 ± 1.4	0.05
		3.0 [2.0-4.0]	2.0 [2.0-3.0]
	Data are means ± SD unless otherwise specified

a SAPS denotes simplified acute physiology score. Modified SAPS II means SAPS II without age inclusion b Includes antimicrobial therapy in preceding 90 days, current hospitalization of 5 days or more, high frequency of antibiotic resistance in the community or in the specific hospital unit, hospitalization for 2 days or more in the preceding 90 days, resident in nursing home or extended care facility, chronic dialysis within 30 days, home wound care, family member with multidrugresistant pathogen, immunosuppressive disease and/or therapy c Data include medians

[interquartile]

Table 2

 2

	Criteria at inclusion	Characteristics	De-escalation group	Continuation group	P
			(n = 59)	(n = 57)
		SOFA a	6.3 ± 2.9	6.4 ± 4.0	0.78
		Catecholamines (%)	54.2	54.4	0.99
		Mechanical ventilation (%)	71.2	59.6	0.19
		Site of infection
		Lung (%)	57.6	40.4	0.06
		Urine (%)	20.3	22.8	0.75
		Abdomen (%)	15.3	21.2	0.42
		Skin and tissue (%)	5.1	10.5	0.32
		Catheter (%)	1.7	1.8	1.00
		Positive blood culture (%)	32.2	35.1	0.74
		Empirical antibiotics			0.54
		Combined therapy (%)	88	91	0.58
		Carbapenems (%)	39.0	17.5	0.01
		Ureidopenicillin plus inhibitor (%)	35.6	50.9	0.09
		Third-generation cephalosporin (%)	25.4	29.8	0.59
		Aminoglycoside (%)	56.0	61.4	0.55
		Fluoroquinolone (%)	13.6	29.8	0.03
		Vancomycin (%)	11.9	12.3	0.94
		Linezolid (%)	23.7	12.3	0.11
		Fluconazole (%)	3.3	3.5	1.0
		Echinocandin (%)	0.0	1.8	0.49

a SOFA denotes sequential organ failure assessment

Table 3

 3 Outcomes of patients included in the two groups

	Duration	De-escalation	Continuation	P
		group (n = 59)	group (n = 57)
	Duration of ICU stay (days)
	From inclusion to discharge	15.2 ± 15.0	11.8 ± 12.6	0.71
		9 [1-79]	8 [1-60]
	From admission to discharge	29.1 ± 50.0	18.1 ± 15.7	0.11
	Number of ICU-free days a	13 [1-375] 13.2 ± 10.6	12 [3-67] 15.0 ± 11.3	0.21
	Ventilator-free days a	18 [0-23] 18.9 ± 11.6	21 [0-25] 19.3 ± 11.8	0.55
	Catecholamine-free days a	23 [6-29] 22.3 ± 10.3	26 [6-29] 21.6 ± 11.2	0.93
		28 [21-29]	28 [16-29]
	Number of antibiotic days	14.1 ± 13.4	9.9 ± 6.6	0.04
		9 [7-15]	7.5 [6-13]
	Number of companion antibiotic days	2.3 ± 0.8	3.2 ± 1.7	\0.00
		2.0 [2.0-3.0]	3.0 [2.8-3.0]
	Number of antibiotic days for the initial episode Number of antipseudomonal agent-free days a	7.9 ± 5.2 23.6 ± 9.2	8.0 ± 4.3 20.1 ± 9.6	0.94 \0.001
	Number of carbapenem-free days a	29 [24-29] 25.6 ± 7.3	24 [15-28] 23.5 ± 8.4	0.17
		29 [26-29]	29 [19-29]

Number of anti-MRSA drug-free days a 25.8 ± 7.1 29 [27-29] 24.1 ± 8.4 29 [21-29] 0.30 Data are means ± SD, followed by medians [interquartile]. Durations are determined after study inclusion MRSA methicillin-resistant Staphylococcus aureus a Free days were calculated from inclusion (day 1) to day 28

Acknowledgments We thank Jean-Charles Reynier, Loundoun Anderson, and Pascal Auquier. We also thank Charlotte Kelway for her attentive reading of our manuscript.

List of co-investigators

The following data are reported as ''unit, hospital, city (number of patients included): names of coinvestigators'':

Polyvalent