Genomic characterization of the commensal Escherichia coli strain A0 34/86 (O83:K24:H31)

Escherichia coli A0 34/86 (O83:K24:H31) est une bactérie commensale, utilisée pour la colonisation de nouveaux-nés. Pour identifier les caractères distinguant cette souche d'autres E. coli, nous avons caractérisé son génome. L hybridation de réseaux d'ADN "coli K12" et pathoarrays , la PCR multiplex, le séquençage des inserts de chromosomes artificiels bactériens (BAC) et le séquençage shotgun ont permis d identifier des gènes codant pour des facteurs de virulence et de fitness. Cette souche appartient à la classe phylogénétique B2. Le séquençage d un BAC de 55 kb a révélé la présence d un îlot génomique de 20 kb (GimA) identifié chez E. coli K1 responsable de méningites. La comparaison génomique entre E. coli A0 34/86 et E. coli K12, CFT073, O157:H7 et Nissle 1917 basée sur les BACs a permis la sélection de deux BACs portant les gènes nécessaires à la synthèse de la vitamine B12 (cob), à la dégradation du propanediol (pdu), des gènes de fimbriae (pix), et des gènes codant pour le système de transport de phosphoglycerate (pgt) de l îlot pathogénique V de la souche uropathogène 536. L'analyse de l opéron hémolysine d'E. coli A0 34/86 a montré que le mutant inactivé dans le locus hly ( hlyA) a une capacité de colonisation des porcelets identique à la souche sauvage. Par contre, dans le modèle du porcelet sans microbe, la survie était plus grande lors d'une colonisation par la souche mutant ( hlyA) comparée à la souche sauvage.PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Characterization of the flexible genome complement of the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31)

International audienceColonization by the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31) has proved to be safe and efficient in the prophylaxis and treatment of nosocomial infections and diarrhoea of preterm and newborn infants in Czech paediatric clinics over the past three decades. In searching for traits contributing to this beneficial effect related to the gut colonization capacity of the strain, the authors have analysed its genome by DNA–DNA hybridization to E. coli K-12 (MG1655) genomic DNA arrays and to ‘Pathoarrays’, as well as by multiplex PCR, bacterial artificial chromosome (BAC) library cloning and shotgun sequencing. Four hundred and ten E. coli K-12 ORFs were absent from A0 34/86, while 72 out of 456 genes associated with pathogenicity islands of E. coli and Shigella were also detected in E. coli A0 34/86. Furthermore, extraintestinal pathogenic E. coli -related genes involved in iron uptake and adhesion were detected by multiplex PCR, and genes encoding the HlyA and cytotoxic necrotizing factor toxins, together with 21 genes of the uropathogenic E. coli 536 pathogenicity island II, were identified by analysis of 2304 shotgun and 1344 BAC clone sequences of A0 34/86 DNA. Multiple sequence comparisons identified 31 kb of DNA specific for E. coli A0 34/86; some of the genes carried by this DNA may prove to be implicated in the colonization capacity of the strain, enabling it to outcompete pathogens. Among 100 examined BAC clones roughly covering the A0 34/86 genome, one reproducibly conferred on the laboratory strain DH10B an enhanced capacity to persist in the intestine of newborn piglets. Sequencing revealed that this BAC clone carried gene clusters encoding gluconate and mannonate metabolism, adhesion ( fim ), invasion ( ibe ) and restriction/modification functions. Hence, the genome of this clinically safe and highly efficient colonizer strain appears to harbour many ‘virulence-associated’ genes. These results highlight the thin line between bacterial ‘virulence’ and ‘fitness' or ‘colonization’ factors, and question the definition of enterobacterial virulence factors