The genome sequence of Escherichia coli strain IMT2125. Escherichia coli IMT2125

Avian pathogenic Escherichia coli (APEC) comprise a diverse subgroup of extra-intestinal pathogenic E. coli (ExPEC) associated with respiratory and systemic disease in poultry. Recent studies have indicated that they may also pose a threat of zoonosis. Infections in poultry are frequently due to serogroup O1, O2 and O78 strains, however APEC are highly heterogenous and the mode and genetics of mucosal colonization and systemic translocation are ill-defined. We sequenced the genomes of sequence-type 23 APEC O78 strains chi7122 (O78:H9) and IMT2125 (O78:H9) and compared them to each other and the re-annotated sequence of APEC O1 (O1:K1:H7, sequence-type 95). This revealed that the O78 strains were far more closely related to each other than to APEC O1, with limited conservation of genomic islands described in APEC O1 and a distinct repertoire of virulence-associated loci. In light of the heterogeneity of APEC genomes, we surveyed the phenotype of 2185 random chi7122 transposon mutants following intra-airsac inoculation of turkeys toward an understanding of the basis of virulence of APEC O78. The insertion site of 78 mutants that were negatively-selected in the lung or liver relative to inocula was assigned by signature-tagged mutagenesis. Phenotypes were supported by negative-selection of defined null mutants constructed by homologous recombination and novel genes and pathways that play strain-specific and tissue-specific roles in infection were identified. For example, genes mediating group 4 (O-antigen) capsule synthesis were required for virulence of chi7122 and were conserved in IMT2125 but absent from the sequenced serogroup O1 strain. Moreover, mutations in several genes were significantly attenuating at systemic sites, but not the lung. Such data will facilitate the development of cross-protective vaccines and other strategies to control a key endemic avian disease.