Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms

Abstract

Avian pathogenic Escherichia coli (APEC) causes respiratory and systemic disease in poultry. Sequencing of a multilocus sequence type 95 (ST95) serogroup O1 strain previously indicated that APEC resembles E. coli causing extraintestinal human diseases. We sequenced the genomes of two strains of another dominant APEC lineage (ST23 serogroup O78 strains χ7122 and IMT2125) and compared them to each other and to the reannotated APEC O1 sequence. For comparison, we also sequenced a human enterotoxigenic E. coli (ETEC) strain of the same ST23 serogroup O78 lineage. Phylogenetic analysis indicated that the APEC O78 strains were more closely related to human ST23 ETEC than to APEC O1, indicating that separation of pathotypes on the basis of their extraintestinal or diarrheagenic nature is not supported by their phylogeny. The accessory genome of APEC ST23 strains exhibited limited conservation of APEC O1 genomic islands and a distinct repertoire of virulence-associated loci. In light of this diversity, we surveyed the phenotype of 2,185 signature-tagged transposon mutants of χ7122 following intra-air sac inoculation of turkeys. This procedure identified novel APEC ST23 genes that play strain- and tissue-specific roles during infection. For example, genes mediating group 4 capsule synthesis were required for the virulence of χ7122 and were conserved in IMT2125 but absent from APEC O1. Our data reveal the genetic diversity of E. coli strains adapted to cause the same avian disease and indicate that the core genome of the ST23 lineage serves as a chassis for the evolution of E. coli strains adapted to cause avian or human disease via acquisition of distinct virulence genes.

Fig 1

Phylogenetic tree generated using RAxML (version 7.0.4) from the concatenated sequences of the 3,153 proteins that are shared by the 12 E. coli strains analyzed (see Materials and Methods). Pathotypes are color-coded according to the key, and serotypes are given at the position of each strain on the tree.

Fig 2

Venn diagram showing the numbers of conserved and strain-specific orthologous proteins predicted by OrthoMCL to be encoded by the chromosomes of strains χ7122, IMT2125, and APEC O1.

Fig 3

Recovery of APEC strain χ7122 mutants from the lung (A), liver (B), and spleen (C) 24 h after intra-air sac inoculation of turkeys. The recovery of the ΔevgS::kan^R and ΔyccC::kan^R mutants relative to that of the parent strain was tested in 4 birds per strain. In a separate study, other mutants were tested relative to the parent strain in three birds each. Asterisks indicate a significant difference (P ≤ 0.05) between the concentration (log₁₀ CFU/g) of the mutant strain recovered and that of the parent strain.