Comparative genomic analysis shows that avian pathogenic Escherichia coli isolate IMT5155 (O2:K1:H5; ST complex 95, ST140) shares close relationship with ST95 APEC O1:K1 and human ExPEC O18:K1 strains

Abstract

Avian pathogenic E. coli and human extraintestinal pathogenic E. coli serotypes O1, O2 and O18 strains isolated from different hosts are generally located in phylogroup B2 and ST complex 95, and they share similar genetic characteristics and pathogenicity, with no or minimal host specificity. They are popular objects for the study of ExPEC genetic characteristics and pathogenesis in recent years. Here, we investigated the evolution and genetic blueprint of APEC pathotype by performing phylogenetic and comparative genome analysis of avian pathogenic E. coli strain IMT5155 (O2:K1:H5; ST complex 95, ST140) with other E. coli pathotypes. Phylogeny analyses indicated that IMT5155 has closest evolutionary relationship with APEC O1, IHE3034, and UTI89. Comparative genomic analysis showed that IMT5155 and APEC O1 shared significant genetic overlap/similarities with human ExPEC dominant O18:K1 strains (IHE3034 and UTI89). Furthermore, the unique PAI I5155 (GI-12) was identified and found to be conserved in APEC O2 serotype isolates. GI-7 and GI-16 encoding two typical T6SSs in IMT5155 might be useful markers for the identification of ExPEC dominant serotypes (O1, O2, and O18) strains. IMT5155 contained a ColV plasmid p1ColV5155, which defined the APEC pathotype. The distribution analysis of 10 sequenced ExPEC pan-genome virulence factors among 47 sequenced E. coli strains provided meaningful information for B2 APEC/ExPEC-specific virulence factors, including several adhesins, invasins, toxins, iron acquisition systems, and so on. The pathogenicity tests of IMT5155 and other APEC O1:K1 and O2:K1 serotypes strains (isolated in China) through four animal models showed that they were highly virulent for avian colisepticemia and able to cause septicemia and meningitis in neonatal rats, suggesting zoonotic potential of these APEC O1:K1 and O2:K1 isolates.

Figure 1. Phylogenomic tree (1,782 concatenated core genes, 1.61 Mb) of 47 E. coli strains.

All MrBayes with the GTR+G+I substitution model (BMCMC) was used for the reconstruction of the phylogenomic tree. The chain length was set to 10,000,000 (1 sample/1000 generations). 47 E. coli strains clearly divided into monophyletically phylogroups (A, B1, B2, D, and E), and ST complex 95 strains were highlighted in phylogenomic tree. 47 E. coli genomes data was listed in File A in File S3.

Figure 2. Chimeric feature and genetic context of PAI I₅₁₅₅ (GI-12).

PAI I₅₁₅₅ was inserted between the cadC and yidC genes of E. coli core genome. Proteins encoded by the ORFs of PAI I₅₁₅₅ represented by arrows, and the direction of the arrows indicated the direction of transcription. The color keys for functions of these proteins were shown at the bottom.

Figure 3. Comparative ORF analysis between IMT5155 and other E. coli strains.

From outside to inside, the circles represent that: a) coordinate of IMT5155 genome; b) IMT5155 genomic island regions (red); c) IMT5155 (pink); d) APEC O1, IHE304, and UTI189 (blue); e) CFT073, ABU 83972 and NA114 (green); f) χ7122 (olive); g) UM146 and NRG857c (orange); h) SE15 (magenta); i) E2348/69 (cyan); j) CE10 and UMN026 (skyblue); k) O157 Sakai and O55:H7 RM12579 (purple); l) MG1655 (yellow); GC% of IMT5155 (calculated by 500 bp sliding window).

Figure 4. Comparative ORF analysis between p1ColV₅₁₅₅ and other plasmids.

From inside to outside, the circles represent that: a) GC% (calculated by 500 bp sliding window); b) common ORFs in pUTI89 (brown); c) common ORFs in pO83_CORR (green); d) common ORFs in pMAR2 (yellow); e) common ORFs in pAPEC-O2-ColV (grey); f) common ORFs in pAPEC-O1-ColBM (purple); g) p1ColV₅₁₅₅ (pink); i) highlighted functional ORFs in the negative strand of p1ColV₅₁₅₅; j) highlighted functional ORFs in the positive strand of p1ColV₅₁₅₅ (orange: RepF IIA, RepF IB, repB; blue: Transfer regions; red: virulence related genes; green: cvaAB locus).

Figure 5. The distribution diagram of 10 sequenced B2 ExPEC pan-genome virulence genes among 46 E. coli strains.

The uppermost row showed six classified clusters: 1, adhesins, green; 2, invasins, magenta; 3, iron acquisition/transport systems, blue; 4, polysialic acid synthesis, aquamarine; 5, toxins, purple; 6, others, darksalmon. Right side of the vertical line showed E. coli strains that were consistent with phylogenetic tree (Figure 1). The red and black body showed distribution of virulence genes among these strains. A red line meant that the virulence gene of interest was present at a particular strain, while a black line implied the gene was absent.