Genetic and phylogenetic characterization of Shiga toxin-producing Escherichia coli and enteropathogenic E. coli from livestock in Jiangsu by using whole-genome sequencing

Abstract

Aims: There are knowledge gaps regarding STEC and EPEC strains in livestock in Jiangsu, China. This study aimed to evaluate the potential public health significance of STEC and EPEC strains isolated from livestock by determining the serotypes, virulence profiles, and genetic relationship with international STEC strains. Methods and Results:A total of 68 STEC and 37 EPEC strains were obtained from 231 faecal sheep samples and 70 faecal cattle samples. By using whole-genome sequencing (WGS) analysis, all STEC belonged to 15 O: H serotypes, and the most prevalent serotypes were O6:H10 (19.1%), O155:H21 (14.7%), and O21:H25 (10.3%). The main Shiga toxin gene subtypes detected were stx1c (41.2%), stx1a (26.5%), stx2b (14.7%), and stx2k (14.7%). Only the STEC from cattle carried eae gene. Other adherence-associated or toxin-related genes, including lpfA (70.6%), iha (48.5%), subA (54.4%), and ehxA (33.8%), were found in STEC. All EPEC strains were bfpA-negative, and the predominant eae variants were eae-β1 (62.2%), eae-ζ (21.6%), and eae-θ (8.1%). The core-genome multilocus sequence typing (cgMLST) analysis revealed nine scattered clusters in STEC and one dominant cluster in EPEC. The strains with the same serotypes, including O22:H8 and O43:H2 in the two towns, possessed a closely genomic distance. The core genome single-nucleotide polymorphism (cgSNP) showed that part of STEC strains in this study was clustered with isolates possessing the same serotypes from the Netherlands, Sweden, and Xinjiang of China. Five serotypes of STEC isolates were associated with the clinical STEC strains from databases. Conclusion:This study provided the diverse serotypes and the virulence genes profiles in STEC and EPEC strains. Local strains possessed widely diverse and scattered clusters by cgMLST. Closely genomic correlation with clinical isolates displayed that part of the STEC strains may threaten to public health.Significance and Impact of the Study: Non-O157 STEC strains act as important pathogens for human infections. This study supports the increased surveillance work of non-O157 STEC rather than just O157 STEC in this region.

High Prevalence and Persistence of Escherichia coli Strains Producing Shiga Toxin Subtype 2k in Goat Herds

“…To determine the phylogenetic relationships of Stx2k-STEC strains isolated from goats in this study and 17 previously reported Stx2k-STEC strains from diverse sources ( 12 , 14 ), a whole-genome phylogeny tree was constructed from the alignment of the concatenated coding sequences (CDSs) of the 1,909 shared loci found in all 187 Stx2k-STEC isolates ( Fig. 3 ).…”

“…Stx2k-producing E. coli strains have been identified from a broad range of hosts and sources, including diarrheal patients, pigs, raw meat (beef and mutton), sheep, and goats, exclusively in China so far ( 12 , 14 ). In this study, 170 Stx2k-STEC strains were isolated from goats, and the proportion of Stx2k (37.95%) was the highest among all Stx subtypes detected.…”

“…Genome assemblies of 170 Stx2k-STEC strains in this study, together with other reported Stx2k-STEC strains ( 12 , 14 ), were assessed by whole-genome multilocus typing (wgMLST) and whole-genome phylogeny. The complete whole-genome sequence of O157:H7 strain Sakai ( NC_002695.2 ) was used as a reference to perform an ad hoc fast-GeP (Fast Genome Profiler) analysis ( https://github.com/jizhang-nz/fast-GeP ) to define wgMLST allelic profiles ( 52 ).…”

“…Of these, Stx2j, Stx2k, Stx2m, and Stx2o subtypes have been identified in clinical isolates ( 11 , 13 ), suggesting clinical relevance of new Stx subtypes. Interestingly, Stx2k-STEC strains have been identified in E. coli strains from a variety of hosts and sources, including diarrheal patients, animals (goats, sheep, and pigs), and raw meat (mutton and beef), in China over time ( 12 , 14 ), while they not yet been reported in any other countries.…”

Distribution, Phylogeny and Evolution of Clinical and Environmental Vibrio vulnificus Antibiotic-Resistant Genes

“… 2 , 34 The biotype 1 clade appeared to contain a significantly higher proportion of clinical isolates, while biotype 2 clade contained both of clinical and environmental isolates, that was also reported by López-Pérez et al 8 Despite the genomic divergence among clusters, a distinct pattern linking strain phylogeny, source of isolation, and virulent capabilities was not identified. This mixed distribution of clinical and environmental V. vulnificus isolates suggested that the genomic difference between 2 groups was subtle, which was also detected in other pathogens, such as Escherichia coli , 35 Legionella pneumophila , 36 Pseudomonas aeruginosa , 37 and Pseudomonas putida . 38 Moreover, this distribution indicated V. vulnificus antibiotic-resistant armory was not only confined to clinical isolates, but to environmental ones as well.…”