Abstract:
Escherichia coli is an indicator micro-organism in One Health antibiotic resistance surveillance programs. The purpose of the study was to describe and compare E. coli isolates obtained from
pigs and human contacts from a commercial farm in South Africa using conventional methods and
whole-genome sequencing (WGS). Porcine E. coli isolates were proportionally more resistant phenotypically and harbored a richer diversity of antibiotic resistance genes as compared to human E. coli
isolates. Different pathovars, namely ExPEC (12.43%, 21/169), ETEC (4.14%, 7/169), EPEC (2.96%,
5/169), EAEC (2.96%, 5/169) and STEC (1.18%, 2/169), were detected at low frequencies. Sequence
type complex (STc) 10 was the most prevalent (85.51%, 59/169) among human and porcine isolates.
Six STcs (STc10, STc86, STc168, STc206, STc278 and STc469) were shared at the human–livestock interface according to multilocus sequence typing (MLST). Core-genome MLST and hierarchical clustering
(HC) showed that human and porcine isolates were overall genetically diverse, but some clustering
at HC2–HC200 was observed. In conclusion, even though the isolates shared a spatiotemporal
relationship, there were still differences in the virulence potential, antibiotic resistance profiles and
cgMLST and HC according to the source of isolation.
Description:
DATA AVAILABILITY STATEMENT: Sequencing data are available at the NCBI’s GenBank under Bioproject number: PRJNA994298 (https://www.ncbi.nlm.nih.gov/sra/PRJNA994298). Additional data generated during this study were placed in an online repository (https://doi.org/10.6084/m9.figshare.23677266.v2). The accession numbers are listed in the Supplementary Material, together with the isolate’s unique identifier.