Whole-Genome Sequencing of Human and Porcine <i>Escherichia coli</i> Isolates on a Commercial Pig Farm in South Africa

• Main Authors: Wilhelmina Strasheim (Author), Michelle Lowe (Author), Anthony M. Smith (Author), Eric M. C. Etter (Author), Olga Perovic (Author)
• Format: Book
• Published: MDPI AG, 2024-06-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.
• Notes: 10.3390/antibiotics13060543; 2079-6382
• Keywords: <i>Escherichia coli</i>; pigs; close human contacts; One Health; antibiotic resistance; whole-genome sequencing; Therapeutics. Pharmacology; RM1-950
• Source: Antibiotics, Vol 13, Iss 6, p 543 (2024)

<i>Escherichia coli</i> is an indicator micro-organism in One Health antibiotic resistance surveillance programs. The purpose of the study was to describe and compare <i>E. coli</i> isolates obtained from pigs and human contacts from a commercial farm in South Africa using conventional methods and whole-genome sequencing (WGS). Porcine <i>E. coli</i> isolates were proportionally more resistant phenotypically and harbored a richer diversity of antibiotic resistance genes as compared to human <i>E. coli</i> 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.