Strasheim, WilhelminaLowe, MichelleSmith, Anthony MariusEtter, Eric Marcel CharlesPerovic, Olga2024-09-022024-09-022024-06Strasheim, W.; Lowe, M.; Smith, A.M.; Etter, E.M.C.; Perovic, O. Whole-Genome Sequencing of Human and Porcine Escherichia coli Isolates on a Commercial Pig Farm in South Africa. Antibiotics 2024, 13, 543. https://doi.org/10.3390/antibiotics13060543.2079-6382 (online)10.3390/antibiotics13060543http://hdl.handle.net/2263/97967DATA 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.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.en© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).Escherichia coliPigsClose human contactsOne HealthAntibiotic resistanceVirulence factorsSequence type complex 10South AfricaWhole genome sequencing (WGS)Multilocus sequence typing (MLST)Core-genome MLSTHierarchical clusteringSDG-03: Good health and well-beingSDG-02: Zero hungerArticle