dc.contributor.author |
Strasheim, Wilhelmina
|
|
dc.contributor.author |
Lowe, Michelle
|
|
dc.contributor.author |
Smith, Anthony Marius
|
|
dc.contributor.author |
Etter, Eric Marcel Charles
|
|
dc.contributor.author |
Perovic, Olga
|
|
dc.date.accessioned |
2024-09-02T08:17:08Z |
|
dc.date.available |
2024-09-02T08:17:08Z |
|
dc.date.issued |
2024-06 |
|
dc.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. |
en_US |
dc.description.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. |
en_US |
dc.description.department |
Medical Microbiology |
en_US |
dc.description.sdg |
SDG-02:Zero Hunger |
en_US |
dc.description.sdg |
SDG-03:Good heatlh and well-being |
en_US |
dc.description.sponsorship |
The South African Medical Research Council via a sub-grant received from the Bill and Melinda Gates Foundation, the University of the Witwatersrand and the University of Pretoria. |
en_US |
dc.description.uri |
https://www.mdpi.com/journal/antibiotics |
en_US |
dc.identifier.citation |
Strasheim, 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. |
en_US |
dc.identifier.issn |
2079-6382 (online) |
|
dc.identifier.other |
10.3390/antibiotics13060543 |
|
dc.identifier.uri |
http://hdl.handle.net/2263/97967 |
|
dc.language.iso |
en |
en_US |
dc.publisher |
MDPI |
en_US |
dc.rights |
© 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/). |
en_US |
dc.subject |
Escherichia coli |
en_US |
dc.subject |
Pigs |
en_US |
dc.subject |
Close human contacts |
en_US |
dc.subject |
One Health |
en_US |
dc.subject |
Antibiotic resistance |
en_US |
dc.subject |
Virulence factors |
en_US |
dc.subject |
Sequence type complex 10 |
en_US |
dc.subject |
South Africa |
en_US |
dc.subject |
Whole genome sequencing (WGS) |
en_US |
dc.subject |
Multilocus sequence typing (MLST) |
en_US |
dc.subject |
Core-genome MLST |
en_US |
dc.subject |
Hierarchical clustering |
en_US |
dc.subject |
SDG-03: Good health and well-being |
en_US |
dc.subject |
SDG-02: Zero hunger |
en_US |
dc.title |
Whole-genome sequencing of human and porcine Escherichia coli isolates on a commercial pig farm in South Africa |
en_US |
dc.type |
Article |
en_US |