Whole-genome sequencing of human and porcine Escherichia coli isolates on a commercial pig farm in South Africa

Strasheim Wilhelmina, Lowe Michelle, Smith Anthony M., Etter Eric, Perovic Olga. 2024. Whole-genome sequencing of human and porcine Escherichia coli isolates on a commercial pig farm in South Africa. Antibiotics, 13 (6), n.spéc. Antimicrobial Resistance in Animals and Animal Products and Its Environmental Transmission Aspects, 22 p.

Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/sra/PRJNA994298 / Url - jeu de données - Entrepôt autre : https://doi.org/10.6084/m9.figshare.23677266.v2

Résumé : 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.

Mots-clés Agrovoc : Résistance aux antibiotiques, Escherichia coli, transmission des maladies, phylogénie, genre humain, antibiotique, porcin, génie génétique, mycose, virulence, approche Une seule santé

Mots-clés géographiques Agrovoc : Afrique du Sud

Mots-clés libres : Escherichia coli, Whole-genome sequencing, Virulence factors, Hierarchical clustering, Core-genome MLST, Sequence type complex 10, South Africa, Antibiotic resistance, One Health, Close human contacts, Pigs

Classification Agris : L70 - Sciences et hygiène vétérinaires - Considérations générales
S50 - Santé humaine

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Agences de financement hors UE : South African Medical Research Council, Bill and Melinda Gates Foundation, Department of Health and Social Care

Projets sur financement : (GBR) SEQAFRICA

Auteurs et affiliations

• Strasheim Wilhelmina, University of Pretoria (ZAF) - auteur correspondant
• Lowe Michelle, National Institute for Communicable Diseases (ZAF)
• Smith Anthony M., University of Pretoria (ZAF)
• Etter Eric, CIRAD-BIOS-UMR ASTRE (GLP) ORCID: 0000-0002-6438-7828
• Perovic Olga, National Institute for Communicable Diseases (ZAF) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/612203/)

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