Genome Analysis of ESBL-Producing Escherichia coli Isolated from Pigs

Luria Leslie Founou; Raspail Carrel Founou; Mushal Allam; Arshad Ismail; Sabiha Yusuf Essack

doi:10.3390/pathogens11070776

Genome Analysis of ESBL-Producing Escherichia coli Isolated from Pigs

Pathogens. 2022 Jul 7;11(7):776. doi: 10.3390/pathogens11070776.

Authors

Luria Leslie Founou^{1

2

3}, Raspail Carrel Founou^{1

4

5}, Mushal Allam^{6

7}, Arshad Ismail⁶, Sabiha Yusuf Essack¹

Affiliations

¹ Antimicrobial Research Unit, University of KwaZulu-Natal, Durban 4000, South Africa.
² Reproductive, Maternal, Newborn and Child Health (ReMarch) Research Unit, Research Institute of the Centre of Expertise and Biological Diagnostic of Cameroon (CEDBCAM-RI), Yaoundé P.O. Box 8242, Cameroon.
³ Bioinformatics and Applied Machine Learning Research Unit, EDEN Foundation, Yaoundé P.O. Box 8242, Cameroon.
⁴ Department of Microbiology, Haematology and Immunology, Faculty of Medicine and Pharmaceutical Sciences, University of Dschang, Dschang P.O. Box 96, Cameroon.
⁵ Antimicrobial Resistance and Infectious Diseases (ARID) Research Unit, Research Institute of the Centre of Expertise and Biological Diagnostic of Cameroon (CEDBCAM-RI), Yaoundé P.O. Box 8242, Cameroon.
⁶ Sequencing Core Facility, National Health Laboratory Service, Johannesburg 2131, South Africa.
⁷ Department of Genetics and Genomics, College of Medicine and Genomics, Al Ain 15551, United Arab Emirates.

Abstract

The resistome, virulome and mobilome of extended spectrum ß-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec) isolated from pigs in Cameroon and South Africa were assessed using whole genome sequencing (WGS). Eleven clonally related phenotypic ESBL-Ec isolates were subjected to WGS. The prediction of antibiotic resistance genes, virulence factors (VFs) and plasmids was performed using ResFinder, VirulenceFinder and PlasmidFinder, respectively. Diverse sequence types (STs) were detected with ST2144 and ST88 being predominant and bla_CTX-M-15 (55%) being the principal ESBL gene. All except two isolates harboured various aminoglycoside resistance genes, including aph(3″)-Ib (6/11, 55%) and aph(6)-1d (6/11, 55%), while the qnrS1 gene was identified in four of the isolates. The ESBL-Ec isolates showed a 93.6% score of being human pathogens. The fim, ehaB, ibeB/C were the leading virulence factors detected. All isolates harboured at least three extraintestinal pathogenic E. coli (ExPEC) VFs, with one isolate harbouring up to 18 ExPEC VFs. Five isolates (45.45%) harboured the plasmid incompatibility group IncF (FII, FIB, FIC, FIA). The study revealed that there is an urgent need to implement effective strategies to contain the dissemination of resistant and virulent ESBL-Ec through the food chain in Cameroon and South Africa.

Keywords: Antibiotic resistance; ESBL-E. coli; food safety; genomics.

Abstract

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