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

Luria Leslie Founou^*, Raspail Carrel Founou, Mushal Allam, Arshad Ismail, Sabiha Yusuf Essack

^*Corresponding author for this work

School of Medicine

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	776
Number of pages	18
Journal	Pathogens
Volume	11
Issue number	7
DOIs	https://doi.org/10.3390/pathogens11070776
Publication status	Published - 7 Jul 2022

Keywords

Antibiotic resistance
ESBL-E. coli
Food safety
Genomics

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This output contributes to the following UN Sustainable Development Goals (SDGs)

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Cite this

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title = "Genome analysis of ESBL-producing Escherichia coli isolated from pigs",

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 blaCTX-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",

author = "Founou, {Luria Leslie} and Founou, {Raspail Carrel} and Mushal Allam and Arshad Ismail and Essack, {Sabiha Yusuf}",

note = "Funding: L.L.F. Founou and R.C. Founou were funded by the Antimicrobial Research Unit (ARU) and College of Health Sciences (CHS) of the University of KwaZulu-Natal, South Africa. The National Research Foundation funded this study through the NRF Incentive Funding for Rated Researchers (Grant No. 85595), and the DST/NRF South African Research Chair in Antibiotic Resistance and One Health (Grant No. 98342) awarded to S.Y. Essack. The South African Medical Research Council also funded the study through the Self-Initiated Researcher (SIR) Grant awarded to S.Y Essack.",

year = "2022",

month = jul,

day = "7",

doi = "10.3390/pathogens11070776",

language = "English",

volume = "11",

journal = "Pathogens",

issn = "2076-0817",

publisher = "MDPI AG",

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TY - JOUR

T1 - Genome analysis of ESBL-producing Escherichia coli isolated from pigs

AU - Founou, Luria Leslie

AU - Founou, Raspail Carrel

AU - Allam, Mushal

AU - Ismail, Arshad

AU - Essack, Sabiha Yusuf

N1 - Funding: L.L.F. Founou and R.C. Founou were funded by the Antimicrobial Research Unit (ARU) and College of Health Sciences (CHS) of the University of KwaZulu-Natal, South Africa. The National Research Foundation funded this study through the NRF Incentive Funding for Rated Researchers (Grant No. 85595), and the DST/NRF South African Research Chair in Antibiotic Resistance and One Health (Grant No. 98342) awarded to S.Y. Essack. The South African Medical Research Council also funded the study through the Self-Initiated Researcher (SIR) Grant awarded to S.Y Essack.

PY - 2022/7/7

Y1 - 2022/7/7

N2 - 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 blaCTX-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.

AB - 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 blaCTX-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.

KW - Antibiotic resistance

KW - ESBL-E. coli

KW - Food safety

KW - Genomics

U2 - 10.3390/pathogens11070776

DO - 10.3390/pathogens11070776

M3 - Article

AN - SCOPUS:85135609660

SN - 2076-0817

VL - 11

JO - Pathogens

JF - Pathogens

IS - 7

M1 - 776

ER -