Genome Sequencing of Extended-Spectrum β-Lactamase (ESBL)-Producing Klebsiella pneumoniae Isolated from Pigs and Abattoir Workers in Cameroon

Frontiers in Microbiology
Luria L FounouSabiha Y Essack

Abstract

Background and objectives: Extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae is a serious public health issue globally. In this study, the antibiotic resistance genes, virulence factors, mobile genetic elements, and genetic lineages of circulating ESBL-producing K. pneumoniae strains isolated from pigs and humans in Cameroonian abattoirs were investigated using whole genome sequencing (WGS), in order to ascertain zoonotic transmission (viz. from animals to humans and/or vice-versa) in the food chain. Methods: During March-October 2016, 288 nasal and rectal pooled samples from 432 pigs as well as nasal and hand swabs from 82 humans were collected from Cameroon and South Africa. Seven ESBL-producing K. pneumoniae circulating in Cameroonian pig abattoirs were selected and their genomic DNA sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using the Qiagen CLC Genomics Workbench and SPAdes. The assembled contigs were annotated using RAST and antibiotic resistance genes, virulence factors, plasmids, and bacteriophages were identified with ResFinder, Virulence Finder, PlasmidFinder, and PHAST, respectively. Results: ESBL-producing K. pneumoniae were detected in pigs (34/158; 21.52%)...Continue Reading

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Citations

Mar 8, 2019·Microbial Drug Resistance : MDR : Mechanisms, Epidemiology, and Disease·Golnaz MobasseriKwai Lin Thong
Mar 11, 2020·Microbial Drug Resistance : MDR : Mechanisms, Epidemiology, and Disease·Nadezhda K FursovaNikolay V Volozhantsev
May 1, 2021·Antibiotics·Zoi AthanasakopoulouCharalambos Billinis

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Datasets Mentioned

BETA
CP020841
PRJNA412434
CP006918
CP020847

Methods Mentioned

BETA
electrophoresis
genotyping

Software Mentioned

Mauve genome
ResFinder
CGView Server
Bionumerics
PlasmidFind
RAST SEED viewer
CLC Genomics Workbench
VirulenceFinder
RAST
FastTree

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