Whole Genome Sequence Analysis of <i>Listeria monocytogenes</i> Isolates Obtained from the Beef Production Chain in Gauteng Province, South Africa

James Gana; Nomakorinte Gcebe; Rian Edward Pierneef; Yi Chen; Rebone Moerane; Abiodun Adewale Adesiyun

doi:10.3390/microorganisms12051003

Microorganisms (May 2024)

Whole Genome Sequence Analysis of <i>Listeria monocytogenes</i> Isolates Obtained from the Beef Production Chain in Gauteng Province, South Africa

James Gana,
Nomakorinte Gcebe,
Rian Edward Pierneef,
Yi Chen,
Rebone Moerane,
Abiodun Adewale Adesiyun

Affiliations

James Gana: Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, Pretoria 0110, South Africa
Nomakorinte Gcebe: Bacteriology Department, Onderstepoort Veterinary Research, Agricultural Research Council, Pretoria 0110, South Africa
Rian Edward Pierneef: Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0001, South Africa
Yi Chen: Center for Food Safety and Applied Nutrition, US Food and Drug Administration, 5001 Campus Dr. Room 4E-007/Mailstop HFS-710, College Park, MD 20740, USA
Rebone Moerane: Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, Pretoria 0110, South Africa
Abiodun Adewale Adesiyun: Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, Pretoria 0110, South Africa

DOI: https://doi.org/10.3390/microorganisms12051003
Journal volume & issue: Vol. 12, no. 5
p. 1003

Abstract

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The study used whole-genome sequencing (WGS) and bioinformatics analysis for the genomic characterization of 60 isolates of Listeria monocytogenes obtained from the beef production chain (cattle farms, abattoirs, and retail outlets) in Gauteng province, South Africa. The sequence types (STs), clonal complexes (CCs), and the lineages of the isolates were determined using in silico multilocus sequence typing (MLST). We used BLAST-based analyses to identify virulence and antimicrobial genes, plasmids, proviruses/prophages, and the CRISPR-Cas system. The study investigated any association of the detected genes to the origin in the beef production chain of the L. monocytogenes isolates. Overall, in 60 isolates of Listeria monocytogenes, there were seven STs, six CCs, forty-four putative virulence factors, two resistance genes, one plasmid with AMR genes, and three with conjugative genes, one CRISPR gene, and all 60 isolates were positive for proviruses/prophages. Among the seven STs detected, ST204 (46.7%) and ST2 (21.7%) were the most prominent, with ST frequency varying significantly (p Listeria Pathogenicity Islands, LIPIs) were present in all the isolates. The difference in the detection frequency varied significantly (p fosX and vga(G)) detected were present in all 60 (100%) isolates of L. monocytogenes. The only plasmid, NF033156, was present in three (5%) isolates. A CRISPR-Cas system was detected in six (10%), and all the isolates carried proviruses/prophages. The source and sample type significantly affected the frequencies of STs and virulence factors in the isolates of L. monocytogenes. The presence of fosX and vga(G) genes in all L. monocytogenes isolates obtained from the three industries of the beef production chain can potentially cause therapeutic implications. Our study, which characterized L. monocytogenes recovered from the three levels in the beef production chain, is the first time genomics was performed on this type of data set in the country, and this provides insights into the health implications of Listeria.

Published in Microorganisms

ISSN: 2076-2607 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Science: Biology (General)
Website: https://www.mdpi.com/journal/microorganisms

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