Comparative Genomics of Listeria Species Recovered from Meat and Food Processing Facilities

T Mafuna; I Matle; K Magwedere; R E Pierneef; O N Reva

doi:10.1128/spectrum.01189-22

Comparative Genomics of Listeria Species Recovered from Meat and Food Processing Facilities

Microbiol Spectr. 2022 Oct 26;10(5):e0118922. doi: 10.1128/spectrum.01189-22. Epub 2022 Sep 6.

Authors

T Mafuna^{1

2}, I Matle³, K Magwedere⁴, R E Pierneef², O N Reva⁵

Affiliations

¹ Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa.
² Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa.
³ Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa.
⁴ Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa.
⁵ Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.

Abstract

Listeria species (spp.) are contaminants that can survive in food, on equipment, and on food processing premises if appropriate hygiene measures are not used. Homologous stress tolerance genes, virulence gene clusters such as the prfA cluster, and clusters of internalin genes that contribute to the pathogenic potential of the strains can be carried by both pathogenic and nonpathogenic Listeria spp. To enhance understanding of the genome evolution of virulence and virulence-associated properties, a comparative genome approach was used to analyze 41 genome sequences belonging to L. innocua and L. welshimeri isolated from food and food processing facilities. Genetic determinants responsible for disinfectant and stress tolerance were identified, including the efflux cassette bcrABC and Tn6188_qac_1 disinfectant resistance determinant, and stress survival islets. These disinfectant-resistant genes were more frequently found in L. innocua (12%) than in L. welshimeri (2%). Several isolates representing the presumed nonpathogenic L. innocua still carried virulence-associated genes, including LGI2, LGI3, LIPI-3, and LIPI-4 which were absent in all L. welshimeri isolates. The mobile genetic elements identified were plasmids (pLGUG1 and J1776) and prophages (PHAGE_Lister_vB_LmoS_188, PHAGE_Lister_LP_030_3, PHAGE_Lister_A118, PHAGE_Lister_B054, and PHAGE_Lister_vB_LmoS_293). The results suggest that the presumed nonpathogenic isolates especially L. innocua can carry genes relevant to the strain's virulence and stress tolerance in the food and food processing facilities. IMPORTANCE This study provides genomic insights into the recently expanded genus in order to gain valuable information about the evolution of the virulence and stress tolerance properties of the genus Listeria and the distribution of these genetic elements pertinent to the pathogenic potential across Listeria spp. and clonal lineages in South Africa (SA).

Keywords: benzalkonium chloride resistance (BC); plasmid analysis; plasmids; prophages; sequence type; stress tolerance; virulence profiles.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Disinfectants*
Food Handling
Food Microbiology
Genomics
Listeria* / genetics
Meat

Substances

Disinfectants