Comparative Genomics of <i>Listeria</i> Species Recovered from Meat and Food Processing Facilities

Abstract

<i>Listeria</i> 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 <i>prfA</i> cluster, and clusters of internalin genes that contribute to the pathogenic potential of the strains can be carried by both pathogenic and nonpathogenic <i>Listeria</i> 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 <i>L. innocua</i> and <i>L. welshimeri</i> isolated from food and food processing facilities. Genetic determinants responsible for disinfectant and stress tolerance were identified, including the efflux cassette <i>bcrABC</i> and <i>Tn6188_qac_1</i> disinfectant resistance determinant, and stress survival islets. These disinfectant-resistant genes were more frequently found in <i>L. innocua</i> (12%) than in <i>L. welshimeri</i> (2%). Several isolates representing the presumed nonpathogenic <i>L. innocua</i> still carried virulence-associated genes, including <i>LGI</i>2, <i>LGI</i>3, <i>LIPI-</i>3, and <i>LIPI-</i>4 which were absent in all <i>L. welshimeri</i> isolates. The mobile genetic elements identified were plasmids (<i>pLGUG1</i> and <i>J1776</i>) 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 <i>L. innocua</i> can carry genes relevant to the strain's virulence and stress tolerance in the food and food processing facilities. <b>IMPORTANCE</b> 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 <i>Listeria</i> and the distribution of these genetic elements pertinent to the pathogenic potential across <i>Listeria</i> spp. and clonal lineages in South Africa (SA).