Whole Genome-Based Characterization of Listeria monocytogenes Isolates Recovered From the Food Chain in South Africa

Abstract

<i>Listeria monocytogenes</i> is an important foodborne pathogen which has the ability to adapt and survive in food and food processing facilities where it can persist for years. In this study, a total of 143 <i>L. monocytogenes</i> isolates in South Africa (SA) were characterized for their strain's genetic relatedness, virulence profiles, stress tolerance and resistance genes associated with <i>L. monocytogenes</i>. The Core Genome Multilocus Sequence Typing (cgMLST) analysis revealed that the most frequent serogroups were IVb and IIa; Sequence Types (ST) were ST204, ST2, and ST1; and Clonal Complexes (CC) were CC204, CC1, and CC2. Examination of genes involved in adaptation and survival of <i>L. monocytogenes</i> in SA showed that ST1, ST2, ST121, ST204, and ST321 are well adapted in food processing environments due to the significant over-representation of Benzalkonium chloride (BC) resistance genes (<i>bcrABC</i> cassette, <i>ermC, mdrL</i> and <i>Ide</i>), stress tolerance genes (SSI-1 and SSI-2), Prophage (φ) profiles (LP_101, vB LmoS 188, vB_LmoS_293, and B054 phage), plasmids profiles (N1-011A, J1776, and pLM5578) and biofilm formation associated genes. Furthermore, the <i>L. monocytogenes</i> strains that showed hyper-virulent potential were ST1, ST2 and ST204, and hypo-virulent were ST121 and ST321 because of the presence and absence of major virulence factors such as LIPI-1, LIPI-3, LIPI-4 and the internalin gene family members including <i>inlABCEFJ</i>. The information provided in this study revealed that hyper-virulent strains ST1, ST2, and ST204 could present a major public health risk due to their association with meat products and food processing environments in SA.