Genomic Diversity of Common Sequence Types of Listeria monocytogenes Isolated from Ready-to-Eat Products of Animal Origin in South Africa

Abstract

Listeria monocytogenes is a highly fatal foodborne causative agent that has been implicated in numerous outbreaks and related deaths of listeriosis in the world. In this study, six L. monocytogenes isolated from ready-to-eat (RTE) meat products were analysed using Whole Genome Sequencing (WGS) to identify virulence and resistance genes, prophage sequences, PCR-serogroups, and sequence types (STs). The WGS identified four different STs (ST1, ST121, ST204, and ST876) that belonged to serogroup 4b (lineage I) and 1/2a (lineage II). Core genome, and average nucleotide identity (ANI) phylogenetic analyses showed that the majority of strains from serogroup 4b (lineage I) clustered together. However, two isolates that belong to serogroup 1/2a (lineage II) grouped far from each other and the other strains. Examination of reference-guided scaffolds for the presence of prophages using the PHAge Search Tool Enhanced Release (PHASTER) software identified 24 diverse prophages, which were either intact or incomplete/questionable. The National Center for Biotechnology Information- Nucleotide Basic Local Alignment Search Tool (NCBI-BLASTn) revealed that Listeria monocytogenes strains in this study shared some known major virulence genes that are encoded in Listeria pathogenicity islands 1 and 3. In general, the resistance profiles for all the isolates were similar and encoded for multidrug, heavy metal, antibiotic, and sanitizer resistance genes. All the isolates in this study possessed genes that code for resistance to common food processing antiseptics such as Benzalkonium chloride.

Molecular Typing of Listeria monocytogenes IVb Serogroup Isolated from Food and Food Production Environments in Poland

“…In the present study, several intact prophages were detected. Similar results were previously obtained by Matle et al [ 54 ], who found almost the same phages among L. monocytogenes isolated from food in South Africa. Such prophage sequences were also reported in strains associated with survival evolution and persistence of L. monocytogenes in food-processing facilities [ 55 , 56 , 57 ].…”

“…However, the genes responsible for resistance to fosfomycin, quinolones, sulphonamides, and lincosamides were identified. These molecular markers were often detected also in L. monocytogenes by other authors [ 26 , 34 , 46 , 54 ]. It has been previously described that L. monocytogenes and other Listeria species are characterized by a low resistance to antimicrobials [ 36 , 41 ].…”

“…It has been suggested that prophage sequences present in the L. monocytogenes genome were probably one of the main causes of molecular diversity of the isolates classified to the same STs [ 9 , 13 , 58 , 59 ]. Furthermore, the presence of some prophages has been connected with the increased virulence and pathogenicity of L. monocytogenes [ 54 ]. Therefore, identification of prophage sequences in several currently tested strains may suggest the possibility of these isolates acquiring genetic material that would have an influence on a higher infection potential of such L. monocytogenes for humans.…”

Whole-Genome Sequencing-Based Characterization of Listeria monocytogenes from Fish and Fish Production Environments in Poland

“…The LIPI-3 pathogenic island, characteristic for L. monocytogenes hypervirulent clones, was identified in only one strain belonging to the IVb serogroup. It was previously shown that this gene cluster was strongly associated with IVb strains, which was also confirmed in the current study, although only one such isolate was identified [ 32 ]. Furthermore, it has also been described that hypervirulent L. monocytogenes strains were connected with the presence of LIPI-4, which was not found in any of the examined isolates [ 14 , 31 ].…”

“…Several sequences encoding the presence of prophages were detected among 28 L. monocytogenes isolates tested, including intact, questionable, or incomplete molecular markers ( Table S4 ). These prophages were originated from different Listeria phages such as LP101, A006, and LmoS188, and were commonly found in Listeria strains by other authors [ 32 , 50 ]. It has been previously described that the presence of prophage genes in L. monocytogenes had an influence on bacterial virulence and their persistence in food processing environments as well as intracellular survival in the human host [ 17 , 18 ].…”