Comparative genomic analysis of foodborne Listeria monocytogenes and Listeria innocua

Abstract

ObjectiveTo utilize whole genome sequencing to comprehensively compare and analyze the genomic characteristics of Listeria monocytogenes （L. monocytogenes） and Listeria innocua （L. innocua） isolated from commercially available foods in Gansu Province.MethodsDuring 2021 and 2022， 25 strains of L. monocytogenes and 7 strains of L. innocua were isolated from commercially available food sources within Gansu Province and subjected to whole genome sequencing for phylogenetic lineage， clonal complex （CC）， sequence type （ST）， virulence gene， resistance gene， and pan-genome analyses.ResultsThe 32 Listeria strains examined could be classified into three distinct groups： L. monocytogenes lineages Ⅰ and Ⅱ and L. innocua. Considering their CC types， further subdivision into 10 subgroups was observed for L. monocytogenes， whereas L. innocua had 5 subgroups. Core genome multi-locus sequence typing effectively differentiated strains with different CC types within each lineage， with lineage Ⅰ showing a closer evolutionary relationship with L. innocua. All 25 L. monocytogenes strains carried Listeria pathogenicity island 1 （LIPI-1） and internalin genes； none carried LIPI-3， and 2 strains of ST87 carried LIPI-4. Conversely， none of the seven strains of L. innocua carried LIPI-1 or internalin genes； however， they all carried LIPI-4， and 5 carried LIPI-3. Among the L. monocytogenes strains， 16 carried surface sensory island 1 （SSI-1）， and 3 carried SSI-2； all 7 L. innocua strains did not carry SSI-1， but 6 of them carried SSI-2. The pan-genome size of L. monocytogenes increased linearly with the number of sequenced genomes. Upon reaching 15 strains， the number of core genes stabilized at 2 272， accounting for 46.2% of the pan-genome genes. Furthermore， 1 487 common core genes were shared between the 25 L. monocytogenes strains and 7 L. innocua strains， with the count tending to stabilize when the strain count reached 10.ConclusionMulti-locus sequence typing of the core genome can effectively distinguish among Listeria strains originating from different lineages and CCs. The similarity in the biochemical characteristics of L. monocytogenes and L. innocua is due to their close genetic relationship， while the differences in their pathogenicity can be attributed to the presence of certain virulence genes in L. monocytogenes.

Keywords

• listeria monocytogenes
• listeria innocua
• whole genome sequencing
• virulence genes
• pan-genome