Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak

From May 2015 to March 2016, a severe outbreak due to Listeria monocytogenes ST7 strain occurred in Central Italy and caused 24 confirmed clinical cases. The epidemic strain was deeply investigated using whole-genome sequencing (WGS) analysis. In the interested area, the foodborne outbreak investigation identified a meat food-producing plant contaminated by the outbreak strain, carried by pork-ready-to-eat products. In the same region, in March 2018, the epidemic strain reemerged causing one listeriosis case in a 10-month-old child. The aim of this study was to investigate the phylogeny of the epidemic and reemergent strains over time and to compare them with a closer ST7 clone, detected during the outbreak and with different pulsed-field gel electrophoresis (PFGE) profiles, in order to identify genomic features linked to the persistence and the reemergence of the outbreak. An approach combining phylogenetic analysis and genome-wide association study (GWAS) revealed that the epidemic and reemergent clones were genetically closer to the ST7 clone with different PFGE profiles and strictly associated with the pork production chain. The repeated detection of both clones was probably correlated with (i) the presence of truly persistent clones and the repeated introduction of new ones and (ii) the contribution of prophage genes in promoting the persistence of the epidemic clones. Despite that no significant genomic differences were detected between the outbreak and the reemergent strain, the two related clones detected during the outbreak can be differentiated by transcriptional factor and phage genes associated with the phage LP-114.

Automated summary

The study investigated a severe outbreak of Listeria monocytogenes ST7 strain in Central Italy, linked to a meat food-producing plant contaminated by the outbreak strain, which reemerged in the same region causing another listeriosis case. The epidemic and reemergent strains were genetically closer to a ST7 clone with different PFGE profiles, and were associated with the pork production chain. The persistence and reemergence of the outbreak were likely due to both the presence of truly persistent clones and the repeated introduction of new ones, along with the contribution of prophage genes promoting their survival. Despite no significant genomic differences between the outbreak and reemergent strains, transcriptional factor and phage genes associated with the phage LP-114 helped differentiate the related clones detected during the outbreak.