Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Outbreak.
Alexandra Chiaverini, Fabrizia Guidi, Marina Torresi, Vicdalia Aniela Acciari, Gabriella Centorotola, Alessandra Cornacchia, Patrizia Centorame, Cristina Marfoglia, Giuliana Blasi, Marco Di Domenico, Giacomo Migliorati, Sophie Roussel, Francesco Pomilio, Yann Sevellec
Author Information
Alexandra Chiaverini: National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy.
Fabrizia Guidi: Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", Perugia, Italy.
Marina Torresi: National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy.
Vicdalia Aniela Acciari: National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy.
Gabriella Centorotola: National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy.
Alessandra Cornacchia: National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy.
Patrizia Centorame: National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy.
Cristina Marfoglia: National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy.
Giuliana Blasi: Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", Perugia, Italy.
Marco Di Domenico: National Reference Centre for Whole Genome Sequencing of Microbial Pathogens Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy.
Giacomo Migliorati: National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy.
Sophie Roussel: Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Université PARIS-EST, Maisons-Alfort, France.
Francesco Pomilio: National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale, Teramo, Italy.
Yann Sevellec: Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Université PARIS-EST, Maisons-Alfort, France.
From May 2015 to March 2016, a severe outbreak due to 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.
