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 investiga...

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Autores principales:	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
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	Listeria monocytogenes GWAS outbreak WGS ST7 Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/fb7c28e44683464b868a9466947071c5
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spelling	oai:doaj.org-article:fb7c28e44683464b868a9466947071c52021-11-04T09:30:57ZPhylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak1664-302X10.3389/fmicb.2021.750065https://doaj.org/article/fb7c28e44683464b868a9466947071c52021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmicb.2021.750065/fullhttps://doaj.org/toc/1664-302XFrom 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.Alexandra ChiaveriniFabrizia GuidiMarina TorresiVicdalia Aniela AcciariGabriella CentorotolaAlessandra CornacchiaPatrizia CentorameCristina MarfogliaGiuliana BlasiMarco Di DomenicoGiacomo MiglioratiSophie RousselFrancesco PomilioYann SevellecFrontiers Media S.A.articleListeria monocytogenesGWASoutbreakWGSST7MicrobiologyQR1-502ENFrontiers in Microbiology, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Listeria monocytogenes GWAS outbreak WGS ST7 Microbiology QR1-502
spellingShingle	Listeria monocytogenes GWAS outbreak WGS ST7 Microbiology QR1-502 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 Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak
description	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.
format	article
author	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_facet	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_sort	Alexandra Chiaverini
title	Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak
title_short	Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak
title_full	Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak
title_fullStr	Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak
title_full_unstemmed	Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak
title_sort	phylogenetic analysis and genome-wide association study applied to an italian listeria monocytogenes outbreak
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/fb7c28e44683464b868a9466947071c5
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Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak

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