Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States

被引：57

作者：

Chen, Yi ^{[1
]}

Luo, Yan ^{[1
]}

Curry, Phillip ^{[1
]}

Timme, Ruth ^{[1
]}

Melka, David ^{[1
]}

Doyle, Matthew ^{[1
]}

Parish, Mickey ^{[1
]}

Hammack, Thomas S. ^{[1
]}

Allard, Marc W. ^{[1
]}

Brown, Eric W. ^{[1
]}

Strain, Errol A. ^{[1
]}

机构：

[1] US FDA, Ctr Food Safety & Appl Nutr, College Pk, MD 20740 USA

来源：

PLOS ONE | 2017年 / 12卷 / 02期

关键词：

SINGLE-NUCLEOTIDE POLYMORPHISMS; MOBILE GENETIC ELEMENTS; PROCESSING PLANTS; SEQUENCE DATA; STRAINS; PHYLOGENIES; VIRULENCE; CLONES; PHAST; FOOD;

D O I：

10.1371/journal.pone.0171389

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

A listeriosis outbreak in the United States implicated contaminated ice cream produced by one company, which operated 3 facilities. We performed single nucleotide polymorphism (SNP)-based whole genome sequencing (WGS) analysis on Listeria monocytogenes from food, environmental and clinical sources, identifying two clusters and a single branch, belonging to PCR serogroup IIb and genetic lineage I. WGS Cluster I, representing one outbreak strain, contained 82 food and environmental isolates from Facility I and 4 clinical isolates. These isolates differed by up to 29 SNPs, exhibited 9 pulsed-field gel electrophoresis (PFGE) profiles and multilocus sequence typing (MLST) sequence type (ST) 5 of clonal complex 5 (CC5). WGS Cluster II contained 51 food and environmental isolates from Facility II, 4 food isolates from Facility I and 5 clinical isolates. Among them the isolates from Facility II and clinical isolates formed a clade and represented another outbreak strain. Isolates in this clade differed by up to 29 SNPs, exhibited 3 PFGE profiles and ST5. The only isolate collected from Facility III belonged to singleton ST489, which was in a single branch separate from Clusters I and II, and was not associated with the outbreak. WGS analyses clustered together outbreak-associated isolates exhibiting multiple PFGE profiles, while differentiating them from epidemiologically unrelated isolates that exhibited outbreak PFGE profiles. The complete genome of a Cluster I isolate allowed the identification and analyses of putative prophages, revealing that Cluster I isolates differed by the gain or loss of three putative prophages, causing the banding pattern differences among all 3 AscI-PFGE profiles observed in Cluster I isolates. WGS data suggested that certain ice cream varieties and/or production lines might have contamination sources unique to them. The SNP-based analysis was able to distinguish CC5 as a group from non-CC5 isolates and differentiate among CC5 isolates from different outbreaks/incidents.

引用

页数：19

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