Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes
Authors: Chen Poyin , den Bakker Henk C. , Korlach Jonas , Kong Nguyet , Storey Dylan B. , Paxinos Ellen E. , Ashby Meredith , Clark Tyson , Luong Khai , Wiedmann Martin , Weimer Bart C. 
Published: November 2016

ABSTRACT

Listeria monocytogenes
is a bacterial pathogen that is found in a wide variety of anthropogenic and natural environments. Genome sequencing technologies are rapidly becoming a powerful tool in facilitating our understanding of how genotype, classification phenotypes, and virulence phenotypes interact to predict the health risks of individual bacterial isolates. Currently, 57 closed
L. monocytogenes
genomes are publicly available, representing three of the four phylogenetic lineages, and they suggest that
L. monocytogenes
has high genomic synteny. This study contributes an additional 15 closed
L. monocytogenes
genomes that were used to determine the associations between the genome and methylome with host invasion magnitude. In contrast to previous findings, large chromosomal inversions and rearrangements were detected in five isolates at the chromosome terminus and within rRNA genes, including a previously undescribed inversion within rRNA-encoding regions. Each isolate's epigenome contained highly diverse methyltransferase recognition sites, even within the same serotype and methylation pattern. Eleven strains contained a single chromosomally encoded methyltransferase, one strain contained two methylation systems (one system on a plasmid), and three strains exhibited no methylation, despite the occurrence of methyltransferase genes. In three isolates a new, unknown DNA modification was observed in addition to diverse methylation patterns, accompanied by a novel methylation system. Neither chromosome rearrangement nor strain-specific patterns of epigenome modification observed within virulence genes were correlated with serotype designation, clonal complex, or
in vitro
infectivity. These data suggest that genome diversity is larger than previously considered in
L. monocytogenes
and that as more genomes are sequenced, additional structure and methylation novelty will be observed in this organism.

IMPORTANCE
Listeria monocytogenes
is the causative agent of listeriosis, a disease which manifests as gastroenteritis, meningoencephalitis, and abortion. Among
Salmonella
,
Escherichia coli
,
Campylobacter
, and
Listeria
—causing the most prevalent foodborne illnesses—infection by
L. monocytogenes
carries the highest mortality rate. The ability of
L. monocytogenes
to regulate its response to various harsh environments enables its persistence and transmission. Small-scale comparisons of
L. monocytogenes
focusing solely on genome contents reveal a highly syntenic genome yet fail to address the observed diversity in phenotypic regulation. This study provides a large-scale comparison of 302
L. monocytogenes
isolates, revealing the importance of the epigenome and restriction-modification systems as major determinants of
L. monocytogenes
phylogenetic grouping and subsequent phenotypic expression. Further examination of virulence genes of select outbreak strains reveals an unprecedented diversity in methylation statuses despite high degrees of genome conservation.