Genomic Characterization of Listeria monocytogenes Isolates Associated with Clinical Listeriosis and the Food Production Environment in Ireland

Abstract

Listeria monocytogenes is a major human foodborne pathogen that is prevalent in the natural environment and has a high case fatality rate. Whole genome sequencing (WGS) analysis has emerged as a valuable methodology for the classification of L. monocytogenes isolates and the identification of virulence islands that may influence infectivity. In this study, WGS was used to provide an insight into 25 L. monocytogenes isolates from cases of clinical infection in Ireland between 2013 and 2015. Clinical strains were either lineage I (14 isolates) or lineage II (11 isolates), with 12 clonal complexes (CC) represented, of which CC1 (6) and CC101 (4) were the most common. Single nucleotide polymorphism (SNP) analysis demonstrated that clinical isolates from mother–infant pairs (one isolate from the mother and one from the infant) were highly related (3 SNP differences in each) and also identified close similarities between isolates from otherwise distinct cases (1 SNP difference). Clinical strains were positive for common virulence-associated loci and 13 isolates harbour the LIPI-3 locus. Pulsed-field gel electrophoresis (PFGE) was used to compare strains to a database of 1300 Irish food and food processing environment isolates and determined that 64% of clinical pulsotypes were previously encountered in the food or food processing environment. Five of the matching food and food processing environment isolates were sequenced and results demonstrated a correlation between pulsotype and genotype. Overall, the work provides insights into the nature of L. monocytogenes strains currently causing clinical disease in Ireland and indicates that similar isolates can be found in the food or food processing environment.

Genomic Diversity of Common Sequence Types of Listeria monocytogenes Isolated from Ready-to-Eat Products of Animal Origin in South Africa

“…The LIPI4 is a newly described Listeria pathogenicity island [56] which encodes for the genes that annotated as a cellobiose family PTS system [55], and it was not identified in any of the strains identified in this study. The LIPI4 appears to be strongly associated with ST4 isolates [1]; hence, it was not observed in the current study. Several studies have identified mutations that are important in L. monocytogenes virulence markers [40,[56][57][58].…”

“…LIPI3 is overrepresented among lineage I strains in human isolates and is strongly associated with serotype 4b isolates [55]. The absence of LIPI3 in two samples of lineage II was expected as the sequence types have been reported to lack it LIPI [1]. The LIPI4 is a newly described Listeria pathogenicity island [56] which encodes for the genes that annotated as a cellobiose family PTS system [55], and it was not identified in any of the strains identified in this study.…”

“…The WGS can also be used to identify the presence of pathogenicity islands linked to virulence or particular modes of pathogenesis [47]. In the present study, each of the six L. monocytogenes samples encode LIPI-1, which harbour Prf-A dependent virulence cluster genes that are critical in the infectious cycle of L. monocytogenes [1]. This could explain the reason why all sequenced isolates share about 40% similar genes that are strongly associated with LIPI-1.…”

“…Listeria species are ubiquitous bacteria widely distributed in the environment of which Listeria monocytogenes is the most important zoonotic species of global public health and economic importance in the genus [1]. The general approach to prevent listeriosis in the human population is to restrict the exposure of the human and animal populations to foods contaminated with L. monocytogenes; however, in the case of a listeriosis outbreak, timeous removal of suspected foods during ongoing epidemiological investigations limits human exposure and spread of the disease [2,3].…”

Listeria monocytogenes isolates from ready to eat plant produce are diverse and have virulence potential

“…Overall, the L. monocytogenes population in the UK fresh produce supply chain is diverse, in line with food isolates other countries such as Ireland (Hilliard et al, 2018), France (Moura et al, 2017), and Australia (Kwong et al, 2015). While some isolates have the necessary genomic components to cause disease and are closely related to outbreak strains, others are distantly related and are of less concern.…”