scholarly journals Application of Whole Genome Sequencing to Aid in Deciphering the Persistence Potential of Listeria monocytogenes in Food Production Environments

2021 ◽  
Vol 9 (9) ◽  
pp. 1856
Author(s):  
Natalia Unrath ◽  
Evonne McCabe ◽  
Guerrino Macori ◽  
Séamus Fanning
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Biofilm Formation ◽  
Food Production ◽  
Mortality Rates ◽  
Foodborne Illness ◽  
Whole Genome ◽  
Bioinformatic Tools ◽  
Production Environments

Listeria monocytogenes is the etiological agent of listeriosis, a foodborne illness associated with high hospitalizations and mortality rates. This bacterium can persist in food associated environments for years with isolates being increasingly linked to outbreaks. This review presents a discussion of genomes of Listeria monocytogenes which are commonly regarded as persisters within food production environments, as well as genes which are involved in mechanisms aiding this phenotype. Although criteria for the detection of persistence remain undefined, the advent of whole genome sequencing (WGS) and the development of bioinformatic tools have revolutionized the ability to find closely related strains. These advancements will facilitate the identification of mechanisms responsible for persistence among indistinguishable genomes. In turn, this will lead to improved assessments of the importance of biofilm formation, adaptation to stressful conditions and tolerance to sterilizers in relation to the persistence of this bacterium, all of which have been previously associated with this phenotype. Despite much research being published around the topic of persistence, more insights are required to further elucidate the nature of true persistence and its implications for public health.

scholarly journals Whole-Genome Sequencing-Based Characterization of Listeria monocytogenes from Fish and Fish Production Environments in Poland

2020 ◽  
Vol 21 (24) ◽  
pp. 9419
Author(s):  
Kinga Wieczorek ◽  
Arkadiusz Bomba ◽  
Jacek Osek
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Foodborne Pathogen ◽  
Whole Genome ◽  
Antimicrobial Resistance Profile ◽  
Production Environments ◽  
Long Time ◽  
Sequence Types

Listeria monocytogenes, an important foodborne pathogen, may be present in different kinds of food and in food processing environments where it can persist for a long time. In this study, 28 L. monocytogenes isolates from fish and fish manufactures were characterized by whole genome sequencing (WGS). Core genome multilocus sequence typing (cgMLST) analysis was applied to compare the present isolates with publicly available genomes of L. monocytogenes strains recovered worldwide from food and from humans with listeriosis. All but one (96.4%) of the examined isolates belonged to molecular serogroup IIa, and one isolate (3.6%) was classified to serogroup IVb. The isolates of group IIa were mainly of MLST sequence types ST121 (13 strains) and ST8 (four strains) whereas the isolate of serogroup IVb was classified to ST1. Strains of serogroup IIa were further subtyped into eight different sublineages with the most numerous being SL121 (13; 48.1% strains) which belonged to six cgMLST types. The majority of strains, irrespective of the genotypic subtype, had the same antimicrobial resistance profile. The cluster analysis identified several molecular clones typical for L. monocytogenes isolated from similar sources in other countries; however, novel molecular cgMLST types not present in the Listeria database were also identified.

scholarly journals Whole-Genome Sequencing Allows for Improved Identification of Persistent Listeria monocytogenes in Food-Associated Environments

2015 ◽  
Vol 81 (17) ◽  
pp. 6024-6037 ◽  
Author(s):  
Matthew J. Stasiewicz ◽  
Haley F. Oliver ◽  
Martin Wiedmann ◽  
Henk C. den Bakker
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genetic Determinants ◽  
Single Nucleotide ◽  
Content Type ◽  
Food Borne ◽  
Clonal Spread

ABSTRACTWhile the food-borne pathogenListeria monocytogenescan persist in food associated environments, there are no whole-genome sequence (WGS) based methods to differentiate persistent from sporadic strains. Whole-genome sequencing of 188 isolates from a longitudinal study ofL. monocytogenesin retail delis was used to (i) apply single-nucleotide polymorphism (SNP)-based phylogenetics for subtyping ofL. monocytogenes, (ii) use SNP counts to differentiate persistent from repeatedly reintroduced strains, and (iii) identify genetic determinants ofL. monocytogenespersistence. WGS analysis revealed three prophage regions that explained differences between three pairs of phylogenetically similar populations with pulsed-field gel electrophoresis types that differed by ≤3 bands. WGS-SNP-based phylogenetics found that putatively persistentL. monocytogenesrepresent SNP patterns (i) unique to a single retail deli, supporting persistence within the deli (11 clades), (ii) unique to a single state, supporting clonal spread within a state (7 clades), or (iii) spanning multiple states (5 clades). Isolates that formed one of 11 deli-specific clades differed by a median of 10 SNPs or fewer. Isolates from 12 putative persistence events had significantly fewer SNPs (median, 2 to 22 SNPs) than between isolates of the same subtype from other delis (median up to 77 SNPs), supporting persistence of the strain. In 13 events, nearly indistinguishable isolates (0 to 1 SNP) were found across multiple delis. No individual genes were enriched among persistent isolates compared to sporadic isolates. Our data show that WGS analysis improves food-borne pathogen subtyping and identification of persistent bacterial pathogens in food associated environments.

scholarly journals Characteristics of Listeria Monocytogenes Strains Persisting in a Meat Processing Facility over a 4-Year Period

Pathogens ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 32 ◽  
Author(s):  
Andrea Stoller ◽  
Marc Stevens ◽  
Roger Stephan ◽  
Claudia Guldimann
Keyword(s):  
Listeria Monocytogenes ◽  
Genome Sequencing ◽  
Peracetic Acid ◽  
Benzalkonium Chloride ◽  
Food Production ◽  
Whole Genome ◽  
Meat Processing ◽  
Minimal Inhibitory Concentrations ◽  
Processing Facility ◽  
Young Old

Listeria monocytogenes can persist in food production facilities, resulting in serious threats to consumers due to the high mortality associated with listeriosis, especially in the very young, old and pregnant. We subtyped 124 strains of L. monocytogenes isolated from a meat processing facility in Switzerland by serotyping, multi locus sequence typing (MLST) typing and whole genome sequencing. We then analyzed their ability to form biofilms and their resistance to the disinfectants benzalkonium chloride (BC) and peracetic acid (PAA). The genotyping results of the strains showed that several clonal populations of L. monocytogenes belonging to CC9, CC204 and CC121 had persisted in this meat processing facility for at least four years. All of the strains showed biofilm forming capacity comparable to a known high biofilm forming strain. Known efflux pumps for BC were present in CC204, CC9 (brcABC) and CC121 (qacH) strains, while strains from other CC showed very low minimal inhibitory concentrations (MICs) for BC. For PAA, minimal bactericidal concentrations of 1.2–1.6% for 20 min and minimal inhibitory concentrations between 0.1 and 0.2% were observed. These values were close to or above the recommended concentration for use (0.5–1%), suggesting that PAA might be ineffective at controlling L. monocytogenes in this and potentially other meat processing facilities.

scholarly journals Genome Sequence of Listeria monocytogenes Strain F4244, a 4b Serotype

2017 ◽  
Vol 5 (49) ◽  
Author(s):  
Taylor W. Bailey ◽  
Naila C. do Nascimento ◽  
Arun K. Bhunia
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Illumina Sequencing ◽  
Foodborne Pathogen ◽  
Whole Genome ◽  
Content Type ◽  
Serotype 1 ◽  
Serotype 4B

ABSTRACT Listeria monocytogenes is an opportunistic invasive foodborne pathogen. Here, we performed whole-genome sequencing of L. monocytogenes strain F4244 (serotype 4b) using Illumina sequencing. The sequence showed 94.5% identity with strain F2365, serotype 4b, and 90.6% with EGD-e, serotype 1/2a.

scholarly journals Short communication: Persistent contamination by Listeria monocytogenes of bovine raw milk investigated by whole-genome sequencing

2019 ◽  
Vol 102 (7) ◽  
pp. 6032-6036
Author(s):  
M. Ricchi ◽  
E. Scaltriti ◽  
G. Cammi ◽  
C. Garbarino ◽  
N. Arrigoni ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Short Communication ◽  
Raw Milk ◽  
Whole Genome

Utility of Whole Genome Sequencing To Describe the Persistence and Evolution of Listeria monocytogenes Strains within Crabmeat Processing Environments Linked to Two Outbreaks of Listeriosis

2018 ◽  
Vol 82 (1) ◽  
pp. 30-38 ◽  
Author(s):  
RICHARD ELSON ◽  
ADEDOYIN AWOFISAYO-OKUYELU ◽  
TREVOR GREENER ◽  
CRAIG SWIFT ◽  
ANAÏS PAINSET ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Surveillance Data ◽  
Control Measures ◽  
Whole Genome ◽  
Typing Method ◽  
Outbreak Investigations ◽  
Molecular Typing Method ◽  
Clinical Cases

ABSTRACT This article describes the identification and investigation of two extended outbreaks of listeriosis in which crabmeat was identified as the vehicle of infection. Comparing contemporary and retrospective typing data of Listeria monocytogenes isolates from clinical cases and from food and food processing environments allowed the detection of cases going back several years. This information, combined with the analysis of routinely collected enhanced surveillance data, helped to direct the investigation and identify the vehicle of infection. Retrospective whole genome sequencing (WGS) analysis of isolates provided robust microbiological evidence of links between cases, foods, and the environments in which they were produced and demonstrated that for some cases and foods, identified by fluorescent amplified fragment length polymorphism, the molecular typing method in routine use at the time, were not part of the outbreak. WGS analysis also showed that the strains causing illness had persisted in two food production environments for many years and in one producer had evolved into two strains over a period of around 8 years. This article demonstrates the value of reviewing L. monocytogenes typing data from clinical cases together with that from foods as a means of identifying potential vehicles and sources of infection in outbreaks of listeriosis. It illustrates the importance of reviewing retrospective L. monocytogenes typing alongside enhanced surveillance data to characterize extended outbreaks and inform control measures. Also, this article highlights the advantages of WGS analysis for strain discrimination and clarification of evolutionary relationships that refine outbreak investigations and improve our understanding of L. monocytogenes in the food chain.

scholarly journals Genome Sequence ofListeria monocytogenesStrain HPB2088 (Serotype 1/2a), an Environmental Isolate Collected in Canada in 1994

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Arthur W. Pightling ◽  
Hugh Rand ◽  
Errol Strain ◽  
Franco Pagotto
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Real Time ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Foodborne Pathogen ◽  
Environmental Isolate ◽  
Severe Illness ◽  
Whole Genome ◽  
Serotype 1

Listeria monocytogenesis a foodborne pathogen that causes severe illness. Thus, ongoing efforts at real-time whole-genome sequencing are of utmost importance. However, it is also important that retrospective analyses that place these data into context be performed. Here, we present the genome sequence of strain HPB2088, which was collected in 1994.

scholarly journals Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of InvasiveStaphylococcus aureusin Europe

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
David M. Aanensen ◽  
Edward J. Feil ◽  
Matthew T. G. Holden ◽  
Janina Dordel ◽  
Corin A. Yeats ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Bacterial Pathogens ◽  
Epidemiological Surveillance ◽  
Data Sets ◽  
Whole Genome ◽  
Bioinformatic Tools ◽  
Road Map

ABSTRACTThe implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasiveStaphylococcus aureusisolates corresponding to a pan-European population snapshot, with epidemiological and resistance data. Geospatial visualization of the data is made possible by a generic software tool designed for public health purposes that is available at the project URL (http://www.microreact.org/project/EkUvg9uY?tt=rc). Our analysis demonstrates that high-risk clones can be identified on the basis of population level properties such as clonal relatedness, abundance, and spatial structuring and by inferring virulence and resistance properties on the basis of gene content. We also show thatin silicopredictions of antibiotic resistance profiles are at least as reliable as phenotypic testing. We argue that this work provides a comprehensive road map illustrating the three vital components for future molecular epidemiological surveillance: (i) large-scale structured surveys, (ii) WGS, and (iii) community-oriented database infrastructure and analysis tools.IMPORTANCEThe spread of antibiotic-resistant bacteria is a public health emergency of global concern, threatening medical intervention at every level of health care delivery. Several recent studies have demonstrated the promise of routine whole-genome sequencing (WGS) of bacterial pathogens for epidemiological surveillance, outbreak detection, and infection control. However, as this technology becomes more widely adopted, the key challenges of generating representative national and international data sets and the development of bioinformatic tools to manage and interpret the data become increasingly pertinent. This study provides a road map for the integration of WGS data into routine pathogen surveillance. We emphasize the importance of large-scale routine surveys to provide the population context for more targeted or localized investigation and the development of open-access bioinformatic tools to provide the means to combine and compare independently generated data with publicly available data sets.

Sign in / Sign up

Export Citation Format

Share Document