Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes

Early detection and population dynamics of Listeria monocytogenes in naturally contaminated drains from a meat processing plant

Listeria monocytogenes, a significant foodborne pathogen, often contaminates ready-to-eat foods through cross-contamination in food processing environments, and floor drains represent one of the most common sites of persistence. Subtyping of L. monocytogenes from food processing plants for the purpose of source tracking is usually performed on a single colony obtained after selective enrichment. This study investigates the temporal variation and population dynamics of L. monocytogenes in drains, focusing on the diversity of L. monocytogenes and the impact of the resident microbiota. Six different drains in a meat processing plant were each sampled four times over a period of 8 weeks and subjected to two-step selective enrichment in Half Fraser and Full Fraser broths. The clonal complexes (CCs) of at least 20 individual L. monocytogenes isolates from each positive sample (460 isolates in total) were determined using either the GenoListeria Multiplex qPCR assay or whole genome sequencing (WGS). The microbiota in drains and enrichment cultures was analyzed by 16S rRNA gene amplicon sequencing and metagenomic or quasimetagenomic sequencing. L. monocytogenes was detected in the majority of samples and four different CCs were identified - CC9, CC11 (ST451), CC121 and CC8 - with up to three CCs in the same sample and with different CCs dominating in different drains. The same clones of CC9, CC11, and CC121 had persisted in the facility for 3-5 years. The composition of the drain microbiota remained relatively stable over time, with Pseudomonas, Acinetobacter, Janthinobacterium, Chryseobacterium, Staphylococcus, and Sphingomonas as the most commonly identified genera. There were no apparent differences in the microbial genera present in L. monocytogenes positive and negative drains or samples. The study highlights the use of techniques such as qPCR and quasimetagenomics for monitoring and controlling the risk of L. monocytogenes contamination in processing environments.

Evaluating serotype-specific survival of Listeria monocytogenes and Listeria innocua on wax-coated Granny Smith apples during storage

Listeria monocytogenes serotypes 1/2a, 1/2b, and 4b are implicated in over 90 % of human listeriosis cases; however, information regarding the serotype-specific survival of L. monocytogenes on apples remains limited. This study evaluated the survival dynamics of these serotypes, using two sets of strains, on Granny Smith apples (GSA) and examined the impact of wax-coating on their survivability during storage. The fate of Listeria innocua on GSA during commercial refrigerated air (RA) storage was also investigated. Results revealed distinct behaviors among L. monocytogenes serotypes. The culturable count of the serotype 4b strain on apples decreased significantly (P < 0.05) by 1.36 log CFU/apple within the first 48 h post-inoculation at ambient temperature. In contrast, counts of serotypes 1/2a and 1/2b strains significantly increased (P < 0.05) by 0.44 and 0.50 log CFU/apple, respectively, during this 48-h attachment period. Over the subsequent 12 weeks of cold storage, serotypes 1/2a and 4b remained stable on GSA, while 1/2b decreased by 1.68 log CFU/apple. Wax coating had a minor impact on L. monocytogenes survival on GSA under both cold and ambient storage conditions, regardless of serotypes. During 18 weeks of commercial RA storage, L. innocua exhibited a gradual decrease of 1.76-1.96 log CFU/apple on wax-coated GSA. Yeasts and molds showed no significant changes in populations due to wax coating, maintaining counts between 5.5 and 5.7 log CFU/apple by the end of the 18-week storage. Additionally, wax coating enhanced quality attributes, significantly preventing (P < 0.05) firmness loss and internal browning compared to unwaxed apples at the conclusion of storage. This study highlights the serotype-specific survival traits of selected L. monocytogenes produce-outbreak isolates on apples, emphasizing the importance of understanding the distinct behaviors of different serotypes.

Current methodologies available to evaluate the virulence potential among Listeria monocytogenes clonal complexes

Listeria monocytogenes is a foodborne pathogen that causes listeriosis in humans, the severity of which depends on multiple factors, including intrinsic characteristics of the affected individuals and the pathogen itself. Additionally, emerging evidence suggests that epigenetic modifications may also modulate host susceptibility to infection. Therefore, different clinical outcomes can be expected, ranging from self-limiting gastroenteritis to severe central nervous system and maternal-neonatal infections, and bacteremia. Furthermore, L. monocytogenes is a genetically and phenotypically diverse species, resulting in a large variation in virulence potential between strains. Multilocus sequence typing (MLST) has been widely used to categorize the clonal structure of bacterial species and to define clonal complexes (CCs) of genetically related isolates. The combination of MLST and epidemiological data allows to distinguish hypervirulent CCs, which are notably more prevalent in clinical cases and typically associated with severe forms of the disease. Conversely, other CCs, termed hypovirulent, are predominantly isolated from food and food processing environments and are associated with the occurrence of listeriosis in immunosuppressed individuals. Reports of genetic traits associated with this diversity have been described. The Food and Agriculture Organization (FAO) is encouraging the search for virulence biomarkers to rapidly identify the main strains of concern to reduce food waste and economical losses. The aim of this review is to comprehensively collect, describe and discuss the methodologies used to discriminate the virulence potential of L. monocytogenes CCs. From the exploration of in vitro and in vivo models to the study of expression of virulence genes, each approach is critically explored to better understand its applicability and efficiency in distinguishing the virulence potential of the pathogen.

Long-term persistence of diverse clones shapes the transmission landscape of invasive Listeria monocytogenes

BACKGROUND

The foodborne bacterium Listeria monocytogenes (Lm) causes a range of diseases, from mild gastroenteritis to invasive infections that have high fatality rate in vulnerable individuals. Understanding the population genomic structure of invasive Lm is critical to informing public health interventions and infection control policies that will be most effective especially in local and regional communities.

METHODS

We sequenced the whole draft genomes of 936 Lm isolates from human clinical samples obtained in a two-decade active surveillance program across 58 counties in New York State, USA. Samples came mostly from blood and cerebrospinal fluid. We characterized the phylogenetic relationships, population structure, antimicrobial resistance genes, virulence genes, and mobile genetic elements.

RESULTS

The population is genetically heterogenous, consisting of lineages I-IV, 89 clonal complexes, 200 sequence types, and six known serogroups. In addition to intrinsic antimicrobial resistance genes (fosX, lin, norB, and sul), other resistance genes tetM, tetS, ermG, msrD, and mefA were sparsely distributed in the population. Within each lineage, we identified clusters of isolates with ≤ 20 single nucleotide polymorphisms in the core genome alignment. These clusters may represent isolates that share a most recent common ancestor, e.g., they are derived from the same contamination source or demonstrate evidence of transmission or outbreak. We identified 38 epidemiologically linked clusters of isolates, confirming eight previously reported disease outbreaks and the discovery of cryptic outbreaks and undetected chains of transmission, even in the rarely reported Lm lineage III (ST3171). The presence of animal-associated lineages III and IV may suggest a possible spillover of animal-restricted strains to humans. Many transmissible clones persisted over several years and traversed distant sites across the state.

CONCLUSIONS

Our findings revealed the bacterial determinants of invasive listeriosis, driven mainly by the diversity of locally circulating lineages, intrinsic and mobile antimicrobial resistance and virulence genes, and persistence across geographical and temporal scales. Our findings will inform public health efforts to reduce the burden of invasive listeriosis, including the design of food safety measures, source traceback, and outbreak detection.

Fitness Differences Between Listeria monocytogenes Serotypes 1/2a, 4b, and 4bv-1 in Competition for Growth on Lettuce Leaf Sections

Listeria monocytogenes is a foodborne pathogen that lives in nature as a saprophyte. Two of the three most common serotypes that cause foodborne listeriosis are 1/2a and 4b. Within serotype 4b, there is a variant called 4bv-1. In the last decade, several produce-related outbreaks (linked to leafy salad, caramel apples, and stone fruit) were linked to 4bv-1 strains, specifically those of Sequence Type 382. This study assessed the fitness of ST 382 strains on lettuce leaf sections to determine if they are more fit on produce than strains of other serotypes. Strains of serotypes 1/2a, 4b, and ST 382 were inoculated as mixtures onto lettuce and incubated at 4 °C for 7 days or 25 °C for 24 h. Thirty L. monocytogenes colonies resulting from the growth on each lettuce piece were characterized for serotype by multiplex PCR, and the percentages of each serotype recovered were compared. In the individual mixtures with three strains, none of the ST 382 strains showed better fitness for growth on lettuce at either 4 °C or 25 °C. Overall, ST 382 strains showed better recovery from lettuce sections grown at 4 °C than at 25 °C. Statistical analysis of the recovery of twelve strains tested in competition experiments indicated that ST 382 strains were less fit for lettuce growth when competing against the other serotypes. The data indicate that ST 382 strains do not have a competitive fitness advantage on cut lettuce sections.

[Molecular characterization of Listeria monocytogenes isolates from human and food sources in Argentina, 2018-2023]

Human listeriosis is an infectious disease caused by Listeria monocytogenes. The invasive form of this disease leads to a high rate of hospitalizations and fatality. The main mode of transmission is through contaminated ready-to-eat foods such as dairy, vegetables and meat products. The knowledge of the diversity and population dynamics of isolates collected from human and food sources is essential for the detection of clusters and the identification of common sites of infection. The aim of this study was the molecular characterization of L. monocytogenes isolates in Argentina. We sequenced a total of 63 isolates, 35 from human and 28 from food sources, collected between 2018 and 2023. Our genomic study divided the isolates into two lineages, four serogroups, 17 sequence types and 15 clonal complexes (CCs). The hypervirulent clone CC1 (lineage I; serogroup IVb) predominated in human and food samples. The phylogenomic analysis showed a high and possible epidemiological relationship between isolates from human and/or food sources, suggesting the presence of transmission chains in our country. These findings highlight the need to strengthen genomic surveillance of L. monocytogenes in Argentina. The identification of geographic distribution and characteristics of predominant and emerging clones from human and food sources might help to focus action plans and public health policies better directed at the control and prevention of listeriosis.

Genomic epidemiology of hypervirulent Listeria monocytogenes CC619: Population structure, phylodynamics and virulence

Listeria monocytogenes is a ubiquitous foodborne pathogen causing human and animal listeriosis with high mortality. Neurological and maternal-neonatal listeriosis outbreaks in Europe and the United States were frequently associated with clonal complexes CC1, CC2 and CC6 harboring Listeria Pathogenicity Island-1 (LIPI-1), as well as CC4 carrying both LIPI-1 and LIPI-4. However, human listeriosis in China was predominantly linked to CC87 and CC619 from serotype 1/2b. To understand the genetic evolution and distribution patterns of CC619, we characterized the epidemic history, population structure, and transmission feature of CC619 strains through analysis of 49,421 L. monocytogenes genomes globally. We found that CC619 was uniquely distributed in China, and closely related with perinatal infection. As CC619 strains were being mainly isolated from livestock and poultry products, we hypothesized that pigs and live chicken were the reservoirs of CC619. Importantly, all CC619 strains not only harbored the intact LIPI-1 and LIPI-4, but these also carried LIPI-3 that could facilitate host colonization and invasion. The deficiency of LIPI-3 or LIPI-4 markedly decreased L. monocytogenes colonization capacity in a model of intragastric infection in the mouse. Altogether, our findings suggest that the hypervirulent CC619 harboring three pathogenicity islands LIPI-1, LIPI-3 and LIPI-4 is a putatively persistent population in various foods, environment, and human population, warranting the further research for deciphering its pathogenicity and strengthening epidemiological surveillance.

Diverse Listeria monocytogenes in-house clones are present in a dynamic frozen vegetable processing environment

Listeria (L.) monocytogenes is of global concern for food safety as the listeriosis-causing pathogen is widely distributed in the food processing environments, where it can survive for a long time. Frozen vegetables contaminated with L. monocytogenes were recently identified as the source of two large listeriosis outbreaks in the EU and US. So far, only a few studies have investigated the occurrence and behavior of Listeria in frozen vegetables and the associated processing environment. This study investigates the occurrence of L. monocytogenes and other Listeria spp. in a frozen vegetable processing environment and in frozen vegetable products. Using whole genome sequencing (WGS), the distribution of sequence types (MLST-STs) and core genome sequence types (cgMLST-CT) of L. monocytogenes were assessed, and in-house clones were identified. Comparative genomic analyses and phenotypical characterization of the different MLST-STs and isolates were performed, including growth ability under low temperatures, as well as survival of freeze-thaw cycles. Listeria were widely disseminated in the processing environment and five in-house clones namely ST451-CT4117, ST20-CT3737, ST8-CT1349, ST8-CT6243, ST224-CT5623 were identified among L. monocytogenes isolates present in environmental swab samples. Subsequently, the identified in-house clones were also detected in product samples. Conveyor belts were a major source of contamination in the processing environment. A wide repertoire of stress resistance markers supported the colonization and survival of L. monocytogenes in the frozen vegetable processing facility. The presence of ArgB was significantly associated with in-house clones. Significant differences were also observed in the growth rate between different MLST-STs at low temperatures (4 °C and 10 °C), but not between in-house and non-in-house isolates. All isolates harbored major virulence genes such as full length InlA and InlB and LIPI-1, yet there were differences between MLST-STs in the genomic content. The results of this study demonstrate that WGS is a strong tool for tracing contamination sources and transmission routes, and for identifying in-house clones. Further research targeting the co-occurring microbiota and the presence of biofilms is needed to fully understand the mechanism of colonization and persistence in a food processing environment.

Hypervirulent clonal complex (CC) of Listeria monocytogenes in fresh produce from urban communities

Introduction

This study aimed to determine the prevalence and virulome of Listeria in fresh produce distributed in urban communities.

Methods

A total of 432 fresh produce samples were collected from farmer's markets in Michigan and West Virginia, USA, resulting in 109 pooled samples. Listeria spp. were isolated and L. monocytogenes was subjected to genoserogrouping by PCR and genotyping by pulsed-field gel electrophoresis (PFGE). Multi-locus sequence typing (MLST) and core-genome multi-locus sequence typing (cgMLST) were conducted for clonal identification.

Results

Forty-eight of 109 samples (44.0%) were contaminated with Listeria spp. L. monocytogenes serotype 1/2a and 4b were recovered from radishes, potatoes, and romaine lettuce. Four clonal complexes (CC) were identified and included hypervirulent CC1 (ST1) and CC4 (ST219) of lineage I as well as CC7 (ST7) and CC11 (ST451) of lineage II. Clones CC4 and CC7 were present in the same romaine lettuce sample. CC1 carried Listeria pathogenicity island LIPI-1 and LIPI-3 whereas CC4 contained LIPI-1, LIPI-3, and LIPI-4. CC7 and CC11 had LIPI-1 only.

Discussion

Due to previous implication in outbreaks, L. monocytogenes hypervirulent clones in fresh produce pose a public health concern in urban communities.

Genomic Characterization of Listeria innocua Isolates Recovered from Cattle Farms, Beef Abattoirs, and Retail Outlets in Gauteng Province, South Africa

Whole-genome sequencing (WGS) was used for the genomic characterization of one hundred and ten strains of Listeria innocua (L. innocua) isolated from twenty-three cattle farms, eight beef abattoirs, and forty-eight retail outlets in Gauteng province, South Africa. In silico multilocus sequence typing (MLST) was used to identify the isolates' sequence types (STs). BLAST-based analyses were used to identify antimicrobial and virulence genes. The study also linked the detection of the genes to the origin (industries and types of samples) of the L. innocua isolates. The study detected 14 STs, 13 resistance genes, and 23 virulence genes. Of the 14 STs detected, ST637 (26.4%), ST448 (20%), 537 (13.6%), and 1085 (12.7%) were predominant, and the frequency varied significantly (p < 0.05). All 110 isolates of L. innocua were carriers of one or more antimicrobial resistance genes, with resistance genes lin (100%), fosX (100%), and tet(M) (30%) being the most frequently detected (p < 0.05). Of the 23 virulence genes recognized, 13 (clpC, clpE, clpP, hbp1, svpA, hbp2, iap/cwhA, lap, lpeA, lplA1, lspA, oatA, pdgA, and prsA2) were found in all 110 isolates of L. innocua. Overall, diversity and significant differences were detected in the frequencies of STs, resistance, and virulence genes according to the origins (source and sample type) of the L. innocua isolates. This, being the first genomic characterization of L. innocua recovered from the three levels/industries (farm, abattoir, and retail) of the beef production system in South Africa, provides data on the organism's distribution and potential food safety implications.

Top-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas

Control of hospital-associated Enterococcus faecium infection is a strenuous task due to the difficulty of identifying transmission routes and the persistence of this nosocomial pathogen despite the implementation of infection control measures that have been successful with other important nosocomial pathogens. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from 66 cancer patients at the University of Arkansas for Medical Sciences (UAMS) between June 2018 and May 2019. In the top-down approach used in this study, we employed, in addition to the 106 E. faecium UAMS isolates, a filtered set of 2,167 E. faecium strains from the GenBank database to assess the current population structure of E. faecium species and, consequently, to identify the lineages associated with our clinical isolates. We then evaluated the antibiotic resistance and virulence profiles of hospital-associated strains from the species pool, focusing on antibiotics of last resort, to establish an updated classification of high-risk and multidrug-resistant nosocomial clones. Further investigation of the clinical isolates collected from UAMS patients using whole-genome sequencing analytical methodologies (core genome multilocus sequence typing [cgMLST], core single nucleotide polymorphism [coreSNP] analysis, and phylogenomics), with the addition of patient epidemiological data, revealed a polyclonal outbreak of three sequence types occurring simultaneously in different patient wards. The integration of genomic and epidemiological data collected from the patients increased our understanding of the relationships and transmission dynamics of the E. faecium isolates. Our study provides new insights into genomic surveillance of E. faecium to assist in monitoring and further limiting the spread of multidrug-resistant E. faecium. IMPORTANCE Enterococcus faecium is a member of the gastrointestinal microbiota. Although its virulence is low in healthy, immunocompetent individuals, E. faecium has become the third leading cause of health care-associated infections in the United States. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from cancer patients at the University of Arkansas for Medical Sciences (UAMS). We employed a top-down analytical approach (from population genomics to molecular biology) to classify our clinical isolates into their genetic lineages and thoroughly evaluate their antibiotic resistance and virulence profiles. The addition of patient epidemiological data to the whole-genome sequencing analytical methodologies performed in the study allowed us to increase our understanding of the relationships and transmission dynamics of the E. faecium isolates. This study provides new insights into genomic surveillance of E. faecium to help monitor and further limit the spread of multidrug-resistant E. faecium.

Application of a core genome sequence typing (cgMLST) pipeline for surveillance of Clostridioides difficile in China

Introduction

Clostridioides difficile (C. difficile) is a nosocomial bacterial pathogen that causes antibiotic-associated diarrhea mediated by cellular exotoxins secreted into the intestine during bacterial growth. Multilocus sequence typing (MLST) and PCR ribotyping are the main molecular typing for C. difficile. Whole genome sequencing (WGS) core genome multilocus sequence typing (cgMLST) was developed for genetic evolution and outbreak investigation of C. difficile with higher precision and accuracy.

Methods

A total of 699 whole (complete and draft) genome sequences of distinct C. difficile strains were used in this study to identify core gene set (2469 core genes) and the cgMLST scheme for the phylogeny analysis of C. difficile. This cgMLST pipeline was then carried the Chinese Pathogen Identification Net (China PIN) for surveillance of C. difficile in China. Within the China PIN, 195 WGS of C. difficile and an outbreak of CDI with 12 WGS of C. difficile were used to evaluate the cgMLST pipeline.

Results

The result displayed that mostly tested C. difficile isolates could be successfully divided into 5 classic clades and the outbreak event was also successfully identified.

Discussion

The results are meaningful and offer a practicable pipeline for a national-wide surveillance of C. difficile in China.

Horizontal Gene Transfer and Loss of Serotype-Specific Genes in Listeria monocytogenes Can Lead to Incorrect Serotype Designations with a Commonly-Employed Molecular Serotyping Scheme

Listeria monocytogenes is a Gram-positive, facultative intracellular foodborne pathogen capable of causing severe, invasive illness (listeriosis). Three serotypes, 1/2a, 1/2b, and 4b, are leading contributors to human listeriosis, with 4b including the major hypervirulent clones. The multiplex PCR scheme developed by Doumith and collaborators employs primers targeting specific lineages (e.g., lineage II-specific lmo0737, lineage I-specific LMOf2365_2059) or serotypes (e.g., serotype 4b-specific LMOf2365_1900). The Doumith scheme (DS) is extensively employed for molecular serotyping of L. monocytogenes due to its high accuracy, relative ease, and affordability. However, for certain strains, the DS serotype designations are in conflict with those relying on antibody-based schemes or whole-genome sequence (WGS) analysis. In the current study, all 27 tested serotype 4b strains with sequence type 782 (ST782) within the hypervirulent clonal complex 2 (CC2) were designated 1/2b/3b using the DS. These strains lacked the serotype 4b-specific gene LMOf2365_1900, while retaining LMOf2365_2059, which, together with prs, yields the DS 1/2b/3b profile. Furthermore, 15 serotype 1/2a strains of four STs, mostly from water, were designated 1/2b/3b using the DS. These strains lacked the lmo0737 cassette but harbored genomic islands with LMOf2365_2059, thus yielding the DS 1/2b/3b profile. Lastly, we investigated a novel, dual 1/2a-1/2b profile obtained using the DS with 21 serotype 1/2a strains of four STs harboring both the lmo0737 cassette and genomic islands with LMOf2365_2059. The findings suggest that for certain strains and clones of L. monocytogenes the DS designations should be viewed with caution and complemented with alternative tools, e.g., traditional serotyping or WGS analysis. IMPORTANCE Listeria monocytogenes is a foodborne pathogen responsible for severe illness (listeriosis), especially in pregnant women and their fetuses, immunocompromised individuals, and the elderly. Three serotypes, 1/2a, 1/2b, and 4b, account for most human listeriosis, with certain serotype 4b clonal complexes (CCs) overrepresented in human disease. Serotyping remains extensively employed in Listeria epidemiologic investigations, and a multiplex PCR-based serotyping scheme is widely used. However, the PCR gene targets can be lost or gained via horizontal gene transfer, leading to novel PCR profiles without known serotype designations or to incorrect serotype assignments. Thus, an entire serotype 4b clone of the hypervirulent CC2 would be misidentified as serotype 1/2b, and several strains of serotype 1/2a would be identified as serotype 1/2b. Such challenges are especially common in novel clones from underexplored habitats, e.g., wildlife and surface water. The findings suggest caution in application of molecular serotyping, while highlighting Listeria's diversity and potential for horizontal gene transfer.

Growth and inactivation of Listeria monocytogenes in sterile extracts of fruits and vegetables: Impact of the intrinsic factors pH, sugar and organic acid content

Intrinsic characteristics of fresh produce, such as pH, water activity, acid content and nutrient availability are critical factors in determining the survival and growth of Listeria monocytogenes (Lm). In this study, sterile fresh produce juice was used to analyze Lm growth potential among 14 different commodities and to identify physicochemical characteristics in those juices that affect Lm growth. Significant growth of Lm was observed in juices with pH ≥5.6 and low acidity (0.04-0.07 % titratable acidity (TA)) (cantaloupe, carrot, celery, green pepper, parsley, and romaine lettuce), slight reduction of Lm was observed in juices with pH 4.1 (tomato) and pH 3.9 (mango), and no Lm counts were recovered from juices with pH ≤3.8 and high acidity (0.28-1.17 % TA) (apple, blueberry, grape, peach, and pineapple). Although these acidic fruit juices possessed a high sugar content, the pH and acidity of produce juice seemed to be the primary determinants for Lm growth. The neutralization of acidic juices (i.e., Fuji and Gala apple, blueberry, grape, mango, pineapple, peach, and tomato) enabled Lm growth at 37 °C in all juices except for Gala apple and peach. Strong decline in Lm populations in Gala apple, grape and peach juices might be linked to sensitivity to organic acids, such as malic acid. Furthermore, Lm populations significantly decreased in pH-neutral (7.6) cauliflower juice, suggesting that potential antilisterial substances may play a role in Lm decline in cauliflower juice.

Wholegenome sequencing as the gold standard approach for control of Listeria monocytogenes in the food chain

Listeria monocytogenes has been implicated in numerous outbreaks and related deaths of listeriosis. In food production, L. monocytogenes occurs in raw food material and above all, through postprocessing contamination. The use of next-generation sequencing technologies such as whole-genome sequencing (WGS) facilitates foodborne outbreak investigations, pathogen source tracking and tracing geographic distributions of different clonal complexes, routine microbiological/epidemiological surveillance of listeriosis, and quantitative microbial risk assessment. WGS can also be used to predict various genetic traits related to virulence, stress, or antimicrobial resistance, which can be of great benefit for improving food safety management as well as public health.

Characterisation of Listeria monocytogenes Isolates from Hunted Game and Game Meat from Finland

Listeria monocytogenes is an important foodborne zoonotic bacterium. It is a heterogeneous species that can be classified into lineages, serogroups, clonal complexes, and sequence types. Only scarce information exists on the properties of L. monocytogenes from game and game meat. We characterised 75 L. monocytogenes isolates from various game sources found in Finland between 2012 and 2020. The genetic diversity, presence of virulence and antimicrobial genes were studied with whole genome sequencing. Most (89%) of the isolates belonged to phylogenetic lineage (Lin) II and serogroup (SG) IIa. SGs IVb (8%) and IIb (3%) of Lin I were sporadically identified. In total, 18 clonal complexes and 21 sequence types (STs) were obtained. The most frequent STs were ST451 (21%), ST585 (12%) and ST37 (11%) found in different sample types between 2012 and 2020. We observed 10 clusters, formed by closely related isolates with 0-10 allelic differences. Most (79%) of the virulence genes were found in all of the L. monocytogenes isolates. Only fosX and lin were found out of 46 antimicrobial resistance genes. Our results demonstrate that potentially virulent and antimicrobial-sensitive L. monocytogenes isolates associated with human listeriosis are commonly found in hunted game and game meat in Finland.

Whole-Genome Sequence Comparisons of Listeria monocytogenes Isolated from Meat and Fish Reveal High Inter- and Intra-Sample Diversity

Interpretation of whole-genome sequencing (WGS) data for foodborne outbreak investigations is complex, as the genetic diversity within processing plants and transmission events need to be considered. In this study, we analyzed 92 food-associated Listeria monocytogenes isolates by WGS-based methods. We aimed to examine the genetic diversity within meat and fish production chains and to assess the applicability of suggested thresholds for clustering of potentially related isolates. Therefore, meat-associated isolates originating from the same samples or processing plants as well as fish-associated isolates were analyzed as distinct sets. In silico serogrouping, multilocus sequence typing (MLST), core genome MLST (cgMLST), and pangenome analysis were combined with screenings for prophages and genetic traits. Isolates of the same subtypes (cgMLST types (CTs) or MLST sequence types (STs)) were additionally compared by SNP calling. This revealed the occurrence of more than one CT within all three investigated plants and within two samples. Analysis of the fish set resulted in predominant assignment of isolates from pangasius catfish and salmon to ST2 and ST121, respectively, potentially indicating persistence within the respective production chains. The approach not only allowed the detection of distinct subtypes but also the determination of differences between closely related isolates, which need to be considered when interpreting WGS data for surveillance.

Sugar Modification of Wall Teichoic Acids Determines Serotype-Dependent Strong Biofilm Production in Listeria monocytogenes

Biofilm production is responsible for persistent food contamination by Listeria monocytogenes, threatening food safety and public health. Human infection and food contamination with L. monocytogenes are caused primarily by serotypes 1/2a, 1/2b, and 4b. However, the association of biofilm production with phylogenic lineage and serotype has not yet been fully understood. In this study, we measured the levels of biofilm production in 98 clinical strains of L. monocytogenes at 37°C, 25°C, and 4°C. The phylogenetic clusters grouped by core genome multilocus sequence typing (cgMLST) exhibited association between biofilm production and phylogenetic lineage and serotype. Whereas clusters 1 and 3 consisting of serotype 4b strains exhibited weak biofilm production, clusters 2 (serotype 1/2b) and 4 (serotype 1/2a) were composed of strong biofilm formers. Particularly, cluster 2 (serotype 1/2b) strains exhibited the highest levels of biofilm production at 37°C, and the levels of biofilm production of cluster 4 (serotype 1/2a) strains were significantly elevated at all tested temperatures. Pan-genome analysis identified 22 genes unique to strong biofilm producers, most of which are related to the synthesis and modification of teichoic acids. Notably, a knockout mutation of the rml genes related to the modification of wall teichoic acids with l-rhamnose, which is specific to serogroup 1/2, significantly reduced the level of biofilm production by preventing biofilm maturation. Here, the results of our study show that biofilm production in L. monocytogenes is related to phylogeny and serotype and that the modification of wall teichoic acids with l-rhamnose is responsible for serotype-specific strong biofilm formation in L. monocytogenes. IMPORTANCE Biofilm formation on the surface of foods or food-processing facilities by L. monocytogenes is a serious food safety concern. Here, our data demonstrate that the level of biofilm production differs among serotypes 1/2a, 1/2b, and 4b depending on the temperature. Furthermore, sugar decoration of bacterial cell walls with l-rhamnose is responsible for strong biofilm production in serotypes 1/2a and 1/2b, commonly isolated from foods and listeriosis cases. The findings in this study improve our understanding of the association of biofilm production with phylogenetic lineage and serotype in L. monocytogenes.

Whole-Genome Sequencing-Based Characterization of Listeria Isolates from Produce Packinghouses and Fresh-Cut Facilities Suggests Both Persistence and Reintroduction of Fully Virulent L. monocytogenes

The contamination of ready-to-eat produce with Listeria monocytogenes (LM) can often be traced back to environmental sources in processing facilities and packinghouses. To provide an improved understanding of Listeria sources and transmission in produce operations, we performed whole-genome sequencing (WGS) of LM (n = 169) and other Listeria spp. (n = 107) obtained from 13 produce packinghouses and three fresh-cut produce facilities. Overall, a low proportion of LM isolates (9/169) had inlA premature stop codons, and a large proportion (83/169) had either or both of the LIPI-3 or LIPI-4 operons, which have been associated with hypervirulence. The further analysis of the WGS data by operation showed a reisolation (at least 2 months apart) of highly related isolates (<10 hqSNP differences) in 7/16 operations. Two operations had highly related strains reisolated from samples that were collected at least 1 year apart. The identification of isolates collected during preproduction (i.e., following sanitation but before the start of production) that were highly related to isolates collected during production (i.e., after people or products have entered and begun moving through the operation) provided evidence that some strains were able to survive standard sanitation practices. The identification of closely related isolates (<20 hqSNPs differences) in different operations suggests that cross-contamination between facilities or introductions from common suppliers may also contribute to Listeria transmission. Overall, our data suggest that the majority of LM isolates collected from produce operations are fully virulent and that both persistence and reintroduction may lead to the repeat isolation of closely related Listeria in produce operations.

IMPORTANCEListeria monocytogenes is of particular concern to the produce industry due to its frequent presence in natural environments as well as its ability to survive in packinghouses and fresh-cut processing facilities over time. The use of whole-genome sequencing, which provides high discriminatory power for the characterization of Listeria isolates, along with detailed source data (isolation date and sample location) shows that the presence of Listeria in produce operations appears to be due to random and continued reintroduction as well as to the persistence of highly related strains in both packinghouses and fresh-cut facilities. These findings indicate the importance of using high-resolution characterization approaches for root cause analyses of Listeria contamination issues. In cases of repeat isolation of closely related Listeria in a given facility, both persistence and reintroduction need to be considered as possible root causes.

Pervasive Listeria monocytogenes Is Common in the Norwegian Food System and Is Associated with Increased Prevalence of Stress Survival and Resistance Determinants

To investigate the diversity, distribution, persistence, and prevalence of stress survival and resistance genes of Listeria monocytogenes clones dominating in food processing environments in Norway, genome sequences from 769 L. monocytogenes isolates from food industry environments, foods, and raw materials (512 of which were sequenced in the present study) were subjected to whole-genome multilocus sequence typing (wgMLST), single-nucleotide polymorphism (SNP), and comparative genomic analyses. The data set comprised isolates from nine meat and six salmon processing facilities in Norway collected over a period of three decades. The most prevalent clonal complex (CC) was CC121, found in 10 factories, followed by CC7, CC8, and CC9, found in 7 factories each. Overall, 72% of the isolates were classified as persistent, showing 20 or fewer wgMLST allelic differences toward an isolate found in the same factory in a different calendar year. Moreover, over half of the isolates (56%) showed this level of genetic similarity toward an isolate collected from a different food processing facility. These were designated as pervasive strains, defined as clusters with the same level of genetic similarity as persistent strains but isolated from different factories. The prevalence of genetic determinants associated with increased survival in food processing environments, including heavy metal and biocide resistance determinants, stress response genes, and inlA truncation mutations, showed a highly significant increase among pervasive isolates but not among persistent isolates. Furthermore, these genes were significantly more prevalent among the isolates from food processing environments compared to in isolates from natural and rural environments (n = 218) and clinical isolates (n = 111) from Norway.

IMPORTANCEListeria monocytogenes can persist in food processing environments for months to decades and spread through the food system by, e.g., contaminated raw materials. Knowledge of the distribution and diversity of L. monocytogenes is important in outbreak investigations and is essential to effectively track and control this pathogen in the food system. The present study presents a comprehensive overview of the prevalence of persistent clones and of the diversity of L. monocytogenes in Norwegian food processing facilities. The results demonstrate extensive spread of highly similar strains throughout the Norwegian food system, in that 56% of the 769 collected isolates from food processing factories belonged to clusters of L. monocytogenes identified in more than one facility. These strains were associated with an overall increase in the prevalence of plasmids and determinants of heavy metal and biocide resistance, as well as other genetic elements associated with stress survival mechanisms and persistence.

Delineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing

Mycobacterium abscessus is an emerging multidrug-resistant non-tuberculous mycobacterium that causes a wide spectrum of infections and has caused several local outbreaks worldwide. To facilitate standardized prospective molecular surveillance, we established a novel core genome multilocus sequence typing (cgMLST) scheme. Whole genome sequencing data of 1991 isolates were employed to validate the scheme, re-analyze global population structure and set genetic distance thresholds for cluster detection and taxonomic identification. We confirmed and amended the nomenclature of the main dominant circulating clones and found that these also correlate well with traditional 7-loci MLST. Dominant circulating clones could be linked to a corresponding reference genome with less than 250 alleles while 99% of pairwise comparisons between epidemiologically linked isolates were below 25 alleles and 90% below 10 alleles. These thresholds can be used to guide further epidemiological investigations. Overall, the scheme will help to unravel the apparent global spread of certain clonal complexes and as yet undiscovered transmission routes.

Surveillance and examination of microbial contamination in ice cream in China

This study investigated the microbial contamination of ice cream in China. A total of 2,887 ice cream samples were collected from different regions of China. Contamination by the aerobic plate count (APC), coliforms, and three foodborne pathogens, such as Listeria monocytogenes, Staphylococcus aureus, and Salmonella spp., was detected in the samples. L. monocytogenes isolates were further analyzed for antibiotic susceptibility and multi-locus sequence typing (MLST). The results showed that APC was more than 10 5 CFU/g in 6.10% (176/2887) and coliform was more than 10 2 CFU/g in 15.69% (453/2887) of all samples. The positive rates of S. aureus, L. monocytogenes, and Salmonella spp. were 0.66%, 0.62%, and 0.10%, respectively. Of these, S. aureus contamination was more than 10 2 CFU/g in two samples, and L. monocytogenes in the positive sample was in the range of 0.3–240 MPN/g, with a median of 4.3 MPN/g. The hygienic status of the packaged samples was much better than that of the bulk samples (P &lt; 0.05). Catered samples were more frequently and heavily contaminated than samples from retail and wholesale outlets (P &lt; 0.05). No significant differences were observed in samples bought from urban and rural areas (P &gt;0.05). For 18 L. monocytogenes strains isolated from ice cream, the resistance rate of nine antibiotics was 5.56% (1/18). By MLST, the L. monocytogenes strains were classified into 9 sequence types (STs), of which ST8 was most common (6 isolates). These above results indicate that a potential health risk to the public may be caused by ice cream, particularly susceptible populations.

Biofilm formation and genomic features of Listeria monocytogenes strains isolated from meat and dairy industries located in Piedmont (Italy)

Listeria monocytogenes is considered a major challenge for the food industry as it can persist for long periods in food processing plants by forming biofilms. The aims of this study were: i) to assess the biofilm producing ability of 57 Listeria monocytogenes isolates previously subjected to whole-genome sequencing (WGS); ii) to compare the levels of biofilm formation with the presence or absence of biofilm associated genes. To determine the presence or absence of a known set of biofilm associated genes, a comparative genomic analysis was performed on each strain. Among Listeria monocytogenes isolates, 58 %, 38.5 % and 3.5 % exhibited weak, moderate or strong biofilm production, respectively. No difference in biofilm production was observed between food and environmental isolates. The percentage of Listeria monocytogenes strains isolated from meat products (57 %) classified as moderate or strong biofilm producers was higher than the percentage obtained for strains isolated from dairy products (28 %). The presence of the Stress Survival Islet 1, the arsD stress gene and the truncated inlA protein was significantly associated with increased levels of biofilm. Combining biofilm phenotype with molecular and genotyping data may provide the opportunity to better understand the relationship between genes linked to biofilm formation in Listeria monocytogenes.

Whole-Genome Sequencing Reveals Multiple Subpopulations of Dominant and Persistent Lineage I Isolates of Listeria monocytogenes in Two Meat Processing Facilities during 2011-2015

Listeria monocytogenes is a foodborne pathogen with a highly clonal population structure comprising multiple phylogenetic sub-groups that can persist within food processing environments and contaminate food. The epidemiology of L. monocytogenes is well-described in some developed countries; however, little is known about the prevalence and population structure of this pathogen in food and food processing environments located in less developed regions. The aim of this study was to determine the genetic characteristics and clonal relatedness of L. monocytogenes that were isolated from two Jamaican meat processing facilities. Of the 37 isolates collected between 2011 and 2015, only a single lineage II isolate was recovered (serotype 1/2c), and the remaining were lineage I isolates representing serotypes 4b, 1/2b, 3b, and two untypeable isolates. Pulsed-field gel electrophoresis (PFGE) delineated isolates into seven pulsotypes, and whole-genome sequencing (WGS) categorized most isolates within one of three clonal complexes (CC): CC2 (N = 12), CC5 (N = 11), and CC288 (N = 11). Isolates representing CC1 (N = 2) and CC9 (N = 1) were also recovered. Virulence-associated genes such as inlA and the LIPI-3 cluster were detected in multiple isolates, along with the stress survival islet cluster-1 (SSI-1), and benzalkonium (bcrABC) and cadmium (cad1, cad2, cad4) resistance cassettes. Multiple isolates that belong to the same CC and matching PFGE patterns were isolated from food and the environment from both facilities across multiple years, suggesting the presence of persistent strains of L. monocytogenes, and/or constant re-entry of the pathogens into the facilities from common sources. These findings highlight the ability of lineage I isolates of L. monocytogenes to colonize, persist, and predominate within two meat-producing environments, and underscores the need for robust surveillance strategies to monitor and mitigate against these important foodborne pathogens.

Prevalence and Clonal Diversity of over 1,200 Listeria monocytogenes Isolates Collected from Public Access Waters near Produce Production Areas on the Central California Coast during 2011 to 2016

A 5-year survey of public access surface waters in an agricultural region of the Central California Coast was done to assess the prevalence of the foodborne pathogen Listeria monocytogenes. In nature, L. monocytogenes lives as a saprophyte in soil and water, which are reservoirs for contamination of preharvest produce. Moore swabs were deployed biweekly in lakes, ponds, streams, and rivers during 2011 to 2016. L. monocytogenes was recovered in 1,224 of 2,922 samples, resulting in 41.9% prevalence. Multiple subtypes were isolated from 97 samples, resulting in 1,323 L. monocytogenes isolates. Prevalence was higher in winter and spring and after rain events in some waterways. Over 84% of the isolates were serotype 4b. Whole-genome sequencing was done on 1,248 isolates, and in silico multilocus sequence typing revealed 74 different sequence types (STs) and 39 clonal complexes (CCs). The clones most isolated, CC639, CC183, and CC1, made up 27%, 19%, and 13%, respectively, of the sequenced isolates. Other types were CC663, CC6, CC842, CC4, CC2, CC5, and CC217. All sequenced isolates contained intact copies of core L. monocytogenes virulence genes, and pathogenicity islands LIPI-3 and LIPI-4 were identified in 73% and 63%, respectively, of the sequenced isolates. The virulence factor internalin A was predicted to be intact in all but four isolates, while genes important for sanitizer and heavy metal resistance were found in <5% of the isolates. These waters are not used for crop irrigation directly, but they are available to wildlife and can flood fields during heavy rains. IMPORTANCE Listeria monocytogenes serotype 4b and 1/2a strains are implicated in most listeriosis, and hypervirulent listeriosis stems from strains containing pathogenicity islands LIPI-3 and LIPI-4. The waters and sediments in the Central California Coast agricultural region contain widespread and diverse L. monocytogenes populations, and all the isolates contain intact virulence genes. Emerging clones CC183 and CC639 were the most abundant clones, and major clones CC1, CC4, and CC6 were well represented. CC183 was responsible for three produce-related outbreaks in the last 7 years. Most of the isolates in the survey differ from those of lesser virulence that are often isolated from foods and food processing plants because they contain genes encoding an intact virulence factor, internalin A, and most did not contain genes for sanitizer and heavy metal resistance. This isolate collection is important for understanding L. monocytogenes populations in agricultural and natural regions.

In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes

Background

Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinformatics tools to define cgMLST alleles, our aim was to identify parameters influencing the precision of cgMLST profiles.

Methods

We used three L. monocytogenes reference genomes from different phylogenetic lineages and assessed the impact of in vitro (i.e. tested genomes, successive platings, replicates of DNA extraction and sequencing) and in silico parameters (i.e. targeted depth of coverage, depth of coverage, breadth of coverage, assembly metrics, cgMLST workflows, cgMLST completeness) on cgMLST precision made of 1748 core loci. Six cgMLST workflows were tested, comprising assembly-based (BIGSdb, INNUENDO, GENPAT, SeqSphere and BioNumerics) and assembly-free (i.e. kmer-based MentaLiST) allele callers. Principal component analyses and generalized linear models were used to identify the most impactful parameters on cgMLST precision.

Results

The isolate’s genetic background, cgMLST workflows, cgMLST completeness, as well as depth and breadth of coverage were the parameters that impacted most on cgMLST precision (i.e. identical alleles against reference circular genomes). All workflows performed well at ≥40X of depth of coverage, with high loci detection (> 99.54% for all, except for BioNumerics with 97.78%) and showed consistent cluster definitions using the reference cut-off of ≤7 allele differences.

Conclusions

This highlights that bioinformatics workflows dedicated to cgMLST allele calling are largely robust when paired-end reads are of high quality and when the sequencing depth is ≥40X.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08437-4.

Genotyping of Listeria monocytogenes isolates by high-resolution melting curve (HRM) analysis of tandem repeat locus

Listeria monocytogenes is responsible for causing listeriosis, a type of food poisoning with high mortality. This bacterium is mainly transmitted to humans through the consumption of contaminated foods. Detection of L. monocytogenes through molecular methods is crucial for food safety and clinical diagnosis. Present techniques are characterized by low discrimination power and high cost, as well as being time-consuming and taking several days to give the final result. In our study, MLVA-HRM (Multiple-Locus Variable-number tandem repeats Analysis ‒ High-Resolution Melting) was investigated as an alternative method for a fast and precise method for the genotyping of L. monocytogenes isolates. Forty-eight isolates of L. monocytogenes obtained from the microbial bank of Department of Microbiology, Iran University of Medical Sciences, were typed by MLVA-HRM analysis using five Variable Numbers of Tandem Repeat (VNTR) loci. A total of 43 different types were obtained. This research demonstrated the usefulness of the MLVA-HRMA method and its ability to discriminate L. monocytogenes isolates. Since this method is easier and more efficient than existing methods, it can be widely used in food processing plants and diagnostic laboratories as a fast and accurate method.

Genetic Diversity of Listeria monocytogenes Isolated From Three Commercial Tree Fruit Packinghouses and Evidence of Persistent and Transient Contamination

Whole genome analysis was performed on 501 isolates obtained from a previous survey which recovered 139 positive environmental sponge samples (i.e., up to 4 isolates per sample) from a total of 719 samples collected at 40 standardized sites in 3 commercial apple packinghouse facilities (i.e., P1, P2, and P3) over 3 successive seasons in a single production year. After excluding duplicated isolates, the data from 156 isolates revealed the clonal diversity of L. monocytogenes and allowed the detection of transient contamination, persistent contamination, and cross-area transmission events. Facility P2 with the poorest sanitary conditions had the least diversity (Shannon's index of 0.38). P2 contained a Clonal Complex (CC) 554, serogroup IVb-v1 strain that persisted throughout the year and spread across the entire facility, a singleton Sequence Type (ST) 1003, lineage III strain that persisted through two seasons and spread across two areas of the facility, and 3 other clones from transient contaminations. P1 and P3, facilities with better sanitary conditions, had much higher diversity (i.e., 15 clones with a Shannon's index of 2.49 and 10 clones with a Shannon's index of 2.10, respectively) that were the result of transient contamination. Facilities P1 and P3 had the highest incidence (43.1%) of lineage III isolates, followed by lineage I (31.3%) and lineage II (25.5%) isolates. Only 1 isolate in the three facilities contained a premature stop codon in virulence gene inlA. Fourteen samples yielded 2-3 clones per sample, demonstrating the importance of choosing appropriate methodologies and selecting a sufficient number of isolates per sample for studying L. monocytogenes diversity. Only 1 isolate, belonging to CC5 and from facility P3, contained a known plasmid, and this was also the only isolate containing benzalkonium chloride tolerance genes. The persistent CC554 strain did not exhibit stronger sanitizer resistance than other isolates and did not contain any confirmed molecular determinants of L. monocytogenes stress resistance that were differentially present in other isolates, such as genes involved in sanitizer tolerance, heavy metal resistance, biofilm-forming, stress survival islet 1 (SSI-1), stress survival islet 2 (SSI-2) or Listeria genomic island (LGI2).

Landscape of Stress Response and Virulence Genes Among Listeria monocytogenes Strains

The pathogenic microorganism Listeria monocytogenes is ubiquitous and responsible for listeriosis, a disease with a high mortality rate in susceptible people. It can persist in different habitats, including the farm environment, the food production environments, and in foods. This pathogen can grow under challenging conditions, such as low pH, low temperatures, and high salt concentrations. However, L. monocytogenes has a high degree of strain divergence regarding virulence potential, environmental adaption, and stress response. This review seeks to provide the reader with an up-to-date overview of clonal and serotype-specific differences among L. monocytogenes strains. Emphasis on the genes and genomic islands responsible for virulence and resistance to environmental stresses is given to explain the complex adaptation among L. monocytogenes strains. Moreover, we highlight the use of advanced diagnostic technologies, such as whole-genome sequencing, to fine-tune quantitative microbiological risk assessment for better control of listeriosis.

Molecular subtyping for source tracking of Escherichia coli using core genome multilocus sequence typing at a food manufacturing plant

When harmful bacteria are detected in the final product at a food manufacturing plant, it is necessary to identify and eliminate the source of contamination so that it does not occur again. In the current study, the source of contamination was tracked using core genome multilocus sequence typing (cgMLST) analysis in cases where Escherichia coli was detected in the final product at a food manufacturing plant. cgMLST analysis was performed on 40 strains of E. coli collected from the environment [floor (26 strains), drainage ditch (5 strains), container (4 strains), post-heating production line (1 strain)] and products [final product (3 strains) and intermediate product (1 strain)]. In total, 40 E. coli isolates were classified into 17 genogroups by cgMLST analysis. The 4 E. coli strains isolated from the intermediate and final products were classified into two genogroups (I and II). Certain isolates collected from the environment also belonged to those genogroups, it was possible to estimate the transmission of E. coli in the manufacturing plant. Thus, the dynamics of E. coli in the food manufacturing location were clarified by using cgMLST analysis. In conclusion, our results indicate that cgMLST analysis can be effectively used for hygiene management at food manufacturing locations.

A machine learning-based typing scheme refinement for Listeria monocytogenes core genome multilocus sequence typing with high discriminatory power for common source outbreak tracking

Background

As whole-genome sequencing for pathogen genomes becomes increasingly popular, the typing methods of gene-by-gene comparison, such as core genome multilocus sequence typing (cgMLST) and whole-genome multilocus sequence typing (wgMLST), are being routinely implemented in molecular epidemiology. However, some intrinsic problems remain. For example, genomic sequences with varying read depths, read lengths, and assemblers influence the genome assemblies, introducing error or missing alleles into the generated allelic profiles. These errors and missing alleles might create “specious discrepancy” among closely related isolates, thus making accurate epidemiological interpretation challenging. In addition, the rapid growth of the cgMLST allelic profile database can cause problems related to storage and maintenance as well as long query search times.

Methods

We attempted to resolve these issues by decreasing the scheme size to reduce the occurrence of error and missing alleles, alleviate the storage burden, and improve the query search time. The challenge in this approach is maintaining the typing resolution when using fewer loci. We achieved this by using a popular artificial intelligence technique, XGBoost, coupled with Shapley additive explanations for feature selection. Finally, 370 loci from the original 1701 cgMLST loci of Listeria monocytogenes were selected.

Results

Although the size of the final scheme (LmScheme_370) was approximately 80% lower than that of the original cgMLST scheme, its discriminatory power, tested for 35 outbreaks, was concordant with that of the original cgMLST scheme. Although we used L. monocytogenes as a demonstration in this study, the approach can be applied to other schemes and pathogens. Our findings might help elucidate gene-by-gene–based epidemiology.

The Persistence of Bacterial Pathogens in Surface Water and Its Impact on Global Food Safety

Water is vital to agriculture. It is essential that the water used for the production of fresh produce commodities be safe. Microbial pathogens are able to survive for extended periods of time in water. It is critical to understand their biology and ecology in this ecosystem in order to develop better mitigation strategies for farmers who grow these food crops. In this review the prevalence, persistence and ecology of four major foodborne pathogens, Shiga toxin-producing Escherichia coli (STEC), Salmonella, Campylobacter and closely related Arcobacter, and Listeria monocytogenes, in water are discussed. These pathogens have been linked to fresh produce outbreaks, some with devastating consequences, where, in a few cases, the contamination event has been traced to water used for crop production or post-harvest activities. In addition, antimicrobial resistance, methods improvements, including the role of genomics in aiding in the understanding of these pathogens, are discussed. Finally, global initiatives to improve our knowledge base of these pathogens around the world are touched upon.

Genome Typing and Epidemiology of Human Listeriosis in New Zealand, 1999 to 2018

This study describes the epidemiology of listeriosis in New Zealand between 1999 and 2018 as well as the retrospective whole-genome sequencing (WGS) of 453 Listeria monocytogenes isolates corresponding to 95% of the human cases within this period. The average notified rate of listeriosis was 0.5 cases per 100,000 population, and non-pregnancy-associated cases were more prevalent than pregnancy-associated cases (averages of 19 and 5 cases per annum, respectively). WGS data was assessed using multilocus sequencing typing (MLST), including core-genome and whole-genome MLST (cgMLST and wgMLST, respectively) and single-nucleotide polymorphism (SNP) analysis. Thirty-nine sequence types (STs) were identified, with the most common being ST1 (21.9%), ST4 (13.2%), ST2 (11.3%), ST120 (6.1%), and ST155 (6.4%). A total of 291 different cgMLST types were identified, with the majority (n = 243) of types observed as a single isolate, consistent with the observation that listeriosis is predominately sporadic. Among the 49 cgMLST types containing two or more isolates, 18 cgMLST types were found with 2 to 4 isolates each (50 isolates in total, including three outbreak-associated isolates) that shared low genetic diversity (0 to 2 whole-genome alleles), some of which were dispersed in time or geographical regions. SNP analysis also produced results comparable to those from wgMLST. The low genetic diversity within these clusters suggests a potential common source, but incomplete epidemiological data impaired retrospective epidemiological investigations. Prospective use of WGS analysis together with thorough exposure information from cases could potentially identify future outbreaks more rapidly, including those that may have been undetected for some time over different geographical regions.

Harnessing Whole Genome Sequence Data for Facility-Specific Signatures for Listeria monocytogenes: A Case Study With Turkey Processing Plants in the United States

Listeria monocytogenes is a Gram-positive foodborne pathogen responsible for the severe disease listeriosis and notorious for its ability to persist in food processing plants, leading to contamination of processed, ready-to-eat foods. L. monocytogenes persistence in various food processing environments (FPEs) has been extensively investigated by various subtyping tools, with increasing use of whole genome sequencing (WGS). However, major knowledge gaps remain. There is a need for facility-specific molecular signatures not only for adequate attribution of L. monocytogenes to a specific FPE but also for improved understanding of the ecology and evolution of L. monocytogenes in the food processing ecosystem. Furthermore, multiple strains can be recovered from a single FPE sample, but their diversity can be underestimated with common molecular subtyping tools. In this study we investigated a panel of 54 L. monocytogenes strains from four turkey processing plants in the United States. A combination of WGS and phenotypic assays was employed to assess strain persistence as well as identify facility-specific molecular signatures. Comparative analysis of allelic variation across the whole genome revealed that allelic profiles have the potential to be specific to individual processing plants. Certain allelic profiles remained associated with individual plants even when closely-related strains from other sources were included in the analysis. Furthermore, for certain sequence types (STs) based on the seven-locus multilocus sequence typing scheme, presence and location of premature stop codons in inlA, inlB length, prophage sequences, and the sequence content of a genomic hotspot could serve as plant-specific signatures. Interestingly, the analysis of different isolates from the same environmental sample revealed major differences not only in serotype and ST, but even in the sequence content of strains of the same ST. This study highlights the potential for WGS data to be deployed for identification of facility-specific signatures, thus facilitating the tracking of strain movement through the food chain. Furthermore, deployment of WGS for intra-sample strain analysis allows for a more complete environmental surveillance of L. monocytogenes in food processing facilities, reducing the risk of failing to detect strains that may be clinically relevant and potentially novel.

An economic evaluation of the Whole Genome Sequencing source tracking program in the U.S

The U.S. Food and Drug Administration (FDA) created the GenomeTrakr Whole Genome Sequencing (WGS) Network in 2013, as a tool to improve food safety. This study presents an analysis of Whole Genome source tracking implementation on potential food contamination and related illnesses through theoretical, empirical, and cost benefit analyses. We conduct empirical tests using data from FDA regulated food commodity outbreaks garnering FDA response from 1999 through 2019 and examine the effect of the National Center for Biotechnology Information (NCBI) Pathogen detection program of source tracking WGS isolates collected in the U.S. on outbreak illnesses for three pilot pathogens (E. coli, Listeria, and Salmonella). Empirical results are consistent with the theoretical model and suggest that each additional 1,000 WGS isolates added to the public NCBI database is associated with a reduction of approximately 6 illnesses per WGS pathogen, per year. Empirical results are connected to existing literature for a Monte Carlo analysis to estimate benefits and costs. By 2019, annual health benefits are estimated at nearly $500 million, compared to an approximately $22 million investment by public health agencies. Even under conservative assumptions, the program likely broke even in its second year of implementation and could produce increasing public health benefits as the GenomeTrakr network matures.

Prevalence, Genetic Diversity and Factors Associated with Distribution of Listeria monocytogenes and Other Listeria spp. in Cattle Farms in Latvia

Listeria spp. is a diverse genus of Gram-positive bacteria commonly present in the environment while L. monocytogenes and L. ivanovii are well known human and ruminant pathogens. The aim of the present study was to reveal the prevalence and genetic diversity of L. monocytogenes and other Listeria spp. and to identify the factors related to the abundance of pathogen at cattle farms. A total of 521 animal and environmental samples from 27 meat and dairy cattle farms were investigated and the genetic diversity of L. monocytogenes isolates was studied with WGS. The prevalence of Listeria was 58.9%, while of L. monocytogenes it was −11%. The highest prevalence of L. monocytogenes was found in the environment—soil samples near to manure storage (93%), mixed feed from the feeding trough and hay (29%), water samples from farms drinking trough (28%) and cattle feces (28%). Clonal complexes (CC) of CC37 (30%), CC11 (20%) and CC18 (17%) (all IIa serogroup) were predominant L. monocytogenes clones. CC18, CC37 and CC8 were isolated from case farms and CC37, CC11 and CC18 from farms without listeriosis history. Only one hypervirulent CC4 (1%) was isolated from the case farm. Sequence types (STs) were not associated with the isolation source, except for ST7, which was significantly associated with soil (p < 0.05). The contamination of soil, feeding tables and troughs with L. monocytogenes was associated with an increased prevalence of L. monocytogenes at farms. Our study indicates the importance of hygienic practice in the prevention of the dissemination of L. monocytogenes in the cattle farm environment.

A Systematic Review of Listeria Species and Listeria monocytogenes Prevalence, Persistence, and Diversity throughout the Fresh Produce Supply Chain

Listeria monocytogenes is an increasing food safety concern throughout the produce supply chain as it has been linked to produce associated outbreaks and recalls. To our knowledge, this is the first systematic literature review to investigate Listeria species and L. monocytogenes prevalence, persistence, and diversity at each stage along the supply chain. This review identified 64 articles of 4863 candidate articles obtained from four Boolean search queries in six databases. Included studies examined naturally detected/isolated Listeria species and L. monocytogenes in fresh produce-related environments, and/or from past fresh produce associated outbreaks or from produce directly. Listeria species and L. monocytogenes were detected in each stage of the fresh produce supply chain. The greatest prevalence of Listeria species was observed in natural environments and outdoor production, with prevalence generally decreasing with each progression of the supply chain (e.g., packinghouse to distribution to retail). L. monocytogenes prevalence ranged from 61.1% to not detected (0.00%) across the entire supply chain for included studies. Listeria persistence and diversity were also investigated more in natural, production, and processing environments, compared to other supply chain environments (e.g., retail). Data gaps were identified for future produce safety research, for example, in the transportation and distribution center environment.

Large Nationwide Outbreak of Invasive Listeriosis Associated with Blood Sausage, Germany, 2018-2019

Invasive listeriosis is a severe foodborne infection in humans and is difficult to control. Listeriosis incidence is increasing worldwide, but some countries have implemented molecular surveillance programs to improve recognition and management of listeriosis outbreaks. In Germany, routine whole-genome sequencing, core genome multilocus sequence typing, and single nucleotide polymorphism calling are used for subtyping of Listeria monocytogenes isolates from listeriosis cases and suspected foods. During 2018–2019, an unusually large cluster of L. monocytogenes isolates was identified, including 134 highly clonal, benzalkonium-resistant sequence type 6 isolates collected from 112 notified listeriosis cases. The outbreak was one of the largest reported in Europe during the past 25 years. Epidemiologic investigations identified blood sausage contaminated with L. monocytogenes highly related to clinical isolates; withdrawal of the product from the market ended the outbreak. We describe how epidemiologic investigations and complementary molecular typing of food isolates helped identify the outbreak vehicle.

Environmental dissemination of pathogenic Listeria monocytogenes in flowing surface waters in Switzerland

Listeria monocytogenes is an opportunistic pathogen that is widely distributed in the environment. The aquatic environment may represent a potential source for the transmission of L. monocytogenes to animals and the food chain. The present study assessed the occurrence of L. monocytogenes in 191 surface water samples from rivers, streams and inland canals throughout Switzerland. Twenty-five (13%) of the surface water samples contained L. monocytogenes. Whole genome sequence (WGS) data were used to characterize the 25 isolates. The isolates belonged to major lineages I and II, with the majority assigned to either serotype 1/2a (48%), or 4b (44%). The predominant CCs identified were the hypervirulent serotype 4b clones CC1 and CC4, and the serotype CC412; all three have been implicated in listeriosis outbreaks and sporadic cases of human and animal infection worldwide. Two (8%) of the isolates belonged to CC6 which is an emerging hypervirulent clone. All isolates contained intact genes associated with invasion and infection, including inlA/B and prfA. The four CC4 isolates all harbored Listeria pathogenicity island 4 (LIPI-4), which confers hypervirulence. The occurrence of L. monocytogenes in river ecosystems may contribute to the dissemination and introduction of clinically highly relevant strains to the food chain.

Molecular Typing of Listeria monocytogenes IVb Serogroup Isolated from Food and Food Production Environments in Poland

Listeria monocytogenes is one of the most important foodborne pathogens that may be present in food and in food processing environments. In the present study, 91 L. monocytogenes isolates of serogroup IVb from raw meat, ready-to-eat food and food production environments in Poland were characterized by whole genome sequencing (WGS). The strains were also compared, using core genome multi-locus sequence typing (cgMLST) analysis, with 186 genomes of L. monocytogenes recovered worldwide from food, environments, and from humans with listeriosis. The L. monocytogenes examined belonged to three MLST clonal complexes: CC1 (10; 11.0% isolates), CC2 (70; 76.9%), and CC6 (11; 12.1%). CC1 comprised of two STs (ST1 and ST515) which could be divided into five cgMLST, CC2 covered two STs (ST2 and ST145) with a total of 20 cgMLST types, whereas CC6 consisted of only one ST (ST6) classified as one cgMLST. WGS sequences of the tested strains revealed that they had several pathogenic markers making them potentially hazardous for public health. Molecular comparison of L. monocytogenes strains tested in the present study with those isolated from food and human listeriosis showed a relationship between the isolates from Poland, but not from other countries.

Population structure-guided profiling of antibiotic resistance patterns in clinical Listeria monocytogenes isolates from Germany identifies pbpB3 alleles associated with low levels of cephalosporin resistance

Numbers of listeriosis illnesses have been increasing in Germany and the European Union during the last decade. In addition, reports on the occurrence of antibiotic resistance in Listeria monocytogenes in clinical and environmental isolates are accumulating. The susceptibility towards 14 antibiotics was tested in a selection of clinical L. monocytogenes isolates to get a more precise picture of the development and manifestation of antibiotic resistance in the L. monocytogenes population. Based on the population structure determined by core genome multi locus sequence typing (cgMLST) 544 out of 1220 sequenced strains collected in Germany between 2009 and 2019 were selected to cover the phylogenetic diversity observed in the clinical L. monocytogenes population. All isolates tested were susceptible towards ampicillin, penicillin and co-trimoxazole – the most relevant antibiotics in the treatment of listeriosis. Resistance to daptomycin and ciprofloxacin was observed in 493 (91%) and in 71 (13%) of 544 isolates, respectively. While all tested strains showed resistance towards ceftriaxone, their resistance levels varied widely between 4 mg/L and >128 mg/L. An allelic variation of the penicillin binding protein gene pbpB3 was identified as the cause of this difference in ceftriaxone resistance levels. This study is the first population structure-guided analysis of antimicrobial resistance in recent clinical isolates and confirms the importance of penicillin binding protein B3 (PBP B3) for the high level of intrinsic cephalosporin resistance of L. monocytogenes on a population-wide scale.

Prevalence and Genetic Diversity of Listeria monocytogenes Isolated From Retail Pork in Wuhan, China

Listeria monocytogenes is a ubiquitous bacteria and causative agent of zoonotic listeriosis with high mortality. The consumption of contaminated animal-derived foods has been linked with both epidemic and sporadic listeriosis. In this work, a total of 64 L. monocytogenes isolates from 259 pork samples sold in 11 supermarket chains were identified and characterized by comparative whole-genome analysis. All isolates were delineated into eight clonal complexes (CCs), namely CC2, CC8, CC9, CC11, CC155, CC121, CC204, and CC619, spanning two lineages (I and II) and carrying 3–5 antibiotic-resistant genes (fosX, lnu, mprF, tetM, and dhfR). It is noted that Listeria pathogenicity island (LIPI)-1, LIPI-3, and LIPI-4 were distributed in all ST619 isolates from two supermarket chains that were closely related with clinical isolates (<40 SNP). Some of the isolates from different supermarket chains with 0 SNP difference indicated a common pork supply source. Notably, 57.81% of the strains carried types IB, IIA, or IIIB CRISPR-Cas system, CC121 isolates carried both types IB and IIA CRISPR-Cas systems, Cas proteins of CC155 isolates located between two CRISPR loci, each CC has unique organization of Cas proteins as well as CRISPR loci. CRISPR-Cas system-based subtyping improved discrimination of pork-derived L. monocytogenes isolates. Comparisons at the genome level contributed to understand the genetic diversities and variations among the isolates and provided insights into the genetic makeup and relatedness of these pathogens.

Whole Genome Sequence Analysis of Phage-Resistant Listeria monocytogenes Serotype 1/2a Strains from Turkey Processing Plants

Listeria monocytogenes is a Gram-positive bacterial pathogen and the causative agent of listeriosis, a severe foodborne infection. L. monocytogenes is notorious for its ability to persist in food processing environments (FPEs) via a variety of adaptive traits. Even though traits such as cold tolerance, biofilm formation and sanitizer resistance have been extensively investigated for their roles in persistence of L. monocytogenes in FPEs, much less is known about resistance to bacteriophages. Previous studies explored phage resistance mechanisms in laboratory-created mutants but it is imperative to investigate phage resistance that is naturally exhibited in FPE-derived strains. Here, we integrated the analysis of whole genome sequence data from a panel of serotype 1/2a strains of sequence types 321 and 391 from turkey processing plants, with the determination of cell surface substituents required for phage adsorption and phage infection assays with the four wide-host-range phages A511, P100, 20422-1 and 805405-1. Using a specific set of recombinant phage protein probes, we discovered that phage-resistant strains lacked one or both of the serogroup 1/2-specific wall teichoic acid carbohydrate decorations, N-acetylglucosamine and rhamnose. Furthermore, these phage-resistant strains harbored substitutions in lmo1080, lmo1081, and lmo2550, which mediate carbohydrate decoration of the wall teichoic acids.

Making Sense of the Biodiversity and Virulence of Listeria monocytogenes

Listeria monocytogenes is a foodborne pathogen responsible for listeriosis, an infection that can manifest in humans as bacteremia, meningoencephalitis in immunocompromised patients and the elderly, and fetal-placental infection in pregnant women. Reference strains from this facultative intracellular bacterium have been instrumental in the investigation of basic mechanisms in microbiology, immunology, and cell biology. The integration of bacterial population genomics with environmental, epidemiological, and clinical data allowed the uncovering of new factors involved in the virulence of L. monocytogenes and its adaptation to different environments. This review illustrates how these investigations have led to a better understanding of the bacterium's virulence and the driving forces that shaped it.

Serotype Assignment by Sero-agglutination, ELISA, and PCR

For assessing isolates of Listeria monocytogenes, serotype designation is the first subtyping method used. Methodologies used to assign serotype are currently evolving and will eventually be replaced with whole genome sequencing. Traditionally, serotyping has been done with agglutination reactions; however, alternative methods utilizing enzyme linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are common. Described here are the three non-genomic methods and the advantages and disadvantages of each.

An Open-Source Program (Haplo-ST) for Whole-Genome Sequence Typing Shows Extensive Diversity among Listeria monocytogenes Isolates in Outdoor Environments and Poultry Processing Plants

A reliable and standardized classification of Listeria monocytogenes is important for accurate strain identification during outbreak investigations. Current whole-genome sequencing (WGS)-based approaches for strain characterization are either difficult to standardize, rendering them less suitable for data exchange, or are not freely available. Thus, we developed a portable and open-source tool, Haplo-ST, to improve standardization and provide maximum discriminatory potential to WGS data tied to a multilocus sequence typing (MLST) framework. Haplo-ST performs whole-genome MLST (wgMLST) for L. monocytogenes while allowing for data exchangeability worldwide. This tool takes in (i) raw WGS reads as input, (ii) cleans the raw data according to user-specified parameters, (iii) assembles genes across loci by mapping to genes from reference strains, and (iv) assigns allelic profiles to assembled genes and provides a wgMLST subtyping for each isolate. Data exchangeability relies on the tool assigning allelic profiles based on a centralized nomenclature defined by the widely used BIGSdb-Lm database. Tests of Haplo-ST's performance with simulated reads from L. monocytogenes reference strains demonstrated high sensitivity (97.5%), and coverage depths of ≥20× were found to be sufficient for wgMLST profiling. We then used Haplo-ST to characterize and differentiate between two groups of L. monocytogenes isolates derived from the natural environment and poultry processing plants. Phylogenetic reconstruction identified lineages within each group, and no lineage specificity was observed with isolate phenotypes (transient versus persistent) or origins. Genetic differentiation analyses between isolate groups identified 21 significantly differentiated loci, potentially enriched for adaptation and persistence of L. monocytogenes within poultry processing plants.IMPORTANCE We have developed an open-source tool (https://github.com/swarnalilouha/Haplo-ST) that provides allele-based subtyping of L. monocytogenes isolates at the whole-genome level. Along with allelic profiles, this tool also generates allele sequences and identifies paralogs, which is useful for phylogenetic tree reconstruction and deciphering relationships between closely related isolates. More broadly, Haplo-ST is flexible and can be adapted to characterize the genome of any haploid organism simply by installing an organism-specific gene database. Haplo-ST also allows for scalable subtyping of isolates; fewer reference genes can be used for low-resolution typing, whereas higher resolution can be achieved by increasing the number of genes used in the analysis. Our tool enabled clustering of L. monocytogenes isolates into lineages and detection of potential loci for adaptation and persistence in food processing environments. Findings from these analyses highlight the effectiveness of Haplo-ST in subtyping and evaluating relationships among isolates in studies of bacterial population genetics.

Lineage-specific evolution and gene flow in Listeria monocytogenes are independent of bacteriophages

Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracking of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage-specific characteristics call for a more detailed understanding of evolution. In our work, we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage-mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages, we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.

Comparison of three neutralizing broths for environmental sampling of low levels of Listeria monocytogenes desiccated on stainless steel surfaces and exposed to quaternary ammonium compounds

Background

An effective environmental sampling method involves the use of a transport/neutralizing broth with the ability to neutralize sanitizer residues that are collected during sampling and to maintain viability of stressed Listeria monocytogenes (Lm) cells.

Results

We applied Lm onto stainless steel surfaces and then subjected Lm to desiccation stress for 16–18 h at room temperature (RT, 21–24 °C). This was followed by the subsequent application of Whisper™ V, a quaternary ammonium compound (QAC)-based sanitizer, diluted to 400 ppm and 8000 ppm of active quat, for 6 h. We then sampled Lm with sponges pre-moistened in three transport broths, Dey/Engley (D/E) broth, Letheen broth and HiCap™ broth, to generate environmental samples that contained sanitizer residues and low levels of stressed Lm, which were subsequently analyzed by an enrichment-based method. This scheme conformed with validation guidelines of AOAC International by using 20 environmental test portions per broth that contained low levels of Lm such that not all test portions were positive (i.e., fractional positive). We showed that D/E broth, Letheen broth and HiCap™ broth performed similarly when no quat or 400 ppm of quat was applied to the Lm contaminating stainless steel surfaces. However, when 8000 ppm of quat was applied, Letheen broth did not effectively neutralize the QAC in the samples. These comparisons were performed on samples stored under three conditions after collection to replicate scenarios of sample transport, RT for 2 h, 4 °C for 24 h and 4 °C for 72 h. Comparisons under the three different scenarios generally reached the same conclusions. In addition, we further demonstrated that storing Letheen and HiCap™ broths at RT for two months before sampling did not reduce their capacity to neutralize sanitizers.

Conclusions

We developed a scheme to evaluate the ability of transport broths to neutralize QAC sanitizers. The three transport broths performed similarly with a commonly used concentration of quat, but Letheen broth could not effectively neutralize a very high concentration of QAC. The performance of transport broths was not significantly affected under the assessed pre-sampling and post-sampling storage conditions.

Characterization of Mobile Genetic Elements Using Long-Read Sequencing for Tracking Listeria monocytogenes from Food Processing Environments

Recently developed nanopore sequencing technologies offer a unique opportunity to rapidly close the genome and to identify complete sequences of mobile genetic elements (MGEs). In this study, 17 isolates of Listeria monocytogenes (Lm) epidemic clone II (ECII) from seven ready-to-eat meat or poultry processing facilities, not known to be associated with outbreaks, were shotgun sequenced, and among them, five isolates were further subjected to long-read sequencing. Additionally, 26 genomes of Lm ECII isolates associated with three listeriosis outbreaks in the U.S. and South Africa were obtained from the National Center for Biotechnology Information (NCBI) database and analyzed to evaluate if MGEs may be used as a high-resolution genetic marker for identifying and sourcing the origin of Lm. The analyses identified four comK prophages in 11 non-outbreak isolates from four facilities and three comK prophages in 20 isolates associated with two outbreaks that occurred in the U.S. In addition, three different plasmids were identified among 10 non-outbreak isolates and 14 outbreak isolates. Each comK prophage and plasmid was conserved among the isolates sharing it. Different prophages from different facilities or outbreaks had significant genetic variations, possibly due to horizontal gene transfer. Phylogenetic analysis showed that isolates from the same facility or the same outbreak always closely clustered. The time of most recent common ancestor of the Lm ECII isolates was estimated to be in March 1816 with the average nucleotide substitution rate of 3.1 × 10⁻⁷ substitutions per site per year. This study showed that complete MGE sequences provide a good signal to determine the genetic relatedness of Lm isolates, to identify persistence or repeated contamination that occurred within food processing environment, and to study the evolutionary history among closely related isolates.