Tracking of Listeria monocytogenes in meat establishment using Whole Genome Sequencing as a food safety management tool: A proof of concept

Gram-negative postpasteurization contamination patterns of single-serve fluid milk produced in 4 different processing facilities

An analysis of historic data on high temperature, short time (HTST) fluid milk quality showed higher total bacterial counts and lower sensory defect judging scores at d 14 postprocessing for milk packaged in single-serve containers as compared with milk packaged in half-gallon containers from the same processing facilities. As postpasteurization contamination with gram-negative bacteria is likely a major contributor to an increased spoilage risk associated with milk packaged in single-serve containers, we performed a comprehensive assessment of the microbial quality and shelf life of 265 commingled single-serve HTST fluid milk samples (including white [unflavored] skim, white [unflavored] 1%, chocolate skim, and chocolate 1%) collected over 2 visits to 4 commercial fluid milk processing facilities. Over 2 initial sampling visits, the frequency of gram-negative spoilage ranged from 14 to 79% of the product collected from the 4 facilities, with significant differences of gram-negative spoilage frequency between sampling visits, facilities (sampling visit 1, sampling visit 2, and both sampling visits combined), milk types (sampling visit 2), and filler lanes (sampling visit 2). We found no significant differences in the frequency of gram-negative spoilage between sampling time points (e.g., beginning, middle, and end of production run). Across facilities, single-serve containers of milk with gram-negative contamination showed significantly higher bacterial counts on d 7 and 14 and significantly lower sensory scores as compared with those without gram-negative contamination. Follow-up investigations, based on in-facility surveys that identified carton forming mandrels as filler components that frequently failed quality assurance ATP swab checks, found that bacterial genera, including Pseudomonas and Bacillus, isolated from single-serve milk samples were also frequently isolated from mandrels. Although interventions aimed at improving cleaning and sanitation of mandrels did not lead to significant reduction of gram-negative spoilage frequency in a comparison of 398 control and 400 intervention samples, our data still suggest that the unhygienic design of single-serve fillers is likely a root cause of gram-negative contamination of single-serve milk.

Persistence of microbiological hazards in food and feed production and processing environments

Listeria monocytogenes (in the meat, fish and seafood, dairy and fruit and vegetable sectors), Salmonella enterica (in the feed, meat, egg and low moisture food sectors) and Cronobacter sakazakii (in the low moisture food sector) were identified as the bacterial food safety hazards most relevant to public health that are associated with persistence in the food and feed processing environment (FFPE). There is a wide range of subtypes of these hazards involved in persistence in the FFPE. While some specific subtypes are more commonly reported as persistent, it is currently not possible to identify universal markers (i.e. genetic determinants) for this trait. Common risk factors for persistence in the FFPE are inadequate zoning and hygiene barriers; lack of hygienic design of equipment and machines; and inadequate cleaning and disinfection. A well-designed environmental sampling and testing programme is the most effective strategy to identify contamination sources and detect potentially persistent hazards. The establishment of hygienic barriers and measures within the food safety management system, during implementation of hazard analysis and critical control points, is key to prevent and/or control bacterial persistence in the FFPE. Once persistence is suspected in a plant, a 'seek-and-destroy' approach is frequently recommended, including intensified monitoring, the introduction of control measures and the continuation of the intensified monitoring. Successful actions triggered by persistence of L. monocytogenes are described, as well as interventions with direct bactericidal activity. These interventions could be efficient if properly validated, correctly applied and verified under industrial conditions. Perspectives are provided for performing a risk assessment for relevant combinations of hazard and food sector to assess the relative public health risk that can be associated with persistence, based on bottom-up and top-down approaches. Knowledge gaps related to bacterial food safety hazards associated with persistence in the FFPE and priorities for future research are provided.

Identification by High-Throughput Real-Time PCR of 30 Major Circulating Listeria monocytogenes Clonal Complexes in Europe

Listeria monocytogenes is a ubiquitous bacterium that causes a foodborne illness, listeriosis. Most strains can be classified into major clonal complexes (CCs) that account for the majority of outbreaks and sporadic cases in Europe. In addition to the 20 CCs known to account for the majority of human and animal clinical cases, 10 CCs are frequently reported in food production, thereby posing a serious challenge for the agrifood industry. Therefore, there is a need for a rapid and reliable method to identify these 30 major CCs. The high-throughput real-time PCR assay presented here provides accurate identification of these 30 CCs and eight genetic subdivisions within four CCs, splitting each CC into two distinct subpopulations, along with the molecular serogroup of a strain. Based on the BioMark high-throughput real-time PCR system, our assay analyzes 46 strains against 40 real-time PCR arrays in a single experiment. This European study (i) designed the assay from a broad panel of 3,342 L. monocytogenes genomes, (ii) tested its sensitivity and specificity on 597 sequenced strains collected from 24 European countries, and (iii) evaluated its performance in the typing of 526 strains collected during surveillance activities. The assay was then optimized for conventional multiplex real-time PCR for easy implementation in food laboratories. It has already been used for outbreak investigations. It represents a key tool for assisting food laboratories to establish strain relatedness with human clinical strains during outbreak investigations and for helping food business operators by improving their microbiological management plans. IMPORTANCE Multilocus sequence typing (MLST) is the reference method for Listeria monocytogenes typing but is expensive and takes time to perform, from 3 to 5 days for laboratories that outsource sequencing. Thirty major MLST clonal complexes (CCs) are circulating in the food chain and are currently identifiable only by sequencing. Therefore, there is a need for a rapid and reliable method to identify these CCs. The method presented here enables the rapid identification, by real-time PCR, of 30 CCs and eight genetic subdivisions within four CCs, splitting each CC into two distinct subpopulations. The assay was then optimized on different conventional multiplex real-time PCR systems for easy implementation in food laboratories. The two assays will be used for frontline identification of L. monocytogenes isolates prior to whole-genome sequencing. Such assays are of great interest for all food industry stakeholders and public agencies for tracking L. monocytogenes food contamination.

Possible sources of Listeria monocytogenes contamination of fresh-cut apples and antimicrobial interventions during antibrowning treatments: a review

Fresh-cut apples, being rich in antioxidants and other nutrients, have emerged as popular snacks in restaurants, at home and in school lunch programs, partially due to freshness, convenience, and portion size availability. Two major challenges in processing fresh-cut apples are browning of cut surfaces and contamination with human pathogens. Regarding human pathogens, contamination by Listeria monocytogenes is a major concern, as evidenced by two recent outbreaks of whole apples and numerous recalls of fresh-cut apples. Antibrowning agents currently used by the industry have little to no antimicrobial properties. The present review discusses possible origins of L. monocytogenes in fresh-cut apples, including contaminated whole apples, and contamination via the processing environment and the equipment in fresh-cut facilities. Treatment with antibrowning solutions could be an opportunity for Listeria contamination and represents the last chance to inactivate pathogens. The discussion is focused on the antibrowning treatments where formulations and coatings with antibrowning and antimicrobial properties have been developed and evaluated against Listeria and other microorganisms. In addition, several research needs and considerations are discussed to further reduce the chance of pathogen contamination on fresh-cut apples.

Slight Temperature Deviation during a 56-Day Storage Period Does Not Affect the Microbiota of Fresh Vacuum-Packed Pork Loins

It is profitable to export fresh meat overseas, where it is often regarded as a premium commodity. Meeting this demand for fresh meat, however, necessitates long export times, during which uncontrolled temperature increases can affect the microbiological quality of the meat and thereby, reduce shelf life or compromise food safety. To study the impact of temperature deviations on microbial community composition and diversity, we used 16S rRNA gene sequencing for Listeria monocytogenes and Salmonella spp. detection to describe the surface microbiota of eight batches of vacuum-packed loins stored at -1.5 °C (control) for 56 days and subjected to a 2 °C or 10 °C temperature deviation for a few hours (mimicking problems regularly encountered in the industry) at day 15 or 29. The presence of pathogens was negligible. The applied temperature deviations were not associated with different microbiota. Sequencing analysis showed the presence of Yersinia, an unexpected pathogen, and relative abundance increased in the groups subjected to temperature deviations. Over time, Lactobacillales_unclassified genus became the main constituent of the microbiota of vacuum-packed pork loins. Although the microbiota of the eight batches appeared similar at the beginning of storage, differences were revealed after 56 days, suggesting unequal aging of the microbiota.

An Overview of the Public Health Challenges in Diagnosing and Controlling Human Foodborne Pathogens

Pathogens found in food are believed to be the leading cause of foodborne illnesses; and they are considered a serious problem with global ramifications. During the last few decades, a lot of attention has been paid to determining the microorganisms that cause foodborne illnesses and developing new methods to identify them. Foodborne pathogen identification technologies have evolved rapidly over the last few decades, with the newer technologies focusing on immunoassays, genome-wide approaches, biosensors, and mass spectrometry as the primary methods of identification. Bacteriophages (phages), probiotics and prebiotics were known to have the ability to combat bacterial diseases since the turn of the 20th century. A primary focus of phage use was the development of medical therapies; however, its use quickly expanded to other applications in biotechnology and industry. A similar argument can be made with regards to the food safety industry, as diseases directly endanger the health of customers. Recently, a lot of attention has been paid to bacteriophages, probiotics and prebiotics most likely due to the exhaustion of traditional antibiotics. Reviewing a variety of current quick identification techniques is the purpose of this study. Using these techniques, we are able to quickly identify foodborne pathogenic bacteria, which forms the basis for future research advances. A review of recent studies on the use of phages, probiotics and prebiotics as a means of combating significant foodborne diseases is also presented. Furthermore, we discussed the advantages of using phages as well as the challenges they face, especially given their prevalent application in food safety.

Molecular typing and genome sequencing allow the identification of persistent Listeria monocytogenes strains and the tracking of the contamination source in food environments

The presence of Listeria monocytogenes (Lm) in the food processing environment (facilities and products) is a challenging problem in food safety management. Lm is one of the main causes of mortality in foodborne infections, and the trend is continuously increasing. In this study, a collection of 323 Lm strain isolates recovered from food matrices and food industry environments (surfaces and equipment) over four years from 80 food processing facilities was screened using a restriction site-associated tag sequencing (2b-RAD) typing approach developed for Lm. Thirty-six different restriction site-associated DNA (RAD) types (RTs) were identified, most of which correspond to lineage II. RT1, the most represented genotype in our collection and already reported as one of the most prevalent genotypes in the food environment, was significantly associated with meat processing facilities. The sequencing of the genomes of strains belonging to the same RT and isolated in the same facility in different years revealed several clusters of persistence. The definition of the persistent strains (PSs) allowed the identification of the potential source of contamination in the incoming raw meat that is introduced in the facility to be processed. The slaughterhouses, which, according to the European Union (EU) regulation, are not inspected for the presence of Lm could be hotspots for the persistence of Lm PSs.

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.

Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.

Use of an Ecosystem-Based Approach to Shed Light on the Heterogeneity of the Contamination Pattern of Listeria monocytogenes on Conveyor Belt Surfaces in a Swine Slaughterhouse in the Province of Quebec, Canada

The role of the accompanying microbiota in the presence of Listeria monocytogenes on meat processing surfaces is not yet understood, especially in industrial production conditions. In this study, 300 conveyor belt samples from the cutting room of a swine slaughterhouse were collected during production. The samples were subjected to the detection of L. monocytogenes. Recovered strains were characterized by serogrouping-PCR, InlA Sanger sequencing and for their ability to form biofilm. A selection of isolates was compared with core genome multi-locus sequence typing analysis (cgMLST). The sequencing of the V4 region of the 16S RNA gene of the microorganisms harvested from each sample was carried out in parallel using the Illumina MiSeq platform. Diversity analyses were performed and MaAsLin analysis was used to assess the link between L. monocytogenes detection and the surrounding bacteria. The 72 isolates collected showed a low genetic diversity and important persistence characteristics. L. monocytogenes isolates were not stochastically distributed on the surfaces: the isolates were detected on three out of six production lines, each associated with a specific meat cut: the half carcasses, the bostons and the picnics. MaAsLin biomarker analysis identified the taxa Veillonella (p ≤ 0.0397) as a bacterial determinant of the presence of L. monocytogenes on processing surfaces. The results of this study revealed a heterogenous contamination pattern of the processing surfaces by L. monocytogenes and targeted a bacterial indicator of the presence of the pathogen. These results could lead to a better risk assessment of the contamination of meat products.

Listeria environmental sampling tests are compatible with polymorphic locus sequence typing

Food processors invest significant resources into environmental sampling to detect contamination with potential pathogens, particularly Listeria monocytogenes. To facilitate these efforts, multiple environmental sampling tests (ESTs) have been developed and commercialized that minimize workload, turnaround time, and cost while providing convenient colorimetric detection. For presumptive-positive ESTs, we hypothesized that a relatively minor additional investment could provide, in addition to species confirmation, valuable strain typing data for tracking pathogen spread through a facility, identifying harborage sites, and distinguishing sporadic from persistent or resident contaminants. This hypothesis is based on the demonstrated compatibility of polymorphic locus sequence typing (PLST) with crude samples including food enrichments. Five Listeria ESTs were tested here: broth-based InSite (Hygiena), Path-Chek (Mericon), and Pathfinder (Hardy Diagnositics); and gel-based Petrifilm (3M) and HardyChrom (Hardy Diagnostics). ESTs were inoculated with strains representing two common L. monocytogenes serotypes and nonpathogenic Listeria innocua. Following incubation, broths or suspended colonies were heat treated to inactivate bacteria. Lysates or purified DNAs were prepared and used as templates in PCRs targeting the previously described PLST loci LmiMT1 and LisMT2. Single clear products were obtained from all inoculated ESTs; uninoculated controls were negative. PCR products were subjected to Sanger sequencing, yielding high-quality chromatograms. Phylogenetic analysis confirmed identities to previously determined sequences and revealed relatedness to serotype-matched strains represented in GenBank databases. PRACTICAL APPLICATION: Multiple environmental sampling tests have been commercialized in recent years to facilitate the proactive detection of pathogens, particularly Listeria monocytogenes, within food processing facilities. Coupling a positive detection test with strain typing would enhance its value by providing data that can be used to track pathogen spread through a facility, identify harborage sites, and distinguish sporadic from resident contamination.

Genetic Listeria monocytogenes Types in the Pork Processing Plant Environment: From Occasional Introduction to Plausible Persistence in Harborage Sites

The purpose of this study was to investigate the L. monocytogenes occurrence and genetic diversity in three Belgian pork cutting plants. We specifically aim to identify harborage sites and niche locations where this pathogen might occur. A total of 868 samples were taken from a large diversity of food and non-food contact surfaces after cleaning and disinfection (C&D) and during processing. A total of 13% (110/868) of environmental samples tested positive for L. monocytogenes. When looking in more detail, zone 3 non-food contact surfaces were contaminated more often (26%; 72/278) at typical harborage sites, such as floors, drains, and cleaning materials. Food contact surfaces (zone 1) were less frequently contaminated (6%; 25/436), also after C&D. PFGE analysis exhibited low genetic heterogeneity, revealing 11 assigned clonal complexes (CC), four of which (CC8, CC9, CC31, and CC121) were predominant and widespread. Our data suggest (i) the occasional introduction and repeated contamination and/or (ii) the establishment of some persistent meat-adapted clones in all cutting plants. Further, we highlight the importance of well-designed extensive sampling programs combined with genetic characterization to help these facilities take corrective actions to prevent transfer of this pathogen from the environment to the meat.

Perspective on Clinically-Relevant Antimicrobial Resistant Enterobacterales in Food: Closing the Gaps Using Genomics

Antimicrobial resistance is one of the most important public health concerns—it causes 700,000 deaths annually according to the World Health Organization (WHO). Enterobacterales such as E. coli and Klebsiella pneumoniae, have become resistant to many relevant antimicrobials including carbapenems and extended spectrum cephalosporins. These clinically relevant resistant Enterobacterales (CRRE) members are now globally distributed in the environment including different food types (meats, produce, dairy). Unlike known foodborne pathogens, CRRE are not usually part of most food surveillance systems. However, numerous reports of CRRE highlight the importance of these bacteria in food and have been shown to contribute to the overall crisis of antimicrobial resistance. This is especially important in the context of carriage of these pathogens by immuno-compromised individuals. CRRE infections upon consumption of contaminated food could colonize the human gastrointestinal tract and eventually be a source of systemic infections such as urinary tract infections or septicemia. While different aspects need to be considered to elucidate this, whole genome sequencing along with metadata could be used to understand genomic relationships of CRRE obtained from foods and humans, including isolates from clinical infections. Once robust scientific data is available on the role of CRRE in food, countries could move forward to better survey and control CRRE in food.

Identification of Listeria monocytogenes Contamination in a Ready-to-Eat Meat Processing Plant in China

Listeria monocytogenes is the etiologic agent of listeriosis, which remains a significant public health concern in many countries due to its high case-fatality rate. The constant risk of L. monocytogenes transmission to consumers remains a central challenge in the food production industry. At present, there is very little known about L. monocytogenes contamination in ready-to-eat (RTE) processing plants in China. In this study, L. monocytogenes in an RTE meat processing plant in Shanghai municipality was characterized using pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). Furthermore, the biofilm formation ability of the pathogen was also tested. Results revealed that L. monocytogenes isolates were present in 12 samples out of the 48 samples investigated. Most of them (66.7%, 8/12) were identified from the processing facilities irrespective of observed hygiene levels of aerobic plate count (APC) and coliforms. Coliforms were present in only one processing area. ST5 (1/2b) isolates were predominant (83.3%, 10/12) and were identified in two dominant pulsotypes (PTs) (three in PT3 and seven in PT4, respectively). Results of the core-genome multi-locus sequence typing (cgMLST) showed that ST5 in three PTs (PT1, PT3, and PT4) had 0-8 alleles, which confirmed that clonal transmission occurred in the RTE meat processing facilities. In addition, the biofilm formation test confirmed that the isolates from the processing facilities could form biofilms, which helped them colonize and facilitate persistence in the environment. These results indicated that common sanitation procedures regularly applied in the processing environment were efficient but not sufficient to remove L. monocytogenes isolates, especially biofilm of L. monocytogenes. Furthermore, the ST5 isolates in this study exhibited 12 alleles with one ST5 clinical isolate, which contributes to the understanding of the potential pathogenic risk that L. monocytogenes in RTE meat processing equipment posed to consumers. Therefore, strong hygienic measures, especially sanitation procedures for biofilms eradication, should be implemented to ensure the safety of raw materials. Meanwhile, continuous surveillance might be vital for the prevention and control of listeriosis caused by L. monocytogenes.

Study of the transfer of Listeria monocytogenes during the slaughter of cattle using molecular typing

The introduction, transmission, and persistence of Listeria monocytogenes in Belgian beef slaughterhouses was investigated using genetic characterization. During slaughter, samples were taken of the hide, carcass, and environment to detect the pathogen. Remarkably, L. monocytogenes was massively present on the hide of incoming animals (93%; 112/120), regardless of their visual cleanliness, which implies high contamination pressure levels entering the slaughterhouses. Pathogen transfer via cross-contamination was conclusively confirmed in this study, with the same pulsotypes isolated from the hide, carcass, and environmental samples. Despite the important bacterial presence on the hide of incoming animals, most slaughterhouses succeeded in limiting the transfer as cause of carcass contamination. Persistence along the slaughter line seemed to be a more significant problem, as it was clearly linked to most of the L. monocytogenes positive carcasses. In one slaughterhouse, whole genome sequencing (WGS) revealed that the carcass splitter had been contaminating carcasses with the same strain belonging to CC9 for more than one year.

Unraveling the emergence and population diversity of Listeria monocytogenes in a newly built meat facility through whole genome sequencing

The food processing environments of a newly opened meat processing facility were sampled in ten visits carried out during its first 1.5 years of activity and analyzed for the presence of Listeria monocytogenes. A total of 18 L. monocytogenes isolates were obtained from 229 samples, and their genomes were sequenced to perform comparative genomic analyses. An increase in the frequency of isolation of L. monocytogenes and in the diversity of sequence types (STs) detected was observed along time. Although the strains isolated belonged to six different STs (ST8, ST9, ST14, ST37, ST121 and ST155), ST9 was the most abundant (8 out of 18 strains). Low (0 and 2) single nucleotide polymorphism (SNP) distances were found between two pairs of ST9 strains isolated in both cases 3 months apart from the same processing room (Lm-1267 and Lm-1705, with a 2 SNPs distance in the core genome; Lm-1265 and Lm-1706, with a 0 SNPs distance), which suggests that these strains may be persistent L. monocytogenes strains in the food processing environment. Most strains showed an in silico attenuated virulence potential either through the truncation of InlA (in 67% of the isolates) or the absence of other virulence factors involved in cell adhesion or invasion. Twelve of the eighteen L. monocytogenes isolates contained a plasmid, which ranged in size from 4 to 87 Kb and harbored stress survival, in addition to heavy metals and biocides resistance determinants. Identical or highly similar plasmids were identified for various sets of L. monocytogenes ST9 isolates, which suggests the clonal expansion and persistence of plasmid-containing ST9 strains in the processing environments of the meat facility. Finally, the analysis of the L. monocytogenes genomes available in the NCBI database, and their associated metadata, evidenced that strains from ST9 are more frequently reported in Europe, linked to foods, particularly to meat and pork products, and less represented among clinical isolates than other L. monocytogenes STs. It also showed that the ST9 strains here isolated were more closely related to the European isolates, which clustered together and separated from ST9 North American isolates.

Listeria monocytogenes in Cooked Chicken: Detection of an Outbreak in the United Kingdom (2016 to 2017) and Analysis of L. monocytogenes from Unrelated Monitoring of Foods (2013 to 2017)

ABSTRACT

In England and Wales, Public Health England applies whole genome sequencing to cultures of Listeria monocytogenes recovered from human cases of listeriosis, foods, and food production environments. Following the routine inspection of a small retailer in February and March 2016, two unopened packs of cooked chicken produced by the same manufacturer were found to be contaminated with L. monocytogenes at levels of 340 and 20 CFU/g. A public recall of this product was issued in March 2016. Early in 2017, a less than five single-nucleotide polymorphism single-linkage cluster was detected between the L. monocytogenes isolates from the two cooked chicken products and cultures from five cases of human listeriosis in England and Scotland with onsets of illness between March 2016 and February 2017. Epidemiological data provided further supportive evidence that this cluster was an outbreak linked to a manufacturer of cooked chicken whose products were supplied to the small retailer that initiated the outbreak investigation. Unrelated to this outbreak, 34 L. monocytogenes isolates recovered from routine food monitoring of 2,007 samples of cooked chicken during 2013 to 2017 were analyzed by whole genome sequencing. Previously undetected fewer than five single-nucleotide polymorphism single-linkage clusters were identified between cultures from cooked chicken and with those from two clusters and two sporadic cases of human listeriosis that were consistent with foodborne transmission. This analysis identified linkage of L. monocytogenes clusters within specific food chains more readily than traditional manual tracing. Linking of data associated with L. monocytogenes cultures from cases of listeriosis with those from unrelated food testing is a unique source of information for communicable disease risk assessment, epidemiological studies, and disease prevention and control. This report provides further evidence that should act as a reminder of the association between cooked chicken consumption and human listeriosis.

HIGHLIGHTS

An outbreak of human listeriosis associated with frozen sweet corn consumption: Investigations in the UK

The use of Whole genome sequencing (WGS) identified a multi-country outbreak of human listeriosis associated with consumption of frozen sweet corn produced in Hungary. The purpose of this report was to summarise information on the cases occurring in the UK which were part of this outbreak and outline investigations on the presence of Listeria monocytogenes in the affected food chain. Prior to the international recall of this product in 2018, 12 UK cases of listeriosis were identified as infected by the outbreak strain between 2015 and 18. Epidemiological and microbiological investigations confirmed these cases as belonging to the outbreak. A further case occurred in 2019 and a contaminated frozen pack from one of the implicated batches of sweet corn was recovered from the patient's domestic freezer. The outbreak strain was also detected in products from a sandwich manufacturer in 2018 which added frozen sweet corn directly to sandwich fillings. The sandwich manufacturer's sweet corn was supplied by a distributor in England which obtained frozen products from the Hungarian manufacturer implicated in the outbreak. Within the distributor's premises, 208 food and environmental samples were taken: L. monocytogenes was detected in 44% of 70 samples of frozen sweet corn and 5% of 79 other foods. The outbreak strain was detected in the frozen sweet corn, in one other frozen food (mixed vegetables) and in the factory environment. The outbreak strain was also recovered from frozen beans on retail sale in the first four months of 2019. Five other L. monocytogenes strains together with two other Listeria species were detected in samples from the importer's premises. One of the L. monocytogenes strains in the importer's factory, which was distinct from the outbreak strain, was also recovered from sweet corn collected from the sandwich manufacturer, sweet corn tested in England in 2013 and 2016 and the blood of two cases of human listeriosis which occurred in England in 2014. This report shows how analysis by WGS provides evidence to understand complex food chains. This report also highlights risks for transmission of human listeriosis from frozen sweet corn and the potential for misuse of this food as a ready-to-eat product.

The sources and transmission routes of microbial populations throughout a meat processing facility

Microbial food spoilage is responsible for a considerable amount of waste and can cause food-borne diseases in humans, particularly in immunocompromised individuals and children. Therefore, preventing microbial food spoilage is a major concern for health authorities, regulators, consumers, and the food industry. However, the contamination of food products is difficult to control because there are several potential sources during production, processing, storage, distribution, and consumption, where microorganisms come in contact with the product. Here, we use high-throughput full-length 16S rRNA gene sequencing to provide insights into bacterial community structure throughout a pork-processing plant. Specifically, we investigated what proportion of bacteria on meat are presumptively not animal-associated and are therefore transferred during cutting via personnel, equipment, machines, or the slaughter environment. We then created a facility-specific transmission map of bacterial flow, which predicted previously unknown sources of bacterial contamination. This allowed us to pinpoint specific taxa to particular environmental sources and provide the facility with essential information for targeted disinfection. For example, Moraxella spp., a prominent meat spoilage organism, which was one of the most abundant amplicon sequence variants (ASVs) detected on the meat, was most likely transferred from the gloves of employees, a railing at the classification step, and the polishing tunnel whips. Our results suggest that high-throughput full-length 16S rRNA gene sequencing has great potential in food monitoring applications.

In-Depth Longitudinal Study of Listeria monocytogenes ST9 Isolates from the Meat Processing Industry: Resolving Diversity and Transmission Patterns Using Whole-Genome Sequencing

Listeria monocytogenes is a deadly foodborne pathogen that is widespread in the environment, and certain types can be established in food factories. The sequence type ST9 dominates in meat processing environments, and this work was undertaken to obtain data needed for the tracking of this subtype. By using whole-genome sequencing (WGS), we revealed the presence of cross-contamination routes between meat factories as well as within a single factory, including the spread from different reservoirs within the same room. It was also possible to estimate the time frame of persistence in the factory, as well as when and how new clones had entered. The present work contributes valuable information about the diversity of ST9 and exemplifies the potential power of WGS in food safety management, allowing the determination of relationships between strains both in an international context and locally between and within factories.

Listeria monocytogenes is a pathogen mostly associated with the consumption of ready-to-eat foods and can cause severe disease and death. It can be introduced into food chains from raw materials, but often the contamination source is the food production environment, where certain clones can persist for years. In the meat chain, ST9 is one of the most commonly encountered L. monocytogenes sequence types, and for effective source tracking, the divergence and spread of ST9 must be understood. In this study, whole-genome sequencing (WGS) was used to characterize and track 252 L. monocytogenes ST9 isolates collected from four Norwegian meat processing plants between 2009 and 2017. The isolates formed distinct clusters relative to genomes found in public databases, and all but three isolates clustered into two major clonal populations. Different contamination patterns were revealed, e.g., evidence of contamination of two factories with a clone that diverged from its ancestor in the late 1990s through a common source of raw materials; breach of hygienic barriers within a factory, leading to repeated detection of two clones in the high-risk zone during a 4- to 6-year period; entry through the purchase and installation of second-hand equipment harboring a previously established clonal population; and spreading and diversification of two clones from two reservoirs within the same production room over a 9-year period. The present work provides data on the diversity of ST9, which is crucial for epidemiological investigations and highlights how WGS can be used for source tracking within food processing factories.

IMPORTANCEListeria monocytogenes is a deadly foodborne pathogen that is widespread in the environment, and certain types can be established in food factories. The sequence type ST9 dominates in meat processing environments, and this work was undertaken to obtain data needed for the tracking of this subtype. By using whole-genome sequencing (WGS), we revealed the presence of cross-contamination routes between meat factories as well as within a single factory, including the spread from different reservoirs within the same room. It was also possible to estimate the time frame of persistence in the factory, as well as when and how new clones had entered. The present work contributes valuable information about the diversity of ST9 and exemplifies the potential power of WGS in food safety management, allowing the determination of relationships between strains both in an international context and locally between and within factories.

Strain variability in biofilm formation: A food safety and quality perspective

The inherent differences in microbial behavior among identically treated strains of the same microbial species, referred to as "strain variability", are regarded as an important source of variability in microbiological studies. Biofilms are defined as the structured multicellular communities with complex architecture that enable microorganisms to grow adhered to abiotic or living surfaces and constitute a fundamental aspect of microbial ecology. The research studies assessing the strain variability in biofilm formation are relatively few compared to the ones evaluating other aspects of microbial behavior such as virulence, growth and stress resistance. Among the available research data on intra-species variability in biofilm formation, compiled and discussed in the present review, most of them refer to foodborne pathogens as compared to spoilage microorganisms. Molecular and physiological aspects of biofilm formation potentially related to strain-specific responses, as well as information on the characterization and quantitative description of this type of biological variability are presented and discussed. Despite the considerable amount of available information on the strain variability in biofilm formation, there are certain data gaps and still-existing challenges that future research should cover and address. Current and future advances in systems biology and omics technologies are expected to aid significantly in the explanation of phenotypic strain variability, including biofilm formation variability, allowing for its integration in microbiological risk assessment.

Microbiological quality of raw drinking milk and unpasteurised dairy products: results from England 2013-2019

The aim of this study was to review microbiology results from testing >2500 raw drinking milk and dairy products made with unpasteurised milk examined in England between 2013 and 2019. Samples were collected as part of incidents of contamination, investigation of infections or as part of routine monitoring and were tested using standard methods for a range of both pathogens and hygiene indicators. Results from testing samples of raw cow's milk or cheese made from unpasteurised milk for routine monitoring purposes were overall of better microbiological quality than those collected during incident or investigations of infections. Results from routine monitoring were satisfactory for 62% of milks, 82% of cream, 100% of ice-cream, 51% of butter, 63% of kefir and 79% of cheeses, with 5% of all samples being considered potentially hazardous. Analysis of data from cheese demonstrated a significant association between increasing levels of indicator Escherichia coli with elevated levels of coagulase positive staphylococci and decreased probability of isolation of Shiga toxin-producing E. coli. These data highlight the public health risk associated with these products and provide further justification for controls applied to raw drinking milk and dairy products made with unpasteurised milk.

Human foodborne listeriosis in England and Wales, 1981 to 2015

Almost all cases of human listeriosis are foodborne, however the proportion where specific exposures are identified is small. Between 1981 and 2015, 5252 human listeriosis cases were reported in England and Wales. The purpose of this study was to summarise data where consumption of specific foods was identified with transmission and these comprised 11 sporadic cases and 17 outbreaks. There was a single outbreak in the community of 378 cases (7% of the total) which was associated with pâté consumption and 112 cases (2% of the total) attributed to specific foods in all the other incidents. The proportion of food-attributed cases increased during this study with improvements in typing methods for Listeria monocytogenes. Ten incidents (one sporadic case and nine outbreaks of 2-9 cases over 4 days to 32 months) occurred in hospitals: all were associated with the consumption of pre-prepared sandwiches. The 18 community incidents comprised eight outbreaks (seven of between 3 and 17 cases) and 10 sporadic cases: food of animal origin was implicated in 16 of the incidents (sliced or potted meats, pork pies, pâté, liver, chicken, crab-meat, butter and soft cheese) and food of non-animal origin in the remaining two (olives and vegetable rennet).

Next-generation sequencing as a screening tool for foodborne pathogens in fresh produce

Next generation sequencing (NGS) approaches are increasingly applied to tracing microbial contaminants entering the food chain due to NGS' untargeted nature and ability to investigate non-culturable (and/or difficult to culture) organisms while yielding genomic information about the microbiota. So far, a plethora of microbes has been shown to be associated with fresh produce, but few studies have utilised NGS to identify contamination with human pathogens. This study aims to establish the limit of detection (LoD) for Salmonella and phage MS2 (a Norovirus surrogate) contamination of fresh produce employing NGS approaches on the Illumina MiSeq: 16S amplicon-sequencing, and RNA-seq, using ScriptSeq (Illumina) and NEBNext (New England BioLabs) kits. ScriptSeq proved the most sensitive approach; delivering an LoD of 10⁴ CFU reaction^-1 (Colony Forming Units) for Salmonella and 10⁵ PFU reaction^-1 (Plaque Forming Units) for phage MS2. Use of the NEBNext kit resulted in detection of Salmonella at 10⁶ CFU reaction^-1 and phage MS2 at 10⁷ PFU reaction^-1. 16S amplicon-sequencing yielded a similar LoD of 10⁵ CFU reaction^-1 for Salmonella but could not detect MS2. The tested NGS methodologies, in combination with bioinformatics approaches applied, proved less sensitive than conventional microbial detection approaches.

Prevalence, Pathogenicity, Virulence, Antibiotic Resistance, and Phylogenetic Analysis of Biofilm-Producing Listeria monocytogenes Isolated from Different Ecological Niches in Egypt: Food, Humans, Animals, and Environment

Serious outbreaks of foodborne disease have been caused by Listeria monocytogenes found in retail delicatessens and the severity of disease is significant, with high hospitalization and mortality rates. Little is understood about the formidable public health threat of L. monocytogenes in all four niches, humans, animals, food, and environment, in Egypt. This study analyzed the presence of L. monocytogenes collected from the four environmental niches and bioinformatics analysis was implemented to analyze and compare the data. PCR was used to detect virulence genes encoded by pathogenicity island (LIPI-1). prfA amino acid substation that causes constitutive expression of virulence was common in 77.7% of isolates. BLAST analysis did not match other isolates in the NCBI database, suggesting this may be a characteristic of the region associated with these isolates. A second group included the NH1 isolate originating in China, and BLAST analysis showed this prfA allele was shared with isolates from other global locations, such as Europe and North America. Identification of possible links and transmission pathways between the four niches helps to decrease the risk of disease in humans, to take more specific control measures in the context of disease prevention, to limit economic losses associated with food recalls, and highlights the need for treatment options.

Isolate-Based Surveillance of Listeria monocytogenes by Whole Genome Sequencing in Austria

Listeria monocytogenes (L. monocytogenes) is a ubiquitous organism that can easily enter the food chain. Infection with L. monocytogenes can cause invasive listeriosis. Since 2014, in Austria, L. monocytogenes isolates from human and food/food-associated samples have been provided on a mandatory basis by food producers and laboratories to the National Reference Laboratory. Since 2017, isolates undergo routinely whole genome sequencing (WGS) and core genome Multilocus Sequence Typing (cgMLST) for cluster analyses. Aims of this study were to characterize isolates and clusters of 2017 by using WGS data and to assess the usefulness of this isolate-based surveillance for generating hypotheses on sources of invasive listeriosis in real-time. WGS data from 31 human and 1744 non-human isolates originating from 2017, were eligible for the study. A cgMLST-cluster was defined as two or more isolates differing by ≤10 alleles. We extracted the sequence types (STs) from the WGS data and analyzed the food subcategories meat, fish, vegetable and diary for associations with the ten most prevalent STs among food, through calculating prevalence ratios (PR) with 95% confidence intervals (CI). The three most frequent STs among the human isolates were ST1 (7/31; 22.6%), ST155 (4/31; 12.9%) and ST451 (3/31; 9.7%) and among the non-human isolates ST451 (614/1744; 35.2%), ST8 (173/1744, 10.0%) and ST9 (117/1744; 6.7%). We found ST21 associated with vegetables (PR: 11.39, 95% CI: 8.32–15.59), ST121 and ST155 with fish (PR: 7.05, 95% CI: 4.88–10.17, PR: 3.29, 95% CI: 1.86–5.82), and ST511, ST7 and ST451 with dairy products (PR: 8.55, 95% CI: 6.65–10.99; PR: 5.05, 95% CI: 3.83–6.66, PR: 3.03, 95% CI: 2.02–4.55). We identified 132 cgMLST-clusters. Six clusters contained human isolates (ST155, ST1, ST101, ST177, ST37 and ST7) and for five of those cgMLST-based cluster analyses solely was able to hypothesize the source: an Austrian meat processing company, two Austrian cheese manufacturers and two vegetable processing companies, one based in Austria and the other in Belgium. Determining routinely STs in food isolates by WGS allows to associate STs with food products. Real-time WGS of L. monocytogenes isolates provided mandatorily, proved to be useful in promptly generating hypotheses on sources of invasive listeriosis.

Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges

Whole-genome sequencing (WGS) will soon replace traditional phenotypic methods for routine testing of foodborne antimicrobial resistance (AMR). WGS is expected to improve AMR surveillance by providing a greater understanding of the transmission of resistant bacteria and AMR genes throughout the food chain, and therefore support risk assessment activities. At this stage, it is unclear how WGS data can be integrated into quantitative microbial risk assessment (QMRA) models and whether their integration will impact final risk estimates or the assessment of risk mitigation measures. This review explores opportunities and challenges of integrating WGS data into QMRA models that follow the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR. We describe how WGS offers an opportunity to enhance the next-generation of foodborne AMR QMRA modeling. Instead of considering all hazard strains as equally likely to cause disease, WGS data can improve hazard identification by focusing on those strains of highest public health relevance. WGS results can be used to stratify hazards into strains with similar genetic profiles that are expected to behave similarly, e.g., in terms of growth, survival, virulence or response to antimicrobial treatment. The QMRA input distributions can be tailored to each strain accordingly, making it possible to capture the variability in the strains of interest while decreasing the uncertainty in the model. WGS also allows for a more meaningful approach to explore genetic similarity among bacterial populations found at successive stages of the food chain, improving the estimation of the probability and magnitude of exposure to AMR hazards at point of consumption. WGS therefore has the potential to substantially improve the utility of foodborne AMR QMRA models. However, some degree of uncertainty remains in relation to the thresholds of genetic similarity to be used, as well as the degree of correlation between genotypic and phenotypic profiles. The latter could be improved using a functional approach based on prediction of microbial behavior from a combination of 'omics' techniques (e.g., transcriptomics, proteomics and metabolomics). We strongly recommend that methodologies to incorporate WGS data in risk assessment be included in any future revision of the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR.

Assessment of Microbial Populations in the Manufacture of Vacuum-Packaged Ready-to-Eat Roast Beef and in a Related Production Plant

Some microbiological criteria were monitored for 6 months in vacuum-packaged roast beef (15 production batches), raw beef (10 batches), and other meat products (12 batches) produced in an Italian small to medium-size enterprise. Fifty-five environmental swab samples also were analyzed. The main bacterial groups were identified by cultural methods according to International Organization for Standardization standards. Listeria monocytogenes was enumerated with the most-probable-number protocol, and species identification was confirmed with a specific PCR assay. Immediately after vacuum packaging, all ready-to-eat (RTE) products had low mean aerobic colony counts (<10² to 2.4 × 10² CFU g^-1), anaerobic colony counts (1.6 to 6.5 × 10¹ CFU g^-1), Enterobacteriaceae counts (1.1 to 1.4 × 10¹ CFU g^-1), and Escherichia coli counts (generally below the detection limit). Nevertheless, the prevalence of L. monocytogenes in these samples was 3.7%. In roast beef samples, the aerobic and anaerobic colony counts reached unacceptable levels (>10⁶ CFU g^-1) after 14 days of refrigerated storage. Because the prevalence of L. monocytogenes increased to 13.3% during storage, a substantial reduction in the shelf life of these products is recommended. Surfaces without direct contact with food (floors and drains) had the highest mean counts for aerobic colonies (8.0 × 10³ to 9.5 × 10⁵ CFU/cm²), anaerobic colonies (2.9 × 10³ to 3.2 × 10⁴ CFU/cm²), Enterobacteriaceae (1.5 × 10¹ to 8.4 × 10¹ CFU/cm²), and E. coli (6.0 to 7.7 CFU/cm²). The levels of L. monocytogenes on direct food contact surfaces were below the detection limit, but more than 25% of floor samples were contaminated. These results reveal the persistence of L. monocytogenes in food processing environments, although at very low levels, posing a high risk of postcooking recontamination for RTE products. To improve hygienic conditions and reduce cross-contamination, an increase in operator awareness and a reassessment of surface sanitization protocols are needed.

Molecular characterization of Listeria monocytogenes isolates from a small-scale meat processor in Montenegro, 2011-2014

The presence of Listeria monocytogenes was evaluated in a small-scale meat processing facility in Montenegro during 2011-2014. L. monocytogenes isolates from traditional meat products and environmental swabs were subjected to a) molecular characterization b) serotyping by both multiplex PCR and next generation sequencing (NGS) c) potential antimicrobial resistance (AMR) was assessed by extraction of specific genes from NGS data and d) screening for the presence of some disinfectant resistance markers. Overall, traditional meat products were contaminated, most likely from incoming raw materials, with 4 major specific STs of L. monocytogenes (ST515, ST8, ST21, ST121) representing 4 clonal complexes (CC1, CC8, CC21, CC121) identified during the four-year period. These strains belonged to serogroup IIa which predominated, followed by IVb (ST515, CC1). The strains from environmental swabs belonged, exclusively, to ST21 and were isolated from cutting board and floor swabs in 2011. Furthermore, we found Tn6188, a novel transposon conferring tolerance to BC, to be specific to sequence type ST121. In addition, antimicrobial resistance genes mprF and fosX were present in clonal complexes CC21 and CC121, while complexes CC8 and CC1 exclusively harbored the mprF antimicrobial resistance gene.

Tracing of Listeria monocytogenes Contamination Routes in Fermented Sausage Production Chain by Pulsed-Field Gel Electrophoresis Typing

In this study, the presence of Listeria monocytogenes was assessed along the production process of fermented sausages in a small-scale facility. Following the isolation of the pathogen from the final product (ISO 11290-1), retrospective sampling was performed during the production of a new batch of sausages, including raw materials, casings, additives, sausage mixtures, sausages during fermentation, and environmental samples. L. monocytogenes was recovered from the following sampling points: the defrosting room and the cuttering, mixing, stuffing, and fermentation phases. Ten strains were isolated, molecularly confirmed as L. monocytogenes by means of a molecular detection system, and subjected to pulsed-field gel electrophoresis (PFGE) typing. On the basis of an unweighted pair group method with arithmetic mean (UPGMA) dendrogram from Ascl pulsotypes, the strains were indistinguishable (no band difference). The same pulsotypes of strains present in both batches of sausages, as well as in environmental samples, indicated the persistence of L. monocytogenes in the sausage production unit.

Sources and survival of Listeria monocytogenes on fresh, leafy produce

Listeria monocytogenes is an intracellular human pathogen which enters the body through contaminated food stuffs and is known to contaminate fresh leafy produce such as spinach, lettuce and rocket. Routinely, fresh leafy produce is grown and processed on a large scale before reaching the consumer through various products such as sandwiches and prepared salads. From farm to fork, the fresh leafy produce supply chain (FLPSC) is complex and contains a diverse range of environments where L. monocytogenes is sporadically detected during routine sampling of produce and processing areas. This review describes sources of the bacteria in the FLPSC and outlines the physiological and molecular mechanisms behind its survival in the different environments associated with growing and processing fresh produce. Finally, current methods of source tracking the bacteria in the context of the food supply chain are discussed with emphasis on how these methods can provide additional, valuable information on the risk that L. monocytogenes isolates pose to the consumer.