Combined sigB allelic typing and multiplex PCR provide improved discriminatory power and reliability for Listeria monocytogenes molecular serotyping

Role of Whole Genome Sequencing in Assessing Resident and Transient Listeria monocytogenes in a Produce Packinghouse

Whole genome sequencing (WGS) is a powerful tool that may be used to assist in identifying Listeria contamination sources and movement within environments, and to assess persistence. This study investigated sites in a produce packinghouse where Listeria had been historically isolated; and aimed to characterize dispersal patterns and identify cases of transient and resident Listeria. Environmental swab samples (n = 402) were collected from 67 sites at two time-points on three separate visits. Each sample was tested for Listeria, and Listeria isolates were characterized by partial sigB sequencing to determine species and allelic type (AT). Representative isolates from the three most common L. monocytogenes ATs (n = 79) were further characterized by WGS. Of the 144 Listeria species positive samples (35.8%), L. monocytogenes was the most prevalent species. L. monocytogenes was often coisolated with another species of Listeria. WGS identified cases of sporadic and continued reintroduction of L. monocytogenes from the cold storages into the packinghouse and demonstrated cases of L. monocytogenes persistence over 2 years in cold storages, drains, and on a forklift. Nine distinct clusters were found in this study. Two clusters showed evidence of persistence. Isolates in these two clusters (N = 11, with one historical isolate) were obtained predominantly and over multiple samplings from cold storages, with sporadic movement to sites in the packing area, suggesting residence in cold storages with opportunistic dispersal within the packinghouse. The other seven clusters demonstrated evidence of transient Listeria, as isolation was sporadic over time and space during the packing season. Our data provide important insights into likely L. monocytogenes harborage points and transfer in a packinghouse, which is key to root cause analysis. While results support Listeria spp. as a suitable indicator organism for environmental monitoring surveys, findings were unable to establish a specific species as an index organism for L. monocytogenes. Findings also suggest long-term persistence with substantial SNP diversification, which may assist in identifying potential contamination sources and implementing control measures.

Soil Collected in the Great Smoky Mountains National Park Yielded a Novel Listeria sensu stricto Species, L. swaminathanii

Soil samples collected in the Great Smoky Mountains National Park yielded a Listeria isolate that could not be classified to the species level. Whole-genome sequence-based average nucleotide identity BLAST and in silico DNA-DNA Hybridization analyses confirmed this isolate to be a novel Listeria sensu stricto species with the highest similarity to L. marthii (ANI = 93.9%, isDDH = 55.9%). Additional whole-genome-based analysis using the Genome Taxonomy Database Toolkit further supported delineation as a novel Listeria sensu stricto species, as this tool failed to assign a species identification. Phenotypic and genotypic characterization results indicate that this species is nonpathogenic. Specifically, the novel Listeria species described here is phenotypically (i) nonhemolytic and (ii) negative for phosphatidylinositol-specific phospholipase C activity; the draft genome lacks all virulence genes found in the Listeria pathogenicity islands 1, 2, 3, and 4 as well as the internalin genes inlA and inlB. While the type strain contains an apparently intact catalase gene (kat), this strain is phenotypically catalase-negative (an unusual characteristic for Listeria sensu stricto species). Additional analyses identified a nonsynonymous mutation in a conserved codon of kat that is likely linked to the catalase-negative phenotype. Rapid species identification systems, including two biochemical and one matrix-assisted laser desorption/ionization, misidentified this novel species as either L. monocytogenes, L. innocua, or L. marthii. We propose the name L. swaminathanii, and the type strain is FSL L7-0020T (=ATCC TSD-239T). IMPORTANCEL. swaminathanii is a novel sensu stricto species that originated from a US National Park and it will be the first Listeria identified to date without official standing in the nomenclature. Validation was impeded by the National Park's requirements for strain access, ultimately deemed too restrictive by the International Committee on Systematics of Prokaryotes. However, lack of valid status should not detract from the significance of adding a novel species to the Listeria sensu stricto clade. Notably, detection of non-monocytogenes sensu stricto species in a food processing environment indicate conditions that could facilitate the presence of the pathogen L. monocytogenes. If isolated, our data show a potential for L. swaminathanii to be misidentified as another sensu stricto, notably L. monocytogenes. Therefore, developers of Listeria spp. detection and identification methods, who historically only include validly published species in their validation studies, should include L. swaminathanii to ensure accurate results.

Novel Approaches to Environmental Monitoring and Control of Listeria monocytogenes in Food Production Facilities

Listeria monocytogenes is a serious public health hazard responsible for the foodborne illness listeriosis. L. monocytogenes is ubiquitous in nature and can become established in food production facilities, resulting in the contamination of a variety of food products, especially ready-to-eat foods. Effective and risk-based environmental monitoring programs and control strategies are essential to eliminate L. monocytogenes in food production environments. Key elements of the environmental monitoring program include (i) identifying the sources and prevalence of L. monocytogenes in the production environment, (ii) verifying the effectiveness of control measures to eliminate L. monocytogenes, and (iii) identifying the areas and activities to improve control. The design and implementation of the environmental monitoring program are complex, and several different approaches have emerged for sampling and detecting Listeria monocytogenes in food facilities. Traditional detection methods involve culture methods, followed by confirmation methods based on phenotypic, biochemical, and immunological characterization. These methods are laborious and time-consuming as they require at least 2 to 3 days to obtain results. Consequently, several novel detection approaches are gaining importance due to their rapidness, sensitivity, specificity, and high throughput. This paper comprehensively reviews environmental monitoring programs and novel approaches for detection based on molecular methods, immunological methods, biosensors, spectroscopic methods, microfluidic systems, and phage-based methods. Consumers have now become more interested in buying food products that are minimally processed, free of additives, shelf-stable, and have a better nutritional and sensory value. As a result, several novel control strategies have received much attention for their less adverse impact on the organoleptic properties of food and improved consumer acceptability. This paper reviews recent developments in control strategies by categorizing them into thermal, non-thermal, biocontrol, natural, and chemical methods, emphasizing the hurdle concept that involves a combination of different strategies to show synergistic impact to control L. monocytogenes in food production environments.

The Saprophytic Lifestyle of Listeria monocytogenes and Entry Into the Food-Processing Environment

Listeria monocytogenes is an environmentally adapted saprophyte that can change into a human and animal bacterial pathogen with zoonotic potential through several regulatory systems. In this review, the focus is on the occurrence of Listeria sensu stricto and sensu lato in different ecological niches, the detection methods, and their analytical limitations. It also highlights the occurrence of L. monocytogenes genotypes in the environment (soil, water, and wildlife), reflects on the molecular determinants of L. monocytogenes for the saprophytic lifestyle and the potential for antibiotic resistance. In particular, the strain-specific properties with which some genotypes circulate in wastewater, surface water, soil, wildlife, and agricultural environments are of particular interest for the continuously updating risk analysis.

Listeria cossartiae sp. nov., Listeria farberi sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov., isolated from agricultural water and natural environments

A total of 27 Listeria isolates that could not be classified to the species level were obtained from soil samples from different locations in the contiguous United States and an agricultural water sample from New York. Whole-genome sequence-based average nucleotide identity blast (ANIb) showed that the 27 isolates form five distinct clusters; for each cluster, all draft genomes showed ANI values of <95 % similarity to each other and any currently described Listeria species, indicating that each cluster represents a novel species. Of the five novel species, three cluster with the Listeria sensu stricto clade and two cluster with sensu lato. One of the novel sensu stricto species, designated L. cossartiae sp. nov., contains two subclusters with an average ANI similarity of 94.9%, which were designated as subspecies. The proposed three novel sensu stricto species (including two subspecies) are Listeria farberi sp. nov. (type strain FSL L7-0091T=CCUG 74668T=LMG 31917T; maximum ANI 91.9 % to L. innocua), Listeria immobilis sp. nov. (type strain FSL L7-1519T=CCUG 74666T=LMG 31920T; maximum ANI 87.4 % to L. ivanovii subsp. londoniensis) and Listeria cossartiae sp. nov. [subsp. cossartiae (type strain FSL L7-1447T=CCUG 74667T=LMG 31919T; maximum ANI 93.4 % to L. marthii) and subsp. cayugensis (type strain FSL L7-0993T=CCUG 74670T=LMG 31918T; maximum ANI 94.7 % to L. marthii). The two proposed novel sensu lato species are Listeria portnoyi sp. nov. (type strain FSL L7-1582T=CCUG 74671T=LMG 31921T; maximum ANI value of 88.9 % to L. cornellensis and 89.2 % to L. newyorkensis) and Listeria rustica sp. nov. (type strain FSL W9-0585T=CCUG 74665T=LMG 31922T; maximum ANI value of 88.7 % to L. cornellensis and 88.9 % to L. newyorkensis). L. immobilis is the first sensu stricto species isolated to date that is non-motile. All five of the novel species are non-haemolytic and negative for phosphatidylinositol-specific phospholipase C activity; the draft genomes lack the virulence genes found in Listeria pathogenicity island 1 (LIPI-1), and the internalin genes inlA and inlB, indicating that they are non-pathogenic.

Identification, subtyping, and tracking of dairy spoilage-associated Pseudomonas by sequencing the ileS gene

Pseudomonas spp. are important spoilage bacteria that negatively affect the quality of refrigerated fluid milk and uncultured cheese by generating unwanted odors, flavors, and pigments. They are frequently found in dairy plant environments and enter dairy products predominantly as postpasteurization contaminants. Current subtyping and characterization methods for dairy-associated Pseudomonas are often labor-intensive and expensive or provide limited and possibly unreliable classification information (e.g., to the species level). Our goal was to identify a single-copy gene that could be analyzed in dairy spoilage-associated Pseudomonas for preliminary species-level identification, subtyping, and phenotype prediction. We tested 7 genes previously targeted in a Pseudomonas fluorescens multilocus sequence typing scheme for their individual suitability in this application using a set of 113 Pseudomonas spp. isolates representing the diversity of typical pasteurized milk contamination. For each of the 7 candidate genes, we determined the success rate of PCR and sequencing for these 113 isolates as well as the level of discrimination for species identification and subtyping that the sequence data provided. Using these metrics, we selected a single gene, isoleucyl tRNA synthetase (ileS), which had the most suitable traits for simple and affordable single-gene Pseudomonas characterization. This was based on the number of isolates successfully sequenced for ileS (113/113), the number of unique allelic types assigned (83, compared with 50 for 16S rDNA), nucleotide and sequence diversity measures (e.g., number of unique SNP and Simpson index), and tests for genetic recombination. The discriminatory ability of ileS sequencing was confirmed by separation of 99 additional dairy Pseudomonas spp. isolates, which were indistinguishable by 16S rDNA sequencing, into 28 different ileS allelic types. Further, we used whole-genome sequencing data to demonstrate the similarities in ileS-based phylogenetic clustering to whole-genome-based clustering for 27 closely related dairy-associated Pseudomonas spp. isolates and for 178 Pseudomonas type strains. We also found that dairy-associated Pseudomonas within an ileS cluster typically shared the same proteolytic and lipolytic activities. Use of ileS sequencing provides a promising strategy for affordable initial characterization of Pseudomonas isolates, which will help the dairy industry identify, characterize, and track Pseudomonas in their facilities and products.

Complete Genome Sequences of Three Listeria monocytogenes Bacteriophage Propagation Strains

Bacteriophages can be used as a biocontrol for the foodborne pathogen Listeria monocytogenes. Propagation of phages is a necessary step for their use in experimental studies and biocontrol applications. Here, we present the complete genomes of three Listeria monocytogenes strains commonly used as propagation hosts for Listeria phages.

Bacteriophages can be used as a biocontrol for the foodborne pathogen Listeria monocytogenes. Propagation of phages is a necessary step for their use in experimental studies and biocontrol applications. Here, we present the complete genomes of three Listeria monocytogenes strains commonly used as propagation hosts for Listeria phages.

Listeria monocytogenes Prevalence Varies More within Fields Than between Fields or over Time on Conventionally Farmed New York Produce Fields

ABSTRACT

Past studies have shown that the on-farm distribution of Listeria monocytogenes is affected by environmental factors (e.g., weather). However, most studies were conducted at large scales (e.g., across farms), whereas few studies examined drivers of L. monocytogenes prevalence at smaller scales (e.g., within a single field). This study was performed to address this knowledge gap by (i) tracking L. monocytogenes distribution in two fields on one farm over a growing season and (ii) identifying factors associated with L. monocytogenes isolation from drag swab, soil, and agricultural water samples. Overall, L. monocytogenes was detected in 78% (21 of 27), 19% (7 of 36), and 8% (37 of 486) of water, drag swab, and soil samples, respectively. All isolates were characterized by pulsed-field gel electrophoresis. Of the 43 types identified, 14 were isolated on multiple sampling visits and/or from multiple sample types, indicating persistence in or repeated introduction into the farm environment during the study. Our findings also suggest that L. monocytogenes prevalence, even at the small spatial scale studied here, (i) was not uniform and (ii) varied more within fields than between fields or over time. This is illustrated by plot (in-field variation), field (between-field variation), and sampling visit (time), accounting for 18, 2, and 3% of variance in odds of isolating L. monocytogenes, respectively. Moreover, according to random forest analysis, water-related factors were among the top-ranked factors associated with L. monocytogenes isolation from all sample types. For example, the likelihood of isolating L. monocytogenes from drag and soil samples increased monotonically as rainfall increased. Overall, findings from this single-farm study suggests that mitigation strategies for L. monocytogenes in produce fields should focus on water-associated risk factors (e.g., rain and distance to water) and be tailored to specific high-risk in-field areas.

HIGHLIGHTS

Prevalence, Persistence, and Diversity of Listeria monocytogenes and Listeria Species in Produce Packinghouses in Three U.S. States

ABSTRACT

Listeria monocytogenes has emerged as a food safety concern for several produce commodities. Although L. monocytogenes contamination can occur throughout the supply chain, contamination from the packinghouse environment represents a particular challenge and has been linked to outbreaks and recalls. This study aimed to investigate the prevalence, persistence, and diversity of L. monocytogenes and other species of Listeria in produce packinghouses. A longitudinal study was performed in 11 packinghouses (whose commodities included microgreen, peach, apple, tomato, broccoli, cauliflower, and cucumber) in three U.S. states. In each packinghouse, 34 to 47 sites representing zones 2 to 4 were selected and swabbed. Packinghouses were visited four times over the packing season, and samples were tested for Listeria by following the U.S. Food and Drug Administration's Bacteriological Analytical Manual methods. Presumptive Listeria-positive isolates were confirmed by PCR. Species and allelic type (AT) were identified by sigB sequencing for up to eight isolates per sample. Among 1,588 samples tested, 50 (3.2%), 42 (2.7%), and 10 (0.6%) samples were positive for L. monocytogenes only, Listeria spp. (excluding L. monocytogenes) only, and both L. monocytogenes and Listeria spp., respectively. Five species of Listeria (L. monocytogenes, L. innocua, L. seeligeri, L. welshimeri, and L. marthii) were identified, and L. monocytogenes was the most prevalent species. The 102 Listeria-positive samples yielded 128 representative isolates (i.e., defined as isolates from a given sample with a different AT). Approximately 21% (21 of 102) of the Listeria-positive samples contained two or more ATs. A high AT diversity (0.95 Simpson's diversity index) was observed among Listeria isolates. There were three cases of L. monocytogenes or Listeria spp. repeated isolation (site testing positive at least twice) based on AT data. Data from this study also support the importance of drain and moisture management, because Listeria were most prevalent in samples collected from drain, cold storage, and wet nonfood contact surface sites.

HIGHLIGHTS

Assembly and Characterization of a Pathogen Strain Collection for Produce Safety Applications: Pre-growth Conditions Have a Larger Effect on Peroxyacetic Acid Tolerance Than Strain Diversity

Effective control of foodborne pathogens on produce requires science-based validation of interventions and control strategies, which typically involves challenge studies with a set of bacterial strains representing the target pathogens or appropriate surrogates. In order to facilitate these types of studies, a produce-relevant strain collection was assembled to represent strains from produce outbreaks or pre-harvest environments, including Listeria monocytogenes (n = 11), Salmonella enterica (n = 23), shiga-toxin producing Escherichia coli (STEC) (n = 13), and possible surrogate organisms (n = 8); all strains were characterized by whole genome sequencing (WGS). Strain diversity was assured by including the 10 most common S. enterica serotypes, L. monocytogenes lineages I-IV, and E. coli O157 as well as selected "non-O157" STEC serotypes. As it has previously been shown that strains and genetic lineages of a pathogen may differ in their ability to survive different stress conditions, a subset of representative strains for each "pathogen group" (e.g., Salmonella, STEC) was selected and assessed for survival of exposure to peroxyacetic acid (PAA) using strains pre-grown under different conditions including (i) low pH, (ii) high salt, (iii) reduced water activity, (iv) different growth phases, (v) minimal medium, and (vi) different temperatures (21°C, 37°C). The results showed that across the three pathogen groups pre-growth conditions had a larger effect on bacterial reduction after PAA exposure as compared to strain diversity. Interestingly, bacteria exposed to salt stress (4.5% NaCl) consistently showed the least reduction after exposure to PAA; however, for STEC, strains pre-grown at 21°C were as tolerant to PAA exposure as strains pre-grown under salt stress. Overall, our data suggests that challenge studies conducted with multi-strain cocktails (pre-grown under a single specific condition) may not necessarily reflect the relevant phenotypic range needed to appropriately assess different intervention strategies.

Evaluation of Third-Party Deep Cleaning as a Listeria monocytogenes Control Strategy in Retail Delis

The objective of this study was to develop and assess the efficacy of an aggressive deep cleaning sanitation standard operating procedure (DC-SSOP) in nine retail delicatessens to reduce persistent Listeria monocytogenes environmental contamination. The DC-SSOP was developed from combined daily SSOPs recommended by the Food Marketing Institute and input from experts in Listeria control from food manufacturing and sanitation. The DC-SSOP was executed by a trained professional cleaning service during a single 12-h shutdown period. A modified protocol from the U.S. Food and Drug Administration Bacteriological Analytical Manual was used to detect L. monocytogenes in samples from 28 food and nonfood contact surfaces that were collected immediately before and after each cleaning and in samples collected monthly for 3 months. The DC-SSOP significantly reduced L. monocytogenes prevalence overall during the 3-month follow-up period and produced variable results for persistent L. monocytogenes isolates. Six delis with historically low to moderate L. monocytogenes prevalence had no significant changes in the number of samples positive for L. monocytogenes after deep cleaning. Deep cleaning in very high prevalence delis (20 to 30% prevalence) reduced L. monocytogenes by 25.6% (Padj < 0.0001, n = 294) overall during the follow-up period. Among delis with extremely high prevalence (>30%), positive samples from nonfood contact surfaces were reduced by 19.6% (Padj = 0.0002, n = 294) during the follow-up period. The inability of deep cleaning to completely eliminate persistent L. monocytogenes was likely due to the diverse infrastructures in each deli, which may require more individualized intervention strategies.

Enhanced Sanitation Standard Operating Procedures Have Limited Impact on Listeria monocytogenes Prevalence in Retail Delis

In a recent longitudinal surveillance study in 30 U.S. retail delicatessens, 9.7% of environmental surfaces were positive for Listeria monocytogenes, and we found substantial evidence of persistence. In this study, we aimed to reduce the prevalence and persistence of L. monocytogenes in the retail deli environment by developing and implementing practical and feasible intervention strategies (i.e., sanitation standard operating procedures; SSOPs). These SSOPs were standardized across the 30 delis enrolled in this study. SSOP implementation was verified by systems inherent to each retailer. Each deli also was equipped with ATP monitoring systems to verify effective sanitation. We evaluated intervention strategy efficacy by testing 28 food and nonfood contact surfaces for L. monocytogenes for 6 months in all 30 retail delis. The efficacy of the intervention on the delis compared with preintervention prevalence level was not statistically significant; we found that L. monocytogenes could persist despite implementation of enhanced SSOPs. Systematic and accurate use of ATP monitoring systems varied widely among delis. The findings indicate that intervention strategies in the form of enhanced daily SSOPs were not sufficient to eliminate L. monocytogenes from highly prevalent and persistently contaminated delis and that more aggressive strategies (e.g., deep cleaning or capital investment in redesign or equipment) may be necessary to fully mitigate persistent contamination.

Genetic Stability and Evolution of the sigB Allele, Used for Listeria Sensu Stricto Subtyping and Phylogenetic Inference

Sequencing of single genes remains an important tool that allows the rapid classification of bacteria. Sequencing of a portion of sigB, which encodes a stress-responsive alternative sigma factor, has emerged as a commonly used molecular tool for the initial characterization of diverse Listeria isolates. In this study, evolutionary approaches were used to assess the validity of sigB allelic typing for Listeria For a data set of 4,280 isolates, sigB allelic typing showed a Simpson's index of diversity of 0.96. Analyses of 164 sigB allelic types (ATs) found among the 6 Listeriasensu stricto species, representing these 4,280 isolates, indicate that neither frequent homologous recombination nor positive selection significantly contributed to the evolution of sigB, confirming its genetic stability. The molecular clock test provided evidence for unequal evolution rates across clades; Listeria welshimeri displayed the lowest sigB diversity and was the only species in which sigB evolved in a clocklike manner, implying a unique natural history. Among the four L. monocytogenes lineages, sigB evolution followed a molecular clock only in lineage IV. Moreover, sigB displayed a significant negative Tajima D value in lineage II, suggesting a recent population bottleneck followed by lineage expansion. The absence of positive selection along with the violation of the molecular clock suggested a nearly neutral mechanism of Listeriasensu strictosigB evolution. While comparison with a whole-genome sequence-based phylogeny revealed that the sigB phylogeny did not correctly reflect the ancestry of L. monocytogenes lineage IV, the availability of a large sigB AT database allowed accurate species classification.IMPORTANCEsigB allelic typing has been widely used for species delineation and subtyping of Listeria However, an informative evaluation of this method from an evolutionary perspective was missing. Our data indicate that the genetic stability of sigB is affected by neither frequent homologous recombination nor positive selection, which supports that sigB allelic typing provides reliable subtyping and classification of Listeria sensu stricto strains. However, multigene data are required for accurate phylogeny reconstruction of Listeria This study thus contributes to a better understanding of the evolution of sigB and confirms the robustness of the sigB subtyping system for Listeria.

Development and Validation of Pathogen Environmental Monitoring Programs for Small Cheese Processing Facilities

Pathogen environmental monitoring programs (EMPs) are essential for food processing facilities of all sizes that produce ready-to-eat food products exposed to the processing environment. We developed, implemented, and evaluated EMPs targeting Listeria spp. and Salmonella in nine small cheese processing facilities, including seven farmstead facilities. Individual EMPs with monthly sample collection protocols were designed specifically for each facility. Salmonella was detected in only one facility, with likely introduction from the adjacent farm indicated by pulsed-field gel electrophoresis data. Listeria spp. were isolated from all nine facilities during routine sampling. The overall Listeria spp. (other than Listeria monocytogenes ) and L. monocytogenes prevalences in the 4,430 environmental samples collected were 6.03 and 1.35%, respectively. Molecular characterization and subtyping data suggested persistence of a given Listeria spp. strain in seven facilities and persistence of L. monocytogenes in four facilities. To assess routine sampling plans, validation sampling for Listeria spp. was performed in seven facilities after at least 6 months of routine sampling. This validation sampling was performed by independent individuals and included collection of 50 to 150 samples per facility, based on statistical sample size calculations. Two of the facilities had a significantly higher frequency of detection of Listeria spp. during the validation sampling than during routine sampling, whereas two other facilities had significantly lower frequencies of detection. This study provides a model for a science- and statistics-based approach to developing and validating pathogen EMPs.

Coliform detection in cheese is associated with specific cheese characteristics, but no association was found with pathogen detection

Coliform detection in finished products, including cheese, has traditionally been used to indicate whether a given product has been manufactured under unsanitary conditions. As our understanding of the diversity of coliforms has improved, it is necessary to assess whether coliforms are a good indicator organism and whether coliform detection in cheese is associated with the presence of pathogens. The objective of this study was (1) to evaluate cheese available on the market for presence of coliforms and key pathogens, and (2) to characterize the coliforms present to assess their likely sources and public health relevance. A total of 273 cheese samples were tested for presence of coliforms and for Salmonella, Staphylococcus aureus, Shiga toxin-producing Escherichia coli, Listeria monocytogenes, and other Listeria species. Among all tested cheese samples, 27% (75/273) tested positive for coliforms in concentrations >10cfu/g. Pasteurization, pH, water activity, milk type, and rind type were factors significantly associated with detection of coliforms in cheese; for example, a higher coliform prevalence was detected in raw milk cheeses (42% with >10cfu/g) compared with pasteurized milk cheese (21%). For cheese samples contaminated with coliforms, only water activity was significantly associated with coliform concentration. Coliforms isolated from cheese samples were classified into 13 different genera, including the environmental coliform genera Hafnia, Raoultella, and Serratia, which represent the 3 genera most frequently isolated across all cheeses. Escherichia, Hafnia, and Enterobacter were significantly more common among raw milk cheeses. Based on sequencing of the housekeeping gene clpX, most Escherichia isolates were confirmed as members of fecal commensal clades of E. coli. All cheese samples tested negative for Salmonella, Staph. aureus, and Shiga toxin-producing E. coli. Listeria spp. were found in 12 cheese samples, including 5 samples positive for L. monocytogenes. Although no association was found between coliform and Listeria spp. detection, Listeria spp. were significantly more likely to be detected in cheese with the washed type of rind. Our data provide information on specific risk factors for pathogen detection in cheese, which will facilitate development of risk-based strategies to control microbial food safety hazards in cheese, and suggest that generic coliform testing cannot be used to assess the safety of natural cheese.

Aerobic plate counts and ATP levels correlate with Listeria monocytogenes detection in retail delis

Listeria monocytogenes is a foodborne pathogen that causes an estimated 1,591 cases of illness and 255 deaths annually in the United States, the majority of which are attributed to ready-to-eat deli meats processed in retail delis. Because retail delis distribute product directly to consumers, rapid methods to validate cleaning and sanitation are needed to improve retail food safety. This study investigated the relationships among ATP levels, standard aerobic plate count (APC), and L. monocytogenes presence in fully operational delis. Fifteen full-service delis were concurrently sampled for ATP, APC, and L. monocytogenes during preoperational hours once monthly for 3 months. Fifteen additional delis were recruited for 6 months of operational sampling (n = 30). A 1-log increase in APC was equivalent to a 3.3-fold increase in the odds of detecting L. monocytogenes (P < 0.001) and a 1.9-log increase in L monocytogenes population (P = 0.03). An ATP level increase of 1 log relative light unit correlated to a 0.22-log increase in APC (P < 0.001). A preoperational ATP level mean increase by 1 log relative light unit increased the odds of detecting L. monocytogenes concurrently fourfold. A 0.5-log increase in mean ATP level during preoperational sampling corresponded to a 2% increase in the predicted L. monocytogenes prevalence during operation (P < 0.01). Additionally, 10 statistically representative sites were identified and recommended for use in sanitation monitoring programs. Our data support the use of ATP as a rapid method to validate effective cleaning and sanitation to reduce L. monocytogenes in retail delis.

Listeria monocytogenes and Listeria spp. contamination patterns in retail delicatessen establishments in three U.S. states

Postprocessing contamination in processing plants has historically been a significant source of Listeria monocytogenes in ready-to-eat delicatessen meats, and therefore a major cause of human listeriosis cases and outbreaks. Recent risk assessments suggest that a majority of human listeriosis cases linked to consumption of contaminated deli meats may be due to L. monocytogenes contamination that occurs at the retail level. To better understand the ecology and transmission of Listeria spp. in retail delicatessens, food and nonfood contact surfaces were tested for L. monocytogenes and other Listeria spp. in a longitudinal study conducted in 30 retail delis in three U.S. states. In phase I of the study, seven sponge samples were collected monthly for 3 months in 15 delis (5 delis per state) prior to start of daily operation; in phase II, 28 food contact and nonfood contact sites were sampled in each of 30 delis during daily operation for 6 months. Among the 314 samples collected during phase I, 6.8% were positive for L. monocytogenes. Among 4,503 samples collected during phase II, 9.5% were positive for L. monocytogenes; 9 of 30 delis showed low L. monocytogenes prevalence (<1%) for all surfaces. A total of 245 Listeria spp. isolates, including 184 Listeria innocua, 48 Listeria seeligeri, and 13 Listeria welshimeri were characterized. Pulsed-field gel electrophoresis (PFGE) was used to characterize 446 L. monocytogenes isolates. PFGE showed that for 12 of 30 delis, one or more PFGE types were isolated on at least three separate occasions, providing evidence for persistence of a given L. monocytogenes subtype in the delis. For some delis, PFGE patterns for isolates from nonfood contact surfaces were distinct from patterns for occasional food contact surface isolates, suggesting limited cross-contamination between these sites in some delis. This study provides longitudinal data on L. monocytogenes contamination patterns in retail delis, which should facilitate further development of control strategies in retail delis.

Risk factors associated with Salmonella and Listeria monocytogenes contamination of produce fields

Identification of management practices associated with preharvest pathogen contamination of produce fields is crucial to the development of effective Good Agricultural Practices (GAPs). A cross-sectional study was conducted to (i) determine management practices associated with a Salmonella- or Listeria monocytogenes-positive field and (ii) quantify the frequency of these pathogens in irrigation and nonirrigation water sources. Over 5 weeks, 21 produce farms in New York State were visited. Field-level management practices were recorded for 263 fields, and 600 environmental samples (soil, drag swab, and water) were collected and analyzed for Salmonella and L. monocytogenes. Management practices were evaluated for their association with the presence of a pathogen-positive field. Salmonella and L. monocytogenes were detected in 6.1% and 17.5% of fields (n = 263) and 11% and 30% of water samples (n = 74), respectively. The majority of pathogen-positive water samples were from nonirrigation surface water sources. Multivariate analysis showed that manure application within a year increased the odds of a Salmonella-positive field (odds ratio [OR], 16.7), while the presence of a buffer zone had a protective effect (OR, 0.1). Irrigation (within 3 days of sample collection) (OR, 6.0), reported wildlife observation (within 3 days of sample collection) (OR, 6.1), and soil cultivation (within 7 days of sample collection) (OR, 2.9) all increased the likelihood of an L. monocytogenes-positive field. Our findings provide new data that will assist growers with science-based evaluation of their current GAPs and implementation of preventive controls that reduce the risk of preharvest contamination.

Molecular approaches to the identification of pathogenic and nonpathogenic listeriae

The genus Listeria consists of a closely related group of Gram-positive bacteria that commonly occur in the environment and demonstrate varied pathogenic potential. Of the 10 species identified to date, L. monocytogenes is a facultative intracellular pathogen of both humans and animals, L. ivanovii mainly infects ungulates (eg., sheep and cattle), while other species (L. innocua, L. seeligeri, L. welshimeri, L. grayi, L. marthii, L. rocourtiae, L. fleischmannii and L. weihenstephanensis) are essentially saprophytes. Within the species of L. monocytogenes, several serovars (e.g., 4b, 1/2a, 1/2b and 1/2c) are highly pathogenic and account for a majority of clinical isolations. Due to their close morphological, biological, biochemical and genetic similarities, laboratory identification of pathogenic and nonpathogenic Listeria organisms is technically challenging. With the development and application of various molecular approaches, accurate and rapid discrimination of pathogenic and nonpathogenic Listeria organisms, as well as pathogenic and nonpathogenic L. monocytogenes strains, has become possible.

Landscape and meteorological factors affecting prevalence of three food-borne pathogens in fruit and vegetable farms

Produce-related outbreaks have been traced back to the preharvest environment. A longitudinal study was conducted on five farms in New York State to characterize the prevalence, persistence, and diversity of food-borne pathogens in fresh produce fields and to determine landscape and meteorological factors that predict their presence. Produce fields were sampled four times per year for 2 years. A total of 588 samples were analyzed for Listeria monocytogenes, Salmonella, and Shiga toxin-producing Escherichia coli (STEC). The prevalence measures of L. monocytogenes, Salmonella, and STEC were 15.0, 4.6, and 2.7%, respectively. L. monocytogenes and Salmonella were detected more frequently in water samples, while STEC was detected with equal frequency across all sample types (soil, water, feces, and drag swabs). L. monocytogenes sigB gene allelic types 57, 58, and 61 and Salmonella enterica serovar Cerro were repeatedly isolated from water samples. Soil available water storage (AWS), temperature, and proximity to three land cover classes (water, roads and urban development, and pasture/hay grass) influenced the likelihood of detecting L. monocytogenes. Drainage class, AWS, and precipitation were identified as important factors in Salmonella detection. This information was used in a geographic information system framework to hypothesize locations of environmental reservoirs where the prevalence of food-borne pathogens may be elevated. The map indicated that not all croplands are equally likely to contain environmental reservoirs of L. monocytogenes. These findings advance recommendations to minimize the risk of preharvest contamination by enhancing models of the environmental constraints on the survival and persistence of food-borne pathogens in fields.

Diversity of Listeria species in urban and natural environments

A total of 442 Listeria isolates, including 234 Listeria seeligeri, 80 L. monocytogenes, 74 L. welshimeri, 50 L. innocua, and 4 L. marthii isolates, were obtained from 1,805 soil, water, and other environmental samples collected over 2 years from four urban areas and four areas representing natural environments. Listeria spp. showed similar prevalences in samples from natural (23.4%) and urban (22.3%) environments. While L. seeligeri and L. welshimeri were significantly associated with natural environments (P ≤ 0.0001), L. innocua and L. monocytogenes were significantly associated with urban environments (P ≤ 0.0001). Sequencing of sigB for all isolates revealed 67 allelic types with a higher level of allelic diversity among isolates from urban environments. Some Listeria spp. and sigB allelic types showed significant associations with specific urban and natural areas. Nearest-neighbor analyses also showed that certain Listeria spp. and sigB allelic types were spatially clustered within both natural and urban environments, and there was evidence that these species and allelic types persisted over time in specific areas. Our data show that members of the genus Listeria not only are common in urban and natural environments but also show species- and subtype-specific associations with different environments and areas. This indicates that Listeria species and subtypes within these species may show distinct ecological preferences, which suggests (i) that molecular source-tracking approaches can be developed for Listeria and (ii) that detection of some Listeria species may not be a good indicator for L. monocytogenes.

Recombination and positive selection contributed to the evolution of Listeria monocytogenes lineages III and IV, two distinct and well supported uncommon L. monocytogenes lineages

Listeriamonocytogenes lineages III and IV represent two uncommon lineages of the human and animal pathogen L. monocytogenes, characterized by occurrence of unusual phenotypic and genetic characteristics that differentiate them from the common lineages I and II. To gain further insights into the evolution of lineages III and IV, we amplified and sequenced housekeeping genes (i.e., gap, prs, purM, ribC, and sigB), internalin genes (i.e., inlA, inlB, inlC, inlG, inlC2, inlD, inlE, inlF, and inlH) and the virulence gene cluster containing prfA, plcA, hly, mpl, actA, and plcB for lineages III (n = 7) and IV (n = 4) isolates. Phylogenetic analyses of the sequences obtained along with previously reported sequence data for 40 isolates representing lineages I (n = 18), II (n = 21), and III (n = 1), showed that lineages III and IV represent divergent and monophyletic lineages. The virulence gene cluster as well as the inlAB operon were present in all isolates, with inlF absent from all lineages III and IV isolates. While all lineage IV isolates contained only inlC (in addition to inlAB), lineage III isolates showed considerable diversity with regard to internalin gene presence, including presence of (i) only inlC (n = 2), (ii) inlC and inlGC2DE (n = 3), (iii) only inlGC2DE (n = 2), and (iv) inlC and inlC2DE (n = 1). In addition to evidence for horizontal gene transfer events, among lineages III and IV isolates, in prs, actA, plcB, mpl, inlA, inlB, inlG, inlD, and inlE, we also found significant evidence for positive selection in the hly promoter region and, along the lineages III and IV branches, for actA (including in sites recognized for interactions with proteins involved in actin tail polymerization). In conclusion, lineages III and IV represent two distinct monophyletic groups with contributions of intragenic recombination to the evolution of their internalin genes as well as contributions of positive selection to evolution of the virulence genes island.

Listeriosis Outbreak in Dairy Cattle Caused by an Unusual Listeria Monocytogenes Serotype 4b Strain

A listeriosis outbreak, in dairy cattle, with a high case mortality and acute death after onset of symptoms was investigated using gross pathology and bacteriologic approaches, including molecular characterization of a clinical Listeria monocytogenes isolate. In a herd of 315 animals, 9 animals showed clinical symptoms consistent with listeriosis, including 3 animals that died within 2–4 days after acute onset of clinical signs, 4 animals that were euthanized, and 2 that survived. Initial EcoRI ribotyping and serotyping indicated that this outbreak was caused by an unusual L. monocytogenes serotype 4b strain, which was classified into lineage III. Further characterization of this isolate by DNA sequencing–based subtyping methods indicated that the strain responsible for this outbreak represented a unique genotype as supported by its classification into a new sigB allelic type, which has not been identified previously among >290 isolates, and by compelling phylogenetic evidence. While lineage III isolates are generally rare, they seem to be more common among L. monocytogenes isolates from animals with clinical signs of listeriosis. This is the first report of a particularly severe clinical course of disease associated with infection by a lineage III strain. The high prevalence of Listeria spp., including L. monocytogenes, in the farm environments may favor emergence and evolution of novel, and possibly more virulent, L. monocytogenes strains. Continued monitoring of animal listeriosis cases and outbreaks may not only improve animal health but also aid in the early discovery of newly emerging L. monocytogenes strains.

Salt stress phenotypes in Listeria monocytogenes vary by genetic lineage and temperature

Listeria monocytogenes can survive and grow under wide-ranging environmental stress conditions encountered both in foods and in the host. The ability of certain L. monocytogenes subtypes to thrive under stress conditions present in specific niches was hypothesized to reflect genetic characteristics and phenotypic capabilities conserved among strains within a subtype. To quantify variations in salt stress phenotypes among 40 strains selected to represent the diversity of the three major L. monocytogenes genetic lineages and to determine if salt stress phenotypes were associated with genetic relatedness, we measured growth under salt stress at both 7°C and 37°C. At 7°C, in brain-heart infusion with 6% NaCl, average growth rates among the lineages were similar. A comparison of doubling times after exposure to salt stress at 7°C or 37°C indicated that growth at 7°C provided crossprotection to subsequent salt stress for strains in lineages I and II. At 37°C, in brain-heart infusion with 6% NaCl, lineage I and III strains grew significantly faster (p<0.0001) than lineage II strains. Under salt stress at 37°C, differences in growth parameters were significantly (p<0.005) associated with genetic relatedness of the strains. Compatible solute uptake is part of the L. monocytogenes salt stress response, but growth differences between the lineages were not related to differences in transcript levels of osmolyte transporter-encoding genes betL, gbuA, oppA, and opuCA. The combination of phylogenetic and phenotypic data suggests that L. monocytogenes lineage I and III strains, which are most commonly associated with human and animal disease, may be better adapted to osmotic stress at 37°C, conditions that are present in the host gastrointestinal tract.

Observation of a new pattern in serogroup-related PCR typing of Listeria monocytogenes 4b isolates

Molecular serogroup-related PCR typing has made the determination of serotypes of Listeria monocytogenes isolates easy and rapid. Amplification of selected lineage- and serotype-related genes can produce serotype patterns reflecting the four major serotypes, 1/2a, 1/2b, 1/2c, and 4b. We found that four isolates in our routine testing had a pattern with the four bands lmo0737, ORF2110, ORF2819, and prs positive, a pattern which has not been previously reported in the literature. After testing with a lineage-specific PCR, hybridization, and conventional agglutination serotyping, the isolates with the new pattern were considered to be serotype 4b.

A population genetics-based and phylogenetic approach to understanding the evolution of virulence in the genus Listeria

The genus Listeria includes (i) the opportunistic pathogens L. monocytogenes and L. ivanovii, (ii) the saprotrophs L. innocua, L. marthii, and L. welshimeri, and (iii) L. seeligeri, an apparent saprotroph that nevertheless typically contains the prfA virulence gene cluster. A novel 10-loci multilocus sequence typing scheme was developed and used to characterize 67 isolates representing six Listeria spp. (excluding L. grayi) in order to (i) provide an improved understanding of the phylogeny and evolution of the genus Listeria and (ii) use Listeria as a model to study the evolution of pathogenicity in opportunistic environmental pathogens. Phylogenetic analyses identified six well-supported Listeria species that group into two main subdivisions, with each subdivision containing strains with and without the prfA virulence gene cluster. Stochastic character mapping and phylogenetic analysis of hly, a gene in the prfA cluster, suggest that the common ancestor of the genus Listeria contained the prfA virulence gene cluster and that this cluster was lost at least five times during the evolution of Listeria, yielding multiple distinct saprotrophic clades. L. welshimeri, which appears to represent the most ancient clade that arose from an ancestor with a prfA cluster deletion, shows a considerably lower average sequence divergence than other Listeria species, suggesting a population bottleneck and a putatively different ecology than other saprotrophic Listeria species. Overall, our data suggest that, for some pathogens, loss of virulence genes may represent a selective advantage, possibly by facilitating adaptation to a specific ecological niche.

Listeria marthii sp. nov., isolated from the natural environment, Finger Lakes National Forest

Four isolates (FSL S4-120(T), FSL S4-696, FSL S4-710, and FSL S4-965) of Gram-positive, motile, facultatively anaerobic, non-spore-forming bacilli that were phenotypically similar to species of the genus Listeria were isolated from soil, standing water and flowing water samples obtained from the natural environment in the Finger Lakes National Forest, New York, USA. The four isolates were closely related to one another and were determined to be the same species by whole genome DNA-DNA hybridization studies (>82 % relatedness at 55 degrees C and >76 % relatedness at 70 degrees C with 0.0-0.5 % divergence). 16S rRNA gene sequence analysis confirmed their close phylogenetic relatedness to Listeria monocytogenes and Listeria innocua and more distant relatedness to Listeria welshimeri, L. seeligeri, L. ivanovii and L. grayi. Phylogenetic analysis of partial sequences for sigB, gap, and prs showed that these isolates form a well-supported sistergroup to L. monocytogenes. The four isolates were sufficiently different from L. monocytogenes and L. innocua by DNA-DNA hybridization to warrant their designation as a new species of the genus Listeria. The four isolates yielded positive reactions in the AccuProbe test that is purported to be specific for L. monocytogenes, did not ferment L-rhamnose, were non-haemolytic on blood agar media, and did not contain a homologue of the L. monocytogenes virulence gene island. On the basis of their phenotypic characteristics and their genotypic distinctiveness from L. monocytogenes and L. innocua, the four isolates should be classified as a new species within the genus Listeria, for which the name Listeria marthii sp. nov. is proposed. The type strain of L. marthii is FSL S4-120(T) (=ATCC BAA-1595(T) =BEIR NR 9579(T) =CCUG 56148(T)). L. marthii has not been associated with human or animal disease at this time.

Pulsed-field gel electrophoresis (PFGE) analysis of Listeria monocytogenes isolates from different sources and geographical origins and representative of the twelve serovars

Multiplex-PCR (MPCR) serogrouping and pulsed-field gel electrophoresis (PFGE) subtyping analysis are currently used by several public and private laboratories for the characterization of Listeria monocytogenes. In this study a set of 80 L. monocytogenes isolates belonging to the twelve serovars was used to investigate (i) the typeability of the rare serovars, (ii) the ability of PFGE analysis with ApaI and AscI to differentiate serovars within MPCR serogroups and (iii) the association of molecular types with the specific source or geographical origin of the isolates. With the exception of three isolates (rare serovars 4a and 4c) that were not amenable to restriction with ApaI, all the other analyzed isolates were subtyped by both enzymes. PFGE discriminated the 80 isolates into 62 combined ApaI and AscI PFGE patterns (pulsotypes), but could not differentiate serovars within MPCR serogroups, in which isolates from different serovars displaying the same pulsotype were found. Clustering analysis suggests that for some pulsotypes grouping according to Portuguese origin or source can be suggested. On the other hand, some L. monocytogenes clones are widely distributed. Two pulsotypes from Portuguese human isolates were identical to the ones displayed by human outbreak clones in the UK and in the USA and Switzerland, respectively, although they were not temporally matched. Computer-assisted data analysis of large and diverse PFGE type databases will improve the correct interpretation of subtyping data in epidemiological studies and in tracing routes and sources of contamination in the food industry.

The use of multiplex PCR to detect and differentiate food- and beverage-associated microorganisms: a review

Regarding food safety, rapid detection of microbial species is crucial to develop effective preventive and/or adjustment measures. Classical methods for determining the presence of certain species are time-consuming and labor-intensive, hence, molecular methods, which offer speed, sensitivity and specificity, have been developed to address this problem. Multiplex PCR (MPCR) is widely applied in the various fields of microbiology for the rapid differentiation of microbial species without compromising accuracy. This paper describes the method and reports on the state-of-the-art application of this technique to the identification of microorganisms vehiculated with foods and beverages. The identification of both pathogens and probiotics and the species important for food fermentation or deterioration will be discussed. Applications of MPCR in combination with other techniques are also reviewed. Potentials, pitfalls, limitations and future prospects are summarised.