Diversity of Listeria species in urban and natural environments

Complete genome sequence of Listeria seeligeri strain 43-1 isolated from a Danish forest freshwater swamp

Here, we report the genome sequence of Listeria seeligeri 43-1 isolated from a Danish freshwater swamp using Oxford Nanopore sequencing. The isolate shared a high genomic similarity to two other L. seeligeri isolates from soil and water.

Application of Environmental Monitoring Programs and Root Cause Analysis to Identify and Implement Interventions to Reduce or Eliminate Listeria Populations in Apple Packinghouses

Controlling Listeria in produce packinghouses can be challenging due to the large number of potential contamination routes. For example, repeated isolation of the same Listeria subtype in a packinghouse could indicate persistence in the packinghouse or reintroduction of the same Listeria from an upstream source. To improve understanding of Listeria transmission patterns in packinghouses, we performed a longitudinal study in four apple packinghouses, including testing of 1,339 environmental sponges and whole genome sequencing (WGS)-based characterization of 280 isolates. Root cause analysis and subsequent intervention implementation were also performed and assessed for effectiveness. Listeria prevalence among environmental sponges collected from the four packinghouses was 20% (range of 5-31% for individual packinghouses). Sites that showed high Listeria prevalence included drains, forklift tires and forks, forklift stops, and waxing area equipment frames. A total of 240/280 WGS-characterized isolates were represented in 41 clusters, each containing two or more isolates that differed by ≤50 high-quality single nucleotide polymorphisms (hqSNPs); 21 clusters were isolated from one packinghouse over ≥2 samplings (suggesting persistence or possibly reintroduction), while 11 clusters included isolates from >2 packinghouses, suggesting common upstream sources. Some interventions successfully (i) reduced Listeria detection on forklift tires and forks (across packinghouses) and (ii) mitigated packinghouse-specific Listeria issues (e.g., in catch pans). However, interventions that lacked enhanced equipment disassembly when persistence was suspected typically appeared to be unsuccessful. Overall, while our data suggest a combination of intensive environmental sampling with subtyping and root cause analysis can help identify effective interventions, implementation of effective interventions continues to be a challenge in packinghouses.

Methodological differences between studies confound one-size-fits-all approaches to managing surface waterways for food and water safety

Even though differences in methodology (e.g., sample volume and detection method) have been shown to affect observed microbial water quality, multiple sampling and laboratory protocols continue to be used for water quality monitoring. Research is needed to determine how these differences impact the comparability of findings to generate best management practices and the ability to perform meta-analyses. This study addresses this knowledge gap by compiling and analyzing a data set representing 2,429,990 unique data points on at least one microbial water quality target (e.g., Salmonella presence and Escherichia coli concentration). Variance partitioning analysis was used to quantify the variance in likelihood of detecting each pathogenic target that was uniquely and jointly attributable to non-methodological versus methodological factors. The strength of the association between microbial water quality and select methodological and non-methodological factors was quantified using conditional forest and regression analysis. Fecal indicator bacteria concentrations were more strongly associated with non-methodological factors than methodological factors based on conditional forest analysis. Variance partitioning analysis could not disentangle non-methodological and methodological signals for pathogenic Escherichia coli, Salmonella, and Listeria. This suggests our current perceptions of foodborne pathogen ecology in water systems are confounded by methodological differences between studies. For example, 31% of total variance in likelihood of Salmonella detection was explained by methodological and/or non-methodological factors, 18% was jointly attributable to both methodological and non-methodological factors. Only 13% of total variance was uniquely attributable to non-methodological factors for Salmonella, highlighting the need for standardization of methods for microbiological water quality testing for comparison across studies.IMPORTANCEThe microbial ecology of water is already complex, without the added complications of methodological differences between studies. This study highlights the difficulty in comparing water quality data from projects that used different sampling or laboratory methods. These findings have direct implications for end users as there is no clear way to generalize findings in order to characterize broad-scale ecological phenomenon and develop science-based guidance. To best support development of risk assessments and guidance for monitoring and managing waters, data collection and methods need to be standardized across studies. A minimum set of data attributes that all studies should collect and report in a standardized way is needed. Given the diversity of methods used within applied and environmental microbiology, similar studies are needed for other microbiology subfields to ensure that guidance and policy are based on a robust interpretation of the literature.

Taxonomy, ecology, and relevance to food safety of the genus Listeria with a particular consideration of new Listeria species described between 2010 and 2022

Since 2010, the genus Listeria has had the addition of 22 new species that more than tripled the number of species identified until 2010. Sixteen of these 22 new species are distantly related to the type species, Listeria monocytogenes, and several of these present phenotypes that distinguish them from classical Listeria species (L. monocytogenes, Listeria innocua, Listeria ivanovii, Listeria seeligeri, Listeria welshimeri, and Listeria grayi). These 22 newly described species also show that Listeria is more genetically diverse than previously estimated. While future studies and surveys are needed to clarify the distribution of these species, at least some of these species may not be widely spread, while other species may be frequently found spread to human-related settings (e.g., farms and processing facilities), and others may be adapted to specific environmental habitats. Here, we review the taxonomic, phylogenetic, and ecological characteristics of these new Listeria species identified since 2010 and re-iterate the suggestion of re-classification of some species into three new genera: Murraya, Mesolisteria, and Paenilisteria. We also provide a review of current detection issues and the relevance to food safety related to the identification of these new species. For example, several new non-pathogenic species could be misidentified as the pathogen L. monocytogenes, based on methods that do not target L. monocytogenes-specific virulence genes/factors, leading to unnecessary product recalls. Moreover, eight species in the proposed new genus Mesolisteria are not good indicators of environmental conditions that could allow L. monocytogenes to grow since Mesolisteria species are unable to grow at low temperatures.

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.

Predicting Food Sources of Listeria monocytogenes Based on Genomic Profiling Using Random Forest Model

Listeria monocytogenes can cause severe foodborne illness, including miscarriage during pregnancy or death in newborn infants. When outbreaks of L. monocytogenes illness occur, it may be possible to determine the food source of the outbreak. However, most reported L. monocytogenes illnesses do not occur as part of a recognized outbreak and most of the time the food source of sporadic L. monocytogenes illness in people cannot be determined. In the United States, L. monocytogenes isolates from patients, foods, and environments are routinely sequenced and analyzed by whole genome multilocus sequence typing (wgMLST) for outbreak detection by PulseNet, the national molecular surveillance system for foodborne illnesses. We investigated whether machine learning approaches applied to wgMLST allele call data could assist in attribution analysis of food source of L. monocytogenes isolates. We compiled isolates with a known source from five food categories (dairy, fruit, meat, seafood, and vegetable) using the metadata of L. monocytogenes isolates in PulseNet, deduplicated closely genetically related isolates, and developed random forest models to predict the food sources of isolates. Prediction accuracy of the final model varied across the food categories; it was highest for meat (65%), followed by fruit (45%), vegetable (45%), dairy (44%), and seafood (37%); overall accuracy was 49%, compared with the naive prediction accuracy of 28%. Our results show that random forest can be used to capture genetically complex features of high-resolution wgMLST for attribution of isolates to their sources.

Enhancing the efficacy of peracetic acid against Listeria monocytogenes and Listeria innocua on fresh apples using commercial acidic and alkaline cleaners

Peracetic acid (PAA) is a commonly used antimicrobial in brush-bed spray bar interventions during apple packing. Prior to sanitizer application on the brush-bed, specific fruit cleaners, such as Acidex Duo (AD), EpiClean (EC), Nature's Shield 220-ACL (NS 220), or Nature's Shield 330-ALK (NS 330), are used to remove of soil, debris, and natural wax from the surfaces of apples. This study evaluated the effectiveness of commonly used cleaners in the apple industry to improve the antimicrobial efficacy of PAA against Listeria monocytogenes on apple surfaces during brush-bed spray bar interventions. Granny Smith apples, 48 h post-inoculation, underwent submersion treatment with different cleaners, as well as PAA alone or in combination with the cleaners. A 30-sec treatment of 5.0% AD, 4.2% EC, 10.0% NS 220, and 10.0% NS 330 resulted in 0.65, 0.50, 0.68, and 0.51 log10 CFU/apple reduction of L. monocytogenes on apples, respectively. Incorporating AD, NS 220, and EC significantly enhanced the antimicrobial efficacy of an 80 ppm PAA intervention. The enhancing effects were not impacted whether the cleaner was applied consecutively with PAA (sequentially) or in combination with PAA (simultaneously), nor were they impacted by a post-treatment water rinse. A 30-120 s wash of 80 ppm PAA with AD, EC, and NS 220 at their suggested concentration resulted in 2.46-2.55, 1.87-2.03, and 2.34-2.48 log10 CFU/apple reduction of L. monocytogenes, respectively, compared to 1.39-1.64 log10 CFU/apple in PAA treatment alone. The inclusion of AD or NS 220 in 80 ppm PAA solution resulted in a reduction of 1.51-1.63 log10 CFU/apple of Listeria after 30-60 s brush-bed spray wash. This enhancement in efficacy was significant compared to the treatment with 80 ppm PAA alone, which resulted in a reduction of 0.94-1.03 log10 CFU/apple. This study demonstrated that using certain commercially available cleaners along with PAA can enhance the effectiveness of PAA in reducing L. monocytogenes on fresh apples.

Tetracycline resistance in Listeria monocytogenes and L. innocua from wild black bears (Ursus americanus) in the United States is mediated by novel transposable elements

IMPORTANCE

Listeria monocytogenes causes severe foodborne illness and is the only human pathogen in the genus Listeria. Previous surveys of AMR in Listeria focused on clinical sources and food or food processing environments, with AMR in strains from wildlife and other natural ecosystems remaining under-explored. We analyzed 185 sequenced strains from wild black bears (Ursus americanus) from the United States, including 158 and 27 L. monocytogenes and L. innocua, respectively. Tetracycline resistance was the most prevalent resistance trait. In L. monocytogenes, it was encountered exclusively in serotype 4b strains with the novel Tn916-like element Tn916.1039. In contrast, three distinct, novel tetracycline resistance elements (Tn5801.UAM, Tn5801.551, and Tn6000.205) were identified in L. innocua. Interestingly, Tn5801.551 was identical to elements in L. monocytogenes from a major foodborne outbreak in the United States in 2011. The findings suggest the importance of wildlife and non-pathogenic Listeria species as reservoir for resistance elements in Listeria.

Comparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environments

Comprehending bacterial genomic variation linked to distinct environments can yield novel insights into mechanisms underlying differential adaptation and transmission of microbes across environments. Gaining such insights is particularly crucial for pathogens as it benefits public health surveillance. However, the understanding of bacterial genomic variation is limited by a scarcity of investigations in genomic variation coupled with different ecological contexts. To address this limitation, we focused on Listeria, an important bacterial genus for food safety that includes the human pathogen L. monocytogenes, and analyzed a large-scale genomic dataset collected by us from natural and food-associated environments across the United States. Through comparative genomics analyses on 449 isolates from the soil and 390 isolates from agricultural water and produce processing facilities representing L. monocytogenes, L. seeligeri, L. innocua, and L. welshimeri, we find that the genomic profiles strongly differ by environments within each species. This is supported by the environment-associated subclades and differential presence of plasmids, stress islands, and accessory genes involved in cell envelope biogenesis and carbohydrate transport and metabolism. Core genomes of Listeria species are also strongly associated with environments and can accurately predict isolation sources at the lineage level in L. monocytogenes using machine learning. We find that the large environment-associated genomic variation in Listeria appears to be jointly driven by soil property, climate, land use, and accompanying bacterial species, chiefly representing Actinobacteria and Proteobacteria. Collectively, our data suggest that populations of Listeria species have genetically adapted to different environments, which may limit their transmission from natural to food-associated environments.

Surface water quality, public health, and ecological risks in Bangladesh-a systematic review and meta-analysis over the last two decades

Water quality has recently emerged as one of the utmost severe ecological problems being faced by the developing countries all over the world, and Bangladesh is no exception. Both surface and groundwater sources contain different contaminants, which lead to numerous deaths due to water-borne diseases, particularly among children. This study presents one of the most comprehensive reviews on the current status of water quality in Bangladesh with a special emphasis on both conventional pollutants and emerging contaminants. Data show that urban rivers in Bangladesh are in a critical condition, especially Korotoa, Teesta, Rupsha, Pashur, and Padma. The Buriganga River and few locations in the Turag, Balu, Sitalakhya, and Karnaphuli rivers have dissolvable oxygen (DO) levels of almost zero. Many waterways contain traces of NO3, NO2, and PO4-3 pollutants. The majority of the rivers in Bangladesh also have Zn, Cu, Fe, Pb, Cd, Ni, Mn, As, and Cr concentrations that exceed the WHO permissible limits for safe drinking water, while their metal concentrations exceed the safety threshold for irrigation. Mercury poses the greatest hazard with 90.91% of the samples falling into the highest risk category. Mercury is followed by zinc 57.53% and copper 29.16% in terms of the dangers they pose to public health and the ecosystem. Results show that a considerable percentage of the population is at risk, being exposed to contaminated water. Despite hundreds of cryptosporidiosis cases reported, fecal contamination, i.e., Cryptosporidium, is totally ignored and need serious considerations to be regularly monitored in source water.

Efficacy of combined caprylic acid and thymol treatments for inactivation of Listeria monocytogenes on enoki mushrooms in household and food-service establishments

Raw enoki mushroom is a high-risk vector for listeriosis, which led to foodborne outbreaks resulting in four deaths in the United States in 2020. This study aimed to investigate the washing method for the inactivation of L. monocytogenes in enoki mushrooms for household and food service establishments. Five methods of washing fresh agricultural products without using disinfectants were selected: (1) rinsing under running water (2 L/min, 10 min), (2-3) dipping in water (200 ml/20 g) at 22 or 40 °C for 10 min, and using (4) 10% NaCl or (5) 5% vinegar at 22 °C for 10 min. The antibacterial efficacy of each washing method along with the final rinse was tested with enoki mushrooms inoculated with a 3-strain cocktail of L. monocytogenes (ATCC 19111, 19115, 19117; ca. 6 log CFU/g). The 5% vinegar showed a significant difference in antibacterial effect compared to the other treatments except 10% NaCl (P < 0.05), with the maximum elimination of L. monocytogenes by 1.23 log CFU/g. Therefore, a disinfectant for enoki mushrooms that can complement the commonly used washing method was developed using antimicrobials (caprylic acid, CA: 0, 0.20, 0.40%; thymol, TM: 0, 0.075, 0.15%). By combined treatment of 0.40% CA and 0.15% TM at 22 °C for 10 min, L. monocytogenes was completely inactivated (>5.55 log reduction CFU/g) and did not recover after enrichment, although individual treatments of antimicrobials showed low bactericidal effects of <1.50 log reduction CFU/g. The bacterial membrane disintegration induced by the disinfectant was analyzed through flow cytometry. Additionally, the sensory scores (odor and appearance) and color parameters (L*, a*, and b*) of enoki mushrooms treated with the disinfectant were not significantly different from those of enoki mushrooms washed with water (P > 0.05). Our findings suggest a washing disinfectant consisting of low concentrations of CA and TM with synergistic antibacterial effects without quality deterioration that can ensure the safe consumption of raw enoki mushrooms in homes and food service establishments.

Soil Collected from a Single Great Smoky Mountains Trail Contains a Diversity of Listeria monocytogenes and Listeria spp

Listeria monocytogenes, a foodborne pathogen, and other Listeria spp. are present in natural environments. Isolating and characterizing strains from natural reservoirs can provide insight into the prevalence and diversity of Listeria spp. in these environments, elucidate their contribution to contamination of agricultural and food processing environments and food products, and lead to the discovery of novel species. In this study, we evaluated the diversity of Listeria spp. isolated from soil in a small region of the Great Smoky Mountains National Park, the most biodiverse national park in the U.S. National Park system. Of the 17 Listeria isolates recovered, whole-genome sequencing revealed that 14 were distinct strains. The strains represented a diversity of Listeria species (L. monocytogenes [n = 9], L. cossartiae subsp. cossartiae [n = 1], L. marthii [n = 1], L. booriae [n = 1], and a potentially novel Listeria sp. [n = 2]), as well as a diversity of sequence types based on multilocus sequence typing (MLST) and core genome MLST, including many novel designations. The isolates were not closely related (≥99.99% average nucleotide identity) to any isolates in public databases (NCBI, PATRIC), which also indicated novelty. The Listeria samples isolated in this study were collected from high-elevation sites near a creek that ultimately leads to the Mississippi River; thus, Listeria present in this natural environment could potentially travel downstream to a large region that includes portions of nine southeastern and midwestern U.S. states. This study provides insight into the diversity of Listeria spp. in the Great Smoky Mountains and indicates that this environment is a reservoir of novel Listeria spp. IMPORTANCE Listeria monocytogenes is a foodborne pathogen that can cause serious systemic illness that, although rare, usually results in hospitalization and has a relatively high mortality rate compared to other foodborne pathogens. Identification of novel and diverse Listeria spp. can provide insights into the genomic evolution, ecology, and evolution and variance of pathogenicity of this genus, especially in natural environments. Comparing L. monocytogenes and Listeria spp. isolates from natural environments, such as those recovered in this study, to contamination and/or outbreak strains may provide more information about the original natural sources of these strains and the pathways and mechanisms that lead to contamination of food products and agricultural or food processing environments.

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.

Structural Equation Models Suggest That On-Farm Noncrop Vegetation Removal Is Not Associated with Improved Food Safety Outcomes but Is Linked to Impaired Water Quality

While growers have reported pressures to minimize wildlife intrusion into produce fields through noncrop vegetation (NCV) removal, NCV provides key ecosystem services. To model food safety and environmental tradeoffs associated with NCV removal, published and publicly available food safety and water quality data from the Northeastern United States were obtained. Because data on NCV removal are not widely available, forest-wetland cover was used as a proxy, consistent with previous studies. Structural equation models (SEMs) were used to quantify the effect of forest-wetland cover on (i) food safety outcomes (e.g., detecting pathogens in soil) and (ii) water quality (e.g., nutrient levels). Based on the SEMs, NCV was not associated with or had a protective effect on food safety outcomes (more NCV was associated with a reduced likelihood of pathogen detection). The probabilities of detecting Listeria spp. in soil (effect estimate [EE] = -0.17; P = 0.005) and enterohemorrhagic Escherichia coli in stream samples (EE = -0.27; P < 0.001) were negatively associated with the amount of NCV surrounding the sampling site. Larger amounts of NCV were also associated with lower nutrient, salinity, and sediment levels, and higher dissolved oxygen levels. Total phosphorous levels were negatively associated with the amount of NCV in the upstream watershed (EE = -0.27; P < 0.001). Similar negative associations (P < 0.05) were observed for other physicochemical parameters, such as nitrate (EE = -0.38). Our findings suggest that NCV should not be considered an inherent produce safety risk or result in farm audit demerits. This study also provides a framework for evaluating environmental tradeoffs associated with using specific preharvest food safety strategies. IMPORTANCE Currently, on-farm food safety decisions are typically made independently of conservation considerations, often with detrimental impacts on agroecosystems. Comanaging agricultural environments to simultaneously meet conservation and food safety aims is complicated because farms are closely linked to surrounding environments, and management decisions can have unexpected environmental, economic, and food safety consequences. Thus, there is a need for research on the conservation and food safety tradeoffs associated with implementing specific preharvest food safety practices. Understanding these tradeoffs is critical for developing adaptive comanagement strategies and ensuring the short- and long-term safety, sustainability, and profitability of agricultural systems. This study quantifies tradeoffs and synergies between food safety and environmental aims, and outlines a framework for modeling tradeoffs and synergies between management aims that can be used to support future comanagement research.

The efficacy of nisin against Listeria monocytogenes on cold-smoked salmon at natural contamination levels is concentration-dependent and varies by serotype

Cold-smoked salmon is a ready-to-eat food product capable of supporting Listeria monocytogenes growth at refrigeration temperatures. While the FDA-approved antimicrobial nisin can be used to mitigate L. monocytogenes contamination, stresses associated with cold-smoked salmon and the associated processing environments may reduce nisin efficacy. A previous study in our laboratory showed that, at high inoculation levels, pre-exposure of L. monocytogenes to sublethal concentrations of quaternary ammonium compounds had an overall detrimental effect on nisin efficacy. The objective of this study was to investigate the impact of nisin concentration and storage temperature on nisin efficacy against L. monocytogenes inoculated on salmon at natural contamination levels. Three L. monocytogenes strains were pre-grown in the presence of sublethal levels of benzalkonium chloride prior to inoculation at ~10² CFU/g on salmon slices that were pre-treated with either 0, 25, or 250 ppm nisin, followed by vacuum-packing and incubation at 4 or 7°C for up to 30 days. L. monocytogenes was enumerated on days 1, 15, and 30 using direct plating and/or most probable number methods. A hurdle model was constructed to describe the odds of complete elimination of L. monocytogenes on salmon and the level of L. monocytogenes when complete elimination was not achieved. Our data showed that (i) nisin efficacy (defined as L. monocytogenes reduction relative to the untreated control) was concentration-dependent with increased efficacy at 250 ppm nisin, and that (ii) 250 ppm nisin treatments led to a reduction in L. monocytogenes prevalence, independent of storage temperature and serotype; this effect of nisin could only be identified since low inoculation levels were used. While lower storage temperatures (i.e., 4°C) yielded lowered absolute L. monocytogenes counts on days 15 and 30 (as compared to 7°C), nisin efficacy did not differ between these two temperatures. Finally, the serotype 1/2b strain was found to be more susceptible to nisin compared with serotype 1/2a and 4b strains on samples incubated at 7°C or treated with 25 ppm nisin. This variation of nisin susceptibility across serotypes, which is affected by both the storage temperature and nisin concentration, needs to be considered while evaluating the efficacy of nisin.

Persistent Spatial Patterns of Listeria monocytogenes and Salmonella enterica Concentrations in Surface Waters: Empirical Orthogonal Function Analysis of Data from Maryland

High spatiotemporal variability of pathogen concentrations in surface waters complicates the design and interpretation of microbial water quality monitoring. Empirical orthogonal function (EOF) analysis can provide spatial patterns (EOFs) of variability in deviations of concentrations in specific locations from the average concentration across the study area. These patterns can be interpreted to assess the effect of environmental factors on pathogen levels in the water. The first and the second EOFs for Listeria monocytogenes explained 84.4% and 9.7% of the total variance of deviations from average, respectively. That percentage was 50.8% and 45.0% for Salmonella enterica. The precipitation also had a strong explanatory capability (79%) of the first EOF. The first EOFs of Listeria and precipitation were similar at pond sites but were opposite to the precipitation at the stream sites. The first EOF of S. enterica and precipitation demonstrated opposite trends, whereas the second S. enterica EOF pattern had similar signs with the precipitation EOF at pond sites, indicating a relationship between rainfall and Salmonella at these sites. Overall, the rainfall data could inform on persistent spatial patterns in concentrations of the two pathogens at the pond sites in farm settings but not at stream sites located in forested areas.

Listeria monocytogenes in Irrigation Water: An Assessment of Outbreaks, Sources, Prevalence, and Persistence

As more fresh fruits and vegetables are needed to meet the demands of a growing population, growers may need to start depending on more varied sources of water, including environmental, recycled, and reclaimed waters. Some of these sources might be susceptible to contamination with microbial pathogens, such as Listeria monocytogenes. Surveys have found this pathogen in water, soil, vegetation, and farm animal feces around the world. The frequency at which this pathogen is present in water sources is dependent on multiple factors, including the season, surrounding land use, presence of animals, and physicochemical water parameters. Understanding the survival duration of L. monocytogenes in specific water sources is important, but studies are limited concerning this environment and the impact of these highly variable factors. Understanding the pathogen’s ability to remain infectious is key to understanding how L. monocytogenes impacts produce outbreaks and, ultimately, consumers’ health.

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

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

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.

Occurrence of Fecal Bacteria and Zoonotic Pathogens in Different Water Bodies: Supporting Water Quality Management

Water contaminated with microbiological and chemical constituents can cause a variety of diseases. Water bodies may become contaminated by wild and domestic animal feces, agricultural runoff or sewage, and are often overlooked as a reservoir and source of human infection by pathogenic microorganisms. The objectives of this study were to evaluate the presence of the zoonotic pathogens, Salmonella spp. and Listeria monocytogenes, in various water bodies located in urban and rural areas in the north of Portugal. Water samples were collected from six sites, including natural and artificial ponds, in two different time periods. Several water quality physicochemical parameters, as well as fecal indicator bacteria, were evaluated. High levels of total coliforms (>1.78 log CFU/100 mL) were detected in all samples, and substantial numbers of Enterococcus (>2.32 log CFU/100 mL) were detected in two ponds located in a city park and in an urban garden. Escherichia coli counts ranged from undetectable to 2.76 log CFU/100 mL. Salmonella spp. was isolated from two sites, the city park and the natural pond, while L. monocytogenes was isolated from three sites: the city garden, the natural pond and the artificial pond, both in the rural area. These data show that artificial and natural ponds are a reservoir of fecal indicator bacteria and enteric and zoonotic pathogens. This may impact the potential risks of human infections by potential contaminants during recreational activities, being important for assessing the water quality for strategic management of these areas.

Characterization of Listeria monocytogenes isolated from wildlife in central New York

Background

Listeria monocytogenes (Lm) present in farming soil and food‐processing facilities threatens food safety, but little is known about the carriage of Lm by wildlife.

Objectives

We estimated the prevalence of faecal Lm shedding among wildlife admitted to a veterinary medical teaching hospital in central New York and characterized a subset of the Lm isolates.

Methods

Wildlife samples were collected between May 2018 and December 2019. We characterized the Lm isolates by assessing the growth at three temperatures approximating the body temperatures of reptiles (25°C), mammals (37°C), and birds (42°C) and identifying genotypic characteristics related to transmission and virulence.

Results

The apparent prevalence of faecal Lm shedding was 5.6% [18/324; 95% confidence interval (CI), 3.3%–8.6%]. Among 13 isolates that represented two lineages and 11 clonal complexes, three and five isolates were grouped into the same SNP clusters with human clinical isolates and environmental isolates, respectively. However, specific SNP difference data showed that Lm from wildlife was generally not closely related (>22 SNP differences) to Lm from human clinical sources and the food‐processing environment. While the stress response locus SSI‐2 was absent, SSI‐1 was found in four isolates. Virulence genes prfA, plcA, hly, mpl, actA, plcB, inlA, inlB, inlC, inlE, inlH, inlJ, and inlK were present, without any premature stop codons, in all isolates. Virulence loci Listeria pathogenicity island 3 (LIPI‐3) and LIPI‐4, which have been linked to hypervirulence, and inlG were found in four, three, and seven isolates, respectively.

Conclusions

Wildlife represents a potential reservoir for genetically diverse and putatively hypervirulent Lm strains. No statistically significant association between growth parameters and hosts was observed. However, compared to lineage I isolates, lineage II isolates showed significantly (p < 0.05) faster growth at 25°C and significantly slower growth at 42°C, suggesting that wildlife Lm isolates that belong to lineages I and II differ in their ability to grow at 25°C and 42°C.

WGS analysis of Listeria monocytogenes from rural, urban, and farm environments in Norway: Genetic diversity, persistence, and relation to clinical and food isolates

Listeria monocytogenes is a ubiquitous environmental bacterium associated with a wide variety of natural and human-made environments, such as soil, vegetation, livestock, food processing environments, and urban areas. It is also among the deadliest foodborne pathogens, and knowledge about its presence and diversity in potential sources is crucial to effectively track and control it in the food chain. Isolation of L. monocytogenes from various rural and urban environments showed higher prevalence in agricultural and urban developments than in forest or mountain areas, and that detection was positively associated with rainfall. Whole-genome sequencing (WGS) was performed for the collected isolates and for L. monocytogenes from Norwegian dairy farms and slugs (218 isolates in total). The data were compared to available data sets from clinical and food-associated sources in Norway collected within the last decade. Multiple examples of clusters of isolates with 0 to 8 whole-genome multilocus sequence typing (wgMLST) allelic differences were collected over time in the same location, demonstrating persistence of L. monocytogenes in natural, urban, and farm environments. Furthermore, several clusters with 6 to 20 wgMLST allelic differences containing isolates collected across different locations, times, and habitats were identified, including nine clusters harboring clinical isolates. The most ubiquitous clones found in soil and other natural and animal ecosystems (CC91, CC11, and CC37) were distinct from clones predominating among both clinical (CC7, CC121, and CC1) and food (CC9, CC121, CC7, and CC8) isolates. The analyses indicated that ST91 was more prevalent in Norway than other countries and revealed a high proportion of the hypovirulent ST121 among Norwegian clinical cases.

IMPORTANCEListeria monocytogenes is a deadly foodborne pathogen that is widespread in the environment. For effective management, both public health authorities and food producers need reliable tools for source tracking, surveillance, and risk assessment. For this, whole-genome sequencing (WGS) is regarded as the present and future gold standard. In the current study, we use WGS to show that L. monocytogenes can persist for months and years in natural, urban, and dairy farm environments. Notably, clusters of almost identical isolates, with genetic distances within the thresholds often suggested for defining an outbreak cluster, can be collected from geographically and temporally unrelated sources. The work highlights the need for a greater knowledge of the genetic relationships between clinical isolates and isolates of L. monocytogenes from a wide range of environments, including natural, urban, agricultural, livestock, food production, and food processing environments, to correctly interpret and use results from WGS analyses.

Occurrence and Diversity of Listeria monocytogenes Isolated from Two Pig Manure Treatment Plants in France

The presence of Listeria monocytogenes in piggery effluents intended for irrigation crops may be a source of bacterial dissemination in agriculture. The occurrence and diversity of L. monocytogenes in the farm environment were examined in two pig manure treatment systems (S1 and S2). Samples collected over the course of one year consisted of manure, the liquid fraction of treated manure (lagoon effluent), and soil surrounding the lagoon. L. monocytogenes was enumerated using the Most Probable Number (MPN) method, serotyped by PCR, genotyped by pulsed-field gel electrophoresis (PFGE), and sequenced for multilocus sequence typing (MLST). L. monocytogenes was detected in 92% of manure samples and in approximately 50% of lagoon effluent and soil samples. Concentrations ranged between 5 and 10³ MPN 100‍ ‍mL^-1. Serogroups IIa, IIb, and IVb were identified. Diversity was high with 44 PFGE profiles (252 isolates) and 17 clonal complexes (CCs) (96 isolates) with higher diversity in manure at site S1 supplied by four farms. Some PFGE profiles and CCs identified in manure or in pig feces from a previous study were also detected in lagoons and/or soil, reflecting pig L. monocytogenes circulation throughout the manure treatment and in the vicinity of the sampling sites. However, some PFGE profiles and CCs were only found in the lagoon and/or in soil, suggesting an origin other than pigs. The present study highlights the limited ability of biological treatments to eliminate L. monocytogenes from pig manure. The persistence of some PFGE profiles and CCs throughout the year in the lagoon and soil shows the ability of L. monocytogenes to survive in this type of environment.

Genomic characteristics of Listeria monocytogenes isolated during mushroom (Agaricus bisporus) production and processing

Listeria monocytogenes is a foodborne pathogen ubiquitously found in nature and which has been isolated from food and food processing environments. This study aimed to characterize L. monocytogenes strains isolated from the production and processing environments of frozen sliced mushrooms (Agaricus bisporus). An analysis was executed along the mushroom processing chain including one mushroom grower and two mushroom processing factories. A total of 153 L. monocytogenes strains were isolated, which could be grouped in three PCR serogroups, namely, serogroup 1/2a-3a (39.2%), serogroup 1/2b-3b-7 (34.0%) and serogroup 4b-4d-4e (26.8%). A selection of 44 L. monocytogenes strains isolated from the processing environment after cleaning and disinfection (C&D) and from frozen sliced mushrooms was genotyped by whole genome sequencing (WGS), because these strains pose a potential risk for product contamination after C&D and for human consumption. Multilocus sequence typing (MLST) revealed 11 clonal complexes (CCs), with strains belonging to CC1, CC4, CC37 and CC87 being detected in both processing factories. Comparative WGS analysis of the 44 strains showed the presence of Listeria pathogenicity island 1 (LIPI-1) with a disrupted version of actA in all CC1, CC4, CC5, CC59 strains, and all but one CC224 strains. Notably, both inlA and inlB were detected as full-length loci in every strain, except for inlA in a CC6 strain that harbored a three amino acid deletion. LIPI-3 was detected in all CC1, CC4, CC6 and CC224 strains, while LIPI-4 was detected in all CC4 and CC87 strains. In addition, antibiotic susceptibility tests showed susceptibility towards fourteen antibiotics tested. The bcrABC operon was found in one CC5 strain, that showed a higher tolerance towards benzalkonium chloride than any other strain tested with confluent growth till 12.5 μg/ml for the CC5 strain compared to 2.5 μg/ml for the other strains. This study highlights that the ecology of L. monocytogenes in the frozen sliced mushroom production chain is highly diverse, and shows the importance of hygienic measures to control L. monocytogenes along the frozen sliced mushroom production chain.

Ruminant-associated Listeria monocytogenes isolates belong preferentially to dairy-associated hypervirulent clones: a longitudinal study in 19 farms

Studies have shown that ruminants constitute reservoirs of Listeria monocytogenes, but little is known about the epidemiology and genetic diversity of this pathogen within farms. Here we conducted a large-scale longitudinal study to monitor Listeria spp. in 19 dairy farms during three consecutive seasons (N = 3251 samples). L. innocua was the most prevalent species, followed by L. monocytogenes. Listeria monocytogenes was detected in 52.6% of farms and more frequently in cattle (4.1%) and sheep (4.5%) than in goat farms (0.2%). Lineage I accounted for 69% of L. monocytogenes isolates. Among animal samples, the most prevalent sublineages (SL) and clonal complexes (CC) were SL1/CC1, SL219/CC4, SL26/CC26 and SL87/CC87, whereas SL666/CC666 was most prevalent in environmental samples. Sixty-one different L. monocytogenes cgMLST types were found, 28% common to different animals and/or surfaces within the same farm and 21% previously reported elsewhere in the context of food and human surveillance. Listeria monocytogenes prevalence was not affected by farm hygiene but by season: higher prevalence was observed during winter in cattle, and during winter and spring in sheep farms. Cows in their second lactation had a higher probability of L. monocytogenes faecal shedding. This study highlights dairy farms as a reservoir for hypervirulent L. monocytogenes.

Ruminant-associated Listeria monocytogenes isolates belong preferentially to dairy-associated hypervirulent clones: a longitudinal study in 19 farms

Studies have shown that ruminants constitute reservoirs of Listeria monocytogenes, but little is known about the epidemiology and genetic diversity of this pathogen within farms. Here we conducted a large-scale longitudinal study to monitor Listeria spp. in 19 dairy farms during three consecutive seasons (N = 3251 samples). L. innocua was the most prevalent species, followed by L. monocytogenes. Listeria monocytogenes was detected in 52.6% of farms and more frequently in cattle (4.1%) and sheep (4.5%) than in goat farms (0.2%). Lineage I accounted for 69% of L. monocytogenes isolates. Among animal samples, the most prevalent sublineages (SL) and clonal complexes (CC) were SL1/CC1, SL219/CC4, SL26/CC26 and SL87/CC87, whereas SL666/CC666 was most prevalent in environmental samples. Sixty-one different L. monocytogenes cgMLST types were found, 28% common to different animals and/or surfaces within the same farm and 21% previously reported elsewhere in the context of food and human surveillance. Listeria monocytogenes prevalence was not affected by farm hygiene but by season: higher prevalence was observed during winter in cattle, and during winter and spring in sheep farms. Cows in their second lactation had a higher probability of L. monocytogenes faecal shedding. This study highlights dairy farms as a reservoir for hypervirulent L. monocytogenes.

Listeria monocytogenes faecal carriage is common and depends on the gut microbiota

Listeria genus comprises two pathogenic species, L. monocytogenes (Lm) and L. ivanovii, and non-pathogenic species. All can thrive as saprophytes, whereas only pathogenic species cause systemic infections. Identifying Listeria species' respective biotopes is critical to understand the ecological contribution of Listeria virulence. In order to investigate the prevalence and abundance of Listeria species in various sources, we retrieved and analyzed 16S rRNA datasets from MG-RAST metagenomic database. 26% of datasets contain Listeria sensu stricto sequences, and Lm is the most prevalent species, most abundant in soil and host-associated environments, including 5% of human stools. Lm is also detected in 10% of human stool samples from an independent cohort of 900 healthy asymptomatic donors. A specific microbiota signature is associated with Lm faecal carriage, both in humans and experimentally inoculated mice, in which it precedes Lm faecal carriage. These results indicate that Lm faecal carriage is common and depends on the gut microbiota, and suggest that Lm faecal carriage is a crucial yet overlooked consequence of its virulence.

Rhizobacteria Impact Colonization of Listeria monocytogenes on Arabidopsis thaliana Roots

In spite of its relevance as a foodborne pathogen, we have limited knowledge about Listeria monocytogenes in the environment. L. monocytogenes outbreaks have been linked to fruits and vegetables; thus, a better understanding of the factors influencing its ability to colonize plants is important. We tested how environmental factors and other soil- and plant-associated bacteria influenced L. monocytogenes' ability to colonize plant roots using Arabidopsis thaliana seedlings in a hydroponic growth system. We determined that the successful root colonization of L. monocytogenes 10403S was modestly but significantly enhanced by the bacterium being pregrown at higher temperatures, and this effect was independent of the biofilm and virulence regulator PrfA. We tested 14 rhizosphere-derived bacteria for their impact on L. monocytogenes 10403S, identifying one that enhanced and 10 that inhibited the association of 10403S with plant roots. We also characterized the outcomes of these interactions under both coinoculation and invasion conditions. We characterized the physical requirements of five of these rhizobacteria to impact the association of L. monocytogenes 10403S with roots, visualizing one of these interactions by microscopy. Furthermore, we determined that two rhizobacteria (one an inhibitor, the other an enhancer of 10403S root association) were able to similarly impact 10 different L. monocytogenes strains, indicating that the effects of these rhizobacteria on L. monocytogenes are not strain specific. Taken together, our results advance our understanding of the parameters that affect L. monocytogenes plant root colonization, knowledge that may enable us to deter its association with and, thus, downstream contamination of, food crops. IMPORTANCE Listeria monocytogenes is ubiquitous in the environment, being found in or on soil, water, plants, and wildlife. However, little is known about the requirements for L. monocytogenes' existence in these settings. Recent L. monocytogenes outbreaks have been associated with contaminated produce; thus, we used a plant colonization model to investigate factors that alter L. monocytogenes' ability to colonize plant roots. We show that L. monocytogenes colonization of roots was enhanced when grown at higher temperatures prior to inoculation but did not require a known regulator of virulence and biofilm formation. Additionally, we identified several rhizobacteria that altered the ability of 11 different strains of L. monocytogenes to colonize plant roots. Understanding the factors that impact L. monocytogenes physiology and growth will be crucial for finding mechanisms (whether chemical or microbial) that enable its removal from plant surfaces to reduce L. monocytogenes contamination of produce and eliminate foodborne illness.

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

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

The Natural Antimicrobial trans-Cinnamaldehyde Interferes with UDP-N-Acetylglucosamine Biosynthesis and Cell Wall Homeostasis in Listeria monocytogenes

Trans-cinnamaldehyde (t-CIN), an antimicrobial compound from cinnamon essential oil, is of interest because it inhibits various foodborne pathogens. In the present work, we investigated the antimicrobial mechanisms of t-CIN in Listeria monocytogenes using a previously isolated yvcK::Himar1 transposon mutant which shows hypersensitivity to t-CIN. Time-lapse microscopy revealed that t-CIN induces a bulging cell shape followed by lysis in the mutant. Complementation with wild-type yvcK gene completely restored the tolerance of yvcK::Himar1 strain to t-CIN and the cell morphology. Suppressor mutants which partially reversed the t-CIN sensitivity of the yvcK::Himar1 mutant were isolated from evolutionary experiments. Three out of five suppression mutations were in the glmU-prs operon and in nagR, which are linked to the biosynthesis of the peptidoglycan precursor uridine-diphosphate-N-acetylglucosamine (UDP-GlcNAc). GlmU catalyzes the last two steps of UDP-GlcNAc biosynthesis and NagR represses the uptake and utilization of N-acetylglucosamine. Feeding N-acetylglucosamine or increasing the production of UDP-GlcNAc synthetic enzymes fully or partially restored the t-CIN tolerance of the yvcK mutant. Together, these results suggest that YvcK plays a pivotal role in diverting substrates to UDP-GlcNAc biosynthesis in L. monocytogenes and that t-CIN interferes with this pathway, leading to a peptidoglycan synthesis defect.

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

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

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

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

Characterization of a Novel Group of Listeria Phages That Target Serotype 4b Listeria monocytogenes

Listeria monocytogenes serotype 4b strains are the most prevalent clinical isolates and are widely found in food processing environments. Bacteriophages are natural viral predators of bacteria and are a promising biocontrol agent for L. monocytogenes. The aims of this study were to characterize phages that specifically infect serotype 4b strains and to assess their ability to inhibit the growth of serotype 4b strains. Out of 120 wild Listeria phages, nine phages were selected based on their strong lytic activity against the model serotype 4b strain F2365. These nine phages can be divided into two groups based on their morphological characteristics and host range. Comparison to previously characterized phage genomes revealed one of these groups qualifies to be defined as a novel species. Phages LP-020, LP-027, and LP-094 were selected as representatives of these two groups of phages for further characterization through one-step growth curve and inhibition of serotype 4b L. monocytogenes experiments. Listeria phages that target serotype 4b showed an inhibitory effect on the growth of F2365 and other serotype 4 strains and may be useful for biocontrol of L.monocytogenes in food processing environments.

Identification and Characterization of a Novel Genomic Island Harboring Cadmium and Arsenic Resistance Genes in Listeria welshimeri

Listeria monocytogenes, the bacterial foodborne pathogen responsible for the severe disease listeriosis, frequently exhibits heavy metal resistance. Concurrent resistance to cadmium and arsenic in L. monocytogenes is strongly associated with the 35-kb chromosomal island LGI2. LGI2 has been encountered repeatedly among L. monocytogenes serotype 4b hypervirulent clones but, surprisingly, not among non-pathogenic Listeria spp. Here we describe a novel LGI2 variant, LGI2-3, in two L. welshimeri strains from an urban aquatic environment. Whole genome sequence analysis revealed that the genomes were closely related except for one prophage region and confirmed a chromosomally integrated LGI2-3. It harbored a cystathionine beta-lyase gene previously only encountered in LGI2-1 of L. monocytogenes clonal complex 1 but was otherwise most closely related to LGI2. LGI2-3 harbored a novel cadAC cassette (cadA7C7) that, like LGI2's cadA4C4, was associated with lower-level tolerance to cadmium (MIC 50 μg/mL) than other cadAC cassettes (MIC ≥ 140 μg/mL). CadA sequence analysis identified two amino acids that may be important for mediating different levels of cadmium tolerance. Our findings clearly demonstrated the potential for LGI2-like islands to be harbored by non-pathogenic Listeria spp. and generate intriguing hypotheses on the genetic diversity mediated by this island and its transfer among Listeria spp.

Multidrug-Resistant Listeria Species Shows Abundance in Environmental Waters of a Key District Municipality in South Africa

The prevalence of bacteria with multidrug-resistance (MDR) is a significant threat to public health globally. Listeria spp. are naturally ubiquitous, with L. monocytogenes particularly being ranked as important foodborne disease-causing microorganisms. This study aimed to evaluate the incidence and determine the antimicrobial resistance (AMR) profiles of multidrug-resistant Listeria spp. (MDRL) isolated from different environmental samples (river and irrigation water) in the Sarah Baartman District Municipality (SBDM), Eastern Cape Province (ECP), South Africa. Molecular identification and characterization were carried out using polymerase chain reaction (PCR) and isolates that exhibited phenotypic resistance were further screened for relevant antimicrobial-resistant genes (ARGs). Findings revealed a total of 124 presumptive Listeria isolates; 69 were molecularly confirmed Listeria species. Out of the confirmed species, 41 isolates (59%) were classified as L. monocytogenes while 9 (13%) were classified as L. welshimeri. All Listeria spp. exhibited phenotypic resistance against ampicillin, penicillin, and trimethoprim-sulphamethoxazole and further screening revealed ARGs in the following proportions: sulI (71%), blaTEM (66%), tetA (63%), and blaCIT (33%). Results confirmed the occurrence of ARGs among Listeria inhabiting surface waters of ECP. The present study indicates that the river water samples collected from SBDM are highly contaminated with MDRL, hence, constituting a potential health risk.

Virulence Characterization of Listeria monocytogenes, Listeria innocua, and Listeria welshimeri Isolated from Fish and Shrimp Using In Vivo Early Zebrafish Larvae Models and Molecular Study

Listeriosis is one of the most notable foodborne diseases and is characterized by high rates of mortality. L. monocytogenes is the main cause of human listeriosis outbreaks, however, there are isolated cases of disease caused by other species of the genus Listeria. The aim of this study was to evaluate strains of L. monocytogenes (n = 7), L. innocua (n = 6), and L. welshimeri (n = 2) isolated from fish and shrimps for their virulence based on the presence of virulence genes and the in vivo Danio rerio (zebrafish) larvae models. A total of 15 strains were analyzed. The zebrafish larvae model showed that the larvae injected with L. monocytogenes strains were characterized by the lowest survival rate (46.5%), followed by L. innocua strains (64.2%) and L. welshimeri (83.0%) strains. Multiplex PCRs were used for detection of selected virulence genes (luxS, actA2, prfA, inlB, rrn, iap, sigB, plcB, actA, hlyA), the majority of which were present in L. monocytogenes. Only a few virulence-related genes were found in L. welshimeri, however, no correlation between the occurrence of these genes and larval survival was confirmed. This research highlights the importance of the potential impact that Listeria spp. strains isolated from fish and shrimps may have on consumers.

Genetic Carriers and Genomic Distribution of cadA6-A Novel Variant of a Cadmium Resistance Determinant Identified in Listeria spp

Listeria monocytogenes is a pathogen responsible for severe cases of food poisoning. Listeria spp. strains occurring in soil and water environments may serve as a reservoir of resistance determinants for pathogenic L. monocytogenes strains. A large collection of Listeria spp. strains (155) isolated from natural, agricultural, and urban areas was screened for resistance to heavy metals and metalloids, and the presence of resistance determinants and extrachromosomal replicons. Of the tested strains, 35% were resistant to cadmium and 17% to arsenic. Sequence analysis of resistance plasmids isolated from strains of Listeria seeligeri and Listeria ivanovii, and the chromosome of L. seeligeri strain Sr73, identified a novel variant of the cadAC cadmium resistance efflux system, cadA6, that was functional in L. monocytogenes cells. The cadA6 cassette was detected in four Listeria species, including strains of L. monocytogenes, isolated from various countries and sources-environmental, food-associated, and clinical samples. This resistance cassette is harbored by four novel composite or non-composite transposons, which increases its potential for horizontal transmission. Since some cadAC cassettes may influence virulence and biofilm formation, it is important to monitor their presence in Listeria spp. strains inhabiting different environments.

Occurrence and molecular characteristics of Listeria monocytogenes isolated from ready-to-eat meats in Hanoi, Vietnam

Listeria monocytogenes represents one of the most serious threats to food safety. Several studies have shown that Ready-To- Eat (RTE) meats are an important vehicle responsible for listeriosis in human. In Vietnam, little is known about the occurrence and molecular characteristics of L. monocytogenes in meat products, which are essential for developing monitoring plans and control measures. In the present study, we investigated the occurrence of L. monocytogenes in 258 sausage and sliced meat samples collected during the period of 2013-2015 and determined the genetic diversity of the isolates using multi-locus sequence typing (MLST). Overall, L. monocytogenes was present in 19/129 (14.7 %) and 40/129 (31.0 %) sausage and sliced meat samples respectively, with the peak of occurrence being in summer. Furthermore, a minimum spanning tree was constructed based on MLST data of 47 isolates. A total of 15 sequence types were found, with five being novel. Notably, the majority of the isolates (34/47) belonged to the hypervirulent clonal complexes 1, 2, and 3.

Planar Interdigitated Aptasensor for Flow-Through Detection of Listeria spp. in Hydroponic Lettuce Growth Media

Irrigation water is a primary source of fresh produce contamination by bacteria during the preharvest, particularly in hydroponic systems where the control of pests and pathogens is a major challenge. In this work, we demonstrate the development of a Listeria biosensor using platinum interdigitated microelectrodes (Pt-IME). The sensor is incorporated into a particle/sediment trap for the real-time analysis of irrigation water in a hydroponic lettuce system. We demonstrate the application of this system using a smartphone-based potentiostat for rapid on-site analysis of water quality. A detailed characterization of the electrochemical behavior was conducted in the presence/absence of DNA and Listeria spp., which was followed by calibration in various solutions with and without flow. In flow conditions (100 mL samples), the aptasensor had a sensitivity of 3.37 ± 0.21 k log-CFU-1 mL, and the LOD was 48 ± 12 CFU mL-1 with a linear range of 102 to 104 CFU mL-1. In stagnant solution with no flow, the aptasensor performance was significantly improved in buffer, vegetable broth, and hydroponic media. Sensor hysteresis ranged from 2 to 16% after rinsing in a strong basic solution (direct reuse) and was insignificant after removing the aptamer via washing in Piranha solution (reuse after adsorption with fresh aptamer). This is the first demonstration of an aptasensor used to monitor microbial water quality for hydroponic lettuce in real time using a smartphone-based acquisition system for volumes that conform with the regulatory standards. The aptasensor demonstrated a recovery of 90% and may be reused a limited number of times with minor washing steps.

A review of Listeria monocytogenes from meat and meat products: Epidemiology, virulence factors, antimicrobial resistance and diagnosis

Listeria monocytogenes is a zoonotic food-borne pathogen that is associated with serious public health and economic implications. In animals, L. monocytogenes can be associated with clinical listeriosis, which is characterised by symptoms such as abortion, encephalitis and septicaemia. In human beings, listeriosis symptoms include encephalitis, septicaemia and meningitis. In addition, listeriosis may cause gastroenteric symptoms in human beings and still births or spontaneous abortions in pregnant women. In the last few years, a number of reported outbreaks and sporadic cases associated with consumption of contaminated meat and meat products with L. monocytogenes have increased in developing countries. A variety of virulence factors play a role in the pathogenicity of L. monocytogenes. This zoonotic pathogen can be diagnosed using both classical microbiological techniques and molecular-based methods. There is limited information about L. monocytogenes recovered from meat and meat products in African countries. This review strives to: (1) provide information on prevalence and control measures of L. monocytogenes along the meat value chain, (2) describe the epidemiology of L. monocytogenes (3) provide an overview of different methods for detection and typing of L. monocytogenes for epidemiological, regulatory and trading purposes and (4) discuss the pathogenicity, virulence traits and antimicrobial resistance profiles of L. monocytogenes.

Detection and Prevalence of Listeria in U.S. Produce Packinghouses and Fresh-Cut Facilities

ABSTRACT

Listeria monocytogenes (LM) contamination of produce can often be traced back to the environment of packinghouses and fresh-cut facilities. Because there is limited information on the detection, prevalence, and distribution of this pathogen in produce operations, environmental "routine sampling" plans for LM and other Listeria spp. were developed and implemented in three packinghouses and five fresh-cut facilities in the United States. For routine sampling, a total of 2,014 sponge samples were collected over six to eight separate samplings per operation, performed over 1 year; vector and preproduction samples (n = 156) were also collected as needed to follow up on positive findings. In addition, a single "validation sampling" visit by an outside expert was used to evaluate the routine sampling. Among the 2,014 routine sponge samples collected, 35 and 30 were positive for LM and Listeria species other than LM (LS), respectively. LM prevalence varied from 0.8 to 5.8% for packinghouses and <0.4 to 1.6% for fresh-cut facilities. Among the 394 validation sponge samples, 23 and 13 were positive for LM and LS, respectively. Validation sampling found statistically significantly higher LM prevalence compared with routine sampling for three of eight operations. For all samples collected, up to eight isolates per sample were characterized by sequencing of sigB, which allowed for classification into sigB allelic types. Among the 97 samples with more than one Listeria isolate characterized, 28 had more than one sigB allelic type present, including 18 sponges that were positive for LM and another Listeria species and 13 sponges that were positive for more than one LM subtype. This indicates that collection of multiple isolates is necessary to capture Listeria diversity present in produce operations. Additionally, 17 of 77 sponges that were positive for LM were positive at only one enrichment time (i.e., 24 or 48 h), indicating that LM testing after two different enrichment times provides enhanced sensitivity.

HIGHLIGHTS

Listeria monocytogenes environmental sampling program in ready-to-eat processing facilities: A practical approach

Listeria monocytogenes is a foodborne pathogen that is frequently found in the environment. It can easily enter food processing environments and contaminate food, potentially causing public health issues. Food business operators (FBOs) are responsible for the control of L. monocytogenes in the food processing environment, particularly in facilities producing ready-to-eat food. The design and implementation of an effective environmental monitoring program (EMP) for L. monocytogenes is an integral part of controlling L. monocytogenes. An effective EMP, including all aspects from sampling, to analysis, to data interpretation, to implementation of corrective actions (including food disposition), is a tool that will help with identification and control of L. monocytogenes contamination. It should be used in conjunction with end product testing, not as a replacement for it. An EMP should be specifically designed for a particular facility on a case-by-case risk-based approach, by a food safety team within the facility. It should be reviewed regularly (at least every 6 months) and verified for its effectiveness. The control of L. monocytogenes in the food industry involves the full commitment of management and of all personnel involved with the safety of foods placed on the market, thus reducing the risk of listeriosis to consumers. Several regulatory and guidance documents provide recommendations for designing aspects of an effective L. monocytogenes EMP. However, a comprehensive review of the key components of an EMP in a single document is lacking. The objective of the present review is to provide FBOs with a practical guide to design, implementation, and verification of an EMP tailored by the food safety team for each food business.

Listeria monocytogenes at the human-wildlife interface: black bears (Ursus americanus) as potential vehicles for Listeria

Listeria monocytogenes is the causative agent of the foodborne illness listeriosis, which can result in severe symptoms and death in susceptible humans and other animals. L. monocytogenes is ubiquitous in the environment and isolates from food and food processing, and clinical sources have been extensively characterized. However, limited information is available on L. monocytogenes from wildlife, especially from urban or suburban settings. As urban and suburban areas are expanding worldwide, humans are increasingly encroaching into wildlife habitats, enhancing the frequency of human-wildlife contacts and associated pathogen transfer events. We investigated the prevalence and characteristics of L. monocytogenes in 231 wild black bear capture events between 2014 and 2017 in urban and suburban sites in North Carolina, Georgia, Virginia and United States, with samples derived from 183 different bears. Of the 231 captures, 105 (45%) yielded L. monocytogenes either alone or together with other Listeria. Analysis of 501 samples, primarily faeces, rectal and nasal swabs for Listeria spp., yielded 777 isolates, of which 537 (70%) were L. monocytogenes. Most L. monocytogenes isolates exhibited serotypes commonly associated with human disease: serotype 1/2a or 3a (57%), followed by the serotype 4b complex (33%). Interestingly, approximately 50% of the serotype 4b isolates had the IVb-v1 profile, associated with emerging clones of L. monocytogenes. Thus, black bears may serve as novel vehicles for L. monocytogenes, including potentially emerging clones. Our results have significant public health implications as they suggest that the ursine host may preferentially select for L. monocytogenes of clinically relevant lineages over the diverse listerial populations in the environment. These findings also help to elucidate the ecology of L. monocytogenes and highlight the public health significance of the human-wildlife interface.

Contamination Pathways can Be Traced along the Poultry Processing Chain by Whole Genome Sequencing of Listeria innocua

Foodborne infection with Listeria causes potentially life-threatening disease listeriosis. Listeria monocytogenes is widely recognized as the only species of public health concern, and the closely related species Listeria innocua is commonly used by the food industry as an indicator to identify environmental conditions that allow for presence, growth, and persistence of Listeria spp. in general. In our study, we analyze the occurrence of Listeria spp. in a farm-to-fork approach in a poultry production chain in Egypt and identify bacterial entry gates and transmission systems. Prevalence of Listeria innocua at the three production stages (farm, slaughterhouse, food products) ranged from 11% to 28%. The pathogenic species Listeria monocytogenes was not detected, and Listeria innocua strains under study did not show genetic virulence determinants. However, the close genetic relatedness of Listeria innocua isolates (maximum 63 SNP differences) indicated cross-contamination between all stages from farm to final food product. Based on these results, chicken can be seen as a natural source of Listeria. Last but not least, sanitary measures during production should be reassessed to prevent bacterial contamination from entering the food chain and to consequently prevent human listeriosis infections. For this purpose, surveillance must not be restricted to pathogenic species.

From Root to Tips: Sporulation Evolution and Specialization in Bacillus subtilis and the Intestinal Pathogen Clostridioides difficile

Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of highly resistant, dormant endospores. Endospores allow environmental persistence, dissemination and for pathogens, are also infection vehicles. In both the model Bacillus subtilis, an aerobic organism, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. Their expression is coordinated between the forespore and the mother cell, the two cells that participate in the process, and is kept in close register with the course of morphogenesis. The evolutionary mechanisms by which sporulation emerged and evolved in these two species, and more broadly across Firmicutes, remain largely unknown. Here, we trace the origin and evolution of sporulation using the genes known to be involved in the process in B. subtilis and C. difficile, and estimating their gain-loss dynamics in a comprehensive bacterial macroevolutionary framework. We show that sporulation evolution was driven by two major gene gain events, the first at the base of the Firmicutes and the second at the base of the B. subtilis group and within the Peptostreptococcaceae family, which includes C. difficile. We also show that early and late sporulation regulons have been coevolving and that sporulation genes entail greater innovation in B. subtilis with many Bacilli lineage-restricted genes. In contrast, C. difficile more often recruits new sporulation genes by horizontal gene transfer, which reflects both its highly mobile genome, the complexity of the gut microbiota, and an adjustment of sporulation to the gut ecosystem.

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.

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