Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution

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.

A comparative analysis reveals the genomic diversity among 8 Muscovy duck populations

The Muscovy duck (Cairina moschata) is a waterfowl indigenous to the neotropical regions of Central and South America. It has low demand for concentrated feed and strong adaptability to different rearing conditions. After introduced to China through Eurasian commercial trade, Muscovy ducks have a domestication history of around 300 years in the Fujian Province of China. In the 1990s, the commodity Muscovy duck breed "Crimo," cultivated in Europe, entered the Chinese market for consumption and breeding purposes. Due to the different selective breeding processes, Muscovy ducks have various populational traits and lack transparency of their genetic background. To remove this burden in the Muscovy duck breeding process, we analyzed genomic data from 8 populations totaling 83 individuals. We identify 11.24 million single nucleotide polymorphisms (SNPs) and categorized these individuals into the Fujian-bred and the Crimo populations according to phylogenetic analyses. We then delved deeper into their evolutionary relationships through assessing population structure, calculating fixation index (FST) values, and measuring genetic distances. Our exploration of runs of homozygosity (ROHs) and homozygous-by-descent (HBD) uncovered genomic regions enriched for genes implicated in fatty acid metabolism, development, and immunity pathways. Selective sweep analyses further indicated strong selective pressures exerted on genes including TECR, STAT2, and TRAF5. These findings provide insights into genetic variations of Muscovy ducks, thus offering valuable information regarding genetic diversity, population conservation, and genome associated with the breeding of Muscovy ducks.

Factors Associated with the Prevalence of Salmonella, Generic Escherichia coli, and Coliforms in Florida's Agricultural Soils

Limited data exist on the environmental factors that impact pathogen prevalence in the soil. The prevalence of foodborne pathogens, Salmonella and Listeria monocytogenes, and the prevalence and concentration of generic E. coli in Florida's agricultural soils were evaluated to understand the potential risk of microbial contamination at the preharvest level. For all organisms but L. monocytogenes, a longitudinal field study was performed in three geographically distributed agricultural areas across Florida. At each location, 20 unique 5 by 5 m field sampling sites were selected, and soil was collected and evaluated for Salmonella presence (25 g) and E. coli and coliform concentrations (5 g). Complementary data collected from October 2021 to April 2022 included: weather; adjacent land use; soil properties, including macro- and micro-nutrients; and field management practices. The overall Salmonella and generic E. coli prevalence was 0.418% (1/239) and 11.3% (27/239), respectively; with mean E. coli concentrations in positive samples of 1.56 log CFU/g. Farm A had the highest prevalence of generic E. coli, 22.8% (18/79); followed by Farm B, 10% (8/80); and Farm C 1.25% (1/80). A significant relationship (p < 0.05) was observed between generic E. coli and coliforms, and farm and sampling trip. Variation in the prevalence of generic E. coli and changes in coliform concentrations between farms suggest environmental factors (e.g. soil properties) at the three farms were different. While Salmonella was only detected once, generic E. coli was detected in Florida soils throughout the duration of the growing season meaning activities that limit contact between soil and horticultural crops should continue to be emphasized. Samples collected during an independent sampling trip were evaluated for L. monocytogenes, which was not detected. The influence of local environmental factors on the prevalence of indicator organisms in the soil presents a unique challenge when evaluating the applicability of more global models to predict pathogen prevalence in preharvest produce environments.

Evolutionary dynamics of the accessory genomes of Staphylococcus aureus

Staphylococcus aureus is a ubiquitous commensal and opportunistic bacterial pathogen that can cause a wide gamut of infections, which are exacerbated by the presence of multidrug-resistant and methicillin-resistant S. aureus. S. aureus is genetically heterogeneous and consists of numerous distinct lineages. Using 558 complete genomes of S. aureus, we aim to determine how the accessory genome content among phylogenetic lineages of S. aureus is structured and has evolved. Bayesian hierarchical clustering identified 10 sequence clusters, of which seven contained major sequence types (ST 1, 5, 8, 30, 59, 239, and 398). The seven sequence clusters differed in their accessory gene content, including genes associated with antimicrobial resistance and virulence. Focusing on the two largest clusters, BAPS8 and BAPS10, and each consisting mostly of ST5 and ST8, respectively, we found that the structure and connected components in the co-occurrence networks of accessory genomes varied between them. These differences are explained, in part, by the variation in the rates at which the two sequence clusters gained and lost accessory genes, with the highest rate of gene accumulation occurring recently in their evolutionary histories. We also identified a divergent group within BAPS10 that has experienced high gene gain and loss early in its history. Together, our results show highly variable and dynamic accessory genomes in S. aureus that are structured by the history of the specific lineages that carry them.IMPORTANCEStaphylococcus aureus is an opportunistic, multi-host pathogen that can cause a variety of benign and life-threatening infections. Our results revealed considerable differences in the structure and evolution of the accessory genomes of major lineages within S. aureus. Such genomic variation within a species can have important implications on disease epidemiology, pathogenesis of infection, and interactions with the vertebrate host. Our findings provide important insights into the underlying genetic basis for the success of S. aureus as a highly adaptable and resistant pathogen, which will inform current efforts to control and treat staphylococcal diseases.

Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics

Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.

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.

Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem

Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.

Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses

BACKGROUND

A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multicopy gene families, which are recognizable by synteny conservation, and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes.

RESULTS

Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, allowing robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables.

CONCLUSIONS

Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.

Relation of pest insect-killing and soilborne pathogen-inhibition abilities to species diversification in environmental Pseudomonas protegens

Strains belonging to the Pseudomonas protegens phylogenomic subgroup have long been known for their beneficial association with plant roots, notably antagonising soilborne phytopathogens. Interestingly, they can also infect and kill pest insects, emphasising their interest as biocontrol agents. In the present study, we used all available Pseudomonas genomes to reassess the phylogeny of this subgroup. Clustering analysis revealed the presence of 12 distinct species, many of which were previously unknown. The differences between these species also extend to the phenotypic level. Most of the species were able to antagonise two soilborne phytopathogens, Fusarium graminearum and Pythium ultimum, and to kill the plant pest insect Pieris brassicae in feeding and systemic infection assays. However, four strains failed to do so, likely as a consequence of adaptation to particular niches. The absence of the insecticidal Fit toxin explained the non-pathogenic behaviour of the four strains towards Pieris brassicae. Further analyses of the Fit toxin genomic island evidence that the loss of this toxin is related to non-insecticidal niche specialisation. This work expands the knowledge on the growing Pseudomonas protegens subgroup and suggests that loss of phytopathogen inhibition and pest insect killing abilities in some of these bacteria may be linked to species diversification processes involving adaptation to particular niches. Our work sheds light on the important ecological consequences of gain and loss dynamics for functions involved in pathogenic host interactions of environmental bacteria.

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.

Microdiversity of the vaginal microbiome is associated with preterm birth

Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield insights into these associations. Here, we analyze metagenomic data from 705 vaginal samples collected during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative. We find that the vaginal microbiome of pregnancies that ended preterm exhibited unique genetic profiles. It was more genetically diverse at the species level, a result which we validate in an additional cohort, and harbored a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species drove this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. underwent more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our population genetics analyses reveal associations between the vaginal microbiome and PTB and suggest that evolutionary processes acting on vaginal microbes may play a role in adverse pregnancy outcomes such as PTB.

Metal-organic frameworks (MOFs) based luminescent and electrochemical sensors for food contaminant detection

With the increasing population, food toxicity has become a prevalent concern due to the growing contaminants of food products. Therefore, the need for new materials for toxicant detection and food quality monitoring will always be in demand. Metal-organic frameworks (MOFs) based on luminescence and electrochemical sensors with tunable porosity and active surface area are promising materials for food contaminants monitoring. This review summarizes and studies the most recent progress on MOF sensors for detecting food contaminants such as pesticides, antibiotics, toxins, biomolecules, and ionic species. First, with the introduction of MOFs, food contaminants and materials for toxicants detection are discussed. Then the insights into the MOFs as emerging materials for sensing applications with luminescent and electrochemical properties, signal changes, and sensing mechanisms are discussed. Next, recent advances in luminescent and electrochemical MOFs food sensors and their sensitivity, selectivity, and capacities for common food toxicants are summarized. Further, the challenges and outlooks are discussed for providing a new pathway for MOF food contaminant detection tools. Overall, a timely source of information on advanced MOF materials provides materials for next-generation food sensors.

Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth

Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield new insights into these associations. To this end, we analyzed metagenomic data from 705 vaginal samples collected longitudinally during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative (MOMS-PI). We find that the vaginal microbiome of pregnancies that ended preterm exhibits unique genetic profiles. It is more genetically diverse at the species level, a result which we validate in an additional cohort, and harbors a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species, a group of central vaginal pathobionts, are driving this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. undergoes more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our results reveal novel associations between the vaginal microbiome and PTB using population genetics analyses, and suggest that evolutionary processes acting on the vaginal microbiome may play a vital role in adverse pregnancy outcomes such as preterm birth.

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

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

Accessory microbiomes

In microbiome research, considerable effort has been invested in finding core microbiomes, which have been hypothesized to contain the species most important for host function. Much less attention has been paid to microbiome members that are present in only a subset of hosts. Such accessory microbiomes must in large part consist of species that have no effect on fitness, but some will have deleterious effects on fitness (pathogens), and it is also possible that some accessory microbiome members benefit an ecologically distinct subset of hosts. This short paper discusses what we know about accessory microbiomes, specifically by comparing it with the concept of accessory genomes.

Salmonella Prevalence Is Strongly Associated with Spatial Factors while Listeria monocytogenes Prevalence Is Strongly Associated with Temporal Factors on Virginia Produce Farms

The heterogeneity of produce production environments complicates the development of universal strategies for managing preharvest produce safety risks. Understanding pathogen ecology in different produce-growing regions is important for developing targeted mitigation strategies. This study aimed to identify environmental and spatiotemporal factors associated with isolating Salmonella and Listeria from environmental samples collected from 10 Virginia produce farms. Soil (n = 400), drag swab (n = 400), and irrigation water (n = 120) samples were tested for Salmonella and Listeria, and results were confirmed by PCR. Salmonella serovar and Listeria species were identified by the Kauffmann-White-Le Minor scheme and partial sigB sequencing, respectively. Conditional forest analysis and Bayesian mixed models were used to characterize associations between environmental factors and the likelihood of isolating Salmonella, Listeria monocytogenes (LM), and other targets (e.g., Listeria spp. and Salmonella enterica serovar Newport). Surrogate trees were used to visualize hierarchical associations identified by the forest analyses. Salmonella and LM prevalence was 5.3% (49/920) and 2.3% (21/920), respectively. The likelihood of isolating Salmonella was highest in water samples collected from the Eastern Shore of Virginia with a dew point of >9.4°C. The likelihood of isolating LM was highest in water samples collected in winter from sites where <36% of the land use within 122 m was forest wetland cover. Conditional forest results were consistent with the mixed models, which also found that the likelihood of detecting Salmonella and LM differed between sample type, region, and season. These findings identified factors that increased the likelihood of isolating Salmonella- and LM-positive samples in produce production environments and support preharvest mitigation strategies on a regional scale. IMPORTANCE This study sought to examine different growing regions across the state of Virginia and to determine how factors associated with pathogen prevalence may differ between regions. Spatial and temporal data were modeled to identify factors associated with an increased pathogen likelihood in various on-farm sources. The findings of the study show that prevalence of Salmonella and L. monocytogenes is low overall in the produce preharvest environment but does vary by space (e.g., region in Virginia) and time (e.g., season), and the likelihood of pathogen-positive samples is influenced by different spatial and temporal factors. Therefore, the results support regional or scale-dependent food safety standards and guidance documents for controlling hazards to minimize risk. This study also suggests that water source assessments are important tools for developing monitoring programs and mitigation measures, as spatiotemporal factors differ on a regional scale.

Pan-Genomics of Escherichia albertii for Antibiotic Resistance Profiling in Different Genome Fractions and Natural Product Mediated Intervention: In Silico Approach

Escherichia albertii is an emerging, enteric pathogen of significance. It was first isolated in 2003 from a pediatric diarrheal sample from Bangladesh. In this study, a comprehensive in silico strategy was followed to first list out antibiotic-resistant genes from core, accessory and unique genome fractions of 95 available genomes of E. albertii. Then, 56 drug targets were identified from the core essential genome. Finally, ZipA, an essential cell division protein that stabilizes the FtsZ protofilaments by cross-linking them and serves as a cytoplasmic membrane anchor for the Z ring, was selected for further downstream processing. It was computationally modeled using a threading approach, followed by virtual screening of two phytochemical libraries, Ayurvedic (n = 2103 compounds) and Traditional Chinese Medicine (n = 36,043 compounds). ADMET profiling, followed by PBPK modeling in the central body compartment, in a population of 250 non-diseased, 250 cirrhotic and 250 renally impaired people was attempted. ZINC85624912 from Chinese medicinal library showed the highest bioavailability and plasma retention. This is the first attempt to simulate the fate of natural products in the body through PBPK. Dynamics simulation of 20 ns for the top three compounds from both libraries was also performed to validate the stability of the compounds. The obtained information from the current study could aid wet-lab scientists to work on the scaffold of screened drug-like compounds from natural resources and could be useful in our quest for therapy against antibiotic-resistant E. albertii.

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.

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.

Addition of carbon sources and nutrient salts can inhibit gangue acidification by changing microbial community structure

Acidic pollution from gangue oxidation has become a primary environmental problem in coal mining areas in China. The use of microorganisms to remediate acidic pollution in coal gangue piles has been indicated to be effective, but environmental differences and carbon sources in different mining areas have become important factors restricting microbial activity. Instead of the addition of new functional bacteria to gangue piles, carbon sources and nutrient salts were added to recently discharged gangue to enhance the activity of beneficial bacteria in the indigenous microbial community. The changes in pH and electrical conductivity (EC) of the gangue leachate as well as the composition and abundance of the functional microbial community on the surface of the gangue were analyzed by leaching simulation experiments and 16S rRNA sequencing. The results showed that the addition of a carbon source maintained the pH of the gangue leachate at 6.31~6.65 in 14 d, which was significantly higher than that of the control group, but the pH of the leachate decreased significantly after the addition of the carbon source was stopped. The most effective treatment is adding a low concentration of nutrient salt (20% concentration) and sodium lactate (0.02 g/L) to the gangue first, and then adding sodium lactate (0.1 mg/L) every 7 days. The addition of carbon sources and nutrient salts changed the microbial community composition on the surface of the gangue, and the species diversity index decreased. The dominant genera in the experimental group were Listeria, Arthrobacter, and Enterococcus. The functional gene types in the experimental and control groups were almost the same, but their relative abundance changed. The abundance of functional genes related to the sulfur cycle increased substantially in the experimental group, and the abundance of genes involved in the nitrogen and carbon cycles also increased, albeit to different degrees.

Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types

The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification, depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that ongoing gene gain and loss in the E. coli pangenome is sequence type-specific, which may be a consequence of distinct sequence type-specific evolutionary drivers.

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

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

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

Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations

Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell–MGEs interactions, and those among MGEs, result in complex evolutionary processes where the source, or even the existence of selection for maintaining a function in the genome, is often unclear. For example, MGE-driven HGT depends on cell envelope structures and defense systems, but many of these are transferred by MGEs themselves. MGEs can spur periods of intense gene transfer by increasing their own rates of horizontal transmission upon communicating, eavesdropping, or sensing the environment and the host physiology. This may result in high-frequency transfer of host genes unrelated to the MGE. Here, we review how MGEs drive HGT and how their transfer mechanisms, selective pressures and genomic traits affect gene flow, and therefore adaptation, in microbial populations. The encoding of many adaptive niche-defining microbial traits in MGEs means that intragenomic conflicts and alliances between cells and their MGEs are key to microbial functional diversification.

This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.

Genomic analysis of Listeria monocytogenes from US food processing environments reveals a high prevalence of QAC efflux genes but limited evidence of their contribution to environmental persistence

Background

Quaternary ammonium compound (QAC) efflux genes increase the minimum inhibitory concentration of Listeria monocytogenes (Lm) to benzalkonium chloride sanitizer, but the contribution of these genes to persistence in food processing environments is unclear. The goal of this study was to leverage genomic data and associated metadata for 4969 Lm isolates collected between 1999 and 2019 to: (1) evaluate the prevalence of QAC efflux genes among Lm isolates from diverse US food processors, (2) use comparative genomic analyses to assess confounding factors, such as clonal complex identity and stress tolerance genotypes, and (3) identify patterns in QAC efflux gene gain and loss among persistent clones within specific facilities over time.

Results

The QAC efflux gene cassette bcrABC was present in nearly half (46%) of all isolates. QAC efflux gene prevalence among isolates was associated with clonal complex (𝛘² < 0.001) and clonal complex was associated with the facility type (𝛘² < 0.001). Consequently, changes in the prevalence of QAC efflux genes within individual facilities were generally attributable to changes in the prevalence of specific clonal complexes. Additionally, a GWAS and targeted BLAST search revealed that clonal complexes with a high prevalence of QAC efflux genes commonly possessed other stress tolerance genes. For example, a high prevalence of bcrABC in a clonal complex was significantly associated with the presence of the SSI-1 gene cluster (p < 0.05). QAC efflux gene gain and loss were both observed among persistent populations of Lm in individual facilities, suggesting a limited direct role for QAC efflux genes as predictors of persistence.

Conclusion

This study suggests that although there is evidence that QAC efflux genes are part of a suite of adaptations common among Lm isolated from some food production environments, these genes may be neither sufficient nor necessary to enhance persistence. This is a crucial distinction for decision making in the food industry. For example, changes to sanitizer regimen targeting QAC tolerance would not address other contributing genetic or non-genetic factors, such as equipment hygienic design which physically mediates sanitizer exposure.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08695-2.

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.

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.

Differentiated Evolutionary Strategies of Genetic Diversification in Atlantic and Pacific Thaumarchaeal Populations

Some marine microbes are seemingly “ubiquitous,” thriving across a wide range of environmental conditions. While the increased depth in metagenomic sequencing has led to a growing body of research on within-population heterogeneity in environmental microbial populations, there have been fewer systematic comparisons and characterizations of population-level genetic diversity over broader expanses of time and space. Here, we investigated the factors that govern the diversification of ubiquitous microbial taxa found within and between ocean basins. Specifically, we use mapped metagenomic paired reads to examine the genetic diversity of ammonia-oxidizing archaeal (“Candidatus Nitrosopelagicus brevis”) populations in the Pacific (Hawaii Ocean Time-series [HOT]) and Atlantic (Bermuda Atlantic Time Series [BATS]) Oceans sampled over 2 years. We observed higher nucleotide diversity in “Ca. N. brevis” at HOT, driven by a higher rate of homologous recombination. In contrast, “Ca. N. brevis” at BATS featured a more open pangenome with a larger set of genes that were specific to BATS, suggesting a history of dynamic gene gain and loss events. Furthermore, we identified highly differentiated genes that were regulatory in function, some of which exhibited evidence of recent selective sweeps. These findings indicate that different modes of genetic diversification likely incur specific adaptive advantages depending on the selective pressures that they are under. Within-population diversity generated by the environment-specific strategies of genetic diversification is likely key to the ecological success of “Ca. N. brevis.”

IMPORTANCE Ammonia-oxidizing archaea (AOA) are one of the most abundant chemolithoautotrophic microbes in the marine water column and are major contributors to global carbon and nitrogen cycling. Despite their ecological importance and geographical pervasiveness, there have been limited systematic comparisons and characterizations of their population-level genetic diversity over time and space. Here, we use metagenomic time series from two ocean observatories to address the fundamental questions of how abiotic and biotic factors shape the population-level genetic diversity and how natural microbial populations adapt across diverse habitats. We show that the marine AOA “Candidatus Nitrosopelagicus brevis” in different ocean basins exhibits distinct modes of genetic diversification in response to their selective regimes shaped by nutrient availability and patterns of environmental fluctuations. Our findings specific to “Ca. N. brevis” have broader implications, particularly in understanding the population-level responses to the changing climate and predicting its impact on biogeochemical cycles.

Pangenome evolution in environmentally transmitted symbionts of deep-sea mussels is governed by vertical inheritance

Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared to core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent horizontal gene transfer between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained.​.

Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species "L. swaminathanii"

Recently, a new Listeria species, “Listeria swaminathanii”, was proposed. Here, we phenotypically and genotypically characterize two additional strains that were previously obtained from soil samples and compare the results to the type strain. Complete genomes for both strains were assembled from hybrid Illumina and Nanopore sequencing reads and annotated. Further genomic analysis including average nucleotide identity (ANI) and detection of mobile genetic elements and genes of interest (e.g., virulence-associated) were conducted. The strains showed 98.7–98.8% ANI with the type strain. The UTK C1-0015 genome contained a partial monocin locus and a plasmid, while the UTK C1-0024 genome contained a full monocin locus and a prophage. Phenotypic characterization consistent with those performed on the proposed type strain was conducted to assess consistency of phenotypes across a greater diversity of the proposed species (n = 3 instead of n = 1). Only a few findings were notably different from those of the type strain, such as catalase activity, glycerol metabolism, starch metabolism, and growth at 41 °C. This study further expands our understanding of this newly proposed sensu stricto Listeria species.

Interfacing Machine Learning and Microbial Omics: A Promising Means to Address Environmental Challenges

Microbial communities are ubiquitous and carry an exceptionally broad metabolic capability. Upon environmental perturbation, microbes are also amongst the first natural responsive elements with perturbation-specific cues and markers. These communities are thereby uniquely positioned to inform on the status of environmental conditions. The advent of microbial omics has led to an unprecedented volume of complex microbiological data sets. Importantly, these data sets are rich in biological information with potential for predictive environmental classification and forecasting. However, the patterns in this information are often hidden amongst the inherent complexity of the data. There has been a continued rise in the development and adoption of machine learning (ML) and deep learning architectures for solving research challenges of this sort. Indeed, the interface between molecular microbial ecology and artificial intelligence (AI) appears to show considerable potential for significantly advancing environmental monitoring and management practices through their application. Here, we provide a primer for ML, highlight the notion of retaining biological sample information for supervised ML, discuss workflow considerations, and review the state of the art of the exciting, yet nascent, interdisciplinary field of ML-driven microbial ecology. Current limitations in this sphere of research are also addressed to frame a forward-looking perspective toward the realization of what we anticipate will become a pivotal toolkit for addressing environmental monitoring and management challenges in the years ahead.

Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions

Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.

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.

Assessment of Reference Method Selective Broth and Plating Media with 19 Listeria Species Highlights the Importance of Including Diverse Species in Listeria Method Evaluations

ABSTRACT

Reference methods developed for detection of Listeria monocytogenes are commonly used for detection of Listeria at the genus level. Improved method performance data are needed because this genus has expanded from 6 to 26 species and now includes several Listeria sensu lato species, which can have phenotypes distinct from those of Listeria sensu stricto. We evaluated growth of 19 Listeria species, including 12 recently described Listeria sensu lato species, using the media specified by (i) the U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual, (ii) the U.S. Department of Agriculture (USDA) Microbiology Laboratory Guidebook, and (iii) the International Organization for Standardization (ISO). The FDA broth enrichment procedure allowed all species to grow to detectable levels (≥4 log CFU/mL), yielded the highest mean growth (7.58 log CFU/mL), and was the only procedure with which no Listeria sensu lato species yielded significantly higher growth than did a comparison Listeria sensu stricto species. With the USDA and ISO broth enrichment procedures, several Listeria sensu lato species yielded significantly higher growth than did either Listeria seeligeri or Listeria ivanovii, suggesting that these two Listeria sensu stricto species could be outgrown by Listeria sensu lato species. On selective and differential agar media, L. seeligeri, L. ivanovii, and Listeria grayi produced colonies with atypical morphology and/or growth of these species was inhibited (which may lead to incorrect classification of a sample as negative), whereas several newly described Listeria sensu lato species grew to high levels and produced colonies with typical morphology. Overall, our study results indicate that the ability to detect various Listeria species can be impacted by the specific broth and selective and differential agar used. Our data can help guide selection of appropriate media and detection methods for environmental Listeria monitoring programs and methods that are most likely to detect the targeted Listeria groups (e.g., Listeria sensu stricto, which appear to be the most appropriate index organisms for the pathogen L. monocytogenes).

HIGHLIGHTS

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.

Prokaryote pangenomes are dynamic entities

Prokaryote pangenomes are influenced heavily by environmental factors and the opportunity for gene gain and loss events. As the field of pangenome analysis has expanded, so has the need to fully understand the complexity of how eco-evolutionary dynamics shape pangenomes. Here, we describe current models of pangenome evolution and discuss their suitability and accuracy. We suggest that pangenomes are dynamic entities under constant flux, highlighting the influence of two-way interactions between pangenome and environment. New classifications of core and accessory genes are also considered, underscoring the need for continuous evaluation of nomenclature in a fast-moving field. We conclude that future models of pangenome evolution should incorporate eco-evolutionary dynamics to fully encompass their dynamic, changeable nature.

Adaptation to a Commercial Quaternary Ammonium Compound Sanitizer Leads to Cross-Resistance to Select Antibiotics in Listeria monocytogenes Isolated From Fresh Produce Environments

The effective elimination of Listeria monocytogenes through cleaning and sanitation is of great importance to the food processing industry. Specifically in fresh produce operations, the lack of a kill step requires effective cleaning and sanitation to mitigate the risk of cross-contamination from the environment. As facilities rely on sanitizers to control L. monocytogenes, reports of the development of tolerance to sanitizers and other antimicrobials through cross-resistance is of particular concern. We investigated the potential for six L. monocytogenes isolates from fresh produce handling and processing facilities and packinghouses to develop cross-resistance between a commercial sanitizer and antibiotics. Experimental adaptation of isolates belonging to hypervirulent clonal complexes (CC2, CC4, and CC6) to a commercial quaternary ammonium compound sanitizer (cQAC) resulted in elevated minimum inhibitory concentrations (2–3 ppm) and minimum bactericidal concentrations (3–4 ppm). Susceptibility to cQAC was restored for all adapted (qAD) isolates in the presence of reserpine, a known efflux pump inhibitor. Reduced sensitivity to 7/17 tested antibiotics (chloramphenicol, ciprofloxacin, clindamycin, kanamycin, novobiocin, penicillin, and streptomycin) was observed in all tested isolates. qAD isolates remained susceptible to antibiotics commonly used in the treatment of listeriosis (i.e., ampicillin and gentamicin). The whole genome sequencing of qAD strains, followed by comparative genomic analysis, revealed several mutations in fepR, the regulator for FepA fluoroquinolone efflux pump. The results suggest that mutations in fepR play a role in the reduction in antibiotic susceptibility following low level adaptation to cQAC. Further investigation into the cross-resistance mechanisms and pressures leading to the development of this phenomenon among L. monocytogenes isolates recovered from different sources is needed to better understand the likelihood of cross-resistance development in food chain isolates and the implications for the food industry.

The Fate of Foodborne Pathogens in Manure Treated Soil

The aim of this review was to provide an update on the complex relationship between manure application, altered pathogen levels and antibiotic resistance. This is necessary to protect health and improve the sustainability of this major farming practice in agricultural systems based on high levels of manure production. It is important to consider soil health in relation to environment and land management practices in the context of the soil microflora and the introduction of pathogens on the health of the soil microbiome. Viable pathogens in manure spread on agricultural land may be distributed by leaching, surface run-off, water source contamination and contaminated crop removal. Thus it is important to understand how multiple pathogens can persist in manures and on soil at farm-scale and how crops produced under these conditions could be a potential transfer route for zoonotic pathogens. The management of pathogen load within livestock manure is a potential mechanism for the reduction and prevention of outbreaks infection with Escherichia coli, Listeria Salmonella, and Campylobacter. The ability of Campylobacter, E. coli, Listeria and Salmonella to combat environmental stress coupled with their survival on food crops and vegetables post-harvest emphasizes the need for further study of these pathogens along with the emerging pathogen Providencia given its link to disease in the immunocompromised and its’ high levels of antibiotic resistance. The management of pathogen load within livestock manure has been widely recognized as a potential mechanism for the reduction and prevention of outbreaks infection but any studies undertaken should be considered as region specific due to the variable nature of the factors influencing pathogen content and survival in manures and soil. Mediocre soils that require nutrients could be one template for research on manure inputs and their influence on soil health and on pathogen survival on grassland and in food crops.

Bacterial cooperation through horizontal gene transfer

Cooperation exists across all scales of biological organization, from genetic elements to complex human societies. Bacteria cooperate by secreting molecules that benefit all individuals in the population (i.e., public goods). Genes associated with cooperation can spread among strains through horizontal gene transfer (HGT). We discuss recent findings on how HGT mediated by mobile genetic elements promotes bacterial cooperation, how cooperation in turn can facilitate more frequent HGT, and how the act of HGT itself may be considered as a form of cooperation. We propose that HGT is an important enforcement mechanism in bacterial populations, thus creating a positive feedback loop that further maintains cooperation. To enforce cooperation, HGT serves as a homogenizing force by transferring the cooperative trait, effectively eliminating cheaters.

Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources

Recent listeriosis outbreaks linked to fresh produce suggest the need to better understand and mitigate L. monocytogenes contamination in packing and processing environments. Using whole genome sequencing (WGS) and phenotype screening assays for sanitizer tolerance, we characterized 48 L. monocytogenes isolates previously recovered from environmental samples in five produce handling facilities. Within the studied population there were 10 sequence types (STs) and 16 cgMLST types (CTs). Pairwise single nucleotide polymorphisms (SNPs) ranged from 0 to 3047 SNPs within a CT, revealing closely and distantly related isolates indicative of both sporadic and continuous contamination events within the facility. Within Facility 1, we identified a closely related cluster (0-2 SNPs) of isolates belonging to clonal complex 37 (CC37; CT9492), with isolates recovered during sampling events 1-year apart and in various locations inside and outside the facility. The accessory genome of these CC37 isolates varied from 94 to 210 genes. Notable genetic elements and mutations amongst the isolates included the bcrABC cassette (2/48), associated with QAC tolerance; mutations in the actA gene on the Listeria pathogenicity island (LIPI) 1 (20/48); presence of LIPI-3 (21/48) and LIPI-4 (23/48). This work highlights the potential use of WGS in tracing the pathogen within a facility and understanding properties of L. monocytogenes in produce settings.