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The serovars of Salmonella enterica display dramatic differences in pathogenesis and host preferences. We developed a process (patent pending) for grouping Salmonella isolates and serovars by their public health risk. We collated a curated set of 12,337 S . enterica isolate genomes from human, beef, and bovine sources in the US. After annotating a virulence gene catalog for each isolate, we used unsupervised random forest methods to estimate the proximity (similarity) between isolates based upon the genomic presentation of putative virulence traits We then grouped isolates (virulence clusters) using hierarchical clustering (Ward’s method), used non-parametric bootstrapping to assess cluster stability, and externally validated the clusters against epidemiological virulence measures from FoodNet, the National Outbreak Reporting System (NORS), and US federal sampling of beef products. We identified five stable virulence clusters of S . enterica serovars. Cluster 1 (higher virulence) serovars yielded an annual incidence rate of domestically acquired sporadic cases roughly one and a half times higher than the other four clusters combined (Clusters 2–5, lower virulence). Compared to other clusters, cluster 1 also had a higher proportion of infections leading to hospitalization and was implicated in more foodborne and beef-associated outbreaks, despite being isolated at a similar frequency from beef products as other clusters. We also identified subpopulations within 11 serovars. Remarkably, we found S . Infantis and S . Typhimurium subpopulations that significantly differed in genome length and clinical case presentation. Further, we found that the presence of the pESI plasmid accounted for the genome length differences between the S . Infantis subpopulations. Our results show that S . enterica strains associated with highest incidence of human infections share a common virulence repertoire. This work could be updated regularly and used in combination with foodborne surveillance information to prioritize serovars of public health concern.

An outbreak of highly pathogenic avian influenza A, subtype H5N1, first reported in U.S. dairy cattle in March 2024, raised concerns of an emerging food safety threat from the virus in the milk supply. To support potential regulatory responses, we conducted a rapid assessment of the predicted risk to U.S. consumers of cow’s milk with two complementary and parallel approaches: a “bottom-up” quantitative risk assessment model that integrated data on virus levels in milk, milk consumption, and dose response; and a “top-down” epidemiological analysis that linked current novel flu illness detection to the consumption of raw and pasteurized milk. The dynamic use of the approaches accommodated rapidly evolving data in a range of risk scenarios. The risk assessment model identified pasteurization as a critical control for H5N1 in milk and highlighted the need for i) the targeted sampling of bulk tank raw milk in affected states pre-pasteurization, ii) raw milk herd surveillance and sampling, and iii) a better understanding of ingestion as a route of H5N1 infections for humans. This novel approach and the findings from this study promoted informed decision-making in an evolving outbreak investigation. This methodology can be leveraged in the conduct of future risk assessments to address emerging pathogen outbreaks that impact the food supply.

Whole genome sequencing (WGS) was performed on 201 Listeria monocytogenes isolates recovered from 102 of 27,389 refrigerated ready-to-eat (RTE) food samples purchased at retail in U.S. FoodNet sites as part of the 2010-2013 interagency L. monocytogenes Market Basket Survey (Lm MBS). Core genome multi-locus sequence typing (cgMLST) and in-silico analyses were conducted, and these data were analyzed with metadata for isolates from five food groups: produce, seafood, dairy, meat, and combination foods. Six of 201 isolates, from 3 samples, were subsequently confirmed as L. welshimeri. Three samples contained one isolate per sample; mmong the 96 samples that contained two isolates per sample, 3 samples each contained two different strains and 93 samples each contained duplicate isolates. After 93 duplicate isolates were removed, the remaining 102 isolates were delineated into 29 clonal complexes (CCs) or singletons based on their sequence type. The five most prevalent CCs were CC155, CC1, CC5, CC87, and CC321. The Shannon's diversity index for clones per food group ranged from 1.49 for dairy to 2.32 for produce isolates, which were not significantly different in pairwise comparisons. The most common molecular serogroup as determined by in-silico analysis was IIa (45.6%), followed by IIb (27.2%), IVb (20.4%), and IIc (4.9%). The proportions of isolates within lineages I, II, and III were 48.0%, 50.0% and 2.0%, respectively. Full-length inlA was present in 89.3% of isolates. Listeria pathogenicity island 3 (LIPI-3) and LIPI-4 were found in 51% and 30.6% of lineage I isolates, respectively. Stress survival islet 1 (SSI-1) was present in 34.7% of lineage I isolates, 80.4% of lineage II isolates and the 2 lineage III isolates; SSI-2 was present only in the CC121 isolate. Plasmids were found in 48% of isolates, including 24.5% of lineage I isolates and 72.5% of lineage II isolates. Among the plasmid-carrying isolates, 100% contained at least one cadmium resistance cassette and 89.8% contained bcrABC, involved in quaternary ammonium compound tolerance. Multiple clusters of isolates from different food samples were identified by cgMLST which, along with available metadata, could aid in the investigation of possible cross-contamination and persistence events.

Food safety risk assessments and large-scale epidemiological investigations have the potential to provide better and new types of information when whole genome sequence (WGS) data are effectively integrated. Today, the NCBI Pathogen Detection database WGS collections have grown significantly through improvements in technology, coordination, and collaboration, such as the GenomeTrakr and PulseNet networks. However, high-quality genomic data is not often coupled with high-quality epidemiological or food chain metadata. We have created a set of tools for cleaning, curation, integration, analysis and visualization of microbial genome sequencing data. It has been tested using Salmonella enterica and Listeria monocytogenes data sets provided by NCBI Pathogen Detection (160,000 sequenced isolates in 2018). GenomeGraphR presents foodborne pathogen WGS data and associated curated metadata in a user-friendly interface that allows a user to query a variety of research questions such as, transmission sources and dynamics, global reach, and persistence of genotypes associated with contamination in the food supply and foodborne illness across time or space. The application is freely available (https://fda-riskmodels.foodrisk.org/genomegraphr/).

Background. Quantitative estimates of the relative risk (RR) of listeriosis among higher-risk populations and a nuanced understanding of the age-specific risks are crucial for risk assessments, targeted interventions, and policy decisions. Method. The RR of invasive listeriosis was evaluated by age, pregnancy status, and ethnicity using 2004—2009 data from the Foodborne Diseases Active Surveillance Network (FoodNet). Nonparametric logistic regression was used to characterize changes in risk with age and ethnicity. Adjusted RRs and 95% confidence intervals (CIs) were evaluated using negative binomial generalized linear models. Results. Among non—pregnancy-associated cases, listeriosis incidence rates increased gradually with age (45—59 years: RR, 4.7; 95% CI, 3.3—6.8; >85 years: RR, 53.8; 95% CI, 37.3—78.9; reference: 15—44 years). The RR was significantly higher for Hispanics than for non-Hispanics (RR, 1.8; 95% CI, 1.3—2.5). Among women of reproductive age (15—44 years), pregnant women had a markedly higher listeriosis risk (RR, 114.6; 95% CI, 68.9—205.1) than nonpregnant women. The RR was higher for Hispanic than non-Hispanic women, regardless of pregnancy status, and this increased during the study period (2004—2006: RR, 1.9; 95% CI, 1.0—3.3; 2007—2009: RR, 4.8; 95% CI, 3.1—7.1). Conclusions. This study quantifies the increases in risk of listeriosis among older persons, pregnant women, and Hispanics in the United States. Additional research is needed to better describe the independent effects of age on risk while accounting for underlying conditions. These estimates are needed both to optimize risk assessment models and to inform targeted interventions and policy decisions.

This study introduces a farm-to-fork quantitative risk assessment (QRA) model for invasive listeriosis from ready-to-eat diced cantaloupe. The modular model comprises seven stages—preharvest (soil and irrigation contamination), harvest (cross-contamination and survival), pre-processing (brushing), processing (flume tank washing, dicing and equipment cross-contamination), lot testing, cold-chain transport and retail growth, and consumer storage/handling. Each stage employs stochastic functions to simulate microbial prevalence and concentration changes (growth, inactivation, removal, partitioning, cross-contamination) using published data. In a reference scenario—good agricultural practices (soil barriers, no preharvest irrigation), hygienic processing and proper cold storage—the model predicts low lot- and pack-level contamination, with few packs >10 CFU/g and most servings below detection; the mean risk per serving is very low. “What-if” analyses highlight critical control points: the absence of soil barriers with preharvest irrigation can increase the risk by 10,000-fold; flume tank water contamination has a greater impact than harvest-stage cross-contamination; and poor consumer storage can raise the risk by up to 500-fold. This flexible QRA framework enables regulators and industry to evaluate and optimize interventions—from improved agricultural measures to targeted sampling plans and consumer guidance—to mitigate listeriosis risk from RTE diced cantaloupe.

Background. Listeriosis can cause severe disease, especially in fetuses, neonates, older adults, and persons with certain immunocompromising and chronic conditions. We summarize US population-based surveillance data for invasive listeriosis from 2004 through 2009. Methods. We analyzed Foodborne Diseases Active Surveillance Network (FoodNet) data for patients with Listeria monocytogenes isolated from normally sterile sites. We describe the epidemiology of listeriosis, estimate overall and specific incidence rates, and compare pregnancy-associated and nonpregnancy-associated listeriosis by age and ethnicity. Results. A total of 762 listeriosis cases were identified during the 6-year reporting period, including 126 pregnancy-associated cases (17%), 234 nonpregnancy-associated cases(31%) in patients aged <65 years, and 400 nonpregnancy-associated cases (53%) in patients aged ≥65 years. Eighteen percent of all cases were fatal. Meningitis was diagnosed in 44% of neonates. For 2004—2009, the overall annual incidence of listeriosis varied from 0.25 to 0.32 cases per 100 000 population. Among Hispanic women, the crude incidence of pregnancy-associated listeriosis increased from 5.09 to 12.37 cases per 100 000 for the periods of 2004—2006 and 2007—2009, respectively; among non-Hispanic women, pregnancy-associated listeriosis increased from 1.74 to 2.80 cases per 100 000 for the same periods. Incidence rates of nonpregnancy-associated listeriosis in patients aged ≥65 years were 4—5 times greater than overall rates annually. Conclusions. Overall listeriosis incidence did not change significantly from 2004 through 2009. Further targeted prevention is needed, including food safety education and messaging (eg, avoiding Mexican-style cheese during pregnancy). Effective prevention among pregnant women, especially Hispanics, and older adults would substantially affect overall rates.

Deli meat was ranked as the highest-risk ready-to-eat food vehicle of Listeria monocytogenes within the 2003 U.S. Food and Drug Administration and U.S. Department of Agriculture, Food Safety and Inspection Service risk assessment. The comparative risk of L. monocytogenes in retail-sliced versus prepackaged deli meats was evaluated with a modified version of this model. Other research has found that retail-sliced deli meats have both higher prevalence and levels of L. monocytogenes than have product sliced and packaged at the manufacturer level. The updated risk assessment model considered slicing location as well as the use of growth inhibitors. The per annum comparative risk ratio for the number of deaths from retail-sliced versus prepackaged deli meats was found to be 4.89, and the per-serving comparative risk ratio was 4.27. There was a significant interaction between the use of growth inhibitors and slicing location. Almost 70% of the estimated deaths occurred from retail-sliced product that did not possess a growth inhibitor. A sensitivity analysis, assessing the effect of the model's consumer storage time and shelf life assumptions, found that even if retail-sliced deli meats were stored for a quarter of the time prepackaged deli meats were stored, retail-sliced product is 1.7 times more likely to result in death from listeriosis. Sensitivity analysis also showed that the shelf life assumption had little effect on the comparative risk ratio.

Dengue is not well documented in Africa. In Cameroon, data are scarce, but dengue infection has been confirmed in humans. We conducted a study to document risk factors associated with anti-dengue virus Immunoglobulin G seropositivity in humans in three major towns in Cameroon. A cross sectional survey was conducted in Douala, Garoua and Yaounde, using a random cluster sampling design. Participants underwent a standardized interview and were blood sampled. Environmental and housing characteristics were recorded. Randomized houses were prospected to record all water containers, and immature stages of Aedes mosquitoes were collected. Sera were screened for anti-dengue virus IgG and IgM antibodies. Risk factors of seropositivity were tested using logistic regression methods with random effects. Anti-dengue IgG were found from 61.4% of sera in Douala (n = 699), 24.2% in Garoua (n = 728) and 9.8% in Yaounde (n = 603). IgM were found from 0.3% of Douala samples, 0.1% of Garoua samples and 0.0% of Yaounde samples. Seroneutralization on randomly selected IgG positive sera showed that 72% (n = 100) in Douala, 80% (n = 94) in Garoua and 77% (n = 66) in Yaounde had antibodies specific for dengue virus serotype 2 (DENV-2). Age, temporary house walls materials, having water-storage containers, old tires or toilets in the yard, having no TV, having no air conditioning and having travelled at least once outside the city were independently associated with anti-dengue IgG positivity in Douala. Age, having uncovered water containers, having no TV, not being born in Garoua and not breeding pigs were significant risk factors in Garoua. Recent history of malaria, having banana trees and stagnant water in the yard were independent risk factors in Yaounde. In this survey, most identified risk factors of dengue were related to housing conditions. Poverty and underdevelopment are central to the dengue epidemiology in Cameroon.

This study introduces a quantitative risk assessment (QRA) model aimed at evaluating the risk of invasive listeriosis linked to the consumption of ready-to-eat (RTE) smoked and gravad fish. The QRA model, based on published data, simulates the production process from fish harvest through to consumer intake, specifically focusing on smoked brine-injected, smoked dry-salted, and gravad fish. In a reference scenario, model predictions reveal substantial probabilities of lot and pack contamination at the end of processing (38.7% and 8.14% for smoked brined fish, 34.4% and 6.49% for smoked dry-salted fish, and 52.2% and 11.1% for gravad fish), although the concentrations of L. monocytogenes are very low, with virtually no packs exceeding 10 CFU/g at the point of sale. The risk of listeriosis for an elderly consumer per serving is also quantified. The lot-level mean risk of listeriosis per serving in the elderly population was 9.751 × 10−8 for smoked brined fish, 9.634 × 10−8 for smoked dry-salted fish, and 2.086 × 10−7 for gravad fish. Risk reduction strategies were then analyzed, indicating that the application of protective cultures and maintaining lower cold storage temperatures significantly mitigate listeriosis risk compared to reducing incoming fish lot contamination. The model also addresses the effectiveness of control measures during processing, such as minimizing cross-contamination. The comprehensive QRA model has been made available as a fully documented qraLm R package. This facilitates its adaptation for risk assessment of other RTE seafood, making it a valuable tool for public health officials to evaluate and manage food safety risks more effectively.