Multistate outbreak of multidrug-resistant Salmonella newport infections associated with ground beef, October to December 2007

Food safety incidents in the red meat industry: A review of foodborne disease outbreaks linked to the consumption of red meat and its products, 1991 to 2021

Red meat is a significant source of human nutrition, and the red meat industry contributes to the economy of nations. Nonetheless, there is a widespread global concern about public health issues posed by severe food safety incidents within the red meat industry. Most of these incidents are associated with foodborne disease outbreaks that impact individual consumers, food businesses and society. This study adopts a systematic search and review approach to identify three decades of published investigation reports of global foodborne disease outbreaks linked with the consumption of red meat and products made from them. The review aims to evaluate the critical features of these outbreak incidents to get insight into their contributing factors and root causes. In particular, this review discusses the transmission setting (origin of pathogenic agents), the food vehicles mostly incriminated, the causative pathogens (bacteria, viruses, and parasites) causing the most illnesses, and the most commonly reported contributing factors to the outbreaks. This information can help researchers and food business operators (FBOs) inform future risk assessment studies and support risk management activities in developing risk-mitigating strategies for the industry. Findings from this study suggest that implementing food safety management strategies which include adequate control measures at all stages of the food chain, from farm to fork, is imperative in preventing outbreak incidents. Of equal importance is the need for enhanced and sustained public education about the risk of foodborne illnesses associated with meat and its products whilst discouraging the consumption of raw meat products, especially by high-risk groups.

Heuristic and Hierarchical-Based Population Mining of Salmonella enterica Lineage I Pan-Genomes as a Platform to Enhance Food Safety

The recent incorporation of bacterial whole-genome sequencing (WGS) into Public Health laboratories has enhanced foodborne outbreak detection and source attribution. As a result, large volumes of publicly available datasets can be used to study the biology of foodborne pathogen populations at an unprecedented scale. To demonstrate the application of a heuristic and agnostic hierarchical population structure guided pan-genome enrichment analysis (PANGEA), we used populations of S. enterica lineage I to achieve two main objectives: (i) show how hierarchical population inquiry at different scales of resolution can enhance ecological and epidemiological inquiries; and (ii) identify population-specific inferable traits that could provide selective advantages in food production environments. Publicly available WGS data were obtained from NCBI database for three serovars of Salmonella enterica subsp. enterica lineage I (S. Typhimurium, S. Newport, and S. Infantis). Using the hierarchical genotypic classifications (Serovar, BAPS1, ST, cgMLST), datasets from each of the three serovars showed varying degrees of clonal structuring. When the accessory genome (PANGEA) was mapped onto these hierarchical structures, accessory loci could be linked with specific genotypes. A large heavy-metal resistance mobile element was found in the Monophasic ST34 lineage of S. Typhimurium, and laboratory testing showed that Monophasic isolates have on average a higher degree of copper resistance than the Biphasic ones. In S. Newport, an extra sugE gene copy was found among most isolates of the ST45 lineage, and laboratory testing of multiple isolates confirmed that isolates of S. Newport ST45 were on average less sensitive to the disinfectant cetylpyridimium chloride than non-ST45 isolates. Lastly, data-mining of the accessory genomic content of S. Infantis revealed two cryptic Ecotypes with distinct accessory genomic content and distinct ecological patterns. Poultry appears to be the major reservoir for Ecotype 1, and temporal analysis further suggested a recent ecological succession, with Ecotype 2 apparently being displaced by Ecotype 1. Altogether, the use of a heuristic hierarchical-based population structure analysis that includes bacterial pan-genomes (core and accessory genomes) can (1) improve genomic resolution for mapping populations and accessing epidemiological patterns; and (2) define lineage-specific informative loci that may be associated with survival in the food chain.

ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses

Whole Genome Sequence (WGS) data from bacterial species is used for a variety of applications ranging from basic microbiological research, diagnostics, and epidemiological surveillance. The availability of WGS data from hundreds of thousands of individual isolates of individual microbial species poses a tremendous opportunity for discovery and hypothesis-generating research into ecology and evolution of these microorganisms. Flexibility, scalability, and user-friendliness of existing pipelines for population-scale inquiry, however, limit applications of systematic, population-scale approaches. Here, we present ProkEvo, an automated, scalable, reproducible, and open-source framework for bacterial population genomics analyses using WGS data. ProkEvo was specifically developed to achieve the following goals: (1) Automation and scaling of complex combinations of computational analyses for many thousands of bacterial genomes from inputs of raw Illumina paired-end sequence reads; (2) Use of workflow management systems (WMS) such as Pegasus WMS to ensure reproducibility, scalability, modularity, fault-tolerance, and robust file management throughout the process; (3) Use of high-performance and high-throughput computational platforms; (4) Generation of hierarchical-based population structure analysis based on combinations of multi-locus and Bayesian statistical approaches for classification for ecological and epidemiological inquiries; (5) Association of antimicrobial resistance (AMR) genes, putative virulence factors, and plasmids from curated databases with the hierarchically-related genotypic classifications; and (6) Production of pan-genome annotations and data compilation that can be utilized for downstream analysis such as identification of population-specific genomic signatures. The scalability of ProkEvo was measured with two datasets comprising significantly different numbers of input genomes (one with ~2,400 genomes, and the second with ~23,000 genomes). Depending on the dataset and the computational platform used, the running time of ProkEvo varied from ~3-26 days. ProkEvo can be used with virtually any bacterial species, and the Pegasus WMS uniquely facilitates addition or removal of programs from the workflow or modification of options within them. To demonstrate versatility of the ProkEvo platform, we performed a hierarchical-based population structure analyses from available genomes of three distinct pathogenic bacterial species as individual case studies. The specific case studies illustrate how hierarchical analyses of population structures, genotype frequencies, and distribution of specific gene functions can be integrated into an analysis. Collectively, our study shows that ProkEvo presents a practical viable option for scalable, automated analyses of bacterial populations with direct applications for basic microbiology research, clinical microbiological diagnostics, and epidemiological surveillance.

Community composition and antibiotic resistance of bacteria in bottlenose dolphins Tursiops truncatus - Potential impact of 2010 BP Oil Spill

Aquatic contamination, oil spills in particular, could lead to the accumulation of antibiotic resistance by promoting selection for and/or transfer of resistance genes. However, there have been few studies on antibiotic resistance in marine mammals in relation to environmental disturbances, specifically oil contaminations. Here we initiated a study on antibiotic resistance bacteria in bottlenose dolphins Tursiops truncatus in relation to oil contamination following the 2010 BP Oil Spill in the northern Gulf of Mexico. Bacterial communities and antibiotic resistance prevalence one year after the 2010 BP Oil Spill were compared between Barataria Bay (BB) and Sarasota Bay (SB) by applying the rarefaction curve method, and (generalized) linear mixed models. The results showed that the most common bacteria included Vibrio, Shewanella, Bacillus and Pseudomonas. The prevalence of antibiotic resistance was high in the bacterial isolates at both bays. Though bacterial diversity did not differ significantly among water or dolphin samples, and antibiotic resistance did not differ significantly among water samples between the two bays, antibiotic resistance and multi-drug resistance in dolphin samples was significantly higher in the BB than in the SB, mainly attributed to the resistance to E, CF, FEP and SXT. We also found sulfamethoxazole-trimethoprim-resistant Stenotrophomonas maltophilia the first time in the natural aquatic environment. The higher antibiotic resistance in the dolphins in BB is likely attributed to 2010 BP Oil Spill as we expected SB, a more urbanized bay area, would have had higher antibiotic resistance based on the previous studies. The antibiotic resistance data gathered in this research will fill in the important data gaps and contributes to the broader spatial-scale emerging studies on antibiotic resistance in aquatic environments.

Outbreak of Salmonella Newport associated with internationally distributed raw goats' milk cheese, France, 2018

Raw milk cheeses are commonly consumed in France and are also a common source of foodborne outbreaks (FBOs). Both an FBO surveillance system and a laboratory-based surveillance system aim to detect Salmonella outbreaks. In early August 2018, five familial FBOs due to Salmonella spp. were reported to a regional health authority. Investigation identified common exposure to a raw goats' milk cheese, from which Salmonella spp. were also isolated, leading to an international product recall. Three weeks later, on 22 August, a national increase in Salmonella Newport ST118 was detected through laboratory surveillance. Concomitantly isolates from the earlier familial clusters were confirmed as S. Newport ST118. Interviews with a selection of the laboratory-identified cases revealed exposure to the same cheese, including exposure to batches not included in the previous recall, leading to an expansion of the recall. The outbreak affected 153 cases, including six cases in Scotland. S. Newport was detected in the cheese and in the milk of one of the producer's goats. The difference in the two alerts generated by this outbreak highlight the timeliness of the FBO system and the precision of the laboratory-based surveillance system. It is also a reminder of the risks associated with raw milk cheeses.

Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance

Whole-genome sequencing (WGS) is used increasingly in public-health laboratories for typing and characterizing foodborne pathogens. To evaluate the performance of existing bioinformatic tools for in silico prediction of antimicrobial resistance (AMR) and serotypes of Salmonella enterica, WGS-based genotype predictions were compared with the results of traditional phenotyping assays. A total of 111 S. enterica isolates recovered from a Canadian baseline study on broiler chicken conducted in 2012-2013 were selected based on phenotypic resistance to 15 different antibiotics and isolates were subjected to WGS. Both SeqSero2 and SISTR accurately determined S. enterica serotypes, with full matches to laboratory results for 87.4 and 89.2% of isolates, respectively, and partial matches for the remaining isolates. Antimicrobial resistance genes (ARGs) were identified using several bioinformatics tools including the Comprehensive Antibiotic Resistance Database – Resistance Gene Identifier (CARD-RGI), Center for Genomic Epidemiology (CGE) ResFinder web tool, Short Read Sequence Typing for Bacterial Pathogens (SRST2 v 0.2.0), and k-mer alignment method (KMA v 1.17). All ARG identification tools had ≥ 99% accuracy for predicting resistance to all antibiotics tested except streptomycin (accuracy 94.6%). Evaluation of ARG detection in assembled versus raw-read WGS data found minimal observable differences that were gene- and coverage- dependent. Where initial phenotypic results indicated isolates were sensitive, yet ARGs were detected, repeat AMR testing corrected discrepancies. All tools failed to find resistance-determining genes for one gentamicin- and two streptomycin-resistant isolates. Further investigation found a single nucleotide polymorphism (SNP) in the nuoF coding region of one of the isolates which may be responsible for the observed streptomycin-resistant phenotype. Overall, WGS-based predictions of AMR and serotype were highly concordant with phenotype determination regardless of computational approach used.

Worldwide Epidemiology of Salmonella Serovars in Animal-Based Foods: a Meta-analysis

Salmonella spp. are among the most important foodborne pathogens and the third leading cause of human death among diarrheal diseases worldwide. Animals are the primary source of this pathogen, and animal-based foods are the main transmission route to humans. Thus, understanding the global epidemiology of Salmonella serovars is key to controlling and monitoring this bacterium. In this context, this study aimed to evaluate the prevalence and diversity of Salmonella enterica serovars in animal-based foods (beef, pork, poultry, and seafood) throughout the five continents (Africa, the Americas [North and Latin America], Asia, Europe, and Oceania). The meta-analysis consisted of a chemometric assessment (hierarchical cluster analysis and principal component analysis) to identify the main epidemiological findings, including the prevalence and diversity of the Salmonella serovars in each matrix. Regarding the serovar distribution, S Typhimurium presented a cosmopolitan distribution, reported in all four assessed matrices and continents; poultry continues to play a central role in the dissemination of the Enteritidis serovar to humans, and Anatum and Weltevreden were the most frequently found in beef and seafood, respectively. Additionally, we recommended careful monitoring of certain serovars, such as Derby, Agona, Infantis, and Kentucky. Finally, given the scientific data regarding the most frequently reported serovars and which matrices constitute the main vehicles for the transmission of this pathogen, control programs may be improved, and specific interventions may be implemented in an attempt to reduce the risk of this pathogen reaching humans.IMPORTANCE Salmonellosis is caused by Salmonella spp. and is the third leading cause of death among food-transmitted diseases. This pathogen is commonly disseminated in domestic and wild animals, and the infection's symptoms are characterized by acute fever, nausea, abdominal pain, and diarrhea. The animals are the primary source of salmonellae, and animal-based foods are the main transmission route to humans. Therefore, data collected from these sources could contribute to future global interventions for effective control and surveillance of Salmonella along the food chain. In light of this, the importance of our research is in identifying the prevalence of Salmonella serovars in four animal-based food matrices (pork, poultry, beef, and seafood) and to evaluate the importance that each matrix has as the primary source of this pathogen to humans.

Prevalence and Serotype Diversity of Salmonella in Apparently Healthy Cattle: Systematic Review and Meta-Analysis of Published Studies, 2000-2017

Salmonellosis is a leading cause of foodborne illnesses in humans with cattle being one of the reservoirs for Salmonella. We estimated a pooled prevalence of Salmonella in apparently healthy cattle and examined serotype diversity through systematic review and meta-analysis of studies published between 2000 and 2017. Peer reviewed publications reporting the prevalence of Salmonella in cattle were searched through five electronic databases (PubMed, Google scholar, Agricola, Scopus, CAB direct) and through manual search. We obtained 71 publications with 75 datasets consisting a total of 52,766 animals examined and 5,010 Salmonella positive cattle from 29 countries in six continents (except from Antarctica). Pooled prevalence of Salmonella in cattle was 9% (95% confidence interval: 7-11%). Significantly high heterogeneity (I 2 = 98.7%, P < 0.01) was observed among all studies as well as within continents. Prevalence varied from 2% (Europe) to 16% (North America). Overall, 143 different serotypes were reported with the most diverse serotypes being reported from Africa (76 different serotypes) followed by North America (49 serotypes). The 10 most frequently reported serotypes (Montevideo, Typhimurium, Kentucky, Meleagridis, Anatum, Cerro, Mbandaka, Muenster, Newport, and Senftenberg) accounted for 65% of the isolates for which specific serotype information was reported. Salmonella Montevideo and S. Dublin are the most frequently reported serotypes in North America and Europe, respectively, while S. Typhimurium was the most frequent in Africa, Asia and Australasia. Our results indicated variability both in the prevalence and serotype diversity of Salmonella in cattle across continents. Although all Salmonella serotypes are potentially pathogenic to humans, five (Montevideo, Typhimurium, Anatum, Mbandaka, and Newport) of the top 10 serotypes identified in this study are among the serotypes most commonly associated with clinical illnesses in humans.

Analysis of consumer food purchase data used for outbreak investigations, a review

BackgroundInvestigations of food-borne outbreaks are frequently unsuccessful and new investigation methods should be welcomed. Aim: Describe the use of consumer purchase datasets in outbreak investigations and consider methodological and practical difficulties. Methods: We reviewed published papers describing the use of consumer purchase datasets, where electronic data on the foods that case-patients had purchased before onset of symptoms were obtained and analysed as part of outbreak investigations. Results: For the period 2006-17, scientific articles were found describing 20 outbreak investigations. Most outbreaks involved salmonella or Shiga toxin-producing Escherichia coli and were performed in eight different countries. The consumer purchase datasets were most frequently used to generate hypotheses about the outbreak vehicle where case-interviews had not been fruitful. Secondly, they were used to aid trace-back investigation, where a vehicle was already suspected. A number of methodological as well as (in some countries) legal and practical impediments exist. Conclusions: Several of the outbreaks were unlikely to have been solved without the use of consumer purchase datasets. The method is potentially powerful and with future improved access to big data purchase information, may become a widely applicable tool for outbreak investigations, enabling investigators to quickly find hypotheses and at the same time estimate odds ratios or relative risks hereof. We suggest using the term 'consumer purchase data' to refer to the approach in the future.

Salmonella in Peripheral Lymph Nodes of Healthy Cattle at Slaughter

To more fully characterize the burden of Salmonella enterica in bovine peripheral lymph nodes (PLN), PLN (n = 5,450) were collected from healthy cattle at slaughter in 12 commercial abattoirs that slaughtered feedlot-fattened (FF) cattle exclusively (n = 7), cattle removed (or culled) from breeding herds (n = 3), or both FF and cull cattle (n = 2). Qualitative and quantitative methods were used to estimate prevalence and concentration of Salmonella in PLN. Isolates were subjected to a variety of phenotypic, serological, and molecular assays. Overall, Salmonella prevalence in PLN from FF and cull cattle was 7.1 and 1.8%. However, burden varied by season in that observed prevalence in PLN collected in cooler or warmer seasons was 2.4 and 8.2%, respectively. Prevalence in PLN from cull cattle in the southwest region of the US was 2.1 and 1.1% for cool and warm seasons, respectively; however, prevalence in FF PLN was far greater in that it was 6.5 and 31.1%, respectively. Salmonella was recovered from 289 (5.6%) PLN and 2.9% (n = 160) of all PLN tested had quantifiable concentrations that varied from 1.6 to 4.9 log₁₀ colony forming units/PLN. The most common serotypes isolated from PLN were Montevideo (26.9%), Lille (14.9%), Cerro (13.0%), Anatum (12.8%), and Dublin (6.9%). In all, 376 unique isolates were collected from the 289 Salmonella-positive PLN. Antimicrobial susceptibility testing revealed the majority (80.6%) of these isolates were pansusceptible; however, 10.7% of isolates were found to be resistant to two or more antimicrobial classes. We were able to document an observed increased in prevalence of Salmonella in PLN during the warmer season, particularly in FF cattle from the southwest region of the US. The mechanisms underlying the observed association between season, region, and production source have yet to be elucidated. Nevertheless, these findings increase our understanding of the sources of contamination of beef products and shed light on transmission dynamics that may be useful in targeting these sources.

Bacteriophages Contribute to the Spread of Antibiotic Resistance Genes among Foodborne Pathogens of the Enterobacteriaceae Family - A Review

Foodborne illnesses continue to have an economic impact on global health care systems. There is a growing concern regarding the increasing frequency of antibiotic resistance in foodborne bacterial pathogens and how such resistance may affect treatment outcomes. In an effort to better understand how to reduce the spread of resistance, many research studies have been conducted regarding the methods by which antibiotic resistance genes are mobilized and spread between bacteria. Transduction by bacteriophages (phages) is one of many horizontal gene transfer mechanisms, and recent findings have shown phage-mediated transduction to be a significant contributor to dissemination of antibiotic resistance genes. Here, we review the viability of transduction as a contributing factor to the dissemination of antibiotic resistance genes in foodborne pathogens of the Enterobacteriaceae family, including non-typhoidal Salmonella and Shiga toxin-producing Escherichia coli, as well as environmental factors that increase transduction of antibiotic resistance genes.

Whole-Genome Comparative Analysis of Salmonella enterica Serovar Newport Strains Reveals Lineage-Specific Divergence

Salmonella enterica subsp. enterica serovar Newport has been associated with various foodborne outbreaks in humans and animals. Phylogenetically, serovar Newport is one of several Salmonella serovars that are polyphyletic. To understand more about the polyphyletic nature of this serovar, six food, environment, and human isolates from different Newport lineages were selected for genome comparison analyses. Whole genome comparisons demonstrated that heterogeneity mostly occurred in the prophage regions. Lineage-specific characteristics were also present in the Salmonella pathogenicity islands and fimbrial operons.

Effects of antimicrobial use in agricultural animals on drug-resistant foodborne salmonellosis in humans: A systematic literature review

Controversy continues concerning antimicrobial use in food animals and its relationship to drug-resistant infections in humans. We systematically reviewed published literature for evidence of a relationship between antimicrobial use in agricultural animals and drug-resistant meat or dairy-borne non-typhoidal salmonellosis in humans. Based on publications from the United States (U.S.), Canada, and Denmark from January 2010 to July 2014, 858 articles received title and abstract review, 104 met study criteria for full article review with 68 retained for which data are presented. Antibiotic exposure in both cattle and humans found an increased likelihood of Salmonella colonization, whereas in chickens, animals not exposed to antibiotics (organic) were more likely to be Salmonella positive and those that had antibiotic exposure were more likely to harbor antimicrobial resistant Salmonella organisms. In swine literature, only tylosin exposure was examined and no correlation was found among exposure, Salmonella colonization, or antimicrobial resistance. No studies that identified farm antimicrobial use also traced antimicrobial-resistant Salmonella from farm to fork.

The risk of carriage of Salmonella spp. and Listeria monocytogenes in food animals in dynamic populations

Salmonella spp. and Listeria monocytogenes are foodborne pathogens of global importance. We assessed their risks and associated factors in a highly dynamic population of animals. Animal and environmental samples were collected from dairy cattle, sheep, camel and chickens at either the farms or the abattoirs. The pathogens were detected using a combination of bacterial enrichment culture and real‐time polymerase chain reaction (PCR). Data on putative risk factors were collect and analysed for their significance of association with these pathogens.

Salmonella spp. were detected at higher proportions in sheep faeces and sheep carcasses in comparison to cattle faeces (odds ratio = 2.4 and 2.2, respectively). This pathogen was less common in milk or carcasses samples from cattle or chickens. Sheep and camel carcass samples were highly contaminated with Salmonella spp. Faecal samples from cattle had the most diverse serovars of Salmonella enterica including S. Newport, S. Haifa, S. Kedougou, S. Kentucky, S. Mbandaka and S. Goettingen. Exotic serovars in sheep included S. Eastbourne, S. Chester and S. Kottnus. Serovars that were shed in camel faeces included S. Newport, S. Bovismorbificans and S. Infantis. In all sampled populations, detection of Salmonella spp. was more likely during warmer months than cold months. Listeria monocytogenes was not common in the targeted populations and was detected at a rate of 2.4%, mainly from sheep carcasses. The study highlights the role of food animals as reservoirs of pathogens across boundaries since all feed are imported in that population from different parts of the world.

Prevalence and Characteristics of Salmonella Serotypes Isolated from Fresh Produce Marketed in the United States

Salmonella continues to rank as one of the most costly foodborne pathogens, and more illnesses are now associated with the consumption of fresh produce. The U.S. Department of Agriculture Microbiological Data Program (MDP) sampled select commodities of fresh fruit and vegetables and tested them for Salmonella, pathogenic Escherichia coli, and Listeria. The Salmonella strains isolated were further characterized by serotype, antimicrobial resistance, and pulsed-field gel electrophoresis profile. This article summarizes the Salmonella data collected by the MDP between 2002 and 2012. The results show that the rates of Salmonella prevalence ranged from absent to 0.34% in cilantro. A total of 152 isolates consisting of over 50 different serotypes were isolated from the various produce types, and the top five were Salmonella enterica serotype Cubana, S. enterica subspecies arizonae (subsp. IIIa) and diarizonae (subsp. IIIb), and S. enterica serotypes Newport, Javiana, and Infantis. Among these, Salmonella serotypes Newport and Javiana are also listed among the top five Salmonella serotypes that caused most foodborne outbreaks. Other serotypes that are frequent causes of infection, such as S. enterica serotypes Typhimurium and Enteritidis, were also found in fresh produce but were not prevalent. About 25% of the MDP samples were imported produce, including 65% of green onions, 44% of tomatoes, 42% of hot peppers, and 41% of cantaloupes. However, imported produce did not show higher numbers of Salmonella-positive samples, and in some products, like cilantro, all of the Salmonella isolates were from domestic samples. About 6.5% of the Salmonella isolates were resistant to the antimicrobial compounds tested, but no single commodity or serotype was found to be the most common carrier of resistant strains or of resistance. The pulsed-field gel electrophoresis profiles of the produce isolates showed similarities with Salmonella isolates from meat samples and from outbreaks, but there were also profile diversities among the strains within some serotypes, like Salmonella Newport.

Multidrug-resistant pathogens in the food supply

Antimicrobial resistance, including multidrug resistance (MDR), is an increasing problem globally. MDR bacteria are frequently detected in humans and animals from both more- and less-developed countries and pose a serious concern for human health. Infections caused by MDR microbes may increase morbidity and mortality and require use of expensive drugs and prolonged hospitalization. Humans may be exposed to MDR pathogens through exposure to environments at health-care facilities and farms, livestock and companion animals, human food, and exposure to other individuals carrying MDR microbes. The Centers for Disease Control and Prevention classifies drug-resistant foodborne bacteria, including Campylobacter, Salmonella Typhi, nontyphoidal salmonellae, and Shigella, as serious threats. MDR bacteria have been detected in both meat and fresh produce. Salmonellae carrying genes coding for resistance to multiple antibiotics have caused numerous foodborne MDR outbreaks. While there is some level of resistance to antimicrobials in environmental bacteria, the widespread use of antibiotics in medicine and agriculture has driven the selection of a great variety of microbes with resistance to multiple antimicrobials. MDR bacteria on meat may have originated in veterinary health-care settings or on farms where animals are given antibiotics in feed or to treat infections. Fresh produce may be contaminated by irrigation or wash water containing MDR bacteria. Livestock, fruits, and vegetables may also be contaminated by food handlers, farmers, and animal caretakers who carry MDR bacteria. All potential sources of MDR bacteria should be considered and strategies devised to reduce their presence in foods. Surveillance studies have documented increasing trends in MDR in many pathogens, although there are a few reports of the decline of certain multidrug pathogens. Better coordination of surveillance programs and strategies for controlling use of antimicrobials need to be implemented in both human and animal medicine and agriculture and in countries around the world.

Genetic diversity of Salmonella pathogenicity islands SPI-5 and SPI-6 in Salmonella Newport

Salmonella enterica subspecies enterica serotype Newport is one of the common serotypes causing foodborne salmonellosis outbreaks in the United States. Salmonella Newport consists of three lineages exhibiting extensive genetic diversity. Due to the importance of Salmonella pathogenicity islands 5 and 6 (SPI-5 and SPI-6) in virulence of pathogenic Salmonella, the genetic diversity of these two SPIs may relate to different potentials of Salmonella Newport pathogenicity. Most Salmonella Newport strains from North America belong to Salmonella Newport lineages II and III. A total 28 Salmonella Newport strains of lineages II and III from diverse sources and geographic locations were analyzed, and 11 additional Salmonella genomes were used as outgroup in phylogenetic analyses. SPI-5 was identified in all Salmonella Newport strains and 146 single nucleotide polymorphisms (SNPs) were detected. Thirty-nine lineage-defining SNPs were identified, including 18 nonsynonymous SNPs. Two 40-kb genomic islands (SPI5-GI1 and SPI5-GI2) encoding bacteriophage genes were found between tRNA-ser and pipA. SPI5-GI1 was only present in Salmonella Newport multidrug-resistant strains of lineage II. SPI-6 was found in all strains but three Asian strains in Salmonella Newport lineage II, whereas the three Asian strains carried genomic island SPI6-GI1 at the same locus as SPI-6 in other Salmonella. SPI-6 exhibited 937 SNPs, and phylogenetic analysis demonstrated that clustering of Salmonella Newport isolates was a reflection of their geographic origins. The sequence diversity within SPI-5 and SPI-6 suggests possible recombination events and different virulence potentials of Salmonella Newport. The SNPs could be used as biomarkers during epidemiological investigations.

Outbreak-associated Salmonella enterica serotypes and food Commodities, United States, 1998-2008

Salmonella enterica infections are transmitted not only by animal-derived foods but also by vegetables, fruits, and other plant products. To clarify links between Salmonella serotypes and specific foods, we examined the diversity and predominance of food commodities implicated in outbreaks of salmonellosis during 1998–2008. More than 80% of outbreaks caused by serotypes Enteritidis, Heidelberg, and Hadar were attributed to eggs or poultry, whereas >50% of outbreaks caused by serotypes Javiana, Litchfield, Mbandaka, Muenchen, Poona, and Senftenberg were attributed to plant commodities. Serotypes Typhimurium and Newport were associated with a wide variety of food commodities. Knowledge about these associations can help guide outbreak investigations and control measures.

An outbreak of Salmonella Newport associated with mung bean sprouts in Germany and the Netherlands, October to November 2011

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Occurrence, serotype diversity, and antimicrobial resistance of salmonella in ground beef at retail stores in Jalisco state, Mexico

The occurrence, serotype diversity, and antimicrobial resistance of Salmonella bacteria in commercial ground beef at retail establishments were investigated. Salmonella was isolated from 135 (56.7%) of 238 ground beef samples collected at the same number of butcher's shops located in three municipalities of Jalisco State, Mexico, during an 11-month period. The isolation frequency differed by municipality (P < 0.05) and was higher (P < 0.05) during the warm season (68.5%) than during the cold season (43.2%). Overall, 25 serotypes and 8 serogroups were identified among 135 Salmonella isolates; predominant were Salmonella group B (9.6%), Salmonella Anatum (8.9%), Salmonella Agona (6.7%), Salmonella Infantis (6.7%), and Salmonella Typhimurium (5.9%). All Salmonella isolates were tested for susceptibility to 11 antimicrobial drugs of human and veterinary use. Resistance to tetracycline was the most commonly observed (40.7%), followed by resistance to streptomycin (35.6%), trimethoprim-sulfamethoxazole (20.7%), and nalidixic acid (19.3%). Thirty-seven Salmonella isolates (27.4%) were multidrug resistant, and the majority corresponded to Salmonella Group B, Salmonella Anatum, and Salmonella Typhimurium. Three Salmonella isolates were resistant to seven different antimicrobials. The frequency of Salmonella in ground beef samples (56.7%) was higher than that observed in our previous investigation on beef carcasses (15.4%) at small abattoirs in the same region of Mexico. This may be a result of increasing contamination at these two points of the raw-beef production chain or may be an effect of the grinding process that facilitates a more-homogeneous pathogen distribution in the product. Poor hygiene, temperature abuse, and practices allowing cross-contamination during ground beef fabrication at these retail establishments increase the consumer's exposure to Salmonella.

Use of global trade item numbers in the investigation of a salmonella newport outbreak associated with blueberries in Minnesota, 2010

In August 2010, the Minnesota Department of Agriculture and Minnesota Department of Health investigated an outbreak of six cases of Salmonella Newport infection occurring in northwestern Minnesota, which identified fresh blueberries as the cause. Initially, traditional traceback methods involving the review of invoices and bills of lading were used to attempt to identify the source of the outbreak. When these methods failed, novel traceback methods were used. Specifically, supplier-specific 12-digit Global Trade Item Numbers (GTINs) and shopper-card information were used to identify a single blueberry grower linked to cases, corroborating the results of a case-control study in which consuming fresh blueberries was statistically associated with illness (5 of 5 cases versus 8 of 19 controls, matched odds ratio [MOR] undefined, P = 0.02). Consuming fresh blueberries from retailer A was also statistically associated with illness (3 of 3 cases versus 3 of 18 controls, MOR undefined, P = 0.03). Based on initially incomplete evidence in this investigation, the invoices pointed to wholesaler A and grower A, based on first-in-first-out product rotation. However, when point-of-sale data were analyzed and linked to shopper-card information, a common GTIN was identified. This information led to an on-site record evaluation at retailer A, and the discovery of additional records at this location documented the supply chain from grower B to wholesaler C to retailer A, shifting the focus of the investigation from grower A to grower B. This investigation demonstrates the emerging concepts of Critical Tracking Events (CTEs) and Key Data Elements (KDE) related to food product tracing. The use of these shopper-cased data and the event data that were queried by investigators demonstrates the potential utility of consciously designed CTEs and KDEs at critical points in the supply chain to better facilitate product tracing.

Reduction of Escherichia coli O157:H7 and Salmonella after application of various sanitizing treatments to harvesting knives

Consumption of food contaminated with Escherichia coli O157:H7 and Salmonella can cause enteric disease in consumers. If not properly sanitized, knives used during animal harvest can spread these and other pathogens. This study evaluated the reduction of E. coli O157:H7 and Salmonella on harvesting knives after nonthermal sanitation. Knives were inoculated in cocktails of E. coli O157:H7 or Salmonella and treated by 30-s immersions in ambient-temperature solutions (unless temperature was specified) of 1.1 % sodium metasilicate (SMS), 200 ppm of quaternary ammonium compounds (QAC), 200 ppm of chlorine (Cl(2)), 5 % lactic acid (LA), 82.2°C water, and 21°C water. Initial and treated counts were determined by plating onto MacConkey and xylose lysine desoxycholate for E. coli O157:H7 and Salmonella, respectively. Initial counts were determined by sampling one side of the knife blade, while treated counts were sampled from the opposite side. Plates were incubated for 24 to 48 h at 37°C. Mean attachment of E. coli O157:H7 and Salmonella was 4.51 and 5.09 log CFU/cm(2), respectively. Mean log reductions on knives inoculated with E. coli O157:H7 were 1.16, 3.51, 3.38, 1.38, 3.82, and 2 0.41 CFU/cm(2) after treatment in SMS, QAC, Cl(2), LA, 82.2°C water, and 21°C water, respectively (P ≤ 0.05). Knives inoculated with Salmonella showed reductions of 0.78, 3.42, 3.40, 2.91, 4.12, and 0.36 log CFU/cm(2) after treatment in SMS, QAC, Cl(2), LA, 82.2°C water, and 21°C water, respectively (P ≤ 0.05). Results indicate that some ambient-temperature sanitizing agents have the potential to significantly reduce E. coli O157:H7 and Salmonella populations on knives used during animal harvest.

Quantifying Salmonella population dynamics in water and biofilms

Members of the bacterial genus Salmonella are recognized worldwide as major zoonotic pathogens often found to persist in non-enteric environments including heterogeneous aquatic biofilms. In this study, Salmonella isolates that had been detected repeatedly over time in aquatic biofilms at different sites in Spring Lake, San Marcos, Texas, were identified as serovars Give, Thompson, Newport and -:z10:z39. Pathogenicity results from feeding studies with the nematode Caenorhabditis elegans as host confirmed that these strains were pathogenic, with Salmonella-fed C. elegans dying faster (mean survival time between 3 and 4 days) than controls, i.e., Escherichia coli-fed C. elegans (mean survival time of 9.5 days). Cells of these isolates inoculated into water at a density of up to 10(6) ml(-1) water declined numerically by 3 orders of magnitude within 2 days, reaching the detection limit of our quantitative polymerase chain reaction (qPCR)-based quantification technique (i.e., 10(3) cells ml(-1)). Similar patterns were obtained for cells in heterogeneous aquatic biofilms developed on tiles and originally free of Salmonella that were kept in the inoculated water. Cell numbers increased during the first days to more than 10(7) cells cm(-2), and then declined over time. Ten-fold higher cell numbers of Salmonella inoculated into water or into biofilm resulted in similar patterns of population dynamics, though cells in biofilms remained detectable with numbers around 10(4) cells cm(-2) after 4 weeks. Independent of detectability by qPCR, samples of all treatments harbored viable salmonellae that resembled the inoculated isolates after 4 weeks of incubation. These results demonstrate that pathogenic salmonellae were isolated from heterogeneous aquatic biofilms and that they could persist and stay viable in such biofilms in high numbers for some time.

The public health impact of food-related illness

PURPOSE OF REVIEW

The purpose of this review is to provide an update on the public health impact of food-related illness in light of recent high-profile outbreaks and advances in the methodology to estimate illness burden. It includes mainly literature from high-income countries, as burden of illness estimations have been focussed in these countries.

RECENT FINDINGS

The public health burden of food-related illness is very high, no matter what method is used to measure it. Outbreaks provide only a partial insight because they represent a small proportion of all cases of food-related illness. Recent outbreaks have demonstrated a very wide variety of contaminated food vehicles and illustrated the challenges in investigations when the contaminated foodstuff is an ingredient of many other food items.

SUMMARY

Outbreaks will continue to challenge public health responses so that maintaining capacity to respond rapidly is crucial. Technological advances, such as whole genome sequencing, pave the way for identifying food-related illness much more rapidly than at present. There is a need to improve diagnostic yield in clinical laboratories and culturing organisms will remain important. Perhaps one of the greatest challenges, though, is to maintain the interest and support of the public when investigating food-related illness.

Efficacy of chemical interventions against Escherichia coli O157:H7 and multidrug-resistant and antibiotic-susceptible Salmonella on inoculated beef trimmings

Studies were conducted to compare the decontamination efficacy of six chemical treatments against Escherichia coli O157:H7 and multidrug-resistant and antibiotic-susceptible Salmonella inoculated on beef trimmings. The inocula, comprising four-strain mixtures of rifampin-resistant E. coli O157:H7 and antibiotic-susceptible or multidrug-resistant (MDR and/or MDR-AmpC) Salmonella Newport and Salmonella Typhimurium, were inoculated (3 log CFU/cm(2)) separately onto samples (10 by 5 by 1 cm) derived from beef chuck rolls. Samples were left untreated (control), were immersed for 30 s in acidified sodium chlorite (0.1%, pH 2.5), peroxyacetic acid (0.02%, pH 3.8), sodium metasilicate (4%, pH 12.6), Bromitize Plus (0.0225% active bromine, pH 6.6), or AFTEC 3000 (pH 1.2), or were immersed for 5 s in SYNTRx 3300 (pH 1.0). Levels of surviving Salmonella on treated trimmings were not influenced by serotype or antibiotic resistance phenotype and were generally similar (P ≥ 0.05) or lower (P < 0.05) than levels of surviving E. coli O157:H7 regardless of antimicrobial treatment. Overall, depending on chemical treatment (reductions within each chemical treatment were similar among all tested inocula), initial counts of E. coli O157:H7 (2.7 to 3.1 log CFU/cm(2)) were reduced (P < 0.05) by 0.2 to 1.4 log CFU/cm(2). Similarly, initial counts of the tested Salmonella inocula (2.8 to 3.3 log CFU/cm(2)) were reduced (P < 0.05) by 0.4 to 1.4 (Salmonella Newport, antibiotic susceptible), 0.3 to 1.4 (Salmonella Newport, MDR-AmpC), 0.2 to 1.5 (Salmonella Typhimurium, antibiotic susceptible), 0.4 to 1.3 (Salmonella Typhimurium, MDR), and 0.4 to 1.5 (Salmonella Typhimurium, MDR-AmpC) log CFU/cm(2), depending on antimicrobial treatment. Reductions obtained with sodium metasilicate were 1.3 to 1.5 log CFU/cm(2), regardless of inoculum, and reductions obtained with the five remaining antimicrobial treatments were 0.2 to 0.7 log CFU/cm(2) (depending on treatment). Findings of this study should be useful to regulatory authorities and the meat industry as they consider Salmonella contamination on beef trimmings.

Impacts of culture-independent diagnostic practices on public health surveillance for bacterial enteric pathogens

For decades, culture has been the mainstay of diagnostic testing for bacterial enteric pathogens. This paradigm is changing as clinical laboratories adopt culture-independent methods, such as antigen-based tests and nucleic acid-based assays. Public health surveillance for enteric infections addresses 4 interrelated but distinct objectives: case investigation for localized disease control; assessment of disease burden and trends to prioritize and assess impact of population-based control measures; outbreak detection; and microbiologic characterization to improve understanding of pathogens, their virulence mechanisms, and epidemiology. We summarize the challenges and opportunities that culture-independent tests present and suggest strategies, such as validation studies and development of culture-independent tests compatible with subtyping, that could be adopted to ensure that surveillance remains robust. Many of these approaches will require time and resources to implement, but they will be necessary to maintain a strong surveillance system. Public health practitioners must clearly explain the value of surveillance, especially how outbreak detection benefits the public, and collaborate with all stakeholders to develop solutions.

Sensitivity of Shiga toxin-producing Escherichia coli, multidrug-resistant Salmonella, and antibiotic-susceptible Salmonella to lactic acid on inoculated beef trimmings

Studies were performed to determine whether lactic acid treatments used to reduce Escherichia coli O157:H7 on beef trimmings are also effective in controlling non-O157 Shiga toxin-producing E. coli (nSTEC), and multidrug-resistant and antibiotic-susceptible Salmonella. Beef trimming pieces (10 by 5 by 1 cm) were inoculated (3 log CFU/cm(2)) separately with four-strain mixtures of rifampin-resistant E. coli O157:H7, O26, O45, O103, O111, O121, and O145. Similarly, in a second study, trimmings were separately inoculated with rifampin-resistant E. coli O157:H7, and antibiotic-susceptible or multidrug-resistant (MDR and/or MDR-AmpC) Salmonella Newport and Salmonella Typhimurium. Inoculated trimmings were left untreated (control) or were immersed for 30 s in 5% lactic acid solutions (25 or 55°C). No differences (P ≥ 0.05) were obtained among surviving counts of E. coli O157:H7 and those of the tested nSTEC serogroups on lactic acid-treated (25 or 55°C) samples. Counts (3.1 to 3.3 log CFU/cm(2)) of E. coli O157:H7 and nSTEC were reduced (P < 0.05) by 0.5 to 0.9 (25°C lactic acid) and 1.0 to 1.4 (55°C lactic acid) log CFU/cm(2). Surviving counts of Salmonella on treated trimmings were not influenced by serotype or antibiotic resistance phenotype and were similar (P ≥ 0.05) or lower (P < 0.05) than surviving counts of E. coli O157:H7. Counts (3.0 to 3.3 log CFU/cm(2)) were reduced (P < 0.05) by 0.5 to 0.8 (E. coli O157:H7) and 1.3 to 1.5 (Salmonella) log CFU/cm(2) after treatment of samples with 25°C lactic acid. Corresponding reductions following treatment with lactic acid at 55°C were 1.2 to 1.5 (E. coli O157:H7) and 1.6 to 1.9 (Salmonella) log CFU/cm(2). Overall, the results indicated that lactic acid treatments used against E. coli O157:H7 on beef trimmings should be similarly or more effective against the six nSTEC serogroups and against multidrug-resistant and antibiotic-susceptible Salmonella Newport and Salmonella Typhimurium.

Nationwide outbreak of Salmonella Montevideo infections associated with contaminated imported black and red pepper: warehouse membership cards provide critical clues to identify the source

In November 2009, we initiated a multistate investigation of Salmonella Montevideo infections with pulsed-field gel electrophoresis pattern JIXX01.0011. We identified 272 cases in 44 states with illness onset dates ranging from 1 July 2009 to 14 April 2010. To help generate hypotheses, warehouse store membership card information was collected to identify products consumed by cases. These records identified 19 ill persons who purchased company A salami products before onset of illness. A case-control study was conducted. Ready-to-eat salami consumption was significantly associated with illness (matched odds ratio 8·5, 95% confidence interval 2·1–75·9). The outbreak strain was isolated from company A salami products from an environmental sample from one manufacturing plant, and sealed containers of black and red pepper at the facility. This outbreak illustrates the importance of using membership card information to assist in identifying suspect vehicles, the potential for spices to contaminate ready-to-eat products, and preventing raw ingredient contamination of these products.

Salmonella diversity and burden in cows on and culled from dairy farms in the Texas High Plains

The objective of this study was to characterize the epidemiology of Salmonella carried by dairy cows culled from herds in the Texas High Plains. Feces were collected from a convenience sample of 706 animals culled from nine dairy farms. In addition, individually paired fecal and hide samples were collected from 70 healthy milking cows on three of the dairies. Samples were cultured for Salmonella using routine methods; isolates were serotyped and subjected to a panel of antimicrobial drugs to determine susceptibility. Salmonella was recovered from 32.6% of culled cows. Whole-herd use of a vaccine containing siderophore receptors and porin proteins was associated (p=0.05) with reduced Salmonella prevalence in that the prevalence among herds that practiced whole-herd vaccination was 8.0% compared to 36.8% among herds that did not use this vaccine. The majority (88.6%) of isolates were pansusceptible or resistant to one drug. Of the 3.1% of isolates resistant to more than four drugs, all were Salmonella Newport and were recovered from one dairy. Various serotypes were recovered from individual fecal and hide samples. Salmonella Montevideo was recovered more frequently (p<0.01) from hide samples, whereas Salmonella Cerro was recovered more frequently (p<0.01) from feces. Salmonella was recovered from at least one cow on all dairies. While our study was not a priori designed to address herd-level factors, we found evidence that the whole-herd use of a siderophore receptor and porin protein-containing vaccine might be a useful aid in the control of Salmonella in groups of cattle. As this is a nonrandomized evaluation of an intervention, other herd-level factors that may be correlated with vaccine use, such as biosecurity, might have been responsible for the observed association.