Foodborne Diseases Active Surveillance Network-2 Decades of Achievements, 1996-2015

MARCKS Inhibition Alters Bovine Neutrophil Responses to Salmonella Typhimurium

Neutrophils are innate immune cells that respond quickly to sites of bacterial infection and play an essential role in host defense. Interestingly, some bacterial pathogens benefit from exuberant neutrophil inflammation. Salmonella is one such pathogen that can utilize the toxic mediators released by neutrophils to colonize the intestine and cause enterocolitis. Because neutrophils can aid gut colonization during Salmonella infection, neutrophils represent a potential host-directed therapeutic target. Myristoylated alanine-rich C-kinase substrate (MARCKS) is an actin-binding protein that plays an essential role in many neutrophil effector responses. We hypothesized that inhibition of MARCKS protein would alter bovine neutrophil responses to Salmonella Typhimurium (STm) ex vivo. We used a MARCKS inhibitor peptide to investigate the role of MARCKS in neutrophil responses to STm. This study demonstrates that MARCKS inhibition attenuated STm-induced neutrophil adhesion and chemotaxis. Interestingly, MARCKS inhibition also enhanced neutrophil phagocytosis and respiratory burst in response to STm. This is the first report describing the role of MARCKS protein in neutrophil antibacterial responses.

An integrated FoodNet in North East India: fostering one health approach to fortify public health

BACKGROUND

Food safety is a critical factor in promoting public health and nutrition, especially in developing countries like India, which experience several foodborne disease outbreaks, often with multidrug-resistant pathogens. Therefore, implementing regular surveillance of enteric pathogens in the human-animal-environment interface is necessary to reduce the disease burden in the country.

OBJECTIVE

To establish a network of laboratories for the identification of major food and waterborne pathogens prevailing in the northeast region of India through integrated surveillance of animal, food, human, and environment and investigate the antimicrobial susceptibility pattern of the pathogens of public health significance.

METHODS

The Indian Council of Medical Research (ICMR) has identified FoodNet laboratories; based on their geographical location, inclination to undertake the study, preparedness, proficiency, and adherence to quality assurance procedures, through an 8-step process to systematically expand to cover the Northeastern Region (NER) with comprehensive diagnostic capacities for foodborne pathogens and diarrhea outbreak investigations. Network initiated in the NER given the unique food habits of the ethnic population.

FINDINGS

This surveillance network for foodborne enteric pathogens was established in Assam, Arunachal Pradesh, Tripura, and Sikkim, and expanded to other four states, i.e., Manipur, Mizoram, Meghalaya, and Nagaland, thereby covering the entire NER by including nine medical and three veterinary centers. All these centers are strengthened with periodic training, technical support, funding, capacity building, quality assurance, monitoring, centralized digital data management, and website development.

RESULTS

The ICMR-FoodNet will generate NER-specific data with close to real-time reporting of foodborne disease and outbreaks, and facilitate the updating of food safety management protocols, policy reforms, and public health outbreak response. During 2020-2023, 13,981 food samples were tested and the detection of enteric pathogens ranged from 3 to 4%. In clinical samples, the detection rate of the pathogens was high in the diarrheal stools (8.9%) when 3,107 samples were tested. Thirteen outbreaks were investigated during the study period.

CONCLUSION

Foodborne diseases and outbreaks are a neglected subject. Given the frequent outbreaks leading to the deaths of children, it is crucial to generate robust data through well-established surveillance networks so that a strong food safety policy can be developed for better public health.

Predicting Salmonella MIC and Deciphering Genomic Determinants of Antibiotic Resistance and Susceptibility

Salmonella spp., a leading cause of foodborne illness, is a formidable global menace due to escalating antimicrobial resistance (AMR). The evaluation of minimum inhibitory concentration (MIC) for antimicrobials is critical for characterizing AMR. The current whole genome sequencing (WGS)-based approaches for predicting MIC are hindered by both computational and feature identification constraints. We propose an innovative methodology called the "Genome Feature Extractor Pipeline" that integrates traditional machine learning (random forest, RF) with deep learning models (multilayer perceptron (MLP) and DeepLift) for WGS-based MIC prediction. We used a dataset from the National Antimicrobial Resistance Monitoring System (NARMS), comprising 4500 assembled genomes of nontyphoidal Salmonella, each annotated with MIC metadata for 15 antibiotics. Our pipeline involves the batch downloading of annotated genomes, the determination of feature importance using RF, Gini-index-based selection of crucial 10-mers, and their expansion to 20-mers. This is followed by an MLP network, with four hidden layers of 1024 neurons each, to predict MIC values. Using DeepLift, key 20-mers and associated genes influencing MIC are identified. The 10 most significant 20-mers for each antibiotic are listed, showcasing our ability to discern genomic features affecting Salmonella MIC prediction with enhanced precision. The methodology replaces binary indicators with k-mer counts, offering a more nuanced analysis. The combination of RF and MLP addresses the limitations of the existing WGS approach, providing a robust and efficient method for predicting MIC values in Salmonella that could potentially be applied to other pathogens.

Epidemiology of Salmonellosis Among Infants in the United States: 1968-2015

OBJECTIVES

Describe characteristics of gastroenteritis, bacteremia, and meningitis caused by nontyphoidal Salmonella among US infants.

METHODS

We analyze national surveillance data during 1968-2015 and active, sentinel surveillance data during 1996-2015 for culture-confirmed Salmonella infections by syndrome, year, serotype, age, and race.

RESULTS

During 1968-2015, 190 627 culture-confirmed Salmonella infections among infants were reported, including 165 236 (86.7%) cases of gastroenteritis, 6767 (3.5%) bacteremia, 371 (0.2%) meningitis, and 18 253 (9.7%) with other or unknown specimen sources. Incidence increased during the late 1970s-1980s, declined during the 1990s-early 2000s, and has gradually increased since the mid-2000s. Infants' median age was 4 months for gastroenteritis and bacteremia and 2 months for meningitis. The most frequently reported serotypes were Typhimurium (35 468; 22%) for gastroenteritis and Heidelberg for bacteremia (1954; 29%) and meningitis (65; 18%). During 1996-2015 in sentinel site surveillance, median annual incidence of gastroenteritis was 120, bacteremia 6.2, and meningitis 0.25 per 100 000 infants. Boys had a higher incidence of each syndrome than girls in both surveillance systems, but most differences were not statistically significant. Overall, hospitalization and fatality rates were 26% and 0.1% for gastroenteritis, 70% and 1.6% for bacteremia, and 96% and 4% for meningitis. During 2004-2015, invasive salmonellosis incidence was higher for Black (incident rate ratio, 2.7; 95% confidence interval, 2.6-2.8) and Asian (incident rate ratio, 1.8; 95% confidence interval, 1.7-1.8) than white infants.

CONCLUSIONS

Salmonellosis causes substantial infant morbidity and mortality; serotype heidelberg caused the most invasive infections. Infants with meningitis were younger than those with bacteremia or gastroenteritis. Research into risk factors for infection and invasive illness could inform prevention efforts.

Prevalence and Antimicrobial Resistance Profiles of Foodborne Pathogens Isolated from Dairy Cattle and Poultry Manure Amended Farms in Northeastern Ohio, the United States

Foodborne pathogens significantly impact public health globally. Excessive antimicrobial use plays a significant role in the development of the public health crisis of antibiotic resistance. Here, we determined the prevalence and antimicrobial resistance profiles of E. coli O157, Salmonella, L. monocytogenes, and Campylobacter isolated between 2016 and 2020 from small scale agricultural settings that were amended with dairy cattle or poultry manure in Northeastern Ohio. The total prevalence of the foodborne pathogens was 19.3%: Campylobacter 8%, Listeria monocytogenes 7.9%, Escherichia coli O157 1.8%, and Salmonella 1.5%. The prevalence was significantly higher in dairy cattle (87.7%) compared to poultry (12.2%) manure amended farms. Furthermore, the prevalence was higher in manure samples (84%) compared to soil samples (15.9%; p < 0.05). Multiple drug resistance was observed in 73%, 77%, 100%, and 57.3% of E. coli O157, Salmonella, L. monocytogenes, and Campylobacter isolates recovered, respectively. The most frequently observed resistance genes were mphA, aadA, and aphA1 in E. coli O157; blaTEM, tet(B), and strA in Salmonella; penA, ampC, lde, ermB, tet(O), and aadB in L. monocytogenes and blaOXA-61, tet(O), and aadE in Campylobacter. Our results highlight the critical need to address the dissemination of foodborne pathogens and antibiotic resistance in agricultural settings.

Interpretative labor and the bane of non-standardized metadata in public health surveillance and food safety

Open source DNA sequence databases have long been touted as beneficial to public health, including the facilitation of earlier detection and response to infectious disease outbreaks. Of critical importance to harnessing these benefits is the metadata which describes general and other domain specific attributes (e.g., collection location, isolate type, etc.) of a sample. Unlike the sequence data, the metadata is often incomplete and lacks adherence to an international standard. We describe the problem posed by such variable and incomplete metadata in terms of interpretative labor costs (the time and energy necessary to make sense of the signal in the genetic data), and the impact such metadata has on foodborne outbreak detection and response. Improving the quality of sequence-associated metadata would allow for earlier detection of emerging food safety hazards and allow faster response to foodborne outbreaks.

An analecta of visualizations for foodborne illness trends and seasonality

Disease surveillance systems worldwide face increasing pressure to maintain and distribute data in usable formats supplemented with effective visualizations to enable actionable policy and programming responses. Annual reports and interactive portals provide access to surveillance data and visualizations depicting temporal trends and seasonal patterns of diseases. Analyses and visuals are typically limited to reporting the annual time series and the month with the highest number of cases per year. Yet, detecting potential disease outbreaks and supporting public health interventions requires detailed spatiotemporal comparisons to characterize spatiotemporal patterns of illness across diseases and locations. The Centers for Disease Control and Prevention's (CDC) FoodNet Fast provides population-based foodborne-disease surveillance records and visualizations for select counties across the US. We offer suggestions on how current FoodNet Fast data organization and visual analytics can be improved to facilitate data interpretation, decision-making, and communication of features related to trend and seasonality. The resulting compilation, or analecta, of 436 visualizations of records and codes are openly available online.

Development of a bivalent food poisoning vaccine: augmented antigenicity of the C-terminus of Clostridium perfringens enterotoxin by fusion with the B subunit of Escherichia coli Shiga toxin 2

Food poisonings caused by Clostridium perfringens and Shiga toxin (Stx)-producing Escherichia coli (STEC) occur frequently worldwide; however, no vaccine is currently available. Therefore, we aimed to develop a bivalent vaccine against C. perfringens and STEC infections. Although it has been considered that the C-terminal region of C. perfringens enterotoxin (C-CPE) could be a good vaccine antigen to block the binding to its receptor, it was insufficient for induction of a protective immune response because of the low antigenicity. However, the fusion of C-CPE with Stx2 B subunit (Stx2B) augmented the antigenicity of C-CPE without affecting the antigenicity of Stx2B. Indeed, high levels of C-CPE-specific neutralizing IgG were found in the serum of mice immunized with the fusion protein Stx2B-C-CPE. Additionally, comparable and substantial levels of Stx2B-specific neutralizing IgG were induced in mice receiving Stx2B-C-CPE or Stx2B alone. These antibody responses against C-CPE and Stx2B lasted for at least 48 weeks, which were sufficient for protective immunity in vitro and in vivo, indicating that Stx2B-C-CPE could induce long-term protective immunity. As an underlying mechanism, ex vivo stimulation with Stx2B, but not with C-CPE, induced cytokine production from splenic T cells collected from mice immunized with Stx2B-C-CPE, suggesting that Stx2B-specific, but not C-CPE-specific, T cells were induced by the immunization with Stx2B-C-CPE and plausibly promoted immunoglobulin class switching of both Stx2B- and C-CPE-specific B cells from IgM to IgG. These findings collectively indicate that Stx2B-C-CPE is a T-cell-antigen-supplement-type bivalent vaccine, which could be an efficient against C. perfringens and STEC infections.

Identifying emerging trends in antimicrobial resistance using Salmonella surveillance data in poultry in Spain

Despite of controls and preventive measures implemented along the food chain, infection with non-typhoidal Salmonella (NTS) remains one of the major causes of foodborne disease worldwide. Poultry is considered one of the major sources of NTS. This has led to the implementation of monitoring and control programmes in many countries (including Spain) to ensure that in poultry flocks infection is kept to a minimum and to allow the identification and monitoring of circulating NTS strains and their antimicrobial resistance (AMR) phenotypes. Here, we investigated the information from the monitoring programme for AMR in Salmonella from poultry in Spain in 2011-2017 to assess the diversity in phenotypic resistance and to evaluate the programme's ability to detect multi-resistance patterns and emerging strains in the animal reservoir. Data on serotype and AMR to nine antimicrobials obtained from 3,047 NTS isolates from laying hens (n = 1,060), broiler (n = 765) and turkey (n = 1,222) recovered during controls performed by the official veterinary services and food business operators were analysed using univariate and multivariate methods in order to describe host and serotype-specific profiles. Diversity and prevalence of phenotypic resistance to all but one of the antimicrobials (colistin) were higher in NTS from broiler and turkey compared with laying hen isolates. Certain combinations of serotype and AMR pattern (resistotype) were particularly linked with certain hosts (e.g. susceptible Enteritidis with laying hens, multi-drug resistant (MDR) Derby in turkey, MDR Kentucky in turkey and broiler). The widespread presence of certain serotype-resistotype combinations in certain hosts/years suggested the possible expansion of MDR strains in the animal reservoir. This study demonstrates the usefulness of the analysis of data from monitoring programmes at the isolate level to detect emerging threats and suggests aspects that should be subjected to further research to identify the forces driving the expansion/dominance of certain strains in the food chain.

Relationship Between Census Tract–Level Poverty and Domestically Acquired Salmonella Incidence: Analysis of Foodborne Diseases Active Surveillance Network Data, 2010–2016

Background

The relationships between socioeconomic status and domestically acquired salmonellosis and leading Salmonella serotypes are poorly understood.

Methods

We analyzed surveillance data from laboratory-confirmed cases of salmonellosis from 2010–2016 for all 10 Foodborne Disease Active Surveillance Network (FoodNet) sites, having a catchment population of 47.9 million. Case residential data were geocoded, linked to census tract poverty level, and then categorized into 4 groups according to census tract poverty level. After excluding those reporting international travel before illness onset, age-specific and age-adjusted salmonellosis incidence rates were calculated for each census tract poverty level, overall and for each of the 10 leading serotypes.

Results

Of 52 821geocodable Salmonella infections (&gt;96%), 48 111 (91.1%) were domestically acquired. Higher age-adjusted incidence occurred with higher census tract poverty level (P &lt; .001; relative risk for highest [≥20%] vs lowest [&lt;5%] census tract poverty level, 1.37). Children &lt;5 years old had the highest relative risk (2.07). Although this relationship was consistent by race/ethnicity and by serotype, it was not present in 5 FoodNet sites or among those aged 18–49 years.

Conclusion

Children and older adults living in higher-poverty census tracts have had a higher incidence of domestically acquired salmonellosis. There is a need to understand socioeconomic status differences for risk factors for domestically acquired salmonellosis by age group and FoodNet site to help focus prevention efforts.

Public health delivery in the information age: the role of informatics and technology

AIM

Public health systems have embraced health informatics and information technology as a potential transformational tool to improve real-time surveillance systems, communication, and sharing of information among various agencies. Global pandemic outbreaks like Zika and Ebola were quickly controlled due to electronic surveillance systems enabling efficient information access and exchange. However, there is the need for a more robust technology to enhance adequate epidemic forecasting, data sharing, and effective communication. The purpose of this review was to examine the use of informatics and information technology tools and its impact on public health delivery.

METHOD

Investigators searched six electronic databases. These were MEDLINE, Cumulative Index to Nursing and Allied Health Literature (CINAHL) Complete, Cochrane Database of Systematic Reviews, COMPENDEX, Scopus, and Academic Search Premier from January 2000 to 31 March 2016.

RESULTS

A total of 60 articles met the eligibility criteria for inclusion. These studies were organized into three areas as (1) definition of the term public health informatics; (2) type of public health surveillance systems and implications for public health; and (3) electronic surveillance systems functionality, capability, training, and challenges. Our analysis revealed that due to the growing expectations to provide real-time response and population-centered evidence-based public health in this information-driven age there has been a surge in informatics and information technology adoption. Education and training programs are now available to equip public health students and professionals with skills in public health informatics. However, obstacles including interoperability, data standardization, privacy, and technology transfer persist.

CONCLUSION

Re-engineering the delivery of public health is necessary to meet the demands of the 21st century and beyond. To meet this expectation, public health must invest in workforce development and capacity through education and training in informatics.

Genetic Susceptibility to Postdiarrheal Hemolytic-Uremic Syndrome After Shiga Toxin-Producing Escherichia coli Infection: A Centers for Disease Control and Prevention FoodNet Study

Background

Postdiarrheal hemolytic-uremic syndrome (D+HUS) following Shiga toxin-producing Escherichia coli (STEC) infection is a serious condition lacking specific treatment. Host immune dysregulation and genetic susceptibility to complement hyperactivation are implicated in non-STEC-related HUS. However, genetic susceptibility to D+HUS remains largely uncharacterized.

Methods

Patients with culture-confirmed STEC diarrhea, identified through the Centers for Disease Control and Prevention FoodNet surveillance system (2007-2012), were serotyped and classified by laboratory and/or clinical criteria as having suspected, probable, or confirmed D+HUS or as controls and underwent genotyping at 200 loci linked to nondiarrheal HUS or similar pathologies. Genetic associations with D+HUS were explored by multivariable regression, with adjustment for known risk factors.

Results

Of 641 enrollees with STEC O157:H7, 80 had suspected D+HUS (41 with probable and 32 with confirmed D+HUS). Twelve genes related to cytokine signaling, complement pathways, platelet function, pathogen recognition, iron transport, and endothelial function were associated with D+HUS in multivariable-adjusted analyses (P ≤ .05). Of 12 significant single-nucleotide polymorphisms (SNPs), 5 were associated with all levels of D+HUS (intergenic SNP rs10874639, TFRC rs3804141, EDN1 rs5370, GP1BA rs121908064, and B2M rs16966334), and 7 SNPs (6 non-complement related) were associated with confirmed D+HUS (all P < .05).

Conclusions

Polymorphisms in many non-complement-related genes may contribute to D+HUS susceptibility. These results require replication, but they suggest novel therapeutic targets in patients with D+HUS.

Post-Campylobacter Guillain Barré Syndrome in the USA: secondary analysis of surveillance data collected during the 2009-2010 novel Influenza A (H1N1) vaccination campaign

Guillain Barré syndrome (GBS), which is triggered by autoantibodies produced in response to antigenic stimuli such as certain infections and vaccinations, is the most common cause of acute flaccid paralysis worldwide. Campylobacter, the most common bacterial enteric infection in the USA, is reported to be the most commonly diagnosed antecedent of GBS, yet little information is available about the risk of post-Campylobacter GBS. Data collected through active, population-based surveillance in the Emerging Infections Program during the 2009-2010 novel Influenza A (H1N1) vaccination campaign allowed us to compare confirmed and probable GBS cases to non-cases to determine whether antecedent Campylobacter infection (or a diarrhoeal illness consistent with campylobacteriosis) was more common among cases and to assess the risk of GBS following Campylobacter infection. We estimate that 8-12% of GBS cases in the USA are attributable to Campylobacter infection (or a diarrhoeal illness consistent with campylobacteriosis), with 434-650 cases of post-diarrhoeal GBS annually and about 49 cases of GBS per 100 000 Campylobacter infections. These results provide updated estimates for post-Campylobacter GBS incidence in the USA and highlight an important benefit of effective measures to prevent Campylobacter infections.

The Relationship Between Census Tract Poverty and Shiga Toxin-Producing E. coli Risk, Analysis of FoodNet Data, 2010-2014

Background

The relationship between socioeconomic status and Shiga toxin-producing Escherichia coli (STEC) is not well understood. However, recent studies in Connecticut and New York City found that as census tract poverty (CTP) decreased, rates of STEC increased. To explore this nationally, we analyzed surveillance data from laboratory-confirmed cases of STEC from 2010-2014 for all Foodborne Disease Active Surveillance Network (FoodNet) sites, population 47.9 million.

Methods

Case residential data were geocoded and linked to CTP level (2010-2014 American Community Survey). Relative rates were calculated comparing incidence in census tracts with <20% of residents below poverty with those with ≥20%. Relative rates of age-adjusted 5-year incidence per 100 000 population were determined for all STEC, hospitalized only and hemolytic-uremic syndrome (HUS) cases overall, by demographic features, FoodNet site, and surveillance year.

Results

There were 5234 cases of STEC; 26.3% were hospitalized, and 5.9% had HUS. Five-year incidence was 10.9/100 000 population. Relative STEC rates for the <20% compared with the ≥20% CTP group were >1.0 for each age group, FoodNet site, surveillance year, and race/ethnic group except Asian. Relative hospitalization and HUS rates tended to be higher than their respective STEC relative rates.

Conclusions

Persons living in lower CTP were at higher risk of STEC than those in the highest poverty census tracts. This is unlikely to be due to health care-seeking or diagnostic bias as it applies to analysis limited to hospitalized and HUS cases. Research is needed to better understand exposure differences between people living in the lower vs highest poverty-level census tracts to help direct prevention efforts.

Monitoring the Results of Foodborne Diseases in Sentinel Hospitals in Wenzhou City, China from 2014 to 2015

BACKGROUND

To investigate the epidemiologic distribution of foodborne diseases in Wenzhou City from 2014-2015, we analyzed the characteristics and main pathogens of foodborne disease outbreaks to provide a reference for the prevention, control, and early warning of foodborne diseases.

METHODS

A total of 9139 patients with foodborne diseases were included in the database of active monitoring from sentinel hospitals in Wenzhou City, China. Salmonella, Shigella, Vibrio parahaemolyticus, enteropathogenic Escherichia coli, and norovirus in the stool samples collected from patients with foodborne diseases were detected according to national standards.

RESULTS

There were 82 cases of Salmonella, 6 cases of Shigella, 393 cases of V. parahaemolyticus, 9 cases of diarrhoeagenic E. coli, and 143 cases of norovirus in the 9139 stool and anal swab samples, for a total detection rate of 6.98%. The peak season in which foodborne diseases occurred was from Jun-Oct. The high-risk populations were the 0-5, 16-25, 26-35, 35-45, and 46-55 yr age groups. Aquatic products accounted for the greatest proportion of suspected food, followed by meat, poultry, fruits, and vegetables.

CONCLUSION

V. parahaemolyticus was the main pathogen of foodborne diseases in the Wenzhou urban area; Salmonella and norovirus were also foodborne disease pathogens. To prevent foodborne diseases, it is necessary to strengthen active monitoring, especially the sanitary management of seafood.

Optimized Co-extraction and Quantification of DNA From Enteric Pathogens in Surface Water Samples Near Produce Fields in California

Pathogen contamination of surface water is a health hazard in agricultural environments primarily due to the potential for contamination of crops. Furthermore, pathogen levels in surface water are often unreported or under reported due to difficulty with culture of the bacteria. The pathogens are often present, but require resuscitation, making quantification difficult. Frequently, this leads to the use of quantitative PCR targeted to genes unique to the pathogens. However, multiple pathogen types are commonly in the same water sample, both gram + and gram -, leading to problems with DNA extraction. With Shiga toxin-producing Escherichia coli (STEC), Salmonella enterica and Listeria monocytogenes as target, a method was optimized to co-extract all three and quantify the level of each using droplet digital PCR (ddPCR). Multiplexed target genes in STEC were virulence genes, shiga toxin 2 (stx2) and hemolysin (ehx). Likewise, multiplexed targets in Listeria and Salmonella were the virulence genes listeriolysin (hly) and invasion protein A (invA). Water samples were processed using microbiological techniques for each of the pathogens and duplicate water samples were quantified by ddPCR. A significant correlation was found between culture and ddPCR results indicating detection primarily of culturable cells by ddPCR. Average virulence gene levels were 923, 23 k, 69 and 152 copies per sample for stx2, ehx, hly and invA, respectively. Additionally, stx2, ehx and inv levels were significantly correlated (P < 0.05, R = 0.34) with generic E. coli MPN levels in the duplicate samples. Indirect quantification with ddPCR will improve understanding of prevalence of the pathogens and may reduce risks associated with contaminated surface water.

Distinct fermentation and antibiotic sensitivity profiles exist in salmonellae of canine and human origin

Background

Salmonella enterica is a recognised cause of diarrhoea in dogs and humans, yet the potential for transfer of salmonellosis between dogs and their owners is unclear, with reported evidence both for and against Salmonella as a zoonotic pathogen. A collection of 174 S. enterica isolates from clinical infections in humans and dogs were analysed for serotype distribution, carbon source utilisation, chemical and antimicrobial sensitivity profiles. The aim of the study was to understand the degree of conservation in phenotypic characteristics of isolates across host species.

Results

Serovar distribution across human and canine isolates demonstrated nine serovars common to both host species, 24 serovars present in only the canine collection and 39 solely represented within the human collection. Significant differences in carbon source utilisation profiles and ampicillin, amoxicillin and chloramphenicol sensitivity profiles were detected in isolates of human and canine origin. Differences between the human and canine Salmonella collections were suggestive of evolutionary separation, with canine isolates better able to utilise several simple sugars than their human counterparts. Generally higher minimum inhibitory concentrations of three broad-spectrum antimicrobials, commonly used in veterinary medicine, were also observed in canine S. enterica isolates.

Conclusions

Differential carbon source utilisation and antimicrobial sensitivity profiles in pathogenic Salmonella isolated from humans and dogs are suggestive of distinct reservoirs of infection for these hosts. Although these findings do not preclude zoonotic or anthroponotic potential in salmonellae, the separation of carbon utilisation and antibiotic profiles with isolate source is indicative that infectious isolates are not part of a common reservoir shared frequently between these host species.

High Throughput Sequencing for Detection of Foodborne Pathogens

High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic "natural" strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.

National Antimicrobial Resistance Monitoring System: Two Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance

Drug-resistant bacterial infections pose a serious and growing public health threat globally. In this review, we describe the role of the National Antimicrobial Resistance Monitoring System (NARMS) in providing data that help address the resistance problem and show how such a program can have broad positive impacts on public health. NARMS was formed two decades ago to help assess the consequences to human health arising from the use of antimicrobial drugs in food animal production in the United States. A collaboration among the Centers for Disease Control and Prevention, the U.S. Food and Drug Administration, the United States Department of Agriculture, and state and local health departments, NARMS uses an integrated "One Health" approach to monitor antimicrobial resistance in enteric bacteria from humans, retail meat, and food animals. NARMS has adapted to changing needs and threats by expanding surveillance catchment areas, examining new isolate sources, adding bacteria, adjusting sampling schemes, and modifying antimicrobial agents tested. NARMS data are not only essential for ensuring that antimicrobial drugs approved for food animals are used in ways that are safe for human health but they also help address broader food safety priorities. NARMS surveillance, applied research studies, and outbreak isolate testing provide data on the emergence of drug-resistant enteric bacteria; genetic mechanisms underlying resistance; movement of bacterial populations among humans, food, and food animals; and sources and outcomes of resistant and susceptible infections. These data can be used to guide and evaluate the impact of science-based policies, regulatory actions, antimicrobial stewardship initiatives, and other public health efforts aimed at preserving drug effectiveness, improving patient outcomes, and preventing infections. Many improvements have been made to NARMS over time and the program will continue to adapt to address emerging resistance threats, changes in clinical diagnostic practices, and new technologies, such as whole genome sequencing.

Salmonella epidemiology: A whirlwind of change

The field of infectious disease epidemiology for Salmonella and other enteric pathogens is undergoing some of the most profound changes since the time of Kauffman and White. Rapid advances in "big data" technologies such as genomics and metagenomics are making it possible to monitor and control salmonellosis in new and exciting ways. Epidemiological methods are becoming increasingly robust through the routine use of standardized hypothesis-generating questionnaires, iterative open-ended interviewing, informational trace-backs and new modeling techniques for describing the attribution of disease to food sources. In addition, Salmonella epidemiology is facing important challenges and new opportunities due to the rapid adoption of culture independent diagnostic test panels by clinical laboratories. Where is this unprecedented wave of change taking us? This chapter will examine emerging trends in Salmonella epidemiology, and take a peek into the not-so-distant future.

Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California

Escherichia coli serotype O157:H7 is a zoonotic food- and waterborne bacterial pathogen that causes a high hospitalization rate and can cause life-threatening complications. Increasingly, E. coli O157:H7 infections appear to originate from fresh produce. Ruminants, such as cattle, are a prominent reservoir of E. coli O157:H7 in the United States. California is one of the most agriculturally productive regions in the world for fresh produce, beef, and milk. The close proximity of fresh produce and cattle presents food safety challenges on a uniquely large scale. We performed a survey of E. coli O157:H7 on 20 farms in California to observe the regional diversity and prevalence of E. coli O157:H7. Isolates were obtained from enrichment cultures of cow feces. Some farms were sampled on two dates. Genomes from isolates were sequenced to determine their relatedness and pathogenic potential. E. coli O157:H7 was isolated from approximately half of the farms. The point prevalence of E. coli O157:H7 on farms was highly variable, ranging from zero to nearly 90%. Within farms, generally one or a few lineages were found, even when the rate of isolation was high. On farms with high isolation rates, a single clonal lineage accounted for most of the isolates. Farms that were visited months after the first visit might have had the same lineages of E. coli O157:H7. Strains of E. coli O157:H7 may be persistent for months on farms.IMPORTANCE This survey of 20 cow-calf operations from different regions of California provides an in depth look at resident Escherichia coli O157:H7 populations at the molecular level. E. coli O157:H7 is found to have a highly variable prevalence, and with whole-genome sequencing, high prevalences in herds were found to be due to a single lineage shed from multiple cows. Few repeat lineages were found between farms in this area; therefore, we predict that E. coli O157:H7 has significant diversity in this area beyond what is detected in this survey. All isolates from this study were found to have pathogenic potential based on the presence of key virulence gene sequences. This represents a novel insight into pathogen diversity within a single subtype and will inform future attempts to survey regional pathogen populations.

Cultivation of an Adaptive Domestic Network for Surveillance and Evaluation of Emerging Infections

Accomplishments of this program have provided numerous dividends and might benefit areas outside infectious diseases.