Current aspects ofSalmonellacontamination in the US poultry production chain and the potential application of risk strategies in understanding emerging hazards

Evaluation of the in vitro and in vivo efficiency of in-feed bacteriophage cocktail application to control Salmonella Typhimurium and Salmonella Enteritidis infection in broiler chicks

RESEARCH HIGHLIGHTS

Bacteriophage (BP) cocktail was partially resistant to different temperatures and pH values.The BP cocktail showed lytic effects on different Salmonella isolates.The BP cocktail reduced Salmonella colonization in the internal organs of broilers.

Genomic perspectives on foodborne illness

Whole-genome sequencing of bacterial pathogens is used by public health agencies to link cases of food poisoning caused by the same source of contamination. The vast majority of these appear to be sporadic cases associated with small contamination episodes and do not trigger investigations. We analyzed clusters of sequenced clinical isolates of Salmonella, Escherichia coli, Campylobacter, and Listeria that differ by only a small number of mutations to provide a new understanding of the underlying contamination episodes. These analyses provide new evidence that the youngest age groups have greater susceptibility to infection from Salmonella, Escherichia coli, and Campylobacter than older age groups. This age bias is weaker for the common Salmonella serovar Enteritidis than Salmonella in general. Analysis of these clusters reveals significant regional variations in relative frequencies of Salmonella serovars across the United States. A large fraction of the contamination episodes causing sickness appear to have long duration. For example, 50% of the Salmonella cases are in clusters that persist for almost three years. For all four pathogen species, the majority of the cases were part of genetic clusters with illnesses in multiple states and likely to be caused by contaminated commercially distributed foods. The vast majority of Salmonella cases among infants < 6 months of age appear to be caused by cross-contamination from foods consumed by older age groups or by environmental bacteria rather than infant formula contaminated at production sites.

Comprehensive Assessment of Subtyping Methods for Improved Surveillance of Foodborne Salmonella

High-resolution and efficient typing for the bacterial pathogen is essential for tracking the sources, detecting or diagnosing variants, and conducting a risk assessment. However, a systematic in-field investigation of Salmonella along the food chain has not been documented. This study assessed 12 typing methods, such as antimicrobial-resistance (AMR) gene profile typing, Core Genome Multilocus Sequence Typing (cgMLST), and CRISPR multi-virulence locus sequence typing (CRISPR-MVLST), to evaluate their effectiveness for use in routine monitoring of foodborne Salmonella transmission along the poultry production chain. During 2015-16, a total of 1,064 samples were collected from poultry production chain, starting from breeding farms and slaughterhouses to the markets of Zhejiang province in China. A total of 61 consecutive unique Salmonella isolates recovered from these samples were selected for genome sequencing and further comparative typing analysis. Traditional typing methods, including serotyping, AMR phenotype-based typing, as well as modern genotyping approaches, were evaluated and compared by their discrimination index (DI). The results showed that the serotyping method identified nine serovars. The gold standard cgMLST method indicated only 18 different types (DI = 0.8541), while the CRISPR-MVLST method detected 30 types (DI = 0.9628), with a higher DI than all examined medium-resolution WGS-based genotyping methods. We demonstrate that the CRISPR-MVLST might be used as a tool with high discriminatory power, comparable ease of use, ability of tracking the source of Salmonella strains along the food chain and indication of genetic features especially virulence genes. The available methods with different purposes and laboratory expertise were also illustrated to assist in rational implementation. IMPORTANCE In public health field, high-resolution and efficient typing of the bacterial pathogen is essential, considering source-tracking and risk assessment are fundamental issues. Currently, there are no recommendations for applying molecular characterization methods for Salmonella along the food chain, and a systematic in-field investigation comparing subtyping methods in the context of routine surveillance was partially addressed. Using 1,064 samples along a poultry production chain with a considerable level of Salmonella contamination, we collected representative isolates for genome sequencing and comparative analysis by using 12 typing techniques, particularly with whole-genome sequence (WGS) based methods and a recently invented CRISPR multi-virulence locus sequence typing (CRISPR-MVLST) method. CRISPR-MVLST is identified as a tool with higher discriminatory power compared with medium-resolution WGS-based typing methods, comparable ease of use and proven ability of tracking Salmonella isolates. Besides, we also offer recommendations for rational choice of subtyping methods to assist in better implementation schemes.

Virulence and antimicrobial resistance factors in Salmonella enterica serotypes isolated from pigs and chickens in central Chile

Salmonella enterica is a food-borne pathogen with a wide host-range that during decades has been of public health concern in developed and developing countries. In Chile, the poultry and pig industries represent the biggest contribution of meat consumption in the population, and sanitary regulations have been imposed for Salmonella control. The aim of this work was to determine and characterize Salmonella strains isolated from pigs and chicken raised on commercials farms in Chile. For this, isolates belonging to pigs (n = 46) and poultry (n = 57) were genotyped by two multiplex PCR reactions and virulotyped by the PCR detection of virulence-associated genes. In addition, isolates were serotyped and analyzed by the Kirby Bauer assay to determine their antimicrobial resistance phenotypes. From these analyses 52 genotypes, six serotypes and several multidrug resistance phenotypes and different combinations of virulence-associated genes were detected. These results suggest that S. enterica in pigs and poultry in central Chile should be monitored due to potential consequences in public and animal health.

Antagonistic activity and mechanism of Lactobacillus rhamnosus SQ511 against Salmonella enteritidis

Salmonella enteritidis is an important food-borne pathogen. The use of antibiotics is a serious threat to animal and human health, owing to the existence of resistant strains and drug residues. Lactic acid bacteria, as a new alternative to antibiotics, has attracted much attention. In this study, we investigated the antibacterial potential and underlying mechanism of Lactobacillus rhamnosus SQ511 against S. enteritidis ATCC13076. The results revealed that L. rhamnosus SQ511 significantly inhibited S. enteritidis ATCC13076 growth or even caused death. Laser confocal microscopic imaging revealed that the cell-free supernatant (CFS) of L. rhamnosus SQ511 elevated the reactive oxygen species level and bacterial membrane depolarization in S. enteritidis ATCC13076, leading to cell death. Furthermore, L. rhamnosus SQ511 CFS had severely deleterious effects on S. enteritidis ATCC13076, causing membrane destruction and the release of cellular materials. In addition, L. rhamnosus SQ511 CFS significantly reduced the expression of virulence, motility, adhesion, and invasion genes in S. enteritidis ATCC13076 (P < 0.05), and considerably inhibited motility and biofilm formation capacity (P < 0.05). Thus, antimicrobial compounds produced by L. rhamnosus SQ511 strongly inhibited S. enteritidis growth, mobility, biofilm formation, membrane disruption, and reactive oxygen species generation, and regulated virulence-related gene expressions, presenting promising applications as a probiotic agent.

Salmonella Broiler Meat's Contamination in Tunisia: Prevalence, Serotypes, Antimicrobial Resistance and Molecular Characterization of Isolated Strains

This study was conducted in north-eastern Tunisia to estimate the contamination prevalence of Salmonella in broilers' meat, to rank serotypes and to characterize the isolated multidrug-resistant (MDR) strains. A total number of 1288 meat samples were collected from 322 broiler batches; Salmonella isolates were identified by the alternative technique VIDAS Easy Salmonella. The susceptibility of Salmonella isolates was assessed against 21 antimicrobials using the disc diffusion method on Mueller-Hinton agar. Some antimicrobial resistance genes were identified using Polymerase Chain Reaction (PCR). The prevalence rates of Salmonella in the neck skin and the breast muscle contamination were estimated at 11.8% (38/322) and 0.9% (3/322), respectively. The prevalence rate of Salmonella in meat cutting parts contamination was estimated at 5.1% (33/644). Eight serotypes of Salmonella were identified, namely S. Enteritidis, S. Kentucky, S. Anatum, S. Infantis, S. Mbandaka, S. Zanzibar, S. Hadar and S. Agona. High rate of resistance was identified against amoxicillin (91.9%), nalidixic acid (83.8%), tetracycline (75.7%), streptomycin (73%), ciprofloxacin (70%), sulfamides (68.9%), cefalotin (68.9%), cefotaxim (67.6%) and cefoxitin (60.8%). The majority (90.5%; 67/74) of isolated strains was recognized as MDR. Nine MDR strains were identified as Extended-Spectrum β-Lactamase (ESBL) producers. The bla_CTX-M gene was identified by PCR in all the nine ESBL strains. TetA, tetB and dfrA1 genes were amplified in 3.6% (2/56), 1.8% (1/56) and 19.3% (5/26) of tetracycline and trimethoprim-resistant strains, respectively. The integrase gene (class 2) was identified in only 8.1% (6/74) of the Salmonella-isolated strains. Our findings highlight the emergence of MDR Salmonella isolates in Tunisia.

Regional Salmonella Differences in United States Broiler Production from 2016 to 2020 and the Contribution of Multiserovar Populations to Salmonella Surveillance

Poultry remains a considerable source of foodborne salmonellosis despite significant reduction of Salmonella incidence during processing. There are multiple entry points for Salmonella during production that can lead to contamination during slaughter, and it is important to distinguish the serovars present between the different stages to enact appropriate controls. National Salmonella data from the U.S. Department of Agriculture-Food Safety Inspection Service (USDA-FSIS) monitoring of poultry processing was analyzed from 2016 to 2020. The overall Salmonella incidence at processing in broiler carcasses and intact parts (parts) decreased from 9.00 to 6.57% over this period. The incidence in parts was higher (11.15%) than in carcasses (4.78%). Regional differences include higher proportions of serovars Infantis and Typhimurium in the Atlantic and higher proportion of serovar Schwarzengrund in the Southeast. For Georgia, the largest broiler-producing state, USDA-FSIS data were compared to Salmonella monitoring data from breeder flocks over the same period, revealing serovar Kentucky as the major serovar in breeders (67.91%) during production but not at processing, suggesting that it is more effectively removed during antimicrobial interventions. CRISPR-SeroSeq was performed on breeder samples collected between 2020 and 2021 to explain the incongruence between pre- and postharvest and showed that 32% of samples contain multiple serovars, with up to 11 serovars found in a single flock. High-resolution sequencing identifies serovar patterns at the population level and can provide insight to develop targeted controls. The work presented may apply to other food production systems where Salmonella is a concern, since it overcomes limitations associated with conventional culture. IMPORTANCE Salmonella is a leading cause of bacterial foodborne illness in the United States, with poultry as a significant Salmonella reservoir. We show the relative decrease in Salmonella over a 5-year period from 2016 to 2020 in processed chicken parts and highlight regional differences with respect to the prevalence of clinically important Salmonella serovars. Our results show that the discrepancy between Salmonella serovars found in pre- and postharvest poultry during surveillance are due in part by the limited detection depth offered by traditional culture techniques. Despite the reduction of Salmonella at processing, the number of human salmonellosis cases has remained stable, which may be attributed to differences in virulence among serovars and their associated risk. When monitoring for Salmonella, it is imperative to identify all serovars present to appropriately assess public health risk and to implement the most effective Salmonella controls.

Phages and Enzybiotics in Food Biopreservation

Presently, biopreservation through protective bacterial cultures and their antimicrobial products or using antibacterial compounds derived from plants are proposed as feasible strategies to maintain the long shelf-life of products. Another emerging category of food biopreservatives are bacteriophages or their antibacterial enzymes called "phage lysins" or "enzybiotics", which can be used directly as antibacterial agents due to their ability to act on the membranes of bacteria and destroy them. Bacteriophages are an alternative to antimicrobials in the fight against bacteria, mainly because they have a practically unique host range that gives them great specificity. In addition to their potential ability to specifically control strains of pathogenic bacteria, their use does not generate a negative environmental impact as in the case of antibiotics. Both phages and their enzymes can favor a reduction in antibiotic use, which is desirable given the alarming increase in resistance to antibiotics used not only in human medicine but also in veterinary medicine, agriculture, and in general all processes of manufacturing, preservation, and distribution of food. We present here an overview of the scientific background of phages and enzybiotics in the food industry, as well as food applications of these biopreservatives.

Salmonella in Chicken Meat: Consumption, Outbreaks, Characteristics, Current Control Methods and the Potential of Bacteriophage Use

The control of Salmonella in chicken processing plants is an ongoing challenge for many factories around the globe, especially with the increasing demand for poultry escalating processing throughputs. Foodborne outbreaks due to Salmonella still pose a prominent risk to public health. As chicken meat is a good reservoir for Salmonella, it is important for chicken processing plants to continuously optimize methods to reduce the incidence of Salmonella on their products. Current methods include the use of chemical antimicrobials such as chlorine-containing compounds and organic acids. However, these current methods are decreasing in popularity due to the rising rate of Salmonella resistance, coupled with the challenge of preserving the sensory properties of the meat, along with the increasing stringency of antimicrobial use. Bacteriophages are becoming more appealing to integrate into the large-scale hurdle concept. A few factors need to be considered for successful implementation, such as legislation, and application volumes and concentrations. Overall, bacteriophages show great potential because of their host specificity, guaranteeing an alternative outcome to the selective pressure for resistant traits placed by chemicals on whole microbial communities.

Mapping foodborne pathogen contamination throughout the conventional and alternative poultry supply chains

Recently, there has been a consumer push for natural and organic food products. This has caused alternative poultry production, such as organic, pasture, and free-range systems, to grow in popularity. Due to the stricter rearing practices of alternative poultry production systems, different types of levels of microbiological risks might be present for these systems when compared to conventional production systems. Both conventional and alternative production systems have complex supply chains that present many different opportunities for flocks of birds or poultry meat to be contaminated with foodborne pathogens. As such, it is important to understand the risks involved during each step of production. The purpose of this review is to detail the potential routes of foodborne pathogen transmission throughout the conventional and alternative supply chains, with a special emphasis on the differences in risk between the two management systems, and to identify gaps in knowledge that could assist, if addressed, in poultry risk-based decision making.

Occurrence of Escherichia coli and Salmonella species in Some Livestock (Poultry) Feeds in Mando, Kaduna, Nigeria

The study aimed at assessing the proximate composition, isolation, characterization of some Enterobacteriaceae from two (2) brands of poultry feeds marketed in Mando, Kaduna, Nigeria. A total of sixteen (16) samples of two (2) different poultry feeds (starter and finisher) from four (4) poultry farms in mando were collected and subjected to proximate and microbiological analysis. The proximate analysis was carried out using standard techniques and procedures. All the feed samples were cultured on separate media which include Eosin methylene blue (EMB), nutrient Agar (NA) and Salmonella-Shigella Agar (SSA) media using standard procedures. The antibiogram of the selected antibiotics was evaluated against the test isolates. The result of proximate analysis of the starter and finisher feeds indicated that the Dry matter of starter feed had the highest percentage composition of 95.02% and crude fiber of the finisher feed had the lowest composition of 3.78%. The highest number of bacterial load was recorded to be 10.0×104 CFU/g for the feed sample A (starter feed) and 12.0x104CFU/g was recorded for the feed sample B (finisher feed) which had the highest number of bacterial load recorded among the two (2) different poultry feeds analyzed. The bacteria isolates were identified as Salmonella species and Escherichia coli. Total viable count (TVC) of Salmonella species and E. coli in the feed samples (starter and finisher) ranges from 3.0×104CFU/g to 12.0×104CFU/g. Both organisms (Salmonella species, E. coli) were found as 37.5% and 25% of the analyzed feeds (Broiler starter and broiler finisher) samples, respectively. There was no level of significant (p>0.05) difference between the level of contamination of Salmonella species and E. coli in the two different feeds analyzed, as p=0.06 and p=0.13 for Salmonella species, and E. coli respectively. Sample A and B (Starter and Finisher) feeds had the highest number of Salmonella species occurrence with six ( 6) positive samples while E. coli was recorded in four (4) samples of A and B (Starter and Finisher) feeds. The result of the antibiogram indicated that ciprofloxacin (30 µg), Gentamycin (30µg), Perfloxacin (30µg) and Tarvid (30µg) was effective against Salmonella species and Escherichia coli. The significant of spread of the species of the Enterobacteriaceae in livestock feeds requires the need for effective quality assurance and control, good hygiene practices in production and proper handling of the poultry feeds.

Prevalence and Molecular Characterization of Salmonella Isolated from Broiler Farms at the Tolima Region-Colombia

Simple Summary

Salmonella spp. is a major foodborne pathogen with a worldwide distribution that is responsible for salmonellosis in animals and humans. Salmonella contamination of poultry and derivative products occurs at different levels. The aim of this study was to estimate the prevalence of Salmonella in broilers farms and to conduct a phenotypic and molecular characterization of Salmonella isolates. The prevalence at the broiler farm level was 26.67%, and all isolates were found to belong to the serovar Salmonella Paratyphi B. These results suggest a common source of Salmonella contamination between broiler farms, presumably via feed, parent flocks or hatchery machines. Salmonella Paratyphi B is present in different segments of the poultry chain in the Tolima region. Additional studies are needed to identify the main source of Salmonella in broilers, chicken carcasses, and eggs commercialized in the Tolima region.

Abstract

Salmonella is an important animal and human pathogen responsible for Salmonellosis, and it is frequently associated with the consumption of contaminated poultry products. The aim of this study was to estimate the prevalence of Salmonella in the poultry farms and to determine the genetic relationship. A total of 135 samples collected from fifteen broiler farms, including cloacal, feed, water, environmental and farm operator faeces samples were subjected to microbiological isolation. Molecular confirmation of Salmonella isolates was carried out by amplification of the invA gene, discrimination of d-tartrate-fermenting Salmonella isolates using multiplex PCR, and subsequently analysed by pulsed-field gel electrophoresis (PFGE). A survey questionnaire was conducted to identify potential risk factors for Salmonella presence in broiler farms. The prevalence of Salmonella at the farm level was 26.67%, and Salmonella isolates were serotyped as S. Paratyphi B and all isolates were d-tartrate-fermenting (dT+). PFGE showed three highly similar clusters and one significantly different Salmonella isolate. S. Paratyphi B continued to be present in different links of the poultry chain in the Tolima region, and identification of its main source is necessary to control its dissemination.

Evaluation of transfer of maternal immunity to the offspring of broiler breeders vaccinated with a candidate recombinant vaccine against Salmonella Enteritidis

Salmonella Enteritidis (SE) is a major cause of foodborne diseases in humans being frequently related to the consumption of poultry products. Therefore, guaranteeing early immunity to chicks is an important tool to prevent the colonization and infection by this pathogen. The present study evaluated the effectiveness of a candidate recombinant vaccine against SE. Thirty female and five male broiler breeders that were ten weeks-old were divided into 3 groups: unvaccinated (UV), vaccinated with recombinant vaccine candidate (VAC) and vaccinated with commercial bacterin (BAC). Samples of serum and embryonated egg were collected at seven and twelve weeks after the booster dose to quantify the transfer rate of IgY to egg yolks and offspring. Subsequently, forty day-old offspring were divided into two groups (UV and VAC) and challenged on the following day with 10⁷ CFU/chick of SE. Samples of serum, intestine, liver, and cecal content were harvested. Throughout the experiment period, significantly higher levels of IgY were observed in the egg yolk and also in the serum of broiler breeders and offspring of the VAC group in comparison to the UV group. In addition, increased transfer rates of IgY were observed in the VAC group when compared to the BAC group. Furthermore, higher villus-crypt ratios were found out in duodenum, jejunum and ileum at four days post-infection in the offspring from the VAC group. A high challenge dose of SE (10⁷ CFU per chick) was used and despite the stronger humoral immune response provoked by the candidate vaccine, there were no statistical differences in the recovery of viable SE cells from the offspring cecal contents. Therefore, the effect of vaccination to improve intestinal quality may affect the development of the chickens and consequently increase the resistance to lower SE challenge doses.

Salmonella Contamination of Broiler Chicken Carcasses at Critical Steps of the Slaughter Process and in the Environment of Two Slaughter Plants: Prevalence, Genetic Profiles, and Association with the Final Carcass Status

ABSTRACT

Salmonella is a foodborne pathogen commonly associated with poultry products. The aims of this work were to (i) estimate the impact of critical steps of the slaughter process on Salmonella detection from broiler chicken carcasses in two commercial poultry slaughter plants in Quebec, Canada; (ii) investigate the presence of Salmonella in the slaughter plant environment; (iii) describe, using a high-resolution melting (HRM) approach, the HRM Salmonella profiles and serotypes present on carcasses and in the slaughter plant environment; and (iv) evaluate whether the HRM flock status after chilling could be predicted by the flock status at previous steps of the slaughter process, the status of previous flocks, or the status of the processing environment, for the same HRM profile. Eight visits were conducted in each slaughter plant over a 6-month period. In total, 379 carcass rinsates from 79 flocks were collected at five critical steps of the slaughter process. Environmental samples were also collected from seven critical sites in each slaughter plant. The bleeding step was the most contaminated, with >92% positive carcasses. A decrease of the contamination along the slaughtering process was noted, with carcasses sampled after dry-air chilling showing ≤2.5% Salmonella prevalence. The most frequently isolated serotypes were Salmonella Heidelberg, Kentucky, and Schwarzengrund. The detection of the Salmonella Heidelberg 1-1-1 HRM profile on carcasses after chilling was significantly associated with its detection at previous steps of the slaughter process and in previously slaughtered flocks from other farms during a same sampling day. Results highlight the importance of the chilling step in the control of Salmonella on broiler chicken carcasses and the need to further describe and compare the competitive advantage of Salmonella serotypes to survive processing. The current study also illustrates the usefulness of HRM typing in investigating Salmonella contamination along the slaughter process.

HIGHLIGHTS

Modeling Salmonella Spread in Broiler Production: Identifying Determinants and Control Strategies

The presence of Salmonella spp. in broiler production is a food safety concern as the bacterium can be transmitted to humans via contaminated meat and derived products. Salmonella detection in litter at the pre-slaughter period has been linked to increased odds of contaminated broiler carcasses and meat derived products. To determine risk factors related to farm and broiler house characteristics and management practices, this study uses a unique longitudinal data set from a Brazilian integrated broiler enterprise, which contains official results of Salmonella spp. isolation from drag swabs collected at the end of the grow-out period. A Bayesian hierarchical spatio-temporal model found significant spatial and time influence on the odds of isolating Salmonella spp. from litter as well as significant effects from the size of a broiler house, total housing area per farm, type of broiler house, and number of litter recycles. Results indicate that recycling litter beyond 6 rearing cycles significantly increased the odds of isolating Salmonella before slaughter, and the bacterium was more likely to persist in conventional broiler houses, compared to broiler houses with controlled environment. Evidence of a potential principal-agent problem was also found in setting strategies to control the bacterium from litter, which suggests strong incentives to adopt the strategies aiming to reduce prevalence of the bacterium in the integrated enterprise. Our findings could be used to develop alternative measures to reduce the risk of persistence of the bacterium in the broiler production chain.

Review of Quantitative Microbial Risk Assessment in Poultry Meat: The Central Position of Consumer Behavior

Food of animal origin, especially meat products, represent the main vehicle of foodborne pathogens and so are implicated in foodborne outbreaks. Poultry meat is a widely consumed food in various forms, but it is also a reservoir of thermotolerant Campylobacter and Salmonella bacterial species. To assess human health risks associated with pathogenic bacteria in poultry meat, the use of quantitative microbial risk assessment (QMRA) has increased over the years as it is recognized to address complex food safety issues and is recommended by health authorities. The present project reviewed poultry meat QMRA, identified key steps of the farm-to-fork chain with significant impacts on food safety, highlighted current knowledge gaps, and provided risk mitigation advices. A PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses)-based systematic analysis was carried out and enabled the collection of 4056 studies including 42 QMRA kept for analysis after screening. The latter emphasized Campylobacter spp. and Salmonella spp. contaminations during the consumer stage as the main concern. The role of consumer handling on cross-contamination and undercooking events were of major concern. Thus, proper hygiene and safety practices by consumers have been suggested as the main intervention and would need to be followed with regular surveys to assess behavior changes and reduce knowledge gaps.

Antibiotic resistance in Salmonella spp. isolated from poultry: A global overview

Salmonella enterica is the most important foodborne pathogen, and it is often associated with the contamination of poultry products. Annually, Salmonella causes around 93 million cases of gastroenteritis and 155,000 deaths worldwide. Antimicrobial therapy is the first choice of treatment for this bacterial infection; however, antimicrobial resistance has become a problem due to the misuse of antibiotics both in human medicine and animal production. It has been predicted that by 2050, antibiotic-resistant pathogens will cause around 10 million deaths worldwide, and the WHO has suggested the need to usher in the post-antibiotic era. The purpose of this review is to discuss and update the status of Salmonella antibiotic resistance, in particular, its prevalence, serotypes, and antibiotic resistance patterns in response to critical antimicrobials used in human medicine and the poultry industry. Based on our review, the median prevalence values of Salmonella in broiler chickens, raw chicken meat, and in eggs and egg-laying hens were 40.5% ( interquartile range [IQR] 11.5-58.2%), 30% (IQR 20-43.5%), and 40% (IQR 14.2-51.5%), respectively. The most common serotype was Salmonella Enteritidis, followed by Salmonella Typhimurium. The highest antibiotic resistance levels within the poultry production chain were found for nalidixic acid and ampicillin. These findings highlight the need for government entities, poultry researchers, and producers to find ways to reduce the impact of antibiotic use in poultry, focusing especially on active surveillance and finding alternatives to antibiotics.

Prevalence of Salmonella and Campylobacter spp. in Alternative and Conventionally Produced Chicken in the United States: A Systematic Review and Meta-Analysis

ABSTRACT

The burden of foodborne illness linked to the consumption of contaminated broiler meat is high in the United States. With the increase in popularity of alternative poultry rearing and production systems, it is important to identify the differences in food safety risks presented by alternative systems compared with conventional methods. Although many studies have been conducted that surveyed foodborne pathogen prevalence along the broiler supply chain, a systematic overview of all of the results is lacking. In the current study, a systematic review and meta-analysis were conducted to quantify the differences in prevalence of Salmonella and Campylobacter spp. in farm environment, rehang, prechill, postchill, and retail samples between conventional and alternative production systems. A systematic search of Web of Science and PubMed databases was conducted to identify eligible studies. Studies were then evaluated by inclusion criteria, and the included studies were qualitatively and quantitatively analyzed. In total, 137 trials from 72 studies were used in the final meta-analysis. Meta-analysis models were individually constructed for subgroups that were determined by sample type, pathogen, and production type. All subgroups possessed high amounts of heterogeneity (I2 > 75%). For environmental sample subgroups, Campylobacter prevalence was estimated to be 15.8 and 52.8% for conventional and alternative samples, respectively. Similar prevalence estimates for both production types were observed for Salmonella environmental samples and all retail samples. For conventional samples, Campylobacter and Salmonella prevalence was highest in prechill samples followed by rehang and postchill samples, respectively. The results herein will be useful in future quantitative microbial risk assessments for characterizing the differences in foodborne illness risks presented by different broiler production systems.

HIGHLIGHTS

A Review of Salmonella and Campylobacter in Broiler Meat: Emerging Challenges and Food Safety Measures

Poultry is one of the largest sources of animal-based protein in the United States. Poultry processing has grown from a small local network of plants to nearly 500 plants nationwide. Two of the most persistent bacteria in poultry processing are Salmonella and Campylobacter. It was not until the introduction of Hazard Analysis and Critical Control Point systems in 1996 that major efforts to reduce bacterial contamination were developed. Traditionally, chlorine has been the industry standard for decontaminating chicken meat. However, antimicrobials such as peracetic acid, cetylpyridinium chloride, and acidified sodium chlorite have replaced chlorine as primary antimicrobials. Despite current interventions, the emergence of stress-tolerant and biofilm-forming Salmonella and Campylobacter is of primary concern. In an effort to offset growing tolerance from microbes, novel techniques such as cold plasma treatment, electrostatic spraying, and bacteriophage-based applications have been investigated as alternatives to conventional treatments, while new chemical antimicrobials such as Amplon and sodium ferrate are investigated as well. This review provides an overview of poultry processing in the United States, major microbes in poultry processing, current interventions, emerging issues, and emerging technologies in antimicrobial treatments.

Poultry processing and the application of microbiome mapping

Chicken is globally one of the most popular food animals. However, it is also one of the major reservoirs for foodborne pathogens, annually resulting in continued morbidity and mortality incidences worldwide. In an effort to reduce the threat of foodborne disease, the poultry industry has implemented a multifaceted antimicrobial program that incorporates not only chemical compounds, but also extensive amounts of water application and pathogen monitoring. Unfortunately, the pathogen detection methods currently used by the poultry industry lack speed, relying on microbiological plate methods and molecular detection systems that take time and lack precision. In many cases, the time to data acquisition can take 12 to 24 h. This is problematic if shorter-term answers are required which is becoming more likely as the public demand for chicken meat is only increasing, leading to new pressures to increase line speed. Therefore, new innovations in detection methods must occur to mitigate the risk of foodborne pathogens that could result from faster slaughter and processing speeds. Future technology will have 2 tracks: rapid methods that are meant to detect pathogens and indicator organisms within a few hours, and long-term methods that use microbiome mapping to evaluate sanitation and antimicrobial efficacy. Together, these methods will provide rapid, comprehensive data capable of being applied in both risk-assessment algorithms and used by management to safeguard the public.

A within-flock model of Salmonella Heidelberg transmission in broiler chickens

As part of the development of a quantitative microbial risk assessment (QMRA) model of third-generation cephalosporins (3GC)-resistant Salmonella Heidelberg, a compartmental (SEIR) model for S. Heidelberg transmission within a typical Canadian commercial broiler chicken flock was developed. The model was constructed to estimate the within-flock prevalence and the bacterial concentration in the barn environment at pre-harvest, and to assess the effect of selected control measures. The baseline scenario predicted an average within-flock prevalence of 23.5 % (95 % tolerance interval: 15.7-31.4) and an average bacterial concentration of 3.579 (0-4.294) log CFU/g of feces in the barn environment at pre-harvest (on the day the flock is sent to slaughter). Because vertical introduction of S. Heidelberg into the barn was already uncommon in the baseline scenario, vaccination of broiler parent flocks appeared to have a negligible effect, while vaccination of broiler chicken flocks substantially reduced the bacterial concentration at pre-harvest. Cleaning and disinfection between batches markedly reduced the within-flock prevalence at pre-harvest, but the effect on bacterial concentration was limited outside of the beginning of the production period. Extending downtime between batches by 7 days had little effect on within-flock prevalence or bacterial concentration of S. Heidelberg when compared to the baseline scenario. This study provides a basis to describe S. Heidelberg dynamics within a broiler chicken flock and to predict the within-flock prevalence and bacterial concentration at pre-harvest, and includes a description of the limitations and data gaps. The results of these analyses and associated uncertainties are critical information for populating QMRA models of the downstream impacts on public health from on-farm and other food-chain practices. Specifically, the study findings will be integrated into a broader farm-to-fork QMRA model to support the risk-based control of S. Heidelberg resistant to 3GC in broiler chicken in Canada.

Modeling the Reduction and Cross-Contamination of Salmonella in Poultry Chilling Process in China

: The study was to establish a predictive model for reduction and cross-contamination of Salmonella on chicken in chilling process. Reduction of Salmonella on chicken was 0.75 ± 0.04, 0.74 ± 0.08, and 0.79 ± 0.07 log CFU/g with 20, 50, and 100 mg/L of chlorine, respectively. No significant differences of bacterial reductions with 20-100 mg/L of chlorine were found and a Normal (-0.75, 0.1) distribution could describe the uncertainty of bacterial reductions. Inoculated and non-inoculated chicken samples were washed together and bacterial transfer rates among them were 0.13%-0.004% with 20-100 mg/L of chlorine. No significant differences of transfer rates with 50-100 mg/L of chlorine were observed and a Triangle (-2.5, -1.5, -1.1) distribution could describe the log transfer rate. Additionally, a 3-factor response surface model based on the central composite design was developed to evaluate the effects of initial contamination level (1-5 log CFU/g), pre-chill incidence (3%-40%) and chlorine concentration (0-100 mg/L) on post-chill incidence. The post-chill incidences in these treatments were within 30%-91.7%. The developed model showed a satisfactory performance to predict the post-chill incidence as evidenced by statistical indices (pseudo-R2 = 0.9; p < 0.0001; RMSE = 0.21) and external validation parameters (Bf = 1.02; Af = 1.11).

Modeling the Reduction of Salmonella spp. on Chicken Breasts and Wingettes during Scalding for QMRA of the Poultry Supply Chain in China

The objective of this study was to develop predictive models for describing the inoculated Salmonella reductions on chicken during the scalding process in China. Salmonella reductions on chicken breasts at a 100 s treatment were 1.12 ± 0.07, 1.38 ± 0.01, and 2.17 ± 0.11 log CFU/g at scalding temperatures of 50, 60 and 70 °C, respectively. For chicken wingettes, 0.87 ± 0.02, 0.99 ± 0.14 and 1.11 ± 0.17 log CFU/g reductions were obtained at 50, 60 and 70 °C after the 100 s treatment, respectively. Greater bacterial reductions were observed on chicken breasts than on chicken wingettes (p < 0.05). A logistic (−1.12, 0.06) distribution could describe the bacterial reductions on chicken breasts at 50–60 °C. Weibull, exponential and log-linear models were compared for describing the bacterial reduction on chicken breasts at 70 °C and the Weibull model showed the best fit as indicated by the pseudo-R², root mean square error (RMSE) and standard error of prediction (SEP) values. For chicken wingettes, a logistic (−0.95, 0.07) distribution could be used to describe the bacterial reduction at 50–70 °C. The developed predictive models could provide parts of the input data for microbial risk assessment of the poultry supply chain in China.

Quantitative Risk Assessment Model for Salmonellosis in Chicken Skewers from Street Food Vendors in South Korea

HIGHLIGHTS

Extended holding time increases likelihood of illness in warmer than it does in cooler months. Split heating is less effective than continuous heating for inactivation of microbes. Longer holding times make meat more vulnerable to microbes.

Comparison between random forest and gradient boosting machine methods for predicting Listeria spp. prevalence in the environment of pastured poultry farms

Foodborne pathogens such as Listeria spp. contain the ability to survive and multiply in poultry farming environments, which provides a route of contamination for poultry processing environments and final poultry products. An understanding of the effect of meteorological variables on the prevalence of Listeria spp. in the farming environment is lacking. Soil and feces samples were collected from 11 pastured poultry farms from 2014 to 2017. Random forest (RF) and gradient boosting machine (GBM) predictive models were generated to describe and predict Listeria spp. prevalence in feces and soil samples based on meteorological factors at the farming location. This study attempted to demonstrate the use of GBM models in a food safety context and compare their use to RF models. Both feces models performed very well, with area under the curve (AUC) values of 0.905 and 0.855 for the RF and GBM models, respectively. The soil GBM model outperformed the RF model with AUCs of 0.873 and 0.700, respectively. The developed models can be used to predict the prevalence of Listeria spp. in pastured poultry farm environments and should be of great use to poultry farmers, producers, and risk managers.

Quantitative Risk Assessment Model of Human Salmonellosis Resulting from Consumption of Broiler Chicken

(1) Background: Salmonella infections are a major cause of illnesses in the United States. Each year around 450 people die from the disease and more than 23,000 people are hospitalized. Salmonella outbreaks are commonly associated with eggs, meat and poultry. In this study, a quantitative risk assessment model (QRAM) was developed to determine Salmonella infections in broiler chicken. (2) Methods: Data of positive Salmonella infections were obtained from the United States Department of Agriculture (USDA) and the Centers for Disease Control and Prevention (CDC) Foodborne Disease Outbreak Surveillance System, in addition to published literature. The Decision Tools @RISK add-in software was used for various analyses and to develop the QRAM. The farm-to-fork pathway was modeled as a series of unit operations and associated pathogen events that included initial contamination at the broiler house (node 1), contamination at the slaughter house (node 2), contamination at retail (node 3), cross-contamination during serving and cooking (node 4), and finally the dose–response model after consumption. (3) Results: QRAM of Salmonella infections from broiler meat showed highest contribution of infection from the retail node (33.5%). (4) Conclusions: This QRAM that predicts the risk of Salmonella infections could be used as a guiding tool to manage the Salmonella control programs

Semi-Quantification of Total Campylobacter and Salmonella During Egg Incubations Using a Combination of 16S rDNA and Specific Pathogen Primers for qPCR

Rapid molecular techniques that evaluate eggs for the presence of foodborne pathogens is an essential component to poultry food safety monitoring. Interestingly, it is not just table eggs that contribute to outbreaks of foodborne disease. Broiler layer production actively contributes to sustaining of foodborne pathogens within a flock. The surface contamination of production eggs with invasive pathogens such as Salmonella enterica, Campylobacter jejuni, and Listeria monocytogenes during embryogenesis results in gastrointestinal tract (GIT) colonization. Pathogens that secure a niche within the GIT during embryonic development are nearly impossible to eradicate from the food chain. Therefore, current monitoring paradigms are not comprehensive because they fail to capture the presence of invasive pathogens within the embryonic GIT rapidly. By developing tools to recognize the pathogens' presence in the GIT during embryogenesis, producers are then able to spot evaluate broiler eggs for their potential risk as carriers of foodborne pathogens. In this study a novel qPCR assay was developed to semi-quantify pathogen load relative to total bacterial burden. Eggs sampled from three independent production broiler flocks of different ages were assayed for S. enterica (invA), C. jejuni (HipO), and L. monocytogenes (HlyA) against total microbial load (16s). The eggs were sampled at 1-day post-set within each flock, 2 weeks post-set, after vaccination (at 2.5 weeks) and 1-day post-hatch. The eggs were washed, and the yolk and embryonic chick GIT were collected. The DNA was extracted and subjected to a qPCR assay. The results confirm a novel technique for pathogen monitoring relative to total bacterial load and a unique method for monitoring the dynamics of foodborne pathogen invasion throughout broiler egg production.

Occurrence, antimicrobial resistance and whole-genome sequencing analysis of Salmonella isolates from chicken carcasses imported into Iraq from four different countries

Salmonella is a major cause of human foodborne illnesses worldwide; however, little is known about its occurrence and genomic characteristics in food sources in many developing countries. This study investigates the occurrence, serotypes distribution, antimicrobial resistance, and multilocus sequence types (ST) of Salmonella isolated from 400 imported frozen chicken carcasses sold in the markets of Thi-Qar, south-eastern Iraq. Salmonella was detected in 46 out of 400 tested samples [11.5% (95% confidence interval: 8.5%-15.0%)]. S. Typhimurium was the most abundant (30.4%) among 14 different serotypes recovered from the tested frozen carcasses. Antimicrobial resistance was most frequently detected against tetracycline (84.4%), nalidixic acid (80.4%), streptomycin (69.6%) and trimethoprim/sulfamethoxazole (65.2%). Whole-genome sequencing (WGS) analysis revealed that 18 isolates harbored four β-lactamase resistance genes, with bla_CARB-2 was the most commonly (14/18) detected. It was possible to identify 8 multilocus sequence types from the WGS analysis of 40 out of the 46 Salmonella isolates; with ST-11 (among S. Enteritidis) and ST-19 (among S. Typhimurium) were the most frequently detected. These results add to our understanding of the global epidemiology of Salmonella. Our work stands as one of the first reports on WGS analysis of Salmonella from retail chicken in a Middle-Eastern country. Results from this study could be valuable for guiding an informed import risk analysis aiming at reducing the exposure risk from Salmonella through imported chicken carcasses into Iraq. This work demonstrates the value of WGS as a promising tool for supporting evidence-based food safety hazard characterization.

Molecular-based identification and detection of Salmonella in food production systems: current perspectives

Salmonella remains a prominent cause of foodborne illnesses and can originate from a wide range of food products. Given the continued presence of pathogenic Salmonella in food production systems, there is a consistent need to improve identification and detection methods that can identify this pathogen at all stages in food systems. Methods for subtyping have evolved over the years, and the introduction of whole genome sequencing and advancements in PCR technologies have greatly improved the resolution for differentiating strains within a particular serovar. This, in turn, has led to the continued improvement in Salmonella detection technologies for utilization in food production systems. In this review, the focus will be on recent advancements in these technologies, as well as potential issues associated with the application of these tools in food production. In addition, the recent and emerging research developments on Salmonella detection and identification methodologies and their potential application in food production systems will be discussed.

An Attenuated Salmonella enterica Serovar Typhimurium Strain and Galacto-Oligosaccharides Accelerate Clearance of Salmonella Infections in Poultry through Modifications to the Gut Microbiome

Salmonella is estimated to cause one million foodborne illnesses in the United States every year. Salmonella-contaminated poultry products are one of the major sources of salmonellosis. Given the critical role of the gut microbiota in Salmonella transmission, a manipulation of the chicken intestinal microenvironment could prevent animal colonization by the pathogen. In Salmonella, the global regulator gene fnr (fumarate nitrate reduction) regulates anaerobic metabolism and is essential for adapting to the gut environment. This study tested the hypothesis that an attenuated Fnr mutant of Salmonella enterica serovar Typhimurium (attST) or prebiotic galacto-oligosaccharides (GOS) could improve resistance to wild-type Salmonella via modifications to the structure of the chicken gut microbiome. Intestinal samples from a total of 273 animals were collected weekly for 9 weeks to evaluate the impact of attST or prebiotic supplementation on microbial species of the cecum, duodenum, jejunum, and ileum. We next analyzed changes to the gut microbiome induced by challenging the animals with a wild-type Salmonella serovar 4,[5],12:r:- (Nal^r) strain and determined the clearance rate of the virulent strain in the treated and control groups. Both GOS and the attenuated Salmonella strain modified the gut microbiome but elicited alterations of different taxonomic groups. The attST produced significant increases of Alistipes and undefined Lactobacillus, while GOS increased Christensenellaceae and Lactobacillus reuteri The microbiome structural changes induced by both treatments resulted in a faster clearance after a Salmonella challenge.IMPORTANCE With an average annual incidence of 13.1 cases/100,000 individuals, salmonellosis has been deemed a nationally notifiable condition in the United States by the Centers for Disease Control and Prevention (CDC). Earlier studies demonstrated that Salmonella is transmitted by a subset of animals (supershedders). The supershedder phenotype can be induced by antibiotics, ascertaining an essential role for the gut microbiota in Salmonella transmission. Consequently, modulation of the gut microbiota and modification of the intestinal microenvironment could assist in preventing animal colonization by the pathogen. Our study demonstrated that a manipulation of the chicken gut microbiota by the administration of an attenuated Salmonella strain or prebiotic galacto-oligosaccharides (GOS) can promote resistance to Salmonella colonization via increases of beneficial microorganisms that translate into a less hospitable gut microenvironment.

Lactobacillus bulgaricus, Lactobacillus rhamnosus and Lactobacillus paracasei Attenuate Salmonella Enteritidis, Salmonella Heidelberg and Salmonella Typhimurium Colonization and Virulence Gene Expression In Vitro

Salmonella Enteritidis (SE), Salmonella Typhimurium (ST), and Salmonella Heidelberg (SH) have been responsible for numerous outbreaks associated with the consumption of poultry meat and eggs. Salmonella colonization in chicken is characterized by initial attachment to the cecal epithelial cells (CEC) followed by dissemination to the liver, spleen, and oviduct. Since cecal colonization is critical to Salmonella transmission along the food chain continuum, reducing this intestinal association could potentially decrease poultry meat and egg contamination. Hence, this study investigated the efficacy of Lactobacillus delbreuckii sub species bulgaricus (NRRL B548; LD), Lactobacillus paracasei (DUP-13076; LP), and Lactobacillus rhamnosus (NRRL B442; LR) in reducing SE, ST, and SH colonization in CEC and survival in chicken macrophages. Additionally, their effect on expression of Salmonella virulence genes essential for cecal colonization and survival in macrophages was evaluated. All three probiotics significantly reduced Salmonella adhesion and invasion in CEC and survival in chicken macrophages (p < 0.05). Further, the probiotic treatment led to a significant reduction in Salmonella virulence gene expression (p < 0.05). Results of the study indicate that LD, LP, and LR could potentially be used to control SE, ST, and SH colonization in chicken. However, these observations warrant further in vivo validation.

Characterization of a Multidrug-Resistant Salmonella enterica Serovar Heidelberg Outbreak Strain in Commercial Turkeys: Colonization, Transmission, and Host Transcriptional Response

In recent years, multidrug-resistant (MDR) Salmonella enterica serovar Heidelberg (S. Heidelberg) has been associated with numerous human foodborne illness outbreaks due to consumption of poultry. For example, in 2011, an MDR S. Heidelberg outbreak associated with ground turkey sickened 136 individuals and resulted in 1 death. In response to this outbreak, 36 million pounds of ground turkey were recalled, one of the largest meat recalls in U.S. history. To investigate colonization of turkeys with an MDR S. Heidelberg strain isolated from the ground turkey outbreak, two turkey trials were performed. In experiment 1, 3-week-old turkeys were inoculated with 10⁸ or 10¹⁰ CFU of the MDR S. Heidelberg isolate, and fecal shedding and tissue colonization were detected following colonization for up to 14 days. Turkey gene expression in response to S. Heidelberg exposure revealed 18 genes that were differentially expressed at 2 days following inoculation compared to pre-inoculation. In a second trial, 1-day-old poults were inoculated with 10⁴ CFU of MDR S. Heidelberg to monitor transmission of Salmonella from inoculated poults (index group) to naive penmates (sentinel group). The transmission of MDR S. Heidelberg from index to sentinel poults was efficient with cecum colonization increasing 2 Log10 CFU above the inoculum dose at 9 days post-inoculation. This differed from the 3-week-old poults inoculated with 10¹⁰ CFU of MDR S. Heidelberg in experiment 1 as Salmonella fecal shedding and tissue colonization decreased over the 14-day period compared to the inoculum dose. These data suggest that young poults are susceptible to colonization by MDR S. Heidelberg, and interventions must target turkeys when they are most vulnerable to prevent Salmonella colonization and transmission in the flock. Together, the data support the growing body of literature indicating that Salmonella establishes a commensal-like condition in livestock and poultry, contributing to the asymptomatic carrier status of the human foodborne pathogen in our animal food supply.