Enumeration of Salmonella and Campylobacter spp. in environmental farm samples and processing plant carcass rinses from commercial broiler chicken flocks

Microbial profile of broiler carcasses processed at a university scale mobile poultry processing unit

Chicken and chicken products have been associated with foodborne pathogens such as Salmonella, Campylobacter, and Escherichia coli (E. coli). Poultry comprises an important segment of the agricultural economy (75 million birds processed as of 2019) in West Virginia (WV). The risk of pathogens on processed chickens has risen with the increased popularity of mobile poultry processing units (MPPUs). This study evaluated the microbial safety of broilers processed in a MPPU in WV. This study assessed aerobic plate counts (APCs), E. coli counts and the presence/absence of Salmonella and Campylobacter on 96 broiler carcasses following each MPPU step of scalding, eviscerating, and chilling. Samples were either chilled in ice water only (W) or ice water with 5 ppm chlorine (CW). The highest number of bacteria recovered from carcasses were APCs (4.21 log10CFU/mL) and E. coli (3.77 log10CFU/mL; P = 0.02). A total reduction of 0.30 (P = 0.10) and 0.63 (P = 0.01) log10CFU/mL for APCs and E. coli, respectively, occurred from chilling carcasses in CW. Overall, results show that E. coli, Salmonella, and Campylobacter were significantly (P < 0.05) reduced from the initial scalding to the chilling step. However, Salmonella frequency doubled (15.63-34.38%) after the evisceration step, indicating that washing carcasses after evisceration may be a critical control point in preventing cross-contamination by Salmonella. Proper chilling is also an important microbial mitigation step in MPPU processing. Results indicate that Campylobacter was more resistant to chilling than Salmonella. Campylobacter was not completely inactivated until carcasses were chilled in CW, whereas W was sufficient to reduce Salmonella on carcasses. The results led to the conclusion that although 5 ppm chlorine (Cl2) achieved more bacterial reductions than water alone, the reductions were not always significant (P > 0.05). Further MPPU studies are needed to verify more effective chilling and processing strategies.

High Salmonella load with serovar virchow dominance pose major public safety risk in postchill broiler carcasses

The objective of this study was to determine Salmonella contamination levels, presence and serovar distribution in broiler carcasses before and after chilling, as well as to evaluate the effectiveness of chilling process. A total of 96 pooled neck skin samples (PNSS) of 48 prechill (PreC) and 48 postchill (PosC) carcasses, representing 480 broilers collected in 6 mo' period were analyzed using ISO 6579-2:2012 Miniaturized Most Probable Number (ISO-mMPN) technique. Species confirmation and serovar identification was performed by Salmonella-specific real-time PCR (Salm-PCR) and conventional serotyping, respectively. Mean Salmonella count was 1.84 log10 MPN/g in PreC, and 1.48 log10 MPN/g in PosC samples, indicating a statistically significant reduction of 0.36 log10 MPN/g (p < 0.05) in the counts by plant's air chill system. Salmonella positivity reduced from 97.9% (47/48) in PreC to 85.42% (41/48) in PosC samples, confirmed by Salm-PCR with identified serovars as S. Virchow (89.77 %) followed by S. Schwarzengrund (9.09%) and S. Bredeney (1.14%). Persistence of high load and prevalence of Salmonella with serovar Virchow dominance (other than the ones mandated in current guidelines) in the final product contributes significant and up to date data to relevant literature, and provides unbiased epidemiological reference to legal authorities for future relevant revisions.

Quantitative microbial risk assessment of Salmonella in fresh chicken patties

Quantitative microbial risk assessment (QMRA) has witnessed rapid development within the context of food safety in recent years. As a means of contributing to these advancements, a QMRA for Salmonella spp. in fresh chicken patties for the general European Union (EU) population was developed. A two-dimensional (Second Order) Monte-Carlo simulation method was used for separating variability and uncertainty of model's parameters. The stages of industrial processing, retail storage, domestic storage, and cooking in the domestic environment were considered in the exposure assessment. For hazard characterization, a dose-response model was developed by combining 8 published dose-response models using a Pert distribution for describing uncertainty. The QMRA model predicted a mean probability of illness of 1.19*10-4 (5.28*10-5 - 3.57*10-4 95 % C.I.), and a mean annual number of illnesses per 100,000 people of 2.13 (0.96 - 6.59 95 % C.I.). Moreover, sensitivity analysis was performed, and variability in cooking preferences was found to be the most influential model parameter (r = -0.39), followed by dose-response related variability (r = 0.22), and variability in the concentration of Salmonella spp. at the time of introduction at the processing facility (r = 0.11). Various mitigation strategy scenarios were tested, from which, "increasing the internal temperature of cooking" and "decreasing shelf life" were estimated to be the most effective in reducing the predicted risk of illness. Salmonella-related illnesses exhibit particularly high severity, making them some of the most prominent zoonotic diseases in the EU. Regular monitoring of this hazard in order to further highlight its related parameters and causes is a necessary procedure. This study not only provides an updated assessment of Salmonella spp. risk associated with chicken patties, but also facilitates the identification of crucial targets for scientific investigation and implementation of real-world intervention strategies.

A systematic review and meta-analysis of the sources of Campylobacter in poultry production (preharvest) and their relative contributions to the microbial risk of poultry meat

A systematic review and meta-analysis were conducted to idetnify the relative contributions of the sources of Campylobacter in poultry live production to Campylobacter prevalence of broiler meat. The keywords of Campylobacter, prevalence, live production, and broiler were used in Google Scholar to address the research interest. A total of 16,800 citations were identified, and 63 relevant citations were included in the meta-analysis after applying predetermined inclusion and exclusion criteria. A generalized linear mixed model approach combined with logit transformation was used in the current meta-analysis to stabilize the variance. The analysis revealed that Campylobacter is ubiquitous in the poultry house exterior environment including surroundings, wildlife, domestic animals, and farm vehicle, with a predicted prevalence of 14%. The recovery of Campylobacter in the interior environment of the poultry house is far less abundant than in the exterior, with a prevalence of 2%, including litter, water, insects, mice, feed, and air. A lack of evidence was observed for vertical transmission due to the day-old chicks being free of Campylobacter from 4 studies identified. Live birds are the predominant carrier of Campylobacter, with a predicted prevalence of 41%. Transportation equipment used for live haul had an overall prevalence of 39%, with vehicles showing a predicted prevalence of 44% and crates with a predicted prevalence of 22%. The results of this meta-analysis highlight the need to implement effective biosecurity measures to minimize the risk of Campylobacter in poultry meat, as human activity appears to be the primary factor for Campylobacter introduction.

Aerotolerance and Multi-Locus Sequence Typing of Campylobacter jejuni Isolated from Commercial Broiler Processing Plants

Campylobacter jejuni is one of the leading causes of acute diarrhea in the United States. Despite being a microaerophilic pathogen, C. jejuni continues to endure within the domain of food production, especially in poultry processing. Recent research on aerotolerance indicates that close monitoring of this pathogen is necessary. A total of 40 C. jejuni isolates previously obtained from commercial broiler processing plants were analyzed for aerotolerance and genetic diversity. In addition, the effect of aerotolerance and storage time (days) on the survival of C. jejuni on broiler drumsticks at refrigeration (4 °C) and freezing conditions (-20 °C) was also evaluated. Out of 40 isolates, 25 (62.5%) were aero-sensitive (AS), 10 (25%) were intermediately aerotolerant (IAT), and 5 (12.5%) were hyper aerotolerant (HAT). The isolates belonged to four clonal complexes (CCs) and six sequence types, with the majority of isolates assigned to the CC-353 clonal complex. C. jejuni counts were reduced by 0.40 log CFU/g after 7 days at 4 °C and by 1.50 log CFU/g after 14 days at -20 °C, respectively, irrespective of aerotolerance (p < 0.001). At both refrigeration (p < 0.013) and freezing (p < 0.001), HAT showed greater reductions as compared to AS and IAT. These findings suggest that both refrigeration and freezing reduce C. jejuni counts.

Dominant Salmonella Serovars in Australian Broiler Breeder Flocks and Hatcheries: a Longitudinal Study

A longitudinal study was conducted to determine the dominance and prevalence of Salmonella enterica subsp in Australian broiler breeder flocks and hatcheries. Twenty-two flocks (n = 3339 samples) were sampled over 6 time points beginning at placement until week 40. Hatcheries (n = 274 samples) were sampled following removal of chicks hatched from eggs originating from the 22 donor parent flocks. The percent of positive flocks (36%) and frequency of positive samples (15.6%) were highest during rearing at week 7. The frequency of positive samples decreased over the 40 weeks; however, the number of positive flocks remained relatively consistent. Geographical location had a greater influence on Salmonella detection frequency than company sample origin, despite differing management and vaccination protocols within and between companies. Twelve serovars were detected in total. The predominant serovars during rearing were Salmonella Mbandaka (32%), S. Saintpaul (27%), and S. Liverpool (18%). The predominant serovars detected during production were S. Cubana (27%), S. Saintpaul (24%), and S. Havana (13%). Salmonella Typhimurium, S. Ohio, and S. Hessarek were detected in the hatcheries. Of the serovars detected, only S. Typhimurium and S. Ohio were found in both broiler breeder flocks and hatcheries. However, detection did not correspond to the status of the flock eggs feeding into the hatchery. This study provides an up-to-date capture of the current Salmonella serovars circulating in the broiler breeder industry. Continued surveillance within the Australian Chicken Meat industry is imperative to mitigate and reduce the risk of salmonellosis in the community related to chicken meat. IMPORTANCE This study identified prevalent and dominant Salmonella enterica subsp in Australian Broiler Breeder flocks, as well as in hatcheries post chick hatch and removal, from eggs originating from these donor parent flocks. The captured Salmonella data was further compared to the most common Salmonella serovars isolated from broilers, as well as human salmonellosis notification data, which is useful for consideration of the circulating serovars within the chicken meat industry and their significance in public health. As there are multiple entry points for Salmonella during the entire chicken meat production chain that can lead to carcass contamination, it is important to distinguish serovars present between the different stages of vertical integration to implement and enable Salmonella control strategies.

Conditions Necessary for the Transfer of Antimicrobial Resistance in Poultry Litter

Animal manures contain a large and diverse reservoir of antimicrobial resistance (AMR) genes that could potentially spillover into the general population through transfer of AMR to antibiotic-susceptible pathogens. The ability of poultry litter microbiota to transmit AMR was examined in this study. Abundance of phenotypic AMR was assessed for litter microbiota to the antibiotics: ampicillin (Ap; 25 μg/mL), chloramphenicol (Cm; 25 μg/mL), streptomycin (Sm; 100 μg/mL), and tetracycline (Tc; 25 μg/mL). qPCR was used to estimate gene load of streptomycin-resistance and sulfonamide-resistance genes aadA1 and sul1, respectively, in the poultry litter community. AMR gene load was determined relative to total bacterial abundance using 16S rRNA qPCR. Poultry litter contained 10⁸ CFU/g, with Gram-negative enterics representing a minor population (<10⁴ CFU/g). There was high abundance of resistance to Sm (10⁶ to 10⁷ CFU/g) and Tc (10⁶ to 10⁷ CFU/g) and a sizeable antimicrobial-resistance gene load in regards to gene copies per bacterial genome (aadA1: 0.0001-0.0060 and sul1: 0.0355-0.2455). While plasmid transfer was observed from Escherichia coli R100, as an F-plasmid donor control, to the Salmonella recipient in vitro, no AMR Salmonella were detected in a poultry litter microcosm with the inclusion of E. coli R100. Confirmatory experiments showed that isolated poultry litter bacteria were not interfering with plasmid transfer in filter matings. As no R100 transfer was observed at 25 °C, conjugative plasmid pRSA was chosen for its high plasmid transfer frequency (10^-4 to 10^-5) at 25 °C. While E. coli strain background influenced the persistence of pRSA in poultry litter, no plasmid transfer to Salmonella was ever observed. Although poultry litter microbiota contains a significant AMR gene load, potential to transmit resistance is low under conditions commonly used to assess plasmid conjugation.

A systematic review and meta-analysis of the sources of Salmonella in poultry production (pre-harvest) and their relative contributions to the microbial risk of poultry meat

Salmonella is a major foodborne pathogen associated with poultry and poultry products and a leading cause for human salmonellosis. Salmonella is known to transmit in poultry flocks both vertically and horizontally. However, there is a lack of knowledge on relative contribution of the factors on Salmonella prevalence in poultry live production system including hatchery, feed, water, environment-interior, and -exterior. Therefore, a systematic review and meta-analysis was conducted to quantify the potential sources of Salmonella during preharvest and their relative contributions to the microbial risk of poultry meat. A total of 16,800 studies identified from Google Scholar and 37 relevant studies were included in the meta-analysis for relative contributions to Salmonella positivity on broilers after applying exclusion criteria. A generalized linear mixed model approach combined with logit transformation was used in the current study to stabilize the variance. The analysis revealed that the hatchery is the most significant contributor of Salmonella with a prevalence of 48.5%. Litter, feces, and poultry house internal environment were the other 3 major contributing factors with a prevalence of 25.4, 16.3, and 7.9%, respectively. Moreover, poultry house external environment (4.7%), feed (4.8%), chicks (4.7%), and drinker water also contributed to the Salmonella positivity. Results from this meta-analysis informed the urgent need for controls in live production to further reduce Salmonella in fresh, processed poultry. The control strategies can include eliminating the sources of Salmonella and incorporating interventions in live production to reduce Salmonella concentrations in broilers.

Combined Quantification and Deep Serotyping for Salmonella Risk Profiling in Broiler Flocks

Despite a reduction of Salmonella contamination on final poultry products, the level of human salmonellosis cases attributed to poultry has remained unchanged over the last few years. There needs to be improved effort to target serovars which may survive antimicrobial interventions and cause illness, as well as to focus on lessening the amount of contamination entering the processing plant. Advances in molecular enumeration approaches allow for the rapid detection and quantification of Salmonella in pre- and postharvest samples, which can be combined with deep serotyping to properly assess the risk affiliated with a poultry flock. In this study, we collected a total of 160 boot sock samples from 20 broiler farms across four different integrators with different antibiotic management programs. Overall, Salmonella was found in 85% (68/80) of the houses, with each farm having at least one Salmonella-positive house. The average Salmonella quantity across all four complexes was 3.6 log10 CFU/sample. Eleven different serovars were identified through deep serotyping, including all three key performance indicators (KPIs; serovars Enteritidis, Infantis, and Typhimurium) defined by the U.S. Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS). There were eight multidrug resistant isolates identified in this study, and seven which were serovar Infantis. We generated risk scores for each flock based on the presence or absence of KPIs, the relative abundance of each serovar as calculated with CRISPR-SeroSeq (serotyping by sequencing the clustered regularly interspaced palindromic repeats), and the quantity of Salmonella organisms detected. The work presented here provides a framework to develop directed processing approaches and highlights the limitations of conventional Salmonella sampling and culturing methods. IMPORTANCE Nearly one in five foodborne Salmonella illnesses are derived from chicken, making it the largest single food category to cause salmonellosis and indicating a need for effective pathogen mitigation. Although industry has successfully reduced Salmonella incidence in poultry products, there has not been a concurrent reduction in human salmonellosis linked to chicken consumption. New efforts are focused on improved control at preharvest, which requires improved Salmonella surveillance. Here, we present a high-resolution surveillance approach that combines quantity and identity of Salmonella in broiler flocks prior to processing which will further support improved Salmonella controls in poultry. We developed a framework for this approach, indicating that it is possible and important to harness deep serotyping and molecular enumeration to inform on-farm management practices and to minimize risk of cross-contamination between flocks at processing. Additionally, this framework could be adapted to Salmonella surveillance in other food animal production systems.

Development and Verification of a Poultry Management Tool to Quantify Salmonella from Live to Final Product Utilizing RT-PCR

The United States Department of Agriculture Food Safety and Inspection Service (USDA FSIS) does not maintain a zero-tolerance policy for Salmonella in poultry and poultry products, despite being a known food safety hazard throughout the poultry industry. In 2016, USDA FSIS established performance standards for a 52-week moving window with the maximum acceptable percent positive for comminuted turkey (325 g sample) at 13.5% (7 of 52 samples). Based upon FSIS verification sampling results from one 52-week moving window, the Salmonella prevalence for each poultry establishment in category 1 (below limit), 2 (meeting limit), or 3 (exceeding limit) are published for public viewing. Moreover, many poultry producers continue to have post-intervention samples test positive. Therefore, the use of quantification would be more valuable to determine the efficacy of process control interventions, corrective actions, and final product Log CFU/g of Salmonella to make rapid, within shift, food safety decisions. Therefore, the objectives of these studies are to develop, verify, and validate a rapid and reliable quantification method utilizing RT-PCR to enumerate Salmonella in the poultry industry from flock to final product and to utilize the method in an application study. BAX® System SalQuant® is an application of the BAX® System Real-Time PCR Assay for Salmonella to enumerate low levels of Salmonella with shortened enrichment times. Curve development encompassed inoculating poultry matrix samples at four levels with an ATCC strain of Salmonella, with three biological replicates per inoculation level, and five technical replicates being run on the BAX® System for various timepoints, gathering the data, and creating a linear-fit equation. A linear-fit equation was provided for each timepoint. The ideal timepoint, based on the statistical parameters surrounding the equation (R2 > 0.80, Log RMSE < 0.60, and enumerable range 0.00 to 4.00 Log CFU/mL (g)) that most accurately estimate Salmonella compared to most probable number (MPN), was chosen to be utilized for further studies.

The Prolonged Treatment of Salmonella enterica Strains with Human Serum Effects in Phenotype Related to Virulence

Salmonella enterica as common pathogens of humans and animals are good model organisms to conduct research on bacterial biology. Because these bacteria can multiply in both the external environments and in the living hosts, they prove their wide adaptability. It has been previously demonstrated that prolonged exposition of Salmonella serotype O48 cells to normal human serum led to an increase in resistance to sera in connection with the synthesis of very long O-antigen. In this work, we have studied the phenotype connected to virulence of Salmonella enterica strains that were subjected to consecutive passages in 50% human serum from platelet-poor plasma (SPPP). We found that eight passages in SPPP may not be enough for the bacteria to become serum-resistant (S. Typhimurium ATCC 14028, S. Senftenberg). Moreover, C1q and C3c complement components bound to Salmonellae (S. Typhimurium ATCC 14028, S. Hammonia) membrane proteins, which composition has been changed after passaging in sera. Interestingly, passages in SPPP generated genetic changes within gene fljB, which translated to cells’ motility (S. Typhimurium ATCC 14028, S. Erlangen). One strain, S. Hammonia exposed to a serum developed a multi-drug resistance (MDR) phenotype and two S. Isaszeg and S. Erlangen tolerance to disinfectants containing quaternary ammonium salts (QAS). Furthermore, colonial morphotypes of the serum adaptants were similar to those produced by starter cultures. These observations suggest that overcoming stressful conditions is manifested on many levels. Despite great phenotypic diversity occurring after prolonged exposition to SPPP, morphotypes of colonies remained unchanged in basic media. This work is an example in which stable morphotypes distinguished by altered virulence can be confusing during laboratory work with life-threatening strains.

Case-control investigation of invasive Salmonella disease in Malawi reveals no evidence of environmental or animal transmission of invasive strains, and supports human to human transmission

BACKGROUND

Invasive Salmonella infections cause significant morbidity and mortality in Sub-Saharan Africa. However, the routes of transmission are uncertain. We conducted a case-control study of index-case and geographically-matched control households in Blantyre, Malawi, sampling Salmonella isolates from index cases, healthy people, animals, and the household environment.

METHODOLOGY

Sixty index cases of human invasive Salmonella infection were recruited (March 2015-Oct 2016). Twenty-eight invasive Non-Typhoidal Salmonella (iNTS) disease and 32 typhoid patients consented to household sampling. Each index-case household was geographically matched to a control household. Extensive microbiological sampling included stool sampling from healthy household members, stool or rectal swabs from household-associated animals and boot-sock sampling of the household environment.

FINDINGS

1203 samples from 120 households, yielded 43 non-Typhoidal Salmonella (NTS) isolates from 25 households (overall sample positivity 3.6%). In the 28 iNTS patients, disease was caused by 3 STs of Salmonella Typhimurium, mainly ST313. In contrast, the isolates from households spanned 15 sequence types (STs). Two S. Typhimurium isolates from index cases closely matched isolates from their respective asymptomatic household members (2 and 3 SNP differences respectively). Despite the recovery of a diverse range of NTS, there was no overlap between the STs causing iNTS disease with any environmental or animal isolates.

CONCLUSIONS

The finding of NTS strains from index cases that matched household members, coupled with lack of related animal or environmental isolates, supports a hypothesis of human to human transmission of iNTS infections in the household. The breadth of NTS strains found in animals and the household environment demonstrated the robustness of NTS sampling and culture methodology, and suggests a diverse ecology of Salmonella in this setting. Healthy typhoid (S. Typhi) carrier state was not detected. The lack of S. Typhi isolates from the household environment suggests that further methodological development is needed to culture S. Typhi from the environment.

Management and environmental factors influence the prevalence and abundance of food-borne pathogens and commensal bacteria in peanut hull-based broiler litter

In this study, we conducted a longitudinal sampling of peanut hull-based litter from a farm under a "no antibiotics ever" program. Our objective was to determine broiler management practices and environmental factors that are associated with the occurrence of food-borne pathogens (Salmonella and Campylobacter) and the abundance of commensal bacteria (Escherichia coli, Enterococcus spp., and Staphylococcus spp.). Litter (n = 288) was collected from 4 broiler houses over three consecutive flocks, starting with a complete house cleanout and fresh peanut hull. Litter was sampled at the beginning of each grow-out cycle and at the end of the cycle. Logistic and linear regression models were used to model the relationships between pathogen prevalence, commensal abundance and management practices, and environmental factors. The number of flocks raised on litter, grow-out period, broiler house, litter pH, litter moisture, and house temperature were associated with the prevalence of pathogens and the abundance of commensal bacteria in litter. The final logistic model for pathogens showed that a higher probability of detecting Salmonella in litter was associated with the number of flocks raised on litter and the grow-out period. A higher probability of detecting Campylobacter in litter was associated with the number of flocks raised on litter, broiler house and the sections of the house, and the pH of litter. Our results suggest that management practices and environmental factors affect Salmonella and Campylobacter differently and suggest that each pathogen will require its own tailored intervention to stop their persistence in broiler litter.

Roles of Aerotolerance, Biofilm Formation, and Viable but Non-Culturable State in the Survival of Campylobacter jejuni in Poultry Processing Environments

Campylobacter jejuni is one of the most common causes of foodborne human gastroenteritis in the developed world. This bacterium colonizes in the ceca of chickens, spreads throughout the poultry production chain, and contaminates poultry products. Despite numerous on farm intervention strategies and developments in post-harvest antimicrobial treatments, C. jejuni is frequently detected on broiler meat products. This indicates that C. jejuni is evolving over time to overcome the stresses/interventions that are present throughout poultry production and processing. The development of aerotolerance has been reported to be a major survival strategy used by C. jejuni in high oxygen environments. Recent studies have indicated that C. jejuni can enter a viable but non-culturable (VBNC) state or develop biofilm in response to environmental stressors such as refrigeration and freezing stress and aerobic stress. This review provides an overview of different stressors that C. jejuni are exposed to throughout the poultry production chain and the genotypic and phenotypic survival mechanisms, with special attention to aerotolerance, biofilm formation, and development of the VBNC state.

Longitudinal Changes in Campylobacter and the Litter Microbiome throughout the Broiler Production Cycle

Broiler chickens are an important source of Campylobacter to humans and become colonized on the farm, but the role of the litter in the ecology of Campylobacter is still not clear. The aim of this study was to examine the relationship between Campylobacter and the changes in the litter microbiome throughout the broiler production cycle. Twenty-six commercial broiler flocks representing two production types (small and big broilers) were followed from 1 to 2 weeks after placement to the end of the production cycle. Composite litter samples from the broiler chicken house were collected weekly. Litter DNA was extracted and used for Campylobacter jejuni and Campylobacter coli qPCR as well as for 16S rRNA gene V4 region sequencing. Campylobacter jejuni concentration in litter significantly differed by production type and flock age. Campylobacter jejuni concentration in litter from big broilers was 2.4 log₁₀ units higher, on average, than that of small broilers at 3 weeks of age. Sixteen amplicon sequence variants (ASVs) differentially abundant over time were detected in both production types. A negative correlation of Campylobacter with Bogoriella and Pseudogracilibacillus was observed in the litter microbiome network at 6 weeks of flock age. Dynamic Bayesian networks provided evidence of negative associations between Campylobacter and two bacterial genera, Ornithinibacillus and Oceanobacillus, at 2 and 4 weeks of flock age, respectively. In conclusion, dynamic associations between Campylobacter and the litter microbiome were observed during grow-out, suggesting a potential role of the litter microbiome in the ecology of Campylobacter colonization and persistence on farm. IMPORTANCE This study interrogated the longitudinal association between Campylobacter and broiler litter microbiome in commercial broiler flocks. The results of this investigation highlighted differences in Campylobacter dynamics in the litter throughout the broiler production cycle and between small and big broilers. Besides documenting the changing nature of the microbial networks in broiler litter during grow-out, we detected bacterial genera (Oceanobacillus and Ornithinibacillus) negatively associated with Campylobacter abundance and concentration in litter via the Bayesian network framework. These bacteria should be investigated as possible antagonists to Campylobacter colonization of the broiler environment.

Intra-cluster correlations for ceca Salmonella prevalence and enumeration from 40 experimental floor pen trials in broiler chickens using a seeder bird challenge model

Floor pen trials are an efficient way to evaluate the effectiveness of potential Salmonella control interventions in broiler chickens. When treatments are allocated at the pen level, and outcomes are measured at the individual bird level, floor pen studies are considered to be cluster randomized trials. Estimating the sample size required to achieve a desired level of statistical power for a cluster randomized trial requires an estimate of the intra-cluster correlation (ICC) as an input. In this study, ICCs were estimated for the untreated challenged control group from 40 broiler chicken Salmonella pen trials performed using a seeder bird challenge model. The ICCs for ceca Salmonella prevalences ranged from 0.00 to 0.64, with a median of 0.17. The ICCs for ceca Salmonella log₁₀(MPN/g + 1) ranged from 0.00 to 0.52, with a median of 0.14. These findings indicate that the effect of pen-level clustering is substantial in Salmonella floor pen trials, and it must be considered during both the study design and analysis. In a multivariable regression analysis, ICCs for ceca Salmonella prevalences were associated with the challenge status of sampled birds, age of birds at the time of challenge, and Salmonella serovar. ICCs were lower for studies in which a combination of direct (seeder) and indirect (horizontal) challenged birds were sampled, and for studies in which birds were challenged on the day of hatch or at one day of age. ICCs were higher for studies in which Salmonella Heidelberg was used as the challenge strain. These findings may be useful for investigators that are planning pen trials to evaluate Salmonella control interventions in broiler chickens. Choosing study design elements associated with a lower ICC may improve efficiency by leading to a larger effective sample size for the same number of experimental units.

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.

Dietary Inclusion of a Saccharomyces cerevisiae-Derived Postbiotic Is Associated with Lower Salmonella enterica Burden in Broiler Chickens on a Commercial Farm in Honduras

Postbiotic feed additives may aid foodborne pathogen reduction during poultry rearing. The study objective was to evaluate a postbiotic additive in parallel to an industry control diet and the subsequent associated burden of Salmonella enterica on a single, commercial broiler farm in Honduras. Twelve houses were matched and assigned the standard diet (CON) or standard diet plus postbiotic (SCFP). New litter was placed in each house and retained across flock cycles with sampling prior to each chick placement and three consecutive rearing cycles. At ~33–34 days, 25 ceca were collected on-farm from each house, treatment, and cycle. Salmonella prevalence in litter for CON (30.6%) and SCFP (27.8%) were equivalent; however, Salmonella load within positive samples was lower (p = 0.04) for SCFP (3.81 log10 MPN/swab) compared to CON (5.53 log10 MPN/swab). Cecal prevalence of Salmonella was lower (p = 0.0006) in broilers fed SCFP (3.4%) compared to CON (12.2%). Salmonella load within positive ceca were numerically reduced (p = 0.121) by 1.45 log10 MPN/g for SCFP (2.41 log10 MPN/g) over CON (3.86 log10 MPN/g). Estimated burden was lower (p = 0.003) for SCFP flocks (3.80 log10 MPN) compared to CON (7.31 log10 MPN). These data demonstrate the preharvest intervention potential of postbiotics to reduce Salmonella enterica in broiler chickens.

Re-used or New Bedding Are Not Drivers of Salmonella Levels and Serovar Emergence in Commercially Farmed Broilers in Australia

To inform Salmonella on-farm management during broiler rearing, a 2-year study on two farms compared the Australian practices of new bedding use, partial litter re-use and an alternative, full litter re-use. Six sequential commercial cycles of ~50 days each were tested on each farm, on ~day 7 from placement (litter only), prior to first thin-out, and prior to final removal (litter and ceca). A random number sample collection occurred, defined by shed supports (33, 39), different drinkers, feeders, and shed center. Across the six cycles on both farms, Salmonella levels in ceca just prior to thin-out on full re-use litter were higher (log 3.11 MPN/g, P = 0.008) than for new bedding (log 2.04 MPN/g) and partial re-use (log 2.43 MPN/g) litter (the latter two were not significantly different). Prior to final removal across all practices the Salmonella levels in ceca from new bedding (log 1.72 MPN/g), partial re-use litter (log 1.77 MPN/g), and full re-use litter (log 2.33 MPN/g) were not statistically different, suggesting no effect of litter practice. The Salmonella levels in litter prior to the first (log 1.96–2.31 MPN/g) and second (log 2.24–2.48 MPN/g) removals were also not statistically different. The emergence of Salmonella serovars in the partitioned chicken-free grow-out end (back) of all sheds at ~day 7 did not suggest carry-over. Both the pattern of emergence of Salmonella serovars and Salmonella levels in litter ~day 7 in the brooder-end with chickens (front), suggested the Salmonella present were due to flock contribution and not practice driven. The dominant Salmonella serovar across cycles on both farms was S. Sofia (75 and 77% isolates) followed by S. Typhimurium (11 and 17%). Irrespective of initial serovars, Salmonella Sofia rapidly gained dominance and displaced 14 other serovars including S. Typhimurium on both farms. This study demonstrates that the litter practices are not the major driver of Salmonella prevalence in broiler farming, supporting the commercial re-use of bedding as a sustainable farming practice in Australia. The major contributor of Salmonella load in production is the Salmonella status of the incoming flock, indicating this is the key area to focus future control measures.

Antimicrobial resistance and virulence genes in Salmonella enterica serovars isolated from droppings of layer chicken in two farms in Nigeria

AIM

This study aimed to investigate the isolation rate, antibiotic resistance, and virulence genes of Salmonella enterica serovar from two commercial farms in Nigeria.

METHODS AND RESULTS

Salmonella isolation was performed according to the United States Food and Drug Agency (USFDA) method. Serotyping, antimicrobial susceptibility testing, detection of resistance and virulence genes were done using the Kauffman-White Scheme, disc diffusion, minimum inhibitory concentration, and real-time polymerase chain reaction techniques. Salmonella serovars were isolated from only farm A at 22/50 (44.0%) while none were isolated from farm B. Salmonella Typhi, 9 (40.9%); Salmonella Typhimurium, 2 (9.1%), Salmonella Enteritidis, 2 (9.1%), Salmonella Pullorum, 1 (4.5%), Salmonella Kentucky, 4 (18.2%) were identified while 4 (18.2%) were untypable. Sixteen isolates (72.7%) showed multiple drug resistance and 17 different resistance profile types with AMP-CHL-TRM-SXT as the most prevalent pattern. Resistance genes (blaTEM, 12/22 (54.5%) and virulence genes (InvA, sopB, mgtC, and spi4D, 22/22 (100.0%), ssaQ, 16/22 (72.7%), and spvC, 13/22 (59.1%) were found, while blaSHV, blaCTX-M, floR, tetA, tetB, tetG, and LJSGI-1 genes were absent.

CONCLUSION

Pathogenic Salmonella were isolated from the chicken droppings in this study. Most of these strains were resistant to antibiotics and possessed characteristics of virulence.

SIGNIFICANCE AND IMPACT OF THE STUDY

Chicken droppings from this study area contained pathogenic strains of Salmonella and a rare occurrence of Salmonella Typhi. The study revealed that the environment and the food chain could be at risk of contamination of highly virulent and antimicrobial-resistant strains of Salmonella. These could affect the profitability of the poultry industry and food consumption. There is a need for caution in indiscriminate disposal of poultry waste and the use of uncomposted chicken droppings in soil amendment.

Comparison of Statistical Methods for Identifying Risk Factors for Salmonella Contamination of Whole Chicken Carcasses

ABSTRACT

The complexity of the food system makes analyzing microbiological data from food studies challenging because many of the assumptions (e.g., linear relationship between independent and dependent variable and independence of observations) associated with common analytical approaches (e.g., analysis of variance) are violated. Repeated sampling within an establishment introduces longitudinal correlation that must be accounted for during analyses. In this study, statistical methods for clustered or correlated data were used to determine how correlation impacts conclusions and to compare how assumptions associated with statistical methods impact the appropriateness of these methods within the context of food safety. Risk factor analyses for Salmonella contamination of whole chicken carcasses were conducted as a case study with regulatory data collected by the U.S. Department of Agriculture Food Safety and Inspection Service between May 2015 and December 2019 from 203 regulated establishments. Three models, generalized estimating equation, random effects, and logistic, were fit to Salmonella presence or absence data with establishment demographics and inspection history included as potential covariates. Beta parameter estimates and their standard errors and odds ratios and their 95% confidence intervals were compared across models. Conclusions drawn from the three models differed with respect to geographic region, whether the chicken establishment also slaughters turkeys, and establishment noncompliance with 9 CFR §417.4 (hazard analysis critical control point system validation, verification, and reassessment) in the 84 days leading up to sample collection. The results of this study reveal the need to consider clustering and correlation when analyzing food microbiological data, provide context for selecting a statistical method, and suggest that generalized estimating equation and random effects models are preferrable over logistic regression when analyzing correlated food data. These results support a renewed focus on statistical methodology in food safety.

HIGHLIGHTS

A systematic review and meta-analysis of the efficacy of processing stages and interventions for controlling Campylobacter contamination during broiler chicken processing

Systematic review and meta-analysis were conducted to quantify the effects of processing stages and interventions on the prevalence and concentration of Campylobacter on broiler carcasses. To comprehensively capture relevant evidence, six databases were searched using the keywords "Campylobacter" and "broiler chicken." The literature search yielded 10,450 unique citations, and after applying predetermined inclusion and exclusion criteria, 72 and 53 relevant citations were included in meta-analyses for processing stages and interventions, respectively. As the two primary outcomes, log reduction and prevalence changes were estimated for each stage or intervention using a random-effects meta-analysis approach whenever possible. The outcome-level quality assessment was conducted following the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. The analysis revealed that scalding and chilling majorly reduces the prevalence and concentration of Campylobacter. Immersion chilling reduces the concentration regardless of chemical additives, but its effect on prevalence is not conclusive. The effects of carcass washing applications remain uncertain due to the inconsistency and imprecision of both outcomes. Defeathering and evisceration were identified as stages that can increase both prevalence and concentration. Both chemical and physical processing interventions provide limited efficacy in concentration and prevalence reduction. Major limitations of the review were inconsistency and imprecision at the outcome level and reporting issues and data gaps at the study level. The results are expected to inform quantitative microbial risk assessment model development and support evidence-based decision-making.

Efficacy of Salmonella Bacteriophage S1 Delivered and Released by Alginate Beads in a Chicken Model of Infection

Modern bacteriophage encapsulation methods based on polymers such as alginate have been developed recently for their use in phage therapy for veterinary purposes. In birds, it has been proven that using this delivery system allows the release of the bacteriophage in the small intestine, the site of infection by Salmonella spp. This work designed an approach for phage therapy using encapsulation by ionotropic gelation of the lytic bacteriophage S1 for Salmonella enterica in 2% w/v alginate beads using 2% w/v calcium chloride as crosslinking agent. This formulation resulted in beads with an average size of 3.73 ± 0.04 mm and an encapsulation efficiency of 70%. In vitro, the beads protected the bacteriophages from pH 3 and released them at higher pH. To confirm that this would protect the bacteriophages from gastrointestinal pH changes, we tested the phage infectivity in vivo assay. Using a model chicken (Gallus gallus domesticus) infected with Salmonella Enteritidis, we confirmed that after 3 h of the beads delivery, infective phages were present in the chicken’s duodenal and caecal sections. This study demonstrates that our phage formulation is an effective system for release and delivery of bacteriophage S1 against Salmonella Enteritidis with potential use in the poultry sector.

Immunity and Protection Provided by Live Modified Vaccines Against Paratyphoid Salmonella in Poultry-An Applied Perspective

Several serotypes of non-host-specific or paratyphoid Salmonella have been linked with contamination of poultry meat, and eggs, resulting in foodborne outbreaks in humans. Vaccination of poultry against paratyphoid Salmonella is a frequent strategy used to reduce the levels of infection and transmission, which ultimately can lead to lower rates of human infections. Live vaccines have been developed and used in poultry immediately after hatching as a result of their ability to colonize the gut, stimulate a mucosal immune response, induce a competitive inhibitory effect against homologous wild strains, and reduce colonization and excretion of Salmonella. Furthermore, vaccines can competitively exclude some heterologous strains of Salmonella from colonizing the gastrointestinal tract when young poultry are immunologically immature. In addition, various studies have suggested that booster vaccination with live vaccines a few weeks after initial vaccination is essential to increase the level of protection and achieve better cross-protective immunity. Vaccination of breeders, broilers, layers, and turkeys with modified live Salmonella vaccines is a common intervention that has become an important component in poultry companies' multistep prevention programs to meet increasingly demanding customer and regulatory food safety requirements. Both live and inactivated vaccines play a critical role in a comprehensive control program for chicken and turkey breeders and commercial layers. This review examines the response and protection conferred by live modified vaccines against non-host-specific Salmonella that can be considered for the design and implementation of vaccination strategies in poultry.

Effect of dietary direct-fed microbial and yeast cell walls on cecal digesta microbiota of layer chicks inoculated with nalidixic acid resistant Salmonella Enteritidis

Salmonella enterica serovar Enteritidis (SE) has consistently been the most common serotype associated with the foodborne Salmonellosis worldwide. In this study, the effect of a dietary direct-fed microbial (DFM) and yeast cell walls (YCW) under a challenge of nalidixic acid resistant SE strain using layer chicks has been investigated. A total of 160 newly hatched Dekalb White female chicks were randomly assigned into 2 experimental groups (80 birds/treatment), control group (CON) and treatment group (DY). Chicks were fed ad libitum a non–medicated-corn-soy based diet and DY was supplemented with the combination of DFM and YCW. At 8 days of age, 2.1 × 10⁹ CFU/bird of the SE was given to all chicks by oral administration. On 3 days postinoculation (dpi), 20 chicks/group were euthanized and all cecal contents were collected for analysis. On 6, 10, and 14 dpi, the cecal contents were sampled from 16 chicks per group. The number of SE in the cecal contents was counted using culture-based methods. A 16S rRNA-based microbiota analysis was performed for additional microbial profiling. The CON and DY showed difference (P ≤ 0.05) in β diversity throughout the trial. Prevalence of SE in cecal contents was lower (P ≤ 0.05) in DY across all time-points. Lower abundance of Salmonella spp. was also shown in DY by liner discriminant analysis effect size (LEfSe). DY increased (P ≤ 0.05) diversity of bacterial species in the cecal contents in DY at 10 and 14 dpi. For the SE challenged birds, SE reduction in DY was observed at 3 dpi and until the end of the trial at 14 dpi confirming a numerically larger difference between groups as well as an increase in bacterial species diversity in DY. It could be hypothesized that the SE reduction shown immediately after the challenge and the greater SE reduction shown after 10 dpi may be the synergistic effect of the combined feed additives.

Prebiotics and alternative poultry production

Alternative poultry production systems continue to expand as markets for organic and naturally produced poultry meat and egg products increase. However, these production systems represent challenges associated with variable environmental conditions and exposure to foodborne pathogens. Consequently, there is a need to introduce feed additives that can support bird health and performance. There are several candidate feed additives with potential applications in alternative poultry production systems. Prebiotic compounds selectively stimulate the growth of beneficial gastrointestinal microorganisms leading to improved health of the host and limiting the establishment of foodborne pathogens. The shift in the gastrointestinal microbiota and modulation of fermentation can inhibit the establishment of foodborne pathogens such as Campylobacter and Salmonella. Both current and potential applications of prebiotics in alternative poultry production systems will be discussed in this review. Different sources and types of prebiotics that could be developed for alternative poultry production will also be explored.

Association of Broiler Litter Microbiome Composition and Campylobacter Isolation

Infection with Campylobacter species is one of the leading causes of bacterial diarrhea in humans in the US. Chickens, which become colonized on the farm, are important reservoirs of this bacterium. Campylobacter can establish itself in the broiler house via a variety of sources, can survive in the litter of the house, and possibly persist over successive flock cycles. However, the role of the broiler litter microbiome on Campylobacter persistence is not clear. A matched case-control study was conducted to determine whether the broiler litter microbiome composition was associated with Campylobacter isolation within the broiler house. Flocks were classified as cases when either Campylobacter jejuni or Campylobacter coli was isolated in boot sock samples, or as controls otherwise. Case and control flocks were matched at the broiler house level. Composite broiler litter samples were collected and used for DNA extraction and 16S rRNA gene V4 region sequencing. Reads were processed using the DADA2 pipeline to obtain a table of amplicon sequence variants. Alpha diversity and differential bacterial relative abundance were used as predictors of Campylobacter isolation status in conditional logistic regression models adjusting for flock age and sampling season. Beta diversity distances were used as regressors in stratified PERMANOVA with Campylobacter isolation status as predictor, and broiler house as stratum. When Campylobacter was isolated in boot socks, broiler litter microbiome richness and evenness were lower and higher, respectively, without reaching statistical significance. Campylobacter isolation status significantly explained a small proportion of the beta diversity (genus-level Aitchison dissimilarity distance). Clostridium and Anaerostipes were positively associated with Campylobacter isolation status, whereas Bifidobacterium, Anaerosporobacter, and Stenotrophomonas were negatively associated. Our results suggest the presence of bacterial interactions between Campylobacter and the broiler litter microbiome. The negative association of Campylobacter with Bifidobacterium, Anaerosporobacter, and Stenotrophomonas in litter could be potentially exploited as a pre-harvest control strategy.

Characterization of Salmonella Isolates Recovered from Stages of the Processing Lines at Four Broiler Processing Plants in Trinidad and Tobago

This cross-sectional study determined the prevalence, characteristics, and risk factors for contamination of chicken with Salmonella at four operating broiler processing plants in Trinidad. Standard methods were used to isolate and characterize the Salmonella isolates. The overall prevalence of Salmonella at the four processing plants was 27.0% (107/396). The whole carcass enrichment (WCE) method yielded a statistically significantly (p = 0.0014) higher frequency of isolation (53.9%; 97/180) than the whole carcass rinse (35.0%; 63/180) and neck skin methods (42.2%; 38/90). S. enterica serotypes Enteritidis, Javiana, and Infantis were the predominant serotypes isolated accounting for 20.8%, 16.7% and 12.5%, respectively, of the serotyped isolates. Risk factors included the use of over 100 contract farmers (OR 4.4), pre-chiller (OR 2.3), addition of chlorine to chiller (OR 3.2), slaughtering sick broilers (OR 4.4), and flocks with >50% mortality. Multi-drug resistance was detected in 12.3% (14/114) of the isolates of Salmonella. Resistance was high to kanamycin (85.7%) and doxycycline (74.6%) but low to amoxicillin-clavulanic acid (2.4%) and sulphamethoxazole-trimethoprim (0.8%). The occurrence of resistant Salmonella in chickens processed at commercial broiler processing plants has implications for salmonellosis and therapeutic failure in consumers of improperly cooked contaminated chickens from these plants in the country.

Selective pre-enrichment method to lessen time needed to recover Salmonella from commercial poultry processing samples

Conventional Salmonella detection is time consuming, often employing a 24-h pre-enrichment step in buffered peptone water (BPW), followed by a 24-h selective enrichment in either Rappaport Vassiliadis (RV) or tetrathionate (TT) broths before streaking onto selective indicator agar. To reduce this time, we sought to optimize pre-enrichment for Salmonella recovery by evaluating the addition of selective chemicals to BPW. Duplicate samples each representative of 500 carcasses were collected by catching processing water drip under moving carcass shackle lines immediately after feather removal in each of nine commercial processing plants. Carcass drip samples were cultured under selective pre-enrichment conditions in parallel with BPW pre-enrichment followed by RV and TT selective enrichment. Addition of bile salts (1 g/L) and novobiocin (0.015 g/L) resulted in Salmonella recovery from 89% samples when plated directly after pre-enrichment compared to 67% recovery in non-selective BPW alone. Salmonella serovar identities were determined using CRISPR-SeroSeq. Overall, serovars matched between selective pre-enrichment and traditional enrichment methods. These data suggest that increasing the selectivity of Salmonella pre-enrichment step may lessen the need for a separate selective enrichment step thereby reducing time required for Salmonella isolation by 24 h.

Mitigating the Spread and Translocation of Salmonella Enteritidis in Experimentally Infected Broilers under the Influence of Different Flooring Housing Systems and Feed Particle Sizes

This study aimed to evaluate the influences of different flooring designs and feed particle sizes on the spread of Salmonella (S.) in broiler chickens. Birds (n = 480) were allocated to four different housing systems (fully littered with and without floor heating, partially and fully slatted flooring with sand bath) and two dietary treatments (finely and coarsely ground diets) in 24 boxes. Two broilers per box were experimentally infected with S. Enteritidis (8.00 log10 CFU/bird) at d 17. Salmonella prevalence in caecal contents and the liver was highest in broilers housed on fully slatted floor until d 36/37 (88.1% and 91.5%, respectively), and lowest in litter flooring (caecal content 64.4%) and litter flooring with floor heating (liver 61.7%). In turn, broilers on littered flooring expressed the lowest Salmonella counts in caecal content at d 36/37 (2.21 ± 1.75 log10 CFU/g), partial slatted flooring the highest (3.76 ± 1.46 log10 CFU/g). The mean Salmonella count in the caecal content was significantly lower for birds fed a coarsely ground diet (0.96 and 1.94 log10 CFU/g) than a finely ground diet (5.07 and 3.34 log10 CFU/g) at d 23 and d 36/37, respectively (p < 0.0001). Slatted flooring with a sand bath did not show advantages in terms of Salmonella reduction, whereas the coarsely ground diet markedly reduced the spread of Salmonella.

Prevalence of Campylobacter spp. in Chicken Carcasses in Slaughterhouses from South of Brazil

Campylobacteriosis has become common cause of diarrhea in humans and is associated with Guillain-Barré Syndrome, Reactive Arthritis and Irritable Bowel Syndrome is caused mainly by contaminated food and water intake in which the majority occurs from manipulation, preparation and consumption of poultry meat. The aim of this study was to estimate the prevalence of Campylobacter in chicken carcasses from slaughterhouses located in the states of Parana, Santa Catarina and Rio Grande do Sul in the South of Brazil. The samples were analyzed for Campylobacter enumeration using the ISO method 10272-2 and the species C. jejuni and C. coli, important for public health, were identified through Maldi-TOF mass spectrometry. From July 2017 to July 2018, 816 samples were analyzed, indicating the prevalence of 35.84%, with higher occurrence of C. jejuni (78.47%). No difference in prevalence was observed in relation to the size of the slaughterhouses. However, significant differences were noted among the three states in the southern region of the country, with the lowest prevalence being observed in Parana. The results reinforce the need to advance in the implementation of strategies to control this pathogen in the country, in order to safeguard consumer's health and contribute for the maintenance of Brazil's position in the international poultry meat market.

Using farm management practices to predict Campylobacter prevalence in pastured poultry farms

Contamination of poultry products by Campylobacter is often associated with farm management practices and processing plant practices. A longitudinal study was conducted on 11 pastured poultry farms in southeastern United States from 2014 to 2017. In this study, farm practices and processing variables were used as predictors for a random forest (RF) model to predict Campylobacter prevalence in pastured poultry farms and processing environments. Individual RF models were constructed for fecal, soil and whole carcass rinse after processing (WCR-P) samples. The performance of models was evaluated by the area under curve (AUC) from the receiver operating characteristics curve. The AUC values were 0.902, 0.894, and 0.864 for fecal, soil, and WCR-P models, respectively. Relative importance plots were generated to predict the most important variable in each RF model. Animal source of feces was identified as the most important variable in fecal model and the soy content of the brood feed was the most important variable for soil model. For WCR-P model, the average flock age showed the strongest impact on RF model. These RF models can help pastured poultry growers with food safety control strategies to reduce Campylobacter prevalence in pastured poultry farms.

Salmonella Genomics and Population Analyses Reveal High Inter- and Intraserovar Diversity in Freshwater

Freshwater can support the survival of the enteric pathogen Salmonella, though temporal Salmonella diversity in a large watershed has not been assessed. At 28 locations within the Susquehanna River basin, 10-liter samples were assessed in spring and summer over 2 years. Salmonella prevalence was 49%, and increased river discharge was the main driver of Salmonella presence. The amplicon-based sequencing tool, CRISPR-SeroSeq, was used to determine serovar population diversity and detected 25 different Salmonella serovars, including up to 10 serovars from a single water sample. On average, there were three serovars per sample, and 80% of Salmonella-positive samples contained more than one serovar. Serovars Give, Typhimurium, Thompson, and Infantis were identified throughout the watershed and over multiple collections. Seasonal differences were evident: serovar Give was abundant in the spring, whereas serovar Infantis was more frequently identified in the summer. Eight of the ten serovars most commonly associated with human illness were detected in this study. Crucially, six of these serovars often existed in the background, where they were masked by a more abundant serovar(s) in a sample. Serovars Enteritidis and Typhimurium, especially, were masked in 71 and 78% of samples where they were detected, respectively. Whole-genome sequencing-based phylogeny demonstrated that strains within the same serovar collected throughout the watershed were also very diverse. The Susquehanna River basin is the largest system where Salmonella prevalence and serovar diversity have been temporally and spatially investigated, and this study reveals an extraordinary level of inter- and intraserovar diversity.IMPORTANCESalmonella is a leading cause of bacterial foodborne illness in the United States, and outbreaks linked to fresh produce are increasing. Understanding Salmonella ecology in freshwater is of importance, especially where irrigation practices or recreational use occur. As the third largest river in the United States east of the Mississippi, the Susquehanna River is the largest freshwater contributor to the Chesapeake Bay, and it is the largest river system where Salmonella diversity has been studied. Rainfall and subsequent high river discharge rates were the greatest indicators of Salmonella presence in the Susquehanna and its tributaries. Several Salmonella serovars were identified, including eight commonly associated with foodborne illness. Many clinically important serovars were present at a low frequency within individual samples and so could not be detected by conventional culture methods. The technologies employed here reveal an average of three serovars in a 10-liter sample of water and up to 10 serovars in a single sample.

Effect of Feeding a Postbiotic Derived from Saccharomyces cerevisiae Fermentation as a Preharvest Food Safety Hurdle for Reducing Salmonella Enteritidis in the Ceca of Layer Pullets

ABSTRACT

Salmonella Enteritidis is responsible for a significant proportion of foodborne salmonellosis in the United States and continues to be attributable to table eggs despite increased federal oversight. Technologies, including feed additives, continue to be evaluated for preharvest application and their potential food safety benefits. Diamond V Original XPC, a Saccharomyces cerevisiae fermentation-based postbiotic (SCFP), was evaluated for its effectiveness in reducing Salmonella Enteritidis (SE) colonization in young layer pullets. A total of 40 day-old Hy-Line W-36 layer pullets were equally divided and randomly assigned to one of two dietary treatments, with SCFP or without SCFP (PCON), and orally gavaged on day 28 with SE at 106 CFU/mL. Another 20 day-old pullets were fed the same control feed without SCFP and blank inoculated on day 28 with 1 mL of sterile phosphate-buffered saline to serve as a negative control. Qualitative and quantitative analyses of cecal contents for Salmonella were performed for all birds on day 32. The prevalence of SE in the ceca of all directly challenged birds was 100%; however, the SE concentration in birds fed SCFP diet (3.35 log CFU/g) was significantly lower (P < 0.0001) than that of the PCON birds not fed SCFP (4.49 log CFU/g). The proportion of birds with enumerable SE concentrations was lower in SCFP-fed pullets (57.9%) than in the PCON pullets (95.0%). These data suggest that inclusion of SCFP in the diet may aid in the reduction of SE within the ceca of commercial laying hens and could serve as an additional preharvest food safety hurdle.

HIGHLIGHTS

Hygiene management in newborn individually housed dairy calves focusing on housing and feeding practices

In calf rearing, the first weeks of life are critical and associated with the highest mortality due to enteric and respiratory diseases. A well-implemented hygiene management can help to protect calves' health preventively by reducing the load of pathogenic bacteria and interrupting infection chains. The aim of this study was to identify deficiencies in hygiene management of individually housed dairy calves by surveying current practice and examining feeding and housing equipment with different hygiene indicators. On 11 farms, different locations in 2 pens or hutches for individual calf rearing prepared for restocking and 2 feeding buckets per farm, including the inner and outer surfaces of artificial teats, were visually scored for cleanliness and sampled with swabs (housing equipment: n = 167; feeding equipment: n = 120). The sanitation of floors was tested with sock samples (n = 41). A total of 328 samples were analyzed for adenosine triphosphate (ATP) and protein residues, aerobic total viable count (TVC), total coliform count (TCC), Escherichia coli, methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum β-lactamase-producing bacteria (ESBL), and Salmonella spp. After evaluation of these results, the farmers were informed about the findings and trained on improvement in hygiene management personally. The sampling was repeated after 1 year to detect possible changes in hygiene management. The highest bacterial loads (TVC, TCC, and E. coli) were observed in feeding equipment, especially the inner teat of milk feeding buckets. Environmental samples, primarily the sidewalls and back walls of tested pens and hutches, exhibited the lowest bacterial counts and ATP and protein residues. All samples were negative for MRSA and Salmonella spp. In 10.5% of all samples, ESBL was detected, and in 6.8%, ESBL E. coli was detected, predominately in sock samples, followed by feeding equipment samples. Training in hygiene management showed only limited effects. In conclusion, there is still great potential to improve the implementation of hygiene measures in individual calf housing. In particular, more attention should be paid to the cleaning of feeding buckets and artificial teats, as this is a simple means of interrupting the possible spread of pathogens among calves.

Pseudomonas putida as a potential biocontrol agent against Salmonella Java biofilm formation in the drinking water system of broiler houses

Background

Environmental biofilms can induce attachment and protection of other microorganisms including pathogens, but can also prevent them from invasion and colonization. This opens the possibility for so-called biocontrol strategies, wherein microorganisms are applied to control the presence of other microbes. The potential for both positive and negative interactions between microbes, however, raises the need for in depth characterization of the sociobiology of candidate biocontrol agents (BCAs). The inside of the drinking water system (DWS) of broiler houses is an interesting niche to apply BCAs, because contamination of these systems with pathogens plays an important role in the infection of broiler chickens and consequently humans. In this study, Pseudomonas putida, which is part of the natural microbiota in the DWS of broiler houses, was evaluated as BCA against the broiler pathogen Salmonella Java.

Results

To study the interaction between these species, an in vitro model was developed simulating biofilm formation in the drinking water system of broilers. Dual-species biofilms of P. putida strains P1, P2, and P3 with S. Java were characterized by competitive interactions, independent of P. putida strain, S. Java inoculum density and application order. When equal inocula of S. Java and P. putida strains P1 or P3 were simultaneously applied, the interaction was characterized by mutual inhibition, whereas P. putida strain P2 showed an exploitation of S. Java. Lowering the inoculum density of S. Java changed the interaction with P. putida strain P3 also into an exploitation of S. Java. A further increase in S. Java inhibition was established by P. putida strain P3 forming a mature biofilm before applying S. Java.

Conclusions

This study provides the first results showing the potential of P. putida as BCA against S. Java in the broiler environment. Future work should include more complex microbial communities residing in the DWS, additional Salmonella strains as well as chemicals typically used to clean and disinfect the system.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-020-02046-5.

Prevalence, Concentration, and Antimicrobial Resistance Profiles of Salmonella Isolated from Florida Poultry Litter

ABSTRACT

For over a decade, Salmonella contamination has increasingly led to outbreaks of foodborne illness associated with fresh produce. The use of untreated animal manures, or biological soil amendments of animal origin, to amend agricultural soils holds a risk of contamination from foodborne pathogens, such as Salmonella. This study was conducted to determine the prevalence, concentration, serotypes, and antimicrobial resistance profiles of Salmonella in poultry litter from Florida farms. Litter pH, total Kjeldahl nitrogen, total ammonia nitrogen, total phosphorus (P2O5), total potassium (K2O), moisture content, total solids, total ash, organic matter, and aerobic plate count (APC) were also measured. Litter samples (n = 54) were collected from 18 broiler farms across three seasons (spring, summer, and winter). Salmonella concentrations were enumerated using a most-probable-number (MPN) method, and antimicrobial susceptibility testing was performed. The prevalence of Salmonella in litter samples was 61.1%, with a geometric mean of 0.21 ± 20.7 MPN/g. Across all seasons, Salmonella concentrations were not influenced by the chemical, physical, or microbial properties measured. Recovered Salmonella isolates (n = 290) were grouped into serogroups O:4 (43.1%), O:7 (26.9%), O:8 (11.0%), O:1,3,10,19 (7.9%), and O:9,46 (7.2%). Serotyping Salmonella isolates (n = 47) resulted in 12 serotypes, with the most common being Typhimurium (27.7%), Kentucky (17.0%), Enteritidis (14.9%), and Mbandaka (14.9%). Antimicrobial resistance to tetracycline (29.8%), sulfisoxazole (23.4%), and streptomycin (14.9%) was observed. No isolates were resistant to more than two antimicrobial agents. This study provides valuable information for future risk assessments for the use of poultry litter as an untreated biological soil amendment of animal origin.

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Strategies to Improve Poultry Food Safety, a Landscape Review

Food safety remains a significant public health issue for the poultry industry. Foodborne pathogens can be in contact at all phases of poultry production, from initial hatch to processing and ultimately to retail and meal preparation. Salmonella and Campylobacter have been considered the primary foodborne pathogens associated with poultry. Both organisms are major causative agents of human foodborne illness. Limiting these pathogens in poultry production requires identifying their sources and routes of transmission. This involves the ability to isolate and precisely identify them using methodologies capable of discernment at the genome level. Interventions to reduce their occurrence in poultry production employ two basic strategies: prevention of establishment and elimination of already-established pathogens. This review provides an overview of current findings and prospects for further research on poultry food safety issues.

Prevalence and antibiotic resistance of Campylobacter coli isolated from broiler farms in the Marrakesh Safi region, Morocco

BACKGROUND AND AIM

Campylobacteriosis is a common foodborne disease epidemiologically linked to the consumption of poultry products. However, other sources, such as raw or contaminated milk, contaminated water or ice, contact with infected livestock, and pets, are reported. This study aimed to evaluate the prevalence and resistance to microbial resistance of Campylobacter coli in broiler farms in the region of Marrakesh Safi, Morocco.

MATERIALS AND METHODS

The study was conducted between May and December 2017 and involved 35 broiler farms. One hundred and five cloacal swabs were collected from the eight provinces in the region of Marrakesh Safi, Morocco. Bacteriology method NM ISO/TS 10272-3: 2013 was used to isolate and identify Campylobacter spp. Molecular identification (polymerase chain reaction) was used for confirmation. A disk diffusion method on Mueller-Hinton agar was used for susceptibility testing. Five antibiotic agents, including first-line drugs, were evaluated.

RESULTS

Among 105 samples, 71.4% (75/105) were positive for Campylobacter spp. test and 56% (42/75) of isolates belonged to the species coli. Susceptibility profiles showed that 95.2% of C. coli strains were resistant to ampicillin, 92.8% to erythromycin and tetracycline, 85.7% to ciprofloxacin, and 7.1% to gentamicin.

CONCLUSION

This study underlines the need to strengthen implementation of specific control procedures to decrease contamination of poultry meat with Campylobacter spp. and to reduce the use of antibiotics in the poultry sector.

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.

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