The prevalence and concentration of Salmonella enterica in poultry litter in the southern United States

Sampling method influences Salmonella detection and quantification in pre-harvest commercial broiler production

Effective pre-harvest Salmonella monitoring in broilers relies on accurate, reliable, and reproducible evaluation of pre-harvest Salmonella. In this study, six sampling methods were evaluated and compared to assess Salmonella prevalence and quantification during broiler production across three iterative experiments. In experiment one, bootsocks, electrostatic pad-rollers, feather swabs, cloacal swabs, fecal grabs, and litter grabs were collected from 24 houses across 10 farms (n = 288 samples). In the second experiment, bootsocks, bootsock-rollers, and feather swabs were collected in 16 houses on seven farms (n = 128). Bootsocks and bootsock-rollers were selected as the most reproducible sampling method. In experiment three both methods were performed in triplicate in 20 houses on 10 farms (n = 240). In all experiments, prevalence was determined by qPCR and by culture, then compared by Fisher's Exact test between and McNemar's test within methods. Salmonella was quantified by qPCR and Ct-values were compared using one-sided F-test. In experiment one, prevalence differed between methods by qPCR (p = 0.0150) only and the best performing sampling methods were bootsocks (42/48 culture and 41/48 qPCR positive), feather swabs (42/48 and 36/48), and electrostatic pad-rollers (35/48 and 34/48). In experiment 2, feather swabs differed by qPCR prevalence (p = 0.0004). Bootsocks (30/32 culture and 28/32 qPCR positive) and bootsock-rollers (31/32 and 32/32) performed best. In experiment 3, qPCR prevalence (210/240) was greater than culture (167/240) (p = 0.0021), but no differences were observed between methods or replicates. The average Ct-value for bootsocks and bootsock-rollers were 37.8 and 38.9, respectively and there was no difference in their variance (p = 0.8061). A linear mixed-effect model found that farm contributed 36.34 % of the variance observed while house, house-side, and replicate accounted for 24.69 %, 4.68 % and 3.85 %, respectively. This study shows that sampling methods directly influence both Salmonella detection and load recovery. For surveillance sampling, bootsocks and bootsock-rollers were found to best indicate pre-harvest Salmonella. These two methods were highly reproducible, user friendly, and provide the most reliable Salmonella results indicating the Salmonella prevalence in broiler flocks during production.

Dose-response study of a fenugreek-based antibiotic alternative in Bábolna Tetra-SL chicks (1-42 days old) with mixed bacterial infections

Introduction

Combating antimicrobial resistance is one of the most pressing public health challenges of our time. The rapid spread of resistant, zoonotic bacterial strains in livestock farming is increasingly raising concerns about the need to reduce antibiotic use. Because of this, there is an urgent need for safe and effective alternatives in animal husbandry.

Methods

This study aimed to perform an in vivo the dose-response analysis of fenugreek (Trigonella foenum-graecum), as a plant-based antibiotic alternative feed supplement in Bábolna Tetra-SL chicks (1-42 days old) with a 1:1 sex ratio. A total of 270 chicks were randomly assigned to 18 groups (15 birds per group) and subjected to six different treatment groups in three replicates: fenugreek at 1×, 10×, and 100× doses, an antibiotic-treated group (enrofloxacin), a positive control group (infection only), and a negative control group (no infection or treatment). The infection was induced using mixed Salmonella Enteritidis and Escherichia coli, administered via gavage on days 3 and 4 of life. The birds were monitored for clinical symptoms, body weight, feed intake, and Salmonella shedding through cloacal swab samples. Statistical analyses included mixed-effect logistic regression for mortality, mixed-effect linear models for weight gain, two-way ANOVA for feed efficiency, and random effects continuation ratio models for Salmonella isolation.

Results

Significant interactions for Group:Day and Sex:Day in weight gain were identified (p < 0.0001 for both). Additionally, the 1 × dose group showed significantly reduced Salmonella shedding compared to the positive control group on day 33 (p = 0.0031). The low-dose group (1×) demonstrated the most promising results, showing a 63% reduction in Salmonella shedding on day 10 and 31% on day 17. This group exhibited the fewest clinical symptoms, no diarrhea, and the lowest individual and specific feed intake up to day 24.

Discussion

The findings of this study suggest that low-dose fenugreek supplementation could be a viable strategy for reducing Salmonella shedding in poultry, potentially contributing to reduced antibiotic use in poultry farming and thus playing a role in the global effort to combat antimicrobial resistance. Future research will involve large-scale industrial trials and next-generation sequencing to evaluate the additive's impact on gut microbiota composition.

Broiler litter moisture and trace metals contribute to the persistence of Salmonella strains that harbor large plasmids carrying siderophores

Broiler litter sampling has proven to be an effective method for determining the Salmonella status of a broiler chicken flock and understanding the ecology of Salmonella prior to harvest. In this study, we investigated the ecology of Salmonella within the litter (n = 224) from two commercial broiler houses in the United States. We employed culture enrichment methods and quantitative polymerase chain reaction to determine the prevalence and load of Salmonella and utilized antimicrobial susceptibility testing and whole-genome sequencing (WGS) to characterize select isolates. Additionally, we applied machine learning algorithms and in vitro experiments to identify environmental selective pressures that may contribute to the persistence of Salmonella in litter. Our findings indicate that the prevalence and abundance of Salmonella in broiler litter are influenced by the downtime between flocks as well as by the flock raised on the litter. A Decision Tree Classifier model developed demonstrated that the moisture in the caked part of litter was the most influential environmental parameter for predicting the prevalence of viable Salmonella. WGS analysis revealed that Typhimurium, Infantis, and Kentucky strains that harbored large self-conjugative plasmids encoding fitness factors for iron siderophore production were the dominant Salmonella population found in litter, and exposure to iron-limiting and copper-enriched culture media affected Salmonella growth. Our results suggest that trace metals may select for siderophores harbored on plasmids, and interventions that reduce litter moisture can potentially curtail the persistence of Salmonella in pre-harvest environments.IMPORTANCEBroiler chicken meat is the most consumed protein worldwide, and global poultry imports are projected to reach 17.5 million tons by 2031. To raise billions of chickens, litter is reused multiple times by the top global producers and exporters of chicken (Brazil and the United States). Chickens are in continuous contact with litter and depend on it for warmth and coprophagy. Consequently, litter serves as a major route for pathogens such as Salmonella to infect chickens, making it crucial to understand the environmental and genetic selective pressures that might explain why certain Salmonella strains persist on broiler farms more than others. In this study, we demonstrated that Salmonella strains that harbored siderophores on large conjugative plasmids persisted in litter and suggested that reducing litter moisture would significantly control Salmonella prevalence. However, a complete eradication of persisting Salmonella strains will require novel, innovative, and multifaceted approaches.

Salmonella enterica serovar Braenderup shows clade-specific source associations and a high proportion of molecular epidemiological clustering

Salmonella enterica serovar Braenderup (S. enterica ser. Braenderup) is an important clinical serovar in the United States. This serovar was reported by the CDC in 2017 as the fifth most common Salmonella enterica serovar associated with outbreaks in the United States, which have been linked to both fresh produce and food animal products. The goals of this study were to compare the relatedness of human clinical isolates from southeastern USA (Tennessee (n = 106), Kentucky (n = 48), Virginia (n = 252), South Carolina (n = 109), Georgia (n = 159), Alabama (n = 8), Arkansas (n = 26), and Louisiana (n = 91)) and global clinical (n = 5,153) and nonclinical (n = 1,053) isolates obtained from the NCBI. Additionally, we also examined the population structure of S. enterica ser. Braenderup strains (n = 3,131) on EnteroBase and found that all the strains of this serovar are associated with a single cgMLST eBurst group (ceBG 185), confirming that this serovar is monophyletic. We divided the S. enterica ser. Braenderup population into two clades (Clade I and Clade II) and one clade group (Clade Group III). The composition of distinct environmental isolates in the clades differed: Clade I was significantly associated with produce (90.7%; P < 0.0001) and water, soil, and sediment (76.9%; P < 0.0001), and Clade II was significantly associated with poultry environments (62.8%; P < 0.0001). The clade-specific gene associations (e.g., Clade I-associated competence proteins and cytochrome_c_asm protein and Clade II-associated heme-exporter protein and dimethyl sulfoxide [DMSO] reductase-encoding genes) provide potential insights into possible mechanisms driving environmental adaptation and host-pathogen interaction. Phylogenetic analyses identified 218 molecular epidemiological clusters in the current study, which represented a greater proportion of potentially outbreak-related isolates than previously estimated.

IMPORTANCE

This study provides insights into the genomic diversity of S. enterica ser. Braenderup by revealing distinct clade-specific source attribution patterns and showing that a greater proportion of isolates were associated with epidemiological clusters based on the genomic relatedness than previously estimated. Specifically, we analyzed the diversity of human clinical isolates from southeastern USA and compared them with the global clinical and nonclinical isolates. Our analysis showed different clades of S. enterica ser. Braenderup linked to different environments, providing insights on the potential source of human sporadic infection and outbreaks. These findings can enhance public health surveillance and response strategies targeting S. enterica serovar Braenderup by expanding our understanding of potential transmission pathways and the genomic diversity of clinical and environmental isolates.

Detection and antimicrobial resistance profiles of Salmonella enterica recovered from house fly intestinal tracts and environments of selected broiler farms in Texas

The entry of drug-resistant Salmonella enterica into the food supply is a challenge to public health and food safety. One emerging concern is the role of synanthropic insects for moving microbial pathogens throughout poultry production systems, where insects commonly thrive. We investigated the presence and phenotypic antimicrobial susceptibility of S. enterica from insect and environmental samples from broiler farms. Insects were collected throughout the broiler house and adjacent compost barn. Environmental samples (poultry feed, drinking water, fresh litter, and feces) were collected simultaneously (n = 80). Insect gastrointestinal tracts were dissected and pooled (n = 57). Recovered Salmonella isolates were serotyped and subjected to antimicrobial susceptibility testing against 14 medically important antimicrobials. Overall, six isolates were recovered from 137 total samples (4.4%): 3.5% (2/57) from adult house flies (Musca domestica), 15% (3/20) from poultry feed, and 4.8% (1/21) from litter. Salmonella Montevideo (16.7%; 1/6), Typhimurium (33.3%; 2/6), and Kentucky (50%, 3/6) were identified. All but one Salmonella isolate (83.3%; 5/6) demonstrated resistance to at least one antimicrobial. Further research should investigate movement patterns between broiler operations and food processing facilities to establish efficient biosecurity measures to prevent any instances of foodborne pathogen transmission into human food systems.

Survival of Twelve Pathogenic and Generic Escherichia coli Strains in Agricultural Soils as Influenced by Strain, Soil Type, Irrigation Regimen, and Soil Amendment

Biological soil amendments of animal origin (BSAAO) play an important role in agriculture but can introduce pathogens into soils. Pathogen survival in soil is widely studied, but data are needed on the impacts of strain variability and field management practices. This study monitored the population of 12 Escherichia coli strains (generic, O157, and non-O157) in soils while evaluating the interactions of soil type, irrigation regimen, and soil amendment in three independent, greenhouse-based, randomized complete block design trials. Each E. coli strain (4-5 log10 CFU/g) was homogenized in bovine manure amended or nonamended sandy-loam or clay-loam soil. E. coli was enumerated in 25 g samples on 0, 0.167 (4 h), 1, 2, 4, 7, 10, 14, 21, 28, 56, 84, 112, 168, 210, 252, and 336 days postinoculation (dpi). Regression analyses were developed to understand the impact of strain, soil type, irrigation regimen, and soil amendment on inactivation rates. E. coli survived for 112 to 336 dpi depending on the treatment combination. Pathogenic and generic E. coli survived 46 days [95% Confidence interval (CI) = 20.85, 64.72; p = 0.001] longer in soils irrigated weekly compared to daily and 146 days (CI = 114.50, 184.50; p < 0.001) longer in amended soils compared to unamended soils. Pathogenic E. coli strains were nondetectable 69 days (CI = 39.58, 98.66, p = 0.015) earlier than generic E. coli strains. E. coli inactivation rates demonstrated a tri-phasic pattern, with breakpoints at 26 dpi (CI = 22.3, 29.2) and 130 dpi (CI = 121.0, 138.1). The study findings demonstrate that using bovine manure as BSAAO in soil enhances E. coli survival, regardless of strain, and adequate food safety practices are needed to reduce the risk of crop contamination. The findings of this study contribute data on E. coli concentrations in amended soils to assist stakeholders and regulators in making risk-based decisions on time intervals between the application of BSAAO and the production and harvest of fruits and vegetables.

Effects of Organic Soil Amendments on Antimicrobial-Resistant Bacteria in Urban Agriculture Environments

Biological soil amendments of animal origin (BSAAOs) are widely used in urban agriculture to improve soil quality. Although BSAAO use is regulated due to risks for introducing foodborne pathogens, effects on antimicrobial-resistant (AMR) bacteria are not well established. Here, we aimed to explore the impacts of BSAAOs on levels of resident AMR bacteria in leafy vegetable production environments (i.e., kale, lettuce, chard, cabbage) across urban farms and community gardens in the greater Washington D.C. area (n = 7 sites). Leaf tissue (LT), root zone soil (RZS; amended soil in crop beds), and bulk soil (BS; site perimeter) were collected and analyzed for concentrations of total heterotrophic bacteria (THB), ampicillin (Amp) or tetracycline (Tet) resistant THB, and coliforms. As expected, amended plots harbored significantly higher concentrations of THB than bulk soil (P < 0.001). The increases in total bacteria associated with reduced fractions of Tet-resistant bacteria (P = 0.008), as well as case-specific trends for reduced fractions of Amp-resistant bacteria and coliforms. Site-to-site variation in concentrations of AMR bacteria in soil and vegetable samples reflected differences in land history and crop management, while within-site variation was associated with specific amendment sources, as well as vegetable type and cultivar. Representative isolates of the AMR bacteria and coliforms were further screened for multidrug resistance (MDR) phenotypes, and a high frequency was observed for the former. In amended soils, as the soil pH (range 6.56-7.80) positively correlated with the fraction of Tet-resistant bacteria (rho = 0.529; P < 0.001), crop management strategies targeting pH may have applications to control related risks. Overall, our findings demonstrate that soil amendments promote soil bacteria concentrations and have important implications for limiting the spread of AMR bacteria, at least in the urban landscape.

A Review on Microbiological Source Attribution Methods of Human Salmonellosis: From Subtyping to Whole-Genome Sequencing

Salmonella is one of the main causes of human foodborne illness. It is endemic worldwide, with different animals and animal-based food products as reservoirs and vehicles of infection. Identifying animal reservoirs and potential transmission pathways of Salmonella is essential for prevention and control. There are many approaches for source attribution, each using different statistical models and data streams. Some aim to identify the animal reservoir, while others aim to determine the point at which exposure occurred. With the advance of whole-genome sequencing (WGS) technologies, new source attribution models will greatly benefit from the discriminating power gained with WGS. This review discusses some key source attribution methods and their mathematical and statistical tools. We also highlight recent studies utilizing WGS for source attribution and discuss open questions and challenges in developing new WGS methods. We aim to provide a better understanding of the current state of these methodologies with application to Salmonella and other foodborne pathogens that are common sources of illness in the poultry and human sectors.

Genetic Characteristics of Salmonella Isolates Recovered From Reused Broiler Litter Over Three Successive Flocks

Salmonella infections are a leading cause of bacterial food-borne illness worldwide. Infections are highly associated with the consumption of contaminated food, and in particular, chicken meat. The severity of Salmonella infections depends on the presence of antimicrobial resistance genes and virulence factors. While there are many studies which have investigated Salmonella strains isolated from postharvest chicken samples, there is a gap in our understanding of the genetic properties that influence the persistence of Salmonella in preharvest and in particular their makeup of antimicrobial resistance genes and virulence factors. We used whole genome sequencing and hierarchical clustering to characterize and classify the genetic diversity of Salmonella enterica isolates (n = 55) recovered from the litter of commercial broiler chicken raised in four colocated broiler houses of one integrated farm over three consecutive flocks. The chicken were raised under a newly adopted "No Antibiotics Ever" program, and copper sulfate was administered via drinking water. In-silico serovar prediction identified three S. enterica serovars: Enteritidis (n = 12), Kentucky (n = 40), and Senftenberg (n = 3). Antimicrobial susceptibility testing revealed that only one S. Kentucky isolate was resistant to streptomycin, while the remaining isolates were susceptible to all antibiotics tested. Metal resistance operons, including copper and silver, were identified chromosomally and on plasmids in serovar Senftenberg and Kentucky isolates, respectively, while serovar Enteritidis carried several virulence factors on plasmids. Serovar Kentucky isolates harboring metal resistance operons were the only Salmonella isolates recovered from the litter of third flock cohort. These results suggest that there might be environmental selection for Salmonella strains carrying plasmid-associated metal resistance and virulence genes, which could play a role in their persistence in litter.

The Probiotic Potential and Metabolite Characterization of Bioprotective Bacillus and Streptomyces for Applications in Animal Production

Probiotics are increasingly recognized for their potential in managing bacterial challenges in animal production. This study aimed to evaluate the probiotic potential of Bacillus and Streptomyces strains, specifically their bioprotective ability against Salmonella. In agar inhibition assays, these bacteria supported Salmonella-inhibition zones, ranging from 2.5 ± 0.5 to 6.3 ± 2.0 mm. Analyses of antimicrobial metabolites revealed their capacity to produce compounds with anti-Salmonella properties, except for Bacillus subtilis MLB2. When Salmonella was exposed to lyophilized metabolites, inhibition occurred in both liquid (at concentrations between 250 and 500 g/L) and solid cultures (at 500 g/L). To confirm their probiotic potential, the S. griseus and Bacillus strains underwent evaluations for antimicrobial resistance, bile salt tolerance, auto- and co-aggregation, pH resistance, and their ability to adhere to and inhibit Salmonella in Caco-2 cells. These assessments confirmed their probiotic potential. The probiotic strains were further encapsulated and subjected to simulated swine and poultry digestion. They demonstrated survival potential through the gastrointestinal tract and significantly reduced the Salmonella population. Thus, these strains exhibit considerable promise for producing biotechnological products aimed at controlling Salmonella in animal production. This approach ensures the health and hygiene of farming facilities, mitigates the spread of zoonotic bacteria, and contributes positively to public health.

Vaccines to Control Salmonella in Poultry

This review is focused on describing and analyzing means by which Salmonella enterica serotype strains have been genetically modified with the purpose of developing safe, efficacious vaccines to present Salmonella-induced disease in poultry and to prevent Salmonella colonization of poultry to reduce transmission through the food chain in and on eggs and poultry meat. Emphasis is on use of recently developed means to generate defined deletion mutations to eliminate genetic sequences conferring antimicrobial resistance or residual elements that might lead to genetic instability. Problems associated with prior means to develop vaccines are discussed with presentation of various means by which these problems have been lessened, if not eliminated. Practical considerations are also discussed in hope of facilitating means to move lab-proven successful vaccination procedures and vaccine candidates to the marketplace to benefit the poultry industry.

Research Note: Role of darkling beetles (Alphitobius diaperinus) and litter in spreading and maintaining Salmonella Enteritidis and Campylobacter jejuni in chicken flocks

Salmonella and Campylobacter are common foodborne pathogens in chickens, but their persistence mechanisms within flocks are not fully understood. In this study, 4 groups of SPF Leghorn chickens (n = 50) were orally inoculated with 108Salmonella Enteritidis and 108Campylobacter jejuni, housed in BSL-2 rooms inside containers with autoclaved bedding and beetles (n = 200). Phase I (wk 1-3): the infected chickens remained in the containers and were then euthanized while beetles and litter remained in the container (group A), beetles were removed and litter remained in the container (group B), beetles remained and litter was removed (group C), and beetles and litter were removed (group D). Phase II (wk 5-7): autoclaved bedding was added to containers in groups C and D, and new SPF chickens (n = 50) were introduced and kept. Phase III (wk 8-20): all chickens were euthanized, and the litter and/or beetles remained in the containers for 17 wk. The prevalence of Salmonella Enteritidis and Campylobacter was significantly higher when detected by PCR compared to culture. In phase II, when infected chickens were removed and new chickens were introduced, 1 fecal sample in group B and 3 litter samples in groups B and C were found positive for Salmonella Enteritidis, and Campylobacter was still detected in groups A, B, and C litter samples, but not in beetles. In phase III, when all chickens were removed, Salmonella Enteritidis was identified in beetle samples from group A and the litter samples of all tested groups A, B, and C, and C. jejuni was positive in litter samples from groups A and B but not in the beetle. Sixty-nine days after removing infected chickens, culturable Salmonella was still found in beetles. Salmonella and Campylobacter were detectable in litter up to 127 d after removing infected chickens. This study highlights the transmission of Salmonella and Campylobacter via beetles and litter to new flocks in successive rearing cycles. Intensive control programs should target insect exclusion and implement strict poultry litter management or litter changes between flocks.

Application of Eugenol in Poultry to Control Salmonella Colonization and Spread

The poultry sector is an essential component of agriculture that has experienced unprecedented growth during the last few decades. It is especially true for the United States, where the average intake of chicken meat increased from 10 pounds (4.5 kg) per person in 1940 to 65.2 pounds (29.6 kg) per person in 2018, while the country produced 113 billion eggs in 2019 alone. Besides providing nutrition and contributing significantly to the economy, chicken is also a natural reservoir of Salmonella, which is responsible for salmonellosis in humans, one of the significant foodborne illnesses around the globe. The increasing use of chicken manure and antibiotics increases the spread of Salmonella and selects for multi-drug resistant strains. Various plant extracts, primarily essential oils, have been investigated for their antimicrobial activities. The multiple ways through which these plant-derived compounds exert their antimicrobial effects make the development of resistance against them unlikely. Eugenol, an aromatic oil primarily found in clove and cinnamon, has shown antimicrobial activities against various pathogenic bacteria. A few reports have also highlighted the anti-Salmonella effects of eugenol in chicken, especially in reducing the colonization by Salmonella Enteritidis and Salmonella Typhimurium, the primary Salmonella species responsible for human salmonellosis. Besides limiting Salmonella infection in chicken, the supplementation of eugenol also significantly improves intestinal health, improving overall well-being. In this review, we highlight the rising incidences of salmonellosis worldwide and the factors increasing its prevalence. We then propose the usage of eugenol as a natural feed supplement for containing Salmonella in chicken.

E-learning is a burden for the deaf and hard of hearing

When considering deaf and hard of hearing (DHH) population, research recognizes that fatigue due to communication challenges and multi-focal attention allocation is a significant concern. Given the putative heightened demands of distance learning on deaf and hard of hearing students, we investigate how an online environment might differently affect deaf and hard of hearing participants, compared to hearing participants, Portuguese Sign Language (PSL) users and non-users. Our findings show that the deaf and hard of hearing group present higher values in the post-task fatigue rates with significant differences from the hearing group (non-PSL users). Furthermore, our results revealed an association between post-task fatigue rates and lower performance scores for the deaf and hard of hearing group, and the gap is significantly bigger when compared with the hearing group (non-PSL users). We also found evidence for high levels of post-task fatigue and lower performance scores in the hearing group PSL users. These novel data contribute to the discussion concerning of the pros and cons of digital migration and help redesign more accessible and equitable methodologies and approaches, especially in the DHH educational field, ultimately supporting policymakers in redefining optimal learning strategies.