Impact of poultry litter Salmonella levels and moisture on transfer of Salmonella through associated in vitro generated dust

Vaccine protection of broilers against various doses of wild-type Salmonella Typhimurium and changes in gut microbiota

This study evaluated the impact of vaccine diluents (peptone or water) on the protective effects of Salmonella Typhimurium (S. Typhimurium) vaccine. Vaccinated broilers were challenged with different doses of wild-type S. Typhimurium through dust. At the time of cull, vaccine load was highest in caeca and lowest in spleen. Wild-type S. Typhimurium was detectable after 24 hrs only in the vaccinated birds challenged with 108 CFU and positive control. S. Typhimurium load was lower in the organs of the groups challenged with 104 and 106 compared to the 108 CFU group. The caecal microbiota alpha diversity of the vaccinated or vaccinated and challenged chickens differed from the positive and negative control groups. Beta diversity of the positive control clustered separately from all other treatment groups, showing that vaccine caused minimal changes in gut microbiota structure. The vaccinated and/or wild-type challenged chickens showed significantly higher abundance of Anaerostignum, Lachnoclostridium, Intestinimonas, Colidextribacter, Monoglobus, Acetanaerobacterium and Subdoligranulum. Outcomes from this study demonstrate that the vaccine effectively protected broiler chickens from S. Typhimurium infection and helped maintain a more stable gut microbiota structure, reducing the impact of S. Typhimurium on gut health. Vaccine diluent did not affect gut microbiota composition.

Outbreaks Linked to Melons, United States, 2012-2021

The Centers for Disease Control and Prevention (CDC), working closely with public health and regulatory partners, investigate outbreaks of foodborne illness. Outbreak investigations continue to identify melons as an important source of outbreak-associated illness. We characterized the epidemiology of outbreaks linked to melons from 2012-2021, summarized public health responses to these outbreaks, and identified potential opportunities for prevention efforts and interventions. We queried CDC's Foodborne Disease Outbreak Surveillance System (FDOSS) for all Salmonella, Escherichia coli (E. coli), and Listeria monocytogenes outbreaks linked to melons and collected data from the U.S. Food and Drug Administration's (FDA) Coordinated Outbreak Response & Evaluation (CORE) Network internal databases for information regarding outbreak investigations that involved FDA's evaluation and response activities. Descriptive statistics were calculated for outbreaks overall, by melon type, and by etiology, including the number of outbreaks, illnesses, hospitalizations, deaths, patient demographics including sex and age, outbreak duration, investigation duration, seasonality, serotypes, and food preparation and consumption settings. During 2012-2021, 18 outbreaks were linked to melons. The median number of outbreaks per year was 2 (range: 0-3); there were no melon-associated outbreaks reported in 2015. These 18 outbreaks resulted in 821 illnesses, 251 hospitalizations, and 10 deaths. More than half of the melon-associated Salmonella outbreaks in this reporting timeframe were linked to cantaloupe. Outbreak illnesses clustered in the U.S. Midwest and in outbreaks where the growing area was known, most were produced domestically (4/7, 57%), frequently grown in Indiana. Traceback and epidemiologic investigations demonstrated that contamination can occur at all points along the farm-to-fork continuum, requiring the need for pathogen control at every step.

Environmental contamination and horizontal transmission of Salmonella Enteritidis among experimentally infected layer pullets in indoor cage-free housing

The persistence and transmission of the egg-associated pathogen Salmonella Enteritidis in laying flocks are significantly influenced by the poultry housing environment. The present study assessed environmental contamination and horizontal transmission of S. Enteritidis within groups of layer pullets in cage-free housing after infection just before the age of sexual maturity. In each of 3 trials, 144 pullets were transferred from a rearing facility at 15 wk of age and randomly distributed between 2 isolation rooms simulating commercial cage-free barns with perches and nest boxes (72 birds/room). One wk after placement in the containment facility, a proportion of the 72 pullets in each room were orally inoculated with approximately 6 × 107 cfu of S. Enteritidis: 1/3 in trial 1, 1/6 in trial 2, and 1/12 in trial 3. At 2 wk post-inoculation in each trial, samples of liver, spleen, and intestinal tract were collected from 40 uninoculated (contact-exposed) birds in each room for bacteriologic culturing to detect horizontal transmission of S. Enteritidis. At 6 intervals between inoculation and necropsy, 5 types of environmental samples (wall dust swab, nest box swab, perch swab, flooring substrate drag swab, and flooring substrate composite) were collected and cultured for S. Enteritidis. The overall frequencies of S. Enteritidis recovery from both environmental samples and internal organs from contact-exposed pullets after initial oral inoculation of 1/3 of the birds in each room (97 % and 75 %, respectively) were significantly greater than after initial infection of 1/6 of the birds (78 % and 58 %), and S. Enteritidis recovery from birds inoculated at a 1/12 proportion (10 % of environmental samples and 18 % of organs) was significantly lower than from the 1/6 inoculation group. Flooring substrate composites were the most efficient environmental sample type for all 3 trials combined (72 % positive), providing significantly better S. Enteritidis recovery than the least efficient samples (flooring substrate drag swabs; 53 % positive). These data suggest that a high frequency of environmental contamination may be an important contributor to horizontal transmission of S. Enteritidis infections among pullets in cage-free housing.

Impact of FortiPhi-S bacteriophage solution on the environmental microbiome in poultry litter systems from commercial operations

The uprising demand of poultry products has led to an increase in the production of chickens. Nonetheless, this increase also gives way for an uprise in different types of issues such as food safety, human and animal health. While postharvest intervention strategies are considerably studied and established, preharvest food safety is considered more challenging. Therefore, anti-microbials like antibiotics are commonly used in poultry production to address and prevent contamination by pathogens. As a result of the many drawbacks associated with antibiotics, there is a growing demand for alternatives in animal production. Consequently, the use of bacteriophages in this field has been on the rise. This study highlights the effect of the application of the bacteriophage treatment FortiPhi-S on commercial poultry litter at different concentrations. The results demonstrate a significant difference by decreasing the richness of samples and increasing the diversity. The treatment also reduced the pathogenic families Staphylococcaceae and maintaining beneficial families such as Lachnospiraceae and Bacteroidaceae. Furthermore, pathogenic strains of Salmonella, Clostridia, and Escherichia-Shigella were significantly reduced or eliminated. The results demonstrated that the bacteriophage treatment FortiPhi-S has a significant effect on the microbial composition and diversity of poultry litter.

Whole-genome sequencing and phylogenetic analysis of Salmonella isolated from pullets through final raw product in the processing plant of a conventional broiler complex: a longitudinal study

Salmonella are Gram-negative, rod-shaped, entero-invasive foodborne bacteria and are frequently detected in chicken houses and facilities of poultry broiler complexes. The objective of this study was to determine the prevalence, critical entry points, and movement pattern of Salmonella along different stages of a complex. A total of 1,071 environmental samples were collected from 38 production houses (8 pullet, 10 breeder, and 20 broiler), a hatchery, 6 transport trucks, and a processing plant. Samples were screened with 3M Molecular Detection System and were further processed for the confirmation of results. Whole-genome sequencing and phylogenetic analysis were performed to determine genetic relatedness among bacterial strains. Using multivariable model, the odds ratios and 95% confidence limits were compared for stages, sample types, environments, and seasons (α < 0.05). Altogether 18% of samples and 42% of production houses tested Salmonella positive. Interestingly, the odds of Salmonella detection were more likely (P ≤ 0.001) in facilities like hatchery, transport, and processing plant as compared to production farms such as pullet, breeder, and broiler farms. The predominant serotype identified was S. Kentucky followed by S. Enteritidis, S. Typhimurium, S. Johannesburg, S. Montevideo, S. Mbandaka, S. Newport, S. Senftenberg, S. Inverness, S. Ohio, S. Uganda, and N/A (9:z29:-). Phylogenetic analysis showed strong genetic relationship among bacterial strains isolated from different stages. It also suggests diverse movement patterns of bacterial strains and possibility of multiple critical points for bacterial pathogens entering the complex. From the above results, we can conclude that Salmonella from chicken houses/facilities' environment can enter the broiler complex and can potentially contaminate the final raw product in the processing plant. A multifaceted comprehensive control strategy focusing on both facilities and production farms might be essential for improved control strategies.

IMPORTANCE

Salmonella continues to be the leading human bacterial foodborne pathogen, a serious food safety concern. The major challenges are to reduce the risk of introduction or spread of such bacteria in flocks, to minimize the persistence of such bacteria within the broiler complex, and to achieve USDA FSIS final product standards at the processing plants. Not well understood are the possible entry points and movement patterns of Salmonella along different stages of an integrated broiler complex. For this study, environmental sampling was considered from parent pullets through the final raw product at the processing plant, and SNP-based analysis of Salmonella isolates was conducted to determine the genetic relatedness and movement patterns. Interestingly, the samples from facilities (hatchery, transport, and processing plant) were more likely to be contaminated with Salmonella as compared to production farms (parent pullets, breeders, and broilers). Similarly, the phylogenetic analysis showed strong genetic relationship among strains isolated from different locations within the same stage and between different stages. The results show complex diversity of Salmonella serotypes along the chain and the possibility of multiple critical points for the entry of pathogen into the broiler complex and contaminate the final raw product at the processing plant. Furthermore, improper cooking or handling of contaminated raw chicken meat and meat products with Salmonella and other zoonotic pathogens can potentially cause foodborne illness in humans.

Pre-Harvest Non-Typhoidal Salmonella Control Strategies in Commercial Layer Chickens

Non-typhoidal Salmonella (NTS) infections in poultry, particularly in commercial-layer chickens, pose a critical risk to food safety and public health worldwide. NTS bacteria can remain undetected in poultry flocks, contaminating products and potentially leading to gastroenteritis in humans. This review examines pre-harvest control strategies for NTS in layer chickens, including biosecurity protocols, vaccinations, feed additives, genetic selection, and environmental management. These strategies have substantially reduced Salmonella colonization and product contamination rates in the commercial layer industry. By evaluating these strategies, this review highlights the importance of integrated control measures to limit NTS colonization, reduce antimicrobial resistance, and improve poultry health. This review aims to provide producers, researchers, and policymakers with insights into effective practices to minimize Salmonella contamination and enhance both animal and human health outcomes.

Assessment and genomic analysis of Salmonella and Campylobacter from different stages of an integrated no-antibiotics-ever (NAE) broiler complex: a longitudinal study

The objective of this study was to determine prevalence and perform genomic analysis of Salmonella spp. and Campylobacter spp. isolated from different stages of an integrated NAE broiler complex. Environmental samples were screened with 3M-Molecular Detection System (MDS) and MDS positive samples were further processed for confirmation of results and identification. Core genome-based phylogenies were built for both bacteria isolated from this study along with selected NCBI genomes. The odds ratios and 95% confidence limits were compared among stages and sample types (α < 0.05) using multivariable model. Based on MDS results, 4% and 18% of total samples were positive for Salmonella spp. and Campylobacter spp. respectively. The odds of Salmonella detection in hatchery samples were 2.58 times as likely as compared to its detection in production farms' samples (P = 0.151) while the odds of Campylobacter detection in production farms' samples were 32.19 times as likely as its detection in hatchery (P = 0.0015). Similarly, the odds of Campylobacter detection in boot swabs, soil, water, and miscellaneous samples were statistically significant (P < 0.05) as compared with fly paper as reference group. The serovars identified for Salmonella were Typhimurium, Barranquilla, Liverpool, Kentucky, Enteritidis, Luciana, and Rough_O:r:1,5. For Campylobacter, the species identified were Campylobacter jejuni and Campylobacter coli. Phylogeny results show close genetic relatedness among bacterial strains isolated from different locations within the same stage and between different stages. The results show possibility of multiple entry points of such bacteria entering broiler complex and can potentially contaminate the final raw product in the processing plant. It suggests the need for a comprehensive control strategy with strict biosecurity measures and best management practices to minimize or eliminate such pathogens from the poultry food chain.

Analysis of Microbial Composition of Edible Insect Products Available for Human Consumption within the United States Using Traditional Microbiological Methods and Whole Genome Sequencing

Edible insects offer a promising protein source for humans, but their food safety risks have not been previously investigated within the United States. Therefore, the aim of this study was to investigate the microbial content of processed edible insect products. A total of eight different types of edible insect products, including diving beetles, silkworms, grasshoppers, Jamaican crickets, mealworms, mole crickets, whole roasted crickets, and 100% pure cricket powder, were purchased from a large online retailer for the analysis. All the products were purchased in August 2022 and examined between August 2022 and November 2022. Traditional microbiological methods were employed to determine microbial counts for each product type using three replicates (total number of samples = 24). This included assessing aerobic bacterial spore, lactic acid bacteria, Enterobacteriaceae, total viable counts, and the presence of Salmonella. Additionally, whole genome sequencing was employed to further characterize selected colonies (n = 96). Microbial counts data were statistically analyzed using one-way ANOVA, while sequence data were taxonomically classified using Sepia.Bacilluscereusgroup isolates underwent additional characterization with Btyper3. Product type significantly influenced total viable counts, bacterial spore counts, and lactic acid bacteria counts (P = 0.00391, P = 0.0065, and P < 0.001, respectively), with counts ranging from < 1.70 to 6.01 Log10 CFU/g, <1.70 to 5.25 Log10 CFU/g, and < 1.70 to 4.86 Log10 CFU/g, respectively. Enterobacteriaceae were only detected in mole crickets (<2.30 Log10 CFU/g) and house cricket powder (<2.15 Log10 CFU/g). All samples were negative for Salmonella. Whole genome sequencing revealed the presence of 12 different bacterial genera among the analyzed isolates, with a majority belonging to the Bacillus genus. Some of the isolates of Bacillus cereus group were identified as biovar Emeticus. Overall, although edible insects offer a promising food alternative, the presence of Bacillus cereus group in some products could raise concerns regarding food safety.

Dust sprinkling as an effective method for infecting layer chickens with wild-type Salmonella Typhimurium and changes in host gut microbiota

Role of dust in Salmonella transmission on chicken farms is not well characterised. Salmonella Typhimurium (ST) infection of commercial layer chickens was investigated using a novel sprinkling method of chicken dust spiked with ST and the uptake compared to a conventional oral infection. While both inoculation methods resulted in colonisation of the intestines, the Salmonella load in liver samples was significantly higher at 7 dpi after exposing chicks to sprinkled dust compared to the oral infection group. Infection of chickens using the sprinkling method at a range of doses showed a threshold for colonisation of the gut and organs as low as 1000 CFU/g of dust. Caecal content microbiota analysis post-challenge showed that the profiles of chickens infected by the sprinkling and oral routes were not significantly different; however, both challenges induced differences when compared to the uninfected negative controls. Overall, the study showed that dust sprinkling was an effective way to experimentally colonise chickens with Salmonella and alter the gut microbiota than oral gavage at levels as low as 1000 CFU/g dust. This infection model mimics the field scenario of Salmonella infection in poultry sheds. The model can be used for future challenge studies for effective Salmonella control.

Salmonella enterica in farm environments in the Ashanti Region of Ghana

BACKGROUND

Salmonella enterica are important foodborne pathogens and the third leading cause of death among diarrheal infections worldwide. This cross-sectional study investigated the frequency of antibiotic-resistant Salmonella enterica in commercial and smallholder farm environments in the Ashanti Region of Ghana. A total of 1490 environmental samples, comprising 800 (53.7%) soil (from poultry, pigs, sheep, goats and cattle farms), 409 (27.4%) pooled poultry fecal and 281 (18.9%) dust (from poultry farms) samples, were collected from 30 commercial and 64 smallholder farms. All samples were processed using standard culture methods. Isolates were identified by biochemical methods and confirmed using the VITEK 2 System. Antibiotic susceptibility testing was carried out by disk diffusion following the EUCAST guidelines. Serotyping was performed using the Kauffman White Le Minor Scheme.

RESULTS

The overall Salmonella frequency was 6.0% (n/N = 90/1490); the frequency varied according to the type of sample collected and included: 8.9% for dust (n/N = 25/281), 6.5% for soil (n/N = 52/800) and 3.2% for pooled poultry fecal samples (n/N = 13/409). Salmonella was also recovered from commercial farm environments (8.6%, n/N = 68/793) than from smallholder farms (3.2%, n/N = 22/697) (PR = 2.7, CI: 1.7 - 4.4). Thirty-four different Salmonella serovars were identified, the two most common being Rubislaw (27.8%, n/N = 25/90) and Tamale (12.2%, n/N = 11/90). Serovar diversity was highest in strains from soil samples (70.6%, n/N = 24/34) compared to those found in the dust (35.2%, n/N = 12/34) and in fecal samples (29.4%, n/N = 10/34). Salmonella frequency was much higher in the rainy season (8.4%, n/N = 85/1007) than in the dry season (1.0%, n/N = 5/483) (PR = 8.4, 95% CI: 3.3 - 20.0). Approximately 14.4% (n/N = 13/90) of the isolates were resistant to at least one of the tested antimicrobials, with 84.6% (n/N = 11/13) being resistant to multiple antibiotics. All Salmonella Kentucky (n = 5) were resistant to ciprofloxacin.

CONCLUSION

This study showed that farm environments represent an important reservoir for antibiotic-resistant Salmonella, which warrants monitoring and good husbandry practices, especially in commercial farms during the rainy season, to control the spread of this pathogen.

Composting: A biosecurity measure to maximize the benefit of broilers̕ litter

Objective

This study was conducted to evaluate the effect of composting on the count of Salmonella spp., Clostridium perfringens, and New Castle virus (NDV) isolated from broilers' litter. Moreover, to verify the impact of compost thermal stress on the expression of thermal genes harbored in the isolated bacteria.

Materials and Methods

The prevalence of enteric aerobic and anaerobic infections by Salmonella spp., C. perfringens, and viral infections by NDV were investigated in litter samples collected from 100 broiler flocks by conventional methods and polymerase chain reaction.

Results

The samples were positive for Salmonella spp., C. perfringens, and NDV, with prevalence rates of 60%, 55%, and 30%, respectively. An experiment to study the effect of compost on the microbiological quality of litter was applied using five compost heaps with an initial average count of Salmonella typhimurium (3.2 × 105CFU CFU/gm), C. perfringens (6.4 × 105 CFU/gm), and an average titer NDV (105.5 embryo infectious dose50/gm). The microbiological count of heaps after 15 days of composting revealed a reduction in the count of S. typhimurium and C. perfringens by 4 log10 CFU/gm and 3 log10 CFU/gm, respectively. Moreover, the hemagglutinating test revealed no detection of NDV after 15 days of composting. A high degree of downregulation of expression of the thermal genes, dnaK in S. typhimurium isolates and cpe gene in C. perfringens isolates, was detected by quantitative reverse transcription PCR.

Conclusion

The reduction of pathogen counts, the simplicity, and the low cost associated with composting for only 15 days advocate the recommendation for raising awareness of composting as a routine biosecurity measure to prevent the spreading of infection and promote its safe use in agribusiness.

Practical Preventive Considerations for Reducing the Public Health Burden of Poultry-Related Salmonellosis

With poultry products as one of the leading reservoirs for the pathogen, in a typical year in the United States, it is estimated that over one million individuals contract non-typhoidal Salmonella infections. Foodborne outbreaks associated with Salmonella infections in poultry, thus, continue to remain a significant risk to public health. Moreover, the further emergence of antimicrobial resistance among various serovars of Salmonella is an additional public health concern. Feeding-based strategies (such as use of prebiotics, probiotics, and/or phytobiotics as well as essential oils), non-feeding-based strategies (such as use of bacteriophages, vaccinations, and in ovo strategies), omics tools and surveillance for identifying antibiotic-resistance genes, post-harvest application of antimicrobials, and biosecurity measures at poultry facilities are practical interventions that could reduce the public health burden of salmonellosis and antibiotic resistance associated with poultry products. With the escalating consumption of poultry products around the globe, the fate, prevalence, and transmission of Salmonella in agricultural settings and various poultry-processing facilities are major public health challenges demanding integrated control measures throughout the food chain. Implementation of practical preventive measures discussed in the current study could appreciably reduce the public health burden of foodborne salmonellosis associated with poultry products.

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.

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.

Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles

Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae, Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside (aac(6′)-Ib(aka aacA4), aadA5), tetracycline (tetG), vancomycin (vanC), phenicol (floR) and MLSB (mphB) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus, which was linked to vancomycin (vanSA, vanC1), MLSB (vatE, ermB) and tetracycline (tetK) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.

Investigation of the potential of aerosolized Salmonella Enteritidis on colonization and persistence in broilers from day 3 to 21

The presence of Salmonella in air of poultry houses has been previously confirmed. Therefore, it is important to investigate the entry of Salmonella into broilers through air. The present study aimed to evaluate different levels of Salmonella Enteritidis aerosol inoculations in broiler chicks for colonization of ceca, trachea, and liver/spleen and persistence over time. In 3 independent trials, 112 one-day-old birds were randomly divided into 4 groups (n = 28/group). On d 1 of age, one group was exposed to an aerosol of sterile saline and the remaining three groups were exposed to an aerosol generated from one of 3 doses (10³, 10⁶, or 10⁹ CFU/mL) of S. Enteritidis inoculum. Aerosol exposure time was 30 min/group and was performed using a nebulizer. On d 3, 7, 14, and 21 of age, ceca, trachea, and liver/spleen were aseptically removed. Ceca were cultured for Salmonella counts (log₁₀ CFU/g) and all tissues were cultured for Salmonella prevalence. All tissues from the control group were Salmonella negative for all sampling days. On sampling d 3 and 7, ceca Salmonella counts were highest (5.14 and 5.11, respectively) when challenged with 10⁹Salmonella (P ≤ 0.0281). Ceca Salmonella counts increased from d 3 (2.43) to d 7 (4.43), then remained constant when challenged at 10³Salmonella, and counts decreased over time for all other groups. Tissue Salmonella prevalence increased with increasing challenge levels at all sampling timepoints (P ≤ 0.0213). Salmonella prevalence was low (0/18 to 4/18) and did not change over time following 10³Salmonella challenge (P ≥ 0.2394). Prevalence decreased over time in ceca and trachea following 10⁶ and 10⁹Salmonella challenge (P ≤ 0.0483). Liver/spleen Salmonella prevalence increased from d 3 (13/18) to d 14 (18/18) and then decreased at d 21 (10/18) in birds exposed to an aerosol of 10⁹Salmonella but remained constant over time for rest of the Salmonella inoculated groups. Overall, this study demonstrated the Salmonella colonization and persistence in different tissues in broilers following exposure to aerosolized Salmonella.