Population dynamics and antimicrobial resistance of the most prevalent poultry-associated Salmonella serotypes

Risk Assessment Predicts Most of the Salmonellosis Risk in Raw Chicken Parts is Concentrated in Those Few Products with High Levels of High-Virulence Serotypes of Salmonella

Salmonella prevalence declined in U.S. raw poultry products since adopting prevalence-based Salmonella performance standards, but human illnesses did not reduce proportionally. We used Quantitative Microbial Risk Assessment (QMRA) to evaluate public health risks of raw chicken parts contaminated with different levels of all Salmonella and specific high- and low-virulence serotypes. Lognormal Salmonella level distributions were fitted to 2012 USDA-FSIS Baseline parts survey and 2023 USDA-FSIS HACCP verification sampling data. Three different Dose-Response (DR) approaches included (i) a single DR for all serotypes, (ii) DR that reduces Salmonella Kentucky ST152 virulence, and (iii) multiple serotype-specific DR models. All scenarios found risk concentrated in the few products with high Salmonella levels. Using a single DR model with Baseline data (μ = -3.19, σ = 1.29 Log CFU/g), 68% and 37% of illnesses were attributed to the 0.7% and 0.06% of products with >1 and >10 CFU/g Salmonella, respectively. Using distributions from 2023 HACCP data (μ = -5.53, σ = 2.45), 99.8% and 99.0% of illnesses were attributed to the 1.3% and 0.4% of products with >1 and >10 CFU/g Salmonella, respectively. Scenarios with serotype-specific DR models showed more concentrated risk at higher levels. Baseline data showed 92% and 67% and HACCP data showed >99.99% and 99.96% of illnesses attributed to products with >1 and >10 CFU/g Salmonella, respectively. Regarding serotypes using Baseline or HACCP input data, 0.002% and 0.1% of illnesses were attributed to the 0.2% and 0.4% of products with >1 CFU/g of Kentucky ST152, respectively, while 69% and 83% of illnesses were attributed to the 0.3% and 0.6% of products with >1 CFU/g of Enteritidis, Infantis, or Typhimurium, respectively. Therefore, public health risk in chicken parts is concentrated in finished products with high levels and specifically high levels of high-virulence serotypes. Low-virulence serotypes like Kentucky contribute few human cases.

Oral vaccination of young broilers with a live Salmonella Typhimurium vaccine reduces caecal and internal organ colonization following a Salmonella Infantis challenge in a seeder-bird model

Poultry products are an important source of foodborne Salmonella infections in humans. Amongst these, the prevalence of S. Infantis is rising. In this study, the protection efficacy of an authorized live-attenuated S. Typhimurium vaccine against S. Infantis, was examined using a seeder-bird model in broilers. Vaccinated birds displayed a significantly lower colonization of S. Infantis bacteria in the caeca compared to the non-vaccinated counterparts (P = 0.017), with no significant differences observed in the spleen among the groups, three days post-infection. Thirty-two days post-infection, the disparity in average S. Infantis concentration between all-vaccinated and non-vaccinated birds was significant in both caeca (P = 0.0003) and spleen (P = 0.0002). Interestingly, a third group, consisting of seeder birds that were not vaccinated but housed with vaccinated penmates, exhibited significantly lower S. Infantis levels in both caeca (P = 0.0014) and spleen (P < 0.0001) compared to the non-vaccinated group. These findings underscore the potential of a live-attenuated S. Typhimurium vaccine administered to 2-day-old chicks in conferring protection against S. Infantis in broilers up to slaughter age.

Thermal inactivation kinetics of Salmonella and Campylobacter in chicken livers

Salmonella and Campylobacter are major foodborne pathogens that cause outbreaks associated with contaminated chicken liver. Proper cooking is necessary to avoid the risk of illness to consumers. This study tested the thermal inactivation of a 4-strain Salmonella cocktail and a 3-strain Campylobacter cocktail in chicken livers separately at temperatures ranging from 55.0 to 62.5°C. Inoculated livers were sealed in aluminum cells and immersed in a water bath. The decimal reduction time (D-values) of Salmonella in chicken livers were 9.01, 2.36, 0.82, and 0.23 min at 55.0, 57.5, 60.0, and 62.5°C, respectively. The D-values of Campylobacter ranged from 2.22 min at 55.0°C to 0.19 min at 60.0°C. Salmonella and Campylobacter had similar z-values in chicken livers of 4.8 and 4.6°C, respectively. Chicken livers can be heated to internal temperatures of 70.0 to 73.9°C for at least 1.6 to 0.2 s to achieve a 7-log reduction of Salmonella. Validation tests demonstrated that heating chicken livers to internal temperatures of 70.0 to 73.9°C for 2 to 0 s resulted in a reduction of Salmonella exceeding 7 logs. Collectively, these data show that Salmonella exhibits higher heat resistance than Campylobacter in chicken livers. Therefore, Salmonella could be considered as the target pathogen when designing thermal treatments or cooking instructions for liver products. These findings will aid in designing effective thermal processing for both industrial and home cooking to eliminate Salmonella and Campylobacter, ensuring consumer safety when consuming chicken liver products.

Prevalence and transmission of extensively drug-resistant Salmonella enterica serovar Kentucky ST198 based on whole-genome sequence in an intensive laying hen farm in Jiangsu, China

Salmonella, which is widely distributed in nature, is an important zoonotic pathogen affecting humans, livestock, and other animals. Salmonella infection not only hinders the development of livestock and poultry-related industries but also poses a great threat to human health. In this study, we collected 1,537 samples including weak chicks, dead embryos, fecal samples and environmental samples from 2020 to 2023 (for a period of 1 to 2 months per year) to keep a long-term monitor the prevalence of Salmonella in an intensive laying hen farm, 105 Salmonella strains were isolated with an isolation rate of 6.83% (105/1,537). It revealed a significant decrease in prevalence rates of Salmonella over time (P < 0.001). Before 2020, the predominant serotype was S. Enteritidis. S. Kentucky was first detected in November 2020 and its proportion was gradually found to exceed that of S. Enteritidis since then. S. Kentucky isolates were distributed in various links of the four regions in the poultry farm. A total of 55 S. Kentucky strains, were assigned to ST198 based on whole genome sequencing. Among them, 54 strains were resistant to 12 to 16 antibiotics, indicating that they were extensively drug-resistant (XDR). Seventeen antimicrobial resistance genes were detected in 55 S. Kentucky isolates. For most of these isolates, antibiotic resistance phenotypes were concordant with their genotypes. All S. Kentucky strains isolated from this farm in 2020 to 2023 showed a high similarity based on their core-genome SNP-based phylogeny. The traceability analysis revealed that S. Kentucky was introduced to the farm through newly purchased flocks. The long-term existence of XDR S. Kentucky ST198 poses a substantial risk because of the multiage management and circulation of workers in this poultry farm. Thus, this study is the first to report extensively drug-resistant S. Kentucky ST198 detected in this intensive poultry farm in China.

Effects of in ovo injection of bacterial peptides and CpG-ODN on Salmonella enterica serovar Heidelberg infection in specific pathogen-free (SPF) chicks

RESEARCH HIGHLIGHTS

Peptides + CpG-ODN reduced SH in caeca at the first week post-infection.Administered formulations did not reduce SH-faecal excretion.Levels of intestinal IgA were similar between all groups.CpG-ODN improved some parameters associated with chick intestinal health.

Microdiversity of Salmonella Kentucky During Long-Term Colonization of a Dairy Herd

Salmonella enterica subsp. enterica serovar Kentucky was repeatedly isolated from a commercial dairy herd that was enrolled in a longitudinal study where feces of asymptomatic dairy cattle were sampled intensively over an 8-year period. The genomes of 5 Salmonella Kentucky isolates recovered from the farm 2 years before the onset of the long-term colonization event and 13 isolates collected during the period of endemicity were sequenced. A phylogenetic analysis inferred that the Salmonella Kentucky strains from the farm were distinct from poultry strains collected from the same region, and three subclades (K, A1, and A2) were identified among the farm isolates, each appearing at different times during the study. Based on the phylogenetic analysis, three separate lineages of highly similar Salmonella Kentucky were present in succession on the farm. Genomic heterogeneity between the clades helped identify regions, most notably transcriptional regulators, of the Salmonella Kentucky genome that may be involved in competition among highly similar strains. Notably, a region annotated as a hemolysin expression modulating protein (Hha) was identified in a putative plasmid region of strains that colonized a large portion of cows in the herd, suggesting that it may play a role in asymptomatic persistence within the bovine intestine. A cell culture assay of isolates from the three clades with bovine epithelial cells demonstrated a trend of decreased invasiveness of Salmonella Kentucky isolates over time, suggesting that clade-specific interactions with the animals on the farm may have played a role in the dynamics of strain succession. Results of this analysis further demonstrate an underappreciated level of genomic diversity within strains of the same Salmonella serovar, particularly those isolated during a long-term period of asymptomatic colonization within a single dairy herd.

Poultry Processing Interventions Reduce Salmonella Serovar Complexity on Postchill Young Chicken Carcasses as Determined by Deep Serotyping

Nearly 20% of salmonellosis cases are attributed to broilers, with renewed efforts to reduce Salmonella during broiler production and processing. A limitation to Salmonella culture is that often a single colony is picked for characterization, favoring isolation of the most abundant serovar found in a sample, while low abundance serovars can remain undetected. We used a deep serotyping approach, CRISPR-SeroSeq (serotyping by sequencing the clustered regularly interspaced palindromic repeats), to assess Salmonella serovar complexity during broiler processing and to determine the impact of antimicrobial interventions upon serovar population dynamics. Paired hot rehang and postchill young chicken carcasses were collected from establishments across the United States from August to November 2022. CRISPR-SeroSeq was performed on Salmonella culture-positive hot rehang (n = 153) and postchill (n = 38) samples, including 31 paired hot rehang and postchill samples. Multiple serovars were detected in 48.4% (74/153) and 7.9% (3/38) of hot rehang and postchill samples, respectively. On average, hot rehang carcasses contained 1.6 serovars, compared to 1.1 serovars at postchill (Mann Whitney U, p = 0.00018). Nineteen serovars were identified with serovar Kentucky the most common at hot rehang (72.5%; 111/153) and postchill (73.7%; 28/38). Serovar Infantis prevalence was higher at hot rehang (39.9%; 61/153) than in postchill (7.9%; 3/38). At hot rehang, serovar Enteritidis was outnumbered by other serovars 81.3% (13/16) of the time but was always the single or most abundant serovar detected when it was present at postchill (n = 5). We observed 98.4% (188/191) concordance between traditional isolation with serotyping and CRISPR-SeroSeq. Deep serotyping was able to explain serovar discrepancies between paired hot rehang and postchill samples when only traditional isolation and serotyping methods were used. These data demonstrate that processing interventions are effective in reducing Salmonella serovar complexity.

In silico and PCR Screening for a Live Attenuated Salmonella Typhimurium Vaccine Strain

The application of live attenuated Salmonella Typhimurium vaccines has significantly helped control Salmonella in poultry products. Because the U.S. Department of Agriculture-Food Safety Inspection Service (USDA-FSIS) scores all Salmonella as positive, regardless of serovar, attenuated vaccine strains that are identified at processing contribute negatively toward Salmonella performance standards. This study was designed to determine the incidence of a live attenuated Salmonella serovar Typhimurium vaccine identified in broiler products by FSIS and to develop a PCR assay for screening of isolates. Salmonella Typhimurium short-read sequences from broiler samples uploaded to the National Center for Biotechnology Information (NCBI) Pathogen Detection database by the USDA-FSIS from 2016 to 2022 were downloaded and assembled. These were analyzed using the Basic Local Alignment Search Tool (BLAST) with a sequence unique to field strains, followed by a sequence unique to the vaccine strain. The PCR assays were developed against field and vaccine strains by targeting transposition events in the crp and cya genes and validated by screening Salmonella serovar Typhimurium isolates. Between 2016 and 2022, 1708 Salmonella Typhimurium isolates of chicken origin were found in the NCBI Pathogen Detection database, corresponding to 7.99% of all Salmonella identified. Of these, 104 (5.97%) were identified as the vaccine strain. The PCR assay differentiated field strains from the vaccine strain when applied to isolates and was also able to detect the vaccine strain from DNA isolated from mixed serovar overnight Salmonella enrichment cultures. Live attenuated Salmonella vaccines are a critical preharvest tool for Salmonella control and are widely used in industry. With forthcoming regulations that will likely focus on Salmonella Typhimurium, along with other serovars, there is a need to distinguish between isolates belonging to the vaccine strain and those that are responsible for causing human illness.

Salmonella enterica serotypes isolated for the first time in laying hens, and their susceptibility to antibiotics

In this study, a total of 323 drag swab samples were taken from laying hen fresh feces from 3 different provinces (Kırklareli, Edirne, and Tekirdağ), which are located in the European part of Türkiye. According to the ISO 6579: 2002 method, 17.3% of the samples were found positive for Salmonella. Obtained 56 Salmonella isolates were serotyped by slide agglutination using antisera according to Kauffmann White Le Minor Scheme. Sixteen serotypes of Salmonella were identified as S. Typhimurium (28.6%), S. Kentucky (17.9%), S. Abony (16.1%), S. Infantis (8.9%), S. Enteritidis (5.4%), S. Anatum (3.6%), S. Saintpaul (3.6%), S. Szentes (1.8%), S. Dibra (1.8%), S. Fallowfield (1.8%), S. Kimuenza (1.8%), S. Escanaba (1.8%), S. Nagoya (1.8%), S. Mbandaka (1.8%), S. Agona (1.8%), and Salmonella II 17: e, n, x, z15: 1,6 (1.8%). Isolations of S. Kimuenza, S. Escanaba, and S. Nagoya from laying hens are reported for the first time in Türkiye. The isolations of S. Dibra, S. Fallowfield, S. Szentes, and Salmonella II 17: e, n, x, z15: 1,6 from laying hens are the first report in the world. A total of 56 Salmonella isolates were tested for susceptibility to amoxicillin-clavulanic acid, cefepime, azithromycin, cefoxitin, and trimethoprim/sulfamethoxazole by the disk diffusion method. While 10% of S. Kentucky isolates were resistant to ofloxacin, and S. Kimuenza was only resistant to chloramphenicol.

Ligilactobacillus salivarius 7247 Strain: Probiotic Properties and Anti-Salmonella Effect with Prebiotics

The Ligilactobacillus salivarius 7247 (LS7247) strain, originally isolated from a healthy woman's intestines and reproductive system, has been studied for its probiotic potential, particularly against Salmonella Enteritidis (SE) and Salmonella Typhimurium (ST) as well as its potential use in synbiotics. LS7247 showed high tolerance to gastric and intestinal stress and effectively adhered to human and animal enterocyte monolayers, essential for realizing its probiotic properties. LS7247 showed high anti-Salmonella activity. Additionally, the cell-free culture supernatant (CFS) of LS7247 exhibited anti-Salmonella activity, with a partial reduction upon neutralization with NaOH (p < 0.05), suggesting the presence of anti-Salmonella factors such as lactic acid (LA) and bacteriocins. LS7247 produced a high concentration of LA, reaching 124.0 ± 2.5 mM after 48 h of cultivation. Unique gene clusters in the genome of LS7247 contribute to the production of Enterolysin A and metalloendopeptidase. Notably, LS7247 carries a plasmid with a gene cluster identical to human intestinal strain L. salivarius UCC118, responsible for class IIb bacteriocin synthesis, and a gene cluster identical to porcine strain L. salivarius P1ACE3, responsible for nisin S synthesis. Co-cultivation of LS7247 with SE and ST pathogens reduced their viability by 1.0-1.5 log, attributed to cell wall damage and ATP leakage caused by the CFS. For the first time, the CFS of LS7247 has been shown to inhibit adhesion of SE and ST to human and animal enterocytes (p < 0.01). The combination of Actigen prebiotic and the CFS of LS7247 demonstrated a significant combined effect in inhibiting the adhesion of SE and ST to human and animal enterocytes (p < 0.001). These findings highlight the potential of using the LS7247 as a preventive strategy and employing probiotics and synbiotics to combat the prevalence of salmonellosis in animals and humans caused by multidrug resistant (MDR) strains of SE and ST pathogens.

Prevention and Control of Human Salmonella enterica Infections: An Implication in Food Safety

Salmonella is a foodborne zoonotic pathogen causing diarrhoeal disease to humans after consuming contaminated water, animal, and plant products. The bacterium is the third leading cause of human death among diarrhoeal diseases worldwide. Therefore, human salmonellosis is of public health concern demanding integrated interventions against the causative agent, Salmonella enterica. The prevention of salmonellosis in humans is intricate due to several factors, including an immune-stable individual infected with S. enterica continuing to shed live bacteria without showing any clinical signs. Similarly, the asymptomatic Salmonella animals are the source of salmonellosis in humans after consuming contaminated food products. Furthermore, the contaminated products of plant and animal origin are a menace in food industries due to Salmonella biofilms, which enhance colonization, persistence, and survival of bacteria on equipment. The contaminated food products resulting from bacteria on equipment offset the economic competition of food industries and partner institutions in international business. The most worldwide prevalent broad-range Salmonella serovars affecting humans are Salmonella Typhimurium and Salmonella Enteritidis, and poultry products, among others, are the primary source of infection. The broader range of Salmonella serovars creates concern over multiple strategies for preventing and controlling Salmonella contamination in foods to enhance food safety for humans. Among the strategies for preventing and controlling Salmonella spread in animal and plant products include biosecurity measures, isolation and quarantine, epidemiological surveillance, farming systems, herbs and spices, and vaccination. Other measures are the application of phages, probiotics, prebiotics, and nanoparticles reduced and capped with antimicrobial agents. Therefore, Salmonella-free products, such as beef, pork, poultry meat, eggs, milk, and plant foods, such as vegetables and fruits, will prevent humans from Salmonella infection. This review explains Salmonella infection in humans caused by consuming contaminated foods and the interventions against Salmonella contamination in foods to enhance food safety and quality for humans.

Probiotic Escherichia coli Nissle 1917 protect chicks from damage caused by Salmonella enterica serovar Enteritidis colonization

As a foodborne pathogen of global importance, Salmonella enterica serovar Enteritidis (S. Enteritidis) is a threat to public health that is mainly spread by poultry products. Intestinal Enterobacteriaceae can inhibit the colonization of S. Enteritidis and are regarded as a potential antibiotic substitute. We investigated, in chicks, the anti-S. Enteritidis effects of Escherichia coli (E. coli) Nissle 1917, the most well-known probiotic member of Enterobacteriaceae. Eighty 1-d-old healthy female AA broilers were randomly divided into 4 groups, with 20 in each group, namely the negative control (group P), the E. coli Nissle 1917-treated group (group N), the S. Enteritidis-infected group (group S) and the E. coli Nissle 1917-treated and S. Enteritidis-infected group (group NS). From d 5 to 7, chicks in groups N and NS were orally gavaged once a day with E. coli Nissle 1917 and in groups P and S were administered the same volume of sterile PBS. At d 8, the chicks in groups S and NS were orally gavaged with S. Enteritidis and in groups P and N were administered the same volume of sterile PBS. Sampling was conducted 24 h after challenge. Results showed that gavage of E. coli Nissle 1917 reduced the spleen index, Salmonella loads, and inflammation (P < 0.05). It improved intestinal morphology and intestinal barrier function (P < 0.05). S. Enteritidis infection significantly reduced mRNA expression of angiotensin-converting enzyme 2 (ACE2) and solute carrier family 6-member 19 (SLC6A19) in the cecum and the content of Gly, Ser, Gln, and Trp in the serum (P < 0.05). Pretreatment with E. coli Nissle 1917 yielded mRNA expression of ACE2 and SLC6A19 in the cecum and levels of Gly, Ser, Gln, and Trp in the serum similar to that of uninfected chicks (P < 0.05). Additionally, E. coli Nissle 1917 altered cecum microbiota composition and enriched the abundance of E. coli, Lactobacillales, and Lachnospiraceae. These findings reveal that the probiotic E. coli Nissle 1917 reduced S. Enteritidis infection and shows enormous potential as an alternative to antibiotics.

Systemic salmonellosis in 4 cats

Clinical signs in 4 cases of salmonellosis in cats included vomiting, diarrhea (2 cases each), fever, dystocia, icterus, and seizures (1 case each). Three cats died, and one was euthanized. Grossly, all cats were in poor body condition and had yellow-to-dark-red perianal feces (3 cases), oral and ocular pallor (2 cases) or icterus (1 case), fluid or pasty yellow intestinal contents (4 cases), white or dark-red-to-black depressed areas on the hepatic surface (2 cases), yellow abdominal fluid with swollen abdominal lymph nodes (1 case), and fibrin strands on the placental chorionic surface (1 case). Histologically, all cats had necrotizing enterocolitis and random hepatocellular necrosis. Other histologic findings included mesenteric (4 cases) or splenic (2 cases) lymphoid necrosis, and endometrial and chorioallantoic necrosis (1 case). Gram-negative bacilli were observed within neutrophils and macrophages in the intestinal lamina propria (4 cases), liver, spleen, lymph node, endometrium, and placenta (1 case each). Aerobic bacterial culture on frozen samples of small intestine, mesenteric lymph node, lung, and liver yielded Salmonella enterica subsp. enterica. Serotyping was consistent with S. Enteritidis (cases 1, 3) and S. Typhimurium (cases 2, 4).

Comparison of Phenotype Nutritional Profiles and Phosphate Metabolism Genes in Four Serovars of Salmonella enterica from Water Sources

The surveillance of foods for Salmonella is hindered by bias in common enrichment media where serovars implicated in human illness are outgrown by less virulent serovars. We examined four Salmonella serovars, two common in human illness (Enteritidis and Typhimurium) and two that often dominate enrichments (Give and Kentucky), for factors that might influence culture bias. The four serovars had similar growth kinetics in Tryptic Soy Broth and Buffered Peptone Water. Phenotype microarray analysis with 950 chemical substrates to assess nutrient utilization and stress resistance revealed phenotype differences between serovars. Strains of S. Enteritidis had better utilization of plant-derived sugars such as xylose, mannitol, rhamnose, and fructose, while S. Typhimurium strains were able to metabolize tagatose. Strains of S. Kentucky used more compounds as phosphorus sources and grew better with inorganic phosphate as the sole phosphorus source. The sequences of nine genes involved in phosphate metabolism were compared, and there were differences between serovars in the catalytic ATP-binding domain of the histidine kinase phoR. Analysis of the predicted PhoR amino acid sequences from additional Salmonella genomes indicated a conservation of sequences each within the Typhimurium, Give, and Enteritidis serovars. However, three different PhoR versions were observed in S. Kentucky.

Review: Current challenges in poultry nutrition, health, and welfare

The poultry industry has benefited greatly from advances in genetics, nutrition, housing and management strategies. Geneticists have made welfare and health traits important components of selection programs, and in general, modern, high-producing poultry are healthier than 30 years ago. However, increased productivity means that the birds are closer to their physiological limits, and nutrition, environment and management have become increasingly important. The move away from in-feed antibiotic growth promotors has resulted in challenges in maintaining gut health and consequently, bird performance. However, as the industry adapts to production without the use of antibiotic growth promotors, long-term benefits may be realized due to a reduction in antimicrobial resistance. Intensive selection for meat yield and efficiency are associated with an increased risk of muscle myopathies that affect bird health and meat quality. As genetic selection increased broiler production traits, it became necessary to restrict parent stock nutrient intake in order to prevent excessive muscle and fat deposition, reduce metabolic disease, and maintain ovarian control. With continued selection for broiler production traits, the degree of restriction implemented has become a welfare issue. Additionally, recent research suggests that highly efficient broiler lines may have limited fat deposition and therefore energy reserves to support sexual maturation and egg production, especially if typical broiler breeder BW targets are maintained. A re-examination of broiler breeder feeding programs is necessary to maintain productivity and welfare. Modern laying hens are capable of laying cycles in excess of 100 weeks of age. This has reduced the use of stress-inducing forced molting programs and reduces the total number of hens needed to meet the demand for egg production. The important role of the skeletal system in eggshell deposition demands that skeletal development during rearing be carefully managed to avoid shell and skeletal problems at the end of the production cycle. As the production potential of modern poultry continues to increase through genetic and genomic selection, even greater care must be paid in order to maintain bird health and welfare. The poultry industry has successfully faced many challenges in the past and is likely to overcome the existing challenges as well.

Isolation, susceptibility profiles and genomic analysis of a colistin-resistant Salmonella enterica serovar Kentucky strain COL-R

Salmonella enterica serovar Kentucky is a frequent cause for clinical infections in human patients. They are isolated and reported with multidrug resistance from the foods of animal origin from various countries. However, studies inferring the colistin resistance are limited. Hence, the current study reports the genetic factors and genomic analysis of the colistin-resistant Salmonella enterica serovar Kentucky strain COL-R for better understanding of its pathogenic potential and phylogenetic relatedness. The S. Kentucky strain COL-R was successfully isolated from chicken meat during ongoing surveillance of food of animal origin. Antimicrobial susceptibility testing revealed resistance to cefoxitin, erythromycin, gentamicin, tetracycline, and most disturbingly to ciprofloxacin and colistin (broth microdilution method). Whole-genome sequence of the COL-R strain was subjected to various in silico analysis to identify the virulence factors, antimicrobial resistance genes, pathogenicity islands and sequence type. The S. Kentucky COL-R strain belonged to sequence type (ST) 198 with a high probability (0.943) of being a human pathogen. Besides presence of integrated phage in the S. Kentucky COL-R genome, 38 genes conferring resistance to various antimicrobials and disinfectants were also identified. Nucleotide Polymorphism analysis indicated triple mutations in gyrA and parC genes conferring fluoroquinolone resistance. Phylogenomic analysis with 31 other S. Kentucky genomes revealed discernible clusters with S. Kentucky COL-R strain latching onto a cluster of high diversity (geographic location and isolation sources). Taken together, our results document the first occurrence of colistin resistance in a fluoroquinolone resistant S. Kentucky COL-R strain isolated from retail chicken and provide crucial information on the genomic features of the strain.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03559-2.

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.

Assessment of multidrug-resistant profile, multi-locus sequence typing and efflux pump activity in Salmonella Typhimurium isolated from hospital sewage

Salmonella enterica serovar Typhimurium is becoming a leading cause of gastroenteritis and mortality. The use of antibiotics has increased natural resistance of S. Typhimurium to antibiotics. This study aims to isolate and characterize multi-drug-resistant (MDR) Salmonella strains from hospital sewage samples in Bhopal City, central India. The MDR isolates were characterized by molecular identification, antimicrobial resistance patterns, multi-locus sequence typing, and efflux pump activity. Specific genes (hilA, stn, invA, typh, and iroB) were used to confirm S. Typhimurium isolates. The Kirbey-Bauer method was employed to profile antimicrobial resistance using 20 antibiotics. Multi-locus sequence typing confirmed S. Typhimurium using seven housekeeping genes (aroC, dnaN, hemD, hisD, purE, sucA, and thr). Out of five strains, only four were confirmed as S. Typhimurium during MLST analysis. Efflux pump activity was determined using the ethidium bromide (EtBr) cartwheel test. Of the 160 isolates, 38 were presumptively confirmed as S. Typhimurium based on biochemical characterization, and only five MDR Salmonella strains were selected for their resistance against most antibiotics. Efflux pump activity revealed that five out of the four MDR isolates did not retain EtBr inside the cells, indicating pronounced efflux activity. Additionally, the isolated strains showed a specific correlation between the antimicrobial phenotypes and genotypes. The results of this study provide a better understanding of the characterization of S. Typhimurium serotype in Bhopal City. Future studies should focus on understanding changing antimicrobial resistance patterns, pathogenicity, and the genetic background of Salmonella serotypes. Further surveillance activities for antimicrobial-resistant Salmonella in different environmental sources should be prioritized.

Antimicrobial susceptibility of Salmonella and Escherichia coli from equids sampled in the NAHMS 2015-16 equine study and association of management factors with resistance

Several studies have investigated antimicrobial resistance (AMR) in Salmonella spp. and Escherichia coli isolated from hospitalized horses, but studies conducted on community-based populations of equids are limited. The factors associated with AMR in these bacteria in the general horse population are not well understood. The primary objective of our study was to estimate the prevalence of Salmonella and describe antimicrobial susceptibility of Salmonella and E. coli from equids across the United States. The second objective was to identify associations between health management and biosecurity practices and AMR. Fecal samples submitted from 1357 equids on 199 operations were tested for Salmonella, identifying 27 positive samples with 29 isolates belonging to 18 serotypes. Fecal sample and operation-level prevalence of Salmonella was 2.0% (27/1357) and 7.0% (14/199), respectively. Most (25/29) isolates were pan-susceptible while four isolates exhibited resistance, three of which were multidrug resistant. Of the 721 samples cultured for E. coli, 85% (613/721) were positive. Eighty-six percent of the E. coli isolates recovered were pan-susceptible (529/612). Ten isolates were intermediate to one antimicrobial drug and susceptible to all others. Seventy-three E. coli isolates (11.9%, SE=1.3) were resistant to one or more antimicrobials, corresponding to a 33.0% (64/194) operation-level prevalence. Resistance to sulfonamide drugs was most common with 63 isolates (10.3%) resistant to sulfisoxazole, 57 of which (9.3%) were resistant to trimethoprim-sulfamethoxazole. MDR in E. coli was rare (1.8%, SE=0.5). Univariate and multivariable regression were used to evaluate associations between health management and biosecurity questionnaire items and AMR in E. coli. The outcome modeled was resistance to any of the 14 tested antimicrobials. Depending on the operation type, operations with greater than 20 resident equids were significantly associated with resistance. In addition, performance operations were significantly associated with resistance when compared to farm/ranch operations. Operations with feed containers that prevent fecal contamination and those that had treated any equids for illness or injury were associated with a lower AMR. The study results suggest that equids in the general population appear to pose low risk of shedding antimicrobial resistant strains of Salmonella and E. coli, and therefore low transmission potential to other equids, animals, humans, or the environment. However, it is prudent to practice good hand hygiene to prevent spread of Salmonella as well as AMR, and to protect both animal and human health. Despite study limitations, potential management factors that may influence prevalence and prevent spread of AMR shed by equids were identified.

Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line

The presence of mobile genetic elements in Salmonella isolated from a chicken farm constitutes a potential risk for the appearance of emerging bacteria present in the food industry. These elements contribute to increased pathogenicity and antimicrobial resistance through genes that are related to the formation of biofilms and resistance genes contained in plasmids, integrons, and transposons. One hundred and thirty-three Salmonella isolates from different stages of the production line, such as feed manufacturing, hatchery, broiler farm, poultry farm, and slaughterhouse, were identified, serotyped and sequenced. The most predominant serotype was Salmonella Infantis. Phylogenetic analyses demonstrated that the diversity and spread of strains in the pipeline are serotype-independent, and that isolates belonging to the same serotype are very closely related genetically. On the other hand, Salmonella Infantis isolates carried the pESI IncFIB plasmid harboring a wide variety of resistance genes, all linked to mobile genetic elements, and among carriers of these plasmids, the antibiograms showed differences in resistance profiles and this linked to a variety in plasmid structure, similarly observed in the diversity of Salmonella Heidelberg isolates carrying the IncI1-Iα plasmid. Mobile genetic elements encoding resistance and virulence genes also contributed to the differences in gene content. Antibiotic resistance genotypes were matched closely by the resistance phenotypes, with high frequency of tetracycline, aminoglycosides, and cephalosporins resistance. In conclusion, the contamination in the poultry industry is described throughout the entire production line, with mobile genetic elements leading to multi-drug resistant bacteria, thus promoting survival when challenged with various antimicrobial compounds.

Comparison of antimicrobial resistance among Salmonella enterica serovars isolated from Canadian turkey flocks, 2013-2021

The emergence of antimicrobial resistance (AMR) in Salmonella from turkeys has raised a food safety concern in Canada as certain serovars have been implicated in human salmonellosis outbreaks in recent years. While several studies evaluated AMR in broiler chickens in Canada, there are limited studies that assess AMR in turkey flocks. This study analyzed data collected between 2013 and 2021 by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) farm turkey surveillance program to determine the prevalence of AMR and differences in resistance patterns among Salmonella serovars recovered from turkey flocks. Salmonella isolates were tested for susceptibility to 14 antimicrobials using a microbroth dilution method. Hierarchical clustering dendrograms were constructed to compare the individual AMR status of Salmonella serovars. Differences in the probability of resistance between Salmonella serovars were determined using generalized estimating equation logistic regression models to account for farm-level clustering. Of the 1,367 Salmonella isolates detected, 55.3% were resistant to at least one antimicrobial and 25.3% were multidrug resistant (MDR) (resistant to ≥3 antimicrobial classes). The Salmonella isolates exhibited high resistance to tetracycline (43.3%), streptomycin (47.2%), and sulfisoxazole (29.1%). The 3 most frequently occurring serovars were S. Uganda (22.9%), S. Hadar (13.5%), and S. Reading (12.0%). Streptomycin-sulfisoxazole-tetracycline (n = 204) was the most frequent MDR pattern identified. Heatmaps showed that S. Reading exhibited coresistance to the quinolone class antimicrobials, ciprofloxacin, and nalidixic acid; S. Heidelberg to gentamicin and sulfisoxazole; and S. Agona to ampicillin and ceftriaxone. Salmonella Hadar isolates had higher odds of resistance to tetracycline (OR: 152.1, 95% CI: 70.6-327.4) while the probability of being resistant to gentamicin and ampicillin was significantly higher in S. Senftenberg than in all the other serovars. Moreover, S. Uganda had the highest odds of being MDR (OR: 4.7, 95% CI: 3.7-6.1). The high resistance observed warrants a reassessment of the drivers for AMR, including AMU strategies and other production factors. Differences in AMR patterns highlight the need to implement serovar-specific mitigation strategies.

Temporal Study of Salmonella enterica Serovars Isolated from Environmental Samples from Ontario Poultry Breeder Flocks between 2009 and 2018

This study's goal was to determine the prevalence, temporal trends, seasonal patterns, and temporal clustering of Salmonella enterica isolated from environmental samples from Ontario's poultry breeding flocks between 2009 and 2018. Clusters of common serovars and those of human health concern were identified using a scan statistic. The period prevalence of S. enterica was 25.3% in broiler breeders, 6.4% in layer breeders, and 28.6% in turkey breeders. An overall decreasing trend in S. enterica prevalence was identified in broiler breeders (from 27.8% in 2009 to 22.1% in 2018) and layer breeders (from 15.4% to 4.9%), while an increasing trend was identified in turkey breeders (from 12.0% to 24.5%). The most common serovars varied by commodity. Among broiler breeders, S. enterica serovars Kentucky (42.4% of 682 submissions), Heidelberg (19.2%), and Typhimurium (5.4%) were the most common. Salmonella enterica serovars Thompson (20.0% of 195 submissions) and Infantis (16.4%) were most common among layer breeders, and S. enterica serovars Schwarzengrund (23.6% of 1368 submissions), Senftenberg (12.9%), and Heidelberg and Uganda (9.6% each) were most common among turkey breeders. Salmonella enterica ser. Enteritidis prevalence was highest in submissions from broiler breeders (3.7% of 682 broiler breeder submissions). Temporal clusters of S. enterica serovars were identified for all poultry commodities. Seasonal effects varied by commodity, with most peaks occurring in the fall. Our study provides information on the prevalence and temporality of S. enterica serovars within Ontario's poultry breeder flocks that might guide prevention and control programs at the breeder level.

High frequency of non-susceptibility to ciprofloxacin in nontyphoid Salmonella recovered from Brazilian broiler chicken

1. This study evaluated the minimal inhibitory concentration (MIC) of ciprofloxacin and the presence of plasmid-mediated quinolone resistance (PMQR) mechanisms in 97 nontyphoidal Salmonella spp. isolated from broilers and carcases from three different regions in Brazil. The presence of mutations in quinolone resistance determination regions (QRDRS) was investigated in the ciprofloxacin-resistant strain by DNA sequencing.2. Most of the Salmonella spp. (85.6%) had intermediate resistance to ciprofloxacin and only one isolate was resistant. MIC breakpoints ranged from ≤0.03 to 1 µg/ml and 67.0% of the strains had a MIC of 0.25 µg/ml (n=65). Thirteen strains (13.4%) were susceptible to ciprofloxacin with MIC ≤0.06 µg/ml. The qnrB gene was detected in eight isolates with intermediate resistance and in two susceptible strains. The other PMQR genes, qnrA, qnrC, qnrD, qnrS, qnrVC, aac(6')-Ib, qepA, oqxAB and mutations in QRDR were not detected in any strain.3. There was a high frequency of ciprofloxacin intermediate resistant Salmonella from broiler and broiler carcases from Brazil. The presence of these strains in poultry and derived products poses a risk to public health.

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.

Pretreatment with probiotics Enterococcus faecium NCIMB 11181 attenuated Salmonella Typhimurium-induced gut injury through modulating intestinal microbiome and immune responses with barrier function in broiler chickens

Background

Preventing Salmonella infection and colonization in young birds is key to improving poultry gut health and reducing Salmonella contamination of poultry products and decreasing salmonellosis for human consumption (poultry meat and eggs). Probiotics can improve poultry health. The present study was conducted to investigate the impact of a probiotics, Enterococcus faecium NCIMB 11181 (E. faecium NCIMB 11181) on the intestinal mucosal immune responses, microbiome and barrier function in the presence or absence of Salmonella Typhimurium (S. Typhimurium, ST) infection.

Methods

Two hundred and forty 1-day-old Salmonella-free male broiler chickens (Arbor Acres AA⁺) were randomly allocated to four groups with 6 replicate cages of 10 birds each. The four experimental groups were follows: (1) negative control (NC), (2) S. Typhimurium, challenged positive control (PC), (3) the E. faecium NCIMB 11181-treated group (EF), (4) the E. faecium NCIMB 11181-treated and S. Typhimurium-challenged group (PEF).

Results

Results indicated that, although continuous feeding E. faecium NCIMB 11181 did not obviously alleviate growth depression caused by S. Typhimurium challenge (P > 0.05), E. faecium NCIMB 11181 addition significantly blocked Salmonella intestinal colonization and translocation (P < 0.05). Moreover, supplemental E. faecium NCIMB 11181 to the infected chickens remarkably attenuated gut morphological structure damage and intestinal cell apoptosis induced by S. Typhimurium infection, as evidenced by increasing gut villous height and reducing intestinal TUNEL-positive cell numbers (P < 0.05). Also, E. faecium NCIMB 11181 administration notably promoting the production of anti-Salmonella antibodies in intestinal mucosa and serum of the infected birds (P < 0.05). Additionally, 16S rRNA sequencing analysis revealed that E. faecium NCIMB 11181 supplementation ameliorated S. Typhimurium infection-induced gut microbial dysbiosis by enriching Lachnospiracease and Alistipes levels, and suppressing Barnesiella abundance. Predicted function analysis indicated that the functional genes of cecal microbiome involved in C5-branched dibasic acid metabolism; valine, leucine and isoleucine biosynthesis; glycerolipid metabolism and lysine biosynthesis were enriched in the infected chickens given E. faecium NCIMB 11181. While alanine, asparate and glutamate metabolism; MAPK signal pathway-yeast; ubiquine and other terpenoid-quinore biosynthesis, protein processing in endoplasmic reticulum; as well as glutathione metabolism were suppressed by E. faecium NCIMB 11181 addition.

Conclusion

Collectively, our data suggested that dietary E. faecium NCIBM 11181 supplementation could ameliorate S. Typhimurium infection-induced gut injury in broiler chickens. Our findings also suggest that E. faecium NCIMB 11181 may serve as an effective non-antibiotic feed additive for improving gut health and controlling Salmonella infection in broiler chickens.

Phenotypic and genotypic characterization of antimicrobial resistance profiles in Salmonella isolated from waterfowl in 2002–2005 and 2018–2020 in Sichuan, China

Salmonella enterica is a widespread foodborne pathogen with concerning antimicrobial resistance (AMR). Waterfowl are a major source of Salmonella transmission, but there are few systematic studies on Salmonella prevalence in waterfowl species. In this study, 126 Salmonella isolates (65 collected in 2018–2020 and 61 collected in 2002–2005) were obtained from waterfowl samples in Sichuan, China. Their serotypes, pulsed-field gel electrophoresis (PFGE) types, and phenotypic and genotypic AMR profiles were systematically examined. The isolates were distributed in 7 serotypes, including serovars Enteritidis (46.0%), Potsdam (27.8%), Montevideo (7.9%), Cerro (6.3%), Typhimurium (4.8%), Kottbus (4.0%) and Apeyeme (3.2%). Their PFGE characteristics were diverse; all isolates were distributed in four groups (cutoff value: 60.0%) and 20 clusters (cutoff value: 80.0%). Moreover, all isolates were multidrug resistant, and high rates of AMR to lincomycin (100.0%), rifampicin (100.0%), sulfadiazine (93.7%), erythromycin (89.7%), ciprofloxacin (81.0%), and gentamicin (75.4%) were observed. Finally, 49 isolates were subjected to whole-genome sequencing, and a wide variety of AMR genes were found, including multiple efflux pump genes and specific resistance genes. Interestingly, the tet(A)/tet(B) and catII resistance genes were detected in only isolates obtained in the first collection period, while the gyrA (S83F, D87N and D87G) and gyrB (E466D) mutations were detected at higher frequencies in the isolates obtained in the second collection period, supporting the findings that isolates from different periods exhibited different patterns of resistance to tetracycline, chloramphenicol and nalidixic acid. In addition, various incompatible plasmid replicon fragments were detected, including Col440I, Col440II, IncFIB, IncFII, IncX1, IncX9, IncI1-I and IncI2, which may contribute to the horizontal transmission of AMR genes and provide competitive advantages. In summary, we demonstrated that the Salmonella isolates prevalent in Sichuan waterfowl farms exhibited diverse serotypes, multiple AMR phenotypes and genotypes, and AMR changes over time, indicating their potential risks to public health.

Salmonella enterica frequency in backyard chickens in Vermont and biosecurity knowledge and practices of owners

The popularity of backyard chickens has been growing steadily over the past 10 years, with Covid-19 stay at home orders in 2020 yielding an added boost in popularity. Concurrently, cases of salmonellosis from live poultry exposure have also risen. Previous research on backyard chicken owners has focused primarily on urban chicken owners, which may have differing knowledge and biosecurity habits from rural backyard chicken owners. The goal of this study was to investigate the prevalence of S. enterica in rural and urban flocks of chickens in the state of Vermont and to determine what attitudes toward and knowledge about S. enterica owners had, as well as what biosecurity practices they used. We conducted two surveys in Vermont between 2019–2022; a pilot study tied to sampling for Salmonella enterica in backyard chicken flocks from 2019–2021 and a statewide study in 2022 to determine the prevalence of backyard chickens in Vermont and obtain representative survey data from backyard chicken owners. We found (i) overall, 19% (8/42) backyard chicken flocks from 2019–2021 had S. enterica, but S. enterica rates varied substantially by year; (ii) backyard chicken owners were wealthier and more educated than the average Vermonter and generally lived in rural areas; (iii) participants in the statewide survey had much lower uptake of good biosecurity habits compared to the pilot survey; (iv) despite increased messaging about backyard chicken-associated salmonellosis and good biosecurity measures over the past several years, uptake of biosecurity measures is inconsistent, and rates of unsafe practices such as kissing or cuddling chickens have increased in Vermont. Overall, the data indicate the need for improved messaging on biosecurity and risks associated with backyard chickens

Characterization of extended-spectrum cephalosporins and fluoroquinolone resistance of a Salmonella enterica serovar Thompson isolate from ready-to-eat pork product in China

Salmonella is a leading cause of foodborne illness worldwide and is a common concern in food safety. Salmonella enterica displaying resistance to extended-spectrum cephalosporins (ESCs) and fluoroquinolone (FQs) has been deemed a high-priority pathogen by the World Health Organization. Co-resistance to ESCs and FQs has been reported in S. enterica serovar Thompson (S. Thompson). However, the genetic context of ESCs and FQs resistance genes in S. Thompson lacks sufficient characterization. In this study, we characterized a multi-drug resistant (MDR) S. Thompson isolate recovered from a retail ready-to-eat (RTE) pork product in China. Short- and long-read sequencing (HiSeq and MinION) of the genome identified the presence of bla_CMY−2, qnrS1, and qepA8, along with 11 additional acquired antimicrobial resistance genes, residing on a 152,940 bp IncA/C plasmid. Specifically, the bla_CMY−2, qnrS1, and qepA8 genes were located in insertion sequences (ISs) and integron mediated mobile genetic structure, sugE-blc-bla_CMY−2-ISEc9, IS26-orf6-qnrS1-orf5-ISKpn19, and intl1-qepA8-orf10-IS91-orf1-dfrA12-orf11-aadA2-qacEΔ1-sul1, respectively. Each gene was identified in various bacteria species, indicating their high transfer ability. The plasmid was found to be transferable to Escherichia coli J53 by conjugation and resulted in the acquiring of multiple resistances in the transconjugants. The plasmid is closely related to plasmids from two human S. Thompson strains isolated in different regions and years in China. Moreover, core-genome Multi Locus Sequence Typing (cgMLST) and phylogenetic analysis based on global 1,868 S. Saintpaul isolates showed that the S. Thompson isolate was highly epidemiologically linked to a human isolate in China. Our findings suggest that Chinese RTE pork products are a possible source of human pathogenic ESCs and FQs co-resistant S. Thompson. Furthermore, the results underline the important role of conjugative plasmids in acquiring and transmission of ESCs and FQs resistance in S. Thompson isolates, which need continuous investigation.

Silver nanoparticle effect on Salmonella enterica isolated from Northern West Egypt food, poultry, and calves

A total no. of 65 Salmonella enterica isolates recovered from food samples, feces of diarrheic calves, poultry, and hospital patient in large five cities at Northern West Egypt were obtained from the Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt. The 65 Salmonella enterica isolates had the invA gene were grouped into 11 Salmonella enterica serovars with dominance of S. Enteritidis and S. Kentucky serovars. Their resistance pattern were characterized by using 18 antibiotics from different classes. Approximately 80% of the isolates were multidrug resistant (MDR). Enterobacterial repetitive intergenic consequences polymerase chain reaction (ERIC-PCR) typing of 7 strains of S. Enteritidis showed 5 clusters with dissimilarity 25%. S. Enteritidis clusters in 2 main groups A and B. Group A have 2 human strain (HE2 and HE3) and one food origin (FE7) with a similarity 99%. Group B divided into B1 (FE2) and B2 (FE3) with a similarity ratio ≥ 93%, while ERIC-PCR analysis of 5 strains of S. Kentucky revealed 4 ERIC types, clustered in 2 main groups A and B with similarity 75%. We studied the effect of silver nanoparticles (Ag-NPs) on 10 antibiotic resistant strains of S. Enteritidis and S. Kentucky. The broth microdilution minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were detected. Evaluation of the affection using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) showed different ratios of Ag-NPs and microorganism as well as at different contact time ended finally with morphological alteration of the bacteria. We submitted new method in vivo to explore the activity of nanosilver in chicken. KEY POINTS: • Importance of ERIC-PCR to determine the relatedness between Salmonella isolates. • Effect of silver nanoparticles to confront the antibacterial resistance. • Studying the effect of silver nanoparticles in vivo on infected chicken with Salmonella.

Emergence, Dissemination and Antimicrobial Resistance of the Main Poultry-Associated Salmonella Serovars in Brazil

Simple Summary

Salmonellosis is a human and animal disease caused by Salmonella, a bacterial genus classified into different species, subspecies, and serological variants (serovars) according to adaptation to one or more different hosts (animals and humans), pathogenicity profiles, and antigenic properties. Some specific Salmonella serovars can spread more easily in the enteric microbiota of avian species, often causing disease in birds and/or being transmitted to humans through food (such as chicken and eggs). Antimicrobial resistance (AMR) has also been reported in poultry-associated Salmonella isolates due to the widespread use of antimicrobials on farms. The availability of comprehensive data on the emergence and spread of Salmonella serovars, as well as their AMR profiles in farms and food products in Brazil (a major producer of poultry in the World), is necessary to understand their relevance in all avian production chains and also occurrence in poultry-derived foods. This article aims to provide an overview of the genus Salmonella and the main serovars that emerged in Brazilian poultry over time (Gallinarum, Typhimurium, Enteritidis, Heidelberg, and Minnesota), reviewing the scientific literature and suggesting more effective prevention and control for the future.

Abstract

Salmonella infects poultry, and it is also a human foodborne pathogen. This bacterial genus is classified into several serovars/lineages, some of them showing high antimicrobial resistance (AMR). The ease of Salmonella transmission in farms, slaughterhouses, and eggs industries has made controlling it a real challenge in the poultry-production chains. This review describes the emergence, dissemination, and AMR of the main Salmonella serovars and lineages detected in Brazilian poultry. It is reported that few serovars emerged and have been more widely disseminated in breeders, broilers, and layers in the last 70 years. Salmonella Gallinarum was the first to spread on the farms, remaining as a concerning poultry pathogen. Salmonella Typhimurium and Enteritidis were also largely detected in poultry and foods (eggs, chicken, turkey), being associated with several human foodborne outbreaks. Salmonella Heidelberg and Minnesota have been more widely spread in recent years, resulting in frequent chicken/turkey meat contamination. A few more serovars (Infantis, Newport, Hadar, Senftenberg, Schwarzengrund, and Mbandaka, among others) were also detected, but less frequently and usually in specific poultry-production regions. AMR has been identified in most isolates, highlighting multi-drug resistance in specific poultry lineages from the serovars Typhimurium, Heidelberg, and Minnesota. Epidemiological studies are necessary to trace and control this pathogen in Brazilian commercial poultry production chains.

Safety of bivalent live attenuated Salmonella vaccine and its protection against bacterial shedding and tissue invasion in layers challenged with Salmonella

Nontyphoidal Salmonella infection was one of the predominant foodborne illnesses in humans. The medical burden and antimicrobial resistance of salmonellosis gained importance in public health and requested the poultry industry to seek effective measures to control the disease. The objective of this study was to evaluate the safety and effectiveness of a commercial bivalent live attenuated vaccine (AviPro Salmonella DUO) in specific-pathogen-free (SPF) chickens and field layers. It explored its safety and efficacy against medically important strains, Salmonella Enteritidis (SE) and S. Typhimurium (ST). The results demonstrated that ten vaccine doses in SPF chickens and regular doses in commercial layers showed desirable safety without affecting chicken health. Vaccinated layers demonstrated lower flock mortality and higher egg production performance than the unvaccinated layers during the raising and egg production periods. Additionally, no visceral colonization and egg contaminations were detected. Cloacal shedding of vaccine strains was noted, but the colonization of Salmonella disappeared within four weeks of the last vaccination. Regarding vaccine efficacy, one dose significantly reduced Salmonella cloacal shedding (P = 0.037 for SE and P = 0.027 for ST) and viable cell counts (P = 0.003 for SE and ST) on day 7 post the challenges. Significantly low Salmonella loads of cloacal samples on day 14 after the challenges were also determined in the vaccinated group (P = 0.006 for SE; P = 0.041 for ST). Triple immunizations effectively prevented layers from the cloacal shedding on either day 7 or day 14 post Salmonella challenges. Total viable counts of SE and ST in tissues of vaccinated layers were also reduced on day 14 after the challenges (P = 0.026 for SE; P = 0.002 for ST). To conclude, one dose of vaccine exhibited inhibitory effects on Salmonella shedding and tissue invasions in young layers. Following the regimen of triple vaccinations, Salmonella shedding was completely inhibited, and tissue invasions were significantly reduced. Incorporating this vaccine into a comprehensive Salmonella control program is promising to protect layers from the risks of contaminating the flocks and egg products.

Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa

Since its emergence in the beginning of the 90’s, multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Salmonella Kentucky ST198 genomes (n=229). All the 19 sequenced Salmonella Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the aac(3)-Id, aadA7, strA-strB, bla_TEM-1B, sul1, and tet(A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and gyrA and parC mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Salmonella Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Salmonella Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1–4, SPI 9 or C63PI) was identified among the 229 public Salmonella Kentucky genomes. The phylogenetic analysis revealed that almost all Salmonella Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Salmonella Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Salmonella Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated.

Assessing Salmonella Prevalence and Complexity Through Processing Using Different Culture Methods

Conventional Salmonella surveillance requires a week for isolation, confirmation, and subsequent serotyping. We previously showed that this could be reduced by 24 h by combining the pre-enrichment and enrichment steps into a single selective pre-enrichment step and was tested on directly after picking. The goal of this study was 2-fold: 1) to evaluate the use of selective pre-enrichment through each step of processing, including postintervention when the Salmonella load is reduced, and 2) to assess any changes in serovar populations in Salmonella positive samples. Duplicate carcass drip samples, each representative of 500 broiler carcasses, were collected by catching processing water drip under moving carcass shackle lines in each of three commercial broiler slaughter plants. Samples were collected post-pick, post-inside-outside bird wash (IOBW), and post-chill; duplicate wing rinses were performed pre- and post-antimicrobial parts dip. Each processing plant was sampled 6 times for a total of 180 samples collected. The number of Salmonella positives identified with selective pre-enrichment conditions (48/180) was similar to traditional selective enrichment culture conditions (52/180), showed good concordance in recovery rate between the 2 culture methods (Fisher's exact test, P = 0.72). We also found that the incidence of Salmonella reduced dramatically after antimicrobial intervention (post-pick 66.7% vs. post chill 8.3%). When serovar populations were evaluated in Salmonella positive samples using CRISPR-SeroSeq, we detected four different Salmonella serovars, Kentucky, Infantis, Schwarzengrund, and Typhimurium, and their incidence rose between post-pick and post-IOBW. The relative abundance of Infantis within individual samples increased between post-pick and post-IOBW while the relative abundance of the other 3 serovars decreased. These results suggest that a selective pre-enrichment step reduces the time required for Salmonella isolation without negatively affecting detection and serovar profiles in culture positive samples were not altered between culture conditions used.

A national study through a 'Farm-to-fork' Approach to determine Salmonella dissemination along with the Lebanese poultry production chain

This cross-sectional study was conducted to determine the prevalence of Salmonella at different stages of the broiler production chain and layer flocks in addition to their antibiotic resistance profile and molecular patterns. Over a period of 3 years, different sample matrices were collected from Lebanese farms, slaughterhouses and retail markets. Out of 672 Salmonella serotyped, 514 were analysed for antimicrobial resistance and 214 for clonality using Pulsed-field gel electrophoresis (PFGE). The results highlighted an important prevalence of Salmonella, 30% in farms, 35.8% in slaughterhouses and 22.4% at retail level. A large diversity of serotypes was identified with predominance among Salmonella Infantis (32.9%), Salmonella Enteritidis (28.4%) and Salmonella Kentucky (21.4%). High resistance to nalidixic acid was revealed in all the isolates. The most prominent resistance was exhibited in S. Kentucky and S. Infantis. The latter was resistant to tetracycline (99%), streptomycin (88.2%) and remarkable multi-drug resistance (MDR) (89.7%). All S. Kentucky isolates were resistant to ciprofloxacin, MDR (62.4%) and 6% were resistant to extended-spectrum cephalosporin (ESCs). One persistent clone of S. Enteritidis was found common between poultry and humans. Similar genomic profiles were detected between farms, slaughterhouses and retail suggesting the dissemination of identical clones throughout the food chain possibly due to weak barriers preventing such transmission.

Investigating the dynamics of Salmonella contamination in integrated poultry companies using a whole genome sequencing approach

The study of non-typhoid Salmonella in broiler integrations has been limited by the resolution of typing techniques. Although serotyping of Salmonella isolates is used as a traditional approach, it is not of enough resolution to clearly understand the dynamics of this pathogen within poultry companies. The aim of this research was to investigate the epidemiology and population dynamics of Salmonella serotypes in 2 poultry integrations using a whole genome sequencing approach. Two hundred and forty-three Salmonella isolates recovered from the broiler production chain of 2 integrated poultry companies were whole genome sequenced and analyzed with dedicated databases and bioinformatic software. The analyses of sequences revealed that S. Infantis was the most frequent serotype (82.3%). Most isolates showed a potential for resistance against medically important antibiotics and disinfectants. Furthermore, 97.5% of isolates harbored the pESI-like mega plasmid, that plays an important role in the global dissemination of AMR. SNP tree analysis showed that there were clones that are niche-specific while other ones were distributed throughout the broiler production chains. In this study, we demonstrated the potential of whole genome sequencing analysis for a comprehensive understanding of Salmonella distribution in integrated poultry companies. Data obtained with these techniques allow determination of the presence of genetic factors that play an important role in the environmental fitness and pathogenicity of Salmonella.

Development of a Genomics-Based Approach To Identify Putative Hypervirulent Nontyphoidal Salmonella Isolates: Salmonella enterica Serovar Saintpaul as a Model

While differences in human virulence have been reported across nontyphoidal Salmonella (NTS) serovars and associated subtypes, a rational and scalable approach to identify Salmonella subtypes with differential ability to cause human diseases is not available. Here, we used NTS serovar Saintpaul (S. Saintpaul) as a model to determine if metadata and associated whole-genome sequence (WGS) data in the NCBI Pathogen Detection (PD) database can be used to identify (i) subtypes with differential likelihoods of causing human diseases and (ii) genes and single nucleotide polymorphisms (SNPs) potentially responsible for such differences. S. Saintpaul SNP clusters (n = 211) were assigned different epidemiology types (epi-types) based on statistically significant over- or underrepresentation of human clinical isolates, including human associated (HA; n = 29), non-human associated (NHA; n = 23), and other (n = 159). Comparative genomic analyses identified 384 and 619 genes overrepresented among isolates in 5 HA and 4 NHA SNP clusters most significantly associated with the respective isolation source. These genes included 5 HA-associated virulence genes previously reported to be present on Gifsy-1/Gifsy-2 prophages. Additionally, premature stop codons in 3 and 7 genes were overrepresented among the selected HA and NHA SNP clusters, respectively. Tissue culture experiments with strains representing 4 HA and 3 NHA SNP clusters did not reveal evidence for enhanced invasion or intracellular survival for HA strains. However, the presence of sodCI (encoding a superoxide dismutase), found in 4 HA and 1 NHA SNP clusters, was positively correlated with intracellular survival in macrophage-like cells. Post hoc analyses also suggested a possible difference in intracellular survival among S. Saintpaul lineages. IMPORTANCE Not all Salmonella isolates are equally likely to cause human disease, and Salmonella control strategies may unintentionally focus on serovars and subtypes with high prevalence in source populations but are rarely associated with human clinical illness. We describe a framework leveraging WGS data in the NCBI PD database to identify Salmonella subtypes over- and underrepresented among human clinical cases. While we identified genomic signatures associated with HA/NHA SNP clusters, tissue culture experiments failed to identify consistent phenotypic characteristics indicative of enhanced human virulence of HA strains. Our findings illustrate the challenges of defining hypo- and hypervirulent S. Saintpaul and potential limitations of phenotypic assays when evaluating human virulence, for which in vivo experiments are essential. Identification of sodCI, an HA-associated virulence gene associated with enhanced intracellular survival, however, illustrates the potential of the framework and is consistent with prior work identifying specific genomic features responsible for enhanced or reduced virulence of nontyphoidal Salmonella.

Non-Antibiotics Strategies to Control Salmonella Infection in Poultry

Salmonella spp. is a facultative intracellular pathogen causing localized or systemic infections, involving economic and public health significance, and remains the leading pathogen of food safety concern worldwide, with poultry being the primary transmission vector. Antibiotics have been the main strategy for Salmonella control for many years, which has allowed producers to improve the growth and health of food-producing animals. However, the utilization of antibiotics has been reconsidered since bacterial pathogens have established and shared a variety of antibiotic resistance mechanisms that can quickly increase within microbial communities. The use of alternatives to antibiotics has been recommended and successfully applied in many countries, leading to the core aim of this review, focused on (1) describing the importance of Salmonella infection in poultry and the effects associated with the use of antibiotics for disease control; (2) discussing the use of feeding-based (prebiotics, probiotics, bacterial subproducts, phytobiotics) and non-feeding-based (bacteriophages, in ovo injection, vaccines) strategies in poultry production for Salmonella control; and (3) exploring the use of complementary strategies, highlighting those based on -omics tools, to assess the effects of using the available antibiotic-free alternatives and their role in lowering dependency on the existing antimicrobial substances to manage bacterial infections in poultry effectively.

Infection dynamics of Salmonella Infantis strains displaying different genetic backgrounds - with or without pESI-like plasmid - vary considerably

Food-borne infections with Salmonella are among the most common causes of human diseases worldwide, and infections with the serovar Infantis are becoming increasingly important. So far, diverse phenotypes and genotypes of S. Infantis have been reported. Therefore, the present study aimed to investigate the infection dynamics of two different S. Infantis strains in broilers. For this purpose, 15 birds were infected on day 2 of life with 108 CFU/ml of a pESI+ or a pESI- S. Infantis strain, respectively. Ten uninfected birds served as in-contact birds to monitor transmission. In both groups, an increase of infection was observed from 7 days of age onwards, reaching its peak at 28 days. However, the pESI+ strain proved significantly more virulent being re-isolated from most cloacal swabs and organs by direct plating. In contrast, the pESI- strain could be re-isolated from cloacal swabs and caeca only when enrichment was applied. Although the excretion of this strain was limited, the transmission level to in-contact birds was similar to the pESI+ strain. Differences in infection dynamics were also reflected in the antibody response: whereas the pESI+ strain provoked a significant increase in antibodies, antibody levels following infection with the pESI- strain remained in the range of negative control birds. The actual findings provide for the first time evidence of S. Infantis strain-specific infectivity in broilers and confirm previous observations in the field regarding differences in persistence on farms and resistance against disinfectants.

Quantitative phosphoproteomics reveals the effect of baeSR and acrB genes on protein phosphorylation in Salmonella enterica serovar Typhimurium

The BaeSR two-component system and the AcrB efflux pump are closely associated with Salmonella resistance to antibiotics. However, the relationship between the two-component system, efflux pumps and protein phosphorylation of Salmonella is poorly understood. In this study, S. typhimurium ciprofloxacin-resistant strain CR, baeSR gene deletion strain CR^ΔbaeSR, acrB gene deletion strain CR^ΔacrB, and double gene deletion strain CR^{ΔbaeSRΔacrB} were used to explore phosphorylated proteins with significant difference, based on non-marker, quantitative phosphorylation modified proteomics technique. Consequently, 363 phosphosites of 213 phosphoproteins were identified in the four strains. More than 70% of the phosphosites were serine phosphorylation. In the CR^ΔbaeSR/CR, CR^ΔacrB/CR and CR^{ΔbaeSRΔacrB}/CR comparison groups, 36, 37 and 49 phosphosites were significantly altered, respectively. Bioinformatic analysis revealed that the main enrichment pathways of these differentially phosphorylated proteins were metabolic pathways, biosynthesis of antibiotics, phosphotransferase system (PTS), ABC transporters, and lipopolysaccharide biosynthesis. Furthermore, 21 differentially phosphorylated proteins were identified to be associated with antibiotic resistance. These results suggest that the BaeSR two-component system and the AcrB efflux pump affect the phosphorylation of proteins in S. typhimurium and may influence the drug resistance and virulence of S. typhimurium by affecting protein phosphorylation, providing a new idea to explore the mechanism of drug resistance in Salmonella.

Genomic Analysis of Ciprofloxacin-Resistant Salmonella enterica Serovar Kentucky ST198 From Spanish Hospitals

Salmonella enterica serovar Kentucky (S. Kentucky) with sequence type (ST) 198 and highly resistant to ciprofloxacin (ST198-Cip^R) has emerged as a global MDR clone, posing a threat to public health. In the present study, whole genome sequencing (WGS) was applied to characterize all Cip^RS. Kentucky detected in five Spanish hospitals during 2009–2018. All Cip^R isolates (n = 13) were ST198 and carried point mutations in the quinolone resistance-determining regions (QRDRs) of both gyrA (resulting in Ser83Phe and Asp87Gly, Asp87Asn, or Asp87Tyr substitutions in GyrA) and parC (with Thr57Ser and Ser80Ile substitutions in ParC). Resistances to other antibiotics (ampicillin, chloramphenicol, gentamicin, streptomycin, sulfonamides, and tetracycline), mediated by the bla_TEM–1B, catA1, aacA5, aadA7, strA, strB, sul1, and tet(A) genes, and arranged in different combinations, were also observed. Analysis of the genetic environment of the latter resistance genes revealed the presence of multiple variants of SGI1 (Salmonella genomic island 1)-K and SGI1-P, where all these resistance genes except catA1 were placed. IS26 elements, found at multiple locations within the SGI1 variants, have probably played a crucial role in their generation. Despite the wide diversity of SGI1-K- and SGI1-P-like structures, phylogenetic analysis revealed a close relationship between isolates from different hospitals, which were separated by a minimum of two and a maximum of 160 single nucleotide polymorphisms. Considering that S. enterica isolates resistant to fluoroquinolones belong to the high priority list of antibiotic-resistant bacteria compiled by the World Health Organization, continuous surveillance of the S. Kentucky ST198-CIP^R clone is required.

Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil

Salmonella enterica serovar Heidelberg is isolated from poultry-producing regions around the world. In Brazil, S. Heidelberg has been frequently detected in poultry flocks, slaughterhouses, and chicken meat. The goal of the present study was to assess the population structure, recent temporal evolution, and some important genetic characteristics of S. Heidelberg isolated from Brazilian poultry farms. Phylogenetic analysis of 68 S. Heidelberg genomes sequenced here and additional whole-genome data from NCBI demonstrated that all isolates from the Brazilian poultry production chain clustered into a monophyletic group, here called S. Heidelberg Brazilian poultry lineage (SH-BPL). Bayesian analysis defined the time of the most recent common ancestor (tMRCA) as 2004, and the overall population size (N_e) was constant until 2008, when an ∼10-fold N_e increase was observed until circa 2013. SH-BPL presented at least two plasmids with replicons ColpVC (n = 68; 100%), IncX1 (n = 66; 97%), IncA/C2 (n = 65; 95.5%), ColRNAI (n = 43; 63.2%), IncI1 (n = 32; 47%), ColMG828, Col156, IncHI2A, IncHI2, IncQ1, IncX4, IncY, and TrfA (each with n < 4; <4% each). Antibiotic resistance genes were found, with high frequencies of fosA7 (n = 68; 100%), mdf(A) (n = 68; 100%), tet(34) (n = 68; 100%), sul2 (n = 64; 94.1%), and blaCMY-2 (n = 56; 82.3%), along with an overall multidrug resistance (MDR) profile. Ten Salmonella pathogenicity islands (SPI1 to SPI5, SPI9, and SPI11 to SPI14) and 139 virulence genes were also detected. The SH-BPL profile was like those of other previous S. Heidelberg isolates from poultry around the world in the 1990s. In conclusion, the present study demonstrates the recent introduction (2004) and high level of dissemination of an MDR S. Heidelberg lineage in Brazilian poultry operations. IMPORTANCE S. Heidelberg is the most frequent serovar in several broiler farms from the main Brazilian poultry-producing regions. Therefore, avian-source foods (mainly chicken carcasses) commercialized in the country and exported to other continents are contaminated with this foodborne pathogen, generating several national and international economic losses. In addition, isolates of this serovar are usually resistant to antibiotics and can cause human invasive and septicemic infection, representing a public health concern. This study demonstrates the use of whole-genome sequencing (WGS) to obtain epidemiological information for one S. Heidelberg lineage highly spread among Brazilian poultry farms. This information will help to define biosecurity measures to control this important Salmonella serovar in Brazilian and worldwide poultry operations.

Prevalence, Serotypes, and Antimicrobial Resistance of Salmonella from Mink Feces and Feed in the United States

Nontyphoidal Salmonella is a leading cause of foodborne illnesses, and concentrated animal production such as commercial mink farming can be a reservoir. The objective of this study was to determine the prevalence, serotypes, antimicrobial resistance, virulence genes and mobile genetic elements, and phylogenetic characterization of Salmonella from mink fecal (n = 42) and feed (n = 8) samples at a commercial mink farm in the United States. Salmonella was detected from 11 (26.2%) fecal and 1 (12.5%) feed samples. Twelve fecal isolates obtained from the positive samples were identified into four serotypes: Salmonella Uganda (eight isolates; two isolates were obtained from one sample), Salmonella Reading (two isolates), Salmonella Heidelberg (one isolate), and Salmonella Orion (one isolate). Two isolates from the positive feed sample were identified as Salmonella Cerro. Twelve isolates, one isolate per positive sample, were whole genome sequenced for further characterization. The two Salmonella Reading isolates were multidrug resistant (MDR) with the classical ASSuT (ampicillin, streptomycin, sulfisoxazole, and tetracycline) phenotype. Genotypically, the isolates were correspondingly positive, both by polymerase chain reaction and by whole-genome sequencing (WGS), for bla_TEM-1, aph(3″)-Ib and aph(6)-Id, sul2, and tet(A). WGS additionally identified trimethoprim resistance gene dfrA8 in Salmonella Reading, and fosfomycin resistance gene fosA7 in Salmonella Heidelberg. All isolates carried Salmonella-specific multidrug resistance (mdsA/B), gold resistance, and intimin-like virulence genes. In addition, Salmonella Orion carried copper and silver resistance gene clusters. The two Salmonella Reading isolates also carried a cytolethal distension toxin (cdtB) gene. Salmonella Reading isolates belonged to ST412, a predominant sequence type among turkey and human isolates obtained in relation to recent salmonellosis outbreaks in North America. Phylogenetically, Salmonella Uganda, Salmonella Heidelberg, and Salmonella Reading were mostly associated with historic human/clinical, and poultry and swine source isolates. This study indicates that mink production can be a reservoir for foodborne pathogens such as Salmonella with MDR serovars commonly associated with human illnesses.