Prevalence and characterization of salmonellae in commercial ground beef in the United States

The effect of a direct-fed microbial (10-G) on live animal performance, carcass characteristics, and Salmonella prevalence of fed beef heifers

The objective of this study was to determine the efficacy of the direct-fed microbial 10-G upon cattle growth performance, liver and lung health, carcass quality, and yield outcomes, as well as prevalence and enumeration of Salmonella in feces and lymph nodes. Fed beef heifers (N = 1,400; initial shrunk body weight [BW] 343.3 ± 36.2 kg) were blocked by the day of arrival and randomly allocated to one of two treatments (0 [negative control, CON] or 2 g of a direct-fed microbial [10-G] that provided 1 billion CFUs per animal per day of Lactobacillus acidophilus, Enterococcus faecium, Pediococcus pentosaceus, L. brevis, and L. plantarum) with 10 pens per treatment. Recto-anal mucosal fecal samples (RAMs; n = 477) and subiliac lymph nodes (SLNs; n = 479) were collected longitudinally at harvest from 23 to 25 heifers per pen. Data were analyzed using mixed models; pen served as the experimental unit; block and harvest date were random effects. No differences were detected in dry matter intake (P = 0.78), final BW (P = 0.64), average daily gain (P = 0.51), gain to feed (P = 0.71), hot carcass weight (P = 0.54), dressed carcass yield (P = 0.52), 12th rib fat depth (P = 0.13), longissimus muscle area (P = 0.62), calculated empty body fat (P = 0.26), or marbling score (P = 0.82). Distributions of liver scores (P ≥ 0.34), quality grades (P ≥ 0.23), and yield grades (P ≥ 0.11) were also not different between treatments. A tendency was detected for more normal lungs (P = 0.08; 10-G = 65.96%, CON = 61.12%) and fewer inflated lungs at harvest for cattle fed 10-G (P = 0.10; 10-G = 0.29%, CON = 1.16%); other lung outcomes did not differ (P ≥ 0.54). Salmonella prevalence did not differ for RAM samples (P = 0.41; 10-G = 97.74%, CON = 96.82%) or SLN (P = 0.22; 10-G = 17.92%, CON = 13.66%). Salmonella concentration of RAM samples (P = 0.25; 10-G = 3.87 log CFU/g, CON = 3.32 log CFU/g) or SLN (P = 0.37; 10-G = 1.46 log CFU/g, CON = 1.14 log CFU/g) also did not differ between treatments at harvest. These results do not demonstrate any difference in live animal performance, carcass characteristics, or Salmonella carriage for heifers fed 10-G.

Growth assessment of Salmonella enterica multi-serovar populations in poultry rinsates with commonly used enrichment and plating media

Isolation of Salmonella from enrichment cultures of food or environmental samples is a complicated process. Numerous factors including fitness in various selective enrichment media, relative starting concentrations in pre-enrichment, and competition among multi-serovar populations and associated natural microflora, come together to determine which serovars are identified from a given sample. A recently developed approach for assessing the relative abundance (RA) of multi-serovar Salmonella populations (CRISPR-SeroSeq or Deep Serotyping, DST) is providing new insight into how these factors impact the serovars observed, especially when different selective enrichment methods are used to identify Salmonella from a primary enrichment sample. To illustrate this, we examined Salmonella-positive poultry pre-enrichment samples through the selective enrichment process in Tetrathionate (TT) and Rappaport Vassiliadis (RVS) broths and assessed recovery of serovars with each medium. We observed the RA of serovars detected post selective enrichment varied depending on the medium used, initial concentration, and competitive fitness factors, all which could result in minority serovars in pre-enrichment becoming dominant serovars post selective enrichment. The data presented provide a greater understanding of culture biases and lays the groundwork for investigations into robust enrichment and plating media combinations for detecting Salmonella serovars of greater concern for human health.

Salmonellosis: An Overview of Epidemiology, Pathogenesis, and Innovative Approaches to Mitigate the Antimicrobial Resistant Infections

Salmonella is a major foodborne pathogen and a leading cause of gastroenteritis in humans and animals. Salmonella is highly pathogenic and encompasses more than 2600 characterized serovars. The transmission of Salmonella to humans occurs through the farm-to-fork continuum and is commonly linked to the consumption of animal-derived food products. Among these sources, poultry and poultry products are primary contributors, followed by beef, pork, fish, and non-animal-derived food such as fruits and vegetables. While antibiotics constitute the primary treatment for salmonellosis, the emergence of antibiotic resistance and the rise of multidrug-resistant (MDR) Salmonella strains have highlighted the urgency of developing antibiotic alternatives. Effective infection management necessitates a comprehensive understanding of the pathogen's epidemiology and transmission dynamics. Therefore, this comprehensive review focuses on the epidemiology, sources of infection, risk factors, transmission dynamics, and the host range of Salmonella serotypes. This review also investigates the disease characteristics observed in both humans and animals, antibiotic resistance, pathogenesis, and potential strategies for treatment and control of salmonellosis, emphasizing the most recent antibiotic-alternative approaches for infection control.

DNA methylation in poultry: a review

As an important epigenetic modification, DNA methylation is involved in many biological processes such as animal cell differentiation, embryonic development, genomic imprinting and sex chromosome inactivation. As DNA methylation sequencing becomes more sophisticated, it becomes possible to use it to solve more zoological problems. This paper reviews the characteristics of DNA methylation, with emphasis on the research and application of DNA methylation in poultry.

Efficacy of Common Antimicrobial Interventions at and above Regulatory Allowable Pick-Up Levels on Pathogen Reduction

The objective of this study was to evaluate the food safety efficacy of common antimicrobial interventions at and above required uptake levels for processing aids on the reduction of Shiga-toxin producing E. coli (STEC) and Salmonella spp. through spray and dip applications. Beef trim was inoculated with specific isolates of STEC or Salmonella strains. Trim was intervened with peracetic or lactic acid through spray or dip application. Meat rinses were serially diluted and plated following the drop dilution method; an enumerable range of 2-30 colonies was used to report results before log transformation. The combination of all treatments exhibits an average reduction rate of 0.16 LogCFU/g for STEC and Salmonella spp., suggesting that for every 1% increase in uptake there is an increase of 0.16 LogCFU/g of reduction rate. There is a statistical significance in the reduction rate of Shiga-toxin producing Escherichia coli in relation to the uptake percentage (p < 0.01). The addition of explanatory variables increases the R² of the regression for STEC, where all the additional explanatory variables are statistically significant for reduction (p < 0.01). The addition of explanatory variables increases the R² of the regression for Salmonella spp., but only trim type is statistically significant for reduction rate (p < 0.01). An increase in uptake percentages showed a significant increase in reduction rate of pathogens on beef trimmings.

Longitudinal evaluation of Salmonella in environmental components and peripheral lymph nodes of fed cattle from weaning to finish in three distinct feeding locations

Salmonella prevalence in bovine lymph nodes (LNs) varies due to seasonality, geographic location, and feedyard environment. The objectives of this study were to (1) establish prevalence rates of Salmonella in environmental components (trough water, pen soil, individual feed ingredients, prepared rations, and fecal samples) and LNs from weaning to finish in three feeding locations, and (2) characterize recovered salmonellae. Calves (n = 120) were raised at the Texas A&M University McGregor Research Center; in lieu of beginning the backgrounding/stocker phase, thirty weanling calves were harvested. Of the remaining ninety calves, thirty were retained at McGregor and sixty were transported to commercial feeding operations (Location A or B; thirty calves each). Locations A and B have historically produced cattle with relatively "low" and "high" rates of Salmonella-positive LNs, respectively. Ten calves per location were harvested at the conclusion of (1) the backgrounding/stocker phase, (2) 60 d on feed, and (3) 165 d on feed. On each harvest day, peripheral LNs were excised. Environmental samples were obtained from each location before and after each phase, and every 30 d during the feeding period. In line with previous work, no Salmonella-positive LNs were recovered from cattle managed at Location A. Salmonella-positive LNs (30%) and environmental components (41%) were most commonly recovered from Location B. Of 7 and 36 total serovars recovered from Salmonella-positive LN and environmental samples, respectively, Anatum was identified most frequently. Data from this study provide insight into Salmonella prevalence differences among feeding locations and the possible influence of environmental and/or management practices at each. Such information can be used to shape industry best practices to reduce Salmonella prevalence in cattle feeding operations, resulting in a decreased prevalence of Salmonella in LNs, and thus, minimizing risks to human health.

Thermal Death Kinetics of Three Representative Salmonella enterica Strains in Toasted Oats Cereal

Several reports have indicated that the thermal tolerance of Salmonella at low-water activity increases significantly, but information on the impact of diverse food matrices is still scarce. The goal of this research was to determine the kinetic parameters (decimal reduction time, D; time required for the first decimal reduction, δ) of thermal resistance of Salmonella in a previously cooked low water activity food. Commercial toasted oats cereal (TOC) was used as the food model, with or without sucrose (25%) addition. TOC samples were inoculated with 108 CFU/mL of a single strain of one of three Salmonella serovars (Agona, Tennessee, Typhimurium). TOC samples were ground and equilibrated to aw values of 0.11, 0.33 and 0.53, respectively. Ground TOC was heated at temperatures between 65 °C and 105 °C and viable counts were determined over time (depending on the temperature for up to 6 h). Death kinetic parameters were determined using linear and Weibull regression models. More than 70% of Weibull’s adjusted regression coefficients (Radj2) and only 38% of the linear model’s Radj2 had values greater than 0.8. For all serovars, both D and δ values increased consistently at a 0.11 aw compared to 0.33 and 0.53. At 0.33 aw, the δ values for Typhimurium, Tennessee and Agona were 0.55, 1.01 and 2.87, respectively, at 85 °C, but these values increased to 65, 105 and 64 min, respectively, at 0.11 aw. At 100 °C, δ values were 0.9, 5.5 and 2.3 min, respectively, at 0.11 aw. The addition of sucrose resulted in a consistent reduction of eight out of nine δ values determined at 0.11 aw at 85, 95 and 100 °C, but this trend was not consistent at 0.33 and 0.53 aw. The Z values (increase of temperature required to decrease δ-value one log) were determined with modified δ values for a fixed β (a fitting parameter that describes the shape of the curve), and ranged between 8.9 °C and 13.4 °C; they were not influenced by aw, strain or sugar content. These findings indicated that in TOC, high thermal tolerance was consistent among serovars and thermal tolerance was inversely dependent on aw.

Genomic characterization of Salmonella enterica serovar Kentucky and London recovered from food and human salmonellosis in Zhejiang Province, China (2016–2021)

Increasing human salmonellosis caused by Salmonella enterica serovar Kentucky and London has raised serious concerns. To better understand possible health risks, insights were provided into specific genetic traits and antimicrobial resistance of 88 representative isolates from human and food sources in Zhejiang Province, China, during 2016–2021. Phylogenomic analysis revealed consistent clustering of isolates into the respective serovar or sequence types, and identified plausible interhost transmission via distinct routes. Each serovar exhibited remarkable diversity in host range and disease-causing potential by cgMLST analyses, and approximately half (48.6%, 17/35) of the food isolates were phylogenetically indistinguishable to those of clinical isolates in the same region. S. London and S. Kentucky harbored serovar-specific virulence genes contributing to their functions in pathogenesis. The overall resistance genotypes correlated with 97.7% sensitivity and 60.2% specificity to the identified phenotypes. Resistance to ciprofloxacin, cefazolin, tetracycline, ampicillin, azithromycin, chloramphenicol, as well as multidrug resistance, was common. High-level dual resistance to ciprofloxacin and cephalosporins in S. Kentucky ST198 isolates highlights evolving threats of antibiotic resistance. These findings underscored the necessity for the development of effective strategies to mitigate the risk of food contamination by Salmonella host-restricted serovars.

Efficacy of Antimicrobial Interventions Used in Meat Processing Plants against Antimicrobial Tolerant Non-Antibiotic-Resistant and Antibiotic-Resistant Salmonella on Fresh Beef

ABSTRACT

Salmonella is a common cause of foodborne illness in the United States, and several strains of Salmonella have been identified as resistant to antibiotics. It is not known whether strains that are antibiotic resistant (ABR) and that have some tolerance to antimicrobial compounds are also able to resist the inactivation effects of antimicrobial interventions used in fresh meat processing. Sixty-eight Salmonella isolates (non-ABR and ABR strains) were treated with half concentrations of lactic acid (LA), peracetic acid (PAA), and cetylpyridinium chloride (CPC), which are used in beef processing plants to screen for tolerant strains. Six strains each from non-ABR and ABR Salmonella that were most tolerant of LA (2%), PAA (200 ppm), and CPC (0.4%) were selected. Selected strains were inoculated on surfaces of fresh beef and subjected to spray wash treatment with 4% LA, 400 ppm PAA, or 0.8% CPC for the challenge study. Tissue samples were collected before and after each antimicrobial treatment for enumeration of survivors. Spray treatment with LA, PAA, or CPC significantly reduced non-ABR Salmonella and ABR Salmonella on surfaces of fresh beef by 1.95, 1.22, and 1.33 log CFU/cm2, and 2.14, 1.45, and 1.43 log CFU/cm2, respectively. The order of effectiveness was LA > PAA = CPC. The findings also indicated that LA, PAA, and CPC were equally (P ≤ 0.05) effective against non-ABR and ABR Salmonella on surfaces of fresh beef. These data contribute to the body of work that indicates that foodborne pathogens that have acquired both antibiotic resistance and antimicrobial tolerance are still equally susceptible to meat processing antimicrobial intervention treatments.

HIGHLIGHTS

Effect of a direct-fed microbial (10-G Armor) on feedlot performance, carcass characteristics, and prevalence of Salmonella in fed-beef heifers

Crossbred beef heifers [N = 1,394; initial shrunk body weight (BW) 291 ± 9.9 kg] were used to investigate the efficacy of 10-G Armor (Life Products, Inc., Norfolk, NE; 10-G) upon feedlot performance, carcass characteristics, and fecal and subiliac lymph nodes Salmonella prevalence. Heifers were blocked by day of arrival and allocated to 1 of 20 pens (N = 70 heifers/pen) and assigned one of two treatments (10 pens/treatment) : no direct fed microbial (CON) or 2g/heifer/d of L. acidophilus, E. faecium, P. pentosaceus, L. brevis and L. plantarum respectively (Life Products, Inc., Norfolk, NE; 10-G). Twenty four animals were randomly selected from each pen for Salmonella sampling. Recto-anal mucosal swab samples (RAMS) were obtained at initial processing and harvest; subiliac lymph nodes were collected at harvest. In addition, pen surface fecal pats were collected and composited by pen (10 pats per composite, 5 composites per pen) on day 0, 52, 120 and 192. Data were analyzed as a generalized complete block design and pen served as the experimental unit. No differences were observed in live growth performance metrics (P ≥ 0.55). Yield grade distributions did not differ between treatments (P ≥ 0.62), however cattle fed 10-G tended (P = 0.06; 14.6 vs 18.9%) to have fewer USDA Select carcasses and more (P = 0.09; 73.6 vs 78.0%) USDA Choice carcasses. Cattle fed 10-G tended (P = 0.10; 9.2% vs 12.3%) to have fewer liver abscesses and had fewer (P = 0.04; 5.3 vs 8.5%) severe liver abscesses. Salmonella prevalence of RAMS did not differ between treatments at initial processing (P = 0.97; CON = 11.6%, 10-G = 11.5%) or at harvest (P = 0.91; CON = 99.0%, 10-G = 98.6%), however RAMS differed (P &lt; 0.01) in Salmonella prevalence between the two collection times. Cattle fed 10-G had a lower frequency of Salmonella positive lymph nodes (P = 0.01; CON = 15.8%, 10-G = 7.4%) than CON. However, Salmonella log (mpn/g) of lymph nodes did not differ between treatments at harvest (P = 0.34; CON = 0.73, 10-G = 0.34). These data indicate that cattle fed 10-G have decreased rates of severe liver abscesses without altering live animal performance or carcass characteristics. Supplementation of 10-G significantly reduced prevalence rate of Salmonella recovered from the subiliac lymph nodes. The factors responsible for the observed difference in the effects of 10-G on Salmonella warrants further investigation

Evidence of sheep and abattoir environment as important reservoirs of multidrug resistant Salmonella and extended-spectrum beta-lactamase Escherichia coli

The increase in antimicrobial-resistant (AMR) foodborne pathogens, including E. coli and Salmonella in animals, humans, and the environment, is a growing public health concern. Among animals, cattle, pigs, and chicken are reservoirs of these pathogens worldwide. There is a knowledge gap on the prevalence and AMR of foodborne pathogens in small ruminants (i.e., sheep and goats). This study investigates the prevalence and antimicrobial resistance of extended-spectrum beta-lactamase (ESBL) E. coli and Salmonella from sheep and their abattoir environment in North Carolina. We conducted a year-round serial cross-sectional study and collected a total of 1128 samples from sheep (n = 780) and their abattoir environment (n = 348). Sheep samples consisted of feces, cecal contents, carcass swabs, and abattoir resting area feces. Environmental samples consisted of soil samples, lairage swab, animal feed, and drinking water for animals. We used CHROMAgar EEC with 4 μg/ml of Cefotaxime for isolating ESBL E. coli, and ESBL production was confirmed by double-disk diffusion test. Salmonella was isolated and confirmed using standard methods. All of the confirmed isolates were tested against a panel of 14 antimicrobials to elucidate susceptibility profiles. The prevalence of ESBL E. coli and Salmonella was significantly higher in environmental samples (47.7% and 65.5%) compared to the sheep samples (19.5% and 17.9%), respectively (P < 0.0001). We recovered 318 ESBL E. coli and 368 Salmonella isolates from sheep and environmental samples. More than 97% (310/318) of ESBL E. coli were multidrug-resistant (MDR; resistant to ≥3 classes of antimicrobials). Most Salmonella isolates (77.2%, 284/368) were pansusceptible, and 10.1% (37/368) were MDR. We identified a total of 24 different Salmonella serotypes by whole genome sequencing (WGS). The most common serotypes were Agona (19.8%), Typhimurium (16.2%), Cannstatt (13.2%), Reading (13.2%), and Anatum (9.6%). Prevalence and percent resistance of ESBL E. coli and Salmonella isolates varied significantly by season and sample type (P < 0.0001). The co-existence of ESBL E. coli in the same sample was associated with increased percent resistance of Salmonella to Ampicillin, Chloramphenicol, Sulfisoxazole, Streptomycin, and Tetracycline. We presumed that the abattoir environment might have played a great role in the persistence and dissemination of resistant bacteria to sheep as they arrive at the abattoir. In conclusion, our study reaffirms that sheep and their abattoir environment act as important reservoirs of AMR ESBL E. coli and MDR Salmonella in the U.S. Further studies are required to determine associated public health risks.

Determining the DNA Fingerprinting Profiles of Salmonella Isolates from Raw Poultry Meats and Human Clinical Samples from the Same Geographic Area Using Pulsed-Field Gel Electrophoresis

ABSTRACT

Foods of animal origin, such as poultry, eggs, and pork, are recognized sources of Salmonella infections, but determination of the proportion of foodborne infections associated with various food sources has been challenging. In the present study, 141 Salmonella isolates recovered from 1,322 poultry product samples purchased over a 1-year period from retail stores across Seattle, WA were subtyped by pulsed-field gel electrophoresis (PFGE) using restriction enzyme XbaI. The objectives of the study were (i) to analyze the longitudinal distribution of Salmonella PFGE profiles throughout the sampling period and their clonality within and between poultry processing establishments, (ii) to determine the association between PFGE profiles of Salmonella isolates from locally distributed poultry products and those of clinical isolates submitted to the Washington State Department of Health (WA-DOH) laboratories, and (iii) to compare the PFGE profiles of Salmonella isolates from the National Antimicrobial Resistance Monitoring System (NARMS) retail meats program. During the 1-year sampling period, multiple indistinguishable PFGE patterns were found across multiple poultry processing establishments. Twelve of the 30 unique PFGE profiles of Salmonella isolates from locally purchased poultry products were indistinguishable from the PFGE profiles of clinical Salmonella isolates submitted to the WA-DOH. When the PFGE profiles from the poultry samples were compared with those found in the NARMS database, eight indistinguishable PFGE matches were found with isolates recovered from chicken breasts, ground turkey, and ground beef from multiple states. Although this study revealed some association between PFGE profiles from raw poultry products and those of clinical isolates from the same geographical area, these results do not prove that all of those clinical isolates were from infections acquired through consumption or handling of poultry.

HIGHLIGHTS

Differential Bacteriophage Efficacy in Controlling Salmonella in Cattle Hide and Soil Models

Asymptomatic Salmonella carriage in beef cattle is a food safety concern and the beef feedlot environment and cattle hides are reservoirs of this pathogen. Bacteriophages present an attractive non-antibiotic strategy for control of Salmonella in beef. In this study, four diverse and genetically unrelated Salmonella phages, Sergei, Season12, Sw2, and Munch, were characterized and tested alone and in combination for their ability to control Salmonella in cattle hide and soil systems, which are relevant models for Salmonella control in beef production. Phage Sergei is a member of the genus Sashavirus, phage Season12 was identified as a member of the Chivirus genus, Sw2 was identified as a member of the T5-like Epseptimavirus genus, and Munch was found to be a novel “jumbo” myovirus. Observed pathogen reductions in the model systems ranged from 0.50 to 1.75 log₁₀ CFU/cm² in hides and from 0.53 to 1.38 log₁₀ CFU/g in soil, with phages Sergei and Sw2 producing greater reductions (∼1 log₁₀ CFU/cm² or CFU/g) than Season12 and Munch. These findings are in accordance with previous observations of phage virulence, suggesting the simple ability of a phage to form plaques on a bacterial strain is not a strong indicator of antimicrobial activity, but performance in liquid culture assays provides a better predictor. The antimicrobial efficacies of phage treatments were found to be phage-specific across model systems, implying that a phage capable of achieving bacterial reduction in one model is more likely to perform well in another. Phage combinations did not produce significantly greater efficacy than single phages even after 24 h in the soil model, and phage-insensitive colonies were not isolated from treated samples, suggesting that the emergence of phage resistance was not a major factor limiting efficacy in this system.

Prevalence, Risk Factors, and Antibiogram of Nontyphoidal Salmonella from Beef in Ambo and Holeta Towns, Oromia Region, Ethiopia

Background

Salmonella has been recognized as a major cause of food-borne illness associated with the consumption of food of animal origin. The present cross-sectional study was conducted from December 2017 to May 2018 in Ambo and Holeta towns to assess the prevalence, risk factors, and antimicrobial susceptibility patterns of nontyphoidal Salmonella isolates from raw beef samples from abattoirs, butchers, and restaurants in Ambo and Holeta towns, Oromia region, Ethiopia.

Methods

A total of 354 beef samples were collected from abattoirs, butchers, and restaurants. Salmonella isolation and identification were carried out using standard bacteriological methods recommended by the International Organization for Standardization. Antimicrobial susceptibility testing was performed using the disk diffusion method. Besides, a structured questionnaire was used to collect sociodemographic data and potential risk factors for contamination of meat. Chi-square tests and logistic regression were used for data analyses.

Results

Of the total 354 meat samples examined, 20 (5.7%, 95% confidence interval (CI): 3.5–8.6) were positive for Salmonella. Two serotypes belonging to S. typhimurium (11 isolates) and I:4,5,12: i:- (9 isolates) were identified. The Salmonella detection rate in abattoirs, butchers, and restaurants was 4.2% (5/118), 8.5% (10/118), and 4.2% (5/118), respectively. The antimicrobial susceptibility test showed that 40%, 30%, and 20% of the Salmonella isolates were resistant to azithromycin, amoxicillin, and ceftriaxone, respectively. The odds of Salmonella isolation when meat handlers are illiterate were 7.8 times higher than those when they are educated to the level of secondary and above (P=0.032). Similarly, the likelihood of Salmonella isolation was 6.3 and 7.6 times higher among workers of butcher and restaurants, respectively, who had no training (P=0.003) and no knowledge (P=0.010) on food safety and hygiene.

Conclusions

The study showed widespread multidrug-resistant Salmonella isolates in the study areas. Therefore, raw meat consumption and indiscriminate use of antimicrobial drugs should be discouraged. Provision of food safety education for meat handlers and further surveillance of antimicrobial-resistant isolates are suggested.

Consecutive Treatments with a Multicomponent Sanitizer Inactivate Biofilms Formed by Escherichia coli O157:H7 and Salmonella enterica and Remove Biofilm Matrix

ABSTRACT

Many foodborne pathogens, including Escherichia coli O157:H7 and Salmonella enterica, can develop biofilms on contact surfaces at meat processing plants. Owing to the high tolerance of the biofilm cells associated with the three-dimensional biofilm structure and the well-expressed bacterial extracellular polymeric substances, it is a real challenge to completely inactivate and remove mature biofilms, as well as further prevent biofilm reoccurrence and pathogen survival. In the present study, we evaluated the effectiveness of consecutive treatments (10 to 120 min per treatment) by repeatedly applying a multicomponent sanitizer, based on a functional mechanism by synergistic combination of hydrogen peroxide and quaternary ammonia compounds, against biofilms formed by E. coli O157:H7 and S. enterica strains. Biofilms on stainless steel surfaces were treated with 2.5, 5, or 10% (recommended working concentration) of the sanitizer applied as a foam or liquid solution. Our results showed that the multicomponent sanitizer significantly (P < 0.05) reduced the amount of viable biofilm cells at all concentrations, as enumerable bacteria were only detected after low-concentration treatments (2.5 or 5%) with short exposure periods (10 or 20 min per treatment). Treatments with high concentrations (5 or 10%) of the sanitizer, multiple consecutive treatments (2 or 3 treatments), and sufficient exposure time (>60 min per treatment) effectively controlled pathogen survival postsanitization. Examination with a scanning electron microscope showed that treatment with the sanitizer at 5% strength significantly dissolved the connecting extracellular polysaccharide matrix and removed the majority of the biofilm matrix. No intact biofilm structure was detected after the 10% sanitizer treatment; instead, scattered individual bacteria with visibly altered cell morphology were observed. The treated bacteria exhibited indented and distorted shapes with shortened cell length and increased surface roughness, indicating severe cell injury and death. Our observations indicated that consecutive treatments with the multicomponent sanitizer was effective in inactivating E. coli O157:H7 and S. enterica biofilms and preventing pathogen reoccurrence.

HIGHLIGHTS

A review of chemical and microbial contamination in food: What are the threats to a circular food system?

A circular food system is one in which food waste is processed to recover plant nutrients and returned to the soil to enable the production of more food, rather than being diverted to landfill or incineration. The approach may be used to reduce energy and water use in food production and contribute to the sustainability of the system. Anaerobic digestion and composting are common food waste treatment technologies used to stabilize waste and produce residual materials that can replenish the soil, thus contributing to a circular food system. This approach can only be deemed safe and feasible, however, if food waste is uncontaminated or any contaminants are destroyed during treatment. This review brings together information on several contaminant classes at different stages of the food supply chain, their possible sources, and their fates during composting and digestion. The main aim is to identify factors that could impede the transition towards a safe, reliable and efficient circular food system. We investigated heavy metals, halogenated organic compounds, foodborne pathogens and antibiotic resistance genes (ARGs) in the food system and their fates during digestion and composting. Production and processing stages were identified as major entry points for these classes of contaminants. Heavy metals and foodborne pathogens pose less risk in a circular system than halogenated organics or antibiotic resistance. Given the diversity of properties among halogenated organic compounds, there is conflicting evidence about their fate during treatment. There are relatively few studies on the fate of ARGs during treatment, and these have produced variable results, indicating a need for more research to clarify their fate in the final products. Repeated land application of contaminated food waste residuals can increase the risk of accumulation and jeopardize the safety of a circular food system. Thus, careful management of the system and research into the fate of the contaminants during treatment is needed.

Microbial Communities of Meat and Meat Products: An Exploratory Analysis of the Product Quality and Safety at Selected Enterprises in South Africa

Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard identification and evaluation of potential pathogen risks from farm to the consumer. The aim of this study was to determine the microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Samples (n = 2017) were analyzed for Yersinia enterocolitica, Salmonella species, Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, and Clostridium botulinum using culture-based methods. PCR was used for confirmation of selected pathogens. Of the 2017 samples analyzed, microbial ecology was assessed for selected subsamples where next generation sequencing had been conducted, followed by the application of computational methods to reconstruct individual genomes from the respective sample (metagenomics). With the exception of Clostridium botulinum, selective culture-dependent methods revealed that samples were contaminated with at least one of the tested foodborne pathogens. The data from metagenomics analysis revealed the presence of diverse bacteria, viruses, and fungi. The analyses provide evidence of diverse and highly variable microbial communities in products of animal origin, which is important for food safety, food labeling, biosecurity, and shelf life limiting spoilage by microorganisms.

Evaluation of Autogenous Vaccine Use in Mitigating Salmonella in Lymph Nodes from Feedlot Cattle in Texas

ABSTRACT

Managing the presence of Salmonella in ground beef has been an ongoing challenge for the beef industry. Salmonella prevalence can vary regionally, seasonally, and within the animal, making the development of interventions difficult. The objective of this study was to assess the efficacy of an autogenous Salmonella vaccine in mitigating Salmonella in lymph nodes (LNs) of feedlot cattle. An autogenous vaccine was developed using the most common Salmonella enterica serovars (Salmonella Kentucky, Salmonella Anatum, Salmonella Muenchen, Salmonella Montevideo, and Salmonella Mbandaka) identified from cattle managed at a South Texas feedlot with historically high Salmonella prevalence. Fifty-five heifers were selected for even distribution across five groups: (i) BASE, which received no autogenous vaccinations and were harvested after the stocker stage, (ii) CNTRL, which received no autogenous vaccinations, (iii) FARM, which received autogenous vaccinations at the ranch only, (iv) SPLIT, which received autogenous vaccinations at both the ranch and feedlot, and (v) YARD, which received vaccinations at the feedlot only. One heifer each from the BASE and CNTRL groups did not complete the study. All treatment groups except BASE were harvested after reaching market weight. Left and right superficial cervical and subiliac LNs from each carcass were collected and analyzed for Salmonella presence, and positive samples were serotyped. No salmonellae were recovered from LNs derived from BASE, FARM, SPLIT, or YARD groups. Cattle in the BASE group were expected to have a low occurrence of Salmonella based on previous research. However, the percentage of Salmonella-positive animals in the CNTRL group was 20.0% (2 of 10), which is lower than expected based on historical data from the same feeding location. There could be several causes of decreased Salmonella presence in the LNs of control cattle, creating an opportunity for future investigation into the development of preharvest interventions to combat Salmonella in feedlots.

HIGHLIGHTS

Chicken cecal DNA methylome alteration in the response to Salmonella enterica serovar Enteritidis inoculation

BACKGROUND

Salmonella enterica serovar Enteritidis (SE) is one of the pathogenic bacteria, which affects poultry production and poses a severe threat to public health. Chicken meat and eggs are the main sources of human salmonellosis. DNA methylation is involved in regulatory processes including gene expression, chromatin structure and genomic imprinting. To understand the methylation regulation in the response to SE inoculation in chicken, the genome-wide DNA methylation profile following SE inoculation was analyzed through whole-genome bisulfite sequencing in the current study.

RESULTS

There were 185,362,463 clean reads and 126,098,724 unique reads in the control group, and 180,530,750 clean reads and 126,782,896 unique reads in the inoculated group. The methylation density in the gene body was higher than that in the upstream and downstream regions of the gene. There were 8946 differentially methylated genes (3639 hypo-methylated genes, 5307 hyper-methylated genes) obtained between inoculated and control groups. Methylated genes were mainly enriched in immune-related Gene Ontology (GO) terms and metabolic process terms. Cytokine-cytokine receptor interaction, TGF-beta signaling pathway, FoxO signaling pathway, Wnt signaling pathway and several metabolism-related pathways were significantly enriched. The density of differentially methylated cytosines in miRNAs was the highest. HOX genes were widely methylated.

CONCLUSIONS

The genome-wide DNA methylation profile in the response to SE inoculation in chicken was analyzed. SE inoculation promoted the DNA methylation in the chicken cecum and caused methylation alteration in immune- and metabolic- related genes. Wnt signal pathway, miRNAs and HOX gene family may play crucial roles in the methylation regulation of SE inoculation in chicken. The findings herein will deepen the understanding of epigenetic regulation in the response to SE inoculation in chicken.

Rapid estimation of Salmonella enterica contamination level in ground beef - Application of the time-to-positivity method using a combination of molecular detection and direct plating

Little progress has been made in decreasing the incidence rate of salmonellosis in the US over the past decade. Mitigating the contribution of contaminated raw meat to the salmonellosis incidence rate requires rapid methods for quantifying Salmonella, so that highly contaminated products can be removed before entering the food chain. Here we evaluated the use of Time-to-Positivity (TTP) as a rapid, semi-quantitative approach for estimating Salmonella contamination levels in ground beef. Growth rates of 14 Salmonella strains (inoculated at log 1 to -2 CFU/g) were characterized in lean ground beef mTSB enrichments and time-to-detection was determined using culture and molecular detection methods. Enrichments were sampled at five timepoints and results were used to construct a prediction model of estimated contamination level by TTP (superscript indicates time in hours) defined as TTP⁴: ≥5 CFU/g; TTP⁶: ≤5, ≥1 CFU/g; TTP⁸: ≤1, ≥0.01 CFU/g; with samples negative at 8 h estimated ≤0.01 CFU/g. Model performance measures showed high sensitivity (100%) and specificity (83% and 93% for two detection methods) for samples with a TTP⁴, with false negative rates of 0%.

Emerging Meat Processing Technologies for Microbiological Safety of Meat and Meat Products

A consumer trend toward convenient, minimally processed meat products has exerted tremendous pressure on meat processors to ensure the safety of meat and meat products without compromising product quality and the meeting of consumer demands. This has led to challenges in developing and implementing novel processing technologies as the use of newer technologies may affect consumer choices and opinions of meat and meat products. Novel technologies adopted by the meat industry for controlling foodborne pathogens of significant public health implications, gaps in the technologies, and the need for scaling up technologies that have been proven to be successful in research settings or at the pilot scale will be discussed. Novel processing technologies in the meat industry warrant microbiological validation prior to becoming commercially viable options and enacting infrastructural changes. This review presents the advantages and shortcomings of such technologies and provides an overview of technologies that can be successfully implemented and streamlined in existing processing environments.

Antibiotic resistance and biofilm formation ability of Salmonella serotypes isolated from beef, mutton, and meat contact surfaces at retail

In this study, Salmonella isolates recovered from meat (beef and mutton) and meat contact surfaces at retail were investigated to determine their serotype, antibiotic resistance, and biofilm formation ability. Salmonella was found in 29 (24.17%) samples out of 120 samples including 14/50 (28%) of beef, 10/40 (25%) of mutton, and 5/30 (16.67%) of meat contact surfaces. Seven isolates were identified as S. Enteritidis, three as S. Typhimurium, and two as S. Typhi, while the rest of the isolates were considered as other Salmonella spp. All of the isolates were resistant to at least one antimicrobial agent and 48.27% of them were identified as multidrug-resistant (MDR) Salmonella. All (100%) of meat contact surfaces isolates, 42.8% of beef isolates, and 30% of mutton isolates were found to be MDR Salmonella. Resistance to nalidixic acid (100%), tetracycline (79.3%), and sulphamethoxazole/trimethoprim (44.8%) were observed. The gyrA gene was detected in 19 of 29 isolates, but tetA was found in one isolate. All of the serotypes were able to form biofilm (75.86 % moderate and 24.14 % strong) and S. Enteritidis was the strongest biofilm producer. The findings indicated that the majority of Salmonella isolates in this study were MDR and biofilm producer. Then, safety measures such as cleaning and disinfection must be taken to control Salmonella and promote public health. PRACTICAL APPLICATION: The present study provides useful information on the prevalence of Salmonella serotypes in meat and meat contact surfaces and their antibiotic resistance patterns as well as biofilm formation capacities. Improving hygiene practices in livestock, slaughterhouses, and at retails may reduce the risk of meat contamination to Salmonella. Meanwhile, high levels of antibiotic resistance in Salmonella isolates emphasized on the improper use of antibiotics.

Translocation of Orally Inoculated Salmonella Following Mild Immunosuppression in Holstein Calves and the Presence of the Salmonella in Ground Beef Samples

The objective of this study was to determine if immunosuppression through daily dexamethasone (DEX) infusion altered Salmonella translocation from the gastrointestinal tract. Weaned Holstein steers (n = 20; body weight [BW] = 102 ± 2.7 kg) received DEX (n = 10; 0.5 mg/kg BW) or saline (control [CON]; n = 10;) for 4 days (from day -1 to 2) before oral inoculation of naldixic acid-resistant Salmonella enterica Typhimurium (SAL; 3.4 × 10⁶ colony-forming units [CFU]/animal) on day 0. Fecal swabs were obtained daily, and blood was collected daily for hematology. At harvest (day 5), ileum, cecal fluid, lymph nodes (ileocecal, mandibular, popliteal, and subscapular), and synovial (stifle, coxofemoral, and shoulder) samples were collected for isolation of the inoculated strain of SAL. White blood cell (WBC) and neutrophil concentrations were elevated (p < 0.01) in DEX calves following each administration event. Following inoculation, 100% of DEX calves shed the experimental strain of SAL for all 5 days, 90% of CON calves shed from day 1 to 3, and 100% of CON calves shed from day 4 to 5. Greater (p < 0.01) concentrations of SAL were quantified from the cecum of DEX calves (3.86 ± 0.37 log CFU/g) compared with CON calves (1.37 ± 0.37 log CFU/g). There was no difference in SAL concentrations between DEX and CON calves in ileal tissue (p = 0.07) or ileocecal (p = 0.57), mandibular (p = 0.12), popliteal (p = 0.99), or subscapular (p = 0.83) lymph nodes. Of the stifle samples collected, 3.3% were positive for SAL, highlighting a contamination opportunity during hindquarter breakdown. While more research is needed to elucidate the interactions of immunosuppression and pathogen migration patterns, these data confirm that orally inoculated SAL can translocate from the gastrointestinal tract and be harbored in atypical locations representing a food safety risk.

Effectiveness and Functional Mechanism of a Multicomponent Sanitizer against Biofilms Formed by Escherichia coli O157:H7 and Five Salmonella Serotypes Prevalent in the Meat Industry

ABSTRACT

Biofilm formation by Escherichia coli O157:H7 and Salmonella enterica at meat processing plants poses a potential risk of meat product contamination. Many common sanitizers are unable to completely eradicate biofilms formed by these foodborne pathogens because of the three-dimensional biofilm structure and the presence of bacterial extracellular polymeric substances (EPSs). A novel multifaceted approach combining multiple chemical reagents with various functional mechanisms was used to enhance the effectiveness of biofilm control. We tested a multicomponent sanitizer consisting of a quaternary ammonium compound (QAC), hydrogen peroxide, and the accelerator diacetin for its effectiveness in inactivating and removing Escherichia coli O157:H7 and Salmonella enterica biofilms under meat processing conditions. E. coli O157:H7 and Salmonella biofilms on common contact surfaces were treated with 10, 20, or 100% concentrations of the multicomponent sanitizer solution for 10 min, 1 h, or 6 h, and log reductions in biofilm mass were measured. Scanning electron microscopy (SEM) was used to directly observe the effect of sanitizer treatment on biofilm removal and bacterial morphology. After treatment with the multicomponent sanitizer, viable E. coli O157:H7 and Salmonella biofilm cells were below the limit of detection, and the prevalence of both pathogens was low. After treatment with a QAC-based control sanitizer, surviving bacterial cells were countable, and pathogen prevalence was higher. SEM analysis of water-treated control samples revealed the three-dimensional biofilm structure with a strong EPS matrix connecting bacteria and the contact surface. Treatment with 20% multicomponent sanitizer for 10 min significantly reduced biofilm mass and weakened the EPS connection. The majority of the bacterial cells had altered morphology and compromised membrane integrity. Treatment with 100% multicomponent sanitizer for 10 min dissolved the EPS matrix, and no intact biofilm structure was observed; instead, scattered clusters of bacterial aggregates were detected, indicating the loss of cell viability and biofilm removal. These results indicate that the multicomponent sanitizer is effective, even after short exposure with dilute concentrations, against E. coli O157:H7 and S. enterica biofilms.

HIGHLIGHTS

Viability of Shiga Toxin-Producing Escherichia coli, Salmonella, and Listeria monocytogenes within Plant versus Beef Burgers during Cold Storage and following Pan Frying

ABSTRACT

The viability of Shiga toxin-producing Escherichia coli (STEC), Salmonella, and Listeria monocytogenes within plant- and beef-based burgers was monitored during storage and cooking. When inoculated (ca. 3.5 log CFU/g) into 15-g portions of plant- or beef-based burgers, levels of STEC and Salmonella decreased slightly (≤0.5-log decrease) in both types of burgers when stored at 4°C, but increased ca. 2.4 and 0.8 log CFU/g, respectively, in plant-based burgers but not beef-based burgers (≤1.2-log decrease), after 21 days at 10°C. For L. monocytogenes, levels increased by ca. 1.3 and 2.6 log CFU/g in plant burgers after 21 days at 4 and 10°C, respectively, whereas pathogen levels decreased slightly (≤0.9-log decrease) in beef burgers during storage at 4 and 10°C. Regarding cooking, burgers (ca. 114 g each) were inoculated with ca. 7.0 log CFU/g STEC, Salmonella, or L. monocytogenes and cooked in a sauté pan. Cooking plant- or beef-based burgers to 62.8°C (145°F), 68.3°C (155°F), or 73.9°C (165°F) delivered reductions ranging from ca. 4.7 to 6.8 log CFU/g for STEC, ca. 4.4 to 7.0 log CFU/g for L. monocytogenes, and ca. 3.5 to 6.7 log CFU/g for Salmonella. In summary, the observation that levels of all three pathogens increased by ca. 1.0 to ca. 2.5 log CFU/g in plant-based burgers when stored at an abusive temperature (10°C) highlights the importance of proper storage (4°C) to lessen risk. However, because all three pathogens responded similarly to heat in plant-based as in beef-based burgers, well-established cooking parameters required to eliminate STEC, Salmonella, or L. monocytogenes from ground beef should be as effective for controlling cells of these same pathogens in a burger made with plant-sourced protein.

HIGHLIGHTS

Molecular Characterization Of Pathogenic Salmonella Spp From Raw Beef In Karachi, Pakistan

The aim of the present study was to estimate the prevalence of Salmonella and investigate the dominant serovars distribution in raw beef and to screen the isolated serovars for the prescense of beta-lactamases and virulence genes. A total of 150 samples of raw beef sold at butcher shops (n = 75) and supermarkets (n = 75) in Karachi city were collected (50 samples each from muscles, lymph nodes, and minced beef). The samples were cultured according to the ISO-6579-1guidlines. The overall prevalence of Salmonella strains was found to be 21.34%. A total of 56 isolates of Salmonella belonging to four serogroups (Salmonella Pullorum, Salmonella Enteritidis, Salmonella Typhimurium and Salmonella Choleraesuis) were isolated from beef muscles (12%), lymph nodes (24%) and minced beef (28%) samples collected from butcher shops (av. 21.34%). No Salmonella was detected in beef samples collected from supermarkets. S. Enteritidis contamination was highest (37.5 %), followed by S. Choleraesuis (30.4%), S. Pullorum (19.6%) and S. Typhimurium (12.5 %). Antibiotic susceptibility testing revealed that Salmonella isolates were highly resistant to Oxytetracycline (90%), Ampicillin (90.5%), Amoxicillin (81.1%), Tetracycline (76%), Neomycin, (79.8%) and Ciprofloxacin (61.4%). The Salmonella isolates examined were more susceptible to the Cephalosporin antibiotics such as Cefixime (43.2%), Cefepime (48.2) and Cefoxitin (49.8%). PCR based screening of blaTEM, blaCTX-M and blaSHV revealed that blaCTX-M and blaTEM were the dominant resistant genes in S. Enteritidis and S. Typhimurium followed by S. Pullorum and S. Choleraesuis whereas blaSHV was the least detected beta-lactamase in Salmonella isolates. Virulence genes screening revealed that at least five genes were present in all the serovars, highest being present in S. Enteritidis (12/17) and S. Typhimurium (12/17). S. Cholerasuis (5/17) carried the least number of virulence genes followed by S. Pullorum (6/17). The present data suggest that beef samples from butcher shops of Karachi city are heavily contaminated with MDR Salmonella. The presence of resistance and virulence genes in MDR strains of Salmonella may play a significant role in transmission and development of Salmonella infection in humans.

Evaluation of Bactericidal Effects of Phenyllactic Acid on Escherichia coli O157:H7 and Salmonella Typhimurium on Beef Meat

Bactericidal effects of various concentrations of phenyllactic acid on Shiga toxin-producing Escherichia coli (STEC), including E. coli O157:H7, O26:H11, O103:H2, and O121:H19, and on Salmonella Typhimurium DT104 in pure culture and microplates assays were studied. Beef cuts were surface sprayed with phenyllactic acid or lactic acid for inactivation of E. coli O157:H7 and Salmonella Typhimurium. The 1.5% phenyllactic acid inactivated all inoculated E. coli O157:H7, O26:H11, O103:H2, and O121:H19 and Salmonella Typhimurium DT104 (>6-log reduction) within 1 min of contact at 21°C, whereas 1.5% lactic acid did not result in microbial reduction. Microplate assays (for STEC and Salmonella Typhimurium DT104 at 10 to 100 CFU per well) indicated that concentrations of 0.25% phenyllactic acid or 0.25% lactic acid inhibited the growth of STEC and Salmonella Typhimurium DT104 incubated at 37°C for 24 h. Treatment of beef with 1.5% lactic acid or 1.5% phenyllactic acid reduced E. coli O157:H7 by 0.22 and 0.38 log CFU/cm², respectively, within 5 min and reduced Salmonella Typhimurium DT104 by 0.12 and 0.86 log CFU/cm², respectively. When meat treated with 1.5% phenyllactic acid was frozen at -20°C, inactivation of E. coli O157 and Salmonella Typhimurium DT104 was enhanced by 1.06 and 1.46 log CFU/cm², respectively. Thus, treatment of beef with 1.5% phenyllactic acid significantly reduced the population of E. coli O157:H7 and Salmonella.

Prevalence and Antibiotic Resistance of Salmonella Enteritidis and Salmonella Typhimurium in Ground Beef and Meatball Samples in Samsun, Turkey

The aims of this study were to evaluate the prevalence of Salmonella spp., including S. Enteritidis and S. Typhimurium, their antibiotic resistance profiles, and the presence/absence of class 1 integron (intI1) in 50 raw ground beef and 50 raw, meatball samples collected in the Samsun Province, Turkey. For the detection of Salmonella, conventional culture technique and PCR assay were used. The antibiotic resistance profiles of the isolates against nine antibiotics were tested. Salmonella spp. was detected in 20 (n = 86 isolates) samples, namely 12 ground beef and 8 meatball samples. Salmonella Enteritidis (n = 12; 24 isolates) or S. Typhimurium (n = 3; 6 isolates) was detected in 15 (75.00%, n = 30 isolates) samples. At least one species-specific gene (oriC or invA) was detected in the isolates. All isolates were sensitive to two of the third-generation cephalosporins and also nalidixic acid. There was a different level of multidrug resistance (MDR) between S. Enteritidis and Typhimurium isolates. Class 1 integron was detected in four samples (n = 7 isolates); seven isolates were S. Enteritidis and four out of the seven S. Enteritidis isolates were also MDR. In conclusion, the presence of Salmonella, particularly S. Enteritidis and S. Typhimurium, in ground beef and meatballs may cause foodborne infections. The presence of antibiotic-resistant Salmonella and S. Enteritidis with the Cls1integron is important for horizontal antibiotic gene transfer.

Prevalence and Characterization of Salmonella Present during Veal Harvest

Beef and veal products have been vehicles implicated in the transmission of Salmonella enterica, a gastroenteritis-causing bacteria. Recent regulatory samples collected from veal have indicated bob veal, or calves harvested within days of birth, have higher rates of Salmonella than samples collected from formula-fed veal, or calves raised 20 weeks on milk replacer formula before harvest. To investigate this problem, we collected samples from veal calf hides, preevisceration carcasses, and final carcasses at five veal processors that harvested bob or formula-fed veal or both. Prevalence and concentrations of Salmonella were determined, and then the isolates were characterized for serovar and antibiotic susceptibility. Salmonella was more prevalent (P < 0.05) among bob veal than formula-fed veal hides, preevisceration carcasses, and final carcass (84.2 versus 15.6%, 62.8 versus 10.1%, and 12.0 versus 0.4%, respectively). Concentrations of Salmonella could be estimated by using regression order statistics on hides and preevisceration carcasses at two veal plants, with one harvesting bob veal and the other bob and formula-fed veal. The concentration of Salmonella on bob veal hides at the plants was 1.45 ± 0.70 and 2.04 ± 1.00 log CFU/100 cm², greater (P < 0.05) than on formula-fed veal hides, which was 1.10 ± 1.51 log CFU/100 cm². Concentrations on carcasses, however, were very low. Seventeen Salmonella serovars were identified among 710 isolates. Salmonella serovars London, Cerro, and Muenster were most common to bob veal and made up 50.7, 18.7, and 6.3% of the isolates, respectively, while serovar Montevideo (6.8% of isolates) was most common to formula-fed veal. Although bob veal had increased prevalence and concentrations of Salmonella, one group of formula-fed veal was found to harbor human disease-related antibiotic-resistant Salmonella serovars Heidelberg and the monophasic variant of Typhimurium (1,4,[5],12:i:-). Veal processors have made changes to improve the safety of veal, but further efforts are necessary from both bob and formula-fed veal to address Salmonella.

Assessment of Salmonella Prevalence in Lymph Nodes of U.S. and Mexican Cattle Presented for Slaughter in Texas

Foodborne salmonellosis has been traced to undercooked ground beef and other beef products in the past, and peripheral lymph node (LN) presence in the fatty tissues of beef carcasses is one possible source of Salmonella contamination. Researchers have previously reported higher rates of Salmonella prevalence in LNs from cattle raised and harvested in Mexico compared with rates typically observed from cattle harvested in the United States. With cattle of Mexican origin comprising the majority of U.S. live cattle imports, the objectives of this study were designed to determine whether Salmonella prevalence in LNs differed (i) between cattle of Mexican and U.S. origins when exposed to the same South Texas feeding operation and (ii) between warm and cool seasons. To meet these objectives, paired (left and right sides) subiliac LNs ( n = 800 LNs; n = 400 pooled samples) were collected from 100 carcasses per origin (Mexico and United States) per season (cool, December to January; warm, July to September). Overall, Salmonella prevalence in LN samples was 52.0% (208 of 400). No difference ( P = 0.4836) was seen in Salmonella prevalence as a function of origin, with 54.0% (108 of 200) and 50.0% (100 of 200) of LN samples returning Salmonella-positive results from cattle of Mexican and U.S. origin, respectively. Salmonella prevalence differed ( P = 0.0354) between seasons, with 46.5% (93 of 200) of cool and 57.5% (115 of 200) of warm season samples returning Salmonella-positive results. Serotyping of PCR-confirmed positive samples resulted in 14 different serovars being identified, with Cerro (21.6%), Anatum (19.7%), Muenchen (17.8%), Montevideo (14.4%), and Kentucky (12.0%) comprising the majority of serovars. These results suggest that factors other than cattle origin may be impacting Salmonella prevalence rates in bovine LNs and that additional research is needed to better understand the role of environment and management-related factors on Salmonella prevalence in bovine LNs.

Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle

Background

Salmonella enterica subspecies enterica is an animal and zoonotic pathogen of global importance. Cattle are a significant reservoir of human non-typhoidal salmonellosis and can suffer enteric and systemic disease owing to the ability of Salmonella to survive within the bovine lymphatic system and intestines. Contamination of food can occur due to the incorporation of contaminated peripheral lymph nodes or by direct contamination of carcasses with gut contents. It is essential to understand the mechanisms used by Salmonella to enter and persist within the bovine lymphatic system and how they differ from those required for intestinal colonization to minimize zoonotic infections.

Results

Transposon-directed insertion site sequencing (TraDIS) was applied to pools of mutants recovered from mesenteric lymph nodes (MLNs) draining the distal ileum of calves after oral inoculation with a library of 8550 random S. Typhimurium mini-Tn5Km2 mutants in pools of 475 mutants per calf. A total of 8315 mutants representing 2852 different genes were detected in MLNs and their in vivo fitness was calculated. Using the same improved algorithm for analysis of transposon-flanking sequences, the identity and phenotype of mutants recovered from the distal ileal mucosa of the same calves was also defined, enabling comparison with previously published data and of mutant phenotypes across the tissues. Phenotypes observed for the majority of mutants were highly significantly correlated in the two tissues. However, 32 genes were identified in which transposon insertions consistently resulted in differential fitness in the ileal wall and MLNs, suggesting niche-specific roles for these genes in pathogenesis. Defined null mutations affecting ptsN and spvC were confirmed to result in tissue-specific phenotypes in calves, thus validating the TraDIS dataset.

Conclusions

This validation of the role of thousands of Salmonella genes and identification of genes with niche-specific roles in a key target species will inform the design of control strategies for bovine salmonellosis and zoonotic infections, for which efficacious and cross-protective vaccines are currently lacking.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5319-0) contains supplementary material, which is available to authorized users.

Herd-level prevalence of Salmonella Dublin among New York dairy farms based on antibody testing of bulk tank milk

Salmonella Dublin is an important cause of salmonellosis among dairy cattle and poses a considerable threat to public health. This serotype is increasingly being identified among bovine Salmonella isolates from clinical samples in the north-eastern United States, and these isolates are generally multidrug resistant. Our objective was to estimate the herd-level prevalence of Salmonella Dublin among dairy cattle herds throughout New York. Bulk tank milk samples from nearly all commercial dairy herds in New York were collected from milk quality testing laboratories during the first half of 2013. Antibody testing of bulk tank milk was performed using a Salmonella Dublin ELISA kit. Samples representing 4,896 commercial dairies were collected, and antibodies against Salmonella Dublin were detected in 46 herds (0.9%; 95% CI, 0.7%-1.3%). Given the herd-level sensitivity of ELISA testing for Salmonella Dublin in bulk tank milk at a single timepoint, this approach presumably underestimated the true prevalence. Some Salmonella Dublin-positive herds had both positive and negative bulk tanks at the same sampling time, indicating that herds with multiple tanks should test all of them when using this ELISA. Further research is needed to better understand the epidemiologic features of Salmonella Dublin in the north-eastern United States, including risk factors for introduction into dairy herds and principal transmission pathways.

Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association

Salmonella enterica serovar Montevideo has been linked to recent foodborne illness outbreaks resulting from contamination of products such as fruits, vegetables, seeds and spices. Studies have shown that Montevideo also is frequently associated with healthy cattle and can be isolated from ground beef, yet human salmonellosis outbreaks of Montevideo associated with ground beef contamination are rare. This disparity fuelled our interest in characterizing the genomic differences between Montevideo strains isolated from healthy cattle and beef products, and those isolated from human patients and outbreak sources. To that end, we sequenced 13 Montevideo strains to completion, producing high-quality genome assemblies of isolates from human patients (n=8) or from healthy cattle at slaughter (n=5). Comparative analysis of sequence data from this study and publicly available sequences (n=72) shows that Montevideo falls into four previously established clades, differentially occupied by cattle and human strains. The results of these analyses reveal differences in metabolic islands, environmental adhesion determinants and virulence factors within each clade, and suggest explanations for the infrequent association between bovine isolates and human illnesses.

Antimicrobial resistance trends in fecal Salmonella isolates from northern California dairy cattle admitted to a veterinary teaching hospital, 2002-2016

Nontyphoidal Salmonella infections contribute to approximately 1.2 million annual illnesses in the United States. Historical and recent outbreaks have been associated with dairy products, ground beef, and direct contact with cattle. Salmonella antimicrobial resistance (AMR) is a serious concern that can reduce successful treatment of infections, increasing recovery time, medical costs, and mortality rates in humans and animals. This highlights the need to track AMR in Salmonella isolated from cattle to improve treatment plans, manage trends in AMR, and prevent future AMR development. A total of 242 Salmonella isolates were retrieved from 9,162 cattle fecal samples submitted to the University of California, Davis Veterinary Medical Teaching Hospital from 2002 to 2016. These isolates were tested for antimicrobial susceptibility using a standardized broth dilution panel. Multidrug resistance (MDR) to three or more classes of antimicrobials was observed in 50.8% of isolates, and the most common MDR pattern was amoxicillin-ampicillin-cefoxitin-ceftiofur-ceftriaxone-chloramphenicol-streptomycin-tetracycline (23.2%). There were significantly greater odds for antimicrobial resistance to aminoglycosides (OR: 2.03, 95% CI: 1.1–3.7), penicillins (OR: 1.87, 95% CI: 1.007–3.5), and tetracyclines (OR: 1.87, 95% CI: 1.017–3.4) for the 2002–2009 period when compared to the 2010–2016 period. The most prevalent MDR serotypes were Newport (100% MDR, n = 52), Typhimurium (100%, n = 20), and Dublin (71% MDR, n = 46). Risk factors associated with higher odds for isolating MDR Salmonella included isolates from calves when compared to adult cattle (OR: 22.0; 95% C.I.: 3.9–125.7), and isolates obtained from cattle suspect of having salmonellosis versus from the infectious disease control surveillance program (OR:13.7; 95%C.I.: 2.8–66.8). Despite a temporal trend for reduced AMR to most antimicrobial drug classes, a lack of this observed in the 2002–2009 period when compared to the 2010–2016 period for important drug classes such as cephalosporins (OR: 1.6, 95% CI: 0.87–3.1), and a trend for temporal increase in resistant to quinolones drugs (P value 0.004) highlight the relevance of AMR surveillance in cattle with Salmonella infections with the aim of targeting future prophylactic interventions.

Quantifying the Survival of Multiple Salmonella enterica Serovars In Vivo via Massively Parallel Whole-Genome Sequencing To Predict Zoonotic Risk

Salmonella enterica is an animal and zoonotic pathogen of worldwide importance. Salmonella serovars that differ in their host and tissue tropisms exist. Cattle are an important reservoir of human nontyphoidal salmonellosis, and contaminated bovine peripheral lymph nodes enter the food chain via ground beef. The relative abilities of different serovars to survive within the bovine lymphatic system are poorly understood and constrain the development of control strategies. This problem was addressed by developing a massively parallel whole-genome sequencing method to study mixed-serovar infections in vivo. Salmonella serovars differ genetically by naturally occurring single nucleotide polymorphisms (SNPs) in certain genes. It was hypothesized that these SNPs could be used as markers to simultaneously identify serovars in mixed populations and quantify the abundance of each member in a population. The performance of the method was validated in vitro using simulated pools containing up to 11 serovars in various proportions. It was then applied to study serovar survival in vivo in cattle challenged orally with the same 11 serovars. All the serovars successfully colonized the bovine lymphatic system, including the peripheral lymph nodes, and thus pose similar risks of zoonosis. This method enables the fates of multiple genetically unmodified strains to be evaluated simultaneously in a single animal. It could be useful in reducing the number of animals required to study mixed-strain infections and in testing the cross-protective efficacy of vaccines and treatments. It also has the potential to be applied to diverse bacterial species which possess shared but polymorphic alleles.

IMPORTANCE While some Salmonella serovars are more frequently isolated from lymph nodes rather than the feces and environment of cattle, the relative abilities of serovars to survive within the lymphatic system of cattle remain ill defined. A sequencing-based method which used available information from sequenced Salmonella genomes to study the dynamics of mixed-serovar infections in vivo was developed. The main advantages of the method include the simultaneous identification and quantification of multiple strains without any genetic modification and minimal animal use. This approach could be used in vaccination trials or in epidemiological surveys where an understanding of the dynamics of closely related strains of a pathogen in mixed populations could inform the prediction of zoonotic risk and the development of intervention strategies.

Salmonella in Peripheral Lymph Nodes of Healthy Cattle at Slaughter

To more fully characterize the burden of Salmonella enterica in bovine peripheral lymph nodes (PLN), PLN (n = 5,450) were collected from healthy cattle at slaughter in 12 commercial abattoirs that slaughtered feedlot-fattened (FF) cattle exclusively (n = 7), cattle removed (or culled) from breeding herds (n = 3), or both FF and cull cattle (n = 2). Qualitative and quantitative methods were used to estimate prevalence and concentration of Salmonella in PLN. Isolates were subjected to a variety of phenotypic, serological, and molecular assays. Overall, Salmonella prevalence in PLN from FF and cull cattle was 7.1 and 1.8%. However, burden varied by season in that observed prevalence in PLN collected in cooler or warmer seasons was 2.4 and 8.2%, respectively. Prevalence in PLN from cull cattle in the southwest region of the US was 2.1 and 1.1% for cool and warm seasons, respectively; however, prevalence in FF PLN was far greater in that it was 6.5 and 31.1%, respectively. Salmonella was recovered from 289 (5.6%) PLN and 2.9% (n = 160) of all PLN tested had quantifiable concentrations that varied from 1.6 to 4.9 log₁₀ colony forming units/PLN. The most common serotypes isolated from PLN were Montevideo (26.9%), Lille (14.9%), Cerro (13.0%), Anatum (12.8%), and Dublin (6.9%). In all, 376 unique isolates were collected from the 289 Salmonella-positive PLN. Antimicrobial susceptibility testing revealed the majority (80.6%) of these isolates were pansusceptible; however, 10.7% of isolates were found to be resistant to two or more antimicrobial classes. We were able to document an observed increased in prevalence of Salmonella in PLN during the warmer season, particularly in FF cattle from the southwest region of the US. The mechanisms underlying the observed association between season, region, and production source have yet to be elucidated. Nevertheless, these findings increase our understanding of the sources of contamination of beef products and shed light on transmission dynamics that may be useful in targeting these sources.

Occurrence of Salmonella enterica and Escherichia coli in raw chicken and beef meat in northern Egypt and dissemination of their antibiotic resistance markers

BACKGROUND

The global incidence of foodborne infections and antibiotic resistance is recently increased and considered of public health concern. Currently, scarcely information is available on foodborne infections and ESBL associated with poultry and beef meat in Egypt.

METHODS

In total, 180 chicken and beef meat samples as well as internal organs were collected from different districts in northern Egypt. The samples were investigated for the prevalence and antibiotic resistance of Salmonella enterica serovars and Escherichia coli. All isolates were investigated for harbouring class 1 and class 2 integrons.

RESULTS

Out of 180 investigated samples 15 S. enterica (8.3%) and 21 E. coli (11.7%) were isolated and identified. S. enterica isolates were typed as 9 S. Typhimurium (60.0%), 3 S. Paratyphi A (20.0%), 2 S. Enteritidis (13.3%) and 1 S. Kentucky (6.7%). Twenty-one E. coli isolates were serotyped into O1, O18, O20, O78, O103, O119, O126, O145, O146 and O158. The phenotypic antibiotic resistance profiles of S. enterica serovars to ampicillin, cefotaxime, cefpodoxime, trimethoprim/sulphamethoxazole and tetracycline were 86.7, 80.0, 60.0, 53.3 and 40.0%, respectively. Isolated E. coli were resistant to tetracycline (80.9%), ampicillin (71.4%), streptomycin, trimethoprim/sulphamethoxazole (61.9% for each) and cefotaxime (33.3%). The dissemination of genes coding for ESBL and AmpC β-lactamase in S. enterica isolates included bla_CTX-M (73.3%), bla_TEM (73.3%) and bla_CMY (13.3%). In E. coli isolates bla_TEM, bla_CTX-M and bla_OXA were identified in 52.4, 42.9 and 14.3%, respectively. The plasmid-mediated quinolone resistance genes identified in S. enterica were qnrA (33.3%), qnrB (20.0%) and qnrS (6.7%) while qnrA and qnrB were detected in 33.3% of E. coli isolates. Class 1 integron was detected in 13.3% of S. enterica and in 14.3% of E. coli isolates. Class 2 integron as well as the colistin resistance gene mcr-1 was not found in any of E. coli or S. enterica isolates.

CONCLUSIONS

This study showed high prevalence of S. enterica and E. coli as foodborne pathogens in raw chicken and beef meat in Nile Delta, Egypt. The emergence of antimicrobial resistance in S. enterica and E. coli isolates is of public health concern in Egypt. Molecular biological investigation elucidated the presence of genes associated with antibiotic resistance as well as class 1 integron in S. enterica and E. coli.

Biofilm Formation, Antimicrobial Resistance, and Sanitizer Tolerance of Salmonella enterica Strains Isolated from Beef Trim

In the beef industry, product contamination by Salmonella enterica is a serious public health concern, which may result in human infection and cause significant financial loss due to product recalls. Currently, the precise mechanism and pathogen source responsible for Salmonella contamination in commercial establishments are not well understood. We characterized 89 S. enterica strains isolated from beef trim with respect to their biofilm-forming ability, antimicrobial resistance, and biofilm cell survival/recovery growth after sanitizer exposure. A total of 28 Salmonella serovars was identified within these strains. The most common serovars identified were Anatum, Dublin, Montevideo, and Typhimurium, with these accounting for nearly half of the total strains. The vast majority (86%) of the strains was able to develop strong biofilms, and the biofilm-forming ability was highly strain dependent and related to cell surface expression of extracellular polymeric structures. These strains also demonstrated strong tolerance to quaternary ammonium chloride (QAC) and chlorine dioxide (ClO₂), but were more sensitive to chlorine treatment. Sanitizer tolerance and bacterial postsanitization recovery growth were closely associated with strains' biofilm-forming ability. Thirty percent of the examined strains were found resistant to multiple antimicrobial agents and the resistance phenotypes were serovar associated, but not related to strains' biofilm-forming ability. Pulsed-field gel electrophoresis analysis tended to group strains by serovar rather than by biofilm-forming ability. Collectively, these data indicate that the strong biofilm formers of certain S. enterica strains/serovars possess significant potential for causing meat product contamination in meat processing environment.

Rapid Detection and Classification of Salmonella enterica Shedding in Feedlot Cattle Utilizing the Roka Bioscience Atlas Salmonella Detection Assay for the Analysis of Rectoanal Mucosal Swabs

With an increasing focus on preharvest food safety, rapid methods are required for the detection and quantification of foodborne pathogens such as Salmonella enterica in beef cattle. We validated the Atlas Salmonella Detection Assay (SEN), a nucleic acid amplification technology that targets Salmonella rRNA, for the qualitative detection of S. enterica with sample enrichment using immunomagnetic separation as a reference test, and we further evaluated its accuracy to predict pathogen load using SEN signal-to-cutoff (SCO) values from unenriched samples to classify animals as high or nonhigh shedders. Rectoanal mucosal swabs (RAMS) were collected from 238 beef cattle from five cohorts located in the Midwest or southern High Plains of the United States between July 2015 and April 2016. Unenriched RAMS samples were used for the enumeration and SEN SCO analyses. Enriched samples were tested using SEN and immunomagnetic separation methods for the detection of Salmonella. The SEN method was 100% sensitive and specific for the detection of Salmonella from the enriched RAMS samples. A SEN SCO value of 8, with a sensitivity of 93.5% and specificity of 94.3%, was found to be an optimum cutoff value for classifying animals as high or nonhigh shedders from the unenriched RAMS samples. The SEN assay is a rapid and reliable method for the qualitative detection and categorization of the shedding load of Salmonella from RAMS in feedlot cattle.

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

Salmonella spp. is the most predominant bacterial cause of foodborne gastroenteritis in humans. Due to the risk of human infection associated with poultry products and the prevalence of antimicrobial resistance, Salmonella also poses a significant challenge to commercial poultry production. During the last decade (2002 to 2012), the 12 most prevalent poultry-associated Salmonella serotypes (MPPSTs) were frequently and consistently isolated from poultry products in the United States. These MPPSTs and their percent prevalence in poultry products include Kentucky (4%), Enteritidis (2%) Heidelberg (2%), Typhimurium (2%), S. I 4,[5],12:i:- (0.31%), Montevideo (0.20%), Infantis (0.16%) Schwarzengrund (0.15%), Hadar (0.15%), Mbandaka (0.13%), Thompson (0.12%), and Senftenberg (0.04%). All MPPSTs except Kentucky are among the top 30 clinically significant serotypes that cause human illnesses in the United States. However with the exception of a few widely studied serotypes such as S. Enteritidis and Typhimurium, the ecology and epidemiology of the majority of MPPSTs still remain poorly investigated. Published data from the United States suggests that MPPSTs such as Heidelberg, Typhimurium, Kentucky, and Sentfenberg are more likely to be multi-drug resistant (MDR, ≥3 antimicobial classes) whereas Enteritidis, Montevideo, Schwarzengrund, Hadar, Infantis, Thompson, and Mbandaka are generally pan-susceptible or display resistance to fewer antimicobials. In contrast, the majority of MPPSTs isolated globally have been reported to display MDR phenotype. There also appears to be an international spread of a few MDR serotypes including Kentucky, Schwarzengrund, Hadar, Thomson, Sentfenberg, and Enteritidis, which may pose significant challenges to the public health. The current knowledge gaps on the ecology, epidemiology, and antimicrobial resistance of MPPSTs are discussed.

Comparison of the Efficacy of a Sulfuric Acid-Sodium Sulfate Blend and Lactic Acid for the Reduction of Salmonella on Prerigor Beef Carcass Surface Tissue

A study was conducted to compare the efficacy of a commercially available sulfuric acid-sodium sulfate blend (SSS) and lactic acid (LA) in reducing inoculated Salmonella populations on beef. Sixty pieces of prerigor beef carcass surface brisket tissue, collected directly from the processing line of a commercial beef processing plant, were cut into two sections (10 by 10 cm each) and spot inoculated (6 to 7 log CFU/cm2) on the adipose side with a six-strain mixture of Salmonella. One section per piece of brisket tissue was left untreated (control), while the second section was spray treated (5 s, 15 lb/in2, and 33 mL/s flow rate) with unheated (21°C) or heated (52°C) solutions of SSS (pH 1.1) or LA (4%). Unheated and heated SSS lowered (P < 0.05) total bacterial counts from 6.3 to 4.6 and 4.3 log CFU/cm2, respectively. Likewise, unheated and heated LA reduced (P < 0.05) total bacterial counts from 6.3 to 4.7 and 4.4 log CFU/cm2, respectively. Initial counts of inoculated Salmonella populations (6.1 to 6.2 log CFU/cm2) were reduced (P < 0.05) to 4.2 and 3.9 log CFU/cm2 following treatment with unheated and heated SSS, respectively, and to 3.7 and 3.8 log CFU/cm2 after treatment with unheated and heated LA, respectively. Overall, the temperature of the chemical solutions had a small (0.3 log CFU/cm2), but significant (P < 0.05), effect on total bacterial counts but not (P > 0.05) on Salmonella counts. Regardless of solution temperature, Salmonella counts for LA-treated samples were 0.3 log CFU/cm2 lower (P < 0.05) than those of samples treated with SSS. These results indicate that both unheated and heated solutions of SSS and LA are effective interventions for reducing Salmonella contamination on prerigor beef carcass surface tissue.

A Meta-Analysis of the Global Prevalence Rates of Staphylococcus aureus and Methicillin-Resistant S. aureus Contamination of Different Raw Meat Products

Previous research has indicated that raw meats are frequently contaminated with Staphylococcus aureus, but data regarding the pooled prevalence rates of S. aureus and methicillin-resistant S. aureus (MRSA) contamination in different types of raw meat products (beef, chicken, and pork) and across different periods, regions, and purchase locations remain inconsistent. We systematically searched the PubMed, EMBASE, Ovid, Web of Science, and HighWire databases to identify studies published up to June 2016. The STROBE guidelines were used to assess the quality of the 39 studies included in this meta-analysis. We observed no significant differences in the pooled prevalence rates of S. aureus and MRSA contamination identified in various raw meat products, with overall pooled prevalence rates of 29.2% (95% confidence interval [CI], 22.8 to 35.9%) and 3.2% (95% CI, 1.8 to 4.9%) identified for the two contaminants, respectively. In the subgroup analyses, the prevalence of S. aureus contamination in chicken products was highest in Asian studies and significantly decreased over time worldwide. In European studies, the prevalence rates of S. aureus contamination in chicken and pork products were lower than those reported on other continents. The pooled prevalence rates of S. aureus contamination in chicken and pork products and MRSA contamination in beef and pork products were significantly higher in samples collected from retail sources than in samples collected from slaughterhouses and processing plants. These results highlight the need for good hygiene during transportation to and manipulation at retail outlets to reduce the risk of transmission of S. aureus and MRSA from meat products to humans.

Cecal MicroRNAome response to Salmonella enterica serovar Enteritidis infection in White Leghorn Layer

Background

Salmonella enterica serovar Enteritidis (SE) is a food-borne pathogen and of great threat to human health through consuming the contaminated poultry products. MicroRNAs (miRNAs) play an important role in different biological activities and have been shown to regulate the innate immunity in the bacterial infection. The objective of this study is to identify miRNAs associated with SE infection in laying chicken cecum.

Results

Average number of reads of three libraries constructed from infected and non-infected chickens was 12,476,156 and 10,866,976, respectively. There were 598 miRNAs including 194 potential novel miRNAs identified in which 37 miRNAs were significantly differentially expressed between infected and non-infected chickens. In total, 2897 unique target genes regulated by differentially expressed miRNAs were predicted, in which, 841 genes were uniquely regulated by up-regulated miRNAs (G1), 636 genes were uniquely regulated by down-regulated miRNAs (G2), and 1420 were co-regulated by both up and down- regulated miRNAs (G3). There were 118, 73 and 178 GO (Gene ontology) BP (Biological process) terms significantly enriched in G1, G2 and G3 groups, respectively. More immune-related GO BP terms than metabolism-related terms were found in G1. Expression of 12 immune-related genes of four differentially expressed miRNAs was detected through qRT-PCR. The regulatory direction of gga-miR-1416-5p, gga-miR-1662, and gga-miR-34a-5p were opposite with the target genes of TLR21, BCL10, TLR1LA, NOTCH2 and THBS1, respectively.

Conclusion

The miRNAs contribute to the response to SE infection at the onset of egg laying through regulating the homeostasis between metabolism and immunity. The gga-miR-125b-5p, gga-miR-34a-5p, gga-miR-1416-5p and gga-miR-1662 could play an important role in SE infection through regulating their target genes. The finding herein will pave the foundation for the studies of microRNA regulation in SE infection in laying hens.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3413-8) contains supplementary material, which is available to authorized users.

Prevalence and Characterization of Salmonella enterica and Salmonella Bacteriophages Recovered from Beef Cattle Feedlots in South Texas

Asymptomatic Salmonella carriage in beef cattle is a food safety concern, and the beef feedlot environment may function as a reservoir of this pathogen. The goal of this study was to identify and isolate Salmonella and Salmonella bacteriophages from beef cattle feedlot environments in order to better understand the microbial ecology of Salmonella and identify phages that might be useful as anti-Salmonella beef safety interventions. Three feedlots in south Texas were visited, and 27 distinct samples from each source were collected from dropped feces, feed from feed bunks, drinking water from troughs, and soil in cattle pens (n = 108 samples). Preenrichment, selective enrichment, and selective/differential isolation of Salmonella were performed on each sample. A representative subset of presumptive Salmonella isolates was prepared for biochemical identification and serotyping. Samples were pooled by feedlot and sample type to create 36 samples and enriched to recover phages. Recovered phages were tested for host range against two panels of Salmonella hosts. Salmonella bacteria were identified in 20 (18.5%) of 108 samples by biochemical and/or serological testing. The serovars recovered included Salmonella enterica serovars Anatum, Muenchen, Altona, Kralingen, Kentucky, and Montevideo; Salmonella Anatum was the most frequently recovered serotype. Phage-positive samples were distributed evenly over the three feedlots, suggesting that phage prevalence is not strongly correlated with the presence of culturable Salmonella. Phages were found more frequently in soil and feces than in feed and water samples. The recovery of bacteriophages in the Salmonella-free feedlot suggests that phages might play a role in suppressing the Salmonella population in a feedlot environment.

Assessing Transmission of Salmonella to Bovine Peripheral Lymph Nodes upon Horn Fly Feeding

Biting arthropods are implicated in the transdermal transmission of Salmonella to bovine peripheral lymph nodes, and such contamination can contribute to increased Salmonella prevalence in processed beef. Since horn flies can acquire Salmonella and then excrete the bacteria in their feces, on-animal fly infestations were conducted in this study to assess whether horn flies have a role in this bacterial transmission. Three Salmonella serotypes were used to assess fly acquisition from and excretion onto cattle. The results indicated that flies can acquire Salmonella from the hide, as assessed by recovery from homogenates of surfacesterilized flies, and that Salmonella persists for at least 5 days in the fly. Fly fecal excreta serves as a bacterial contaminant on the hide, and the overall mean probable estimate of the quantity shed was ≈10(5) most probable number per fly cage area. In 5 days, no transmission of the bacteria to bovine peripheral lymph nodes was evident, prompting an assessment of the effects of prolonged horn fly feeding on transmission. Three groups of animals were infested with flies that had consumed a blood meal containing Salmonella Senftenberg. After 5 days, the study was either terminated or the flies were removed and the cages replenished with unfed flies either once or twice over the course of an 11- or 19-day fly exposure period, respectively. A microlancet-inoculated positive-control animal was included in each group for comparison. The impact of prolonged horn fly feeding was evident, as 8% of lymph nodes cultured were positive from the 5-day exposure, whereas 50 and 42% were positive from 11- and 19-day exposures, respectively. Higher concentrations of Salmonella were recovered from fly-infested animals than from the microlancet-inoculated control, likely a result of repeated inoculations over time by flies versus a single introduction. The data described provide new insights into the transmission dynamics of Salmonella in cattle populations, highlighting a role for biting flies as an important reservoir.

Diagnostic Accuracy of Rectoanal Mucosal Swab of Feedlot Cattle for Detection and Enumeration of Salmonella enterica

Cattle are noted carriers of the foodborne pathogen Salmonella enterica. The perceived need to decrease the potential human health risk posed by excretion of this pathogen has resulted in numerous studies examining the factors that influence Salmonella shedding in cattle. Fecal grab (FG) samples have been the predominant method used to identify cattle colonized or infected with Salmonella; however, FG sampling can be impractical in certain situations, and rectoanal mucosal swabs (RAMS) are a more convenient sample type to collect. Despite a lack of studies comparing FG and RAMS for the detection and enumeration of Salmonella fecal shedding, RAMS is perceived as less sensitive because a smaller amount of feces is cultured. In a cross-sectional study to address these concerns, paired RAMS and FG samples were collected from 403 adult feedlot cattle approximately 90 days prior to harvest. Samples were processed for Salmonella enumeration (direct plating) and detection (enrichment and immunomagnetic separation). In all, 89.6% of RAMS and 98.8% of FG samples were positive for Salmonella, and concordant prevalence outcomes were observed for 90.8% of samples. Mean enumeration values were 3.01 and 3.12 log CFU/ml for RAMS and FG, respectively. The sensitivity and specificity of RAMS were 91% (95% confidence interval [CI]: 87.5 to 93%) and 100% (95% CI: 48 to 100%), respectively, for Salmonella detection. Furthermore, RAMS Salmonella enumeration was substantially concordant (ρc = 0.89; 95% CI: 0.86 to 0.91) with FG values. We conclude that RAMS are a reliable alternative to FG for assessing cattle Salmonella fecal shedding status, especially for cattle shedding high levels of Salmonella.