Substantial within-animal diversity of Salmonella isolates from lymph nodes, feces, and hides of cattle at slaughter

An Experimental Infection Model in Sheep and Goats to Evaluate Salmonella Colonization in Deep Tissue Lymph Nodes and after Carcass Vascular Rinsing with Bacteriophages in Goats

An animal infection model was evaluated on sheep and goats to confirm which species infected with Salmonella enterica serovar Enteritidis C StR (SE13) would provide a consistent and high frequency of Salmonella colonization in lymph nodes (LNs) without causing undue animal morbidity. Sheep and goats (n = 5) were intradermally inoculated with Salmonella, postincubated for 7 days, and euthanized. Superficial cervical, medial iliac, subiliac, mammary, and popliteal LNs were excised from each carcass. Goat LNs had approximately 53% greater Salmonella level compared to sheep. Also, Salmonella was inconsistently recovered from the sheep LNs. Thus, goats were selected to determine the ability of carcass vascular rinsing (with and without bacteriophages) to reduce Salmonella in infected LNs. Goats with similar characteristics were grouped together before being randomly assigned to 3 postharvest treatments; control (CN, not vascularly rinsed; n = 10), vascularly rinsed with a standard Rinse & Chill® solution (RC; 98.5% water and a blend of saccharides and phosphates; n = 10), or vascularly rinsed with a standard Rinse & Chill® solution plus the addition of bacteriophages (BP; n = 10). Rinse & Chill® system was able to successfully deliver a mean 7.0 log PFU/g to the S. Enteritidis-infected LNs (mean 3.5 log CFU/g). However, neither Rinse & Chill® without bacteriophages nor with bacteriophages caused Salmonella reduction (P > 0.05) compared to the nonrinsed goat carcasses.

Medium-term storage of calf beddings affects bacterial community and effectiveness to inactivate zoonotic bacteria

Land-spreading of animal faecal wastes -such as animal beddings- can introduce zoonotic enteropathogens into the food system environment. The study evaluated the effectiveness of animal beddings naturally contaminated by calf manure to reduce E. coli O157:H7 or Salmonella enterica. The two pathogens were introduced separately as a four strains-cocktail and at high (>6.5 Log10 g-1) concentration into bedding materials, and their inactivation over a 10 weeks-period was monitored by using a Most Probable Number (MPN) enumeration method. Inactivation of E. coli O157:H7 was more effective in the bedding inoculated immediately after collection from calf pens than in the beddings inoculated after a 2 months-pre-storage period: E. coli O157:H7 levels were reduced by 6.6 Log10 g-1 in unstored bedding (0.5 Log10 g-1 recovered; 95%CI: 0.0-1.2), and by 4.9 Log10 g-1 in pre-stored bedding (2.2 Log10 g-1 recovered; 95%CI: 1.5-2.8) with a significant (p<0.05) difference between unstored and pre-stored. S. enterica was inactivated less effectively as counts were reduced by one order of magnitude, with no significant difference in inactivation between unstored and pre-stored beddings. Low levels of naturally occurring E. coli O157 and Salmonella spp. were detected in the non-inoculated beddings, as well as in the straw prior to use in the animal facility. To better understand the possible biological processes involved, the bacterial community present in the beddings was characterised by short-read 16S rRNA sequencing. Pre-storage of the bedding affected the composition but not the diversity of the bacterial community. Analyses of the key bacterial phyla suggested that the presence of a diverse and stable bacterial community might facilitate inactivation of the introduced pathogens, and a possible role of bacterial orders associated with lignocellulolytic resources. Overall, the study contributed to the understanding of the fate of zoonotic bacteria introduced in animal beddings during storage and identified bedding storage practices pre-and post-use in animal facilities that could be important to prevent the risk of zoonosis dissemination to the environment or to the dairy herds.

Class 1 integron carrying qacEΔ1 gene confers resistance to disinfectant and antibiotics in Salmonella

Salmonella has presented increasingly alarming rates of antimicrobial resistance believed to be a result of a high prevalence of integrons. It is speculated that disinfectant-resistant isolates are due to the expression of qacEΔ1, an efflux pump located in the 3' conserved sequence (3'CS) of class 1 integrons. With this concern, we tested the antibiotic and disinfectant resistance of 581 Salmonella strains collected from different sources, and characterized their integron structures. Gene expression and induction experiments were also performed. Results showed that Salmonella have high resistance to antimicrobials, especially to sulfonamides (SAs, 78.83 %), tetracyclines (TCs, 75.04 %) and benzalkonium chloride (BC, 87.26 %). The multi-drug resistance (MDR) frequency reached up to 63.17 %, and the prevalence of intI1 was 45.78 %. Molecular characterization of class 1 integrons exhibited nine different gene cassette arrays, of these, dfrA12-orf-aadA2 (n = 75), EstX (n = 25) and aadA2 (n = 14) were the most frequent. Importantly, 74.06 % of intI1-positive isolates were carrying qacEΔ1-sul1 genes in the 3'CS. This study also demonstrated that phenotypic resistance to both antibiotics and disinfectants was significantly correlated with the emergence of intI1 (p < 0.05). 91.37 % of qacEΔ1-sul1 positive Salmonella were found with disinfectant resistance. Additionally, expression of qacEΔ1 gene in Escherichia coli confirmed qacEΔ1 is predominantly involved in conferring disinfectant resistance. Disinfectant induction experiments further implicated qacEΔ1 in disinfectant resistance. RT-qPCR revealed a disinfectant-mediated increase in the relative expression of antibiotic-resistant genes (ARGs), aadA2 and dfrA12 on the integron, and efflux pump genes (mdtH and acrD) indicating that disinfectant could trigger co or cross-resistance. Therefore, our study confirmed that using disinfectant could provide selection pressure for strains with acquired resistance to antibiotics, providing new insights into the public health impact of Salmonella and guide continued efforts in antimicrobial stewardship and prevention of antibiotic resistance.

Longitudinal Assessment of Prevalence and Incidence of Salmonella and Escherichia coli O157 Resistance to Antimicrobials in Feedlot Cattle Sourced and Finished in Two Different Regions of the United States

The objective was to investigate the influence of cattle origin and region of finishing on the prevalence of Salmonella, Escherichia coli O157:H7, and select antimicrobial resistance in E. coli populations. Yearling heifers (n = 190) were utilized in a 2 × 2 factorial arrangement. After determining fecal Salmonella prevalence, heifers were sorted into one of four treatments: heifers originating from South Dakota (SD) and finished in SD (SD-SD); heifers originating from SD and finished in Texas (SD-TX); heifers originating from TX and finished in SD (TX-SD); and heifers originating from TX and finished in TX (TX-TX). Fecal, pen, and water scum line samples were collected longitudinally throughout the study; hide swab and subiliac lymph node (SLN) samples were collected at study end. A treatment × time interaction was observed (p ≤ 0.01) for fecal Salmonella prevalence, with prevalence being greatest for TX-TX and TX-SD heifers before transport. From day (d) 14 through study end, prevalence was greatest for TX-TX and SD-TX heifers compared with SD-SD and TX-SD heifers. Salmonella prevalence on hides were greater (p ≤ 0.01) for heifers finished in TX compared with SD. Salmonella prevalence in SLN tended (p = 0.06) to be greater in TX-TX and SD-TX heifers compared with TX-SD and SD-SD. Fecal E. coli O157:H7 prevalence had a treatment × time interaction (p = 0.04), with SD-TX prevalence being greater than TX-SD on d 56 and SD-SD and TX-TX being intermediate. A treatment × time interaction was observed for fecal trimethoprim-sulfamethoxazole-resistant and cefotaxime-resistant E. coli O157:H7 prevalence (p ≤ 0.01). Overall, these data suggest that the region of finishing influences pathogenic bacterial shedding patterns, with the initial 14 d after feedlot arrival being critical for pathogen carriage.

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.

Metaphylactic antimicrobial effects on occurrences of antimicrobial resistance in Salmonella, Escherichia coli, and Enterococcus spp. measured longitudinally from feedlot arrival to harvest in high-risk beef cattle

Aims

Our objective was to determine how injectable antimicrobials affected populations of Salmonella enterica, Escherichia coli and Enterococcus spp. in feedlot cattle.

Methods and Results

Two arrival date blocks of high‐risk crossbred beef cattle (n = 249; mean BW = 244 kg) were randomly assigned one of four antimicrobial treatments administered on day 0: sterile saline control (CON), tulathromycin (TUL), ceftiofur (CEF) or florfenicol (FLR). Faecal samples were collected on days 0, 28, 56, 112, 182 and study end (day 252 for block 1 and day 242 for block 2). Hide swabs and subiliac lymph nodes were collected the day before and the day of harvest. Samples were cultured for antimicrobial‐resistant Salmonella, Escherichia coli and Enterococcus spp. The effect of treatment varied by day across all targeted bacterial populations (p ≤ 0.01) except total E. coli. Total E. coli counts were greatest on days 112, 182 and study end (p ≤ 0.01). Tulathromycin resulted in greater counts and prevalence of Salmonella from faeces than CON at study end (p ≤ 0.01). Tulathromycin and CEF yielded greater Salmonella hide prevalence and greater counts of 128ERY^RE. coli at study end than CON (p ≤ 0.01). No faecal Salmonella resistant to tetracyclines or third‐generation cephalosporins were detected. Ceftiofur was associated with greater counts of 8ERY^REnterococcus spp. at study end (p ≤ 0.03). By the day before harvest, antimicrobial use did not increase prevalence or counts for all other bacterial populations compared with CON (p ≥ 0.13).

Conclusions

Antimicrobial resistance (AMR) in feedlot cattle is not caused solely by using a metaphylactic antimicrobial on arrival, but more likely a multitude of environmental and management factors.

Prevalence and Sources of Salmonella Lymph Node Infection in Special-Fed Veal Calves

ABSTRACT

Peripheral lymph nodes (LNs) have been implicated as potential contaminants of ground beef, yet the source and timing of Salmonella LN infection in cattle is still unclear, limiting targeted intervention. The aim of this study was to leverage the vertical integration of special-fed veal production to identify preharvest environmental exposures, specifically in livestock trailers and harvest facility holding pens where calves spend 30 min to 4 h, that result in Salmonella LN infection. Ten cohorts of 80 to 82 veal calves were followed through the harvest process, and environmental samples were collected in barns, trailers, and holding pens. Mesenteric LNs from 35 calves were collected at harvest, and 25 prefemoral LNs per cohort were pooled. Within the same cohort, for 12 samples for which the serovar of the environmental and calf LN Salmonella isolates matched, the isolates were submitted for whole genome sequencing to determine whether environmental exposure resulted in LN infection. Cohort-level Salmonella mesenteric LN prevalence ranged from 0% (0 of 35 samples) to 80% (28 of 35 samples), and pooled prefemoral LNs were positive for Salmonella in 3 of the 10 cohorts. Salmonella prevalence in samples from barns, livestock trailers, and harvest facility holding pens was 22% (13 of 60 samples), 74% (59 of 80 samples), and 93% (74 of 80 samples), respectively. Some environmental and LN isolates were multidrug resistant. Four instances of Salmonella transmission from trailers and/or holding pens to calf LNs were supported by sequence data. Salmonella serovars Agona, Give, and Muenster were identified in transmission events. One instance of transmission from the livestock trailer, two instances from holding pens, and one instance from either trailer or holding pens were observed. Further research is needed to evaluate the extent of environmental Salmonella transmission in cattle and to determine whether targeted interventions in trailers or holding pens could reduce novel Salmonella LN infection in veal calves before harvest.

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

Salmonella Carriage in Peripheral Lymph Nodes and Feces of Cattle at Slaughter Is Affected by Cattle Type, Region, and Season

Salmonella is a significant food safety concern in commercial beef production, and some contamination is thought to occur by inclusion of Salmonella-infected peripheral lymph nodes (LN) in ground beef and through fecal contamination. Surveillance in processing plants assists packers in risk management of Salmonella by understanding seasonal trends and risks associated with different cattle types. Approximately 25 fecal samples and 20 LN were collected from animals representing each of five cattle types (cull beef cattle, cull dairy cows, conventional feedlot cattle, all-natural feedlot cattle raised without pharmaceuticals, and grass-finished cattle) and each of five climate regions (mixed-temperatures and dry, mixed-temperatures and humid, hot and humid, hot and dry, cold) during each of three seasons (summer, fall, winter) to better characterize Salmonella inputs into a commercial cattle processing facility. In total, 1,840 fecal samples and 1,550 LN samples were collected. Fecal samples and LN were cultured for Salmonella, and select isolates were serogrouped and screened for antimicrobial resistance. Conventional feedlot cattle had the highest LN Salmonella concentrations (1.17 log10 CFU/g LN) in this data set, while cull dairy cows had the highest fecal Salmonella concentrations (1.96 log10 CFU/g feces). Conventional feedlot cattle and cull dairy cows had the greatest Salmonella prevalence in both LN (32 and 18%, respectively) and feces (37 and 49%, respectively), while all-natural feedlot cattle had the lowest prevalence in the LN (3%) and feces (7%). As expected, Salmonella prevalence and concentration was lowest for all cattle types during winter compared to warmer seasons. When examined by climate region, a greater Salmonella prevalence in both feces and LN was observed in climate region 4 (hot-dry), than the other regions. Only 21 of 50 Salmonella isolates examined for antimicrobial susceptibility were identified as multidrug resistant (MDR); cull dairy cows were responsible for 48% of MDR isolates, cull beef cattle were responsible for 38%, and conventional feedlot, grass-fed, and all-natural feedlot cattle were each responsible for 4.8%. These results indicate that different production schemes, season, and climate region may influence which cattle are most likely to introduce Salmonella to the abattoir, allowing for greater risk awareness during the slaughter process.

The Impact of Overstocking and Negative Energy Balance on Quantitative Measurement of Non-typhoidal Salmonella in Periparturient Dairy Cattle

Stressful conditions in animal production facilities may exacerbate the fecal shedding and foodborne transmission of non-typhoidal Salmonella enterica subsp. enterica. Dairy cows are reservoirs of this zoonotic microorganism, and its prevalence has roughly doubled in the past decade on dairy farms in United States. Dairy cows are commonly overstocked at the feed bunk, and stressors placed on the animal prior to parturition may exacerbate Salmonella shedding. However, no studies have evaluated the impact of overstocking and metabolic stress on fecal concentrations of the pathogen. Therefore, we conducted a field trial with 120 multiparous dairy cows randomized into one of four treatment groups with different stocking densities at the feed bunk during the periparturient period as follows: US, understocked from −60 to −1 DRC; OS, overstocked from −60 to −1 DRC; USOS, understocked from −60 to −26 DRC/overstocked from −25 to −1 DRC; and OSUS, overstocked from −60 to −26 DRC/ understocked from −25 to −1 DRC. Fecal and blood samples were collected at four time points relative to calving. qPCR assays were used to quantify Salmonella invA gene and total bacterial community from fecal samples, and a subset of isolates recovered from fecal bacterial culture were characterized using pulsed field gel electrophoresis and serotyping. Serum non-esterified fatty acids (NEFA) were measured as a metabolic stress indicator using an immunoassay. Multivariable analyses were performed to test if changes in Salmonella concentrations were associated with stocking density, energy balance, or days relative to calving. From fecal isolates, three Salmonella serovars were identified, S. Cerro; Kentucky; Meleagridis. Concentrations of Salmonella increased as cows approached calving. Higher stocking densities at the feed bunk did not impact total bacterial community or NEFA; however, cows in the overstocked groups had higher Salmonella fecal concentrations. Further, cows with higher NEFA concentrations after calving had a higher likelihood of detection of Salmonella. Future farm interventions should aim to reduce environmental and metabolic stress during the periparturient period to decrease the dissemination of Salmonella to cattle, the environment, and humans.

Systematic Review: Nontyphoidal Salmonella in Food from Latin America

In Latin America, nontyphoidal Salmonella (NTS) is one of the most important etiological agents of foodborne infections; it can survive in soil, water, and food even after processing. Here, we aimed to perform a systematic review by collecting data on the prevalence, serotypes, and antimicrobial resistance (AMR) of NTS isolated from different food products in Latin America, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Out of 1766 studies screened, 244 reports from 13 Latin American countries were eligible. Among these, 182 reported NTS prevalence, 87 reported NTS serotypes, and 83 reported serotypes with AMR patterns. The NTS prevalence ranged from 0.005% to 93.3%, regardless of country and food. Meat showed the highest NTS prevalence. Enteritidis, Typhimurium, and Derby were the most frequently observed serotypes in different food products. The serotypes Enteritidis, Typhimurium, and Infantis, isolated from animal products, showed the highest AMR rate. The presence of NTS in fruits and vegetables, which are generally consumed raw or as ready-to-eat food, indicates a high risk of salmonellosis from consuming these foods. Thus, the reduction of this pathogen in the food chain requires a One Health approach, involving good agricultural and manufacturing practices, low antimicrobial use, and proper waste management.

High-Resolution Genomic Comparisons within Salmonella enterica Serotypes Derived from Beef Feedlot Cattle: Parsing the Roles of Cattle Source, Pen, Animal, Sample Type, and Production Period

Salmonella enterica is a major foodborne pathogen, and contaminated beef products have been identified as one of the primary sources of Salmonella-related outbreaks. Pathogenicity and antibiotic resistance of Salmonella are highly serotype and subpopulation specific, which makes it essential to understand high-resolution Salmonella population dynamics in cattle. Time of year, source of cattle, pen, and sample type (i.e., feces, hide, or lymph nodes) have previously been identified as important factors influencing the serotype distribution of Salmonella (e.g., Anatum, Lubbock, Cerro, Montevideo, Kentucky, Newport, and Norwich) that were isolated from a longitudinal sampling design in a research feedlot. In this study, we performed high-resolution genomic comparisons of Salmonella isolates within each serotype using both single-nucleotide polymorphism-based maximum-likelihood phylogeny and hierarchical clustering of core-genome multilocus sequence typing. The importance of the aforementioned features in clonal Salmonella expansion was further explored using a supervised machine learning algorithm. In addition, we identified and compared the resistance genes, plasmids, and pathogenicity island profiles of the isolates within each subpopulation. Our findings indicate that clonal expansion of Salmonella strains in cattle was mainly influenced by the randomization of block and pen, as well as the origin/source of the cattle, i.e., regardless of sampling time and sample type (i.e., feces, lymph node, or hide). Further research is needed concerning the role of the feedlot pen environment prior to cattle placement to better understand carryover contributions of existing strains of Salmonella and their bacteriophages. IMPORTANCE Salmonella serotypes isolated from outbreaks in humans can also be found in beef cattle and feedlots. Virulence factors and antibiotic resistance are among the primary defense mechanisms of Salmonella, and are often associated with clonal expansion. This makes understanding the subpopulation dynamics of Salmonella in cattle critical for effective mitigation. There remains a gap in the literature concerning subpopulation dynamics within Salmonella serotypes in feedlot cattle from the beginning of feeding up until slaughter. Here, we explore Salmonella population dynamics within each serotype using core-genome phylogeny and hierarchical classifications. We used machine learning to quantitatively parse the relative importance of both hierarchical and longitudinal clustering among cattle host samples. Our results reveal that Salmonella populations in cattle are highly clonal over a 6-month study period and that clonal dissemination of Salmonella in cattle is mainly influenced spatially by experimental block and pen, as well by the geographical origin of the cattle.

Antimicrobial Resistance Hidden within Multiserovar Salmonella Populations

Salmonella enterica can exist in food animals as multiserovar populations, and different serovars can harbor diverse antimicrobial resistance (AMR) profiles. Conventional Salmonella isolation assesses AMR only in the most abundant members of a multiserovar population, which typically reflects their relative abundance in the initial sample. Therefore, AMR in underlying serovars is an undetected reservoir that can readily be expanded upon antimicrobial use. CRISPR-SeroSeq profiling demonstrated that 60% of cattle fecal samples harbored multiple serovars, including low levels of Salmonella serovar Reading in 11% of samples, which were not found by culture-based Salmonella isolation. An in vitro challenge revealed that Salmonella serovar Reading was tetracycline resistant, while more abundant serovars were susceptible. This study highlights the importance of AMR surveillance in multiserovar populations.

Genomic surveillance of antimicrobial resistance shows cattle and poultry are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico

Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is a public health concern globally. This study reports the phenotypic and genotypic antimicrobial resistance (AMR) profiles of NTS isolates from bovine lymph nodes (n = 48) and ground beef (n = 29). Furthermore, we compared genotypic AMR data of our isolates with those of publicly available NTS genomes from Mexico (n = 2400). The probability of finding MDR isolates was higher in ground beef than in lymph nodes:χ2 = 12.0, P = 0.0005. The most common resistant phenotypes involved tetracycline (40.3%), carbenicillin (26.0%), amoxicillin-clavulanic acid (20.8%), chloramphenicol (19.5%) and trimethoprim-sulfamethoxazole (16.9%), while more than 55% of the isolates showed decreased susceptibility to ciprofloxacin and 26% were MDR. Conversely, resistance to cephalosporins and carbapenems was infrequent (0-9%). MDR phenotypes were strongly associated with NTS serovar (χ2 = 24.5, P<0.0001), with Typhimurium accounting for 40% of MDR strains. Most of these (9/10), carried Salmonella genomic island 1, which harbors a class-1 integron with multiple AMR genes (aadA2, blaCARB-2, floR, sul1, tetG) that confer a penta-resistant phenotype. MDR phenotypes were also associated with mutations in the ramR gene (χ2 = 17.7, P<0.0001). Among public NTS isolates from Mexico, those from cattle and poultry had the highest proportion of MDR genotypes. Our results suggest that attaining significant improvements in AMR meat safety requires the identification and removal (or treatment) of product harboring MDR NTS, instead of screening for Salmonella spp. or for isolates showing resistance to individual antibiotics. In that sense, massive integration of whole genome sequencing (WGS) technologies in AMR surveillance provides the shortest path to accomplish these goals.

A Preliminary Study on the Presence of Salmonella in Lymph Nodes of Sows at Processing Plants in the United States

Salmonella-contaminated lymph nodes (LN), when included into edible meat products, are a potential source of Salmonella foodborne disease. In this survey, ventral superficial cervical and mandibular LN were tested for the presence of Salmonella from two sow processing plants in the midwestern United States. Results indicate that both LN can be contaminated with Salmonella; mandibular LN have higher prevalence (p < 0.05) of Salmonella than cervical LN (16% vs. 0.91%), and the majority (>90%) of Salmonella isolates are pan-susceptible or resistant to one antimicrobial, while 9.78% of isolates were multi-drug-resistant (MDR-resistant to three or more classes of antimicrobials). Intervention methods to prevent foodborne disease could include elimination of these LN from pork products or inclusion of LN only into products that are destined for cooking. Integrated multi-faceted intervention methods need to be developed to reduce Salmonella in the food chain.

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.

Prevalence and antimicrobial resistance of Listeria monocytogenes, Salmonella enterica and Escherichia coli O157:H7 in imported beef cattle in Jordan

This study characterized Listeria monocytogenes, Salmonella enterica, and E. coli O157:H7 by collecting rectoanal mucosal swabs and fecal samples from 518 imported beef cattle at Jordan's major abattoir. A unique 53 L. monocytogenes, 287 S. enterica, and 17 E. coli O157:H7 were isolated from 37, 120 and 9 different animals; respectively. The prevalence of S. enterica, L. monocytogenes and E. coli O157:H7 were 23.2 % (95 % CI, 19.7-27.0 %), 7.1 % (95 % CI, 5.2-9.7 %) and 1.7 % (95 % CI, 0.9-3.3 %); respectively. All L. monocytogenes, all E. coli O157:H7 and 93.0 % of S. enterica isolates resisted at least one antimicrobial class. All L. monocytogenes, 94.1 % of E. coli O157:H7 and 69.7 % of S. enterica isolates exhibited multidrug resistance (resistant to ≥3 antimicrobials classes). Moreover, high percentages of L. monocytogenes (98.1 %), E. coli O157:H7 (64.7 %) and S. enterica (45.3 %) isolates resisted ≥5 antimicrobial classes. More than 90 % of the L. monocytogenes isolates resisted ampicillin, penicillin and erythromycin and more than 75 % resisted vancomycin. S. enterica isolates resisted several treatment-of-choice antimicrobials such as nalidixic acid (85.4 %), ciprofloxacin (26.8 %) and ceftriaxone (19.5 %). Furthermore, greater than 50 % of the E. coli O157:H7 isolates resisted streptomycin, nalidixic acid, tetracycline, ampicillin, sulfamethoxazole-trimethoprim, kanamycin, chloramphenicol and ciprofloxacin. The high prevalence and the high resistance percentages of the studied pathogens toward clinically important antimicrobials is alarming. Thus, applying strict sanitation procedures at the abattoirs in Jordan is crucial to lower the risk of carcasses contamination.

Interventions Targeting Deep Tissue Lymph Nodes May Not Effectively Reduce the Risk of Salmonellosis from Ground Pork Consumption: A Quantitative Microbial Risk Assessment

The inclusion of deep tissue lymph nodes (DTLNs) or nonvisceral lymph nodes contaminated with Salmonella in wholesale fresh ground pork (WFGP) production may pose risks to public health. To assess the relative contribution of DTLNs to human salmonellosis occurrence associated with ground pork consumption and to investigate potential critical control points in the slaughter-to-table continuum for the control of human salmonellosis in the United States, a quantitative microbial risk assessment (QMRA) model was established. The model predicted an average of 45 cases of salmonellosis (95% CI = [19, 71]) per 100,000 Americans annually due to WFGP consumption. Sensitivity analysis of all stochastic input variables showed that cooking temperature was the most influential parameter for reducing salmonellosis cases associated with WFGP meals, followed by storage temperature and Salmonella concentration on contaminated carcass surface before fabrication. The input variables were grouped to represent three main factors along the slaughter-to-table chain influencing Salmonella doses ingested via WFGP meals: DTLN-related factors, factors at processing other than DTLNs, and consumer-related factors. The evaluation of the impact of each group of factors by second-order Monte Carlo simulation showed that DTLN-related factors had the lowest impact on the risk estimate among the three groups of factors. These findings indicate that interventions to reduce Salmonella contamination in DTLNs or to remove DTLNs from WFGP products may be less critical for reducing human infections attributable to ground pork than improving consumers' cooking habits or interventions of carcass decontamination at processing.

Worldwide Epidemiology of Salmonella Serovars in Animal-Based Foods: a Meta-analysis

Salmonella spp. are among the most important foodborne pathogens and the third leading cause of human death among diarrheal diseases worldwide. Animals are the primary source of this pathogen, and animal-based foods are the main transmission route to humans. Thus, understanding the global epidemiology of Salmonella serovars is key to controlling and monitoring this bacterium. In this context, this study aimed to evaluate the prevalence and diversity of Salmonella enterica serovars in animal-based foods (beef, pork, poultry, and seafood) throughout the five continents (Africa, the Americas [North and Latin America], Asia, Europe, and Oceania). The meta-analysis consisted of a chemometric assessment (hierarchical cluster analysis and principal component analysis) to identify the main epidemiological findings, including the prevalence and diversity of the Salmonella serovars in each matrix. Regarding the serovar distribution, S Typhimurium presented a cosmopolitan distribution, reported in all four assessed matrices and continents; poultry continues to play a central role in the dissemination of the Enteritidis serovar to humans, and Anatum and Weltevreden were the most frequently found in beef and seafood, respectively. Additionally, we recommended careful monitoring of certain serovars, such as Derby, Agona, Infantis, and Kentucky. Finally, given the scientific data regarding the most frequently reported serovars and which matrices constitute the main vehicles for the transmission of this pathogen, control programs may be improved, and specific interventions may be implemented in an attempt to reduce the risk of this pathogen reaching humans.IMPORTANCE Salmonellosis is caused by Salmonella spp. and is the third leading cause of death among food-transmitted diseases. This pathogen is commonly disseminated in domestic and wild animals, and the infection's symptoms are characterized by acute fever, nausea, abdominal pain, and diarrhea. The animals are the primary source of salmonellae, and animal-based foods are the main transmission route to humans. Therefore, data collected from these sources could contribute to future global interventions for effective control and surveillance of Salmonella along the food chain. In light of this, the importance of our research is in identifying the prevalence of Salmonella serovars in four animal-based food matrices (pork, poultry, beef, and seafood) and to evaluate the importance that each matrix has as the primary source of this pathogen to humans.

In-Plant Validation Study of Harvest Process Controls in Two Beef Processing Plants in Honduras

Imported meat in the United States can become a food safety hazard if proper food safety programs are not fully implemented in foreign meat processing plants. Thus, exporting countries' food safety inspection systems must be equivalent to the U.S. federal inspection system to become eligible to export meat to the United States. The objective of this study was to validate the beef harvest Hazard Analysis and Critical Control Points and food safety programs of two beef processing plants in Honduras operating under U.S. equivalency standards by evaluating the presence of Salmonella (plant A) and Shiga toxin-producing Escherichia coli (STEC; plant B) on hides. Additionally, evaluating pathogen transfer from hides to carcasses, as detected by preevisceration sampling, and the mitigation of transferred pathogens, by application of carcass spray interventions and determination of Salmonella presence in lymph nodes, was also conducted. In plant A, the presence of Salmonella on hides ( n = 30 of 687; 4.4%) was significantly greater ( P < 0.10) than on carcasses swabbed at preevisceration ( n = 7 of 687; 1.0%), after intervention ( n = 13 of 678; 1.9%), and in lymph nodes ( n = 14 of 691; 2.0%). In plant B, Salmonella was not detected on hide samples; therefore, data could not be used for validation of the harvest Hazard Analysis and Critical Control Points program. Alternatively, STEC presence on hides ( n = 21 of 85; 24.7%) was greater ( P < 0.10) than on carcasses at preevisceration ( n = 3 of 85; 3.5%) and after intervention ( n = 1 of 85; 1.2%). Pathogen presence in plant B did not differ ( P = 0.306) between carcasses in preevisceration and postintervention stages; both, however, were substantially low. Both plants' controls effectively reduced Salmonella and STEC presence in postintervention carcasses.

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.

Characterization of Antimicrobial Resistant (AMR) Salmonella Enterica Isolates Associated With Cattle at Harvest in Mexico

Despite being the target of control efforts for many decades, Salmonella enterica continues to be linked with a large amount of foodborne illnesses and outbreaks worldwide. Over the years, Salmonella isolated from meat products have exhibited a high level of antibiotic resistance. In this study, a total of 351 Salmonella isolates, recovered from cattle fecal samples (n = 31), hides (n = 105), and beef carcasses (n = 215) from 3 abattoirs in Mexico were analyzed for antimicrobial susceptibility. Resistance to at least one antimicrobial drug was found in 205 (58.4%) isolates and 20 different resistance phenotypes were observed among this Salmonella isolates set. Resistance to tetracycline (40.2%) and nalidixic acid (21.1%) was most commonly observed. Additionally, the most common multidrug-resistant (MDR) phenotypes shared resistance to chloramphenicol, streptomycin, tetracycline, and trimethopin/sulfamethoxazole (11.3%), resistance to ampicillin, tetracycline, and trimethopin/sulfamethoxazole (3.4%), and resistance to ampicillin, streptomycin, and tetracycline (2.5%). When it came to antimicrobial resistance phenotypes in each abattoir, we determined there was no statistical difference in the frequency of resistant vs. susceptible Salmonella isolates among the three abattoirs (P > 0.05). These data indicate that Salmonella isolates recovered from beef cattle in Mexico are commonly resistant to antimicrobials and often multiple antimicrobials. In Mexico, antimicrobial resistance, and in particular, multidrug-resistance, maybe of particular concern due to the much higher prevalence of Salmonella in retail beef. This may lead to the spread of resistance and to the reduction of antibiotic efficacy for the control of animal and human infections. Promoting control measures and inspection standards on imported animals and food products should be applied to avoid the spread of antibiotic resistance in various populations and among countries.

Complete Genome Sequences of Four Salmonella enterica Strains (Including Those of Serotypes Montevideo, Mbandaka, and Lubbock) Isolated from Peripheral Lymph Nodes of Healthy Cattle

Salmonella enterica serotype Lubbock emerged most likely from a Salmonella enterica serotype Mbandaka ancestor that acquired by recombination the fliC operon from Salmonella enterica serotype Montevideo. Here, we report the complete genome sequence of two S. Lubbock, one S. Montevideo, and one S. Mbandaka strain isolated from bovine lymph nodes.

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.

Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae

The ability of pathogenic bacteria to affect higher organisms and cause disease is one of the most dramatic properties of microorganisms. Some pathogens can establish transient colonization only, but others are capable of infecting their host for many years or even for a lifetime. Long-term infection is called persistence, and this phenotype is fundamental for the biology of important human pathogens, including Helicobacter pylori, Mycobacterium tuberculosis, and Salmonella enterica Both typhoidal and nontyphoidal serovars of the species Salmonella enterica can cause persistent infection in humans; however, as these two Salmonella groups cause clinically distinct diseases, the characteristics of their persistent infections in humans differ significantly. Here, following a general summary of Salmonella pathogenicity, host specificity, epidemiology, and laboratory diagnosis, I review the current knowledge about Salmonella persistence and discuss the relevant epidemiology of persistence (including carrier rate, duration of shedding, and host and pathogen risk factors), the host response to Salmonella persistence, Salmonella genes involved in this lifestyle, as well as genetic and phenotypic changes acquired during prolonged infection within the host. Additionally, I highlight differences between the persistence of typhoidal and nontyphoidal Salmonella strains in humans and summarize the current gaps and limitations in our understanding, diagnosis, and curing of persistent Salmonella infections.

Whole genome sequencing reveals widespread distribution of typhoidal toxin genes and VirB/D4 plasmids in bovine-associated nontyphoidal Salmonella

Nontyphoidal Salmonella (NTS) is a common pathogen in food-producing animals and a public health concern worldwide. Various NTS serovars may be present in apparently healthy animals. This could result in carcass contamination during the slaughter process leading to human exposure. While most genomic research has focused on Salmonella pathogenesis, little is known on the factors associated with subclinical infections and environmental persistence. We report here the widespread distribution of typhoidal toxin genes (i. e. the cdtB islet, hlyE, taiA), among NTS strains from a beef slaughter operation (n = 39) and from epidemiologically unconnected ground beef (n = 20). These genes were present in 76% of the strains, regardless of serovar, isolation source or geographical location. Moreover, strains that predominated in the slaughterhouse carry plasmid-borne type IV secretion systems (T4SS), which have been linked to persistent infections in numerous pathogens. Population genomics supports clonal dissemination of NTS along the food production chain, highlighting its role as reservoir of genetic variability in the environment. Overall, the study provides a thorough characterization of serovar diversity and genomic features of beef-associated NTS in Mexico. Furthermore, it reveals how common genetic factors could partially explain the emergence and persistence of certain NTS serovars in the beef industry.

Neutral barcoding of genomes reveals the dynamics of Salmonella colonization in cattle and their peripheral lymph nodes

Feedlot cattle often contain Salmonella. The number of bacteria that initiate colonization of different cattle organs and the bacterial migration within these large animals are poorly understood. To investigate these questions, we constructed wild-type isogenic tagged strains (WITS) of Salmonella by inserting 21-base barcodes flanked by Illumina sequencing primers into a neutral genome location. We then delivered several different pools of uniquely barcoded clones orally and into multiple intradermal sites, in individual Holstein steers, and subsequently performed Salmonella-directed sequence tag-based analysis of microbial populations (STAMP). Using high-throughput sequencing of the barcodes of Salmonella grown from steer lymph nodes, organs and feces, we monitored how individual barcoded clones travel from different entry sites within animals. Data showed that gastrointestinal colonization was established by up to hundreds of Salmonella founder cells, whereas peripheral lymph nodes were usually colonized by very low numbers of founding bacteria, often originating from the nearest draining intradermal delivery site. Transmission of Salmonella from the gastrointestinal tract to the lymphatic system was frequently observed, whereas entry of intradermally delivered bacteria into the gut was rare. Bacteria undergo limited extraintestinal proliferation within or prior to arrival at peripheral lymph nodes. Overall, the application of the STAMP technique facilitated characterization of the migration routes and founder population size of Salmonella within feedlot cattle and their organs and lymph nodes in unprecedented detail.

Relationship between Salmonella infection, shedding and serology in fattening pigs in low-moderate prevalence areas

Salmonella is a major foodborne pathogen causing important zoonosis worldwide. Pigs asymptomatically infected in mesenteric lymph nodes (MLN) can be intermittent shedders of the pathogen through faeces, being considered a major source of human infections. European baseline studies of fattening pig salmonellosis are based on Salmonella detection in MLN. This work studies the relationship between Salmonella infection in MLN and intestinal content (IC) shedding at slaughter and the relationship between the presence of the pathogen and the serologic status at farm level. Mean Salmonella prevalence in the selected pigs (vertically integrated production system of Navarra, Spain) was 7.2% in MLN, 8.4% in IC and 9.6% in serum samples. In this low-moderate prevalence context, poor concordance was found between MLN infection and shedding at slaughter and between bacteriology and serology. In fact, most of shedders were found uninfected in MLN (83%) or carrying different Salmonella strains in MLN and in IC (90%). The most prevalent Salmonellae were Typhimurium resistant to ACSSuT ± Nx or ASSuT antibiotic families, more frequently found invading the MLN (70%) than in IC (33.9%). Multivariable analysis revealed that risk factors associated with the presence of Salmonella in MLN or in IC were different, mainly related either to good hygiene practices or to water and feed control, respectively. Overall, in this prevalence context, detection of Salmonella in MLN is an unreliable predictor of faecal shedding at abattoir, indicating that subclinical infections in fattening pigs MLN could have limited relevance in the IC shedding.

A multiplex real-time PCR assay, based on invA and pagC genes, for the detection and quantification of Salmonella enterica from cattle lymph nodes

Cattle lymph nodes can harbor Salmonella and potentially contaminate beef products. We have developed and validated a new real-time PCR (qPCR) assay for the detection and quantification of Salmonella enterica in cattle lymph nodes. The assay targets both the invA and pagC genes, the most conserved molecular targets in Salmonella enterica. An 18S rRNA gene assay that amplifies from cattle and other animal species was also included as an internal control. Available DNA sequences for invA, pagC and 18S rRNA genes were used for primer and probe selections. Three Salmonella serotypes, S. Typhimurium, S. Anatum, and S. Montevideo, were used to assess the assay's analytical sensitivity. Correlation coefficients of standard curves generated for each target and for all three serotypes were >99% and qPCR amplification efficiencies were between 93% and 110%. Assay sensitivity was also determined using standard curve data generated from Salmonella-negative cattle lymph nodes spiked with 10-fold dilutions of the three Salmonella serotypes. Assay specificity was determined using Salmonella culture method, and qPCR testing on 36 Salmonella strains representing 33 serotypes, 38 Salmonella strains of unknown serotypes, 252 E. coli strains representing 40 serogroups, and 31 other bacterial strains representing 18 different species. A collection of 647 cattle lymph node samples from steers procured from the Midwest region of the US were tested by the qPCR, and compared to culture-method of detection. Salmonella prevalence by qPCR for pre-enriched and enriched lymph nodes was 19.8% (128/647) and 94.9% (614/647), respectively. A majority of qPCR positive pre-enriched samples (105/128) were at concentrations between 10⁴ and 10⁵ CFU/mL. Culture method detected Salmonella in 7.7% (50/647) and 80.7% (522/647) of pre- and post-enriched samples, respectively; 96.0% (48/50) of pre-enriched and 99.4% (519/522) of post-enriched culture-positive samples were also positive by qPCR. More samples tested positive by qPCR than by culture method, indicating that the real-time PCR assay was more sensitive. Our data indicate that this triplex qPCR can be used to accurately detect and quantify Salmonella enterica strains from cattle lymph node samples. The assay may serve as a useful tool to monitor the prevalence of Salmonella in beef production systems.

Comparison of Salmonella Prevalence Rates in Bovine Lymph Nodes across Feeding Stages

Peripheral lymph nodes (LNs) located in the fatty tissues of beef carcasses have been shown to harbor Salmonella and, thus, potentially contaminate ground beef. Salmonella prevalence within LNs is known to differ among feedlots. Two South Texas feeding operations (identified as locations A and B) known to harbor salmonellae in the feedlot environment, while historically producing cattle with opposing rates (one "high" and one "low") of Salmonella prevalence in LNs, were used in this study. To determine whether this difference was due to cattle source or factors associated with different stages of feeding, weanling steers of common and known origin were followed through normal feeding stages at both operations. Eighty Angus-sired beef steers were harvested at each of four feeding stages: 1, postweaning; 2, background or stocker; 3, 60 days on feed; and 4, 120 days on feed. Left and right subiliac and superficial cervical LNs ( n = 304) were collected from each carcass, and similar node types were pooled by animal ( n = 152). Results showed a difference ( P < 0.05) in prevalence of Salmonella in bovine lymph nodes between location A and location B and among feeding stages in location B. Salmonella was not isolated from any feeding stage 1 (postweaning) or location A LN samples. Within location B, there was an increase in Salmonella prevalence as cattle moved into later stages of feeding: at 22.2% (4 of 18), 77.8% (14 of 18), and 94.4% (17 of 18) for feeding stages 2, 3, and 4, respectively. Although the reasons for the differences seen between feeding operations and for increased Salmonella prevalence in LNs at later feeding stages remain unexplained, these results indicate that factors other than cattle source are likely influencing Salmonella prevalence in LNs.

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.

Recovery of Salmonella isolated from eggs and the commercial layer farms

BACKGROUND

Salmonella is recognized as a common bacterial cause of foodborne diarrheal illness worldwide, and animal or its food products have been the most common vehicles of the Salmonella infections. This study aimed to investigate the distribution of Salmonella in two commercial layer farms and to determine the genetic relatedness between these strains. The Salmonella isolates were serotyped by slide agglutination using commercial antisera and analyzed for genetic relatedness using pulsed-field gel electrophoresis (PFGE).

RESULTS

The internal environment had the highest prevalence of Salmonella (14/15, 93.3%), followed by external environment (60/96, 62.5%) and egg samples (23/84, 27.3%). The prevalence of Salmonella in the environment was significantly higher than that in egg samples (p < 0.05). The occurrence of Salmonella in the internal environment (93.3%) was relatively higher than in the external environment (55.6-77.2%). The 111 isolates were distributed among 15 PFGE types, and the PFGE results suggested that there existed cross-contamination between these strains not only from eggs, but also from the environments.

CONCLUSIONS

The findings indicated ongoing Salmonella cross-contamination inside or outside of the layer farms, and that Salmonella could also spread along the egg production line.

Molecular Characterization of Salmonella from Beef Carcasses and Fecal Samples from an Integrated Feedlot and Abattoir in Mexico

Nontyphoid Salmonella strains are some of the leading causes of foodborne illnesses worldwide; however, there is very limited information on the presence and characteristics of Salmonella in the food production chain in developing countries. In this study, pulsed-field gel electrophoresis (PFGE) was used for molecular subtyping and for monitoring the ecology and transmission of Salmonella isolates in a slaughter facility in Mexico in an attempt to determine specific steps that need to be improved to reduce Salmonella contamination in beef carcasses. A total of 94 isolates from a Salmonella stock culture collection originally obtained from a single vertically integrated feedlot and beef abattoir in Mexico were analyzed. A total of 26 unique PFGE patterns were identified, 38.5% of them corresponding to a single serotype. High concordance (88.4%) was found between serotype and PFGE banding subtype. Salmonella Kentucky and Salmonella Give were the most clonal subtypes in this study, and Salmonella Muenster was the most diverse, with 11 banding patterns identified. A total of 73.7, 70.6, and 85.7% of the PFGE subtypes identified from preevisceration, precooler, and chilled carcasses, respectively, were identified only at those specific points and not at any previous or subsequent steps of the slaughter process, suggesting that each step is in itself a source of Salmonella contamination. Salmonella Mbandaka was more likely to be recovered from feces than from any of the steps of the slaughter process. The genetic diversity and distribution of PFGE subtypes in the processing facility highlight the need to implement antimicrobial interventions and improve sanitation procedures at various points to avoid further Salmonella dissemination into the meat supply.

Low Prevalence of Salmonella and Shiga Toxin-Producing Escherichia coli in Lymph Nodes of Australian Beef Cattle

Salmonella contamination of ground beef has been viewed as originating from the surface of carcasses. Recent studies have identified lymph nodes as a potential source of Salmonella contamination because these tissues play an active role in containment of pathogens in the live animal and because some lymph nodes are unavoidably present in manufacturing beef trimmings or primal cuts that may be incorporated into ground beef. A survey was conducted of the microbiological status of lymph nodes from Australian cattle at the time of slaughter to determine the prevalence of microbiological contamination. Sets of lymph nodes (n = 197), consisting of the superficial cervical (prescapular), prepectoral, axillary, presternal, popliteal, ischiatic, subiliac (precrural), coxalis, and iliofemoralis (deep inguinal), were collected from five geographically separated Australian abattoirs over a period of 14 months. Samples were tested for the presence of Salmonella spp. and Shiga toxin-producing Escherichia coli by BAX PCR assay. Aerobic plate count, E. coli, and coliforms were enumerated with a lower limit of detection of 80 CFU per node. The observed prevalence of Salmonella within peripheral lymph nodes was 0.48% (7 of 1,464). Two of the seven lymph nodes in which Salmonella organisms were detected came from the same animal. Grass-fed, grain-fed, and cull dairy cattle were all found to have detectable Salmonella in lymph nodes. All Salmonella detections occurred during cooler months of the year. No Shiga toxin-producing E. coli were detected. Aerobic microorganisms were detected above the limit of quantification in 3.2% of nodes (median count 2.24 log per node), and E. coli was detected in 0.8% of nodes (median count 3.05 log per node). The low prevalence of Salmonella and low concentration of aerobic microorganisms in Salmonella-positive lymph nodes of Australian cattle at the time of slaughter suggest that the likelihood of lymph nodes contributing significantly to the presence of Salmonella in ground beef is low.

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.

Population dynamics of enteric Salmonella in response to antimicrobial use in beef feedlot cattle

A randomized controlled longitudinal field trial was undertaken to assess the effects of injectable ceftiofur crystalline-free acid (CCFA) versus in-feed chlortetracycline on the temporal dynamics of Salmonella enterica spp. enterica in feedlot cattle. Two replicates of 8 pens (total 176 steers) received one of 4 different regimens. All, or one, out of 11 steers were treated with CCFA on day 0 in 8 pens, with half of the pens later receiving three 5-day regimens of chlortetracycline from day 4 to day 20. Salmonella was isolated from faecal samples and antimicrobial susceptibility was analysed via microbroth dilution. Serotype was determined by whole-genome sequencing. On day 0, mean Salmonella prevalence was 75.0% and the vast majority of isolates were pansusceptible. Both antimicrobials reduced overall prevalence of Salmonella; however, these treatments increased the proportion of multi-drug resistant (MDR) Salmonella from day 4 through day 26, which was the last day of faecal collection. Only six Salmonella serotypes were detected. Salmonella serotype Reading isolates were extensively MDR, suggesting a strong association between serotype and resistance. Our study demonstrates that the selection pressures of a 3^rd generation cephalosporin and chlortetracycline during the feeding period contribute to dynamic population shifts between antimicrobial susceptible and resistant Salmonella.

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.

A Stochastic Model to Assess the Effect of Meat Inspection Practices on the Contamination of the Pig Carcasses

The objective of meat inspection is to promote animal and public health by preventing, detecting, and controlling hazards originating from animals. With the improvements of sanitary level in pig herds, the hazards profile has shifted and the inspection procedures no longer target major foodborne pathogens (i.e., not risk based). Additionally, carcass manipulations performed when searching for macroscopic lesions can lead to cross-contamination. We therefore developed a stochastic model to quantitatively describe cross-contamination when consecutive carcasses are submitted to classic inspection procedures. The microbial hazard used to illustrate the model was Salmonella, the data set was obtained from Brazilian slaughterhouses, and some simplifying assumptions were made. The model predicted that due to cross-contamination during inspection, the prevalence of contaminated carcass surfaces increased from 1.2% to 95.7%, whereas the mean contamination on contaminated surfaces decreased from 1 logCFU/cm² to -0.87 logCFU/cm², and the standard deviations decreased from 0.65 to 0.19. These results are explained by the fact that, due to carcass manipulations with hands, knives, and hooks, including the cutting of contaminated lymph nodes, Salmonella is transferred to previously uncontaminated carcasses, but in small quantities. These small quantities can easily go undetected during sampling. Sensitivity analyses gave insight into the model performance and showed that the touching and cutting of lymph nodes during inspection can be an important source of carcass contamination. The model can serve as a tool to support discussions on the modernization of pig carcass inspection.

Preharvest Food Safety Challenges in Beef and Dairy Production

Foods of animal origin, including beef and dairy products, are nutritious and important to global food security. However, there are important risks to human health from hazards that are introduced to beef and dairy products on the farm. Food safety hazards may be chemical, biological, or physical in nature. Considerations about protecting the safety of beef and dairy products must begin prior to harvest because some potential food safety hazards introduced at the farm (e.g., chemical residues) cannot be mitigated by subsequent postharvest food processing steps. Also, some people have preferences for consuming food that has not been through postharvest processing even though those foods may be unsafe because of microbiological hazards originating from the farm. Because of human fallibility and complex microbial ecologies, many of the preharvest hazards associated with beef and dairy products cannot entirely be eliminated, but the risk for most can be reduced through systematic interventions taken on the farm. Beef and dairy farms differ widely in production practices because of differences in natural, human, and capital resources. Therefore, the actions necessary to minimize on-farm food safety hazards must be farm-specific and they must address scientific, political, economic, and practical aspects. Notable successes in controlling and preventing on-farm hazards to food safety have occurred through a combination of voluntary and regulatory efforts.

Outbreak of Salmonella Reading in persons of Eastern Mediterranean origin in Canada, 2014-2015

Background

Salmonella Reading (S. Reading) is a rare serotype of Salmonella subspecies (spp.) in Canada with less than nine cases reported each year (2011-2013). An increase in S. Reading was identified in several Canadian provinces in early 2015, prompting the initiation of a national outbreak investigation.

Objectives

To describe a multi-provincial S. Reading outbreak in Canada that affected over 30 people.

Methods

Cases were defined as laboratory-confirmed S. Reading with related pulsed-field gel electrophoresis (PFGE) patterns. Onset dates were between November 2014 and September 2015.​: Early in the investigation, investigators noted cases were predominantly of Eastern Mediterranean origin, mainly Afghan and Lebanese and many of those affected had consumed food items not typically captured on standard enteric outbreak hypothesis-generating questionnaires. An open-ended three day food consumption survey was conducted with a convenience sample of community informants to better understand food preferences of the affected ethnocultural populations. Results of the survey were used to design a focused questionnaire for case re-interviews and subsequent outbreak cases. Public health investigators obtained food samples from case homes and relevant food premises. Food safety authorities conducted traceback of suspected food items and collected food samples for laboratory testing.

Results

There were 31 confirmed cases (Ontario=23, Alberta=7, New Brunswick=1) and three probable (Ontario=2, Alberta=1) cases of S. Reading identified as part of the outbreak. The median age was 31 years (range less than one to 85 years) and 53% (18/34) of cases were female. Seven cases were hospitalized. No deaths were reported. Most cases were of Eastern Mediterranean origin (n=23) or had reported consuming Eastern Mediterranean foods (n=3). The predominant ethnic origins reported by cases were Afghan in Ontario (n=12) and Lebanese in Alberta (n=3). Genetic similarity of clinical isolates was further confirmed using whole genome sequencing.​: Three ethnic bakeries were identified as possible common exposures for the cases; however, traceback of foods of interest from these bakeries did not identify a common supplier and the source of the illness was not identified. In total, 227 food samples from retail premises (n=142), restaurants (n=13) and case homes (n=72) were tested; two food samples, kalonji seeds and tahini, were positive for S. Ruiru and S. Meleagridis. These products were recalled from the marketplace.

Conclusion

Despite extensive epidemiological, microbiological and food traceback investigations, a common source was not identified for this S. Reading outbreak. Challenges included lack of familiarity with the food items consumed in affected ethnocultural groups, as well as a lack of background data on expected food exposures in the outbreak population. Engaging local partners helped build understanding of food preferences in affected communities. Given Canada's ethnic and cultural diversity, culturally competent approaches to enteric outbreak investigations and food consumption surveys may be useful.

Salmonella Presence in Mandibular, Mesenteric, and Subiliac Lymph Nodes Collected from Sheep and Goats in the United States

Even though often underappreciated in the United States, meat derived from goats and lambs is a valuable global commodity. Although extensive studies have been conducted examining pathogen prevalence in beef, pork, and poultry species, less research is available about pathogen presence in small ruminants. Understanding the presence of Salmonella in small ruminants can influence processing method improvements for these species to minimize food safety risks. The objective of this study was to establish the Salmonella presence in lymph nodes from sheep (n = 311) and goats (n =357) in the United States. Mandibular, mesenteric, and subiliac lymph nodes were collected from animals at abattoirs located in California, New Mexico, and Texas over a 14-month period. Lymph nodes were analyzed for Salmonella presence by using standard isolation methods, and presumptive isolates were confirmed with latex agglutination. Salmonella was detected in 3.15% of mandibular lymph nodes (n = 222), 5.83% of mesenteric lymph nodes (n = 223), and 7.62% of subiliac lymph nodes (n = 223). A total of 30 animals (13.39%) were found to have one or more Salmonella -positive lymph nodes. Our data indicate Salmonella is harbored within the lymph nodes of small ruminants. With this knowledge, further work can target strategies and interventions to minimize the risk associated with this pathogen during the processing of small ruminants.

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.

Efficacy of a Salmonella Siderophore Receptor Protein Vaccine on Fecal Shedding and Lymph Node Carriage of Salmonella in Commercial Feedlot Cattle

The efficacy of a Salmonella vaccine for reducing fecal shedding of Salmonella during the finishing period and lymph node (LN) carriage at harvest was investigated in commercial feedlot cattle. The study was designed as a pen-level randomized complete block with two treatment groups, a Salmonella Newport siderophore receptor and porin proteins-based vaccine (VAC) and a nonvaccinated control (CON). Cattle were randomly allocated into 24 pens within 12 blocks based on the time of allocation. Twenty to 25 fecal pats were collected from each of the study pen floors once a month from June to August 2013. During harvest, a minimum of 25 sub-iliac LN were collected from carcasses within each study pen. Fecal and pulverized LN samples were cultured for Salmonella quantification and detection. Mixed models were used to analyze the effect of vaccination on fecal shedding and LN carriage of Salmonella. Montevideo and Anatum were the predominant Salmonella serotypes among fecal samples and LNs; no Newport isolates were recovered. Vaccination was not significantly associated (p = 0.57) with the prevalence of Salmonella in feces over time; the mean within-pen prevalence was 62.3% and 66.0% among VAC and CON, respectively. Sampling month was significantly associated (p < 0.01) with fecal prevalence; mean prevalence was 71.4% for June, 48.6% for July, and 70.8% for August. Across all pens, the cumulative prevalence of Salmonella in LN was 86.4%. Vaccination resulted in no significant reduction in LN prevalence (p = 0.52); mean prevalence was 85.7% for VAC and 87.4% for CON groups. Although vaccinated cattle had numerically fewer Salmonella LN and fecal positives, there were no statistically significant vaccine effects. Potential reasons for the lack of vaccine efficacy could include an overwhelming Salmonella exposure, a lack of cross-protection against non-Newport serotypes, and insufficient duration of immunity relative to harvest.

Salmonella contamination, serovars and antimicrobial resistance profiles of cattle slaughtered in South Africa

Antimicrobial resistant Salmonella are among the leading causes of foodborne infections. Our aim was to determine Salmonella contamination during cattle slaughter in South African rural abattoirs (n = 23) and environmental samples. Furthermore, antimicrobial resistance patterns of the Salmonella isolates were determined. Samples of cattle faeces (n = 400), carcass sponges (n = 100), intestinal contents (n = 62), hides (n = 67), and water from the abattoirs (n = 75) were investigated for Salmonella species using microbiological techniques and species-specific polymerase chain reaction targeting the invA gene. In total 92 Salmonella species isolates were recovered. The Salmonella mean frequency of occurrence on hides, carcasses, and intestinal contents was 35.37% (n = 81). Eleven faecal samples (2.75%) tested positive for Salmonella. The predominant serovar was Salmonella Enteritidis. Diverse serovars that were identified on carcasses were not necessarily found on the hides and intestinal contents. The inconsistent occurrence of the diverse Salmonella serovars on hides, carcasses, and intestinal contents implies that in addition to carriage on hides and in intestinal contents, other external factors also play an important role regarding carcass contamination. The 92 Salmonella were serotyped and tested for susceptibility towards the following antimicrobials: ampicillin, cefotaxime, enrofloxacin, kanamycin, and oxytetracycline using the disk diffusion method. Most Salmonella (n = 66; 71.7%) isolates were resistant to at least one antimicrobial with highest resistance observed towards oxytetracycline (51.90%), which highlights the need for strict hygiene during slaughter and prudent antimicrobial use during animal production. In conclusion, cattle slaughtered in South African rural abattoirs harbour diverse Salmonella serovars that are resistant to antimicrobials, which could be a public health risk. The findings should assist policymakers with improving implementation of hygienic slaughter of cattle in rural abattoirs, which is paramount from socioeconomic, public health, and epidemiological standpoints.

Investigation into Possible Differences in Salmonella Prevalence in the Peripheral Lymph Nodes of Cattle Derived from Distinct Production Systems and of Different Breed Types

Previous research demonstrated significant variation in the prevalence of Salmonella in peripheral lymph nodes (LNs) of feedlot cattle and cull cows, with greater prevalence in feedlot cattle. Therefore, we performed experiments to investigate whether these differences in Salmonella prevalence in subiliac LNs are due to, or influenced by, breed, which in many respects is a proxy for the production system in which the animal is derived. Holstein steers are a by-product of dairy systems, and beef steers are an intended product of commercial beef operations. For the first experiment, Holstein and beef steers originating from the same feedlot and harvested on the same day were sampled. Of the 467 Holstein and 462 beef cattle LNs collected, 62.1% of Holstein and 59.7% of beef cattle samples harbored Salmonella (P = 0.46; qualitative culture), with 51.2 and 48.9% of samples containing quantifiable concentrations (P = 0.49), respectively. The concentration of Salmonella within the LN followed a decreasing trend over the collection period (May to October), averaging 1.4 log CFU/g of LN for both Holstein and beef cattle samples (P = 0.78). In a second experiment, we compared 100% Brahman cattle to their beef cattle counterparts, as we hypothesized that the resistance of Brahman cattle to insects may reduce Salmonella transmission via biting insects. Of the 42 Brahman and 31 beef cattle LNs collected, the concentration of Salmonella within the LN averaged 3.0 log CFU/g for Brahman cattle and 2.9 log CFU/g for beef cattle samples (P = 0.30). Using qualitative culture, we recovered Salmonella from 100% of LNs from Brahman cattle and 97% of beef cattle samples (P = 0.25). Results of this research indicate that the differences observed are not due to breed and are likely a function of age, immune function, or other factors yet to be identified. Understanding which cattle are more likely to harbor Salmonella within LNs will aid in targeting both pre- and postharvest intervention strategies.

Microbiological Testing Results of Boneless and Ground Beef Purchased for the National School Lunch Program, 2011 to 2014

The Agricultural Marketing Service (AMS) purchases boneless and ground beef for distribution to recipients through federal nutrition assistance programs, including the National School Lunch Program, which represents 93% of the overall volume. Approximately every 2,000 lb (ca. 907 kg) of boneless beef and 10,000 lb (ca. 4,535 kg) of ground beef are designated a "lot" and tested for Escherichia coli O157:H7, Salmonella, standard plate count organisms (SPCs), E. coli, and coliforms. Any lot of beef positive for E. coli O157:H7 or for Salmonella, or any beef with concentrations of organisms exceeding critical limits for SPCs (100,000 CFU g(-1)), E. coli (500 CFU g(-1)), or coliforms (1,000 CFU g(-1)) is rejected for purchase by AMS and must be diverted from federal nutrition assistance programs. From July 2011 through June 2014, 537,478,212 lb (ca. 243,795,996 kg) of boneless beef and 428,130,984 lb (ca. 194,196,932 kg) of ground beef were produced for federal nutrition assistance programs. Of the 230,359 boneless beef samples collected over this period, 82 (0.04%) were positive for E. coli O157:H7, 924 (0.40%) were positive for Salmonella, 222 (0.10%) exceeded the critical limit for SPCs, 69 (0.03%) exceeded the critical limit for E. coli, and 123 (0.05%) exceeded the critical limit for coliforms. Of the 46,527 ground beef samples collected over this period, 30 (0.06%) were positive for E. coli O157:H7, 360 (0.77%) were positive for Salmonella, 20 (0.04%) exceeded the critical limit for SPCs, 22 (0.05%) exceeded the critical limit for E. coli, and 17 (0.04%) exceeded the critical limit for coliforms. Cumulatively, these data suggest beef produced for the AMS National School Lunch Program is done so under an adequate food safety system, as indicated by the low percentage of lots that were pathogen positive or exceeded critical limits for indicator organisms.

Two Draft Genome Sequences of a New Serovar of Salmonella enterica, Serovar Lubbock

Salmonella enterica is principally a foodborne pathogen that shows considerable serovar diversity. In this report, we present two draft genome sequences of Salmonella enterica subsp. enterica serovar Lubbock, a novel serovar.