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

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.

Disease Occurrence in- and the Transferal of Zoonotic Agents by North American Feedlot Cattle

North America is a large producer of beef and contains approximately 12% of the world's cattle inventory. Feedlots are an integral part of modern cattle production in North America, producing a high-quality, wholesome protein food for humans. Cattle, during their final stage, are fed readily digestible high-energy density rations in feedlots. Cattle in feedlots are susceptible to certain zoonotic diseases that impact cattle health, growth performance, and carcass characteristics, as well as human health. Diseases are often transferred amongst pen-mates, but they can also originate from the environment and be spread by vectors or fomites. Pathogen carriage in the gastrointestinal tract of cattle often leads to direct or indirect contamination of foods and the feedlot environment. This leads to the recirculation of these pathogens that have fecal-oral transmission within a feedlot cattle population for an extended time. Salmonella, Shiga toxin-producing Escherichia coli, and Campylobacter are commonly associated with animal-derived foods and can be transferred to humans through several routes such as contact with infected cattle and the consumption of contaminated meat. Brucellosis, anthrax, and leptospirosis, significant but neglected zoonotic diseases with debilitating impacts on human and animal health, are also discussed.

Microbial Dynamics in Mixed-Culture Biofilms of Salmonella Typhimurium and Escherichia coli O157:H7 and Bacteria Surviving Sanitation of Conveyor Belts of Meat Processing Plants

Biofilm formation can lead to the persistence of Salmonella Typhimurium (ST) and E. coli O157:H7 (O157). This study investigated the impact of meat processing surface bacteria (MPB) on biofilm formation by O157 (non-biofilm former; NF) and ST (strong biofilm former; BF). MPB were recovered from the contacting surfaces (CS), non-contacting surfaces (NCS), and roller surfaces (RS) of a beef plant conveyor belt after sanitation. O157 and ST were co-inoculated with MPB (CO), or after a delay of 48 h (IS), into biofilm reactors containing stainless steel coupons and incubated at 15 °C for up to 144 h. Coupons were withdrawn at various intervals and analyzed by conventional plating and 16S rRNA gene amplicon sequencing. The total bacterial counts in biofilms reached approximately 6.5 log CFU/cm², regardless of MPB type or development mode. The mean counts for O157 and ST under equivalent conditions mostly did not differ (p > 0.05), except for the IS set at 50 h, where no O157 was recovered. O157 and ST were 1.6 ± 2.1% and 4.7 ± 5.0% (CO) and 1.1 ± 2.2% and 2.0 ± 2.8% (IS) of the final population. Pseudomonas dominated the MPB inocula and biofilms, regardless of MPB type or development mode. Whether or not a pathogen is deemed BF or NF in monoculture, its successful integration into complex multi-species biofilms ultimately depends on the presence of certain other residents within the biofilm.

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.

Salmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle

Salmonella enterica subsp. enterica (S.) serovar Cerro is rarely isolated from human clinical cases of salmonellosis but represents the most common serovar isolated from cattle without clinical signs of illness in the United States. In this study, using a large, diverse set of 316 isolates, we utilized genomic methods to further elucidate the evolutionary history of S. Cerro and to identify genomic features associated with its apparent virulence attenuation in humans. Phylogenetic analyses showed that within this polyphyletic serovar, 98.4% of isolates (311/316) represent a monophyletic clade within section Typhi and the remaining 1.6% of isolates (5/316) form a monophyletic clade within subspecies enterica Clade A1. Of the section Typhi S. Cerro isolates, 93.2% of isolates (290/311) clustered into a large clonal clade comprised of predominantly sequence type (ST) 367 cattle and environmental isolates, while the remaining 6.8% of isolates (21/311), primarily from human clinical sources, clustered outside of this clonal clade. A tip-dated phylogeny of S. Cerro ST367 identified two major clades (I and II), one of which overwhelmingly consisted of cattle isolates that share a most recent common ancestor that existed circa 1975. Gene presence/absence and rarefaction curve analyses suggested that the pangenome of section Typhi S. Cerro is open, potentially reflecting the gain/loss of prophage; human isolates contained the most open pangenome, while cattle isolates had the least open pangenome. Hypothetically disrupted coding sequences (HDCs) displayed clade-specific losses of intact speC and sopA virulence genes within the large clonal S. Cerro clade, while loss of intact vgrG, araH, and vapC occurred in all section Typhi S. Cerro isolates. Further phenotypic analysis suggested that the presence of a premature stop codon in speC does not abolish ornithine decarboxylase activity in S. Cerro, likely due to the activity of the second ornithine decarboxylase encoded by speF, which remained intact in all isolates. Overall, our study identifies specific genomic features associated with S. Cerro's infrequent isolation from humans and its apparent adaptation to cattle, which has broader implications for informing our understanding of the evolutionary events facilitating host adaptation in Salmonella.

Prevalence and Antimicrobial Resistance of Nontyphoidal Salmonella enterica from Head Meat and Trim for Ground Product at Pork Processing Facilities

ABSTRACT

Pork head meat may harbor Salmonella and contaminate other carcass by-products during harvest and fabrication. A large pork processing plant in the United States was sampled bimonthly for 11 months to determine the concentration, prevalence, seasonality, serotype diversity, and antimicrobial susceptibility of Salmonella enterica isolated from cheek meat and head trim of swine carcasses. Each collection consisted of 25 samples on two consecutive days in the morning and afternoon shifts, for a total of 100 cheek meat and 100 head trim samples each month. Tissues were cultured for Salmonella by using restrictive media and enrichment techniques, and a subset of isolates was serotyped, analyzed for antimicrobial susceptibility, and genome sequenced. Salmonella postenrichment prevalence did not differ (P = 0.20) between cheek meat (63%) and head trim (66%). Postenrichment prevalence differed (P < 0.05) by month (January, 94%; March, 80%; May, 54%; July, 59%; September, 47%; and November, 55%) and by processing shift (morning, 68%; afternoon, 62%). The subset (n = 618) of isolates selected for serotyping yielded 21 distinct serotypes: Typhimurium (49%), Infantis (10%), Heidelberg (8%), I 4,[5],12:i:- (8%), and 17 other types (≤5%). In total, 407 multidrug-resistant (MDR; resistance to three or more antibiotic classes) isolates were identified. There were 120 isolates that exhibited the penta-resistant ACSSuT phenotype. In addition, 113 isolates exhibited decreased susceptibility to ciprofloxacin (MIC ≥ 0.12 μg/mL). Resistance genes blaCARB, blaSHV, blaTEM, aac(6')-Ib-cr,qnrB, sul2, and dfrA were expressed in numerous MDR Salmonella isolates. The data herein suggest that pork products from the head, compared with data reported for carcasses, may have a relatively high prevalence of Salmonella with diverse serotypes and MDR.

HIGHLIGHTS

A Commentary on Salmonella From a Pre-Harvest Perspective

Salmonella occurs in all the major meat producing livestock species (ruminants, swine and poultry), most often residing within the gastrointestinal tract asymptomatically. While considerable success has been achieved post-harvest, the design of effective pre-harvest interventions to control Salmonella has lagged. A simplistic view of the extremely complex host/pathogen interaction suggests that the pathogen has a vested interest in not causing illness or death to the host. The former would initiate an immune response from the host and/or the application of therapeutic antibacterial agents, while the latter would require finding another suitable host. Due to the widespread prevalence of Salmonella within livestock and poultry, and the relatively few salmonellosis cases in comparison, it appears, and is supported by new research, that Salmonella has developed methods to avoid detection by the animal’s immune system and live essentially as a commensal organism within the gastrointestinal tract of the animal. Yet, for reasons that are not fully understood, this “commensal” Salmonella does on occasion become virulent, in young and mature animals alike. Indeed, these researchers have documented Salmonella carriage throughout the year in cattle, but only rarely, if at all, was salmonellosis observed. Further, evaluation of Salmonella isolates (serotype and antimicrobial resistance patterns) from sick and healthy cattle failed to explain that while Salmonella was present in the majority of cattle sampled on that farm, only a few developed salmonellosis. Virulence, as well as multi-drug resistance, in both livestock and humans appears to cluster within a few serotypes. As a result, petitions are circulating calling for the labeling of some Salmonella serotypes as adulterants, as was done with Escherichia coli O157:H7 and other enterohemorrhagic E. coli strains. Regulators are considering approaching the Salmonella problem by serotype, such as focusing specifically on the top 10 reported serotypes causing human illness. Herein, the authors will discuss the many challenges of controlling Salmonella pre-harvest, reflecting on the significant research portfolio that has been generated over the last 25 years, as well as challenging existing paradigms surrounding this pathogen and the experimental methods used to further our understanding of Salmonella and/or evaluate methods of control.

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.

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.

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

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.

Microbiological Testing Results of Boneless and Ground Beef Purchased for the U.S. National School Lunch Program, School Years 2015 to 2018

The Agricultural Marketing Service (AMS) purchases beef for the National School Lunch Program and other federal nutrition assistance programs. For beef that will be delivered to food service facilities raw, each ca. 900-kg lot of boneless beef raw material and each ca. 4,500-kg sublot of resultant ground beef is tested for standard plate count (SPC) organisms, coliforms, Escherichia coli, Salmonella, and E. coli O157:H7. In addition, 1 of every 10 lots of boneless beef, randomly selected, is tested for E. coli O26, O45, O103, O111, O121, and O145. For beef that will be cooked using a validated lethality step at a federally inspected establishment before delivery, each lot of boneless beef and each sublot of ground beef is tested for SPC organisms, coliforms, and E. coli only. Any lot or sublot exceeding predefined critical limits (CLs) of 100,000 CFU g^-1 for SPC organisms, 1,000 CFU g^-1 for coliforms, or 500 CFU g^-1 for E. coli or for beef containing Salmonella or any of previously mentioned E. coli serotypes is rejected for purchase. For school years 2015 through 2018 (July 2014 through June 2018), 220,497,254 kg of boneless beef and 189,347,318 kg of ground beef were produced for AMS. For boneless beef, 133 (0.06%), 164 (0.07%), and 106 (0.04%) of 240,488 lots exceeded CLs for SPC organisms, coliforms, and E. coli, respectively; 2,038 (1.30%) and 116 (0.07%) of 156,671 lots were positive for Salmonella and E. coli O157:H7, respectively; and 59 (0.36%) of 16,515 lots were positive for non-O157 Shiga toxin-producing E. coli. For ground beef, 46 (0.10%), 27 (0.06%), and 19 (0.04%) of 45,769 sublots exceeded CLs for SPC organisms, coliforms, and E. coli, respectively; and 329 (1.40%) and 18 (0.08%) of 23,475 sublots were positive for Salmonella and E. coli O157:H7, respectively. All lots and sublots found to exceed indicator organism CLs or to contain pathogens were identified, rejected for purchase, and diverted from federal nutrition assistance programs.