Occurrence of Antimicrobial-Resistant Escherichia coli and Salmonella enterica in the Beef Cattle Production and Processing Continuum

Impact of "Raised without Antibiotics" Beef Cattle Production Practices on Occurrences of Antimicrobial Resistance

The specific antimicrobial resistance (AMR) decreases that can be expected from reducing antimicrobial (AM) use in U.S. beef production have not been defined. To address this data gap, feces were recovered from 36 lots of "raised without antibiotics" (RWA) and 36 lots of "conventional" (CONV) beef cattle. Samples (n = 719) were collected during harvest and distributed over a year. AMR was assessed by (i) the culture of six AM-resistant bacteria (ARB), (ii) quantitative PCR (qPCR) for 10 AMR genes (ARGs), (iii) a qPCR array of 84 ARGs, and (iv) metagenomic sequencing. Generally, AMR levels were similar, but some were higher in CONV beef cattle. The prevalence of third-generation cephalosporin-resistant (3GC^r) Escherichia coli was marginally different between production systems (CONV, 47.5%; RWA, 34.8%; P = 0.04), but the seasonal effect (summer, 92.8%; winter, 48.3%; P < 0.01) was greater. Erythromycin-resistant (ERY^r) Enterococcus sp. concentrations significantly differed between production systems (CONV, 1.91 log₁₀ CFU/g; RWA, 0.73 log₁₀ CFU/g; P < 0.01). Levels of aadA1, ant(6)-I, bla _ACI, erm(A), erm(B), erm(C), erm(F), erm(Q), tet(A), tet(B), tet(M), and tet(X) ARGs were higher (P < 0.05) in the CONV system. Aggregate abundances of all 43 ARGs detected by metagenomic sequencing and the aggregate abundances of ARGs in the aminoglycoside, β-lactam, macrolide-lincosamide-streptogramin B (MLS), and tetracycline AM classes did not differ (log₂ fold change < 1.0) between CONV and RWA systems. These results suggest that further reductions of AM use in U.S. beef cattle production may not yield significant AMR reductions beyond MLS and tetracycline resistance.IMPORTANCE The majority of antimicrobial (AM) use in the United States is for food-animal production, leading to concerns that typical AM use patterns during "conventional" (CONV) beef cattle production in the United States contribute broadly to antimicrobial resistance (AMR) occurrence. In the present study, levels of AMR were generally similar between CONV and "raised without antibiotics" (RWA) cattle. Only a limited number of modest AMR increases was observed in CONV cattle, primarily involving macrolide-lincosamide-streptogramin B (MLS) and tetracycline resistance. Macrolides (tylosin) and tetracyclines (chlortetracycline) are administered in-feed for relatively long durations to reduce liver abscesses. To ensure judicious AM use, the animal health, economic, and AMR impacts of shorter duration in-feed administration of these AMs should be examined. However, given the modest AMR reductions observed, further reductions of AM use in U.S. beef cattle production may not yield significant AMR reductions beyond MLS and tetracycline resistance.

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

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

Surface-Modified Mesh Filter for Direct Nucleic Acid Extraction and its Application to Gene Expression Analysis

Rapid and convenient isolation of nucleic acids (NAs) from cell lysate plays a key role for onsite gene expression analysis. Here, this study achieves one-step and efficient capture of NA directly from cell lysate by developing a cationic surface-modified mesh filter (SMF). By depositing cationic polymer via vapor-phase deposition process, strong charge interaction is introduced on the surface of the SMF to capture the negatively charged NAs. The NA capturing capability of SMF is confirmed by X-ray photoelectron spectroscopy, fluorescent microscopy, and zeta potential measurement. In addition, the genomic DNAs of Escherichia Coli O157:H7 can be extracted by the SMF from artificially infected food, and fluorescent signal is observed on the surface of SMF after amplification of target gene. The proposed SMF is able to provide a more simplified, convenient, and fast extraction method and can be applied to the fields of food safety testing, clinical diagnosis, or environmental pollutant monitoring.

National Antimicrobial Resistance Monitoring System: Two Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance

Drug-resistant bacterial infections pose a serious and growing public health threat globally. In this review, we describe the role of the National Antimicrobial Resistance Monitoring System (NARMS) in providing data that help address the resistance problem and show how such a program can have broad positive impacts on public health. NARMS was formed two decades ago to help assess the consequences to human health arising from the use of antimicrobial drugs in food animal production in the United States. A collaboration among the Centers for Disease Control and Prevention, the U.S. Food and Drug Administration, the United States Department of Agriculture, and state and local health departments, NARMS uses an integrated "One Health" approach to monitor antimicrobial resistance in enteric bacteria from humans, retail meat, and food animals. NARMS has adapted to changing needs and threats by expanding surveillance catchment areas, examining new isolate sources, adding bacteria, adjusting sampling schemes, and modifying antimicrobial agents tested. NARMS data are not only essential for ensuring that antimicrobial drugs approved for food animals are used in ways that are safe for human health but they also help address broader food safety priorities. NARMS surveillance, applied research studies, and outbreak isolate testing provide data on the emergence of drug-resistant enteric bacteria; genetic mechanisms underlying resistance; movement of bacterial populations among humans, food, and food animals; and sources and outcomes of resistant and susceptible infections. These data can be used to guide and evaluate the impact of science-based policies, regulatory actions, antimicrobial stewardship initiatives, and other public health efforts aimed at preserving drug effectiveness, improving patient outcomes, and preventing infections. Many improvements have been made to NARMS over time and the program will continue to adapt to address emerging resistance threats, changes in clinical diagnostic practices, and new technologies, such as whole genome sequencing.

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

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

Antimicrobial usage and resistance in beef production

Antimicrobials are critical to contemporary high-intensity beef production. Many different antimicrobials are approved for beef cattle, and are used judiciously for animal welfare, and controversially, to promote growth and feed efficiency. Antimicrobial administration provides a powerful selective pressure that acts on the microbial community, selecting for resistance gene determinants and antimicrobial-resistant bacteria resident in the bovine flora. The bovine microbiota includes many harmless bacteria, but also opportunistic pathogens that may acquire and propagate resistance genes within the microbial community via horizontal gene transfer. Antimicrobial-resistant bovine pathogens can also complicate the prevention and treatment of infectious diseases in beef feedlots, threatening the efficiency of the beef production system. Likewise, the transmission of antimicrobial resistance genes to bovine-associated human pathogens is a potential public health concern. This review outlines current antimicrobial use practices pertaining to beef production, and explores the frequency of antimicrobial resistance in major bovine pathogens. The effect of antimicrobials on the composition of the bovine microbiota is examined, as are the effects on the beef production resistome. Antimicrobial resistance is further explored within the context of the wider beef production continuum, with emphasis on antimicrobial resistance genes in the food chain, and risk to the human population.

Effects of In-Feed Chlortetracycline Prophylaxis in Beef Cattle on Animal Health and Antimicrobial-Resistant Escherichia coli

Concerns have been raised that in-feed chlortetracycline (CTC) may increase antimicrobial resistance (AMR), specifically tetracycline-resistant (TET^r) Escherichia coli and third-generation cephalosporin-resistant (3GC^r) E. coli We evaluated the impact of a 5-day in-feed CTC prophylaxis on animal health, TET^r E. coli, and 3GC^r E. coli A control group of cattle (n = 150) received no CTC, while a CTC group (n = 150) received in-feed CTC (10 mg/lb of body weight/day) from the 5th to the 9th day after feedlot arrival. Over 25% (38/150) of the animals in the control group developed illnesses requiring therapeutic treatment with antimicrobials critically important to human medicine. Only two animals (1.3%) in the CTC group required such treatments. Fecal swab and pen surface occurrences of generic E. coli (isolated on media that did not contain antimicrobials of interest and were not isolated based on any specific resistance), TET^r E. coli, and 3GC^r E. coli were determined on five sampling occasions: arrival at the feedlot, 5 days posttreatment (5 dpt), 27 dpt, 75 dpt, and 117 dpt. On 5 dpt, TET^r E. coli concentrations were higher for the CTC group than the control group (P < 0.01). On 27 dpt, 75 dpt, and 117 dpt, TET^r E. coli concentrations did not differ between groups. 3GC^r E. coli occurrences did not differ between control and CTC groups on any sampling occasion. For both groups, generic, TET^r, and 3GC^r E. coli occurrences were highest on 75 dpt and 117 dpt, suggesting that factors other than in-feed CTC contributed more significantly to antimicrobial-resistant E. coli occurrence.

IMPORTANCE

The occurrence of human bacterial infections resistant to antimicrobial therapy has been increasing. It has been postulated that antimicrobial resistance was inevitable, but the life span of the antimicrobial era has been prematurely compromised due to the misuse of antimicrobials in clinical and agricultural practices. Direct evidence relating the use of antimicrobials in livestock production to diminished human health outcomes due to antimicrobial resistance is lacking, and the U.S. Food and Drug Administration has taken an approach to maximize therapeutic efficacy and minimize the selection of resistant microorganisms through judicious use of antimicrobials. This study demonstrated that prophylactic in-feed treatment of chlortetracycline administered for 5 days to calves entering feedlots is judicious, as this therapy reduced animal morbidity, reduced the use of antimicrobials more critical to human health, and had no long-term impact on the occurrence of antimicrobial-resistant E. coli.

Escherichia coli O157:H7 Strains Isolated from High-Event Period Beef Contamination Have Strong Biofilm-Forming Ability and Low Sanitizer Susceptibility, Which Are Associated with High pO157 Plasmid Copy Number

In the meat industry, a high-event period (HEP) is defined as a time period when beef processing establishments experience an increased occurrence of product contamination by Escherichia coli O157:H7. Our previous studies suggested that bacterial biofilm formation and sanitizer resistance might contribute to HEPs. We conducted the present study to further characterize E. coli O157:H7 strains isolated during HEPs for their potential to cause contamination and to investigate the genetic basis for their strong biofilm-forming ability and high sanitizer resistance. Our results show that, compared with the E. coli O157:H7 diversity control panel strains, the HEP strains had a significantly higher biofilm-forming ability on contact surfaces and a lower susceptibility to common sanitizers. No difference in the presence of disinfectant-resistant genes or the prevalence of antibiotic resistance was observed between the HEP and control strains. However, the HEP strains retained significantly higher copy numbers of the pO157 plasmid. A positive correlation was observed among a strain's high plasmid copy number, strong biofilm-forming ability, low sanitizer susceptibility, and high survival and recovery capability after sanitization, suggesting that these specific phenotypes could be either directly correlated to gene expression on the pO157 plasmid or indirectly regulated via chromosomal gene expression influenced by the presence of the plasmid. Our data highlight the potential risk of biofilm formation and sanitizer resistance in HEP contamination by E. coli O157:H7, and our results call for increased attention to proper and effective sanitization practices in meat processing facilities.

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

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

Antimicrobial-Resistant Bacterial Populations and Antimicrobial Resistance Genes Obtained from Environments Impacted by Livestock and Municipal Waste

This study compared the populations of antimicrobial-resistant bacteria and the repertoire of antimicrobial resistance genes in four environments: effluent of three municipal wastewater treatment facilities, three cattle feedlot runoff catchment ponds, three swine waste lagoons, and two "low impact" environments (an urban lake and a relict prairie). Multiple liquid and solid samples were collected from each environment. The prevalences and concentrations of antimicrobial-resistant (AMR) Gram-negative (Escherichia coli and Salmonella enterica) and Gram-positive (enterococci) bacteria were determined from individual samples (n = 174). The prevalences of 84 antimicrobial resistance genes in metagenomic DNA isolated from samples pooled (n = 44) by collection date, location, and sample type were determined. The prevalences and concentrations of AMR E. coli and Salmonella were similar among the livestock and municipal sample sources. The levels of erythromycin-resistant enterococci were significantly higher in liquid samples from cattle catchment ponds and swine waste lagoons than in liquid samples from municipal wastewater treatment facilities, but solid samples from these environments did not differ significantly. Similarly, trimethoprim/sulfamethoxazole-resistant E. coli concentrations were significantly higher in swine liquid than in municipal liquid samples, but there was no difference in solid samples. Multivariate analysis of the distribution of antimicrobial resistance genes using principal coordinate analysis showed distinct clustering of samples with livestock (cattle and swine), low impact environment and municipal samples forming three separate clusters. The numbers of class A beta-lactamase, class C beta-lactamase, and fluoroquinolone resistance genes detected were significantly higher (P < 0.05) in municipal samples than in cattle runoff or swine lagoon samples. In conclusion, we report that AMR is a very widespread phenomenon and that similar prevalences and concentrations of antimicrobial-resistant bacteria and antimicrobial resistance genes exist in cattle, human, and swine waste streams, but a higher diversity of antimicrobial resistance genes are present in treated human waste discharged from municipal wastewater treatment plants than in livestock environments.