Antimicrobial-Resistant Fecal Bacteria from Ceftiofur-Treated and Nonantimicrobial-Treated Comingled Beef Cows at a Cow–Calf Operation

Salmonella spp. in Domestic Ruminants, Evaluation of Antimicrobial Resistance Based on the One Health Approach-A Systematic Review and Meta-Analysis

Salmonella spp. pose a global threat as a leading cause of foodborne illnesses, particularly prevalent in the European Union (EU), where it remains the second cause of foodborne outbreaks. The emergence of antimicrobial resistance (AMR) in Salmonella spp. has become a critical concern, complicating treatment strategies and escalating the risk of severe infections. The study focuses on large and small ruminants, identifying a prevalence of Salmonella spp. in slaughterhouses and revealing varied AMR rates across antimicrobial families throughout a meta-analysis. Also, comparison with AMR in human medicine was carried out by a systematic review. The results of the present meta-analysis displayed a prevalence of Salmonella spp. in large and small ruminants at slaughterhouses of 8.01% (8.31%, cattle; 7.04%, goats; 6.12%, sheep). According to the AMR of Salmonella spp., 20, 14, and 13 out of 62 antimicrobials studied were classified as low (<5%), high (>5% but <10%), and very high (>10%), respectively. Salmonella spp. did not display AMR against aztreonam, mezlocillin, ertapenem, meropenem, cefoxitin, ceftazidime, levofloxacin, tilmicosin, linezolid, fosfomycin, furazolidone, quinupristin, trimethoprim and spectinomycin. In contrast, a prevalence of 100% of AMR has been described against ofloxacin, lincomycin, and cloxacillin. In the context of the main antibiotics used in the treatment of human salmonellosis, azithromycin was shown to have the highest resistance among Salmonella spp. isolates from humans. Regarding cephalosporins, which are also used for the treatment of salmonellosis in humans, the prevalence of Salmonella spp. resistance to this class of antibiotics was similar in both human and animal samples. Concerning quinolones, despite a heightened resistance profile in Salmonella spp. isolates from ruminant samples, there appears to be no discernible compromise to the efficacy of salmonellosis treatment in humans since lower prevalences of AMR in Salmonella spp. isolated from human specimens were observed. Although the resistance of Salmonella spp. indicates some degree of concern, most antibiotics are not used in veterinary medicine. Thus, the contribution of cattle, sheep and goats to the rise of antibiotic resistance of Salmonella spp. and its potential impact on public health appears to be relatively insignificant, due to their low prevalence in carcasses and organs. Nevertheless, the observed low prevalence of Salmonella spp. in ruminants at slaughterhouse and the correspondingly low AMR rates of Salmonella spp. to key antibiotics employed in human medicine do not indicate that ruminant livestock poses a substantial public health risk concerning the transmission of AMR. Thus, the results observed in both the meta-analysis and systematic review suggests that AMR is not solely attributed to veterinary antibiotic use but is also influenced by factors such as animal health management (i.e., biosecurity measures, prophylactic schemes) and human medicine.

Reducing transmission of high-risk antibiotic resistance genes in whole-crop corn silage through lactic acid bacteria inoculation and increasing ensiling temperature

The microbial hosts of antibiotic resistance genes (ARGs) found epiphytically on plant materials could grow and flourish during silage fermentation. This study employed metagenomic analysis and elucidated the occurrence and transmission mechanisms of ARGs and their microbial hosts in whole-crop corn silage inoculated with homofermentative strain Lactiplantibacillus plantarum or heterofermentative strain Lentilactobacillus buchneri ensiled under different temperature (20 and 30 °C). The results revealed that the corn silage was dominated by Lactobacillus, Leuconostoc, Lentilactobacillus, and Latilactobacillus. Both the ensiling temperature and inoculation had greatly modified the silage microbiota. However, regardless of the ensiling temperature, L. buchneri had significantly higher ARGs, while it only exhibited significantly higher mobile genetic elements (MGEs) in low temperature treatments. The microbial community of the corn silage hosted highly diverse form of ARGs, which were primarily MacB, RanA, bcrA, msbA, TetA (58), and TetT and mainly corresponded to macrolides and tetracyclines drug classes. Plasmids were identified as the most abundant MGEs with significant correlation with some high-risk ARGs (tetM, TolC, mdtH, and NorA), and their abundances have been reduced by ensiling process. Furthermore, higher temperature and L. buchneri reduced abundances of high-risk ARGs by modifying their hosts and reduced their transmission in the silage. Therefore, ensiling, L. buchneri inoculation and higher storage temperature could improve the biosafety of corn silage.

Prevalence and antimicrobial resistance profiles of extended-spectrum beta-lactamase-producing Escherichia coli in East Tennessee dairy farms

Introduction

The extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, such as Escherichia coli, are emerging as a serious threat to global health due to their rapid spread and their multidrug-resistant (MDR) phenotypes. However, limited information is available regarding the prevalence and antimicrobial resistance (AMR) profile of ESBL-E. coli in the United States dairy farms. This study aimed to determine the prevalence and AMR pattern of ESBL-E. coli in East Tennessee dairy cattle farms.

Methods

Rectal fecal samples from dairy cattle (n = 508) and manure (n = 30), water (n = 19), and feed samples (n = 15) were collected from 14 farms. The presumptive E. coli was isolated on CHROMagar™ ESBL and confirmed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Antimicrobial susceptibility testing was performed on the ESBL-E. coli isolates.

Results and discussion

From 572 fecal and farm environmental samples, a total of 233 (41%, n = 572) ESBL-E. coli were identified. The prevalence of fecal ESBL-E. coli was 47.5% (95% CI: 46.2-49.2). The within-farm prevalence of ESBL-E. coli ranged from 8 to 100%. Recent treatment history with third-generation cephalosporins (3GC), cow parity ≥3, and calves were the independent risk factors associated (P < 0.05) with fecal carriage of ESBL-E. coli. Overall, 99.6% (n = 231) ESBL-E. coli tested were phenotypically resistant to at least one of the 14 antimicrobial agents tested. The most common AMR phenotypes were against beta-lactam antibiotics, ampicillin (99.1%; n = 231 isolates), and ceftriaxone (98.7%, n = 231). Most ESBL-E. coli isolates (94.4%) were MDR (resistance to ≥3 antimicrobial classes), of which 42.6% showed co-resistance to at least six classes of antimicrobials. ESBL-E. coli isolates with concurrent resistance to ceftriaxone, ampicillin, streptomycin, tetracycline, sulfisoxazole, and chloramphenicol are widespread and detected in all the farms. The detection of MDR ESBL-E. coli suggests that dairy cattle can be a reservoir for these bacteria, highlighting the associated public health risk.

A Scoping Review of Antimicrobial Usage and Antimicrobial Resistance in Beef Cow-Calf Herds in the United States and Canada

BACKGROUND

The magnitude and knowledge gaps regarding antimicrobial use (AMU) and antimicrobial resistance (AMR) have not been summarized for the North American cow-calf production sector, although estimates of AMU and AMR are essential to AMR risk analysis. The objectives of this scoping review were to map AMU and AMR in the beef cow-calf sector in Canada and the United States, summarize published AMU/AMR predictors, and identify research gaps.

METHODS

An electronic search was conducted of four bibliographic databases and Google Scholar, augmented by a hand-search of captured studies.

RESULTS

Twenty-three of three-hundred and forty-three publications screened advanced to data extraction. Of these, 10 were conducted in the USA and 13 in Canada. Thirteen studied AMR and twelve studied AMU, with two reporting both. Of twelve captured AMU studies, nine presented counts of herd AMU by antimicrobial class or specific antimicrobial. Antimicrobial resistance in Escherichia coli (E. coli) was reported in nine studies. Risk factors for AMU include herd size, vaccine use, and start date of calving season.

CONCLUSIONS

Overall, a small number of AMR studies were available for synthesis in primarily one population (cows) reporting E. coli AMR. Additional studies targeting reasons for AMU in calves, the impact of management procedures on AMU, potential environmental AMR sources, and AMR in respiratory pathogens and enteric organisms other than E. coli for pre-weaning calves are required to inform AMR risk mitigation strategies.

Antibimicrobial Susceptibility of Trimethoprim-Sulfamethoxazole and 3rd-Generation Cephalosporin-Resistant Escherichia coli Isolates Enumerated Longitudinally from Feedlot Arrival to Harvest in High-Risk Beef Cattle Administered Common Metaphylactic Antimicrobials

Multidrug resistant (MDR) Escherichia coli threaten the preservation of antimicrobials to treat infections in humans and livestock. Thus, it is important to understand where antimicrobial-resistant E. coli persist and factors that contribute to its their development. Crossbred cattle (n = 249; body weight = 244 kg ±25 kg standard deviation) were blocked by arrival date and assigned metaphylactic antimicrobial treatments of sterile saline control, tulathromycin (TUL), ceftiofur, or florfenicol at random. Trimethoprim-sulfamethoxazole (COTR) and third-generation cephalosporin (CTXR)-resistant E. coli were isolated from fecal samples on days 0, 28, 56, 112, 182, and study END (day 252 for block 1 and day 242 for block 2). Then, susceptibility testing was conducted on all confirmed isolates. MDR was detected in both COTR and CTXR E. coli isolates. In COTR isolates, the number of antimicrobials each isolate was resistant to and the minimum inhibitory concentration (MIC) for amoxicillin-clavulanic acid, ceftriaxone, and gentamicin was greatest on day 28 compared with all other days (p ≤ 0.04). Similarly, chloramphenicol MIC was greater on day 28 than on day 0 (p < 0.01). Overall, sulfisoxazole MIC was less for TUL than all other treatments (p ≤ 0.02), and trimethoprim-sulfamethoxazole MIC was greater for TUL than all other treatments (p ≤ 0.03). Finally, there was no effect of treatment, day, or treatment × day for tetracycline or meropenem MIC (p ≥ 0.07). In CTXR isolates, there was an effect of day for all antimicrobials tested except ampicillin and meropenem (p ≤ 0.06). In conclusion, administering a metaphylactic antimicrobial at feedlot arrival did influence the susceptibility of COTR and CTXR E. coli. However, MDR E. coli are widely distributed, and the MIC for most antimicrobials was not different from the initial value upon completion of the feeding period.

Prevalence of antimicrobial resistance in fecal Escherichia coli and Enterococcus spp. isolates from beef cow-calf operations in northern California and associations with farm practices

Antimicrobials are necessary for the treatment of bacterial infections in animals, but increased antimicrobial resistance (AMR) is becoming a concern for veterinarians and livestock producers. This cross-sectional study was conducted on cow-calf operations in northern California to assess prevalence of AMR in Escherichia coli and Enterococcus spp. shed in feces of beef cattle of different life stages, breeds, and past antimicrobial exposures and to evaluate if any significant factors could be identified that are associated with AMR status of the isolates. A total of 244 E. coli and 238 Enterococcus isolates were obtained from cow and calf fecal samples, tested for susceptibility to 19 antimicrobials, and classified as resistant or non-susceptible to the antimicrobials for which breakpoints were available. For E. coli, percent of resistant isolates by antimicrobial were as follows: ampicillin 100% (244/244), sulfadimethoxine 25.4% (62/244), trimethoprim-sulfamethoxazole 4.9% (12/244), and ceftiofur 0.4% (1/244) while percent of non-susceptible isolates by antimicrobial were: tetracycline 13.1% (32/244), and florfenicol 19.3% (47/244). For Enterococcus spp., percent of resistant isolates by antimicrobial were as follows: ampicillin 0.4% (1/238) while percent of non-susceptible isolates by antimicrobial were tetracycline 12.6% (30/238) and penicillin 1.7% (4/238). No animal level or farm level management practices, including antimicrobial exposures, were significantly associated with differences in isolate resistant or non-susceptible status for either E. coli or Enterococcus isolates. This is contrary to the suggestion that administration of antibiotics is solely responsible for development of AMR in exposed bacteria and demonstrates that there are other factors involved, either not captured in this study or not currently well understood. In addition, the overall use of antimicrobials in this cow-calf study was lower than other sectors of the livestock industry. Limited information is available on cow-calf AMR from fecal bacteria, and the results of this study serve as a reference for future studies to support a better understanding and estimation of drivers and trends for AMR in cow-calf operations.

Factors associated with antimicrobial resistant enterococci in Canadian beef cattle: A scoping review

Introduction

Antimicrobial resistance (AMR) is a global health concern, occurring when bacteria evolve to render antimicrobials no longer effective. Antimicrobials have important roles in beef production; however, the potential to introduce AMR to people through beef products is a concern. This scoping review identifies factors associated with changes in the prevalence of antimicrobial-resistant Enterococcus spp. applicable to the Canadian farm-to-fork beef continuum.

Methods

Five databases (MEDLINE, BIOSIS, Web of Science, Embase, and CAB Abstracts) were searched for articles published from January 1984 to March 2022, using a priori inclusion criteria. Peer-reviewed articles were included if they met all the following criteria: written in English, applicable to the Canadian beef production context, primary research, in vivo research, describing an intervention or exposure, and specific to Enterococcus spp.

Results

Out of 804 screened articles, 26 were selected for inclusion. The included articles discussed 37 factors potentially associated with AMR in enterococci, with multiple articles discussing at least two of the same factors. Factors discussed included antimicrobial administration (n = 16), raised without antimicrobials (n = 6), metal supplementation (n = 4), probiotics supplementation (n = 3), pen environment (n = 2), essential oil supplementation (n = 1), grass feeding (n = 1), therapeutic versus subtherapeutic antimicrobial use (n = 1), feeding wet distiller grains with solubles (n = 1), nutritional supplementation (n = 1) and processing plant type (n = 1). Results were included irrespective of their quality of evidence.

Discussion

Comparability issues arising throughout the review process were related to data aggregation, hierarchical structures, study design, and inconsistent data reporting. Findings from articles were often temporally specific in that resistance was associated with AMR outcomes at sampling times closer to exposure compared to studies that sampled at longer intervals after exposure. Resistance was often nuanced to unique gene and phenotypic resistance patterns that varied with species of enterococci. Intrinsic resistance and interpretation of minimum inhibitory concentration varied greatly among enterococcal species, highlighting the importance of caution when comparing articles and generalizing findings.

Systematic Review Registration

[http://hdl.handle.net/1880/113592].

Tetracycline-Resistant, Third-Generation Cephalosporin-Resistant, and Extended-Spectrum β-Lactamase-Producing Escherichia coli in a Beef Cow-Calf Production System

ABSTRACT

Cow-calf production plays a significant role in the beef production chain. However, bacteria in these systems are not typically monitored for antimicrobial resistance (AMR). We determined the baseline level of AMR in fecal bacteria collected from preweaned calves prior to feedlot entry and evaluated the effects of type of graze and age on AMR occurrence. Two grazing experiments (16 cow-calf pairs each) were conducted on tall fescue or wheat. Fecal samples were cultured for the detection of tetracycline-resistant (TETr), third-generation cephalosporin-resistant (3GCr), and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli. Isolates were characterized for resistance to other antibiotics and resistance mechanisms. Concentrations (P < 0.001) and prevalence (P = 0.007) of TETrE. coli isolates were significantly higher in the calves (5.1 log CFU/g and 93%, respectively) than in the cows (4.4 log CFU/g and 80%, respectively). Wheat grazing did not affect TETr isolates phenotypically; however, it significantly expanded (P = 0.005) the resistant population carrying tet(A) over that carrying tet(B). Fecal prevalence of 3GCr and ESBL-producing isolates was 31.3 and 3.4%, respectively, with no significant effects of age (P = 0.340) or wheat grazing (P = 0.597). All 3GCr and ESBL-producing isolates were multidrug resistant (resistant to at least three antimicrobial classes). 3GCr isolates were positive for blaCMY-2 (73%) or blaCTX-M (27%), and blaCTX-M-15 was the most prevalent gene (94%, n = 17) among the CTX-M-positive isolates. Wheat grazing significantly expanded (P < 0.001) the 3GCr population carrying blaCTX-M and reduced the population carrying blaCMY-2. Five of the seven ESBL-producing isolates were positive for blaCTX-M. Our study revealed age-dependent occurrence of TETrE. coli and that wheat grazing expanded the resistant population carrying certain resistance genes. Cow-calf production is a significant reservoir for antibiotic-resistant bacteria of significant public health importance such as 3GCr and CTX-M ESBL-producing E. coli.

HIGHLIGHTS

Extended-Spectrum Beta-Lactamases Producing Enterobacteriaceae in the USA Dairy Cattle Farms and Implications for Public Health

Antimicrobial resistance (AMR) is one of the top global health threats of the 21th century. Recent studies are increasingly reporting the rise in extended-spectrum beta-lactamases producing Enterobacteriaceae (ESBLs-Ent) in dairy cattle and humans in the USA. The causes of the increased prevalence of ESBLs-Ent infections in humans and commensal ESBLs-Ent in dairy cattle farms are mostly unknown. However, the extensive use of beta-lactam antibiotics, especially third-generation cephalosporins (3GCs) in dairy farms and human health, can be implicated as a major driver for the rise in ESBLs-Ent. The rise in ESBLs-Ent, particularly ESBLs-Escherichia coli and ESBLs-Klebsiella species in the USA dairy cattle is not only an animal health issue but also a serious public health concern. The ESBLs-E. coli and -Klebsiella spp. can be transmitted to humans through direct contact with carrier animals or indirectly through the food chain or via the environment. The USA Centers for Disease Control and Prevention reports also showed continuous increase in community-associated human infections caused by ESBLs-Ent. Some studies attributed the elevated prevalence of ESBLs-Ent infections in humans to the frequent use of 3GCs in dairy farms. However, the status of ESBLs-Ent in dairy cattle and their contribution to human infections caused by ESBLs-producing enteric bacteria in the USA is the subject of further study. The aims of this review are to give in-depth insights into the status of ESBL-Ent in the USA dairy farms and its implication for public health and to highlight some critical research gaps that need to be addressed.

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.

Tetracycline- and Macrolide-Resistant Enterococcus Species Isolated from a Mink Farm in the United States

Enterococcus species are a normal flora of animals and humans. However, life-threatening opportunistic infections can be caused by antimicrobial resistant strains. Fecal (n = 42) and feed (n = 8) samples were obtained from a mink farm and cultured for the enumeration and detection of erythromycin-resistant (a macrolide; ERY^r)- and tetracycline-resistant (TET^r) enterococci. ERY^r and TET^r enterococci were detected from all fecal (mean concentrations = 6 and 7 logs, respectively) and feed (mean concentrations = 5 and 4 logs, respectively) samples. While Enterococcus faecalis and Enterococcus faecium were detected at equal proportions among the fecal TET^r isolates, E. faecium predominated among ERY^r fecal isolates. All ERY^r and 90% of the TET^r isolates (n = 50) were multidrug resistant (resistant to three or more antimicrobial classes). Among ERY^r isolates, while 83% of E. faecalis (n = 12) were positive for erm(B), 58% of E. faecium (n = 38) isolates were positive for msr(C). Among ERY^r isolates, tet(M) was detected from 92% of E. faecalis (n = 12) and 97% of E. faecium (n = 38) isolates. Conversely, however, erm(B) was detected in 18% of E. faecalis (n = 22) and 33% of E. faecium (n = 27) TET^r isolates. Our study provides a baseline for future efforts to reduce antimicrobial resistance and improve antimicrobial stewardship in commercial mink production facilities.

Prevalence of Antimicrobial Resistant and Extended-Spectrum Beta-Lactamase-producing Escherichia coli in Dairy Cattle Farms in East Tennessee

Antimicrobials have been widely used in dairy farms to prevent and control dairy cattle diseases since 1960s. This led to the emergence of antimicrobial resistant bacteria (ARB) that, along with their antimicrobial resistance genes (ARGs), can spread from dairy farms to humans. Therefore, regular antimicrobial resistance (AMR) monitoring is important to implement proper mitigation measures. The objective of this study was to determine the prevalence of AMR and extended-spectrum beta-lactamases (ESBLs)-producing Escherichia coli in dairy cattle. A cross-sectional study was conducted in four dairy cattle farms (A-D) in East Tennessee. A total of 80 samples consisting of 20 samples each of bulk tank milk, feces, dairy cattle manure-amended soil, and prairie soil adjacent to the farms were collected and cultured for the isolation of E. coli. Tetracycline (TET^r)-, third-generation cephalosporin (TGC^r)- and nalidixic acid (NAL^r)-resistant E. coli (n = 88) were isolated and identified on agar media supplemented with TET, cefotaxime, and NAL, respectively. TGC^r E. coli were tested for ESBLs and other coselected ARGs. TET^r (74%, n = 88) was the most common, followed by TGC^r (20%) and NAL^r (8%). Farms had significant (p < 0.001) differences: the highest prevalence of TGC^r (55%) and TET^r (100%) were observed in farm D, while all NAL^r isolates were from farm C. Over 83% of TGC^r isolates (n = 18) harbored ESBL gene bla_CTX-M. Majority (78%) of the E. coli isolates were multidrug-resistant (MDR), being positive for beta-lactams (bla_CTX-M), TETs tet(A), tet(B), tet(M)), sulfonamides (sul2), aminoglycosides (strA), and phenicols (floR). This study indicated the widespread occurrence of MDR ESBLs-E. coli in dairy cattle farms. AMR surveillance of more dairy farms and identification of farm-level risk factors are important to mitigate the occurrence and spread of ARB of significant public health importance, such as ESBLs-E. coli.

Management-intensive grazing impacts on total Escherichia coli, E. coli O157:H7, and antibiotic resistance genes in a riparian stream

The impacts of management-intensive grazing (MIG) of cattle on concentrations of total Escherichia coli, total suspended solids (TSS), and nitrate-nitrite nitrogen (NO₃ + NO₂-N), and occurrence of E. coli O157:H7 and selected antibiotic resistance genes (ARGs) in stream water and/or sediments were evaluated. Cattle were grazed for two-week periods in May in each of three years. Overall, grazing increased total E. coli in downstream water by 0.89 log₁₀ MPN/100 mL (p < 0.0001), and downstream total E. coli concentrations were higher than upstream over all sampling intervals. Downstream TSS levels also increased (p ≤ 0.0294) during grazing. In contrast, there was a main effect of treatment for downstream NO₃ + NO₂-N to be lower than upstream (3.59 versus 3.70 mg/L; p = 0.0323). Overwintering mallard ducks increased total E. coli and TSS concentrations in January and February (p < 0.05). For precipitation events during the 24 h before sampling, each increase of 1.00 cm of rainfall increased total E. coli by 0.49 log₁₀ MPN/100 mL (p = 0.0005). In contrast, there was no association of previous 24 h precipitation volume on TSS (p = 0.1540), and there was a negative linear effect on NO₃ + NO₂-N (p = 0.0002). E. coli O157:H7 prevalence was low, but the pathogen was detected downstream up to 2½ months after grazing. Examination of ARGs sul1, ermB, bla_ctx-m-32, and intI1 identified the need for additional research to understand the impact of grazing on the ecology of these resistance determinants in pasture-based cattle production. While E. coli remained higher in downstream water compared to upstream, MIG may reduce the magnitude of the downstream E. coli concentrations. Likewise, the MIG strategy may prevent large increases in TSS and NO₃ + NO₂-N concentrations during heavy rain events. Results indicate that MIG can limit the negative effects of cattle grazing on stream water quality.

A Farm-to-Fork Quantitative Microbial Exposure Assessment of β-Lactam-Resistant Escherichia coli among U.S. Beef Consumers

Integrated quantitative descriptions of the transmission of β-lactam-resistant Escherichia coli (BR-EC) from commercial beef products to consumers are not available. Here, a quantitative microbial exposure assessment model was established to simulate the fate of BR-EC in a farm-to-fork continuum and provide an estimate of BR-EC exposure among beef consumers in the U.S. The model compared the per-serving exposures from the consumption of intact beef cuts, non-intact beef cuts, and ground beef. Additionally, scenario analysis was performed to evaluate the relative contribution of antibiotic use during beef cattle production to the level of human exposure to BR-EC. The model predicted mean numbers of BR-EC of 1.7 × 10⁻⁴, 8.7 × 10⁻⁴, and 6.9 × 10⁻¹ CFU/serving for intact beef cuts, non-intact beef cuts, and ground beef, respectively, at the time of consumption. Sensitivity analyses using the baseline model suggested that factors related to sectors along the supply chain, i.e., feedlots, processing plants, retailers, and consumers, were all important for controlling human exposure to BR-EC. Interventions at the processing and post-processing stages are expected to be most effective. Simulation results showed that a decrease in antibiotic use among beef cattle might be associated with a reduction in exposure to BR-EC from beef consumption. However, the absolute reduction was moderate, indicating that the effectiveness of restricting antibiotic use as a standalone strategy for mitigating human exposure to BR-EC through beef consumption is still uncertain. Good cooking and hygiene practices at home and advanced safety management practices in the beef processing and post-processing continuum are more powerful approaches for reducing human exposure to antibiotic-resistant bacteria in beef products.

Resistomes and microbiome of meat trimmings and colon content from culled cows raised in conventional and organic production systems

Background

The potential to distribute bacteria resistant to antimicrobial drugs in the meat supply is a public health concern. Market cows make up a fifth of the U.S. beef produced but little is known about the entire population of bacteria (the microbiome) and entirety of all resistance genes (the resistome) that are found in this population. The objective of this study was to characterize and compare the resistomes and microbiome of beef, dairy, and organic dairy market cows at slaughter.

Methods

Fifty-four (N = 54) composite samples of both colon content and meat trimmings rinsate samples were collected over six visits to two harvest facilities from cows raised in three different production systems: conventional beef, conventional dairy, and organic dairy (n = 3 samples per visit per production system). Metagenomic DNA obtained from samples were analyzed using target-enriched sequencing (resistome) and 16S rRNA gene sequencing (microbiome).

Results

All colon content samples had at least one identifiable antimicrobial resistance gene (ARG), while 21 of the 54 meat trimmings samples harbored at least one identifiable ARGs. Tetracycline ARGs were the most abundant class in both colon content and carcass meat trimmings. The resistome found on carcass meat trimmings was not significantly different by production system (P = 0.84, R² = 0.00) or harvest facility (P = 0.10, R² = 0.09). However, the resistome of colon content differed (P = 0.01; R² = 0.05) among production systems, but not among the harvest facilities (P = 0.41; R² = 0.00). Amplicon sequencing revealed differences (P < 0.05) in microbial populations in both meat trimmings and colon content between harvest facilities but not production systems (P > 0.05).

Conclusions

These data provide a baseline characterization of an important segment of the beef industry and highlight the effect that the production system where cattle are raised and the harvest facilities where an animal is processed can impact associated microbiome and resistomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00166-z.

The resistome of the bovine gastrointestinal tract

The gastrointestinal tracts of beef and dairy cattle are reservoirs of antimicrobial-resistant bacteria, and our knowledge of the ecology of resistance in these animals has changed with the advent of novel molecular technologies. Application of metagenomics and qPCR to the study of bovine gut ecology has demonstrated that there is overlap, with some differences, between beef and dairy cattle fecal resistomes, that treatment with antimicrobials often transiently influences the resistome, and young calves carry a high abundance of ARGs. Future work should harness emerging metagenome sequencing technologies to better describe the taxa harboring ARGs and collocated non-resistance genes and use these data along with identifying the multiplicity of factors driving resistance to develop strategies to reduce AMR carriage in cattle.

Prevalence of Mastitis and Antibiotic Resistance of Bacterial Isolates from CMT Positive Milk Samples Obtained from Dairy Cows, Camels, and Goats in Two Pastoral Districts in Southern Ethiopia

Simple Summary

A study was carried out from August 2017 to February 2018 on lactating dairy cows, one-humped dromedary camels, and goats to determine mastitis in the Bule Hora and Dugda Dawa districts of in Southern Ethiopia. Milk samples from 564 udder quarters and udder halves from 171 animals consisting of 60 dairy cows, 51 camels, and 60 goats were tested for mastitis. Sixty-four positive udder milk samples were cultured, and bacterial mastitis pathogens were isolated and identified. The antibiotic resistance of bacterial isolates from milk with mastitis was tested against nine antimicrobials commonly used in the study area. Cow-level prevalence of mastitis in dairy cows, camels, and goats was 33.3%, 26.3%, and 25%, respectively. The quarter-level prevalence of mastitis in cows, camels and goats was 17.6%, 14.5%, and 20%, respectively. In cattle, the prevalence was significantly higher in Dugda Dawa than in Bule Hora. Major bacterial isolates were coagulase-negative Staphylococcus species (39.1%), S. aureus (17.2%), S. hyicus (14.1%), and S. intermedius and Escherichia coli (9.4% each). In camels, udder abnormality and mastitis were significantly higher in late lactation than in early lactation. Mastitis tends to increase with parity in camels. E. coli isolates were highly resistant to spectinomycin, vancomycin, and doxycycline, whereas most S. aureus isolates were multidrug-resistant. Most of the rural and periurban communities in this area consume raw milk, which indicates a high risk of infection with multidrug-resistant bacteria. We recommend community-focused training programs to improve community awareness of the risk of raw milk consumption and the need to boil milk.

Abstract

A study was carried out from August 2017 to February 2018 on lactating dairy cows, one-humped dromedary camels, and goats to determine mastitis in the Bule Hora and Dugda Dawa districts of in Southern Ethiopia. Milk samples from 564 udder quarters and udder halves from 171 animals consisting of 60 dairy cows, 51 camels, and 60 goats were tested for mastitis. Sixty-four positive udder milk samples were cultured, and bacterial mastitis pathogens were isolated and identified. The antibiotic resistance of bacterial isolates from milk with mastitis was tested against nine antimicrobials commonly used in the study area. Cow- and quarter-level prevalence of mastitis in dairy cows, camels, and goats was 33.3%, 26.3%, and 25% and 17.6%, 14.5%, and 20%, respectively. In cattle, the prevalence was significantly higher in Dugda Dawa than in Bule Hora. Major bacterial isolates were coagulase-negative Staphylococcus species (39.1%), S. aureus (17.2%), S. hyicus (14.1%), and S. intermedius and Escherichia coli (9.4% each). In camels, udder abnormality and mastitis were significantly higher in late lactation than in early lactation. Mastitis tends to increase with parity in camels. E. coli isolates were highly resistant to spectinomycin, vancomycin, and doxycycline, whereas most S. aureus isolates were multidrug-resistant. Most of the rural and periurban communities in this area consume raw milk, which indicates a high risk of infection with multidrug-resistant bacteria. We recommend a community-focused training program to improve community awareness of the need to boil milk and the risk of raw milk consumption.

Antimicrobial Resistance in U.S. Retail Ground Beef with and without Label Claims Regarding Antibiotic Use

ABSTRACT

Antibiotics used during food animal production account for approximately 77% of U.S. antimicrobial consumption by mass. Ground beef products labeled as raised without antibiotics (RWA) are perceived to harbor lower levels of antimicrobial-resistant bacteria than conventional (CONV) products with no label claims regarding antimicrobial use. Retail ground beef samples were obtained from six U.S. cities. Samples with an RWA or U.S. Department of Agriculture Organic claim (n = 299) were assigned to the RWA production system. Samples lacking these claims (n = 300) were assigned to the CONV production system. Each sample was cultured for the detection of five antimicrobial-resistant bacteria. Genomic DNA was isolated from each sample, and a quantitative PCR assay was used to determine the abundance of 10 antimicrobial resistance (AMR) genes. Prevalence of tetracycline-resistant Escherichia coli (CONV, 46.3%; RWA, 34.4%; P < 0.01) and erythromycin-resistant Enterococcus (CONV, 48.0%; RWA, 37.5%; P = 0.01) was higher in CONV ground beef. Salmonella was detected in 1.2% of samples. The AMR gene blaCTX-M (CONV, 4.1 log-normalized abundance; RWA, 3.8 log-normalized abundance; P < 0.01) was more abundant in CONV ground beef. The AMR genes mecA (CONV, 4.4 log-normalized abundance; RWA, 4.9 log-normalized abundance; P = 0.05), tet(A) (CONV, 3.9 log-normalized abundance; RWA, 4.5 log-normalized abundance; P < 0.01), tet(B) (CONV, 3.9 log-normalized abundance; RWA, 4.5 log-normalized abundance; P < 0.01), and tet(M) (CONV, 5.4 log-normalized abundance; RWA, 5.8 log-normalized abundance; P < 0.01) were more abundant in RWA ground beef. Although these results suggest that antimicrobial use during U.S. cattle production does not increase human exposure to antimicrobial-resistant bacteria via ground beef, quantitative microbiological risk assessments are required for authoritative determination of the human health impacts of the use of antimicrobial agents during beef production.

HIGHLIGHTS

Impact of Ceftiofur Administration in Steers on the Prevalence and Antimicrobial Resistance of Campylobacter spp

Bacterial resistance to ceftiofur raises health concerns due to ceftiofur’s extensive veterinary usage and structural similarity with the human antibiotic ceftriaxone. Ceftiofur crystalline-free acid (CCFA) and ceftiofur hydrochloride (CHCL) are ceftiofur types used therapeutically in cattle, but their potential impacts on Campylobacter prevalence and antimicrobial resistance remain unclear. In this study two groups of steers were each treated with CCFA or CHCL. In vivo active drug concentrations were measured and fecal samples were analyzed for Campylobacter for up to 42 days post-treatment. Following administration, the colonic concentration of ceftiofur initially increased then dropped to pre-treatment levels by day 8. The estimated prevalence of Campylobacter spp. was significantly (p = 0.0009) higher during the first week after CCFA treatment than after CHCL treatment (81.3% vs. 45.2%). Campylobacter jejuni predominated overall, with other Campylobacter spp. mainly identified in the first week after CCFA treatment. No treatment impacts were noted on ceftiofur minimum inhibitory concentration (MIC) for C. jejuni (10–20 μg/mL). More C. jejuni genotypes were detected in CCFA-treated than CHCL-treated steers. These findings suggest that ceftiofur did not significantly impact Campylobacter prevalence or ceftiofur MIC. However, CHCL may be preferable due to the lower likelihood of temporary increases in Campylobacter prevalence.

Antimicrobial Resistance at Two U.S. Cull Cow Processing Establishments

ABSTRACT

Culled beef cows (cows that have reached the end of their productive life span in cow-calf operations) and culled dairy cows represent approximately 18% of the cattle harvested in the United States annually, but data on antimicrobial resistance (AMR) in these cull cattle are extremely limited. To address this data gap, colon contents were obtained from 180 culled conventional beef cows, 179 culled conventional dairy cows, and 176 culled organic dairy cows (produced without using antimicrobials). Sponge samples were also collected from 181 conventional beef, 173 conventional dairy, and 180 organic dairy cow carcasses. These samples were obtained on 6 days (3 days each at two beef harvest and processing establishments). At one establishment, 30 samples of beef manufacturing trimmings from conventional cows and 30 trim samples from organic dairy cows were acquired. All 1,129 samples were cultured for Escherichia coli, tetracycline-resistant (TETr) E. coli, third-generation cephalosporin-resistant (3GCr) E. coli, Salmonella, and 3GCrSalmonella. Metagenomic DNA was isolated from 535 colon content samples, and quantitative PCR assays were performed to assess the abundances of the following 10 antimicrobial resistance genes: aac(6')-Ie-aph(2″)-Ia, aadA1, blaCMY-2, blaCTX-M, blaKPC-2, erm(B), mecA, tet(A), tet(B), and tet(M). For colon contents, only TETrE. coli (P < 0.01), 3GCrE. coli (P < 0.01), and erm(B) (P = 0.03) levels were higher in conventional than in organic cows. Sampling day also significantly affected (P < 0.01) these levels. Production system did not affect the levels of any measured AMR on carcasses or trim. The human health impact of the few significant AMR differences could not be determined due to the lack of standards for normal, background, safe, or basal values. Study results provide key heretofore unavailable data that may inform quantitative microbial risk assessments to address these gaps.

HIGHLIGHTS

SMART Antimicrobial Resistance Goals to Drive Meat Safety Improvement

Concerns that food-animal production significantly contributes to antibiotic-resistant human infections have persisted for more than 20 years. Most antibiotic resistance concerns are generalized, not specific. By their nature, non- specific concerns are unfalsifiable and can never be scientifically alleviated or remediated. Therefore, antibiotic resistance meat safety improvement begins with defining SMART (Specific, Measurable, Attainable, Relevant, and Time bound) antibiotic resistance goals. Two SMART goals related to high-priority antibiotic resistance in beef production are described as an example to facilitate scientific goal attainment

Effects of Bacillus subtilis PB6 and/or chromium propionate supplementation on serum chemistry, complete blood count, and fecal Salmonella spp. count in high-risk cattle during the feedlot receiving and finishing periods. Transl Anim Sci 2020;4:txaa164. [PMID: 33134874 PMCID: PMC7584394 DOI: 10.1093/tas/txaa164]

The study objective was to determine the effects of Bacillus subtilis PB6 and/or chromium propionate supplementation on serum chemistry, complete blood count, and fecal Salmonella spp. count in high-risk beef cattle during a 56-d feedlot receiving period and the subsequent finishing period. Four truckload blocks of crossbred beef bulls (n = 300) and steers [n = 84; total n = 384; average initial body weight (BW) = 220 ± 16.2 kg] were sourced from regional auction markets and assigned randomly to treatments arranged in a 2 × 2 factorial. Blood samples were collected from two bulls nearest to the median BW on arrival in each pen (n = 96) and fecal samples were collected from cattle in block 3 (n = 96). The generalized complete block design consisted of 12 pen replications per treatment with pen as the experimental unit. Treatments were: 1) negative control (CON); 2) 13 g per animal daily of prepared B. subtilis PB6 product (CST); 3) 450 ppb dry matter (DM) chromium propionate (CHR); and 4) 13 g per animal daily of prepared B. subtilis PB6 product and 450 ppb DM chromium propionate (CST + CHR). Treatments were top dressed in feed bunks daily using 0.45 kg per animal ground corn carrier immediately following feed delivery. Data were analyzed using mixed models with repeated measures. Day affected all serum chemistry variables (P ≤ 0.03) except total CO2 (P = 0.34) and all complete blood count variables during receiving (P ≤ 0.02) except percentage basophils (P ≥ 0.12). During the overall receiving period, serum calcium was decreased (P = 0.02) by CHR. Cattle fed CHR had greater total leukocyte count (P = 0.04) and neutrophil count (P = 0.02) during the overall receiving period. Fecal Salmonella spp. count was markedly reduced in cattle fed CST on day 28 (P = 0.01) and overall (P = 0.07). Overall, these data provide metabolic and hematologic insight into the unique challenges presented by lightweight, high-risk feeder cattle. Notably, CST was found to be effective in mitigating fecal enumeration and presumably replication of Salmonella spp. in the gastrointestinal tract.

Dihydrofolate reductase inhibitors for use as antimicrobial agents

Drug-resistant bacteria pose an increasingly serious threat to mankind all over the world. However, the currently available clinical treatments do not meet the urgent demand.Therefore, it is desirable to find new targets and inhibitors to overcome the problems of antibiotic resistance. Dihydrofolate reductase (DHFR) is an important enzyme required to maintain bacterial growth, and hence inhibitors of DHFR have been proven as effective agents for treating bacterial infections. This review provides insights into the recent discovery of antimicrobial agents targeting DHFR. In particular, three pathogens, Escherichia coli (E. coli), Mycobacterium tuberculosis(Mtb) and Staphylococcus aureus(S. aureus), and research strategies are emphasized. DHFR inhibitors are expected to be good alternatives to fight bacterial infections.

In-Feed Tylosin Phosphate Administration to Feedlot Cattle Minimally Affects Antimicrobial Resistance

ABSTRACT

The macrolide class antimicrobial tylosin (trade name Tylan) is approved by the U.S. Food and Drug Administration for continuous inclusion in feed for liver abscess prevention. To address concerns that this antimicrobial application may threaten human health, a population of feedlot steers was split into a control treatment (n = 42) and a tylosin treatment (n = 42). Feed rations were identical except for the inclusion of tylosin at 60 to 90 mg per head per day. Fecal swab (n = 335), pen surface material (n = 256), feed (n = 56), and water trough (n = 32) samples were obtained over four sample occasions: November (1 day before the start of tylosin inclusion in feed), January (80 days of tylosin in feed), April (167 days), and June (253 days). These samples were cultured for Escherichia coli, tetracycline-resistant E. coli, third-generation cephalosporin-resistant E. coli, Enterococcus, tetracycline-resistant Enterococcus, and erythromycin-resistant Enterococcus. Metagenomic DNA was isolated from each June fecal swab and pen surface material sample. Metagenomic DNA samples were pooled by pen for 14 fecal and 14 pen surface material samples. Quantitative PCR was employed to assess the abundances of the following 10 antimicrobial resistance genes: aac(6')-Ie-aph(2″)-Ia, aadA1, blaCMY-2, blaCTX-M, blaKPC-2, erm(B), mecA, tet(A), tet(B), and tet(M). Nasal swab samples (n = 335) were obtained from each steer during each sample period and cultured for the presence of Staphylococcus aureus and methicillin-resistant S. aureus. Of these measurements, only January and June mean fecal swab erythromycin-resistant Enterococcus colony counts for tylosin-treated cattle were significantly higher (P ≤ 0.05) than the range of mean values for control treatments. These results suggest that in-feed tylosin through the end of finishing has a narrow and minimal antimicrobial resistance impact.

HIGHLIGHTS

Food Service Pork Chops from Three U.S. Regions Harbor Similar Levels of Antimicrobial Resistance Regardless of Antibiotic Use Claims

Pork products from animals "raised without antibiotics" (RWA) are assumed to harbor lower levels of antimicrobial resistance (AMR) than conventional (CONV) pork products with no claims regarding use of antimicrobial agents during production. A total of 372 pork chop samples from CONV (n = 190) and RWA (n = 182) production systems were collected over 13 months from three food service suppliers. The following bacteria were cultured: Escherichia coli, tetracycline-resistant (TET^r) E. coli, third-generation cephalosporin-resistant (3GC^r) E. coli, Salmonella enterica, TET^r Salmonella, 3GC^r Salmonella, nalidixic acid-resistant Salmonella, Enterococcus spp., TET^r Enterococcus, erythromycin-resistant Enterococcus, Staphylococcus aureus, and methicillin-resistant S. aureus. Production system did not significantly impact the detection of cultured bacteria (P > 0.05). Metagenomic DNA was isolated from each sample, and equal amounts of metagenomic DNA were pooled by supplier, month, and production system for 75 pooled samples (38 CONV, 37 RWA). Quantitative PCR was used to assess the abundances of the following 10 AMR genes: aac(6')-Ie-aph(2″)-Ia, aadA1, bla_CMY-2, bla_CTX-M, bla_KPC-2, erm(B), mecA, tet(A), tet(B), and tet(M). For all 10 AMR genes, abundances did not differ significantly (P > 0.05) between production systems. These results suggest that use of antimicrobial agents during swine production minimally impacts the AMR of bacteria in pork chops.

Antimicrobial Usages and Antimicrobial Resistance in Commensal Escherichia coli From Veal Calves in France: Evolution During the Fattening Process

Extended-Spectrum-Cephalosporin (ESC)-resistant Enterobacteriaceae have widely spread in all settings worldwide. In animals, Extended-Spectrum Beta-Lactamase (ESBL) producers have been frequently identified in veal calves. The objectives of this study were to investigate the trends in the ESBL load and antimicrobial resistance (AMR) proportions, and antimicrobial usages (AMU) in veal calves during the fattening process. Ten fattening farms were selected and 50 animals per farm were sampled. AMR was assessed in bacteria from the dominant flora (collected on non-selective MacConckey agar) and in ESBL/AmpC-carrying bacteria from the subdominant flora (selected on ChromID ESBL selective plates) upon arrival and 5-6 months later before slaughter. The number and types of treatments during fattening were also collected. Rates of ESBL-producing E. coli from the subdominant flora significantly decreased in all farms (arrival: 67.7%; departure: 20.4%) whereas rates of multidrug-resistant E. coli from the dominant flora have significantly increased (arrival: 60.2%; departure: 67.2%; p = 0.025). CTX-M-1 was the most frequently identified ESBL enzyme (arrival: 59.3%; departure: 52.0%). The plasmid-mediated mcr-1 gene was also identified occasionally. In parallel, levels of resistances to non-critically important antimicrobials were already high upon arrival but have still further increased over time until slaughter. Our study also highlighted that if only ESBL-producing isolates were monitored, it might have led to a partial (and partly false) picture of AMR rates globally decreasing during the fattening period. The mean number of antimicrobial treatments per calf (NTPC) was 8.75 but no association between AMU and AMR was evidenced. Most ESBL producers were clonally unrelated suggesting multiple sources and not cross-contaminations among calves during transportation. Feeding milk containing antimicrobial residues to veal calves is hypothesized to explain the high ESBL loads in animals at the entrance on farms.

Persistence of antibiotic resistance genes in beef cattle backgrounding environment over two years after cessation of operation

Confined animal feeding operations can facilitate the spread of genes associated with antibiotic resistance. It is not known how cattle removal from beef cattle backgrounding operation affects the persistence of antibiotic resistance genes (ARGs) in the environment. We investigated the effect of cessation of beef cattle backgrounding operation on the persistence and distribution of ARGs in the beef cattle backgrounding environment. The study was conducted at a pasture-feedlot type beef cattle backgrounding operation which consisted of feeding and grazing areas that were separated by a fence with an access gate. Backgrounding occurred for seven years before cattle were removed from the facility. Soil samples (n = 78) from 26 georeferenced locations were collected at the baseline before cattle were removed, and then one year and two years after cattle were removed. Metagenomic DNA was extracted from the soil samples and total bacterial population (16S rRNA), total Enterococcus species and class 1 integrons (intI1), and erythromycin (ermB and ermF), sulfonamide (sul1 and sul2) and tetracycline (tetO, tetW and tetQ) resistance genes were quantified. Concentrations of total bacteria, Enterococcus spp., class 1 integrons, and ARGs were higher in the feeding area and its immediate vicinity (around the fence and the gate) followed by a gradient decline along the grazing area. Although the concentrations of total bacteria, Enterococcus spp., class 1 integrons and ARGs in the feeding area significantly decreased two years after cattle removal, their concentrations were still higher than that observed in the grazing area. Higher concentrations over two years in the feeding area when compared to the grazing area suggest a lasting effect of confined beef cattle production system on the persistence of bacteria and ARGs in the soil.

Similar Levels of Antimicrobial Resistance in U.S. Food Service Ground Beef Products with and without a "Raised without Antibiotics" Claim

U.S. ground beef with "raised without antibiotics" (RWA) label claims are perceived as harboring fewer bacteria with antimicrobial resistance (AMR) than are found in conventional (CONV) ground beef with no such label claim. A total of 370 ground beef samples from CONV ( n = 191) and RWA ( n = 179) production systems were collected over 13 months from three food service suppliers. The following bacteria were cultured: Escherichia coli, tetracycline-resistant (TET^r) E. coli, third-generation cephalosporin-resistant (3GC^r) E. coli, Salmonella enterica, TET^r S. enterica, 3GC^r S. enterica, nalidixic acid-resistant S. enterica, Enterococcus spp., erythromycin-resistant Enterococcus spp., TET^r Enterococcus spp., Staphylococcus aureus, and methicillin-resistant S. aureus. TET^r E. coli was more frequently detected in CONV ground beef (CONV, 54.2%; RWA, 35.2%; P < 0.01), but supplier ( P < 0.01) and production system × suppler interaction ( P < 0.01) effects were also significant. Metagenomic DNA was isolated from each sample, and equal amounts of metagenomic DNA were pooled by supplier, month, and production system for 75 pooled samples (38 CONV, 37 RWA). The abundance of aac(6')-Ie-aph(2″)-Ia, aadA1, bla_CMY-2, bla_CTX-M, bla_KPC-2, erm(B), mecA, tet(A), tet(B), and tet(M) genes was assessed by quantitative PCR. The tet(A) (2.9-log₂-fold change, P = 0.04) and tet(B) (5.6-log₂-fold change) ( P = 0.03) genes were significantly more abundant in RWA ground beef. Phylogenetic analyses revealed that ground beef microbiomes differed more by supplier than by production system. These results were consistent with prior research suggesting antimicrobial use in U.S. beef cattle has minimal impact on the AMR of bacteria found in these products. These results should spur a reevaluation of assumptions regarding the impact of antimicrobial use during U.S. beef production on the AMR of bacteria in ground beef.

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.

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.