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

Exploring bacterial diversity and antimicrobial resistance gene on a southern Brazilian swine farm

The bacterial composition of and the circulation of antimicrobial resistance genes (ARGs) in waste from Brazilian swine farms are still poorly understood. Considering that antimicrobial resistance (AMR) is one of the main threats to human, animal, and environmental health, the need to accurately assess the load of ARGs released into the environment is urgent. Therefore, this study aimed to characterize the microbiota in a swine farm in southern Brazil and the resistome in swine farm wastewater treated in a series of waste stabilization ponds (WSPs). Samples were collected from farm facilities and the surrounding environment, representing all levels of swine manure within the treatment system. Total metagenomic sequencing was performed on samples from WSPs, and 16S-rDNA sequencing was performed on all the collected samples. The results showed increased bacterial diversity in WSPs, characterized by the presence of Caldatribacteriota, Cloacimonadota, Desulfobacterota, Spirochaetota, Synergistota, and Verrucomicrobiota. Furthermore, resistance genes to tetracyclines, lincosamides, macrolides, rifamycin, phenicol, and genes conferring multidrug resistance were detected in WSPs samples. Interestingly, the most abundant ARG was linG, which confers resistance to the lincosamides. Notably, genes conferring macrolide (mphG and mefC) and rifamycin (rpoB_RIF) resistance appeared in greater numbers in the late WSPs. These drugs are among the high-priority antibiotic classes for human health. Moreover, certain mobile genetic elements (MGEs) were identified in the samples, notably tnpA, which was found in high abundance. These elements are of particular concern due to their potential to facilitate the dissemination of ARGs among bacteria. In summary, the results indicate that, in the studied farm, the swine manure treatment system could not eliminate ARGs and MGEs. Our results validate concerns about Brazil's swine production system. The misuse and overuse of antimicrobials during animal production must be avoided to mitigate AMR.

Intervention effects of fructooligosaccharide and astragalus polysaccharide, as typical antibiotic alternatives, on antibiotic resistance genes in feces of layer breeding: advantages and defects

Although antibiotic alternatives are widely used in livestock and poultry breeding industry after in-feed antibiotics ban, their intervention effects on antibiotic resistance genes (ARGs) in these food animals' feces remain poorly understood. Here effects of fructooligosaccharide (FOS) and astragalus polysaccharide (APS), as typical antibiotic alternatives in China, on ARGs in layer feces were estimated by performing metagenomic sequencings and fluorescence quantitative PCR. Fructooligosaccharide significantly reduced sum abundance of ARGs and mobile genetic elements (MGEs) by increasing Lactobacillus clones and reducing Escherichia clones which had relatively higher abundances of ARG subtypes and MGE subtypes in layer feces. However, at least parts of core ARGs and MGEs categories were not reduced by FOS, such as aminoglycosides- and tetracyclines-resistant genes, Tn916, Integrase, and so on. MGEs and microbiome, especially Escherichia genus and Lactobacillus genus, were the key factors affecting ARGs' sum abundance. MGEs had a higher correlation coefficient with ARGs' sum abundance than Escherichia genus and Lactobacillus genus. These findings firstly reveal the defects of antibiotic alternatives in controlling bacterial resistance in livestock and poultry breeding after in-feed antibiotics ban, and more strategies are needed to control pollutions and risks of core ARGs and MGEs in food animals' feces under a special environment.

Validation of a New Method of Sampling Beef Manufacturing Trimmings for Pathogen Testing Using a Manual Sampling Mitt Approach

The USDA Food Safety Inspection Service has declared Escherichia coli O157:H7, and six additional Shiga toxin-producing E. coli (STEC) are adulterants for nonintact raw beef products. The U. S. beef processing industry has implemented several antimicrobial intervention technologies throughout the carcass dressing process to remove or destroy foodborne pathogens present on beef carcasses. Despite these efforts, STEC have been shown to cause finished product contamination, albeit at prevalences typically <0.5%. Recent work described the development and validation of improved methods for collecting samples from raw beef trimmings. One of the methods, the Manual Sampling Device (MSD) method, uses the manual implementation of the MicroTally® Swab (MT-Swab) to vigorously scrub the surface of raw beef manufacturing trimmings for pathogen detection. The work described herein reports the data from an evaluation of a novel MSD method using the MicroTally® Mitt (MT-Mitt). The MT-Mitt provides a more user-friendly option for sample collection than the MT-Swab. A series of trials were conducted with a total of 360 matched samples comparing manual sampling of raw beef manufacturing trimmings using the MT-Swab, N60-excision, or N60-plus methods to a novel method using the MT-Mitt. The results of these trials collectively demonstrate that manual sampling of raw beef manufacturing trimmings using the MT-Mitt provides organism recovery that is not significantly different from that of the MT-Swab, N60-excision, and N60-plus methods. Thus, the MT-Mitt method provides an alternative sampling method with organism recovery that is not significantly different from previous methods for sampling beef manufacturing trimmings for pathogen detection and some implementation advantages pertaining to labor and ease of use.

Antimicrobial Susceptibility in Respiratory Pathogens and Farm and Animal Variables in Weaned California Dairy Heifers: Logistic Regression and Bayesian Network Analyses

Weaned dairy heifers are a relatively understudied production group. Bovine respiratory disease (BRD) is the most common cause of antimicrobial drug (AMD) use, morbidity, and mortality in this production group. The study of antimicrobial resistance (AMR) is complicated because many variables that may affect AMR are related. This study generates hypotheses regarding the farm- and animal-level variables (e.g., vaccination, lane cleaning, and AMD use practices) that may be associated with AMR in respiratory isolates from weaned dairy heifers. A cross-sectional study was performed using survey data and respiratory isolates (Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni) collected from 341 weaned dairy heifers on six farms in California. Logistic regression and Bayesian network analyses were used to evaluate the associations between farm- and animal-level variables with minimum inhibitory concentration (MIC) classification of respiratory isolates against 11 AMDs. Farm-level variables associated with MIC classification of respiratory isolates included the number of source farms of a calf-rearing facility, whether the farm practiced onsite milking, the use of lagoon water for flush lane cleaning, and respiratory and pinkeye vaccination practices. Animal-level variables associated with a MIC classification included whether the calf was BRD-score-positive and time since the last phenicol treatment.

Two-Dose Ceftiofur Treatment Increases Cephamycinase Gene Quantities and Fecal Microbiome Diversity in Dairy Cows Diagnosed with Metritis

Antimicrobial resistance is a significant concern worldwide; meanwhile, the impact of 3rd generation cephalosporin (3GC) antibiotics on the microbial communities of cattle and resistance within these communities is largely unknown. The objectives of this study were to determine the effects of two-dose ceftiofur crystalline-free acid (2-CCFA) treatment on the fecal microbiota and on the quantities of second-and third-generation cephalosporin, fluoroquinolone, and macrolide resistance genes in Holstein-Friesian dairy cows in the southwestern United States. Across three dairy farms, 124 matched pairs of cows were enrolled in a longitudinal study. Following the product label regimen, CCFA was administered on days 0 and 3 to cows diagnosed with postpartum metritis. Healthy cows were pair-matched based on lactation number and calving date. Fecal samples were collected on days 0, 6, and 16 and pooled in groups of 4 (n = 192) by farm, day, and treatment group for community DNA extraction. The characterization of community DNA included real-time PCR (qPCR) to quantify the following antibiotic resistance genes: blaCMY-2, blaCTX-M, mphA, qnrB19, and the highly conserved 16S rRNA back-calculated to gene copies per gram of feces. Additionally, 16S rRNA amplicon sequencing and metagenomics analyses were used to determine differences in bacterial community composition by treatment, day, and farm. Overall, blaCMY-2 gene copies per gram of feces increased significantly (p ≤ 0.05) in the treated group compared to the untreated group on day 6 and remained elevated on day 16. However, blaCTX-M, mphA, and qnrB19 gene quantities did not differ significantly (p ≥ 0.05) between treatment groups, days, or farms, suggesting a cephamycinase-specific enhancement in cows on these farms. Perhaps unexpectedly, 16S rRNA amplicon metagenomic analyses showed that the fecal bacterial communities from treated animals on day 6 had significantly greater (p ≤ 0.05) alpha and beta diversity than the untreated group. Two-dose ceftiofur treatment in dairy cows with metritis elevates cephamycinase gene quantities among all fecal bacteria while paradoxically increasing microbial diversity.

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.

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.

Effect of continuous in-feed administration of tylosin to feedlot cattle on macrolide and tetracycline resistant enterococci in a randomized field trial

Liver abscess causes substantial economic loss to the beef cattle industry through liver condemnation, reduced animal performance, and carcass yield. Continuous in-feed use of tylosin is the most effective and a commonly used practice in beef cattle production to prevent liver abscess. However, such mass medication can increase the level of antimicrobial resistant bacteria. We investigated the effect of continuous in-feed use of tylosin in feedlot cattle on (i) concentrations and prevalence of erythromycin-resistant (ERY^r) and tetracycline-resistant (TET^r) enterococci; (ii) associated antimicrobial resistance genes (ARGs) for resistance; (iii) species distribution; iv) macrolide and tetracycline resistance gene concentrations; and (v) tylosin concentration. A cohort of weaned calves were randomized to receive tylosin-medicated feed (Tylosin; n = 10) or nonmedicated feed (Control; n = 10) for a full feedlot cycle. Feces, feed and pen-surface samples were collected and processed by culture, droplet digital PCR, and liquid chromatography/mass spectroscopy for bacterial enumeration, detection and characterization, ARG quantification, and tylosin concentration, respectively. Data were analyzed by mixed effects linear- or binary-regression models depending on the outcomes. Tylosin administration significantly increased fecal concentration (P < 0.001) and prevalence (P = 0.021) of ERY^r enterococci and erm(B) gene concentration (P < 0.001), compared to the control group. Interestingly, tylosin administration significantly reduced (P = 0.037) fecal TET^r enterococci concentration compared to the control group, with no significant effect (P = 0.758) on fecal tet(M) concentration. In both treatment groups, enterococci concentrations increased over time, peaking on 174 days in feed before returning to the baseline. ERY^r enterococci concentration was significantly (P = 0.012) higher in tylosin medicated feeds, with no significant effect (P = 0.321) on TET^r enterococci concentration. Pen-surface concentration of ermB was significantly (P = 0.024) higher in the tylosin group, with no significant effect (P > 0.05) on bacterial concentrations. Increased diversity and a shift in the composition of enterococcal species and ARGs were observed over time, although tylosin use did not significantly affect (P > 0.05) their prevalence. Tylosin concentration was significantly higher in the feces of tylosin administered cattle (P < 0.001) and medicated feed (P = 0.027), with numerically higher pen-surface concentration (P = 0.065) in the tylosin group. In conclusion, continuous in-feed use of tylosin in feedlot cattle increases macrolide resistant enterococci and its fecal excretion, while decreasing tetracycline resistance. Two medically important species, E. faecium and E. faecalis, were predominant regardless of resistance status or sample source. Risk-based approaches including label changes to limit tylosin use such as withdrawal period, and development of effective manure treatments are potential areas of research to reduce environmental and public health impacts.

Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods

BACKGROUND

With the escalating risk of antimicrobial resistance (AMR), there are limited analytical options available that can comprehensively assess the burden of AMR carried by clinical/environmental samples. Food can be a potential source of AMR bacteria for humans, but its significance in driving the clinical spread of AMR remains unclear, largely due to the lack of holistic-yet-sensitive tools for surveillance and evaluation. Metagenomics is a culture-independent approach well suited for uncovering genetic determinants of defined microbial traits, such as AMR, present within unknown bacterial communities. Despite its popularity, the conventional approach of non-selectively sequencing a sample's metagenome (namely, shotgun-metagenomics) has several technical drawbacks that lead to uncertainty about its effectiveness for AMR assessment; for instance, the low discovery rate of resistance-associated genes due to their naturally small genomic footprint within the vast metagenome. Here, we describe the development of a targeted resistome sequencing method and demonstrate its application in the characterization of the AMR gene profile of bacteria associated with several retail foods.

RESULT

A targeted-metagenomic sequencing workflow using a customized bait-capture system targeting over 4,000 referenced AMR genes and 263 plasmid replicon sequences was validated against both mock and sample-derived bacterial community preparations. Compared to shotgun-metagenomics, the targeted method consistently provided for improved recovery of resistance gene targets with a much-improved target detection efficiency (> 300-fold). Targeted resistome analyses conducted on 36 retail-acquired food samples (fresh sprouts, n = 10; ground meat, n = 26) and their corresponding bacterial enrichment cultures (n = 36) reveals in-depth features regarding the identity and diversity of AMR genes, most of which were otherwise undetected by the whole-metagenome shotgun sequencing method. Furthermore, our findings suggest that foodborne Gammaproteobacteria could be the major reservoir of food-associated AMR genetic determinants, and that the resistome structure of the selected high-risk food commodities are, to a large extent, dictated by microbiome composition.

CONCLUSIONS

For metagenomic sequencing-based surveillance of AMR, the target-capture method presented herein represents a more sensitive and efficient approach to evaluate the resistome profile of complex food or environmental samples. This study also further implicates retail foods as carriers of diverse resistance-conferring genes indicating a potential impact on the dissemination of AMR.

Short-Term Impact of Oxytetracycline Administration on the Fecal Microbiome, Resistome and Virulome of Grazing Cattle

Antimicrobial resistance (AMR) is an important public health concern around the world. Limited information exists about AMR in grasslands-based systems where antibiotics are seldom used in beef cattle. The present study investigated the impacts of oxytetracycline (OTC) on the microbiome, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in grazing steers with no previous exposure to antibiotic treatments. Four steers were injected with a single dose of OTC (TREAT), and four steers were kept as control (CONT). The effects of OTC on fecal microbiome, ARGs, and VFGs were assessed for 14 days using 16S rRNA sequencing and shotgun metagenomics. Alpha and beta microbiome diversities were significantly affected by OTC. Following treatment, less than 8% of bacterial genera had differential abundance between CONT and TREAT samples. Seven ARGs conferring resistance to tetracycline (tet32, tet40, tet44, tetO, tetQ, tetW, and tetW/N/W) increased their abundance in the post-TREAT samples compared to CONT samples. In addition, OTC use was associated with the enrichment of macrolide and lincosamide ARGs (mel and lnuC, respectively). The use of OTC had no significant effect on VFGs. In conclusion, OTC induced short-term alterations of the fecal microbiome and enrichment of ARGs in the feces of grazing beef cattle.

Determination of Verification Parameters for Using the Manual Sampling Device for Fresh Raw Beef Trim

Multifaceted food safety systems are used by the beef processing industry to minimize risk of bacterial contamination of the finished product. These systems are comprised of several parts including the conditional release of product requiring a sample to produce a negative result on a pathogen test prior to sending the product into the food supply. The methods of sample collection require verification activities that ensure the sampling protocols are performed adequately. The research described herein was done to determine the parameters for use in verifying adequate beef trim sampling for the Manual Sampling Device (MSD) method. In addition, the efficacy of repeated sampling via multiple applications of the MSD procedure on a fresh raw beef trim combo was investigated. The results show that MSD sample collection thatcoversless than the entire combo surface, but at least one-halfof the combo surface and is collected for a minimum of 90 s, is adequate for the recovery of organisms and prevalence targets from fresh raw beef trim. In addition, the evidence that MSD sample collection thatoccurs forless than the recommended time, butnot less than 30 s per side of the swab, is adequate for the recovery of organisms and prevalence targets from raw beef trim. Finally, results show that in a scenario where an in-plant MSD sample and a regulatory MSD sample are required from the same combo, two MSD samples can be collected from the same combo bin with similar test results for both samples. While the recommended MSD protocol specifications will not be changed, the data presented herein provide support for some flexibility in accepting test results when verification activities indicate that sampling did not occur as specified in the recommended procedure.

More than an anthropogenic phenomenon: Antimicrobial resistance in ungulates from natural and agricultural environments

Widely considered an anthropogenic phenomenon, antimicrobial resistance (AMR) is a naturally occurring mechanism that microorganisms use to gain competitive advantage. AMR represents a significant threat to public health and has generated criticism towards the overuse of antimicrobial drugs. Livestock have been proposed as important reservoirs for AMR accumulation. Here, we show that assemblages of AMR genes in cattle and ungulates from natural environments (Yellowstone and Rocky Mountain National Parks) are all dominated by genes conferring resistance to tetracyclines. However, cattle feces contained higher proportions of erm(A-X) genes conferring resistance to macrolide antibiotics. Medically important AMR genes differed between cattle and natural ungulates, but cumulatively were more predominant in natural soils. Our findings suggest that the commonly described predominance of tetracycline resistance in cattle feces is a natural phenomenon among multiple ungulate species and not solely a result of antimicrobial drug exposure. Yet, the virtual absence of macrolide resistance genes in natural ungulates suggests that macrolide usage in agriculture may enrich these genes in cattle. Our results show that antimicrobial use in agriculture may be promoting a potential reservoir for specific types of AMR (i.e., macrolide resistance) but that a significant proportion of the ungulate resistome appears to have natural origins.

The differential plasma and ruminal metabolic pathways and ruminal bacterial taxa associated with divergent residual body weight gain phenotype in crossbred beef steers

We applied ruminal and plasma metabolomics and ruminal 16S rRNA gene sequencing to determine the metabolic pathways and ruminal bacterial taxa associated with divergent residual body weight gain phenotype in crossbred beef steers. A group of 108 crossbred growing beef steers (average BW = 282.87 ± 30 kg) were fed a forage-based diet for a period of 56 d in a confinement dry lot equipped with GrowSafe intake nodes to determine their residual body weight gain (RADG) phenotype. After RADG identification, blood and rumen fluid samples were collected from beef steers with the highest RADG (most efficient; n = 16; 0.76 kg/d) and lowest RADG (least efficient; n = 16; -0.65 kg/d). Quantitative untargeted metabolome analysis of the plasma and rumen fluid samples were conducted using chemical isotope labelling/liquid chromatography-mass spectrometry. Differentially abundant metabolites in each of the plasma and rumen fluid samples between the two groups of beef steers were determined using a false discovery rate (FDR)-adjusted P-values ≤ 0.05 and area under the curve (AUC) > 0.80. Rumen and plasma metabolic pathways that were differentially enriched or depleted (P ≤ 0.05) in beef steers with positive RADG compared to those with negative RADG were determined by the quantitative pathway enrichment analysis. A total of 1,629 metabolites were detected and identified in the plasma of the beef steers; eight metabolites including alanyl-phenylalanine, 8-hydroxyguanosine, and slaframine were differentially abundant (FDR ≤ 0.05; AUC > 0.80) in beef steers with divergent RADG; five metabolic pathways including steroid hormone biosynthesis, thiamine metabolism, propanoate metabolism, pentose phosphate pathway, and butanoate metabolism were enriched (P ≤ 0.05) in beef steers with positive RADG, relative to negative RADG steers. A total of 1,908 metabolites were detected and identified in the rumen of the beef steers; results of the pathway enrichment analysis of all the metabolites revealed no metabolic pathways in the rumen were altered (P > 0.05). The rumen fluid samples were also analyzed using 16S rRNA gene sequencing to assess the bacterial community composition. We compared the rumen bacterial community composition at the genus level using a linear discriminant analysis effect size (LEfSe) to identify the differentially abundant taxa between the two groups of beef steers. The LEfSe results showed greater relative abundance of Bacteroidetes_vadinHA17 and Anaerovibrio in steers with positive RADG compared to the negative RADG group, while steers in the negative RADG group had greater relative abundance of Candidatus_Amoebophilus, Clostridium_sensu_stricto_1, Pseudomonas, Empedobacter, Enterobacter, and Klebsiella compared to the positive RADG group. Our results demonstrate that beef steers with positive or negative RADG exhibit differences in plasma metabolic profiles and some ruminal bacterial taxa which probably explain their divergent feed efficiency phenotypes.

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].

Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle

Introduction

Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle.

Methods

This study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics.

Results

Overall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively).

Discussion

Results of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.

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.

Genomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum

Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E. hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.

The Multi-Omics Analysis Revealed Microbiological Regulation of Rabbit Colon with Diarrhea Fed an Antibiotic-Free Diet

Diarrhea symptoms appeared after antibiotics were banned from animal feed based on the law of the Chinese government in 2020. The colon and its contents were collected and analyzed from diarrheal and healthy rabbits using three omics analyses. The result of the microbial genomic analysis showed that the abundance of Bacteroidetes and Proteobacteria increased significantly (p-value < 0.01). Transcriptomes analysis showed that differentially expressed genes (DEGs) are abundant in the IL-17 signaling pathway and are highly expressed in the pro-inflammatory pathway. The metabolome analysis investigated differential metabolites (DMs) that were mainly enriched in tryptophan metabolism and bile secretion, which were closely related to the absorption and immune function of the colon. The results of correlation analysis showed that Bacteroidetes was positively correlated with 4-Morpholinobenzoic acid, and 4-Morpholinobenzoic acid could aggravate inflammation through its influence on the bile secretion pathway. The enriched DMs L-Tryptophan in the tryptophan metabolism pathway will lead to the functional disorder of inhibiting inflammation by affecting the protein digestion and absorption pathway. Thus, the colonic epithelial cells were damaged, affecting the function of the colon and leading to diarrhea in rabbits. Therefore, the study provided an idea for feed development and a theoretical basis for maintaining intestinal tract fitness in rabbits.

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.

Characterization of Escherichia coli harboring colibactin genes (clb) isolated from beef production and processing systems

Certain strains of Escherichia coli possess and express the toxin colibactin (Clb) which induces host mutations identical to the signature mutations of colorectal cancer (CRC) that lead to tumorigenic lesions. Since cattle are a known reservoir of several Enterobacteriaceae including E. coli, this study screened for clb amongst E. coli isolated from colons of cattle-at-harvest (entering beef processing facility; n = 1430), across the beef processing continuum (feedlot to finished subprimal beef; n = 232), and in ground beef (n = 1074). Results demonstrated that clb⁺E. coli were present in cattle and beef. Prevalence of clb⁺E. coli from colonic contents of cattle and ground beef was 18.3% and 5.5%, respectively. clb⁺E. coli were found susceptible to commonly used meat processing interventions. Whole genome sequencing of 54 bovine and beef clb⁺ isolates showed clb occurred in diverse genetic backgrounds, most frequently in phylogroup B1 (70.4%), MLST 1079 (42.6%), and serogroup O49 (40.7%).

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.

Twenty-Four-Month Longitudinal Study Suggests Little to No Horizontal Gene Transfer In Situ between Third-Generation Cephalosporin-Resistant Salmonella and Third-Generation Cephalosporin-Resistant Escherichia coli in a Beef Cattle Feedyard

ABSTRACT

Third-generation cephalosporins (3GCs) are preferred treatments for serious human Salmonella enterica infections. Beef cattle are suspected to contribute to human 3GC-resistant Salmonella infections. Commensal 3GC-resistant Escherichia coli are thought to act as reservoirs of 3GC resistance because these strains are isolated more frequently than are 3GC-resistant Salmonella strains at beef cattle feedyards. During each of 24 consecutive months, four samples of pen surface material were obtained from five pens (N = 480) at a Nebraska feedyard to determine to the contribution of 3GC-resistant E. coli to the occurrence of 3GC-resistant Salmonella. Illumina whole genome sequencing was performed, and susceptibility to 14 antimicrobial agents was determined for 121 3GC-susceptible Salmonella, 121 3GC-resistant Salmonella, and 203 3GC-resistant E. coli isolates. 3GC-susceptible Salmonella isolates were predominantly from serotypes Muenchen (70.2%) and Montevideo clade 1 (23.1%). 3GC-resistant Salmonella isolates were predominantly from serotypes Montevideo clade 2 (84.3%). One bla gene type (blaCMY-2) and the IncC plasmid replicon were present in 100 and 97.5% of the 3GC-resistant Salmonella, respectively. Eleven bla gene types were detected in the 3GC-resistant E. coli, which were distributed across 42 multilocus sequence types. The blaCMY-2 gene and IncC plasmid replicon were present in 37.9 and 9.9% of the 3GC-resistant E. coli, respectively. These results suggest that 3GC resistance in Salmonella was primarily due the persistence of Salmonella Montevideo clade 2 with very minimal or no contribution from 3GC-resistant E. coli via horizontal gene transfer and that 3GC-resistant E. coli may not be a useful indicator for 3GC-resistant Salmonella in beef cattle production environments.

HIGHLIGHTS

Prevalence, antimicrobial resistance, and genotype diversity of Salmonella isolates recovered from retail meat in Hebei Province, China

This study investigated the prevalence of Salmonella in 210 retail meat samples (105 raw chicken and 105 raw pork) collected from supermarkets and wet markets in 13 areas of Hebei Province, China, from June to October 2018. Whole-genome sequencing was performed on all 125 Salmonella isolates to investigate their genetic relationship. Core genome multilocus sequence typing of 77 representative isolates was used to further elucidate the genetic relatedness among the Salmonella isolated from retail meat. The mean detection rate of Salmonella in all samples was 59.5% (125/210). The prevalence of Salmonella was 53.3% (56/105) in chicken and 65.7% (69/105) in pork. Chicken and pork samples collected in July had the highest detection rate of Salmonella among the sampling months. The isolates were assigned to 19 serotypes, with S. Derby, S. London, and S. Thompson being the most frequent serotypes. Resistance to tetracycline (primarily used for the treatment of bacterial infections) was observed in 89.6% of the isolates, and 84.0% were resistant to doxycycline (also a tetracycline antibiotic) or gemifloxacin (commonly used for clinical treatment of human acute bronchitis). More than 80% of the isolates were multidrug resistant. A total of 21 sequence types were identified. Sequence type 40 (ST-40), the predominant genotype among all isolates, was found only in pork; the sequence types of chicken isolates were more diverse. A total of 58 different antibiotic resistance genes (ARGs) were detected in the 125 isolates. Most types of ARGs were associated with aminoglycoside and β-lactam resistance. Nevertheless, the tetracycline resistance gene tet(A) was the most frequently occurring ARG in all isolates at 78.4%. Multiple isolates of ST-26 contained 20 ARGs. All isolates of ST-40 were divided into two clusters, with at least 160 allelic differences between them. The findings highlight the need to continually monitor ARGs in foodborne Salmonella with particular emphasis on ST-40 and ST-26; the monitoring should include as many retail meat types as possible in the study area.

A review of the resistome within the digestive tract of livestock

Antimicrobials have been widely used to prevent and treat infectious diseases and promote growth in food-production animals. However, the occurrence of antimicrobial resistance poses a huge threat to public and animal health, especially in less developed countries where food-producing animals often intermingle with humans. To limit the spread of antimicrobial resistance from food-production animals to humans and the environment, it is essential to have a comprehensive knowledge of the role of the resistome in antimicrobial resistance (AMR), The resistome refers to the collection of all antimicrobial resistance genes associated with microbiota in a given environment. The dense microbiota in the digestive tract is known to harbour one of the most diverse resistomes in nature. Studies of the resistome in the digestive tract of humans and animals are increasing exponentially as a result of advancements in next-generation sequencing and the expansion of bioinformatic resources/tools to identify and describe the resistome. In this review, we outline the various tools/bioinformatic pipelines currently available to characterize and understand the nature of the intestinal resistome of swine, poultry, and ruminants. We then propose future research directions including analysis of resistome using long-read sequencing, investigation in the role of mobile genetic elements in the expression, function and transmission of AMR. This review outlines the current knowledge and approaches to studying the resistome in food-producing animals and sheds light on future strategies to reduce antimicrobial usage and control the spread of AMR both within and from livestock production systems.

Characterization and comparison of the microbiomes and resistomes of colostrum from selectively treated dry cows

Professionals in animal agriculture promote prudent use of antimicrobials to address public and animal health concerns, such as reduction of antimicrobial residues and antimicrobial resistance (AMR) in products. Few studies evaluate the effect of selective dry-cow therapy on preservation of the milk microbiome or the profile of AMR genes (the resistome) present at freshening. Our objectives were to characterize and compare the microbiomes and resistomes in the colostrum of cows with low somatic cell count that were treated or not treated with intramammary cephapirin benzathine at dry-off. From a larger parent study, cows on a New York dairy farm eligible for dry-off and with histories of somatic cell counts ≤200,000 cells/mL were enrolled to this study (n = 307). Cows were randomly assigned to receive an intramammary antimicrobial and external teat sealant (ABXTS) or sealant only (TS) at dry-off. Composite colostrum samples taken within 4 h of freshening, and quarter milk samples taken at 1 to 7 d in milk were subjected to aerobic culture. The DNA extraction was performed on colostrum from cows with culture-negative samples (ABXTS = 43; TS = 33). The DNA from cows of the same treatment group and parity were pooled (26 pools; ABXTS = 12; TS = 14) for 16S rRNA metagenomic sequencing. Separately, the resistome was captured using a custom RNA bait library for target-enriched sequencing. Sequencing reads were aligned to taxonomic and AMR databases to characterize the microbiome and resistome, respectively. The R statistical program was used to tabulate abundances and to analyze differences in diversity measures and in composition between treatment groups. In the microbiome, the most abundant phyla were Firmicutes (68%), Proteobacteria (23%), Actinobacteria (4%), and Bacteroidetes (3%). Shannon and richness diversity means were 0.93 and 14.7 for ABXTS and 0.94 and 13.1 for TS, respectively. Using analysis of similarities (ANOSIM), overall microbiome composition was found to be similar between treatment groups at the phylum (ANOSIM R = 0.005), class (ANOSIM R = 0.04), and order (ANOSIM R = -0.04) levels. In the resistome, we identified AMR gene accessions associated with 14 unique mechanisms of resistance across 9 different drug classes in 14 samples (TS = 9, ABXTS = 5). The majority of reads aligned to gene accessions that confer resistance to aminoglycoside (TS = ABXTS each 35% abundance), tetracycline (TS = 22%, ABXTS = 54%), and β-lactam classes (TS = 15%, ABXTS = 12%). Shannon diversity means for AMR class and mechanism, respectively, were 0.66 and 0.69 for TS and 0.19 and 0.19 for ABXTS. Resistome richness diversity means for class and mechanism were 3.1 and 3.4 for TS and 1.4 and 1.4 for ABXTS. Finally, resistome composition was similar between groups at the class (ANOSIM R = -0.20) and mechanism levels (ANOSIM R = 0.01). Although no critical differences were found between treatment groups regarding their microbiome or resistome composition in this study, a larger sample size, deeper sequencing, and additional methodology is needed to identify more subtle differences, such as between lower-abundance features.

Stockpiling versus Composting: Effectiveness in Reducing Antibiotic-Resistant Bacteria and Resistance Genes in Beef Cattle Manure

Manure storage methods can affect the concentration and prevalence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in cattle manure prior to land application. The objective of this study was to compare stockpiling and composting with respect to their effectiveness in reducing ARB and ARGs in beef cattle manure in a field-scale study. Field experiments were conducted in different seasons with different bulking agents for composting. For both the winter-spring cycle and the summer-fall cycle, ARB concentrations declined below the limit of quantification rapidly in both composting piles and stockpiles; however, ARB prevalence was significantly greater in the composting piles than in the stockpiles. This was likely due to the introduction of ARB from bulking agents. There was no significant change in ARG concentrations between initial and final concentrations for either manure storage treatment during the winter-spring cycle, but a significant reduction of the ARGs erm(B), tet(O), and tet(Q) over time was observed for both the composting pile and stockpile during the summer-fall cycle. Results from this study suggest that (i) bulking agent may be an important source of ARB and ARGs for composting; (ii) during cold months, the heterogeneity of the temperature profile in composting piles could result in poor ARG reduction; and (iii) during warm months, both stockpiling and composting can be effective in reducing ARG abundance. IMPORTANCE Proper treatment of manure is essential to reduce the spread of antibiotic resistance and protect human health. Stockpiling and composting are two manure storage methods which can reduce antibiotic-resistant bacteria and resistance genes, although few field-scale studies have examined the relative efficiency of each method. This study examined the ability of both methods in both winter-spring and summer-fall cycles, while also accounting for heterogeneity within field-scale manure piles. This study determined that bulking agents used in composting could contribute antibiotic-resistant bacteria and resistance genes. Additionally, seasonal variation could hinder the efficacy of composting in colder months due to heterogeneity in temperature within the pile; however, in warmer months, either method of manure storage could be effective in reducing the spread of antibiotic resistance.

Prevalence of antimicrobial resistance genes and its association with restricted antimicrobial use in food-producing animals: a systematic review and meta-analysis

BACKGROUND

There is ongoing debate regarding potential associations between restrictions of antimicrobial use and prevalence of antimicrobial resistance (AMR) in bacteria.

OBJECTIVES

To summarize the effects of interventions reducing antimicrobial use in food-producing animals on the prevalence of AMR genes (ARGs) in bacteria from animals and humans.

METHODS

We published a full systematic review of restrictions of antimicrobials in food-producing animals and their associations with AMR in bacteria. Herein, we focus on studies reporting on the association between restricted antimicrobial use and prevalence of ARGs. We used multilevel mixed-effects models and a semi-quantitative approach based on forest plots to summarize findings from studies.

RESULTS

A positive effect of intervention [reduction in prevalence or number of ARGs in group(s) with restricted antimicrobial use] was reported from 29 studies for at least one ARG. We detected significant associations between a ban on avoparcin and diminished presence of the vanA gene in samples from animals and humans, whereas for the mecA gene, studies agreed on a positive effect of intervention in samples only from animals. Comparisons involving mcr-1, blaCTX-M, aadA2, vat(E), sul2, dfrA5, dfrA13, tet(E) and tet(P) indicated a reduced prevalence of genes in intervention groups. Conversely, no effects were detected for β-lactamases other than blaCTX-M and the remaining tet genes.

CONCLUSIONS

The available body of scientific evidence supported that restricted use of antimicrobials in food animals was associated with an either lower or equal presence of ARGs in bacteria, with effects dependent on ARG, host species and restricted drug.

Detection of Extended-Spectrum Beta-Lactamase-Producing and Carbapenem-Resistant Bacteria from Mink Feces and Feed in the United States

Antibiotic-resistant infections caused by extended-spectrum β-lactamases (ESBLs) and carbapenemases are increasing worldwide. Bacteria resistant to extended-spectrum cephalosporins and last resort carbapenems have been reported from food animals and their environments. Other concentrated nonfood-producing animals such as mink farming can be a reservoir of bacteria resistant to these critically important antibiotics. The objective of this study was to determine the prevalence of ESBL-producing bacteria and carbapenem-resistant (CR) bacteria from mink fecal (n = 42) and feed (n = 8) samples obtained from a commercial mink farm in the United States. The most prevalent ESBL-producing bacteria identified from the fecal samples were Escherichia coli (93%), Klebsiella pneumoniae (76%), and Proteus species (88%). E. coli (100%) and K. pneumoniae (75%) were also the most prevalent ESBL-producing bacteria identified from feed samples. All ESBL E. coli isolates were resistant to penicillin and most cephem beta-lactam antibiotics. Among the ESBL E. coli isolates, co-resistance was observed to ciprofloxacin (33%) and gentamicin (28%) indicating multidrug resistance. ESBL E. coli isolates predominantly carried bla_CTX-M-14 and bla_CTX-M-15 genes. Although all feed K. pneumoniae isolates carried bla_CTX-M-9, all fecal K. pneumoniae isolates carried bla_SHV. CR Pseudomonas species (7%), Hafnia alvei (24%), and Myroides odoratimimus (9.5%) were detected from fecal samples. H. alvei (37.5%) was the only CR bacteria detected from the feed samples. All CR isolates were polymerase chain reaction negative for the tested carbapenemases that are commonly reported, which may indicate intrinsic rather than acquired resistance. This study indicates that mink production can be a reservoir for bacteria resistant to the highest priority critically important antibiotics for human health.

Using the heat generated from electrically conductive concrete slabs to reduce antibiotic resistance in beef cattle manure

Proper treatment is necessary to reduce antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in livestock manure before land application. Conventional stockpiling suffers unreliable removal efficiency, while composting can be complicated and expensive. The objective of this study was to test the feasibility of a novel heat-based technology, i.e., stockpiling manure on conductive concrete slabs, to inactivate ARB and ARGs in beef cattle manure. In this study, two independent bench-scale trials were conducted. In both trials, samples were taken from manure piles on conductive concrete slabs and regular slabs (i.e., heated and unheated piles). In the heated pile of the first trial, 25.9% and 83.5% of the pile volume met the EPA Class A and Class B biosolids standards, respectively. For the heated pile of the second trial, the two values were 43.9% and 74.2%. In both trials, nearly all forms of the total and resistant Escherichia coli and enterococci were significantly lower in the heated piles than in the unheated piles. Besides, significant reduction of ARGs in heated piles was observed in the first trial. Through this proof-of-concept study, the new technology based on conductive concrete slabs offers an alternative manure storage method to conventional stockpiling and composting with respect to reduce ARB and ARGs in manure.

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

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

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

A Comparative Quantitative Assessment of Human Exposure to Various Antimicrobial-Resistant Bacteria among U.S. Ground Beef Consumers

ABSTRACT

Consumption of animal-derived meat products is suspected as an important exposure route to antimicrobial resistance, as the presence of antimicrobial-resistant bacteria (ARB) along the beef supply chain is well documented. A retail-to-fork quantitative exposure assessment was established to compare consumers' exposure to various ARB due to the consumption of ground beef with and without "raised without antibiotics" claims and to inform potential exposure mitigation strategies related to consumer practices. The microbial agents evaluated included Escherichia coli, tetracycline-resistant (TETr) E. coli, third-generation cephalosporin-resistant E. coli,Salmonella enterica, TETrS. enterica, third-generation cephalosporin-resistant S. enterica, nalidixic acid-resistant S. enterica, Enterococcus spp., TETrEnterococcus spp., erythromycin-resistant Enterococcus spp., Staphylococcus aureus, and methicillin-resistant S. aureus. The final model outputs were the probability of exposure to at least 0 to 6 log CFU microorganisms per serving of ground beef at the time of consumption. It was estimated that tetracycline resistance was more prevalent in ground beef compared with other types of resistance, among which the predicted average probability of ingesting TETrEnterococcus was highest (6.2% of ingesting at least 0 log CFU per serving), followed by TETrE. coli (3.1%) and TETrSalmonella (0.0001%), given common product purchase preferences and preparation behaviors among beef consumers in the United States. The effectiveness of consumer-related interventions was estimated by simulating the differences in exposure as a result of changes in consumer practices in purchasing, handling, and preparing ground beef. The results indicated that proper use of recommended safe cooking and food preparation practices mitigates ARB exposure more effectively than choosing raised without antibiotics compared with conventional beef.

HIGHLIGHTS

System Economic Costs of Antibiotic Use Elimination in the US Beef Supply Chain

There is consumer pressure on the US beef cattle industry to minimize antibiotic use (ABU) in order to aid in the global antimicrobial resistance mitigation efforts. Our objective was to estimate the economic costs of ABU constraints in a conceptual US integrated beef supply chain (IBSC) to aid the beef industry in mitigating the ever-increasing risk of antimicrobial resistance, by reducing their ABU. An IBSC network model was developed and differentiated into 37 different nodes of production. Each node could only raise a specific type of animals, differentiated based on the production technique and animal health status. The cost, as well as the weight gain coefficient, was estimated for each node, using an IBSC cost of production model. Linear programming solutions to this network model provided the least cost path of beef supply through the system, under various ABU constraints. The cost as well as weight gain coefficient of the 37 nodes, initial supply of 28.5 million calves weighing 0.65 million metric tons, and final demand of 16.14 million metric tons of slaughter-ready fed cattle were used as inputs/constraints to the three different linear programming scenarios, with different ABU constraints. Our first scenario, which placed no constraint on ABU, estimated that the minimum total economic cost to meet the final beef demand was $38.6 billion. The optimal solution was to use only the high health status calves for beef production. Because low health calves occur in the beef system, our second scenario required all the calves irrespective of their health status to be used, which increased the system cost to $41.5 billion. Thus, the value of only producing high health status calves is $2.9 billion. Our third scenario, which restricted feedlots from using antibiotics even for low health calves, incurred a total cost of $41.9 billion for antibiotic-free beef production. We concluded that the additional cost of $367 million for implementing antibiotic-free beef production is relatively low, ~0.90% of the minimum cost incurred for the conventional beef supply chain (model 2 cost of $41.5 billion). However, a much higher cost savings is obtained by producing only high health status calves.

Validation of Additional Approaches and Applications for Using the Continuous and Manual Sampling Devices for Raw Beef Trim

ABSTRACT

In this work, the goal was to determine the efficacy of MicroTally-based sampling in scenarios commonly encountered in the commercial beef processing industry, but outside of the parameters evaluated during the initial proof-of-concept work. The data were derived from 1,650 matched samples collected from 540 individual combo bins at six commercial beef processing plants, comparing MicroTally-based sampling (continuous and manual sampling devices [CSD and MSD]) to N60 Excision and/or N60 Plus methods. Mounting a 61-cm CSD cartridge to a 30-cm-wide conveyor provided sampling that is equivalent to N60 Excision and N60 Plus methods. Mounting a CSD to a chute instead of a conveyor was equivalent to the N60 Plus sampling method. The CSD was shown to be effective for sampling when used in conjunction with a "swinging arm trim diverter" and receiving product in batch mode as opposed to continuous flow. MSD sampling of oval combo bins with trim surface area (≈0.93 m2 [≈1,439 in2]) less than 1 m2 (1,600 in2) was shown to be equivalent to the N60 Plus sample collection method. Peracetic acid applied at the end of the trim conveyor did not negatively impact pathogen index target detection of the CSD even if the samples were shipped overnight before analysis. Pathogen index targets were demonstrated to be useful tools for validating methods designed to measure pathogen prevalence. The data presented herein support equivalency criteria of within 0.5 log CFU per sample for indicator organism counts. These data collectively support various alternative applications of MicroTally-based trim sampling and the application and interpretation of alternative methods for pathogen detection.

HIGHLIGHTS

Antimicrobial resistance in non-Typhoidal Salmonella from retail poultry meat by antibiotic usage-related production claims - United States, 2008-2017

Antimicrobial resistance (AMR) in non-typhoidal Salmonella from poultry is a public health concern. Injudicious use of antibiotics in humans and agriculture fuels the emergence of resistance. The objective of this study was to characterize the prevalence, antibiotic susceptibility profiles and genetic resistance mechanisms of Salmonella isolated from US retail poultry meat samples with and without antibiotic-related claims. We reviewed data from 46,937 poultry meat samples collected from 2008 to 2017 through the FDA NARMS retail meat program. Antibiotic usage claims on the poultry packaging were used to categorize the sample as 'conventionally raised' or 'reduced or no antibiotic use'. The results show that the prevalence of Salmonella in conventional poultry samples (8.6%) was higher than reduced or no antibiotic use poultry samples (5.1%). The odds of resistance to three or more antimicrobial classes (multi-drug resistant) were 2.61 times higher for Salmonella isolates from conventional samples, compared to isolates from reduced antibiotic use samples. The frequency of the aminoglycoside resistance gene, strB, and the beta-lactam resistant gene, blaCMY-2, were higher in isolates from conventional meat. This study suggests that conventionally raised poultry meat was more likely to be contaminated with multi-drug resistant Salmonella, and those Salmonella are more likely to carry genes for antibiotics resistance.

Metagenomic Analysis of the Microbial Communities and Resistomes of Veal Calf Feces

Antimicrobial resistance (AMR) is a major public health concern, and dairy calves, including veal calves, are known reservoirs of resistant bacteria. To investigate AMR in the fecal microbial communities of veal calves, we conducted metagenomic sequencing of feces collected from individual animals on four commercial veal operations in Pennsylvania. Fecal samples from three randomly selected calves on each farm were collected soon after the calves were brought onto the farms (n = 12), and again, just before the calves from the same cohorts were ready for slaughter (n = 12). Results indicated that the most frequently identified phyla were Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Fecal microbial communities in samples collected from the calves at the early and late stages of production were significantly different at the genus level (analysis of similarities [ANOSIM] on Bray-Curtis distances, R = 0.37, p < 0.05), but not at the phylum level. Variances among microbial communities in the feces of the younger calves were significantly higher than those from the feces of calves at the late stage of production (betadisper F = 8.25, p < 0.05). Additionally, our analyses identified a diverse set of mobile antimicrobial resistance genes (ARGs) in the veal calf feces. The fecal resistomes mostly consisted of ARGs that confer resistance to aminoglycosides, tetracyclines, and macrolide-lincosamide-streptogramin B (MLS), and these ARGs represented more than 70% of the fecal resistomes. Factors that are responsible for selection and persistence of resistant bacteria in the veal calf gut need to be identified to implement novel control points and interrupt detrimental AMR occurrence and shedding.

Antibiotic-resistant bacteria and gut microbiome communities associated with wild-caught shrimp from the United States versus imported farm-raised retail shrimp

In the United States, farm-raised shrimp accounts for ~ 80% of the market share. Farmed shrimp are cultivated as monoculture and are susceptible to infections. The aquaculture industry is dependent on the application of antibiotics for disease prevention, resulting in the selection of antibiotic-resistant bacteria. We aimed to characterize the prevalence of antibiotic-resistant bacteria and gut microbiome communities in commercially available shrimp. Thirty-one raw and cooked shrimp samples were purchased from supermarkets in Florida and Georgia (U.S.) between March-September 2019. The samples were processed for the isolation of antibiotic-resistant bacteria, and isolates were characterized using an array of molecular and antibiotic susceptibility tests. Aerobic plate counts of the cooked samples (n = 13) varied from < 25 to 6.2 log CFU/g. Isolates obtained (n = 110) were spread across 18 genera, comprised of coliforms and opportunistic pathogens. Interestingly, isolates from cooked shrimp showed higher resistance towards chloramphenicol (18.6%) and tetracycline (20%), while those from raw shrimp exhibited low levels of resistance towards nalidixic acid (10%) and tetracycline (8.2%). Compared to wild-caught shrimp, the imported farm-raised shrimp harbored distinct gut microbiota communities and a higher prevalence of antibiotic-resistance genes in their gut. The presence of antibiotic-resistant strains in cooked shrimps calls for change in processing for their mitigation.

The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania

BACKGROUND

Antimicrobial resistance is a serious concern. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial resistance genes (ARG) in farm environments, little is known about whether antimicrobial use affects distribution of ARG in livestock systems. This study compared the distribution of microbiomes and resistomes (collections of ARG) across different farm sectors in dairy herds that differed in their use of antimicrobials. Feces from heifers, non-lactating, and lactating cows, manure storage, and soil from three conventional (antimicrobials used to treat cows) and three organic (no antimicrobials used for at least four years) farms in Pennsylvania were sampled. Samples were extracted for genomic DNA, processed, sequenced on the Illumina NextSeq platform, and analyzed for microbial community and resistome profiles using established procedures.

RESULTS

Microbial communities and resistome profiles clustered by sample type across all farms. Overall, abundance and diversity of ARG in feces was significantly higher in conventional herds compared to organic herds. The ARG conferring resistance to betalactams, macrolide-lincosamide-streptogramin (MLS), and tetracyclines were significantly higher in fecal samples of dairy cows from conventional herds compared to organic herds. Regardless of farm type, all manure storage samples had greater diversity (albeit low abundance) of ARG conferring resistance to aminoglycosides, tetracyclines, MLS, multidrug resistance, and phenicol. All soil samples had lower abundance of ARG compared to feces, manure, and lagoon samples and were comprised of ARG conferring resistance to aminoglycosides, glycopeptides, and multi-drug resistance. The distribution of ARG is likely driven by the composition of microbiota in the respective sample types.

CONCLUSIONS

Antimicrobial use on farms significantly influenced specific groups of ARG in feces but not in manure storage or soil samples.

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

Metagenomic Characterization of the Microbiome and Resistome of Retail Ground Beef Products

Ground beef can be a reservoir for a variety of bacteria, including spoilage organisms, and pathogenic foodborne bacteria. These bacteria can exhibit antimicrobial resistance (AMR) which is a public health concern if resistance in pathogens leads to treatment failure in humans. Culture-dependent techniques are commonly used to study individual bacterial species, but these techniques are unable to describe the whole community of microbial species (microbiome) and the profile of AMR genes they carry (resistome), which is critical for getting a holistic perspective of AMR. The objective of this study was to characterize the microbiome and resistome of retail ground beef products labeled as coming from conventional or raised without antibiotics (RWA) production systems. Sixteen ground beef products were purchased from 6 retail grocery outlets in Fort Collins, CO, half of which were labeled as produced from cattle raised conventionally and half of products were from RWA production. Total DNA was extracted and isolated from each sample and subjected to 16S rRNA amplicon sequencing for microbiome characterization and target-enriched shotgun sequencing to characterize the resistome. Differences in the microbiome and resistome of RWA and conventional ground beef were analyzed using the R programming software. Our results suggest that the resistome and microbiome of retail ground beef products with RWA packaging labels do not differ from products that do not carry claims regarding antimicrobial drug exposures during cattle production. The resistome predominantly consisted of tetracycline resistance making up more than 90% of reads mapped to resistance gene accessions in our samples. Firmicutes and Proteobacteria predominated in the microbiome of all samples (69.6% and 29.0%, respectively), but Proteobacteria composed a higher proportion in ground beef from conventionally raised cattle. In addition, our results suggest that product management, such as packaging type, could exert a stronger influence on the microbiome than the resistome in consumer-ready products. Metagenomic analyses of ground beef is a promising tool to investigate community-wide shifts in retail ground beef. Importantly, however, results from metagenomic sequencing must be carefully considered in parallel with traditional methods to better characterize the risk of AMR in retail products.

Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes

Chicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey, we established the chicken microbiome as a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information and retain systematic signals characteristic of overall processing environments.

Microorganisms and their communities on foods are important determinants and indicators of food safety and quality. Despite growing interests in studying food and food-related microbiomes, how effective and practical it is to glean various food safety and quality information from food commodity microbiomes remains underinvestigated. Microbiomes of retail chicken breast from 4 processing establishments in 3 major U.S. broiler production states displayed longitudinal consistency over 7 months and cross-sectional distinctiveness associated with individual processing environments. Packaging type and processing environment but not antibiotic usage and seasonality affected composition and diversity of the microbiomes. Low abundances of antimicrobial resistance genes were found on chicken breasts, and no significant resistome difference was observed between antibiotic-free and conventional products. Benchmarked by culture enrichment, shotgun metagenomics sequencing delivered sensitive and specific detection of Salmonella enterica from chicken breasts.

IMPORTANCE Chicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey, we established the chicken microbiome as a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information and retain systematic signals characteristic of overall processing environments.

No Change in Risk for Antibiotic-Resistant Salmonellosis from Beef, United States, 2002-2010

Restricting antibiotic use in food production animals is a target for reducing antimicrobial drug–resistant infections in humans. To estimate the probability of antibiotic-resistant nontyphoidal salmonellosis per meal made with beef during 2002–2010, we used US surveillance data. Applying data for nontyphoidal Salmonella in raised-without-antibiotics cattle, we tested the effect of removing antibiotic use from all beef cattle production. We found an average of 1.2 antibiotic-resistant nontyphoidal salmonellosis cases per 1 million beef meals made with beef initially contaminated with antibiotic-resistant nontyphoidal Salmonella at slaughter or retail and 0.031 cases per 1 million meals irrespective of beef contamination status. Neither outcome showed sustained change except for increases in 2003 and 2009 (>98% confidence) when larger or more outbreaks occurred. Switching all beef production to a raised-without-antibiotics system may not have a significant effect on antibiotic-resistant nontyphoidal salmonellosis (94.3% confidence).

Corn stalk residue may add antibiotic-resistant bacteria to manure composting piles

Manure is commonly used as a fertilizer or soil conditioner; however, land application of untreated manure may introduce pathogens and antibiotic-resistant bacteria (ARB) into the soil, with harmful implications for public health. Composting is a manure management practice wherein a carbon-rich bulking agent, such as corn (Zea mays L.) stalk residue, is added to manure to achieve desirable carbon/nitrogen ratios to facilitate microbial activities and generate enough heat to inactivate pathogens, including antibiotic-resistant pathogens. However, when comparing compost piles and stockpiles for ARB reduction, we noticed that bulking agents added ARB to composting piles and compromised the performance of composting in reducing ARB. We hypothesized that ARB could be prevalent in corn stalk residues, a commonly used bulking agent for composting. To test this hypothesis, corn stalk residue samples throughout Nebraska were surveyed for the presence of ARB. Of the samples tested, 54% were positive for antibiotic-resistant Escherichia coli or enterococci using direct plating or after enrichment. Although not statistically significant, there was a trend wherein the use of pesticides tended to result in a greater prevalence of some ARB. Results from this study suggest that bulking agents can be a source of ARB in manure composting piles and highlight the importance of screening bulking agents for effective ARB reduction in livestock manure during composting.

Differences in the Microbial Community and Resistome Structures of Feces from Preweaned Calves and Lactating Dairy Cows in Commercial Dairy Herds

Preweaned dairy calves and lactating dairy cows are known reservoirs of antibiotic-resistant bacteria. To further understand the differences in the resistomes and microbial communities between the two, we sequenced the metagenomes of fecal composite samples from preweaned dairy calves and lactating dairy cows on 17 commercial dairy farms (n = 34 samples). Results indicated significant differences in the structures of the microbial communities (analysis of similarities [ANOSIM] R = 0.81, p = 0.001) and resistomes (ANOSIM R = 0.93 to 0.96, p = 0.001) between the two age groups. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the predominant members of the communities, but when the groups were compared, Bacteroidetes and Verrumicrobia were significantly more abundant in calf fecal composite samples, whereas Firmicutes, Spirochaetes, Deinococcus-Thermus, Lentisphaerae, Planctomycetes, Chlorofexi, and Saccharibacteria-(TM7) were more abundant in lactating cow samples. Diverse suites of antibiotic resistance genes (ARGs) were identified in all samples, with the most frequently detected being assigned to tetracycline and aminoglycoside resistance. When the two groups were compared, ARGs were significantly more abundant in composite fecal samples from calves than those from lactating cows (calf median ARG abundance = 1.8 × 10⁰ ARG/16S ribosomal RNA [rRNA], cow median ARG abundance = 1.7 × 10^-1 ARG/16S rRNA) and at the antibiotic resistance class level, the relative abundance of tetracycline, trimethoprim, aminoglycoside, macrolide-lincosamide-streptogramin B, β-lactam, and phenicol resistance genes was significantly higher in calf samples than in cow samples. Results of this study indicate that composite feces from preweaned calves harbor different bacterial communities and resistomes than composite feces from lactating cows, with a greater abundance of resistance genes detected in preweaned calf feces.

Investigation of a Reduction in Tylosin on the Prevalence of Liver Abscesses and Antimicrobial Resistance in Enterococci in Feedlot Cattle

Recent concerns over linkages between antimicrobial resistance in human pathogens and antimicrobial use in livestock have prompted researchers to investigate management strategies that reduce the current reliance on in-feed tylosin to control liver abscesses in feedlot cattle. A total of 7,576 crossbred yearlings were allocated to the study (~253 animals/pen, 10 replicate pens per treatment) and individually randomized to one of three treatments. Tylosin phosphate (11 ppm) was included in-feed (1) for the first 125 days on feed (DOF) (FIRST-78%), (2) for DOF 41 to 161 (LAST-75%), or (3) for the entire feeding period (CON; day 0–161). Fecal composites were collected from the pen floor on days 0, 81, and 160 of the finishing period. Serial dilutions were spread plated for enumeration of enterococci on Bile Esculin Azide (BEA) agar and BEA amended with 8 μg/ml erythromycin. Results indicated that although the proportion of Ery^R enterococci increased with DOF (P < 0.01), neither treatment (P = 0.34) or treatment × DOF (P = 0.37) affected antimicrobial resistance. Of the 538 isolates, 97% were enterococci, with mixed species isolated early in the feeding period and only Enterococcus hirae isolated at the end. Isolates were most frequently resistant to tylosin (86%), erythromycin (84%), and doxycycline (31%). Macrolide and tetracycline resistant isolates harbored erm(B), msrC, and tet(L), tet(M), tet(O) genes, respectively. Overall, the proportion of Ery^R enterococci increased (P < 0.05) in all three treatments over the feeding period. Compared to the control cattle, FIRST-78% cattle had more severe (P < 0.05) liver abscesses, while there was a trend (P < 0.08) for this response in LAST-75% cattle. There was no difference (P > 0.05) in total liver abscesses, growth performance, carcass traits, morbidity, or mortality among treatments. These results support the potential to reduce the duration and therefore quantity of tylosin administered to feedlot cattle during the feeding period without impacting animal productivity.

Antimicrobial Resistance in Members of the Bacterial Bovine Respiratory Disease Complex Isolated from Lung Tissue of Cattle Mortalities Managed with or without the Use of Antimicrobials

Over a two-year period, Mannheimia haemolytica (MH; n = 113), Pasteurella multocida (PM; n = 47), Histophilus somni (HS; n = 41) and Mycoplasma bovis (MB; n = 227) were isolated from bovine lung tissue at necropsy from cattle raised conventionally (CON, n = 29 feedlots) or without antimicrobials [natural (NAT), n = 2 feedlots]. Excluding MB, isolates were assayed by PCR to detect the presence of 13 antimicrobial resistance (AMR) genes and five core genes associated with integrative and conjugative elements (ICEs). Antimicrobial susceptibility phenotypes and minimum inhibitory concentrations (MICs, µg/mL) were determined for a subset of isolates (MH, n = 104; PM, n = 45; HS, n = 23; and MB, n = 61) using Sensititre analyses. A subset of isolates (n = 21) was also evaluated by whole-genome sequencing (WGS) based on variation in AMR phenotype. All five ICE core genes were detected in PM and HS by PCR, but only 3/5 were present in MH. Presence of mco and tnpA ICE core genes in MH was associated with higher MICs (p < 0.05) for all tetracyclines, and 2/3 of all macrolides, aminoglycosides and fluoroquinolones evaluated. In contrast, association of ICE core genes with MICs was largely restricted to macrolides for PM and to individual tetracyclines and macrolides for HS. For MH, the average number of AMR genes markedly increased (p < 0.05) in year 2 of the study due to the emergence of a strain that was PCR positive for all 13 PCR-tested AMR genes as well as two additional AMR genes (aadA31 and bla_ROB-1) detected by WGS. Conventional management of cattle increased (p < 0.05) MICs of tilmicosin and tulathromycin for MH; neomycin and spectinomycin for PM; and gamithromycin and tulathromycin for MB. The average number of PCR-detected AMR genes in PM was also increased (p < 0.05) in CON mortalities. This study demonstrates increased AMR especially to macrolides by bovine respiratory disease organisms in CON as compared to NAT feedlots and a rapid increase in AMR following dissemination of strain(s) carrying ICE-associated multidrug resistance.

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

Raising Animals Without Antibiotics: U.S. Producer and Veterinarian Experiences and Opinions

Ensuring the safety, health, and overall well-being of animals raised for food is both an ethical obligation and a critical component of providing safe food products. The use of antibiotics for maintaining animal health has come under scrutiny in recent years due to the rise of antibiotic resistance globally. Some U.S. producers, especially in the poultry industry, have responded by eliminating their antibiotic use. The number of animals raised without antibiotics (RWA) is growing in the U.S., but there are concerns that RWA practices might negatively impact animal health and welfare. Therefore, the objective of this study was to survey U.S. veterinarians and producers about their experiences and opinions regarding RWA production. Veterinarians, farmers, ranchers, producers, and other stakeholders involved in raising broilers, turkeys, swine, beef cattle or dairy cattle were surveyed. Of the 565 completed responses received, 442 self-reported as practicing veterinarians or producers. Just over half of respondents reported having past or current experience with RWA programs. The main indicated reasons for raising animals without antibiotics were market driven; switching to RWA production was less commonly made for health-related reasons, such as to reduce antibiotic resistance or to improve animal health and welfare. Although respondents felt that RWA production has negative impacts on animal health and welfare, they overwhelmingly (>70%) indicated that the customer (retailer/restaurant/food service) believes that animal and health welfare will be significantly improved. Veterinarians and producers indicated that RWA programs will increase production costs with questionable effect on meat, egg or dairy consumer demand. Many respondents felt that there are times when the RWA label takes priority over animal health and welfare. Respondents generally felt that there was a need for increased auditing/assessment of animal health and welfare in RWA systems.