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Lee C, Zaheer R, Munns K, Holman DB, Van Domselaar G, Zovoilis A, McAllister TA. Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome. Microorganisms 2023; 11:2982. [PMID: 38138126 PMCID: PMC10745953 DOI: 10.3390/microorganisms11122982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of "natural" feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems.
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Affiliation(s)
- Catrione Lee
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
| | - Krysty Munns
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; (C.L.); (R.Z.); (K.M.)
| | - Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 6000 C and E Trail, Lacombe, AB T4L 1W1, Canada;
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Government of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada;
| | - Athanasios Zovoilis
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
| | - Tim A. McAllister
- Southern Alberta Genomic Sciences Centre, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada;
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Patience JF, Ramirez A. Invited review: strategic adoption of antibiotic-free pork production: the importance of a holistic approach. Transl Anim Sci 2022; 6:txac063. [PMID: 35854972 PMCID: PMC9278845 DOI: 10.1093/tas/txac063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/13/2022] [Indexed: 02/07/2023] Open
Abstract
The discovery of the use of antibiotics to enhance growth in the 1950s proved to be one of the most dramatic and influential in the history of animal agriculture. Antibiotics have served animal agriculture, as well as human and animal medicine, well for more than seven decades, but emerging from this tremendous success has been the phenomenon of antimicrobial resistance. Consequently, human medicine and animal agriculture are being called upon, through legislation and/or marketplace demands, to reduce or eliminate antibiotics as growth promotants and even as therapeutics. As explained in this review, adoption of antibiotic-free (ABF) pork production would represent a sea change. By identifying key areas requiring attention, the clear message of this review is that success with ABF production, also referred to as "no antibiotics ever," demands a multifaceted and multidisciplinary approach. Too frequently, the topic has been approached in a piecemeal fashion by considering only one aspect of production, such as the use of certain feed additives or the adjustment in health management. Based on the literature and on practical experience, a more holistic approach is essential. It will require the modification of diet formulations to not only provide essential nutrients and energy, but to also maximize the effectiveness of normal immunological and physiological capabilities that support good health. It must also include the selection of effective non-antibiotic feed additives along with functional ingredients that have been shown to improve the utility and architecture of the gastrointestinal tract, to improve the microbiome, and to support the immune system. This holistic approach will require refining animal management strategies, including selection for more robust genetics, greater focus on care during the particularly sensitive perinatal and post-weaning periods, and practices that minimize social and environmental stressors. A clear strategy is needed to reduce pathogen load in the barn, such as greater emphasis on hygiene and biosecurity, adoption of a strategic vaccine program and the universal adoption of all-in-all-out housing. Of course, overall health management of the herd, as well as the details of animal flows, cannot be ignored. These management areas will support the basic biology of the pig in avoiding or, where necessary, overcoming pathogen challenges without the need for antibiotics, or at least with reduced usage.
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Affiliation(s)
| | - Alejandro Ramirez
- College of Veterinary Medicine, University of Arizona, Oro Valley, AZ 85737, USA
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Tunsagool P, Mhuantong W, Tangphatsornruang S, Am-In N, Chuanchuen R, Luangtongkum T, Suriyaphol G. Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics. Appl Environ Microbiol 2021; 87:AEM. [PMID: 33547058 DOI: 10.1128/AEM.02684-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study aimed to detect the cecal microbiome, antimicrobial resistance (AMR) and heavy metal resistance genes (MRGs) in fattening pigs raised under antibiotic-free (ABF) conditions compared with ordinary industrial pigs (control, C) using whole-genome shotgun sequencing. ABF pigs showed the enrichment of Prevotella (33%) and Lactobacillus (13%), whereas Escherichia coli (40%), Fusobacterium and Bacteroides (each at 4%) were notably observed in the C group. Distinct clusters of cecal microbiota of ABF and C pigs were revealed; however, microbiota of some C pigs (C1) appeared in the same cluster as ABF and were totally separated from the remaining C pigs (C2). For AMR genes, the highest abundance tet(Q) (35.7%) and mef(A) (12.7%) were markedly observed in the ABF group whereas tet(Q) (26.2%) and tet(W) (10.4%) were shown in the C group. tet(Q) was positively correlated to Prevotella in ABF and C1 samples. In the C2 group, the prominent tet(W) was positively correlated to Fusobacterium and Bacteroides Pigs have never received tetracycline but pregnant sows used chlortetracycline once 7 d before parturition. Chromosomal Cu and Zn resistance genes were also shown in both groups regardless the received Cu and Zn feed additives. A higher abundance of multi-metal resistance genes was observed in the C group (44%) compared with the ABF group (41%). In conclusion, the microbiome clusters in some C pigs were similar to that in ABF pigs. High abundant tetracycline resistance genes interrelated to major bacteria were observed in both ABF and C pigs. MRGs were also observed.IMPORTANCE: Owing to the increased problem of AMR in farm animals, raising farm animals without antibiotics is one method that could solve this problem. Our study showed that only some tetracycline and macrolide resistance genes, tet(Q), tet(W) and mef(A), were markedly abundant in ABF and C groups. The tet(Q) and tet(W) genes interrelated to different predominant bacteria in each group, showing the potential role of major bacteria as reservoirs of AMR genes. In addition, chromosomal Cu and Zn resistance genes were also observed in both pig groups, not depending on the use of Cu and Zn additives in both farms. The association of MRGs and AMR genotypes and phenotypes together with the method to re-sensitize bacteria to antibiotics should be studied further to unveil the cause of high resistance genes and solve the problems.
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Doster E, Thomas KM, Weinroth MD, Parker JK, Crone KK, Arthur TM, Schmidt JW, Wheeler TL, Belk KE, Morley PS. Metagenomic Characterization of the Microbiome and Resistome of Retail Ground Beef Products. Front Microbiol 2020; 11:541972. [PMID: 33240224 PMCID: PMC7677504 DOI: 10.3389/fmicb.2020.541972] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
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.
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Affiliation(s)
- Enrique Doster
- Texas A&M University, VERO Program, Canyon, TX, United States.,Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States.,Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Kevin M Thomas
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Maggie D Weinroth
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Jennifer K Parker
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Kathryn K Crone
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Terrance M Arthur
- U.S. Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - John W Schmidt
- U.S. Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Tommy L Wheeler
- U.S. Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Keith E Belk
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Paul S Morley
- Texas A&M University, VERO Program, Canyon, TX, United States.,Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
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Vikram A, Rovira P, Agga GE, Arthur TM, Bosilevac JM, Wheeler TL, Morley PS, Belk KE, Schmidt JW. Impact of " Raised without Antibiotics" Beef Cattle Production Practices on Occurrences of Antimicrobial Resistance. Appl Environ Microbiol 2017; 83:e01682-17. [PMID: 28887421 DOI: 10.1128/AEM.01682-17] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/05/2017] [Indexed: 01/04/2023] Open
Abstract
The specific antimicrobial resistance (AMR) decreases that can be expected from reducing antimicrobial (AM) use in U.S. beef production have not been defined. To address this data gap, feces were recovered from 36 lots of "raised without antibiotics" (RWA) and 36 lots of "conventional" (CONV) beef cattle. Samples (n = 719) were collected during harvest and distributed over a year. AMR was assessed by (i) the culture of six AM-resistant bacteria (ARB), (ii) quantitative PCR (qPCR) for 10 AMR genes (ARGs), (iii) a qPCR array of 84 ARGs, and (iv) metagenomic sequencing. Generally, AMR levels were similar, but some were higher in CONV beef cattle. The prevalence of third-generation cephalosporin-resistant (3GCr) Escherichia coli was marginally different between production systems (CONV, 47.5%; RWA, 34.8%; P = 0.04), but the seasonal effect (summer, 92.8%; winter, 48.3%; P < 0.01) was greater. Erythromycin-resistant (ERYr) Enterococcus sp. concentrations significantly differed between production systems (CONV, 1.91 log10 CFU/g; RWA, 0.73 log10 CFU/g; P < 0.01). Levels of aadA1, ant(6)-I, bla ACI, erm(A), erm(B), erm(C), erm(F), erm(Q), tet(A), tet(B), tet(M), and tet(X) ARGs were higher (P < 0.05) in the CONV system. Aggregate abundances of all 43 ARGs detected by metagenomic sequencing and the aggregate abundances of ARGs in the aminoglycoside, β-lactam, macrolide-lincosamide-streptogramin B (MLS), and tetracycline AM classes did not differ (log2 fold change < 1.0) between CONV and RWA systems. These results suggest that further reductions of AM use in U.S. beef cattle production may not yield significant AMR reductions beyond MLS and tetracycline resistance.IMPORTANCE The majority of antimicrobial (AM) use in the United States is for food-animal production, leading to concerns that typical AM use patterns during "conventional" (CONV) beef cattle production in the United States contribute broadly to antimicrobial resistance (AMR) occurrence. In the present study, levels of AMR were generally similar between CONV and "raised without antibiotics" (RWA) cattle. Only a limited number of modest AMR increases was observed in CONV cattle, primarily involving macrolide-lincosamide-streptogramin B (MLS) and tetracycline resistance. Macrolides (tylosin) and tetracyclines (chlortetracycline) are administered in-feed for relatively long durations to reduce liver abscesses. To ensure judicious AM use, the animal health, economic, and AMR impacts of shorter duration in-feed administration of these AMs should be examined. However, given the modest AMR reductions observed, further reductions of AM use in U.S. beef cattle production may not yield significant AMR reductions beyond MLS and tetracycline resistance.
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