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O'Hara E, Zaheer R, Andrés-Lasheras S, McAllister TA, Gruninger RJ. Evaluating the liver abscess microbiota of beef cattle during a reduction in tylosin supplementation shows differences according to abscess size and fraction. FEMS Microbiol Ecol 2024; 100:fiae002. [PMID: 38373802 PMCID: PMC10960635 DOI: 10.1093/femsec/fiae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/04/2024] [Accepted: 02/19/2024] [Indexed: 02/21/2024] Open
Abstract
Liver abscesses (LA) resulting from bacterial infection in cattle pose a significant global challenge to the beef and dairy industries. Economic losses from liver discounts at slaughter and reduced animal performance drive the need for effective mitigation strategies. Tylosin phosphate supplementation is widely used to reduce LA occurrence, but concerns over antimicrobial overuse emphasize the urgency to explore alternative approaches. Understanding the microbial ecology of LA is crucial to this, and we hypothesized that a reduced timeframe of tylosin delivery would alter LA microbiomes. We conducted 16S rRNA sequencing to assess severe liver abscess bacteriomes in beef cattle supplemented with in-feed tylosin. Our findings revealed that shortening tylosin supplementation did not notably alter microbial communities. Additionally, our findings highlighted the significance of sample processing methods, showing differing communities in bulk purulent material and the capsule-adhered material. Fusobacterium or Bacteroides ASVs dominated LA, alongside probable opportunistic gut pathogens and other microbes. Moreover, we suggest that liver abscess size correlates with microbial community composition. These insights contribute to our understanding of factors impacting liver abscess microbial ecology and will be valuable in identifying antibiotic alternatives. They underscore the importance of exploring varied approaches to address LA while reducing reliance on in-feed antibiotics.
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Affiliation(s)
- Eóin O'Hara
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave S, Lethbridge, AB, T1J 4B1, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave S, Lethbridge, AB, T1J 4B1, Canada
| | - Sara Andrés-Lasheras
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave S, Lethbridge, AB, T1J 4B1, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave S, Lethbridge, AB, T1J 4B1, Canada
| | - Robert J Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave S, Lethbridge, AB, T1J 4B1, Canada
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Strickland AH, Murray SA, Vinasco J, Auvermann BW, Bush KJ, Sawyer JE, Scott HM, Norman KN. Comparative microbiome analysis of beef cattle, the feedyard environment, and airborne particulate matter as a function of probiotic and antibiotic use, and change in pen environment. Front Microbiol 2024; 15:1348171. [PMID: 38389541 PMCID: PMC10883649 DOI: 10.3389/fmicb.2024.1348171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Introduction Intensive beef cattle production systems are frequently implicated as a source of bacteria that can be transferred to nearby humans and animals via effluent water, manure used as fertilizer, or airborne particulate matter. It is crucial to understand microbial population dynamics due to manure pack desiccation, antibiotic usage, and antibiotic alternatives within beef cattle and their associated feedyard environment. Understanding how bacterial communities change in the presence of antibiotics can also improve management practices for reducing the spread of foodborne bacteria. Methods In this study, we aimed to compare the microbiomes within cattle feces, the feedyard environment and artificially produced airborne particulate matter as a function of pen change and treatment with tylosin or probiotics. We utilized 16S rRNA sequencing to compare bacterial communities among sample types, study days, and treatment groups. Results Bacterial community diversity varied as a function of sampling day and pen change (old or new) within fecal and manure pack samples. Manure pack samples from old pens and new pens contained diverse communities of bacteria on days 0 and 84; however, by day 119 of the study these taxonomic differences were less evident. Particulate matter samples exhibited significant differences in community diversity and predominant bacterial taxa compared to the manure pack they originated from. Treatment with tylosin did not meaningfully impact bacterial communities among fecal, environmental, or particulate matter samples; however, minor differences in bacterial community structure were observed in feces from cattle treated with probiotics. Discussion This study was the first to characterize and compare microbial communities within feces, manure pack, and airborne particulate matter from the same location and as a function of tylosin and probiotic treatment, and pen change. Although fecal and environmental samples are commonly used in research studies and other monitoring programs to infer public health risk of bacteria and antimicrobial resistance determinants from feedyard environments, our study suggests that these samples may not be appropriate to infer public health risk associated with airborne particulate matter.
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Affiliation(s)
- A. H. Strickland
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - S. A. Murray
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - J. Vinasco
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - B. W. Auvermann
- Texas A&M AgriLife Research and Extension Center at Amarillo, Amarillo, TX, United States
| | - K. J. Bush
- Texas A&M AgriLife Research and Extension Center at Amarillo, Amarillo, TX, United States
| | - J. E. Sawyer
- Department of Animal Sciences, Texas A&M University, College Station, TX, United States
| | - H. M. Scott
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - K. N. Norman
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
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Collis RM, Biggs PJ, Burgess SA, Midwinter AC, Brightwell G, Cookson AL. Impact of systemic antimicrobial therapy on the faecal microbiome in symptomatic dairy cows. PLoS One 2024; 19:e0296290. [PMID: 38180967 PMCID: PMC10769045 DOI: 10.1371/journal.pone.0296290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 12/10/2023] [Indexed: 01/07/2024] Open
Abstract
Antimicrobial resistance is a global threat to human and animal health, with the misuse and overuse of antimicrobials suggested as the main drivers of resistance. Antimicrobial therapy can alter the bacterial community composition and the faecal resistome in cattle. Little is known about the impact of systemic antimicrobial therapy on the faecal microbiome in dairy cows in the presence of disease. Therefore, this study aimed to assess the impact of systemic antimicrobial therapy on the faecal microbiome in dairy cows in the pastoral farm environment, by analysing faecal samples from cattle impacted by several different clinically-defined conditions and corresponding antimicrobial treatments. Analysis at the individual animal level showed a decrease in bacterial diversity and richness during antimicrobial treatment but, in many cases, the microbiome diversity recovered post-treatment when the cow re-entered the milking herd. Perturbations in the microbiome composition and the ability of the microbiome to recover were specific at the individual animal level, highlighting that the animal is the main driver of variation. Other factors such as disease severity, the type and duration of antimicrobial treatment and changes in environmental factors may also impact the bovine faecal microbiome. AmpC-producing Escherichia coli were isolated from faeces collected during and post-treatment with ceftiofur from one cow while no third-generation cephalosporin resistant E. coli were isolated from the untreated cow samples. This isolation of genetically similar plasmid-mediated AmpC-producing E. coli has implications for the development and dissemination of antibiotic resistant bacteria and supports the reduction in the use of critically important antimicrobials.
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Affiliation(s)
- Rose M. Collis
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J. Biggs
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Sara A. Burgess
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C. Midwinter
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Gale Brightwell
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Adrian L. Cookson
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
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Kim MJ, Kim JY, Choi JD, Moon G. Re-evaluation of a microbiological acceptable daily intake for tylosin based on its impact on human intestinal microflora. Toxicol Res 2024; 40:23-30. [PMID: 38223671 PMCID: PMC10786802 DOI: 10.1007/s43188-023-00179-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 03/06/2023] [Accepted: 03/29/2023] [Indexed: 01/16/2024] Open
Abstract
As veterinary drugs available for fish is very restricted, there is growing trials for repurposing livestock drugs as aquatic animal drugs. Tylosin is one of the most effective antibiotics to treat bacterial infections approved for livestock, and would be used in fish. Hence, we investigated the toxicological and microbiological aspects of tylosin to establish health-based guidance value (HBGV) and maximum residue limit (MRL) in fishes, and reevaluated the microbiological acceptable daily intake (mADI) based on updated relevant data and international guildeline. Lastly, exposure assessment was performed to confirm the appropriateness of MRL. By investigating available microbiologcial studies on tylosin, the microbiological point of departure was determined as 0.308 μg/mL, which was mean 50% minimum inhibitory concentration (MIC50), obtained from the Food Safety Committee of Japan (FSCJ) evaluation report. Furthermore, as a factor for the derivation of mADI, the volume of colon content was recently changed to 500 mL in compliance with the International Cooperation on Harmonization of Technical Requirements for Registration of Veterinary Medicinal Products (VICH) guidelines. This was previously defined as the mass of colon content (220 g). We applied correction factor 0.224 to the mean MIC50 for tylosin in the equation of mADI, since the drug is transformed to metabolites with reduced activity prior to entering the colon and bound to fecal materials within the colon of human. The mADI was evaluated as 0.01 mg/kg bw/day. Finally, the hazard index, calculated by dividing the estimated chronic dietary exposure by mADI, did not exceed 100%, suggesting that chronic dietary exposure to tylosin residues from veterinary use was unlikely to be a public health concern. Overall, this study contributes significantly in updating HBGV by application of the concept of mADI for the first time in Korea based on the revised microbiological risk assessment guidelines and in providing scientific rationale for the risk management of veterinary drug residues in food. Supplementary Information The online version contains supplementary material available at 10.1007/s43188-023-00179-z.
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Affiliation(s)
- Min Ji Kim
- Pesticide and Veterinary Drug Residues Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong, Cheongju, Chungcheongbuk-do 28159 Republic of Korea
| | - Ji Young Kim
- Pesticide and Veterinary Drug Residues Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong, Cheongju, Chungcheongbuk-do 28159 Republic of Korea
| | - Jang Duck Choi
- Pesticide and Veterinary Drug Residues Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong, Cheongju, Chungcheongbuk-do 28159 Republic of Korea
| | - Guiim Moon
- Pesticide and Veterinary Drug Residues Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong, Cheongju, Chungcheongbuk-do 28159 Republic of Korea
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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] [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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Pinnell LJ, Young JD, Thompson TW, Wolfe CA, Bryant TC, Nair MN, Richeson JT, Morley PS. Establishing the link between microbial communities in bovine liver abscesses and the gastrointestinal tract. Anim Microbiome 2023; 5:58. [PMID: 37986094 PMCID: PMC10662489 DOI: 10.1186/s42523-023-00278-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Liver abscesses (LAs) are one of the most common and important problems faced by the beef industry. The most efficacious method for the prevention of LAs in North America is through dietary inclusion of low doses of antimicrobial drugs such as tylosin, but the mechanisms by which this treatment prevents LAs are not fully understood. LAs are believed to result from mucosal barrier dysfunction in the gastrointestinal tract (GIT) allowing bacterial translocation to the liver via the portal vein, yet differences in the GIT microbiome of cattle with and without LAs have not been explored. Here, we characterized microbial communities from LAs, rumen, ileum, and colon from the same cattle for the first time. RESULTS Results demonstrate that tylosin supplementation was associated with differences in microbial community structure in the rumen and small intestine, largely because of differences in the predominance of Clostridia. Importantly, we show for the first time that microbial communities from multiple LAs in one animal's liver are highly similar, suggesting that abscesses found at different locations in the liver may originate from a localized source in the GIT (rather than disparate locations). A large portion of abscesses were dominated by microbial taxa that were most abundant in the hindgut. Further, we identified taxa throughout the GIT that were differentially abundant between animals with and without liver abscesses. Bifidobacterium spp.-a bacteria commonly associated with a healthy GIT in several species-were more abundant in the rumen and ileum of animals without LAs compared to those with LAs. CONCLUSIONS Together these results provide the first direct comparison of GIT and LA microbial communities within the same animal, add considerable evidence to the hypothesis that some LA microbial communities arise from the hindgut, and suggest that barrier dysfunction throughout the GIT may be the underlying cause of LA formation in cattle.
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Affiliation(s)
- Lee J Pinnell
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, 79015, USA
| | - J Daniel Young
- Department of Agricultural Sciences, West Texas A&M University, Canyon, TX, 79015, USA
| | - Tyler W Thompson
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Cory A Wolfe
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, 79015, USA
| | - Tony C Bryant
- Five Rivers Cattle Feeding, Johnstown, CO, 80534, USA
| | - Mahesh N Nair
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - John T Richeson
- Department of Agricultural Sciences, West Texas A&M University, Canyon, TX, 79015, USA
| | - Paul S Morley
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, 79015, USA.
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7
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Rovira P. Short-Term Impact of Oxytetracycline Administration on the Fecal Microbiome, Resistome and Virulome of Grazing Cattle. Antibiotics (Basel) 2023; 12:antibiotics12030470. [PMID: 36978337 PMCID: PMC10044027 DOI: 10.3390/antibiotics12030470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
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.
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Affiliation(s)
- Pablo Rovira
- Instituto Nacional de Investigación Agropecuaria (INIA Uruguay), Treinta y Tres 33000, Uruguay
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8
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Bryant TC, Jennings J. Roughage and Dietary Influence on Liver Abscesses. Vet Clin North Am Food Anim Pract 2022; 38:405-419. [DOI: 10.1016/j.cvfa.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Teseo S, Otani S, Brinch C, Leroy S, Ruiz P, Desvaux M, Forano E, Aarestrup FM, Sapountzis P. A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle. MICROBIOME 2022; 10:155. [PMID: 36155629 PMCID: PMC9511753 DOI: 10.1186/s40168-022-01357-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/24/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries. RESULTS Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes. CONCLUSIONS Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task. Video Abstract.
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Affiliation(s)
- S Teseo
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - S Otani
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - C Brinch
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - S Leroy
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - P Ruiz
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - M Desvaux
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - E Forano
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - F M Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - P Sapountzis
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France.
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Mansilla FI, Ficoseco CA, Miranda MH, Puglisi E, Nader-Macías MEF, Vignolo GM, Fontana CA. Administration of probiotic lactic acid bacteria to modulate fecal microbiome in feedlot cattle. Sci Rep 2022; 12:12957. [PMID: 35902668 PMCID: PMC9334624 DOI: 10.1038/s41598-022-16786-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 07/15/2022] [Indexed: 11/20/2022] Open
Abstract
Modulation of animal gut microbiota is a prominent function of probiotics to improve the health and performance of livestock. In this study, a large-scale survey to evaluate the effect of lactic acid bacteria probiotics on shaping the fecal bacterial community structure of feedlot cattle during three experimental periods of the fattening cycle (163 days) was performed. A commercial feedlot located in northwestern Argentina was enrolled with cattle fed mixed rations (forage and increasing grain diet) and a convenience-experimental design was conducted. A pen (n = 21 animals) was assigned to each experimental group that received probiotics during three different periods. Groups of n = 7 animals were sampled at 40, 104 and 163 days and these samples were then pooled to one, thus giving a total of 34 samples that were subjected to high-throughput sequencing. The microbial diversity of fecal samples was significantly affected (p < 0.05) by the administration period compared with probiotic group supplementation. Even though, the three experimental periods of probiotic administration induced changes in the relative abundance of the most representative bacterial communities, the fecal microbiome of samples was dominated by the Firmicutes (72–98%) and Actinobacteria (0.8–27%) phyla, while a lower abundance of Bacteroidetes (0.08–4.2%) was present. Probiotics were able to modulate the fecal microbiota with a convergence of Clostridiaceae, Lachnospiraceae, Ruminococcaceae and Bifidobacteriaceae associated with health and growth benefits as core microbiome members. Metabolic functional prediction comparing three experimental administration periods (40, 104 and 163 days) showed an enrichment of metabolic pathways related to complex plant-derived polysaccharide digestion as well as amino acids and derivatives during the first 40 days of probiotic supplementation. Genomic-based knowledge on the benefits of autochthonous probiotics on cattle gastrointestinal tract (GIT) microbiota composition and functions will contribute to their selection as antibiotic alternatives for commercial feedlot.
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Affiliation(s)
| | | | | | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy
| | | | | | - Cecilia Alejandra Fontana
- Instituto Nacional de Tecnología Agropecuaria INTA EEA-Famaillá, Tucumán, Argentina. .,Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy.
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11
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Resistomes and microbiome of meat trimmings and colon content from culled cows raised in conventional and organic production systems. Anim Microbiome 2022; 4:21. [PMID: 35272712 PMCID: PMC8908682 DOI: 10.1186/s42523-022-00166-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/04/2022] [Indexed: 11/21/2022] Open
Abstract
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.
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Sapountzis P, Teseo S, Otani S, Aarestrup FM, Forano E, Suen G, Tsiamis G, Haley B, Van Kessel JA, Huws SA. FI: The Fecobiome Initiative. Foodborne Pathog Dis 2021; 19:441-447. [PMID: 34936494 PMCID: PMC9297326 DOI: 10.1089/fpd.2021.0082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Animal husbandry has been key to the sustainability of human societies for millennia. Livestock animals, such as cattle, convert plants to protein biomass due to a compartmentalized gastrointestinal tract (GIT) and the complementary contributions of a diverse GIT microbiota, thereby providing humans with meat and dairy products. Research on cattle gut microbial symbionts has mainly focused on the rumen (which is the primary fermentation compartment) and there is a paucity of functional insight on the intestinal (distal end) microbiota, where most foodborne zoonotic bacteria reside. Here, we present the Fecobiome Initiative (or FI), an international effort that aims at facilitating collaboration on research projects related to the intestinal microbiota, disseminating research results, and increasing public availability of resources. By doing so, the FI can help mitigate foodborne and animal pathogens that threaten livestock and human health, reduce the emergence and spread of antimicrobial resistance in cattle and their proximate environment, and potentially improve the welfare and nutrition of animals. We invite all researchers interested in this type of research to join the FI through our website: www.fecobiome.com
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Affiliation(s)
| | - Serafino Teseo
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Saria Otani
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Evelyne Forano
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Garett Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - George Tsiamis
- Lab of Systems Microbiology and Applied Genomics, University of Patras, Agrinio, Greece
| | - Bradd Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, USA
| | - Jo Ann Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, USA
| | - Sharon A Huws
- School of Biological Sciences, Institute for Global Food Security, Queens University Belfast (QUB), Belfast, United Kingdom
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13
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Ma T, McAllister TA, Guan LL. A review of the resistome within the digestive tract of livestock. J Anim Sci Biotechnol 2021; 12:121. [PMID: 34763729 PMCID: PMC8588621 DOI: 10.1186/s40104-021-00643-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/07/2021] [Indexed: 12/25/2022] Open
Abstract
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.
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Affiliation(s)
- Tao Ma
- Key laboratory of Feed Biotechnology of the Ministry of Agriculture, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Department of Agricultural, Food and Nutritional Science, University of Alberta, T6G2P5, Edmonton, AB, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4P4, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, T6G2P5, Edmonton, AB, Canada.
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14
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Breiner-Goldstein E, Eyal Z, Matzov D, Halfon Y, Cimicata G, Baum M, Rokney A, Ezernitchi A, Lowell A, Schmidt J, Rozenberg H, Zimmerman E, Bashan A, Valinsky L, Anzai Y, Sherman D, Yonath A. Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida. Nucleic Acids Res 2021; 49:9560-9573. [PMID: 34417608 PMCID: PMC8450085 DOI: 10.1093/nar/gkab684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 02/02/2023] Open
Abstract
Macrolides have been effective clinical antibiotics for over 70 years. They inhibit protein biosynthesis in bacterial pathogens by narrowing the nascent protein exit tunnel in the ribosome. The macrolide class of natural products consist of a macrolactone ring linked to one or more sugar molecules. Most of the macrolides used currently are semi-synthetic erythromycin derivatives, composed of a 14- or 15-membered macrolactone ring. Rapidly emerging resistance in bacterial pathogens is among the most urgent global health challenges, which render many antibiotics ineffective, including next-generation macrolides. To address this threat and advance a longer-term plan for developing new antibiotics, we demonstrate how 16-membered macrolides overcome erythromycin resistance in clinically isolated Staphylococcus aureus strains. By determining the structures of complexes of the large ribosomal subunit of Deinococcus radiodurans (D50S) with these 16-membered selected macrolides, and performing anti-microbial studies, we identified resistance mechanisms they may overcome. This new information provides important insights toward the rational design of therapeutics that are effective against drug resistant human pathogens.
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Affiliation(s)
- Elinor Breiner-Goldstein
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Zohar Eyal
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Donna Matzov
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Yehuda Halfon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Giuseppe Cimicata
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Moti Baum
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Assaf Rokney
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Analia V Ezernitchi
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Andrew N Lowell
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Jennifer J Schmidt
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Haim Rozenberg
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Lea Valinsky
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Yojiro Anzai
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-0072, Japan
| | - David H Sherman
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Ada Yonath
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
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15
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Trott DJ, Turnidge J, Kovac JH, Simjee S, Wilson D, Watts J. Comparative macrolide use in humans and animals: should macrolides be moved off the World Health Organisation's critically important antimicrobial list? J Antimicrob Chemother 2021; 76:1955-1961. [PMID: 33956974 DOI: 10.1093/jac/dkab120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Macrolide antibiotics are categorized by the WHO as Highest Priority, Critically Important Antimicrobials due to their recommendation as treatment for severe cases of campylobacteriosis in humans; a self-limiting, rarely life-threatening, zoonotic foodborne infection. Low rates of macrolide resistance in Campylobacter jejuni and the availability of alternative treatments have prompted some regulatory schemes to assign macrolides to a lower importance category. Apart from rare, specific infections, macrolides largely play a supportive role to other drug classes in human medicine. By contrast, although the advent of alternative control methods has seen significant reductions in macrolide use in intensive livestock, they still have a crucial role in the treatment/control of respiratory infections and liver abscesses in cattle. Whilst acknowledging that ongoing surveillance is required to reduce the spread of recently emerged, transferable macrolide resistance among Campylobacter, this article recommends that macrolides should be moved to the WHO Highly Important category.
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Affiliation(s)
- Darren J Trott
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - John Turnidge
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Jessica H Kovac
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Shabbir Simjee
- Elanco Animal Health, Form 2, Bartley Way, Bartley Wood Business Park, Hook, England
| | - Danny Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, South Australia, Australia
| | - Jeffrey Watts
- Veterinary Medicine Research and Development, Zoetis, Inc, Kalamazoo, MI, USA
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16
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McDermott PF, Davis JJ. Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring. J Vet Pharmacol Ther 2020; 44:223-237. [PMID: 33010049 DOI: 10.1111/jvp.12913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/25/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022]
Abstract
The laboratory identification of antibacterial resistance is a cornerstone of infectious disease medicine. In vitro antimicrobial susceptibility testing has long been based on the growth response of organisms in pure culture to a defined concentration of antimicrobial agents. By comparing individual isolates to wild-type susceptibility patterns, strains with acquired resistance can be identified. Acquired resistance can also be detected genetically. After many decades of research, the inventory of genes underlying antimicrobial resistance is well known for several pathogenic genera including zoonotic enteric organisms such as Salmonella and Campylobacter and continues to grow substantially for others. With the decline in costs for large scale DNA sequencing, it is now practicable to characterize bacteria using whole genome sequencing, including the carriage of resistance genes in individual microorganisms and those present in complex biological samples. With genomics, we can generate comprehensive, detailed information on the bacterium, the mechanisms of antibiotic resistance, clues to its source, and the nature of mobile DNA elements by which resistance spreads. These developments point to a new paradigm for antimicrobial resistance detection and tracking for both clinical and public health purposes.
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Affiliation(s)
- Patrick F McDermott
- Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - James J Davis
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA.,University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
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17
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Ran T, Jiao P, AlZahal O, Xie X, Beauchemin KA, Niu D, Yang W. Fecal bacterial community of finishing beef steers fed ruminally protected and non-protected active dried yeast. J Anim Sci 2020; 98:skaa058. [PMID: 32068850 PMCID: PMC7105065 DOI: 10.1093/jas/skaa058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 02/17/2020] [Indexed: 12/11/2022] Open
Abstract
Our previous study suggested that supplementation of high-grain diets with ruminally protected and non-protected active dried yeast (ADY) may potentially reduce manure pathogen excretion by feedlot cattle. We hypothesized that feeding ruminally protected ADY might change the fecal bacterial community of finishing cattle. The objective of this study was to investigate the effects of feeding ruminally protected and non-protected ADY to finishing beef steers on their fecal bacterial community. Fresh fecal samples were collected on day 56 from 50 steers fed one of five treatments: 1) control (no monensin, tylosin, or ADY), 2) antibiotics (ANT, 330 mg monensin + 110 mg tylosin·steer-1d-1), 3) ADY (1.5 g·steer-1d-1), 4) encapsulated ADY (EDY; 3 g·steer-1d-1), and 5) a mixture of ADY and EDY (MDY; 1.5 g ADY + 3 g EDY·steer-1d-1). Bacterial DNA was extracted from fecal samples and sequenced using a MiSeq high-throughput sequencing platform. A total number of 2,128,772 high-quality V4 16S rRNA sequences from 50 fecal samples were analyzed, and 1,424 operational taxonomic units (OTU) were detected based on 97% nucleotide sequence identity among reads, with 769 OTU shared across the five treatments. Alpha diversity indices, including species observed, Chao estimate, abundance-based coverage estimator, Shannon, Simpson, and coverage, did not differ among treatments, and principal coordinate analysis revealed a high similarity among treatments without independent distribution. Bacteroidetes and Firmicutes were dominant phyla in the fecal bacterial community for all treatments, with a tendency (P < 0.10) for greater relative abundance of Bacteroidetes but lesser Firmicutes with ANT, EDY, and MDY compared with control steers. Prevotella was the dominant genus in all treatments and steers supplemented with ANT, EDY, and MDY had greater (P < 0.05) relative abundance of Prevotella than control steers, but lesser (P < 0.03) relative abundance of Oscillospira. No differences between ADY and control were observed for the aforementioned variables. Fecal starch contents were not different among treatments, but the relative abundance of Bacteroidetes, as well as Prevotella at genera level, tended (P < 0.06) to be positively correlated to fecal starch content. We conclude that supplementing ruminally protected or non-protected ADY or ANT had no effect on diversity and richness of fecal bacteria of finishing beef cattle, whereas feeding protected ADY or ANT to finishing beef steers altered the dominant fecal bacteria at phylum and genus levels. Therefore, supplementation of ruminally protected ADY may potentially improve intestinal health by stimulating the relative abundance of Prevotella.
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Affiliation(s)
- Tao Ran
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
- Institute of Subtropical Agriculture, the Chinese Academy of Sciences, Changsha, Hunan, China
- College of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Peixin Jiao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | | | - Xiaolai Xie
- College of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Karen A Beauchemin
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
| | - Dongyan Niu
- College of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Wenzhu Yang
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
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