Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm
Abstract Introduction The widespread use of antimicrobials in the livestock industry has raised global concerns regarding the emergence and spread of antimicrobial resistance genes (ARGs). Comprehensive databases of ARGs specific to different farm animal species can greatly improve the surveillance...
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BMC
2025-06-01
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| Series: | Animal Microbiome |
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| Online Access: | https://doi.org/10.1186/s42523-025-00432-w |
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| author | Nahidur Rahman Taylor McCullough Daniel Flores Orozco Sean Walkowiak Abdolvahab Farzan Shahrokh Shekarriz Michael G. Surette Nazim Cicek Hooman Derakhshani |
| author_facet | Nahidur Rahman Taylor McCullough Daniel Flores Orozco Sean Walkowiak Abdolvahab Farzan Shahrokh Shekarriz Michael G. Surette Nazim Cicek Hooman Derakhshani |
| author_sort | Nahidur Rahman |
| collection | DOAJ |
| description | Abstract Introduction The widespread use of antimicrobials in the livestock industry has raised global concerns regarding the emergence and spread of antimicrobial resistance genes (ARGs). Comprehensive databases of ARGs specific to different farm animal species can greatly improve the surveillance of ARGs within the agri-food sector and beyond. In particular, defining the association of ARGs with mobile genetic elements (MGEs)—the primary agents responsible for the spread and acquisition of resistant phenotypes among bacterial populations—could help assess the transmissibility potential of clinically relevant ARGs. Recognizing the gut microbiota as a vast reservoir of ARGs, we aimed to generate a representative isolate collection and genome database of the swine gut microbiome, enabling high-resolution characterization of ARGs in relation to bacterial host range and their association with MGEs. Results We generated a biobank of bacteria from different sections of the gastrointestinal tracts of four clinically healthy pigs housed at a research farm in Ontario, Canada. The culturing was performed under anaerobic conditions using both selective and general enrichment media to ensure the capture of a diverse range of bacterial families within the swine gut microbiota. We sequenced the genomes of 129 unique isolates encompassing 44 genera and 25 distinct families of the swine gut microbiome. Approximately 85.3% (110 isolates) contained one or more ARGs, with a total of 246 ARGs identified across 38 resistance gene families. Tetracycline and macrolide resistance genes were the most prevalent across different lineages of the swine gut microbiota. Additionally, we observed a wide range of MGEs, including integrative conjugative elements, plasmids, and phages, frequently associated with ARGs, indicating that the swine gut ecosystem is conducive to the horizontal transfer of ARGs. High-throughput alignment of the identified ARG-MGE complexes to large-scale metagenomics datasets of the swine gut microbiome suggests the presence of highly prevalent and conserved resistome sequences across diverse pig populations. Conclusion Our findings reveal a highly diverse and relatively conserved reservoir of ARGs and MGEs within the gut microbiome of pigs. A deeper understanding of the microbial host range and potential transmissibility of prevalent ARGs in the swine microbiome can inform development of targeted antimicrobial resistance surveillance and disease control programs. |
| format | Article |
| id | doaj-art-4b8caa0bdc7b416dbf8a69773c64ffea |
| institution | DOAJ |
| issn | 2524-4671 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BMC |
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| series | Animal Microbiome |
| spelling | doaj-art-4b8caa0bdc7b416dbf8a69773c64ffea2025-08-20T03:22:57ZengBMCAnimal Microbiome2524-46712025-06-017111510.1186/s42523-025-00432-wGenomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farmNahidur Rahman0Taylor McCullough1Daniel Flores Orozco2Sean Walkowiak3Abdolvahab Farzan4Shahrokh Shekarriz5Michael G. Surette6Nazim Cicek7Hooman Derakhshani8Department of Animal Sciences, Faculty of Agricultural and Food Sciences, University of ManitobaDepartment of Animal Sciences, Faculty of Agricultural and Food Sciences, University of ManitobaDepartment of Animal Sciences, Faculty of Agricultural and Food Sciences, University of ManitobaDepartment of Animal Sciences, Faculty of Agricultural and Food Sciences, University of ManitobaOntario Veterinary College, University of GuelphFarncombe Family Digestive Health Research Institute, McMaster UniversityFarncombe Family Digestive Health Research Institute, McMaster UniversityDepartment of Biosystems Engineering, Faculty of Agricultural and Food Sciences, University of ManitobaDepartment of Animal Sciences, Faculty of Agricultural and Food Sciences, University of ManitobaAbstract Introduction The widespread use of antimicrobials in the livestock industry has raised global concerns regarding the emergence and spread of antimicrobial resistance genes (ARGs). Comprehensive databases of ARGs specific to different farm animal species can greatly improve the surveillance of ARGs within the agri-food sector and beyond. In particular, defining the association of ARGs with mobile genetic elements (MGEs)—the primary agents responsible for the spread and acquisition of resistant phenotypes among bacterial populations—could help assess the transmissibility potential of clinically relevant ARGs. Recognizing the gut microbiota as a vast reservoir of ARGs, we aimed to generate a representative isolate collection and genome database of the swine gut microbiome, enabling high-resolution characterization of ARGs in relation to bacterial host range and their association with MGEs. Results We generated a biobank of bacteria from different sections of the gastrointestinal tracts of four clinically healthy pigs housed at a research farm in Ontario, Canada. The culturing was performed under anaerobic conditions using both selective and general enrichment media to ensure the capture of a diverse range of bacterial families within the swine gut microbiota. We sequenced the genomes of 129 unique isolates encompassing 44 genera and 25 distinct families of the swine gut microbiome. Approximately 85.3% (110 isolates) contained one or more ARGs, with a total of 246 ARGs identified across 38 resistance gene families. Tetracycline and macrolide resistance genes were the most prevalent across different lineages of the swine gut microbiota. Additionally, we observed a wide range of MGEs, including integrative conjugative elements, plasmids, and phages, frequently associated with ARGs, indicating that the swine gut ecosystem is conducive to the horizontal transfer of ARGs. High-throughput alignment of the identified ARG-MGE complexes to large-scale metagenomics datasets of the swine gut microbiome suggests the presence of highly prevalent and conserved resistome sequences across diverse pig populations. Conclusion Our findings reveal a highly diverse and relatively conserved reservoir of ARGs and MGEs within the gut microbiome of pigs. A deeper understanding of the microbial host range and potential transmissibility of prevalent ARGs in the swine microbiome can inform development of targeted antimicrobial resistance surveillance and disease control programs.https://doi.org/10.1186/s42523-025-00432-wSwine gut microbiomeAntimicrobial resistanceMobile genetic elementsIntegrative and conjugative elements |
| spellingShingle | Nahidur Rahman Taylor McCullough Daniel Flores Orozco Sean Walkowiak Abdolvahab Farzan Shahrokh Shekarriz Michael G. Surette Nazim Cicek Hooman Derakhshani Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm Animal Microbiome Swine gut microbiome Antimicrobial resistance Mobile genetic elements Integrative and conjugative elements |
| title | Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm |
| title_full | Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm |
| title_fullStr | Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm |
| title_full_unstemmed | Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm |
| title_short | Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm |
| title_sort | genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a canadian research farm |
| topic | Swine gut microbiome Antimicrobial resistance Mobile genetic elements Integrative and conjugative elements |
| url | https://doi.org/10.1186/s42523-025-00432-w |
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