Evidence map›Paper›PMID 40533851›Full record

ArticleAnimal microbiome2025

Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm.

Nahidur Rahman, Taylor McCullough, Daniel Flores Orozco, Sean Walkowiak, Abdolvahab Farzan, Shahrokh Shekarriz, Michael G Surette, Nazim Cicek, Hooman Derakhshani

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Animal microbiome, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Nahidur RahmanDepartment of Animal Sciences, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada.
Taylor McCulloughDepartment of Animal Sciences, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada.
Daniel Flores OrozcoDepartment of Animal Sciences, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada.
Sean WalkowiakDepartment of Animal Sciences, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada.
Abdolvahab FarzanOntario Veterinary College, University of Guelph, Guelph, ON, Canada.
Shahrokh ShekarrizFarncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada.
Michael G SuretteFarncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada.
Nazim CicekDepartment of Biosystems Engineering, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada.
Hooman DerakhshaniDepartment of Animal Sciences, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada. hooman.derakhshani@umanitoba.ca.

Funding

NSERC Discovery Grant (RGPIN-2023-04359)
6 · The paper itself

Abstract

introductionThe 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.

resultsWe 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.

conclusionOur 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.

Indexed as

Antimicrobial resistanceIntegrative and conjugative elementsMobile genetic elementsSwine gut microbiome

Identifiers

PMID40533851
PMCPMC12175345

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.