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Background
Antimicrobial drugs (AMDs) are used in beef production to treat clinical disease and to prevent or control infections in groups of cattle. Use of 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, but genes that confer AMR are known to be distributed and shared throughout microbial communities. Use of high-throughput metagenomic sequencing provides a holistic perspective on AMR ecology by examining determinants within the entire microbiome. The primary objective of this study was to employ metagenomic sequencing to investigate the effects of AMD use on the microbiome and resistome in beef feedlot cattle.
Results
This study leveraged the use of archived samples that were 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. Samples were analyzed using AMR target-enriched shotgun sequencing to characterize the fecal resistome and 16S rRNA gene sequencing to characterize the microbiome. Overall, the fecal resistome composition was dominated by alignments to gene accessions 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 as the microbiome shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but their contribution to the variance was small compared to other factors measured in this study.
Conclusions
Time in the feedlot was associated with greater changes in the microbiome and resistome for both individual animals and pen-floor samples, although the proportion of the variance associated with this factor was small. Results of this study are consistent with other investigations showing that AMD exposures did not have strong effects on the microbial ecology of beef cattle.
Keywords
Resistome, Microbiome, Microbial ecology, Antimicrobial drug exposure, Antimicrobial resistance
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CURRENT STATUS: Under Review
Version 1
Posted 01 Nov, 2021
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Reviewers invited
Invitations sent on 18 Nov, 2021
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On 27 Oct, 2021
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On 26 Oct, 2021
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On 26 Oct, 2021
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Subject Areas
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This preprint is under consideration at Microbiome. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 01 Nov, 2021
No community comments so far
Reviewers invited
Invitations sent on 18 Nov, 2021
Editor assigned
On 27 Oct, 2021
Submission checks complete
On 26 Oct, 2021
Editor invited
On 26 Oct, 2021
First submitted
On 26 Oct, 2021
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
General Microbiology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
Antimicrobial drugs (AMDs) are used in beef production to treat clinical disease and to prevent or control infections in groups of cattle. Use of 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, but genes that confer AMR are known to be distributed and shared throughout microbial communities. Use of high-throughput metagenomic sequencing provides a holistic perspective on AMR ecology by examining determinants within the entire microbiome. The primary objective of this study was to employ metagenomic sequencing to investigate the effects of AMD use on the microbiome and resistome in beef feedlot cattle.
Results
This study leveraged the use of archived samples that were 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. Samples were analyzed using AMR target-enriched shotgun sequencing to characterize the fecal resistome and 16S rRNA gene sequencing to characterize the microbiome. Overall, the fecal resistome composition was dominated by alignments to gene accessions 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 as the microbiome shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but their contribution to the variance was small compared to other factors measured in this study.
Conclusions
Time in the feedlot was associated with greater changes in the microbiome and resistome for both individual animals and pen-floor samples, although the proportion of the variance associated with this factor was small. Results of this study are consistent with other investigations showing that AMD exposures did not have strong effects on the microbial ecology of beef cattle.
Figure 1
Figure 2
Figure 3
Figure 4
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