Assessing antimicrobial resistance in pasture-based dairy farms: a 15-month surveillance study in New Zealand.

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dc.citation.volumeOnline First
dc.contributor.authorCollis RM
dc.contributor.authorBiggs PJ
dc.contributor.authorBurgess SA
dc.contributor.authorMidwinter AC
dc.contributor.authorLiu J
dc.contributor.authorBrightwell G
dc.contributor.authorCookson AL
dc.coverage.spatialUnited States
dc.date.accessioned2024-10-28T22:54:45Z
dc.date.available2024-10-28T22:54:45Z
dc.date.issued2024-10-23
dc.description.abstractAntimicrobial resistance is a global public and animal health concern. Antimicrobial resistance genes (ARGs) have been detected in dairy farm environments globally; however, few longitudinal studies have utilized shotgun metagenomics for ARG surveillance in pasture-based systems. This 15-month study aimed to undertake a baseline survey using shotgun metagenomics to assess the relative abundance and diversity of ARGs in two pasture-based dairy farm environments in New Zealand with different management practices. There was no statistically significant difference in overall ARG relative abundance between the two dairy farms (P = 0.321) during the study period. Compared with overseas data, the relative abundance of ARG copies per 16S rRNA gene in feces (0.08-0.17), effluent (0.03-0.37), soil (0.20-0.63), and bulk tank milk (0.0-0.12) samples was low. Models comparing the presence or absence of resistance classes found in >10% of all feces, effluent, and soil samples demonstrated no statistically significant associations (P > 0.05) with "season," and only multi-metal (P = 0.020) and tetracycline (P = 0.0003) resistance were significant at the "farm" level. Effluent samples harbored the most diverse ARGs, some with a recognized public health risk, whereas soil samples had the highest ARG relative abundance but without recognized health risks. This highlights the importance of considering the genomic context and risk of ARGs in metagenomic data sets. This study suggests that antimicrobial resistance on pasture-based dairy farms is low and provides essential baseline ARG surveillance data for such farming systems. IMPORTANCE: Antimicrobial resistance is a global threat to human and animal health. Despite the detection of antimicrobial resistance genes (ARGs) in dairy farm environments globally, longitudinal surveillance in pasture-based systems remains limited. This study assessed the relative abundance and diversity of ARGs in two New Zealand dairy farms with different management practices and provided important baseline ARG surveillance data on pasture-based dairy farms. The overall ARG relative abundance on these two farms was low, which provides further evidence for consumers of the safety of New Zealand's export products. Effluent samples harbored the most diverse range of ARGs, some of which were classified with a recognized risk to public health, whereas soil samples had the highest ARG relative abundance; however, the soil ARGs were not classified with a recognized public health risk. This emphasizes the need to consider genomic context and risk as well as ARG relative abundance in resistome studies.
dc.description.confidentialfalse
dc.edition.editionOct 2024
dc.format.paginatione0139024-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/39440981
dc.identifier.citationCollis RM, Biggs PJ, Burgess SA, Midwinter AC, Liu J, Brightwell G, Cookson AL. (2024). Assessing antimicrobial resistance in pasture-based dairy farms: a 15-month surveillance study in New Zealand.. Appl Environ Microbiol. Online First. (pp. e0139024-).
dc.identifier.doi10.1128/aem.01390-24
dc.identifier.eissn1098-5336
dc.identifier.elements-typejournal-article
dc.identifier.issn0099-2240
dc.identifier.numbere0139024
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/71853
dc.languageeng
dc.publisherAmerican Society for Microbiology
dc.publisher.urihttps://journals.asm.org/doi/10.1128/aem.01390-24
dc.relation.isPartOfAppl Environ Microbiol
dc.rights(c) 2024 The Author/s
dc.rightsCC BY 4.0
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectNew Zealand
dc.subjectantimicrobial resistance
dc.subjectantimicrobial resistance genes
dc.subjectdairy farm environment
dc.subjectpasture-based system
dc.subjectresistome
dc.subjectshotgun metagenomic sequencing
dc.titleAssessing antimicrobial resistance in pasture-based dairy farms: a 15-month surveillance study in New Zealand.
dc.typeJournal article
pubs.elements-id492022
pubs.organisational-groupCollege of Health
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