Extended-Spectrum Beta-Lactamase-Producing <i>Enterobacteriaceae</i> in Dairy Farm Environments: A New Zealand Perspective

Collis, Rose M.; Burgess, Sara; Biggs, Patrick J.; Midwinter, Anne C.; French, Nigel P.; Toombs-Ruane, Leah; Cookson, Adrian L.

doi:10.1089/fpd.2018.2524

Cited by 29 publications

(36 citation statements)

References 102 publications

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“…Environmental (non-clinical and non-human) populations of Enterobacterales may act as a genetic reservoir for antimicrobial resistance (AMR). This includes livestock [1][2][3][4][5] and water-borne [6] resistance. Frequent horizontal gene transfer (HGT) in Enterobacterales populations results in a large and open pangenome, enabling the wide-spread transmission of the genes conferring AMR [7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Genomic network analysis of environmental and livestock F-type plasmid populations

et al. 2021

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F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.

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Section: Introductionmentioning

confidence: 99%

Genomic network analysis of environmental and livestock F-type plasmid populations

et al. 2021

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“…Additionally, many dairy farms practice dry cow therapy and use intramammary antibiotics following the last milking of lactation (Oliver et al, 2011). However, dairy cattle production tends to be less reliant on antimicrobials than swine or poultry production (Burgess & French, 2017;Collis et al, 2019;Van Boeckel et al, 2015).…”

Section: Structure Of Reviewmentioning

confidence: 99%

“…Antibiotic-resistant bacteria and their genes can also contaminate the environment (Aitken et al, 2016;Oliver et al, 2011;Tripathi & Tripathi, 2017) and have been isolated from dairy wastewater; soil from dairy farms; dairy manure; and the dairy farm environment (Collis et al, 2019;Noyes et al, 2016;Oliver et al, 2011;Pitta et al, 2016). Antibiotic-resistant bacteria have also been detected in surface water, groundwater, sediments, and wetlands (Aitken et al, 2016;Oliver et al, 2011;Tripathi & Tripathi, 2017).…”

Section: Biological Pollutantsmentioning

confidence: 99%

A Review of Potential Public Health Impacts Associated With the Global Dairy Sector

et al. 2020

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Strong demand for dairy products has led to a global increase in dairy production. In many parts of the world, dairy systems are undergoing rapid intensification. While increased production may contribute to food security, higher dairy stocking rates in some regions have resulted in increased pressure on natural resources with the potential to affect public health and wellbeing. The aim of this review was to identify and describe the potential health harms and benefits associated with dairy production and consumption. Electronic databases Medline, Embase, Scopus, Web of Science, PubMed, and Google Scholar were searched for published literature that investigated human health impacts of dairy production and consumption. Occupational hazards, environmental health impacts, ecosystem health impacts, foodborne hazards, and diet‐related chronic diseases were identified as potential public health hazards. Some impacts, notably climate change, extend beyond directly exposed populations. Dairy production and consumption are also associated with important health benefits through the provision of nutrients and economic opportunities. As the global dairy sector increases production, exposure to a range of hazards must be weighed with these benefits. The review of impacts presented here can provide an input into decision making about optimal levels of dairy production and consumption, local land use, and identification and management of specific hazards from this sector. Future research should consider multiple exposure routes, socioeconomic implications, and environmental factors, particularly in regions heavily dependent on dairy farming.

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“…Environmental (non-clinical, non-human) populations of Enterobacteriaceae may act as a genetic reservoir for antimicrobial resistance (AMR). This includes livestock [1][2][3][4][5] and water-borne [6] resistance. Frequent horizontal gene transfer (HGT) in Enterobacteriaceae populations results in a large and open pangenome, enabling the wide-spread transmission of the genes conferring AMR [7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Genomic network analysis of an environmental and livestock IncF plasmid population

Matlock

Chau

AbuOun

et al. 2020

Preprint

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IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacteriaceae. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of IncF plasmids from environmental (influent, effluent, and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable IncF plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The recent association of IncF plasmids with AMR likely reflects their suitability for rapid niche adaptation.

show abstract

Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Dairy Farm Environments: A New Zealand Perspective

Cited by 29 publications

References 102 publications

Genomic network analysis of environmental and livestock F-type plasmid populations

Genomic network analysis of environmental and livestock F-type plasmid populations

A Review of Potential Public Health Impacts Associated With the Global Dairy Sector

Genomic network analysis of an environmental and livestock IncF plasmid population

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