Exploring the Antibiotic Resistance Burden in Livestock, Livestock Handlers and Their Non-Livestock Handling Contacts: A One Health Perspective

Hickman, Rachel A.; Leangapichart, Thongpan; Lunha, Kamonwan; Jiwakanon, Jatesada; Magnusson, Ulf; Sunde, Marianne; Järhult, Josef D.

doi:10.3389/fmicb.2021.651461

Cited by 21 publications

(19 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…However, these more comprehensive approaches could reveal important insights into ARG gene flow that cannot be observed using WGS methods, especially in these settings. For example, the movement of mobile elements carrying ARGs has been observed to be more influential on ARG flow than bacterial lineage in LMIC farms [41]. Hence, given the dynamic nature of the resistome [42], studying the core and mobile resistome, can provide an insight into which ARGs pose the greatest risks to humans [40].…”

Section: Introductionmentioning

confidence: 99%

Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock

Maciel-Guerra

Baker

et al. 2022

The ISME Journal

View full text Add to dashboard Cite

A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.

show abstract

Section: Introductionmentioning

confidence: 99%

Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock

Maciel-Guerra

Baker

et al. 2022

The ISME Journal

View full text Add to dashboard Cite

show abstract

“…In a previous study, we show that ESBL-producing E. coli were highly prevalent in both small and medium pig farms and that pigs and humans shared the same sequence types [32]. The transmission of these resistant microorganisms between pigs and farmers was hypothesized but not confirmed [32,33]. Here, we investigate the impact of farm size and host on the accessory-genome of ESBL and/or AmpC-producing E. coli recovered from pigs and humans and investigate the inter-host transmission of these microorganisms using whole genome sequencing.…”

Section: Introductionmentioning

confidence: 90%

Section: Introductionmentioning

confidence: 90%

“…We retrieved 363 ESBL and/or AmpC-producing E. coli from a study performed across 155 farms Khon Kaen province of Northeast Thailand from September to December, 2018 [32]. Isolates were recovered from fecal swabs of healthy pigs, pig-farmers (human contacts), and people living in the same household of pigfarmers but not in contact with the farm environment (human non-contacts).…”

Section: Bacterial Genomesmentioning

confidence: 99%

See 1 more Smart Citation

Genome-associations of extended-spectrum ß-lactamase producing (ESBL) or AmpC producing E. coli in small and medium pig farms from Khon Kaen province, Thailand

et al. 2022

View full text Add to dashboard Cite

Thailand is undergoing rapid intensification of livestock production where small subsistence farms and medium sized commercial farms coexist. In medium farms, antimicrobials are prescribed by a veterinarian, whereas in small farms antimicrobial use remains largely unsupervised. The impact of these differences as well as other farming practices on the emergence and composition of antimicrobial resistance genes (ARGs) remains largely unknown. We analyzed 363 genomes of extended-spectrum ß-lactamase producing (ESBL) and/or AmpC producing Escherichia coli recovered from humans and pigs at small and medium farms from the Khon Kaen province, Thailand. We tested for genome-wide associations to identify links between ARGs, host, and farm size. Pig isolates from small farms were associated with mcr and qnr genes conferring resistance to colistin and fluoroquinolones, respectively. In contrast, pig isolates from medium farms were associated with ARGs conferring resistance to drugs commonly used on medium farms (i.e., streptomycin). ESBL plasmids from small farms co-carried ARGs conferring resistance to critically important antimicrobials more frequently compared to plasmid from medium farms. Frequent ARG combinations included blaCTX-M-55 + qnrS1 (29.8% vs 17.5% in small and medium farms, respectively), blaCTX-M-55 + qnrS1 + mcr-3.19 (5% vs 0%), blaCTX-M-14 + qnrS1 (9.3% vs 6.2%), and blaCTX-M-14 + qnrS1 + mcr-1.1 (3.1% vs 0%). The co-location on plasmids of ARGs conferring resistance to critically important antimicrobials as defined by the World Health Organization is concerning, and actions to curb their spread are urgently needed. Legislation on limiting antimicrobial sales and initiatives to better inform farmers and veterinarians on appropriate antimicrobial usage and farm biosecurity could help reduce antimicrobial use on farms.

show abstract

“…These data were then further processed in Python (3.8.3rc1 Documentation, 2020) using the matplotlib, pandas and seaborn packages. All processing of the whole genome sequences was done with open software with an in-house bioinformatics pipeline as described in Hickman et al (2021). The genomic data processing was done on the Uppsala Multidisciplinary Centre for Advance Computational cluster (UPPMAX).…”

Section: Antimicrobial Resistance Profiling and Genomic Analysismentioning

confidence: 99%

Dissemination of Resistant Escherichia coli Among Wild Birds, Rodents, Flies, and Calves on Dairy Farms

et al. 2022

Self Cite

View full text Add to dashboard Cite

Antimicrobial resistance (AMR) in bacteria in the livestock is a growing problem, partly due to inappropriate use of antimicrobial drugs. Antimicrobial use (AMU) occurs in Swedish dairy farming but is restricted to the treatment of sick animals based on prescription by a veterinary practitioner. Despite these strict rules, calves shedding antimicrobial resistant Enterobacteriaceae have been recorded both in dairy farms and in slaughterhouses. Yet, not much is known how these bacteria disseminate into the local environment around dairy farms. In this study, we collected samples from four animal sources (fecal samples from calves, birds and rodents, and whole flies) and two environmental sources (cow manure drains and manure pits). From the samples, Escherichia coli was isolated and antimicrobial susceptibility testing performed. A subset of isolates was whole genome sequenced to evaluate relatedness between sources and genomic determinants such as antimicrobial resistance genes (ARGs) and the presence of plasmids were assessed. We detected both ARGs, mobile genetic elements and low rates of AMR. In particular, we observed four potential instances of bacterial clonal sharing in two different animal sources. This demonstrates resistant E. coli dissemination potential within the dairy farm, between calves and scavenger animals (rodents and flies). AMR dissemination and the zoonotic AMR risk is generally low in countries with low and restricted AMU. However, we show that interspecies dissemination does occur, and in countries that have little to no AMU restrictions this risk could be under-estimated.

show abstract

Exploring the Antibiotic Resistance Burden in Livestock, Livestock Handlers and Their Non-Livestock Handling Contacts: A One Health Perspective

Cited by 21 publications

References 49 publications

Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock

Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock

Genome-associations of extended-spectrum ß-lactamase producing (ESBL) or AmpC producing E. coli in small and medium pig farms from Khon Kaen province, Thailand

Dissemination of Resistant Escherichia coli Among Wild Birds, Rodents, Flies, and Calves on Dairy Farms

Contact Info

Product

Resources

About