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Influence of antibiotic selection on genetic composition of Escherichia coli populations from conventional and organic dairy farms.

ABSTRACT: The widespread agricultural use of antimicrobials has long been considered a crucial influence on the prevalence of resistant genes and bacterial strains. It has been suggested that antibiotic applications in agricultural settings are a driving force for the development of antimicrobial resistance, and epidemiologic evidence supports the view that there is a direct link between resistant human pathogens, retail produce, farm animals, and farm environments. Despite such concerns, little is understood about the population processes underlying the emergence and spread of antibiotic resistance and the reversibility of resistance when antibiotic selective pressure is removed. In this study, hierarchical log-linear modeling was used to assess the association between farm type (conventional versus organic), age of cattle (calf versus cow), bacterial phenotype (resistant versus susceptible), and the genetic composition of Escherichia coli populations (E. coli Reference Collection [ECOR] phylogroup A, B1, B2, or D) among 678 susceptible and resistant strains from a previously published study of 60 matched dairy farms (30 conventional and 30 organic) in Wisconsin. The analysis provides evidence for clonal resistance (ampicillin resistance) and genetic hitchhiking (tetracycline resistance [Tet(r)]), estimated the rate of compositional change from conventional farming to organic farming (mean, 8 years; range, 3 to 15 years), and discovered a significant association between low multidrug resistance, organic farms, and strains of the numerically dominant phylogroup B1. These data suggest that organic farming practices not only change the frequency of resistant strains but also impact the overall population genetic composition of the resident E. coli flora. In addition, the results support the hypothesis that the current prevalence of Tet(r) loci on dairy farms has little to do with the use of this antibiotic.

SUBMITTER: Walk ST

PROVIDER: S-EPMC2074991 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Biases of antimicrobial use (AMU) reporting systems pose a challenge to monitoring of AMU. Our study aimed to cross-compare three data sources of AMU in Swedish dairy herds to provide an account of the validity of AMU reports. We studied AMU differences between two production systems, to investigate how the reporting system affected this comparison. On-farm quantification of AMU via a manual collection of empty drug containers (BIN) took place in organic (n = 30) and conventional (n = 30) dairy herds during two periods between February 2016 and March 2017. A data extract mirroring these periods was obtained from two linked datasets that contain AMU data as reported by the prescribing veterinarians. These included data from the Swedish Board of Agriculture system (SBA) and Växa milk recording system (VXA). Using the European Medicines Agency technical units, the total number of defined daily doses (DDDvet), and defined course doses (DCDvet) per animal/year were calculated for each herd/period/dataset. Descriptive statistics and Bland-Altman plots were used to evaluate the agreement and systematic bias between the datasets. Mixed models for repeated measures were used to assess AMU differences between production systems. We found consistent numerical differences for the calculated AMU metrics, with BIN presenting higher usage compared to the SBA and VXA. This was driven by a disparity in intramammary tubes (IMt) which appear to be underreported in the national datasets. A statistically significant interaction (BIN dataset) between the production system and drug administration form was found, where AMU for injectable and lactating cow IMt drug forms differed by the production system, but no difference was found for dry-cow IMt. We conclude that calculating AMU using DDDvet and DCDvet metrics at a herd level based on Swedish national datasets is useful, with the caveat of IMt potentially being misrepresented. The BIN method offers an alternative to monitoring AMU, but scaling up requires considerations. The lower disease caseload in organic herds partly explains the lower AMU in particular drug forms. The fact that organic and conventional herds' had equally low AMU for dry-cow IMt, coupled with mismatches in IMt report across herds indicated an area of further research.

Project description:The United States regulates the use of antibiotics in agricultural settings to address the global antibiotic resistance problem. Conventional dairy cows treated with antibiotics are kept in the herd and after the withholding period milk is harvested. On organic farms, the US organic standard on antibiotic use requires sick dairy cows to be treated, but treated cows must be removed from the herd and their milk can never again be sold as certified organic. This study investigated the US public's perceptions of the organic dairy farming, antibiotic use on dairy farms, and whether these perceptions affect consumer's self-reported purchasing behavior for organic. We used a nationally representative phone-based survey of 1000 US adults and characterized participants' self-reported (i) knowledge of the legality of antibiotic use on dairy farms (conventional and organic) and (ii) frequency of purchasing organic instead of conventional dairy products, as well as several demographic and other variables. The results indicated that participants' knowledge about antibiotic use practices in dairy farming have no effect on their self-reported purchasing behavior for organic or conventional dairy products. However, respondents who were familiar with the regulations of antibiotic use on dairy farms were more likely to oppose the US organic standard on antibiotic use in dairy farming and thought that past antibiotic use should not permanently remove a cow's organic status. These findings contribute to understanding of public perceptions that shape the US dairy organic market. PRACTICAL APPLICATION: Income, employment, health and political values, but not consumers' knowledge about antibiotic use in dairy farming, affect self-reported purchasing behavior for organic dairy products. However, consumers who are familiar with the regulations of antibiotic use on US dairy farms disagree with the US organic standard on antibiotic use mandating loss of organic status for any cattle treated with antibiotics. These findings may be useful to organic markets.

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Influence of antibiotic selection on genetic composition of Escherichia coli populations from conventional and organic dairy farms.

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