Dataset Information

Gut carriage of antimicrobial resistance genes in women exposed to small-scale poultry farms in rural Uganda: A feasibility study.

ABSTRACT:

Background

Antibiotic use for livestock is presumed to be a contributor to the acquisition of antimicrobial resistance (AMR) genes in humans, yet studies do not capture AMR data before and after livestock introduction.

Methods

We performed a feasibility study by recruiting a subset of women in a delayed-start randomized controlled trial of small-scale chicken farming to examine the prevalence of clinically-relevant AMR genes. Stool samples were obtained at baseline and one year post-randomization from five intervention women who received chickens at the start of the study, six control women who did not receive chickens until the end of the study, and from chickens provided to the control group at the end of the study. Stool was screened for 87 clinically significant AMR genes using a commercially available qPCR array (Qiagen).

Results

Chickens harbored 23 AMR genes from classes found in humans as well as additional vancomycin and β-lactamase resistance genes. AMR patterns between intervention and control women appeared more similar at baseline than one year post randomization (PERMANOVA R2 = 0.081, p = 0.61 at baseline, R2 = 0.186, p = 0.09 at 12 months) Women in the control group who had direct contact with the chickens sampled in the study had greater similarities in AMR gene patterns to chickens than those in the intervention group who did not have direct contact with chickens sampled (p = 0.01). However, at one year there was a trend towards increased similarity in AMR patterns between humans in both groups and the chickens sampled (p = 0.06).

Conclusions

Studies designed to evaluate human AMR genes in the setting of animal exposure should account for high baseline AMR rates. Concomitant collection of animal, human, and environmental samples over time is recommended to determine the directionality and source of AMR genes.

Trial registration

ClinicalTrials.gov Identifier NCT02619227.

SUBMITTER: Weil AA

PROVIDER: S-EPMC7289395 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:IntroductionAntimicrobial resistance (AMR) is a global public health threat. Worse still, there is a paucity of data from low- and middle-income countries to inform rational antibiotic use.ObjectiveAssess the feasibility of setting up microbiology capacity for AMR testing and estimate the cost of setting up microbiology testing capacity at rural district hospitals in Rwanda.MethodsLaboratory needs assessments were conducted, and based on identified equipment gaps, appropriate requisitions were processed. Laboratory technicians were trained on microbiology testing processes and open wound samples were collected and cultured at the district hospital (DH) laboratories before being transported to the National Reference Laboratory (NRL) for bacterial identification and antibiotic susceptibility testing. Quality control (QC) assessments were performed at the DHs and NRL. We then estimated the cost of three scenarios for implementing a decentralized microbiology diagnostic testing system.ResultsThere was an eight-month delay from the completion of the laboratory needs assessments to the initiation of sample collection due to the regional unavailability of appropriate supplies and equipment. When comparing study samples processed by study laboratory technicians and QC samples processed by other laboratory staff, there was 85.0% test result concordance for samples testing at the DHs and 90.0% concordance at the NRL. The cost for essential equipment and supplies for the three DHs was $245,871. The estimated costs for processing 600 samples ranged from $29,500 to $92,590.ConclusionThere are major gaps in equipment and supply availability needed to conduct basic microbiology assays at rural DHs. Despite these challenges, we demonstrated that it is feasible to establish microbiological testing capacity in Rwandan DHs. Building microbiological testing capacity is essential for improving clinical care, informing rational antibiotics use, and ultimately, contributing to the establishment of robust national antimicrobial stewardship programs in rural Rwanda and comparable settings.