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.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1. Heatmap demonstrating whether antimicrobial resistance (AMR) genes were present, absent, or indeterminate in human and chicken samples at different timepoints.

Fig 2. Ordination plot of the Jaccard dissimilarity index of AMR gene patterns between groups.

The proportion of unshared AMR genes out of the total number of AMR genes detected between any two samples is shown. More similar samples will appear closer together on the plot. The ellipse depicts the 95% confidence ellipse around each sample group. At baseline, there were no statistically significant differences between AMR gene patterns between intervention and control groups (PERMANOVA R2 = 0.081), whereas at 12 months, there was a trend towards different AMR gene patterns (PERMANOVA p = 0.09) between intervention and control groups.

Fig 3. Boxplot of the distance between sample groups and the centroid of the chicken stool samples based on AMR gene pattern.

To demonstrate the comparison of the AMR gene pattern of each human sample to the chicken samples at baseline and follow up, we computed the distance between the Jaccard index of each sample to the centroid of all chicken samples. Here, a shorter distance indicates increased similarity in AMR gene pattern of the human sample in relation to the centroid of the chicken samples gene patterns, whereas a longer distance indicates decreased similarity in AMR gene pattern of that human sample compared to the chicken samples gene patterns. The chicken sample centroid is set at zero. The AMR gene pattern of the chicken samples is more similar to the AMR gene pattern in the control group rather than the intervention group (p = 0.014); note that chicken samples were obtained from the control group. Differences in AMR gene patterns over time did not reach statistical significance (p = 0.059), although at follow-up, the AMR gene patterns in both control and intervention group humans were more similar to AMR gene patterns in chicken samples.