High abundance of antimicrobial resistance genes in chicken flocks receiving antimicrobial treatment in Vietnamese poultry production

Abstract

Abstract Background and objectives Studies focussing on measuring antimicrobial resistance (AMR) rely on phenotyping or low throughput PCR detection of limited AMR genes (ARGs); high-throughput qPCR (HT-qPCR) may be a scalable approach for measuring AMR. We applied Fluidigm HT-qPCR to measure the impact of flock-level antimicrobial use (AMU) on genotypic AMR in the Mekong Delta area of Vietnam.

Methods AMU-related data and pooled faecal samples were collected longitudinally from 20 meat chicken flocks, divided into flocks treated with antimicrobials and untreated controls. Samples were analysed for 94 ARGs using Fluidigm HT-qPCR. Normalized ARG abundance was measured in reference to 16S rRNA. A regression model was constructed to weigh the effect of AMU factors on AMR.

Results The frequency of ARGs per sample was significantly higher in antimicrobial treatment group chicken samples (56.4; 95% CI 55.3–57.6) compared with the controls (52.1, 95% CI 50.9–53.4). Similarly, the normalized ARG abundance was significantly greater in treatment flock samples (3.2; 95% CI 2.9–3.4) than in control samples (2.0; 95% CI 1.7–2.3), except for tetracycline ARGs. Overall, ARG frequency negatively correlated with the average ARG abundance (R = −0.27 and P < 0.05). The time series analysis of ARG abundance revealed three distinct and equally prevalent patterns of ARG persistence. Among all the AMU factors, the number of antimicrobial classes and the total AMU duration showed the highest impact on flock ARG abundance.

Conclusion The findings of this study highlight the utility of molecular AMR profiling in areas with heavy AMU for poultry production.