title: The transmission and dynamics of antimicrobial resistance in small-holder chicken flocks in Vietnam
Creators: name: Nguyen Thi Nhung, 
Publisher: name: The Open University
Year: 2023

description: Antimicrobial resistance (AMR) is a top global public health threat. Antimicrobial use (AMU) and AMR in food producing animals have been identified as sources that significantly contribute to the overall burden of AMR worldwide. Using the framework of longitudinal and cross-sectional cohorts of small-scale native chicken flocks in the Mekong Delta region of Vietnam, I characterized the dynamics of AMR over time and its relation to AMU and investigated potential transmission of AMR between chickens and humans and of <i>Streptococcus suis</i> between pigs and chickens.<br><br> Firstly, I developed and evaluated a microdilution method to quantitative estimate colistin resistance based on the testing of mixtures of <i>Escherichia coli</i> strains from pooled faecal samples. This method correlates well with single-colony analysis and may allow affordable monitoring colistin resistance in animal feces from flocks/herds.<br><br> Secondly, using data and samples collected longitudinally from 83 chicken flocks over the production cycle, I quantified antimicrobial resistance genes (ARGs) in chickens at day-old, mid- (2 months) and end-production (4-6 months). ARG abundance significantly increased from day-old to mid production chickens (p= 0.007) and slightly decreased at the end of the cycle (p= 0.198). Despite the higher degree of AMU in the early stage (average 736.7 ADD<sub>kg</sub> per 1,000 chicken-days) compared to the later period of chicken life (average 52.1), the association of AMU and ARG abundance was stronger during later period (increase 254%). Next, I investigated the impact of an intervention consisting of the provision of veterinary support to farmers on chicken gut resistome. The intervention resulted in a 74.2% reduction in AMU (p= 0.002) in flocks, associated with a 17.5% reduction in ARG abundance (p= 0.438).<br><br> Next, I described the phenotypic AMR patterns of <i>E. coli</i> from humans and chickens using a cross-sectional study design. Crucially levels of AMU were about 19 times greater in chicken flocks than in humans, even though AMR prevalence were comparable. <i>E. coli</i> from chickens and humans living on same farms had a higher degree of similarity in their AMR pattern than humans and animals from different farms. Interestingly, prevalence of colistin resistance was slightly higher in human than chicken isolates (2.1% vs 1.3%) and there was epidemiological evidence of transmission of colistin resistance from chicken flocks to in-contact humans.<br><br> In addition, I found a high prevalence of chickens colonized with the serious zoonotic pathogen <i>S. suis</i>(~34%). The isolates had no epidemiological linkage with pigs in the same and neighbor farms, suggesting an important role of the environment in chicken infection. The isolates displayed high prevalence of resistance against tetracycline, clindamycin, erythromycin and penicillin but they were unrelated to AMU in chicken flocks.<br><br> Overall, findings from this thesis highlight the contribution of factors other than AMU (i.e., low biosecurity, water and feed sources, carry-over from previous flocks) on transmission and persistence of AMR in chicken flocks.<br>