Feasibility, acceptability, and bacterial recovery for community-based biological sample collection to estimate antibiotic resistance in commensal gut and upper respiratory tract bacteria: a cross-sectional mixed-methods study

BackgroundVietnam has high rates of antibiotic resistance, driven by overuse in agriculture, hospital, and community healthcare. Measures of resistance in commensal bacteria could provide a hard indicator for progress in evaluating the impact of interventions to reduce antibiotic use in the community. This study aimed to evaluate the feasibility, acceptability, and bacterial recovery for health-worker (HW) administered compared to self-administered swabs to recover Streptococcus pneumoniae, and stool collection to recover Enterobacterales in a community-based pilot study.MethodsWe conducted a cross-sectional mixed methods study in a rural community in Ha Nam Province, northern Vietnam. Between 16 July 2018 and 10 April 2019, 389 households were invited to participate in a household survey, Households were randomly selected and allocated in a 2:1 ratio to provide self-administered nasal swabs, or HW-administered nasopharyngeal swabs. Structured interviews were conducted with each household, and stool samples were self-collected from all household members. In-depth interviews with participants and health-workers were conducted in August 2018 to explore perspectives about different sample collection methods.Results324 households participated (83%), representing 1502 individuals. Stool samples were collected from 1498 individuals, self-administered nasal swabs from 1002 and HW-administered nasopharyngeal swabs from 496. S. pneumoniae were recovered from 11.1% (128/1,149) of the total population and 26.2% (48/183) of those under 5-years. Recovery was higher for HW-administered swabs (13.7%, 48/350) than self-administered swabs (10.0%, 80/799) (OR 2.06, 95% CI 1.07-3.96). Five main themes related to feasibility emerged through qualitative interviews: workload for data collectors; sample collection procedures; concerns about quality; storage and transportation; and disruptions. Nasopharyngeal swabs administered by health-workers took longer to collect, caused more discomfort and were more difficult to take from children. Costs per swab were cheaper for self-administered ($7.26) than HW-administered swabs ($8.63), but the total cost for 100 positive samples was higher ($7,260 and $6,300 respectively). Only 3 households refused to participate, representing a high acceptability of taking part. Factors affecting motivation to participate included sense of contribution, perceived trade-offs between benefits and effort, influence from others. Reluctance was related to stool sampling and negative perceptions of research. ConclusionsThis study provides important evidence for planning community-based carriage studies, including cost, logistics, and participant feedback about acceptability of different methods. Self-administered swabs had lower recovery, and though cheaper and quicker, this would translate to higher costs for large population-based studies requiring adequate numbers of positive samples for further testing. Factors that might improve recovery for self-administered swabs include swab-type, transport medium, and improved cold-chain to lab.