Cross-sectional study of antimicrobial resistance and ecology in gastrointestinal and oral microbial communities of urban Pakistani adults

Background and AimsAntimicrobial resistance (AMR) is one of the most serious global public health threats affecting lower-middle-income countries (LMICs) due to lack of awareness, inadequate healthcare and sanitation infrastructure, plus other environmental factors. In this study, we aimed to link microbial assembly and covariates (body mass index, smoking, use of antibiotics) to gut microbiome structure and correlate AMR gene prevalence. MethodsWe examined the gastrointestinal and oral microbial profiles of healthy adults in Pakistan through 16S rRNA gene sequencing with a focus on different ethnicities, antibiotic usage, drinking water type, smoking, and other demographic measures. We then utilised a suite of innovative statistical tools, driven by numerical ecology and machine learning, to address the above aims. ResultsWe observed tap water as the main contributor for development of AMR in the Pakistani cohort. In addition, microbial niche breadth analysis based on null modelling procedures highlighted an aberrant gut microbial signature of smokers with increased age. ConclusionsDrinking water plays a more important role in AMR spread in Pakistan rather than other factors considered. Moreover, covariates such as smoking, and age impact the human microbial community structure in this Pakistani cohort. To the best of our knowledge, this is one of the first studies that provide a snapshot of the microbiomes of healthy individuals in Pakistan and considers AMR profiles with an emphasis on potential sources of AMR prevalence. Background and ContextPakistan is categorized as a low-and-middle-income country by the World Bank where misuse of antibiotics is widespread, and multidrug resistance is prevalent. Thus, it is imperative that we understand antimicrobial resistance and the drivers of human microbiomes in Pakistan. New FindingsIn a healthy Pakistani cohort, individuals that consumed Tap Water had almost 6-fold more associations with AMRs. Therefore, drinking water source could be a strong driver in the spread of AMR. LimitationsA limitation is the use of predictive functional profiles. However, shotgun metagenomics may be prohibitively costly for LMICs given the urgent need for AMR surveillance. Clinical Research RelevanceOur research shows strong associations of key microbial taxa with covariates such as age, BMI, and gender. Additionally, we show correlations between specific outlier taxa that are present both in the gut and oral communities, highlighting potential future feasibility for use of the oral microbiome as a proxy to gut dysbiosis in some cases. Basic Research RelevanceWe have applied recent advancements in analytical tools to link both AMR prevalence and human microbiome composition with factors such as age, BMI, gender, ethnicity, smoking status, use of antibiotics, and drinking water source. Additionally, we use null modelling to show that the microbial communities are subject to strong environmental pressure and dispersal limitation. Lay SummaryWe analysed gut and oral microbes from healthy individuals in Pakistan and found that the potential for antibiotic resistance was increased in those who drank tap water.