Assessment of the household antibiotic resistance genes, virulence factor genes, and pathogen profiles from three global cities

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Abstract This study assessed the prevalence of antibiotic resistance genes (ARGs) and virulence factor genes (VFs), DNA viruses, and medically-relevant pathogens in three major cities around the globe – Mysuru (India), Dubai (United Arab Emirates), and Tucson (Arizona, United States of America). Ten households were sampled in each city, at ten sites in the bathroom, kitchen, and living spaces. The alpha diversity of ARGs significantly differed between household locations in each country (ANOVA, p<0.05) and beta diversity (dissimilarity) analysis showed a significant association between the ARGs and the geographic locations (PERMANOVA, p<0.01). A set of ARGs were found in every location across the dataset (the core ARG profile) included 25 different genes. The alpha diversity of virulence factors differed across the household locations within the three cities (ANOVA, p<0.01). The beta diversity of VFs was not well explained by geographic location or location within the household (PERMANOVA, p=0.129 (geographic), p=0.127 (household)). There were 341 unique VFs found in the study, but only 5 core VFs across the dataset. Bacterial pathogens detected across the household included Escherichia coli , Acinetobacter baumanii , Klebsiella pneumoniae , and more. The DNA (and bacteriophage) virome varied between countries and was more diverse in Tucson and Dubai (top viral families included Poxviridae and Orthoherpesviridae - two families which contain human pathogens - and Steitzviridae, a family of bacteriophages) compared to Mysuru, where nearly all viruses were a part of the Muvirus genus (a bacteriophage which contributes to horizontal gene transfer by phage transduction). Importance The diversity of the built environment microbiome is not well characterized globally. Household occupants interact with the built microbiome on a daily basis, and the built microbiome may have the potential to influence human health. The presence of pathogens in the built environment and the key genes contributing to microorganism pathogenicity were investigated in this study, as information on this is lacking on an international scale. The diversity of ARG and VFs across the globe, as well as the presence of medically relevant pathogens within the house that were found in this study highlights the need to explore further the factors which influence the household microbiome, virome, and resistome. This may aid in identify how the build microbiome may be shaped by humans and influence human health. Impact Statement This research contributes to the understanding of the built microbiome, specifically how it varies within the house, within cities, and across the globe. This can aid in our understanding of microbial dynamics in environments with heavy human influence and help develop and improve hygiene habits and products which are mindful of the existing microbiome.

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