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Although studies have shown that urban environments and mass-transit systems have distinct genetic profiles, there are no systematic studies of these dense, human/microbial ecosystems around the world. To address this gap in knowledge, we created a global metagenomic and antimicrobial resistance (AMR) atlas of urban mass transit systems from 58 cities, spanning 3,741 samples and 4,424 taxonomically-defined microorganisms collected for from 2015-2017. The map provides annotated, geospatial details about microbial strains, functional genetics, antimicrobial resistance, and novel genetic elements, including 10,928 novel predicted viral species. Urban microbiomes often resemble human commensal microbiomes from the skin and airways, but also contain a consistent "core" of 61 species which are predominantly not human commensal species. Conversely, samples may be accurately (91.4%) classified to their city-oforigin using a linear support vector machine over taxa. These data also show that AMR density across cities varies by several orders of magnitude, including many AMRs present on plasmids with specific cosmopolitan distributions. Together, these results constitute a high-resolution global metagenomic atlas, which enables the discovery of new genetic components of the built human environment, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the world's cities.

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The prevalence of ARV resistance among treatment-naive MSM in Peru is low, reflecting limited access to treatment before 2004, and contrasts with the history of ARV treatment in developed countries, where high levels of nucleoside reverse transcriptase inhibitor resistance occurred before introduction of highly active antiretroviral therapy. Linking ARV resistance and HIV sentinel surveillance in developing settings is feasible and should be considered in third-generation HIV sentinel surveillance programs.

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