Highlights d Cities possess a consistent ''core'' set of non-human microbes d Urban microbiomes echo important features of cities and city-life d Antimicrobial resistance genes are widespread in cities d Cities contain many novel bacterial and viral species

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.

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.

Foxp3+ cells are an integral component of acute rejection of allografts but may be dominated by pathogenic effectors.