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

Accurate exposure assessments are needed to evaluate health hazards caused by airborne microorganisms and require air samplers that efficiently capture representative samples. This highlights the need for samplers with well-defined performance characteristics. While generic aerosol performance measurements are fundamental to evaluate/compare samplers, the added complexity caused by the diversity of microorganisms, especially in combination with cultivation-based analysis methods, may render such measurements inadequate to assess suitability for bioaerosols. Specific performance measurements that take into account the end-toend sampling process, targeted bioaerosol and analysis method could help guide selection of air samplers.Nine different samplers (impactors/impingers/cyclones/ electrostatic precipitators/filtration samplers) were subjected to comparative performance testing in this work. Their end-to-end cultivation-based biological sampling efficiencies (BSEs) and PCR-/microscopy-based physical sampling efficiencies (PSEs) relative to a reference sampler (BioSampler) were determined for gram-negative and gram-positive vegetative bacteria, bacterial spores, and viruses.Significant differences were revealed among the samplers and shown to depend on the bioaerosol's stress-sensitivity and particle size. Samplers employing dry collection had lower BSEs for stresssensitive bioaerosols than wet collection methods, while nonfilterbased samplers showed reduced PSEs for 1 μm compared to 4 μm bioaerosols. Several samplers were shown to underestimate bioaerosol concentration levels relative to the BioSampler due to having lower sampling efficiencies, although they generally obtained samples that were more concentrated due to having higher concentration factors.Our work may help increase user awareness about important performance criteria for bioaerosol sampling, which could contribute to methodological harmonization/standardization and result in more reliable exposure assessments for airborne pathogens and other bioaerosols of interest.

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.

The reliable detection of airborne biological threat agents depends on several factors, including the performance criteria of the detector and its operational environment. One step in improving the detector's performance is to increase our knowledge of the biological aerosol background in potential operational environments. Subway stations are enclosed public environments, which may be regarded as potential targets for incidents involving biological threat agents. In this study, the airborne bacterial community at a subway station in Norway was characterized (concentration level, diversity, and virulence-and survival-associated properties). In addition, a SASS 3100 high-volume air sampler and a matrix-assisted laser desorption ionization-time of flight mass spectrometry-based isolate screening procedure was used for these studies. The daytime level of airborne bacteria at the station was higher than the nighttime and outdoor levels, and the relative bacterial spore number was higher in outdoor air than at the station. The bacterial content, particle concentration, and size distribution were stable within each environment throughout the study (May to September 2010). The majority of the airborne bacteria belonged to the genera Bacillus, Micrococcus, and Staphylococcus, but a total of 37 different genera were identified in the air. These results suggest that anthropogenic sources are major contributors to airborne bacteria at subway stations and that such airborne communities could harbor virulence-and survival-associated properties of potential relevance for biological detection and surveillance, as well as for public health. Our findings also contribute to the development of realistic testing and evaluation schemes for biological detection/surveillance systems by providing information that can be used to mimic real-life operational airborne environments in controlled aerosol test chambers.