Characterization of the public transit air microbiome and resistome reveals geographical specificity

Abstract

Background The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized. Results City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes. Conclusions Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.

Detection and isolation of airborne SARS‐CoV‐2 in a hospital setting

“…Cumulatively, our results provide support for aerosol transmission of SARS-CoV-2 and demonstrate the applicability of targeted sampling approaches that deploy air and surface monitoring of respiratory pathogens as previously applied in subway systems. 32 Detection of SARS-CoV-2 on the patient's bed rail and floor may reflect respiratory droplet deposition. We did not quantify PFUs from these sites.…”

An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics

“…Two negative media controls were included in each sampling session, which were unopened media with swabs from the same lot. Each collected control was split into triplicate and processed along with samples 53,74 . Negative filter controls were included in triplicate for each pore size by letting sterile PBST flow through the vacuum filtration system attached with blank filter papers.…”

A Journey on the Skin Microbiome: Pitfalls and Opportunities

“…The amount of skin bacteria on humans is relatively high, and they are constantly shed in the surrounding environment together with dead cells of the stratum corneum of the skin, so the fact that they are often the major microbial component in the air, soil, and other surfaces in a crowded urban area is not surprising [ 49 , 50 ].…”