Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes

Abstract

We describe the sampling of sixty-three uncultured hospital air samples collected over a six-month period and analysis using shotgun metagenomic sequencing. Our primary goals were to determine the longitudinal metagenomic variability of this environment, identify and characterize genomes of potential pathogens and determine whether they are atypical to the hospital airborne metagenome. Air samples were collected from eight locations which included patient wards, the main lobby and outside. The resulting DNA libraries produced 972 million sequences representing 51 gigabases. Hierarchical clustering of samples by the most abundant 50 microbial orders generated three major nodes which primarily clustered by type of location. Because the indoor locations were longitudinally consistent, episodic relative increases in microbial genomic signatures related to the opportunistic pathogens Aspergillus, Penicillium and Stenotrophomonas were identified as outliers at specific locations. Further analysis of microbial reads specific for Stenotrophomonas maltophilia indicated homology to a sequenced multi-drug resistant clinical strain and we observed broad sequence coverage of resistance genes. We demonstrate that a shotgun metagenomic sequencing approach can be used to characterize the resistance determinants of pathogen genomes that are uncharacteristic for an otherwise consistent hospital air microbial metagenomic profile.

Correction: Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes

“…The attached Supporting Information file provides additional information about the version of ZovaSeq used for King et al 2016 [1], which is currently available for use from Zova Systems (contact robert.yamamoto@zovasystems.com; also see https://lnkd.in/gxkRCVV). ZovaSeq has since been updated and further optimized.…”

Measuring bioaerosol concentrations generated from toilet flushes during hospital-based patient care

“…Metagenomics has emerged as a new molecular method to characterize diverse bioaerosols, which first quantified and identified bioaerosols in agriculture and has most recently been used for healthcare aerosols (King et al, 2016;Nonnenmann et al, 2010;O'Brien et al, 2016). Within the healthcare setting, several of the microorganisms cultured from previous studies were identified to exist as well as other microorganisms that have not yet been cultured (King et al, 2016). Results suggest healthcare settings may consist of more microorganism species than originally hypothesized (King et al, 2016) Challenges of Sampling Bioaerosols in a Healthcare Setting…”

“…Molecular based analysis occurs when bioaerosols are collected or extracted into liquid solution where the DNA or RNA are analyzed, however viability of the microorganism may not be determined (ACGIH, 1999). Molecular analysis can include techniques such as polymerase chain reaction (PCR) or metagenomic techniques (e.g., shotgun sequencing) (King et al, 2016;Mukoda, Todd, & Sobsey, 1994;Nonnenmann, Bextine, Dowd, Gilmore, & Levin, 2010;O'Brien et al, 2016;Stetzenbach, Buttner, & Cruz, 2004). PCR is the oldest molecular method that quantifies microorganisms obtained in a sample and is limited for use in microorganisms which have a fully or partially sequenced genome (Mukoda et al, 1994).…”

“…However, some microorganisms do not conserve either of the 16S or 18S genes or have multiple copies in their genome which leads to error in estimates of quantification (Stetzenbach et al, 2004). Metagenomics has emerged as a new molecular method to characterize diverse bioaerosols, which first quantified and identified bioaerosols in agriculture and has most recently been used for healthcare aerosols (King et al, 2016;Nonnenmann et al, 2010;O'Brien et al, 2016). Within the healthcare setting, several of the microorganisms cultured from previous studies were identified to exist as well as other microorganisms that have not yet been cultured (King et al, 2016).…”

“…Both filter materials are smooth and flat, which are good surfaces to observe collected bioaerosols under a microscope (ACGIH, 1999). Bioaerosols can be removed for analysis by rinsing the filter with an extraction fluid, and have been used in a healthcare setting to measure and characterize bioaerosol exposures (King et al, 2016;Wang et al, 2015). Wang et al, (2015) found that all filter materials do not collect bioaerosols equally and that more culturable bacteria is extracted from polycarbonate filters.…”