Metagenomic characterization of ambulances across the USA

Microbiome

Rachid Ounit¹  Ebrahim Afshinnekoo²  Harry J. Reed²  Erin Butler²  Christopher E. Mason²  Gail Rosen³  Stephen Woloszynek³  Shawn Levy⁴  Niamh B. O’Hara⁵  Donell Harvin⁶  Nora Caplan⁶  Brook Frye⁷ 

[1] Department of Computer Science and Engineering, University of California;Department of Physiology and Biophysics, Weill Cornell Medicine;Electrical and Computer Engineering, Drexel University;Hudson Alpha;Jacobs Technion-Cornell Institute, Cornell Tech;SUNY Downstate Medical Center, State University of New York;School of Public Health and Health Sciences, University of Massachusetts;

关键词: Ambulance;    Classification;    Taxonomy;    Pre-hospital setting;    Hospital-acquired infections;    Nosocomial pathogens;   

DOI  :  10.1186/s40168-017-0339-6

来源: DOAJ

【 摘 要 】

Abstract Background Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some healthcare settings. However, there has been no study to date that has used this approach in pre-hospital settings, such as ambulances, an important first point-of-contact between patients and hospitals. Results We sequenced 398 samples from 137 ambulances across the USA using shotgun sequencing. We analyzed these data to explore the microbial ecology of ambulances including characterizing microbial community composition, nosocomial pathogens, patterns of diversity, presence of functional pathways and antimicrobial resistance, and potential spatial and environmental factors that may contribute to community composition. We found that the top 10 most abundant species are either common built environment microbes, microbes associated with the human microbiome (e.g., skin), or are species associated with nosocomial infections. We also found widespread evidence of antimicrobial resistance markers (hits ~ 90% samples). We identified six factors that may influence the microbial ecology of ambulances including ambulance surfaces, geographical-related factors (including region, longitude, and latitude), and weather-related factors (including temperature and precipitation). Conclusions While the vast majority of microbial species classified were beneficial, we also found widespread evidence of species associated with nosocomial infections and antimicrobial resistance markers. This study indicates that metagenomics may be useful to characterize the microbial ecology of pre-hospital ambulance settings and that more rigorous testing and cleaning of ambulances may be warranted.

【 授权许可】

Unknown