Additional file 1: of Aspergillus fumigatus during COPD exacerbation: a pair-matched retrospective study

Table S1. Detection of pathogenic bacteria and other fungi. (DOCX 14 kb

Metagenomic Human Repiratory Air in a Hospital Environment

<div><p>Hospital-acquired infection (HAI) or nosocomial infection is an issue that frequent hospital environment. We believe conventional regulated Petri dish method is insufficient to evaluate HAI. To address this problem, metagenomic sequencing was applied to screen airborne microbes in four rooms of Beijing Hospital. With air-in amount of sampler being setup to one person’s respiration quantity, metagenomic sequencing identified huge numbers of species in the rooms which had already qualified widely accepted petridish exposing standard, imposing urgency for new technology. Meanwhile,the comparative culture only got small portion of recovered species and remain blind for even cultivable pathogens reminded us the limitations of old technologies. To the best of our knowledge, the method demonstrated in this study could be broadly applied in hospital indoor environment for various monitoring activities as well as HAI study. It is also potential as a transmissible pathogen real-time modelling system worldwide.</p></div

Number of metagenomic recovered species for each group of microorganisms.

<p>a) sampling equipment, the soft tube connected to sampling head allows it to be easily fixed at any position, even could be put before the mouth. b) the sampling filter paper at Nov.6,2013. Left: blank; right: after work for 24 hours. c) Numbers of species and d) proportions of species number in each group of microbes in four rooms.</p

Heatmap of metagenomic recoverd species for each group of microorganisms in four rooms.

<p>For bacteria and eukaryote, top 100 abundant species for the heatmap.</p

Species intersection of each group of microbes in four rooms.

<p>Species intersection of each group of microbes in four rooms.</p

Results in bacteria comparative culture of parallel hospital samples (Filter paper elution half to metagenomic sequencing and half to conventional Peri dish culture).

<p>(For those not identified to species such as Bacillus, Genus abundance instead of species abundance was used).</p><p>Results in bacteria comparative culture of parallel hospital samples (Filter paper elution half to metagenomic sequencing and half to conventional Peri dish culture).</p

Reported pathogens among metagenomic recovered top 100 abundant bacteria species, missed by regulated culture-based technology from parallel control.

<p>Reported pathogens among metagenomic recovered top 100 abundant bacteria species, missed by regulated culture-based technology from parallel control.</p

PCoA analysis for indoor and outdoor air.

<p>Data were normalized between 0 and 1 and compared with PM2.5 and PM10 data set[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139044#pone.0139044.ref047" target="_blank">47</a>]. (red: Indoor results; blue: outdoor results).</p

Main routes of transmission for nosocomial infection.

<p>Main routes of transmission for nosocomial infection.</p

Rarefaction Curve for data effectiveness.

<p>Abscissa: number of reads, coordinate: number of species.</p