High diversity of airborne fungi in the hospital environment as revealed by meta-sequencing-based microbiome analysis

Abstract

Invasive fungal infections acquired in the hospital have progressively emerged as an important cause of life-threatening infection. In particular, airborne fungi in hospitals are considered critical pathogens of hospital-associated infections. To identify the causative airborne microorganisms, high-volume air samplers were utilized for collection, and species identification was performed using a culture-based method and DNA sequencing analysis with the Illumina MiSeq and HiSeq 2000 sequencing systems. Few bacteria were grown after cultivation in blood agar. However, using microbiome sequencing, the relative abundance of fungi, Archaea species, bacteria and viruses was determined. The distribution characteristics of fungi were investigated using heat map analysis of four departments, including the Respiratory Intensive Care Unit, Intensive Care Unit, Emergency Room and Outpatient Department. The prevalence of Aspergillus among fungi was the highest at the species level, approximately 17% to 61%, and the prevalence of Aspergillus fumigatus among Aspergillus species was from 34% to 50% in the four departments. Draft genomes of microorganisms isolated from the hospital environment were obtained by sequence analysis, indicating that investigation into the diversity of airborne fungi may provide reliable results for hospital infection control and surveillance.

Fungi diversity in PM<sub>2. 5</sub> and PM<sub>1</sub> at the summit of Mt. Tai: abundance, size distribution, and seasonal variation

“…This protocol can extract sufficient DNA from low-biomass environmental samples (e.g., aerosol particles) and boosted the DNA extraction efficiency by more than twice as compared to the non-optimized extraction method. Besides, it has been applied for studying airborne microbial diversity in different environments (Cao et al, 2014;Deng et al, 2016;Tong et al, 2017;Gao et al, 2017b). Half of the filters (about 121.64 cm 2 in area) were cut into small pieces, inserted into 50 mL Falcon tubes that were filled with sterilized 1× PBS buffer, and centrifuged at 200 × g for 3 h at 4 • C. The resuspension was collected into a 0.2 µm Supor 200 PES membrane disc filter.…”

Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol

“…This enhances the efficiency of the REPLI-g SensiPhi DNA polymerase during the multiple displacement amplification (MDA) reaction and, if used for populations of single cells from singular organisms, the impact on downstream quantification of transcripts is negligible. However, given the high efficiency and fidelity of the SensiPhi DNA polymerase, these kits have been attractive for meta-omics studies, with populations of multiple species, from low diversity, low biomass environments or investigations with minimal biological sample material 60–62 . For short-read sequencing technologies (i.e., Illumina), the confounding effects of the ligation step, and subsequent chimeric cDNAs, are negligible, or an acceptable trade-off for the efficacy of SensiPhi DNA polymerase.…”

The dynamic surface proteomes of allergenic fungal conidia

“…Airborne fungi, especially in outdoor and hospital environments remain difficult to rapidly detect, despite their potential to contribute to invasive fungal disease and allergic exacerbation in susceptible patient populations. 34,35 Therefore, improved methods for rapid detection of airborne fungi are greatly needed in managing allergic responses and invasive fungal disease. The ortholog analysis presented here provides numerous candidate proteins likely accessible to both the immune system and potential diagnostic assays.…”

“…33 Our capacity to detect airborne fungi remains particularly limited and slow, despite the obvious importance of fungal conidia in initiating invasive lung infections or allergic reactions in susceptible populations. [34][35][36] As the burden of fungal pathogens in the clinic increases, improvements in each of these realms are desperately needed. 37 In this study we further elucidated the surface-exposed proteome and secreted/shed proteins of allergyinducing fungal conidia to reveal new fungal surface antigens as potential diagnostic or therapeutic targets.…”