key: cord-0847950-xw7u8qhc
authors: Fan, Jun; Li, Xiang; Gao, Yong; Zhou, Junjie; Wang, Sihua; Huang, Bo; Wu, Junhua; Cao, Qin; Chen, Yajun; Wang, Zhenkao; Luo, Danju; Zhou, Ting; Li, Ruiting; Shang, You; Nie, Xiu
title: The Lung Tissue Microbiota Features of 20 Deceased Patients with COVID-19
date: 2020-06-21
journal: J Infect
DOI: 10.1016/j.jinf.2020.06.047
sha: 68105bccc101a456c2d1f0b19fa1ac68544155d9
doc_id: 847950
cord_uid: xw7u8qhc

nan

(10 [50.0%]) and fatigue or myalgia (10 [50.0%]). One-fifth of the patients had diarrhoea (4 [20%] ). Other symptoms included chest pain, vomiting and headache. All 20 (100.0%) patients had findings of bilateral infiltrates on radiographic imaging. Fifteen were more vulnerable to SARS-CoV-2 infection. Notably, sepsis was the most frequently observed complication. Immediately after death, postmortem needle core biopsies were performed on bilateral lungs in the negative-pressure isolation ward. The procedures were guided with ultrasound, and specimens were collected aseptically. Tissue cores were fixed in 10% neutral formalin immediately after being removed from the body, fixed for over 24 hours, dehydrated in a graded series of ethanol, cleared in xylene, and then embedded in paraffin. A QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany) was used to extract the total DNA from every FFPE tissue. The V3-V4 regions of the 16S rRNA samples were amplified by PCR, and the specific primers were 338F: 5-ACTCCTACGGGAGGCAGCA-3 and 806R: 5-GGACTACHVGGGT WTCTAAT-3. The ITS1 genes were amplified using barcoded ITS 5F: 5-GGAAGTAAAAGTCGTAACAAGG-3 and Although originally believed to be sterile, the lung exhibits a microbiota that varies in both physiological and pathological conditions (4) . Many authors agree that healthy lung tissue has a low density of microbial populations, represented mainly by genera such as Prevotella, Veillonella, Streptococcus and Tropheryma (5) . In our study, disorder of the lung microbiome was characterized by enrichment with the OTU of the Acinetobacter spp., which is usually comprised of Acinetobacter calcoaceticus, Acinetobacter baumannii, Acinetobacter nosocomialis, and Acinetobacter pittii, with Acinetobacter baumannii (AB) being the most clinically important species responsible for the highest incidence of multidrug resistance and mortality (6) . It should be noted that Enterobacteriaceae spp., a kind of abundant taxonomic group in the human gut microbiome, was common in the lung tissues of fatal COVID-19 patients. The Enterobacteriaceae family of bacteria (a kind of taxon comprising many potentially pathogenic bacteria including Klebsiella, Escherichia coli, Proteus, Enterobacter, etc.) might release a large amount of endotoxin in the intestinal lumen, which would inhibit protein synthesis in intestinal epithelial cells (7) . Significantly, we observed that the fungal communities in lung specimens were usually dominated by Cryptococcus spp. Cryptococcus infections have high morbidity and mortality rates worldwide, particularly in the context of immune suppression and central nervous system involvement (8) . Moreover, we successfully detected Issatchenkia spp., Cladosporium spp., Cladosporium spp., Alternaria spp., Aspergillus spp., and Candida spp., all of which are important species for opportunistic invasive mycosis in immunocompromised patients. In general, persistent lymphocytic depletion, mechanical ventilation, corticosteroid therapy and prolonged hospital stays may lead to the development of opportunistic infections in fatal COVID-19. What is more important is that fatal COVID-19 is associated with complex mixed bacteria and fungal infections in the lungs. Therefore, it is urgent to serially monitor the microbiota in the lower respiratory tract for timely personalized treatment.

The study was approved by the health commission of Hubei Province and the ethics committee of Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (approval number: 2020-0043-1).

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We thank all patients and their families involved in the study. 

All authors declare no competing interests.