About: Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients

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About: Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients Goto Sponge NotDistinct Permalink

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients
Creator	Wang, Jian Wang, Yanqun Ye, Feng Zhao, Jingxian Chen, Weijun Zhang, Lu Zhong, Nanshan Li, Fang He, Weiqun Gan, Mian Zhang, Zhaoyong Zhu, Airu Yang, Huanming Xiao, Fei Li, Jiandong Li, Fuqiang Li, Li, Junhua Tun, Hein Ren, Huahui Ren, Peidi Wang, Daxi Xu, Xun Zhong, Huanzi Zhu, Shida Liang, Tianzhu Zhong, Bei Kristiansen, Karsten Ruan, Shicong Shi, Zhun Yang, Fangming
Source	MedRxiv
abstract	Summary Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, microbial composition of the respiratory tract and other infected tissues, as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear. Method Between January 27 and February 26, 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients (requiring ICU admission and mechanical ventilation), in the Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. Co-infection rates, the prevalence and abundance of microbial communities in these COVID-19 patients were determined. Findings Notably, respiratory microbial co-infections were exclusively found in 84.6% of severely ill patients (11/13), among which viral and bacterial co-infections were detected by sequencing in 30.8% (4/13) and 69.2% (9/13) of the patients, respectively. In addition, for 23.1% (3/13) of the patients, bacterial co-infections with Burkholderia cepacia complex (BCC) and Staphylococcus epidermidis were also confirmed by bacterial culture. Further, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes in one severely ill patient was demonstrated, which might be the primary cause of his disease deterioration and death one month after ICU admission. Interpretation Our findings identified distinct patterns of co-infections with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking of BCC-associated nosocomial infections are recommended to improve the pre-emptive treatment regimen and reduce fatal outcomes of hospitalized patients infected with SARS-CoV-2. Funding National Science and Technology Major Project of China, National Major Project for Control and Prevention of Infectious Disease in China, the emergency grants for prevention and control of SARS-CoV-2 of Ministry of Science and Technology and Guangdong province, Guangdong Provincial Key Laboratory of Genome Read and Write, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, and Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics.
has issue date	2020-07-05(xsd:dateTime)
bibo:doi	10.1101/2020.07.02.20143032
has license	medrxiv
sha1sum (hex)	d32b768e194315e416afd988bf9f02c8296e96f7
schema:url	https://doi.org/10.1101/2020.07.02.20143032
resource representing a document's title	Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients
resource representing a document's body	covid:d32b768e194315e416afd988bf9f02c8296e96f7#body_text
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