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2.1. Data and sample collection

SC Shuyan Chen
QZ Qing Zhu
YX Yanyu Xiao
CW Chi Wu
ZJ Zhaofang Jiang
LL Lei Liu
JQ Jiuxin Qu
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On 8 January 2020, Shenzhen Centers for Disease Control (CDC) identified the first case of pneumonia with unknown cause. The Shenzhen Third People's Hospital is the only government‐mandated hospital for the treatment of COVID‐19 patients in this metropolis of 20 million people. Between 11 January 2020 and 1 March 2020, a total of 418 patients diagnosed with SARS‐CoV‐2 infections were admitted to our hospital. A total of 408 patients who received at least one microbiological test were enrolled in this study (Figure 1) and their clinical and laboratory findings, microbiological investigation results, and thoracic computed tomography scans were retrospectively collected.

Patients enrollment and microbiological testing

Furthermore, patients were classified into disease groups based on COVID‐19 severity. 13 Mild cases were defined as patients presenting with mild clinical symptoms without pneumonia manifestation on imaging. Moderate cases were patients presenting with a fever and respiratory symptoms, along with radiological findings of pneumonia. Severe cases met any one of the following criteria: respiratory distress, hypoxia (SpO2 ≤ 93%), or abnormal blood gas analysis (PaO2 < 60 mmHg, PaCO2 > 50 mmHg). Lastly, critical cases met any one of the following criteria: respiratory failure requiring mechanical ventilation or shock accompanied by other organ failure that required ICU care. The patients were then divided into three groups: mild and moderate, severe, and critically ill.

Blood samples and nasopharyngeal swabs were routinely collected from each patient, and lower respiratory samples, including sputum and bronchoalveolar lavage fluid (BAL), were collected when available and clinically indicated. Blood cultures were also obtained when clinically indicated. All samples were sent to the clinical laboratory of the hospital for pathogen detection by molecular assay and/or conventional culture. This study was approved by the Institutional Review Board of Shenzhen Third People's Hospital (number 2020‐100).

Copyright and License information:  ©2021 John Wiley & Sons Ltd
This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.

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