Optimization of Microbiological Laboratory Detection Strategy for Patients in A Designated Hospital Treating Novel Coronavirus Pneumonia in Anhui Province

  1. Wenjiao Chang
  2. Yuru Shi
  3. Yingjie Qi
  4. Jiaxing Liu
  5. Ting Liu
  6. Zhaowu Chen
  7. Wenjing Zhang
  8. Mengmeng Wang
  9. Dongfeng Liu
  10. Ming Yin
  11. Jing Xu
  12. Yun Yang
  13. Xiaowu Zhu
  14. Jing Ge
  15. Shu Zhu
  16. Yong Gao
  17. Xiaoling Ma

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Abstract

Novel coronavirus pneumonia (NCP) is an emerging, highly contagious community acquired pneumonia (CAP) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Highly efficient and accurate microbiological laboratory assay is essential to confirm the SARS-CoV-2 infection, rule out other pathogens that can cause CAP, and monitor secondary infections. Here, we enrolled and provide microbiological analysis for 129 suspected and 52 transferred confirmed NCP patients hospitalized in the First Affiliated Hospital of University of Science and Technology of China (USTC) from Jan 21 to Feb 29, 2020. By analyzing the dual swab samples (sputum and pharyngeal) from 129 suspected patients with realtime RT-PCR, we confirmed 33 SARS-CoV-2 infections, with two co-infection cases with adenovirus or rhinovirus. We also used multiplex PCR to detect 13 common respiratory tract pathogens in 96 non-NCP patients, and found that 30 patients (31.25%) were infected with at least one respiratory tract pathogen that may cause CAP. Further, we performed bacterial and fungal cultures as well as fungal serologic tests and found that there is no secondary bacterial/fungal infections in confirmed NCP patients. Our studies suggest that, during the epidemic of NCP in Anhui province, there was a certain proportion of infection and co-infection of other common pathogens of CAP, and the secondary bacterial and fungal infection is not detectable in NCP patients. In comparison with SARS-CoV-2 detection alone, this optimized strategy combining multiple pathogen detection for identification of NCP and other CAP patients as well as cultures and serologic tests for confirmed patients increases the diagnosis efficiency and facilitates the personalized medication.

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    SciScore for 10.1101/2020.03.21.20039065: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: Written consents were obtained from all of the patients and the study was approved by the Ethics Review Committee of the First Affiliated Hospital of USTC
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.03.21.20039065v1 on medRxiv