Incidence and Characteristics of Co-infection and Secondary Infection in Patients with COVID-19

  1. Yingyi Guo
  2. Jiuxin Qu
  3. Lingling Cheng
  4. Xiaohe Li
  5. Ningjing Liu
  6. Tungngai Li
  7. Ying Jiang
  8. Qiao Wan
  9. Chuyue Zhuo
  10. Shunian Xiao
  11. Baomo Liu
  12. Yan Chen
  13. lin Fu
  14. Zhixu Chen
  15. Mingcong Ma
  16. Chao zhuo
  17. Nanshan Zhong

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Abstract

Objective

The etiology and epidemiology of co-infection and secondary infection in COVID-19 patients remain unknown. The study aims to investigate the occurrence and characteristics of co-infection and secondary infection in COVID-19 patients, mainly focusing on Streptococcus pneumoniae co-infections.

Methods

This study was a prospective, observational cohort study of the inpatients diagnosed with COVID-19 in two designated hospitals in south China enrolled between Jan 11 and Feb 22, 2020. The urine specimen was collected on admission and applied for pneumococcal urinary antigen tests (PUATs). Demographic, clinical and microbiological data of patients were recorded simultaneously.

Result

A total of 146 patients with a confirm diagnosis of COVID-19 at the median age of 50.0 years (IQR 36.0-61.0) were enrolled, in which, 16 (11.0%) were classified as severe cases and 130 (89.0%) as non-severe cases. Of the enrolled patients, only 3 (2.1%) were considered to present the co-infection, in which 1 was co-infected with S.pneumoniae, 1 with B. Ovatus infection and the other one with Influenza A virus infection. Secondary infection occurred in 16 patients, with S. maltophilia as the most commonly isolated pathogen (43.8%), followed by P. aeruginosa (25.0%), E. aerogenes (25.0%), C. parapsilosis (25.0%) and A. fumigates (18.8%).

Conclusion

Patients with confirmed COVID-19 were rarely co-infected with Streptococcus pneumoniae or other pathogens, indicating that the application of antibiotics against CAP on admission may not be necessary in the treatment of COVID-19 cases.

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  1. ScreenIT

    SciScore for 10.1101/2021.01.06.425542: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: After obtaining the informed consents of all enrolled patients, urine samples were collected on admission to accomplish PUATs.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    12] Secondary infections are patients with positive culture of new pathogens from blood, sputum, balf and urine samples 48 hours after admission.[4] Bacteremia was determined in patients with positive blood cultures.[13] Statistical analysis: All statistical analysis was completed using SPSS v.25.0.
    SPSS
    suggested: (SPSS, RRID:SCR_002865)

    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: We detected the following sentences addressing limitations in the study:
    Last but not least, PUAT could be performed on a bench under proper precautions and without biological safety cabinets since it meets the criteria of POC (Point of care or near-POC), making the screening process of S. pneumoniae co-infection much more convenient.[10] Limitations existed also in our study. First, the empirical use of broad-spectrum antibiotics at the time of admission might produce the difficulty in detection of sensitive bacterial strains and induce the false negative results. Nevertheless, the effects of antibiotics could be neglected in this study since only 20.7% patients with negative etiology test had used antimicrobial drugs, indicating a restrained use of broad-spectrum antibiotics. Also, the low PCT levels in most patients suggest the negative results in our study are credible. Second, since this study was conducted in south China, the generalizability may be limited. Further study should be condcuted in more regions. Third, the sample size was too small to do more statistical analysis such as multivariate analysis to discover more eloquent difference among patients with or without co-infection and secondary infection. Further studies with more patients are required.

    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 10.1101/2021.01.06.425542v1 on bioRxiv