Prevalence of bacterial coinfection and patterns of antibiotics prescribing in patients with COVID-19: A systematic review and meta-analysis

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1. Version published to 10.1371/journal.pone.0272375

   Aug 1, 2022
2. 

   ScreenIT

   Mar 7, 2022

   SciScore for 10.1101/2022.03.02.22271779: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	Data Extraction and quality assessment: Data was extracted into a standardised collection form that was created using Microsoft Excel 2016, by reviewers FA and ON. Data collected for information regarding the demographics of the studies included the following variables: first author; publication year; country of publication; study design (Retrospective, prospective, RCTs etc…); is the study multicentre; study setting (Community, hospital, mixed etc…); if the study was peer-reviewed; number of positive COVID-19 patients; proportion of male population; and the average age.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table …

   SciScore for 10.1101/2022.03.02.22271779: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	Data Extraction and quality assessment: Data was extracted into a standardised collection form that was created using Microsoft Excel 2016, by reviewers FA and ON. Data collected for information regarding the demographics of the studies included the following variables: first author; publication year; country of publication; study design (Retrospective, prospective, RCTs etc…); is the study multicentre; study setting (Community, hospital, mixed etc…); if the study was peer-reviewed; number of positive COVID-19 patients; proportion of male population; and the average age.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   The databases searched included OVID MEDLINE, OVID EMBASE, Cochrane library and MedRxiv, with articles published between December 2019 and 29th June 2021.	EMBASE suggested: (EMBASE, RRID:SCR_001650) Cochrane library suggested: (Cochrane Library, RRID:SCR_013000)
   Data Extraction and quality assessment: Data was extracted into a standardised collection form that was created using Microsoft Excel 2016, by reviewers FA and ON. Data collected for information regarding the demographics of the studies included the following variables: first author; publication year; country of publication; study design (Retrospective, prospective, RCTs etc…); is the study multicentre; study setting (Community, hospital, mixed etc…); if the study was peer-reviewed; number of positive COVID-19 patients; proportion of male population; and the average age.	Microsoft Excel suggested: (Microsoft Excel, RRID:SCR_016137)
   All analyses were carried out using STATA/BE 17.0 for Windows (64-bit x 86-64) using the Metaprop command package.	Metaprop suggested: None

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   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).

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   Strengths and Limitations: We believe the key strengths of this review included a comprehensive search strategy spanning several databases, including both pre-prints and peer-reviewed studies, resulting in 22 studies being included, representing over 76,000 patients. However, we are aware that this review was not without limitations. During the screening process, a significant number of studies have been excluded as they did not meet the inclusion criteria. The majority of the excluded studies included non-lab confirmed COVID-19 patients, therefore, bacterial coinfection and antibiotic use may be under- or over-reported. Disproportionate representation from North America and failure to include studies from regions other than Europe and Asia can also limit the generalizability of the results to other regions impacted by COVID-19. Additionally, the majority of studies included were conducted within the first 6 month of pandemic. Consequently, data included might not be up to date, which again, can compromise the generalizability of the results. Notably, the emergence of new variants, updated treatment regimens and variations in measures for SARS-CoV-2 testing, might impact the prevalence of bacterial coinfection and antibiotic use[77]. In addition, the majority of studies included in the meta-analyses were retrospective studies with their inherently associated bias and limitations. Alongside this, determining the appropriateness and justifiable need of antibiotic therapy, which...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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

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

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   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.

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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2022.03.02.22271779 on medRxiv

   Mar 4, 2022