Microbial infection among SARS-COV-2-infected patients in a COVID-19-dedicated tertiary care hospital of Bangladesh: a cross-sectional study
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Objectives. This study aimed to determine patterns of respiratory, blood-borne and uropathogenic microbial pathogens among SARS-CoV-2-infected patients in a COVID-19-(coronavirus disease 2019) dedicated tertiary care hospital in Dhaka, Bangladesh.
Design. This was a cross-sectional study.
Setting. In a COVID-19-dedicated tertiary care hospital in Dhaka, Bangladesh, conducted from March to June 2021.
Participants. Hospitalized individuals with COVID-19 infection regardless of age or sex.
Primary and secondary outcome measures. The percentage of co-infected COVID-19 patients and the characterization of the micro-organisms responsible for co-infection served as the primary outcome measures. Finding any associations between co-infection and age, co-infection and sex and co-infection and comorbidity was the secondary outcome variable.
Interventions. Not applicable.
Results. Out of 79 patients, 61 % were male, and the mean age was 49.53 years. Co-infection was seen in 7.7 % of patients, out of which 5.1 % of isolates were from urine samples, followed by 2.6 % from blood. Bacteria isolated from urine were Enterococcus (2.6 %), coagulase-negative Staphylococcus (CONS) (1.3 %) and Enterobacter spp. (1.3 %). Pseudomonas spp. was the only organism isolated from blood sample. Mixed growth was found in nasopharyngeal and throat swabs, with the predominant species being Staphylococcus aureus and Streptococcus spp. At the time of data collection, 55.7 % of patients had been given antimicrobials, and 30.4 % of patients had been given a single antimicrobial. HBsAg was positive in 1.3 % of patients and none were anti-hepatitis C or dengue NS1Ag positive.
Conclusion. Microbial infection has been seen to be associated with SARS-CoV-2 infections and is of great value in prescribing antimicrobials and reducing fatal outcomes of hospitalized patients.
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I am pleased to tell you that your article has now been accepted for publication in Access Microbiology.
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Comments to Author
The authors have addressed my points.
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Thank you for submitting your paper to Access Microbiology. It has now been reviewed and I would like you to revise the paper in line with the reviewers' reports and any Editorial Office requirements below. The reviewer reports can be found at the bottom of the email.
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Comments to Author
In this study, Shamsul Islam and colleagues have investigated microbial infection in SARS-COV-2 infected patients from Bangladesh. The cohort data is from 2021 based on which microbial screening has been undertaken. I have following observations with the present version of manuscript Major comments Given the cohorts data are from 2021, what new information does it reveal besides the routine information that have been stated in manuscript? For example, did the authors work further with the bacterial isolates and identified eco-genomic characteristics or genes linked to antimicrobial resistance as an example? Such information would bring in novelty, in addition to the need for having a geographical understanding of infection in cohorts linked to COVID-19. The authors have reported cohort data …
Comments to Author
In this study, Shamsul Islam and colleagues have investigated microbial infection in SARS-COV-2 infected patients from Bangladesh. The cohort data is from 2021 based on which microbial screening has been undertaken. I have following observations with the present version of manuscript Major comments Given the cohorts data are from 2021, what new information does it reveal besides the routine information that have been stated in manuscript? For example, did the authors work further with the bacterial isolates and identified eco-genomic characteristics or genes linked to antimicrobial resistance as an example? Such information would bring in novelty, in addition to the need for having a geographical understanding of infection in cohorts linked to COVID-19. The authors have reported cohort data representing 79 individuals. What is the geographical coverage of the cohorts ? What was their food habit when the antibiotics dosage was ongoing? What was the infection rate between males and females as well as age less or greater than 50? Such information needs to be discussed thoroughly with published studies from other geographic locations. Minor comments The subsection of data source/management needs to be written down under separate subheadings. In particular, the work on cultured based microbiology has to be a separate subsection. Cohort data in terms of height and weight seems missing.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Comments to Author
The methodology and design section is quite detailed and well-organized, covering all the essential components such as study design, setting, participants, variables, diagnostic criteria, data sources/measurement, statistical analysis, and patient and public involvement. However, I have some suggestions and comments to improve the clarity and rigor of the methodology: 1. Study Design and Methodology: * The choice of a cross-sectional study design is appropriate for the research objective. However, it would be helpful to explain why this design was chosen over other possible designs. 2. Setting: * The setting is well-described, but it would be useful to include information about the capacity and facilities of the hospital, as this can impact the study results. 3. Participants: * The inclusion and …
Comments to Author
The methodology and design section is quite detailed and well-organized, covering all the essential components such as study design, setting, participants, variables, diagnostic criteria, data sources/measurement, statistical analysis, and patient and public involvement. However, I have some suggestions and comments to improve the clarity and rigor of the methodology: 1. Study Design and Methodology: * The choice of a cross-sectional study design is appropriate for the research objective. However, it would be helpful to explain why this design was chosen over other possible designs. 2. Setting: * The setting is well-described, but it would be useful to include information about the capacity and facilities of the hospital, as this can impact the study results. 3. Participants: * The inclusion and exclusion criteria are clearly stated. However, the reason for excluding critically ill and mentally unstable patients should be explained, as this could introduce selection bias. 4. Variables: * The variables are listed, but it would be helpful to provide more detail on how each variable was measured or defined. 5. Diagnostic Criteria: * The diagnostic criteria for UTI and BSI are well-explained, but it would be useful to include the diagnostic criteria for COVID-19 as well. 6. Data Sources/Measurement: * The data collection and sample processing procedures are well-detailed. However, it would be helpful to include information about the quality control measures taken to ensure the accuracy and reliability of the results. 7. Statistical Analysis: * The statistical analysis methods are appropriate, but it would be useful to include information about how missing data was handled. 8. Patient and Public Involvement: * The statement about patient and public involvement is a good addition, but it would be helpful to include more details about how the study findings will be disseminated to the public. Any other relevant comments: * The sample size is relatively small, which may limit the generalizability of the study findings. It would be useful to discuss the implications of the sample size in the discussion section. * The study uses non-probability (convenience) sampling, which may introduce selection bias. The potential impact of this bias should be addressed in the discussion section. * The exclusion of critically ill and mentally unstable patients may also introduce selection bias. The reason for this exclusion should be explained, and the potential impact on the study findings should be discussed. Results and Conclusions section: o How significant are the findings described in the article, and do they represent an advance in knowledge and understanding? * The findings of this study add to the growing body of knowledge regarding co-infections in COVID-19 patients, specifically within a tertiary care hospital in Dhaka, Bangladesh. By analyzing data from 79 patients, the authors were able to determine the prevalence of co-infections in this specific population. The identification of specific bacteria and their prevalence adds valuable data to the existing literature. While these findings are significant for the specific population studied, it may be limited in its generalizability to other populations or geographical areas. o Have the results been interpreted properly? * The results appear to have been interpreted properly and in line with the data presented. However, it is important to note that the study is limited by its sample size and the fact that certain tests for specific pathogens could not be conducted due to a lack of resources. These limitations should be considered when interpreting the results. o Are the conclusions based on sound data, with reasonable reference to the published literature? * The conclusions are based on the data presented in the study and are supported by references to the published literature. The authors acknowledge the limitations of their study and provide recommendations for future research, which adds credibility to their conclusions. However, it is important to note that the conclusions may be limited by the specific population studied and may not be generalizable to other populations or geographical areas. Overall, the study adds valuable data to the existing literature on co-infections in COVID-19 patients and provides a foundation for future research in this area. * Specific Comments for the result section: * P-value interpretation: In line 191, you mention the p-value but do not provide an interpretation of what it means in the context of your study. It would be helpful to explain the significance of the p-value in relation to your findings. Some specific comments for the discussion section: * In lines 204-208, you mentioned that urine analysis could not be done for 1 patient due to insufficient quantity. It would be helpful to mention how this missing data was handled in the analysis. * In lines 215-224, you discussed the prevalence of bacterial co-infection in COVID-19 patients based on meta-analyses and literature surveys. It would be helpful to provide some context on how these findings relate to your study results. * In lines 237-260, you discussed the findings of urine microscopy and culture. It would be helpful to mention any limitations or challenges faced during this part of the study. * In lines 261-271, you discussed the nasopharyngeal and throat microbiota findings. It would be helpful to provide some context on how these findings relate to your study results. * In lines 273-287, you discussed the blood borne pathogen findings. It would be helpful to mention any limitations or challenges faced during this part of the study. * In lines 288-307, you discussed viral co-infection findings. It would be helpful to provide some context on how these findings relate to your study results. * In lines 312-327, you provided a conclusion and recommendations. It would be helpful to mention any limitations or challenges faced during the study and how they may have affected the results. * Overall, the discussion section is well-written and provides a comprehensive overview of the study results. With a few minor additions, it will be even more informative and helpful for the reader.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
No: The manuscript provides valuable insights into the prevalence of coinfections in COVID-19 patients and the types of pathogens involved. However, there are several concerns that need to be addressed to strengthen the validity and generalizability of the findings. Small Sample Size: The study is based on a small sample of patients, which may limit the ability to detect significant differences between groups and may not be representative of the larger population of COVID-19 patients. Lack of Certain Tests: The study relies on hospital records for data collection, and it is unclear whether all patients were tested for all relevant pathogens. The lack of certain tests for specific pathogens may affect the accuracy of the findings. Reliance on Hospital Records: The study relies on hospital records for data collection, which may not provide a complete and accurate picture of the patients' clinical status and coinfections. Comparison with Existing Literature: The manuscript could be strengthened by a more thorough comparison with the existing literature. This would help to contextualize the findings and highlight the contribution of the study to the field. Implications for Clinical Practice and Future Research: The conclusions could be further strengthened by a more detailed discussion of the implications of the findings for clinical practice and future research. This would help to demonstrate the relevance and significance of the study. Overall, while the manuscript has the potential to make a valuable contribution to the field, further work is needed to address these concerns and enhance the rigor and reliability of the study.
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