Viral-bacterial codetection among patients with pneumonia during the COVID-19 pandemic in Jakarta, Indonesia

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1. 

   Version published to 10.1099/acmi.0.000888.v2 on Access Microbiology

   Apr 25, 2025
2. 

   Access Microbiology

   Mar 24, 2025

   Thank you for submitting your manuscript for publication in Access Microbiology. It has been examined by expert reviewers who have concluded that the work is of potential interest to the readership of Access Microbiology. However, based on the comments received, a major revision of this manuscript will be required before a decision can be made on its publication. I will be pleased to consider a revised manuscript along with a document including a point by point response to each of the reviewers comments. Your revised manuscript may be returned to one or more of the original reviewers, along with your itemised response to the reviewers’ comments.

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3. 

   Access Microbiology

   Mar 21, 2025

   Comments to Author

   Interesting paper, just needs some clarity in parts. Unclear in the abstract when you are talking about the bacterial screening if this is single bacterial infections or co-infections. Page 13 Table 1- no column for gender, female Methods don't mention what the statistical test is that was performed for statistical analysis of data. Table 3- Slightly misleading as the titles state viral-bacterial co-detection but some are viral- viral. Could you change the table titles or split out the viral-viral/ viral- bacterial samples. Other tables (table 2)/ in text state viral-bacterial co-detection stated, but a number of these refer to viral-viral co-detection. So perhaps throughout you need to either edit to pathogen co-detection, or state viral-viral/ viral-bacterial. Throughout it is unclear what …

   Comments to Author

   Interesting paper, just needs some clarity in parts. Unclear in the abstract when you are talking about the bacterial screening if this is single bacterial infections or co-infections. Page 13 Table 1- no column for gender, female Methods don't mention what the statistical test is that was performed for statistical analysis of data. Table 3- Slightly misleading as the titles state viral-bacterial co-detection but some are viral- viral. Could you change the table titles or split out the viral-viral/ viral- bacterial samples. Other tables (table 2)/ in text state viral-bacterial co-detection stated, but a number of these refer to viral-viral co-detection. So perhaps throughout you need to either edit to pathogen co-detection, or state viral-viral/ viral-bacterial. Throughout it is unclear what findings are statistically significant. It would be good to clearly state this throughout. Also ensure this is very clear in the abstract and discussion. P16 - Supp table typo S.pneumoniae. E missed off end of pathogen name. Same for H. influenzae.

   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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4. 

   Access Microbiology

   Oct 27, 2024

   Comments to Author

   1.The objectives and significance of this research are not clearly stated in the end of introduction. 2.The authors didn't explain what appropriate statistical tools and methods are used to address the findings. 3.The methods described are not all in enough detail to permit someone to reproduce the experiments, e.g. how are the bacterial loads of Haemophilus influenzae and Streptococcus pneumoniae measured in patients？what is the exclusion criteria of this study? 4. Methods are suggested to be stated including subheadings: 1. Patient population, 2. Virus detection, 3. Bacteria detection, 4. Statistical analysis 5. Molecular detection of S. pneumoniae and H. influenzae was carried out using real-time PCR to detect lyt A and Hi hpd genes respectively. Line 115, 'two RT-PCR bacterial panels' is not …

   Comments to Author

   1.The objectives and significance of this research are not clearly stated in the end of introduction. 2.The authors didn't explain what appropriate statistical tools and methods are used to address the findings. 3.The methods described are not all in enough detail to permit someone to reproduce the experiments, e.g. how are the bacterial loads of Haemophilus influenzae and Streptococcus pneumoniae measured in patients？what is the exclusion criteria of this study? 4. Methods are suggested to be stated including subheadings: 1. Patient population, 2. Virus detection, 3. Bacteria detection, 4. Statistical analysis 5. Molecular detection of S. pneumoniae and H. influenzae was carried out using real-time PCR to detect lyt A and Hi hpd genes respectively. Line 115, 'two RT-PCR bacterial panels' is not correctly described, it should be 'two real-time PCR bacterial panels'. RT-PCR is often short for reverse transcription PCR. 6. Whether there was a significant difference in the virus-bacterial co-detection rates between positive (19%,15/80) and negative (6%,10/165) RT-PCR cases? 7. Line 117-119, Our consensus pan-coronavirus PCR testing detected eight additional positives from the previously negative COVID-19, making a total of 33% (n=80) SARS CoV-2 positive. Therefore, Line 30, in the abstract, of the 245 pneumonia cases, 80 (33%) were confirmed positive for SARS CoV-2. 8. Line 30-31, Among other viruses, paramyxovirus was the predominant virus identified (7%) followed by herpesvirus (6%) and influenza virus (4%). The numbers of the three additional viruses should be presented in the abstract. 9. Line 34-36, Overall, the higher rate of viral-bacterial codetection was observed in the SARS-CoV-2 positive cases than in the negative cases. The co-detection rates of virus-bacteria between the two groups are best listed. 10. What was the study design? Prospective or retrospective? Whether the sample size meets the requirements of the study design? 11.Line 112-113, Overall, 207 were inpatients, 23 absconded, and 5 died. It should be rewrited to '207 patients were hospitalized, 23 absconded and 5 died'. 12. In this study, authors found 10% of viral-bacterial codetection without any significant association with clinical manifestation, patient outcome or severity. This should be presented in the abstracted. 13. What are the limitations of the study and the direction of future efforts?

   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

   Read the original source
5. 

   Version published to 10.1099/acmi.0.000888.v1 on Access Microbiology

   Jul 26, 2024