PONE-D-23-38915Protocol for the systematic review of the Pneumocystis jirovecii-associated pneumonia in non-HIV immunocompromised patientsPLOS ONE

Dear Dr. Orozco Ugarriza,

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We look forward to receiving your revised manuscript.

Kind regards,

Benjamin M. Liu, MBBS, PhD, D(ABMM), MB(ASCP)

Academic Editor

PLOS ONE

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Additional Editor Comments:

Editor's comments

1. line 91-103: the authors failed to provide updated introduction on the novel molecular testing for PCP. Please cite the following reference and discuss the progress/advantages (e.g., increased sensitivity and fast turnaournd time, sample to answer detection) and challenges (difficulty in differentiating colocalization vs true infection) of PCR for PJP:

Liu B, Totten M, Nematollahi S, Datta K, Memon W, Marimuthu S, Wolf LA, Carroll KC, Zhang SX. Development and Evaluation of a Fully Automated Molecular Assay Targeting the Mitochondrial Small Subunit rRNA Gene for the Detection of Pneumocystis jirovecii in Bronchoalveolar Lavage Fluid Specimens. J Mol Diagn. 2020 Dec;22(12):1482-1493. doi: 10.1016/j.jmoldx.2020.10.003. Epub 2020 Oct 15. Erratum in: J Mol Diagn. 2021 Apr;23(4):506. PMID: 33069878.

2. The authors have written six paragraphs for Introduction. However, Discussion is just one paragraph, which is unacceptable. The authors are encouraged to discuss different aspects of PCP.

Comments from PLOS Editorial Office:

We noted that the decision includes recommendations that you cite specific previously published works. As always, we recommend that you please review and evaluate the requested works to determine whether they are relevant and should be cited. It is not a requirement to cite these works. We appreciate your attention to this request.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Does the manuscript provide a valid rationale for the proposed study, with clearly identified and justified research questions?

The research question outlined is expected to address a valid academic problem or topic and contribute to the base of knowledge in the field.

Reviewer #1: Yes

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2. Is the protocol technically sound and planned in a manner that will lead to a meaningful outcome and allow testing the stated hypotheses?

The manuscript should describe the methods in sufficient detail to prevent undisclosed flexibility in the experimental procedure or analysis pipeline, including sufficient outcome-neutral conditions (e.g. necessary controls, absence of floor or ceiling effects) to test the proposed hypotheses and a statistical power analysis where applicable. As there may be aspects of the methodology and analysis which can only be refined once the work is undertaken, authors should outline potential assumptions and explicitly describe what aspects of the proposed analyses, if any, are exploratory.

Reviewer #1: Yes

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3. Is the methodology feasible and described in sufficient detail to allow the work to be replicable?

Reviewer #1: Yes

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4. Have the authors described where all data underlying the findings will be made available when the study is complete?

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Reviewer #1: Yes

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Reviewer #1: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above and, if applicable, provide comments about issues authors must address before this protocol can be accepted for publication. You may also include additional comments for the author, including concerns about research or publication ethics.

You may also provide optional suggestions and comments to authors that they might find helpful in planning their study.

(Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: A systematic review of the epidemiology, pathogen biology, pathogenesis, diagnosis and treatment, prevention, and other information of non-HIV PJP patients is of great practical significance.

This research protocol has been standardized, registered, and obtained a CRD number. We look forward to future research results.

Although this systematic review will be using published data, please confirm with the ethics committee of your faculty or university whether ethical approval is required, including the researcher's information, for instance. (Line 234)

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Reviewer #1: No

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Protocol for the systematic review of the Pneumocystis jirovecii-associated pneumonia in non-HIV immunocompromised patients

PONE-D-23-38915R1

Dear Dr. Ugarriza,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Benjamin M. Liu, MBBS, PhD, D(ABMM), MB(ASCP)

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

When performing proofreading, please change "Li" to "Liu" in line 104

Reviewers' comments: