Prevalence of Cryptococcal Antigenemia and associated factors among HIV/AIDS patients on second-line antiretroviral therapy at two hospitals in Western Oromia, Ethiopia

Nuguse Geda; Tafese Beyene; Regea Dabsu; Hylemariam Mihiretie Mengist

doi:10.1371/journal.pone.0225691

Peer Review History

Original SubmissionJuly 27, 2019
27 Sep 2019 Decision Letter - Kirsten Nielsen, Editor PONE-D-19-20216 Prevalence of Cryptococcal Antigenemia and Associated Factors Among HIV/AIDS Patients on Second-Line Antiretroviral Therapy at Two Hospitals in Western Oromia, Ethiopia PLOS ONE Dear Mr Mengist, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. REQUIRED: Clarify the CD4 count and the population being studied, as described in the reviewer comments. REQUIRED: Address All reviewer comments individually in the "Response to Reviewers" document included with the resubmission. We would appreciate receiving your revised manuscript by Nov 11 2019 11:59PM. 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The PLOS ONE style templates can be found at http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Additional Editor Comments (if provided): [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 3. 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Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Authorship order is different on the manuscript than in the PLoS One system. Abstract Results: would prefer you to specify the median age (with interquartile range). % married is of no value and is distracting. Would remove that. % living with HIV and/or on ART -consider changing units to years instead of months. This is more intuitive/understandable for readers Introduction: Line 59 -Define MLICs Line 61 -CrAg isn't antibodies, it's antigen. would remove the term anti-cryptococcal antibodies. replace with "antigen", same with line 63 Methods: Line 90 -don't use contractions in formal writing. Same with line 132. Results: Line 162: don't capitalize "second line ART" Line 162 -saying 35% were in one age group is unhelpful. State the median age and interquartile range. Line 168 -change to years Line 170 -is this an error? the baseline CD4 was 163 +/- 182? That doesn't make sense. Line 173 -the prevalence is 7.7%. is this among peoplew ith CD4<100? On line 170 it says mean CD4 was 434. Very confused about the population you're describing. Line 221: Men tend to have more advanced HIV disease (ie. lower CD4 counts) Line 229: It's not clear from your results what the CD4 counts were of your patient population and those who were CrAg+ Line 257: higher than what? In your figure, label your Y axis. Don't use decimal places unless it's useful. And put percentages behind your numbers. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files to be viewed.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0225691.r001
Revision 1
30 Sep 2019 Author Response Response to the reviewer 1. Authorship order is different on the manuscript than in the PLoS One system. Response: We have communicated with the journal office for another paper and confirmed the authorship order in the manuscript is the final acceptable order. The journal has similar rules which we thought will be applicable for this manuscript, too. It was difficult for the corresponding author to put his name last in the editorial manager. 2. Abstract Results: would prefer you to specify the median age (with interquartile range). % married is of no value and is distracting. Would remove that. % living with HIV and/or on ART -consider changing units to years instead of months. Response: The age was described with median and IQR and we removed % marriage. And we changed unit of stay with HIV or ART in years instead of months. 3. Introduction: Line 59 -Define MLICs Line 61 -CrAg isn't antibodies, it's antigen. would remove the term anti-cryptococcal antibodies? replace with "antigen", same with line 63 Response: We defined MLICs (Middle and low income countries) and HICs (High income countries). We removed the term “anti-cryptoccocal antibodies” and changed the “antibody” miswording to “antigen”. 4. Methods: Line 90 -don't use contractions in formal writing. Same with line 132. Response: We fixed the abovementioned issue. 5. Results: Line 162: don't capitalize "second line ART" Line 162 -saying 35% were in one age group is unhelpful. State the median age and interquartile range. Response: We modified the phrase “Second Line ART” into “second line ART” and the median age was used than mean age. 6. Line 168 -change to years. Line 170 -is this an error? the baseline CD4 was 163 +/- 182? That doesn't make sense. Line 173 -the prevalence is 7.7%. is this among people with CD4<100? On line 170 it says mean CD4 was 434. Very confused about the population you're describing. Response: We changed months to years in line 168. Line 170…it was error. Baseline CD4+ T cell count was 163 +/- 82, not 163 +/- 182. In line 173….the prevalence of CrAg test positivity was 7.7% from all study participants. But 50% prevalence was among participants whose current mean CD4+ T cell count <100 cells/µL. plus the phrase saying “….CD4 was 434….” is about the current mean CD4 T cell count. Thus our study population are those with current mean CD4 T cell count of 434, but their baseline (before starting treatment) was 163+/-82. 7. Line 221: Men tend to have more advanced HIV disease (ie. lower CD4 counts). Line 229: It's not clear from your results what the CD4 counts were of your patient population and those who were CrAg+ Response: Line 221…it doesn’t necessarily mean men has advanced disease than women rather men usually have outdoor activities in Ethiopia which exposes them for Cryptococcosis infection which in turn resulted higher prevalence of CrAg test positivity among men. Line 229……We included the proportion of CrAg positive with respect to CD+ T cell count in results section. 8. Line 257: higher than what? Response: Line 260….higher. it is corrected into “….was significantly ‘high’ in the study area”. 9. In your figure, label your Y axis. Don't use decimal places unless it's useful. And put percentages behind your numbers. Response: The figure was modified accordingly. Attachments Attachment Submitted filename: Rebutal letter.docx https://doi.org/10.1371/journal.pone.0225691.r002
12 Nov 2019 Decision Letter - Kirsten Nielsen, Editor Prevalence of Cryptococcal Antigenemia and Associated Factors Among HIV/AIDS Patients on Second-Line Antiretroviral Therapy at Two Hospitals in Western Oromia, Ethiopia PONE-D-19-20216R1 Dear Dr. Mengist, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. With kind regards, Kirsten Nielsen, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0225691.r003
Formally Accepted
22 Nov 2019 Acceptance Letter - Kirsten Nielsen, Editor PONE-D-19-20216R1 Prevalence of Cryptococcal Antigenemia and Associated Factors Among HIV/AIDS Patients on Second-Line Antiretroviral Therapy at Two Hospitals in Western Oromia, Ethiopia Dear Dr. Mengist: I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Kirsten Nielsen Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0225691.r004

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