Prevalence of enteric pathogens, intestinal parasites and resistance profile of bacterial isolates among HIV infected and non-infected diarrheic patients in Dessie Town, Northeast Ethiopia

Assefa Belay; Melaku Ashagrie; Berhanu Seyoum; Mekuanent Alemu; Aster Tsegaye

doi:10.1371/journal.pone.0243479

Peer Review History

Original SubmissionSeptember 1, 2020
25 Sep 2020 Decision Letter - Iddya Karunasagar, Editor PONE-D-20-27382 Prevalence of EntericPathogens,Intestinal Parasites and High Resistance rate of Bacterial Isolates to Commonly Prescribed Antibiotics in HIVInfected and Non-Infected Diarrheic Patients from selected Health Facilities in Dessie town,Northeast Ethiopia PLOS ONE Dear Dr. Tsegaye, 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. ============================== A number of aspects of manuscript need improvement particularly outlining the objectives of statistical analysis and discussing the results rather than just comparing data to that reported by others. ============================== Please submit your revised manuscript by Nov 02 2020 11:59PM. 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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Please include additional information regarding the survey or questionnaire used in the study and ensure that you have provided sufficient details that others could replicate the analyses. For instance, if you developed a questionnaire as part of this study and it is not under a copyright more restrictive than CC-BY, please include a copy, in both the original language and English, as Supporting Information. 3.Thank you for stating the following in the Funding Section of your manuscript: [No external funds were obtained; only institutional support from Dessie Regional Health Research Laboratory.] We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: [The author(s) received no specific funding for this work.] Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 4. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. 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Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. Please see http://www.bmj.com/content/340/bmj.c181.long for guidelines on how to de-identify and prepare clinical data for publication. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. We will update your Data Availability statement on your behalf to reflect the information you provide. 6.Please upload a copy of Supporting Information S1 Questionnaire. which you refer to in your text on page 29. 7.We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: Belete MA. Bacterial Profile and ESBL Screening of Urinary Tract Infection Among Asymptomatic and Symptomatic Pregnant Women Attending Antenatal Care of Northeastern Ethiopia Region. Infect Drug Resist. 2020;13:2579-2592 https://doi.org/10.2147/IDR.S258379 In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed." Additional Editor Comments (if provided): The reviewer has pointed out number of aspects of the manuscript that need improvement. Please address all comments point by point. [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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: No ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. 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: This is a well written manuscript that provides some useful data about pathogen prevalences and antimicrobial resistance in one area of Ethiopia. The methods seem good and well reported (the random selection of facilities is particularly commendable, as is the detailed description lab methods employed). Congratulations to the authors! I do have a few comments: Major comments: 1) The authors need to discuss the recommended care of salmonella and shigella (both Ethiopian guidelines and WHO guidelines). For example, current WHO Shigella recommendation are to treat with Cipro. Your study suggest that guideline would work well in this region, which is reassuring. However, you then suggest Cipro as an “alternative” treatment, when in fact perhaps it should be the first line (as per guidelines)? I would suggest including the current treatment recommendation in the introduction and discussing how your results should inform these recommendation in the discussion. 2) I’m not sure that your conclusion that “the prevalence of these pathogens are high” (paraphrased) is valid. You only recruited children with diarrhea, so you were always going to see a high prevalence of enterics pathogens, and your discuss of other studies suggest that your prevalence is the same or lower than other studies have observed. 3) The discussion focus heavily on comparing your results with other work. While this is somewhat necessary for a discussion, many of the paragraphs do not appear to have an overarching point to the comparison. The discussion would be greatly improved by the authors make it clear to the reader what they should take away from each comparison. For example, in the second paragraph you compare prevalences of Shigella to other studies, what is your conclusion from this comparison? 4) In the statistical methods it would be better to identify which methods are answering which questions, i.e. you used descriptive methods to estimate the prevalences, and then model to associate exposures with the presence of pathogens. This would make it crystal clear to the reader what you are going to do. 5) You do not mention that you’re going to do a corelates of pathogen infection analysis in the introduction, you only mention looking at the prevalence. I was surprised by your correlates of infection analysis when I reached it in the results. Making this a clear goal of the paper in the introduction would be helpful. Minor comments 1) There are some minor grammar errors, although the paper is generally well written: Background, first paragraph, third line: “safe water is limited” Background, fourth paragraph, seventh line: “5 times more bacteraemia” Methods, first para, second line, “and two randomly” Conclusion, fourth line, “On the other hand” 2) In the methods the sentence beginning “ A total of 354 HIV infected…” should be moved to the results. 3) In the antimicrobial susceptibility testing paragraph in the methods, you define the abbreviation CLSI two times. ****** 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.] 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 PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0243479.r001
Revision 1
2 Nov 2020 Author Response Manuscript ID number: PONE-D-20-27382 Title of paper: Prevalence of Enteric Pathogens, Intestinal Parasites and High Resistance rate of Bacterial Isolates to Commonly Prescribed Antibiotics in HIV Infected and Non-Infected Diarrheic Patients from selected Health Facilities in Dessie town, Northeast Ethiopia General We thank all the reviewers for critically reviewing our manuscript which helps us to give better clarity to the paper and make it scientifically strong. We thank the PLOS ONE academic editors for their valuable comments and for giving us an opportunity to revise the manuscript. All the questions raised by the Reviewers and Editor have been addressed; and the manuscript is modified accordingly. Moreover, the requested Editorial corrections are addressed in both the revised manuscript and the response letter. Changes are shown with track changes in the file labeled ‘Revised Manuscript with Track Changes’. The point by point response is given below. Editor Comments: 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. Author’s Response: Thanks for the significant editorial comment. The revised manuscript is now updated and meets PLOS ONE's style requirements, including those for file naming. 2. Please include additional information regarding the survey or questionnaire used in the study and ensure that you have provided sufficient details that others could replicate the analyses. For instance, if you developed a questionnaire as part of this study and it is not under a copyright more restrictive than CC-BY, please include a copy, in both the original language and English, as Supporting Information. Author’s Response: Thank you for the comment. Copy of the questionnaire in both the original language and English is attached as Supporting Information. 3. We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: [The author(s) received no specific funding for this work.] Author’s Response: Thank you and corrections are made as per the comment; the Funding Statement is amended and written as: “The authors received no specific funding for this work.” Moreover, the amended statement is included within the cover letter. 4. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. Author’s Response: Thank you for the valuable comment. Based up on the comment, pre-existing ORCID iD of the corresponding author is authenticated in the PLOS ONE Editorial Manager. 5. We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. Author’s Response: Thanks for the comment. Since the study included HIV positive patients, ethical restrictions do not allow us to share their data. However, the manuscript contains all the necessary information. 6. Please upload a copy of Supporting Information S1 Questionnaire. which you refer to in your text on page 29. Author’s Response: Thanks, Supporting Information S1 Questionnaire is uploaded with the revised manuscript. 7. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed. Author’s Response: Thanks, comment well taken; we have tried to rephrase overlapping and duplicated texts as per the comments. Reviewer #1 comments 1. The authors need to discuss the recommended care of salmonella and shigella (both Ethiopian guidelines and WHO guidelines). For example, current WHO Shigella recommendation are to treat with Cipro. Your study suggest that guideline would work well in this region, which is reassuring. However, you then suggest Cipro as an “alternative” treatment, when in fact perhaps it should be the first line (as per guidelines)? I would suggest including the current treatment recommendation in the introduction and discussing how your results should inform these recommendations in the discussion. Author’s Response: Thanks for the invaluable comment. We addressed this in both sections [Ref 21-23] 2. I’m not sure that your conclusion that “the prevalence of these pathogens are high” (paraphrased) is valid. You only recruited children with diarrhea, so you were always going to see a high prevalence of enterics pathogens, and your discuss of other studies suggest that your prevalence is the same or lower than other studies have observed. Author’s Response: Thank you for the substantial comment. We have revised as per the comment. 3. The discussion focuses heavily on comparing your results with other work. While this is somewhat necessary for a discussion, many of the paragraphs do not appear to have an overarching point to the comparison. The discussion would be greatly improved by the authors make it clear to the reader what they should take away from each comparison. For example, in the second paragraph you compare prevalences of Shigella to other studies, what is your conclusion from this comparison? Author’s Response: Comment well taken and after each comparison a concluding sentence is added, we thank you very much for this. 4. In the statistical methods it would be better to identify which methods are answering which questions, i.e. you used descriptive methods to estimate the prevalences, and then model to associate exposures with the presence of pathogens. This would make it crystal clear to the reader what you are going to do. Author’s Response: Thank you for the valuable comment. The statistical methods part is amended accordingly. 5. You do not mention that you’re going to do a corelates of pathogen infection analysis in the introduction, you only mention looking at the prevalence. I was surprised by your correlates of infection analysis when I reached it in the results. Making this a clear goal of the paper in the introduction would be helpful. Author’s Response: Thanks, and we have added a clear statement stating about the goal of the paper to do corelates of pathogen infection analysis and assess possible associated risk factors at the end of the introduction part of the revised manuscript. 6. There are some minor grammar errors, although the paper is generally well written: Background, first paragraph, third line: “safe water is limited” Background, fourth paragraph, seventh line: “5 times more bacteraemia” Methods, first para, second line, “and two randomly” Conclusion, fourth line, “On the other hand” Author’s Response: Comments well taken and the manuscript corrected accordingly, thanks. 7. In the methods the sentence beginning “ A total of 354 HIV infected…” should be moved to the results. Author’s Response: Thanks; we really appreciate the comment which helped us to notice a gap. Since the result section has the similar information, we rather felt the data collection section lacks about how the data was collected. Hence, we revised the sentence and included it under this section to make the reader aware from the beginning that data was collected from the study participants conveniently. 8. In the antimicrobial susceptibility testing paragraph in the methods, you define the abbreviation CLSI two times. Author’s Response: Comment addressed in the method section, thanks. Finally we thank you for your critical review of the paper. Sincerely, Aster Tsegaye, PhD Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0243479.r002
23 Nov 2020 Decision Letter - Iddya Karunasagar, Editor Prevalence of Enteric Pathogens, Intestinal Parasites and Resistance Profile of Bacterial Isolates among HIV Infected and Non-Infected Diarrheic Patients in Dessie Town, Northeast Ethiopia PONE-D-20-27382R1 Dear Dr. Tsegaye, 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. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. 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 help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- 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. Kind regards, Iddya Karunasagar Academic Editor PLOS ONE Additional Editor Comments (optional): All reviewer comments addressed satisfactorily Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed ******** 2. 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: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ****** 6. 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: Thank you for the change you've made. I have no further comments, good luck with you continued work. ****** 7. 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 https://doi.org/10.1371/journal.pone.0243479.r003
Formally Accepted
4 Dec 2020 Acceptance Letter - Iddya Karunasagar, Editor PONE-D-20-27382R1 Prevalence of Enteric Pathogens, Intestinal Parasites and Resistance Profile of Bacterial Isolates among HIV Infected and Non-Infected Diarrheic Patients in Dessie Town, Northeast Ethiopia Dear Dr. Tsegaye: I'm 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 let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Iddya Karunasagar Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0243479.r004

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