Phenotypic identification of Metallo-ß- lactamase resistance Gram negative bacteria from a clinical specimen in Sidama, Ethiopia

Tsegaye Alemayehu; Wondwesson Abera; Musa Mohammed Ali; Bethelihem Jimma; Henok Ayalew; Limenih Habte; Frezer Teka; Demissie Asegu

doi:10.1371/journal.pone.0313431

Peer Review History

Original SubmissionMarch 2, 2024
5 Jun 2024 Decision Letter - Mihret Tilahun, Editor PONE-D-24-02706Phenotypic Identification of Metallo-ß- lactamase resistance Gram Negative bacteria from a clinical specimen in Sidama, EthiopiaPLOS ONE Dear Dr. Alemeyhu, 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. Please submit your revised manuscript by Jul 19 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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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. During our evaluation of the documents provided, we noted that your ethics approval letter did not cover the entire date range for participant recruitment. Before we can proceed further with the submission, please provide the ethics approval extension document for the study. If the document is in another language, please also provide an English translation. Please note that if this document is not included when your manuscript is resubmitted, it may be rejected 3. Ethics statement appears in the Methods section of the manuscript AND at the end of the manuscript: Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please delete it from any other section. 4. Please amend the manuscript submission data (via Edit Submission) to include author Henok Ayalew. 5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. Additional Editor Comments: To the author please revise your paper based on the the reviwer comments and the language needs revision please attach authore response point by point and the clear and highlighted revised manuscript [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 Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 Reviewer #2: Yes ****** 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 Reviewer #2: 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: The manuscript titled “Phenotypic Identification of Metallo-ß- lactamase resistance Gram Negative bacteria from a clinical specimen in Sidama, Ethiopia” is important in that the authors have highlighted the detection of Carbapenemase and MBL producers by phenotypes of Gram-negative bacteria in Sidama, Ethiopia. Undoubtedly the study has a profound impact as the WHO (2017) highlighted drug-resistant GNB as a priority pathogen. It can be understood that there is no laboratory molecular setup in developing countries to perform confirmatory tests. As well as low-budget research it is difficult to do molecular tests. However, the study has several deficits, and gaps without addressing these concerns the manuscript is not recommended for publication. The authors have shown only Carbapenem resistance without testing tigecycline and polymyxin-b how XDR and PDR strain detection which is unclear in the methods section. It is important to learn whether these stains have colistin or other last-resort antibacterial agents’ resistance. There are several recent papers the authors have missed, there is no comparison or discussion between these papers and the author’s findings. The discussion should be improved and the conclusion should be revised. It makes no sense merely comparing percentage occurrence of one trait or phenotype with other studies. The methods used to detect these traits may be different for the previous studies. Just comparing if the percent occurrence in the present study was similar to, or greater or smaller than the previous study does not suggest anything in the current frame of discussion. The authors need to elaborate more on the results obtained in the present study and draw inferences from the same. Research results should be highlighted as the major outcome and recommendation is required. Reviewer #2: In Page1: City and country of each author should be added to the Authors’ affiliation. Abstract: • Page 1: Method section needs more explanation about the practical work. • Page 2, lines 40-42: The sentence “The rates of multi, extensive and pan-drug resistance bacteria accounted for 83.7%, 50.3%, and 17.0%, respectively” needs more explanation. What do these numbers mean? Introduction • Page 3, Line 67: What does the abbreviation “ESBLs” mean? • Page 3, Line 89: Correct “20.9 o C”. Materials and Methods • Page 4, line 101: delete “&”. • Page 4, line 110: delete “Study Methodology” • Page 4, line 125: correct “37 C0” • Page 5, line 142: correct the sentence “Twelve different antibacterial will be performed” to be “Twelve different antibacterial agents were used”. • Page 5, line 142: Write the full name of “mCIM” and similar abbreviations in other pages. • Page 6, lines 186, 187: the sentence “Gram-negative bacilli that produced serine carbapenemases were those that were carbapenemases positive but Metallo carbapenemases negative” is not necessary. • Page 6, line 195: add the IRB number. Results: • Some typing errors need correction in the whole results section, specifically spaces between numbers. • Page 7, line 225: what do you mean by this sentence “from this most of them 226 used more than two types of external devices 62 (40.5%)”? • Page 8: abbreviations of the antibiotics used should be added to the Table 1 capture. • Page 10, line 259: correct the word “statical” to be “statistical”. Discussion: • Please remove some “comma symbol where is not necessary. • Please revise the text without “Italic” typing other than the name of bacteria. • Write the full name for the abbreviations. • Some typing errors should be revised. Conclusion: • Page 13, line 323: correct the word “Impenem” to “imipenem” ****** 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 Reviewer #2: 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. Attachments Attachment Submitted filename: Decision PONE-D-24-02706.docx https://doi.org/10.1371/journal.pone.0313431.r001
Revision 1
21 Jul 2024 Author Response Point by point response General Response Dear Editor and reviewers, thank you very much for your expertise and time to review and edit our manuscript. As per your recommendation we modify and include the data set as supporting file. Here we tried to make a modification based on your comments. Even if, the reviewer 1 comments are not specific and difficult to address as per your comments we tried to address a general response. For reviewer 2 since his comment is specific, we tried to address point by point and shaded on the manuscript with yellow color for both modifications. Reviewer 1: Comment: The manuscript titled “Phenotypic Identification of Metallo-ß- lactamase resistance Gram Negative bacteria from a clinical specimen in Sidama, Ethiopia” is important in that the authors have highlighted the detection of Carbapenemase and MBL producers by phenotypes of Gram-negative bacteria in Sidama, Ethiopia. Undoubtedly the study has a profound impact as the WHO (2017) highlighted drug-resistant GNB as a priority pathogen. Response: Thank for recognizing our work Comment: It can be understood that there is no laboratory molecular setup in developing countries to perform confirmatory tests. As well as low-budget research it is difficult to do molecular tests. However, the study has several deficits, and gaps without addressing these concerns the manuscript is not recommended for publication. The authors have shown only Carbapenem resistance without testing tigecycline and polymyxin-b how EDR and PDR strain detection which is unclear in the methods section. It is important to learn whether these stains have colistin or other last-resort antibacterial agents’ resistance. Response: We write this idea in the limitation but the CLSI recommend as to check the presence of Carbapenem resistance phenotypically with carbapenem class of antibiotics. At this time, we couldn’t improve as per your comment. I hope you understand the shortage of antibiotics in the local market. Comment: There are several recent papers the authors have missed, there is no comparison or discussion between these papers and the author’s findings. The discussion should be improved and the conclusion should be revised. It makes no sense merely comparing percentage occurrence of one trait or phenotype with other studies. The methods used to detect these traits may be different for the previous studies. Just comparing if the percent occurrence in the present study was similar to, or greater or smaller than the previous study does not suggest anything in the current frame of discussion. The authors need to elaborate more on the results obtained in the present study and draw inferences from the same. Response: We tried to modify the discussion as per your comment and add a justification. Comment: Research results should be highlighted as the major outcome and recommendation is required. Response: We tried to modify the conclusion and recommendation. Reviewer #2: Comment: In Page 1: City and country of each author should be added to the Authors’ affiliation. Response: modified as per your comment Comment: Abstract: • Page 1: Method section needs more explanation about the practical work. Response: modified • Page 2, lines 40-42: The sentence “The rates of multi, extensive and pan-drug resistance bacteria accounted for 83.7%, 50.3%, and 17.0%, respectively” needs more explanation. What do these numbers mean? Response: modified Comments: Introduction • Page 3, Line 67: What does the abbreviation “ESBLs” mean? Response: modified • Page 3, Line 89: Correct “20.9 o C”. Response: modified Comments: Materials and Methods • Page 4, line 101: delete “”. Response: modified • Page 4, line 110: delete “Study Methodology” Response: Accepted • Page 4, line 125: correct “37 C0” Response: modified • Page 5, line 142: correct the sentence “Twelve different antibacterial will be performed” to be “Twelve different antibacterial agents were used” Response: modified .• Page 5, line 142: Write the full name of “mCIM” and similar abbreviations in other pages. Response: modified • Page 6, lines 186, 187: the sentence “Gram-negative bacilli that produced serine carbapenemase were those that were carbapenemase positive but Metallo carbapenemase negative” is not necessary. Response: modified • Page 6, line 195: add the IRB number. Response: modified Comments Results: • Some typing errors need correction in the whole results section, specifically spaces between numbers. Response: modified • Page 7, line 225: what do you mean by this sentence “from this most of them 226 used more than two types of external devices 62 (40.5%)”? Response: this is modified • Page 8: abbreviations of the antibiotics used should be added to the Table 1 capture. Response: modified • Page 10, line 259: correct the word “statical” to be “statistical”. Response: modified Comments Discussion: • Please remove some “comma symbol where is not necessary. Response: modified • Please revise the text without “Italic” typing other than the name of bacteria. Response: modified • Write the full name for the abbreviations. Response: modified •Some typing errors should be revised. Response: modified Comments Conclusion: • Page 13, line 323: correct the word “Impenem” to “imipenem” Response: modified The end https://doi.org/10.1371/journal.pone.0313431.r002
22 Aug 2024 Decision Letter - Mihret Tilahun, Editor PONE-D-24-02706R1Phenotypic Identification of Metallo-ß- lactamase resistance Gram Negative bacteria from a clinical specimen in Sidama, EthiopiaPLOS ONE Dear Dr. Alemeyhu, 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. During our evaluation of the documents provided, we noted that your ethics approval letter did not cover the entire date range for participant recruitment and data collection. Before we can proceed further with the submission, please provide the ethics approval extension document(s) for the study that cover the study period from 1st March 2023 - June 2023. If the document is in another language, please also provide an English translation. Please note that if this document is not included when your manuscript is resubmitted, it may be rejected. Please submit your revised manuscript by Oct 04 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Emma Campbell, Ph.D Staff Editor PLOS ONE Journal Requirements: 1. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. 2. During our evaluation of the documents provided, we noted that your ethics approval letter did not cover the entire date range for participant recruitment and data collection. Before we can proceed further with the submission, please provide the ethics approval extension document(s) for the study that cover the study period from 1st March 2023 - June 2023. If the document is in another language, please also provide an English translation. Please note that if this document is not included when your manuscript is resubmitted, it may be rejected. 3. Please amend the manuscript submission data (via Edit Submission) to include author Henok Ayalew. 4. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [Note: HTML markup is below. Please do not edit.] [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.0313431.r003
Revision 2
3 Sep 2024 Author Response Dear Editor, Thank you very much for your effort to make our manuscript imporved a lot through regress review. Here we made a modification as per your comments and suggestion and attached as point by point response. Attachments Attachment Submitted filename: Point by Point Response.docx https://doi.org/10.1371/journal.pone.0313431.r004
24 Oct 2024 Decision Letter - Mihret Tilahun, Editor Phenotypic Identification of Metallo-ß- lactamase resistance Gram Negative bacteria from a clinical specimen in Sidama, Ethiopia PONE-D-24-02706R2 Dear Dr. Alemeyhu, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Mihret Tilahun, MSc Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0313431.r005
Formally Accepted
4 Nov 2024 Acceptance Letter - Mihret Tilahun, Editor PONE-D-24-02706R2 PLOS ONE Dear Dr. Alemayehu, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, 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 customercare@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. Mihret Tilahun Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0313431.r006

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