Isolation, identification and antibiotic resistance profile of thermophilic Campylobacter species from Bovine, Knives and personnel at Jimma Town Abattoir, Ethiopia

Motuma Debelo; Nezif Mohammed; Abebaw Tiruneh; Tadele Tolosa

doi:10.1371/journal.pone.0276625

Peer Review History

Original SubmissionJuly 1, 2022
8 Aug 2022 Decision Letter - Monica Cartelle Gestal, Editor PONE-D-22-17337Isolation, identification and antibiogram profile of thermophilic Campylobacter species from bovine, knives and personnel at Jimma Town abattoir, EthiopiaPLOS ONE Dear Dr. Debelo, 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 Sep 22 2022 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, Monica Cartelle Gestal, PhD Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. 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. Thank you for stating the following financial disclosure: "Authors who received each award; Motuma Debelo, Nezif Mohammed, Abebaw Tiruneh and Tadele Tolosa No Specific Grant numbers awarded to each author. This research work was funded by Jimma University College of Agriculture and Veterinary Medicine. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." At this time, please address the following queries: a) Please clarify the sources of funding (financial or material support) for your study. List the grants or organizations that supported your study, including funding received from your institution. b) State what role the funders took in the study. If the funders had no role in your study, please state: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” c) If any authors received a salary from any of your funders, please state which authors and which funders. d) If you did not receive any funding for this study, please state: “The authors 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. 3. "Thank you for stating the following in the Acknowledgments Section of your manuscript: "We thank Jimma Town abattoir workers for their support and participation in this study. We are also thankful to technical staff of School of Veterinary Medicine for their assistance during laboratory works and Jimma University, College of Agriculture and Veterinary Medicine for their facilitation and some funds." 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: "Authors who received each award; Motuma Debelo, Nezif Mohammed, Abebaw Tiruneh and Tadele Tolosa No Specific Grant numbers awarded to each author. This research work was funded by Jimma University College of Agriculture and Veterinary Medicine. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 4. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. "Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. 5. Please ensure that you refer to Figure 1 in your text as, if accepted, production will need this reference to link the reader to the figure. 6. Please include a caption for figure 1. Additional Editor Comments: As you can see on the reviewers comments, it was some controversy with this manuscript. Please pay special attention to the comments provided by reviewer 1 and 3 prior to resubmission. Thanks [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: No Reviewer #2: Yes Reviewer #3: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: Yes Reviewer #3: 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: Yes Reviewer #2: Yes Reviewer #3: 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: No Reviewer #2: Yes Reviewer #3: 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: Comments to the Author: The paper described the “Isolation, identification and antibiogram profile of thermophilic Campylobacter species from bovine, knives and personnel at Jimma Town abattoir, Ethiopia”. Major comment: After carefully reading this paper, it was observed that the findings of the paper are of local interest and importance. Other readers may not be benefited by the data. Further, the study carried out at only one abattoir and therefore the limited number of isolates (n=38) obtained in this study are not sufficiently addressed to draw any logistic conclusion. The article does not have any novelty of data or any molecular characterization of isolates. Further, the data of the study is also not presented well in the manuscript. Keeping in view of the facts, the article may not be found suitable for publication in the reputed and high impact Plos One journal. XXXXXXXX Minor comments : The manuscript presents the research to understand the current status of Antimicrobial Resistance (AMR) in Campylobacter isolates from faecal samples of bovine, carcases of slaughtered animals, knives and personnel employed at abattoir. Overall, the manuscript requires editing on the grammar at many places to improve the clarity and data presentation. Some sentences are not clear and difficult to understand. Objective to rephrase, not clear, and to show novelity or improvement from previous studies carried in this era. In Methodology, what i am missing is the absence of molecular study for identification of different species and for detection of different AMR and Virulence genes. Emphasize the new and important aspects of your study and put your findings in the context of the totality of the relevant evidence. I didn’t find any standard strains of campylobacter( be it jejuni, coli, lari) were used for this study? As a general comment, no limitations of the study were given in manuscript. In my mind the major limitation is the absence of genotypic studies for AMR and virulence of isolates it could have made your study more meaningful and interesting. The objective of this manuscript was to estimate the occurrence and antimicrobial resistance of thermophilic Campylobacter strains isolated from from faecal samples of bovine, carcases of slaughtered animals, knives and personnel employed at abattoir in Ethiopia. There are many articles with similar objectives and I do not observe in this any original element beyond the region studied. However, this fact seems to me not to be enough and perhaps the authors should consider a journal with local impact. Reviewer #2: Review Report: Line 15 – make the campylobacter italics “Campylobacter species from bovine” make. Line 18 – make the italics “in vitro” Line 23 – Check the spelling “specious” Line 76 --- Looking at the sample data, the samples have not been collected on a regular basis to estimate the prevalence, and it does not comply with cross-sectional study norms! Again please correct for grammatical errors. The manuscript has been looked at for minor grammar mistakes and the manuscript suffers from a huge amount of grammatical errors. This manuscript has to be handed over a native English speaker and revised accordingly. Reviewer #3: The authors should improved their manuscript following the reviewer comment uploaded. The authors should improved their manuscript following the reviewer comment uploaded.The authors should improved their manuscript following the reviewer comment uploaded.The authors should improved their manuscript following the reviewer comment uploaded. ****** 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: Yes: Bilal Ahmad Malla Reviewer #2: No Reviewer #3: 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: comments to authors.docx Attachment Submitted filename: Reviewer comments.docx https://doi.org/10.1371/journal.pone.0276625.r001
Revision 1
20 Sep 2022 Author Response Reviewer #1 1. We thank the reviewer for the fruitful comments Major comment: a. We the authors agree with the reviewer comment that it was better if the study was done at national level. However, Jimma Town is not as such small town and it is home for more than 207,573 (projected population in 2021/not actual) with 50.52km2 in south-western Ethiopia. There is only one abattoir in the town delivering service for the vast population in the town. The research finding will benefit the local and national government to take measures in Jimma abattoir in particular and abattoirs in the country in general. Researchers/scientific community will be benefitted to prepare review articles, taking this findings as a baseline research and to consider the aggravation of antimicrobial resistance pattern both in human and animal populations. To make it very clear to the international readers, we elaborated the background of our study setting. b. It was better if the number of isolates obtained (n=38) was increased. However, our finding is consistent (relatively high) with similar previous researches done in Ethiopia. c. We strongly agree with the comment not to use molecular characterization as diagnostic method and we included in the study limitation. It was also our plan and tried our best to get primers from abroad, but we missed due to COVID-19 pandemic lockdown in the world. Minor comment a. We thank the reviewer comment to edit the grammar and sentence structure. We improved the grammar and unclear sentences in the revised manuscript. b. We thank the reviewer for the comment ‘absence of molecular study’. We took as limitation of the study. c. We thank the reviewer comments on the objectives. We improved/rephrased our objectives in the revised manuscript. d. We thank the reviewer for the comment. We included the importance of our finding in the revised manuscript. e. We thank the reviewer for the comment to use standard strain of Campylobacter. We could not find standard strain for Campylobacter species from the national laboratory and we have used E. coli (ATCC 25922) as standard and included in the limitation of the study in the revised manuscript. f. We thank the reviewer for the comment and the revised manuscript included ‘limitations of the study’. g. We respect the reviewer comment and strongly disagree with the idea ‘study region is not enough reason to conduct research’. There are millions of prevalence studies for the same disease in different regions and/or time frame. In previous works, prevalence as well AMR was only determined from faecal but in our case it was from faecal, carcasses, personnel hands and knife samples. Therefore, our study is not out of this fact and we believe it is very important and respected to show the gaps and identify AMR Campylobacter strains in the region. Reviewer #2 a. We thank the reviewer for the comments Line 15,18 and 23. We corrected accordingly in the revised manuscript. b. We thank the reviewer comment on study design. We trimmed the full description of sample collection methods to make it shorter previously. It is included now (the regular basis) in the revised manuscript. c. We thank the reviewer comment for the English language. Senior professors edited the English language of our revised manuscript. Reviewer #3 a. We thank the reviewer comment on the tittle of the manuscript. We reformulated the tittle as ‘Isolation, identification and antibiotic resistance profile of thermophilic Campylobacter species from bovine, knives and personnel at Jimma Town abattoir, Ethiopia’. b. We thank the reviewer for the comment on the English language improvement and our revised manuscript is edited by senior professors. c. We thank the reviewer comment on capitalizing genus name initials in the manuscript and corrected accordingly. d. We thank the reviewer for the comment to include molecular techniques (PCR) for confirmation of Campylobacter species. We also strongly agree with the comment, and there was no Campylobacter primer in Ethiopia and difficult to get from abroad due to COVID-19 pandemic at a time. We included in the limitation of the study in the revised manuscript. e. We appreciate and thank the reviewer for suggesting very important research findings to compare with our work. We discussed our findings comparing with suggested studies. f. We thank the reviewer comment and the discussion part was improved in the revised manuscript. g. We thank the reviewer for critical review and the mentioned words in line 35 & 36 were eliminated in the revised manuscript. h. We thank the reviewer for the comment and some points were added after reference (1,2) in the revised manuscript. i. We thank the reviewer for the comments and paragraphs in line 38-39, 81-83 and 88-89 were reformulated in the revised manuscript. j. We thank the reviewer for the comments and words mentioned in line 93 and 96 were replaced accordingly. Authors’ response to academic editor We thank the academic editor for the detailed comments on the format of the manuscript and other comments. 1. The manuscript was checked according to the journal formats. 2. The funding section was revised based on the comments given in the revised manuscript. 3. The acknowledgement part is corrected in the revised manuscript. 4. Supporting files were uploaded as indicated by the academic editor. 5. The authors prefer to display tables than figure, and figure 1 is deleted from the revised manuscript. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0276625.r002
11 Oct 2022 Decision Letter - Monica Cartelle Gestal, Editor Isolation, Identification and Antibiotic Resistance Profile of Thermophilic Campylobacter Species from Bovine, Knives and Personnel at Jimma Town Abattoir, Ethiopia PONE-D-22-17337R1 Dear Dr. Debelo, 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, Monica Cartelle Gestal, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): 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 #2: All comments have been addressed Reviewer #3: 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 #2: Yes Reviewer #3: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes Reviewer #3: 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 #2: Yes Reviewer #3: 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 #2: Yes Reviewer #3: 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 #2: The manuscript has been revised and as per the suggestion of the reviewer. So it may be accepted for publication. Reviewer #3: accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte accepte ****** 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 #2: Yes: Amit Kumar Verma Reviewer #3: No ******** https://doi.org/10.1371/journal.pone.0276625.r003
Formally Accepted
14 Oct 2022 Acceptance Letter - Monica Cartelle Gestal, Editor PONE-D-22-17337R1 Isolation, Identification and Antibiotic Resistance Profile of Thermophilic Campylobacter Species from Bovine, Knives and Personnel at Jimma Town Abattoir, Ethiopia Dear Dr. Debelo: 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. Monica Cartelle Gestal Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0276625.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .