Multidrug-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae isolated from chicken droppings in poultry farms at Gondar City, Northwest Ethiopia

Mitkie Tigabie; Sirak Biset; Teshome Belachew; Azanaw Amare; Feleke Moges

doi:10.1371/journal.pone.0287043

Peer Review History

Original SubmissionMarch 18, 2023
13 Apr 2023 Decision Letter - Md. Tanvir Rahman, Editor PONE-D-23-06358Multidrug-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae isolated from chicken droppings in poultry farms at Gondar city, Northwest EthiopiaPLOS ONE Dear Dr. Tigabie, 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 May 28 2023 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, Md. Tanvir Rahman, DVM, MSc, 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. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. Additional Editor Comments (if provided): Dear Authors, Please see the comments of the reviewers and take the necessary actions. Best wishes, Tanvir == Prof. Md. Tanvir Rahman DVM, MSc (Canada), Ph.D. (UK), Postdoc (Germany) Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh. Phone. + 88-01913323307; Fax + 88-09161510 E.mail: tanvirahman@bau.edu.bd http://vmh.bau.edu.bd/profile/VMH1005 https://orcid.org/0000-0001-5432-480X https://sites.google.com/site/tanvirahman/Home https://www.researchgate.net/profile/DrMdTanvir_Rahman/research [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 Reviewer #2: Partly ******** 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: Yes 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: No ****** 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: 1. There are many places in the manuscript written wrongly used words, phrases and sentences. The English correction is needed for sentence to sentence. 2. The theme of the abstract is not highlighted/reflected to emphasize the title. Please modify the abstract with noting a brief primary objective. 3. The Introduction section is very weak and uninformative. Please strengthen the introduction with relevant citations. There is so much languages problem. Please modify it by Native English Speaker. What is the significance of the study? How is the study different from others?…….Please note it down and rectify accordingly? 4. Results and discussion portion is haphazardly written and difficult to correlate with each other. Please modify the discussion in systemic manner with relevant references. Please modify the discussion by strengthening the results. There is also lacuna of the representation of the discussion in the present endeavor. Please modify the discussion with proper justification and analysis by strengthening the novelty of the work. Reviewer #2: Abstract While the author aimed to Enterobacteriaceae, they have mentioned only enrichment and isolation of Salmonella. They said isolation of E. coli, Salmonella and P. mirabilis. But, just next to that they mentioned 9.1% of K. pneumonia as ESBL!! Strange, why didn’t they mention K. pneumonia earlier? Introduction The importance is nicely described with necessary references; however, this could be further improved with information on ESBL. Few typo mistakes. Materials and methods Although they targeted Enterobacteriaceae, isolation was performed on MacConkey and XLD agar which limits the isolation of other enterobacteriae and increasing the chance of missing bacteria that does not grow on those media properly. So, my suggestion is, instead of saying Enterobacteriaceae, they could mention specific bacteria like E. coli and Salmonella… Isolation techniques are not properly described. The authors didn’t mention, how they calculated sample size, i.e. no sample size calculation was performed!! Line 158: 5%??? Results Nicely presented with easy going Tables. In Prevalence, they didn’t mention about K. pneumonia, although it’s prevalence was not that low. I think it worth to mention in the prevalence section. In addition, they also isolated E. cloacae, but no mention in the prevalence or isolation section (Table 4) But, in Antibiotic resistance K. pneumonia suddenly came (Table 3)!! Discussion The authors have discussed the findings nicely with evidences from different part of the world. However, the authors have identified several general characteristics significantly associated with the occurrence of ESBL, but they didn’t discussion anything about them. The discussion feels very monotonous. It could be improved with suggestion from a person with good English writing skill. Conclusion and recommendations Waste disposal was not significantly associated with occurrence of ESBL according to their findings (Table 1). Rather, some critical factors were identified, which could be highlighted in the conclusion section. ****** 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: Yes: Jayedul Hassan ******** [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.0287043.r001
Revision 1
17 May 2023 Author Response PONE-D-23-06358 Multidrug-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae isolated from chicken droppings in poultry farms at Gondar city, Northwest Ethiopia PLOS ONE Dear Dr. Tigabie, 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 May 28 2023 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, Md. Tanvir Rahman, DVM, MSc, 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. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. Additional Editor Comments (if provided): Dear Authors, Please see the comments of the reviewers and take the necessary actions. Best wishes, Tanvir == Prof. Md. Tanvir Rahman DVM, MSc (Canada), Ph.D. (UK), Postdoc (Germany) Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh. Phone. + 88-01913323307; Fax + 88-09161510 E.mail: tanvirahman@bau.edu.bd http://vmh.bau.edu.bd/profile/VMH1005 https://orcid.org/0000-0001-5432-480X https://sites.google.com/site/tanvirahman/Home https://www.researchgate.net/profile/DrMdTanvir_Rahman/research [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 Reviewer #2: Partly 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: Yes 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: No 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: 1. There are many places in the manuscript written wrongly used words, phrases and sentences. The English correction is needed for sentence to sentence. 2. The theme of the abstract is not highlighted/reflected to emphasize the title. Please modify the abstract with noting a brief primary objective. 3. The Introduction section is very weak and uninformative. Please strengthen the introduction with relevant citations. There is so much languages problem. Please modify it by Native English Speaker. What is the significance of the study? How is the study different from others?…….Please note it down and rectify accordingly? 4. Results and discussion portion is haphazardly written and difficult to correlate with each other. Please modify the discussion in systemic manner with relevant references. Please modify the discussion by strengthening the results. There is also lacuna of the representation of the discussion in the present endeavor. Please modify the discussion with proper justification and analysis by strengthening the novelty of the work. Reviewer #2: Abstract While the author aimed to Enterobacteriaceae, they have mentioned only enrichment and isolation of Salmonella. They said isolation of E. coli, Salmonella and P. mirabilis. But, just next to that they mentioned 9.1% of K. pneumonia as ESBL!! Strange, why didn’t they mention K. pneumonia earlier? Introduction The importance is nicely described with necessary references; however, this could be further improved with information on ESBL. Few typo mistakes. Materials and methods Although they targeted Enterobacteriaceae, isolation was performed on MacConkey and XLD agar which limits the isolation of other enterobacteriae and increasing the chance of missing bacteria that does not grow on those media properly. So, my suggestion is, instead of saying Enterobacteriaceae, they could mention specific bacteria like E. coli and Salmonella… Isolation techniques are not properly described. The authors didn’t mention, how they calculated sample size, i.e. no sample size calculation was performed!! Line 158: 5%??? Results Nicely presented with easy going Tables. In Prevalence, they didn’t mention about K. pneumonia, although it’s prevalence was not that low. I think it worth to mention in the prevalence section. In addition, they also isolated E. cloacae, but no mention in the prevalence or isolation section (Table 4) But, in Antibiotic resistance K. pneumonia suddenly came (Table 3)!! Discussion The authors have discussed the findings nicely with evidences from different part of the world. However, the authors have identified several general characteristics significantly associated with the occurrence of ESBL, but they didn’t discussion anything about them. The discussion feels very monotonous. It could be improved with suggestion from a person with good English writing skill. Conclusion and recommendations Waste disposal was not significantly associated with occurrence of ESBL according to their findings (Table 1). Rather, some critical factors were identified, which could be highlighted in the conclusion section. 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: Yes: Jayedul Hassan [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: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0287043.r002
30 May 2023 Decision Letter - Md. Tanvir Rahman, Editor Multidrug-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae isolated from chicken droppings in poultry farms at Gondar city, Northwest Ethiopia PONE-D-23-06358R1 Dear Dr. Tigabie, 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, Md. Tanvir Rahman, DVM, MSc, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Thanks for addressing the comments of the reviewers and revising the manuscrot. Reviewers' comments: https://doi.org/10.1371/journal.pone.0287043.r003
Formally Accepted
2 Jun 2023 Acceptance Letter - Md. Tanvir Rahman, Editor PONE-D-23-06358R1 Multidrug-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae isolated from chicken droppings in poultry farms at Gondar City, Northwest Ethiopia Dear Dr. Tigabie: 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 Professor Md. Tanvir Rahman Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0287043.r004

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