PONE-D-24-37013Occurrence of virulence genes bfp, ompA, traT, eaeA, and stx1 in multidrug-resistant Escherichia coli isolates from humans, animals, and the environment: One Health perspectivePLOS ONE

Dear Dr. Niccodem,

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.

I have completed my evaluation of your manuscript. The reviewers recommend reconsideration of your manuscript following minor revision and modification. I invite you to resubmit your manuscript after addressing the comments below. 

Please submit your revised manuscript by Jan 17 2025 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,

Reham Mokhtar ELTarabili

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 your Data Availability Statement is currently as follows: 

“All relevant data are within the manuscript and its Supporting Information files.”

Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. PLOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods (https://journals.plos.org/plosone/s/data-availability#loc-minimal-data-set-definition).

For example, authors should submit the following data:

- The values behind the means, standard deviations and other measures reported;

- The values used to build graphs;

- The points extracted from images for analysis.

Authors do not need to submit their entire data set if only a portion of the data was used in the reported study.

If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories.

If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If data are owned by a third party, please indicate how others may request data access.

3. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels.   

In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions.

4. Please include a separate caption for each figure in your manuscript.

5. Please upload a copy of Supporting Information Tables S1 to S5 which you refer to in your text on pages 20 to 21.

6. 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.

Additional Editor Comments:

After evaluating this manuscript well , there are some tables and titles must be merged as one table or one title and statistical analysis was missed so this manuscript must be statistically analysis .The manuscript received positive feedback from both reviewers. Reviewer #1 suggests minor revisions, including rephrasing certain lines for clarity and correcting the tense in one instance. Reviewer #2 suggests minor revision, including modifications in manner of writing. Based on the reviewers' comments, the manuscript is generally well-received but requires minor revisions for clarity and grammatical accuracy. The authors are requested to address the specific comments provided by Reviewers to improve the overall quality of the 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: 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: 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: Dear Editor

The manuscript "Occurrence of virulence genes bfp, ompA, traT, eaeA, 1 and stx1 in multidrug-resistant Escherichia coli isolates from humans, animals, and the environment: One Health Perspective" is quite an interesting article that comprehensively described the AMR paradigm in One Health Perspective.

Comments:

1. The names of resistance genes are not necessarily to be described in the title. It could be "Occurrence of virulence genes among multidrug-resistant Escherichia coli isolates from humans, animals, and the environment: A One Health Perspective".

2. There are lots of grammar or English mistakes in the article.

3. Novelty statement or the need of project should be more focused, need revision of Line 81. Here describe more objective of the study.

More references should be added from other parts of the world including Veterinary settings, to provide strong One Health Perspective and Global Concern.

http://dx.doi.org/10.29261/pakvetj/2023.041

https://doi.org/10.1155/2022/8224883

http://dx.doi.org/10.29261/pakvetj/2023.062

http://dx.doi.org/10.29261/pakvetj/2022.049

https://doi.org/10.1016/j.onehlt.2023.100586

4. Line 90-92, this is not required to describe the link.

5. Line 102-103: Dates are not required to be mentioned.

6. Tables are good, however, it is suggested to add at least one figure using data of Table 3.

7. Discussion section is more focused on results. Some of the critical points should be added.

Thanks and Regards

Reviewer #2: Comments to Author:

Minor points

1- In Background; page3, 49 line: You wrote virulence genes (VRs)!!! That’s

incorrect abbreviation; kindly correct it to (VGs).

2- In Background; page3, 53 line: you wrote blaOXA-4!!! That’s incorrect; kindly

correct it to blaOXA-48

3- In Background; page4, 81 line and 85 line: The rule of manuscript writing is to

avoid using (We). So you should delete (We) and use formal scientific words

(This study or The current study or The present study).

4- In Biochemical identification of the isolates; page5, 105 line: you wrote

Isolates were identified as described previously [4,26,29,31]. Briefly…..!!!

Kindly delete this sentence and directly write: The isolates were identified by

colonial morphology, Gram stain…. Do not repeat the sentences because this

makes your manuscript weak.

5- In DNA extraction for the screening of virulence genes; page6, 124 line: you

wrote whole the practical method but without writing any references!!! Kindly

mention the references that you dependent on them.

6- In PCR mixture for the detection of virulence genes; page7, 136 line: The rule

of manuscript writing is to avoid using (We). So you should delete (We) and use

formal scientific words (This study or The current study or The present study).

7- In Visualization of PCR products by electrophoresis; page7, 154 line: you

wrote whole the practical method but without writing any references again!!!

Kindly mention the references that you dependent on them.

8- In discussion; page16, 268 line, 270,283, 287, 311, 315, 321, 325, 351 and

353line: The rule of manuscript writing is to avoid using (Our) and (We). So you

should delete (Our) and (We) and use formal scientific words (This study or

The current study or The present study).

9- In discussion; page16, 274 line: you wrote the occurrence of 274 virulence

gene stx1 was low, being 4% in Karatu and 0% in this study!!! Why? You did

not suggest any reason for it!!! Try to mention accurate scientific reason.

10- In conclusion; page20, 359 line, 361 and 363line: The rule of manuscript

writing is to avoid using (We). So you should delete (We) and use formal

scientific words (This study or The current study or The present study).

11- In conclusion; page20: You should shortly mention the fact that you

explained about the PCA because this make your research stronger scientifically;

you wrote it in discussion only “PCA showed that isolates from pigs had a higher

proportion of virulence genes, followed by those isolated from the environment,

with those from poultry and humans having the lowest proportion, which indicates

their respective potential as a reservoir for the genes”.

Best regards

**********

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: Muhammad Asif Zahoor

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: PONE-D-24-37013.pdf

Occurrence of virulence genes in multidrug-resistant Escherichia coli isolates from humans, animals, and the environment: One Health Perspective

PONE-D-24-37013R1

Dear Dr. Niccodem,

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,

Reham Mokhtar ELTarabili

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: