PONE-D-21-26629Analysis of migration of pathogenic drug-resistant bacteria to soils and groundwater after fertilization with sewage sludgePLOS ONE

Dear Dr. Stańczyk-Mazanek,

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 consider the comments of both reviewers carefully and address them as much as possible as they are required for acceptance.
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Reginald B. Kogbara, Ph.D.

Academic Editor

PLOS ONE

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When submitting your revision, we need you to address these additional requirements.

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2. In your Methods section, please provide additional details regarding the experimental materials (soils, sludge) used in your study and ensure you have described the source. For more information regarding PLOS' policy on materials sharing and reporting, see https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-materials.

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"The scientific research was funded by the statute subvention of Czestochowa University of Technology, Faculty of Infrastructure and Environment"

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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: 

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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

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: N/A

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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

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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

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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 article entitled "Analysis of migration of pathogenic drug-resistant bacteria to soils and ground water after fertilization with sewage sludge" aimed to study the effect of using sewage sludge as fertilizer for contamination with drug-resistant bacteria in the environment.

In my opinion, the article needs major revision for publication in PLOS one as the structure and quality of the manuscript is not up to quality. The experiment used a novel approach but fail to design and represent the study in a scientifically coherent manner.

The abstract is not organized in a coherent manner. There is no proper introduction and concluding remark. Author should provide a summary of what is known, the rationale for the study, the method used, the outcome obtained, and conclusions drawn.

The introduction should focus on more how sewage sludge led to migration of pathogenic drug-resistant bacteria, the consequence and why the experiment need to be done

The materials and methods should be written in a way of how experiment is done and condensed by removing description not related to materials and methods.

In table 3 and 4, I am not sure why increased dose of sewage sludge applied for soil fertilization would lead to decreased CFU of bacterial strain such as E. coli.

For Table 5, 6 7 and 8, it does not make any sense to evaluate the antimicrobial resistant pattern of a single strain as it will never represent the while scenario. Author should test more random colony from the same sample to make a logical conclusion. Author should find a way to compare results of table 5, 6 and 7 together.

The results should be quantitatively compared in conclusion with other published data.

Reviewer #2: Analysis of migration of pathogenic drug-resistant bacteria to soils and groundwater after fertilization with sewage sludge

The study entitled “Analysis of migration of pathogenic drug-resistant bacteria to soils and groundwater after fertilization with sewage sludge” deals with one of the most alarming threat connected with the environmental safety and human and animal health. The strong side of this article is the duration devoted to the experiment and the genus identification of the obtained strains with antibiotic-resistance analysis in the further part of research. All the needed data is acquired in the manuscript. The manuscript is well organized and it is carrying the proper scientific soundness. However, in some places, there is no precise description of results, errors in discussion, and vocabulary mistakes throughout the manuscript. Here follows the detailed questions and concerns which could help with correction of the manuscript.

Abstract line 13-23:

The Abstract contained well described aim of the study and used methods, but clearly it is lacking the brief characterization of most important results.

Materials and Methods line 99-100

Authors based sanitary analysis on Polish laboratory exercises book (references number 23), in my opinion this could be not sufficient. I encouraged authors to make references on what detailed regulation they based their methods.

Materials and Methods line 135

I think, it is supposed to be “discs soaked” not “dishes soaked”

Results Table 1. line 168-171

In my opinion the Table 1 structure it can be difficult to read which Unit stands for what Parameter. I encouraged to add some additional horizontal lines.

Results line 223-225

In the sentence “According to the standards, water used e.g. for bathing purposes should not contain more than 100 CFU per 100 ml.”, in my opinion this should be clarified to which group of bacteria it refers.

Results line 231-233

The last sentence of the paragraph is unclear and it could be clarified with references to specific Table/Tables.

Results Table 6. and Table 7. line 240 and 252

In those tables I found the column named “Dose of sewage sludge applied for soil fertilization [t/ha]” with it values very unclear. Is this values represent sewage sludge concentrations in which resistant bacteria occurred ? In my opinion additional description should appear.

Discussion line 317-320

Please verify if defined percentage values are correct.

Discussion line 322

Please specify in which samples or stage of the experiment 36.6% of isolated bacteria were resistant to co-amoxiclav.

Manuscript

Please verify the units correctness with SI Units convention.

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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

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PONE-D-21-26629R1Analysis of migration of pathogenic drug-resistant bacteria to soils and groundwater after fertilization with sewage sludgePLOS ONE

Dear Dr. Stańczyk-Mazanek,

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 do address the minor comment of Reviewer 2 as it is required for acceptance.

Please submit your revised manuscript by Jan 06 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,

Reginald B. Kogbara, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

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.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: (No Response)

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Author could have done better in addressing review question but I believe the author efforts are sufficient enough.

Reviewer #2: I am grateful for answering every comment and making corrections. Unfortunately, one of the comments has been wrongly corrected. After solving this issue, the article in my opinion is ready for publication. Therefore, the issue is described below.

- In the revised manuscript Authors removed the sentence in line 260; “A worrying phenomenon was the observed resistance of E. faecalis bacteria to erythromycin.”.

In the Review, I had in mind the other sentence, which is: “It was found that only a dose of 10 t/ha of sewage sludge did not cause significant contamination of sandy soil and infiltrating water.”. I allow myself to recall my comment for this sentence: “The last sentence of the paragraph is unclear and it could be clarified with references to specific Table/Tables.”.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

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.

Analysis of migration of pathogenic drug-resistant bacteria to soils and groundwater after fertilization with sewage sludge

PONE-D-21-26629R2

Dear Dr. Stańczyk-Mazanek,

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.

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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,

Reginald B. Kogbara, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: