PONE-D-24-40234Genomic characterization of foodborne Salmonella enterica and Escherichia coli isolates from Saboba district and Bolgatanga Municipality GhanaPLOS ONE

Dear Dr. Okeke,

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.

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Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN

Academic Editor

PLOS ONE

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3. Thank you for submitting the above manuscript to PLOS ONE. During our internal evaluation of the manuscript, we found significant text overlap between your submission and previous work in the [introduction, conclusion, etc.].

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When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section.

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“Whole genome sequencing and analysis for this project was supported through SEQAFRICA award to INO. The SEQAFRICA project is funded by the Department of Health and Social Care’s Fleming Fund using UK aid. The views expressed in this publication are those of the authors and not necessarily those of the UK Department of Health and Social Care or its Management Agent, Mott MacDonald. INO is a Calestous Juma Fellow supported by the Bill and Melinda Gates Foundation.”

Please state what role the funders took in the study.  If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."

If this statement is not correct you must amend it as needed.

Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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:

In addition to your response to the reviewer's comments, please address the following;

1a. Clarify the Use of Previously Isolated Bacteria in the Study

It would be helpful if the abstract and aim mention that the study will be using previously isolated bacteria. This is a critical detail that should be highlighted early on for clarity and to set appropriate expectations for the reader.

b. Address the Discrepancies in Sampling Methods

• Upon reviewing references 22 and 23, the sampling methodologies differ from those described in this study. Specifically:
  • Neither reference mentions the collection of fresh meat or milk samples.
  • The term lactating cows does not appear in the methods or anywhere else in these papers.
  • There is no mention of samples from handlers’ hands, meat sellers’ tables, knives, or feces in these papers.
  • The sampling procedures of the two references are quite similar in terms of Ready-to-Eat (RTE) sample collection, yet there is no mention of fresh meat, milk, or surfaces like tables or utensils in those papers.
  Suggestions to Address These Points:
  • Provide a clear explanation of how the current study's sampling methods relate to the methods in references 22 and 23.
  • Clarify if the fresh meat, milk, and surface samples mentioned in your manuscript are new, or if they are derived from RTEs as per references 22 and 23.
  • If there is an overlap or distinction between RTE and fresh meat sampling, this should be explicitly discussed in the text. For example, is fresh meat being classified as RTE in some instances? If so, it would be important to explain this decision clearly to avoid confusion.

c. Clarification on the Synonymity Between RTEs and Fresh Meat

If the authors are suggesting that Ready-to-Eat foods (RTEs) are synonymous with fresh meat or that there is some overlap between the two, it is crucial to state this explicitly. Readers may assume a difference between the two categories, and any potential synonymity should be justified with an appropriate explanation.

d. Enhance transparency in sampling descriptions and briefly describe how these bacteria were isolated from these samples.

Consider revising the methods section to provide brief description about how E. coli and Salmonella were isolated from the fresh meat, milk, and RTE samples. Also describe the sampling procedures for fresh meat, milk and other samples if they were conducted separately from the RTE samples. This will help clarify any misconceptions and make it clear how the study builds on or differs from the previously published studies.

By addressing these points, the study will offer greater transparency in its methodology and improve clarity for readers regarding the sampling strategy and its connection to previously published studies. 

2. Highlight key limitations of the present study.

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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

Reviewer #3: Partly

Reviewer #4: Yes

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

Reviewer #1: N/A

Reviewer #2: Yes

Reviewer #3: N/A

Reviewer #4: 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

Reviewer #3: Yes

Reviewer #4: 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

Reviewer #3: Yes

Reviewer #4: 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: Abstract: Review and either complete the half sentences and remove where not applicable. Eg...."While 7of the Salmonella isolates carry the IncI1-I(Gamma) plasmid replicon."

Review the recommendation and make it more focused on the work and not broad, blanket recommendation.

Introduction:

The role of the equipment such knives and surfaces need to be mentioned in the introduction and not just having it appear in the objectives.

Method:

A lot is described for Salmonella but not much is mentioned about how the E.coli samples were presented.

Results and Discussion:

I was expecting the authors to emphasize the genetic relatedness for the Salmonella and E. coli and their implication on foodborne illnesses and and control.

Other details are available in the body of the manuscript.

Overall this is an excellent work and the presentation is nicely done.

Reviewer #2: The manuscript is technically sound, with experiments conducted rigorously, including appropriate controls, replication, and sample sizes. The conclusions are well-supported by the data presented, without any overreach or misinterpretation. The statistical analysis has been performed appropriately and rigorously, ensuring that the findings are valid and reliable. The manuscript is also presented in an intelligible fashion, written in clear and standard English, making it easy to follow and understand for the intended scientific audience.

Reviewer #3: Undoubtedly, this study is of value from a public health and One Health point of view. And the authors are commended for carrying it out.

An initial read showed that the abstract lacked an aim by which to appraise the paper. However, line 63 in the introduction section tells us that "this study aims to characterize the resistance, virulence and plasmid profile of Salmonella and E. coli isolated from fresh different retail meats, milk, and associated samples (handler’s hand swab, table, knife and faecal samples) in in Saboba district and Bolgatanga Municipality of Ghana" Neither the abstract or the aim reproduced above apprises the reader that the study will be using previously isolated bacteria. Mention is made in the the methods' section and 2 published papers (22 & 23) are referenced.

However, despite intense perusal of the methods section, questions arise and clarifications are thus required:

1. None of the aforementioned 2 references mentioned fresh, meat and milk samples being collected in their methods' section

2. None of these references mentioned 'lactating cows' in their methods' section or any where else in the papers.

3. None of these references mentioned (handler’s hand or milkers’ hands swab, meat sellers’ tables, knife collecting utensils, and faecal) samples being collected in their methods' section.

4. Both of these references had very similar sampling methods such that they collected 300 RTEs during almost the same period from the same (n=6) species, 50 sample per specie. But no mention is made of fresh meat, milk or tables. Why?

5. Are the authors suggesting RTEs are synonymous with fresh meat?

The authors need to clarify the above to make understanding and comprehension easy for PLoS One readers. Only then can conclusions like "This study has characterized the genomes of Salmonella and E. coli in milk, meat and their associated utensils" (line 294) have true validity as per the methods.

Reviewer #4: Review Comments

• Line 24: It is suggested to authors to use “carried mobile genetic elements” and not “carry mobile elements”.

• Line 44: Organism names must be italized

• Line 48: Authors must choose between using either Salmonella or S. enterica and keep it consistent throughout the paper.

• Line 55: It is suggested to authors to introduce “to” between “and” and “determine” to allow for a smooth read

• Line 70: How many of the isolates belonged to the various sources of isolation? This must be stated

• Line 85: In its current state, the terminal extension at 72 oC for 5 minutes appears to be part of the 35 cycles of PCR which I do not think it is. The sentence muct be revised to reflect such.

• Line 99: Do authors mean SPAdes? and was the quality of the reads assessed before assembly?

• Line 105: Multi-locus sequence types (MLST) for the isolates were determined and core-genome MLST was calculated using what tools or programs?

• Line 170: Were these just the only amr genes found considering the origin of the isolates from west Africa? Was this confirmed using other programs? I used Resfinder in Abricate (https://github.com/tseemann/abricate) and I found other genes like mdf(A) which act against macrolides in some of the isolates

• Line 226: “All multidrug resistant strains encode pO111 or IncY replicons”. What is the basics for the claim? Is it from published literature or the authors performed plasmid analysis?

• Line 246: Cite some examples of non-pathogenic ecoli for better discourse

• Line 262: It is suggested to authors to change the “possess” to "possessed"

• Line 289: “gene” should be added to “beta-lactamase”.

• Line 289: Were the ARGs identified on the plasmids or the chromosomes? This must be stated if that analysis was done?

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Reviewer #1: No

Reviewer #2: Yes: Ayomide Adeyeye

Reviewer #3: No

Reviewer #4: Yes: Kingsley Emmanuel Bentum

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PONE-D-24-40234R1Genomic characterization of foodborne Salmonella enterica and Escherichia coli isolates from Saboba district and Bolgatanga Municipality GhanaPLOS ONE

Dear Dr. Okeke,

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  Jan 10 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,

Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN

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.

[Note: HTML markup is below. Please do not edit.]

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

Reviewer #3: All comments have been addressed

Reviewer #4: (No Response)

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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

Reviewer #3: Yes

Reviewer #4: Yes

**********

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

Reviewer #1: N/A

Reviewer #2: Yes

Reviewer #3: N/A

Reviewer #4: N/A

**********

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: (No Response)

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: 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 #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: 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 #1: Great work. The authors have addressed all the comments from the initial submission. There are no comments from me at this time.

Reviewer #2: (No Response)

Reviewer #3: (No Response)

Reviewer #4: • Line 25: Authors must understand that research publication is a reported work done hence all verbs must be in the past tense. Hence “belong” must be “belonged” and “carrying” be “carried”. The manuscript is rife with such errors and must be corrected

• Line 25: I again ask the authors to define which mobile elements as there are several. If it is a plasmid, then authors must state it.

• Line 98-99: This implies that apart from the VITEK no initial confirmation was done for the E. coli strains like Salmonella. Any reason for that?

• Line 128: Please provide a reference or link for the VFDB platform or publication

• Line 183: Same comment as Line 25

• Line 190: The “,” between “other” and “tetA” is not needed.

• Line 191-192: The plasmid information is conspicuously missing in the Figure 1

• Line 196: I suggest the addition of sequence type to the title like in Salmonella

• Line 294- 296: The sentence is not reading right. Authors must rephrase it

• Line 303: It is suggested to authors to be more specific by writing “ association of the Inc1 plasmid replicon

• Line 313: Same comment as in Line 25

• Line 326: Should read “multidrug-resistant”

• Line 330-331: The sentence is not reading right

• Line 333: Saying “elsewhere in West Africa” is vague. Rather authors should say “and by extension West Africa”.

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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

Reviewer #3: No

Reviewer #4: 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.

Genomic characterization of foodborne Salmonella enterica and Escherichia coli isolates from Saboba district and Bolgatanga Municipality Ghana

PONE-D-24-40234R2

Dear Dr. Okeke,

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,

Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: