PONE-D-20-09327

Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes

PLOS ONE

Dear Mr Iramiot,

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PLOS ONE

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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: Yes

Reviewer #2: Yes

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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: No

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 study provided by Authors gives an overview on genetic profile of collected strains (n=42) from cattle and human in Kasese District, Uganda. The Authors concluded that major results stays contrary to thesis that antimicrobial resistance (AMR) may be passed to human from livestock as a result of antibiotic use in the farm.

Methods provided by Authors are sound and well based. However discussion section and conclusion should be revised, please find following remarks below:

A) Major remarks:

1. Please highlight the exact number of tested strains in abstract. Cattle (n=12) and human (n=30). In abstract we can found: […] 21/42 isolates were ESBL producers; 13/42 from human and 8/42 from cattle – it remains unclear, and suggest there were 84 samples. I suggest to use 13/30 and 8/12 instead, respectively.

2. Please indicate the exact number of tested strains in Methods section, subsection Bacterial strains as mentioned above

3. Major conclusion made by Authors stays a little bit contrary to data provided in Figure 2. According to Figure 2 about 8 cattle E. coli strains (60% of all cattle samples) are closely related to this found in human and the several of them have similar or wider pattern of AMR.

4. Could you explain why only cattle was designated to the study? If the cattle is the most important meat donor in Uganda, such thing should be mentioned in the background section.

5. Consider discuss other work i.e work of Okubo et al (1) in meaning possibility of obtaining AMR genes from other livestock

6. Because of relative small number of samples in case of cattle (n=12), and no comparison to other livestock (lack of discussion i.e abovementioned) the conclusion may be misleading.

B) Minor remarks:

1. consider the necessity of Figure 1. It is not essential for study.

- Please correct:

2. Method section: Whole genome-sequencing: “Briefly, gDNA was fragmented and

tagged with […]”

3. Figure 2: last strain: Catt-BWE_048B – should be probably Bovine not Human in Host section.

4. I suggest to revise paper by native English speaker.

In conclusion, the study provided by authors are interesting and presents valuable data. I recommend to publish it after revision.

1. Okubo T, Yossapol M, Maruyama F, Wampande EM, Kakooza S, Ohya K, et al. Phenotypic and genotypic analyses of antimicrobial resistant bacteria in livestock in Uganda. Transbound Emerg Dis [Internet]. 2019 Jan 22;66(1):317–26. Available from: https://doi.org/10.1111/tbed.13024

Reviewer #2: The article prepare by the authors present a serious problem which is E. coli multi-drug resistance. It is very interesting that it was observed similar pattern of antibiotic resistance both in human and cattle. Paper is written correctly, the Figures are very impressing, however there are small details which should be corrected.

In Manuscript draft there are missing keywords, however there are present in main document so I assumed that this is omission. In some places like in page 5 Escherichia coli is not written in italic. When you once use shortcut "E. coli" in the text do not use full name in further part. You should write "ng/µl" not "ng/ul" (page 4).

In Results I thought that it will be more genetic data, knowing the title of article. That part could be improved. In addition despite the fact that the Discussion is written correctly and in scientific way, it also could be improved. For a research article the Discussion is to short, try write more about importance of your results regarding to other papers.

Summary, the article is very interesting and the data are important equally for human health and agriculture. I recommend this paper for publication after minor revision.

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Reviewer #1: No

Reviewer #2: No

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Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes

PONE-D-20-09327R1

Dear Dr. Iramiot,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

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With kind regards,

Grzegorz Woźniakowski, PhD ScD

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 #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: (No Response)

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

Reviewer #1: Yes

Reviewer #2: (No Response)

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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: (No Response)

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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: No

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: Dear Author

Thank you for applying indicated remarks.

Please verify english by native speaker.

I've got no further comments.

I recommend to publish manuscript after english verification.

Kind regards.

Reviewer #2: (No Response)

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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