PONE-D-23-32355One Health surveillance of colistin-resistant Enterobacterales in Belgium and the Netherlands between 2017 and 2019PLOS ONE

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   "The i-4-1-Health project was financed by the Interreg V Flanders-The Netherlands program, the cross-border cooperation program with financial support from the European Regional Development Fund (ERDF) (0215). Additional financial support was received from the Dutch Ministry of Health, Welfare and Sport (325911), the Dutch Ministry of Economic Affairs (DGNR-RRE/14191181), the Province of Noord-Brabant (PROJ-00715/PROJ-01018/PROJ-00758), the Belgian Department of Agriculture and Fisheries (no reference), the Province of Antwerp (1564470690117/1564470610014) and the Province of East-Flanders (E01/subsidie/VLNL/i-4-1-Health). The authors are free to publish the results from the project without interference from the funding bodies. FecalSwabs and tryptic soy broths were provided by Copan. The authors were free to publish the results from the project without interference by Copan."

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Reviewers' comments:

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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: 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: No

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: This manuscript explore colistin resistance bacteria and AMR genes in each one-health sector. This is interesting and attract the readers in the field. My minor comments appear below:

1. M & M: How the author selected the setting of the study? random or clustering or other?

2. M & M: Line 142-146, I think it will be better to move this paragraph to be ethical approval and inform consent.

3. M & M: How to choose farms? (line 155-157).

4. M 7 M: Line 167, please shortly described of Kluytmans-van der Bergh et al.

5. M & M: Line 173, What is antibiotics used in this study, please mention.

6. Result: What is genetic relationship of E. coli/Klebsiella/Enterobacter in this study? Do author perform core genome SNP?

7. Discussion: Line 562-563, Are they used colistin? I think it may be not, however, hospital stay is possible to get colistin resistance organism via oral-route.

8. In this study found mcr-9 and mcr-10 from human, that is different from several previous study which reported mcr-1 in healthy humans and patients. Especially, one report in Thailand showed mcr-1 carrying in carbapenem-resistant Enterobacterales. Please see https://www.frontiersin.org/articles/10.3389/fmicb.2020.586368/full and https://www.nature.com/articles/s41598-022-21836-7

This might be useful for the reader to discussion.

Reviewer #2: - Line 127, please write: ‘...in hospital patient, long term care facility (LTCF) residents and healthy.....’

- Line 133, the term ‘i-4-1-Health’ is not really known, so please provide one to two sentences to define.

- Line 363, write ‘mcr-5.1 sequences from Belgian pigs..’ also line 365 ‘mcr-9 and mcr-10- containing plasmids’. I mean that in all case the ‘mcr’ must be written with low letter even in the beginning of the sentence (not Mcr).

- Line 457, write ‘..atypical enteropathogenic E. coli (aEPEC, n=18 from all One Health sectors)......

- Line 466, you can use the term ‘high risk clonal lineages’ instead of ‘pandemic clones’.

- Line 468, write ‘K. pneumoniae ST15 (n=2), ST45 469 (n=7), ST101 (n=1), ST147 (n=1) and ST307 (n=1), and E. cloacae ST171 (n=1)..’

- Line 488, you wrote ‘Inter-host transmission between humans and livestock animals was not detected. However, clusters of related isolates were detected in all sectors indicating that transmission of ColR-E occurred in broiler and in pig farms, between children within the day care centres, and between patients residing in the LTCFs and the hospitals’. WHAT is the difference between ‘Inter-host transmission between humans and livestock animals was not detected’ and ‘However, clusters of related isolates were detected .... occurred in broiler and in pig farms, between children within the day care centres, and between patients residing in the LTCFs and the hospitals’. IT SEEMS that there is a contradiction. If you find same clone in different niches so this is ‘Inter-host transmission between humans and livestock animals’. You can explain this to me or you can verify or improve the sentences.

- Line 517, write ‘..However, colistin screening in humans is not included [17]’.

- Line 570, just a question, you wrote ‘Adenosine triphosphate (ATP) measurements also ...’ I am not specialized in this but what is the link between ATP and environmental contamination.

- I believe that mcr genes are mainly co-localized with ESBL genes, it is not clear if you find this linkage or not. Please highlight this phenomenon (if there is linkage or even there not) in the discussion section.

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Reviewer #1: No

Reviewer #2: Yes: Mohamed Salah Abbassi

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One Health surveillance of colistin-resistant Enterobacterales in Belgium and the Netherlands between 2017 and 2019

PONE-D-23-32355R1

Dear Dr. De Koster,

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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Kind regards,

Zhi Ruan, Ph.D.

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

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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

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

Reviewer #1: 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

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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

**********

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: (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.

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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

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