PONE-D-19-31583

Elevated plasma cotinine is associated with an increased risk of developing IBD, especially among users of combusted tobacco

PLOS ONE

Dear Dr. Lovisa Widbom,

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Additional Editor Comments (if provided):

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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: Partly

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

Reviewer #1: No

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: I found this very interesting. The novel finding is that cotinine levels do not predict the risk of IBD developing in snuff users (higher levels of cotinine than smokers but not higher levels of IBD) suggesting some component of cigarette smoke other than nicotine is the causative factor increasing the risk of IBD.

However the manuscript does need significant revision and I do not think it can be accepted in its current form. The results section is very unclear and difficult to read. The authors describe their results in the text but do not put the actual statistics in the text. Rather they require the reader to look at "Table 2" to look up the relevant statistic. I think it would be better to follow the convention of having the statistic in brackets e.g. (OR x.xx, 95% CI x.xx-x.xx, Table 2).

I also find some of the results section misleading. For example "A higher number of self-reported cigarettes per day was associated with higher OR for developing IBD (Table 2)." When looking at table two I see that none of the ORs are statistically significant, all of the 95% CIs cross 1.0 but instead the authors are reporting a "p trend" on the values of the odds ratios themselves in relation to the number of cigarettes smoked. This is not described in the methods section and it should be clear exactly which statistical test was used.

My other major concern is that in supplementary table 2 it suggests the OR for developing Crohn's in a heavy smoker is 148631 relative to a non-smoker. This is clearly incorrect and likely results from the study being very under-powered. While I am not a statistician by training my experience is that such outlandish results are almost always incorrect and the statistical analysis has been performed incorrectly.

I also note that they have pre-defined cut-off levels of cotinine to determine smoking status. How did these concur with the patients' self reported smoking? Also when reading reference 20 I couldn't see these cut-off levels used but perhaps I missed this.

Finally the English, while intelligible and certainly better than my Swedish, is non-standard. In the first paragraph the authors refer to the 21th rather than the 21st century. They also refer to "medical journals" which to me would mean publications such as PLOS ONE but I believe they mean "medical records". I think it would be important to have a native English speaker to proof read the manuscript before re-submission.

Reviewer #2: Thank you for the opportunity to review the manusrcipt entitled "Elevated plasma cotinine is associated with an increased risk of developing IBD, especially among users of combusted tobacco". The topic is highly interesting but the manuscript would need a bit of a revision.

The Introduction is brief and clear.

In the Materials and Methods it should be added that the matching was not complete in a 1:2 maner.

Why were not previous smokers/snuff users as previous users rather than non-users? This may affect the findings.

Also, and even more important, there is a continuous unclearity throughout the manuscript (and tables) on cotinine levels being the cut off for smokers. Should this not be changed to tobacco users instead as smokers and snuff users later are analysed separately? Causes confusion in it's present form.

In the Results I would prefer to have cotinine levels evaluated first and then separate for smokers and snuff users.

Regarding all tables I would like to have them moved from a separate column at the end to be added in each column respectively. Further you should add % in the columns as this is unclear at the moment.

I do not get the numbers in the tables to add up as expected. E.g. in table 1 Smoking (tobacco user?) is 87/170 but regarding # of cigarettes/day 83/164. In table 2 # cig/day is only 83/156. Non-smokers in table 1 is 96/161 while in table 2 85/188. Same disparities apply for tables 3 and 4.

Was there any data on smoking status at time of diagnosis? Would be highly interesting, especially regarding the increased risk for UC patients.

In the discussion there I would like more discussion on the found risk for UC among smokers/tobacco users. Also there is a recent Swedish publication for incidence for late onset of IBD (Everhov et al) which might be more appropriate in a national epidemiological maner.

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Reviewer #1: No

Reviewer #2: No

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Elevated plasma cotinine is associated with an increased risk of developing IBD, especially among users of combusted tobacco

PONE-D-19-31583R1

Dear Dr. Widbom,

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,

Stefanos Bonovas, M.D., M.Sc., 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 #2: All comments have been addressed

Reviewer #3: 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 #2: Yes

Reviewer #3: Yes

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

Reviewer #2: Yes

Reviewer #3: Yes

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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 #2: Yes

Reviewer #3: 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 #2: Yes

Reviewer #3: Yes

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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 #2: I find that the authors have commented to all questions and changed the manuscript accordingly and improving the manuscript satisfactory.

Reviewer #3: Authors regurarly responded to all the questions, and the suggestions, posed by the previous reviewers. No major issues arised from this second revision.

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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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Reviewer #2: No

Reviewer #3: No