PONE-D-19-25985

Pneumococcal Colonisation is an Asymptomatic Event in Healthy Adults using an Experimental Human Colonisation Model.

PLOS ONE

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Reviewers' comments:

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Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: The manuscript by Trimble and colleagues present additional results from an experimental human challenge model, describing whether experimental pneumococcal colonisation in healthy adults is a symptomatic event. This manuscript is a resubmission from 2016 (but due to time limits is now a new submission) which has addressed some of the queries from the initial review. This study reports some interesting data but is nevertheless limited mainly due to the small sample size, especially for the secondary analyses.

Some points for consideration:

1. The pneumococcal colonisation rate was 30.4% (14/46), which was solely due to serotype 6B, and actually 48% if only those who were inoculated with 6B are included. This seems quite high for an otherwise healthy adult population. The authors state that this model mimics natural pneumococcal exposure but the high carriage rate may suggest otherwise. Can the authors provide some comment on the colonisation rate they observed with respect to what has been reported among UK healthy adults or more generally? Some explanation of this would greatly benefit the manuscript. The authors also argued against providing some comment on the lack of 23F colonisation but I tend to think that this would also be worth noting in the discussion, given that both these are commonly carried serotypes.

2. Figures 2 and 3 could be combined since they are both essentially reporting the same data but with a different comparison. Also, it should be Fisher’s exact test, not Fischer’s exact test.

3. Can the authors comment on the apparent high rate of nasal and non-nasal symptoms in the control group and whether they believe this could have contributed to the lack of any clinical symptoms being demonstrated for the other groups? An independent assessor may have been useful here.

4. There are a couple of instances where what is reported in the results is inconsistent with the data or discussion. For example, on lines 192-193 it states that “This study does not however report the effect of co-colonisation (SPN and virus) on symptoms” when this is clearly shown in Figure 5. Also on lines 207-208, it states that “…experimental SPN colonisation does not increase nasal or non-nasal symptoms” when in the results (lines 156-157) it states that “Experimental SPN colonisation rates were higher in the presence of virus….(p<0.05)”. Please correct. The p-value, if indeed significant, should be included in the Figure.

5. What were the viruses that were detected, and were there any associations between specific viruses?

6. For most of the reported p-values there are no = sign. Please include.

Reviewer #2: General comments

This study uses a human challenge model to examine if symptoms are experienced in the context of pneumococcal colonisation among adults. The structure of the paper is acceptable, however there could be improvement made in the finer details, e.g. error bars/confidence intervals and raw numbers

I think it is also important to mention the limitations of this study e.g. not an RCT, low sample size, and only one serotype successfully colonised. Consequently I think some of the statements in the discussion should have the language softened, as this study is not the definitive study which demonstrates that colonisation is asymptomatic among adults. Rather it might suggest this, but further work using more serotypes, in larger RCTs is needed.

Specific comments

#Abstract

Methods section line 46

" ... reported between groups was compared ..." to groups were compared

Results section line 49

S. pneumoniae (29 with serotype 6B, 17 with serotype 23F ...

Conclusion section line 58

Pneumococcal colonisation using the EHPC was asymptomatic ...

#Introduction

line 69 - correct typo, H. influenzae

line 70-73 - could be better worded

lines 83-87 - suggest rearranging this paragraph e.g.

The experimental pneumococcal challenge model (EHPC) mimics natural colonisation in healthy ....vaccines in randomised control trials. We aimed to use the EHPC to investigate if the process is symptomatic....

#Methods

Was a sample size calculation conducted?

#Results

line 134-137

please provide actual numbers, proportions, confidence intervals, and p-values.

figures - please add in confidence intervals.

#Discussion

Lines 164 and 212

I would tone down the language here e.g.

This study provides evidence supporting the hypothesis that SPN colonisation among adults is asymptomatic

line 171

Other than sample size, key limitations also include: the study wasn't randomised, only one serotype was assessed in this study, and pre-existing immunity.

line 213

I would suggest adding a sentence to say that larger randomised studies using a wider variety of

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Reviewer #1: No

Reviewer #2: Yes: Rama Kandasamy

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Pneumococcal Colonisation is an Asymptomatic Event in Healthy Adults using an Experimental Human Colonisation Model.

PONE-D-19-25985R1

Dear Dr. Robinson,

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.

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With kind regards,

Ray Borrow, Ph.D., FRCPath

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

**********

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

**********

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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Reviewer #1: No