Reviewer’ s report
Title: Prevalence of non Helicobacter pylori gastric Helicobacters in Iranian dyspeptic patients
Version: 1Date: 21 May 2019
Reviewer: Research Square Reviewer 1
Reviewer's report:
PEER REVIEWER ASSESSMENTS: OBJECTIVE - Full research articles: is there a clear
objective that addresses one or several testable research questions? (Brief or other article types: isthere a clear objective?)Yes - there is a clear objectiveDESIGN - Is the current approach (includingcontrols and analysis protocols) appropriate for the objective?No - there are minorissuesEXECUTION - Are the experiments and analyses performed with sufficient technical rigorto allow confidence in the results?No - there are minor issuesSTATISTICS - Is the use of statisticsin the manuscript appropriate?Yes - appropriate statistical analyses have been used in thestudyINTERPRETATION - Is the current interpretation/discussion of the results reasonable andnot overstated?No - there are minor issuesOVERALL MANUSCRIPT POTENTIAL - Has theauthor addressed your concerns sufficiently for you to now recommend the work as a technicallysound contribution? If not, can further revisions be made to make the work technicallysound?Probably - with minor revisionsPEER REVIEWER COMMENTS: GENERAL COM-MENTS: The authors have attempted to answer some of this reviewer's comments and haveimproved the manuscript but there are still issues that prevent this work being published in itspresent form. They have corrected errors (e.g. number of Helicobacter species identified, referenceto Gastrospirillum, addition of p values and removal of "16S rRNA PCR of housekeeping genes")and have provided missing information (e.g. location of hospital, inclusion and discussion of other
similar studies). REQUESTED REVISIONS: One important issue that remains is that the authors
did not sequence any of the amplicons that they generated. This means that they distinguishedbetween Helicobacter species by differences in amplicon size only. The problem with this is thatsome of the amplicon sizes, as listed in Table 1, are very similar (e.g. 305 bp for H. felis and 368bp for H. heimannii). In this reviewer's opinion it would be very difficult to distinguish these sizedifferences in standard agarose gels. In addition, this PCR approach does not take the possibility offalse positives into consideration. If the authors are still unable to sequence some of the amplicons(which is still the preferred option) then they should at least provide a gel picture that shows all ofthe 5 possible amplicons (i.e. 253 bp, 172 bp, 350 bp, 219 bp, 368 bp) generated from referencematerial/controls, side by side on the same agarose gel (I recommend a 2.5% w/v gel). Withoutthis, their results are not convincing. It is not clear whether the Real-time PCR was able todistinguish species. This should be clarified. The quality of the English, syntax and style seemsworse than before and needs to be improved.They have still failed to highlight the novelty of thisstudy for Iran. There is no mention of Iran in the Abstract or Introduction.ADDITIONALREQUESTS/SUGGESTIONS: None
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
No
Does the work include the necessary controls?
If not, please specify which controls are required in your comments to the authors.
NoAre the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
No
Are you able to assess any statistics in the manuscript or would you recommend an
additional statistical review?If an additional statistical review is recommended, please specify what aspects require furtherassessment in your comments to the editors.
I am able to assess the statisticsQuality of written English
Please indicate the quality of language in the manuscript:
Needs some language corrections before being publishedDeclaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of thismanuscript, either now or in the future?
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?
4. Have you received reimbursements, fees, funding, or salary from an organization that holds
or has applied for patents relating to the content of the manuscript?
5. Do you have any other financial competing interests?6. Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests' below.
If your reply is yes to any, please give details below.
This reviewer has been recruited by a partner organization, Research Square. Reviewers with
declared or apparent competing interests are not utilized for these reviews. This reviewer hasagreed to publication of their comments online under a Creative Commons Attribution Licenseattributed to Research Square and was paid a small honorarium for completing the review within aspecified timeframe. Honoraria for reviews such as this are paid regardless of the reviewerrecommendation.
I agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named report
including any attachments I upload will be posted on the website along with the authors'
responses. I agree for my report to be made available under an Open Access Creative CommonsCC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any commentswhich I do not wish to be included in my named report can be included as confidential commentsto the editors, which will not be published.
I agree to the open peer review policy of the journal
Reviewer’ s report
Title: Prevalence of non Helicobacter pylori gastric Helicobacters in Iranian dyspeptic patients
Version: 1Date: 21 May 2019
Reviewer: Research Square Reviewer 1
Reviewer's report:
PEER REVIEWER ASSESSMENTS: OBJECTIVE - Full research articles: is there a clear
objective that addresses one or several testable research questions? (Brief or other article types: isthere a clear objective?)Yes - there is a clear objectiveDESIGN - Is the current approach (includingcontrols and analysis protocols) appropriate for the objective?No - there are minorissuesEXECUTION - Are the experiments and analyses performed with sufficient technical rigorto allow confidence in the results?No - there are minor issuesSTATISTICS - Is the use of statisticsin the manuscript appropriate?Yes - appropriate statistical analyses have been used in thestudyINTERPRETATION - Is the current interpretation/discussion of the results reasonable andnot overstated?No - there are minor issuesOVERALL MANUSCRIPT POTENTIAL - Has theauthor addressed your concerns sufficiently for you to now recommend the work as a technicallysound contribution? If not, can further revisions be made to make the work technicallysound?Probably - with minor revisionsPEER REVIEWER COMMENTS: GENERAL COM-MENTS: The authors have attempted to answer some of this reviewer's comments and haveimproved the manuscript but there are still issues that prevent this work being published in itspresent form. They have corrected errors (e.g. number of Helicobacter species identified, referenceto Gastrospirillum, addition of p values and removal of "16S rRNA PCR of housekeeping genes")and have provided missing information (e.g. location of hospital, inclusion and discussion of other
similar studies). REQUESTED REVISIONS: One important issue that remains is that the authors
did not sequence any of the amplicons that they generated. This means that they distinguishedbetween Helicobacter species by differences in amplicon size only. The problem with this is thatsome of the amplicon sizes, as listed in Table 1, are very similar (e.g. 305 bp for H. felis and 368bp for H. heimannii). In this reviewer's opinion it would be very difficult to distinguish these sizedifferences in standard agarose gels. In addition, this PCR approach does not take the possibility offalse positives into consideration. If the authors are still unable to sequence some of the amplicons(which is still the preferred option) then they should at least provide a gel picture that shows all ofthe 5 possible amplicons (i.e. 253 bp, 172 bp, 350 bp, 219 bp, 368 bp) generated from referencematerial/controls, side by side on the same agarose gel (I recommend a 2.5% w/v gel). Withoutthis, their results are not convincing. It is not clear whether the Real-time PCR was able todistinguish species. This should be clarified. The quality of the English, syntax and style seemsworse than before and needs to be improved.They have still failed to highlight the novelty of thisstudy for Iran. There is no mention of Iran in the Abstract or Introduction.ADDITIONALREQUESTS/SUGGESTIONS: None
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
No
Does the work include the necessary controls?
If not, please specify which controls are required in your comments to the authors.
NoAre the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
No
Are you able to assess any statistics in the manuscript or would you recommend an
additional statistical review?If an additional statistical review is recommended, please specify what aspects require furtherassessment in your comments to the editors.
I am able to assess the statisticsQuality of written English
Please indicate the quality of language in the manuscript:
Needs some language corrections before being publishedDeclaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of thismanuscript, either now or in the future?
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?
4. Have you received reimbursements, fees, funding, or salary from an organization that holds
or has applied for patents relating to the content of the manuscript?
5. Do you have any other financial competing interests?6. Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests' below.
If your reply is yes to any, please give details below.
This reviewer has been recruited by a partner organization, Research Square. Reviewers with
declared or apparent competing interests are not utilized for these reviews. This reviewer hasagreed to publication of their comments online under a Creative Commons Attribution Licenseattributed to Research Square and was paid a small honorarium for completing the review within aspecified timeframe. Honoraria for reviews such as this are paid regardless of the reviewerrecommendation.
I agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named report
including any attachments I upload will be posted on the website along with the authors'
responses. I agree for my report to be made available under an Open Access Creative CommonsCC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any commentswhich I do not wish to be included in my named report can be included as confidential commentsto the editors, which will not be published.
I agree to the open peer review policy of the journal
Please review this paper.
user
Reviewer’ s report
Title: Prevalence of non Helicobacter pylori gastric Helicobacters in Iranian dyspeptic patients
Version: 1Date: 21 May 2019
Reviewer: Research Square Reviewer 1
Reviewer's report:
PEER REVIEWER ASSESSMENTS: OBJECTIVE - Full research articles: is there a clear
objective that addresses one or several testable research questions? (Brief or other article types: isthere a clear objective?)Yes - there is a clear objectiveDESIGN - Is the current approach (includingcontrols and analysis protocols) appropriate for the objective?No - there are minorissuesEXECUTION - Are the experiments and analyses performed with sufficient technical rigorto allow confidence in the results?No - there are minor issuesSTATISTICS - Is the use of statisticsin the manuscript appropriate?Yes - appropriate statistical analyses have been used in thestudyINTERPRETATION - Is the current interpretation/discussion of the results reasonable andnot overstated?No - there are minor issuesOVERALL MANUSCRIPT POTENTIAL - Has theauthor addressed your concerns sufficiently for you to now recommend the work as a technicallysound contribution? If not, can further revisions be made to make the work technicallysound?Probably - with minor revisionsPEER REVIEWER COMMENTS: GENERAL COM-MENTS: The authors have attempted to answer some of this reviewer's comments and haveimproved the manuscript but there are still issues that prevent this work being published in itspresent form. They have corrected errors (e.g. number of Helicobacter species identified, referenceto Gastrospirillum, addition of p values and removal of "16S rRNA PCR of housekeeping genes")and have provided missing information (e.g. location of hospital, inclusion and discussion of other
similar studies). REQUESTED REVISIONS: One important issue that remains is that the authors
did not sequence any of the amplicons that they generated. This means that they distinguishedbetween Helicobacter species by differences in amplicon size only. The problem with this is thatsome of the amplicon sizes, as listed in Table 1, are very similar (e.g. 305 bp for H. felis and 368bp for H. heimannii). In this reviewer's opinion it would be very difficult to distinguish these sizedifferences in standard agarose gels. In addition, this PCR approach does not take the possibility offalse positives into consideration. If the authors are still unable to sequence some of the amplicons(which is still the preferred option) then they should at least provide a gel picture that shows all ofthe 5 possible amplicons (i.e. 253 bp, 172 bp, 350 bp, 219 bp, 368 bp) generated from referencematerial/controls, side by side on the same agarose gel (I recommend a 2.5% w/v gel). Withoutthis, their results are not convincing. It is not clear whether the Real-time PCR was able todistinguish species. This should be clarified. The quality of the English, syntax and style seemsworse than before and needs to be improved.They have still failed to highlight the novelty of thisstudy for Iran. There is no mention of Iran in the Abstract or Introduction.ADDITIONALREQUESTS/SUGGESTIONS: None
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
No
Does the work include the necessary controls?
If not, please specify which controls are required in your comments to the authors.
NoAre the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
No
Are you able to assess any statistics in the manuscript or would you recommend an
additional statistical review?If an additional statistical review is recommended, please specify what aspects require furtherassessment in your comments to the editors.
I am able to assess the statisticsQuality of written English
Please indicate the quality of language in the manuscript:
Needs some language corrections before being publishedDeclaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of thismanuscript, either now or in the future?
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?
4. Have you received reimbursements, fees, funding, or salary from an organization that holds
or has applied for patents relating to the content of the manuscript?
5. Do you have any other financial competing interests?6. Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests' below.
If your reply is yes to any, please give details below.
This reviewer has been recruited by a partner organization, Research Square. Reviewers with
declared or apparent competing interests are not utilized for these reviews. This reviewer hasagreed to publication of their comments online under a Creative Commons Attribution Licenseattributed to Research Square and was paid a small honorarium for completing the review within aspecified timeframe. Honoraria for reviews such as this are paid regardless of the reviewerrecommendation.
I agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named report
including any attachments I upload will be posted on the website along with the authors'
responses. I agree for my report to be made available under an Open Access Creative CommonsCC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any commentswhich I do not wish to be included in my named report can be included as confidential commentsto the editors, which will not be published.
I agree to the open peer review policy of the journal
assistant