Reviewer ’s report  
 
Title: Helicobacter pylori vacA, cagA and iceA genotypes  in dyspeptic patients from the 
southwestern region of Saudi Arabia: Distribution and associa tion with clinical outcomes and 
histopathological changes  
 
Version: 1 Date: 09 Oct 2018  
 
Reviewer: Amin Talebi Bezmin Abadi  
 
Reviewer's report:  
 
Please include all comments for the authors in this box rather than uploading your report as an 
attachment. Please only upload as attachments annotated versions of manuscripts, graphs, 
supporting materials or other aspects of your report which cannot be i ncluded in a text format.  
 
Please overwrite this text when adding your comments to the authors.  
 
 
Dear Editor in BMC Gastroenterology  
 
My pleasure to see your invitation addressing this cross sectional paper,  
 
I have some suggestions/critics and modification s to improve this paper which I found it 
interesting for publication in BMC journal.  
 
 
1- The title is too long and descriptive. I would prefer to see more informative one. 
Generally, it is not acceptable to say everything in the title for a cross sectional paper.  
 
 
2- In background section of abstract: the actual aims stated by the authors are in a line, why 
they divided these same goals into two different ones? Please correct it.  
 
 
3- The result section for abstract should be reduced in word count. I see some u nnecessary 
parts in it, so please delete them all.  
 
 
4- The word H. pylori in many of sentences are not italic, please address this correction all 
over the manuscript.  
 
 
5- Basically, if the authors want to talk about the virulence genes, the y should have th ink 
about many of proposed virulence genes for HP. For example, dupA, babA and homB are 
the minimum candidates which deserve more investigation by the researchers before they 
can conclude about virulence determinants of HP. So I would see the rationale for  such 
selection by the authors or performing this survey as I mentioned in revised manuscript 
afterwards.  
 
 
6- The page 3 - line 65, add the word ''bacterial'' before the carcinogen.  
 
 
7- The page 3, line 73, whole line needs a reference, and without the refer ence this section 
should be removed. Mainly from the region authors work. For example, these references 
are suggestive:  
 
 
a-High correlation of babA 2 -positive strains of Helicobacter pylori with the presence of gastric 
cancer  
 
b-Prevalence of Helicobacter p ylori vacA, cagA, cagE, iceA, babA2, and oipA genotypes in 
patients with upper gastrointestinal diseases  
 
c-High frequency of vacA s1m2 genotypes among Helicobacter pylori isolates from patients with 
gastroduodenal disorders in Kermanshah, Iran  
 
d-Clinical relevance of the cagA, tnpA and tnpB genes in Helicobacter pylori  
 
 
8- Whole page -4 needs rewrite in English!  
 
 
9- All genes should be italic, it is large number of genes which wrote not -italic through the 
paper.  
 
10- Of how many biopsies, the auth ors could take 128 positive biopsy specimens which hare 
all positive for HP? This should be clarified in the M&M. This is very important since I 
think this paper designed as cross sectional study but something are lacking in my 
opinion. Howeve, the other c riterias for a cross -sectional study is not met and I think that 
they selected manually those 128 samples! This is a major query should be replied in 
detailed by the authors before final decision.  
 
 
11- Page7 is a bit elongated text, please reduce it.  
 
 
12- PAGE 4 Line 108 -109, should be deleted! Since it is obvious statement and not necessary 
for a scientific paper  
 
 
13- Page4, what was the identity of the positive control applied in the study?  
 
 
14- I think that the paper can be considered as short communication  rather a original paper. 
However, it can be an original paper only after making new experiments such as 
determining the new virulence factors as I suggested in above.  
 
 
15- The first sentence is discussion should be removed since it is not true! If they ins ist on 
their claim, we need to see new references confirming their idea and statics.  
 
 
16- Page 10 -line 232, this sentence is not clear to me! I know what they meant but I need to 
read it once and get the meaning rapidly not think 20 minutes!  
 
 
17- The literat ure review made by the authors to excuse the result in discussion part is not 
enough. I like this study but the authors should have informed that we need better search 
to publish this paper in BMC -Gastro!!!!!  
 
 
Finally, I would see the revision if possible.  
 
 
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls  are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
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 speci fy what aspects require further 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
 
 
Declaration of competing interests  
Please complete a declaration of competing in terests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, f ees, funding, or salary from an 
organisation that may in any way gain or lose financial ly from the publication of this 
manuscript, either now or in t he future?  
 
2. Do you hold any stocks or shares in an organisation t hat 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 th e 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 y ou 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.  
 
no COI.  
 
I agree to the open peer review policy of the journal. I understan d that my name will be included 
on my report to the authors and, if the manuscript is accepted f or publication, my named repor t 
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 Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do not wish to be included in my named report can be in cluded as confidential comments 
to the editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
Reviewer ’s report  
 
Title: Helicobacter pylori vacA, cagA and iceA genotypes  in dyspeptic patients from the 
southwestern region of Saudi Arabia: Distribution and associa tion with clinical outcomes and 
histopathological changes  
 
Version: 1 Date: 09 Oct 2018  
 
Reviewer: Amin Talebi Bezmin Abadi  
 
Reviewer's report:  
 
Please include all comments for the authors in this box rather than uploading your report as an 
attachment. Please only upload as attachments annotated versions of manuscripts, graphs, 
supporting materials or other aspects of your report which cannot be i ncluded in a text format.  
 
Please overwrite this text when adding your comments to the authors.  
 
 
Dear Editor in BMC Gastroenterology  
 
My pleasure to see your invitation addressing this cross sectional paper,  
 
I have some suggestions/critics and modification s to improve this paper which I found it 
interesting for publication in BMC journal.  
 
 
1- The title is too long and descriptive. I would prefer to see more informative one. 
Generally, it is not acceptable to say everything in the title for a cross sectional paper.  
 
 
2- In background section of abstract: the actual aims stated by the authors are in a line, why 
they divided these same goals into two different ones? Please correct it.  
 
 
3- The result section for abstract should be reduced in word count. I see some u nnecessary 
parts in it, so please delete them all.  
 
 
4- The word H. pylori in many of sentences are not italic, please address this correction all 
over the manuscript.  
 
 
5- Basically, if the authors want to talk about the virulence genes, the y should have th ink 
about many of proposed virulence genes for HP. For example, dupA, babA and homB are 
the minimum candidates which deserve more investigation by the researchers before they 
can conclude about virulence determinants of HP. So I would see the rationale for  such 
selection by the authors or performing this survey as I mentioned in revised manuscript 
afterwards.  
 
 
6- The page 3 - line 65, add the word ''bacterial'' before the carcinogen.  
 
 
7- The page 3, line 73, whole line needs a reference, and without the refer ence this section 
should be removed. Mainly from the region authors work. For example, these references 
are suggestive:  
 
 
a-High correlation of babA 2 -positive strains of Helicobacter pylori with the presence of gastric 
cancer  
 
b-Prevalence of Helicobacter p ylori vacA, cagA, cagE, iceA, babA2, and oipA genotypes in 
patients with upper gastrointestinal diseases  
 
c-High frequency of vacA s1m2 genotypes among Helicobacter pylori isolates from patients with 
gastroduodenal disorders in Kermanshah, Iran  
 
d-Clinical relevance of the cagA, tnpA and tnpB genes in Helicobacter pylori  
 
 
8- Whole page -4 needs rewrite in English!  
 
 
9- All genes should be italic, it is large number of genes which wrote not -italic through the 
paper.  
 
10- Of how many biopsies, the auth ors could take 128 positive biopsy specimens which hare 
all positive for HP? This should be clarified in the M&M. This is very important since I 
think this paper designed as cross sectional study but something are lacking in my 
opinion. Howeve, the other c riterias for a cross -sectional study is not met and I think that 
they selected manually those 128 samples! This is a major query should be replied in 
detailed by the authors before final decision.  
 
 
11- Page7 is a bit elongated text, please reduce it.  
 
 
12- PAGE 4 Line 108 -109, should be deleted! Since it is obvious statement and not necessary 
for a scientific paper  
 
 
13- Page4, what was the identity of the positive control applied in the study?  
 
 
14- I think that the paper can be considered as short communication  rather a original paper. 
However, it can be an original paper only after making new experiments such as 
determining the new virulence factors as I suggested in above.  
 
 
15- The first sentence is discussion should be removed since it is not true! If they ins ist on 
their claim, we need to see new references confirming their idea and statics.  
 
 
16- Page 10 -line 232, this sentence is not clear to me! I know what they meant but I need to 
read it once and get the meaning rapidly not think 20 minutes!  
 
 
17- The literat ure review made by the authors to excuse the result in discussion part is not 
enough. I like this study but the authors should have informed that we need better search 
to publish this paper in BMC -Gastro!!!!!  
 
 
Finally, I would see the revision if possible.  
 
 
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls  are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
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 speci fy what aspects require further 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
 
 
Declaration of competing interests  
Please complete a declaration of competing in terests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, f ees, funding, or salary from an 
organisation that may in any way gain or lose financial ly from the publication of this 
manuscript, either now or in t he future?  
 
2. Do you hold any stocks or shares in an organisation t hat 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 th e 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 y ou 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.  
 
no COI.  
 
I agree to the open peer review policy of the journal. I understan d that my name will be included 
on my report to the authors and, if the manuscript is accepted f or publication, my named repor t 
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 Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do not wish to be included in my named report can be in cluded as confidential comments 
to 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: Helicobacter pylori vacA, cagA and iceA genotypes  in dyspeptic patients from the 
southwestern region of Saudi Arabia: Distribution and associa tion with clinical outcomes and 
histopathological changes  
 
Version: 1 Date: 09 Oct 2018  
 
Reviewer: Amin Talebi Bezmin Abadi  
 
Reviewer's report:  
 
Please include all comments for the authors in this box rather than uploading your report as an 
attachment. Please only upload as attachments annotated versions of manuscripts, graphs, 
supporting materials or other aspects of your report which cannot be i ncluded in a text format.  
 
Please overwrite this text when adding your comments to the authors.  
 
 
Dear Editor in BMC Gastroenterology  
 
My pleasure to see your invitation addressing this cross sectional paper,  
 
I have some suggestions/critics and modification s to improve this paper which I found it 
interesting for publication in BMC journal.  
 
 
1- The title is too long and descriptive. I would prefer to see more informative one. 
Generally, it is not acceptable to say everything in the title for a cross sectional paper.  
 
 
2- In background section of abstract: the actual aims stated by the authors are in a line, why 
they divided these same goals into two different ones? Please correct it.  
 
 
3- The result section for abstract should be reduced in word count. I see some u nnecessary 
parts in it, so please delete them all.  
 
 
4- The word H. pylori in many of sentences are not italic, please address this correction all 
over the manuscript.  
 
 
5- Basically, if the authors want to talk about the virulence genes, the y should have th ink 
about many of proposed virulence genes for HP. For example, dupA, babA and homB are 
the minimum candidates which deserve more investigation by the researchers before they 
can conclude about virulence determinants of HP. So I would see the rationale for  such 
selection by the authors or performing this survey as I mentioned in revised manuscript 
afterwards.  
 
 
6- The page 3 - line 65, add the word ''bacterial'' before the carcinogen.  
 
 
7- The page 3, line 73, whole line needs a reference, and without the refer ence this section 
should be removed. Mainly from the region authors work. For example, these references 
are suggestive:  
 
 
a-High correlation of babA 2 -positive strains of Helicobacter pylori with the presence of gastric 
cancer  
 
b-Prevalence of Helicobacter p ylori vacA, cagA, cagE, iceA, babA2, and oipA genotypes in 
patients with upper gastrointestinal diseases  
 
c-High frequency of vacA s1m2 genotypes among Helicobacter pylori isolates from patients with 
gastroduodenal disorders in Kermanshah, Iran  
 
d-Clinical relevance of the cagA, tnpA and tnpB genes in Helicobacter pylori  
 
 
8- Whole page -4 needs rewrite in English!  
 
 
9- All genes should be italic, it is large number of genes which wrote not -italic through the 
paper.  
 
10- Of how many biopsies, the auth ors could take 128 positive biopsy specimens which hare 
all positive for HP? This should be clarified in the M&M. This is very important since I 
think this paper designed as cross sectional study but something are lacking in my 
opinion. Howeve, the other c riterias for a cross -sectional study is not met and I think that 
they selected manually those 128 samples! This is a major query should be replied in 
detailed by the authors before final decision.  
 
 
11- Page7 is a bit elongated text, please reduce it.  
 
 
12- PAGE 4 Line 108 -109, should be deleted! Since it is obvious statement and not necessary 
for a scientific paper  
 
 
13- Page4, what was the identity of the positive control applied in the study?  
 
 
14- I think that the paper can be considered as short communication  rather a original paper. 
However, it can be an original paper only after making new experiments such as 
determining the new virulence factors as I suggested in above.  
 
 
15- The first sentence is discussion should be removed since it is not true! If they ins ist on 
their claim, we need to see new references confirming their idea and statics.  
 
 
16- Page 10 -line 232, this sentence is not clear to me! I know what they meant but I need to 
read it once and get the meaning rapidly not think 20 minutes!  
 
 
17- The literat ure review made by the authors to excuse the result in discussion part is not 
enough. I like this study but the authors should have informed that we need better search 
to publish this paper in BMC -Gastro!!!!!  
 
 
Finally, I would see the revision if possible.  
 
 
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls  are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
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 speci fy what aspects require further 
assessment in your comments to the editors.  
 
I am able to assess the statistics  
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
 
 
Declaration of competing interests  
Please complete a declaration of competing in terests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, f ees, funding, or salary from an 
organisation that may in any way gain or lose financial ly from the publication of this 
manuscript, either now or in t he future?  
 
2. Do you hold any stocks or shares in an organisation t hat 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 th e 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 y ou 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.  
 
no COI.  
 
I agree to the open peer review policy of the journal. I understan d that my name will be included 
on my report to the authors and, if the manuscript is accepted f or publication, my named repor t 
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 Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do not wish to be included in my named report can be in cluded as confidential comments 
to the editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
assistant