Reviewer’s report
Title:  The analysis of virulence factors and antibiotic resistance between Helicobacter pylori strains  
isolated from gastric antrum and body
Version: 0 Date: 04 Feb 2019
Reviewer: Jay Solnick
Reviewer's report:
The manuscript by Seo et al examines diversity in antibiotic resistance and presence of virulence genes  
between H. pylori strains isolated from the same patient. They found that of 80 patients examined, 10  
had strains with different RAPD fingerprints, and several of these differed in antibiotic susceptibility  
and/or virulence genes.
1.How exactly were the patients and strains selected?  For example, were the 80 patients perhaps  
consecutive with positive cultures?  It is implied but not stated that 1 colony from antrum and 1 from  
body were examined; is this true?  If so, then presumably only patients with positive cultures at both  
sites would be eligible.  If many patients with positive cultures in antrum or body only were found but  
excluded, then the true denominator may be greater than 80 and the prevalence of diversity may thus be  
lower.  Also, since apparently multiple colonies within antrum and body were not examined, we don't  
know whether the location is significant.
2.Figure 2, which just shows a band that represents PCR of ureA, should be deleted.  Why show  
this assay to confirm H. pylori and not any of the others.  All these are routine and need not be shown.
3.On the other hand, why not show the primary data for differences in virulence factors, rather  
than a summary?  
4.The clinical data (Table 2) uses unvalidated terms for histopathology that are not in general use,  
and there is no description in the methods for how the histopathology was determined (definitions of  
mild vs moderate; + vs ++).  Gastric histopathology is well known to be variable across observers, so  
needs to be validated.  On the other hand, are these data at all useful?  How do they inform the general  
point? Is the pathology of the 10 patients with > 1 strain different than in those with only 1?
5.Some of the data in Table 3 are confusing or hard to interpret.  What does 3+1 etc mean for  
oipA?  Since oipA and iceA1 are essentially invariant, why show them?  The babA2 data are hard to  
interpret. babA2 is  an old  term used  by Thomas  Boren when he discovered babA, because  that  
particular strain had two copies of babA, one of which (babA2) had an ORF. But this is atypical, so the  
primers used here probably do not reflect the true babA status of these strains.  This is all the more  
likely since most strains that have cagA also have a functional babA, and all of these strains have cagA.
6.The MIC data would be much more informative and believable if there were some mechanistic  
information. For example, one could sequence the 23S gene to look for differences in Clarithromycin  
susceptibility; similarly gyrA and gyrB for quinolone susceptibility.  
7.While there is a general feeling in the field that diversity is more common in high prevalence  
areas, do we really think that the difference between 39% in Japan and 54% in Korea is sufficient to  
account for this?
Minor Points
1.The abstract says that 7 of the 10 strains had different antibiotic susceptibility patterns; the text  
says 9 had different MICs and 7 had different patterns. The meaning of pattern should be clarified.
2.The methods for confirmation of H. pylori include "Campylobacter-like organism test".  This is  
presumably a rapid urease, but it is an old term and should be replaced by a more precise description of  
exactly what was done.
3.How was H. pylori cultured for isolation of DNA?
4.Table 1 should probably be a supplement.
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.
No
Are 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  further  
assessment in your comments to the editors.
Not relevant to this manuscript
Quality of written English
Please indicate the quality of language in the manuscript:
Acceptable
Declaration 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 this
manuscript, 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.
I declare that I have no competing interests
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 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 included 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:  The analysis of virulence factors and antibiotic resistance between Helicobacter pylori strains  
isolated from gastric antrum and body
Version: 0 Date: 04 Feb 2019
Reviewer: Jay Solnick
Reviewer's report:
The manuscript by Seo et al examines diversity in antibiotic resistance and presence of virulence genes  
between H. pylori strains isolated from the same patient. They found that of 80 patients examined, 10  
had strains with different RAPD fingerprints, and several of these differed in antibiotic susceptibility  
and/or virulence genes.
1.How exactly were the patients and strains selected?  For example, were the 80 patients perhaps  
consecutive with positive cultures?  It is implied but not stated that 1 colony from antrum and 1 from  
body were examined; is this true?  If so, then presumably only patients with positive cultures at both  
sites would be eligible.  If many patients with positive cultures in antrum or body only were found but  
excluded, then the true denominator may be greater than 80 and the prevalence of diversity may thus be  
lower.  Also, since apparently multiple colonies within antrum and body were not examined, we don't  
know whether the location is significant.
2.Figure 2, which just shows a band that represents PCR of ureA, should be deleted.  Why show  
this assay to confirm H. pylori and not any of the others.  All these are routine and need not be shown.
3.On the other hand, why not show the primary data for differences in virulence factors, rather  
than a summary?  
4.The clinical data (Table 2) uses unvalidated terms for histopathology that are not in general use,  
and there is no description in the methods for how the histopathology was determined (definitions of  
mild vs moderate; + vs ++).  Gastric histopathology is well known to be variable across observers, so  
needs to be validated.  On the other hand, are these data at all useful?  How do they inform the general  
point? Is the pathology of the 10 patients with > 1 strain different than in those with only 1?
5.Some of the data in Table 3 are confusing or hard to interpret.  What does 3+1 etc mean for  
oipA?  Since oipA and iceA1 are essentially invariant, why show them?  The babA2 data are hard to  
interpret. babA2 is  an old  term used  by Thomas  Boren when he discovered babA, because  that  
particular strain had two copies of babA, one of which (babA2) had an ORF. But this is atypical, so the  
primers used here probably do not reflect the true babA status of these strains.  This is all the more  
likely since most strains that have cagA also have a functional babA, and all of these strains have cagA.
6.The MIC data would be much more informative and believable if there were some mechanistic  
information. For example, one could sequence the 23S gene to look for differences in Clarithromycin  
susceptibility; similarly gyrA and gyrB for quinolone susceptibility.  
7.While there is a general feeling in the field that diversity is more common in high prevalence  
areas, do we really think that the difference between 39% in Japan and 54% in Korea is sufficient to  
account for this?
Minor Points
1.The abstract says that 7 of the 10 strains had different antibiotic susceptibility patterns; the text  
says 9 had different MICs and 7 had different patterns. The meaning of pattern should be clarified.
2.The methods for confirmation of H. pylori include "Campylobacter-like organism test".  This is  
presumably a rapid urease, but it is an old term and should be replaced by a more precise description of  
exactly what was done.
3.How was H. pylori cultured for isolation of DNA?
4.Table 1 should probably be a supplement.
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.
No
Are 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  further  
assessment in your comments to the editors.
Not relevant to this manuscript
Quality of written English
Please indicate the quality of language in the manuscript:
Acceptable
Declaration 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 this
manuscript, 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.
I declare that I have no competing interests
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 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 included 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:  The analysis of virulence factors and antibiotic resistance between Helicobacter pylori strains  
isolated from gastric antrum and body
Version: 0 Date: 04 Feb 2019
Reviewer: Jay Solnick
Reviewer's report:
The manuscript by Seo et al examines diversity in antibiotic resistance and presence of virulence genes  
between H. pylori strains isolated from the same patient. They found that of 80 patients examined, 10  
had strains with different RAPD fingerprints, and several of these differed in antibiotic susceptibility  
and/or virulence genes.
1.How exactly were the patients and strains selected?  For example, were the 80 patients perhaps  
consecutive with positive cultures?  It is implied but not stated that 1 colony from antrum and 1 from  
body were examined; is this true?  If so, then presumably only patients with positive cultures at both  
sites would be eligible.  If many patients with positive cultures in antrum or body only were found but  
excluded, then the true denominator may be greater than 80 and the prevalence of diversity may thus be  
lower.  Also, since apparently multiple colonies within antrum and body were not examined, we don't  
know whether the location is significant.
2.Figure 2, which just shows a band that represents PCR of ureA, should be deleted.  Why show  
this assay to confirm H. pylori and not any of the others.  All these are routine and need not be shown.
3.On the other hand, why not show the primary data for differences in virulence factors, rather  
than a summary?  
4.The clinical data (Table 2) uses unvalidated terms for histopathology that are not in general use,  
and there is no description in the methods for how the histopathology was determined (definitions of  
mild vs moderate; + vs ++).  Gastric histopathology is well known to be variable across observers, so  
needs to be validated.  On the other hand, are these data at all useful?  How do they inform the general  
point? Is the pathology of the 10 patients with > 1 strain different than in those with only 1?
5.Some of the data in Table 3 are confusing or hard to interpret.  What does 3+1 etc mean for  
oipA?  Since oipA and iceA1 are essentially invariant, why show them?  The babA2 data are hard to  
interpret. babA2 is  an old  term used  by Thomas  Boren when he discovered babA, because  that  
particular strain had two copies of babA, one of which (babA2) had an ORF. But this is atypical, so the  
primers used here probably do not reflect the true babA status of these strains.  This is all the more  
likely since most strains that have cagA also have a functional babA, and all of these strains have cagA.
6.The MIC data would be much more informative and believable if there were some mechanistic  
information. For example, one could sequence the 23S gene to look for differences in Clarithromycin  
susceptibility; similarly gyrA and gyrB for quinolone susceptibility.  
7.While there is a general feeling in the field that diversity is more common in high prevalence  
areas, do we really think that the difference between 39% in Japan and 54% in Korea is sufficient to  
account for this?
Minor Points
1.The abstract says that 7 of the 10 strains had different antibiotic susceptibility patterns; the text  
says 9 had different MICs and 7 had different patterns. The meaning of pattern should be clarified.
2.The methods for confirmation of H. pylori include "Campylobacter-like organism test".  This is  
presumably a rapid urease, but it is an old term and should be replaced by a more precise description of  
exactly what was done.
3.How was H. pylori cultured for isolation of DNA?
4.Table 1 should probably be a supplement.
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.
No
Are 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  further  
assessment in your comments to the editors.
Not relevant to this manuscript
Quality of written English
Please indicate the quality of language in the manuscript:
Acceptable
Declaration 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 this
manuscript, 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.
I declare that I have no competing interests
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 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 included as confidential comments to the editors, which will not  
be published.
I agree to the open peer review policy of the journal
assistant