Reviewer's report 
 Helicobacter pylori Genotypes Identified in Gastric Biopsy Specimens from Jordanian patients Title: 
 4  2 August 2006 Version: Date: 
 Barbara Schneider Reviewer: 
Reviewer's report: 
General 
The authors have state that they intend to separate out the histology into a separate paper. It would be 
preferable to have all in a single large paper, rather than the 2 small ones. The investigators have done much work on a good size patient population, and a combined study of histology and genotyping would be of more interest than the 2 smaller, incomplete papers would be. 
------------------------------------------------------------------------------- 
Major Compulsory Revisions (that the author must respond to before a decision on publication can be reached) 
The revised version of the manuscript by Nimri et al. is much better, but still leaves important questions 
unanswered: How did the PCR findings relate to the histology? We are told that they were associated or 
correlated, but how many were positive by histology but failed at PCR? Were any positive by PCR that were 
negative by histology? What controls did the investigators use for PCR ? 
In my previous review, I recommended the use of the term â€œassociatedâ€  instead of 
â€œcorrelatedâ€ . For results obtained with the Spearman rho test, â€œcorrelatedâ€  is the correct term 
to use. However, use of this test requires that the paper include more information regarding how the 
comparisons were done, in a correlation matrix. The test requires some kind of ranking of the non-parametric categories of histology, which means the biopsies had to be categorized and ranked as 
more or less severe in their gastric pathology. If the histological analysis is not to be presented in this paper 
(as recommended by the other reviewer) , then it would be preferable not to include the Spearman analysis 
in this paper. If the goal is to simply look for an association of positivity by histology vs. PCR, this can be done with a Fisherâ€™s or chi square test. â€œAssociatedâ€  is the correct term to use for results from 
those tests.. 
Also, throughout the results section, the text still uses the term â€œwas presentâ€™ where â€œwas 
detectedâ€  should be used. Also the text states that biopsies â€œhadâ€  a certain genotype, when what 
is meant is they â€œshowedâ€  a certain genotype, because some that had it did not show it, in the tests 
used. All of us working in the field know that we sometimes get false negatives, but this language will 
confuse those not familiar with the technical situation. 
Page 2 , Abstract, Conclusions: The reader will be looking here to see what is new. The geographic nature 
of H.pylori genetic diversity is not new, so I suggest changing the sentence to â€œThe results illustrate the 
geographic nature of the genetic diversity of H.pylori, as the identified genotypes are similar to those reported in neighboring countries.â€ 
Similarly, in the conclusions at the end of the paper, the part about the geographic distribution should not be 
listed as if it were new. 
Page 9, line 3: What do the authors mean by â€œobvious differences in two neighboring countriesâ€ ? 
The differences are not obvious to those of us who do not live in those countries. Do the authors mean 
differences in life styles? 
Page 10, line 7: We are told that s2 and m1 are independent of each other, but the p value (0.02) is one 
usually used for a significant association. ------------------------------------------------------------------------------- 
Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author 
can be trusted to correct) 
At the end of the Background section, it appears that each sentence is a new paragraph. These should all 
be combined in the same paragraph. 
Page 6: line 9: â€œSpearmanâ€  should be capitalized. 
Page 9, line 8 from bottom: this is a run-on sentence. After â€œcagA genotypeâ€ , there should be a 
period and start of a new sentence, or at least a semicolon to separate the clauses. 
In several places, the text uses the terms â€œequally presentâ€ . This is an awkward and confusing term, 
as present is not a condition subject to quantitation. Do they mean â€œpresent in approximately equal amountsâ€ ? 
------------------------------------------------------------------------------- 
Discretionary Revisions (which the author can choose to ignore) 
 Unable to decide on acceptance or rejection until the authors have responded to the major What next?: 
compulsory revisions 
 An article whose findings are important to those with closely related research interests Level of interest: 
 Needs some language corrections before being published Quality of written English: 
 Yes Statistical review: 
Declaration of competing interests: 
I have no competing interests. 
Reviewer's report 
 Helicobacter pylori Genotypes Identified in Gastric Biopsy Specimens from Jordanian patients Title: 
 4  2 August 2006 Version: Date: 
 Barbara Schneider Reviewer: 
Reviewer's report: 
General 
The authors have state that they intend to separate out the histology into a separate paper. It would be 
preferable to have all in a single large paper, rather than the 2 small ones. The investigators have done much work on a good size patient population, and a combined study of histology and genotyping would be of more interest than the 2 smaller, incomplete papers would be. 
------------------------------------------------------------------------------- 
Major Compulsory Revisions (that the author must respond to before a decision on publication can be reached) 
The revised version of the manuscript by Nimri et al. is much better, but still leaves important questions 
unanswered: How did the PCR findings relate to the histology? We are told that they were associated or 
correlated, but how many were positive by histology but failed at PCR? Were any positive by PCR that were 
negative by histology? What controls did the investigators use for PCR ? 
In my previous review, I recommended the use of the term â€œassociatedâ€  instead of 
â€œcorrelatedâ€ . For results obtained with the Spearman rho test, â€œcorrelatedâ€  is the correct term 
to use. However, use of this test requires that the paper include more information regarding how the 
comparisons were done, in a correlation matrix. The test requires some kind of ranking of the non-parametric categories of histology, which means the biopsies had to be categorized and ranked as 
more or less severe in their gastric pathology. If the histological analysis is not to be presented in this paper 
(as recommended by the other reviewer) , then it would be preferable not to include the Spearman analysis 
in this paper. If the goal is to simply look for an association of positivity by histology vs. PCR, this can be done with a Fisherâ€™s or chi square test. â€œAssociatedâ€  is the correct term to use for results from 
those tests.. 
Also, throughout the results section, the text still uses the term â€œwas presentâ€™ where â€œwas 
detectedâ€  should be used. Also the text states that biopsies â€œhadâ€  a certain genotype, when what 
is meant is they â€œshowedâ€  a certain genotype, because some that had it did not show it, in the tests 
used. All of us working in the field know that we sometimes get false negatives, but this language will 
confuse those not familiar with the technical situation. 
Page 2 , Abstract, Conclusions: The reader will be looking here to see what is new. The geographic nature 
of H.pylori genetic diversity is not new, so I suggest changing the sentence to â€œThe results illustrate the 
geographic nature of the genetic diversity of H.pylori, as the identified genotypes are similar to those reported in neighboring countries.â€ 
Similarly, in the conclusions at the end of the paper, the part about the geographic distribution should not be 
listed as if it were new. 
Page 9, line 3: What do the authors mean by â€œobvious differences in two neighboring countriesâ€ ? 
The differences are not obvious to those of us who do not live in those countries. Do the authors mean 
differences in life styles? 
Page 10, line 7: We are told that s2 and m1 are independent of each other, but the p value (0.02) is one 
usually used for a significant association. ------------------------------------------------------------------------------- 
Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author 
can be trusted to correct) 
At the end of the Background section, it appears that each sentence is a new paragraph. These should all 
be combined in the same paragraph. 
Page 6: line 9: â€œSpearmanâ€  should be capitalized. 
Page 9, line 8 from bottom: this is a run-on sentence. After â€œcagA genotypeâ€ , there should be a 
period and start of a new sentence, or at least a semicolon to separate the clauses. 
In several places, the text uses the terms â€œequally presentâ€ . This is an awkward and confusing term, 
as present is not a condition subject to quantitation. Do they mean â€œpresent in approximately equal amountsâ€ ? 
------------------------------------------------------------------------------- 
Discretionary Revisions (which the author can choose to ignore) 
 Unable to decide on acceptance or rejection until the authors have responded to the major What next?: 
compulsory revisions 
 An article whose findings are important to those with closely related research interests Level of interest: 
 Needs some language corrections before being published Quality of written English: 
 Yes Statistical review: 
Declaration of competing interests: 
I have no competing interests. 
Please review this paper.
user
Reviewer's report 
 Helicobacter pylori Genotypes Identified in Gastric Biopsy Specimens from Jordanian patients Title: 
 4  2 August 2006 Version: Date: 
 Barbara Schneider Reviewer: 
Reviewer's report: 
General 
The authors have state that they intend to separate out the histology into a separate paper. It would be 
preferable to have all in a single large paper, rather than the 2 small ones. The investigators have done much work on a good size patient population, and a combined study of histology and genotyping would be of more interest than the 2 smaller, incomplete papers would be. 
------------------------------------------------------------------------------- 
Major Compulsory Revisions (that the author must respond to before a decision on publication can be reached) 
The revised version of the manuscript by Nimri et al. is much better, but still leaves important questions 
unanswered: How did the PCR findings relate to the histology? We are told that they were associated or 
correlated, but how many were positive by histology but failed at PCR? Were any positive by PCR that were 
negative by histology? What controls did the investigators use for PCR ? 
In my previous review, I recommended the use of the term â€œassociatedâ€  instead of 
â€œcorrelatedâ€ . For results obtained with the Spearman rho test, â€œcorrelatedâ€  is the correct term 
to use. However, use of this test requires that the paper include more information regarding how the 
comparisons were done, in a correlation matrix. The test requires some kind of ranking of the non-parametric categories of histology, which means the biopsies had to be categorized and ranked as 
more or less severe in their gastric pathology. If the histological analysis is not to be presented in this paper 
(as recommended by the other reviewer) , then it would be preferable not to include the Spearman analysis 
in this paper. If the goal is to simply look for an association of positivity by histology vs. PCR, this can be done with a Fisherâ€™s or chi square test. â€œAssociatedâ€  is the correct term to use for results from 
those tests.. 
Also, throughout the results section, the text still uses the term â€œwas presentâ€™ where â€œwas 
detectedâ€  should be used. Also the text states that biopsies â€œhadâ€  a certain genotype, when what 
is meant is they â€œshowedâ€  a certain genotype, because some that had it did not show it, in the tests 
used. All of us working in the field know that we sometimes get false negatives, but this language will 
confuse those not familiar with the technical situation. 
Page 2 , Abstract, Conclusions: The reader will be looking here to see what is new. The geographic nature 
of H.pylori genetic diversity is not new, so I suggest changing the sentence to â€œThe results illustrate the 
geographic nature of the genetic diversity of H.pylori, as the identified genotypes are similar to those reported in neighboring countries.â€ 
Similarly, in the conclusions at the end of the paper, the part about the geographic distribution should not be 
listed as if it were new. 
Page 9, line 3: What do the authors mean by â€œobvious differences in two neighboring countriesâ€ ? 
The differences are not obvious to those of us who do not live in those countries. Do the authors mean 
differences in life styles? 
Page 10, line 7: We are told that s2 and m1 are independent of each other, but the p value (0.02) is one 
usually used for a significant association. ------------------------------------------------------------------------------- 
Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author 
can be trusted to correct) 
At the end of the Background section, it appears that each sentence is a new paragraph. These should all 
be combined in the same paragraph. 
Page 6: line 9: â€œSpearmanâ€  should be capitalized. 
Page 9, line 8 from bottom: this is a run-on sentence. After â€œcagA genotypeâ€ , there should be a 
period and start of a new sentence, or at least a semicolon to separate the clauses. 
In several places, the text uses the terms â€œequally presentâ€ . This is an awkward and confusing term, 
as present is not a condition subject to quantitation. Do they mean â€œpresent in approximately equal amountsâ€ ? 
------------------------------------------------------------------------------- 
Discretionary Revisions (which the author can choose to ignore) 
 Unable to decide on acceptance or rejection until the authors have responded to the major What next?: 
compulsory revisions 
 An article whose findings are important to those with closely related research interests Level of interest: 
 Needs some language corrections before being published Quality of written English: 
 Yes Statistical review: 
Declaration of competing interests: 
I have no competing interests. 
assistant