Reviewer's report 
 Helicobacter pylori Genotypes Identified in Gastric Biopsy Specimens Title: 
 1  24 May 2006 Version: Date: 
 Barbara Schneider Reviewer: 
Reviewer's report: 
General 
The manuscript reports Helicobacter pylori genotyping data obtained directly from biopsies from Jordanian 
patients. The study appears to have been carefully done. Sample size and statistics are appropriate. ------------------------------------------------------------------------------- Major Compulsory Revisions (that the author must respond to before a decision on publication can be 
reached) 
What the authors have not done is helped the reader understand what is new about their study. In the last sentence of the introduction, the implication is that H.pylori genotyping has not been previously done from 
biopsies, but this is not true. See, for example, Gunn et al. (Eur J Gastroenterol Hepatol 10:683+, 1998) and 
many others. It is valuable to see reports of Helicobacter genotyping from many countries. The authors do 
state that this is the first report on Jordanian patientsâ €™ H.pylori genotypes, but that is easily overlooked, 
as this novelty is not in the title and is in only one sentence in the abstract. The sentence at the end of the introduction does not make clear that the authors mean first in Jordan, if that is what they mean. It is not 
new that H.pylori genotype diversity is geographic, as that has been well-established by the work of van 
Doorn and colleagues. 
It is not clear whether mixed infections were detected. 
On page 9, in the first paragraph, the authors state that â €œvacA s region was presentâ €, when what they 
mean is successfully amplified. False negatives are a big problem in genotyping from biopsies, and there is 
no reason to avoid stating this. On page 10, last sentence, the false negatives are not mentioned when 
explanations for the difference in histology and PCR are proposed. 
Page 10, line 17: The phrase beginning â €œAlthough femalesâ € is not a sentence. 
Question for statistician: Page 8, statistical analysis: Here and elsewhere, the authors use the term 
â€œcorrelatedâ €, when â €œassociatedâ € seems more appropriate. 
Page 10, line 11: What the authors mean by a negative correlation is not clear. Do they simply mean lack of association, or do they have a statistic to present? ------------------------------------------------------------------------------- 
Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author 
can be trusted to correct) In the abstract results section and elsewhere, the proper term is â €œsignificantly associatedâ €, not 
â€œsignificantly associationâ €. 
Page 5, line 15: The correct term is â €œepigastric painâ €. 
Page 7, line 4 from bottom: Omit the word â €œbutâ €. 
Page 9, line 4: Europe is not a country. One could simply state that the genotype was reported in Europe, Central and South American and East Asia. 
Page 9, last line: Here and elsewhere, the term should be â €œindependent ofâ €, not â €œindependent 
onâ €. 
Page 11, line 4: The correct term is â €œproton pump inhibitorsâ €. 
------------------------------------------------------------------------------- 
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 declare that I have no competing interests. 
Reviewer's report 
 Helicobacter pylori Genotypes Identified in Gastric Biopsy Specimens Title: 
 1  24 May 2006 Version: Date: 
 Barbara Schneider Reviewer: 
Reviewer's report: 
General 
The manuscript reports Helicobacter pylori genotyping data obtained directly from biopsies from Jordanian 
patients. The study appears to have been carefully done. Sample size and statistics are appropriate. ------------------------------------------------------------------------------- Major Compulsory Revisions (that the author must respond to before a decision on publication can be 
reached) 
What the authors have not done is helped the reader understand what is new about their study. In the last sentence of the introduction, the implication is that H.pylori genotyping has not been previously done from 
biopsies, but this is not true. See, for example, Gunn et al. (Eur J Gastroenterol Hepatol 10:683+, 1998) and 
many others. It is valuable to see reports of Helicobacter genotyping from many countries. The authors do 
state that this is the first report on Jordanian patientsâ €™ H.pylori genotypes, but that is easily overlooked, 
as this novelty is not in the title and is in only one sentence in the abstract. The sentence at the end of the introduction does not make clear that the authors mean first in Jordan, if that is what they mean. It is not 
new that H.pylori genotype diversity is geographic, as that has been well-established by the work of van 
Doorn and colleagues. 
It is not clear whether mixed infections were detected. 
On page 9, in the first paragraph, the authors state that â €œvacA s region was presentâ €, when what they 
mean is successfully amplified. False negatives are a big problem in genotyping from biopsies, and there is 
no reason to avoid stating this. On page 10, last sentence, the false negatives are not mentioned when 
explanations for the difference in histology and PCR are proposed. 
Page 10, line 17: The phrase beginning â €œAlthough femalesâ € is not a sentence. 
Question for statistician: Page 8, statistical analysis: Here and elsewhere, the authors use the term 
â€œcorrelatedâ €, when â €œassociatedâ € seems more appropriate. 
Page 10, line 11: What the authors mean by a negative correlation is not clear. Do they simply mean lack of association, or do they have a statistic to present? ------------------------------------------------------------------------------- 
Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author 
can be trusted to correct) In the abstract results section and elsewhere, the proper term is â €œsignificantly associatedâ €, not 
â€œsignificantly associationâ €. 
Page 5, line 15: The correct term is â €œepigastric painâ €. 
Page 7, line 4 from bottom: Omit the word â €œbutâ €. 
Page 9, line 4: Europe is not a country. One could simply state that the genotype was reported in Europe, Central and South American and East Asia. 
Page 9, last line: Here and elsewhere, the term should be â €œindependent ofâ €, not â €œindependent 
onâ €. 
Page 11, line 4: The correct term is â €œproton pump inhibitorsâ €. 
------------------------------------------------------------------------------- 
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 declare that I have no competing interests. 
Please review this paper.
user
Reviewer's report 
 Helicobacter pylori Genotypes Identified in Gastric Biopsy Specimens Title: 
 1  24 May 2006 Version: Date: 
 Barbara Schneider Reviewer: 
Reviewer's report: 
General 
The manuscript reports Helicobacter pylori genotyping data obtained directly from biopsies from Jordanian 
patients. The study appears to have been carefully done. Sample size and statistics are appropriate. ------------------------------------------------------------------------------- Major Compulsory Revisions (that the author must respond to before a decision on publication can be 
reached) 
What the authors have not done is helped the reader understand what is new about their study. In the last sentence of the introduction, the implication is that H.pylori genotyping has not been previously done from 
biopsies, but this is not true. See, for example, Gunn et al. (Eur J Gastroenterol Hepatol 10:683+, 1998) and 
many others. It is valuable to see reports of Helicobacter genotyping from many countries. The authors do 
state that this is the first report on Jordanian patientsâ €™ H.pylori genotypes, but that is easily overlooked, 
as this novelty is not in the title and is in only one sentence in the abstract. The sentence at the end of the introduction does not make clear that the authors mean first in Jordan, if that is what they mean. It is not 
new that H.pylori genotype diversity is geographic, as that has been well-established by the work of van 
Doorn and colleagues. 
It is not clear whether mixed infections were detected. 
On page 9, in the first paragraph, the authors state that â €œvacA s region was presentâ €, when what they 
mean is successfully amplified. False negatives are a big problem in genotyping from biopsies, and there is 
no reason to avoid stating this. On page 10, last sentence, the false negatives are not mentioned when 
explanations for the difference in histology and PCR are proposed. 
Page 10, line 17: The phrase beginning â €œAlthough femalesâ € is not a sentence. 
Question for statistician: Page 8, statistical analysis: Here and elsewhere, the authors use the term 
â€œcorrelatedâ €, when â €œassociatedâ € seems more appropriate. 
Page 10, line 11: What the authors mean by a negative correlation is not clear. Do they simply mean lack of association, or do they have a statistic to present? ------------------------------------------------------------------------------- 
Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author 
can be trusted to correct) In the abstract results section and elsewhere, the proper term is â €œsignificantly associatedâ €, not 
â€œsignificantly associationâ €. 
Page 5, line 15: The correct term is â €œepigastric painâ €. 
Page 7, line 4 from bottom: Omit the word â €œbutâ €. 
Page 9, line 4: Europe is not a country. One could simply state that the genotype was reported in Europe, Central and South American and East Asia. 
Page 9, last line: Here and elsewhere, the term should be â €œindependent ofâ €, not â €œindependent 
onâ €. 
Page 11, line 4: The correct term is â €œproton pump inhibitorsâ €. 
------------------------------------------------------------------------------- 
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 declare that I have no competing interests. 
assistant