Reviewer's report
Title:Prevalence of non Helicobacter pylori species in patients presenting with
dyspepsia
Version: 3Date:31 August 2011
Reviewer: Cinthia Goldman
Reviewer's report:
Reviewer’s Report
The authors have fulfilled each of the major compulsory revisions and modified
the introduction and discussion sections as requested. I have the following
further suggestions that in my opinion will improve the quality of the manuscript.
Minor Essential Revisions
1. Please revise the correct use of italics for bacterial nomenclature throughout
the paper.
Introduction
2. Last paragraph: “…and to analyze the effect of coinfection with these
organisms on gastric pathology…” should be replaced by “…and to analyze the
association of coinfection with these organisms with gastric…” (The effect of one
variable on the other can not be assessed on a cross sectional study).
Materials and Methods
Study population
3. First sentence: Cut the verb “were enrolled” and insert it after “in Karachi”.
4. Second sentence: Revise the age range. The minimum age for inclusion was
18 as declared by the authors.
5. “Following EGD 242 (97%) were found have” should read “were found to
have”.
6. Replace “Inclusion criteria included” by “Inclusion criteria were”.
7. The sentence: “Only those patients having RUT or histology with positive…”
should be rephrased as “Criteria for a true positive result was established with
positive RUT or histology and 16S rDNA amplification”.
8. “Patients 90(36%) out 250 had…” should read “Ninety patients (36%) out of
250 had…”.
Polymerase Chain Reaction
9. According to the final volume of the PCR reaction, buffer would have been
10X. Please check.
10. “The amplification cycles for the various H. pylori genes was…” should be
replaced by “The amplification cycles for the different Helicobacter spp. gene
fragments were: …”
11. Concerning the positive control for H. heilmannii amplification, as JF804941.1
sequence was obtained by the authors from a positive sample during this study, I
would declare this in the corresponding sentence.
Sequencing of PCR product and BLAST Query
12. “The sequences were edited to a common length”: please specify how many
base pairs were the final fragments for comparison.
Sequence analysis
13. I suggest to change this subhead to: Nucleotide sequence accession
numbers.
14. “The sequenced PCR products of H. heilmannii and H. felis have GeneBank
accession number….” should be rephrased as: “The sequenced PCR products of
H. heilmannii and H. felis obtained in this study have been deposited in GenBank
under the following accession numbers:…”
15. PCR product sequences “were comparable” should read “were compared to”.
16. “H. heilmannii that is ref…” should read “H. heilmannii sequences…”
Sample size for estimation of H. heilmannii and H. felis incidence
17. I would change the subhead to: Sample size calculation.
18. It would be more comprehensive if this subhead is included at the end of
Study population.
Results
PCR for Helicobacter genus specific and non H. pylori Helicobacter species
19. The authors state that “all the positives at the species level were also positive
for the Helicobacter genus specific 16S rRNA”. This statement does not reflect
what is shown in Table 3. For example, 7 patients were positive for GlmM and
negative for 16S rDNA amplification. For that reason, this sentence should be
deleted (but leave the reference to Table 3).
Distribution of positive PCR for both H. pylori and non H. pylori Helicobacter
species
20. The following sentence should be added for clarification: All the H. heilmannii
and H. felis positive patients were also positive for H. pylori PCR amplification.
Discussion
21. “PCR positives at the species level were also positive for the Helicobacter
genus specific 16S rRNA”: Same comment as above.
22. Last sentence of first paragraph: “PCR product sequences of Urease B gene
of H. heilmannii …” Delete “H. felis strains”.
23. Last sentence of second paragraph: replace “include fluorescent…” by
“including fluorescent…”
24. Third paragraph: “patients gave history of having contact” should read
“patients had history of contact”.
Table 1
25. Please change the title to: Oligonucleotide primers used in this study to
amplify Helicobacter spp. gene fragments
26. Delete the complete references below the table. Instead, add a further
column entitled “Reference” and list the reference numbers of each primer pair
(and remove the numbers from the first column).
27. First column: If the column head is “Gene”, add the amplified genes for H.
heilmannii and H. felis.
Table 3
28. The title should be changed to: PCR results for Helicobacter species.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests
Reviewer's report
Title:Prevalence of non Helicobacter pylori species in patients presenting with
dyspepsia
Version: 3Date:31 August 2011
Reviewer: Cinthia Goldman
Reviewer's report:
Reviewer’s Report
The authors have fulfilled each of the major compulsory revisions and modified
the introduction and discussion sections as requested. I have the following
further suggestions that in my opinion will improve the quality of the manuscript.
Minor Essential Revisions
1. Please revise the correct use of italics for bacterial nomenclature throughout
the paper.
Introduction
2. Last paragraph: “…and to analyze the effect of coinfection with these
organisms on gastric pathology…” should be replaced by “…and to analyze the
association of coinfection with these organisms with gastric…” (The effect of one
variable on the other can not be assessed on a cross sectional study).
Materials and Methods
Study population
3. First sentence: Cut the verb “were enrolled” and insert it after “in Karachi”.
4. Second sentence: Revise the age range. The minimum age for inclusion was
18 as declared by the authors.
5. “Following EGD 242 (97%) were found have” should read “were found to
have”.
6. Replace “Inclusion criteria included” by “Inclusion criteria were”.
7. The sentence: “Only those patients having RUT or histology with positive…”
should be rephrased as “Criteria for a true positive result was established with
positive RUT or histology and 16S rDNA amplification”.
8. “Patients 90(36%) out 250 had…” should read “Ninety patients (36%) out of
250 had…”.
Polymerase Chain Reaction
9. According to the final volume of the PCR reaction, buffer would have been
10X. Please check.
10. “The amplification cycles for the various H. pylori genes was…” should be
replaced by “The amplification cycles for the different Helicobacter spp. gene
fragments were: …”
11. Concerning the positive control for H. heilmannii amplification, as JF804941.1
sequence was obtained by the authors from a positive sample during this study, I
would declare this in the corresponding sentence.
Sequencing of PCR product and BLAST Query
12. “The sequences were edited to a common length”: please specify how many
base pairs were the final fragments for comparison.
Sequence analysis
13. I suggest to change this subhead to: Nucleotide sequence accession
numbers.
14. “The sequenced PCR products of H. heilmannii and H. felis have GeneBank
accession number….” should be rephrased as: “The sequenced PCR products of
H. heilmannii and H. felis obtained in this study have been deposited in GenBank
under the following accession numbers:…”
15. PCR product sequences “were comparable” should read “were compared to”.
16. “H. heilmannii that is ref…” should read “H. heilmannii sequences…”
Sample size for estimation of H. heilmannii and H. felis incidence
17. I would change the subhead to: Sample size calculation.
18. It would be more comprehensive if this subhead is included at the end of
Study population.
Results
PCR for Helicobacter genus specific and non H. pylori Helicobacter species
19. The authors state that “all the positives at the species level were also positive
for the Helicobacter genus specific 16S rRNA”. This statement does not reflect
what is shown in Table 3. For example, 7 patients were positive for GlmM and
negative for 16S rDNA amplification. For that reason, this sentence should be
deleted (but leave the reference to Table 3).
Distribution of positive PCR for both H. pylori and non H. pylori Helicobacter
species
20. The following sentence should be added for clarification: All the H. heilmannii
and H. felis positive patients were also positive for H. pylori PCR amplification.
Discussion
21. “PCR positives at the species level were also positive for the Helicobacter
genus specific 16S rRNA”: Same comment as above.
22. Last sentence of first paragraph: “PCR product sequences of Urease B gene
of H. heilmannii …” Delete “H. felis strains”.
23. Last sentence of second paragraph: replace “include fluorescent…” by
“including fluorescent…”
24. Third paragraph: “patients gave history of having contact” should read
“patients had history of contact”.
Table 1
25. Please change the title to: Oligonucleotide primers used in this study to
amplify Helicobacter spp. gene fragments
26. Delete the complete references below the table. Instead, add a further
column entitled “Reference” and list the reference numbers of each primer pair
(and remove the numbers from the first column).
27. First column: If the column head is “Gene”, add the amplified genes for H.
heilmannii and H. felis.
Table 3
28. The title should be changed to: PCR results for Helicobacter species.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests
Please review this paper.
user
Reviewer's report
Title:Prevalence of non Helicobacter pylori species in patients presenting with
dyspepsia
Version: 3Date:31 August 2011
Reviewer: Cinthia Goldman
Reviewer's report:
Reviewer’s Report
The authors have fulfilled each of the major compulsory revisions and modified
the introduction and discussion sections as requested. I have the following
further suggestions that in my opinion will improve the quality of the manuscript.
Minor Essential Revisions
1. Please revise the correct use of italics for bacterial nomenclature throughout
the paper.
Introduction
2. Last paragraph: “…and to analyze the effect of coinfection with these
organisms on gastric pathology…” should be replaced by “…and to analyze the
association of coinfection with these organisms with gastric…” (The effect of one
variable on the other can not be assessed on a cross sectional study).
Materials and Methods
Study population
3. First sentence: Cut the verb “were enrolled” and insert it after “in Karachi”.
4. Second sentence: Revise the age range. The minimum age for inclusion was
18 as declared by the authors.
5. “Following EGD 242 (97%) were found have” should read “were found to
have”.
6. Replace “Inclusion criteria included” by “Inclusion criteria were”.
7. The sentence: “Only those patients having RUT or histology with positive…”
should be rephrased as “Criteria for a true positive result was established with
positive RUT or histology and 16S rDNA amplification”.
8. “Patients 90(36%) out 250 had…” should read “Ninety patients (36%) out of
250 had…”.
Polymerase Chain Reaction
9. According to the final volume of the PCR reaction, buffer would have been
10X. Please check.
10. “The amplification cycles for the various H. pylori genes was…” should be
replaced by “The amplification cycles for the different Helicobacter spp. gene
fragments were: …”
11. Concerning the positive control for H. heilmannii amplification, as JF804941.1
sequence was obtained by the authors from a positive sample during this study, I
would declare this in the corresponding sentence.
Sequencing of PCR product and BLAST Query
12. “The sequences were edited to a common length”: please specify how many
base pairs were the final fragments for comparison.
Sequence analysis
13. I suggest to change this subhead to: Nucleotide sequence accession
numbers.
14. “The sequenced PCR products of H. heilmannii and H. felis have GeneBank
accession number….” should be rephrased as: “The sequenced PCR products of
H. heilmannii and H. felis obtained in this study have been deposited in GenBank
under the following accession numbers:…”
15. PCR product sequences “were comparable” should read “were compared to”.
16. “H. heilmannii that is ref…” should read “H. heilmannii sequences…”
Sample size for estimation of H. heilmannii and H. felis incidence
17. I would change the subhead to: Sample size calculation.
18. It would be more comprehensive if this subhead is included at the end of
Study population.
Results
PCR for Helicobacter genus specific and non H. pylori Helicobacter species
19. The authors state that “all the positives at the species level were also positive
for the Helicobacter genus specific 16S rRNA”. This statement does not reflect
what is shown in Table 3. For example, 7 patients were positive for GlmM and
negative for 16S rDNA amplification. For that reason, this sentence should be
deleted (but leave the reference to Table 3).
Distribution of positive PCR for both H. pylori and non H. pylori Helicobacter
species
20. The following sentence should be added for clarification: All the H. heilmannii
and H. felis positive patients were also positive for H. pylori PCR amplification.
Discussion
21. “PCR positives at the species level were also positive for the Helicobacter
genus specific 16S rRNA”: Same comment as above.
22. Last sentence of first paragraph: “PCR product sequences of Urease B gene
of H. heilmannii …” Delete “H. felis strains”.
23. Last sentence of second paragraph: replace “include fluorescent…” by
“including fluorescent…”
24. Third paragraph: “patients gave history of having contact” should read
“patients had history of contact”.
Table 1
25. Please change the title to: Oligonucleotide primers used in this study to
amplify Helicobacter spp. gene fragments
26. Delete the complete references below the table. Instead, add a further
column entitled “Reference” and list the reference numbers of each primer pair
(and remove the numbers from the first column).
27. First column: If the column head is “Gene”, add the amplified genes for H.
heilmannii and H. felis.
Table 3
28. The title should be changed to: PCR results for Helicobacter species.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests
assistant