Reviewer's report
Title:Incidence of non Helicobacter pylori species in patients presenting with
dyspepsia
Version: 1Date:30 June 2011
Reviewer: Cinthia Goldman
Reviewer's report:
Reviewer’s Report
According to the authors, this article aimed to investigate the incidence of
non-Helicobacter pylori organisms in dyspeptic patients and to analyze the effect
of coinfection with these organism on gastric pathology.
Major Compulsory Revisions
General comments
1. Gastric non-Helicobacter pylori helicobacters constitute a complex group of
bacterial species. Taxonomy and nomenclature of these bacteria has suffered
several changes during the past years that led to misclassifications. In particular,
the finding of these spiral bacteria in the human stomach has been often
described as “H. heilmannii”, although that species has not been validly
designated until now (this confusing nomenclature is clearly described in an
outstanding review by Haesebrouck et al., 2009). Reference to “H. heilmannii”
represented in that cases several Helicobacter spp., like H. suis (previously
designated ‘H. heilmannii’ type I), or H. felis, H. bizzozeronii, H. salomonis, or
‘Candidatus H. heilmannii’ (previously designated ‘H. heilmannii’ type II). In light
of the very recent isolation and characterization of Helicobacter heilmannii sp.
nov. for the first time (Smet et al., 2011), I suggest the authors of this paper to
clarify whether the species name “H. heilmannii” is validly used.
Haesebrouck F., Pasmans F., Flahou B., Chiers K., Baele M., Meyns T.,
Decostere A., Ducatelle R., 2009. Gastric helicobacters in domestic animals and
nonhuman primates and their significance for human health. Clin. Microbiol. Rev.
22, 202–223.
Smet A., Flahou B., D’Herde K., Vandamme P., Cleenwerck I., Ducatelle R.,
Pasmans, F., Haesebrouck F., 2011. Helicobacter heilmannii sp. nov., isolated
from feline gastric mucosa. Int. J. Syst. Evol. Microbiol. Mar 18. [Epub ahead of
print]
2. Specificity of the PCR primers employed for amplification of Helicobacter at
the species level should also be clearly addressed given the changes occurred in
this field since they were designed in 1997/1998.
3. Accuracy of the citations should be revised along the article. It is my
recommendation to reference and discuss more recent reports in the Introduction
and Discussion sections (in particular publications from the last few years).
Objectives
4. Given that the study design was cross sectional, incidence of gastric non-H.
pylori helicobacters could not has been investigated. Instead, prevalence should
be referred to in the aim of the study, Materials and Methods and Title.
5. The second objective of the study was to analyze the effect of coinfection with
these organism on gastric pathology. Because of the nature of study design,
association between these two variables was addressed and not the effect of one
variable on the other.
Introduction
6. In the second paragraph, the authors describe the pathogenesis and immune
response to H. pylori and how coinfection with H. pylori and several parasites
could modulate immunity. In my opinion this paragraph should be removed.
Instead, a more comprehensive and profound introduction concerning the
description of gastric non-H. pylori helicobacters in particular from humans
should be addressed.
Materials and Methods
7. Statistical methods and parameters set up to calculate the number of patients
to be included in the study, along with the estimation of expected dropouts,
should be stated within the description of the studied population.
8. The authors state that “the enrolled patients were divided into four groups…i to
iv”. If the population is classified in groups at recruitment, the results should be
analyzed according to that classification. In that case, a first descriptive table
should be included where a comparison of the four groups is presented. On the
other hand, if the aim of the study was to investigate the association between the
presence of non- H. pylori Helicobacter spp. with contact of the patient with pets,
this first classification should be avoided.
9. Last paragraph: “Patients who were less likely to turn up for…”. This
paragraph is not clear. Please specify which methods were used to diagnose
Helicobacter spp. infection as a true positive.
10. PCR: Positive controls included H. pylori and H. felis ATCC strains. Which
positive control was used for “H. heilmannii” amplification?
Results
11. The authors should state the percentage of patients which were positive for
the Helicobacter specific 16S rRNA amplification and negative with primers for
the species level. Were all the positives at the species level also positive for the
16S rRNA?
12. Coinfection should be carefully evaluated and deeply discussed taking into
account all the above mentioned points, and the limitations of the methodology
used in this study. In my opinion it would be more appropriate to report the
results as positive for both PCR specific reactions. According to the reported
results, amplification of both “H. heilmannii” and H. pylori was observed in 17/17
(100%) of the “H. heilmannii” positive patients, and not in 7% of the cases. The
same
occurred for H. felis positive patients.
13. Sequence analysis: I would suggest to include a subhead under the head
Materials and Methods to list the nucleotide sequences accession numbers for
PCR positive samples obtained in this study.
14. Sequence analysis: The authors should state within the Materials and
Methods section the methodology used to analyze the sequences, including the
programs used for edition. Were the sequences edited to a common length?
Similarity percentages should have been compared to the sequences of
validated strains in order to avoid confusion (please refer to www.straininfo.net or
www.bacterio.cict.fr ), and the results should be clearly described. The usage of
the terms “aligned well” should be avoided.
Discussion
15. The discussion of the article should include all the above mentioned points,
along with the limitations of the study.
Table 1
16. Is amplicon size for H. pylori glmM correct?
17. This table should include the amplified genes and the references for each
primer.
Table 2
18. RUT and Histopathology results are reported in this table, but no mention
within the text is made to the false positive and false negative results obtained
with each technique. Which results were set as a criteria for a true positive?
Minor Essential Revisions
Materials and Methods
1. Study population. First paragraph: The number and percentage of males
included in the study is not coincident between the abstract and materials and
methods. Please check.
2. Usage of “e.g.” should be avoided.
3. It is not clear what is the meaning of “All these patients underwent history”.
4. The city and country should be declared for reagents and equipments.
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:Incidence of non Helicobacter pylori species in patients presenting with
dyspepsia
Version: 1Date:30 June 2011
Reviewer: Cinthia Goldman
Reviewer's report:
Reviewer’s Report
According to the authors, this article aimed to investigate the incidence of
non-Helicobacter pylori organisms in dyspeptic patients and to analyze the effect
of coinfection with these organism on gastric pathology.
Major Compulsory Revisions
General comments
1. Gastric non-Helicobacter pylori helicobacters constitute a complex group of
bacterial species. Taxonomy and nomenclature of these bacteria has suffered
several changes during the past years that led to misclassifications. In particular,
the finding of these spiral bacteria in the human stomach has been often
described as “H. heilmannii”, although that species has not been validly
designated until now (this confusing nomenclature is clearly described in an
outstanding review by Haesebrouck et al., 2009). Reference to “H. heilmannii”
represented in that cases several Helicobacter spp., like H. suis (previously
designated ‘H. heilmannii’ type I), or H. felis, H. bizzozeronii, H. salomonis, or
‘Candidatus H. heilmannii’ (previously designated ‘H. heilmannii’ type II). In light
of the very recent isolation and characterization of Helicobacter heilmannii sp.
nov. for the first time (Smet et al., 2011), I suggest the authors of this paper to
clarify whether the species name “H. heilmannii” is validly used.
Haesebrouck F., Pasmans F., Flahou B., Chiers K., Baele M., Meyns T.,
Decostere A., Ducatelle R., 2009. Gastric helicobacters in domestic animals and
nonhuman primates and their significance for human health. Clin. Microbiol. Rev.
22, 202–223.
Smet A., Flahou B., D’Herde K., Vandamme P., Cleenwerck I., Ducatelle R.,
Pasmans, F., Haesebrouck F., 2011. Helicobacter heilmannii sp. nov., isolated
from feline gastric mucosa. Int. J. Syst. Evol. Microbiol. Mar 18. [Epub ahead of
print]
2. Specificity of the PCR primers employed for amplification of Helicobacter at
the species level should also be clearly addressed given the changes occurred in
this field since they were designed in 1997/1998.
3. Accuracy of the citations should be revised along the article. It is my
recommendation to reference and discuss more recent reports in the Introduction
and Discussion sections (in particular publications from the last few years).
Objectives
4. Given that the study design was cross sectional, incidence of gastric non-H.
pylori helicobacters could not has been investigated. Instead, prevalence should
be referred to in the aim of the study, Materials and Methods and Title.
5. The second objective of the study was to analyze the effect of coinfection with
these organism on gastric pathology. Because of the nature of study design,
association between these two variables was addressed and not the effect of one
variable on the other.
Introduction
6. In the second paragraph, the authors describe the pathogenesis and immune
response to H. pylori and how coinfection with H. pylori and several parasites
could modulate immunity. In my opinion this paragraph should be removed.
Instead, a more comprehensive and profound introduction concerning the
description of gastric non-H. pylori helicobacters in particular from humans
should be addressed.
Materials and Methods
7. Statistical methods and parameters set up to calculate the number of patients
to be included in the study, along with the estimation of expected dropouts,
should be stated within the description of the studied population.
8. The authors state that “the enrolled patients were divided into four groups…i to
iv”. If the population is classified in groups at recruitment, the results should be
analyzed according to that classification. In that case, a first descriptive table
should be included where a comparison of the four groups is presented. On the
other hand, if the aim of the study was to investigate the association between the
presence of non- H. pylori Helicobacter spp. with contact of the patient with pets,
this first classification should be avoided.
9. Last paragraph: “Patients who were less likely to turn up for…”. This
paragraph is not clear. Please specify which methods were used to diagnose
Helicobacter spp. infection as a true positive.
10. PCR: Positive controls included H. pylori and H. felis ATCC strains. Which
positive control was used for “H. heilmannii” amplification?
Results
11. The authors should state the percentage of patients which were positive for
the Helicobacter specific 16S rRNA amplification and negative with primers for
the species level. Were all the positives at the species level also positive for the
16S rRNA?
12. Coinfection should be carefully evaluated and deeply discussed taking into
account all the above mentioned points, and the limitations of the methodology
used in this study. In my opinion it would be more appropriate to report the
results as positive for both PCR specific reactions. According to the reported
results, amplification of both “H. heilmannii” and H. pylori was observed in 17/17
(100%) of the “H. heilmannii” positive patients, and not in 7% of the cases. The
same
occurred for H. felis positive patients.
13. Sequence analysis: I would suggest to include a subhead under the head
Materials and Methods to list the nucleotide sequences accession numbers for
PCR positive samples obtained in this study.
14. Sequence analysis: The authors should state within the Materials and
Methods section the methodology used to analyze the sequences, including the
programs used for edition. Were the sequences edited to a common length?
Similarity percentages should have been compared to the sequences of
validated strains in order to avoid confusion (please refer to www.straininfo.net or
www.bacterio.cict.fr ), and the results should be clearly described. The usage of
the terms “aligned well” should be avoided.
Discussion
15. The discussion of the article should include all the above mentioned points,
along with the limitations of the study.
Table 1
16. Is amplicon size for H. pylori glmM correct?
17. This table should include the amplified genes and the references for each
primer.
Table 2
18. RUT and Histopathology results are reported in this table, but no mention
within the text is made to the false positive and false negative results obtained
with each technique. Which results were set as a criteria for a true positive?
Minor Essential Revisions
Materials and Methods
1. Study population. First paragraph: The number and percentage of males
included in the study is not coincident between the abstract and materials and
methods. Please check.
2. Usage of “e.g.” should be avoided.
3. It is not clear what is the meaning of “All these patients underwent history”.
4. The city and country should be declared for reagents and equipments.
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:Incidence of non Helicobacter pylori species in patients presenting with
dyspepsia
Version: 1Date:30 June 2011
Reviewer: Cinthia Goldman
Reviewer's report:
Reviewer’s Report
According to the authors, this article aimed to investigate the incidence of
non-Helicobacter pylori organisms in dyspeptic patients and to analyze the effect
of coinfection with these organism on gastric pathology.
Major Compulsory Revisions
General comments
1. Gastric non-Helicobacter pylori helicobacters constitute a complex group of
bacterial species. Taxonomy and nomenclature of these bacteria has suffered
several changes during the past years that led to misclassifications. In particular,
the finding of these spiral bacteria in the human stomach has been often
described as “H. heilmannii”, although that species has not been validly
designated until now (this confusing nomenclature is clearly described in an
outstanding review by Haesebrouck et al., 2009). Reference to “H. heilmannii”
represented in that cases several Helicobacter spp., like H. suis (previously
designated ‘H. heilmannii’ type I), or H. felis, H. bizzozeronii, H. salomonis, or
‘Candidatus H. heilmannii’ (previously designated ‘H. heilmannii’ type II). In light
of the very recent isolation and characterization of Helicobacter heilmannii sp.
nov. for the first time (Smet et al., 2011), I suggest the authors of this paper to
clarify whether the species name “H. heilmannii” is validly used.
Haesebrouck F., Pasmans F., Flahou B., Chiers K., Baele M., Meyns T.,
Decostere A., Ducatelle R., 2009. Gastric helicobacters in domestic animals and
nonhuman primates and their significance for human health. Clin. Microbiol. Rev.
22, 202–223.
Smet A., Flahou B., D’Herde K., Vandamme P., Cleenwerck I., Ducatelle R.,
Pasmans, F., Haesebrouck F., 2011. Helicobacter heilmannii sp. nov., isolated
from feline gastric mucosa. Int. J. Syst. Evol. Microbiol. Mar 18. [Epub ahead of
print]
2. Specificity of the PCR primers employed for amplification of Helicobacter at
the species level should also be clearly addressed given the changes occurred in
this field since they were designed in 1997/1998.
3. Accuracy of the citations should be revised along the article. It is my
recommendation to reference and discuss more recent reports in the Introduction
and Discussion sections (in particular publications from the last few years).
Objectives
4. Given that the study design was cross sectional, incidence of gastric non-H.
pylori helicobacters could not has been investigated. Instead, prevalence should
be referred to in the aim of the study, Materials and Methods and Title.
5. The second objective of the study was to analyze the effect of coinfection with
these organism on gastric pathology. Because of the nature of study design,
association between these two variables was addressed and not the effect of one
variable on the other.
Introduction
6. In the second paragraph, the authors describe the pathogenesis and immune
response to H. pylori and how coinfection with H. pylori and several parasites
could modulate immunity. In my opinion this paragraph should be removed.
Instead, a more comprehensive and profound introduction concerning the
description of gastric non-H. pylori helicobacters in particular from humans
should be addressed.
Materials and Methods
7. Statistical methods and parameters set up to calculate the number of patients
to be included in the study, along with the estimation of expected dropouts,
should be stated within the description of the studied population.
8. The authors state that “the enrolled patients were divided into four groups…i to
iv”. If the population is classified in groups at recruitment, the results should be
analyzed according to that classification. In that case, a first descriptive table
should be included where a comparison of the four groups is presented. On the
other hand, if the aim of the study was to investigate the association between the
presence of non- H. pylori Helicobacter spp. with contact of the patient with pets,
this first classification should be avoided.
9. Last paragraph: “Patients who were less likely to turn up for…”. This
paragraph is not clear. Please specify which methods were used to diagnose
Helicobacter spp. infection as a true positive.
10. PCR: Positive controls included H. pylori and H. felis ATCC strains. Which
positive control was used for “H. heilmannii” amplification?
Results
11. The authors should state the percentage of patients which were positive for
the Helicobacter specific 16S rRNA amplification and negative with primers for
the species level. Were all the positives at the species level also positive for the
16S rRNA?
12. Coinfection should be carefully evaluated and deeply discussed taking into
account all the above mentioned points, and the limitations of the methodology
used in this study. In my opinion it would be more appropriate to report the
results as positive for both PCR specific reactions. According to the reported
results, amplification of both “H. heilmannii” and H. pylori was observed in 17/17
(100%) of the “H. heilmannii” positive patients, and not in 7% of the cases. The
same
occurred for H. felis positive patients.
13. Sequence analysis: I would suggest to include a subhead under the head
Materials and Methods to list the nucleotide sequences accession numbers for
PCR positive samples obtained in this study.
14. Sequence analysis: The authors should state within the Materials and
Methods section the methodology used to analyze the sequences, including the
programs used for edition. Were the sequences edited to a common length?
Similarity percentages should have been compared to the sequences of
validated strains in order to avoid confusion (please refer to www.straininfo.net or
www.bacterio.cict.fr ), and the results should be clearly described. The usage of
the terms “aligned well” should be avoided.
Discussion
15. The discussion of the article should include all the above mentioned points,
along with the limitations of the study.
Table 1
16. Is amplicon size for H. pylori glmM correct?
17. This table should include the amplified genes and the references for each
primer.
Table 2
18. RUT and Histopathology results are reported in this table, but no mention
within the text is made to the false positive and false negative results obtained
with each technique. Which results were set as a criteria for a true positive?
Minor Essential Revisions
Materials and Methods
1. Study population. First paragraph: The number and percentage of males
included in the study is not coincident between the abstract and materials and
methods. Please check.
2. Usage of “e.g.” should be avoided.
3. It is not clear what is the meaning of “All these patients underwent history”.
4. The city and country should be declared for reagents and equipments.
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