Reviewer's report
Title:The EPIYA-ABCC motif pattern in CagA of Helicobacter pylori is associated
with peptic ulcer and gastric cancer in Mexican population
Version:3Date:21 October 2014
Reviewer: Dionyssios Sgouras
Reviewer's report:
Major Compulsory Revisions
1. Authors determine H. pylori status only by PCR amplification of whole genomic
DNA isolated from the gastric biopsies instead of bacterial DNA, extracted from
the corresponding H. pylori isolated clinical strains. I am always very skeptical
because this practice can be problematic, due to the presence of PCR
amplification-inhibiting factors, which can reduce considerably the sensitivity and
specificity in the PCR typing process. Authors should evaluate the effect of such
potential inhibitory factors with the use of an internal positive control, i.e. SPUD.
Alternatively, I would suggest that authors should provide data of congruence
with an alternative method by which H. pylori patient status was assessed in their
study group, such as culture, histological evaluation, CLO test, breath test, stool
test etc.
2. H. pylori seroprevalence in Mexico for patients over 50yo is over 80% (Torres
et al., Cancer Epidemiol Biomarkers Prev 2005;14(8):1874-7). Authors should
offer an explanation of the much lower detected prevalence in their study group.
3. Authors should report levels of congruence between the two CagA PCR
assays they used to determine the cagA-status. In addition, they should confirm
CagA-negative status by a positive-result empty-site PCR (Akopyants et al. 1998
Mol. Microbiol., 28:37–53), in order to convincingly address the same issues with
regards to the effect of potential inhibitory factors in the PCR mix (comment 1),
4. The method used to type EPIYA motifs assumes clonal uniformity, with
reference to EPIYA motif diversity within an isolate, and requires bacterial
genomic DNA. Authors should defend the suitability of their typing practice i.e.
from total DNA of gastric biopsies since, quite often, within the same patient
gastric biopsy, the presence of a mixed infection by strains differing solely in the
number of EPIYA-C repeats, has been reported.
5. When attempting to associate particular virulence characteristics to a clinical
situation, functionality of the particular virulence factor may be crucial to discern
the true biological significance that lies beneath the plasticity of the H. pylori
genome. Have authors been able to detect CagA protein by western blot in the
corresponding patient serum samples or gastric biopsies?
Minor Essential Revisions
1. Line 116: reference needed, about the western-type of strains.
2. Line 242: ABB’C should be corrected to ABBC.
3. Line 248 should be corrected to read: 164 cagA-positive H. pylori patients with
chronic gastritis.
4. Line 260: reference needed about CRPA motifs
5. Authors should correct the percentage of H. pylori-positive patients throughout
the text. There are differences in the different sections that create confusion to
the reader, i.e. line 58: 57%, line 233: 57.5%, line 295: 57.4%.
Discretionary Revisions
1. Table 2 and figure 1 account for the same data. I propose to add the
corresponding percentages to Table 2 and delete figure 1 altogether, as it does
not contribute to the comprehension of the results. Also in table 2, a footnote
should be included in order to clarify the different frequencies with regards to the
number of cases within groups of EPIYA motifs for sections 3 and 4. For
example, the strains classified as ABC were found to be 148, whereas strains
with 1 CagA-EPIYA-C motif are 149. So if different groups were grouped together
for statistical assessment, it should be clearly defined.
2. Other studies have also demonstrated that the presence of CagA EPIYA-C
motifs being an independent risk factor for gastroduodenal ulceration. Authors
might want to include those too.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests
Reviewer's report
Title:The EPIYA-ABCC motif pattern in CagA of Helicobacter pylori is associated
with peptic ulcer and gastric cancer in Mexican population
Version:3Date:21 October 2014
Reviewer: Dionyssios Sgouras
Reviewer's report:
Major Compulsory Revisions
1. Authors determine H. pylori status only by PCR amplification of whole genomic
DNA isolated from the gastric biopsies instead of bacterial DNA, extracted from
the corresponding H. pylori isolated clinical strains. I am always very skeptical
because this practice can be problematic, due to the presence of PCR
amplification-inhibiting factors, which can reduce considerably the sensitivity and
specificity in the PCR typing process. Authors should evaluate the effect of such
potential inhibitory factors with the use of an internal positive control, i.e. SPUD.
Alternatively, I would suggest that authors should provide data of congruence
with an alternative method by which H. pylori patient status was assessed in their
study group, such as culture, histological evaluation, CLO test, breath test, stool
test etc.
2. H. pylori seroprevalence in Mexico for patients over 50yo is over 80% (Torres
et al., Cancer Epidemiol Biomarkers Prev 2005;14(8):1874-7). Authors should
offer an explanation of the much lower detected prevalence in their study group.
3. Authors should report levels of congruence between the two CagA PCR
assays they used to determine the cagA-status. In addition, they should confirm
CagA-negative status by a positive-result empty-site PCR (Akopyants et al. 1998
Mol. Microbiol., 28:37–53), in order to convincingly address the same issues with
regards to the effect of potential inhibitory factors in the PCR mix (comment 1),
4. The method used to type EPIYA motifs assumes clonal uniformity, with
reference to EPIYA motif diversity within an isolate, and requires bacterial
genomic DNA. Authors should defend the suitability of their typing practice i.e.
from total DNA of gastric biopsies since, quite often, within the same patient
gastric biopsy, the presence of a mixed infection by strains differing solely in the
number of EPIYA-C repeats, has been reported.
5. When attempting to associate particular virulence characteristics to a clinical
situation, functionality of the particular virulence factor may be crucial to discern
the true biological significance that lies beneath the plasticity of the H. pylori
genome. Have authors been able to detect CagA protein by western blot in the
corresponding patient serum samples or gastric biopsies?
Minor Essential Revisions
1. Line 116: reference needed, about the western-type of strains.
2. Line 242: ABB’C should be corrected to ABBC.
3. Line 248 should be corrected to read: 164 cagA-positive H. pylori patients with
chronic gastritis.
4. Line 260: reference needed about CRPA motifs
5. Authors should correct the percentage of H. pylori-positive patients throughout
the text. There are differences in the different sections that create confusion to
the reader, i.e. line 58: 57%, line 233: 57.5%, line 295: 57.4%.
Discretionary Revisions
1. Table 2 and figure 1 account for the same data. I propose to add the
corresponding percentages to Table 2 and delete figure 1 altogether, as it does
not contribute to the comprehension of the results. Also in table 2, a footnote
should be included in order to clarify the different frequencies with regards to the
number of cases within groups of EPIYA motifs for sections 3 and 4. For
example, the strains classified as ABC were found to be 148, whereas strains
with 1 CagA-EPIYA-C motif are 149. So if different groups were grouped together
for statistical assessment, it should be clearly defined.
2. Other studies have also demonstrated that the presence of CagA EPIYA-C
motifs being an independent risk factor for gastroduodenal ulceration. Authors
might want to include those too.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests
Please review this paper.
user
Reviewer's report
Title:The EPIYA-ABCC motif pattern in CagA of Helicobacter pylori is associated
with peptic ulcer and gastric cancer in Mexican population
Version:3Date:21 October 2014
Reviewer: Dionyssios Sgouras
Reviewer's report:
Major Compulsory Revisions
1. Authors determine H. pylori status only by PCR amplification of whole genomic
DNA isolated from the gastric biopsies instead of bacterial DNA, extracted from
the corresponding H. pylori isolated clinical strains. I am always very skeptical
because this practice can be problematic, due to the presence of PCR
amplification-inhibiting factors, which can reduce considerably the sensitivity and
specificity in the PCR typing process. Authors should evaluate the effect of such
potential inhibitory factors with the use of an internal positive control, i.e. SPUD.
Alternatively, I would suggest that authors should provide data of congruence
with an alternative method by which H. pylori patient status was assessed in their
study group, such as culture, histological evaluation, CLO test, breath test, stool
test etc.
2. H. pylori seroprevalence in Mexico for patients over 50yo is over 80% (Torres
et al., Cancer Epidemiol Biomarkers Prev 2005;14(8):1874-7). Authors should
offer an explanation of the much lower detected prevalence in their study group.
3. Authors should report levels of congruence between the two CagA PCR
assays they used to determine the cagA-status. In addition, they should confirm
CagA-negative status by a positive-result empty-site PCR (Akopyants et al. 1998
Mol. Microbiol., 28:37–53), in order to convincingly address the same issues with
regards to the effect of potential inhibitory factors in the PCR mix (comment 1),
4. The method used to type EPIYA motifs assumes clonal uniformity, with
reference to EPIYA motif diversity within an isolate, and requires bacterial
genomic DNA. Authors should defend the suitability of their typing practice i.e.
from total DNA of gastric biopsies since, quite often, within the same patient
gastric biopsy, the presence of a mixed infection by strains differing solely in the
number of EPIYA-C repeats, has been reported.
5. When attempting to associate particular virulence characteristics to a clinical
situation, functionality of the particular virulence factor may be crucial to discern
the true biological significance that lies beneath the plasticity of the H. pylori
genome. Have authors been able to detect CagA protein by western blot in the
corresponding patient serum samples or gastric biopsies?
Minor Essential Revisions
1. Line 116: reference needed, about the western-type of strains.
2. Line 242: ABB’C should be corrected to ABBC.
3. Line 248 should be corrected to read: 164 cagA-positive H. pylori patients with
chronic gastritis.
4. Line 260: reference needed about CRPA motifs
5. Authors should correct the percentage of H. pylori-positive patients throughout
the text. There are differences in the different sections that create confusion to
the reader, i.e. line 58: 57%, line 233: 57.5%, line 295: 57.4%.
Discretionary Revisions
1. Table 2 and figure 1 account for the same data. I propose to add the
corresponding percentages to Table 2 and delete figure 1 altogether, as it does
not contribute to the comprehension of the results. Also in table 2, a footnote
should be included in order to clarify the different frequencies with regards to the
number of cases within groups of EPIYA motifs for sections 3 and 4. For
example, the strains classified as ABC were found to be 148, whereas strains
with 1 CagA-EPIYA-C motif are 149. So if different groups were grouped together
for statistical assessment, it should be clearly defined.
2. Other studies have also demonstrated that the presence of CagA EPIYA-C
motifs being an independent risk factor for gastroduodenal ulceration. Authors
might want to include those too.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests
assistant