Antimicrobial susceptibility of clinical Helicobacter pylori isolates and its eradication by standard triple therapy: a study in west central region of Colombia

ABSTRACT The aim of the present study was first to isolate Helicobacter pylori from gastric biopsy specimens and to test their antibiotic susceptibility. Second, it was to evaluate the efficacy of the standard triple therapy from patients of the west central region of Colombia. H. pylori positive patients received standard triple therapy with proton pump inhibitor (PPI) (40 mg b.i.d.), clarithromycin (500 mg b.i.d.), and amoxicillin (1 g b.i.d.) for 14 days. Thereafter, antibiotic susceptibility of the isolates was assessed by E-Test. From 94 patients enrolled, 67 were positive for H. pylori by histology or culture. Overall resistance to metronidazole, levofloxacin, rifampicin, clarithromycin, and amoxicillin was 81%, 26.2%, 23.9%, 19%, and 9.5%, respectively. No resistance was found for tetracycline. A total of 54 patients received standard triple therapy, 48 attended follow-ups testing, and of them, 30 had resistance test reports. Overall eradication rate was 81.2%. Second-line treatment was given to eight patients, four of whom were followed up with a 13C urea breath test (UBT) and remained positive for H. pylori. Eradication was significantly higher in patients with clarithromycin susceptible than in resistant strains (95.6% vs 42.8% P = 0.001). The updated percentages of resistance to clarithromycin in this geographical area had increased, so this value must be considered when choosing the treatment regimen. IMPORTANCE Antibiotic resistance in Helicobacter pylori has increased worldwide, as has resistance to multiple antimicrobials (MDRs), which seriously hampers the successful eradication of the infection. The ideal success rate in eradicating H. pylori infection (≥90%) was not achieved in this study (81.2%). This is the first time that MDR is reported (14.3%) in the region; the resistance to clarithromycin increased over time (3.8%–19%), and levofloxacin (26.2%) and rifampicin (23%) resistant isolates were detected for the first time. With these results, strain susceptibility testing is increasingly important, and the selection of treatment regimen should be based on local antibiotic resistance patterns.

1st Editorial Decision Re: Spectrum00401-24 (Antimicrobial susceptibility of clinical Helicobacter pylori isolates and its eradication by standard triple therapy: A study in west central region of Colombia) Dear Prof. Adalucy Alvarez Aldana: Thank you for the privilege of reviewing your work.After reviewing feedback from reviewers, modifications are required before potential publication.Below you will find my comments, instructions from the Spectrum editorial office, and the reviewer comments.
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Reviewer #1 (Comments for the Author): This is an interesting manuscript "Antimicrobial susceptibility of clinical Helicobacter pylori isolates and its eradication by standard triple therapy: A study in west central region of Colombia" .Given the rising incidence of antibiotic resistance in H. pylori, consider research to be crucial for the population.
Overall, the experiments are performed well, and manuscript was well written, I recommend this research manuscript is appropriate to publish with Major revision mentioned below.
1.The author would think about in addition to Gram staining and biochemical testing, the polymerase chain reaction (PCR) is an extremely sensitive and specific technique for diagnosing Helicobacter pylori.So, the study will be more reliable.

On what basis Helicobacter pylori strains were chosen?
Reviewer #2 (Comments for the Author): This is a generally well-written article describing a small study on Triple therapy of Helicobacter pylori in Colombia.It presents results of a PPI-clarithromycin-amoxicillin regimen for treatment of patients with gastritis and includes data on efficacy, eradication and antibiotic susceptibility of drugs used for H. pylori.The main take home is that clarithromycin resistance is growing and susceptibility to clarithromycin is strongly correlated with eradication.It is recommended that empirical treatment of H. pylori be based on knowledge of local antibiotic resistance patterns.The methods used are appropriate and well described.There are a few instances of rather informal English which should be corrected: Line 64 "figured out as" should be changed to identified as Line 74 "apparition" should be changed to appearance or emergence Line 103 "figure out" should be changed to discover Dear, Editors: Microbiology Spectrum -ASM Please find the revised version of our paper "Antimicrobial susceptibility of clinical Helicobacter pylori isolates and its eradication by standard triple therapy: A study in west central region of Colombia" co-authored by Adalucy Alvarez-Aldana et al., which we would like to submit for publication in your Journal.It contains original results which have not been submitted for publication elsewhere.

Microbiology Spectrum
Manuscript ID: Spectrum00401-24R1 Thank you for your interest on our paper.As recommended, please find hereafter the list of the whole changes amended in our manuscript "Antimicrobial susceptibility of clinical Helicobacter pylori isolates and its eradication by standard triple therapy: A study in west central region of Colombia" co-authored by Adalucy Alvarez-Aldana et al (Manuscript ID: Spectrum00401-24R1) according to your comments for the format of the manuscript.You will find all modifications done in new version of "Marked-Up Manuscript" using blue highlight and will uploaded a clean .DOC/.DOCX version of the revised manuscript and removed the previous version.

Reviewer #1:
This is an interesting manuscript "Antimicrobial susceptibility of clinical Helicobacter pylori isolates and its eradication by standard triple therapy: A study in west central region of Colombia".Given the rising incidence of antibiotic resistance in H. pylori, consider research to be crucial for the population.Overall, the experiments are performed well, and manuscript was well written, I recommend this research manuscript is appropriate to publish with Major revision mentioned below.
Comment 1: The author would think about in addition to Gram staining and biochemical testing, the polymerase chain reaction (PCR) is an extremely sensitive and specific technique for diagnosing Helicobacter pylori.So, the study will be more reliable.
Answer 1: Despite the availability of multiple diagnostic methods, selection of one or more diagnostic tests will depend on the several conditions (e.g sensitivity and specificity).Although PCR method is beneficial to detect H. pylori, the following points were taken into account: -Cultures from gastric biopsies are the gold standard (Bordin et al, 2021) 1 .
-Culture-based diagnostics followed by phenotypic antimicrobial susceptibility testing is the gold standard for detection of resistance patterns (Shakir et al, 2023)  2 .
Since the objective of the research was to follow up a cohort with respect to the eradication rate using triple standard therapy, it was necessary to obtain the resistance patterns of the most reliable method (gold standard) to determine if the treatment failure was due to bacterial resistance.The results of biochemical tests and Gram staining of presumptive H. pylori colonies did not generate doubts, therefore, molecular confirmation (PCR) was not performed.
Comment 2: On what basis Helicobacter pylori strains were chosen?Answer 2: As described in the subtitles of Materials and Methods, "Patient Population", "H.pylori Culture" and "E-Test and Definition of Susceptibility Testing", all H. pylori isolates obtained by the primary culture were subcultured on non-selective Tryptic soy agar and the isolates subcultured were profiled for antimicrobial resistance by E-test.Therefore, the selection of the strains was based on the positive growth in culture.
Reviewer #2: This is a generally well-written article describing a small study on Triple therapy of Helicobacter pylori in Colombia.It presents results of a PPI-clarithromycin-amoxicillin regimen for treatment of patients with gastritis and includes data on efficacy, eradication and antibiotic susceptibility of drugs used for H. pylori.The main take home is that clarithromycin resistance is growing and susceptibility to clarithromycin is strongly correlated with eradication.It is recommended that empirical treatment of H. pylori be based on knowledge of local antibiotic resistance patterns.The methods used are appropriate and well described.
Comment 1: There are a few instances of rather informal English which should be corrected: Line 64 "figured out as" should be changed to identified as Line 74 "apparition" should be changed to appearance or emergence Line 103 "figure out" should be changed to discover Answer 1: All sentences were corrected in the manuscript.