Antibiotics | Highlight Article Title: Whole-Genome Sequencing and Antibiotic Resistance Analysis of Helicobacter pylori from Southern Thailand Hospitals

This study reveals the antibiotic resistance mutations, virulence factors, and phylogenetic features of Helicobacter pylori clinical isolates from southern Thailand through whole-genome sequencing and resistance profiling, providing critical insights for regional-specific therapeutic strategies and genomic surveillance.

 

Literature Overview
The article 'Whole-Genome Sequencing and Antibiotic Resistance Profiling of Helicobacter pylori Isolates from a Tertiary Hospital in Southern Thailand', published in Antibiotics, summarizes the genomic characteristics, antibiotic resistance patterns, and virulence gene distribution of Helicobacter pylori in southern Thailand. Phylogenetic analysis identifies its unique evolutionary lineage, offering essential regional resistance data to support clinical correlation studies between resistance, virulence factors, and disease outcomes. This research holds significant public health and clinical implications.

Background Knowledge
Helicobacter pylori is a Gram-negative, microaerophilic bacterium colonizing human gastric mucosa, strongly associated with upper gastrointestinal diseases such as chronic gastritis, peptic ulcers, and gastric cancer. Classified as a Group 1 carcinogen by the International Agency for Research on Cancer (IARC), its increasing global antibiotic resistance—particularly in Southeast Asia—has led to declining eradication rates, posing major clinical challenges. Resistance mechanisms primarily involve chromosomal point mutations rather than horizontal gene transfer, underscoring the importance of genomic analysis in understanding resistance evolution. Virulence factors like cagA, vacA, and babA play critical roles in disease progression but exhibit geographic variability in distribution and expression. Southern Thailand, with distinct dietary habits and high antibiotic usage, has emerged as a key region for resistance monitoring. While prior studies confirm high resistance rates in this area, systematic analyses linking resistance mutations to virulence factors remain limited. This study fills this gap by integrating phenotypic resistance testing with whole-genome sequencing to characterize resistance genes, virulence profiles, and phylogenetic features of three clinical isolates, offering genomic evidence for region-specific treatment strategies.

 

 

Research Methods and Experiments
The research team collected three Helicobacter pylori clinical isolates (004, 117, 189) from a tertiary hospital in southern Thailand. Isolates were cultured, identified via MALDI-TOF MS, and subjected to whole-genome sequencing. Phenotypic resistance was assessed using E-test methods, while genomic resistance mutations were predicted through bioinformatics analysis. The Roary pipeline facilitated pangenomic analysis, phylogenetic tree construction, and exploration of potential associations between virulence genes and resistance traits through comparative studies.

Key Conclusions and Perspectives

• All isolates exhibited high-level metronidazole resistance (MIC > 256 µg/mL).
• Strain 117 demonstrated resistance to amoxicillin and levofloxacin, qualifying it as a multidrug-resistant strain.
• Genomic analysis identified A2142G and A2143G mutations in the 23S rRNA gene, linked to clarithromycin resistance. However, phenotypic tests showed susceptibility to clarithromycin, suggesting potential genotype-phenotype discrepancies.
• Metronidazole resistance correlated with mutations in rdxA and frxA genes. Strain 189 carried additional mutations (H97T, P106S).
• All strains harbored virulence genes (cagA, vacA, oipA, babA) and genes associated with urease, flagellum, and lipopolysaccharide synthesis, indicating high pathogenic potential.
• Phylogenetic analysis revealed Thai strains formed a distinct monophyletic clade, suggesting localized clonal expansion and regional adaptation.
• The study advocates for region-specific treatment guidelines and genomic surveillance to address dual challenges of resistant and hypervirulent strains.

Research Significance and Prospects
This work provides the first genomic-level evidence correlating antibiotic resistance and virulence factors in southern Thai Helicobacter pylori isolates, supporting the integration of genomic sequencing into clinical resistance diagnostics. Future studies should expand sample sizes and correlate resistance mutations with clinical phenotypes (e.g., gastric cancer) using comprehensive clinical data. Rapid evolution of resistant strains necessitates stricter regional antibiotic stewardship and exploration of gene-editing models for mechanistic studies.

 

 

Conclusion
This study systematically characterized whole-genome features and resistance phenotypes of Helicobacter pylori isolates from southern Thailand, revealing high metronidazole resistance, multidrug-resistant strains, and conserved virulence genes. Notably, clarithromycin resistance mutations did not align with phenotypic resistance, indicating possible regulatory mechanisms or compensatory mutations. Phylogenetic analysis demonstrated Thai isolates form a distinct evolutionary lineage, reflecting regional evolutionary pressures. These findings emphasize the urgency of regional resistance monitoring and personalized treatment strategies, while offering genomic and functional research entry points. Combining genomic data with virulence/resistance profiling supports precision therapy and public health interventions for Helicobacter pylori.

 

Chonticha Romyasamit, Apichat Kaewdech, Pimsiri Sripongpun, Maseetoh Samaeng, and Phoomjai Sornsenee. Whole-Genome Sequencing and Antibiotic Resistance Profiling of Helicobacter pylori Isolates from a Tertiary Hospital in Southern Thailand. Antibiotics.