Microorganisms (Feb 2025)

Beyond Low Prevalence: Exploring Antibiotic Resistance and Virulence Profiles in Sri Lankan Helicobacter pylori with Comparative Genomics

  • Kartika Afrida Fauzia,
  • Jeewantha Rathnayake,
  • Dalla Doohan,
  • Meegahalande Durage Lamawansa,
  • Ricky Indra Alfaray,
  • Saruuljavkhlan Batsaikhan,
  • Bui Hoang Phuc,
  • Langgeng Agung Waskito,
  • Vo Phuoc Tuan,
  • Evariste Tshibangu Kabamba,
  • Shamshul Ansari,
  • Takashi Matsumoto,
  • Junko Akada,
  • Takeshi Matsuhisa,
  • Yoshio Yamaoka

DOI
https://doi.org/10.3390/microorganisms13020420
Journal volume & issue
Vol. 13, no. 2
p. 420

Abstract

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Helicobacter pylori infects at least half the population worldwide, and its highly diverse genomic content correlates with its geographic distribution because of its prolonged relationship with humans. The extremely low infection prevalence alongside low inflammation severity observed in some countries might be caused by strains with low virulence potential. Therefore, this study aimed to investigate whole-genome analysis datasets of Sri Lankan H. pylori strains. H. pylori strains were isolated from biopsy specimens and underwent whole-genome sequencing to investigate their antibiotic resistance and virulence potential. The prevalence of H. pylori infection in Sri Lanka is extremely low (1.7% in a previous study), and only six H. pylori strains were successfully isolated from bacterial culture. Antibiotic resistance analysis showed a high prevalence of metronidazole resistance (83.3%, five out of six strains), and investigation of the related genes showed truncation of the rdxA and frxA genes and single-nucleotide polymorphisms in the rdxA, frxA, ribF, omp11, and fur genes. Most virulence genes of the 144 assessed were present, except for the cag pathogenicity island (cagPAI) (absent in four out of six strains), babA/B/C, and tlpB genes. An incomplete type 4 secretion system (tfs) was found in three strains. A pan-genome analysis with non-Sri Lankan H. pylori strains showed that the htpX gene was found only in Sri Lankan strains (p-corrected = 0.0008). A phylogenetic analysis showed that the Sri Lankan strains clustered with strains from hpAsia2 and hpEurope. This comparative genomic study shows that H. pylori strains with low virulence potential are present in countries with a low prevalence of infection and disease severity, indicating a strain-type geographical pattern. The tailored guidelines for screening and treatment strategy for each region are necessary to obtain effective and efficient eradication.

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