J Bacteriol. 2000 Jun;182(11):3219-27.

Distinctiveness of genotypes of Helicobacter pylori in Calcutta, India.

Mukhopadhyay AK, Kersulyte D, Jeong JY, Datta S, Ito Y, Chowdhury A, Chowdhury S, Santra A, Bhattacharya SK, Azuma T, Nair GB, Berg DE.

Source

Department of Molecular Microbiology, Washington University Medical School, St. Louis, Missouri 63110, USA.

Abstract

The genotypes of 78 strains of Helicobacter pylori from Calcutta, India (55 from ulcer patients and 23 from more-benign infections), were studied, with a focus on putative virulence genes and neutral DNA markers that were likely to be phylogenetically informative. PCR tests indicated that 80 to 90% of Calcutta strains carried the cag pathogenicity island (PAI) and potentially toxigenic vacAs1 alleles of the vacuolating cytotoxin gene (vacA), independent of disease status. This was higher than in the West (where cag PAI(+) vacAs1 genotypes are disease associated) but lower than in east Asia. The iceA2 gene was weakly disease associated in Calcutta, whereas in the West the alternative but unrelated iceA1 gene at the same locus is weakly disease associated. DNA sequence motifs of vacAm1 (middle region) alleles formed a cluster that was distinct from those of east Asia and the West, whereas the cagA sequences of Calcutta and Western strains were closely related. An internal deletion found in 20% of Calcutta iceA1 genes was not seen in any of approximately 200 strains studied from other geographic regions and thus seemed to be unique to this H. pylori population. Two mobile DNAs that were rare in east Asian strains were also common in Calcutta. About 90% of Calcutta strains were metronidazole resistant. These findings support the idea that H. pylori gene pools differ regionally and emphasize the potential importance of studies of Indian and other non-Western H. pylori populations in developing a global understanding of this gastric pathogen and associated disease.

PMID:: 10809703; [PubMed - indexed for MEDLINE]
PMCID:: PMC94510

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FIG. 4

DNA sequence alignments, illustrating motifs found in H. pylori strains from Calcutta. Sequences from non-Indian strains that were used here were from public databases, as indicated. (A) vacAs region sequences, showing differences between vacAs1a, -s1b, and -s1c type alleles. vacAs1a alleles are common in the Calcutta H. pylori strains, whereas vacAs1c alleles are most common elsewhere in Asia. Each of the 97-bp sequences presented here starts at position 27 of a reference vacA open reading frame (GenBank accession no. U07145). Identical nucleotides are indicated by hyphens. GenBank accession numbers for the sequences depicted here are U07145 (NCTC11638), AF217728 (India9), AF217729 (India10), AF217730 (India17), AF217731 (India18), AF217734 (India29), AF217735 (India67), AE001511 (J99), AF217732 (India21), AF091830 (Taiwan34), AF049632 (Japan55), and AF049638 (Japan78). (B) vacAm1 middle region sequences, showing differences among vacAm1a, vacAm1b, and two of the representative vacAm1c allele types that we characterized. The vacAm1c alleles, which were common in Calcutta strains, were rare in populations from outside India that have been studied to date. Each of the 650-bp sequences presented here corresponds to nucleotides (nt) 2060 to 2709 of the vacA gene of reference strain NCTC11638 (Genbank accession no. U07145). GenBank accession numbers for the sequences depicted here are U07145 (NCTC11638), AF035610 (ChinaR13), AF220110 (India18; strain 5 in Fig. 3) and AF220117 (India230; strain 6 in Fig. 3). (C) Alignment of four iceA1 genes of Calcutta isolates, along with reference strain 60190 (GenBank accession no. U43917). The sequences presented here correspond to nt 426 to 558 in India227 (accession no. AF239991), nt 446 to 558 in India34A (accession no. AF239992), nt 430 to 478 in India18A (accession no. AF239993), and nt 423 to 471 in India44A (accession no. AF239994).

Distinctiveness of Genotypes of Helicobacter pylori in Calcutta, India

J Bacteriol. J Bacteriol;182(11):3219-3227.

FIG. 3

Phylogenetic trees of sequences within the cagA gene and vacAm1 alleles. Sequences from non-Indian strains that were used here were from public databases, as indicated. (A) Phylogenetic tree based on an informative 220-bp segment of cagA (62) of H. pylori strains determined in this study (Calcutta strains 5 to 7, 16 to 18, and 23) or reported by others. The tree was generated using PHYLIP (Phylogeny Inference Package), version 3.5c, of J. Felsenstein (see Materials and Methods). The strains used are as follows (GenBank accession numbers are in parentheses): 1, Dutch161A (AJ252965); 2, 26695 (AE000569); 3, Peru8C (AF198478); 4, Lith5-1 (AJ239734); 5, India10 (AF202222); 6, India19 (AF202225); 7, India3 (AF202219); 8, Peru24C (AF198473); 9, Peru2B (AF198474); 10, Dutch292 (AJ252971); 11, Peru35B (AF198476); 12, Dutch79 (AJ252970); 13, Gambia4659 (AF198468); 14, Peru4A (AF198477); 15, Gambia4797 (AF198469); 16, India18 (AF202224); 17, India9 (AF202221); 18, India7 (AF202220); 19, Dutch25 (AJ252968); 20, Dutch419 (AJ252974); 21, Guatemala88 (AF198472); 22, South Africa19 (AF198470); 23, India17 (AF202223); 24, Dutch107 (AJ252963); 25, Peru34B (AF198475); 26, ChinaR47 (AJ252985); 27, HongKong77 (AF198485); 28, Thailand88-28 (AJ239722); 29, ChinaR27 (AJ252979); 30, HongKong97-42 (AJ239733); 31, HongKong81 (AF198486); 32, ChinaR40 (AJ252982); 33, ChinaR59 (AJ252986); 34, ChinaR29 (AJ252980); 35, JapanF32 (AJ239726); 36, JapanGC4 (AF198484); 37, ChinaR48 (AJ252983). (B) Tree based on informative 650-bp segment of vacA gene containing vacAm1 alleles of Calcutta H. pylori strains determined in this study (strains 1 to 9 except strain 7) or reported by others. The tree was generated using PHYLIP (Phylogeny Inference Package), version 3.5c, of J. Felsenstein (see Materials and Methods). The sequences of east Asian and ethnic European vacAm1 alleles were taken from GenBank. Each number in this figure indicates the vacAm1 sequence from a given strain, as follows (GenBank accession numbers in parentheses): 1, India19 (AF220111); 2, India226 (AF220115); 3, India89 (AF220114); 4, India48 (AF220112); 5, India18 (AF220110); 6, India230 (AF220117); 7, GermanyMz19 (AJ006967); 8, India66 (AF220113); 9, India227 (AF220116); 10, JapanF52 (AF049631); 11, JapanF55 (AF049632); 12, ChinaR59 (AF035611); 13, JapanF63 (AF049635); 14, ChinaR13 (AF035610); 15, JapanF42 (AF049626); 16, Japan94 (AF049640); 17, JapanF72 (AF049651); 18, JapanF73 (AF049652); 19, JapanF47 (AF049629); 20, JapanF57 (AF049634); 21, JapanF35 (AF049625); 22, JapanF61 (AF049645); 23, JapanF36 (AF049462); 24, JapanF64 (AF049647); 25, JapanF45 (AF0496628); 26, Poland1492 (AF097570); 27, Poland278 (AF097571); 28, NCTC11637 (AF049653); 29, J99 (AE001511); 30, NCTC11638 (U07145); 31, 26695 (AE000598).

Distinctiveness of Genotypes of Helicobacter pylori in Calcutta, India

J Bacteriol. J Bacteriol;182(11):3219-3227.