Population genetics of Helicobacter pylori in the southern part of Switzerland analysed by sequencing of four housekeeping genes (atpD, glnA, scoB and recA), and by vacA, cagA, iceA and IS605 genotyping The GenBank accession numbers for the sequences reported in this paper are AY004351–AY004662

Solcà, Nadia Maggi; Bernasconi, Marco Valerio; Valsangiacomo, Claudio; Doorn, Leen–Jan van; Piffaretti, Jean-Claude

doi:10.1099/00221287-147-6-1693

Cited by 26 publications

(9 citation statements)

References 61 publications

(66 reference statements)

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“…In this study, the phylogenetic analysis of 34 rdxA nucleotide sequences obtained from Mtz-resistant H. pylori and 30 CLO+ samples revealed high genetic polymorphism. However, no particular characteristic could be clustered by the phylogenetic tree topologies of four H. pylori housekeeping genes (atpD, scoB, glnA, and recA) that arose from frequent recombination, similar to the results obtained in a previous study (Maggi Solca et al, 2001).…”

Section: Discussionsupporting

confidence: 86%

Analysis of allelic variants of rdxA associated with metronidazole resistance in Helicobacter pylori: detection of common genotypes in rdxA by multiplex allele-specific polymerase chain reaction

Butlop¹,

Mungkote²,

Chaichanawongsaroj³

2016

Genet. Mol. Res.

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ABSTRACT. Resistance to metronidazole (Mtz) in Helicobacter pylori is a major problem worldwide, especially in developing countries. Alterations in Mtz nitroreductase enzymes, such as oxygen-insensitive NADPH nitroreductase (RdxA) and NADPH flavin oxidoreductase (FrxA), are the major contributing factors for this resistance. In this study, rdxA and frxA were amplified, sequenced, and analyzed in 34 Mtz-resistant H. pylori isolates (MIC ≥ 8 µg/mL) using multiple allelespecific polymerase chain reaction (MAS-PCR); this method was developed to target the most common genotypes of rdxA in H. pylori. In this study, the rdxA and frxA genes in Mtz-resistant H. pylori strains displayed a large number of point mutations. The rdxA and frxA genes of Mtz-resistant clinical isolates showed a higher percentage of missense mutations (97.1 and 78.6%, respectively) compared to 26695 reference strains; additionally, missense mutations were more common than frameshift (20.6 and 32.1%) and nonsense mutations (8.8 and 10.7%, respectively) in these genes. The most common missense mutations in rdxA were D 59 N (94.1%), T 31 E (88.2%), and R 131 K (85.3%). The most common missense mutations in frxA were F 72 S (57.1%), G 73 S (57.1%), and C 193 S (53.6%). The developed MAS primers, specific to position 175 and 392 of rdxA, successfully amplified the common alleles and distinguished the variants. MAS-PCR could be a useful tool for epidemiological studies of H. pylori, associated with Mtz resistance. rdxA variants must be screened in order to ensure the effectiveness of Mtz-based H. pylori therapies in developing countries.

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Section: Discussionsupporting

confidence: 86%

Analysis of allelic variants of rdxA associated with metronidazole resistance in Helicobacter pylori: detection of common genotypes in rdxA by multiplex allele-specific polymerase chain reaction

Butlop¹,

Mungkote²,

Chaichanawongsaroj³

2016

Genet. Mol. Res.

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“…These analyses yielded comparable mean ρvalues within each species, indicating that LDhat estimates of this parameter are not strongly affected by sample size (see other examples by Jolley et al, 2000;Maggi-Solcà et al, 2001;Feil et al, 2003;Viscidi and Demma, 2003). However, many MLST data sets represent biased samples that are concentrated on disease isolates and confirmation of our results with more population-based samples is desirable.…”

Section: Species Comparisonsmentioning

confidence: 53%

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data

Pérez‐Losada

Browne

Madsen

et al. 2006

Infection, Genetics and Evolution

145

107

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The inference of population recombination (ρ), population mutation (Θ), and adaptive selection is of great interest in microbial population genetics. These parameters can be efficiently estimated using explicit statistical frameworks (evolutionary models) that describe their effect on gene sequences. Within this framework, we estimated ρand Θ using a coalescent approach, and adaptive (or destabilizing) selection under heterogeneous codon-based and amino acid property models in microbial sequences from MLST databases. We analyzed a total of 91 different housekeeping gene regions (loci) corresponding to one fungal and sixteen bacterial pathogens. Our results show that these three population parameters vary extensively across species and loci, but they do not seem to be correlated. For the most part, estimated recombination rates among species agree well with previous studies. Over all taxa, the ρ/Θ ratio suggests that each factor contributes similarly to the emergence of variant alleles. Comparisons of Θ estimated under finite-and infinite-site models indicate that recurrent mutation (i.e., multiple mutations at some sites) can increase Θ by up to 39%. Significant evidence of molecular adaptation was detected in 28 loci from 13 pathogens. Three of these loci showed concordant patterns of adaptive selection in two to four different species.

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“…RAPD typing provides a method of easily producing typeable data based on familial groupings over a short time span. Variation is likely to occur between samples as H. pylori undergoes considerable genetic mutation and recombination due to the pandemic nature of this species [20]. …”

Section: Discussionmentioning

confidence: 99%

Intrafamilial Genotyping ofHelicobacter pylorifrom Faecal DNA

McMillan

Mackay

Williams

et al. 2011

Gastroenterology Research and Practice

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Helicobacter pylori infection, often acquired in early childhood, is a global cause of undernutrition, gastritis, peptic ulcer disease and gastric carcinoma. This study tested the feasibility of using H. pylori shed in the faeces as a source of DNA for non-invasive epidemiological studies. H. pylori DNA was chemically recovered and isolated using a specific biotinylated oligonucleotide probe with magnetic capture from 28 H. pylori positive faecal samples obtained from children attending hospital for the investigation of suspected H. pylori infection, together with close family members. Random amplification of polymorphic DNA (RAPD) was subsequently used to discriminate each isolate. 93% of stool samples selected were typeable. Parent, child and sibling samples were compared and similarities determined. Phylogenetic analysis showed that H. pylori DNA obtained from the faeces can be used to genotype individual strains, offering a means of studying intrafamilial transfer of this microorganism.

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Population genetics of Helicobacter pylori in the southern part of Switzerland analysed by sequencing of four housekeeping genes (atpD, glnA, scoB and recA), and by vacA, cagA, iceA and IS605 genotyping The GenBank accession numbers for the sequences reported in this paper are AY004351–AY004662

Cited by 26 publications

References 61 publications

Analysis of allelic variants of rdxA associated with metronidazole resistance in Helicobacter pylori: detection of common genotypes in rdxA by multiplex allele-specific polymerase chain reaction

Analysis of allelic variants of rdxA associated with metronidazole resistance in Helicobacter pylori: detection of common genotypes in rdxA by multiplex allele-specific polymerase chain reaction

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data

Intrafamilial Genotyping ofHelicobacter pylorifrom Faecal DNA

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