Comparison of Genotyping
            <i>Helicobacter pylori</i>
            Directly from Biopsy Specimens and Genotyping from Bacterial Cultures

Park, Chang-Young; Kwak, Minjung; Gutiérrez, Óscar; Graham, David Y.; Yamaoka, Yoshio

doi:10.1128/jcm.41.7.3336-3338.2003

Cited by 44 publications

(49 citation statements)

References 11 publications

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“…Furthermore, they observed a higher proportion of mixed H. pylori strain infection in biopsy specimens (27%) compared to cultured H. pylori strains (9%) (Park et al, 2003). Similarly, based on cagA EPIYA genotyping we detected a higher proportion of mixed H. pylori strains in biopsy specimens (24%) compared to cultured H. pylori strains (11%).…”

Section: Discussionmentioning

confidence: 67%

“…It has been discussed that PCR-based genotyping directly from biopsy specimens tend to underestimate the prevalence of H. pylori specific virulence genes (Park et al, 2003;Secka et al, 2011). This may be due to limited access of H. pylori DNA, inhibition of PCR amplification due to high level of cellular genomic DNA, other PCR inhibitors or potent nucleases in gastric biopsy specimens (Monstein et al, 2005;Park et al, 2003;Thoreson et al, 1999).…”

Section: Discussionmentioning

confidence: 99%

“…Park and co-workers have suggested that studies identifying associations between virulence factors and disease outcome should be restricted to sites with rare mixed H. pylori strain infection. However, this might lead to false perception of the actual relationship of bacterial strains and disease outcome (Park et al, 2003).…”

Section: Discussionmentioning

confidence: 99%

“…This may be due to limited access of H. pylori DNA, inhibition of PCR amplification due to high level of cellular genomic DNA, other PCR inhibitors or potent nucleases in gastric biopsy specimens (Monstein et al, 2005;Park et al, 2003;Thoreson et al, 1999). Whole genome amplification by multiple displacement amplification (MDA) can be used as a pre-PCR amplification step under conditions where PCR amplifications normally are hampered due to presence of inhibitors (Gonzalez et al, 2005) or where the amount of DNA is not sufficient for analysis (Ryberg et al, 2008).…”

Section: Discussionmentioning

confidence: 99%

“…One such factor may be the occurrence of mutations, selection of a single strain from a sample containing mixed strains, or both, when culturing H. pylori strains (Kraft and Suerbaum, 2005;Marshall et al, 1998). It is still debated whether or not molecular genotyping of cagA should be performed on cultured H. pylori strains or biopsy DNA (Gunn et al, 1998;Kim et al, 2009;Park et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

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Variation in number of cagA EPIYA-C phosphorylation motifs between cultured Helicobacter pylori and biopsy strain DNA

Karlsson¹,

Ryberg²,

Dehnoei³

et al. 2012

Infection, Genetics and Evolution

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The Helicobacter pylori cagA gene encodes a cytotoxin which is activated by phosphorylation after entering the host epithelial cell. Phosphorylation occurs on specific tyrosine residues within EPIYA motifs in the variable 3'-region. Four different cagA EPIYA motifs have been defined according to the surrounding amino acid sequence; EPIYA-A, -B, -C and -D. Commonly, EPIYA-A and -B are followed by one or more EPIYA-C or -D motif. Due to observed discrepancies in cagA genotypes in cultured H. pylori and the corresponding DNA extracts it has been suggested that genotyping assays preferentially should be performed directly on DNA isolated from biopsy specimens. Gastric biopsies randomly selected from a Swedish cohort were homogenised and used for both direct DNA isolation and for H. pylori specific culturing and subsequent DNA isolation. In 123 of 153 biopsy specimens, the cagA EPIYA genotypes were in agreement with the corresponding cultured H. pylori strains. A higher proportion of mixed cagA EPIYA genotypes were found in the remaining 30 biopsy specimens. Cloning and sequencing of selected cagA EPIYA amplicons revealed variations in number of cagA EPIYA-C motifs in the mixed amplicons. The study demonstrates that culturing of H. pylori introduces a bias in the number of EPIYA-C motif. Consistent with other H. pylori virulence genotyping studies, we suggest that cagA EPIYA analysis should be performed using total DNA isolated from biopsy specimens.funding agencies|Research council in the South-East of Sweden (FORSS)||ALF||Clinical Microbiology, Laboratory Centre-DC, University Hospital, Linkoping, Sweden|

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Section: Discussionmentioning

confidence: 67%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Variation in number of cagA EPIYA-C phosphorylation motifs between cultured Helicobacter pylori and biopsy strain DNA

Karlsson¹,

Ryberg²,

Dehnoei³

et al. 2012

Infection, Genetics and Evolution

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PCR Detection of Helicobacter pylori in Clinical Samples

Rimbara¹,

Sasatsu

Graham

2012

PCR Detection of Microbial Pathogens

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Helicobacter pylori is an important pathogen whose primary niche is the human stomach. H. pylori is etio-logically associated with gastric inflammation (gastritis), peptic ulcer disease, and gastric cancer. Both noninvasive (e.g., urea breath and stool antigen tests) and invasive (gastric biopsy for histology, culture, or PCR) tests are used for diagnosis. PCR detection of H. pylori has been reported using a variety of clinical samples including gastric biopsy, gastric juice, saliva, dental plaque, and stools as well as environmental samples. Whenever possibly, noninvasive tests are preferred over invasive tests. H. pylori are excreted in the stool. Culture from stool is variable whereas stool antigen testing is widely used. Stool consists of a complicated mixture of commensal bacteria and chemicals and often includes inhibitors of PCR. Nevertheless, simple extraction methods are available to efficiently extract DNA from human stools and nested-PCR targeting the 23S rRNA gene have proven to be highly sensitive for the detection of H. pylori. Detection of clarithromycin susceptibility/resistance is important clinically and the mutation of the 23S rRNA gene responsible for resistance can also be detected using stool. This described method can be modified for other clinical samples such as gastric juice or biopsy material.

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Differentiation of virulence of Helicobacter pylori by matrix-assisted laser desorption/ionization mass spectrometry and multivariate analyses

Cho¹,

Kuo

Wang

et al. 2013

Clinica Chimica Acta

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Comparison of Genotyping Helicobacter pylori Directly from Biopsy Specimens and Genotyping from Bacterial Cultures

Cited by 44 publications

References 11 publications

Variation in number of cagA EPIYA-C phosphorylation motifs between cultured Helicobacter pylori and biopsy strain DNA

Variation in number of cagA EPIYA-C phosphorylation motifs between cultured Helicobacter pylori and biopsy strain DNA

PCR Detection of Helicobacter pylori in Clinical Samples

Differentiation of virulence of Helicobacter pylori by matrix-assisted laser desorption/ionization mass spectrometry and multivariate analyses

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