Detection of rodent Helicobacter spp. by use of fluorogenic nuclease polymerase chain reaction assays

Polymerase chain reaction (PCR) analysis is the standard method for detection of Helicobacter spp. infections in laboratory rodents, with H. hepaticus, H. bilis, and H. typhlonius considered primary pathogens. Fluorogenic nuclease PCR assays that detect all known rodent Helicobacter spp., or that specifically detect H. hepaticus, H. bilis, or H. typhlonius were developed to eliminate post-PCR processing, enhance specificity, and provide quantitative data on starting template concentration. Each fluorogenic PCR assay detected a minimum of 10 copies of target template, had comparable or greater sensitivity when compared directly with corollary gel detection PCR assays, and detected only targeted species when numerous Helicobacter spp. and other enteric bacteria were analyzed. Fluorogenic nuclease PCR analysis of fecal DNA samples obtained from numerous laboratory mice sources detected all samples with positive results by use of Helicobacter spp., H. hepaticus, H. bilis, and/or H. typhlonius gel detection PCR analysis, except for one sample that had positive results by H. typhlonius gel detection PCR but negative results by H. typhlonius fluorogenic nuclease PCR analysis. Among fecal DNA samples that were Helicobacter spp. negative by use of all gel detection PCR assays, the fluorogenic nuclease PCR assays detected target template in only one sample that was positive by use of the Helicobacter spp. and the H. bilis fluorogenic nuclease PCR assays. In conclusion, fluorogenic nuclease PCR assays provide sensitive, specific, and high-throughput diagnostic assays for detection of Helicobacter spp., H. hepaticus, H. bilis, and H. typhlonius in laboratory rodents, and the quantitative data generated by these assays make them potentially useful for bacterial load determination.     

Template DNA ratio can affect detection by genus-specific PCR-denaturing gradient gel electrophoresis of bacteria present at low abundance in mixed populations

The detection of Helicobacter species by genus-specific polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was compared with that by species-specific PCR in murine intestinal samples. Results suggest that, in samples containing multiple Helicobacter species, genus-specific PCR-DGGE may fail to detect all Helicobacter species present and that this relates to the initial template DNA ratio.     

啮齿类螺杆菌不同检测方法的比较

目的确定用于实验啮齿类动物常规螺杆菌检测方法。方法选用针对螺杆菌属16S rRNA属特异性的4对引物进行了引物选择、取材部位以及与分离培养法比较。结果引物P7/P8的敏感性优于其它3对,检出限可达0.01 pg,对阳性动物群检出率80%-100%;分离培养法检出率40%-50%;盲肠、结肠检出率无显著差异。结论以引物P7/P8的PCR方法作为啮齿类实验动物螺杆菌初筛方法,分离培养法作为验证方法,取材部位可在盲肠或结肠。     

Characterization of the PCR inhibitory effect of bile to optimize real-time PCR detection of Helicobacter species

The inhibitory effect of human and porcine bile samples to detect Helicobacter DNA was studied by adding different concentrations of bile samples to PCR mixtures of six thermostable DNA polymerases containing cagA specific primers and Helicobacter pylori DNA. PCR products were amplified by using the Rotorgene system and SYBR Green I. Among the six DNA polymerases tested, rTth had the lowest sensitivity to bile inhibitors, whereas Taq and Tfl had the highest sensitivity. Bile proteins did not inhibit AmpliTaq DNA polymerase, whereas the fraction containing mainly bile acids and their salts inhibited the amplification capacity of AmpliTaq. Heating human bile at 98 degrees C and adding casein and formamide to the reaction mixture reduced the PCR inhibitory effect of bile. Therefore, a pre-PCR treatment based on dilution and heating of bile, adding casein and formamide to the reaction mixture of rTth DNA polymerase was found efficient to amplify DNA directly in bile.     

Natural colonization with Helicobacter species and the development of inflammatory bowel disease in interleukin-10-deficient mice

BACKGROUND: The interleukin-10-deficient (IL-10-/-) mice maintained in specific-pathogen-free (SPF) conditions develop typhlocolitis when experimentally infected with Helicobacter species. However, there is limited information regarding the role of Helicobacter species that naturally colonize IL-10-/- mice in typhlocolitis development. The aim of this study was to examine in SPF IL-10-/- mice the association between natural colonization specific Helicobacter species and typhlocolitis development. MATERIAL AND METHODS: Cecum and proximal colon from 72 C57BL/6 x 129/Ola IL-10-/- mice (8-20 weeks old) were removed for DNA extraction and histologic evaluation. Genus-specific polymerase chain reaction- denaturing gradient gel electrophoresis (PCR-DGGE) and species-specific PCR were used to detect Helicobacter species. Mice were grouped by age, sex, and Helicobacter colonization status, and their histologic scores were compared. The development of clinical typhlocolitis was observed in a further 12 mice. RESULTS: Species-specific PCR showed that mice were colonized with Helicobacter ganmani and/or Helicobacter hepaticus. The PCR-DGGE detected H. ganmani, H. hepaticus and an H. ganmani-like organism. The histologic scores in mice colonized with H. hepaticus were significantly higher than that in mice colonized with H. ganmani. Male mice showed significantly higher histologic scores than female mice. Four of the 12 mice developed clinical typhlocolitis in 38 weeks. CONCLUSION: Natural colonization with different Helicobacter species was found in IL-10-/- mice within the same breeding colony. The severity of typhlocolitis differed according to the colonizing Helicobacter species. Furthermore, the rate of typhlocolitis development in IL-10-/- mice naturally colonized with Helicobacter species was significantly slower than that reported in experimentally infected mice.     

Quantitative detection for low levels of Helicobacter pylori infection in experimentally infected mice by real-time PCR

Accurate diagnosis of Helicobacter pylori infection is important in both clinical practice and clinical research. Molecular methods are highly specific and sensitive, and various PCR-based tests have been developed to detect H. pylori in gastric biopsy specimens. We optimized a sensitive and specific quantitative SYBR Green I real-time PCR assay for detection of H. pylori based on amplification of the fragment of a 26-kDa Helicobacter species-specific antigen gene that allows for detection of 5 bacterial cells per PCR sample. Under the assay conditions, SYBR Green I real-time PCR is highly reproducible with a precise log-linear relation in the range of six orders of magnitude of bacterial DNA concentrations. For accurate comparison of H. pylori infection in different tissue samples, the amount of total host DNA in each sample is normalized by TaqMan real-time PCR of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) pseudogenes. The developed method was validated in prophilactically immunized and experimentally infected mice and revealed a level of H. pylori gastric colonisation that was below the limit of detection for a rapid urease test. This new method established for a quantitative analysis of H. pylori in the host's stomach may be useful in experimental studies evaluating new anti-H. pylori drugs and vaccines.     

The use of fatty acid methyl ester analysis (FAME) for the identification of heterotrophic bacteria present on three mural paintings showing severe damage by microorganisms

To monitor changes along the entire Helicobacter pylori vac A gene we carried out full-length single-step PCR amplification in 21 gastritis and gastric cancer isolates. HindIII restriction analysis led us to detect a > 400-bp internal insertion in vacA subsequently shown to be a direct 451-bp gene duplication. We found HindIII profiles for 16 genes that allowed their grouping into two restriction patterns that were related to theoretical profiles for previously sequenced Western genes. Comparisons with theoretical HindIII patterns for Japanese isolates appear suggestive of geographical H. pylori clonality. Full-length single-step PCR amplification seems suitable for quick restriction pattern assignment and detection of gene size changes.     

口腔中幽门螺杆菌PCR检测方法的建立

全世界大约有50%的人口感染幽门螺杆菌(Helicobacter pylori, Hp),Hp感染容易造成慢性胃炎、消化性溃疡、低度恶性胃MALT淋巴瘤及胃癌,对人类造成严重的危害。为寻求一种简便、准确、非创伤性的方法用于口腔中Hp的检测,本研究建立了口腔中幽门螺杆菌的PCR检测方法,并对建立的PCR方法的敏感性、特异性进行分析,并应用于检测唾液样品和牙菌斑共50份。结果显示,50份样品中,阳性率为82%。结果表明,本研究建立的口腔中Hp的PCR检测方法特异性强、敏感性高,可以用于临床上Hp诊断的重要参考。     

Prevalence of Helicobacter and Acanthamoeba in natural environment

Aims:  We examined whether the presence of Helicobacter is related to that of Acanthamoeba in river and soil environments.
Methods and Results:  The samples (river n  =   51, soil n  =   75) were collected in Sapporo City, Japan. PCR with primers for Helicobacter genus-specific and standard culture techniques were used to detect helicobacter. Prevalence of acanthamoeba was also evaluated by genus-specific PCR. The prevalence of Helicobacter genus-specific DNA in river water samples and in soil samples was 88% and 0%, respectively. No successful culture of helicobacter was achieved. The prevalence of Acanthamoeba genus-specific DNA in river samples and in soil samples was 61% and 96%, respectively. No statistical correlation between the prevalence of helicobacter and either that of acanthamoeba or water quality parameters (pH, turbidity and coliform group) except for temperature was found.
Conclusions:  We revealed the presence of helicobacter in river water and non-existence of helicobacter in soil. However, the distribution of helicobacter did not overlap with that of acanthamoeba in rivers.
Significance for Impact of the Study:  The role of acanthamoeba on the survival of helicobacter might be limited as the both are coincidentally present in the environment.     

Detection of gastric Helicobacter species in free-ranging lynx (Lynx lynx) and red foxes (Vulpes vulpes) in Sweden

Specimens of gastric mucosa and liver of 25 free-ranging Eurasian lynx (Lynx lynx), and four red foxes (Vulpes vulpes) shot in Sweden during 1999-2000, were investigated for the presence of Helicobacter species. Histopathology, bacteriologic culture and urease test, Helicobacter genus-specific 16S rDNA PCR analysis, and DNA sequence analysis were applied. Numerous Helicobacter-like organisms were observed histologically in the gastric mucosa of one fox. Helicobacter spp. were detected in the stomach by PCR analysis in 17 (68%) of the lynx and in three (75%) of the foxes. Seven of the positive lynx were also positive in the urease test. PCR fragments, amplified from lynx and foxes, were sequenced and compared with those of known Helicobacter species. PCR products from lynx were closely related (>or=98% homology) to H. heilmannii, and PCR fragments from foxes demonstrated close homology to H. heilmannii and H. salomonis. No Helicobacter spp. or Helicobacter-like organisms could be cultured. The PCR analysis of the liver was negative for all animals. The pathologic significance of the presence of Helicobacter spp. in the stomach of free-ranging lynx and foxes remains uncertain.     

Value of PCR technique in detection of Helicobacter pylori in paraffin-embedded material

Methods which permit effective detection of Helicobacter prlori are based on endoscopic sampling of gastric mucosa followed by a direct or indirect demonstration of Helicobacter pylori bacilli, e.g. searching for specific proteins or gene fragments. PCR technique represents one of techniques employed for diagnosing the biopsies. The present study was aimed at examining how effective is the detection of Helicobacter pylori in paraffin-embedded material by PCR technique using primers for the Ure C gene fragment. The material for studies involved gastric biopsies, routinely fixed in formalin and embedded in paraffin. In order to perform PCR, DNA was isolated and purified, subjected to amplification with the use of starters for the Ure C gene fragment. The performed experiments have confirmed suitability of PCR technique for detection of Helicobacter pylori.     

不同部位、分化和起源胃癌中H.pylori、CagA基因的探讨

目的通过检测不同部位和不同组织类型中胃癌组织中幽门螺杆菌(H.pylori)和细胞毒素相关基因(CagA基因),探讨H.pylori、CagA基因与胃癌的关系,以及H.pylori、CagA基因导致胃癌的可能机制。方法应用快速尿素酶试验和组织切片革兰染色及血清H.pylori CagA抗体检测胃癌患者H.pylori,应用PCR检测胃癌组织中H.pylori CagA基因。结果胃癌组织中随活检部位不同,H.pylori检出率也不同,以胃窦部检出率最高为76.9%,与胃体大弯侧、胃角和贲门相比差异均有非常显著性(P0.005),胃体大弯侧、胃角与贲门相比差异均有非常显著性(P0.005),胃底与贲门相比差异无显著性(P0.05)。胃窦部癌的CagA检出率(85.6%)最高,与其他部位相比差异均有非常显著性(P0.005),胃角胃癌CagA检出率显著高于胃体大弯侧和贲门胃癌(P0.005)。高分化胃癌H.pylori检出率为73.1%,低分化胃癌H.pylori检出率为44.1%,二者相比差异均有非常显著性(P0.01)。肠型胃癌H.pylori检出率为76.7%,弥漫型胃癌H.pylori检出率为33.3%,二者相比差异有显著性(P0.05),高分化胃癌CagA检出率为26.3%,低分化胃癌CagA检出率为80.0%,二者相比差异均有非常显著性(P0.01)。肠型胃癌CagA检出率为80.4%,弥漫型胃癌CagA检出率为57.1%,二者相比差异无显著性(P0.05)。结论不同部位和不同组织类型中胃癌组织中H.pylori和CagA基因的表达存在一定差异性,对探讨胃癌的发生及胃癌的防治有一定的指导意义。     

Multiple displacement amplification of isolated DNA from human gallstones: molecular identification of Helicobacter DNA by means of 16S rDNA-based pyrosequencing analysis

BACKGROUND: Molecular typing of Helicobacter spp. in clinical biopsy specimens has become increasingly important. By means of nested polymerase chain reaction (PCR) amplification and Southern blot analysis of the PCR amplicons, we have shown that Helicobacter spp. DNA is present in human gallstones. In this study we have investigated the possibility of using multiple displacement amplification (MDA) of isolated gallstone DNA and pyrosequencing analysis for the molecular identification of Helicobacter spp. MATERIALS AND METHODS: DNA isolated from the nucleus of 33 human gallstones and one control strain were used in a MDA assay. Subsequently, pyrosequencing analysis was performed either directly on MDA-DNA using primers flanking the Helicobacter spp. 16S rDNA variable V3 region or on PCR amplicons derived from broad-range primers flanking the 16S rDNA variable V3, V4, and V9 regions. RESULTS: Pyrosequencing analysis of 16S rDNA derived from MDA-DNA revealed that Helicobacter spp.-like DNA was present in 25 of 33 (approximately 76%) gallstones. Using an H. pylori-specific Southern blot analysis, Helicobacter spp.-like DNA was present in 20 of 33 [approximately 61%] of the gallstones. Using MDA-DNA directly in pyrosequencing analysis, Helicobacter spp.-like DNA was present in 13 of 33 [approximately 39%] gallstones. CONCLUSIONS: We conclude that multiple displacement amplification combined with pyrosequencing enables a rapid and accurate molecular typing of Helicobacter spp. from small and precious biopsy specimens.     

Helicobacter pylori detection in human biopsies: a competitive PCR assay with internal control reveals false results

A polymerase chain reaction assay (PCR) for the diagnosis of Helicobacter pylori in human gastric biopsies was developed. To prevent false-negative results while performing PCR on human tissues, an internal control is necessary. Primer set ACT1-ACT2 which specifically amplifies a 542-bp fragment of the 16S rRNA gene of H. pylori was used. dUTP and hot-start were used to prevent false-positives from carryover of previous products and avoid non-specific extension products. A competitive internal control DNA fragment was constructed to detect the presence of inhibitors. Biopsies from 101 unselected patients with gastric symptoms were tested. PCR results were compared with results from microscopy of histological sections and conventional culturing for H. pylori. Forty-two percent of the biopsies were found to contain compounds inhibiting the PCR. The addition of the internal control assures the performance of the PCR assay and is an important quality control parameter.     

Simple duplex fecal PCR assay that allows identification of false-negative results in Helicobacter sp.-infected mice

We designed a simple and sensitive duplex polymerase chain reaction (PCR) assay for detection of false-negative results during routine Helicobacter sp. feces analysis. We took advantage of the various Lactobacillus species that form part of the normal intestinal flora of laboratory rodents to improve our PCR diagnostic assays. Using this one-step PCR assay, we were able to rule out false-negative results without the need of adding internal standard molecules. This is an important quality control for PCR diagnostic tests, since the presence of inhibitors in feces can prevent detection of Helicobacter infections using PCR analysis. Use of this Lactobacillus group-specific PCR assay can be extended to other feces tests used in mouse quality-control programs.     

Detection of Helicobacter species DNA by quantitative PCR in the gastrointestinal tract of healthy individuals and of patients with inflammatory bowel disease

In many animal species different intestinal Helicobacter species have been described and a few species are associated with intestinal infection. In humans, the only member of the Helicobacter family which is well described in literature is Helicobacter pylori. No other Helicobacter-associated diseases have definitely been shown in humans. We developed a sensitive quantitative PCR to investigate whether Helicobacter species DNA can be detected in the human gastrointestinal tract. We tested gastric biopsies (including biopsies from H. pylori positive persons), intestinal mucosal biopsies and fecal samples from healthy persons, and intestinal mucosal biopsies from patients with inflammatory bowel disease (IBD) for the presence of Helicobacter species. All gastric biopsies, positive for H. pylori by culture, were also positive in our newly developed PCR. No Helicobacter species were found in the mucosal biopsies from patients with IBD (n = 50) nor from healthy controls (n = 25). All fecal samples were negative. Our study suggests that Helicobacter species, other than H. pylori, are not present in the normal human gastrointestinal flora and our results do not support a role of Helicobacter species in IBD.     

Development of a combined PCR-culture technique for the rapid detection of Arcobacter spp. in chicken meat

A combined PCR-culture technique was developed to detect Arcobacter spp. in fresh chicken meat. Following a short selective enrichment of chicken samples, bacterial DNA was extracted and amplified using primers targeted at the genes encoding 16S rRNA of Arcobacter spp. The selected primers amplify a 181-bp fragment from all Arcobacter spp., whereas no PCR product is generated for other bacteria, including the closely related Campylobacter and Helicobacter species. The assay was used to screen 96 retail-purchased chicken samples for the presence of Arcobacter spp. Fifty-three percent of the samples analysed were positive for this micro-organism. The assay is simple and sensitive and reduces the amount of time required to positively detect Arcobacter spp. in poultry meat.     

MIF mRNA在胃窦胃癌组织中的表达及其与幽门螺杆菌感染的关系

目的:探讨胃窦胃癌组织中人巨噬细胞移动抑制因子MIF mRNA的表达,并分析其与幽门螺杆菌感染的关系,分析二者在胃窦胃癌发生中的相关性。方法:选取2013年1月至2014年12月于我院收治的胃窦胃癌患者30例作为观察组,另随机选择10例胃窦胃炎患者作为对照组,采用14C-尿素呼气试验(UBT)检测各组患者有无幽门螺杆菌感染,定量逆转录PCR检测观察组患者及对照组患者组织中MIF mRNA表达。统计分析不同组织中MIF mRNA表达与幽门螺杆菌感染之间的关系。结果:观察组组织中MIF mRNA的表达为(1.09±0.11),高于对照组组织的(0.21±0.08),差异具有统计学意义(P0.05)。进一步亚组分析,观察组合并幽门螺杆菌感染组织中MIF mRNA的表达为(1.24±0.14),高于非幽门螺杆菌感染者的(1.09±0.11),差异具有统计学意义(P0.05)。结论:MIF mRNA在胃窦胃癌组织中高表达,幽门螺杆菌感染促进了MIF mRNA的表达,共同促进了胃窦胃癌的发生发展。     

Detection of Helicobacter pylori in bile of cats

Lymphocytic cholangitis (LC) in cats is a biliary disease of unknown etiology. Helicobacter spp. were recently implicated in human primary sclerosing cholangitis (PSC) and primary biliary cirrhosis (PBC). Because of the similarities between PSC/PBC with LC, we hypothesized that Helicobacter spp. are involved in feline LC. A PCR with Helicobacter genus-specific 16S rRNA primers was performed on DNA isolated from feline bile samples. Four of the 15 (26%) LC samples were positive, whereas only 8/51 (16%) of non-LC samples were PCR positive (p=0.44). Sequence analysis of the amplicons revealed a 100% identity with the Helicobacter pylori specific DNA fragments. Our data suggest an etiological role of H. pylori in feline LC and that cats are a potential zoonotic reservoir.     

Presence of Helicobacter species DNA in Swedish water

Municipal water, treated waste-water and well-water from all 25 counties in Sweden were analysed for the presence of Helicobacter spp. DNA. Bacteria were concentrated by immunomagnetic separation. Culture, Gram staining and urease tests were performed before lysis of bacteria. Two polymerase chain reactionColour RGB 0,0,128 (PCR) assays with high sensitivity (adhesin and 16S rRNA) were followed by Helicobacter spp. specific hybridization. Nine of 24 private wells, three of 25 municipal tapwater and three of 25 wastewater samples were positive for both PCR assays. Positive municipal and waste-water samples originated from the same counties. Non-specificity of PCR methods due to the presence of unknown bacteria within the genus Helicobacter cannot be totally ruled out. Thus, the clinical significance of finding Helicobacter spp. DNA in drinking water needs to be further evaluated.