Bacteriological analysis, antimicrobial susceptibility and detection of 16S rRNA gene of Helicobacter pylori by PCR in drinking water samples of earthquake affected areas and other parts of Pakistan

Helicobacter pylori infection is associated with peptic ulcers and gastric cancer in humans. Transmission of H. pylori is still not certain with some epidemiological data suggesting water as a possible transmission route. The objective of this study was to detect H. pylori 16S rRNA gene in five water systems in the Mexico City area. Samples were taken between 1997 and 2000 from extraction wells (system 1), from dams used as water sources, both pre- and post-treatment (systems 2 and 3), treated wastewater (system 4) and non-treated wastewater (system 5). Detection of the H. pylori 16S rRNA gene in water samples was carried out using nested PCR in 139 water samples and confirmed by using cagA gene detection by PCR-hybridisation. The results showed the presence of H. pylori in 58 (42%) of the water samples in total with a prevalence of 68% in system 1, 100% in system 2, 0% in system 3, 17% in system 4 and 20% in system 5. This first stage showed the presence of H. pylori in the tested water systems; nevertheless, viability of the microorganism in water and vegetables needs to be confirmed as well as demonstration of a relationship between human and environmental strains.

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Identification of Opportunistic Pathogenic Bacteria in Drinking Water Samples of Different Rural Health Centers and Their Clinical Impacts on Humans

BioMed Research International ◽

10.1155/2013/348250 ◽

2013 ◽

Vol 2013 ◽

pp. 1-10 ◽

Cited By ~ 6

Author(s):

Pavan Kumar Pindi ◽

P. Raghuveer Yadav ◽

A. Shiva Shanker

Keyword(s):

Drinking Water ◽

16S Rrna ◽

16S Rrna Gene ◽

Water Samples ◽

Pathogenic Bacteria ◽

Gene Sequence ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

The 16S Rrna Gene

International drinking water quality monitoring programs have been established in order to prevent or to reduce the risk of contracting water-related infections. A survey was performed on groundwater-derived drinking water from 13 different hospitals in the Mahabubnagar District. A total of 55 bacterial strains were isolated which belonged to both gram-positive and gram-negative bacteria. All the taxa were identified based on the 16S rRNA gene sequence analysis based on which they are phylogenetically close to 27 different taxa. Many of the strains are closely related to their phylogenetic neighbors and exhibit from 98.4 to 100% sequence similarity at the 16S rRNA gene sequence level. The most common group was similar toAcinetobacter junii(21.8%) andAcinetobacter calcoaceticus(10.9%) which were shared by 7 and 5 water samples, respectively. Out of 55 isolates, only 3 isolates belonged to coliform group which areCitrobacter freundiiandPantoea anthophila. More than half (52.7%, 29 strains) of the phylogenetic neighbors which belonged to 12 groups were reported to be pathogenic and isolated from clinical specimens. Out of 27 representative taxa are affiliated have eight representative genera in drinking water except for those affiliated with the generaExiguobacterium, Delftia, Kocuria,andLysinibacillus.

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Nocardioides hungaricus sp. nov., isolated from a drinking water supply system

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.022939-0 ◽

2011 ◽

Vol 61 (3) ◽

pp. 549-553 ◽

Cited By ~ 13

Author(s):

Erika M. Tóth ◽

Zsuzsa Kéki ◽

Judit Makk ◽

Zalán G. Homonnay ◽

Károly Márialigeti ◽

...

Keyword(s):

Drinking Water ◽

16S Rrna ◽

16S Rrna Gene ◽

Water Supply ◽

Gene Sequence ◽

Supply System ◽

Drinking Water Supply ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Drinking Water Supply System

Three Gram-positive, rod-shaped bacterial strains were isolated from the drinking water supply system of the Hungarian capital, Budapest. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparison revealed that the isolates represented a distinct cluster within the clade of the genus Nocardioides and were most closely related to Nocardioides pyridinolyticus OS4T, Nocardioides aquiterrae GW-9T, Nocardioides sediminis MSL-01T and N. hankookensis DS-30T. The peptidoglycan based on ll-2,6-diaminopimelic acid, the major menaquinone MK-8(H4), the cellular fatty acid profile with iso-C16 : 0 and anteiso-C17 : 0 as predominating components and the DNA G+C content of 71.4 mol% (strain 1RaM5-12T) were consistent with the affiliation of the isolates to the genus Nocardioides. Because of differences in physiological characteristics, matrix-assisted laser-desorption/ionization time-of-flight mass spectra of protein extracts, PvuII RiboPrinter patterns and 96.1 % 16S rRNA gene sequence similarity between strain 1RaM5-12T and its closest phylogenetic neighbour, N. pyridinolyticus OS4T, a novel species, Nocardioides hungaricus sp. nov., is proposed. The type strain is 1RaM5-12T (=DSM 21673T =NCAIM 02330T).

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Bacillus purgationiresistans sp. nov., isolated from a drinking-water treatment plant

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.028605-0 ◽

2012 ◽

Vol 62 (1) ◽

pp. 71-77 ◽

Cited By ~ 23

Author(s):

Ivone Vaz-Moreira ◽

Vânia Figueira ◽

Ana R. Lopes ◽

Alexandre Lobo-da-Cunha ◽

Cathrin Spröer ◽

...

Keyword(s):

Drinking Water ◽

Water Treatment ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Treatment Plant ◽

Drinking Water Treatment ◽

Water Treatment Plant ◽

Rrna Gene ◽

Rrna Gene Sequence

A Gram-positive, aerobic, non-motile, endospore-forming rod, designated DS22T, was isolated from a drinking-water treatment plant. Cells were catalase- and oxidase-positive. Growth occurred at 15–37 °C, at pH 7–10 and with <8 % (w/v) NaCl (optimum growth: 30 °C, pH 7–8 and 1–3 % NaCl). The major respiratory quinone was menaquinone 7, the G+C content of the genomic DNA was 36.5 mol% and the cell wall contained meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis, strain DS22T was a member of the genus Bacillus. Its closest phylogenetic neighbours were Bacillus horneckiae NRRL B-59162T (98.5 % 16S rRNA gene sequence similarity), Bacillus oceanisediminis H2T (97.9 %), Bacillus infantis SMC 4352-1T (97.4 %), Bacillus firmus IAM 12464T (96.8 %) and Bacillus muralis LMG 20238T (96.8 %). DNA–DNA hybridization, and biochemical and physiological characterization allowed the differentiation of strain DS22T from its closest phylogenetic neighbours. The data supports the proposal of a novel species, Bacillus purgationiresistans sp. nov.; the type strain is DS22T ( = DSM 23494T = NRRL B-59432T = LMG 25783T).

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Genotyping pattern of the vacuolating cytotoxin A and cytotoxin associated gene A of the Helicobacter pylori strains detected in fecal samples of household dogs

Microbiology Research ◽

10.4081/mr.2017.7289 ◽

2017 ◽

Vol 8 (2) ◽

Author(s):

Asieh Bolandi ◽

Saam Torkan ◽

Iman Alavi

Keyword(s):

Helicobacter Pylori ◽

16S Rrna ◽

16S Rrna Gene ◽

Pcr Amplification ◽

Rrna Gene ◽

Fecal Samples ◽

The Status ◽

Cytotoxin Associated Gene A ◽

H Pylori

In despite of the high clinical impact of Helicobacter pylori, its exact sources and routes of transmission are unknown. Dogs may play an imperative role in the transmission of H. pylori to humans. The current investigation was done to study the status of vacA and cagA genotypes in the H. pylori strains of dogs. One-hundred and fifty fecal samples were collected from healthy and complicated household dogs. Genomic DNA was extracted from fecal samples and presence of 16S rRNA gene was studied using the PCR amplification. Distribution of vacA and cagA genotypes were studied by the multiplex PCR. Thirteen out of 150 fecal samples (8.66%) were positive for H. pylori 16S rRNA gene. Prevalence of H. pylori in healthy and complicated dogs were 5.55% and 8.57%, respectively. Male had the higher prevalence of H. pylori (P=0.038). The most commonly detected genotypes among the H. pylori strains were vacAs1A (61.53%), cagA (38.46%), vacAm1a (38.46%), vacAs2 (30.76%) and vacAm2 (30.76%). The most commonly detected combined genotypes were s1aCagA (30.76%), s1am1a (23.07%), s2m1a (23.07%) and s2CagA (23.07%). Iranian household dogs harbor H. pylori in their fecal samples similar in genotypes of the vacA and cagA alleles which suggest that complicated and even healthy dogs may be the latent host of the H. pylori and its genotypes. However, supplementary studies are required to found the exact role of dogs as a definitive host of the H. pylori.

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Lack of Association between Helicobacter pylori Infection and Biliary Tract Diseases

Polish Journal of Microbiology ◽

10.33073/pjm-2012-044 ◽

2012 ◽

Vol 61 (4) ◽

pp. 319-322 ◽

Cited By ~ 4

Author(s):

SOMAYEH JAHANI SHERAFAT ◽

ELAHE TAJEDDIN ◽

MOHAMMAD REZA SEYYED MAJIDI ◽

FARZAM VAZIRI ◽

MASOUD ALEBOUYEH ◽

...

Keyword(s):

Helicobacter Pylori ◽

16S Rrna ◽

16S Rrna Gene ◽

Biliary Tract ◽

Helicobacter Pylori Infection ◽

Rrna Gene ◽

Biliary Tract Diseases ◽

Hepatobiliary Diseases ◽

H Pylori ◽

Bile Samples

There are ambiguous results about the involvement of Helicobacter species in production of hepatobiliary diseases. This study was aimed to investigate any possible association between the presences of Helicobacter spp., their genotypes and occurrence of different biliary diseases. Cultures of 102 bile samples for Helicobacter spp. did not show any growth, but the presence of Helicobacter genus specific DNA (16s rRNA gene) was detected in 3.92% of them. No significant association was found between development of the diseases and presence of the bacteria. All the Helicobacter genus positive samples belonged to H. pylori species and showed vacA+ (s1/m2), cagA- genotypes.

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Utility of a PCR-based method for rapid and specific detection of toxigenic Microcystis spp. in farm ponds

Journal of Veterinary Diagnostic Investigation ◽

10.1177/1040638720916156 ◽

2020 ◽

Vol 32 (3) ◽

pp. 369-381 ◽

Cited By ~ 1

Author(s):

Jian Yuan ◽

Hyun-Joong Kim ◽

Christopher T. Filstrup ◽

Baoqing Guo ◽

Paula Imerman ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Water Samples ◽

Low Cost ◽

Farm Animals ◽

Rrna Gene ◽

Analytical Sensitivity ◽

Water Safety ◽

Farm Ponds ◽

Pcr Method

Microcystis is a widespread freshwater cyanobacterium that can produce microcystin, a potent hepatotoxin harmful to animals and humans. Therefore, it is crucial to monitor for the presence of toxigenic Microcystis spp. to provide early warning of potential microcystin contamination. Microscopy, which has been used traditionally to identify Microcystis spp., cannot differentiate toxigenic from non-toxigenic Microcystis. We developed a PCR-based method to detect toxigenic Microcystis spp. based on detection of the microcystin synthetase C ( mcyC) gene and 16S rRNA gene. Specificity was validated against toxic and nontoxic M. aeruginosa strains, as well as 4 intergeneric freshwater cyanobacterial strains. Analytical sensitivity was as low as 747 fg/µL genomic DNA (or 3 cells/µL) for toxic M. aeruginosa. Furthermore, we tested 60 water samples from 4 farm ponds providing drinking water to swine facilities in the midwestern United States using this method. Although all water samples were positive for Microcystis spp. (i.e., 16S rRNA gene), toxigenic Microcystis spp. were detected in only 34 samples (57%). Seventeen water samples contained microcystin (0.1–9.1 μg/L) determined with liquid chromatography–mass spectrometry, of which 14 samples (82%) were positive for mcyC. A significant correlation was found between the presence of toxigenic Microcystis spp. and microcystin in water samples ( p = 0.0004). Our PCR method can be a low-cost molecular tool for rapid and specific identification of toxigenic Microcystis spp. in farm ponds, improving detection of microcystin contamination, and ensuring water safety for farm animals.

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Highly Specific Sewage-DerivedBacteroidesQuantitative PCR Assays Target Sewage-Polluted Waters

Applied and Environmental Microbiology ◽

10.1128/aem.02696-18 ◽

2019 ◽

Vol 85 (6) ◽

Cited By ~ 10

Author(s):

Shuchen Feng ◽

Sandra L. McLellan

Keyword(s):

Population Structure ◽

16S Rrna ◽

16S Rrna Gene ◽

Water Samples ◽

Rrna Gene ◽

Content Type ◽

Hypervariable Regions ◽

Animal Hosts ◽

Pcr Assays ◽

The 16S Rrna Gene

ABSTRACTThe identification of sewage contamination in water has primarily relied on the detection of human-associatedBacteroidesusing markers within the V2 region of the 16S rRNA gene. Despite the establishment of multiple assays that target the HF183 cluster (i.e.,Bacteroides dorei) and otherBacteroidesorganisms (e.g.,Bacteroides thetaiotaomicron), the potential for more human-associated markers in this genus has not been explored in depth. We examined theBacteroidespopulation structure in sewage and animal hosts across the V4V5 and V6 hypervariable regions. Using near-full-length cloned sequences, we identified the sequences in the V4V5 and V6 hypervariable regions that are linked to the HF183 marker in the V2 region and found these sequences were present in multiple animals. In addition, the V4V5 and V6 regions contained human fecal marker sequences for organisms that were independent of the HF183 cluster. The most abundantBacteroidesin untreated sewage was not human associated but pipe derived. Two TaqMan quantitative PCR (qPCR) assays targeting the V4V5 and V6 regions of this organism were developed. Validation studies using fecal samples from seven animal hosts (n = 76) and uncontaminated water samples (n = 30) demonstrated the high specificity of the assays for sewage. FreshwaterBacteroideswere also identified in uncontaminated water samples, demonstrating that measures of totalBacteroidesdo not reflect fecal pollution. A comparison of two previously described humanBacteroidesassays (HB and HF183/BacR287) in municipal wastewater influent and sewage-contaminated urban water samples revealed identical results, illustrating the assays target the same organism. The detection of sewage-derivedBacteroidesprovided an independent measure of sewage-impacted waters.IMPORTANCEBacteroidesare major members of the gut microbiota, and host-specific organisms within this genus have been used extensively to gain information on pollution sources. This study provides a broad view of the population structure ofBacteroideswithin sewage to contextualize the well-studied HF183 marker for a human-associatedBacteroides. The study also delineates host-specific sequence patterns across multiple hypervariable regions of the 16S rRNA gene to improve our ability to use sequence data to assess water quality. Here, we demonstrate that regions downstream of the HF183 marker are nonspecific but other potential human-associated markers are present. Furthermore, we show the most abundantBacteroidesin sewage is free living, rather than host associated, and specifically found in sewage. Quantitative PCR assays that target organisms specific to sewer pipes offer measures that are independent of the human microbiome for identifying sewage pollution in water.

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Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

Applied and Environmental Microbiology ◽

10.1128/aem.02032-15 ◽

2015 ◽

Vol 81 (20) ◽

pp. 7067-7077 ◽

Cited By ~ 42

Author(s):

W. Ahmed ◽

C. Staley ◽

M. J. Sadowsky ◽

P. Gyawali ◽

J. P. S. Sidhu ◽

...

Keyword(s):

Molecular Markers ◽

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Water Samples ◽

High Throughput Sequencing ◽

Community Analysis ◽

Fecal Pollution ◽

Rrna Gene ◽

Potential Sources

ABSTRACTIn this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways.

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