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1.  Low rate of recurrence of Helicobacter Pylori infection in spite of high clarithromycin resistance in Pakistan 
BMC Gastroenterology  2013;13:33.
The aim was to investigate the reinfection rate of H. pylori during a follow-up period of 12 months in adults who had undergone eradication therapy.
One hundred-twenty patients; 116 with gastritis, 3 with duodenal ulcer and 1 gastric ulcer, were studied. Their mean age was 41 ± 13 years (range 18–77) and male: female ratio of 2:1. H. pylori were cultured and antibiotic sensitivity was determined by Epsilometer test (E-test) for clarithromycin (CLR) and amoxicillin (AMX). Primers of urease C gene of H. pylori and Sau-3 and Hha I restriction enzymes were used for polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP). 14C urea breath test (14C-UBT) was performed 4 weeks after the eradication therapy. The successfully treated patients were observed for 12 months with 14C-UBT to assess H. pylori status. If 14C-UBT was negative, it was repeated after every 12 weeks. If 14C-UBT was positive, endoscopy was repeated with biopsies.
The eradication therapy was successful in 102(85%) patients. Out of forty-seven H. pylori isolates cultured, clarithromycin sensitivity was present in 30(64%) and amoxicillin in 45(98%), respectively. Follow-up 14C-urea breath tests of all 102 patients who eradicated H. pylori remained negative up to 9 months. However, in 6 patients, the 14C-UBT confirmed recurrence at 12 months. The recurrence rate was 6%.
A low rate of recurrence of H. pylori infection was found in patients with dyspeptic symptoms. H. pylori isolates demonstrated a high invitro clarithromycin resistance.
PMCID: PMC3608237  PMID: 23433429
Helicobacter pylori; Clarithromycin resistance; Recurrence; Nonulcer dyspepsia
2.  Prevalence of non Helicobacter pylori species in patients presenting with dyspepsia 
BMC Gastroenterology  2012;12:3.
Helicobacter species associated with human infection include Helicobacter pylori, Helicobacter heilmannii and Helicobacter felis among others. In this study we determined the prevalence of H. pylori and non-Helicobacter pylori organisms H. felis and H. heilmannii and analyzed the association between coinfection with these organisms and gastric pathology in patients presenting with dyspepsia. Biopsy specimens were obtained from patients with dyspepsia on esophagogastroduodenoscopy (EGD) for rapid urease test, histology and PCR examination for Helicobacter genus specific 16S rDNA, H. pylori phosphoglucosamine mutase (glmM) and urease B (ureB) gene of H. heilmannii and H. felis. Sequencing of PCR products of H. heilmannii and H. felis was done.
Two hundred-fifty patients with dyspepsia were enrolled in the study. The mean age was 39 ± 12 years with males 162(65%). Twenty-six percent (66 out of 250) were exposed to cats or dogs. PCR for Helicobacter genus specific 16S rDNA was positive in 167/250 (67%), H. pylori glmM in 142/250 (57%), H. heilmannii in 17/250 (6%) and H. felis in 10/250 (4%), respectively. All the H. heilmannii and H. felis PCR positive patients were also positive for H. pylori PCR amplification. The occurrence of coinfection of H. pylori and H. heilmannii was 17(6%) and with H. felis was 10(4%), respectively. Only one out of 66 exposed to pets were positive for H. heilmannii and two for H. felis. Histopathology was carried out in 160(64%) of 250 cases. Chronic active inflammation was observed in 53(56%) (p = 0.001) of the patients with H. pylori infection alone as compared to 3(37%) (p = 0.73) coinfected with H. heilmannii and H. pylori and 3(60%) coinfected with H. felis and H. pylori (p = 0.66). Intestinal metaplasia was observed in 3(3%)(p = 1.0) of the patients with H. pylori infection alone as compared to 2(25%) (p = 0.02) coinfected with H. heilmannii and H. pylori and 1(20%) coinfected with H. felis and H. pylori (p = 0.15).
The prevalence of H. heilmannii and H. felis was low in our patients with dyspepsia. Exposure to pets did not increase the risk of H. heilmannii or H. felis infection. The coinfection of H. pylori with H. heilmannii was seen associated with intestinal metaplasia, however this need further confirmation.
PMCID: PMC3276444  PMID: 22226326
Dyspepsia; gastric biopsies; H. pylori; H. heilmannii; H. felis; coinfection; cats; dogs
3.  Distribution of Helicobacter pylori virulence markers in patients with gastroduodenal diseases in Pakistan 
BMC Gastroenterology  2009;9:87.
Helicobacter pylori (H. pylori) infection is known to be associated with a spectrum of gastroduodenal diseases. We studied the association of H. pylori virulence markers cytotoxin-associated gene (cagA) and vacuolating associated cytotoxin gene (vacA) alleles in patients with non ulcer dyspepsia (NUD), gastric ulcer (GU), gastric carcinoma (GC) and duodenal ulcer (DU).
H. pylori infection established by both rapid urease test and histology were studied. The cagA and vacA allelic status was determined by polymerase chain reaction (PCR). Sequencing of vacA i1 and i2 PCR product was carried out.
Two hundred and twenty-four patients were included, 141 (63%) were males with a mean age of 45 ± 16, range 16-83 years. The virulence marker cagA was associated with GU in 20(63%) (p = 0.04), DU in 23(72%) (p = 0.003) and GC in 29(73%) (p = 0.001) compared to NUD in 51(42%). VacA s1am1 was associated with GU in 23(72%) (p = 0.001), DU in 17(53%) (p < 0.001) and GC in 23(58%) (p = 0.003) compared to NUD in 38(32%) while vacA s1bm1 was also associated with GU in 9(28%) (p = 0.001), DU in 12(37%) (p < 0.001) and GC 11(28%) (p < 0.001) compared to NUD in 13(11%), respectively. The diagnoses of GU in 21(66%), DU in 16(50%), GC in 20(50%) and NUD in 50(42%) were associated with moderately active chronic inflammation. CagA in 55(45%) (p = 0.037), vacA s1am1 in 51(51%) (P < 0.001), s1bm1 in 25(56%) (p = 0.002), s1am2 32(30%) (p < 0.001) and s1bm2 29(69%) (p = 0.004) were also associated with moderately active chronic inflammation.
CagA was negative in majority of NUD patients with H. pylori infection. However, cagA was associated with peptic ulcer and GC. VacA allele's s1am1 and s1bm1 were associated with H. pylori associated diseases and inflammation.
PMCID: PMC2784790  PMID: 19930551
4.  Acceptability and outcomes of the Percutaneous Endoscopic Gastrostomy (PEG) tube placement- patients' and care givers' perspectives 
BMC Gastroenterology  2006;6:37.
Percutaneous endoscopic gastrostomy tube has now become a preferred option for the long-term nutritional support device for patients with dysphagia. There is a considerable debate about the health issues related to the quality of life of these patients. Our aim of the study was to assess the outcome and perspectives of patients/care givers, about the acceptability of percutaneous endoscopic gastrostomy tube placement.
This descriptive analytic study conducted in patients, who have undergone percutaneous endoscopic gastrostomy tube placement during January 1998 till December 2004. Medical records of these patients were evaluated for their demographic characteristics, underlying diagnosis, indications and complications. Telephonic interviews were conducted till March 2005, on a pre-tested questionnaire to address psychological, social and physical performance status, of the health related quality of life issues.
A total of 191 patients' medical records were reviewed, 120 (63%) were males, and mean age was 63 years. Early complication was infection at PEG tube site in 6 (3%) patients. In follow up over 365 ± 149 days, late complications (occurring 72 hours later) were infection at PEG tube site in 29 (15 %) patient and dislodgment/blockage of the tube in 26 (13.6%). Interviews were possible with 126 patients/caretakers. Karnofsky Performance Score of 0, 1, 2, 3 and 4 was found in 13(10%), 18(14%), 21(17%), 29(23%) and 45(36%) with p-value < 0.001. Regarding the social and psychological aspects; 76(60%) would like to have the PEG tube again if required, 105(83 %) felt ease in feeding, and 76(60%) felt that PEG-tube helped in prolonging the survival. Regarding negative opinions; 49(39 %) felt that the feeding was too frequent, 45(36 %) felt apprehensive about dependency for feeding and 62(49%) were concerned about an increase in the cost of care.
PEG-tube placement was found to be relatively free from serious immediate and long- term complications. Majority of caregivers and patient felt that PEG-tube helped in feeding and prolonging the survival. Studies are needed to assess the real benefit in terms of actual nutritional gain and quality of life in such patients.
PMCID: PMC1676010  PMID: 17125502
5.  Genetic variability in the precore and core promoter regions of hepatitis B virus strains in Karachi 
BMC Gastroenterology  2006;6:20.
Hepatitis B virus (HBV) genotypes have distinct geographic distribution. Moreover, much genetic variability has been described in the precore (PC) and basal core promoter (BCP) regions of the HBV genome. The local prevalence of HBV genotypes and mutations has not been well studied. The aim of the present study is to determine the prevalence of HBV genotypes and mutations in the PC and BCP region in HBV strains in Karachi.
A total of 109 chronic hepatitis B patients with detectable HBV DNA by a PCR assay were enrolled in the study. Sera were tested for HBeAg, anti-HBe antibody and liver profile. HBV genotypes and mutations in the PC and BCP regions were detected by INNO-LiPA line-probe assays.
Of the 109 patients investigated, 38 (35%) were HBeAg positive while 71 (65%) were HBeAg negative. Genotype D was present in 100% of the patients. Two patients had co-infection with genotype A. There was no significant difference in the baseline characteristics, mean ALT levels, and presence of clinical cirrhosis in patients with HBeAg positive or negative strains with or without PC and BCP mutations. Of the 38 HBeAg positive patients, 9 (24%) had PC and BCP mutations. In the HBeAg negative patient group, mutations were detected in 44 (62%) of the strains investigated. More than one mutation was common, seen in 26 (37%) patients with HBeAg negative disease and 6 (16%) patients with HBeAg positive disease. Twelve (17%) HBeAg negative patients had dual T1762 and A1764 mutations. None of the HBeAg positive patients had T1762 mutation. Mutations were undetectable in 27 (38%) of patients with HBeAg negative disease.
Our study shows that type D is the main HBV genotype in Karachi, Pakistan. Significant numbers of patients infected with this genotype have PC and BCP variants. Mutations at more than one site are common. Patients harboring these mutants do not differ significantly in their clinical presentation from patients having wild type infection.
PMCID: PMC1544342  PMID: 16863587
6.  Role of rapid urease test and histopathology in the diagnosis of Helicobacter pylori infection in a developing country 
BMC Gastroenterology  2005;5:38.
The aim of this study was to determine the effect of commonly self-prescribed proton pump inhibitors (PPI) on the results of rapid urease test and histology for the diagnosis of H. pylori infection.
One hundred-nine consecutive patients with dyspeptic symptoms attending the endoscopy suite were enrolled in this study. Antrum biopsy specimens were collected at endoscopy for the rapid urease test (Pronto Dry, Medical Instrument Corp, France) and histopathology. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and like-hood ratio of a positive and negative of Pronto Dry test were compared against histology. The gold standard test for the diagnosis of H. pylori infection was histopathology.
Sixty-one percent (66/109) patients were males with mean age of 43 ± 14.1 years and age range 17–80 years. Fifty-two percent (57/109) were not on any medications while 48% (52/109) used PPI before presentation to the outpatients. Pronto Dry was positive in 40% (44/109) and negative in 60% (65/109). Histopathology was positive for H. pylori in 57% (62/109) and negative in 43% (47/109). The sensitivity, specificity, PPV, NPV and like-hood ratio of a positive and negative Pronto Dry test with and without PPI were 43.3%, 86.4%, 81.3%, 3.18, 0.656 and 52.8% vs 71.9%, 80%, 82.1%, 69%, 3.59 and 0.35.
This study shows that the sensitivity, specificity, NPV and PPV of rapid urease test was reduced in patients who are on PPI. The exclusive use of the rapid urease test for the diagnosis of Helicobacter pylori cannot be recommended in patients with prior PPI use.
PMCID: PMC1316874  PMID: 16309551

Results 1-6 (6)