PCR Based Detection of Phase Variable Genes in Pakistani Based Clinical Helicobacter pylori Strains.
BACKGROUND
The distribution pattern of phase-variable genes varies from strain to strain and from region to region. The present study was carried out to investigate the distribution pattern of phase-variable genes within Pakistan-based Helicobacter pylori strains and to analyze and compare them with strains prevalent in other parts of the world.


OBJECTIVE
To determine the distribution pattern of phase-variable genes in H. pylori strains circulating in Pakistan.


METHODS
Biopsy samples were collected from 85 symptomatic patients suffering from various upper gastrointestinal tract symptoms. The biopsy specimens were chopped, then inoculated on H. pylori-specific media and incubated in a Campylobacter Gas Generating kit. Positive isolates were further confirmed via staining and biochemical procedures. Primers were designed for five phase-variable genes using OligoCalc, an oligonucleotide properties calculator (version 3.26) according to parameters stipulated in the literature. Polymerase chain reaction (PCR) was performed on all positive isolates to determine the presence or absence of phase-variable genes.


RESULTS
On culturing, the prevalence of H. pylori infections in the samples was 44.7%. The prevalence was higher in females than in males, and it increased with age. PCR amplification revealed that the hsdR gene was present in 79% of samples, while the mod and β-subunit genes were present in 16% and 30% of samples, respectively. The streptococcal M protein gene was found in 79%, while the fliP gene was prevalent in 56%.


CONCLUSIONS
The distribution patterns of phase-variable genes in Pakistani H. pylori strains were found to be somewhat different. The dominant prevalence of the hsdR gene was an interesting finding, considering its role in bacterial defense in both micro- and macroenvironments.
Department of Microbiology, Faculty of Biological Sciences, Quaid-i-azam University, Islamabad, Pakistan.
Sajjad
S
Ahmad
Department of Microbiology, Faculty of Biological Sciences, Quaid-i-azam University, Islamabad, Pakistan.
Faisal
F
Ahmad
Department of Microbiology, Faculty of Biological Sciences, Quaid-i-azam University, Islamabad, Pakistan.
Faiz Ur
FU
Rahman
Department of Microbiology, Faculty of Biological Sciences, Quaid-i-azam University, Islamabad, Pakistan.
Salman
S
Khan
Department of Microbiology and Molecular Genetics (MMG), University of Punjab, Lahore, Pakistan.
Waheed
W
Murad
Center of Biotechnology and Microbiology (COBAM), University of Peshawar, Peshawar, Pakistan.
Imran
I
Mughal
DHQ Teaching Hospital, KDA Kohat, Khyber Pukhtoon Khwa, Pakistan.
Amjad
A
Ur Rahman
Bioresource Research Center (BRC), Islamabad, Pakistan.
Fida
F
Muhammad Khan
College of Veterinary Science and Animal Husbandry, Abdul Wali khan University, Mardan, Pakistan.
Imad
I
Khan
Department of Medicine, Khyber Teaching Hospital (KTH), Peshawar, Pakistan.
Hajra
H
Ahmad
Helicobacter pylori; PCR; Phase-Variable Genes; Restriction Modification System
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