Designing a novel multi-epitopes pan-vaccine against SARS-CoV-2 and seasonal influenza: in silico and immunoinformatics approach.

The merger of COVID-19 and seasonal influenza infections is considered a potentially serious threat to public health. These two viral agents can cause extensive and severe lower and upper respiratory tract infections with lung damage with host factors. Today, the development of vaccination has been shown to reduce the risk of hospitalization and mortality from the COVID-19 virus and influenza epidemics. Therefore, this study contributes to an immunoinformatics approach to producing a vaccine that can elicit strong and specific immune responses against COVID-19 and influenza A and B viruses. The NCBI, GISAID, and Uniprot databases were used to retrieve sequences. Linear B cell, Cytotoxic T lymphocyte, and Helper T lymphocyte epitopes were predicted using the online servers. Population coverage of MHC I epitopes worldwide for SARS-CoV-2, Influenza virus H3N2, H3N2, and Yamagata/Victoria were 99.93%, 68.67%, 68.38%, and 85.45%, respectively. Candidate epitopes were linked by GGGGS, GPGPG, and KK linkers. Different epitopes were permutated several times to form different peptides and then screened for antigenicity, allergenicity, and toxicity. The vaccine construct was analyzed for physicochemical properties, conformational B-cell epitopes, interaction with Toll-like receptors, and IFN-gamma-induced. Immune stimulation response of final construct was evaluated using C-IMMSIM. Eventually, the final construct sequence was codon-optimized for Escherichia coli K12 and Homo sapiens to design a multi-epitope vaccine and mRNA vaccine. In conclusion, due to the variable nature of SARS-CoV-2 and influenza proteins, the design of a multi-epitope vaccine can protect against all their standard variants, but laboratory validation is required.Communicated by Ramaswamy H. Sarma.

Potentially Infectious Helicobacter pylori in Tap Water in Kermanshah, Western Iran.

Background: Although the pathogenesis of Helicobacter pylori is well-defined, the origin and transmission of the bacterium have remained largely unknown. The water transmission hypothesis suggested that water acts as a carrier in oral-fecal transmission, especially in high-prevalence areas. We aimed to evaluate the possible contamination of tap water with infective H. pylori in Kermanshah, Iran from Sep-Oct 2020. Methods: Tap water samples were collected from varieties of probable high-alert regions and the viability of H. pylori were achieved using culture and real-time PCR techniques (ureA gene expression). Results: Out of 50 tap water samples, 3 were positive for H. pylori before enrichment and 6 were positive after enrichment by RT qPCR, while H. pylori colonies of two samples were observed on brucella agar plates. Conclusion: The results of positive samples demonstrated the probable presence of viable H. pylori in tap water samples, showing that tap water distribution systems could be a potential route for H. pylori transmission.

High burden of MDR, XDR, PDR, and MBL producing Gram negative bacteria causing infections in Kermanshah health centers during 2019-2020.

Background and Objectives: Microorganisms producing Metallo-Beta-Lactamase (MBL) are a threat and cause of concern as they have become one of the most feared resistance mechanisms. This study was designed to explore the prevalence of MBL production in clinical isolates of Gram negative bacteria using phenotypic MBL detection. Materials and Methods: A total of 248 isolates were collected from various clinical samples and were evaluated for carbapenem resistance and MBL production. All strains were screened for MBL production using Double Disk Confirmatory Test (DDCT). Results: The results of screening for MBL production using phenotypic disk diffusion method showed that in the 85 isolates were carbapenemase positive; including, 10 (16.1%) Klebsiella pneumoniae, 9 (14.5%) Escherichia coli, 58 (93.6%) Acinetobacter baumannii, and 8 (12.9%) Pseudomonas aeruginosa isolates. Also, 83 (97.6) Carbapenemase-producing isolates were resistant to at least four classes of antimicrobials (MDR). Conclusion: A. baumannii was the most common carbapenem resistant bacterium in medical centers in Kermanshah. Significant multiple drug resistance (MDR) incidence was observed compared to different classes of antibiotics.

Prevalence of Mycobacterium tuberculosis mutations associated with isoniazid and rifampicin resistance: A systematic review and meta-analysis.

Tuberculosis (TB) is still one of the leading causes of worldwide death, especially following the emergence of strains resistant to isoniazid (INH) and rifampicin (RIF). This study aimed to systematically review published articles focusing on the prevalence of INH and/or RIF resistance-associated mutations of Mycobacterium tuberculosis isolates in recent years. Literature databases were searched using appropriate keywords. The data of the included studies were extracted and used for a random-effects model meta-analysis. Of the initial 1442 studies, 29 were finally eligible to be included in the review. The overall resistance to INH and RIF was about 17.2% and 7.3%, respectively. There was no difference between the frequency of INH and RIF resistance using different phenotypic or genotypic methods. The INH and/or RIF resistance was higher in Asia. The S315T mutation in KatG (23.7 %), C-15 T in InhA (10.7 %), and S531L in RpoB (13.5 %) were the most prevalent mutations. Altogether, the results showed that due to S531L in RpoB, S315T in KatG, and C-15 T in InhA mutations INH- and RIF-resistant M. tuberculosis isolates were widely distributed. Thus, it would be diagnostically and epidemiologically beneficial to track these gene mutations among resistant isolates.

Global prevalence of Clostridioides difficile in 17,148 food samples from 2009 to 2019: a systematic review and meta-analysis.

BACKGROUND: Clostridioides (Clostridium) difficile is an important infectious pathogen, which causes mild-to-severe gastrointestinal infections by creating resistant spores and producing toxins. Spores contaminated foods might be one of the most significant transmission ways of C. difficile-associated infections. This systematic review and meta-analysis study were conducted to investigate the prevalence of C. difficile in food. METHODS: Articles that published the prevalence of C. difficile in food in PubMed, Web of Science, and Scopus databases were retrieved using selected keywords between January 2009 and December 2019. Finally, 17,148 food samples from 60 studies from 20 countries were evaluated. RESULTS: The overall prevalence of C. difficile in various foods was 6.3%. The highest and lowest levels of C. difficile contamination were detected to seafood (10.3%) and side dishes (0.8%), respectively. The prevalence of C. difficile was 4% in cooked food, 6.2% in cooked chicken and 10% in cooked seafood. CONCLUSIONS: There is still little known concerning the food-borne impact of C. difficile, but the reported contamination might pose a public health risk. Therefore, to improve the food safety and prevent contamination with C. difficile spores, it is necessary to observe hygienic issues during foods preparation, cooking and transfer.

Modified gold nanoparticle colorimetric probe-based biosensor for direct and rapid detection of Mycobacterium tuberculosis in sputum specimens.

The incidence of Mycobacterium tuberculosis (MTB) is increasing due to lack of appropriate diagnostic and therapeutic methods. Therefore, early and accurate detection of this bacteria plays a significant role in controlling tuberculosis. This study aimed to design, develop, and implement a direct and rapid detection method of MTB using modified gold nanoparticle (AuNP) colorimetric probe-based biosensor in sputum specimens. Spherical AuNPs were synthesized by the citrate reduction method and were functionalized using thiol-modified oligonucleotides (AuNP-biosensor). AuNP-biosensor and IS6110 PCR were compared to the gold standard in terms of analytical and clinical sensitivity and specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic odds ratio (DOR), and accuracy in 52 clinical specimens. Gold standard was defined as a positive result in concentrated sputum smear microscopy (SSM), culture, or Xpert MTB/RIF.The AuNP-biosensor had 100% sensitivity and specificity for detection of total sputum DNA in less than 15 min with ready-to-use AuNP-biosensor. PPV, NPV, DOR and accuracy of this method were 100%, 100%, 2325 and 100%, respectively. Considering the promising results of the diagnostic value indices of the AuNP-biosensor, the designed method is an affordable, rapid, reliable, and cost-beneficial way for direct detection of MTB in sputum specimens.

Rapid Detection of vanA Resistance Gene from E. faecalis Clinical Isolates Using Duplex Loop-Mediated Isothermal Amplification and Triplex PCR Assay.

Today, the spread of vancomycin-resistant strains isolated from Enterococcus faecalis (E. faecalis) has become a major health concern worldwide. Therefore, it is essential to provide a rapid and sensitive assay for identifying vanA gene for timely and appropriate antimicrobial control of resistant enterococcal infections. For this purpose, a cross-sectional study was performed on different clinical specimens of enterococci from Imam Reza hospital, Kermanshah, Iran. The antimicrobial susceptibility testing was determined by disk diffusion and MIC methods. Triplex-PCR and duplex-LAMP assays were also used to identify vanA E. faecalis resistance gene isolates. The results of this study shown that out of 108 Enterococcus isolates, 86, 18, 2, 1, and one isolates of E. faecalis, E. faecium, E. avium, E. psudoavium, and E. raffinosus were identified, respectively. On the other hand, E. faecalis was confirmed in 87 and 88 isolates using duplex-LAMP and triplex PCR, respectively. The LAMP primer set designed in this study can reliably identify seven distinct regions of the vanA gene, and finally the sensitivity, specificity, and the positive and negative predictive values of LAMP assay were shown to be 94.19%, 72.73%, 76.19%, and 93.10%, respectively. In general, sample processing, isothermal reaction and result reporting were completed using the LAMP assay in 75 minutes. Our findings suggest that LAMP assay has been approved as an alternative to the vancomycin resistance Enterococcus genotype (vanA and vanB) compared to other methods and has the advantage of being rapid, time-consuming, and easy for diagnosis.

Prevalence of Antibiotic-Resistant Lactobacilli in Sepsis Patients with Long-Term Antibiotic Therapy.

Lactobacilli are the most common probiotic bacteria found in the human gut microbiota, and the presence of acquired antibiotic resistance determinants carried on mobile genetic elements must be screened due to safety concerns. Unnecessary and inappropriate antibiotic therapy, as well as ingested antibiotic resistance bacteria (originating from food or food products), influence the abundance of antibiotic resistance genes in human guts, with serious clinical consequences. The current study looked into the antibiotic resistance of lactobacilli isolated from the guts of sepsis patients on long-term antibiotic therapy. The broth microdilution method was used to investigate the minimum inhibitory concentrations (MICs) of antibiotics such as imipenem, meropenem, erythromycin, tetracycline, cefepime, ciprofloxacin, and gentamycin, and the molecular genetic basis of resistance was studied based on the MIC values. The isolates were phenotypically resistant to tetracycline (20%), fluoroquinolone (20%), and macrolide (5%). Following that, resistance genes for tetracycline [tet(L), tet(O), tet(K), and tet(M)], macrolide [erm(B) and erm(C)], and beta-lactams [bla(CMY)] were investigated. Tetracycline or macrolide resistance genes were not found in the isolates, and only one isolate possessed the bla(CMY) resistance gene. The findings suggested that tetracycline and macrolide resistance may be linked to other resistance genes that were not investigated in this study. Because tetracyclines, fluoroquinolones, and macrolides are commonly used in clinics and animals, there has been concern about the spread of resistance in humans. If acquired antibiotic resistance is passed down through mobile genetic elements, it may serve as a reservoir of resistance for gut pathogens and other microbiome environments.

Characterization of the resistome in Lactobacillus genomic sequences from the human gut.

OBJECTIVES: The gut is a complex environment inhabited by a wide range of bacterial species. Lactobacillus species constitute a significant proportion of this environment and, due to their mobile genetic elements such as plasmids and transposons, are more likely to acquire and transfer antibiotic resistance genes through horizontal gene transfer (HGT). METHODS: The current study obtained and analysed 321 genome assemblies to determine the prevalence of intrinsic and acquired antibiotic resistance genes (ARGs) among Lactobacillus species colonizing the human gastrointestinal tract. RESULTS: A total of four high-frequency resistance genes were identified, including dfra42 (42%), poxtA (17.4%), lmrB (12%), and BJP-1 (7.7%); aside from dfra42, which is an intrinsic resistance gene, the other genes are acquired resistance genes. PoxtA was found in several different species, mainly in L. paracasei, whereas BJP-1 and lmrB were found in only one species, L. rhamnosus. IS5-like elements family transposase flanked 11% and 8% of detected lmrB and BJP-1, respectively, while a variety of insertion sequences surrounded 22% of identified poxtA. Furthermore, to the best of our knowledge, this is the first report of BJP-1 in lactobacilli that would suggest it has transferred from soil microbiota to humans. CONCLUSION: According to the 'One Health' perspective, early detection of a new reservoir would control the global spread of the antibiotic-resistant bacterial species among the three environments, which include humans, the environment, and animals. Finally, the study's findings may then highlight the possibility of lactobacilli acquiring or transmitting resistance to other species within or outside the human intestine.

Prevalence of Clostridioides difficile contamination in the healthcare environment and instruments: A systematic review and meta-analysis.

Introduction: Worldwide, Clostridioides difficile infection is becoming one of the most common healthcare-associated infections. Management and control of this infection in healthcare facilities are associated with screening for environmental and instrumental C. difficile contamination. This systematic review and meta-analysis aimed to assess the overall prevalence of C. difficile in hospital settings, medical devices, and instruments. Methods: Four main databases, PubMed, Web of Science, Google Scholar, and Scopus, were searched using the keywords Clostridioides difficile, Clostridium difficile, C. difficile, clostridia, Clostridium spp., hospital environments, antibiotic associate colitis, intensive care unit, and ward in combination as a search strategy. The PRISMA checklist was used for selecting eligible studies. Results: A total of 11 eligible articles published between 2012 and 2021 were included. The overall pooled prevalence of C. difficile in hospital environments was 14.9%. The highest and lowest prevalence were reported for India (51.1%) and the USA (1.6%), respectively. The highest prevalence was reported for beds (46.3%). A significant heterogeneity was seen between C. difficile prevalence in hospital environments in different samples. The highest and lowest prevalence was reported for floor corners (63.2%) and privacy curtains (1.4%), respectively. Conclusions: In conclusion, hospitals' medical devices and environmental surfaces are considered a crucial source of Clostridioides difficile infection. In this regard, we strongly recommend revising and improving the cleaning and disinfection methods in hospitals and quality control of cleaning adequacy.

A worldwide systematic review and meta-analysis of bacteria related to antibiotic-associated diarrhea in hospitalized patients.

INTRODUCTION: Antibiotic-associated diarrhea (AAD) is a major hospital problem and a common adverse effect of antibiotic treatment. The aim of this study was to investigate the prevalence of the most important bacteria that cause AAD in hospitalized patients. MATERIALS AND METHODS: PubMed, Web of Science and Scopus databases were searched using multiple relevant keywords and screening carried out based on inclusion/exclusion criteria from March 2001 to October 2021. The random-effects model was used to conduct the meta-analysis. RESULTS: Of the 7,377 identified articles, 56 met the inclusion criteria. Pooling all studies, the prevalence of Clostridioides (Clostridium) difficile, Clostridium perfringens, Klebsiella oxytoca, and Staphylococcus aureus as AAD-related bacteria among hospitalized patients were 19.6%, 14.9%, 27%, and 5.2%, respectively. The prevalence of all four bacteria was higher in Europe compared to other continents. The highest resistance of C. difficile was estimated to ciprofloxacin and the lowest resistances were reported to chloramphenicol, vancomycin, and metronidazole. There was no or little data on antibiotic resistance of other bacteria. CONCLUSIONS: The results of this study emphasize the need for a surveillance program, as well as timely public and hospital health measures in order to control and treat AAD infections.

In silico vaccine design and epitope mapping of New Delhi metallo-beta-lactamase (NDM): an immunoinformatics approach.

BACKGROUND: Antibiotic resistance is a global health crisis. The adage that "prevention is better than cure" is especially true regarding antibiotic resistance because the resistance appears and spreads much faster than the production of new antibiotics. Vaccination is an important strategy to fight infectious agents; however, this strategy has not attracted sufficient attention in antibiotic resistance prevention. New Delhi metallo-beta-lactamase (NDM) confers resistance to many beta-lactamases, including important carbapenems like imipenem. Our goal in this study is to use an immunoinformatics approach to develop a vaccine that can elicit strong and specific immune responses against NDMs that prevent the development of antibiotic-resistant bacteria. RESULTS: In this study, 2194 NDM sequences were aligned to obtain a conserved sequence. One continuous B cell epitope and three T cell CD4+ epitopes were selected from NDMs conserved sequence. Epitope conservancy for B cell and HLA-DR, HLA-DQ, and HLA-DP epitopes was 100.00%, 99.82%, 99.41%, and 99.86%, respectively, and population coverage of MHC II epitopes for the world was 99.91%. Permutation of the four epitope fragments resulted in 24 different peptides, of which 6 peptides were selected after toxicity, allergenicity, and antigenicity assessment. After primary vaccine design, only one vaccine sequence with the highest similarity with discontinuous B cell epitope in NDMs was selected. The final vaccine can bind to various Toll-like receptors (TLRs). The prediction implied that the vaccine would be stable with a good half-life. An immune simulation performed by the C-IMMSIM server predicted that two doses of vaccine injection can induce a strong immune response to NDMs. Finally, the GC-Content of the vaccine was designed very similar to E. coli K12. CONCLUSIONS: In this study, immunoinformatics strategies were used to design a vaccine against different NDM variants that could produce an effective immune response against this antibiotic-resistant factor.

Rapid and accurate detection of Helicobacter pylori from biopsy specimens using loop-mediated isothermal amplification.

Loop-mediated isothermal amplification (LAMP) is a promising nucleic acid-based assay for quick, accurate and cost-effective diagnosis of many infectious agents. The purpose of this study was to assess the diagnostic value of LAMP for rapid and accurate detection of Helicobacter pylori in biopsy specimens. Patients suffering from one or several gastroduodenal disorders were enrolled in the study. Specificity, sensitivity, and the positive and negative predictive values of LAMP were compared with the gold standard result, which was the assembled result of culture, rapid urease test and polymerase chain reaction. Sensitivity, specificity, and the positive and negative predictive values of LAMP in comparison with the gold standard result were 100%, 30.76%, and 87.67% and 100% respectively [%95 CI]. As the diagnostic value of LAMP is favourable, the method is an optimum technique for diagnosis the presence of H. pylori in different clinical and environmental samples.

Prevalence of Clostridium difficile and its toxigenic genotype in beef samples in west of Iran.

BACKGROUND AND OBJECTIVES: Clostridium difficile is the leading cause of nosocomial diarrhea and pseudomembranous colitis. The prevalence of C. difficile infection differs in various geographical areas. The aim of this study was to determine the prevalence of C. difficile isolates and the prevalence of cdd3, tcdA and tcdB genes in beef samples in Kermanshah Province. MATERIALS AND METHODS: One hundred ground beef samples were randomly collected from the butchers of Kermanshah province during March 2014 to March 2015. Following alcohol shock, minced meat samples were incubated in a specific culture medium for 5 to 7 days. The suspicious colonies were analyzed by biochemical tests and frequency of C. difficile and cdd3, tcdA and tcdB genes was assessed by PCR using specific primers. RESULTS: In total, 30% samples were positive for C. difficile and all the isolates harbored Cdd3 gene. Combined dual-gene frequency of A+B+, A-B+ and A+B- strains in the positive were 0%, 3.3%, and 26.6% respectively, while 21 samples (70%) were non-toxigenic (A-B-). CONCLUSION: In this study, the presence of C. difficile in beef as a source of contamination was confirmed. It was also shown that the incidence of C. difficile in ground meat was relatively higher than many other studies.

Development and Diagnostic Evaluation of Loop-Mediated Isothermal Amplification Using a New Gene Target for Rapid Detection of Helicobacter pylori.

BACKGROUND: Helicobacter pylori cause chronic gastritis and subsequent diseases like gastric and duodenal ulcers and gastric adenocarcinoma. Current methods for detecting H. pylori have several disadvantages and it is of utmost importance to develop a simple, quick, accurate, and cost-effective diagnostic test. OBJECTIVES: The aim of this study was to set up and evaluate a diagnostic value of loop- mediated isothermal amplification (LAMP) for detecting H. pylori. PATIENTS AND METHODS: The analytical sensitivity values (limit of detection) of LAMP and polymerase chain reaction (PCR) were determined using serial dilutions of H. pylori DNA. Analytical specificity of the methods using new designed primers targeted ureC gene was also determined. RESULTS: The detection limits of the LAMP and PCR assay were similar and were 10 fg of pure DNA of H. pylori, which is equal to 6 copy numbers of H. pylori genome. Analytical specificity of the tests was 100% because the tests were positive only with H. pylori DNA. CONCLUSIONS: The analytical sensitivity of LAMP and PCR methods, using the designed primers, was 8 times more than any other reported methods. The designed methods are specific and sensitive for detection of H. pylori in different clinical and environmental samples.

Loop-Mediated Isothermal Amplification as a Fast Noninvasive Method of Helicobacter pylori Diagnosis.

BACKGROUND: Helicobacter pylori infection is etiologically associated with some important health problems such as gastric cancer. Because of the high clinical importance of H. pylori infection, development of a noninvasive test for the detection of H. pylori is desirable. METHODS: In this study, a loop-mediated isothermal amplification (LAMP) targeted ureC of H. pylori was evaluated on 100 stool specimens and compared with a stool antigen test. Culture and rapid urease test were considered as gold standards. RESULTS: The overall detection rate of the fecal antigen test and LAMP was 58% and 82%, respectively. The analytical sensitivity of the fecal antigen test and LAMP was 500 and 10 H. pylori cells/g and 10 fg DNA/reaction, which is equal to six H. pylori genome. CONCLUSION: LAMP technique has been characterized by high sensitivity and low detection limit for the detection of H. pylori in stool specimen. Clinical diagnostic performance of LAMP was better than the stool antigen test.

Expression and Purification of the Recombinant Cytochrome P450 CYP141 Protein of Mycobacterium Tuberculosis as a Diagnostic Tool and Vaccine Production.

BACKGROUND: Tuberculosis (TB) is regarded as a health problem worldwide, particularly in developing countries. Mycobacterium tuberculosis (M. tuberculosis) is the cause of this disease. Approximately two billion people worldwide are infected by M. tuberculosis and annually about two million individuals die in consequence. Forty million people are estimated to die because of M. tuberculosis over the next 25 years if the measures for controlling this infection are not extensively developed. In the vaccination field, Bacillus Calmette-Guérin (BCG) is still the most effective vaccine but it shows no efficacy in adult pulmonary patients. One of the other problems regarding TB is its appropriate diagnosis. OBJECTIVES: In this experimental study, the recombinant cytochrome P450 CYP141 protein of M. tuberculosis was expressed and purified to be used as a vaccine candidate and diagnostic purpose in subsequent investigations. MATERIALS AND METHODS: The optimization of the cytochrome P450 CYP141 protein expression was evaluated in different conditions. Then, this protein was purified with a resin column of nickel-nitrilotriacetic acid and investigated via Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) and Western Blotting. RESULTS: The highest expression of the cytochrome P450 CYP141 protein was obtained by the addition of 1 mM of isopropyl ß-D-1-thiogalactopyranoside (IPTG) to the bacterial culture grown to an optical density at 600 nm (OD600) of 0.6, 16 hours after induction. This protein was subsequently purified with a purification of higher than 80%. The results of Western Blotting indicated that the purified protein was specifically detected. CONCLUSIONS: In this experimental study, for the first time in Iran the expression and purification of this recombinant protein was done successfully. This recombinant protein could be used as a vaccine candidate and diagnostic purpose in subsequent investigations.

The frequency of Helicobacter pylori in dental plaque is possibly underestimated.

OBJECTIVE: The commonest bacteria, causing infection across the world is Helicobacter pylori, which colonizes the human stomach. This bacteria has also been detected in some extra-gastric ecological niches such as the oral cavity and water. However, the results of H. pylori detection in extra-gastric ecological niche are controversial. The improvement of the sensitivity and the specificity of the detection methods appear to be some of the main bottleneck issues in providing compelling evidence. The aim of this study was to detect the presence of this organism in dental plaque samples using an analytically sensitive and specific Polymerase Chain Reaction (PCR) as well as a new nucleic acid detection method termed the Loop-mediated Isothermal Amplification (LAMP). DESIGN: In a descriptive cross-sectional study 45 participants enrolled and dental plaque samples were collected from at least two teeth surfaces (one anterior and one posterior tooth) using a sterile periodontal curette. The DNA content was extracted from the samples and the presence of H. pylori was determined by PCR and LAMP reactions. RESULTS: The frequency of detection of H. pylori in the dental plaque samples were 44% (20/45), 66.67% (30/45) and 77.78% (35/45) using PCR, LAMP and positivity for both tests, respectively. CONCLUSION: The high frequency of H. pylori was detected in the dental plaque samples of the participants, which concurs with the high prevalence of this bacteria in the population. This is one of the highest reported rates around the world. The results reveal that dental plaque can be one of the main causes of re-infection and also be the cause of oral-oral transmission.

High Frequency of vacA s1m2 Genotypes Among Helicobacter pylori Isolates From Patients With Gastroduodenal Disorders in Kermanshah, Iran.

BACKGROUND: Helicobacter pylori infection and related diseases outcome are mediated by a complex interplay between bacterial, host and environmental factors. Several distinct virulence factors of H. pylori have been shown to be associated with different clinical outcomes. Here we focused on vacA and cagA genotypes of H. pylori strains isolated from patients with gastric disorder. OBJECTIVES: The aim of this study was to determine the frequency of two toxins and genotypes of VacA toxin in patients referred to a central hospital in the west of Iran (Imam Reza hospital, Kermanshah) during 2011 - 2012. PATIENTS AND METHODS: Samples were collected from patients infected with H. pylori. Gastric biopsy specimens from the stomach antrum and corpus were cultured. PCR analysis was performed for genotyping H. pylori vacA and cagA genes. RESULTS: Helicobacter pylori was isolated from 48% (96/200) of patients with gastroduodenal disorders. In 81/96 (84%) cases, the cagA gene was present. Among different genotypes of vacA, two s1m2 and s2m2 genotypes were dominant with frequency of 39.5% and 50%, respectively. The frequency of the s1m1 genotype was 7.2% (7/96), which is much lower than elsewhere. H. pylori isolates with positive results for cagA gene and vacA s1m2 genotypes showed statistically significant correlation with peptic ulcer (s1m2 13/34 [38.2%] P = 0.003). However, isolates of H. pylori infection with cagA gene and vacA s2m2 genotypes were significantly associated with development of gastritis (s2m2 41/42 [97.6%] P = 0.000). CONCLUSIONS: About 90% of H. pylori strains potentially contained vacA s2m2 and s1m2 genotypes. Infection with H. pylori strain containing the cagA gene or the vacA s1m1 and s1m2 genotypes was associated with increased incidence of peptic ulcer disease (PUD).