The variations in the three regions of the Helicobacter pylori vacA gene, the signal (s1 and s2), intermediate (i1 and i2) and middle regions (m1 and m2), are known to cause the differences in ...vacuolating activities. However, it was unclear whether these vacA genotypes are associated with the development of gastric cancer and peptic ulcer in the Middle East. The aim was to identify the prevalence of vacA genotypes in the Middle East and the association with gastroduodenal diseases. We investigated the relationship of vacA genotypes to H. pylori-related disease development by meta-analysis using previous reports of 1,646 patients from the Middle East. The frequency of the vacA s1, m1 and i1 genotypes in the Middle Eastern strains was 71.5% (1,007/1,409), 32.8% (427/1,300) and 40.7% (59/145), respectively. Importantly, the frequency of vacA s- and m-region genotypes significantly differed between the north and south parts of the Middle East countries (P < 0.001). The vacA genotypes significantly increased the risk of gastric cancer (odds ratio OR: 4.02, 95% confidence interval CI: 1.98-8.14 for the s1 genotype; 2.50, 1.62-3.85 for m1; 5.27, 1.97-14.1 for s1m1; 15.03, 4.69-48.17 for i1) and peptic ulcers (OR: 3.07, 95% CI: 2.08-4.52 for s1; 1.81, 1.36-2.42 for m1). The cagA-positive genotype frequently coincided with the s1, m1 and i1 genotypes. The vacA s- and m-region genotypes may be useful risk factors for gastrointestinal diseases in the Middle East, similar to European and American countries. Further studies will be required to evaluate the effects of the i-region genotype.
Blastocystis
is an unusual enteric protozoan parasite of humans and many animals whose pathogenic potential is still controversial. To increase the understanding of the molecular epidemiology of this ...emerging parasite and due to its potential impact on public health, its subtypes (STs) in Iranian symptomatic and asymptomatic individuals were determined. A total of 100
Blastocystis
isolates by microscopy and culture methods were obtained. DNA was extracted from the positive culture isolates, and the
Blastocystis
subtypes were identified using seven subtype-specific sequenced-tagged site (STS) primers. Four subtypes, ST3 as dominant (53 %), followed by ST1 (48 %), ST5 (33 %), and ST2 (7 %) were identified. In this study, ST1 in gastrointestinal patients compared to asymptomatic individuals was significantly dominant (
p =
0.001). From 33 (33 %) mixed subtype infections, ST1, 3 (14 %) was significantly related to GI symptoms (
p =
0.045), and eight mixed infections with three different STs, which are under reported, were also identified.
Blastocystis
is a single-celled intestinal parasite commonly found in humans and a broad range of animals all over the world. In humans, its role in health and disease remains unsettled. The aim of ...our study was to investigate the distribution of
Blastocystis
and
Blastocystis
subtypes (ST) in patients with inflammatory bowel disease (IBD) and control subjects. A total of 71 stool samples were collected from IBD patients, 69 and 2 of whom had ulcerative colitis (UC) and Crohn’s Disease (CD), respectively. Moreover, 166 stool samples from healthy subjects were included as control samples. All stool samples were cultivated, and 550-bp fragments of the small subunit ribosomal RNA gene was amplified from
Blastocystis
-positive cultures. All PCR-positive samples were sequenced.
Blastocystis
was observed in 9 (12.67%) and 35 (21.1%) IBD patients and healthy controls, respectively. There was no statistically significant correlation between IBD and presence of
Blastocystis
(
P
= 0.147). There was a statistically significant correlation between age and
Blastocystis
colonization in the IBD group (
P
< 0.05), but not among healthy controls. No significant correlation between gender and colonization was observed. ST1 and ST3 were obtained from 1 (12.5%) and 7 (87.5%) IBD patients, respectively, while in the healthy control group, subtypes 1, 2, and 3 were found in 14 (40%), 12 (34.28%), and 9 (25.72%), respectively. Phylogenetic analysis showed no variation in the distribution of subtypes nor intra-subtype genetic diversity between samples acquired from IBD patients and healthy controls. This study showed a trend towards a lower prevalence of
Blastocystis
in IBD patients than in control subjects. ST3 sequences isolated from IBD patients and control individuals did not appear to differ genetically.
Non-alcoholic fatty liver disease (NAFLD) is a common liver disease with a rapidly growing incidence worldwide. For prognostication and therapeutic decisions, it is important to distinguish the ...pathological stages of NAFLD: steatosis, steatohepatitis, and liver fibrosis, which are definitively diagnosed on invasive biopsy. Non-invasive ultrasound (US) imaging, including US elastography technique, and clinical parameters can be used to diagnose and grade NAFLD and its complications. Artificial intelligence (AI) is increasingly being harnessed for developing NAFLD diagnostic models based on clinical, biomarker, or imaging data. In this work, we systemically reviewed the literature for AI-enabled NAFLD diagnostic models based on US (including elastography) and clinical (including serological) data.
We performed a comprehensive search on Google Scholar, Scopus, and PubMed search engines for articles published between January 2005 and June 2023 related to AI models for NAFLD diagnosis based on US and/or clinical parameters using the following search terms: "non-alcoholic fatty liver disease", "non-alcoholic steatohepatitis", "deep learning", "machine learning", "artificial intelligence", "ultrasound imaging", "sonography", "clinical information".
We reviewed 64 published models that used either US (including elastography) or clinical data input to detect the presence of NAFLD, non-alcoholic steatohepatitis, and/or fibrosis, and in some cases, the severity of steatosis, inflammation, and/or fibrosis as well. The performances of the published models were summarized, and stratified by data input and algorithms used, which could be broadly divided into machine and deep learning approaches.
AI models based on US imaging and clinical data can reliably detect NAFLD and its complications, thereby reducing diagnostic costs and the need for invasive liver biopsy. The models offer advantages of efficiency, accuracy, and accessibility, and serve as virtual assistants for specialists to accelerate disease diagnosis and reduce treatment costs for patients and healthcare systems.
Background
Health authorities have expanded two strategies to diminish CRC-related influence: CR screening and improve diagnostic process in symptomatic patients. The aim of the current study is to ...design a predictive model to identify the most important risk factors that can efficiently predict patients who have high risk of colorectal neoplasia.
Method
A cross-sectional study was constructed to include all patients who had positive test for FIT or had one or more risk factors for colorectal cancer based on the guidelines of detecting high-risk groups for colorectal cancer in Iran. Multivariable binary logistic regression model was constructed for prediction of colorectal neoplasia. We used sensitivity, specificity, positive and negative predictive value, and positive and negative likelihood ratio to check the accuracy. The Hosmer–Lemeshow test, chi-square test, and
p
value were used to determine the precision of model.
Result
Following an AIC stepwise selection model, only nine potential variables, namely gender, watery diarrhea, IBD, abdominal pain, melena, body mass index, depression drug, anti-inflammatory drug, and age, were found to be a predictor of colorectal neoplasia. The best cut-point probability in the final model was 0.27 and results of sensitivity and specificity, based on maximizing these two criteria, were 66% and 62%, respectively.
Conclusion
Overall, our model prediction was comparable with other risk prediction models for colorectal cancer. It had a modest discriminatory power to distinguish an individual’s neoplasia colorectal risk.
Hepatitis B virus (HBV) infection is a major cause of liver disease worldwide. Eight genotypes and 24 subgenotypes of HBV have been identified. The aim of this study was to determine the distribution ...of HBV genotypes, subgenotypes and subtypes, and to understand HBV genetic variability in the HBV genome circulating in Iranian provinces. Two hundred and forty-nine sera from HBV-infected patients living in 25 provinces of Iran were collected (2004–2007). A part of the HBV S/pol and whole BCP/C genes were amplified, sequenced and then subjected to phylogenetic, recombination and genetic variability analysis. Results revealed genotype D of HBV in all samples and subgenotypes D1 (98.52%), D2 (0.74%) and D3 (0.74%) among Iranian patients living in different provinces of Iran. Subtypes ayw2 (94.4%), ayw1 (2.8%), ayw3 (2%) and ayw4 (0.4%) were deduced, on the basis of HBV small surface antigen (HBsAg) amino acid sequences. The mean percentage intra-genotypic distance of S plus core regions was 2.8%; the mean percentage inter-genotypic distance of this region between Iranian strains and genotype D isolates was 3.1%; and this rate for other genotypes was 5.2–11.4%. Various rates of point mutations have been found within different HBV genes, e.g. HBsAg (17.2%), precore-G1896A (59.5%) and Basal core promoter (BCP) double mutations (49.2%), whereas no recombination was found. In conclusion, these results indicate that the only genotype circulating in the provinces of Iran is genotype D. There exist high genetic variabilities in the S/pol and BCP/C regions among the Iranian HBV isolates.
Summary Introduction Acute diarrhea disease is the second cause of death among all infectious diseases in children younger than 5 years of age worldwide. The aim of this study was to employ a ...combination of biochemical, microbiological and molecular diagnostic techniques to investigate the stools of Iranian children with acute diarrhea for bacterial enteropathogens. Method Diarrheagenic Escherichia coli , Shigella spp., Salmonella spp., Campylobacter spp. and Yersinia spp., were investigated from Jun 2003 to Jun 2005, in 1087 children less than 5 years old with acute diarrhea. Stool specimens from children were studied for enteropathogens both by standard culturing and molecular methods. This study was designed on hospital based. Result The highest incidence values were found in the summer and in children less than 1-year-old (42.7%). The Pathogenic bacteria recovered out from fecal samples of 555 (55.1%) patients had the following profile: Shigella spp. (26.7%) was the most prevalent bacterial pathogen and Shiga-like toxin producing E. coli (STEC) and Enteroaggregative E. coli (EAEC) 105 (18.9%) and 92 (16.6%) had the second and third highest prevalence, respectively. Enteropathogenic E. coli (EPEC), Campylobacter , Salmonella and Enterotoxigenic E. coli (ETEC) were found in 70 (12.6%), 60 (10.8%), 42 (7.6%), and 38 (6.8%) positive samples, respectively. In this study neither Yersinia nor E. coli O157:H7 were found. Of the 30 co-infections detected, Shigella flexneri and Campylobacter jejuni accounted for more than 50%. Conclusion Information about the prevalence of wide-range Shigella and STEC may facilitate the control and management of infant diarrhea diseases in Iran. The results of this study suggest that comprehensive surveys are needed in different parts of the country in order to identify the incidence of different enteropathogenic diarrhea, especially diarrheagenic E. coli in children in Iran.
Microsporida are known as opportunistic unicellular organisms and have recently been reclassified as fungi that have been frequently reported from patients with congenital and acquired immunity ...failure disorders, worldwide. However, use of immunosuppressive medications in inflammatory bowel disease (IBD) patients significantly decreases overall immunity, and increases their susceptibility to opportunistic infections. Totally, 71 stool samples were collected from IBD patients consisted of 69 ulcerative colitis (UC) patients and two Crohn's disease (CD) patients. All patients had taken immunosuppressive and/or immunomodulator drugs for at least 3 weeks. DNA was extracted from all stool samples and Nested PCR was performed using genus-specific primers based on small subunit ribosomal RNA (SSU rRNA) gene. Fisher's Exact Test was applied to evaluate statistical association between microsporidia infection and sex, age and types of IBD. Mean of age ± s.d., women and men percentage of the attended patients were 36·17 ± 11·93, 60·6%, and 39·4%, respectively. A 440-bp fragment of SSU rRNA gene attributed to Enterocytozoon bieneusi was amplified from 12·7% of IBD patients. No Encephalitozoon DNA was detected in the samples. No microsporidia-positive sample was found in CD patients. Fisher's Exact Test showed that there was no statistically significant correlation between intestinal microsporidiosis and age, sex, and IBD types with P values: 0·389, 1·00, and 1·00, respectively. This study has shown IBD patients undergoing immunosuppressive/immunomodulators medications, which may be susceptible to intestinal microsporida infection. E. bieneusi is the commonest intestinal microsporidan reported from IBD patients.
BackgroundRotavirus is the most common causes of severe, acute diarrhea during childhood and is an important cause of morbidity and mortality in developing countries. We established active ...hospital-based surveillance of childhood diarrhea to assess the scope of severe rotavirus disease in Iran MethodsFrom May 2006 through April 2007, prospective surveillance of rotavirus diarrhea among children aged <5 years was conducted in 5 sentinel hospitals in Iran. Stool samples were tested for rotavirus using a commercially available enzyme immunoassay, and rotavirus-positive samples were genotyped using reverse-transcriptase polymerase chain reaction ResultsOf 2198 children admitted to the hospital for acute gastroenteritis, 1298 (59.1%) had stool samples test positive for rotavirus by enzyme immunoassay. Of the rotavirus episodes, 85% occurred during the first 2 years of life, with the peak prevalence of severe rotavirus disease occurring from September through January. Among the 110 rotavirus-positive samples that were genotyped, G4P8 was the most commonly detected rotavirus genotype (30.9% of strains). Other commonly detected genotypes included P8 with G nontypeable (21.8%), G4 with P nontypeable (13.6%), G1P8 (10.9%), and G2P4 (5.5%) ConclusionsRotavirus is the most common cause of severe diarrhea in Iran, which indicates that safe and effective rotavirus vaccination in Iran is a public health priority
Mitochondrial genes have more power than nuclear genes in reconstructing phylogenetic relationships among closely related species because of their faster sequence evolution. The aim of this study was ...to use the complete or near-complete sequences from three mitochondrial genes (cox1, nad1 and atp6) and partial sequences of the 12S rRNA gene to infer relationships among isolates of Echinococcus granulosus from Iran. Two hundred and twenty-nine isolates of E. granulosus were collected from cattle, camels, sheep, buffalo and goats from different geographical areas. Most individuals were found to possess the G1 genotype but some of the camel samples belonged to the G6 genotype. Newly designed primers for cox1, nad1 and atp6 genes amplified bands of 1830, 708 and 1157 bp for the G1 genotype and 1856, 705, 1054 bp for the G6 genotype, respectively. The result of this survey showed that atp6 and nad1 genes are good molecular markers for identifying E. granulosus isolates from a range of hosts in Iran.
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