masoud alebouyeh

Exudative diarrhea is a significant global public health issue, particularly affecting children under the age of 5. Identifying the cause of diarrhea is crucial for epidemiological surveillance and, in some cases, for ensuring appropriate treatment for patients.

The aim of this study was to investigate the frequency of bacteria responsible for exudative diarrhea in samples from children under five years old in a tertiary hospital in Iran.

In this multicenter cross-sectional descriptive study, 104 children with exudative diarrhea who were referred to Mofid Children's Hospital in Tehran, as well as hospitals in Hamedan, Ardebil, and Bandar Abbas, from December 2020 to March 2022 were enrolled. DNA extraction was performed using a commercial kit, and the identification of various causative bacteria was conducted through conventional and real-time PCR. Descriptive and inferential statistics were analyzed using SPSS version 22 software.

Most of the children with exudative diarrhea were under 12 months old (31%) or between 12 and 24 months old (22%). Boys made up 66% of the participants. Additionally, 70% of the children had a fever, and 58% experienced vomiting. Furthermore, 56% of the patients were dehydrated. The most prevalent bacterial causes of exudative diarrhea were Shigella spp., followed by Salmonella spp., Campylobacter spp., Clostridium difficile, E. coli-Stx1 , and E. coli-Stx2 .

The findings indicated that * Shigella * spp. was the leading cause of diarrhea in children under five years old. The most common signs and symptoms associated with exudative diarrhea were fever and vomiting, which physicians should consider in their diagnostic and treatment processes.

 Rotavirus is the most common cause of gastroenteritis among children. Currently, four oral live-attenuated vaccines are available to prevent rotavirus infection. The World Health Organization (WHO) has recommended including rotavirus vaccination in national immunization programs; however, it has not been introduced to the Iranian national immunization program. The study aimed to assess the frequency of rotavirus gastroenteritis in the west of Iran and investigate the necessity of rotavirus vaccination.

Study Design:

 A case series study.

 In this case series study, 284 cases under six years of age who presented with acute gastroenteritis from March 2021 to 2022 to a referral hospital in the west of Iran were evaluated. Data on baseline characteristics, clinical manifestations, results of stool test, ELISA for rotavirus detection, and polymerase chain reaction (PCR) test for genotyping of rotavirus-positive samples were recorded.

 Results showed that the prevalence of rotavirus infection was 36.6%. The highest frequency was observed among children aged 6-12 months and during the autumn. According to the PCR results, G1P[8], G9P[8], G9P[4], and G1P [4] were the dominant genotypes, and 33.75% of samples were infected with multiple rotavirus genotypes.

 The study highlights the considerable prevalence of rotavirus infection among cases of acute gastroenteritis in children under six years of age who were referred to a referral hospital in the west of Iran and the high diversity of rotavirus genotypes in the targeted community. Consequently, physicians and health policymakers should prioritize strategies for the prevention and control of this infection, particularly by considering the rotavirus vaccine as a priority for the Iranian national immunization program.

Complete immunization against Rubella and Measles (MR) in pediatrics is achieved using 2 doses of the Measles, Mumps, and Rubella-containing vaccine (MMR) in Iran at 12 and 18 months of age, where more than 95% of children under 5 years of age are vaccinated. Antibody waning in mothers and older children, and genetic diversity in immune responses may render them susceptible to infections.

This study aimed to investigate the diversity in immunoglobulin G (IgG) antibody levels against these two viruses in pregnant women, infants younger than 2 months, children at 6, 12, and 18 months, and 5 - 6 years of age in Iran.

This study was conducted on serum specimens sent to the National Reference Laboratory for Measles and Rubella in Tehran, Iran, from children under 2 months (n: 50), 6 (n: 54), 12 (n: 54), and 18 (n: 39) months, and 5 - 6 years old (n: 49), as well as women at 37 weeks of pregnancy (n: 53), from May to December 2020. Rubella and Measles-specific IgG were measured using an enzyme-linked immunosorbent assay kit.

Among serum samples from different provinces of Iran, the lowest positive level of Measles IgG was observed in children aged 6 and 12 months (7.41%), while the highest positive level was found in children aged 18 months (84.62%). For Rubella, the lowest IgG-positive level was seen in children aged 11 - 13 months (11.11%), while the highest positive level was observed in the 5 - 6 years old group (83.67%). Antibody levels against measles and rubella were higher in pregnant women than in children.

Measles and Rubella antibody titers were lower in children 12 months before vaccination and reached a positive level in children aged 18 months post-vaccination. Whereas, lower Measles IgG levels in 5 - 6 years old children compared to 18 months old children may be due to waning antibodies. Pregnant women exhibited high levels of protection against these viruses (more than 80% had positive rubella IgG), as anticipated from outcomes of the national vaccination program in 2004.

 Bloodstream infection with multi-drug resistant (MDR) bacteria has been introduced as the main risk factor for in-hospital mortality in vulnerable children worldwide. COVID-19 can complicate the treatment process in patients with bacteremia; however, data about this co-infection in children are scant.

 This was a study on the antimicrobial patterns of Gram-negative bacteria (GNB) isolated from blood samples of children with bacteremia and their correlation with COVID-19.

 In this cross-sectional study, blood samples of children with bacteremia were analyzed using BACTEC bottles. The bacterial isolates were characterized based on standard microbiology laboratory methods, and MDR strains were detected based on a standard protocol. Real-time PCR tests for COVID-19 were recorded from the patients’ hospital documents.

 A total of 255 positive blood samples were detected in children with bacteremia. The bacterial isolates included Enterobacteriaceae spp. 43.5% (111/255), Pseudomonas spp. 33.7% (86/255), Acinetobacter spp. 21.6% (55/255), and Stenotrophomonas spp. 1.2% (3/255). Of 255 GNB, 86.66% (221/255) were MDR, and the frequency of MDR strains was as follows: Enterobacteriaceae spp. 91.8% (102/111), Pseudomonas spp. 77.9% (67/86), Acinetobacter spp. 89% (49/55), and Stenotrophomonas spp. 100% (3/3). Of 255 children with GNB-related bacteremia, COVID-19 infection was confirmed in 25.1% (64/255) of them. Nearly 93.7% (60/64) of these patients had both MDR bacteremia and COVID-19. The correlation was significant between MDR bacteremia and COVID-19 (P-value = 0.002). The death rate was 43.33% (26/60) among these children.

 The results of this study showed that MDR-GNB was the main cause of bacteremia in children. Our findings showed a notable risk of concomitant COVID-19 and GNB-related bacteremia in these patients.

 Widespread and inappropriate use of antibiotics has led to an increase in antibiotic-resistant bacteria worldwide. Extended-spectrum β-lactamases (ESBLs) are among the most important resistance mechanisms in members of Enterobacteriaceae, which can pose a threat to patients.

 This study aimed to investigate the carrier status and alteration in the fecal transmission of ESBL-producing Enterobacteriaceae (ESBL-E) on admission and during the hospital stay, as well as its correlation with the usage of antibiotics among children in a pediatric intensive care unit (PICU). Molecular typing between the primary and secondary isolates was done to detect the homotypic clonal strains.

 Demographic and medical data of PICU children were collected, and the carrier status of ESBL-E was investigated in pairs of their rectal swab samples at the admission and discharge time. Detection of ESBL phenotype and antimicrobial susceptibility to 12 antibiotics were performed by double-disk synergy and disc diffusion methods, respectively. Polymerase chain reaction for detection of blaTEM, blaSHVblaPER, blaCTX-M, and blaVEB genes was performed using specific primers. The phylogenetic relations were analyzed by the enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) method.

 Extended-spectrum β-lactamase-producing Enterobacteriaceae was detected in 48% of the samples at admission and 42% at discharge time. The highest frequency of resistance was observed in cephazolin, amoxicillin-clavulanic acid, and ampicillin. Children with a history of meropenem administration showed a significantly higher frequency of meropenem resistance Enterobacteriaceae in their samples. Moreover, the administration of metronidazole increased the isolation of ESBL-Escherichia species in hospitalized children. The most common gene associated with the ESBL phenotype was blaCTX-M, while blaPER and blaVEB were not detected in the ESBL-E isolates. The phylogenetic analysis did not confirm the occurrence of the cross-transmission of ESBL-E in the patients during hospitalization.

 Our results showed a high frequency of ESBL-E in the feces of children upon admission to the PICU, which did not change significantly during the hospital stay. Although the prescription of metronidazole showed an association with the enrichment of ESBL-E due to observed diversity in the molecular types and resistance phenotypes of the isolates, the community seems to be the primary source of ESBL-E transmission in children. Further investigations are needed to understand the role of hospital stay in the colonization and enrichment of ESBL-E in the intestinal tract of children and their association with infections during the medical interventions in the PICU.

Since several Helicobacter pylori strains have become resistant to metronidazole, new nitroimidazole derivatives based on metronidazole were designed and synthesized with different substituents on imidazole nitrogen. The activity of the synthesized compounds was evaluated against 20 clinically isolated metronidazole-resistant H. pylori strains. Some synthesized compounds were effective against those metronidazole-resistant H. pylori strains. Three compounds exhibited the most potent inhibitory activities (MIC50 = 8 µg/mL and MIC90 = 16 µg/mL).

Identification of rotavirus genotypes in children is clinically important. This study aimed to determine the spectrum of rotavirus genotypes and assess their correlation with demographic variables and clinical manifestations in hospitalized children.

To determine rotavirus genotypes, rotavirus positive stool samples of symptomatic children were included in the study between December 2019 and March 2020. RNA extraction and cDNA synthesis for VP7 and VP4 genes were performed following standard protocols. Genotypes were determined using specific primers. Validation of results was done through sequencing and bioinformatic analysis. Data were statistically analyzed using SPSS version 20 and GraphPad version 9.5.0.

Among the infected patients, three genotypes emerged as dominant in the studied population. The study demonstrated a significant correlation between genotype frequency and seasonal variations (p-value=0.0077), as well as between genotypes, hospitalization, and severity of diarrhea. While significantly more types of rotavirus group A were identified with increasing age, no correlation was observed between the genotypes and gender (p-value=0.473). Furthermore, there was no significant association between genotype, dehydration rates, and the presence or absence of fever.

This study revealed a relatively high diversity of rotavirus genotypes in children. The findings suggest the need for further research to validate the identified correlations between certain genotypes and age groups, seasonal variations, clinical symptoms, and the efficacy of available vaccines.

 Rotavirus (RV) is associated with diarrhea in children under 5 years old. It leads to severe dehydration. RV infection is the third cause of hospitalization and death in children under 5 years old.

 This study aimed to assess the frequency of RV infection in hospitalized children under 5 years old with diarrhea during 2021-2022.

 In this cross-sectional observational study, a total of 190 stool samples from hospitalized children with diarrhea were collected in Mofid Children’s Hospital in Tehran from December 2020 to March 2021. RV infection was detected by an enzyme-linked immunosorbent assay (ELISA). Chi-square tests were performed to determine the difference in age and gender group, time, and symptoms.

 The overall prevalence of RV infection was 28.5% and higher in boys (68.5%), children aged ≤ 12 months (44.4%), and children with mixed feeding (33.3%); it is more common in winter. Vomiting (79.6%), fever (87.03%), and non-exudative stool (88.8%) were observed in most children with RV, but there were no significant differences in children with and without RV.

 Due to the prevalence of RV among children under 5 years of age, establishing a national RV registration system and control programs, like vaccination, seems to be considered.

 Hospital-acquired infection with carbapenem-resistant Enterobacteriaceae (CRE) is a global concern. The administration of antibiotics among the infected and non-infected immunocompromised children with SARS-CoV-2 is associated with an increased risk of intestinal CRE colonization and bacteremia during hospitalization.

 The present study aimed to detect the correlation between the intestinal colonization of carbapenemase encoding Enterobacteriaceae with SARS-CoV-2 infection and antibiotic prescription among immunocompromised children admitted to the oncology and Bone Marrow Transplantation (BMT) wards.

 Stool samples were collected from the immunocompromised children, and the members of Enterobacteriaceae were isolated using standard microbiological laboratory methods. Carbapenem resistance isolates were initially characterized by the disc diffusion method according to CLSI 2021 and further confirmed by the PCR assay. SARS-CoV-2 infection was also recorded according to documented real-time PCR results.

 In this study, 102 Enterobacteriaceae isolates were collected from the stool samples. The isolates were from Escherichia spp. (59/102, 57.8%), Klebsiella spp. (34/102, 33.3%), Enterobacter spp. (5/102, 4.9%), Citrobacter spp. (2/102, 1.9%), and Serratia spp. (2/102, 1.9%). The carbapenem resistance phenotype was detected among 42.37%, 73.52%, 40%, 50%, and 100%of Escherichia spp., Klebsiella spp., Enterobacter spp., Citrobacter spp., and Serratia spp., respectively. Moreover, blaOXA-48 (49.1%) and blaNDM-1 (29.4%), as well as blaVIM (19.6%) and blaKPC (17.6%) were common in the CRE isolates. SARS-CoV-2 infection was detected in 50% of the participants; however, it was confirmed in 65.45% (36/55) of the intestinal CRE carriers. The administration of antibiotics, mainly broad-spectrum antibiotics, had a significant correlation with the CRE colonization in both the infected and non-infected children with SARS-CoV-2 infection.

 Regardless of the COVID-19 status, prolonged hospitalization and antibiotic prescription are major risk factors associated with the CRE intestinal colonization in immunocompromised children.

Isolating Helicobacter pylori (H. pylori) from wastewater and culturing it using a conventional method has always been a controversial issue because the bacterium converts into a coccoid form when exposed to an unfavourable environment like wastewater. To clarify the cultivability behaviour of the bacterium in fresh wastewater samples, the effect of municipal wastewater dilation on the cultivation of the bacterium using a conventional method was examined.

Several dilutions of wastewater samples were inoculated with fresh H. pylori suspension (with McFarland's dilution 0.5) to examine the dilution effect of wastewater on the bacterium isolation.

The H. pylori growth was found to be possible for a dilution factor from 1/106 to 1/107 of raw wastewater. In higher dilution factors the growth of fungi was dominant and could prevent the isolation of the bacterium.

The optimized technique could be applied in future studies for increasing the chance of H. pylori isolation from fresh wastewater environments.

Global growing infections by multi-drug resistance (MDR) or extensively drug-resistant (XDR) bacteria are a serious public health problem which can increase the rate of mortality and morbidity even in children. Carbapenem is the last choice therapy in case of antibiotic-resistant bacteria presence.

This study aimed to evaluate the easy to use method to identify carbapenemase producing bacteria which include in CLSI.

In this descriptive study, 125 carbapenem-resistant and 97 carbapenem-susceptible gram-negative bacteria were included. PCR was used to identify carbapenemase enzymes include VIM, IMP, KPC, NDM-1, SPM-1, OXA-48 as a gold standard method. The modified carbapenem inactivation method (mCIM) was employed to phenotypically identify carbapenemase-producing bacteria. Some modifications were made to the CLSI proposed mCIM to ensure more accurate results in contrast of PCR.

The OXA-48 is the most prevalent detected carbapenemase and SPM-1 was not detected in any of strain. The results of the mCIM according to CLSI guide line demonstrated 100% sensitivity to define carbapenemase-producing bacteria. However, in the cases of non-carbapenemase-producing bacteria, only 4% of mCIM test results were consistent with the outcome of PCR. Decrease of the incubation time and the consider 15mm as a break point could increase the accuracy of mCIM against PCR.

The results of this study endorse that mCIM test is a valuable method to detect carbapenemase producing bacteria if the three hours consider instead of 4 hours with 15mm break point.

Neisseria meningitidis and Streptococcus pneumoniae are serious causes of invasive infections associated with high mortality and morbidity worldwide, particularly meningitis. Efficient diagnostic strategies play a crucial role in the management of disease and the prevention of overtreatment. The low sensitivity and time-consuming nature of culture and gram stain methods have led to the demand for alternative methods in clinical laboratories.

This study aims to design and develop a rapid, sensitive, and cost-effective EvaGreen-based real-time PCR to simultaneously detect N. meningitidis and S. pneumoniae.

We designed and evaluated an accurate, reliable, and inexpensive approach based on EvaGreen dye real-time PCR to simultaneously detect N. meningitidis and S. pneumoniae in a single tube from cerebrospinal fluid. Melting curve analysis was used to differentiate the amplicons of each pathogen. Analytical sensitivity and specificity of the assay were conducted by reference bacterial strains genomes. Besides, in order to clinical validation we used 53 positive CSF samples and 7 negative CSF samples.

Our assay demonstrated no amplification curve with non-target microorganisms indicating 100% analytical specificity. In the EvaGreen multiplex assay, the lower limit of detection (LLD) was nine copies/reaction for N. meningitidis and 13 copies/reaction for S. pneumoniae. The clinical validation of positive CSF samples revealed 100% sensitivity and no false positives. The reproducibility and repeatability of tested replicates indicated low intra-assay and inter-assay CVs of less than 1.5%.

EvaGreen-based multiplex real-time PCR offers a rapid, affordable, and appropriate diagnostic tool to identify the main cause of bacterial meningitis.

Understanding the bacterial community composition of gastric microbes and the relationship between its differences in the development and progression of gastritis can be of great help in the perception of the mechanism of this disease and designing preventive treatment pathways for its progression. We aimed to investigate the simultaneous colonization of bacterial agents in patients with chronic gastritis.

The study was performed on 168 gastric biopsy specimens of patients with gastric complaints who were referred to the endoscopic ward of Firoozgar hospital in Tehran. Biopsy specimens in the pathology department were examined histologically by the hematoxylin-eosin staining method and in the specific culture medium of Helicobacter under microaerophilic growth conditions and in general culture medium under aerobic conditions for the presence of Helicobacter and other bacteria. Identification of Helicobacter pylori (H. pylori) isolates was performed by analyzing colony morphology, gram staining, positive reactions of oxidase and catalase, rapid urease test, and polymerase chain reaction (PCR). Other bacteria were identified by biochemical and phenotypical analysis.

In our study, the recovery rate of H. pylori infection was 27.4 %. The mean age of patients in the two groups with and without H. pylori infection was almost the same. 87.5% of all patients had chronic gastritis, which showed significant associations with H. pylori infection (p-value: 0.00). We identified 140 bacterial colonies that belonged to 12 genera and 3 phyla. At the genus level, Streptococcus and Staphylococcus were predominant followed by Micrococcus, Escherichia coli, Bacillus, Enterococcus, Klebsiella, Pseudomonas, Enterobacter, Citrobacter, and Providencia. The predominant phyla were Proteobacteria and Firmicutes while Actinobacteria was less frequent. Co-infection of H. pylori with other isolated bacteria, especially Streptococcus and Staphylococcus was observed.

The presence of different bacterial genera in the gastric tissue of patients with gastritis in the absence of H. pylori suggests their possible role in the occurrence or progression of this disease. Additional studies to determine the association of the persistence of these bacteria with the use of drugs that modulate gastric acidity and pathological changes can be useful in the prevention and treatment of gastritis.

Crohn's disease (CD) has a chronic course, which its recurrence varies widely among different patients. In this study we prospectively analyzed blood samples of 19 CD patients. Alteration in transcription of inflammatory and anti-inflammatory cytokines was analyzed compared with household members after three month follow up.

CD patients were diagnosed based on clinical symptoms, endoscopic and histopathologic characteristics. Nineteen CD patients and their households were evaluated from Jun 2019 to Feb 2021 at Tehran university hospitals. CD activity score, biological, clinical and demographic data of the patients were recorded at two time point intervals. Bacteriological tests were done using aerobic and anaerobic blood cultures. To investigate transcriptional alterations, peripheral blood mononuclear cells (PBMCs) were isolated using Ficol centrifugation method and relative quantitative real-time PCR was done to determine the expression level of IFN-γ, TNF-α, IL10, and FOXP3 cytokines.

Our results showed a correlation between fecal calprotectin level (709.8 ± 554.6), C-reactive protein concentration (18.1 ± 15.9), and erythrocyte sedimentation rate (30.4 ± 17.9) with disease activity (Flare/remission). IL10 and Foxp3 anti-inflammatory gene’s expression were significantly (P = 0.003 for IL10 and P = 0.008 Foxp3) higher during the flare and remission in patients with active disease respectively. Bacteriological examination showed infection with Streptococcus spp. and Clostridium spp. in two CD patients during flares, which was correlated with upregulation and down-regulation of IL10, TNF-α, IFN-γ and FOXP3 proteins, respectively.

Occurrence of bacteremia, and higher amount of CAP, CRP and ESR are correlated with higher level of transcription for inflammatory cytokines, which could effectively reflect the disease activity. Raise in FoxP3 transcription proposed change in Treg sub-population in PBMC or its activity during the CD remission phase.

The objective of this study was to determine the seroepidemiological history of SARS-CoV-2 infection among asymptomatic children in Tehran.

Blood samples of children younger than 14 years old were collected during the period autumn-winter 2020 and spring 2021 and tested for SARS-CoV-2 IgG antibody using the EUROIMMUN ELISA kit. In addition, questionnaires were used to collect demographic and infection status information in the participants. Data were analyzed using the SPSS software.

Out of the 1142 children collected from the children with no COVID-19 symptoms, 33.3% (381/1142) were found to have had a history of SARS-CoV-2. The positive samples in girls and boys were 34.1% and 33.03%, respectively. Analysis of the data showed no statistically significant differences between the infection rate on the one hand and age, family size, underlying diseases, gender or occupations of the family members on the other hand. In addition, the infection rate was significantly lower in autumn 2020 than in winter 2020 and spring 2021.

SARS-CoV-2 infection can occur in children with no clinical symptoms. In addition, the infection rate is in direct correlation with an increase in age of the children.

Hepatitis B vaccination is necessary to prevent infection with this virus and to prevent the development of chronic hepatocellular carcinoma.

Assessing the immunization status after receiving the vaccine and identifying non-respondents, especially among health care workers and physicians, is important because of the higher risk of contact with infected patients and their body fluids. In this study, the vaccination status of health and medical staff of a children's hospital was investigated to measure the anti-HBs antibody titer and its relationship with body mass index, smoking, and drugs used in individuals with underlying diseases. In this study HBsAb kit, DIA.PRO; Italy was used to measure the antibody titers. Statistical analysis was done using SPSS software version 26.

The results of this study showed that a proper antibody titer is present in 66.6% of the participants. Reduced antibody titers to unsafe levels were measured among the employees older than 50 years, smokers, and employees with low or very high body mass index.

In this study, the decrease in antibody titer did not show any association with underlying diseases and related medications. The presence of an unsafe antibody titer among young vaccinated staff suggested additional studies to identify non-responders after receiving a booster dose of the vaccine.

Source tracking of antimicrobial resistance in Campylobacter is useful for control measures. In this study, Campylobacter-associated diarrhea and homology in antimicrobial resistance of humans and poultry meat isolates were investigated.

A total of 400 stools of patients and 100 poultry meat samples were analyzed. Susceptibility of the isolates was detected by disk diffusion, Etest, and agar dilution methods. Mismatch amplification mutation assay was used for the detection of mutations in the gyrA quinolone resistance determining region (QRDR).

Campylobacter spp., including C. jejuni, C. coli, and C. lari, were detected in 35% of the chicken meat and 6.75% of the stool samples, respectively. The QRDR mutation was detected in most of the stool and chicken meat samples. Although the frequency of resistance to tetracycline (53.5% and 62.8%), erythromycin (39.2% and 37.1%), and gentamicin (32.1% and 31.4%) was relatively similar, higher frequency of resistance to ciprofloxacin (51.4% vs 28.6%) and nalidixic acid (42.15% vs 28.6%) among the chicken meat, and ampicillin (50% and 17.1%) among the human stool was detected.

High percentage of poultry meat samples is contaminated with different Campylobacter species, which shows homology with the patients’ isolates in Tehran.

The main purpose of microbial typing is to evaluate the relationships between microbial isolates. Microbial typing can use for identifying the source of infection by detecting a clonal link between the strains. Moreover, it can analyze outbreaks, antimicrobial-resistant strains, and evaluate the effectiveness of control measures so, the efficiency of monitoring systems would increase. HAIs can affect hospitalized patients in all age ranges with any clinical situation, and lead to death. Molecular epidemiology is useful to determine genetic relatedness between isolated pathogens from patients, and design proper prevention plans to prevent infection through the hospital and community. Nowadays, typing methods for a wide range of bacterial strains are known as essential epidemiological tools to prevent and control infections in hospitals and communities. Although basic typing methods were more focused on phenotypic techniques like antibiogram and serotyping, new methods are based on molecular techniques including PCR-based methods and sequencing-based methods. Due to the high frequency of methods, choosing the right one for research applications seems difficult and requires basic knowledge about all of them. In this review, we aim to introduce the most useful and practical molecular typing techniques. Also, their utilization, advantages, and disadvantages were compared.

Aberrant DNA methylation is a common molecular feature in colorectal cancer (CRC). Hypermethylation of miR-200b promoter, as an epigenetic factor, is involved in CRC tumorigenesis. The methylation status of miR-200b has been examined in CRC and adjacent normal tissues.

This studyaimed to investigate miR-200b methylation in a series of colorectal adenomatous polyps, hyperplastic polyps, and adenocarcinoma tissues as precursors of CRC in the Iranian population for the first time.

In this cross-sectional study (2017-2018), the methylation status of the miR-200b promoter was investigated on 131 fresh samples, including adenocarcinoma specimens (n=30), tumor-adjacent normal tissues(n=17), primary lesions (n=78; 55 adenomatous polyps and 23 hyperplastic polyps) and healthy individuals (n=6) using Methylation-specific polymerase chain reaction.

Methylation of miR-200b was detected in adenocarcinoma samples (86%) and adenomatous polyps (85%); however, most of the hyperplastic polyps were unmethylated (69.6%). Neither control individuals nor tumor-adjacent normal tissues exhibited methylation in the miR-200b promoter. Aberrant methylationof miR-200b wassignificantlymore common in tumor tissues and adenomatous polyps than in hyperplastic polyps (P<0.0001) and tumor-adjacent normal samples (P<0.0001).

The methylation status of the miR-200b promoter was significantly altered during CRC development andmay be identified as an indicative biomarker for the early detection of the disease.

Gastritis is one of the most common diseases affecting the stomach. Helicobacter pylori infection could lead to DNA damage in gastric epithelial cells, followed by error-prone DNA repair pathways that increase the accumulation of damage at the site of DNA double-stranded breaks, exacerbate genome instability, and facilitate the emergence of gastric cancer. This study aimed to examine the expression level of ATM, POLM, and TP53 genes involving in the DNA Damage Response and the cell cycle arrest in the gastric precancerous stage.

Among 180 gastric biopsy specimens, 30 samples taken from patients with moderate chronic gastritis infected by H. Pylori were regarded as the case group, and 30 other samples taken from non-infected patients with mild chronic gastritis were regarded as control. Following that, RNA extraction and cDNA synthesis was performed. Afterward, the expression levels of ATM, POLM, and TP53 genes were evaluated by the Real-Time PCR method. Ethics code: 98-02-27-43392

The ATM, POLM, and TP53 genes in the cases showed a 4.07, 3.35, and 5.13 increase in the gene expression at the transcriptional level, compared to the controls.

In general, ATM, POLM, and TP53 genes showed a higher increased expression level in the case group, compared to the controls, which might indicate the activation of noted genes after H. pylori infection. This may subsequently activate the error-prone DNA repair and non-homologous recombination pathways.

Gastritis is one of the most common diseases of human stomach. Most of the time, it is asymptomatic and if not treated, can cause atrophy in gastric tissue. Gastritis seems to be a consequence of Helicobacter pylori infection. H. pylori can induce DNA double strand breaks in DNA and activates the error-prone DNA repair pathways that result in accumulation of mutations and genomic instability which may mediate gastric carcinogenesis. In this study, we assessed expression of CHEK2, DCLRE1C and XRCC4 genes which are involved in cell cycle arrest and DNA double strand break repair systems happening with Gastritis. One hundred and eighty biopsy specimens were collected from patients who were referred for endoscopic examination. 60 samples including 30 cases (H. pylori positive Moderate chronic gastritis) and 30 controls (H. pylori negative Mild chronic gastritis) were selected for RNA extraction. Later cDNA was synthesized and Real-Time PCR was used to assess expression of CHEK2, DCLRE1C, XRCC4 and B2M genes. CHEK2, DCLRE1C and XRCC genes showed 5.88, 6.7 and 3.4 up-regulation respectively in comparison to the controls. Increasing level of CHEK2, DCLRE1C and XRCC4 genes might be related to activation of these genes after H. pylori infection.

Salmonella is one of the most important bacteria that causes gastroenteritis in humans and the spread of Salmonella strains with multidrug resistance is an acute global problem. Integrons are one of the most important factors responsible for transfering of drug resistance genes among Salmonella serotypes. In the present study, the frequency of class 1 and class 2 integrons as well as their relationship with drug resistance patterns in patients with gastrointestinal symptoms were investigated.

In this cross-sectional study, 400 human fecal samples with gastrointestinal symptoms were collected from 4 hospitals in Tehran. All the samples were analyzed by standard method for microbial culture and the results were confirmed by biochemical and PCR tests. Antimicrobial susceptibility testing was performed by disk diffusion method. After DNA extraction, the presence of class 1 and 2 integrons was investigated by PCR. Statistical analysis for detection of correlation between the presence of integrons and resistance patterns was done using SPSS software and Fisherʼs exact test.

The results showed that Salmonella was present in 5.5% (22.400) of the stool specimens. The prevalence rates of class 1 and 2 integrons for human stool specimens were 40.9% (9/22) and 27.2% (6/22), respectively. MDR phenotype was detected in 4.5% (1.22) of the Salmonella isolates from patients with gastroenteritis.

In this study, high levels of integrons 1 and 2 were observed in the patients' Salmonella isolates with gastroenteritis. The observed relationship between drug resistance patterns and the integrons indicated a possible increased risk of drug resistance genes in Salmonella isolates with human gastroenteritis.

Campylobacter species are among foodborne pathogens that are known as the main cause of inflammatory diarrhea in humans. In this cross-sectional study, we investigated the prevalence of Campylobacter spp. and their drug resistance status in fecal samples of patients with community-acquired gastroenteritis in Tehran.

In this survey, infection with Campylobacter spp. was evaluated in 400 stool samples of patients with diarrhea. Accordingly, microscopic examination to show the presence of exudative diarrhea, rejection of fungi and parasitic infections, enrichment and culture in a specific medium under microaerophilic conditions, determination of biochemical identity, and molecular confirmation at genus and species levels for C. jejuni, C. coli, C. lari, and C. upsaliensis were performed. Antibiotic resistance patterns were determined by E-test and disk diffusion methods, and the presence of the dominant gyrA gene mutations in the quinolone-resistance domain of C. jejuni isolates was determined by using Mismatch Amplification Mutation Assay-polymerase chain reaction (MAMA-PCR)[1].

A total of 28 strains of Campylobacter were isolated from the samples obtained from the patients with diarrhea. The most common species were C. jejuni (6%), C. coli (0.5%), C. lari (0.25%), and other unknown species (0.25%). The highest antibiotic resistance rate was observed against tetracycline and ampicillin (53.5% and 50%, respectively), and the lowest rate was detected for nalidixic acid and ciprofloxacin (28.5% and 28.5%). Multiple drug resistance (MDR) phenotype was detected among 51.8% of the strains.

Results of this study indicated C. jejuni as the main Campylobacter species responsible for community-acquired diarrhea among the studied patients. The high rate of resistance to antibiotics and MDR phenotype in these strains compared with other countries is considered a risk, especially in the treatment of invasive infections.

 This scoping review tries to synthesize early findings on the immunopathogenicity of SARS-CoV-2 to assess the emerging therapies and vaccines by evaluating their impact based on the mechanism of pathogenicity.

The three databases of PubMed, Scopus, and Google Scholar were searched from January 1, 2020, to March 15, 2020. To extract the results from the studies, the content, thematic analysis method was used. In this method, the topics studied were coded in the articles, and then major topics related to the articles were determined. After identifying major issues, the contents of the articles were reviewed.

A total of 2,250 articles were retrieved after deleting duplications, and after reviewing the thematic relevance, 45 of them were selected for the final analysis. Topics studied in the articles were classified into four main areas, including “virus entry inhibition and immune response”, “vaccine and treatment targets”, “genome structure similarity to other coronaviruses,” and “pathogensis”.

Results of this review showed that we have a long way to develop an effective and safe vaccine due to the structural and behavioral complexities of this virus. In the meantime, the scientific community should use results of megatrials, but until their accomplishing them, we have to use results of systematic reviews of randomized controlled trials.

The laboratory diagnosis of SARS-CoV-2 should be done to confirm coronavirus disease 2019 (COVID-19) in suspected patients. Although several diagnostic methods have been developed in this regard, their accuracy for clinical application is not very clear yet. To compare the diagnostic value of laboratory tests for the detection of COVID-19 infection, this study provides an upcoming review of the newly developed detection methods. Sensitivity, specificity, detection limit, and turn-around-time of these methods are compared and challenges for their application in clinical settings are reviewed. PubMed and Google Scholar web sites were used for the systematic search until April 9, 2020 to identify the published studies based on the following keywords: “Detection”, “Coronavirus 2019”, “SARS-CoV-2”, and “Sensitivity”. Out of 526 results, a total of 54 articles, including 46 studies on detection methods, were considered eligible for the review. The results showed that most of the proposed tests focused on molecular methods, while immunological and point-of-care tests were investigated in 13 studies. There were also a few commercial automated methods for the qualitative detection of SARS-CoV-2 in clinical samples, most of which are not examined in the current review, as no data about their sensitivity and specificity were presented. Although the assessment of publication biases showed that 64% sensitivity and nearly 100% specificity for RT-PCR are close to reality, most of the related reports for serological methods are not valid and further studies are needed to confirm their utility in clinical settings. Moreover, the RT-PCR test alone cannot act as a gold standard because of bias in measurements. Therefore, antibody tests and other proposed methods could be used as supplementary diagnostic tests to improve RT-PCR accuracy. Although clinical findings are invaluable, in many cases, they can provide more valuable supportive data than serological tests.