Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 2 2022 04 13 138 144 Abdol Sattar Pagheh Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran Arghavan Asghari Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran Khadijeh Abrari Romenjan Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran Tahoora Mousavi Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell Biology Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences, Sari, Iran Farshid Abedi Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran Arash Ziaee Department of Neuroscience, Mashhad University of Medical Sciences, Mashhad, Iran Hakime Malakimoghadam Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran Masood Ziaee Department of Neuroscience, Mashhad University of Medical Sciences, Mashhad, Iran 2021 09 11 2022 02 24 Background and Objectives: Health care workers (HCWs) are a high-risk group for acquiring and transmitting severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Aim of the study was the evaluation of sero-prevalence of SARS-CoV-2 in a random sample of HCWs at a large acute care hospital in Iran. Materials and Methods: We collected blood samples of 180 medical staffs from September 22, 2020 to January 26, 2021. The enzyme linked immunosorbent assays (ELISA) tests were used for evaluation of the presence of IgG antibodies. Participants completed a self-report questionnaire, comprising demographics, occupational, the work area, and personal protection data. Results: Of the 180 HCWs who participated in this study, 44 (24.4%) were seropositive for anti-SARS-CoV-2 IgG. The percentage of IgG positivity was higher in males than females (P<0.05). Also, there was statistically significant difference between presence of the antibodies and the occupation, location, and infecting family members with Covid -1 (P<0.05). Other factors did not associate significantly to antibody presence against SARS-CoV-2 (P>0.05). Conclusion: According to this point that the number of COVID-19 cases is still growing rapidly among HCWs. So, the epidemiological estimate of SARS-CoV-2 infection remains a major challenge that is needed to prevent the spread of infection in the hospitals. https://ijm.tums.ac.ir/index.php/ijm/article/view/3319 https://ijm.tums.ac.ir/index.php/ijm/article/download/3319/1436

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 2 2022 04 13 145 155 Bi Bi Ayesha Department of Microbiology, St Johns Medical College and Hospital, Bangalore, Karnataka, India Supriya Gachinmath Department of Microbiology, St Johns Medical College and Hospital, Bangalore, Karnataka, India Christobel Sobia Department of Microbiology, St Johns Medical College and Hospital, Bangalore, Karnataka, India 2021 04 28 2021 12 20 Background and Objectives: Obligate anaerobic bacteria are known to cause various infections in human beings. We aimed to determine the prevalence and spectrum of obligate anaerobes encountered in pus aspirate, sterile fluids and tissue samples received for routine bacterial culture and sensitivity. Materials and Methods: A total of 160 samples including tissue, sterile body fluids and pus aspirate were collected , analysed for prevalence and spectrum of obligate anaerobes. Identification of obligate and facultative anaerobes was done by automated MALDI-TOF and Vitek 2 method. Results: Among 160 samples, 75 samples (46.8%) yielded obligate anaerobes out of which 41 samples (26%) yielded obligate anaerobes along with facultative anaerobes which was significant (p value=0.031) and 34 samples (21%) yielded only obligate anaerobes. 90 obligate anaerobes were isolated from 75 samples among which only 34 (37.7%) samples yielded only obligate anaerobes and 56 (62.2%) yielded both obligate and facultative anaerobes. Gram stain with polymicrobial appearance (p value 0.02) was found to be significantly associated with growth of obligate anaerobes. Clinical conditions where obligate anaerobes were commonly associated were appendicular abscess, empyema, fournier’s gangrene, diabetic foot, ludwigs angina and deep abscess. Out of 75 positive samples 30 (40%) patients had predisposing conditions like diabetes mellitus, hypertension etc. Total of 90 obligate anaerobes and 49 facultative anaerobes were isolated. The common obligate anaerobes were Bacteroides fragilis 18 (20%), Prevotella spp. 20 (22.2%), and Clostridium spp. 8 (8.88%). Facultative anaerobes like Escherichia coli 25 (34.7%), Klebsiella species 15 (20.8%), Enterococcus faecalis 19 (26.3%) were isolated. Antibiotic sensitivity was performed for facultative anaerobes by Kirby bauer disc diffusion method. Out of 15 Escherichia coli isolates resistance was commonly seen for ampicillin 13 (86.6%), cephalosporins 11 (73.3%), ciprofloxacin 10 (66.6%) and Piperacillin tazobactum 8 (53.3%). In Klebsiella species resistance were commonly seen to Ampicillin 6 (100%), cephalosporins 2 (33.3%) and ciprofloxacin 2 (33.3%). Conclusion: There was significant isolation of obligate anaerobes along with facultative anaerobes in clinical samples received for aerobic culture and sensitivity. There is a need for isolation of these bacteria routinely and a scope for doing antibiotic susceptibility testing, which will help in evidence-based medicine and a better clinical outcome by giving appropriate therapy. https://ijm.tums.ac.ir/index.php/ijm/article/view/3121 https://ijm.tums.ac.ir/index.php/ijm/article/download/3121/1437

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 2 2022 04 13 156 160 Nouara Ait-Mimoune Department of Biology, Laboratory of Microbiology, Bouira University, Bouira, Algeria Houda Hassaine Department of Biology, Laboratory of Microbiology, Bouira University, Bouira, Algeria; Department of Biological Analysis, Laboratory of Bacteriology, Tizi-Ouzou Hospital, Tizi-Ouzou, Algeria Meriem Boulanoir Department of Biology, Laboratory of Microbiology, Bouira University, Bouira, Algeria; Department of Biological Analysis, Laboratory of Bacteriology, Tizi-Ouzou Hospital, Tizi-Ouzou, Algeria 2021 12 24 2022 03 26 Background and Objectives: Urinary tract infections are one of the most common bacterial infections worldwide. The emergence of antibiotic-resistant bacterial strains is a serious problem and greatest challenge in public health care. The purpose of this study was to determine the prevalence of uropathogenic microorganisms and the antibiotic resistance pattern of Escherichia coli in Algeria. Materials and Methods: Urine samples were collected from 760 outpatients in the hospital of Tizi-Ouzou (Algeria). From the positive cultures, 120 strains of E. coli were isolated and tested for their susceptibility to antibiotics by disk diffusion method on Mueller Hinton agar medium. Results: Among the collected urine specimens, 270 (35.5%) yielded positive cultures for urinary tract infection. Females were more affected with a sex ratio F/M of 1.14. E. coli was the most prevalent isolated bacteria with a rate of 44.44%, followed by Klebsiella pneumoniae (12.21%), Pseudomonas aeruginosa (11.1%) and Proteus mirabilis (5.55%). Isolates of E. coli showed high level of resistance to cephalothin (85.83%), ticarcillin (82.5%), ampicillin (73.3%) and amoxicillin-clavulanic acid (58.33%). Imipenem was the most effective antimicrobial agent. Conclusion: These results highlight the inappropriate utilization of antibiotics and suggest the need to improve prescription practices in our country. https://ijm.tums.ac.ir/index.php/ijm/article/view/3489 https://ijm.tums.ac.ir/index.php/ijm/article/download/3489/1438

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 2 2022 04 13 161 167 Ali Akbar Karami Department of Urology, Qazvin University of Medical Sciences, Qazvin, Iran Amir Javadi Department of Social Sciences, School of Medicine, Qazvin University of Medical Sciences Qazvin, Iran Sohrab Salehi Department of Urology, Qazvin University of Medical Sciences, Qazvin, Iran Neda Nasirian Department of Pathology, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran Amirhosein Maali Department of Immunology, Pasteur Institute of Iran, Tehran, Iran; Department of Medical Biotechnology, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran Maryam Bakhshalizadeh Shadkam Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran Masoumeh Najari Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran Zahra Rousta Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran Safar Ali Alizadeh Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran 2021 11 17 2022 02 24 Background and Objectives: Prostatitis affects about 16% of men in their lifetime and sometimes leading to prostate cancer. Bacterial infections are the most common causes of prostatitis. Diagnosis of the causative agents of bacterial prostate infections plays an essential role in timely treating and preventing secondary complications. This study isolated bacterial infectious agents in patients’ surgical prostate and evaluated them by routine and molecular microbiological methods. Materials and Methods: In this cross-sectional study, 72 prostate biopsy specimens were collected from the Orology Departmen of hospitals of Qazvin University of Medical Sciences. All samples were cultured in aerobic and anaerobic conditions. Antibiotic susceptibility test by Kirby-Bauer standard method was performed for all isolated bacteria. In addition, all isolated bacteria were identified using 16S rDNA PCR and sanger sequencing methods. Also, TaqMan real-time PCR was applied to detect Ureaplasm aurealyticum, Mycoplasma hominins, and Mycoplasma genitalium. Results: In conventional culture method, out of 18 positive samples, 15 samples (83.3%) were Gram-negative bacteria and 3 samples (16.6%) were Gram-positive bacteria, containing Escherichia coli (55.5%), Klebsiella pneumoniae (11.1%), Enterobacter cloacae (5.5%), Pseudomonas aeruginosa (11.1%), Staphylococcus aureus (11.1%), and Enterococcus faecalis (5.5%). The results of molecular identification methods were the same as conventional culture results. Also, four patients were Ureaplasm aurealyticum, and three patients were positive for Mycoplasma hominis. Conclusion: Most bacteria isolated from prostate specimens belonged to the Enterobacteriaceae family, especially Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae. Staphylococcus aureus and Enterococcus faecalis were cocci isolated in the specimens too. Also, Ureaplasma urealyticum, and Mycoplasma hominis were identified in prostatitis. https://ijm.tums.ac.ir/index.php/ijm/article/view/3438 https://ijm.tums.ac.ir/index.php/ijm/article/download/3438/1439

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 2 2022 04 13 168 173 Syeda Mehreen Department of Microbiology, Nizams Institute of Medical Sciences, Hyderabad, Telangana Kanne Padmaja Department of Microbiology, Nizams Institute of Medical Sciences, Hyderabad, Telangana Sukanya Sudhaharan Department of Microbiology, Nizams Institute of Medical Sciences, Hyderabad, Telangana Vijay Teja Department of Microbiology, Nizams Institute of Medical Sciences, Hyderabad, Telangana Mudumba Saradhi Department of Neurosurgery, Nizams Institute of Medical Sciences, Hyderabad, Telangana Y. Krishna Department of Neurosurgery, Nizams Institute of Medical Sciences, Hyderabad, Telangana 2021 06 04 2022 02 18 Background and Objectives: Insertion of an External Ventricular Drain (EVD) is a common and important lifesaving procedure that can lead to morbidity and mortality. This study was conducted to assess the infection rate, risk factors, causative organisms, and outcome of EVDs. Materials and Methods: A prospective study was undertaken in a tertiary care centre from August 1st to October 30th, 2020. Over 192 patients had undergone insertion of EVDs in the neurosurgical intensive care unit. CSF samples were collected in sterile containers and transported to the laboratory. Results: A total of 214 EVDs were inserted in 192 patients for 691 days. The median duration for EVD in situ and the mean time between catheter insertion and onset of infection were 14.5 days and 8 days. EVD related infection rate was 19.4 for 1000 EVD days. The most common risk factor for EVD insertion were tumors (55%) followed by hydrocephalus (40%).We identified 25 patients out of 192 (12%) who had clinical signs and symptoms with deranged CSF counts. A total of 13/25 (52%) specimens were culture positives out of which 10 (76.9%) were Gram negative pathogens and 3 (23%) were Gram positive pathogens and 3/10 (30%) Gram negative pathogens were Multidrug resistant organisms (MDROs). Conclusion: It was observed that longer duration of catheter in situ was an important risk factor for EVD-related infections (ERIs) and also higher frequency of CSF sampling. A proper EVD infection prevention and control protocol must be followed in the form of a checklist at the time of EVD insertion. https://ijm.tums.ac.ir/index.php/ijm/article/view/3184 https://ijm.tums.ac.ir/index.php/ijm/article/download/3184/1440

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 2 2022 04 13 174 180 Morubagal Rao Department of Microbiology, JSS Medical College, JSSAHER, Mysore, India Tejashree Urs Department of Microbiology, JSS Medical College, JSSAHER, Mysore, India Vidyavathi Chitharagi Department of Microbiology, JSS Medical College, JSSAHER, Mysore, India Sowmya Shivappa Department of Microbiology, JSS Medical College, JSSAHER, Mysore, India Rashmi Mahale Department of Microbiology, JSS Medical College, JSSAHER, Mysore, India Ranjitha Gowda Department of Microbiology, JSS Medical College, JSSAHER, Mysore, India Kavya Shree Department of Microbiology, JSS Medical College, JSSAHER, Mysore, India 2021 05 30 2022 03 17 Background and Objectives: Acinetobacter baumannii has emerged as a major organism accounting for hospital acquired infections particularly in intensive care units. Due to production of different kinds of beta lactamases these bacteria have developed drug resistance rendering the treatment of such infections very difficult and expensive. Rapid identification of A. baumannii producing such beta-lactamases is the need of the hour in reducing morbidity and mortality associated with A. baumannii infections. Materials and Methods: A. baumannii was isolated from clinical samples like endotracheal aspirates, sputum, urine, exudates using standard culture techniques. Identification and drug sensitivity was done using Vitek 2 system. All the isolates were subjected to detection of ESBLs using phenotypic confirmatory test, plasmid mediated AmpC beta- lactamase by AmpC disc test, Carbapenemase production by CarbAcineto NP Test and Modified hodge method. Results: 149 A. baumannii isolates were analysed for antimicrobial susceptibility and various beta-lactamase production. Results were evaluated for statistical significance using Chi-Square and P value. 81.8% of isolates were from male patients with majority of them above 50 years of age. 88.5% of samples were from ventilator associated pneumonia patients. 83.8% of isolates were sensitive to tigecycline. Only 10% to 12% of isolates were sensitive to carbapenems. 23.4% of isolates were ESBL producers and 46.9% of them were AmpC producers. Modified Hodge test method identified 63.7% of A. baumannii as carbapenemase producers where as CarbAcineto NP test identified 63% and exibiting 94.74% sensitivity, 93.22% specificity when compared to Modified Hodge test. Conclusion: Multidrug resistant Acinetobacter spp. is on the rise. Present study showed that high percentage of drug resistance in A. baumannii could be due to production of ESBLs, AmpC and carbapenemases. Among all beta lactamases carbapenemase producers are more and quickly raising in A. baumannii. Rapid, cost effective assay which can be adopted in all clinical laboratories is critical to prevent their further transmission particularly in hospital environment. https://ijm.tums.ac.ir/index.php/ijm/article/view/3173 https://ijm.tums.ac.ir/index.php/ijm/article/download/3173/1441

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 2 2022 04 13 181 185 Mohammad Siahpoush Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran Hassan Noorbazargan Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran Shirin Kalantari Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran Mohammad Shayestehpour Autoimmune Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran; Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran Shaghayegh Yazdani epartment of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran 2021 08 10 2022 02 11 Background and Objectives: Torque Teno virus or transfusion-transmitted virus (TTV) is a non-enveloped virus with a single strand circular DNA genome that currently is classified in the Alphatorquevirus genus and the family of Anelloviridae. Unlike other DNA viruses, TTV has an extremely wide genomic diversity. This virus, based on previous studies, infects both healthy people, as well as those who have HCV and human papillomavirus (HPV). This study aimed to evaluate the coinfection of torque teno virus (TTV) and HPV in cervical samples from Iranian women. Materials and Methods: In this case-control study, the fresh cervical cytobrush specimens were collected from 150 women referred to Dena laboratory in Tehran. Viral DNA was extracted from samples. The HPV-DNA was detected and genotyped. Then, nested polymerase chain reaction (Nested PCR) was performed for TTV using specific primers. Results: Among 50 cervical specimens without HPV, 14 were TTV positive (28%); among 50 low-risk HPV cervical specimen, 23 were TTV positive (46%), and from 50 high-risk HPV cervical specimen, 48 were TTV positive (96%). There is a significantly higher prevalence of TTV virus in low-risk and high-risk papillomavirus-infected specimens than in healthy specimens (p 0.0001). Additionally, TTV is more prevalent in samples containing high-risk papillomaviruses than in samples with low-risk papillomaviruses (P = 0.048). Conclusion: The higher prevalence of TTV among people infected with papillomavirus than in non-infected people indicates that both viruses are transmitted by the same mechanism (sexual route). In addition, the prevalence of TTV in samples containing high-risk papillomavirus is significantly higher than that in samples containing low-risk papillomavirus. The presence of papillomaviruses, particularly high-risk types, may be associated with TTV proliferation, which requires further research in the future. https://ijm.tums.ac.ir/index.php/ijm/article/view/3272 https://ijm.tums.ac.ir/index.php/ijm/article/download/3272/1442

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 2 2022 04 13 186 193 Zahra Khosravi Babadi Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University GC, Tehran, Iran; Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Braunschweig, Germany Abolfazl Narmani Department of Plant Protection, Faculty of Agriculture, University of Tabriz, Tabriz, Iran; Department of Microbial Drugs, Helmholtz Centre for Infection Research and German Centre for Infection Research (DZIF), Partner Site Hannover/Braunschweig, Braunschweig, Germany Gholam Hossein Ebrahimipour Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University GC, Tehran, Iran Joachim Wink Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Braunschweig, Germany; German Centre for Infection Research Association (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany 2021 03 02 2022 03 11 Background and Objectives: DNA extraction is an important step of any molecular experiment. DNA could not be easily extracted from members of actinomycetes by the usual methods of lysis. Due to the low efficiency of the conventional DNA extraction methods, development of an effective technique for DNA extraction of actinobacteria in emergency cases seems to be necessary. Since most of the DNA extraction techniques and commercial kits are not efficient enough to extract DNA from actinobacteria, this study was conducted to improve an efficient method obtained from conventional one to extract DNA from this group of bacteria. Materials and Methods: DNA extraction was performed using five methods (an improved method, Invisorb Spin Plant Mini Kit, EZ-10 Spin Column, Sarrbrucken method (HZI, Germany) and Kirby Bauer's method). To evaluate the quantity and quality of extracted genomic DNA, UV absorbance of all samples and efficiency of polymerase chain reaction (PCR) were evaluated. Results: Overall, the results revealed that the highest quantity (up to 4000 ng/µl) and good quality of DNA was obtained using introduced DNA extraction method. Conclusion: Results indicated that recently introduced improved method was more efficient for extraction of DNA from actinobacteria for DDH (DNA–DNA hybridization) test and for those require the high concentration of DNA. https://ijm.tums.ac.ir/index.php/ijm/article/view/3019 https://ijm.tums.ac.ir/index.php/ijm/article/download/3019/1443

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 2 2022 04 13 194 202 EN Warinya Nuwong Department of Biology, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand Chokchai Kittiwongwattana Department of Biology, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand 2021 10 21 2022 02 10 Background and Objectives: House-keeping genes are generally selected as reference genes in gene expression analysis. However, some genes may not be stably expressed across all experimental conditions. Thus, this study aimed to validate seven house-keeping genes for gene expression analysis in Bacillus siamensis 1021. Materials and Methods: Strain 1021 was grown in potato dextrose broth, nutrient broth and mineral salt medium. Reverse-transcription quantitative PCR was used to determine Cq values of seven reference genes including gyrA, gyrB, ssb and dnaB, rpsU, gat_Yqey and udp in these media. Expression stability of these genes was analyzed, using geNorm and Normfinder applications. The target gene ftsZ was used for assessment of the best candidate genes. Results: Based on geNorm and Normfinder, ssb was the most-stably expressed gene, while udp was the least-stably expressed gene. Pairwise variation indicated the combination of ssb, gyrA, gyrB and gatB_Yqey was suitable for the normalization of ftsZ expression. ftsZ expression in potato dextrose broth and mineral salt medium was higher than that in nutrient broth. In contrast, the normalization against udp resulted in an under- and overestimation of ftsZ expression in potato dextrose broth and mineral salt medium, respectively. Conclusion: The combination of ssb, gyrA, gyrB and gatB_Yqey was the best candidate for normalization of target gene expression in B. siamensis 1021 in these media. This study emphasized the significance of reference gene validation for gene expression analysis and provided a guideline for future gene expression studies in B. siamensis. https://ijm.tums.ac.ir/index.php/ijm/article/view/3383 https://ijm.tums.ac.ir/index.php/ijm/article/download/3383/1444

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 2 2022 04 13 203 213 Raheleh Majdani Department of Biology, Faculty of Basic Sciences, University of Maragheh, Maragheh, Iran Elham Shams Ghahfarokhi Department of Biology, Faculty of Basic Sciences, University of Maragheh, Maragheh, Iran 2021 07 16 2022 02 10 Background and Objectives: With the emergence of Pseudomonas aeruginosa antibiotic-resistant strains, using the antibacterial potential of bacteriophages could be an effe 76 83 Mohammad Reza Arabestani Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Nutrition Health Research Center, Hamadan University of Medical Sciences, Hamadan, Iran Farideh Kamarehei Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran Mahya Dini Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran Farid Aziz Jalilian Department of Virology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran Abbas Moradi Department of Community Medicine, Hamadan University of Medical Sciences, Hamadan, Iran Leili Shokoohizadeh Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran 2021 04 30 2021 12 31 Background and Objectives: Staphylococcus aureus is one of the most common causes of food poisoning. This study aimed to identify S. aureus isolated from pastries, the virulence factors, antimicrobial resistance patterns, biofilm formation, and then classification based on SCCmec types, phage types, and also Rep types. Materials and Methods: In this study, 370 creamy and dried pastry samples have been randomly collected from different confectioneries in Hamadan city. The S. aureus isolates were identified by conventional microbiological methods and nuc gene amplification. The virulence factors and prophage genes were detected. After that, the biofilm production and antibiotic susceptibility assay of S. aureus isolates were examined. Finally, the isolates were classified by rep-PCR typing. Results: Among 370 samples, 97 creamy (34.64%) and 3 dried (3.33%) pastry samples were contaminated with S. aureus. Antibiotic sensitivity results showed the highest resistance to penicillin (90%) but none of them were MRSA. According to biofilm formation assay, 14 strains (45%) were strongly adhesive. The dominant phage among isolates was SGF, especially SGFa subgroup. About half of the isolates carried SCCmec Types I and III. Analysis of the genetic linkage between isolates by rep-PCR showed ≥80% genetic similarity and also different rep-types of S. aureus isolates. Conclusion: The presence of different prophage encoded virulence factors and antibiotic resistance enable S. aureus strains to produce a broad range of diseases. Thus, consumption of creamy pastries increases the risk of infection with S. aureus and it is a serious warning to the health system. https://ijm.tums.ac.ir/index.php/ijm/article/view/3123 https://ijm.tums.ac.ir/index.php/ijm/article/download/3123/1427

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 1 2022 02 20 84 89 Fatemeh Razeh Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran Siavosh Salmanzadeh-Ahrabi Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran Roghaieh Zarei Department of Plant Sciences, Faculty of Biological Sciences, Alzahra University, Tehran, Iran Bahareh Attaran Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran 2020 10 20 2021 12 30 Background and Objectives: Pathogenic diseases resulting from microbial contamination of food have been widely distributed in many parts of the world. Among these, Escherichia coli is one of the most important foodborne pathogenic bacteria. Diarrhea is one of the major causes of children’s death in developing countries, with approximately 2 million deaths annually. The current study aimed to determine the frequency of diarrheagenic E. coli pathotypes such as Enteropathogenic E. coli (EPEC), Enterotoxigenic E. coli (ETEC), Enteroaggregative E. coli (EAEC), and Shiga toxin-producing E. coli (STEC) in Brassica oleracea cultivars in order to provide information on the assessment of diarrheagenic E. coli pathogenesis risk. Materials and Methods: 100 samples of vegetables were collected in Tehran, including cabbage, cauliflower, broccoli and Brussels sprouts. After homogenizing samples, enrichment was done in the EC broth medium. Five colonies of pure culture were used for DNA extraction. Pathotypes were identified by PCR using virulence genes. Results: The results showed that the prevalence of diarrheagenic E. coli strains was 7%. The EPEC prevalence was 3%, All EPEC isolates were atypical. The ETEC frequency was 3%, And the EAEC prevalence was 1%. Conclusion: These findings indicated that Brassica oleracea cultivars could be consideredas a source of contamination with diarrhea-causing E. coli strains. https://ijm.tums.ac.ir/index.php/ijm/article/view/2823 https://ijm.tums.ac.ir/index.php/ijm/article/download/2823/1428

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 1 2022 02 20 90 96 Gissou Keyhani Department of Genetics, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran Hamideh Mahmoodzadeh Hosseini Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran Ali Salimi Nanobiotechnology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran 2021 01 02 2021 11 11 Background and Objectives: Almost all living cells secret nano-sized structures enclosed by the lipid bilayer called extracellular vesicles (EVs) into their extracellular milieu. These EVs play important roles in several physiological processes as a cargo delivery system. In probiotics, EVs are the main communication tool with the host. The present study aimed to assess the effect of EVs originated from Lactobacillus rhamnosus GG on the Carcinoembryonic antigen (cea) gene expression and protein (CEA) synthesis in the SW480 and HT-29 cell lines. Materials and Methods: Different concentrations of Lactobacillus rhamnosus GG EVs were applied on the SW480 and HT-29 cell lines. The MTT assay, Real-Time PCR, and ELISA analysis methods were exploited to explore the cell viability and the expression level of the cea gene in comparison with the β-actin gene as the control. Results: The two concentrations of 80 and 100 μg/ml of Lactobacillus rhamnosus GG EVs considerably affected the anti-proliferation and increased the amount of both CEA mRNA and protein (p < 0.05). Conclusion: Our findings showed that EVs of Lactobacillus rhamnosus GG could induce the gene expression and protein synthesis of CEA. Also, they reduced the cell proliferation of HT29 and SW480. Thus, probiotics such as EVs of Lactobacillus rhamnosus GG could be useful for preventing colorectal cancer. https://ijm.tums.ac.ir/index.php/ijm/article/view/2918 https://ijm.tums.ac.ir/index.php/ijm/article/download/2918/1429

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 1 2022 02 20 97 103 Mostafa Al-Musawi Department of Clinical Laboratory Science, College of Pharmacy, University of Al-Mustansiriyah, Baghdad, Iraq Kadhim Ibrahim Department of Plant Biotechnology, College of Biotechnology, Al-Nahrain University, Baghdad, Iraq Salim Albukhaty Department of Chemistry, College of Science, University of Misan, Maysan, Iraq 2021 11 21 2021 12 20 Background and Objectives: Medicinal plants have recently received much interest because of the low production costs and fewer side effects associated with remedies made from them compared with chemical therapies. The current study investigated the antioxidant, antibacterial, and cytotoxicity properties of an ethanol extract of Cordiamyxa fruit (CMF) extract. Materials and Methods: The antioxidant activity of CMF was determined by measuring electron-donating ability with a 1,1-diphenyl-2picrylhydrazyl (DPPH) assay. The phenolic content was calculated as Gallic acid equivalents using the Folin–Ciocalteu assay. To evaluate the efficiency of CMF, five multidrug-resistant bacterial strains (Salmonella enterica, Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Pseudomonas aeruginosa) were tested using the agar diffusion method. Furthermore, the cytotoxic activity of CMF was determined using 3-(4,5-dimethylthiazol-2-yl)-2,5-dipheltetrazolium (MTT) assay against a healthy fibroblast (L929) cell line. Results: The CMF ethanol extract was revealed to have substantial phenol and flavonoid content (113.71± 0.04 mg gallic acid/g dried extract and 68.9 ± 0.002 mg quercetin/g dried extract, respectively) that showed the highest percentage of DPPH inhibition (86.45%), which was achieved by ethanol extract at the concentration of 60 μg/ml,with excellent antibacterial activity against S. aureus, E. coli, S. enterica, B. subtilis, and P. aeruginosa (17.5 ± 1.0, 14.9 ± 1.0, 13.3 ± 1.5, 15.7 ± 1.0, and 13.8 ± 1.5 mm IZ, respectively). In addition, no expressive antiproliferative effect was recorded in the assessment of cytotoxicity on L929 cells. Conclusion: According to the current findings, CMF exhibits low cytotoxicity, antibacterial activity, and antioxidant properties in vitro and can be developed for pharmaceutical and medical uses in the future. https://ijm.tums.ac.ir/index.php/ijm/article/view/3443 https://ijm.tums.ac.ir/index.php/ijm/article/download/3443/1430

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 1 2022 02 20 104 111 EN Manmohan Mishra Department of Virology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India; Department of Microbiology, Province Public Health Laboratory, Janakpurdham, Nepal Santosh Yadav Department of Microbiology, Rajarshi Janak University, Janakpurdham, Nepal Shravan Mishra Department of Microbiology, Province Public Health Laboratory, Janakpurdham, Nepal Radha Ratho Department of Virology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India 2021 06 04 2021 09 23 Background and Objectives: In recent decades, the incidence of dengue has increased dramatically. In dengue-endemic countries, changes in dengue virus serotypes, genotypes, and lineages have been reported. This study was designed to detect and characterize the dengue virus isolates circulating in North India by serological and molecular techniques. Materials and Methods: This study was conducted at the Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India. NS1 antigen and IgM antibody against dengue were detected by ELISA methods, viral RNA was extracted and amplified by conventional PCR and one-step single-tube multiplex PCR. The purified PCR products were cycle sequenced and a database search was implemented for the confirmation of the sequence product. Phylogenetic analysis was carried out with previously reported sequences. Results: Among 1509 samples, 205 (13.6%) were found positive for IgM antibodies with the highest number (n=67) among the 21 to 30 years age group with peak positivity during post-monsoon months. Among acute samples, NS1 antigen was positive in 62.9%. Seven patients out of 13 had dengue viral RNA in PCR. It comprised six DENV-2 serotypes and one DENV-3 serotype. On phylogenetic analysis, DENV-2 strains grouped with genotype IV and DENV-3 with genotype III. Conclusion: Dengue infection was found frequently during post-monsoon season. The positivity rate of the dengue NS1 antigen test was greater than that of the antibody test. The dengue isolates were characterized as genotype IV and genotype III of DENV-2 and DENV-3 respectively. https://ijm.tums.ac.ir/index.php/ijm/article/view/3182 https://ijm.tums.ac.ir/index.php/ijm/article/download/3182/1431

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 1 2022 02 20 112 118 EN Alireza Tabibzadeh Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Mahshid Panahi Gastrointestinal and Liver Diseases Research Center, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Behnaz Bouzari Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Mohammad Taghi Haghi Ashtiani Department of Pathology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran Farhad Zamani Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, IranGastrointestinal and Liver Diseases Research Center, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Hadi Teimoori Arzati Department of Veterinary, Islamic Azad University, Karaj Branch, Karaj, Iran Mohammad Hadi Karbalaie Niya Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Gastrointestinal and Liver Diseases Research Center, School of Medicine, Iran University of Medical Sciences, Tehran, Iran 2021 02 18 2021 10 05 Background and Objectives: The human papillomavirus (HPV) is associated with more than 70% of the cervical neoplasm. The current study aims to evaluate the distribution of HPV genotypes in suspected women cytological specimens from Tehran, Iran. Materials and Methods: In the current cross-sectional study, HPV genotype prevalence was investigated in 433 subject women. DNA extraction was performed by High Pure Viral Nucleic Acid kit. A semi-automatically hybriSpot 24™ (HS24) setting was used for HPV typing and data interpreted by hybriSoft™ software according to instructions. Results: Pathologic data showed 181 (41.8%) had non-malignant lesions, 212 (49%) had inflammation and 40 (9.2%) reported LSIL in primary Pap-smear result. HPV was found in 143 (33%) specimens and the most comment high-risk and low-risk HPV types were HPV-16 and -6, respectively. Also, 62 (43%) were co-infected with multiple genotypes includes, 34 (24%) cases had co-infection with two HPV types, 17 (12%) cases had co-infection with three HPV types, 6 (4%) cases had co-infection with four HPV types and 5 (3%) cases had co-infection with five HPV types. There was statistically different domination on high-risk genotype in most of the co-infected samples (p<0.01). Conclusion: Current study indicates that the lesion pathology assessment was significantly associated with the HPV infection (p<0.01). Furthermore, the age group assessment shows that most of the HPV positive cases were 21 to 40 (p<0.01). The HPV infection prevalence in the current study was 33% and the most frequently reported high-risk and low-risk HPV types were 16 and 6, respectively. https://ijm.tums.ac.ir/index.php/ijm/article/view/2984 https://ijm.tums.ac.ir/index.php/ijm/article/download/2984/1432

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 1 2022 02 20 119 124 EN Hooman Ramezany Department of Immunology, Research Center of Blood Transfusion, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran Maryam Kheirandish Department of Immunology, Research Center of Blood Transfusion, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran Shahram Samiee Department of Immunology, Research Center of Blood Transfusion, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran Mina Khosravifar Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran Seyedeh Melika Hashemi Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran 2021 11 13 2021 12 20 Background and Objectives: Umbilical cord blood (UCB) was used to source hematopoietic stem cells in the past. Despite the apparent advantages of UCB transplantation, virus reactivation poses a considerable danger in allogeneic hematopoietic stem cell transplantation (HSCT). Human Parvovirus B19 is regarded as a potential threat to UCB contamination. This study aimed to evaluate the prevalence of parvovirus B19 in cord blood donors by Semi-Nested PCR. This study is the first large-scale report of the B19 DNA in cord blood donors in Iran. Materials and Methods: A total of 691 umbilical cord blood were collected under standard procedure. Then, DNA from buffy coat and plasma were extracted, and semi-nested PCR was performed for all samples. Results: Two out of 691 samples (0.29%) indicated viremia in plasma and buffy coat. Conclusion: In this line, designing and validating a quantitative PCR assay for detection, quantification, and discrimination of Human B19 DNA genotypes of cord blood donors is necessary to enhance the safety of this source of stem cells. https://ijm.tums.ac.ir/index.php/ijm/article/view/3426 https://ijm.tums.ac.ir/index.php/ijm/article/download/3426/1433

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 14 1 2022 02 20 125 132 Amin Ebadi Student Research Committee, Tabri