Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 565 573 Özgür Appak Department of Medical Microbiology, Division of Medical Virology, School of Medicine, Dokuz Eylul University, Izmir, Turkey Abdurrahman Gülmez Department of Medical Microbiology, Istanbul Basaksehir Cam ve Sakura Hospital, Istanbul, Turkey Irmak Güzel Department of Medical Microbiology, School of Medicine, Dokuz Eylul University, Izmir, Turkey Naciye Gezer Department of Radiology, School of Medicine, Dokuz Eylul University, Izmir, Turkey Özlem Gürsoy Doruk Department of Medical Biochemistry, School of Medicine, Dokuz Eylul University, Izmir, Turkey Osman Ergor Department of Public Health, School of Medicine, Dokuz Eylul University, Izmir, Turkey Nuran Esen Department of Medical Microbiology, School of Medicine, Dokuz Eylul University, Izmir, Turkey Ayca Sayıner Department of Medical Microbiology, Division of Medical Virology, School of Medicine, Dokuz Eylul University, Izmir, Turkey 2021 04 24 2021 08 06 Background and Objectives: In this study, the performance of three different commercial antibody assays for COVID-19 was examined and parameters affecting the antibody response were investigated. The correlation of patients’ chest CT results, procalcitonin, CRP, and D-dimer levels with the antibody response were retrospectively evaluated. Materials and Methods: COVID-19 antibodies were detected by three commercially available assays in each patient. Two of the assays were rapid immunochromatographic tests and - one was an ELISA-based IgG assay. SARS-CoV-2 RNA was tested by “COVID-19 RT-qPCR Detection Kit” using nasopharyngeal swab samples. The results of antibody tests were compared with each other, RT-qPCR, Biochemical parameters and chest CT findings. Results: RT-qPCR was positive in 46.6% (41/88) of the evaluated patients among which 77.3% (68/88) were healthcare workers. Seventeen (41.4%) of viral RNA positive patients had a positive antibody result with at least two assays. Both of the rapid immunochromatographic tests had identical sensitivity of 36.6% and specificity of 100%, compared to RT-qPCR assay; while the sensitivity of the ELISA based Euroimmune test was 43.9%, and the specificity was 95.7%. The sensitivity and specificity of the immunochromatographic tests were 75% and 100% respectively, compared to ELISA test result. There was a correlation between antibody positivity and old age and male gender. The presence of typical chest CT findings increased the antibody positivity 13.62 times. Antibody positivity was also increased with the decrease in Ct value of the PCR assay. There was no significant relationship between the biochemical parameters (CRP, D-dimer and procalcitonin values) and the antibody or RT-qPCR results. Conclusion: There was a correlation between antibody response and male gender, older age, presence of symptoms, typical chest CT findings and low PCR-Ct value. https://ijm.tums.ac.ir/index.php/ijm/article/view/3114 https://ijm.tums.ac.ir/index.php/ijm/article/download/3114/1380

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 724 727 Shervin Shokouhi Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medial Sciences, Tehran, Iran Ghodsieh Kamrani Cancer Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran Iman Ghasemzadeh Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medial Sciences, Tehran, Iran; HIV/STI Surveillance Research Center, WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran Mana Baziboroun Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medial Sciences, Tehran, Iran; Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran 2021 01 03 2021 08 06 Acinetobacter baumannii is an opportunistic bacterial pathogen predominantly associated with hospital-acquired infections. Here we present a case of infective endocarditis of native Mitral and Aorta valves caused by A. baumannii in a 73-year-old man. He underwent surgical excision and Pathologic specimen showed A. baumannii growth after 48 hours that was extensively drug-resistant (XDR). He was treated with colistin and tigecycline. Finally, he discharged with no important complication. To our best knowledge, it is the first case of Acinetobacter endocarditis has ever been reported in Iran. Although XDR A. baumannii is a life-threatening pathogen, proper and timely treatment can be life-saving. https://ijm.tums.ac.ir/index.php/ijm/article/view/2919 https://ijm.tums.ac.ir/index.php/ijm/article/download/2919/1398

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 574 582 EN Shojaat Dashtipour Department of Tuberculin and Mallein, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran Keyvan Tadayon Department of Veterinary Aerobic Bacteria Vaccines, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran Sajjad Yazdansetad Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran Nader Mosavari Department of Tuberculin and Mallein, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran Rouhollah Keshavarz Department of Tuberculin and Mallein, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran 2021 05 09 2021 10 01 Background and Objectives: Glanders is a serious zoonotic disease caused by Burkholderia mallei. Prevention, control, and treatment strategies of glanders are prerequisites for microbial source tracking. The present study was aimed to analyze the genomic pattern of B. mallei Iranian field isolates by pulsed-field gel electrophoresis (PFGE) typing. Materials and Methods: B. mallei isolates were aerobically cultured in nutrient broth/agar supplemented with glycerol 4% for 48 h at 37°C. API 20NE identification system was used for the biochemical characterization. Genomic DNA of bacterial isolates was extracted using OIE-recommended protocol. Molecular identification of bacterial isolates was done based on amplification of BimA and IS407-flip genes. PFGE was applied to prepare the genomic pattern of B. mallei isolates. The guinea pig was used as a suitable model for studying the histopathological characterization of B. mallei. Results: In both enzymatic digestion patterns by using Af1II and VspI, we found three different clonal types; І) PFGE type of B. mallei Razi 325 strain, ІІ) PFGE type of Tiger, Kordan, and Oshnavieh strains, and ІІІ) PFGE type of Semirom strain. B. mallei Razi 325 was categorized as unrelated strain which was belonged to the different cluster differing more than four bands. Conclusion: PFGE showed more discriminatory power and considerable reproducibility for molecular typing of B. mallei strains in our study. It is standardized the approaches for outbreak detection, pathogen phylogeny, molecular epidemiology, and population studies. https://ijm.tums.ac.ir/index.php/ijm/article/view/3140 https://ijm.tums.ac.ir/index.php/ijm/article/download/3140/1381

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 583 591 Ajanta Sharma Department of Microbiology, Gauhati Medical College, Guwahati, Assam Bornali Dutta Department of Microbiology, Gauhati Medical College, Guwahati, Assam Debajit Rabha Department of Microbiology, Gauhati Medical College, Guwahati, Assam Elmy Rasul Department of Microbiology, Fakaruddin Ali Ahmed Medical College, Barpeta, Assam Naba Hazarika Department of Microbiology, Gauhati Medical College, Guwahati, Assam 2020 12 20 2021 08 06 Background and Objectives: Information on the genetic epidemiology of cholera in Assam, a northeastern state of India is lacking despite cholera being a major public health problem. The study aimed to determine the virulence genes and genes encoding antibiotic resistance in Vibrio cholerae isolates and to determine the prevalent genotypes based on the presence or absence of the virulence genes and ctxB genotype. Materials and Methods: Twenty-five V. cholerae strains were subjected to conventional biotyping and serotyping followed by multiplex PCR to detect ctxA, ctxB, zot, ace, O1rfb, tcpA, ompU, ompW, rtxC, hly and toxR and antibiotic resistance genes. Cholera toxin B (ctxB) gene was amplified followed by sequencing. Results: All the V. cholerae O1 isolates were El Tor Ogawa and showed the presence of the core toxin region representing the genome of the filamentous bacteriophage CTXø. The complete cassette of virulence genes was seen in 48% of the isolates which was the predominant genotype. All the isolates possessed amino acid sequences identical to the El Tor ctxB subunit of genotype 3. sulII gene was detected in 68% of the isolates, dfrA1 in 88%, strB in 48% and SXT gene was detected in 36% of the isolates. Conclusion: Toxigenic V. cholerae O1 El Tor Ogawa strains of ctxB genotype 3 carrying a large pool of virulence genes are prevailing in Assam. Presence of a transmissible genetic element SXT in 36% of the strains is of major concern as it indicates the emergence of multiple drug resistance among the V. cholerae isolates. https://ijm.tums.ac.ir/index.php/ijm/article/view/2891 https://ijm.tums.ac.ir/index.php/ijm/article/download/2891/1382

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 592 601 Arjun Bhugra Department of Microbiology, St John’s Medical College, Bengaluru, India Supriya Gachinmath Department of Microbiology, St John’s Medical College, Bengaluru, India 2021 03 15 2021 08 12 Background and Objectives: Urinary tract infections (UTI) are the most common bacterial infections in both outpatient and inpatient department received for routine bacterial culture and sensitivity. We looked for significant bacteriuria in requested repeat urine sample after primary urine culture yielded significant growth (>105 CFU/ml) of ≥3 types of colonies. Also studied, different isolates grown with their sensitivity pattern and contamination rates of urine samples from different departments. Materials and Methods: In routine, primary urine cultures yielding ≥3 types of colonies on Cystine Lactose Electrolyte Deficient (C.L.E.D) were requested for repeat samples, collected with aseptic precautions after proper instructions. Data was analyzed for the Microbiological profile and its clinical correlation. Results: Among 617 received requested urine samples, 292 (47.3%) yielded significant bacteriuria. Clinical details were available for 252 cases out of which 100 (39.7%) showed asymptomatic bacteriuria, 87 (34.5%) complicated UTI and 65 (25.7%) uncomplicated UTI. Null hypothesis was rejected as 292 (47.3%) of the received repeat samples showed significant bacteriuria and 325 (53%) showed normal flora/no growth i.e. there is a 50% chance of getting either a positive culture or normal flora/no growth in repeat urine samples after the primary urine culture showed ≥3 types of colonies. It indicates the importance of requesting repeat urine samples for an accurate urine culture report. Male patients were significantly associated with significant bacteriuria and complicated UTI (p= 0.001). Escherichia coli (n=112, 28%) was the most common followed by Klebsiella species (n=66, 16.4%) and Enterococcus species (n=69, 17.2%). 183 (45.6%) isolates were Multi-Drug Resistant (MDR) Gram Negative Bacilli (GNBs), Escherichia coli (50.3%) being most common. Vancomycin Resistant Enterococcus (VRE) (n=8, 2.0%) was also isolated. Conclusion: Our study justifies the rationale for asking a repeat urine samples which helps in providing an appropriate microbiological report with antibiotic sensitivity pattern, hence preventing unwanted reporting of commensals/contaminants facilitating evidence based therapy. https://ijm.tums.ac.ir/index.php/ijm/article/view/3046 https://ijm.tums.ac.ir/index.php/ijm/article/download/3046/1383

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 602 607 Eun Ju Oh Departmentof Medical Laser, School of Medicine, Dankook University Graduate, Chungnam, South Korea Tae Su Jang Department of Preventive Medicine, Dankook University College of Medicine, Chungnam, South Korea Jae Kyung Kim Departmentof Biomedical Laboratory Science, Dankook University College of Health Sciences, Chungnam, South Korea 2021 07 17 2021 08 30 Background and Objectives: Sexually transmitted infections (STIs) can remain undetected and untreated; therefore, rapid diagnosis and treatment of STIs are important. Mycoplasma genitalium (MG), Mycoplasma hominis (MH), and Ureaplasma urealyticum are sexually transmitted pathogens that cause asymptomatic, organ-specific, and chronic infections, thereby posing a threat to community health. Therefore, we investigated the epidemiological trends of MG and MH infections in South Korea for rapid diagnosis and treatment. Materials and Methods: From September 2018 to December 2020, samples (catheter, pus, tissue, swab, and urine) were collected from outpatients of hospitals in South Korea for molecular biological venereal disease testing. DNA was extracted and analyzed using real-time polymerase chain reaction. Results: Of the 59,381 samples analyzed, 8.78% (n=5,215) were positive for MG and MH. The MH positivity rate (5.51%, n=3,273) was higher than the MG positivity rate (3.27%, n=1,942). MG and MH positivity rates were the highest in patients aged <19 years. Men had higher MG positivity rate, whereas women had higher MH positivity rates. Furthermore, the MGpositivity rate was the highest in the swab samples of both men and women, whereas that of MH was the highest in the urine samples of men and swab samples of women. Conclusion: We identified the differences between MG and MH positivity rates based on sex, specimen, and age. Our findings can provide information for strategies that protect public health and reduce STI incidence and transmission. https://ijm.tums.ac.ir/index.php/ijm/article/view/3238 https://ijm.tums.ac.ir/index.php/ijm/article/download/3238/1384

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 608 616 Mahshid Lalvand ment of Microbiology, Annapurna Research Centre, Kathmandu, Nepal Shiba Kumar Rai Department of Microbiology, Nepal Medical College, Kathmandu, Nepal 2021 04 02 2021 05 09 Background and Objectives: Carbapenems have been the choice of antibiotics for the treatment of infections caused by multidrug-resistant bacteria. The main objective of this study was to determine the prevalence of carbapenemase (blaVIM and blaIMP) producing isolates among Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Materials and Methods: A total of 1,151 clinical samples were collected from the patients visiting Annapurna Neurological Institute and Allied Science and Annapurna Research Centre, Kathmandu, between June 2017 and January 2018. Antibiotic susceptibility testing (AST) was performed on the Enterobacteriaceae, P. aeruginosa and A. baumannii isolates using the Kirby-Bauer disk diffusion method. The modified Hodge test (MHT) was performed on the carbapenem-resistant isolates to confirm carbapenemase production. DNA was extracted and then screened for blaVIM and blaIMP genes by multiplex PCR. Results: Of the total 1,151 clinical samples, 253 (22.0%) showed positive growth. Of them, 226 (89.3%) were identified as Enterobacteriaceae, P. aeruginosa, and A. baumannii. Among the 226 isolates, 106 (46.9%) were multidrug-resistant. Out of the 106, 97 (91.5%) isolates showed resistance to at least one of the carbapenem used. Among the 97 carbapenem-resistant isolates, 67 (69.1%) showed the modified Hodge test (MHT) positive results. blaVIM and blaIMP were detected in 40 and 38 isolates respectively using multiplex PCR assay. Conclusion: This study determined a high prevalence of MDR and carbapenem resistance among Enterobacteriaceae, P. aeruginosa, and A. baumannii as detected by the presence of blaVIM and blaIMP genes. This study recommends the use of rapid and advanced diagnostic tools along with conventional phenotypic detection methods in the clinical settings for early detection and management of drug-resistant pathogens to improve treatment strategies. https://ijm.tums.ac.ir/index.php/ijm/article/view/3072 https://ijm.tums.ac.ir/index.php/ijm/article/download/3072/1347

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 312 318 Manoochehr Makvandi Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Ali Teimoori Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Roya Pirmoradi Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Chiman Karami Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Ahmad Shamsizadeh Division of Pediatric Infectious Diseases, Aboozar Children's Medical Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Abdolnabi Shabani Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Kambiz Ahmadi Angali Department of Biostatistic, School of Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran 2021 02 15 2021 05 12 Background and Objectives: Human parechoviruses (HPeV) and Human enteroviruses (EV) frequently cause a sepsis-like illness in young infants (younger than three months). Therefore, this study was conducted to determine the frequency of HPeV and EV among the young infants with clinical signs and symptoms of sepsis in Ahvaz city, Iran. Materials and Methods: The blood specimens were collected from 100 (younger than 90 days hospitalized infants) including 54 (56.25%) males and 46 (43.75%) females with clinical signs and symptoms of sepsis-like disease. The RNA was extracted and tested for detection of VP1 region of HPeV and 5 UTR (Untranslated Region) of EV by RT-PCR. The sequences of positive of HPeV were further analyzed to determine HPeV genotyping. Results: 5/100 (5%) of patients including 2/46 (2%) females and 3/54 (3%) males tested positive for HPeV (P=0.85). The analysis of 5 positive VP1 region of HPeV revealed the genotype 1. The analysis of sequencing and phylogenetic tree revealed that the isolated HPeVs were genotype 1. While 38/100 (38%) specimens including 16 (16%) females and 22 (22%) males were tested positive for EV (P=0.68). Conclusion: The frequency of HPeV genotype 1 was 5% among the young infants with sepsis. While frequency of EV was 38% among the young infants with sepsis. This study showed HPeV genotype 1 and EV are dominant in this region. https://ijm.tums.ac.ir/index.php/ijm/article/view/2982 https://ijm.tums.ac.ir/index.php/ijm/article/download/2982/1348

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 319 324 Maryam Adabi Brucellosis Research Center, Hamadan University of Medical Sciences, Hamadan, Iran Manoochehr Karami Health Sciences Research Center, Hamadan University of Medical Sciences, Hamadan, Iran; Department of Epidemiology, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran Fariba Keramat Brucellosis Research Center, Hamadan University of Medical Sciences, Hamadan, Iran Mohammad Yousef Alikhani Brucellosis Research Center, Hamadan University of Medical Sciences, Hamadan, Iran Somaye Bakhtiari Brucellosis Research Center, Hamadan University of Medical Sciences, Hamadan, Iran 2021 01 10 2021 03 21 Background and Objectives: Brucella is an intracellular pathogen that causes brucellosis in humans and animals. This study aimed to assess the results of brucellosis seroprevalence among participants of the Famenin brucellosis cohort with molecular investigation technique and determine Brucella-approved species. Materials and Methods: Following the first phase of the Famenin brucellosis cohort in 2016 which investigated the seroprevalence of brucellosis among 2367 participants in Famenin city, a total of 575 people including all seropositive and some seronegative people were examined again by wright serological tests in 2019. The PCR assay was accomplished on all cases that have wright titers ≥ 1/20 for tracing Brucella DNA using BCSP31 target gene and IS711 locus. Results: Out of 575 studied cases, 145 people had wright titers ≥ 1/20. The PCR reactions of these 145 blood samples were positive in 63/145 (43.44%) tested samples using primers (B4/B5) for Brucella genus detection. In the second PCR assay using specific-primers for Brucella abortus and Brucella melitensis, 18/63 (28.57%) of the samples were diagnosed as B. abortus, and 18/63 (28.57%) were diagnosed as B. melitensis. Conclusion: In this study, using the selected specific genes for the diagnosis of Brucella in the genus and species levels, the PCR technique was evaluated as a promising method for the rapid and safe detection of brucellosis besides the serological test for more accurate detection of brucellosis especially in cases that are not definitive. https://ijm.tums.ac.ir/index.php/ijm/article/view/2930 https://ijm.tums.ac.ir/index.php/ijm/article/download/2930/1349

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 325 336 Sadaf Sabzevari Vector-Borne Disease Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran; Preclinical Core Facility, Infection Preclinical Imaging Group, Tehran University of Medical Sciences, Tehran, Iran Hamidreza Shoraka Vector-Borne Disease Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran Mohammad Seyyedin Department of Quality Control, Razi Vaccine and Serum Research Institute, Agricultural Research Education And Extention Organization, Mashhad Branch, Mashhad, Iran 2021 01 18 2021 04 14 Background and Objectives: Brucellosis and Q fever are considered as occupational hazards to people in contact with domestic animals or their carcasses. The present cross-sectional study was carried out to determine the seroprevalence of brucellosis and Q fever among professions at risk in the North Khorasan Province, northeastern Iran during 2020. Materials and Methods: In this study, 185 sera samples were collected from butchers, slaughterhouse workers, farmers, and veterinarians in different counties of the province. The collected sera were tested by ELISA test for the detection of IgG antibodies against Coxiella burnetii and Brucella spp. A questionnaire was filled for each participant to investigate demographic characteristics information (i.e., age, gender, educational status, occupation, years of occupational experience, and location), and any exposure to risk factors (animals Keeping, consumption of unpasteurized dairy products, exposure to ill or dead animals, tick bite, splashing animal fluids, travel history, and use of personal protective equipment) that could be associated with these infections. Results: The seroprevalence of antibodies against C. burnetii and Brucella spp. were 17.2% and 19.4%, respectively. Twelve participants also had Q fever and brucellosis co-infection, with a prevalence of 6.4%. Conclusion: Based on the results, it is concluded that brucellosis and Q fever occur among the high-risk populations in this area and it needs more surveillance to control the diseases by public health and veterinary authorities. https://ijm.tums.ac.ir/index.php/ijm/article/view/2945 https://ijm.tums.ac.ir/index.php/ijm/article/download/2945/1350

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 337 344 Ali Hojabr Rajeoni Department of Microbiology and Immunology, School of Veterinary Medicine, University of Tehran, Tehran, Iran Arash Ghalyanchilangeroudi Department of Microbiology and Immunology, School of Veterinary Medicine, University of Tehran, Tehran, Iran Bahman Khalesi Razi InsDepartment of Poultry Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AEREO), Karaj, Iran Mohammad Sadegh Madadi Department of Microbiology and Immunology, School of Veterinary Medicine, University of Tehran, Tehran, Iran Hossein Hosseini Department of Clinical Sciences, School of Veterinary Medicine, Karaj Branch, Islamic Azad University, Alborz, Iran 2021 01 11 2021 04 14 Background and Objectives: Avian respiratory disease complex (RDC) is one of the most detrimental economic diseases that affected different parts of the world. Various pathogens cause the disease, but the most significant viral pathogens include avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) are the most prevalent. To detect these pathogens, various methods have been discovered in the last decades. Detection and characterization of viruses by metagenomics methods have improved our knowledge about the role of virome in the avian complex respiratory disease. Materials and Methods: This research investigates the viral pathogen populations that mostly participate in emerging these diseases using the NGS method RNA-sequencing. In surveillance of ten broiler farms from different cities with respiratory symptoms, trachea samples were collected to determine the pathogenic virome causing the disease. Results: In this metagenomics analysis, nine viral families were identified, comprising 72.82% of RNA viruses, 24.32% of RT viruses, and 2.86% of DNA viruses. RNA viruses had the highest contribution to the respiratory disease complex instead of disease, including paramyxoviridae, orthomyxoviridae, coronaviridae, and picornaviridae viruses. Other viruses from the RNA viruses and DNA virus families were also identified in addition to these results. Conclusion: This research suggests that studies of pathogenic viromes in different diseases can help monitor different diseases and predict their future occurrence. https://ijm.tums.ac.ir/index.php/ijm/article/view/2933 https://ijm.tums.ac.ir/index.php/ijm/article/download/2933/1351

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 345 351 EN Dumrul Gülen Department of Medical Microbiology, Tekirdağ Namık Kemal University, Faculty of Medicine, Tekirdağ, Turkey Birol Şafak Department of Medical Microbiology, Tekirdağ Namık Kemal University, Faculty of Medicine, Tekirdağ, Turkey Berna Erdal Department of Medical Microbiology, Tekirdağ Namık Kemal University, Faculty of Medicine, Tekirdağ, Turkey Betül Günaydın Department of Medical Microbiology, Tekirdağ Namık Kemal University, Faculty of Medicine, Tekirdağ, Turkey 2020 05 30 2021 05 04 Background and Objectives: The frequency of multiple resistant bacterial infections, including carbapenems, is increasing worldwide. As the decrease in treatment options causes difficulties in treatment, interest in new antimicrobials is increasing. One of the promising natural ingredients is curcumin. It is known to be effective in bacteria such as Pseudomonas aeruginosa, Escherichia coli, Burkholderia pseudomallei through efflux pump inhibition, toxin inhibition and enzymes. However, because its bioavailability is poor, it seffectiveness occurs in combination with antibiotics. In the study, the interaction of meropenem and curcumin in carbapenemase producing strains of Klebsiella pneumoniae was tested. Materials and Methods: Thirty-nine Klebsiella pneumoniae isolates, resistant to meropenem, were used in this study. From those 15 MBL, 6 KPC, 17 OXA-48 and 1 AmpC resistance pattern were detected by combination disk method. Meropenem and Curcumin MIC values were determined by liquid microdilution. Checkerboard liquid microdilution was used to determine the synergy between meropenem and curcumin. Results: Synergistic effects were observed in 4 isolates producing MBL, 3 isolates producing KPC, 4 isolates producing OXA-48, and 1 isolates producing AmpC (totally 12 isolates) according to the calculated FICI. No antagonistic effects were observed in any isolates. Conclusion: Curcumin was thought to be an alternative antimicrobial in combination therapies that would positively contribute to the treatment of bacterial infection. The effectiveness of this combination should be confirmed by other in vitro and clinical studies. https://ijm.tums.ac.ir/index.php/ijm/article/view/2650 https://ijm.tums.ac.ir/index.php/ijm/article/download/2650/1352

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 352 359 EN Mehdi Mirzaii Department of Microbiology, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran Marzieh Yaeghoobi Department of Microbiology, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran Meysam Afzali Department of Microbiology, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran Neginsadat Amirkhalili Young and Elite Research Club, Tehran North Branch, Islamic Azad University, Tehran, Iran Majid Mahmoodi Department of Microbiology, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran Esmaeil Babakhanzadeh Sajirani Department of Horticulture Crops Research, Horticultural Sciences Research Institute, Agricultural and Natural Resources Research Center of Semnan Province, Shahrood, Iran 2020 05 01 2021 01 31 Background and Objectives: Candidiasis and pityriasis versicolor are opportunistic fungal infections that are caused by Candida spp. and Malassezia spp. yeasts. Conventional drugs like azole and amino derivatives are known to treat fungal skin diseases. However, drawbacks like long-term side effects and drug resistance lead to investigate on antifungal properties of phytochemicals as an alternative to available synthetic drugs. Materials and Methods: The herbal nano hydrogel was successfully synthesized from Quince Seed extract followed by ultrasonic treatment and it has been formulated using a mixture of essential oils. We evaluated the antifungal in vitro assay for a mixture of essential oils in combination with herbal nano hydrogel against Candida albicans and Malasezia furfur strains by micro dilution method. Results: The results indicated that essential oils possess antifungal activity with the MIC value of 12.5 and 6.24 mg/ml against C. albicans and M. furfur, respectively. No fungicidal effect was reported for the herbal hydrogel before nanofabrication while it shown some antifungal activity after ultrasonic treatment for 5 and 10 minutes. As anticipated; the antifungal property of essential oil mixture was appreciably improved when it combined with herbal nano hydrogel where the highest level of inhibition was observed at concentration of 3.125 mg/ml for both strains. The loss in biological activity observed when the ultrasonic treatment on herbal nano hydrogel performed for longer time. Conclusion: The proposed plant-based nano formulation shown promising in vitro antifungal activities against C. albicans and M. furfur strains and its antifungal properties were comparable with commercially available agents like clotrimazole. The new formulation expected to be safe with minimum long-term side effects. Further investigations are underway to confirm the safety and the mechanism of the action of this new herbal formulation. https://ijm.tums.ac.ir/index.php/ijm/article/view/2608 https://ijm.tums.ac.ir/index.php/ijm/article/download/2608/1353

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 360 371 Narges Nodeh Farahani Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Behrooz Sadeghi Kalani Department of Medical Microbiology, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran; Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran Seyed Hamidreza Monavari Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Shiva Mirkalantari Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Fatemeh Montazer Firoozabadi Clinical Research and Development Unit (FACRDU), Iran university of Medical Sciences (IUMS), Tehran, Iran Mohammad Sholeh Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Zahra Javanmard Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Gholamreza Irajian Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran 2021 02 10 2021 03 19 Background and Objectives: Helicobacter pylori causes several gastrointestinal diseases, including asymptomatic gastritis, chronic peptic ulcer, duodenal ulcer, lymphoma of the mucosa-associated lymphoid tissue (MALT), and gastric adenocarcinoma. In recent years, failure to eradicate H. pylori infections has become an alarming problem for physicians. It is now clear that the current treatment strategies may become ineffective, necessitating the development of innovative antimicrobial compounds as alternative treatments. Materials and Methods: In this experimental study, a cell-penetrating peptide-conjugated peptide nucleic acid (CPP-PNA) was used to target the cagA expression. cagA expression was evaluated using RT-qPCR assay after treatment by the CPP-PNA in cell culture and animal model. Additionally, immunogenicity and toxicity of the CPP-PNA were assessed in both cell culture and animal models. Results: Our analysis showed that cagA mRNA levels reduced in H. pylori-infected HT29 cells after treatment with CPP-PNA in a dose-dependent manner. Also, cagA expression in bacterial RNA extracted from stomach tissue of mice treated with PNA was reduced compared to that of untreated mice. The expression of inflammatory cytokines also decreased in cells and tissue of H. pylori-infected mice after PNA treatment. The tested CPP-PNA showed no significant adverse effects on cell proliferation of cultured cells and no detectable toxicity and immunogenicity were observed in mice. Conclusion: These results suggest the effectiveness of CPP-PNA in targeting CagA for various research and therapeutic purposes, offering a potential antisense therapy against H. pylori infections. https://ijm.tums.ac.ir/index.php/ijm/article/view/2972 https://ijm.tums.ac.ir/index.php/ijm/article/download/2972/1354

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 372 380 Sepideh Asadi Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran Neda Soleimani Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran Zahra Khosravi Babadi Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran Gholam Hossein Ebrahimipour Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran 2020 08 26 2021 03 21 Background and Objectives: Cancer incidence and recurrence, antibiotic resistance, and overuse of antibiotics have become a global concern. The purpose of this study was to identify and isolate bacteria from the skin of the Rana ridibunda, Iranian swamp frog, which has produced antimicrobial compounds, and investigate its cytotoxic activity on the breast (MCF7) and glioblastoma (U87) cancer cell line. Materials and Methods: An antibiotic-producing bacterium was isolated from the frog skin. The bacterium was identified based on 16S rDNA sequencing and biochemical and morphological characteristics. Antimicrobial activity of the culture supernatant was examined by disc diffusion and MIC methods. Cytoplasmic and cell wall extracts of bacteria were prepared by sonication. SDS-PAGE was then used to examine protein contents of them. The cancer cell lines were treated with cytoplasmic and cell wall extracts at different concentrations. The effects of cytotoxicity were assessed by MTT assay at 24 and 48 h intervals. Finally, the results were analyzed by SPSS. Results: The isolated bacterium was identified as a new strain of Bacillus atrophaeus. MIC and disc diffusion methods showed that the Bacillus atrophaeus antimicrobial activity was broad spectrum. MTT assay showed IC50 values 30 μg/ml and 20 μg/ml for U87 and MCF7 cells after 24-48 h exposure, respectively. Conclusion: The cytoplasmic extracts of Bacillus atrophaeus has anticancer potential and can be used as an alternative or complementary candidate in the treatment of cancer. Further in vivo and in vitro mechanistic studies are suggested to confirm the biological activities. https://ijm.tums.ac.ir/index.php/ijm/article/view/2760 https://ijm.tums.ac.ir/index.php/ijm/article/download/2760/1355

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 381 388 Dita Artanti Departement of Microbiology, Faculty Health of Sciences, University Muhammadiyah of Surabaya, Surabaya, Indonesia Yeti Eka Sispita Sari Departement of Microbiology, Faculty Health of Sciences, University Muhammadiyah of Surabaya, Surabaya, Indonesia Fitrotin Azizah Departement of Microbiology, Faculty Health of Sciences, University Muhammadiyah of Surabaya, Surabaya, Indonesia Nur Vita Puwaningsih Departement of Clinical Pathology, Faculty Health of Sciences, University Muhammadiyah of Surabaya, Surabaya, Indonesia Vella Rohmayani Departement of Microbiology, Faculty Health of Sciences, University Muhammadiyah of Surabaya, Surabaya, Indonesia Dede Nasrullah Departement of Nursing, Faculty Health of Sciences, University Muhammadiyah of Surabaya, Surabaya, Indonesia 2021 02 09 2021 05 06 Background and Objectives: In 2020 the whole world is experiencing a pandemic condition due to infection with the SARS-CoV-2 virus which can cause the COVID-19 disease. This condition results in “Panic Buying”, because everyone tries to avoid the spread and transmission of the COVID-19 disease by doing various ways, one of which is by taking additional supplements such as vitamin C and probiotic supplements. Materials and Methods: The materials used were mice Mus musculus male DDY strain aged 1-2 months. Probiotic supplement Lactobacillus acidophilus La-14 with a viability of 1 × 108 CFU/ml. with a weight of 0.16 grams dissolved in 0.25 ml 0.9% NaCl. Vitamin C used is a commercial vitamin C tablet, weighing 0.06 grams in 0.25 ml 0.9% NaCl. Meanwhile, the feed for mice (Mus musculus) is a complete feed from Pokphand with the code BR1 CP511B. Lung histology preparations data were analysed descriptively and statistically through the test Chi square while the data on the number of lymphocytes were analysed descriptively. Results: The histological observations of lungs of Mus musculus showed that in the treatment of ML, MV, and MKA test was carried out chi square ratio between the groups that did not have lymphocyte infiltration and those that had lymphocyte infiltration showed a significant difference (p <0.05). Meanwhile, the results of the lymphocyte count showed that ML and MV treatment was higher than that of MK treatment. Conclusion: It is suggested that the administration of probiotics can stimulate and modulate the respiratory immune system. https://ijm.tums.ac.ir/index.php/ijm/article/view/2971 https://ijm.tums.ac.ir/index.php/ijm/article/download/2971/1356

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 389 398 Sharmineh Sharafi Department of Food Science and Technology, Faculty of Agriculture, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran Leila Nateghi Department of Food Science and Technology, Faculty of Agriculture, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran Shahriyar Yousefi Department of Food Science and Technology, Faculty of Agriculture, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran 2021 01 13 2021 04 23 Background and Objectives: Gamma-aminobutyric acid (GABA) is a non-protein amino acid produced by lactic acid bacteria. Among GABA-producing bacteria, lactic acid bacteria have received more attention due to their probiotic nature and properties such as inhibiting pathogenic bacteria, strengthening the immune system, and so on. Materials and Methods: Investigation on the effect of three independent variables including pH (4.7, 4.9 and 5.1), glutamic acid (1, 2 and 3 mgg-1) and salt (2, 2.5 and 3%) on GABA production in low fat cheese by probiotic bacteria. Results: By increasing the amount of glutamic acid and decreasing the pH from 5.1 to 4.7, the amount of GABA production in ultra-filtration cheese significantly increased on the 15th and 30th days of production (p≤0.05), while by increasing the amount of salt the production GABA decreased on the 15th and 30th days. Simultaneous optimal conditions to achieve maximum GABA production in cheese on the 15th and 30th production day was respectively 167.7917 mg/kg-1 and 220.125 mg/kg-1 using 3 mg/g glutamic acid, 2% salt at pH 4.7. Conclusion: The results showed that by identifying probiotic bacteria with the highest potential for GABA production and optimizing the culture medium, more GABA can be produced in food products and a positive step can be taken to produce pragmatic products and promote consumer health. https://ijm.tums.ac.ir/index.php/ijm/article/view/2936 https://ijm.tums.ac.ir/index.php/ijm/article/download/2936/1357

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 399 406 Fahimeh Mahmoudnia Department of Biology, Faculty of Sciences, Farhangian University, Tehran, Iran 2020 08 11 2021 04 28 Background and Objectives: Halothermophilic bacteria are adapted to high osmolarity and can grow in high saline environments and high temperatures. This study was aimed at the isolation of halothermophilic bacteria from Howz-e Sultan hypersaline lake in the central desert zone in Iran. Materials and Methods: Samples were collected and after preparing dilutions, the samples were cultured on Molten haloid agar with different salt concentrations (5-35%), then the plates were incubated at 35-70ºC in both aerobic and anaerobic conditions. Biochemical characterizations, utilization of carbon sources, production of exoenzymes and antibiotic susceptibility were investigated. Taxonomic and phylogenetic analyses were performed using 16S rRNA gene sequences. Results: One of the isolated bacteria was found to be Gram-positive, hyperhalophilic, thermophilic, endospore-forming, and was named as 1-9 h isolate. The bacterial cells were bacilli-shaped, which produced endospores at a subterminal position. This isolate was an aerobe and facultative anaerobe and grew between pH 5.0 and 10.0 (optimal growth at pH 7.0-7.5), at temperature between 15°C and 65°C (optimal growth at 40-45°C) and at salinity of 9-32% (w/v) NaCl, growing optimally at 18% (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, isolate 1-9 h belongs to the genus Bacillus within the phylum Firmicutes and showed the closest phylogenetic similarity to Gracilibacillus sp. IBP-V003 (99.0%). Conclusion: Based on the results of its phenotypic and genotypic properties, strain 1-9 h represents a novel strain of the genus Gracilibacillus. It can be used in various fields of industry and biotechnology. https://ijm.tums.ac.ir/index.php/ijm/article/view/2748 https://ijm.tums.ac.ir/index.php/ijm/article/download/2748/1358

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 407 417 EN Doaa Khalil Department of Botany, Faculty of Sciences, Aswan University, Aswan, Egypt; Department of Biological Science, Unit of Environmental Studies and Development, Aswan University, Aswan, Egypt Mohamed Salah Massoud Department of Botany, Faculty of Sciences, Aswan University, Aswan, Egypt; Department of Chemistry, Science & Arts College, Alqurayyat, Jouf University, Al-Jawf, Kingdom of Saudi Arabia Soad El-Zayat Department of Botany, Faculty of Sciences, Aswan University, Aswan, Egypt; Department of Biological Science, Unit of Environmental Studies and Development, Aswan University, Aswan, Egypt Magdi El-Sayed Department of Botany, Faculty of Sciences, Aswan University, Aswan, Egypt; Department of Biological Science, Unit of Environmental Studies and Development, Aswan University, Aswan, Egypt; Department of Biological Science, Molecular Biotechnology Program, Field of Advanced Basic Sciences, Galala University, New Galala City, Egypt 2021 01 17 2021 04 21 Background and Objectives: The use of endophytic fungi for management of phenol residue in paper and pulp industries has been shown as cost-effective and eco-friendly approach. In this study, isolation of endophytic fungi from roots, stems, and leaves of Hibiscus sabdariffa was conducted. Additionally, the isolated fungi were examined for their ability to degrade phenol and its derivatives in paper and pulp industrial samples, using different growth conditions. Materials and Methods: Out of 35 isolated endophyitc fungi, 31 were examined for their phenol biodegradation capacity using Czapek Dox broth medium containing Catechol and Resorcinol as a sole carbon source at final concentrations of 0.4, 0.6 and 0.8%. Results: A total of 35 fungal species belonging to 18 fungal genera were isolated and identified from different parts of H. sabdariffa plants. All strains have the capability for degrading phenol and their derivatives with variable extents. The optimum condition of degrading phenol in paper and pulp effluent samples by Fusarium poae11r7 were at pH 3-5, temperature at 28-35°C, good agitation speed at no agitation and 100 rpm. Conclusion: All endophytic fungal species can utilize phenol and its derivatives as a carbon source and be the potential to degrade phenol in industrial contaminants. https://ijm.tums.ac.ir/index.php/ijm/article/view/2943 https://ijm.tums.ac.ir/index.php/ijm/article/download/2943/1359

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 3 2021 06 05 418 424 Mohammed Al-atrash Middle Technical University Zwida Khadur Baquba Technical Institute ,Middle Technical University Anwar Khadim Baquba Technical Institute ,Middle Technical University 2020 10 31 2021 03 21   Background and Objectives: Yeasts are an important portion of microbial communities of soil due to their bioactivity  for ecosystem safety. Soil yeast abundance and diversity are likely to be affected under harsh environmental and climatic conditions. In Iraq, human activity and climatic changes especially high temperature which may alter microbial communities in soil. Very little is known about yeast abundance and diversity in a hot climatic region. Materials and Methods: By PCR technique, soil yeast abundance and diversity were investigated under extreme environmental and climatic conditions , as well as the effects of soil pr