Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 17 4 2025 07 29 516 527 Kiana Shirani Department of Infectious Diseases, Nosocomial Infection Research Center, Isfahan University of Medical Sciences, Isfahan, Iran Arash Seifi Department of Infectious Diseases, Research Center for Antibiotic Stewardship and Antimicrobial Resistance, Tehran University of Medical Sciences, Tehran, Iran Alireza Assadi Department of Infectious Diseases, Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran Ashkan Mortazavi Department of Infectious Diseases, Immunodeficiency Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran SeyedAhmad SeyedAlinaghi Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High-Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran; Research Development Center, Arash Women's Hospital, Tehran University of Medical Sciences, Tehran, Iran 2024 11 05 2025 07 04 Fungal surgical site infections (SSIs) may be less common than bacterial SSIs but are a significant clinical issue due to their challenging diagnosis, higher morbidity, and rising incidence, particularly in immunocompromised patients. The epidemiology, risk factors, prevalent fungal pathogens, and prevention of SSIs caused by fungi are discussed in this narrative review. Systematic literature search for the period 2000 to 2024 was conducted on top databases using relevant MeSH keywords. The most frequent solitary pathogens were Candida spp., followed by Aspergillus and Mucor spp., especially in transplant, cardiac, and GI infections. The greatest challenge is extended length of hospital stay, broad-spectrum antibiotics, immunosuppression, and invasive interventions with prosthetic device or shunts. While it creates added burden, fungal SSIs go unnoticed by clinical practice and are rarely included in SSI prevention strategies. The review declares the significance of enhanced clinical vigilance and tailored antifungal prophylaxis in high-risk exposure surgical procedures. The review, based on the integration of existing information, provides clinicians and infection control practitioners with a framework of fungal SSIs so that they can be better equipped to assess risk, detect infection sooner, and focus prevention efforts. https://ijm.tums.ac.ir/index.php/ijm/article/view/5117 https://ijm.tums.ac.ir/index.php/ijm/article/download/5117/1794

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 17 4 2025 07 29 528 538 Amir Naddaf Maternal-Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran Mohammad Ansari Nasab Maternal-Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran Mamak Shariat Maternal-Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran Parvaneh Sadeghi-Moghaddam Breastfeeding Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran Samaneh Salarvand Department of Anatomical and Clinical Pathology, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran Zahra Omidi Breastfeeding Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Vali-E-Asr Reproductive Health Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran Neda Sadat Kosari Maternal-Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran Leyla Sahebi Maternal-Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran 2024 11 12 2025 07 01 Background and Objectives: Neonatal septicemia is a significant cause of morbidity and mortality in neonatal intensive care units (NICUs). Understanding the patterns of antibiotic resistance and pathogen prevalence is crucial for effective treatment. Materials and Methods: This cross-sectional study was conducted from 2016 to 2022 in the NICU of Vali-Asr Hospital in Tehran. All neonates diagnosed with septicemia were included. Data were collected using the hospital's registry system. Results: A total of 477 infants were hospitalized with sepsis, with 71.7% classified as early-onset sepsis (EOS) and 28.3% as late-onset sepsis (LOS). The most common pathogens were coagulase-negative Staphylococcus (22.1%), Klebsiella pneumoniae (14.9%), and Staphylococcus epidermidis (14.3%). The highest antibiotic resistance was observed for erythromycin (89.8%), clindamycin (80.6%), gentamicin (66.1%), and ciprofloxacin (63.5%), while vancomycin showed the lowest resistance (11.2%). Significant associations were found between antibiotic resistance with low birth weight and chest tube intervention. Trends in antibiotic resistance varied over the study period, with a notable decrease in resistance in 2021. Conclusion: The study highlights the high prevalence of antibiotic resistance in neonatal sepsis, emphasizing the need for continuous monitoring and tailored antibiotic stewardship programs. The findings underscore the importance of individualized treatment approaches to improve outcomes for neonates with sepsis. https://ijm.tums.ac.ir/index.php/ijm/article/view/5131 https://ijm.tums.ac.ir/index.php/ijm/article/download/5131/1795

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 17 4 2025 07 29 539 548 Touseefa Shafi Department of Microbiology, Sher-i-Kashmir Institute of Medical Sciences, Soura, Jammu & Kashmir, India Anjum Ara Mir Department of Microbiology, Sher-i-Kashmir Institute of Medical Sciences, Soura, Jammu & Kashmir, India Shagufta Roohi Department of Microbiology, Sher-i-Kashmir Institute of Medical Sciences, Soura, Jammu & Kashmir, India Bashir Fomda Department of Microbiology, Sher-i-Kashmir Institute of Medical Sciences, Soura, Jammu & Kashmir, India Sanam Wani Department of Microbiology, Sher-i-Kashmir Institute of Medical Sciences, Soura, Jammu & Kashmir, India Tufail Ahmed Department of Microbiology, Sher-i-Kashmir Institute of Medical Sciences, Soura, Jammu & Kashmir, India Samiah Yousuf Department of Microbiology, Sher-i-Kashmir Institute of Medical Sciences, Soura, Jammu & Kashmir, India 2024 08 03 2025 05 09 Background and Objectives: Carbapenem-resistant Enterobacterales (CRE) pose a major healthcare challenge due to high resistance rates and limited treatment options. This study characterized carbapenemase production among CRE isolates using phenotypic methods—Modified Carbapenem Inactivation Method (mCIM) and EDTA-Carbapenem Inactivation Method (eCIM)—as genotypic methods have limitations like restricted gene targets and mutations. Materials and Methods: This six-month study was conducted at Sher-i-Kashmir Institute of Medical Sciences (SKIMS). Samples including swabs, respiratory specimens, pus, body fluids, and blood were cultured on Blood Agar and MacConkey Agar (HiMedia, India). Enterobacterales were identified using conventional methods and screened for carbapenem resistance. CRE isolates underwent mCIM and eCIM testing per CLSI guidelines. Results: Among 471 Enterobacterales isolates tested, 160 (33.9%) were carbapenem-resistant. Of these, 97 (60.6%) were mCIM positive, indicating carbapenemase production. eCIM further identified 83 (85.5%) as metallo-beta-lactamase (MBL) producers and 14 (14.4%) as serine carbapenemase producers. CRE prevalence was higher in ICU settings and among males. Isolates showed high cephalosporin resistance, with multi-drug resistance (MDR) common in both MBL and serine carbapenemase producers. Conclusion: The prevalence of CRE was found to be 33.9%. The findings underscore the critical need for continuous surveillance and stringent infection control measures to manage the spread of CRE in healthcare settings. https://ijm.tums.ac.ir/index.php/ijm/article/view/4966 https://ijm.tums.ac.ir/index.php/ijm/article/download/4966/1796

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 17 4 2025 07 29 549 558 Sanaz Khashei Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran Hossein Fazeli Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran Fateh Rahimi Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran Vajihe Karbasizade Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran 2024 12 31 2025 06 14 Background and Objectives: Acinetobacter baumannii is considered a troublesome cause of infection in burn units, where its capability to form biofilm and resist antibiotics significantly hampers therapeutic success. This study explored the correlations between antimicrobial resistance profiles, biofilm-producing capacity, and genetic diversity of A. baumannii strains from patients with burn wound infection in Isfahan, Iran. Materials and Methods: Ninety-six isolates were analyzed for antibiotic resistance using the disk diffusion technique and for biofilm formation through the microtiter dish assay. The prevalence of ten biofilm-related genes was investigated using specific primers. Clonal relatedness among bacterial strains was defined by Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR). Results: A vast majority of isolates (99%) exhibited resistance to meropenem, ciprofloxacin, ceftriaxone, cefotaxime, piperacillin-tazobactam, and imipenem, qualifying them as extensively drug-resistant (XDR). Twenty-five percent of the strains were strong biofilm formers, while 68% demonstrated moderate or weak biofilm formation. The most commonly identified biofilm-related genes included bfmR (100%), ompA (100%), and bap (99%). A significant association was found between the production of biofilm, resistance to aminoglycosides, and the presence of csuE and bap genes. ERIC-PCR typing showed the presence of 3 clonal types and 7 single types, with biofilm producers predominantly clustering to clonal type 2. Conclusion: This work highlights a notable prevalence of biofilm-producing XDR A. baumannii in burn patients, underscoring the need for continuous surveillance and enhanced infection control strategies. https://ijm.tums.ac.ir/index.php/ijm/article/view/5225 https://ijm.tums.ac.ir/index.php/ijm/article/download/5225/1797

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 17 4 2025 07 29 559 568 EN Neda Shadvar Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran; Student Research Committee, Bushehr University of Medical Sciences, Bushehr, Iran Forough Yousefi Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran Afshin Barazesh Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran Saeed Tajbakhsh Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran 2024 12 01 2025 07 22 Background and Objectives: This study aimed to investigate the virulence factors and genes associated with biofilm and protease in Stenotrophomonas maltophilia in Bushehr, Iran. Materials and Methods: Eighty-seven S. maltophilia isolates (67 clinical and 20 environmental isolates) were studied. The isolates were assessed for the production of virulence factors including several enzymes and biofilm. To detect rmlA, rpfF, spgM, smf-1, StmPr1 868 bp, StmPr1 1621 bp, and StmPr2 genes, PCR and sequencing were performed. Results: All isolates (100%) produced DNase, hemolysin, protease, lipase, and hyaluronidase. Seventy-eight (89.7%) isolates were gelatinase producers, and 85 (97.7%) isolates were lecithinase producers. All isolates were biofilm producers: 79 (90.8%) isolates produced strong biofilm, 5 (5.7%) isolates produced moderate biofilm, and 3 (3.5%) isolates produced weak biofilm. The frequency of smf-1, rmlA, rpfF, and spgM was 93.1%, 86.2%, 26.4%, and 59.8%, respectively. The frequency of protease genes including StmPr1 868 bp, StmPr1 1621 bp, and StmPr2 was 12.6%, 41.4%, and 18.4%, respectively. Conclusion: Our findings revealed a high frequency of isolates that produce DNase, hemolysin, protease, gelatinase, lipase, lecithinase, hyaluronidase, and biofilm. All isolates that harbored spgM or rpfF or both genes were strong biofilm producers. Notably, the presence of isolates that lacked spgM and rpfF genes but produced strong biofilm indicates that in addition to these two genes, other genes or factors may play a role in the production of strong biofilm. Based on this research, S. maltophilia in our area possesses the capability to produce several factors that could play roles in pathogenicity. https://ijm.tums.ac.ir/index.php/ijm/article/view/5171 https://ijm.tums.ac.ir/index.php/ijm/article/download/5171/1798

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 17 4 2025 07 29 569 576 Fahad Ullah Department of Microbiology, Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar, Pakistan Maqsood Ali Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China Falak Niaz Department of Medical Laboratory Technology, Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Malakand Campus, Malakand, Pakistan Israr Ali Khan Department of Microbiology, Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar, Pakistan Sher Wali Khan Department of Chemistry, Women University Rawalpindi, Rawalpindi, Pakistan Momin Khan Department of Microbiology, Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar, Pakistan Rafaqat Ishaq Department of Biochemistry & Molecular Bio Department of Pathobiology, Science and Research Branch, Islamic Azad university, Tehran, Iran Seyed Jamal Hashemi Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran Mansour Bayat Department of Pathobiology, Science and Research Branch, Islamic Azad university, Tehran, Iran 2021 04 27 2021 09 15 Background and Objectives: Dermatophytosis induced by Trichophyton mentagrophytes is a major human and animal fungal contamination. Antifungals like terbinafine and fluconazole are widely used to treat dermatophytosis; nevertheless, the prevalence of drug resistance has increased. Hence, novel curative strategies are needed. In the present study, we compared the efficacies of conventional and nanoform of antifungals agents in guinea pig model of dermatophytosis. Materials and Methods: Guinea pigs (n=36) were injected (the posterior dorsal portion) with Trichophyton mentagrophytes conidia. The guinea pigs were divided into 6 groups (positive control, negative control, fluconazole 0.5% treated group, nano-fluconazole treated group, terbinafine 1% treated group, and nano-terbinafine treated group), then were scored both clinically (redness and lesion intensity) and mycologically (microscopy and culture) until day 40 of inoculation. The treatment started 5 days after the inoculation and continued until day 40 of inoculation. Results: Assessment of the mean score of clinical lesions in groups treated with nano-drug forms of fluconazole and terbinafine on the first day of treatment showed a score of 3 (significant redness with large scaling) and for the conventional form of terbinafine and fluconazole had a score of 4 (ulcer and scar). The decrease in lesion score in nano-drug treated groups was observed between days 15 and 20 and continued until day 40. On day 40, all groups had zero scores except the positive control group. Conclusion: This study indicated that nano-drugs are more suitable for the treatment of dermatophytosis and could be considered as future alternatives for the treatment of dermatophytosis. https://ijm.tums.ac.ir/index.php/ijm/article/view/3118 https://ijm.tums.ac.ir/index.php/ijm/article/download/3118/1385

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 617 623 Ranjana Rohilla Department of Microbiology, Shri Guru Ram Rai Institute of Medical and Health Sciences, Dehradun, India Dimple Raina Department of Microbiology, Shri Guru Ram Rai Institute of Medical and Health Sciences, Dehradun, India Malvika Singh Department of Microbiology, Shri Guru Ram Rai Institute of Medical and Health Sciences, Dehradun, India Ajay Pandita Department of Community Medicine, Shri Guru Ram Rai Institute of Medical and Health Sciences, Dehradun, India Shiwang Patwal Department of Microbiology, Shri Guru Ram Rai Institute of Medical and Health Sciences, Dehradun, India 2021 06 03 2021 08 27 Background and Objectives: Sphingomonas paucimobilis is an opportunistic pathogen and was rarely encountered in clinical specimens previously. This study aimed to investigate the clinical features, associated co-morbidities, and antimicrobial susceptibility patterns of S. paucimobilis infection in a tertiary hospital in Uttarakhand. Materials and Methods: S. paucimobilis isolates cultured from various sections of hospital and OPDs were identified and analyzed for their antibiograms in the microbiology laboratory for a duration of one year from January 2020 to December 2020. Results: S. paucimobilis was isolated from 49 samples (0.01%) out of 3792 samples processed in VITEK 2 Compact automated ID/AST instrument. The maximum number of isolates were obtained from urine samples (31%), followed by blood (24%). Septicemia (41%), meningitis (17%), lower respiratory tract infections and ventilator associated pneumonia (14%) constituted a major portion of infections caused by this organism. Diabetes mellitus (22%) and steroid usage (16%) were major associated co-morbid conditions. Third and Fourth generation cephalosporins like ceftriaxone (81%) and cefepime (86%) were found to be the most susceptible drugs whereas 61% of isolates were resistant to colistin. Conclusion: This organism is an up-and-coming pathogen and should not be simply labeled as a contaminant. Although the organism is not grossly virulent and still might not be associated with serious life-threatening infections; however their evolving resistance patterns and increased spectrum of infections should be seriously taken into account. https://ijm.tums.ac.ir/index.php/ijm/article/view/3177 https://ijm.tums.ac.ir/index.php/ijm/article/download/3177/1386

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 624 631 Rehan Deshmukh Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, Goa, India; Department of Biology, Faculty of Science, Dr. Vishwanath Karad MIT World Peace University, Pune, India Sunil Bhand Department of Chemistry, Birla Institute of Technology and Sciences, Pilani, Biosensor Laboratory, Goa, India Utpal Roy Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, Goa, India 2021 02 16 2021 08 31 Background and Objectives: Public health protection requires timely evaluation of pathogens in potable water to minimize outbreaks caused by microbial contaminations. The present study was aimed at assessing the microbiological quality of water obtained from Shantinagar (a rural area in the South Goa region of Goa, India) using 5-Bromo-4-Chloro-3-Indoxyl β-D-glucuronide-Sorbitol MacConkey agar (BCIG-SMAC) medium and, propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) assay for differential detection and quantification of viable Escherichia coli cells in water samples. Materials and Methods: Membrane filtration method was used for both BCIG-SMAC medium and PMA-qPCR methods. To determine the efficiency of detection of viable cells, we first evaluated the PMA treatment protocol and established the standard calibration curves using previously reported primers. Results: PMA-qPCR detected as low as 7 femtograms of DNA of E. coli per qPCR reaction whereas the limit of detection (LOD) of BCIG-SMAC medium was 1.8 CFU/100mL. A total of 71 water samples spanning 2017-2018 have been analyzed using BCIG-SMAC medium and PMA-qPCR, of which 95.77% (68/71) and 7.04% (5/71) were found to be total E. coli and E. coli O157:H7, respectively. PMA-qPCR study showed the viable counts of total viable E. coli cells ranging from 3 CFU/100mL to 8.2×102 CFU/100mL. The total E. coli CFU/100mL quantified by PMA-qPCR significantly exceeded (paired t-test; P<0.05) the number on BCIG-SMAC medium. Conclusion: The present study indicates that the microbiological quality of environmental water samples analyzed do not comply with the regulatory standard. Therefore, special attention is warranted to improve the overall portable quality of water in the perspective of public health. https://ijm.tums.ac.ir/index.php/ijm/article/view/2987 https://ijm.tums.ac.ir/index.php/ijm/article/download/2987/1387

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 632 641 Sherein Elgendy Department of Medical Microbiology and Immunology, School of Medicine, Assiut University, Assiut, Egypt Rawan Abd-Elhameed Department of Medical Microbiology and Immunology, School of Medicine, Assiut University, Assiut, Egypt Enas Daef Department of Medical Microbiology and Immunology, School of Medicine, Assiut University, Assiut, Egypt Shereen Mohammed Department of Medical Microbiology and Immunology, School of Medicine, Assiut University, Assiut, Egypt Hebatallah Hassan Department of Medical Microbiology and Immunology, School of Medicine, Assiut University, Assiut, Egypt Mohamed El-Mokhtar Department of Medical Microbiology and Immunology, School of Medicine, Assiut University, Assiut, Egypt Ahmed Nasreldein Department of Neurology and Psychiatry, School of Medicine, Assiut University, Assiut, Egypt Eman Khedr Department of Neurology and Psychiatry, School of Medicine, Assiut University, Assiut, Egypt 2021 05 30 2021 09 05 Background and Objectives: Gut microbiota is assumed to play an essential role in the pathogenesis of multiple sclerosis (MS). This study aimed to investigate the abundance of some gut microbiota among Egyptian patients with relapsing remitting multiple sclerosis (RR-MS). Materials and Methods: Forty cases of RR-MS diagnosed according to McDonald diagnostic criteria (2017) were recruited consecutively from the Department of Neurology, Assiut University Hospitals. The results were compared with 22 healthy age and sex matched control subjects. DNA was extracted from stool and measures made of concentration and copy number of bacterial organisms by real-time PCR using group specific primers for 16S rRNA targeting predominant genera of gut microbiota previously hypothesized to participate in MS pathogenesis. Results: The mean age was 31.4 ± 8.8 yrs; 75% of the patients were women. The mean and SD of EDSS score was 3.43 ± 1.35. Seven cases had cervical cord plaques (17%). There were significantly increased copy numbers of Desulfovibrio, Actinobacteria, Firmcutes, and Lactic acid bacteria in patients compared with the control group. In contrast there was a significantly lower level of Clostridium cluster IV in the patients. Patients who had EDSS < 3.5 had a significantly higher copy number of Actinobacteria, Bacteroidetes, and Bifidobacterium, compared with patients who had EDSS > 3.5. There was a significant negative correlation between duration of illness and copy number of Firmcutes, Akkermansia, and Lactic acid bacteria (P = 0.01, 0.04, and 0.004 respectively). Conclusion: The changes in gut microbiota are associated with exacerbation of MS disease. Disruption of the intestinal microbiota results in the depletion or enrichment of certain bacteria that may affect the immune balance leading to predisposition to MS. https://ijm.tums.ac.ir/index.php/ijm/article/view/3172 https://ijm.tums.ac.ir/index.php/ijm/article/download/3172/1388

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 642 652 Zahra Davoudi Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran Amirhossein Taromchi Department of Medical Biotechnology and Nanotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran Bahram Kazemi Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran Mojgan Bandehpour Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran Nariman Mosaffa Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran 2021 04 23 2021 09 20 Background and Objectives: Immunization is a promising strategy to combat against the life-threatening infections by Multi Drug Resistance Acinetobacter baumannii. In this study, we directed to design and evaluate the efficacy of a recombinant multi-epitope protein against this pathogen. Materials and Methods: Epitopes prediction was performed for candidate proteins OmpA and BAM complex (BamA, BamB, BamC, BamD, BamE) from A. baumannii, using immune-informatics tools with high affinity for the human HLA alleles. After expression and purification of the recombinant protein, its functional activity was confirmed by interaction with positive sera. Results: Cloning and expression of the desired multi-epitopes protein were verified. Circular Dichroism study showed the secondary structure and proper refolding of the recombinant protein was achieved and matched with computational prediction. There was a significant interaction between designed protein with antibodies presented in ICU patients' and staff's sera. Conclusion: The interaction of the recombinant protein with patients' sera antibodies suggests that it may be a promising determinant protein for immunization against of MDR A. baumannii. https://ijm.tums.ac.ir/index.php/ijm/article/view/3112 https://ijm.tums.ac.ir/index.php/ijm/article/download/3112/1389

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 653 663 Elnaz Harifi Mood Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran Alireza Japoni-Nejad Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran Mohammadreza Asadi Karam Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran Mohammad Pooya Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran Saeid Bouzari Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran Nader Shahrokhi Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran 2021 05 25 2021 08 17 Background and Objectives: This study aimed to investigate the accessible regions of the fimH mRNA using computational prediction and dot-blot hybridization to increase the effectiveness of antisense anti-virulence therapeutics against Uropathogenic Escherichia coli. Materials and Methods: We predicted the secondary structure of the E. coli fimH mRNA using the Sfold and Mfold Web servers and RNA structure 5.5 program. Considering the predicted secondary structure, accessible regions in mRNA of fimH were determined and oligonucleotides complementary to these regions were synthesized and hybridization activity of those oligonucleotides to the fimH Digoxigenin (DIG) labeled mRNA was assessed with dot-blot hybridization. Results: When searching the fimH gene in the GenBank database, two lengths for this gene was discovered in different strains of E. coli. The difference was related to the nine bases in the first part of the gene utilizing either of two translation initiation sites. Based on the bioinformatics analyses, five regions lacking obvious stable secondary structures were selected in mRNA of fimH. The result of dot-blot hybridization exhibited strongest hybridization signal between the antisense oligonucleotide number one and fimH labeled mRNA, whereas hybridization signals were not seen for the negative control. Conclusion: The results obtained here demonstrate that the region contains start codon of fimH mRNA could act as the potential mRNA target site for anti-fimH antisense therapeutics. It is recommended in the future both of utilizing translation initiation sites be targeted with antisense oligomers compounds. https://ijm.tums.ac.ir/index.php/ijm/article/view/3166 https://ijm.tums.ac.ir/index.php/ijm/article/download/3166/1390

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 664 670 Mahdiyar Iravancterium which produced 1.96 fold more protease over the parent strain. Conclusion: Random mutation by UV radiation is a simple and convenient method to increase the protease activity of Lysobacter enzymogenes. Furthermore, it seems that the middle time of exposure to UV, 90 s, was the best time because it can induce mutagenesis but did not hamper the bacteria growth and viability. https://ijm.tums.ac.ir/index.php/ijm/article/view/2306 https://ijm.tums.ac.ir/index.php/ijm/article/download/2306/1300

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 6 2020 12 16 607 615 Mohammad Reza Sarjoughian Department of Biotechnology, Faculty of New Sciences and Technologies, Semnan University, Semnan, Iran Fereshte Rahmani Department of Biotechnology, Faculty of New Sciences and Technologies, Semnan University, Semnan, Iran Shamsozoha Abolmaali Department of Biology, Faculty of Basic Science, Semnan University, Semnan, Iran Shakiba Darvish Alipour Astaneh Department of Biotechnology, Faculty of New Sciences and Technologies, Semnan University, Semnan, Iran 2020 04 14 2020 11 03 Background and objective: The great potential of bacteriophage for removing pathogen bacteria via targeting the cell wall is highly concerned. With a priority for drug-resistant, we screened endolysins  targeting Gram-negative bacteria to introduce a new antibacterial agent. The study was aimed to identify endolysins from the lysogenic phage of the Siphoviridea family in Bacillus subtilis. Materials and Methods: The Bacillus subtilis strain DDBCC46 was isolated from a preliminary antibacterial screening program. The endolysin(s) was extracted, concentrated with ammonium sulfate saturation, and their activity evaluated against the indicator bacteria. The phage particles was extracted from the bacteria using the minimum inhibition concentration of mitomycin C, followed by testing the phage inhibitory effect on the growth of indicator bacteria. The NCBI, Virus-Host DB, and EXPASY databases were used to obtain and confirm the sequences of the genes encoding PG hydrolases in Siphoviridea phages hosted in B. subtilis. Results: An  816 bp gene encoding an endolysin enzyme, was approved in the B. subtilis, DDBCC 46, with specific primers of Bacillus phage SPP1. The purified-endolysin indicated antibacterial activity against Klebsiella pneumoniae, Salmonella typhimurium, Proteus (sp), and Escherichia coli. SDS-PAGE profiling followed by silica gel purification, led to introduce lys4630 as a therapeutic product and food preservative. Conclusion: lys4630 showed specific effects on the very known gram-negative pathogens in clinics and food industries; E. coli, P. aeruginosa, Salmonella (sp). https://ijm.tums.ac.ir/index.php/ijm/article/view/2584 https://ijm.tums.ac.ir/index.php/ijm/article/download/2584/1301

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 6 2020 12 16 616 624 EN Sepideh Khalatbari-Limaki Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran Saeid Hosseinzadeh Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran Seyed Shahram Shekarforoush Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran Enayat Berizi Department of Food Hygiene and Quality Control, Nutrition Research Center, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran 2020 04 11 2020 10 17 Background and Objectives: Foodborne pathogens are among the serious problems all around the world and thus a novel and natural strategy to control and to inhibit such pathogens is highly demanded nowadays. The aim of this study was to isolate a specific bacteriophage of Escherichia coli O157:H7 from sewage in Fars province, Iran to determine its morphological and antimicrobial activities. Materials and Methods: In order to isolate the bacteriophage of E. coli O157:H7, 10 samples of slaughterhouse wastewaters were used. Double-Layer Agar method was employed to isolate the bacteriophage. To identify the fine structure of the bacteriophage, electron microscope was employed. Host range and antibacterial activity of the phage was also investigated, in vitro. Results: The morphological and biological characteristics of a virulent Siphoviridae phage, PI, are reported. It was found that infection of E. coli O157:H7 strains with this specific bacteriophage produce clear plaques. In the one-step growth analysis, it was confirmed that the phage has been characterized with a very short rise period (around 15 min), an average burst size of 193 PFU/cell, high infectivity and potent lytic action. The bacteriolytic activity of PI was also investigated, in vitro. It was also clarified that at the MOI of 100, 10 and 1, the phage rapidly lysed the bacterial cells within 0.5 or 2 h. Conclusion: These results indicate that the phage PI is a newly discovered phage against E. coli O157:H7 in Iran which may be recommended to use as bio-control purposes. https://ijm.tums.ac.ir/index.php/ijm/article/view/2577 https://ijm.tums.ac.ir/index.php/ijm/article/download/2577/1302

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 6 2020 12 16 625 628 Tahir Belice Department of Internal Medicine, University of Health Sciences, Izmir Bozyaka Training and Research Hospital, Izmir, Turkey Ismail Demir Department of Internal Medicine, University of Health Sciences, Izmir Bozyaka Training and Research Hospital, Izmir, Turkey 2020 06 19 2020 10 25 Background and Objectives: In a Turkish cohort study, we revealed first time in literature the gender differences in admission to hospital and rates of mortality for diabetic patients with COVID-19. Materials and Methods: The demographics, length of stay, mortality rates and concomitant chronic metabolic diseases of 152 patients diagnosed with COVID-19 were found in our hospital electronic document system (Probel) and recorded in excel files for further statistical analysis. Results: In the mortality group (n:22), the numbers of men and women were 9 (40.9%) and 4 (18.2%), respectively. Comparing gender rates in diabetic group, the mortality risk of diabetic men was higher and statistically significant (p<0.05, Pearson Chi-square value:7.246). Conclusion: We hope that the findings of this research will give scientists an idea of gender differences in viral pandemics for further studies. https://ijm.tums.ac.ir/index.php/ijm/article/view/2677 https://ijm.tums.ac.ir/index.php/ijm/article/download/2677/1303

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 6 2020 12 16 629 635 Seyedeh Zahra Mousavi Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran Vahdat Poortahmasebi Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran AND Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran Talat Mokhtari-Azad Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran Shohreh Shahmahmoodi Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran Mohammad Farahmand Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran Mahdieh Farzanehpour Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran Somayeh Jalilvand Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran 2020 06 26 2020 10 25 Background and Objectives: Human papillomavirus (HPV) is the fourth most common cause of cervical cancer (CC). The aim of the present study was to investigate gene expression levels of previously identified transcriptional signatures for malignant and non-malignant CC. Materials and Methods: To validate of previously analyzed microarray gene expression data, we selected two hub genes (CDK1 and PLK1) and four differentially expressed mRNAs that were common in pre-malignant-normal and malignant-pre-malignant networks (SMS, NNT, UHMK1 and DEPDC1). To this purpose, the study included women diagnosed histologically with malignant CC (n=15), pre-malignant (n=15), and normal subjects (n=15). The expression of six host genes and viral E6/E7 genes were measured by quantitative Real-Time PCR. Results: The results showed higher expression of CDK1/PLK1 hub genes and SMS, NNT and UHMK1 genes in malignant CC group than non-malignant CC group and normal group. A positive correlation was observed between gene expression of viral E6/E7 oncogenes and UHMK1 gene. Conclusion: Dysregulation of several mRNA signatures are a common feature of CC and can be potentially used as diagnostic and prognostic biomarkers as well as can be applied to therapeutic targets for CC treatment. https://ijm.tums.ac.ir/index.php/ijm/article/view/2691 https://ijm.tums.ac.ir/index.php/ijm/article/download/2691/1304

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 6 2020 12 16 636 643 EN Masoud Mardani Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medial Sciences, Tehran, Iran Sara Abolghasemi Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medial Sciences, Tehran, Iran Shiva Shabani Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medial Sciences, Tehran, Iran Farzaneh Tavakoli Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran Anahita Saeedi Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran Sayeh Parkhideh Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran Abbas Hajifathali Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran 2020 05 23 2020 11 03 Background and Objectives: Infections is yet one of the life-threatening complications of the hematopoietic stem cell transplantation (HSCT). The myeloablative and immunosuppressive conditioning regimens, which are administered before HSCT, dampen the defense capacity of the recipients’ immune systems. In this condition, opportunistic infections, especially viral infections such as cytomegalovirus (CMV) can be reactivated and cause morbidity and mortality in HSCT patients. Here, we aimed to find out any possible relationship between types of conditioning regimen and CMV reactivation in allogeneic HSCT patients. Materials and Methods: We retrospectively analyzed the data of 145 CMV-seropositive cases out of total 201 allo-HSCT patients, including age, gender, underlying disease, conditioning regimen, prophylaxis regimen and occurrence of acute graft-versus-host disease (aGVHD) to evaluate their roles in CMV reactivation. Results: Our result showed that conditioning regimen containing Busulfan and Fludarabine (P=0.003) or Cyclophosphamide (P=0.02) significantly decrease the early CMV reactivation. Patients who developed aGVHD (P=0.003) and those who received anti-thymocyte globulin (ATG) as prophylaxis regimen (P=0.002), had 1.84 and 2.63 times higher risks of CMV reactivation, respectively. Conclusion: Our findings suggest the conditioning regimen, aGVHD and ATG as influencing factors for early CMV reactivation post-HSCT which should be considered in the future studies. https://ijm.tums.ac.ir/index.php/ijm/article/view/2640 https://ijm.tums.ac.ir/index.php/ijm/article/download/2640/1305

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 6 2020 12 16 644 649 Anitha Madhavan Department of Microbiology, Government TD Medical College, Alappuzha, Kerala, India Arun Sachu Department of Microbiology, Believers Church Medical College, Thiruvalla, Kerala, India Anu Balakrishnan Department of Virology, National Institute of Virology, Alappuzha, Kerala, India Anu Vasudevan Department of Biostatistics, Amrita Institute of Medical Sciences and Research Centre, Kochi, Kerala, India Sobha Balakrishnan Department of Microbiology, Government TD Medical College, Alappuzha, Kerala, India Jayalakshmi Vasudevapanicker Department of Microbiology, Government TD Medical College, Alappuzha, Kerala, India 2020 08 02 2020 11 11 Background and Objectives: Hepatitis C is the most common hepatotropic viral infection that affects patients on maintenance hemodialysis. Most of the laboratories in India depend on HCV antibody detection by ELISA. PCR based studies on detection of HCV RNA among haemodialysis patients are very scanty in India. The current study was undertaken to find the prevalence of HCV among haemodialysis patients by ELISA and PCR. Materials and Methods: This prospective study was conducted from January to May 2018 in a total of 100 samples. Patients more than 18 years of age, who had undergone at least 15 sessions of dialysis were enrolled in the study. All samples were screened for HCV antibody by ELISA and HCV RNA by PCR. Data regarding age and gender of the patients, history of blood transfusion, duration of hemodialysis, total bilirubin levels were collected from medical records. Results: Among the 100 samples, only one was positive for HCV antibody by ELISA. Eight samples were positive for HCV RNA by PCR. In this study 62.5% of the HCV positives had a previous history of blood transfusion. Duration of dialysis was more among the HCV positive group but there was no statistical significance. Conclusion: This is the first study from the southern state of Kerala in India showing the prevalence of HCV among hemodialysis patients by PCR. Our study showed an overall HCV prevalence of 8% by PCR. All the PCR positive samples were negative by 3rd generation ELISA which is an alarming finding and further justifies the need for PCR for detecting HCV. https://ijm.tums.ac.ir/index.php/ijm/article/view/2732 https://ijm.tums.ac.ir/index.php/ijm/article/download/2732/1306

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 6 2020 12 16 650 656 EN Samira Amini Student of Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran Mazaher Khodabandehloo Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran AND Department of Microbiology, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran 2020 02 05 2020 11 13 Background and Objectives: Co-infection of hepatitis C virus (HCV) with human immunodeficiency virus (HIV) is increasing due to similar transmission pathways. Chronic HCV infection is the most common complication among HIV-infected individuals. Information on the frequency of HCV infection on Iranian HIV-infected individuals is scarce. The aim of this study was the detection of HCV prevalence and genotypes among HIV-infected people in Sanandaj, Iran. Materials and Methods: In this cross-sectional study, whole blood samples were taken from 185 HIV positive individuals referring to Consultation Center for Behavioral Diseases, Sanandaj, Iran. The ELISA test was done on samples for anti-HCV antibodies. RNA was extracted from only anti-HCV antibody positive samples. An RT-PCR test was conducted to detect HCV RNA. Genotypes of HCV were detected by melting curve analysis by specific primers and probes. Test results and demographic information were analyzed by SPSS software. Results: The mean age of individuals was 39.3 ± 9.4 years. Out of 185 individuals 99 (53.5%) were positive for anti-HCV antibodies. Out of 99 antibody positive individuals, 44 had HCV RNA. Among 44 RNA positive individuals, genotypes and subtypes of HCV were as 26 (59.1%) 1a, 17 (38.6%) 3a and one (2.2%) 4. There was a significant association between anti-HCV antibody and demographic variables including, age, gender, occupation, and CD4+ T-cell count (p = 0.0001). Conclusion: The present study reveals that HIV/HCV co-infection is high in the study population. It is recommended similar studies should be done in other HIV infected populations for management of HIV/HCV co-infection. https://ijm.tums.ac.ir/index.php/ijm/article/view/2474 https://ijm.tums.ac.ir/index.php/ijm/article/download/2474/1307

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 6 2020 12 16 657 660 Safin Hussein Department of Medical Laboratory Science, University of Raparin, Rania, Kurdistan, Iraq AND Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran Karzan Qurbani Department of Medical Laboratory Science, University of Raparin, Rania, Kurdistan, Iraq Haide