Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 15 336 342 EN Esmaeil Mohammadnejad Research Center for Antibiotic Stewardship and Antimicrobial Resistance, Department of Medical-Surgical Nursing and Basic Sciences, School of Nursing and Midwifery, Tehran University of Medical Sciences, Tehran, Iran Arash Seifi Research Center for Antibiotic Stewardship and Antimicrobial Resistance, Department of Infectious Disease, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran Reza Ghanei Gheshlagh Social Determinants of Health Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran Amir Aliramezani Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland Samrand Fattah Ghazi Department of Anesthesiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran Mohammadreza Salehi Research Center for Antibiotic Stewardship and Antimicrobial Resistance, Department of Infectious Disease, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran Seyed Ali Dehghan Manshadi Department of Infectious Disease and Tropical Medicine, School of Medicine, Iranian Research Center for HIV/AID, Iranian Institute for reduction of High- Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran Amirhossein Orandi Department of Anesthesiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran 2023 04 07 2023 05 11 Background and Objectives: Antibacterial resistance (AMR) is a serious threat and major concern, especially in developing countries. Therefore, we aimed to determine phenotypical patterns of resistance to antibiotics in COVID-19 patients with associated bacterial infection in intensive care units. Materials and Methods: In this cross-sectional study, 6524 COVID-19 patients admitted for more than 48 h in the ICUs of Imam Khomeini Complex Hospital (IKCH) in Tehran from March 2020 to January 2022 were included in the study with initial diagnosis of COVID-19 (PCR test and chest imaging). Data were collected regarding severity of the illness, primary reason for ICU admission, presence of risk factors, presence of infection, length of ICU and hospital stay, microbial type, and antibiotic resistance. In this study, the pattern of antibiotic resistance was determined using the Kirby–Bauer disk diffusion method. Results: In this study, 439 (37.5%) were ventilator-related events (VAEs), and 46% of all hospitalized patients had an underlying disease. The most common microorganisms in COVID-19 patients were carbapenem resistant Klebsiella pneumoniae (KPCs) (31.6%), Escherichia coli (E. coli) (15.8%), and Acinetobacter baumannii (A. baumannii) (15.7%), respectively. Prevalence of vancomycin-resistant enterococci (VRE) and KPCs were 88% and 82%, respectively. Conclusion: A study on AMR surveillance is the need of the hour as it will help centers to generate local antibiograms that will further help formulate national data. It will guide doctors to choose the appropriate empiric treatment, and these studies will be the basis for establishing antimicrobial surveillance and monitoring and regulating of the use of antimicrobials. https://ijm.tums.ac.ir/index.php/ijm/article/view/4182 https://ijm.tums.ac.ir/index.php/ijm/article/download/4182/1574

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 343 349 EN Sajad Hassanzadeh Department of Internal Medicine, School of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran Seyed Sajjad Khoramrooz Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran Farzad Mazloomirad Student Research Committee, Yasuj University of Medical Sciences, Yasuj, Iran Asghar Sharifi Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran Narges Roustaei Department of Epidemiology and Biostatistics, School of Health and Nutrition Sciences, Social Determinants of Health Research Center, Yasuj University of Medical Sciences, Yasuj, Iran Mohammad Gholamnezhad Department of Internal Medicine, School of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran Esmaeel Jamshidnejad Student Research Committee, Yasuj University of Medical Sciences, Yasuj, Iran 2022 12 22 2023 05 11 Background and Objectives: Community-acquired pneumonia (CAP) is one of the most common life-threatening infections, occurring in the community or within the first 48 hours of a patient's hospitalization. The present study aimed to investigate the frequency of pathogenic bacteria and their antibiotic resistance pattern in the sputum of patients with community-acquired pneumonia in Yasuj from 2018 to 2019. Materials and Methods: In the present study, 128 patients with CAP were included. Under aseptic conditions clinical samples including sputum collected from each patient were sent to the Microbiology Laboratory. Specific culture media and biochemical tests were used to identify the bacteria. Antimicrobial resistance patterns of the isolates were examined by disc diffusion. DNA was extracted from sputum using the phenol-chloroform method. The PCR method was used for the molecular detection of bacteria. Data were analyzed using SPSS software version 22 and the chi-square test. Results: The most common clinical symptoms in patients were sputum (68.8%), fever (64.1%), shortness of breath (60.2%), cough (50.8%), and chest pain (24.2%). A total of 133 bacteria were identified by culture and 117 bacteria by PCR. In the current study, the most prevalent organisms were Streptococcus pneumoniae (24.1%), Hemophilus influenzae (18%), Staphylococcus aureus (13.5%), and Moraxella catarrhalis (11.4%). Antibiogram test showed that most of the Gram-negative bacteria were resistant to levofloxacin (22.6%), rifampin (20.8%) and ceftriaxone (17%), and the highest resistance rate to clindamycin (43.1%), ciprofloxacin (43.1%) and amoxicillin (41.4%) were detected in the Gram-positive bacteria. Cefepime was the most effective antibiotic against Gram negative bacteria. Conclusion: S. pneumoniae was the most prevalent bacteria identified by culture and PCR methods in patients with CAP, indicating an important role of this bacterium in the pathogenesis of CAP. According to the results, cefepime can be used to treat patients with CAP with Gram-negative bacteria. In the present study, S. pneumoniae, S. aureus, P. aeruginosa, H. influenzae, M. catarrhalis, and K. pneumoniae have been isolated from the CAP patient population with varying frequencies. This is consistent with various studies in different parts of the world. https://ijm.tums.ac.ir/index.php/ijm/article/view/4052 https://ijm.tums.ac.ir/index.php/ijm/article/download/4052/1575

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 350 358 Fatemeh Nayeri Maternal-Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran Hosein Dalili Breastfeeding 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 Nahid Farrokhzad Maternal-Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran Kosar Abouhamzeh Students' Scientific Research Center (SSRC), 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 2023 02 10 2023 06 05 Background and Objectives: This study aimed to investigate epidemiology of Staphylococcus epidermidis (S. epidermidis) and Acinetobacter baumannii (A. baumannii) infections in neonatal intensive care unit (NICU) in a period of 8 years. Materials and Methods: This retrospective cohort study was conducted on 46 cases of nosocomial infection by S. epidermidis, and 44 neonates with A. baumannii in NICU of Valiasr hospital, Iran. Results: The trend of A. baumannii and S. epidermidis infection were as follows: 1 and 7 in 2014, 11 and 7 in 2015, 20 and 11 in 2016, 1 and 4 in 2017, 4 and 6 in 2018, 4 and 4 in 2019, 0 and 1 in 2020, and 3 and 6 in 2021-March 2022 respectively. Mortality proportion (%) in neonates with S. epidermidis and A. baumannii infection was at 8.3 and 32.1, respectively. There was a strong positive correlation between number of infected neonates in month and average of prescribed antibiotics before incidence of infection in every baby in that month. Fluconazole prescription before incidence of infection were associated with the A. baumannii infection in month too. Amikacin prescription had adjusted correlation on increasing of A. baumannii and S. epidermidis infection in month. Conclusion: It seems reducing of hospitalization duration and medication prescriptions management plays an important role in reducing of nosocomial infections. https://ijm.tums.ac.ir/index.php/ijm/article/view/4123 https://ijm.tums.ac.ir/index.php/ijm/article/download/4123/1576

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 359 372 EN Sepide Kadivarian Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran Mosayeb Rostamian Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran Shirin Dashtbin Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Sara Kooti Department of Basic Sciences, Behbahan Faculty of Medical Sciences, Behbahan, Iran Zahra Zangeneh Department of Biology, Ilam Branch, Islamic Azad University, Ilam, Iran Ramin Abiri Fertility and Infertility Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran Amirhooshang Alvandi Department of Microbiology, School of Medicine, Medical Technology Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran 2023 02 21 2023 05 20 Background and Objectives: Microorganisms producing Metallo-Beta-Lactamase (MBL) are a threat and cause of concern as they have become one of the most feared resistance mechanisms. This study was designed to explore the prevalence of MBL production in clinical isolates of Gram negative bacteria using phenotypic MBL detection. Materials and Methods: A total of 248 isolates were collected from various clinical samples and were evaluated for carbapenem resistance and MBL production. All strains were screened for MBL production using Double Disk Confirmatory Test (DDCT). Results: The results of screening for MBL production using phenotypic disk diffusion method showed that in the 85 isolates were carbapenemase positive; including, 10 (16.1%) Klebsiella pneumoniae, 9 (14.5%) Escherichia coli, 58 (93.6%) Acinetobacter baumannii, and 8 (12.9%) Pseudomonas aeruginosa isolates. Also, 83 (97.6) Carbapenemase-producing isolates were resistant to at least four classes of antimicrobials (MDR). Conclusion: A. baumannii was the most common carbapenem resistant bacterium in medical centers in Kermanshah. Significant multiple drug resistance (MDR) incidence was observed compared to different classes of antibiotics. https://ijm.tums.ac.ir/index.php/ijm/article/view/4104 https://ijm.tums.ac.ir/index.php/ijm/article/download/4104/1577

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 373 382 Khatereh Faghihi 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 Saeed Tajbakhsh Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran; The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran Moradali Fouladvand Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran Behrouz Latifi Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran Forough Yousefi Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran; The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran 2022 12 20 2023 03 16 Background and Objectives: Plasmid-mediated AmpC producers are considered an increasing concern. The aim of this study was to investigate the prevalence of plasmid-mediated AmpC β-lactamases (pAmpCs) in Klebsiella pneumoniae isolates. Materials and Methods: A total of 228 clinical isolates of K. pneumoniae were collected in Bushehr province, Iran, from December 2017 to February 2019. Cefoxitin disks were applied for screening AmpC-producing isolates. Furthermore, 3 phenotypic confirmatory tests including combine disk test (CDT), double disk synergy test (DDST) and modified three dimensional test (M3DT) were used. Finally, the presence of pAmpC genes was tested by multiplex PCR. Results: We identified 18 pAmpC-KP isolates among the 228 isolates (7.9%): 12 DHA (66.6%) and 6 CMY (33.3%). In the present study only 47% of cefoxitin-resistant isolates were pAmpC producers. The sensitivity of CDT, DDST, and M3DT was 89%, 67% and 100% and the specificity was 90%, 90% and 85%, respectively. In addition, M3DT displayed a higher rate of efficiency (92%) than CDT (89%) and DDST (79%) in detecting plasmid-meditated AmpC producers. Conclusion: DHA was the most prevalent pAmpC beta-lactamase in this study. DDST and CDT tests proved inefficient to detect two and six pAmpC producers, respectively, while M3DT represented the best overall performance. https://ijm.tums.ac.ir/index.php/ijm/article/view/4048 https://ijm.tums.ac.ir/index.php/ijm/article/download/4048/1578

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 383 391 Reza Ghotaslou Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran Shabnam Baghbani Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran Pardis Ghotaslou Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran Solmaz Mirmahdavi Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran Hamed Ebrahimzadeh Leylabadlo Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran 2022 10 03 2023 05 11 Background and Objectives: The immediate emergence of resistant bacteria poses an increasingly growing problem to human society and the increasing prevalence of antibiotic resistance in Escherichia coli strains is one of the most important health problems. This study aimed to review the molecular epidemiology of drug resistance among clinical isolates of E. coli in north-west portion of Iran Azerbaijan. Materials and Methods: A complete of 219 clinical isolates of E. coli had been collected from the various clinical samples. The disk diffusion and agar dilution assays were used to determine antimicrobial susceptibility. The presence of antibiotics resistance genes was carried out by the PCR method. Results: The highest susceptibility was shown to imipenem (3%) and fosfomycin (3%), and the most antibiotic resistance was presented to ampicillin (99%). The highest frequent ESBL gene among isolates was blaCTXM-15 in 70% followed by blaCMY-2 in 67%, and blaTEM-1 in 46%. The most common fluoroquinolone (FQ) resistance genes were oqxB (34%), followed by oqxA (25%), and qnrB (18%). The frequency of tetracycline resistance genes (tetA, tetB, tetC, and tetD) were detected in 24.8%, 31.6%, 1.8%, and 4.2%, respectively. The highest frequent genes to fosfomycin were fosA 10%, fosA3 30%, fosC 40%, and fosX 20%. The dominant founded aminoglycosides resistant genes were armA (12.96%) and npmA (4.93%). Conclusion: The prevalence of antibiotics resistance in the tested E. coli isolates was high in Azerbaijan, Iran and these findings showed that E. coli is one of the major drug-resistant pathogens. https://ijm.tums.ac.ir/index.php/ijm/article/view/3927 https://ijm.tums.ac.ir/index.php/ijm/article/download/3927/1579

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 392 400 Gholamali Riahi Department of Surgery, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran Ebrahimeh Koohsari Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran Seyed Sedigheh Hosseini Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran 2022 12 28 2023 03 16 Background and Objectives: Sternum infection increases the time of the patients stay in the hospital and, as a result, increases the treatment costs. This study aimed to evaluate the fungal and bacterial co-infection in the superficial and deep sternal wounds after open cardiac surgery and its relationship with risk factors, as sternal infection increases the time of the patient's stay in the hospital and, as a result, increases the treatment costs. Materials and Methods: Data were collected using a questionnaire and sampling with two swabs after open heart surgery and hospitalization from 21 March 2018 to 20 March 2019 and sent to the laboratory for diagnosis of microorganisms effective in wound infection. Susceptibility testing for fluconazole and specific antibiotics was performed by the disk diffusion method. Results: Out of 210 patients studied, 2% of patients had deep sternal wound infections. The most common coinfection fungal and bacterial agents in sternal wounds were caused by Staphylococcus aureus with Candida glabrata 4% and Escherichia coli with Candida albicans 2%. S. aureus and E. coli showed the highest antibiotic susceptibility to the antibiotics ciprofloxacin, norfloxacin, meropenem, and imipenem. Candida glabrata and Candida albicans had the highest rate of resistance to fluconazole. Conclusion: According to the results of this study, patients on the 7th day in the cardiac care unit (CCU) and the 28th day are at higher risk of getting confection of fungi with bacteria in the sternal wound. Therefore, timely and appropriate antibiotic therapy, including the use of appropriate antibiotics, can be an important step in the patient's recovery. https://ijm.tums.ac.ir/index.php/ijm/article/view/4058 https://ijm.tums.ac.ir/index.php/ijm/article/download/4058/1580

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 401 407 Leila Heidari Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran Gholamreza Rafiei Dehbidi Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran Ali Farhadi Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran Golnar Sami Kashkooli Shiraz Referral Mycobacteriology Laboratory, Shiraz University of Medical Sciences, Shiraz, Iran Farzaneh Zarghampoor Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran Sepide Namdari Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran Noorossadat Seyyedi Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran Saeid Amirzadh Fard Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran Abbas Behzad-Behbahani Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran 2023 01 14 2023 04 24 Background and Objectives: In clinical diagnostics, molecular methods are used to detect Mycobacterium tuberculosis bacilli (MTB) and to distinguish them from non-tuberculous mycobacteria (NTM). They are also used to make the right treatment decision for the patient as soon as possible. The aim of this study was to establish a rapid and novel multiplex PCR (mPCR) assay for the detection and differentiation of MTB and NTM in a single tube. Materials and Methods: 100 sputum samples positive for acid-fast bacilli (AFB) were included in this study. Mycobacterial culture, biochemical tests, and antibiotic susceptibility testing were performed on samples. After alkaline decontamination, total DNA was extracted from the samples. A primer pair targeting the rpoB gene, encoding the beta-subunit of RNA polymerase, was used to detect MTB and NTM, amplifying a 235-bp fragment of MTB and a 136-bp sequence of NTM. A pair of primers targeting a 190-bp fragment of the IS6110 region of MTB was also used to confirm the results. The sensitivity and specificity of the mPCR assay were evaluated using DNA extracted from standard strains. The amplified products were then analyzed by conventional agarose gel electrophoresis. Results: Of 100 AFB smear-positive sputum samples, 92 MTB DNA, 7 NTM DNA, and one mixed-infection sample were identified in a single tube using mPCR assay. There was no correlation between the AFB degree of smear positivity and PCR results. Of seven NTM isolates, 6 (86%) were resistant to rifampin, isoniazid, and ethambutol, the three first-line anti-tuberculosis drugs. Conclusion: A single-tube mPCR assay based on the rpoB gene provides a rapid and reliable means of detecting and differentiating MTB and NTM in sputum specimens. https://ijm.tums.ac.ir/index.php/ijm/article/view/4085 https://ijm.tums.ac.ir/index.php/ijm/article/download/4085/1581

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 408 413 Behnood Haji Sheikhzadeh Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran Leila Rahbarnia Department of Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran Alireza Dehnad Department of Bacterial Disease Research, Razi Vaccine and Serum Research Institute, AREEO, Tabriz, Iran Behrooz Naghili Department of Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran Parvaneh Saffarian Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran 2022 10 05 2023 05 16 Background and Objectives: Methicillin-resistant Staphylococcus aureus (MRSA) is one of the main causes of high mortality and morbidity in hospitals. This study was aimed to examine virulence factors, molecular typing, and the antibiotic resistance pattern of MRSA isolates in hemodialysis patients and healthy communities. Materials and Methods: Total of 231 and 400 nasal samples were obtained from hemodialysis patients and healthy communities, respectively. Virulence factors profile was examined in two groups by PCR reaction. Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR) was used as a molecular typing approach. Results: Overall, 35.49% (82/231) of hemodialysis patients were positive for S. aureus, and 47.56% (39/82) of isolates were positive for mecA. In a healthy community, 15% (60/400) of samples were positive for S. aureus, and 36.66% (22/60) were positive for mecA. The frequency of MDR was significantly higher in patients group (p-value < 0.00001). The frequency of pvl (p.value = 0.003932, P<0.05) and tsst-1 (p.value = 0.003173, p < .05) were significantly higher in patients group. The highest frequency virulence factors in healthy individuals were related to hla (68.33%, 41/60), hlb (53.33%, 32/60), and Acme/arcA (46.66%) genes. Two groups were clustered by the ERIC-PCR method into 7 clusters and 2 single isolate with a 0.74 similarity index. Based on the results, each cluster was combination with healthy and patient isolates. Conclusion: Our findings indicate a notable variation in the frequency of virulence factors between S. aureus isolates obtained from dialysis patients and the healthy community. https://ijm.tums.ac.ir/index.php/ijm/article/view/3932 https://ijm.tums.ac.ir/index.php/ijm/article/download/3932/1582

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 414 424 Rusul Al-Kahachi Department of Scholarships and Cultural Relationship, Ministry of Higher Education and Scientific Research, Baghdad, Iraq Sura Al-Asadi Department of Laboratory Techniques, College of Health and Medical Techniques, Middle Technical University, Baghdad, Iraq Zainab Ali Department of Laboratory Techniques, College of Health and Medical Techniques, Middle Technical University, Baghdad, Iraq Jamila Rampurawala Department of Applied Genetics, The Oxford College of Science, Bangalore, India 2022 12 22 2023 04 02 Background and Objectives: The study aimed to investigate whether Achromobacter mucicolens IA strain biofilm formation, which contributes to antibiotic resistance, could be enhanced by readily available nutrient sources like carbohydrates and environmental factors such as pH and NaCl. Additionally, the study aimed to identify any inherent genes that support biofilm formation in this strain, which is an opportunistic pathogen that affects immunocompromised patients and is resistant to many antibiotics. Materials and Methods: Biofilm growth in different carbohydrate, pH, and NaCl concentrated media was measured using crystal violet microtiter assay. All the treatments were subjected to biostatistics analysis for normality, Test of Homogeneity, one way ANOVA analysis. Whole-genome sequencing of our IA strain was conducted to identify various gene sequences. Results: Biofilm formation was measured at different carbohydrate concentrations, and the optimum biofilm formation was observed at 3M glucose and 0.5M NaCl, while the lowest results were seen at 2M maltose concentration. Whole-genome sequencing identified potential genes involved in biofilm formation, pathogenicity, protein metabolism, flagellar motility, cell wall component synthesis, and a multidrug efflux pump. Conclusion: These findings suggest that biofilm formation is influenced by extrinsic and intrinsic factors, which could aid in the development of effective treatments for resistant infections. https://ijm.tums.ac.ir/index.php/ijm/article/view/4049 https://ijm.tums.ac.ir/index.php/ijm/article/download/4049/1583

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 425 432 Alireza Keyhanian Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran Mojgan Mohammadimehr Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran Farshad Nojoomi Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran Hamed Naghoosi Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran Mehdi Shakouri Khomartash Medical Biotechnology Research Center, Aja University of Medical Sciences, Tehran, Iran Mohsen Chamanara Toxicology Research Center, Aja University of Medical Sciences, Tehran, Iran 2023 02 07 2023 04 30 Background and Objectives: Biosurfactants are amphiphilic surface-active agents that mainly produced by various microorganisms. In this study, the anti-biofilm and inhibition of bacterial adhesion activities of two bacterial biosurfactants were investigated. Materials and Methods: After extraction and evaluation of Bacillus cereus and Serratia nematodiphila biosurfctants, inhibition of bacterial adhesion and anti-biofilm effects of them on Staphylococcus aureus and Pseudomonas aeruginosa were determined. Results: On average, the synergistic effect of two bacterial biosurfactants, caused about 60% decrease in adhesion and about 80% decrease in biofilm formation of S. aureus and P. aeruginosa. Conclusion: The results of this study showed that combination of B. cereus and S. nematodiphila biosurfactants would increase the potential of attachment inhibition and biofilm eradication with very low toxicity. https://ijm.tums.ac.ir/index.php/ijm/article/view/4117 https://ijm.tums.ac.ir/index.php/ijm/article/download/4117/1584

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 433 438 Mohammed Al-Saadi Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Al-Qadisiyah, Al-Diwaniyah, Iraq Dhama Al-Sallami Department of Physiology, Pharmacology and Biochemistry, College of Veterinary Medicine, University of Al-Qadisiyah, Al-Diwaniyah, Iraq Amjed Alsultan Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Al-Qadisiyah, Al-Diwaniyah, Iraq 2023 02 08 2023 06 05 Background and Objectives: Anaplasmosis is a zoonotic disease caused by Gram- negative bacterium from Anaplasmataceae family. Anaplasma causes high economic losses worldwide. 16S rRNA analysis was used to diagnose Anaplasma platys in Cattle. Phylogenetic tree and estimation of evolutionary divergence between A. platys isolates were performed. Materials and Methods: A total of 60 blood samples were collected from a cattle farm in AL- Diwaniyah province. 16S rRNA gene was identified using nested PCR. Overall, 40% of cattle that were chosen to collect the blood were identified to be infected with A. platys. Results: The results have shown presence of targeting partial region of 16S rRNA gene in 24 samples out of 60. Sequencing results of 10 samples have revealed that the phylogenetic tree was divided in to two separate clades. Five isolates of A. platys- Iraq (accession no. OP646782, OP646783, OP646784, OP646790, and OP646791) were located in one clade with the A. platys- China (accession no. MN193068.1). While, five isolates (accession no. OP646785, OP646786, OP646787, OP646788, OP646789) were in different clade with two isolates of A. platys- Africa and A. platys- Zambia in distinct branches, close to the Rickettsiales. Conclusion: The phylogenetic study of A. platys sequences indicated that the isolates were collected from a cattle farm in Al- Dewaniyah were similar and close related to A. platys- China, A. platys- Zambia and A. platys- Africa). This study suggests that cattle can be considered a reservoir of A. platys. https://ijm.tums.ac.ir/index.php/ijm/article/view/4121 https://ijm.tums.ac.ir/index.php/ijm/article/download/4121/1585

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 439 447 Mohammad Ebrahim Goli Mehdi Abadi Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran Ahmad Hosseini-Safa Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran Sina Habibi Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran Mohammadreza Dehghan Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran Mohamad Javad Forouzani-moghaddam Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran Mojgan Oshaghi Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran 2023 02 19 2023 06 06 Background and Objectives: The lactobacilli are abundant in honey, helping protect against pathogens and providing antimicrobial properties. This study aimed to isolate lactobacillus species from different honey regions and evaluate their potential probiotic properties. Materials and Methods: Eighty-eight samples were collected from different regions, including the northern, central, and southern areas, and obtained through retail stores. All samples were independently examined for the presence of Lactobacillus using both culture and real-time PCR methods. Probiotic tests were performed on the isolated Lactobacillus strains, including hemolytic activity, bile, acid, and pepsin resistance. Additionally, the antibiotic resistance of the obtained strains was investigated using seven different antibiotics. Results: Thirteen Lactobacillus isolates were obtained from 7 (8.0%) honey samples. Of these, eight isolates were identified as L. plantarum (61.54%), four isolates as L. rhamnosus (30.77%), and one isolate as L. acidophilus (7.69%). All strains were devoid of hemolytic activity, and three isolates (23.07%) were found to be resistant to acid, while 2 (15.38%) showed resistance to bile and pepsin. All isolates were resistant to vancomycin (100%). Additionally, only one strain exhibited resistance to all tested antibiotics. Furthermore, the present study demonstrates a significant association (p-value<0.05) between the presence of Lactobacillus in various regions of Iran. Conclusion: Various factors, such as climatic conditions and geographical location, can influence honey's composition and microbial diversity. Identifying and isolating potential probiotic species in honey could significantly expand their use in the food and pharmaceutical industries, offering numerous health benefits and potential therapeutic applications. https://ijm.tums.ac.ir/index.php/ijm/article/view/4131 https://ijm.tums.ac.ir/index.php/ijm/article/download/4131/1586

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 15 3 2023 06 16 448 455 Mohsen Al-Zubaidi Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran Seyed Masoud Hosseini Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran Mohsen Al-Roudhan Department of Pathological Analysis Techniques, Faculty of Medical Technology, Najaf Islamic University, Diwaniyah, Iraq Maather Al-Harmooshee Department of Pathology, College of Medicine, University of Al Qadisiya, Diwaniyah, Iraq 2024 10 22 2025 02 04 Background and Objectives: Human cytomegalovirus (HCMV) infection is the most common cause of congenital infection during pregnancy. It is a major concern worldwide with a wide range of clinical outcomes in fetuses and newborns due to HCMV reactivation or reinfection during pregnancy. Primary maternal infection is best diagnosed by examining IgM and IgG antibodies. The current study aimed epidemiology survey of congenital HCMV infection in pregnant women in Diwaniyah. Materials and Methods: 600 blood samples were collected from pregnant women, between 18-45 years old, in Diwaniyah Governorate for 12 months, from January to December 2022, in regards to their place of residence (urban or rural). All samples were monitored for both IgG and IgM antibodies against HCMV using rapid test and ELISA. Results: Our findings showed a high positive rate for IgG (95.7%) and (96.2%) and a positive rate for IgM (1.5%) and (1.8%) for rapid test and ELISA, respectively. The highest IgG positive rate was in the age group 26-35 years (43.33%), while the lowest rate (13.0%) was in the age group 36-45 years. The HCMV infection rate in rural and urban areas were (96.48%) and (95.26%), respectively, with no significant differences (P value>0.05). Also, the rate of miscarriages among pregnant women infected with HCMV was 28.83%, and the highest infection rate (30.51%) was recorded in the age group 26-35 years. Conclusion: The prevalence of HCMV infection and its related miscarriage among the studied population is relatively high with the highest rate in the age group of 26-35 years. https://ijm.tums.ac.ir/index.php/ijm/article/view/5096 https://ijm.tums.ac.ir/index.php/ijm/article/download/5096/1750

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 17 1 2025 02 05 137 143 EN Mahsa Javadi Cancer Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Department Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Gholamabbas Kaydani Department of Laboratory Sciences, School of Allied Medical Sciences, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Roya Pirmoradi Cancer Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Abdolhassan Talaiezadeh Cancer Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Azadeh Haghi Navand Cancer Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Department Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Mohammad Karimi Baba Ahmadi Department of Medical Biotechnology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Manoochehr Makvandi Cancer Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran 2024 07 29 2025 02 04 Background and Objectives: BK polyomavirus infection is prevalent and primarily asymptomatic, except for complications in kidney transplant recipients. Furthermore, its involvement in a tumorigenic family necessitates consideration in various malignancies such as urogenital tumors, prostate cancer, colorectal cancer (CRC), and brain cancer. Materials and Methods: This investigation encompassed 50 specimens of colorectal adenocarcinoma tumors, 50 adjacent tissues, and 40 urine samples, with patients having a mean age of 61 years ± 12.4 years. The detection of BK virus DNA VP1 gene and genotyping were carried out through nested-PCR and sequencing techniques. Results: Through the utilization of nested-PCR, BK virus DNA was identified in 15/50 (30%) colorectal tumor samples and 3/50 (6%) adjacent tissues (p-value = 0.008). Additionally, 6/40 (15%) urine samples exhibited positive results for BK virus DNA. Notably, among these findings, 9/15 BK virus positive tumor tissues (60%) and 3/6 BK virus positive urine samples (50%) were confirmed to be positive for BK virus subtype 4 (p-value < 0.001), whereas 2 tumor samples and 3 urine samples were attributed to BK virus type 1b2. Conclusion: It is imperative to enhance one's understanding of the etiological and risk factors pertaining to cancers. The present findings offer substantiation of a potential correlation between BK virus infection and colorectal cancer. BK virus genotype 4 was found to be dominant among the CRC patients in this study. https://ijm.tums.ac.ir/index.php/ijm/article/view/4947 https://ijm.tums.ac.ir/index.php/ijm/article/download/4947/1751

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 17 1 2025 02 05 144 152 EN Inès Quadri Department of Cellular and Molecular Biology, Cellular and Molecular Biology Laboratory (Team Microbiology), University of Sciences and Technology Houari Boumediene, Bab Ezzouar, Algiers, Algeria Imene Hassani Department of Cellular and Molecular Biology, Cellular and Molecular Biology Laboratory (Team Microbiology), University of Sciences and Technology Houari Boumediene, Bab Ezzouar, Algiers, Algeria Hocine Hacène Department of Cellular and Molecular Biology, Cellular and Molecular Biology Laboratory (Team Microbiology), University of Sciences and Technology Houari Boumediene, Bab Ezzouar, Algiers, Algeria 2024 04 14 2025 01 16 Background and Objectives: Halophilic archaea commonly produce antimicrobial peptides (halocins), but only a few studies have been conducted on these molecules. This study explores the antimicrobial potential of two strains belonging to Halopiger and Natrialba genera, isolated from hypersaline environments in the Algerian Sahara. Antimicrobial compounds produced by these genera have rarely been studied before. Materials and Methods: The antimicrobial activity of the strains was evaluated, along with the effects of UV radiation and culture conditions on growth and compound production. Stability assays and the effects of extracted compounds on target cells and peripheral blood mononuclear cells (PBMC) were assessed. Results: The strains exhibited high anti-archaeal activities and cross-domain interactions. Producing extracellular compounds associated with halocin, in the cell-free supernatant (CFS). These compounds remained stable at different temperatures (4°C, 60°C, 80°C, and 100°C) and different pH ranges (4-10 and 5-11), with antimicrobial profiles changed in response to UV light. The active compounds resembled known halocins but displayed unique features suggesting the discovery of new halocins. Additionally, Natrialba extracts showed significant activity against PBMC. Conclusion: This investigation confirms that Algerian saline soils are a promising source of interesting antimicrobial compounds. https://ijm.tums.ac.ir/index.php/ijm/article/view/4725 https://ijm.tums.ac.ir/index.php/ijm/article/download/4725/1752

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 17 1 2025 02 05 153 162 Hoai Le Center of Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam Truong Phuong Faculty of Odonto – Stomatology, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam Giang Huy Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam Phuoc-Vinh Nguyen Faculty of Pharmacy, University of Health Sciences, Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam Bac Giang Nguyen Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam 2024 10 03 2024 12 18 Background and Objectives: Candida albicans as pathogenic fungi cause conditions like oral candidiasis and dental caries. The critical role of biofilms in the pathogenicity of C. albicans necessitates the exploration of conditions that promote their growth and development. Our study aimed to delineate the optimal conditions conducive to the proliferation and biofilm production of C. albicans on prevalent dental materials. Materials and Methods: To approximate oral cavity conditions, culture media were enhanced with various glucose concentrations to assess the growth and biofilm-forming capability of the fungus through growth curve analysis and crystal violet assays. Results: The findings suggest that YPG medium augmented with 4% glucose presents as an optimal environment for C. albicans growth. Biofilm formation was most effectively promoted in RPMI medium supplemented with the same concentration of glucose. Composite resin was identified as the substrate most susceptible to biofilm development by C. albicans under these conditions. Conclusion: This investigation highlights the necessity of accounting for microbial activity and material characteristics in the prevention and management of dental biofilm formation. Our research advances the understanding of in vitro cultivation of C. albicans, simulating the oral milieu more accurately and contributing to enhanced oral health management for individuals utilizing temporary dental fixtures. https://ijm.tums.ac.ir/index.php/ijm/article/view/5061 https://ijm.tums.ac.ir/index.php/ijm/article/download/5061/1753

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 17 1 2025 02 05 163 170 Negar Danafar Department of Life Sciences Engineering, School of New Sciences & Technologies, University of Tehran, Tehran, Iran Marzieh Shokoohi Department of Life Sciences Engineering, School of New Sciences & Technologies, University of Tehran, Tehran, Iran 2024 09 03 2025 01 16 Background and Objectives: Diabetes is a metabolic disorder characterized by elevated glucose levels, leading to complications such as infections and impaired wound healing. Diabetic wounds are prone to bacterial infections, with common pathogens including Staphylococcus, Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa. Coelomic fluid of Eisenia fetida (CFEF) exhibits antimicrobial properties, making it a potential alternative to traditional antibiotics. This study aims to evaluate the in vitro antibacterial effects of CFEF on diabetic wound pathogens, alongside analyzing its protein content and antioxidant activities. Materials and Methods: This study used bacterial strains Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, Bacillus subtilis ATCC 19659, and Pseudomonas aeruginosa ATCC 27853. CFEF was extracted using warm water and electric shock methods. Protein concentration was determined using the Bradford method, and protein analysis was conducted via Tricine SDS-PAGE. Antioxidant activities were evaluated using DPPH, FRAP, superoxide dismutase, and catalase assays. Antibacterial activities were tested by disc diffusion, MIC, and MBC methods. Results: The study showed that CFEF exhibited significant antibacterial and antioxidant activities against common bacteria found in diabetic wound infections. The warm water shock method yielded superior results compared to the electric shock method. Conclusion: CFEF demonstrates promising antibacterial and antioxidant properties, suggesting its potential as a natural alternative for treating diabetic wound infections. Further research is needed to evaluate its clinical application and safety. https://ijm.tums.ac.ir/index.php/ijm/article/view/5024 https://ijm.tums.ac.ir/index.php/ijm/article/download/5024/1754

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 17 1 2025 02 05 171 179 Fatemeh Hajmoradi Department of Biology, Faculty of Science, Payame Noor University, Tehran, Iran Hamed Fathi Department of Biology, Faculty of Science, Payame Noor Univers