Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 2 2025 04 01 Determining the Antibiotic Resistance Pattern and the Frequency of the Most Common Resistance Genes in Acinetobacter baumannii Complex Isolates from Two Medical Centers in Tehran 95 104 1984 10.61186/iem.11.2.95 EN Katayoun Borhani Department of Biology, Tehran central branch, Islamic Azad University, Tehran, Iran Maryam Abizadeh Department of Biology, Tehran central branch, Islamic Azad University, Tehran, Iran Fatemeh Nori-Koutenai Department of Biology, Tehran central branch, Islamic Azad University, Tehran, Iran Journal Article 1970 01 01 Background: Acinetobacter baumannii is a major cause of nosocomial infections. Today, the increasing trend of antibiotic resistance in this bacterium has created many therapeutic challenges. This study aimed to assess the antibiotic resistance pattern and the presence of the most important resistance genes in A. baumannii complex clinical isolates collected from two medical centers in Tehran. Materials & Methods: In this study, 73 clinical isolates of A. baumanii complex belong to patients hospitalized in Sina and Shariati hospitals in 2018 were obtained from the university's microbial collection. Standard biochemical tests and PCR (polymerase chain reaction) detection of the 16srRNA gene were performed to confirm A. baumannii complex isolates. Antibiotic sensitivity test was done using disk diffusion method. Isolates with resistance to three or more antibiotic classes were defined as multidrug-resistant (MDR). The frequency of genes encoding aminoglycoside-modifying enzymes and those responsible for resistance to beta-lactam antibiotics was determined using PCR method. Findings: A total of 73 isolates were confirmed as A. baumannii complex. The isolates showed the highest resistance (100%) to ciprofloxacin, cefotaxime, and ceftazidime They also showed high resistance to other antibiotics. Ninety-three percent of the isolates were classified as MDR. Genetic analysis confirmed the presence of blaOXA-2, aphA6, and blaVIM genes in 100% of A. baumannii complex isolates. Furthermore, the isolates contained ant (87.67%), blaIMP (65.75%), aacC1 (76.71%), aadA1 (35.61%), and aadB (61.64%) genes. Conclusion: The prevalence of antibiotic-resistant A. baumannii complex strains has increased among hospitalized patients, leading to significant therapeutic challenges.

https://iem.modares.ac.ir/article_1984_1b36ea1c9b7a1c3ad668b8bb5df7963f.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 2 2025 04 01 Isolation and Identification of Endophytic Fungi of Licorice and Their Effect on Human Pathogenic Fungi 105 113 1985 10.61186/iem.11.2.105 EN Melika Esfandyari Department of Microbiology, Hamedan Branch, Islamic Azad University, Hamedan, Iran Reza Habibipour Department of Microbiology, Hamedan Branch, Islamic Azad University, Hamedan, Iran Mohsen Rajabi Forest and Rangeland Research Department, Hamedan Agriculture and Natural Resources Research and Education Center, AREEO, Hamedan, Iran Journal Article 1970 01 01 Background: Endophytes are microorganisms residing within plants, which have recently gained attention for producing bioactive compounds with pharmacological properties likesuch as antioxidant, anti-inflammatory, anticancer, and antibiotic, anticancer, anti-inflammatory, and antioxidant effects. Licorice plants (Glycyrrhiza glabra) may serve as a source of these bioactive metabolites, particularly those with antifungal potential. This study aimed to evaluateinvestigate the antifungal properties of endophytic fungi residing inisolated from licorice plants against human pathogenic fungi. Materials & Methods: Licorice plant samples were collected from three locations in Hamadan in October 2022. Endophytic fungi were collectedisolated from differentthe plant parts of licorice plants, identified morphologically using microscopy, and confirmed through molecular methods by DNA extraction and amplification, with sequencing results compared to public databases. The isolated fungi were cultured on PDA (potato dextrose agar) medium, and crude extracts were obtained using ethyl acetate. The Aantifungal properties activity of the crude extracts were investigatedwas tested against four pathogenic fungal pathogensi including Aspergillus niger, Candida glabrata, Cryptococcus neoformans, and Pseudallescheria boydii using disc diffusion method and ketoconazole as a positive control. Findings: A total of 21 endophytic fungi were identified, with Fusarium as the dominant genus. F. oxysporum and F. redolens were prevalent in root tissues, while A. niger dominated in stems and leaves. A. niger exhibited strong antifungal effects against A. niger, C. neoformans, and P. boydii. Conclusion: Licorice plant roots hosted the highest number of endophytes, likely due to reduced exposure to pollution. A. niger and F. oxysporum demonstrated significant potential as biocontrol agents against pathogenic fungi, making them promising candidates for sustainable disease management in agriculture and human health.

https://iem.modares.ac.ir/article_1985_1f36c15d6a3d18d52e8d493bc8187cb9.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 2 2025 04 01 Exploring Maternal-Fetal Transmission of Human Herpesvirus 6: A Study of Placental, Embryonic, and Autopsy Samples 115 121 1986 10.61186/iem.11.2.115 EN Somayeh Shatizadeh Malekshahi Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran 0000-0003-2741-2745 Mehdi Gholami Barzoki Student Research Committee, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran Mona Shokoofeh Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran Journal Article 1970 01 01 Background: Considering the limited studies conducted on the possibility of vertical transmission of HHV-6 in humans at different stages of pregnancy, the objective of this research wasis to examine the vertical transmission of HHV-6 (human herpesvirus 6) in various tissues of aborted fetuses atduring different months of pregnancy. Materials & Methods: This research was conducted on used 58 formalin- fixed paraffin- embedded tissues (FFPE) from 26 fetopsies. DNA extraction was performed using the phenol-chloroform technique. The quantity of extracted DNA samples was measured using the NanoDrop spectrophotometric method. PCR of the beta-globin gene confirmed the quality of the extracted DNA, and then the presence of the HHV-6 genome was tested using the Rreal-time PCR method. Findings: Of the 26 fetuses examined, 22 (84.6%) were negative for HHV-6, and four (15.4%) were positive. All six first-trimester fetuses were negative. Among 13 second-trimester fetuses (29 FFPE tissues), two (7.7%) tested positive., wWhile none of the seven third-trimester fetuses (22 FFPE tissues) had placental positive placentasity. However, HHV-6 was detected in non-placental fetal tissues, including the liver of fetus No. 16 and the heart of fetus No. 22, both of which were in the third trimester. Conclusion: These findings suggest that while vertical transmission of HHV-6 may occur, particularly in later stages of pregnancy andor in specific fetal tissues, the overall prevalence in theis sample studied was relatively low. Further investigation is needed to understand the implications of these results for maternal and fetal health.

https://iem.modares.ac.ir/article_1986_8c249675aea6c3cbd91661bbae767ff1.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 2 2025 04 01 SARS-CoV-2 Omicron: Genotyping, Mutational Analysis, and Characterization of Subvariants in Iran 123 133 1987 10.61186/iem.11.2.123 EN Mona Roozbehani Vaccine Research Center, Iran University of Medical Sciences, Tehran, Iran Hossein Keyvani Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Alireza Tabibzadeh Immunoassay Development, Fellowship of Clinical Laboratory Science, Laboratory Director and Chief Medical Laboratory Scientist, Shahid Rajaee Hospital and Training Center, Laboratory Medicine Department, Karaj, Iran Farah Bokharaei-Salim Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Leila Mousavizadeh Vaccine Research Center, Iran University of Medical Sciences, Tehran, Iran. Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran Journal Article 1970 01 01 Background: Several SARS-CoV-2 variants with distinct characteristics have emerged, with Omicron sub-variants such as BA.1 to BA.5 being predominant since late 2021. Distinguishing sub-variants using phylogenetic and molecular analyzes provides a valuable approach in the context of epidemiological research. Materials & Methods: Molecular epidemiology and sub-variants of SARS-CoV-2 omicron were investigated using 150 nasopharyngeal samples from COVID-19 patients in Tehran (Iran) from May 2022 to August 2023. Omicron lineages were differentiated using RT-PCR targeting Q493R, L452R, and ∆69-70 spike mutations. SARS-CoV-2 omicron sub-variants were determined by amplicon sequencing. Findings: The mean age of the study participants was 44±7 years, comprising 38.6% males and 61.4% females , which may have an effect on transmission and susceptibility of different ages. Also, 117 (78%) samples were positive for one of the three lineages, while 33 (22%) was none of the lineages, which were referred to as conclusive and inconclusive results, respectively. 60.7% of the samples was the omicron lineage BA.4 or BA.5. Conclusion: Considering the prevalence of BA.4 and BA.5 in the study population and their differences with the parental SARS-CoV-2 variant, the primary vaccine seems to be not effective against the current omicron sub-variants. These results underscore the importance of vaccination as a critical strategy to prevent the spread of these variants. The suggested primer sets could be an easy way to screen sample variants and lineages and are useful for screening and sequencing samples in countries with limited resources. Continuous monitoring of omicron sub-variants is recommended for preventing the resurgence of COVID-19.

https://iem.modares.ac.ir/article_1987_d68a18275455ae3eaa2c291eebb46e6d.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 2 2025 04 01 Identification and prioritization of safety barriers to prevent and reduce the infection of the COVID-19 using fuzzy DEMATEL-BAYESIAN modeling: lesson learned 135 165 1988 10.61186/iem.11.2.135 EN Omran Ahmadi Department of Occupational Health Engineering, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran Journal Article 1970 01 01 Background: The COVID-19 pandemic resulted in widespread outbreaks and a significant increase in mortality among both the general population and the workforce over a span of two years. This study aimed to identify and prioritize measures for preventing and reducing the incidence of COVID-19 through the application of fuzzy DEMATEL-Bayesian modeling. Materials & Methods: In the first phase, key factors in the prevention and reduction of COVID-19, as identified in past studies, were reviewed and extracted. In the second phase, the cause-and-effect relationships of these factors in the prevention and control of COVID-19 were established using the fuzzy DEMATEL method. In the third phase, the identified factors were integrated into a Bayesian network based on the findings from the previous phase. Findings: The analysis identified seven critical factors in the prevention and control of COVID-19: personal protective equipment, social distancing, technology, training, lessons learned, geographical factors, and attention to sensitive age groups. The results indicated that the prevention and reduction node of COVID-19 was most sensitive to social distancing, more so than any other factor. Conclusion: Based on the sensitivity analysis of the model, the first priority in decision-making for preventing and reducing COVID-19 should be focused on social distancing. The Bayesian network model developed in this study can effectively assist in macro-level decision-making by prioritizing the measures necessary to control and reduce the spread of the COVID-19.

https://iem.modares.ac.ir/article_1988_9d7311ba459f9e45ed746755a32dcd11.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 2 2025 04 01 HLA Class I Genotypes and Their Role in COVID-19 Severity: A Study in the Isfahan Province 167 178 1989 10.61186/iem.11.2.167 EN Leila Khani Laboratory of Transcriptional Regulation, Institute of Medical Biology, Polish Academy of Science, Lodz, Poland. Bio-Med-Chem Doctoral School of the University of Lodz, Lodz, Institutes of the Polish Academy of Sciences, Lodz, Poland Negar Nikfar Department of molecular medicine, University of Pavia, Italy Saghar Zakeri Molecular department of Isfahan Nobel pathology and genetics laboratory, Isfahan, Iran Mahshid Rahmati Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran Saeid Javdan Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran Mohamad Reza Ganjalikhany Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran Hamed Fouladseresht Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran Behrooz Ataei Infectious Disease and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran Reza Didarian Department of Biomedical Engineering, Ankara Yıldırım Beyazıt University, Ankara, Turkey Journal Article 1970 01 01 Background: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a significant global health threat. The host immune response determines the disease severity, with factors like human leukocyte antigen (HLA) genes, age, sex, and nutritional status influencing outcomes. HLA genes, known for their genetic diversity, are implicated in determining susceptibility and severity of infectious diseases. This study investigated the association between HLA class I genotypes and COVID-19 severity in the Isfahan population, Iran. Materials & Methods: Blood samples were collected from 34 COVID-19 patients with varying levels of disease severity (severe, moderate, and mild). HLA genotyping was performed using polymerase chain reaction-sequence specific primers (PCR-SSP), and in silico analysis assessed the affinity of viral peptides to HLA alleles. Findings: Statistical analyses revealed that HLA-C07 was more prevalent in patients with severe COVID-19, suggesting a potential association between this allele and the disease severity. Furthermore, HLA-A01 was more prevalent among severe cases, while HLA-A02 and HLA-A03 were less frequent, indicating a possible predisposing role for HLA-A01 and protective roles for HLA-A02 and HLA-A*03. Conclusion: These findings highlight the role of HLA molecules in COVID-19 severity and offer insights into genetic factors influencing outcomes. Understanding the association of specific HLA alleles, such as HLA-C07, HLA-A01, HLA-A02, and HLA-A03, with the disease progression lays a foundation for advancing personalized preventive and therapeutic approaches. These results contribute to knowledge on host genetics in infectious diseases, paving the way for further research and therapeutic strategies.

https://iem.modares.ac.ir/article_1989_4a3e00961a08879c34f91ca0070ea2f5.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 2 2025 04 01 Investigating the Effect of Hemoperfusion Therapy on Laboratory and Clinical Factors in COVID-19 Patients: A Cross-Sectional Study 179 188 1990 10.61186/iem.11.2.179 EN Mousa Ghelighi-Ghojogh Neonatal and Children’s Research Center, Department of Biostatistics and Epidemiology, School of Health, Faculty of Health, Golestan University of Medical Sciences, Gorgan, Iran Amir Hossein Saberi Medical Doctor, Golestan University of Medical Sciences, Gorgan, Iran Saeid Amirkhanlou Department of Internal Medicine, Clinical Research Development Unit (CRDU), Shahid Sayad Shirazi Hospital, Golestan University of Medical Sciences, Gorgan, Iran Journal Article 1970 01 01 Background: With the epidemic of the emerging COVID-19 disease in the world in 2019 and the lack of a definitive and effective treatment for it, medical science practically faced a new challenge, this study aimed to investigation the effect of hemoperfusion therapy on laboratory and clinical factors in COVID-19 patients. Materials & Methods: In this cross-sectional study, 49 patients with severe COVID-19, who had indications for hemoperfusion were examined in 2020-2021. The patients underwent four hemoperfusion sessions after inserting a vascular catheter and preparing a special filter. Changes in laboratory and clinical factors before and after each hemoperfusion session were carefully recorded, and the data were analyzed using SPSS software. Findings: The results of the study showed that the average age of the patients was 55.5 ± 13.9 years. Changes in the patients’ blood oxygen saturation levels after each hemoperfusion session showed a statistically significant improvement trend, the average values before and after the first session were 86.7±7.2% and 88.5±5.7%, respectively, indicating a significant increase (p= .009). Also, the inflammatory factor CRP (C-reactive protein) and blood platelet levels were significantly reduced after each hemoperfusion session. Conclusion: This study showed that hemoperfusion could improve patients’ blood oxygen saturation values without causing any special complications and could also have a clear effect on clearing inflammatory factors and CRP from the blood.

https://iem.modares.ac.ir/article_1990_dc513ea4fbdaa7a14786ffdebc4ef64e.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 2 2025 04 01 Anti-NMDA Receptor Encephalitis Associated with SARS-CoV-2 Infection in the COVID-19 Pandemic: A Systematic Review 189 203 1991 10.61186/iem.11.2.189 EN Justyna Jachman-Kapułka Department of Internal Medicine and Rheumathology, J. Gromkowski Specialist Regional Hospital, Wroclaw, Poland Marta Rorat Department of Social Sciences and Infectious Diseases, Medical Faculty, Wroclaw University of Science and Technology, Poland Journal Article 1970 01 01 Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is associated with neurological complications, like various autoimmune encephalitis (AE) types. This study aimed to identify and analyze COVID-19 cases diagnosed with anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis (anti-NMDARE). Materials & Methods: This research summarized all post-pandemic reports. The review was conducted based on PRISMA (preferred reporting items for systematic reviews and meta-analyses) 2020 guidelines. Electronic databases were search using search terms to find anti-NMDARE cases associated with COVID-19. Findings: After analyzing 649 records, 16 patients (ten women and six men) with a median age of 19.5 years were identified. All AE cases were confirmed by the presence of anti-NMDAR IgG, dominant behaviour and mental status changes, psychiatric symptoms, epileptic seizures, movement disorders, and sleep and speech problems. Abnormalities were more common in electroencephalography (EEG) and cerebrospinal fluid (CSF) than in brain MRI scans. All patients received first-line guideline-based therapy (intravenous methylprednisolone, intravenous immunoglobulin, plasma exchange), and five patients received second-line immunotherapy (rituximab, azathioprine, cyclophosphamide). Nine out of 16 patients had complete recovery or significant improvement. Conclusion: Considering the magnitude of the pandemic and the few anti-NMDAR encephalitis cases temporally diagnosed with COVID-19, this association was relatively rare. The appearance of characteristic features of encephalitis during SARS-CoV-2 infection necessitates further diagnostic tests, especially detection of auto-antibodies and possible neoplasm, since earlier diagnosis and treatment provide a better prognosis. This review highlights the need for further investigation into the co-occurrence of anti-NMDARE with COVID-19, long-term clinical outcomes, and possible relapses.

https://iem.modares.ac.ir/article_1991_96055f5b06bf9381ac43879351642cf5.pdf