Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 12 1 2026 02 01 Molecular characterizations of vancomycin and methicillin-resistant Staphylococcus aureus strains isolated from intensive care unit patients in Tehran, Iran 1 13 28095 10.66224/iem.12.1.1 EN Fateh Rahimi Department of Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran Sanaz Khashei Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran 0000-0001-8076-9896 Mohammad Katouli Center for Bioinnovation and School of Science, Technology and Education, University of the Sunshine Coast, Queensland, Australia 0000-0001-5486-0469 Journal Article 2025 11 21 Background: We investigated the prevalence, diversity, and antibiotic susceptibility profiles of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant S. aureus (VRSA) strains isolated from ICU patients in Tehran, Iran. Materials & Methods: A total of 247 S. aureus isolates were collected from patients admitted to the ICU of a referral hospital in Tehran between June and August 2022. Antimicrobial susceptibility testing was done on all isolates using the disc diffusion method. MRSA was identified by cefoxitin screening and mecA gene detection. Vancomycin resistance was assessed by E-test and confirmed by the detection of vanA and vanB genes. A combination of Staphylococcal cassette chromosome mec (SCCmec), pulsed-field gel electrophoresis (PFGE), and ccr typing methods was used to measure the genetic diversity of the strains. Findings: Our results revealed that 60 (24%) and 7 (3%) isolates were identified as MRSA and VRSA, respectively. vanA and vanB genes were detected in 100% and 29% of VRSA isolates, respectively. There was a high level of resistance to penicillin, ciprofloxacin, and tobramycin. Out of 205 (83%) strains showing SCCmec, 96 (47%) belonged to type III SCCmec. Typing of the isolates with PFGE showed the presence of 32 pulsotypes consisting of 19 common (CTs) and 13 single types (STs) among the studied strains, with CT3 comprising 43% of VRSA strains. Conclusion: The detection of a dominant VRSA clone and a considerable prevalence of MRSA among ICU patients underscores the role of ICUs as potential reservoirs for MRSA dissemination.

https://iem.modares.ac.ir/article_28095_c4caf9e04a0d4f83565449f2cce9d5d5.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 12 1 2026 02 01 Molecular mechanisms of fluoroquinolone resistance in Streptococcus pneumoniae isolates from Iran 15 23 28715 10.66224/iem.12.1.15 EN Aram Sharifi Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Kurdistan, Iran Amin Tarinjoo Islamic Azad university, Science and Research Branch, Tehran, Iran. Samira Dahaghin Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran. Ali Ahmadi Molecular Biology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran Journal Article 2025 04 24 Background: Due to recent reports of resistance to β-lactams and macrolides, the use of fluoroquinolones (FQs) for treating Streptococcus pneumoniae infections has increased. This study aimed to evaluate the molecular mechanisms of FQ resistance in pneumococcal isolates. Materials & Methods: This study was conducted on 131 pneumococcal isolates (67 nasopharyngeal isolates from healthy individuals and 64 clinical isolates) collected in Tehran, Iran, in 2023. Susceptibility to FQs was determined, and quinolone resistance–determining regions (QRDRs) of gyrA, gyrB, parC, and parE in resistant isolates were amplified and sequenced. Findings: Disk diffusion testing showed that 23 (17.5%) and five (3.8%) isolates were resistant to norfloxacin (5µg) and ofloxacin (5µg), respectively. Minimum inhibitory concentration (MIC) test confirmed resistance in 22 of 23 norfloxacin-resistant isolates. All five ofloxacin-resistant isolates were distinct from the norfloxacin-resistant group, and their resistance was also confirmed by MIC testing. Overall, 28 non-overlapping resistant isolates were selected for sequencing. Among these isolates, mutations in parC and gyrA were detected in four (14.28%) and five (17.85%) isolates, respectively, while two (7.14%) isolates harbored simultaneous mutations in both genes. The most frequent substitutions were Ser81→Leu in parC and Glu85→Lys and Ser81→His/Thr in gyrA. No statistically significant difference was observed between nasopharyngeal (healthy flora) and clinical isolates regarding FQ resistance patterns. Conclusion: This study identified key molecular mechanisms of fluoroquinolone resistance in S. pneumoniae, primarily involving mutations in parC and gyrA, including double mutations. Notably, all isolates remained susceptible to moxifloxacin, supporting its effectiveness in treating pneumococcal infections.

https://iem.modares.ac.ir/article_28715_74a564781bf38f42f6d60ae0c8e2d63a.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 12 1 2026 02 01 Antimicrobial and Anti-Biofilm Potential of Selected Plant Essential Oils against Salmonella enterica Serovar Typhimurium 25 35 28717 10.66224/iem.12.1.25 EN Aram Sharifi Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Kurdistan, Iran Bahar Nayeri Fasaei Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran Sepideh Asadi Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran Fatemeh Yazarloo Department of Aquatic Animal Health, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran Journal Article 2025 07 09 Background: Salmonella enterica serovar Typhimurium is a major foodborne pathogen with growing resistance to antibiotics. Plant-derived essential oils (EOs) have emerged as potential alternatives due to their antimicrobial and anti-virulence properties. This study aimed to investigate the antibacterial, anti-biofilm, and quorum sensing (QS) inhibitory effects of EOs derived from Thymus daenensis and Satureja hortensis. Materials & Methods: The antibacterial activity of the EOs was evaluated by determining the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) using standard microbiological assays. Biofilm inhibition and disruption were assessed via crystal violet staining. Gas chromatography-mass spectrometry (GC-MS) was used to analyze the chemical composition of the EOs. Real-time PCR was performed to measure the expression of QS-related genes. Findings: Both EOs exhibited antibacterial activity against S. Typhimurium, with MICs of 6.25 µg/mL (T. daenensis) and 12.5 µg/mL (S. hortensis) and MBCs of 25 µg/mL for both. GC-MS analysis revealed carvacrol, thymol, γ-terpinene, p-cymene, and α-terpinene as major constituents. At sub-MIC concentrations, T. daenensis EO inhibited biofilm formation by 68% and disrupted mature biofilms by 54%, while S. hortensis EO showed 45 and 37% inhibition, respectively. Both EOs significantly downregulated QS-related genes, indicating strong anti-QS activity. Conclusion: The EOs derived from T. daenensis and S. hortensis exhibited strong antibacterial, anti-biofilm, and anti-QS properties against S. Typhimurium. These findings support their potential as natural therapeutic agents for combating resistant Salmonella infections.

https://iem.modares.ac.ir/article_28717_21e04c4536ac1ee11ab991e1dea13c47.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 12 1 2026 02 01 In-Silico Identification of Phytochemical Inhibitors of Mycobacterium tuberculosis Efflux Pumps: A Potential Strategy against Multidrug Resistance 37 52 28716 10.66224/iem.12.1.37 EN Seyed Akbar Moosavi Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Iran University of Medical Sciences and Health Services, Tehran, Iran Abdorrahim Absalan Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Iran University of Medical Sciences and Health Services, Tehran, Iran Zahra Absalan Department of Microbiology, Faculty of medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran Fereshteh Parto Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Iran University of Medical Sciences and Health Services, Tehran, Iran Journal Article 2025 05 24 Background: Efflux pump-mediated antibiotic extrusion is a key mechanism of multidrug resistance in Mycobacterium tuberculosis (MTB). Inhibiting these pumps is a promising strategy for resensitizing resistant strains to conventional antibiotics. Materials & Methods: An integrated in silico approach was employed to evaluate the interaction of drug-like ligands, primarily phytochemicals, with key MTB efflux pumps. Homology models of DrrA, DrrB, and DrrC proteins and the crystal structure of Rv1819c were used for molecular docking. Top-scoring ligands were subsequently analyzed for drug-likeness, toxicity profile, and binding stability via molecular dynamics (MD) simulations to identify the most promising efflux pump inhibitors (EPIs). Findings: Molecular docking revealed high-affinity binding of several phytochemicals. The top-scoring ligands were curcumin, rosmarinic acid, and pracinostat for DrrA; curcumin, kanzonol C, and Skf-100330A for DrrB; and rosmarinic acid, curcumin, and kanzonol C for DrrC. For the Rv1819c protein, the top-scoring compounds were crocetin, curcumin, and kanzonol C, which were found to bind specifically to the ATP-interacting pocket. An integrated analysis of docking affinity, molecular dynamics stability, toxicity, and drug-likeness identified curcumin, kanzonol C, rosmarinic acid, and crocetin as the most promising candidate EPIs. Conclusion: The present in-silico study identified curcumin, kanzonol C, rosmarinic acid, and crocetin as promising phytochemical inhibitors of key MTB efflux pumps. These compounds exhibited potential for synergistic activity with conventional anti-tuberculosis drugs. Therefore, preclinical and experimental validation is warranted to confirm their efficacy as efflux pump inhibitors.

https://iem.modares.ac.ir/article_28716_8ff28835276bec79658f56f14f699674.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 12 1 2026 02 01 Molecular Epidemiology of Acinetobacter baumannii Isolates Using Single-Locus Sequence Typing of blaOXA-51-like and ampC Genes as a Cost-Effective Method 53 60 28720 10.66224/iem.12.1.53 EN Farzaneh Firoozeh Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran. Evidence-based Phytotherapy and Complementary Medicine Research Center, Alborz University of Medical Sciences, Karaj, Iran. 0000-0002-4026-4110 Zahra Hoseini Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran Mohammad Mohammadzadeh Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran. 0000-0001-8526-4504 Farzad Badmasti Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran 0000-0003-3502-147X Mohammad Zibaei Department of Parasitology and Mycology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran Center for Research of Endemic Parasites of Iran, Tehran University of medical Sciences, Tehran, Iran 0000-0003-2265-7460 Sepeta Zibaei Student Research Committee, Alborz University of Medical Sciences, Karaj, Iran 0009-0006-3630-0314 Journal Article 2025 09 27 Background: Acinetobacter baumannii is a crisis-causing opportunistic pathogen with a high capacity for clonal spread. blaOXA-51-like and ampC sequence-based typing (SBT) is a cost-effective and reliable technique to identify global and widespread lineages of A. baumannii strains. This research aimed to study circulating A. baumannii clones using single-locus sequence typing (SLST) as a reliable and cost-effective method. Materials & Methods: A total of 119 A. baumannii clinical isolates were collected from hospital inpatients from February to September 2024. The antibiotic resistance profile of A. baumannii isolates was determined, and genotyping was performed using SBT of blaOXA-51-like and ampC genes. Findings: All A. baumannii isolates were specified as multidrug-resistant (MDR), and 78.1% were identified as carbapenem resistant. Resistance to colistin was observed in 5% of isolates with a minimum inhibitory concentration (MIC) of ≥128 μg/mL. SBT of the blaOXA-51-like gene revealed four various blaOXA-51-like allele variants: including blaOXA-69 (n=47, 39.5%), blaOXA-64 (n=21, 17.6%), blaOXA-383 (n=44, 37%), and blaOXA-441 (n=7, 5.9%). SBT of the ampC specified two alleles, including ampC-1 (n=47, 39.5%) and ampC-25 (n=21, 17.6%), and 51 (42.9%) isolates showed an undetermined allele variant of the ampC gene. blaOXA-69 /ampC-1 and blaOXA-64 / ampC-25 pertained to sequence type 1/ clonal complex 1 (ST1/CC1) and ST25/CC25, respectively. Conclusion: SBT of the blaOXA-51-like and ampC genes revealed a relatively high prevalence of the international ST1/CC1 clone in MDR A. baumannii isolates in our region. However, the blaOXA-383 allele variant, which could possibly be associated with endemic clones, also had an approximately significant frequency.

https://iem.modares.ac.ir/article_28720_7c08f51438fbd3ee4cbb942a0b87eb9e.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 12 1 2026 02 01 Suppressive Effect of Bifidobacterium bifidum Probiotic Supernatant on Tigecycline Resistance Gene Expression in Clinical Isolates of Streptococcus pyogenes 61 75 28721 10.66224/iem.12.1.61 EN Ghazaleh Moradi Department of Microbiology, TeMS.C.,Islamic Azad University, Tehran, Iran Zahra Shafie Department of Biology, Ro.C.,Islamic Azad University, Roudehen,Iran. Fatemeh Bagheri Department of Microbiology, TeMS.C.,Islamic Azad University, Tehran, Iran Journal Article 2025 11 27 Background: The rapid rise in antibiotic resistance is a grave worldwide concern, with tigecycline being a key treatment here. Inherent resistance is making this common yet sometimes fatal bacterium, Streptococcus pyogenes, difficult to treat. This study looks at whether the liquid from the probiotic Bifidobacterium bifidum can lower the activity of important tigecycline resistance genes: tet(M), tet(O), and tet(X1) in clinical samples of S. pyogenes. Materials and Methods: A total of 60 S. pyogenes isolates were identified from 100 clinical samples using biochemical methods. The tigecycline susceptibility test was carried out, following standard antibiogram procedures. The antimicrobial potential of the supernatant of B. bifidum was assessed by determining the MIC and MBC values of it. Findings: About 58.3% (35 of 60) of isolates were resistant to tigecycline. The most common resistance-associated gene was tet(M) (16.67%), followed by tet(O) (11.67%) and tet(X1) (1.67%). No isolate carried all three genes together. MIC and MBC values of probiotic supernatant were within the range of 8-128 and 16-128 μg/mL, respectively. Crucially, real-time PCR showed that the supernatant significantly reduced the expression of all three resistance genes in treated isolates. Conclusion: These results suggest that B. bifidum supernatant may help suppress tigecycline resistance in S. pyogenes by downregulating the expression of critical resistance genes. This highlights its potential as a natural, supportive strategy to help combat antibiotic resistance and lays the groundwork for future clinical or therapeutic research.

https://iem.modares.ac.ir/article_28721_d5bb9cf6866fa9b987b5b64c6c28f1f3.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 12 1 2026 02 01 Microbial Isolation and Comparison of Antibiotic Resistance Pattern in Rainbow Trout (Oncorhynchus mykiss) from Chaharmahal-va-Bakhtiari Province, Iran (2022-2023) 77 85 28719 10.66224/iem.12.1.77 EN Maryam Karimi-Dehkordi Department of Veterinary, Shk.C., Islamic Azad University, Shahrekord, Iran 0000-0001-6086-2014 Mohammad Ghasemi Shamsabadi Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran Majid Gholami-Ahangaran Department of Veterinary, Shk.C., Islamic Azad University, Shahrekord, Iran Journal Article 2025 10 05 Background: Increased antibiotic resistance due to the overuse and misuse of antibiotics is a severe threat to both the aquaculture industry and human health. This study aimed to determine the antibiotic resistance pattern of bacteria isolated from rainbow trout. Materials & Methods: A total of 79 and 120 fish samples were collected in 2022 and 2023, respectively. Swab samples were enriched in TSB (tryptic soy broth) and cultured on TSA (tryptic soy agar). The grown colonies were evaluated for Aeromonas hydrophila, Lactococcus garvieae, Streptococcus iniae, and Yersinia ruckeri. Antibiotic resistance patterns against 10 common antibiotics were evaluated. Findings: In this study, four types of bacteria (A. hydrophila, L. garvieae, S. iniae, and Y. ruckeri) were isolated. The results of antibiotic resistance analysis during 2022-2023 showed that in all isolated bacteria, the percentage of antibiotic resistance against enrofloxacin and florfenicol was higher in 2023 than in 2022. Conclusion: The isolated bacteria had different resistance patterns, these patterns could be used as a guide for selecting appropriate antibiotics to control infectious diseases in rainbow trout. This finding may be due to improper administration of these antibiotics in rainbow trout production.

https://iem.modares.ac.ir/article_28719_19f560c0fc2e02c530e64152bb9ec137.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 12 1 2026 02 01 Dengue virus infection and Skin Manifestations: A Systematic Review and Meta-Analysis 87 99 28718 10.66224/iem.12.1.87 EN Fatemeh Sameni Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran 0000-0001-5762-1279 Mehrshad Ahmadi Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran Mohammad Mohammadzadeh Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran 0000-0001-8526-4504 Seyed Mehdi Tabaie Department of Medical Laser, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran Amir Bairami Department of Medical Parasitology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran Maedeh Pourali Eshkalak Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran Masoud Dadashi Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran. Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran Journal Article 2025 08 28 Background: Dengue virus infection is a severe systemic condition primarily transmitted by its main vector, Aedes aegypti. Skin rash may be the initial symptom in patients with dengue virus infection, which could be helpful for clinical diagnosis. This research aimed to evaluate the prevalence of skin manifestations associated with dengue virus infection worldwide. Materials & Methods: Electronic resources such as Scopus, Medline (via PubMed), and Web of Science were searched to identify studies focusing on skin manifestations in patients with dengue virus infection between 2000 and 2024. Statistical analysis was conducted using Stata software, and sources of heterogeneity were assessed using I2. Findings: A total of 24 papers (six prevalence studies and 18 case reports/case series) were included. A meta-analysis of prevalence studies revealed that skin manifestations were reported in patients with dengue virus infection in three countries (India, Pakistan, and France), with an overall prevalence of 63.2% (95% CI: 54.4-71.1) among 962 dengue virus infected patients. Analysis of case reports/case series showed that among 19 dengue virus infected cases, skin rash and thrombocytopenia were the most common skin manifestations and laboratory indications, respectively. Conclusion: Dengue virus infection could result in various dermal manifestations with distinct clinical symptoms and laboratory findings. These skin involvements may aid in the timely diagnosis of patients with dengue virus infection.

https://iem.modares.ac.ir/article_28718_c022cf41a12658e227aeb252f734364d.pdf