Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 3 2025 10 01 Prevalence and Genetic Characterization of Foodborne Vibrio spp. Isolated from Persian Gulf Seafood 205 212 27660 10.61882/iem.11.3.205 EN Mohaseneh Ghari Shahid Ashrafi esfahani, university, Esfahan, Iran. Hessam Alizadeh Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran Afsaneh Karmostaji Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran Journal Article 2024 06 30 Backgrounds: Vibrio species are of particular concern due to their association with gastroenteritis after consuming raw seafood. This study aimed to assess the prevalence of Vibrio species and the frequency of virulence genes in Vibrio isolates from the Persian Gulf seafood. Materials & Methods: In this descriptive cross-sectional study, 118 samples of marine fish, shrimp, salted fish, and salted shrimp were collected from seafood markets along the southeastern coast of Iran. The collected samples were enriched in alkaline peptone water and then cultured on thiosulfate citrate bile salt sucrose agar medium. Vibrio species were identified using multiplex polymerase chain reaction (PCR) targeting the sodB, flaE, and hsp genes. Additionally, the virulence genes toxR, trh, and tdh were identified through PCR. Findings: A total of 68 Vibrio isolates were collected from 118 samples, including 48 (70%) V. parahaemolyticus isolates, 14 (20%) V. cholera isolates, and six (9%) V. vulnificus isolates. No isolates of V. mimicus were found. Among the isolates, the Tdh and toxR genes were detected in 16 (23%) and 35 (51%) cases, respectively. Additionally, 12 (18%) isolates contained both genes. The Trh gene was not detected in any of the samples. Conclusion: The seafood market in southeastern Iran serves as a crucial hub for distributing marine products to other provinces. The presence of Vibrio species, particularly V. parahaemolyticus, along with their virulence factors in these marine products may pose a risk of infection to consumers. This underscores the importance of proper handling practices when preparing seafood.

https://iem.modares.ac.ir/article_27660_f72ce9098bc2b98030ed78319d60be6e.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 3 2025 10 01 An Experimental Study on the Potential of Honey Lactobacilli to Combat Multidrug-Resistant Acinetobacter baumannii (MDRAB) in Northern Iran 213 223 27666 10.61882/iem.11.3.213 EN Leila Fozouni Associate Professor in Microbiology, Department of Microbiology, Go.C.,Islamic Azad University, Gorgan, Iran Bent Al- Hoda Barzegar Department of Microbiology, Go.C.,Islamic Azad University, Gorgan, Iran Sara Malekpour Kolbadinezhad Department of Microbiology,Go.C., Islamic Azad University, Gorgan, Iran Journal Article 2025 05 17 Backgrounds: Infections caused by Acinetobacter baumannii represent a global health threat in medical settings. This research aimed to investigate the phenotypic characteristics of antimicrobial resistance in A. baumannii strains isolated from post-burn infections as well as the antagonistic effects of honey probiotics on multidrug-resistant isolates. Materials & Methods: A total of 220 post-burn wound samples were analyzed to identify A. baumannii strains using microbiological and molecular tests. The Kirby-Bauer test was conducted according to CLSI (Clinical and Laboratory Standards Institute)-2021 guidelines to determine resistance phenotypes. Additionally, probiotics were isolated from 11 honey types through phenotypic and molecular methods, and their antagonistic properties were evaluated using the disk diffusion method. Findings: Out of the 63 A. baumannii isolates identified, 76.19% exhibited multidrug-resistance. Most of the isolates were obtained from patients with second-degree burns, accounting for 23.81% of the cases. The highest antibiotic sensitivity was against amikacin, with a sensitivity rate of 58.73%. In the disk diffusion tests, the average growth inhibition zone diameter for all multidrug-resistant A. baumannii isolates was 29 mm when treated with Lactobacillus plantarum derived from Camelthorn honey. This probiotic effect was significantly 1.7 times greater than that of L. delbrueckii and 1.9 times greater than that of L. acidophilus. Conclusion: Although this in vitro study did not investigate the biochemical properties of honey, certain native Iranian honeys were shown to possess desirable anti-Acinetobacter properties due to the presence of lactobacilli.

https://iem.modares.ac.ir/article_27666_344fbbdb875272b916352c8040207bd6.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 3 2025 10 01 Microbiological and Therapeutic Insights into Primary Breast Abscesses: A Retrospective Study 225 238 27664 10.61882/iem.11.3.225 EN Christine Wen Hui Chen Pengiran Anak Puteri Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei Darussalam Kenneth Yuh Yen Kok Pengiran Anak Puteri Rashidah Sa’adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei Darussalam Sonal Tripathi Department of Surgery, Raja Isteri Pengiran Anak Saleha Hospital, Bandar Seri Begawan, Brunei Darussalam Terrence Rohan Chinniah Department of Pathology, Raja Isteri Pengiran Anak Saleha Hospital, Bandar Seri Begawan, Brunei Darussalam Journal Article 2025 02 10 Backgrounds: Breast abscess is a common health issue among women, particularly those who are lactating or of childbearing age. Timely and effective antibiotic therapy along with appropriate surgical intervention is essential for treating bacterial infections associated with breast abscesses. This study aimed to investigate the clinical presentations, common pathogens, and treatment practices (including antibiotic therapy and surgical interventions) of primary breast abscesses in lactating and non-lactating women in a tertiary hospital. Materials & Methods: This retrospective study was conducted on women diagnosed with primary breast abscesses in a tertiary hospital from January 1, 2019 to January 1, 2023. Patients were identified through the hospital microbiology laboratory database and electronic health records. Data were collected on patient demographics, comorbidities, smoking history, clinical presentations, treatment modalities, pus culture and antibiotic sensitivity reports, and clinical outcomes. Findings: The study comprised 85 patients. Bacillus species was the most frequently-identified pathogen (35.3%), followed by methicillin-sensitive Staphylococcus aureus (25.9%). Sensitivity reports indicated that these organisms were generally susceptible to co-amoxiclav, flucloxacillin, and ciprofloxacin. These antibiotics were the most commonly-prescribed and effective medications when used in conjunction with ultrasound-guided aspiration (88%), surgical incision and drainage (19%), or both. Conclusion: Bacillus species emerged as the most common pathogen responsible for primary breast abscesses in this cohort. Although bacterial resistance was not prevalent, understanding the current bacteriological profile of breast abscesses is vital for selecting appropriate empirical antibiotic therapy and developing evidence-based treatment guidelines.

https://iem.modares.ac.ir/article_27664_8af7aa91dea57ef40a8a11afea500470.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 3 2025 10 01 Significant Reduction of Saccharomyces cerevisiae in the Gut Microbiota of Colorectal Cancer Patients from Iran 239 245 27665 10.61882/iem.11.3.239 EN Tayebe Shahbazi Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran Bita Bakhshi Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran Aliakbar Rasekhi Department of Biostatistics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran Mohammad Sadegh Fazeli Division of colon and rectal surgery, Department of Surgery, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran Fatemeh Fallah Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran Journal Article 2025 03 04 Backgrounds: This study aimed to investigate and compare the prevalence of Saccharomyces cerevisiae (S. cerevisiae) in the stool of colorectal cancer (CRC) patients and healthy controls. Materials & Methods: Over a one-year study period from April 2022 to April 2023, 25 patients who met all the necessary conditions for inclusion in the study were selected from among the patients referring to the colonoscopy unit of a teaching hospital in Tehran, considering the exclusion criteria. Stool samples were collected and immediately transported to the laboratory in a cold chain. Also, 25 healthy individuals who were matched with the patients in terms of sex, age, and ethnicity were included as a control group. After DNA extraction, the presence of S. cerevisiae was assayed by TaqMan real-time polymerase chain reaction (PCR) using specific primers and probe. Findings: The cancer stage of all individuals in the CRC group was 3, and the location of tumor formation in all of them was colon. Of the 25 samples in each group, three samples in the CRC group and 18 samples in the healthy group were positive for the presence of S. cerevisiae DNA. This difference was statistically significant (p< .0001). Conclusion: The results may indicate the importance of evaluating S. cerevisiae reduction as an indicator for the diagnosis of CRC. Considering the positive role of S. cerevisiae in maintaining gut health and also in helping treat CRC, it could be used as a probiotic product or adjuvant in this field.

https://iem.modares.ac.ir/article_27665_c9684ee86ee11ae2556ffa8b9eb8cd6b.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 3 2025 10 01 Characterization of High-Risk Human Papillomavirus Genotypes in Formalin-Fixed Paraffin-Embedded Cervical Tissues Using Genexpert® 247 255 27662 10.61882/iem.11.3.247 EN Sheba Joseph Magaji Department of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria Maryam Aminu Department of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria Muhammad Hassan I. Doko Department of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria Adekunle O. Oguntayo Department of Obstetrics and Gynaecology, Ahmadu Bello University Teaching Hospital, Zaria, Kaduna State, Nigeria Jigo D. Yaro Department of Pathology, Ahmadu Bello University, Zaria, Kaduna State, Nigeria. Journal Article 2024 12 10 Backgrounds: There is a growing need for human papillomavirus (HPV) annotation of formalin-fixed paraffin-embedded (FFPE) tissues. This study was carried out to characterize high-risk human papillomavirus genotypes in formalin-fixed paraffin-embedded cervical tissues using GeneXpert® Materials & Methods: In this study, 200 formalin-fixed paraffin-embedded (FFPE) cervical tissue samples were collected from women with pre-invasive and invasive cervical diseases and screened for high-risk human papillomavirus (hrHPV) using GeneXpert®. Findings: Analysis of the results showed that 47 (23.5%) samples were positive for hrHPV, with HPV 16 being the most common type (16.5%), followed by other high risk (OHR) types (31, 33, 35, 52, 58, 51, 59, 39, 56, 66, 68) (4.5%) and HPV 18/45 (2.5%). Ninety-six (48%) samples were negative for hrHPV, while 57 (28.5%) samples were invalid. GeneXpert® had low sensitivity for hrHPV in CIN 1 (cervical intraepithelial neoplasia) (9.1%), CIN 2 (33.3%), CIN 3 (22.2%), and cervical cancer (50.7%). However, the specificity of the test was much better, with values ranging from 64.9-83.8%. Apart from cervical cancer, which had a positive predictive value of 74.5%, the positive predictive value of all pre-invasive diseases was very poor. However, the negative predictive value of the test was very good, with CIN 2 having a high value of 97.9%. Conclusion: This study findings show that FFPE cervical tissue is functional for HPV detection, although HPV detection and characterization by the GeneXpert® assay is still recommended only after full optimization.

https://iem.modares.ac.ir/article_27662_f17e28704bf2b4702992842989431d24.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 3 2025 10 01 Cytomegalovirus Seropositivity and Its Impact on Clinical Progression of Multiple Sclerosis: A Case-Control Study from Northeastern Iran 257 267 27659 10.61882/iem.11.3.257 EN Amirali Ghahremani Department of Internal Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran Mehdi Barati Vector-borne Diseases Research, Center, North Khorasan University of Medical Sciences, Bojnurd, Iran Hasan Namdar Ahmadabad Vector-borne Diseases Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran. Journal Article 2025 03 04 Backgrounds: Investigating the role of cytomegalovirus (CMV) in multiple sclerosis (MS) could clarify its potential impacts on the disease progression and pathogenesis. This study aimed to examine the relationship between CMV seropositivity and MS development as well as its impact on the disease clinical course and patients' disability status in North Khorasan province. Materials & Methods: <span style="mso-ascii-font-family: 'Times New Roman'; mso-ascii-theme-font: major-bidi; mso-hansi-font-family: 'Times New Roman'; mso-hansi-theme-font: major-bidi; mso-bidi-font-family: 'Times New Roman'; mso-bidi-theme-font: major-bidi; color: black; mso-themecolor: text1;">This case-control study assessed 98 MS patients and 100 age- and sex-matched healthy controls using the 2017 McDonald diagnostic criteria. Disability levels were evaluated via the Expanded Disability Status Scale (EDSS). The presence and levels of anti-CMV IgG and IgM antibodies in serum samples of both groups were quantified by ELISA. Findings: <span style="mso-ascii-font-family: 'Times New Roman'; mso-ascii-theme-font: major-bidi; mso-hansi-font-family: 'Times New Roman'; mso-hansi-theme-font: major-bidi; mso-bidi-font-family: 'Times New Roman'; mso-bidi-theme-font: major-bidi; color: black; mso-themecolor: text1;">All MS patients were seropositive for anti-CMV IgG and seronegative for anti-CMV IgM, akin to healthy controls. Interestingly, MS patients exhibited significantly lower serum anti-CMV IgG levels compared to healthy individuals (178.7 ± 61.92 vs. 342.9 ± 3.121, p< .0001). Ethnicity and EDSS scores influenced anti-CMV IgG levels, with higher EDSS scores correlated with lower serum levels. In patients with relapsing-remitting multiple sclerosis (RRMS), serum levels of anti-CMV IgG exhibited significant variations based on age, EDSS scores, and the disease duration. <span style="font-size: 11.0pt; line-height: 107%; mso-ascii-font-family: 'Times New Roman'; mso-ascii-theme-font: major-bidi; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-font-family: 'Times New Roman'; mso-hansi-theme-font: major-bidi; mso-bidi-font-family: 'Times New Roman'; mso-bidi-theme-font: major-bidi; color: black; mso-themecolor: text1; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: FA;">Conclusion<span style="font-size: 11.0pt; line-height: 107%; font-family: 'Times New Roman',serif; mso-ascii-theme-font: major-bidi; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: major-bidi; mso-bidi-theme-font: major-bidi; color: black; mso-themecolor: text1; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: FA;">: <span style="font-size: 11.0pt; line-height: 107%; font-family: 'Times New Roman',serif; mso-ascii-theme-font: major-bidi; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: major-bidi; mso-bidi-theme-font: major-bidi; color: black; mso-themecolor: text1; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: FA;">This study reveals a complex link between CMV infection and MS. While anti-CMV IgG antibodies were found in both MS patients and healthy individuals, lower levels in MS patients might suggest a protective effect against MS progression. Additionally, reduced anti-CMV IgG levels correlated with higher EDSS scores, indicating that diminished CMV-specific immunity could worsen disease severity, especially in RRMS patients.

https://iem.modares.ac.ir/article_27659_0fea24d4edf999326dfa6c1d6f887b99.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 3 2025 10 01 Molecular Docking and Dynamics of 2,5-Pyrrolidinedione Analogue Using the SARS-CoV-2 Main Protease as Target Protein 269 283 27663 10.61882/iem.11.3.269 EN Sultan D. Y. Albakhit Branch of Basic Sciences, College of Dentistry, University of Basrah, Basrah, Iraq Sajjad Hassan Ali Department of Chemical and Petroleum Refining Engineering, College of Oil and Gas Engineering, Basrah University for Oil and Gas, Basrah, Iraq Sajood Qasim Ibrahim Department of Polymer and Petrochemical Engineering, College of Oil and Gas Engineering, Basrah University for Oil and Gas, Basrah, Iraq Kithar Rasheed Majeed Department of Food Science, College of Agriculture, University of Basrah, Basrah, Iraq Noor H. Faisal Department of Chemistry, College of Education for Pure Sciences, University of Basrah, Basrah, Iraq Ali A. A. Al-Shawi Department of Chemistry, College of Education for Pure Sciences, University of Basrah, Basrah, Iraq Kawkab Ali Hussein Department of Chemistry, College of Education for Pure Sciences, University of Basrah, Basrah, Iraq Osama A. Mohsein 1- Department of Medical Laboratory Techniques, Mazaya University College, Thi-Qar, Iraq 2- Thi-Qar Health Directorate, Al Habbobi Teaching Hospital, Thi-Qar, Iraq Wafa Ali Eltayb Biotechnology Department, Faculty of Science and Technology, Shendi University, Shendi 11111, Sudan Romisa Mamoun School of Pharmaceutical Science and Technology,Tianjin university, Tianjin 300072, China Mohnad Abdalla Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, Shandong 250022, China Journal Article 2025 01 21 Backgrounds: The goal of this study was to employ molecular docking and dynamics to investigate the interactions of twelve maleimide and succinimide derivatives (SD1-SD12) with the SARS-CoV-2 main protease (Mpro) (PDB ID:6LU7). Materials & Methods: Molecular docking and molecular dynamics simulations were performed to study the interaction of twelve derivatives (SD1-SD12) of maleimide and succinimide with the SARS-CoV-2 main protease (Mpro) (PDB ID:6LU7). Four compounds (SD1, SD4, SD8, and SD12) were selected for further molecular docking analysis based on their binding energies (-7, -7.3, -7.3, and -7.2 kcal/mol, respectively), which were lower than the other compounds and close to the control crystal (-8.5 kcal/mol). Molecular docking was used to find the binding energy of non-bonding interactions between ligand and receptor in connection to the SARS-CoV-2 main protease (PDB code: 6LU7). Findings: Molecular docking results showed binding energies ranging from -7.3 to -6.5 kcal/mol for the 2,5-pyrrolidinedione analog, the co-crystallized control ligand exhibited a binding energy of -8.5 kcal/mol. SD1 exhibited the best binding mode and drug-like properties to inhibit the SARS-CoV-2 main protease compared to the other ligands. Among the demonstrated interactions with the protein, RMSD (root mean square deviation) values decreased due to the improved and more stable states. Conclusion: Overall, the current study proposed a strategy to combat COVID-19 using pharmaceuticals as prospective agents, which might also serve as a starting point for drug discovery. Additional studies on the target compounds are expected to yield substantial advances in the fight against COVID-19.

https://iem.modares.ac.ir/article_27663_83c15a5063efa34c1e31fc0a00ff04f6.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 11 3 2025 10 01 Investigation of SARS-CoV-2 Genomic Variants in Two Patients: Insights into Initial Isolates from West Kalimantan, Indonesia 285 296 27661 10.61882/iem.11.3.285 EN Puji Astuti Department of Biochemistry and Biomolecular Science, Faculty of Medicine, Universitas Tanjungpura, Pontianak, Indonesia Mahyarudin Mahyarudin Department of Microbiology, Faculty of Medicine, Universitas Tanjungpura, Pontianak, Indonesia 0000-0002-0184-3435 Delima Fajar Liana 1: Department of Microbiology, Faculty of Medicine, Universitas Tanjungpura, Pontianak, Indonesia 2: Universitas Tanjungpura Hospital, Pontianak, Indonesia Virhan Novianry Department of Biochemistry and Biomolecular Science, Faculty of Medicine, Universitas Tanjungpura, Pontianak, Indonesia Sofi Siti Shofiyah Department of Chemistry, Faculty of Natural and Marine Science, Universitas OSO, Pontianak, Indonesia Puspa Amalia Study Program of Medical Technology Laboratory, Polytechnic ‘Aisyiyah of Pontianak, Pontianak, Indonesia Muhammad Faisal Universitas Tanjungpura Hospital, Pontianak, Indonesia Marinus Andre Reynaldi Universitas Tanjungpura Hospital, Pontianak, Indonesia Journal Article 2024 10 31 Backgrounds: The COVID-19 (coronavirus disease-2019) pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has led to significant global health impacts. Understanding the genomic evolution and mutation dynamics of SARS-CoV-2 is crucial for devising effective control measures. This study aimed to perform genomic analysis of early 2020 SARS-CoV-2 isolates from West Kalimantan, Indonesia, focusing on the presence of the D614G mutation. Materials & Methods: Samples were collected from individuals whose COVID-19 was confirmed using RT-PCR at the Microbiology Laboratory of Tanjungpura University Hospital during October to November 2020. Samples were sequenced following standard protocols using GRIDION sequencer at the Genetica Science Sequencing Services Company in Jakarta. Additionally, 53.109 SARS-CoV-2 genome sequences from Indonesia (January 2020- June 2023) were retrieved from the GISAID database. A phylogenetic tree and 3D (dimensional) protein structure were constructed using MEGA X software and I-TASSER. Findings: Genomic sequencing and phylogenetic analysis showed that both West Kalimantan isolates were closely related to the Wuhan Hu-1 strain and belonged to the B.1.459 lineage. Both samples exhibited the D614G mutation in the spike protein, a mutation later found in dominant variants including Delta and Omicron in Indonesia. The identification of B.1.459 in this region contributes to understanding its spread across the archipelago. Conclusion: This study provides genomic evidence of the first SARS-CoV-2 isolates in West Kalimantan, supporting the role of the D614G mutation in increased transmission. It also enhances understanding of the emergence and geographic distribution of the B.1.459 lineage in Indonesia, highlighting the importance of continued genomic surveillance.

https://iem.modares.ac.ir/article_27661_e7c3645a3ea1024d6704a3133c7930a8.pdf