ORIGINAL_ARTICLE Introduction: Malaria remains a significant public health challenge in Aljazeera State, Sudan, substantially contributing to morbidity. This study aimed to determine malaria prevalence and associated risk factors in Al Managil City to inform targeted interventions. Methods: A cross-sectional study was conducted in Al Managil City between August 2022 and April 2023. A random sample of 385 individuals presenting at four healthcare facilities was enrolled. Data on demographics and potential risk factors were collected using a standardized questionnaire. Malaria infection was diagnosed by microscopic examination of thick and thin blood films. Results: The overall malaria prevalence was 63.9% (246/385), with Plasmodium falciparum identified in 98.2% of positive cases. The study population was 54.5% male, and 89.9% resided in rural areas. Age was significantly associated with malaria infection (P = 0.003), with the highest prevalence in those over 15 years (76.2%) and the lowest in children under five years (57.4%). No significant associations were found with gender (P = 0.915) or residency (P = 0.295). Fever was reported in 51.9% of participants. Proximity to irrigated agricultural schemes was significantly associated with malaria infection (P = 0.009). Conclusion: This study demonstrates high malaria prevalence in Al Managil City, primarily due to P. falciparum. The disproportionately high prevalence in individuals over 15 years highlights the need for targeted interventions. Proximity to irrigated agriculture is a significant risk factor, emphasizing the importance of environmental management. These findings support integrated malaria control strategies, including vector control and targeted interventions for young children, to reduce the malaria burden. http://jommid.pasteur.ac.ir/article-1-622-en.pdf 2025-06-01 1 8 10.61186/JoMMID.13.1.1 Malaria Prevalence Risk factors Plasmodium falciparum Cross-sectional study Al Managil city Gezira state Sudan Mohamed Ahmed Salah Mohamed Ahmed Mohammedahmed6218@gmail.com 1 Department of Community Medicine, Faculty of Medicine and Health Sciences, University of Kassala, Sudan AUTHOR Hajrhma Ismael Hajrhma Mohammedahmed 2 Department of Medicine, Alsherg University of Science and Technology,3Microbiology specialist in Al Nasr Medical clinic, Gezira state, Sudan AUTHOR Amgad Albashir Khalid Albashir 3 Microbiology specialist in Al Nasr Medical clinic, Gezira state, Sudan AUTHOR Duha Isam Osman Mustfa 4 Department of Community Medicine, Faculty of Medicine and Health Sciences, University of Kassala, Sudan AUTHOR Mohamed Ali Ahmed Hamid 5 Department of Community Medicine, Faculty of Medicine and Health Sciences, University of Kassala, Sudan AUTHOR Mohamed Hassan Ahmed Kebayer m.hassan101189@gmail.com 6 Department of Parasitology and Medical Entomology, Faculty of Medicine and Health Sciences, University of Kassala, Sudan AUTHOR https://orcid.org/0000-0003-0138-5996 Tafawl Ibrahim Karrar 7 Department of Parasitology and Medical Entomology, Faculty of Medicine and Health Sciences, University of Kassala, Sudan AUTHOR Abobaker Mohamed Al Amin Al basher 8 Department of Clinical Chemistry, Faculty of Medicine and Health Sciences, University of Kassala, Sudan AUTHOR Samah AbulGasim Osman Karoum 9 Department of Pathology, Faculty of Medicine and Health Sciences, University of Kassala, Sudan AUTHOR Nouh Saad Mohamed 10 Department of Molecular Biology, Sennar Malaria Research and Training Centre, Sennar, Sudan AUTHOR

ORIGINAL_ARTICLE Introduction: The COVID-19 pandemic underscored the critical need for robust surveillance of other respiratory viruses due to overlapping clinical presentations, which can complicate accurate diagnosis. Consequently, precise etiological diagnosis remains paramount, particularly in settings where SARS-CoV-2 infection is suspected, given the shared symptomatology with other respiratory pathogens. This retrospective study investigated the prevalence of Respiratory Syncytial Virus (RSV) and Influenza A and B virus infections among individuals who tested negative for SARS-CoV-2 in Oyo State, Nigeria. Methods: Nasopharyngeal samples (n = 206) were collected between January 2023 and June 2023 from both adults and children who tested negative for COVID-19 using RT-qPCR. These samples were subsequently analyzed following a standardized protocol, which included viral RNA extraction and a multiplex one-step RT-qPCR assay. The resulting data were statistically analyzed using IBM SPSS Statistics software (version 25). Results: Among individuals who tested negative for COVID-19, RSV was detected in 2.8% of children and 2.0% of adults. Influenza B was identified in 2.8% of children and 1.0% of adults, while Influenza A was detected in 1.0% of adults but was not found in any children. The mean age of the participants was 2.97 years for children and 33.51 years for adults. Conclusion: Although the observed detection rates were relatively low, our findings underscore the continued necessity of screening for RSV and Influenza A and B viruses in individuals presenting with respiratory symptoms, even in the context of a negative SARS-CoV-2 test result. Sustained surveillance efforts are paramount for a comprehensive understanding of respiratory viral epidemiology, including the dynamics of circulation, potential geographic variations, and the identification of potential outbreak hotspots, thereby informing evidence-based public health interventions and clinical management strategies. Future prospective sentinel surveillance studies will be instrumental in further elucidating the complexities of respiratory viral co-infections and revealing nuanced spatiotemporal and demographic patterns of infection. http://jommid.pasteur.ac.ir/article-1-629-en.pdf 2025-06-01 9 15 10.61186/JoMMID.13.1.9 Respiratory Syncytial Virus Influenza A Influenza B COVID-19 Respiratory co-infections Surveillance Oyo State Nigeria Adefunke Akinola akinolaadefunke2013@gmail.com 1 Department of Biological Sciences, Lead City University, Ibadan, Nigeria AUTHOR https://orcid.org/0009-0003-7640-7368 Oluseyi Adebowale Olayinka 2 Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria AUTHOR https://orcid.org/0000-0003-2224-9061 Toyosi Yekeen Raheem toyosiraheem55@gmail.com 3 Department of Biological Sciences, Lead City University, Ibadan, Nigeria AUTHOR https://orcid.org/0000-0003-1316-3549

REVIEW_ARTICLE The development of expression systems using non-pathogenic microorganisms has enabled efficient and safe platforms for medical and food applications, including functional foods with therapeutic benefits. Among non-pathogenic bacteria, Lactococcus lactis (L. lactis) is widely used in biotechnology for various applications, such as vaccine development and protein expression. L. lactis serves as an effective in vivo expression system for developing vaccines and therapeutics in medical research, particularly for parasitic diseases. This review highlights examples of L. lactis-based vaccines for parasitic diseases, demonstrating their ability to elicit protective cellular and humoral immune responses.   http://jommid.pasteur.ac.ir/article-1-693-en.pdf 2025-06-01 16 29 10.61186/JoMMID.13.1.16 Lactococcus lactis Expression system Live-vector vaccine Parasitic diseases Adjuvant Elaheh Davarpanah elahedavarpanah@yahoo.com 1 Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran AUTHOR https://orcid.org/0000-0002-5898-1732 Negar Seyed negarse@gmail.com 2 Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran AUTHOR https://orcid.org/0000-0001-8249-6692 Tahereh Taheri tahereh_t@yahoo.com 3 Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran AUTHOR https://orcid.org/0000-0002-2619-6879

ORIGINAL_ARTICLE Introduction: Carbapenem resistance, due to the production of carbapenemase enzymes in various bacteria, is responsible for numerous outbreaks and is significantly associated with healthcare-associated infections. Metallo-β-lactamases (MBLs) are carbapenemases that hydrolyze all β-lactam antibiotics except monobactams. The most prominent bacteria exhibiting this resistance mechanism include members of the Enterobacteriaceae family and Pseudomonas aeruginosa. Therefore, this study aims to assess the prevalence of MBL production among Gram-negative bacteria at Kirtipur Hospital. Methods: This study was conducted at Kirtipur Hospital from June 26, 2022, to September 28, 2022. Organisms were isolated and identified from clinical samples including urine, blood, wound swabs, sputum, tissues, pus, catheter tips, and other body fluids, following standard laboratory protocols. Carbapenemase production was detected using the modified Carbapenem Inactivation Method (mCIM), with metallo-β-lactamase (MBL) production confirmed by the EDTA-modified Carbapenem Inactivation Method (eCIM) test. Results were interpreted according to the Clinical and Laboratory Standards Institute (CLSI) guidelines, M100, 31st ed., 2021. Results: From 1988 clinical samples, 388 Gram-negative bacteria were isolated, with Escherichia coli, Klebsiella pneumoniae, and P. aeruginosa being the predominant species. Antibiotic susceptibility testing revealed that Amikacin was the most effective against Enterobacteriaceae, exhibiting a susceptibility rate of 84.05%. In contrast, Cefepime was the most effective against non-Enterobacteriaceae Gram-negative bacteria with susceptibility rate of 60%. Screening identified 23.40% (84/359) of isolates as potential carbapenemase producers, with 15.32% (55/359) confirmed as carbapenemase producers via mCIM. Of these, 56.36% (31/55) were MBL producers, representing 8.63% (31/359) of all screened isolates. Among confirmed carbapenemase producers, P. aeruginosa exhibited the highest MBL production rate at 77.78% (7/9 isolates), followed by K. pneumoniae at 73.68% (14/19), E. coli at 41.18% (7/17), C. koseri at 33.33% (2/6), and P. mirabilis at 25% (1/4). Conclusion: This study underscores the significant threat posed by MBL-producing E. coli, K. pneumoniae, and P. aeruginosa in this healthcare setting. Therefore, implementing routine screening for MBL-producing organisms in diagnostic laboratories is crucial for controlling the spread among hospital patients and guiding effective antibiotic therapy.   http://jommid.pasteur.ac.ir/article-1-681-en.pdf 2025-06-01 30 38 10.61186/JoMMID.13.1.30 Carbapenem resistance eCIM Enterobacteriaceae Metallo-beta-lactamases (MBLs) Pseudomonas aeruginosa Niroj Man Amatya mahaju@gmail.com 1 Department of Medical Microbiology, Nobel College, Kathmandu, Nepal AUTHOR https://orcid.org/0000-0003-3398-7422 Sanjit Shrestha shrestha.s@hotmail.com 2 Pathology Department, Kirtipur Hospital, Kirtipur, Nepal AUTHOR https://orcid.org/0000-0003-4419-5455 Pushpa Thapa Magar pushpathapa79@gmail.com 3 Department of Medical Microbiology, Nobel College, Kathmandu, Nepal AUTHOR https://orcid.org/0009-0007-3370-9031 Rimsa Dhaubadhel rimsa.dh@gmail.com 4 Department of Medical Microbiology, Nobel College, Kathmandu, Nepal AUTHOR https://orcid.org/0009-0007-9762-8660 Srijana Tamang tamangsrijana600@gmail.com 5 Department of Medical Microbiology, Nobel College, Kathmandu, Nepal AUTHOR https://orcid.org/0009-0009-2672-3606 Swostika Pant swostika.panta55@gmail.com 6 Department of Medical Microbiology, Nobel College, Kathmandu, Nepal AUTHOR https://orcid.org/0009-0001-3757-170X

ORIGINAL_ARTICLE Introduction: Colorectal cancer (CRC) remains a significant global health challenge. Specific strains of Escherichia coli elaborating virulence factors, including cyclomodulins and colibactin, have been increasingly implicated in CRC pathogenesis. This study aimed to determine the prevalence of genes encoding these toxins, namely cnf1, cdtB-I, and clbB, alongside genes associated with biofilm formation, csgA and flu, in clinical E. coli isolates from patients diagnosed with CRC or precancerous lesions. Methods: A total of 44 E. coli isolates were obtained from colorectal tissue biopsies of patients diagnosed with CRC or precancerous polyps, and from healthy controls. PCR was employed to screen for the presence of the toxin-encoding genes cnf1, cdtB-I, and clbB, as well as the biofilm-associated genes csgA and flu. Biofilm formation was assessed quantitatively utilizing a standard microtiter plate assay. Results: The toxin-encoding genes cnf1 and cdtB-I were each detected in 14 isolates (31.8%) across all study groups (CRC, polyp, and healthy controls). In contrast, the clbB gene was identified in 5 isolates (11.4%), exclusively within the polyp and healthy control groups. The biofilm-associated genes csgA and flu exhibited the highest prevalence, being detected in 41 (93.2%) and 22 (50.0%) isolates, respectively, across all groups. Notably, none of the tested isolates demonstrated biofilm formation capability under the experimental conditions employed. Conclusions: This study demonstrated the presence of the cdtB-I gene in E. coli isolates from both early-stage CRC (stages I and II), with a notably higher prevalence in stage I. Furthermore, cdtB-I was also detected in precancerous polyps classified as both high-grade dysplasia (HGD) and low-grade dysplasia (LGD). Intriguingly, the clbB gene was conspicuously absent from all CRC isolates of stages I and II. These findings suggest a potential role for cdtB-I in the early stages of CRC development, warranting further research to elucidate its precise impact on the progression of CRC. The presence of these virulence-associated genes, without significant differences across groups, underscores the complexity of E. coli's involvement in colorectal carcinogenesis. http://jommid.pasteur.ac.ir/article-1-691-en.pdf 2025-06-01 39 49 10.61186/JoMMID.13.1.39 E. coli Colorectal neoplasms Cyclomodulin Colibactin Biofilm formation Taghi Amiriani amiriani@goums.ac.ir 1 Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan, Iran AUTHOR https://orcid.org/0000-0002-7750-0367 Behnoush Khasheii bh_kh@yahoo.com 2 Department of Pathobiology, Faculty of Veterinary Sciences, Bu-Ali Sina University Hamedan, Iran AUTHOR https://orcid.org/0000-0002-2981-9090 Samin Zamanii Samin.Zamanii@gmail.com 3 Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran AUTHOR https://orcid.org/0000-0001-7503-7228 Mousa Ghelichi-Ghojogh 4 Children’s Research Center, Golestan University of Medical Sciences, Gorgan, Iran AUTHOR https://orcid.org/0000-0002-0726-5509 Ailar Jamalli jamali@goums.ac.ir 5 Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran AUTHOR https://orcid.org/0000-0002-4612-8144

ORIGINAL_ARTICLE Introduction: Stenotrophomonas maltophilia is a bacterium that increasingly causes respiratory and bloodstream infections, particularly in individuals with compromised immune systems, such as cancer patients. This study investigates a series of S. maltophilia respiratory infections among cancer patients at a large hospital, aiming to describe the clinical and microbiological characteristics of these cases. Methods: We investigated cancer patients presenting with respiratory symptoms between February 1st and February 28th, 2023 in ten of whom S. maltophilia isolates were recovered from clinical specimens through microbiological culture. Identification was initially based on colony morphology, oxidase reaction, glucose fermentation, motility, and other biochemical tests, followed by confirmation using the Vitek® 2 system (BioMérieux). Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method. Results: Ten adult cancer patients (6 females, 4 males) developed S. maltophilia pneumonia between February 1st and February 28th, 2023. Eight patients had hematological malignancies, and two had solid tumors. All patients' infections were susceptible to treatment with trimethoprim-sulfamethoxazole, and all patients recovered fully following treatment. Conclusion: We identified a cluster of S. maltophilia respiratory infections, but it did not meet the criteria for a true outbreak due to the lack of a common source and evidence of transmission between patients. Despite reinforced infection control measures, limitations in surveillance hindered identifying the source and implementing prevention strategies. This cluster emphasizes the need for vigilance in recognizing S. maltophilia infections in cancer patients, enabling timely, susceptibility-guided antimicrobial therapy. http://jommid.pasteur.ac.ir/article-1-534-en.pdf 2025-06-01 50 56 10.61186/JoMMID.13.1.50 Cancer patients Immunocompromised Non-fermenting Gram-negative bacilli Respiratory infections Sporadic Stenotrophomonas maltophilia Mahua Sinha mahuasinha@gmail.com 1 Department of Microbiology, Kidwai Memorial Institute of Oncology, Bengaluru, India AUTHOR https://orcid.org/0000-0002-4155-817X Sumathi BG iimationsumathi@gmail.com 2 Department of Microbiology, Kidwai Memorial Institute of Oncology, Bengaluru, India AUTHOR https://orcid.org/0009-0000-5083-5346 Priyanka Shivashankar priyavij2202@gmail.com 3 Department of Microbiology, Kidwai Memorial Institute of Oncology, Bengaluru, India AUTHOR https://orcid.org/0009-0006-0868-8526 Junia Joseph juniajoseph22@gmail.com 4 Department of Microbiology, Kidwai Memorial Institute of Oncology, Bengaluru, India AUTHOR https://orcid.org/0009-0003-2302-6449 Sahana Shetty sahanashettyns@gmail.com 5 Department of Microbiology, Kidwai Memorial Institute of Oncology, Bengaluru, India AUTHOR https://orcid.org/0009-0003-5283-2669

ORIGINAL_ARTICLE Introduction: Blood culture remains the gold standard for diagnosing bloodstream infections. Contamination during the collection, transport, or processing of blood culture samples can obscure the true pathogens with contaminant growth, thereby complicating or delaying the diagnosis of bacteremia. This study assesses the effectiveness of an educational intervention aimed at reducing blood culture contamination rates in a tertiary care hospital. Methods: This single-center study, aimed at quality improvement, included two phases: an observational phase from December 2022 to February 2023, and an interventional phase from March to May 2023. During the interventional phase, healthcare workers underwent comprehensive training in aseptic blood sample collection techniques. The study involved 980 patients, with 470 blood samples collected during the observational phase (December 2022–February 2023) and 510 during the interventional phase (March–May 2023), all processed using standard microbiological techniques. Blood cultures yielding commensal organisms without corresponding clinical symptoms were classified as contaminants. Results: The contamination rate of blood cultures dropped from 12.1% (57/470) during the observational phase to 8.6% (44/510) post-intervention; however, this reduction was not statistically significant (P = 0.34, chi-square test). Contamination rates during the observational phase were highest in the ward at 16.2%, followed by 13% in the outpatient department, and lowest in the intensive care unit at 7.1%. The predominant contaminants identified were Staphylococcus hominis, followed by Staphylococcus haemolyticus, highlighting common sources of contamination. Conclusion: Although the educational intervention did not yield a statistically significant decrease in blood culture contamination rates, the study underscores the need for multifaceted strategies, including enhanced training, environmental controls, and standardized protocols, to meet international benchmarks for contamination control.   http://jommid.pasteur.ac.ir/article-1-609-en.pdf 2025-06-01 57 65 10.61186/JoMMID.13.1.57 Blood culture contamination Observational phase Interventional phase Quality improvement Healthcare education Wanshisha Wanswett 1 Department of Microbiology, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India AUTHOR https://orcid.org/0009-0007-4773-6145 Sheetal Goenka 2 Department of Microbiology, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India AUTHOR https://orcid.org/0000-0001-8033-8391 Manisha Jain manisha_jain29@yahoo.com 3 Department of Microbiology, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India AUTHOR https://orcid.org/0009-0007-4773-6145 Poonam Loomba 4 Department of Microbiology, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India AUTHOR https://orcid.org/0000-0002-5580-5733 Abha Sharma 5 Department of Microbiology, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India AUTHOR https://orcid.org/0000-0002-6976-3853 Shivani Tyagi 6 Department of Microbiology, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India AUTHOR https://orcid.org/0000-0002-1276-0133

ORIGINAL_ARTICLE Introduction: Understanding the etiological agents, reservoirs, and transmission dynamics of infectious diseases is crucial for developing effective prevention and control strategies, particularly in rural settings where healthcare access and awareness may be limited. Past pandemics, such as COVID-19 and historical influenza pandemics, have highlighted the diverse nature of infectious diseases and underscored the critical importance of public health awareness, particularly in underserved rural communities. This study aimed to assess the knowledge, attitudes, and practices (KAP) of a rural population regarding infectious diseases and their prevention. Methods: This cross-sectional study included adults aged 18 years and older residing in rural areas of Eastern Uttar Pradesh, India. Data were collected using a questionnaire validated through expert review and pilot testing. Descriptive statistics were used to summarize demographic variables. Continuous variables were summarized as mean ± standard deviation, and categorical variables as frequencies and percentages. Associations between categorical variables were assessed using the Chi-square test, while correlations between ordinal or non-normally distributed continuous variables were evaluated using Spearman's rank correlation test. Data were analyzed using SPSS version 26. Results: The study included 1,714 participants, with 56.2% males and 43.8% females. The majority of participants (52.8%) were young adults aged 18–25 years. A majority of participants (58.8%) had attained or were pursuing college-level education or higher. Most respondents (84.2%) lacked knowledge of endemic diseases, and 82% lacked knowledge of vaccine-preventable diseases in the study region. Significant gaps were observed in participants' knowledge of disease transmission modes and preventive practices. Employed participants demonstrated significantly higher attitude and practice scores compared to unemployed participants and students (P < 0.05). A weak positive correlation was observed between knowledge and practice scores (r = 0.202; P < 0.001). No significant associations were observed between knowledge and attitude (r = 0.035, P = 0.704) or between attitude and practice (r = 0.099; P = 0.274). Conclusion: The study highlights significant gaps in knowledge about infectious diseases among the rural population, particularly regarding endemic and vaccine-preventable diseases. The weak correlation between knowledge and practice underscores the need for targeted, behavior-focused health interventions. Community-based programs, such as village workshops, school campaigns, and mobile health outreach, should be integrated with existing national disease control efforts to address the significant knowledge gaps identified and improve preventive practices. Future research should assess the impact of such interventions on health-seeking behaviors in rural communities. http://jommid.pasteur.ac.ir/article-1-674-en.pdf 2025-06-01 66 77 10.61186/JoMMID.13.1.66 Disease prevention Endemic diseases Modes of transmission Infectious disease knowledge Rural health Saumya Shukla iamsaumyashukla12345@gmail.com 1 Department of Microbiology, Maharshi Vashishtha Autonomous State Medical College, Basti, UP, India AUTHOR https://orcid.org/0000-0001-8354-6719 Kumar S Abhishek get.abhi1904@gmail.com 2 Department of Microbiology, AIIMS, Jodhpur, Rajasthan, India AUTHOR https://orcid.org/0000-0001-7019-4478 Laxmi Rathore tina.lrathore@gmail.com 3 Department of Microbiology, Dr. S. N. Medical College, Jodhpur, Rajasthan, India AUTHOR https://orcid.org/0000-0003-0318-299X Vinod Kumar Maurya vinod29m@gmail.com 4 Department of Microbiology, Maharshi Vashishtha Autonomous State Medical College, Basti, UP, India AUTHOR https://orcid.org/0000-0001-9746-8299 Vandana Upadhyay dr.vandana027@gmail.com 5 Department of Microbiology, Maharshi Vashishtha Autonomous State Medical College, Basti, UP, India AUTHOR https://orcid.org/0000-0002-8733-8121 Pawan Kumar Dubey 131093pawan@gmail.com 6 Department of Community Medicine, Maharshi Vashishtha Autonomous State Medical College, Basti, Uttar Pradesh, INDIA AUTHOR https://orcid.org/0000-0003-1871-3546 Amit Kumar Singh amit.singh.dr@gmail.com 7 Department of Microbiology, Maharshi Vashishtha Autonomous State Medical College, Basti, UP, India AUTHOR https://orcid.org/0000-0002-1913-1129