Iranian Journal of Microbiology

A comparative analysis of CRISPR systems, virulence factors, and antibiotic resistance genes in carbapenem-sensitive and carbapenem-resistant Klebsiella pneumoniae

Sat, 14 Feb 2026 14:22:09 +0330

Background and Objectives: Klebsiella pneumoniae is a major cause of healthcare-associated infections, particularly in immunocompromised patients. This study compares the CRISPR systems, virulence factors, and antibiotic resistance genes in carbapenem-sensitive (CSKP) and carbapenem-resistant (CRKP) clinical isolates.
Materials and Methods: Carbapenemase-producing isolates were identified by mCIM/eCIM. PCR and RT-qPCR detected key genes, including cas3, involved in CRISPR-Cas function. In silico analyses included STRING for protein interactions, CRISPRCasdb for CRISPR subtype distribution, and Phyre2/AlphaFold for cas3 structure prediction.
Results: Among the isolates, 35.2% were resistant to carbapenems. Among CRKP strains, high prevalence of bla-NDM-1 (82%) and bla-OXA-48 (64%) was observed. The cas3 expression was significantly upregulated in resistant isolates (P = 0.002). CRISPR subtype I-E was identified in 16% of CRKP and 36% of CSKP isolates. Structural-functional analysis supported the integrity of Cas3 and revealed interactions with regulatory and iron acquisition proteins. Statistically significant differences in virulence and resistance gene profiles were found between CRKP and CSKP groups (P < 0.05).
Conclusion: This study highlights key differences between CRKP and CSKP isolates, particularly in CRISPR-Cas systems, resistance, and virulence. The findings suggest that cas3 plays a critical role in genomic adaptation and resistance mechanisms in K. pneumoniae, offering insights for future therapeutic strategies.

Detection and prevalence of the blaNDM-1 gene in carbapenem-resistant Klebsiella pneumoniae bloodstream isolates from a tertiary care institute

Sat, 14 Feb 2026 14:31:59 +0330

Background and Objectives: Carbapenem resistance mediated by bla_NDM-1 in Klebsiella pneumoniae has emerged as a major challenge, particularly in intensive care settings with high antibiotic pressure. This compromises therapeutic options and contributes to poor clinical outcomes. The present study aimed to determine the prevalence of bla_NDM-1 among isolates of K. pneumoniae from a tertiary care hospital, evaluate the performance of phenotypic tests against PCR-based detection, assess antimicrobial susceptibility profiles, and analyze clinical outcomes.
Materials and Methods: In this study, over 18 months, 130 non-duplicate K. pneumoniae isolates were identified, and antimicrobial susceptibility testing was performed by VITEK-2 Compact and broth microdilution for colistin. Imipenem-resistant isolates were subjected to the Combined disc diffusion test (CDDT) and Double disc synergy test (DDST) for metallo-beta-lactamase (MBL), and conventional PCR targeting bla_NDM-1. Demographic data and outcomes were recorded.
Results: Of the 130 isolates, 111 were imipenem-resistant, of which CDDT detected MBLs in 94.6%, and DDST detected MBLs in 76.6%. PCR confirmed bla_NDM-1 in 77.5% and was more commonly associated with cases of sepsis. bla_NDM-1 -positive isolates were resistant to β-lactams, fluoroquinolones and aminoglycosides. No isolate was found to be colistin-resistant. 26.7% of the patients with bla_NDM-1 -positive bacteremia died.
Conclusion: This study highlights the high prevalence of bla_NDM-1 in K. pneumoniae isolates. Among the phenotypic tests, CDDT outperformed DDST and showed the best agreement with PCR, supporting its use as a screening method for MBL, but confirmatory PCR remains essential. The restricted treatment options underscore the need for stringent infection control and robust antimicrobial stewardship to curb transmission and preserve last-line agents.

Detection and distribution of carbapenemase-encoding genes in clinical Klebsiella pneumoniae isolates from Kayseri, Türkiye

Thowiba Yousif Jameel, Abdurrahman Ayvaz, Pınar Sağıroğlu, Mustafa Altay Atalay — Sat, 14 Feb 2026 14:37:11 +0330

Background and Objectives: Carbapenem Resistance Klebsiella pneumonia (CRKP ), mostly caused by carbapenemase enzymes, poses a serious public health threat due to limited treatment options. This study aimed to genotypically identify carbapenemase-encoding genes in CRKP isolates recovered from fecal swabs and to correlate these genotypes with phenotypic antibiotic resistance profiles.
Materials and Methods: In this study, fecal samples from 150 hospitalized patients were screened for K. pneumoniae. Phenotypic testing included the Phoenix automated system, CHROMagar KPC, biochemical tests, and disk diffusion assays. Genotypic analysis was performed using the BD MAX Checkpoint CPO PCR test, marking its first use in Kayseri, Türkiye, to detect carbapenemase genes in this pathogen.
Results: Out of 150 fecal samples, 47 tested positive for K. pneumoniae, with 28 (59.6%) identified as carbapenem-resistant (CRKP). Molecular analysis identified five distinct carbapenemase gene patterns among these resistant isolates. The most prevalent gene, bla_OXA-48, was found alone in 60.7% of CRKP isolates, followed by bla_NDM in 3.6%; bla_KPC was not detected. Co-occurrence of genes was observed as follows: bla_OXA-48/bla_NDM (14.3%), bla_OXA-48 with bla_VIM/bla_IMP (10.7%), and bla_OXA-48 with bla_NDM and bla_VIM/bla_IMP (10.7%) in CRKP clinical isolates.
Conclusion: The study found that bla_KPC was consistently absent, while bla_OXA-48 was highly prevalent and exhibited co-occurrences of carbapenemase genes. It underscored the need for strict hospital surveillance and effective infection control to prevent the spread of CRKP strains. Rapid molecular methods, such as the BD MAX multiplex PCR, have shown promise in accurately and efficiently identifying carbapenemase genes.

Burden and resistance of Gram-negative pathogens in ICU-acquired infections in Vietnam: a cross-sectional study

Sat, 14 Feb 2026 14:40:56 +0330

Background and Objectives: This study aimed to describe the burden, pathogen distribution, antimicrobial resistance patterns, and selected clinical outcomes of intensive care unit (ICU)-acquired Gram-negative bacteria (GNB) infections in Vietnam, with exploratory comparative analyses of outcomes.
Materials and Methods: A retrospective descriptive study with comparative analyses was conducted among 102 adult patients with culture-confirmed ICU-acquired GNB infections at E Hospital, Hanoi. Demographic, clinical, microbiological, and outcome data were extracted from medical records. Antimicrobial susceptibility testing was performed according to Clinical and Laboratory Standards Institute guidelines. Comparisons between outcome groups were assessed using chi-square test, with effect sizes quantified using Cramer’s V.
Results: Pneumonia was the predominant infection (70.5%), followed by urinary tract (15.2%) and bloodstream infections (10.6%). GNB accounted for 68.3% of all hospital-acquired infections (HAIs), with Acinetobacter baumannii (43.4%), Pseudomonas aeruginosa (24.8%), and Klebsiella pneumoniae (13.9%) being the most frequent pathogens. The predominant pathogens exhibited extensive resistance to β-lactams, cephalosporins, and carbapenems. Susceptibility was largely retained only to colistin, tigecycline, and amikacin. Mechanical ventilation was significantly associated with death or a severe clinical outcome (p = 0.03; Cramer’s V = 0.21).
Conclusion: GNB dominate ICU-acquired infections in Vietnam and demonstrate alarming antimicrobial resistance, underscoring the urgent need for strengthened infection control and antimicrobial stewardship.

Incidence, microbial profile and antimicrobial resistance trends of CLABSI in adult ICUs: a longitudinal prospective study

Sat, 14 Feb 2026 14:43:00 +0330

Background and Objectives: Central line-associated bloodstream infections (CLABSIs) remain a major cause of healthcare-associated mortality, prolonged hospitalization, and increased healthcare costs, especially in resource-poor settings where surveillance data are scarce. This study aimed to determine CLABSI incidence, risk factors, causative organisms, and antimicrobial resistance (AMR) patterns across adult intensive care units (ICUs).
Materials and Methods: A prospective longitudinal study was conducted amongst 200 adult ICU patients with central line (CL) in-situ for >2 calendar days. CLABSI surveillance followed definitions by The Centers for Disease Control and Prevention, National Healthcare Safety Network. Microbiological identification and antimicrobial susceptibility testing were performed according to Clinical and Laboratory Standards Institute (CLSI) guidelines.
Results: The overall CLABSI incidence was 19.25/1,000 catheter days. CLABSI patients demonstrated significantly extended hospitalization (20.22 vs 9.09 days, p<0.001) and CL duration (16.17 vs 7.85 days, p<0.001). Femoral lines had the highest infection rate (42.85%). The median time from CL insertion to the onset of CLABSI was 7.5 days. Gram-negative organisms predominated (75%), with Acinetobacter species being most frequent (36.1%), followed by Candida species (22.23%). Comorbidities such as hypertension, type 2 diabetes mellitus, tuberculosis, and drug abuse showed no significant association with CLABSI. Antimicrobial resistance (AMR) was extensive; all isolates were resistant to most antibiotic classes, including penicillins, cephalosporins, and carbapenems. In contrast, colistin retained 100% susceptibility. CLABSI was associated with significantly higher mortality (69.4% vs. 47%; p = 0.014) and a lower rate of discharge/transfer to a healthy setting (p = 0.0112) compared to non-CLABSI patients.
Conclusion: The study demonstrates high CLABSI incidence and alarming levels of AMR, underscoring the urgent need for strengthening infection prevention practices and antimicrobial stewardship in ICUs.

Chromosome-borne blaCTX-M-65 gene in non-O1/O139 Vibrio cholerae isolated from bile

Haifeng Mao, Xinzhe Wu, Danting Jin — Sat, 14 Feb 2026 14:45:24 +0330

Background and Objectives: Non-O1/O139 Vibrio cholerae (NOVC) has been associated with extraintestinal infections; however, its isolation from bile remains exceedingly rare. This study reports the identification and comprehensive analysis of a NOVC strain isolated from bile, including its antimicrobial resistance profile, virulence gene content, and molecular characteristics.
Materials and Methods: A NOVC isolate was obtained from the bile of a patient with a hepatobiliary tumor. The isolate was identified and subjected to antimicrobial susceptibility testing. Whole-genome sequencing was performed to characterize its molecular features, including antimicrobial resistance genes, virulence genes, and relevant genetic mutations.
Results: The NOVC isolate presents a multi-drug resistance phenotype. Corresponding genomic analysis indicates that this strain belongs to a novel sequence type (ST1736), carrying various drug resistance genes and virulence factors. Moreover, the bla_CTX-M-65 extended-spectrum β-lactamase (ESBL) gene was detected in its chromosomal genome.
Conclusion: This study presents the first report of a multidrug-resistant NOVC strain isolated from bile in mainland China. Notably, the ESBL gene bla_CTX-M-65 was identified chromosomally in NOVC for the first time.

Presence and copy number variations of H. pylori, pks⁺ bacteria, E. faecalis, and B. bifidum in colorectal cancer: an integrated study using FFPE tissue samples

Sat, 14 Feb 2026 14:47:38 +0330

Background and Objectives: Colorectal cancer (CRC) is a leading malignancy with multifactorial etiology, including genetic, environmental, and microbial factors. Bacteria such as Helicobacter pylori, pks⁺ bacteria, Enterococcus faecalis, and Bifidobacterium bifidum have been linked to CRC, though their roles remain controversial. Some may promote inflammation and genotoxicity, while others may confer protective effects. This study assessed the presence and relative abundance of these bacteria in colorectal FFPE tissue samples.
Materials and Methods: This case-control study included three groups of FFPE tissue samples: tumor tissues from CRC patients (Tumor, n=50), normal tissues adjacent to tumors (Adjacent, n=50), and normal tissues from non-CRC individuals (Normal, n=30). Sections were prepared with a microtome, and bacterial gene copy numbers were quantified using species-specific primers and quantitative real-time PCR, normalized to human GAPDH. Associations with age, sex, and neoplastic type were analyzed (p < 0.05).
Results: B. bifidum was significantly higher in Adjacent tissues compared to Tumor and Normal (p < 0.0001). H. pylori detection increased progressively from Normal to Adjacent to Tumor tissues (p = 0.002). pks⁺ bacteria were detected only in individuals ≥60 years (p = 0.014). E. faecalis load was higher in Tumor tissues of females and older adults, though overall presence did not differ significantly among groups.
Conclusion: Enrichment of B. bifidum and increased H. pylori detection near tumors suggest the tumor microenvironment favors bacterial persistence. Age- and sex-related patterns in pks⁺ and E. faecalis highlight host influences on microbial distribution in CRC, supporting further mechanistic studies.

Evaluation of fosfomycin susceptibility using CLSI vs EUCAST criteria among multi drug resistant uropathogens in a tertiary care Hospital

Arun Sachu, Alice David — Sat, 14 Feb 2026 14:52:15 +0330

Background and Objectives: Urinary Tract Infections (UTIs) are most frequently caused by uropathogenic Escherichia coli, which accounts for approximately 80% of the cases. Other causative agents include Klebsiella spp., Proteus spp., Enterobacter spp., Enterococcus spp., and Staphylococcus saprophyticus. The main objectives of the study were to estimate the in vitro antimicrobial activity of fosfomycin against multidrug-resistant uropathogens (MDR) isolated from patients with suspected UTI using CLSI and EUCAST criteria and to describe the antimicrobial susceptibility pattern of uropathogens isolated during the study.
Materials and Methods: This was a descriptive study in which a total of 900 urine samples were collected from patients presenting with physician-assessed signs and symptoms suggestive of a UTI. Only samples exhibiting significant bacteriuria that were also multidrug-resistant (MDR) were included. Although fosfomycin disk diffusion criteria, according to CLSI and EUCAST, are only validated for E. coli, susceptibility among other Gram-negative bacteria was also interpreted using the same criteria. This represents a major limitation of the study.
Results: In the study, 251 samples grew multi drug resistant organisms. Only 57% of the Gram-negative isolates were sensitive according to EUCAST guidelines, while 87.6% of all isolates were sensitive by CLSI criteria. Among the 161 carbapenem-resistant isolates, 135 (83.9%) were fosfomycin-susceptible and 18 (11.2%) were resistant according to CLSI. In contrast, by EUCAST criteria, only 40 (24.9%) isolates were fosfomycin-susceptible, and the remaining 121 (75.1%) were resistant.
Conclusion: Our study showed that using fosfomycin disc diffusion criteria of E. coli for other organisms is not ideal; therefore, performing an alternative form of susceptibility testing for non-E. coli isolates is recommended. Continuous monitoring of fosfomycin susceptibility is warranted to detect any emerging resistance and to guide its clinical application.

The antimicrobial effects of cord blood-derived platelet gel on nosocomial pathogens

Akbar Hashemi Tayer, Gholamreza Shokoohi — Sat, 14 Feb 2026 15:03:53 +0330

Background and Objectives: Umbilical cord blood-derived platelet gel (CBPG) is rich in growth factors (GFs) and antimicrobial peptides. This study evaluated its in vitro antibacterial and antifungal activity against dominant nosocomial pathogens.
Materials and Methods: In this experimental study, CB samples were taken from 12 healthy pregnant women post-cesarean at Motahari Hospital, Jahrom. Platelet -rich plasma (PRP) was isolated using a two-step centrifugation protocol (soft-spin: 200×g, 10 min; hard spin:1000×g, 15 min, 22°C) and activated with calcium and human thrombin to form PG. Antimicrobial effect of PG was determined against Klebsiella pneumoniae, Methicillin-resistant Staphylococcus aureus (MRSA), Acinetobacter baumannii, Pseudomonas aeruginosa, Candida albicans, Aspergillus spp., and Penicillium spp. using broth microdilution and time-kill assays per CLSI guidelines.
Results: PG exhibited strong bacteriostatic activity against MRSA and K. pneumoniae (MIC 2.2–2.8 × 10⁸ platelets/mL; 1.7-1.8 log₁₀ reduction at 24 h, p < 0.001), while PRP was moderately active and PPP was ineffective. No significant activity was observed against P. aeruginosa or A. baumannii (p= 0.2). PG showed sustained fungistatic effects (MIC: 1.9-4.2× 10⁸ platelets/mL up to 72 h).
Conclusion: CBPG exhibits potent bacteriostatic and fungistatic effects, particularly against MDR Gram-positive bacteria, offering a novel autologous antimicrobial.

Prophage typing of Staphylococcus aureus in traditional dairy products of Ilam, Iran

Ali Abbas Hashemi, Mostafa Nemati, Fazel Pourahmad — Sat, 14 Feb 2026 15:06:04 +0330

Background and Objectives: Antimicrobial resistance (AMR), particularly from methicillin-resistant Staphylococcus aureus (MRSA), poses a significant public health threat, exacerbated by antibiotic misuse in livestock and food production. This study aimed to evaluate the prevalence of MRSA in traditional dairy products from Ilam, Iran, and explore the role of prophages in enhancing bacterial virulence and resistance, assessing their implications for food safety.
Materials and Methods: Between January and April 2021, 116 dairy samples (raw milk, traditional cheese, and toof) were collected from Ilam, Iran. Staphylococcus aureus was identified using bacteriological and molecular methods, including PCR targeting femA, mecA, and prophage markers (SGB, SGFa, SGFb). Antibiotic susceptibility was tested via the Kirby-Bauer method, and data were analyzed using SPSS.
Results: S. aureus was detected in 25.9% of samples (30/116), with raw milk showing the highest contamination (57.9%). MRSA, identified by the mecA gene, was present in 6.7% of isolates, and 73.3% exhibited multidrug resistance. Prophages were found in 13.3% of isolates, with SGB linked to β-lactam resistance (p = 0.04). High resistance to doxycycline (87%) and tetracycline (67%) was observed.
Conclusion: The study highlights a significant presence of MRSA and multidrug-resistant S. aureus in Ilam’s dairy products, with prophages contributing to the virulence of these bacteria. Enhanced hygiene and monitoring are crucial for mitigating food safety risks.

Comparative evaluation of outer membrane protein and whole cell antigen vaccine against avian pathogen Escherichia coli infection in broiler chicken

Sat, 14 Feb 2026 15:07:53 +0330

Background and Objectives: Present study was aimed at assessing protective efficacy of outer membrane protein (OMP) vaccine in comparison to inactivated whole cell antigen vaccine after challenge with homologous serogroup (O2) of avian pathogenic Escherichia coli in broiler chickens.
Materials and Methods: The outer membrane proteins were extracted by sarcosyl method and protein concentration was determined by nanodrop spectrophotometer. The study comprised of 120 birds divided into 6 groups. The birds were subcutaneously immunized twice with primary vaccine in the first week followed by booster vaccine in second week.
Results: The protection rate of 82% was found in whole cell inactivated antigen, 91% in OMP vaccine and 27% among the unvaccinated group. The antibody (IgG) response was found significantly higher in OMP vaccine group than whole cell antigen group. In unvaccinated groups chicks, the antibody titer never reached to the protective level till the termination of experiment. The bacteria were re-isolated from the infected broiler chickens for the confirmation of induced infection and were characterized using standard cultural and biochemical tests belonging to O2 serogroup.
Conclusion: Our study demonstrated that the outer membrane protein (OMP) vaccine provided significantly higher protection (91%) and antibody response compared to the inactivated whole cell antigen vaccine (82%) against Escherichia coli O2 infection in broiler chickens. Birds vaccinated with OMP exhibited fewer pathological lesions and a stronger immune response. The findings underscore the potential of OMP-based vaccines as a safer, more immunogenic alternative for controlling colibacillosis.

Immunological and virological response in HIV-1 infected patients receiving active antiretroviral therapy at a tertiary care center in Northern India

Sat, 14 Feb 2026 15:10:00 +0330

Background and Objectives: Human Immunodeficiency Virus (HIV) remains a major global health challenge, with limited Indian data on factors influencing treatment outcomes. This study assessed immunological and virological responses and survival determinants among treatment-naïve HIV-1–positive adults.
Materials and Methods: A retrospective observational study was conducted at a tertiary care centre from May 2022 to April 2023. Adults (≥18 years) who initiated first-line ART (TDF + 3TC + DTG) between January 2019 and December 2020 with 24-month follow-up were included. Baseline demographics, CD4 count, viral load, and adherence were analysed using descriptive statistics and logistic regression.
Results: Of 452 screened patients, 355 were eligible. Mortality at 6, 12, and 24 months was 22%, 26.8%, and 29.9%, respectively, with overall survival of 70.1%. Baseline CD4 count, viral load, adherence, and ART initiation timing significantly influenced outcomes (p < 0.05). Patients with baseline between 200 to 350 had almost 7 times the odds of survival compared to those with <200 cells/µL. Early ART initiation (≤7 days) improved survival (3-fold) and viral suppression (2.4-fold), while adherence >95% was the strongest predictor of success. Older age and high viral load predicted poorer outcomes.
Conclusion: Early ART initiation, strict adherence, and favourable baseline markers significantly improved survival and suppression, supporting the “test-and-treat” approach and the UNAIDS 95-95-95 targets.

Molecular characterization of cytomegalovirus based on glycoprotein B and N among solid organ and hematopoietic stem cell transplant recipients in Jordan

Sat, 14 Feb 2026 15:11:59 +0330

Background and Objectives: Cytomegalovirus (CMV), a prevalent member of the herpesvirus family, poses significant risks to immunocompromised patients, particularly those undergoing hematopoietic stem cell transplantation (HSCT) or solid organ transplantation (SOT). This study aimed to assess the prevalence and genotype distribution of CMV among transplant recipients in Jordan.
Materials and Methods: A retrospective observational study conducted at the Jordan Royal Medical Service's Virology Department from January to October 2024, included all patients who underwent HSCT or SOT. Blood samples collected in EDTA tubes were analyzed for CMV detection and genotyping. Real-time PCR facilitated CMV amplification, while multiplex nested PCR identified gB and gN genotypes.
Results: Among 80 transplant recipients with positive CMV DNA, 15 (18.8%) were from SOT kidney transplants (KT), and 65 (81.2%) were HSCT recipients. Genotype analysis of 44 samples revealed that 21 had the gN genotype and 27 had the gB genotype. Mixed genotypes gB and gN were present in 15 samples. The mixed genotype gN1+gN2 (42.86%) was most common in KT recipients, while gB2 (31%) was prevalent among HSCT recipients.
Conclusion: CMV is a common opportunistic virus that often leads to severe, life-threatening illness and is associated with an increased risk of transplant rejection. Our study demonstrated that the most prevalent genotypes in Jordanian HSCT and SCT recipients with CMV infection were gB2 and gN1+gN2, respectively.

Molecular characterization of human rhinovirus strains detected in pediatric acute respiratory tract infections

Sun, 15 Feb 2026 20:47:50 +0330

Background and Objectives: Acute respiratory tract infections (ARTI) are a leading cause of morbidity and mortality in children worldwide, accounting for approximately 18% of deaths in those <5 years of age. Viruses cause 50-90% of pediatric ARTI cases. Human rhinovirus (HRV) is increasingly associated with lower respiratory tract infections (LRTIs). This study aimed to detect HRV in pediatric ARTI cases and characterize circulating genotypes.
Materials and Methods: Nasopharyngeal swabs from 154 children (≤5 years) presenting with ARTI were screened for HRV using real-time PCR. Thirteen samples with a cycle threshold ≤30 were sequenced. Phylogenetic analysis was performed using 41 global reference sequences representing different geographical regions and HRV types.
Results: HRV was detected in 34.41% (53/154) of the samples. In children aged >1 month to 1 year, HRV positivity was significantly associated with severe acute respiratory infection (SARI) compared with influenza-like illness (ILI). Phylogenetic analysis revealed a predominance of HRV-C strains (n = 7), followed by HRV-A (n = 5) and HRV-B (n = 1).
Conclusion: HRV was detected in a significant proportion of pediatric ARTI cases, with HRV-C as the predominant strain. Infants aged >1 month to 1 year showed a higher association with severe illness, underscoring the need for closer clinical monitoring in this age group.

Detection of echovirus 7 in effluent sewage treatment plant Ahvaz city, Iran

Sun, 15 Feb 2026 20:50:30 +0330

Background and Objectives: The enteroviruses may lead to conditions such as aseptic meningitis, encephalitis, acute flaccid myelitis, epidemic pleurodynia (Bornholm disease), hemorrhagic conjunctivitis, and myopericarditis among pediatric populations. The present study was undertaken to identify the presence of enteroviruses within sewage treatment systems.
Materials and Methods: 24 composite effluent sewage samples (500 ml each) were collected, centrifuged (1000 rpm for 30 minutes), and the first supernatant was saved. The precipitate was resuspended in 10 ml of supernatant, treated with 10% chloroform, and centrifuged again (1000 rpm for 5 minutes) to collect a second supernatant. The first and second supernatants were combined, treated with 2.2% sodium chloride and 7% polyethylene glycol 6000, and the mixture was agitated at 4°C overnight before being centrifuged for two hours at 2000 g. After discarding the supernatant, the pellet was resuspended at a 1:100 dilution. Each sample was then inoculated into RD and HeLa cells for virus isolation, followed by detection via RT-PCR. A phylogenetic tree was constructed to determine the genotypes of the isolated enteroviruses.
Results: Enterovirus was detected in 10 of 24 (41.7%) sewage effluent samples. Phylogenetic analysis of five randomly chosen positive samples identified echovirus 7.
Conclusion: The removal of enteroviruses during the sewage treatment process is of paramount importance, necessitating heightened attention to this critical phase of wastewater management.

Candiduria in catheterized ICU patients: epidemiology, molecular identification, and antifungal susceptibility

Sun, 15 Feb 2026 20:53:03 +0330

Background and Objectives: Candiduria related to urinary catheters is frequently encountered in patients hospitalized in intensive care units. The diagnosis and management of catheter-associated candiduria in hospitalized patients is frequently a gray area for both physicians and microbiologists because of the paucity of clinical and microbiological data.
Materials and Methods: This cross-sectional study aims to enhance the understanding of candiduria among adult ICU patients with urinary catheters across three hospitals in Tehran, Iran. Yeast identification was performed using a two-step multiplex PCR, and antifungal susceptibility testing was performed following the CLSI M27, 4^th edition,
recommendations.
Results: Among the 110 enrolled ICU patients, 38 (35%) had significant candiduria. A total of 45 yeast isolates were collected. The distribution was as follows: Candida glabrata (23/45; 51%), C. albicans (14/45; 31%), and C. tropicalis (4/45; 9%). These three species accounted for 91% of the isolates. Antifungal resistance was detected: six isolates (two C. glabrata, two C. albicans, one C. krusei, and one C. tropicalis) were fluconazole-resistant, and one C. glabrata isolate was resistant to itraconazole, voriconazole, and caspofungin. All isolated species were susceptible to amphotericin B. Symptomatic candiduria occurred in 29% of cases (11/38); only 55% (6/11) were treated, and of those, 50% (3/6) experienced fluconazole treatment failure. One symptomatic patient developed candidemia shortly after acquiring candiduria. The mortality rate was 21% (8/38), with no apparent difference in death rates between symptomatic and asymptomatic candiduric patients.
Conclusion: Our findings reveal that high fluconazole failure rates among patients with symptomatic candiduria are concerning. Furthermore, speciation and antifungal susceptibility testing are crucial, as they guide clinicians in selecting the most effective agent and improving case management.

Clinical profile and outcome of COVID-19 associated mucormycosis in Shiraz, South Iran: a longitudinal study

Sun, 15 Feb 2026 20:55:00 +0330

Background and Objectives: Numerous cases of mucormycosis appeared among COVID-19 patients, predominantly in Asian countries. This study aimed to investigate the clinical profile, in-hospital outcome, and one-year prognosis of COVID-19-associated mucormycosis (CAM).
Materials and Methods: All patients who developed CAM in Shiraz, South Iran, between July and October 2021 were included in this study. We collected data on presentations, comorbidities, risk factors, and outcomes.
Results: Sixty-two patients with CAM were analyzed; the mean age was 59.3 years, and 58.1% were male. Diabetes mellitus was present in 80.6% (11.2% uncontrolled), hypertension in 54.8%, and chronic kidney disease in 11.3%. All patients had sinonasal involvement; ophthalmic, cutaneous, cerebral, gastrointestinal, pulmonary, and renal involvement occurred in 41.9%, 8.1%, 6.4%, 6.4%, 1.6%, and 1.6%, respectively. In-hospital and one-year mortality were 40.3% and 48.3%. Concurrent CAM and COVID-19, hypertension, older age, and radiologically severe COVID-19 lung involvement were associated with higher mortality. In multivariable analysis, age ≥60 years predicted in-hospital (OR: 5.47; 95% CI: 1.53-19.56) and one-year mortality (OR: 7.65; 95% CI: 1.90-30.84). Long-term mortality was also associated with ≥3 risk factors (OR: 4.12; 95% CI: 1.09-15.52) and lung severity index >30 (OR: 9.35; 95% CI: 1.01-86.63).
Conclusion: These findings emphasize the critical role of age in immune responses to opportunistic infections and highlight the impact of multiple comorbidities and severe lung damage on long-term prognosis in CAM.

Drug susceptibility of Candida albicans and non-albicans Candida species isolated from ornamental birds

Zahra Mirhosseini, Jamshid Razmyar, Alireza Khosravi — Sun, 15 Feb 2026 20:57:41 +0330

Background and Objectives: The prevalence of Candida infections, especially by non-albicans Candida species, has led to excessive use of antifungal drugs, resulting in the transfer of resistance and increased minimum inhibitory concentration (MIC) among Candida isolates. This study aimed to investigate the susceptibility of clinical Candida isolates of ornamental birds to three antifungal drugs: amphotericin B, caspofungin, and itraconazole.
Materials and Methods: Totally 126 samples were analyzed, from which 116 distinct colonies were cultured. Of these, 26 were identified as Candida spp., comprising 12 C. albicans (46.1%), 8 C. tropicalis (30%), 1 C. glabrata (3%), 1 C. krusei (3%), and 4 isolates (15%) of other Candida species. The present study aimed to determine the susceptibility and resistance levels of these Candida isolates to three antifungal drugs: amphotericin B, caspofungin, and itraconazole.
Results: According to the CLSI M44 recommended method, by the disk diffusion method, itraconazole (100%) and amphotericin B (86.46%) showed the best susceptibility pattern, compared to caspofungin (0%).
Conclusion: Given that the isolates showed the highest in vitro susceptibility to itraconazole and amphotericin B and the lowest to caspofungin, these findings suggest that itraconazole and amphotericin B could be considered potential first-line agents for treating avian candidiasis.

Aflatoxin-producing Aspergillus flavus from food samples in Nepal

Sun, 15 Feb 2026 20:59:45 +0330

Background and Objectives: Maize and peanuts, staple foods in Nepal, are highly susceptible to fungal contamination, particularly with aflatoxin-producing Aspergillus flavus. This study aimed to detect aflatoxin-producing A. flavus in maize and peanut samples collected from different regions of Nepal.
Materials and Methods: A total of 80 maize and 20 peanut samples were collected randomly from markets and households. Disinfected samples were inoculated on Potato Dextrose Agar and incubated at 28°C for 48 hours. A. flavus was identified by conventional cultural methods. Aflatoxin production was screened on Aspergillus Differential Medium (ADM) and confirmed through Thin Layer Chromatography (TLC) and High Performance Liquid Chromatography (HPLC).
Results: Fungal contamination was detected in 67.0% of samples, with a significantly higher rate in household-stored samples (p = 0.00039). A. flavus was the predominant species, particularly in maize (72.5%). Of 50 A. flavus isolates, 15 (30%) were aflatoxin positive on ADM, with 11 (73.3%) being confirmed by TLC. HPLC revealed AFB1 as the most prevalent in both maize and peanuts, while AFB2 was restricted to maize.
Conclusion: Maize and peanuts are highly susceptible to contamination with aflatoxin producing A. flavus in Nepal, particularly in household-stored samples, emphasizing significant food safety concerns.