Enterococcus faecalis is among the leading causes of hospital-acquired infections worldwide. This bacterium has both intrinsic and acquired resistance to various antibiotics. The continuous development of antibiotic resistance by pathogens poses a challenge that economically and technologically restricts the discovery of next-generation antibiotics. Therefore, many researchers aim to develop new strategies to combat this pathogen. The aim of this study was to evaluate the synergistic antimicrobial and antibiofilm effects of the combination of antimicrobial agents such as chlorhexidine (CHX), ethylenediaminetetraacetic acid (EDTA) and sodium hypochlorite (NaOCl) with nisin against clinical and food isolates of E.faecalis. Nisin produced by wild-type and recombinant Lactococcus lactis strains was purified and their activities were evaluated in comparison with commercial nisin. The minimum inhibitory concentration (MIC) and minimum biofilm eradication concentration (MBEC) of the agents were determined using microplate dilution methods. Antibiofilm activities were visualized using scanning electron microscopy (SEM). The MIC values for CHX, EDTA, and NaOCl were determined as 0.0002%, 5 mM, and 0.50%, respectively. The MIC values of nisin for all tested strains and isolates ranged from 12.5 to 100 IU/ mL. Synergistic interactions of the antimicrobial agents were determined using the checkerboard method, revealing that the most effective combination was the combination of nisin and EDTA. Similarly, the most effective combination for eradicating 24-hour biofilms was nisin + EDTA (1000 IU/mL + 10 mM). The concentration of nisin in this combination was lower than its MBEC value (1500 IU/mL). While the combination of nisin with CHX and NaOCl achieved complete eradication of biofilms, the agents alone were ineffective in achieving such results. SEM images showed that although E.faecalis biofilms were not completely eradicated, they were significantly disrupted as a result of the combined application of nisin with antimicrobial agents. These in vitro findings indicate that the combination of nisin and EDTA may be effective against biofilm structures formed by clinical and food-derived E.faecalis isolates and demonstrate the potential of this combination for practical applications. Considering the different resistance profiles of clinical and food isolates, our study emphasizes the need to tailor treatment strategies according to the distinct characteristics of the bacterial strains involved. The results provide a scientific basis for future combination-based studies aimed at enhancing antibiofilm efficacy against E.faecalis.

Monitoring of viral load is of critical importance in the clinical management of patients at risk of cytomegalovirus (CMV)-related complications following transplantation. Quantitative real-time polymerase chain reaction (qRT-PCR) is one of the most commonly used methods for CMV DNA detection. For this purpose, commercial test kits calibrated according to the International Standard of Quantitation (ISQ) defined by the World Health Organization (WHO) are used. However, measurement variability between different test systems still constitutes a significant problem. The aim of this study was to compare the test results of two different commercial kits, CMV Cobas Ampliprep/Cobas Taqman (CMV-CAP/CTM) (Roche Diagnostics, Mannheim, Germany) and NeuMoDx CMV Quant Assay (Qiagen, Ann Arbor, USA) which have been calibrated with the WHO CMV IQS. The results of 478 plasma samples run simultaneously with the CMV-CAP/CTM and NeuMoDx CMV PCR tests were analyzed. Fully automated steps including extraction, real-time amplification and result analysis were performed according to the manufacturer’s recommendations. CMV DNA was detected in 216 (45.18%) samples and not detected in 82 (17.15%) samples in both tests. A total of 180 (37.65%) samples had discordant results. Statistically, a moderate level of qualitative agreement was found between the qualitative results of both tests (kappa= 0.28, p< 0.001). When the quantitative results obtained in the dynamic measurement range of both tests (n= 104) were examined, the median viral load values measured by CMV-CAP/CTM and NeuMoDx CMV tests were calculated as 1598 IU/mL (range= 137.41-115570) and 2600 IU/mL (range= 55-220000), respectively. According to the correlation analysis, a very strong correlation was found in the comparison of the results of both tests (r= 0.83, p< 0.001). According to the Bland-Altman analysis; the average difference between the CMV-CAP/CTM test and NeuMoDx CMV test values was found to be 0.296 log10 (standard deviation: 0.412) IU/mL (the lowest difference was 0.005 and the highest difference was -1.559 log10 IU/mL), and the CMV-CAP/CTM test gave lower measurements than the NeuMoDx CMV test. In 104 samples with results in the dynamic measurement range of both tests, for log10 IU/mL results, the measurement difference was within ±0.5 log10 IU/mL in 71 (quantitative agreement: 68.3%) samples and the measurement difference was greater than ±0.5 log10 in 33 (31.7%) samples (median= 0.7 log10 IU/ml; range: 0.51-1.56). A measurement difference of more than ±1 log10 was detected in two samples (1.9%). As a result, in the measurements made with CMV-CAP/CTM and NeuMoDx CMV PCR tests, a moderate level of agreement was found for qualitative results in plasma samples, a strong correlation for quantitative values and a biologically significant viral load difference in one-third of the samples was detected. Our study shows that the measurement differences observed between CMV PCR test platforms do not completely disappear even if calibration is provided with the WHO ISQ. In post-transplantation follow-up, considering the measurement differences between test systems and preferring the same sample type and the same test platform in CMV viral load monitoring is important in terms of ensuring consistency in patient management.

Burkholderia cepacia is an environmental bacterium that can cause nosocomial infections, particularly in immunocompromised patients. This study aimed to describe a hospital outbreak caused by B.cepacia. In our hospital, we observed an unusual increase in B.cepacia growth in blood culture samples, prompting the infection control team to initiate a retrospective investigation due to concerns about a potential outbreak. Since February 2023, we have detected a rise in B.cepacia isolations from specimens of patients hospitalized in the intensive care unit (ICU). As a result, we retrospectively reviewed patient data from the ICU with positive cultures in blood, tracheal aspirate, urine and other sterile body fluids between October 2022 and December 2023. The outbreak was defined as starting in February 2023 and ending in December 2023. During this period, we evaluated clinical data from infected patients, laboratory results and environmental samples (including medical devices and hygiene products). Bacteria isolated from patient and environmental samples were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS Microflex LT/SH Smart MS, Bruker Daltonics, USA). The genetic relatedness of B.cepacia isolates identified by MALDI-TOF MS was determined using 16S rRNA typing. To control the outbreak, contact isolation, enhanced hand hygiene protocols, environmental disinfection and discontinuation of foam soap use were implemented. Additionally, based on culture results, we performed de-escalation to reduce unnecessary use of broad-spectrum antibiotics. A total of 155 patients in the ICU were found to have B.cepacia growth, compared to only 13 patients in clinical wards. Among the patients with B.cepacia growth, 55.4% were diagnosed as B.cepacia infection. Of these, 78 (83.9%) had bloodstream infections, seven (7.5%) had ventilator-associated pneumonia, four (4.3%) had hospital-acquired pneumonia, three (3.2%) had urinary tract infections and one (1.1%) had peritonitis. Overall, 39.8% of patients died due to sepsis. Patients without a diagnosis of infection were considered colonized. We detected B.cepacia growth in 43.8% of foam soap samples used in the ICU. The bacterium was also isolated from unopened soap bottles, and 16S rRNA analysis showed that 23 strains isolated from patients and foam soaps were phylogenetically related. Colony counts of B.cepacia in foam soap cultures exceeded 1000 CFU/mL, surpassing the acceptable limits stated in the “Guidelines for the Safety Assessment of Cosmetic Products.” Trimethoprim-sulfamethoxazole was identified as the antibiotic with the highest susceptibility rate among our clinical isolates. We contacted the manufacturer of the foam soaps used in our hospital to identify and eliminate the source of the contamination. The outbreak lasted approximately 270 days, from February to November 2023. This outbreak highlights that despite its low virulence, B.cepacia can pose a serious threat to critically ill ICU patients and underscores the importance of microbiological monitoring of hospital-use products. The absence of adequate quality control procedures for commonly used hygiene products, such as foam soaps, can lead to nosocomial outbreaks associated with high morbidity and mortality. Therefore, strict adherence to infection control measures and regulatory standards is essential in the delivery of healthcare services.

Mucormycosis is a rare, difficult-to-diagnose, angioinvasive fungal disease with high morbidity and mortality. It is classified into clinical categories based on the anatomical regions involved. The most common clinical form is rhino-orbito-cerebral mucormycosis (ROCM). In this study, we aimed to identify the risk factors for mortality in cases of rhino-orbito-cerebral mucormycosis (ROCM). We retrospectively evaluated histopathologically and/or microbiologically confirmed ROCM cases in patients over the age of 18, diagnosed in our clinic between January 1, 2003, and December 31, 2024. A total of 49 patients were diagnosed as ROCM, with a mean age of 56.6 ± 15.5 years, including 22 women (44.9%) and 27 men (55.1%). Patients had diabetes mellitus (65.3%), hematological cancer (24.4%), hematopoietic stem cell transplantation (10.2%), chronic kidney failure (8.1%), solid organ transplantation (8.1%), and solid organ cancer (8.1%). Predisposing factors among the patients included steroid treatment (32.6%), erythrocyte transfusion (26.5%), recent tooth extraction (20.4%), neutropenia (18.3%) and a recent history of coronavirus disease-2019 (12.2%). Periocular pain (81.6%), ophthalmoplegia (75.5%), periorbital cellulitis (69.3%) and ptosis (67.3%) were identified as the most common presenting symptoms and clinical findings. Although antifungal therapy (liposomal amphotericin B), functional endoscopic sinus surgery (FESS) and orbital exenteration were performed when necessary, 24 patients (48.9%) died. Binary logistic regression analysis revealed that the risk of mortality was significantly higher in patients with hematological malignancy (8.2-fold), those receiving steroid therapy (5.2-fold), those undergoing chemotherapy or immunosuppressive treatment (10-fold) and those who received erythrocyte transfusion (9.8-fold). Additionally, patients presenting with orbital apex syndrome (3.5-fold), those with cerebral infarction (6.9-fold) and those whose duration from symptom onset to FESS exceeded 96 hours (4-fold) also had a significantly increased risk of death. As a result, underlying hematological malignancy, immunosuppressive therapy, steroid use, erythrocyte transfusion, the presence of orbital apex syndrome at admission, cerebral infarction and delayed surgical intervention were all found to increase the risk of mortality.

The three step human immunodeficiency virus (HIV) testing algorithm used in Türkiye was updated and implemented in 2019 in accordance with the current HIV testing algorithm of the Centers for Disease Control and Prevention. In this study, it was aimed to obtain HIV test data with a multicenter and multidisciplinary approach in order to reveal the current situation in the diagnosis of HIV/acquired immunodeficiency syndrome in our country and to identify new algorithm applications and problems encountered in HIV diagnosis. For this purpose, 12 HIV testing centers were asked about the HIV testing algorithms they use, the problems they encountered in practice and their suggestions for solution with a 57-question survey. The performance of the current algorithm and the current HIV status of the centers were evaluated with the total number of three-year fourth generation HIV enzyme linked immunsorbent assay (ELISA) tests , the number of repeated reactive tests, the distribution of confirmatory test results and the number of HIV nucleic acid amplification tests (NAT) between 2018 and 2020. Between 2018 and 2020, the total number of anti-HIV ELISA tests were 788261, 871299 and 835498, the repeating reactivity rates were 0.48, 0.51 and 0.70, respectively, while the confirmed HIV test rates were 0.24, 0.25 and 0.21 respectively. During this period the rates of Western Blot (WB) confirmatory test utilization were 25.77%, 12.29% and 9.86%, respectively and are gradually decreasing. The utilization rates of HIV-1/2 antibody differential rapid confirmatory tests recommended in the current algorithm were found to be 25.72%, 38.76% and 45.78%, respectively and it is seen to replace WB. The rates of HIV-1 RNA studied by year were 48.77%, 97.98% and 46.31% respectively. In our study, it has been observed that the use of the rapid HIV-1/2 antibody differential test, which is included in the new algorithm, is gradually increasing and is used more effectively in HIV diagnosis, while the use of HIV-1 NAT has decreased. This situation, which is associated with the shift of NAT opportunities to coronavirus diseases-2019 (COVID-19) polymerase chain reaction studies in the shadow of the COVID-19 pandemic, requires more detailed monitoring in terms of possible changes in the HIV epidemic in our country.

Klebsiella pneumoniae is a major pathogen in ventilator-associated pneumonia (VAP) and poses a significant challenge in healthcare-associated infections due to its multidrug resistance (MDR). Mobile genetic elements such as integrons are key factors in the spread of resistance genes in pathogens like K.pneumoniae. This study aimed to detect class 1 and class 2 integron gene cassettes in K.pneumoniae isolates from VAP patients. A total of 22 isolates were collected between 2022 and 2023 from the intensive care unit of Kırşehir Training and Research Hospital. DNA was extracted using the boiling method and integrons were amplified via polymerase chain reaction with specific primers. Amplified fragments were cloned into the pJET1.2/blunt vector and sequenced. Sequences were processed using BioEdit and compared with the NCBI BLAST GenBank database to identify gene cassette contents. Identified sequences were submitted to GenBank and assigned accession numbers. Class 1 integrons were found in five isolates (22.7%) and class 2 integrons in two isolates (9.1%). Class 1 integrons harboured dfrA12 responsible for trimethoprim resistance and aadA which provides resistance to aminoglycoside group antibiotics. In class 2 integrons, dfrA1, sat2 and aadA1 were identified which confer resistance to trimethoprim, streptothricin and streptomycin/spectinomycin, respectively. The results of this study demonstrate that integrons play a significant role in the spread of hospital-acquired MDR K.pneumoniae isolates. Strengthening infection control measures and monitoring antibiotic resistance mechanisms are crucial for controlling antibiotic-resistant isolates seen in hospitals. This study will contribute to understanding the genetic makeup of VAP-related K.pneumoniae isolates, determining appropriate treatment approaches and controlling hospital-acquired infections.

Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) is widely used in microbiology. Composite index (CI) analyses, which involve evaluating spectra obtained from the device as well as small peak data, are a crucial method for examining microbial differences. When analysing the impact of external factors on cell composition, the composite correlation index (CCI) facilitates the grouping of spectrum data. In recent years, a significant increase in the isolation of Malassezia furfur strains from clinical specimens has been observed. Due to its lipid-dependent growth characteristics, this pathogen does not grow on the media typically used in routine mycology, such as Sabouraud’s dextrose agar. It is therefore recommended that each laboratory prepare and use its own appropriate media when necessary. However, the contents and their quantities in media used to cultivate Malassezia yeasts can vary considerably. Modified Dixon agar (mDA), modified Leeming & Notman agar (mLNA) and Fast Fung agar (FFA) are widely used as both primary culture media and in research. The variation in the composition of these media may lead to different spectra forming. This study aimed to investigate the relationship between MALDI-TOF MS spectra obtained from cultivating lipophilic M.furfur strains on different media and to assess their usability in routine practice. Seventeen M.furfur isolates included in the study were grown on mDA, mLNA and FFA agar. CI analyses of MALDI-TOF MS spectra of the strains were performed and CCI data were compared. While no difference was found in the CI values of the FFA and mLNA media for the strains included in the study (p> 0.05), the CI values of both media were higher than those of the mDA media (p< 0.05). Kurtosis values for the media were calculated as 1.83, -0.56, and -1.16, respectively, for FFA, mLNA and mDA. The platykurtic distribution of the mDA medium data in the study suggests that, despite its widespread use, it may lead to time-consuming spectroscopic analyses. The high CI values observed in FFA and mLNA media prepared with tween 60 indicate that methods such as MALDI-TOF MS are more suitable for standardization in the analysis of M.furfur. Differences in tween will also affect the efficiency of tween removal protocols in MALDI-TOF MS analyses. The acquisition of variable data and the requirement to process minor spectral parameters, such as CI values, underscore the importance of standardizing culture media protocols. Achieving consistency in media formulation will further support the generation of comparable data between laboratories.

Crimean-Congo hemorrhagic fever (CCHF) is a rare but severe viral hemorrhagic disease transmitted to humans through tick bites or contact with the blood, tissues or secretions of infected animals. CCHF can lead to widespread endothelial damage and immune dysfunction, resulting in severe hemorrhagic manifestations and various complications. Although the majority of patients recover without permanent sequelae, unexpected complications such as secondary bacterial infections may rarely occur during the acute phase or convalescence. In this report, the case of a 42-year-old female patient who developed spinal epidural abscess and lumbar spondylodiscitis following real-time polymerase chain reaction testing confirmed CCHF was presented. On the seventh day of illness, the patient admitted to our emergency department with persistent high fever, nausea, vomiting, anorexia, malaise, diffuse body pain, hematuria and vaginal bleeding. The patient’s past medical history was unremarkable except for a lumbar disc herniation surgery 10 years ago. Following recovery from the acute viral illness, the patient developed sudden and severe lower back pain, recurrent high-grade fever and progressive motor weakness in plantar flexion of the right ankle. On the 10th day of hospitalization, spinal magnetic resonance imaging revealed spondylodiscitis and a spinal epidural abscess at the L5-S1 level. The epidural abscess caused compression of the S1 nerve roots, correlating with her neurological symptoms. The patient underwent surgical intervention (abscess drainage and stabilization) by the department of neurosurgery. Growth of Staphylococcus aureus in the blood culture confirmed that the infection was of bacterial origin but since the operation was performed while under 10 days of antibiotic treatment, there was no bacterial growth in the abscess material taken during the surgery. The patient was treated with intravenous cefazolin at a dose of 1000 mg three times daily for six weeks. Clinical improvement was rapid and complete, with no residual neurological deficits. This rare complication is thought to be related to immunoparalysis following a cytokine storm induced by CCHF, predisposing the patient to opportunistic bacterial infections. While leukopenia was observed during the immunosuppressive phase, a subsequent rise in leukocyte counts during recovery unmasked the signs of infection. Additionally, the patient’s history of prior spinal surgery may have created a localized microvascular injury or hematoma, forming a favorable niche for bacterial proliferation. New symptoms in the convalescent phase of CCHF must be carefully evaluated. In patients presenting with spinal pain and progressive localized motor deficits, prompt imaging and advanced diagnostics are essential to ensure early recognition and treatment of rare but potentially serious complications.

Lichtheimia corymbifera (formerly known as Absidia corymbifera) is a mold fungus belonging to the family Mucorales. Mucormycosis caused by L.corymbifera is a newly recognized and rare opportunistic infection in immunocompromised patients. Rapid diagnosis and treatment are crucial due to the high mortality rates, especially in patients with hematologic malignancies. Early clinical suspicion, surgical removal of necrotic tissue and appropriate antifungal chemotherapy constitute the main steps of treatment. Lipid formulations of Amphotericin B are the first-line treatment for mucormycosis. In this report a case of fungal sinusitis and preseptal cellulitis caused by L.corymbifera in a 23-year-old male patient who had been followed for eight years with a diagnosis of acute myeloid leukemia (AML) was presented. The patient, hospitalized due to relapsed AML, development of edema and discharge in the left eye and ophthalmological evaluation revealed preseptal cellulitis. Despite treatment, no clinical improvement was observed and contrast-enhanced orbital and paranasal sinus computed tomography revealed sinusitis. Direct microscopic examination of crusted lesions from the left nasal cavity showed the presence of irregular aseptate hyphae. A panic notification was reported to the relevant clinic with a preliminary diagnosis of mucormycosis. After the clinic and the patient interview, liposomal Amphotericin B treatment was started since the patient did not accept surgical debridement. The material was cultured on two Sabouraud’s Dextrose agar; one was incubated at 22 °C (room temperature) and the other at 37 °C (incubator). On the second day of incubation at 37 °C, colony morphology was observed as light white woolly surfaces with a dark white, non-pigmented base. In the preparations prepared with lactophenol cotton blue; fixed stolons ending in a pyriform funnel-shaped apophysis supporting the sporangium were observed. The agent grown in culture was named to species level with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) (MALDI Biotyper® Sirius System, Bruker, Germany) and diagnosed as L.corymbifera based on characteristic macroscopic and microscopic features. Although the patient refused surgical debridement treatment, early presumptive diagnosis allowed for the administration of liposomal Amphotericin B, resulting in successful treatment In conclusion, rapid preliminary diagnosis is critical to prevent the aggressive clinical course of mucormycosis, improves prognosis and increases survival rate.

Vancomycin-variable enterococci (VVE) are Enterococcus strains that appear phenotypically susceptible to vancomycin but harbor glycopeptide resistance genes, representing a significant diagnostic and therapeutic challenge and posing a risk for therapeutic failure. These strains are often undetectable by conventional susceptibility methods but can be identified by molecular techniques. This study aimed to investigate the prevalence of vanA and vanB resistance genes in vancomycin- and teicoplanin-susceptible Enterococcus faecalis and Enterococcus faecium clinical isolates using multiplex and monoplex polymerase chain reaction (PCR) techniques. A total of 251 clinical Enterococcus isolates phenotypically confirmed as susceptible to vancomycin by disc diffusion test, broth microdilution and gradient diffusion test (Etest®), were retrospectively analyzed. Multiplex PCR targeting vanA and vanB genes was performed on all isolates, followed by monoplex PCR for the confirmation of positive results. Among the 251 isolates screened, only one E.faecalis isolate (0.4%) from a urinary sample of a 91-year-old female patient detected as positive for the vanA gene in both multiplex and monoplex PCR. In contrast, vanB gene was detected as positive in 100 isolates (39.8%) by multiplex PCR, but none of these were confirmed by monoplex PCR. The detection of a vanA-positive E.faecalis isolate that was phenotypically susceptible to vancomycin highlights the risk of missing vancomycin-variable enterococci (VVE) when relying solely on conventional testing. The high rate of false-positive vanB results obtained by multiplex PCR demonstrates the limitations of this method and underscores the necessity of confirmatory testing within molecular workflows. Integrating gene-specific PCR assays into standard diagnostic protocols may facilitate more effective detection of VVE strains and the development of appropriate antimicrobial management strategies, particularly in settings with high glycopeptide use or unexplained treatment failures.

Malaria is a severe infectious disease caused by Plasmodium parasites transmitted by infected female Anopheles mosquitoes. Plasmodium falciparum is the leading cause of malaria-related deaths worldwide and can lead to severe complications such as coma, metabolic acidosis and renal failure. In this report a case of high-parasitemia P.falciparum infection diagnosed and treated with intravenous (IV) artesunate was presented. The patient was a 52-year-old male with a travel history to Liberia who was referred to a university hospital due to thrombocytopenia and hematochezia. Subsequently, the patient developed severe malaria symptoms, including metabolic acidosis and acute renal failure. Laboratory tests revealed a leukocyte count of 9370/mm³, hemoglobin level of 18.3 g/dL, platelet count of 11000/μL, aspartate aminotransferase of 57 U/L, alanine aminotransferase of 28 U/L, gama-glutamyl transferase of 160 U/L, lactate dehydrogenase of 629 U/L, total bilirubin of 8 mg/dL, direct bilirubin of 4.64 mg/ dL, creatinine of 1.69 mg/dL, prothrombin time of 14.9 seconds, international normalized ratio of 1.27, and C-reactive protein level of 247.7 mg/L. Giemsa-stained thin blood smear preparations, the Abbott Bioline™ Malaria Ag P.f/P.v rapid diagnostic test and real-time quantitative polymerase chain reaction confirmed P.falciparum infection. Intravenous artesunate and meropenem for secondary infections were administered, resulting in a rapid response to treatment. Parasite density was regularly monitored during treatment, and the patient was transitioned to oral therapy. According to the treatment algorithms of the World Health Organization and the Turkish Public Health Directorate, IV artesunate is the first-line treatment for severe malaria. In patients who have traveled to endemic regions and present with unexplained fever and flu-like symptoms, malaria should always be considered in the differential diagnosis and prompt diagnosis and treatment are crucial. Early diagnosis and the rapid action of artesunate significantly contribute to reducing morbidity and mortality rates. In this case, the rapid effect of artesunate and the significant decrease in parasitemia follow-up were clearly observed. In this case report, it was evaluated that parasitemia monitoring plays a critical role in directing patient treatment and is an important guide for clinicians and microbiologists.

Ureaplasma parvum and Ureaplasma urealyticum can colonize the urinary and genital tracts and cause various infections. Due to their fastidious growth requirements, these organisms cannot be identified by routine laboratory diagnostic methods. Therefore, more detailed studies are needed to investigate their incidence in the community, resistance characteristics, and clinical manifestations. This study aimed to demonstrate the presence of ureaplasmas in patients with suspected urinary tract infections. As a part of the study objectives, a commercial real-time quantitative polymerase chain reaction (qRt-PCR) panel kit targeting U.urealyticum and U.parvum was used and the results were confirmed by sequence analysis. A total of 603 midstream urine samples submitted to our laboratory from patients with suspected urinary tract infections were analyzed using a urinary tract infection qRt-PCR panel kit (Bioeksen, Türkiye). Of the 195 samples found positive for U.urealyticum and/or U.parvum, 130 with sufficient sample volume were subjected to next generation sequencing (NGS) using the MinION™ system with a rapid barcoding kit (SQK-RBK110.96), both from Oxford Nanopore Technologies® (UK), according to the manufacturer’s instructions after storage at -20 °C. Of the 195 (32.33%) samples found positive by qRt-PCR, 138 (70.76%) were positive for U.parvum, 46 (23.58%) for U.urealyticum and 11 (5.64%) showed the presence of both species. Sequence analysis was performed on 130 of the 195 qPCR-positive samples that had sufficient volume. In 17 of these samples, no amplification product was observed during electrophoresis and five yielded insufficient sequencing data (< 10 coverage). As a result, sequence analysis data could not be obtained for 22 samples, while valid results were obtained for 108 samples. Among these 108 samples, 102 (94.44%) showed concordant results between qPCR and NGS, while six (5.56%) showed discordant results. One of the six discordant samples was identified as U.urealyticum by qPCR, while it was identified as U.parvum in the sequence analysis. In the remaining five samples, only one of the two species detected by qPCR could be demonstrated by NGS, the other could not be demonstrated. In three of the five samples, only U.parvum could be demonstrated by sequence analysis and in two, only U.urealyticum could be demonstrated. In the study, U.parvum and/or U.urealyticum positivity was found at a rate of 32.33% in midstream urine samples. In this study, it was aimed to draw attention to the fact that these microorganisms may be a possible cause of urinary tract infections due to their high positivity rates and they should not be ignored in clinical evaluations.

Method verification or validation studies using quantitative standards are required for diagnostic tests to be used in microbiological diagnostic laboratories. Standards containing whole viruses instead of synthetic nucleic acids or plasmids ensures that all steps of the assay, including extraction, reverse transcription and polymerase chain reaction (PCR), are evaluated as in real life. Commercial quantitative standard materials for nucleic acid tests are limited for respiratory viruses. In this study, we aimed to develop quantitative nucleic acid standards for influenza A (infA), influenza B (infB) viruses and respiratory syncytial virus (RSV) using digital PCR (dPCR). In the study, the amount of viral nucleic acids in samples prepared by pooling nasopharyngeal swab samples known to be positive for RSV, infA, infB RNA were determined by dPCR (QIAcuity, Qiagen) using commercial primer/probe sets (Qiagen, Germany). Nucleic acid extraction was performed using a commercial kit (Xi’an Tianlong Science&Technology Co, China). The analytical sensitivity (LoD) and lower limit of quantitation (LoQ), intra- and inter-study reproducibility and linearity of the dPCR method for infA, infB and RSV were determined. Samples were analysed by both dPCR and real-time RT-PCR (qRT-PCR) and the relationship between Ct values and dPCR quantification results was evaluated by linear regression. Statistical analysis were performed using GraphPad Prism 10.4.0 (GraphPad, USA) and Excel Analysis ToolPak. The LoD values of the dPCR method for infA, infB and RSV were 93.75, 15.59 and 26.23 copies/mL, respectively. The intra-study reproducibility (coefficient of variation, CV%) of the dPCR method ranged from 0.06 to 7.97, being higher in samples with low viral load. Inter-study reproducibility was 0.73 to 5.41. Linearity analysis performed with dilutions in the range of 3-4 log10 for infA and in infB and seven log10 for RSV showed r2≥ 0.99 for all three viruses. The concentrations measured by dPCR were correlated with qRT-PCR Ct results. When the intra- and inter-study reproducibility results of dPCR and qRT-PCR tests were compared, the CV% value of dPCR was significantly lower (p= 0.0312). The results of the study showed that the dPCR method is a highly reproducible and reliable method for obtaining quantitative standards. The quantitative standards obtained can be used to develop assays for viral load determination and/or to perform method confirmation analysis of such assays. In conclusion, in this study reliable quantitative nucleic acid standards for infA, infB and RSV were obtained by dPCR using pooled patient samples and performance analysis of the dPCR method was determined. This study was an example of the production of quantitative viral nucleic acid standards by dPCR.

The most common route of transmission of human immunodeficiency virus (HIV) in children is perinatal transmission. HIV can be transmitted from mother to baby during pregnancy, delivery and breastfeeding. This study aimed to evaluate the characteristics of mothers and babies born to HIV-infected mothers and the methods applied to prevent perinatal HIV transmission and their outcomes. Data of babies born to HIV-infected mothers who were followed up at our tertiary hospital between January 2007 and December 2024 were retrospectively analyzed. Demographic and perinatal information of the patients, breastfeeding status, antiretroviral (ARV) prophylaxis, presence of congenital anomalies, HIV infection of the parents, characteristics of the mothers regarding HIV infection and pregnancy course were recorded. In our study, 65 of the 120 (54.2%) babies born to HIV-infected mothers were male. Of the patients, 62.5% (n= 75) were referred from other centers. Nineteen (15.8%) cases were born preterm and 11 (9.2%) cases were born small for gestational age. Ninety-one (75.8%) of the cases were born via cesarean section. Congenital cardiac anomalies were detected in two (1.7%). It was observed that 70 (58.3%) of the mothers were diagnosed before pregnancy, 40 (33.3%) during pregnancy and 10 (8.3%) at birth. The majority of mothers (59.2%) were between the ages of 20-30 and 26.7% were foreign nationals. ARV treatment was initiated in 70 (58.3%) of the mothers prior to pregnancy and in 30 (25%) during pregnancy. Of the mothers, 73.3% (n= 88) had HIV-1 RNA values < 20 copies/mL and 82.5% (n= 99) had CD4 counts ≥ 200 cells/mm3 in the last trimester. Of these cases, 82 (68.3%) were infants of low-risk mothers and 38 (31.7%) were infants of high-risk mothers. Despite being high risk, 15 cases received only zidovudine prophylaxis due to problems in drug supply. Appropriate prophylaxis could not be provided to five babies referred from external centers due to their late applications (days 3, 5, 2, 3, 29). HIV-RNA values were positive in the follow-up of four (3.1%) of our cases. It is possible to reduce and eliminate perinatal HIV transmission by using effective measures. This study highlights the importance of identifying the problems experienced by referred babies, providing more education on this issue and providing prophylactic drugs that are suitable for newborn formulation.

Diabetic foot ulcers (DFUs) are a serious complication of diabetes, leading to high morbidity and mortality rates. Early diagnosis of DFUs is critical for improving patients’ quality of life and reducing the burden on healthcare systems. This study aimed to identify biomarkers that can predict the early development of DFUs and evaluate their potential for clinical applications. The study included three groups: diabetic patients with DFUs, diabetic patients without ulcers and healthy individuals. Serum levels of hypoxia-inducible factor-1 alpha (HIF-1α), matrix metallopeptidase 9 (MMP-9) and IL-8 were measured in blood samples and these biomarkers were compared with acute phase reactants such as C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and procalcitonin. The diagnostic values of these biomarkers were assessed using receiver operating characteristic (ROC) analysis. HIF-1α levels were found to be significantly elevated in patients with DFUs and ROC analysis revealed that this biomarker had the highest diagnostic sensitivity and specificity [area the under curve (AUC= 0.99, p= 0.001)]. The increase in HIF-1α levels suggested that hypoxic responses remain active during the early stages of DFU but decrease in advanced stages due to impaired tissue response to hypoxia. MMP-9 levels were observed to increase proportionally with Wagner stages and were positively correlated with ESR, indicating its role in chronic inflammation and tissue damage. IL-8 levels were significantly elevated in DFU patients, yet their lack of correlation with other inflammatory markers suggested that IL-8 might have a more specific role in the inflammatory process. HIF-1α emerges as a key biomarker in the early detection of DFUs due to its central role in hypoxia-driven tissue repair and angiogenesis. Owing to its high specificity and sensitivity (AUC= 0.99), it should be considered a promising biomarker for routine clinical monitoring. The role of MMP-9 in chronic inflammation and tissue degradation suggests that this biomarker may contribute to the development of therapies aimed at preventing tissue damage. Similarly, the role of IL-8 in specific inflammatory processes may lead to the development of novel therapeutic approaches targeting neutrophil modulation. Regular monitoring of HIF-1α, MMP-9, and IL-8 could facilitate the early diagnosis and prevention of DFUs. Additionally, the clinical application of these biomarkers may improve patient quality of life while reducing the economic burden on healthcare systems. Future prospective studies may provide more robust evidence to support the widespread clinical use of these biomarkers.

This study aimed to compare the diagnostic performances of monkey esophagus (ME) and monkey liver (MK) preparations in the detection of anti-endomysium (EMA) IgA antibodies used in the diagnosis of celiac disease (CD) and to evaluate their relationship with anti-tissue transglutaminase (anti-TTG) IgA and anti-deamine gliadin peptide (GAF3X) IgA levels.This methodological and cross-sectional study included 123 patients with a preliminary diagnosis of CD who did not have selective IgA deficiency. EMA IgA tests were evaluated using the indirect immunofluorescence microscopy (IIF) method with ME and ML preparations. Serological tests (anti-TTG IgA and GAF3X IgA) were analyzed using the ELISA method and intestinal biopsy results were categorized according to the Marsh classification. The diagnostic performance of the tests was evaluated using sensitivity, specificity, positive and negative predictive values. Differences between groups were analyzed using statistical methods. Among 90 patients with anti-TTG IgA positivity, 96.67% were positive with ML testing, while 88.89% were positive with ME testing. A high agreement was observed between ME and ML tests (Kappa= 0.692, p< 0.001) and both preparations demonstrated similar effectiveness in detecting EMA IgA positivity. A strong relationship was identified between Marsh positivity and serological test results. ML testing showed 100% sensitivity and 50% specificity, with positive and negative predictive values of 86% and 100%, respectively. ME testing exhibited 97.7% sensitivity and 64.3% specificity, with positive and negative predictive values of 89.4% and 90%, respectively. Quantitative test results revealed significant differences between pediatric and adult groups (ML: p= 0.006; ME: p= 0.048). However, age (p= 0.268) and gender (p= 0.775) had no statistically significant impact on Marsh positivity. Correspondence analysis indicated a statistically significant relationship between ME and ML categories (p< 0.001) and a high level of correlation was detected in the positive categories. As a result of the receiver operating characteristic analysis for the antiTTG IgA test, the area under the curve value was calculated as 0.822 which revealed that the test has a good capacity to distinguish between Marsh score positivity and negativity. An optimal cutoff value of 223.84 RU/mL was identified, with sensitivity of 60.5% and specificity of 100%, emphasizing its clinical utility in reducing biopsy requirements. These findings supported the high diagnostic value of EMA IgA and other serological tests in CD diagnosis. The use of EMA IgA tests with ME and ML preparations was shown to be an effective serological method in the diagnosis of CD. ML preparations demonstrated higher sensitivity compared to ME but were more limited in specificity. The optimal cutoff value for anti-TTG IgA testing in relation to Marsh score positivity may assist in clinical decision-making processes. These findings have shed light on diagnostic approaches aimed at reducing the need for biopsy

The human pathogen Cryptococcus neoformans has been isolated from a variety of environmental sources, including avian excreta, soil, trees, and decaying wood. In addition to the biological characteristics of the yeast, the structure and properties of the external environment play a pivotal role in the process of environmental colonization. Peloidotherapy has been used since ancient times in the Aegean Region (near Denizli, Türkiye) as a treatment or supportive therapy for pathological disorders and musculoskeletal conditions. This therapy involves either immersing patients in natural pools or rehydrating dried mud and applying it directly to the body. Notably, the organic content of these peloids is quite low. Additionally, commercially packaged peloidotherapy muds undergo high-temperature treatments, which alter their physicochemical properties. While it is possible that sexual reproduction might occur during environmental colonization by cryptococcal species, even in environments with low organic content, there is currently insufficient data to confirm this phenomenon in peloids. The aim of this study was to investigate the sexual reproduction of C.neoformans in peloids with low organic content, which are used in peloidotherapy practices in our country.The aim of this study was to investigate the sexual reproduction of C.neoformans in muds with poor organic content used in peloidotherapy in our country. In this study, commercially packaged peloid samples (1 g/L, filtered in distilled water) from three active sources in the Denizli Basin -Sarayköy, Gölemezli, and Karahayıt- were used to prepare media with varying pH levels, supplemented with 3 g/L CaCO3 and 1 g/L agar. Two reference strains, C.neoformans KN99 Aa and KN99 Aα, were tested for their ability to mate on these media. Over the course of a month, the plates were periodically examined for sexual structures, including filaments, hyphae, clamp connections, basidia and basidiospores. Sexual structures were observed in two of the three samples, indicating that, despite their low organic content, reusable and commercially available peloids can support C.neoformans, particularly under conditions of immunosuppression. Moreover, the low organic content and the mineral variability of peloids across regions provide a unique environment for studying factors that influence the natural life cycle of significant human pathogens like C.neoformans.

Candida parapsilosis is an important fungal pathogen that is particularly isolated from blood cultures. In recent years, although there are regional differences between centres, resistance to fluconazole which is the most commonly preferred drug for candidemia, has increased in many regions. This increase complicates infection control and adversely affects treatment. In C.parapsilosis, codon 132 Y/F change in ERG11 is accepted as the dominant mechanism and it is reported that some amino acid changes in MRR1 may also contribute to resistance. In this study, we aimed to elucidate the azole resistance mechanisms of ERG11 and MRR1 in C.parapsilosis sensu stricto isolated in our centre. 30 C.parapsilosis sensu stricto obtained from patients with candidemia in 2018 and 2019 were tested for susceptibility to fluconazole by broth microdilution method and amplified by colony polymerase chain reaction approach and DNA sequence analysis was performed on selected regions. As a result of the analysis, Y132F mutation was identified in one susceptible isolate while Y132F, G307A and K143R mutations were detected in resistant isolates in ERG11; R405K mutation was detected in one susceptible isolate whereas G927C mutation was observed in the resistant isolates in MRR1.R398I mutation in ERG11 was detected in dose-dependent susceptible and sensitive isolates. Although Y132F mutation is the primary mechanism and the most frequently detected mutation, potential mechanisms should not be neglected. In our study, the G307A and G927C mutations detected in resistant isolates were observed as single mutations in some of the samples. Similarly, the R398I mutation in susceptible isolates was identified alone. Studies aimed at elucidating these mechanisms will contribute to the proper development of therapeutic strategies.

Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, is one of the most significant neglected tropical diseases. Approximately 6-7 million people worldwide are estimated to be infected with T.cruzi, with about 12000 deaths annually attributed to the disease. In Türkiye, natural transmission does not occur due to the absence of vectors carrying the parasite. However, touristic or commercial travels to endemic areas and migration from these regions increase the risk of Chagas disease emergence in the country. Currently, only two drugs, benznidazole (BENZ) and nifurtimox, are available for the treatment of Chagas disease. These drugs have limitations, including effectiveness only during the acute or early stages of infection, adverse side effects and the potential for the parasite to develop resistance. Consequently, there is an urgent need for new, safe and effective therapeutic alternatives for treating Chagas disease. This study aimed to investigate the efficacy and cytotoxicity of essential oil components (EOCs) such as α-pinene, isoborneol, carvacrol, coumarin and eugenol against T.cruzi and their synergy with BENZ. In this study, the T.cruzi ATCC 50825 reference strain was used. BENZ was selected as the reference drug and α-pinene, isoborneol, carvacrol, coumarin, and eugenol were chosen as EOCs. Cytotoxic activity was evaluated using the L929 mouse fibroblast cell line. Antitrypanosomal and cytotoxic activities were determined using the broth microdilution method and interactions between BENZ and EOCs were assessed using the checkerboard method. The IC50 values indicating the cytotoxic effects of EOCs and BENZ on fibroblast cells at 24, 48, and 72 hours were as follows: α-pinene (26.68-20.79 µg/mL), isoborneol (128.7-73.63 µg/mL), carvacrol (4.56-2.49 µg/mL), coumarin (169.3-108.6 µg/mL), eugenol (6.04-1.65 µg/mL), and BENZ (1011-806.9 µg/mL). The IC50 values for antitrypanosomal activity at 48 hours were 11.8 µg/mL, 114.6 µg/mL, 3.9 µg/mL, 268.6 µg/mL, 19.5 µg/mL, and 11.7 µg/mL for the same compounds, respectively. Carvacrol, α-pinene and eugenol demonstrated the most potent activity and especially carvacrol and α-pinene being comparable to the reference drug BENZ. Selectivity index (SI) calculations revealed high selective activity (SI> 1) for BENZ and α-pinene, while other EOCs exhibited lower selectivity (SI< 1). Nevertheless, synergistic interactions were identified in all combinations of EOCs with BENZ. The mechanisms underlying drug resistance in T.cruzi remain poorly understood. Natural compounds with multiple biological effects, new drug formulations and innovative combinations can contribute to overcoming drug resistance. Among these strategies, essential oil components, known for their biological activities against various microorganisms, offer promising alternatives. In addition to the strong antitrypanosomal activities of EOCs, their synergistic interaction with BENZ may fill important gaps in the literature and guide future studies in designing next-generation drug combinations, reducing side effects and preventing the development of resistance.

There are increasing reports of failure of artemisinin-based combination therapy (ACT) in malaria patients returning from endemic areas. ACT has been used globally as first-line treatment for Plasmodium falciparum malaria. However, with the emergence of artemisinin-resistant strains of P.falciparum and their spread across Southeast Asia, there is a risk that these resistant strains could reach areas of high malaria incidence in Africa and elsewhere. In this case report, two cases of malaria imported from Africa, initially treated with six doses of artemether-lumefantrine (AL) were presented. Two middle-aged men returning from Gabon and Uganda developed symptoms of malaria in Türkiye and were hospitalized and diagnosed as P.falciparum malaria. Both patients were treated with AL. After being discharged from the hospital with marked improvement, they re-admitted to the hospital with high fever and chills and showed late signs of clinical failure. One patient was completely cleared of parasites with six doses of AL treatment and the other after non-ACT antimalarial (quinine and doxycycline) treatment and no recrudescence occurred. AL, an artemisinin-based combination, is a frequently preferred preparation for the treatment of malaria cases seen in Türkiye. It should be kept in mind that even if parasitemia is cleared in the peripheral blood smear after three days of appropriate AL treatment, treatment failure may be seen in patients and this treatment failure may also include cases of African P.falciparum malaria.

Lophomonas blattarum is a protozoan that typically infects the lower respiratory tract and causes bronchopulmonary infections. Although its clinical manifestations are nonspecific, they may include symptoms such as cough, sputum production, fever, chest discomfort, and respiratory distress. The diagnosis of Lophomonas infection relies on the morphological identification of the parasite in respiratory secretions using light microscopy. Differentiating the parasite from ciliated bronchial epithelial cells is challenging and critically important for accurate diagnosis. In this case report a L.blattarum infection in an immunocompetent adult man was presented. A 46-year-old man admitted to our hospital with the complaints of hemoptysis, exertional dyspnea, fatigue, night sweats and productive cough. Thoracic computed tomography revealed a 2 cm abscess/cyst in the right upper lobe, with adjacent consolidation/ atelectasis and ground-glass opacities. Empirical treatment was initiated with a preliminary diagnosis of pneumonia. Due to persistent hemoptysis, fiberoptic bronchoscopy was performed. Sputum and bronchoalveolar lavage (BAL) fluid samples were collected for acid-fast bacilli testing, culture and direct microscopic examination. Trophozoites morphologically consistent with L.blattarum were observed in the BAL specimen by direct microscopy and Giemsa staining. A polymerase chain reaction analysis was performed to confirm the diagnosis; however, no reliable results specific to the target parasite were obtained. Therefore, based on compatible microscopic findings, a presumptive diagnosis of Lophomonas infection was made and nonspecific antibiotic therapies were discontinued in favor of metronidazole. Following the treatment, the patient experienced dramatic clinical and radiological improvement and was discharged in good health. This case highlights that Lophomonas infection can also occur in immunocompetent individuals and may mimic other bronchopulmonary infections. It underscores the critical role of microscopic examination in diagnosis, while also pointing to the need for standardized molecular diagnostic methods. In clinical practice, the possibility of lophomoniasis should not be ignored in cases that do not respond to empirical antibiotic therapy and every suspected case should be carefully evaluated.