Kayhan Çağlar

Aims: Most commercial multiplex polymerase chain reaction (PCR) panels primarily detect bacterial and viral pathogens and usually include only Cryptococcus among fungal targets. However, other fungi such as Candida and Aspergillus are increasingly recognized as important causes of central nervous system (CNS) infections, especially in immunocompromised patients. This study aimed to preliminarily develop a multiplex real-time PCR approach for the detection of selected fungal targets in cerebrospinal fluid (CSF)-based samples. The assay was initially designed as a SYBR Green-based screening method; however, because overlapping melting temperatures limited reliable target discrimination, a three-target probe-based confirmation step was subsequently incorporated for Candida spp., Aspergillus spp., and Fusarium spp.Methods: Target-specific primers were used for Candida spp., Aspergillus spp., Fusarium spp., Mucor spp., Rhizopus spp., and Trichosporon spp. in the SYBR Green-based screening step. In addition, probe-based primer/probe sets were evaluated for Candida spp., Aspergillus spp., and Fusarium spp. to improve target-specific discrimination. The assay was evaluated using CSF-based simulated samples and tested against selected bacterial backgrounds.Results: The SYBR Green-based screening step produced amplification signals for the selected fungal targets, but melting curve analysis alone was insufficient for reliable discrimination because of overlapping Tm values. In the probe-based format, Candida spp., Aspergillus spp., and Fusarium spp. generated target-specific signals in their assigned fluorescence channels, with no off-target amplification in the tested bacterial background. These findings support the added value of probe-based confirmation while highlighting the preliminary nature of the assay.Conclusion: This preliminary study suggests that an in-house multiplex real-time PCR approach may provide a feasible framework for detecting selected fungal targets in CSF-based simulated samples. While SYBR Green-based amplification enabled initial screening, overlapping melting temperatures limited reliable target discrimination. Probe-based testing in a limited subset suggested a potential role in reducing interpretive ambiguity. Further validation with clinically positive CSF samples is required before clinical implementation.

Background: Candida meningitis is a rare but life-threatening infection, most commonly caused by Candida albicans . Candida dubliniensis , despite its close phenotypic similarity to C. albicans , is an uncommon cause of central nervous system (CNS) infections, with limited data available. To date, only 12 cases of C. dubliniensis meningitis have been reported worldwide. This study presents the 13th documented case and the first reported from Türkiye, together with a systematic review of the literature. Case presentation: A 44-year-old immunocompetent male developed meningitis caused by C. dubliniensis following subtotal resection of a clival meningioma. The diagnosis was established through fungal culture, MALDI-TOF MS, and ITS region DNA sequencing. The isolate was deposited in GenBank (accession number PV088619). Antifungal therapy with fluconazole was initiated based on susceptibility results. Despite appropriate antifungal management, the patient developed secondary Klebsiella pneumoniae sepsis and subsequently died, highlighting the complexity and high mortality risk associated with post-neurosurgical fungal CNS infections. Methods: A systematic review was conducted according to PRISMA guidelines using PubMed and Web of Science databases, including studies published up to February 2025. Search terms included “ Candida dubliniensis ” and “meningitis.” Only microbiologically confirmed cases with individual patient data were included. Studies older than 25 years or lacking sufficient diagnostic detail were excluded. Results and conclusion: Thirteen cases were identified. Most patients were immunocompetent, and infections were frequently acquired outside neurosurgical settings. Mortality was reported in four cases. These findings emphasize the extreme rarity of C. dubliniensis meningitis and underscore the importance of early species-level identification strategies.

Background: Hospital indoor environments contain a wide variety of microorganisms. Bacteria, viruses, and fungi in these environments can cause serious healthcare-associated infections in patients. The aim of this study is to show the mycoflora of the hospital by evaluating the distribution of fungal species in hospital indoor air, water, and surfaces. Methods: Air, water, and surface were sampled for fungi at Gazi University Hospital, using active air method, water collection, and swabbing, during a five-month period in 2022-2023. A total of 22 hospital wards were surveyed; overall, 110 air samples, 66 water samples, and 45 surface samples were collected. Results: A total of 1331 fungal colonies were isolated from indoor air, predominantly Penicillium (57.7%) and Cladosporium (31.6%). From outdoor air (n = 471), Cladosporium (66.9%) and Penicillium (22.5%) were most common. Median colony counts per 500 L of air were 11.5 indoors and 30.0 outdoors (range: 4–21.1 and 9–55.6, respectively. Fungal diversity, as evaluated by the Shannon index, peaked in March for both environments. Fungal growth was observed in 17 of 66 water samples (26.0%), with a total of 225 colonies recovered. Penicillium spp. accounted for the majority (85.7%), followed by Exophiala (8.0%) and Aspergillus (5.0%).Among 45 surface samples, only 3 (6.0%) yielded fungal isolates, indicating low environmental fungal burden on high-touch surfaces. Conclusion: The findings demonstrate that hospital environments, especially air and water sources, are significantly colonized by diverse fungal genera—predominantly Penicillium and Cladosporium—highlighting the importance of routine environmental mycological monitoring to mitigate potential nosocomial risks.

Objective: Real-time multiplex polymerase chain reaction (PCR) test increases the detection of viral respiratory tract infections. This study aimed to evaluate the effect of real-time multiplex PCR on antibiotic use in viral respiratory tract infections. Materials and Methods: This retrospective study included patients who underwent respiratory multiplex PCR tests. Patients were grouped into influenza-like illness, viral pneumonia, bacterial pneumonia, and co-infection. These groups were compared in terms of antibiotic use. Results: A total of 352 patients were included in the study. The most frequently detected viral agent was the human rhinovirus (24.3%). The frequency of antibiotic use and the median duration of antibiotic use were higher in the viral pneumonia group compared to the influenza-like illness group (p=0.003 and p<0.007). Conclusion: Despite a confirmed viral etiology by PCR, antibiotic use remained high, particularly in cases of viral pneumonia. These findings underscore the need for targeted antimicrobial stewardship interventions, including clinician education and integration of diagnostic-therapeutic approaches, to optimize antibiotic prescribing in respiratory infections.

Kandidemilerde etken tür dağılımında ve antifungal duyarlılık durumundaki değişimler, hastalarda prognozu etkileyebilmektedir. Bu çalışma, COVID-19 pandemisi öncesi (2016-2019) ve sonrası (2020-2024) dönemlerde kan kültürlerinden izole edilen mantar türlerinin dağılımlarını ve antifungal duyarlılıklarını karşılaştırmayı amaçlamaktadır. Çalışmada, Gazi Üniversitesi Tıp Fakültesi Tıbbi Mikrobiyoloji Laboratuvarı'nda 2016-2024 yılları arasında kan kültürlerinden izole edilen mantar türleri değerlendirilmiştir. Kan kültürleri COVID-19 öncesi ve COVID-19 sonrası dönemde BACT/ALERT® 3D cihazında inkübe edilmiştir. Üreyen mantarların tanımlanmasında pandemiden önce fenotipik yöntemler (ID32C) kullanılırken, pandemi sonrası dönemde VITEK® MS (MALDI-TOF MS) sisteminden yararlanılmıştır. Antifungal duyarlılık testleri CLSI M27-A3 mikrodilüsyon referans yöntemiyle yapılmıştır. Gazi Üniversitesi Hastanesi’nde 2016-2019 ve 2020-2024 dönemlerinde alınan toplam 148734 kan kültürünün analizi yapılmıştır. COVID-19 öncesi dönemde pozitif kültür oranı %16 (8397/53835) ve mantar pozitifliği %5 (391/8397) iken, pandemi sonrası dönemde bu oranlar sırasıyla %17 (16.572/94.899) ve %5 (845/16.572) olarak saptanmıştır. En sık izole edilen dört tür her iki dönemde Candida albicans (%40→%39), Nakaseomyces glabratus (%19→%18), Candida parapsilosis (%14→%23) ve Candida tropicalis (%9→%7) olmuş, C. parapsilosis’teki artış istatistiksel olarak anlamlı bulunmuştur (p=0.011). MİK90 değerleri esas alındığında flukonazol için C. tropicalis’te (4→8 µg/ml), vorikonazol için N. glabratus ve C. tropicalis’te (sırasıyla 0.25→2 ve 0.25→4 µg/ml), amfoterisin B için ise C. albicans ve C. parapsilosis’te (0.25→1 µg/ml) artış izlenmiştir. Bu bulgular, bazı türlerde antifungal duyarlılığın azaldığını ve dikkatli izlenmesi gerektiğini göstermektedir. Pandemi öncesi ve sonrası dönemde etken dağılımlarında sınırlı farklılıklar izlenmiş, antifungal direnç açısından dikkat çekici artışlar gözlemlenmiştir. Klinik mikrobiyoloji laboratuvarlarının düzenli aralıklarla tür ve duyarlılık dağılımlarını değerlendirmesi önerilmektedir.

Objectives: Acute pyelonephritis (APN) caused by extended-spectrum β-lactamase (ESBL)-positive Enterobacteriaceae poses a growing therapeutic challenge in children, as carbapenems remain the mainstay of treatment even when susceptibility to alternative agents such as amikacin is demonstrated. However, the widespread and inappropriate use of carbapenems can lead to carbapenem resistance. The aim of this study was to compare the clinical efficacy of amikacin and carbapenems in the management of pediatric acute pyelonephritis caused by ESBL-positive Enterobacteriaceae. Methods: We analyzed cases of pediatric acute pyelonephritis caused by ESBL-positive Enterobacteriaceae that were treated with either carbapenems or amikacin over a two-year period. This study compared microbiological cure, clinical improvement, and recurrence rates across the amikacin and carbapenem treatment groups. Results: Fifty-five patients were evaluated. The median age of the patients was 3 years (range, 0.1–13 years). The causative agents were E. coli in 43 cases (78.2%) and Klebsiella spp. in 12 cases (21.8%). All were susceptible to both carbapenem and amikacin in vitro. Twenty patients (36.3%) received a carbapenem and thirty-five (63.7%) received amikacin. Twenty-four (43.6%) had an underlying urological disease. No difference was observed between the groups in terms of microbiological cure, clinical improvement, or recurrence rates. Conclusions: Amikacin may be a potential alternative to carbapenems for treating pediatric ESBL-positive APN when in vitro susceptibility is confirmed.

Background: Allogeneic hematopoietic stem cell transplant (Allo-HSCT) recipients are still at increased risk of severe COVID-19 infection. Vaccination is a critical strategy to protect this population. This real-world prospective cohort study aimed to evaluate the immune response and clinical outcomes of COVID-19 vaccines in Allo-HSCT recipients. Methods: Allo-HSCT recipients (median age: 48 years) who received either the BNT162b2 or CoronaVac vaccines were included. Antibodies against the SARS-CoV-2 spike protein were quantitatively measured using the chemiluminescent microparticle immunoassay. Patient- and vaccine-related factors affecting antibody responses were analyzed. Adverse events, including graft-versus-host disease (GVHD) and post-vaccine infections, were recorded. Results: Among 95 Allo-HSCT recipients, 86.3% achieved adequate antibody responses following COVID-19 vaccination. Patients receiving ≥3 vaccine doses showed significantly higher antibody titers compared to those with only 2 doses (OR: 0.11; 95% CI: 0.02–0.53; p = 0.006 **). The use of Ruxolitinib or Ibrutinib was associate with increased odds of low antibody response (OR: 38.39; 95% CI: 3.14–468.95; p = 0.004 **). Hypogammaglobulinemia (low serum IgG levels) was associated with a reduced antibody response (OR: 0.17; 95% CI: 0.03–0.96; p = 0.045 *), while no significant correlation was found between serum IgA levels and antibody responses (p = 0.672). Three cases of post-vaccine GVHD were observed, and no fatalities related to COVID-19 occurred during the study. Conclusions: COVID-19 vaccination is safe and effective in Allo-HSCT recipients, with stronger responses especially following ≥3 vaccine doses. Patients receiving GVHD treatment or with hypogammaglobulinemia exhibited impaired responses, emphasizing the need for tailored vaccination strategies and close monitoring in this population.

Background/aim: Ralstonia species are opportunistic, waterborne microorganisms known for their ability to survive and proliferate in a wide range of water-based environments. They can contaminate solutions used for patient care and cause hospital outbreaks due to contaminated solutions. The aim of this study was to investigate the source and clonal relationship of Ralstonia insidiosa bacteremia detected in 28 patients between August and December 2021, as part of an unusual outbreak.Materials and methods: Active prospective surveillance studies were conducted, and environmental samples, including saline, antiseptic, and antibiotic solutions, injectors, arterial blood gas syringes, tap water, and hand soap, were collected from wards to determine the source of the outbreak. An arbitrary-primed polymerase chain reaction (AP-PCR) genotyping method was used to determine the clonal relationship between the isolates.Results: All the samples were cultured, and R. insidiosa was isolated from arterial blood gas syringes with the same location and time-based identifier (LOT number). All the arterial blood gas syringes were recalled from the hospital departments and sent back to the manufacturer. The outbreak was reported to the national health authorities. Clonal analysis between isolates from the patients and the blood gas syringes was performed using AP-PCR. It was observed that the R. insidiosa isolates were monoclonal and identical.Conclusion: It was concluded that these contaminated arterial blood gas syringes caused the R. insidiosa bacteremia, especially in immunocompromised patients.