Murat Yaman

Objectives: Rapid molecular detection of viral pathogens in cerebrospinal fluid (CSF) supports the timely evaluation of suspected central nervous system (CNS) infections. This study evaluated viral detection patterns and laboratory turnaround time (TAT) of syndromic multiplex RTqPCR testing, with emphasis on age – and season-specific patterns.Methods: This retrospective, laboratory-based study included 3,243 CSF specimens from 3,243 unique patients with suspected CNS infection between January 2021 and May 2026. Viral results were evaluated according to year, age group, sex, season, target distribution, and laboratory TAT. A p-value

AMAÇ: Bu çalışma ile algoritma tabanlı tanısal yaklaşımda akut HIV enfeksiyonlarının önemini, HIV tarama testlerindeki signal-to-cutoff (S/Co) değerlerinin doğrulama test sonuçları ile karşılaştırılmasını ve öngörü potansiyelimizin değerlendirilebilmesini amaçladık.GEREÇ VE YÖNTEM: Bu çalışma, Ocak 2020 – Ekim 2025 tarihleri arasında hastanemiz mikrobiyoloji laboratuvarında dördüncü kuşak enzim immünoassay (EIA) yöntemi ile gerçekleştirilen anti-HIV tarama testi ile İstanbul 3 No’lu Halk Sağlığı Referans Laboratuvarı’nda uygulanan serolojik ve moleküler doğrulama testlerine ait sonuçların, bilgi işletim sistemi ve arşiv kayıtları üzerinden retrospektif olarak elde edilip analiz edilmesine dayanmaktadır.BULGULAR: Yaklaşık beş yıllık çalışma süremiz boyunca dördüncü nesil HIV tarama testleri kullanılarak toplam 258,742 anti-HIV tarama testi gerçekleştirilmiş olup, bu testlerin 724’ü (%0,28) tekrarlayan reaktif olarak saptanmıştır. Tekrarlayan reaktif örneklere ait doğrulama testleri ve moleküler test sonuçları, laboratuvar kayıtları üzerinden retrospektif olarak incelenmiştir. Bu çalışmada, elde edilen S/Co değerleri ile doğrulama testi sonuçları arasındaki uyum ROC analizi ile değerlendirilmiş ve optimal S/Co değeri 28,38 olarak belirlenmiştir. Çalışmamızda hatalı pozitiflik oranı kadınlarda (%59,5), erkeklere (%18,7) kıyasla istatistiksel olarak anlamlı düzeyde yüksek bulunmuştur (p < 0,01). Algoritmaya dayalı yaklaşım sonucunda moleküler yöntem (kantitatif PCR) kullanılarak yapılan analizlerde, akut HIV enfeksiyonlu 11 hasta başarıyla tespit edilmiştir.SONUÇ: Rutin laboratuvar uygulamalarında HIV taramasında elde edilen EIA S/Co değerleri, kesin tanı koydurucu olmamakla birlikte sonuçların yorumlanmasında önemli bir öngörü sağlayabilir. PCR’ın tanısal algoritmaya dahil edilmesi ise, serolojik doğrulama testleriyle saptanamayan akut enfeksiyonların başarıyla tespit edilmesine önemli katkı sunmaktadır.

Background/Objectives: HIV and hepatitis B virus (HBV) share major transmission routes and may coexist in the same individual, making coordinated molecular assessment clinically important. Methods: This retrospective longitudinal laboratory-based study evaluated the patient-level association between HIV-1 RNA detection and HBV DNA detection using routine molecular testing data from a tertiary-care hospital in Istanbul, Türkiye. HIV-1 RNA and HBV DNA results obtained between 1 January 2022 and 1 August 2026 were linked at the patient level. A total of 5303 unique patients had HIV-1 RNA testing and 30,981 unique patient records had HBV DNA testing; these were separate source populations, and 529 individuals with results available for both molecular assays constituted the primary analytical cohort. Results: Among the 529 patients, HIV-1 RNA was detected at least once in 246 (46.5%), while HBV DNA was detected at least once in 147 (27.8%). HBV DNA detection occurred in 83/246 (33.7%) patients with at least one detectable HIV-1 RNA result and in 64/283 (22.6%) patients with no detectable HIV-1 RNA in any available measurement (OR, 1.74; 95% CI, 1.19–2.56; p = 0.005). However, the association was attenuated after adjustment for age and sex and was no longer statistically significant (adjusted OR, 1.28; 95% CI, 0.84–1.94; p = 0.255). HIV-1 RNA magnitude and HIV-1 RNA categories were not significantly associated with HBV DNA detection, and no significant correlation was observed between same-day HIV-1 RNA and HBV DNA levels (Spearman’s ρ = 0.161; p = 0.387) or between the nearest quantitative measurements obtained within ±30 days (ρ = 0.171; p = 0.245). Because treatment exposure and adherence information were unavailable, the observed molecular patterns could not be interpreted as direct measures of treatment response or treatment failure. Conclusions: These findings indicate that HIV-1 RNA detection status or magnitude should not be used as a surrogate for HBV DNA detection and support independent, clinically indicated HBV assessment in people living with HIV.

Respiratory viral detection in large metropolitan clinical settings is shaped by age, seasonality, testing behavior, and environmental context, but these dimensions are rarely evaluated together using multiplex molecular data. Istanbul's transcontinental position, dense urban structure, and heterogeneous climatic and air-quality conditions provide a relevant setting for integrated analysis of respiratory viral detection. This retrospective sample-level study analyzed 21,151 clinician-requested respiratory specimens tested by multiplex reverse transcription polymerase chain reaction in Istanbul, Türkiye, during 2022–2025. The study aimed to characterize age-stratified respiratory viral detection patterns and to explore short-term associations with meteorological and pollutant-specific air-quality exposures. Detection patterns were classified as single-target, dual-target, or ≥3-target positivity. ERA5-derived meteorological variables and station-based pollutant data were linked to specimen collection dates using a predefined incubation-informed 1–9-day pre-sampling exposure window. Environmental analyses were exploratory and interpreted using effect estimates, 95% confidence intervals, nominal p -values, and false-discovery-rate-adjusted q values where applicable; SARS-CoV-2-specific analyses were restricted to 2024–2025. After excluding SARS-CoV-2, at least one evaluated respiratory viral target was detected in 4,836 specimens (22.9%). Positive specimens were obtained from younger patients than target-negative specimens [median age, 6 years (interquartile range, 1–32) vs. 19 years [interquartile range, 4–59]; p = 7.58 × 10 ⁻¹⁴⁶ ]. Children aged 1–5 years accounted for 30.1% of single-target, 44.1% of dual-target, and 48.2% of ≥3-target detections. Enterovirus/rhinovirus was the most frequently detected viral target, identified in 1,604 of 4,836 positive specimens (33.2%). Seasonal patterns varied by age group and viral target. Exploratory exposure analyses showed crude signals linking low temperature and selected pollutant-specific exposures with dual+≥3-target positivity, with attenuation of most estimates after year–month temporal-control sensitivity analyses. Overall, respiratory viral detection in this tertiary-care hospital testing cohort varied mainly by age, viral target, and season, while the environmental analyses provided temporally controlled contextual signals rather than confirmatory causal evidence. These findings support cautious, context-aware interpretation of multiplex respiratory viral testing data in large urban clinical settings.

Background/Objectives: This study aimed to investigate the genital pathogen profile and co-infection dynamics using multiplex RT-qPCR, specifically evaluating the independent associations with age, sex, and HIV status. Methods: Data from 1217 patients who underwent a sexually transmitted infection (STI) panel study at the Microbiology Laboratory of Marmara University Pendik Training and Research Hospital between January 2024 and December 2025 were retrospectively reviewed. Pathogen detection was performed using a commercial kit (Bioeksen, Istanbul, Türkiye) with the multiplex RT-qPCR method. The independent effects of HIV positivity, age, and sex on pathogen frequency and co-infection were analyzed using logistic regression models; results were evaluated using adjusted odds ratio (aOR) and 95% confidence interval (CI). Results: Any-pathogen positivity was detected in 57.8% of patients, with Ureaplasma spp. (36.9%) and Gardnerella vaginalis (32.5%) being the most prevalent. While overall pathogen positivity did not differ significantly by HIV status (p = 0.158), HIV-positive patients exhibited distinct microbiological architectures. Higher positivity rates were observed in women in both groups, and a strong correlation was found between sex and the presence of infection (p < 0.001). Multivariate analysis revealed that HIV positivity was independently associated with an over fivefold increase in HSV-2 detection (aOR = 5.09, 95% CI: 1.47–17.65; p = 0.010). Furthermore, HIV-positive individuals were significantly enriched for complex polymicrobial patterns involving three or more pathogens (p = 0.008). Conversely, male sex was independently associated with a substantially lower risk of co-infection (aOR = 0.17, 95% CI: 0.12–0.22; p < 0.001), and increasing age showed an inverse relationship with co-infection frequency (aOR = 0.98 per year, 95% CI: 0.97–0.99; p = 0.001). Conclusions: This study adds to current epidemiological evidence by showing that genital pathogen distribution is shaped by age- and sex-related heterogeneity, with flora-associated co-infections predominating in women and more classical STI-related agents occurring more often in men. Our findings suggest that multiplex RT-qPCR provides value not only for broad pathogen detection but also for identifying demographic- and HIV-associated co-infection patterns that may support stratified screening and targeted clinical management.

Neisseria meningitidis is an important pathogen that can cause invasive meningococcal diseases, especially with serogroups A, B, C, W and Y, which can be seen endemic or sporadic. Early diagnosis and treatment of invasive meningococcal disease is life-saving. Delay in diagnosis of meningitis infection, especially in the adolescent age group, which initially presents with atypical symptoms, can further increase the risk of morbidity and mortality. In this case report the clinical evaluation and diagnostic process of a 15-year-old female patient who admitted to the emergency department with abdominal pain, fever, cough and hallucinations and was initially considered to have an abdominal pathology was presented. Based on systematic clinical evaluations in the pediatric emergency department, a preliminary diagnosis of meningitis was established and cerebrospinal fluid (CSF) was obtained via lumbar puncture for diagnostic confirmation. The purulent-appearing CSF sample was analyzed using the Bio-Speedy® Meningitis/Encephalitis quantitative polymerase chain reaction (qPCR) MX-17 Panel (Bioeksen, Türkiye) multiplex PCR kit, which identified N.meningitidis as the causative pathogen. We used an real-time (RT)- PCR-based method to identify the serogroup of N.meningitidis and identified as serogroup C. Based on these findings, empirical treatment with ceftriaxone [2 g intravenous (IV)] was initiated and vancomycin (15 mg/kg IV) was subsequently added following the observation of abundant leukocytes in direct examination of cerebrospinal fluid.Chemoprophylaxis was administered to close contacts. The appearance of ecchymotic rashes and laboratory parameters were closely monitored throughout the clinical course. Prompt molecular diagnosis, coupled with efficacious antimicrobial therapy and intensive supportive care enabled the patient's discharge without neurological sequelae. In this case report, we emphasized the potential for meningitis infections to present with atypical clinical courses, the critical importance of rapid molecular diagnostic methods and the necessity of vaccination as a fundamental contribution to the protection of public health.

HIV-1 genotyping and drug resistance tests are routinely performed in virology laboratories in some countries, aiding clinical management. In Istanbul, between January 2021 and March 2024, plasma samples from 1029 HIV-1-infected patients were analyzed using the NGS method, and mutation and drug resistance results were retrospectively evaluated alongside demographic data. Subtype B (54.4%) was most frequent in Turkish patients, while Subtype A1 (43.5%) was predominant among foreign nationals. The most common CRFs were CRF02_AG (3.8%) and CRF56_cpx (1.6%). According to the change in detection rates during the study period, Subtype B decreased, and Subtype A increased. The most frequent mutations detected were A62V (38.7%) and M184V (22.4%) for NRTIs; E138A (55.5%) and E138G (11.5%) for NNRTIs; M46I (33.3%) and M46L (25%) for PIs; and E92Q and G for INIs (total rate: 35.2%). Darunavir/ritonavir had the highest sensitivity rate, while resistance rates for NNRTIs and INIs increased over time. We anticipate that this study, in which we evaluate the routine use of an FDA-approved NGS kit alongside integrated bioinformatics data analysis and automated reporting software for the first time in Türkiye, will contribute to both national and international molecular epidemiological data and public health strategies by providing reliable results that align with international standarts.

Background. Sexual abuse in children can sometimes result in sexually transmitted infections (STIs), which can serve as crucial forensic evidence. Although PCR methods are now accepted as the gold standard for STI screening, they have not yet widely replaced traditional culture methods in Türkiye. This study aims to assess the necessity of implementing PCR-based STI testing at Child Advocacy Centers in Türkiye, where such testing is not routinely available. Methods. Conducted between February and November 2023, this study included children who presented to the Child Advocacy Center of Marmara University Pendik Training and Research Hospital. High-risk victims were identified based on criteria including a history of penetrative sexual abuse and factors such as multiple perpetrators or significant age disparity. Serological tests and genital swabs were collected and analyzed using both bacterial culture methods and a comprehensive STI PCR panel. Results. The study included 20 victims, with a median age of 16 years. STI PCR testing detected pathogens in 19 out of 21 samples, including Chlamydia trachomatis (20%) and Neisseria gonorrhoeae (5%). In contrast, culture methods identified no sexually transmitted pathogens. Conclusion. PCR testing demonstrated significantly higher sensitivity for detecting STIs compared to traditional bacterial culture methods, as expected. Implementing PCR-based STI testing in Child Advocacy Centers is an urgent and essential need for providing an accurate diagnosis and robust forensic evidence, enhancing the care and legal protection of sexually abused children.

Human papilloma virus (HPV) is the most common sexually transmitted viral agent in the world and the most common cause of cervical cancer. HPV prevalence and genotype distribution vary by region and demographic data. In a province in the south of Turkey that constantly receives immigration, we aimed to determine the prevalence of high-risk HPV (HR-HPV) genotypes, evaluate the compatibility between cervical Pap smear cytology results patients and HR-HPVs, and make an up-to-date contribution to the elucidation of epidemiological data. In this single-centre study, a total of 12,641 women aged 18 and over were evaluated retrospectively from January 2019 to July 2022. HPV detection and genotyping were analysed by the PCR method. Bethesda scoring was used for Pap smear cytological evaluation. The overall prevalence of HR-HPV was 12.6% (12.7% in Turkish women, 11.2% in foreign women). Among the typed HPVs that were detected, HPV-16 (31%) was found first, followed by HPV-18 (8%). The prevalence of HR-HPV was higher in women with abnormal cytology (977/1762, 55.4%) than in women with normal cytology (620/10879, 5.7%) (p<0.001). Turkey doesn't yet have a national HPV immunisation program. We think that determining the specific regional frequency of other HR-HPVs separately will be useful in the follow-up of the natural course of the type-specific infection and in vaccine studies in the future.