Ferhat Osman Daşdemir

Background: The association between Helicobacter pylori and the resident gastric microbiota plays a critical role in gastric carcinogenesis; however, the specific microbial alterations accompanying the transition from chronic inflammation to malignancy remain to be fully elucidated. This study aimed to characterize the distinct bacterial signatures associated with gastric cancer (GC) and non-ulcer dyspepsia (NUD) within a Turkish cohort, evaluating these structural shifts in the context of the “hit-and-run” hypothesis. Methods: Genomic DNA was isolated from 158 gastric biopsy specimens obtained from 96 individuals stratified into four homogeneous groups based on clinical H. pylori status and histopathological presentation: H. pylori-positive GC (Hp+GC, n = 37), H. pylori-negative GC (Hp-GC, n = 25), H. pylori-positive NUD (Hp+NUD, n = 17), and H. pylori-negative NUD (Hp-NUD, n = 17). Next-generation amplicon sequencing targeting the V3–V4 hypervariable regions of the 16S rRNA gene was executed, followed by strict quality filtering via the DADA2 pipeline and taxonomic classification against the SILVA database. Results: Alpha diversity analysis demonstrated a significant reduction in microbial richness and evenness within the Hp+GC group compared with all other cohorts (FDR-adjusted q < 0.001). Beta diversity metrics revealed distinct ecological trajectories, with the overall microbial community structure of the Hp+GC group diverging sharply from non-malignant controls. Taxonomic profiling unveiled a profound dysbiotic shift in the Hp+GC microenvironment, characterized by a massive depletion of the Firmicutes phylum and a concomitant overrepresentation of Proteobacteria (66.56%). While the Helicobacter genus predominated in the non-malignant Hp+NUD group, its relative abundance declined to negligible levels (Enterobacteriaceae family, showing highly significant enrichment of Morganella (11.14% mean relative abundance; FDR-adjusted q < 0.001), Providencia (3.43%; FDR-adjusted q < 0.001), and Klebsiella (2.03%; FDR-adjusted q < 0.001). Conclusions: These findings support the “hit-and-run” model, indicating that H. pylori acts as an initiator of carcinogenesis but is progressively outcompeted by an aggressive, nitrate-reducing, and pro-inflammatory Enterobacteriaceae-dominated dysbiotic bacterial community as mucosal atrophy and hypochlorhydria neutralize the typical acidic gastric barrier.

Understanding microbial survival mechanisms in aquatic environments is essential for public health. This study investigates the potential role of free-living amoebae (FLA) as environmental shelters for Helicobacter pylori in Istanbul’s potable and wastewater treatment plants. Sampling was conducted during wet (February–March 2024) and dry (May–June 2024) seasons from influent and effluent points across various facilities. Standardized protocols for water collection, filtration, DNA extraction, and sequencing were employed. Metagenomic analysis revealed the presence of Dictyostelium discoideum as the only detected FLA and identified Helicobacter DNA fragments, with an average of 31.8% assigned to H. pylori within this genus. Given that D. discoideum is primarily a soil-dwelling social amoebae rather than a typical aquatic FLA of public health concern, its detection in the water treatment systems likely reflects soil runoff following precipitation events or environmental contamination during sample collection and filtration. However, qPCR and propidium monoazide–droplet digital PCR (PMA-ddPCR)—used to assess bacterial viability—yielded negative results for all water samples. Similarly, axenic culturing and microscopic analysis failed to isolate viable amoebae. Although metagenomic signals suggested prior microbial presence, the absence of viable organisms indicates possible inactivation due to environmental or treatment-related factors. This study is the first to apply PMA-ddPCR for H. pylori detection, offering high specificity for viable cells. The findings underscore a key limitation in using DNA-based assays alone to assess pathogen viability and interspecies interactions. Despite negative results for viable H. pylori and FLA, the study raises concerns about waterborne transmission and highlights the importance of integrating viability-focused techniques. Broader sampling and longitudinal monitoring are recommended to fully assess the risk of amoebae-mediated survival and environmental persistence of pathogenic bacteria like H. pylori. These findings support a One Health approach, linking environmental microbiology to human and animal health risk management in urban water systems.

This study aimed to assess the humoral immune response following administration of a BNT162b2 mRNA COVID‐19 booster dose and to evaluate its association with the development of SARS‐CoV‐2 infection after vaccination. Between July 2021 and February 2022, serum samples were collected from 313 individuals 28 days after receiving a COVID‐19 booster dose. Quantitative SARS‐CoV‐2 IgG antibodies directed against the receptor‐binding domain (RBD) of the spike protein were measured using a chemiluminescent microparticle immunoassay. Neutralizing antibody activity, defined as inhibition of the RBD–ACE2 interaction, was evaluated semi‐quantitatively by a competitive ELISA. Participants were followed for 6 months after the final dose to identify confirmed SARS‐CoV‐2 infections. The cohort included 97 males (31%) and 216 females (69%), with a mean age of 39.43 years. The median SARS‐CoV‐2 IgG antibody level at day 28 was 7713.3 AU/mL, and the median neutralizing antibody inhibition rate was 99.2%. Antibody levels were not significantly associated with age or comorbidities. Booster vaccination induced a strong humoral immune response in all participants. However, the occurrence of post‐vaccination infections despite high antibody levels suggests immune escape by emerging variants. While vaccines may not fully prevent infection, they provide substantial protection against severe disease and mortality.

This study aimed to comparatively evaluate the conventional hepatitis B surface antigen (HBsAg) assay and the next-generation HBsAg NEXT (HBsAgNx) assay in samples with low-level HBsAg positivity and in cases of occult hepatitis B infection (OBI). A total of 497 individuals were included in the study, comprising 300 individuals with low-level HBsAg positivity, 100 OBI cases (64 seropositive and 36 seronegative) and 97 healthy controls. Serum samples were analyzed using the Abbott ARCHITECT HBsAg Qualitative II assay (Abbott Diagnostics, Wiesbaden, Germany) and the Abbott Alinity i HBsAg NEXT assay (Abbott Diagnostics, Wiesbaden, Germany). The presence of HBV DNA was confirmed by real-time polymerase chain reaction (Rt-PCR) using the COBAS AmpliPrep/COBAS TaqMan HBV test v2.0 (Roche Diagnostics, Mannheim, Germany). HBV DNA (Rt-PCR) was accepted as the gold standard reference for diagnostic performance evaluation. To minimize potential bias arising from sample selection, individuals with lowlevel HBsAg positivity and OBI cases were analyzed separately. In the low-level HBsAg-positive group, semi-quantitative S/CO values of the assays were compared, whereas in the OBI group, only the detection rates of HBV DNA-positive cases were evaluated. A total of 17 OBI cases (17%) were identified that were tested negative by the conventional assay but positive by the HBsAgNx assay. Differences between the assays were evaluated using the McNemar test and p< 0.05 was considered statistically significant. Median values obtained with the HBsAgNx assay were significantly higher than those obtained with the conventional assay (p< 0.001). The HBsAgNx assay provides clinically significant contributions particularly in the OBI group, by detecting cases that cannot be identified by conventional assays. These findings indicate that the integration of high-sensitivity HBsAg assays into current HBV diagnostic algorithms would increase case detection and contribute to both transfusion safety and the clinical management of OBI.

Aims: This study retrospectively evaluates the serological (CMV IgM and IgG) and molecular (CMV DNA PCR) test results of patients admitted to İstanbul Faculty of Medicine Hospital between 2021 and 2023 due to suspected cytomegalovirus (CMV) infection. The aim is to assess the diagnostic value of combining serological and molecular methods and to analyze CMV positivity across age and gender groups. Methods: This cross-sectional observational study included 1.649 patients who underwent CMV testing (CMV IgM, CMV IgG, and/or CMV DNA PCR) at the Medical Microbiology Laboratory of İstanbul Faculty of Medicine between January 1, 2021, and December 31, 2023. Serological tests were performed using ELISA (Vircell, Spain), and CMV DNA was quantified using real time PCR (QIAsymphony/Artus CMV QS-RGQ and cobas® 6800). Data were anonymized and analyzed statistically using SPSS v26.0. Mann-Whitney U, Chi-square, McNemar, and ROC tests were applied; p0.05), CMV DNA positivity varied significantly across age groups (p

This study aimed to evaluate the performance characteristics of a rapid antigen test developed to detect SARS-CoV-2 (COVID-19), influenza A virus (IAV), and influenza B virus (IBV) (flu) compared with those of the real-time reverse transcription-polymerase chain reaction (rRT-PCR) method. One hundred SARS-CoV-2, one hundred IAV, and twenty-four IBV patients whose diagnoses were confirmed by clinical and laboratory methods were included in the patient group. Seventy-six patients, who were negative for all respiratory tract viruses, were included as the control group. The Panbio™ COVID-19/Flu A&B Rapid Panel test kit was used in the assays. The sensitivity values of the kit were 97.5%, 97.9%, and 33.33% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load below 20 Ct values. The sensitivity values of the kit were 16.7%, 36.5%, and 11.11% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load above 20 Ct. The kit’s specificity was 100%. In conclusion, this kit demonstrated high sensitivity to SARS-CoV-2 and IAV for viral loads below 20 Ct values, but the sensitivity values were not compatible with PCR positivity for lower viral loads over 20 Ct values. Rapid antigen tests may be preferred as a routine screening tool in communal environments, especially in symptomatic individuals, when diagnosing SARS-CoV-2, IAV, and IBV with high caution.

Giriş: Günümüzde COVID-19 aşı ya da enfeksiyon sonrasında humoral immün yanıtı değerlendirmek amacıyla pek çok immünolojik test yöntemleri kullanılmaktadır. Çalışmamızda da CoronaVac, BNT162b2 ve COVID-19 geçiren kişilerde SARS-CoV-2 humoral immün yanıtı farklı prensipli immünolojik test yöntemleriyle değerlendirmeyi amaçladık. Materyal-metot: COVID-19 tanısı alan 30, CoronaVac aşısı olan 35 ve BNT162b2 aşısı olan 35 kişinin 28 gün sonra alınan serum örnekleri çalışmaya dahil edilmiştir. SARS-CoV 2’nin spike proteini S1 alt biriminin reseptör bağlayıcı bölgesine (RBD) karşı nötralize edici antikorlar üç farklı prensibe yönelik (CMIA, ELISA, LFA) antikor testleri ile (ARCHITECT IgG II Quant test, Abbott, USA/SARS-CoV-2 NeutraLISA, Euroimmun, Lübeck, Almanya/ NeutraXpress™, JOYSBIO Biotechnology Co. Ltd., Tianjin China) çalışıldı. Verilerin istatistiksel değerlendirmesinde IBM SPSS statistic 21 paket programı kullanıldı. Bulgular: Tüm olguların SARS-CoV-II kantitatif antikor titreleri 2635,150 (391,1-8053,425) AU/mL olarak saptandı. Gruplar arasındaki istatistiksel değerlendirmede, COVID-19 geçiren ve BNT162b2aşısı olan kişilerin SARS-CoV-II kantitatif antikor titreleri CoronaVac grubuna kıyasla anlamlı olarak yüksek saptandı (p<0.001). SARS-CoV-II nötralizan antikor inhibisyon yüzdesi tüm olgularda %88,411 (32,904-98,832) iken, COVID-19 geçiren ve BNT162b2 aşısı olan anlamlı olarak yüksek saptandı (p<0.001). Lateral-flow yöntemine göre bağlanan total antikor varlığı 75 (%75) kişide pozitif olarak saptanırken, Nötralizan antikor 60 (%60) kişide pozitif olarak saptandı. Sonuç: Çalışmamıza göre, enfeksiyon ve aşılama sonrası SARS-CoV-2’ ye spesifik humoral immün yanıtın geliştiği görülmektedir. Ayrıca, immunolojik yöntemlerle humoral immün yanıtın değerlendirilmesinde, duyarlılığı ve özgüllüğü yüksek olan testlerin tercih edilmesi gerektiğini düşünmekteyiz.

This study aimed to determine the anti-S (receptor binding protein) RBD IgG antibody titers formed against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and the neutralizing antibody inhibition percentages (nAb IH%) in blood samples taken after two doses of inactive or mRNA-based vaccine and a booster dose. Volunteers with two doses of inactivated CoronaVac (heterologous group; n = 75) and BioNTech (BNT)162b2 mRNA vaccine (homologous group; n = 75) were included in this study. All participants preferred the BNT162b2 vaccine as a booster dose. First, peripheral blood samples were taken 3 months after the second vaccine dose. Second, peripheral blood samples were taken 1 month after the booster dose. Anti-S-RBD IgG titers were determined by CMIA (SARS-CoV-2 IgG II Quant). Neutralizing antibodies were detected by a surrogate neutralization assay (SARS-CoV-2 NeutraLISA, Euroimmun, Lübeck, Germany). The median age of the volunteers was 40 (IQR 29–47) years old. After the heterologous booster dose, anti-S-RBD IgG levels and neutralizing antibodies increased approximately 50-fold and 9-fold, respectively. Anti-S-RBD IgG titers increased by 9 and 57 times, respectively, while nAb IH% increased by 1.5 and 16 times, respectively, among those with heterologous reminder doses and those with and without a prior history of coronavirus disease (COVID-19). This study showed that after the administration of a heterologous booster dose with BNT162b2 to those whose primary vaccination was with inactivated CoronaVac, the binding and neutralizing antibody levels were similar to those who received a homologous BNT162b2 booster dose. It was observed that the administration of heterologous and homologous booster doses resulted in the development of similar levels of neutralizing antibodies, independently from a prior history of COVID-19.