Nida Özcan

Background/Objectives: Streptococcus pyogenes (Group A Streptococcus, GAS) remains a major human pathogen. This study aimed to determine the phenotypic profiles of macrolide resistance in S. pyogenes isolates from southeastern Turkey and to investigate underlying genotypic mechanisms using Oxford Nanopore sequencing. Methods: A total of 83 clinical isolates of S. pyogenes were collected between January 2024 and June 2025. Antimicrobial susceptibility was assessed by disk diffusion following EUCAST guidelines. Macrolide resistance phenotypes (iMLSB, cMLSB, M) were determined by the D‑zone test. Whole‑genome sequencing of erythromycin‑resistant isolates was performed using Oxford Nanopore technology, and resistance determinants were analyzed with the CARD/RGI pipeline.Results: All isolates were susceptible to penicillin. Six isolates (7.2%) exhibited erythromycin resistance: three iMLSB, two cMLSB, and one M phenotype. Adult isolates were exclusively iMLSB, whereas pediatric isolates included one M and two cMLSB phenotypes. Genotypic analysis revealed erm(A) in all iMLSB isolates, mef(A)/msr(D) in the M phenotype, and absence of major resistance genes in cMLSB isolates, which instead carried chromosomal lmrP and mef(E)‑like sequences. Co‑occurrence of tetracycline resistance genes (tetM/O) was observed in several isolates.Conclusions: Penicillin remains the cornerstone of GAS therapy; however, macrolide resistance persists through diverse mechanisms. The coexistence of erm(A)‑mediated iMLSB, mef(A)/msr(D)‑associated M phenotype, and unexplained cMLSB resistance highlights the need for routine D‑testing and genomic surveillance. These findings emphasize the importance of integrating phenotypic and genotypic approaches to monitor resistance evolution in GAS.

Adenovirus may cause life‐threatening infections. While outcomes in immunocompromised patients are well documented, data on critically ill, immunocompetent adults remain limited. To describe the clinical characteristics and outcomes of adenovirus infection in adult intensive care unit (ICU) patients and to identify factors associated with 30‐day mortality. This retrospective observational study included adult patients (≥ 16 years) admitted to ICUs between January 2020 and May 2025 with PCR‐confirmed adenovirus infection and compatible clinical syndromes, with a primary focus on describing patient characteristics rather than analyzing virological features of the infection. Data were collected from 24 centers in 11 countries. Demographics, comorbidities, clinical characteristics, laboratory findings, treatments, and outcomes were recorded. The primary outcome was 30‐day all‐cause in‐hospital mortality. Variables associated with mortality in univariate analyses were entered into a stepwise multivariable logistic regression model. A total of 126 patients were included; 40 (31.7%) died within 30 days of PCR positivity. The mean age of the entire cohort of patients was 44.9 ± 20.4 years (median 48; 16–95), and 38.9% were female. Pneumonia was the most common presentation (108/126, 85.7%), followed by upper respiratory tract infection (18.3%), gastroenteritis (6.3%), conjunctivitis (4.8%), meningoencephalitis (2.4%), and cystitis (1.6%). Significant immunosuppression was present in 29.4%. In multivariable analysis, independent predictors of 30‐day mortality included mean arterial pressure ≤ 65 mmHg, SOFA score ≥ 5, increasing Charlson Comorbidity Index, central venous catheter placement, platelet count <50,000/µL (borderline significance), procalcitonin ≥ 0.1 ng/mL, and significant immunosuppression. The final model had 84.9% accuracy, 72.5% sensitivity, and 90.7% specificity. A high percentage of ICU patients with PCR‐confirmed adenovirus infection died within 30 days. Hemodynamic instability, organ failure severity, comorbidity burden, inflammatory response, thrombocytopenia, and immunosuppression are key determinants of poor outcome.

The present study investigated the protective effects of Plantago major extract on cecal histopathology and microbiota composition in rats with ethanol-induced gastric injury. A total of 28 male Wistar albino rats were randomly divided into four groups: control, extract-treated, ethanol-treated, and ethanol + extract groups (n = 7). Gastric injury was induced by oral administration of absolute ethanol, while Plantago major extract (100 mg/kg) was administered by gavage throughout the experimental period. Cecal tissues were evaluated macroscopically and histologically, and microbiological analyses were performed using conventional culture methods. Histopathological examination of the ethanol-treated group revealed marked epithelial vacuolization, disruption of Lieberkuhn crypt architecture, inflammatory cell infiltration, vascular congestion, and edema. In contrast, the extract- treated group preserved normal cecal morphology, whereas partial histological recovery was observed in the ethanol + extract group. Microbiological analyses demonstrated no statistically significant differences among most bacterial groups (P > 0.05). However, Ruminococcus spp. levels were significantly increased in the alcohol- treated group (P < 0.001). These findings suggest that Plantago major extract may exert protective effects against ethanol-induced intestinal damage and partially preserve cecal tissue integrity.

Hepatitis C virus (HCV) is a virus that can cause hepatitis, hepatic steatosis, cirrhosis and hepatocellular carcinoma. The distribution of HCV genotypes and subtypes varies according to geographical regions. The choice and duration of treatment for hepatitis C infection are influenced by genotype. This study aimed to investigate the distribution of HCV genotypes in chronic hepatitis C patients who admitted to a university hospital in Diyarbakır and to evaluate the impact of migration on this distribution. This crosssectional retrospective study included patients who tested positive for HCV RNA between January 2011 and December 2020. One sample per patient was included in the study. Genotype determination was performed by sequencing the HCV genome obtained after amplification in serum samples containing HCV RNA. Of the 815 samples included in the study, genotype 1 was detected in 768 (94.2%), genotype 2 in five (0.6%), genotype 3 in 27 (3.3%), genotype 4 in 14 (1.7%) and genotype 5 in one (0.12%). It was determined that the sample in which genotype 5 was detected, belonged to a Syrian patient. It was determined that the prevalence of genotype 1 decreased over the years, while the prevalence of genotype 4 increased. An increase in genotype 3 was observed in the last two years of the study (2019- 2020). The majority of patients with genotype 3 were male (88.8% male, 11.2% female). The study suggests that the increase in genotype 4 rates over the years and the identification of genotype 5 indicate that migration from Syria has altered the genotype distribution. Furthermore, the increasing prevalence of genotype 3, known to be more common in intravenous drug users, highlights the involvement of various factors influencing genotype distribution. While cure rates have increased with the use of directly effective antiviral drugs, the presence of rare mutations means that regular monitoring of genotype determination and molecular epidemiological data can contribute to the development of treatment modalities.

Infection with nontuberculous mycobacterium (NTM) has been on the rise worldwide. Although the incidence rate of NTM infection has increased, little is known about its species diversity and clinical significance. Investigating the variety and load of NTM species in pulmonary and extrapulmonary clinical isolates from a community in southeast Turkey is the goal of this study. The prevalence of NTM and the clinical significance of pulmonary NTM (PNTM) are evaluated in this cross-sectional study. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and multiplex PCR were used to identify NTM species. Between 2014 and 2023, a total of 30,539 clinical samples from 14,586 tuberculosis (TB)-suspected patients were analyzed. Among the 1159 mycobacterial isolates, 85.25% were identified as Mycobacterium tuberculosis complex (MTBC), while 14.75% were identified as NTM. Of the NTM isolates, 88.88% were pulmonary, while 11.11% were extrapulmonary. The majority of NTM isolates consisted of slow-growing species (67.84%). MTBC rate has decreased while the NTM rate has increased over the years. Of the 171 NTM isolates, identification was performed for 66 isolates. Overall, 16 different NTM species were identified. The most frequently isolated species were Mycobacterium simiae 28.78% (19/66), Mycobacterium avium complex 21.21% (14/66), and Mycobacterium abscessus complex 13.63% (9/66). Among the 66 patients with NTM isolation, the mean age was 39 (±23.10). On applying the American Thoracic Society/Infectious Disease Society of America (ATS/IDSA) criteria to determine the clinical relevance of the 61 patients with PNTM isolation, only 36.06% had nontuberculous mycobacterial pulmonary disease (NTMPD), and the majority were caused by M. simiae (40.9%). Chronic obstructive pulmonary disease was significantly more common in the American Thoracic Society criteria -positive group (22.7%, P = .004). Nodular bronchiectatic patterns occurred significantly more often in the American Thoracic Society criteria-positive group (77.3%, P <.001). A statistically significant correlation was determined between NTMPD and fatigue, although fatigue was not specific for a diagnosis of NTMPD. Cough was the predominant symptom. In conclusion, our findings indicate that the species diversity of NTM isolates in our region differs from that observed in other cities across Turkey. M. simiae emerged as the species with the highest isolation frequency and clinical significance.

Vibrio, Campylobacter ve Helicobacter cinsleri doğada yaygın bulunan Gram negatif kıvrık basillerdir. Vibriolar deniz suyu ve akarsularda bulunur, kontamine sular ve bu suların kirlettiği gıdaların ağız yoluyla alınması veya bütünlüğü bozulan deriden girerek bulaşır. Vibrio cholerae salgıladığı enterotoksinler ile bol sulu ishal, dehidratasyon ve ölüme yol açabilen kolera hastalığının etkenidir, tedavide su ve elektrolitlerin yerine konması önemlidir. Diğer Vibrio türleri akut gastroenterit, sepsis veya yara yeri enfeksiyonlarına yol açar.Campylobacter spp., kümes hayvanları dahil olmak üzere birçok hayvanda bulunur, kontamine gıdaların ağız yoluyla alınması ile insana bulaşır. Campylobacter jejuni insanda en sık gastroenterit etkenlerindendir, ancak kültürde üretmek için mikroaerofilik ortam ve özel besiyerleri gerektirir. Etkenin kültür ile izolasyonu altın standart olmakla beraber klinik mikrobiyoloji laboratuvarlarında kültüre dayalı olmayan hassas teknikler de yaygın olarak kullanılmaktadır.Helikobakter türleri insan ve diğer memeli hayvanların gastrointestinal sistem ve safra yollarında, yabani kuş ve kümes hayvanlarında bulunur. Helicobacter pylori, insanda mide ve duodenum ülseri, mide adenokarsinomu ve MALT lenfomaları gibi üst gastrointestinal hastalıklarla ilişkilidir. Bakteri kendisini mide asiditesine karşı koruyan üreaz enzimine sahiptir. Tanı, biyopsi, üre nefes testleri ve dışkı antijeni gibi çeşitli yöntemlerle yapılır. Başarılı tedavi için PPI’ları içeren üçlü ve dörtlü antibiyotik rejimleri gereklidir.

Aim: Given the significant mortality and sequelae due to meningitis, rapid diagnosis and initiation of treatment have a major impact on patient outcomes. In many cases of meningitis/meningoencephalitis, empirical treatment should be initiated immediately. This empirical treatment regimen is initiated based on the cumulative antibiotic susceptibility results in the region. The aim of our study was to retrospectively determine the causative agents in cerebrospinal fluid samples of patients who received a presumptive diagnosis of meningitis, using Multiplex Polymerase Chain Reaction (PCR) tests. Materials and Methods: The study included 206 cerebrospinal fluid samples from different patients with a preliminary diagnosis of meningitis sent from various clinics. The Biospeedy viral nucleic acid isolation kit (Bioeksen, Türkiye) was used for the isolation of genetic material. Genetic materials (DNA/RNA) related to Herpes simplex virus 1-2, Humman herpesvirus 6-7-8, Varicella zoster virus, Enterovirus, Cytomegalovirus, Human Parechoviruses, Haemophilus influenzae, Listeria monocytogenes, Streptococcus pneumoniae, Neisseria meningitidis, Streptococcus agalactiae, Escherichia coli K1, Cryptococcus gattii/neoformans in cerebrospinal fluid samples were investigated using the Meningitis/Encephalitis RT-qPCR MX-17 Panel (RT-qPCR MX-17S Panel, Bio-Speedy®, Bioeksen, Türkiye) multiplex PCR kit. Results: According to the PCR results, the causative agent was identified in a total of 19 patients. Nine patients were found to have Streptococcus pneumoniae, two had Varicella zoster virus, and two had Enterovirus. Additionally, six patients had separate detections of Haemophilus influenzae, Cytomegalovirus, Herpes simplex virus 1, Human herpesvirus 6, Human herpesvirus 8, and Parechoviruses. Conclusion: Recently, simple and rapid molecular tests such as PCR have contributed to an increase in the early detection of causative agents. Based on the performance of diagnostic tests, we propose an algorithm for the use of both syndromic and specific tests in patients at risk for meningitis/encephalitis.

Aim: Given the significant mortality and sequelae due to meningitis, rapid diagnosis and initiation of treatment have a major impact on patient outcomes. In many cases of meningitis/meningoencephalitis, empirical treatment should be initiated immediately. This empirical treatment regimen is initiated based on the cumulative antibiotic susceptibility results in the region. The aim of our study was to retrospectively determine the causative agents in cerebrospinal fluid samples of patients who received a presumptive diagnosis of meningitis, using Multiplex Polymerase Chain Reaction (PCR) tests. Materials and Methods: The study included 206 cerebrospinal fluid samples from different patients with a preliminary diagnosis of meningitis sent from various clinics. The Biospeedy viral nucleic acid isolation kit (Bioeksen, Türkiye) was used for the isolation of genetic material. Genetic materials (DNA/RNA) related to Herpes simplex virus 1-2, Humman herpesvirus 6-7-8, Varicella zoster virus, Enterovirus, Cytomegalovirus, Human Parechoviruses, Haemophilus influenzae, Listeria monocytogenes, Streptococcus pneumoniae, Neisseria meningitidis, Streptococcus agalactiae, Escherichia coli K1, Cryptococcus gattii/neoformans in cerebrospinal fluid samples were investigated using the Meningitis/Encephalitis RT-qPCR MX-17 Panel (RT-qPCR MX-17S Panel, Bio-Speedy®, Bioeksen, Türkiye) multiplex PCR kit. Results: According to the PCR results, the causative agent was identified in a total of 19 patients. Nine patients were found to have Streptococcus pneumoniae, two had Varicella zoster virus, and two had Enterovirus. Additionally, six patients had separate detections of Haemophilus influenzae, Cytomegalovirus, Herpes simplex virus 1, Human herpesvirus 6, Human herpesvirus 8, and Parechoviruses. Conclusion: Recently, simple and rapid molecular tests such as PCR have contributed to an increase in the early detection of causative agents. Based on the performance of diagnostic tests, we propose an algorithm for the use of both syndromic and specific tests in patients at risk for meningitis/encephalitis.

Brucellosis remains a critical zoonotic infection with profound implications for public health across diverse regions, including the Middle East, Asia, the Arabian Peninsula, the Mediterranean, Africa, and South and Central American countries. This global threat necessitates ongoing investigation and surveillance. Accordingly, this study aimed to elucidate the presence and characteristics of Brucella spp. isolated from patients in a province of eastern Türkiye. A combination of conventional and molecular techniques was employed to achieve comprehensive species and biovar determination. A total of 189 human Brucella spp. strains isolated from blood cultures at Bitlis State Hospital between 2010 and 2020 were included in the study. Identification tests for the isolates comprised assessing serum requirement for growth, oxidase and urease production, as well as lysis testing with Tbilisi phage and R/C phage. Additional conventional biotyping tests involved evaluating hydrogen sulfide (H2S) production, carbon dioxide (CO2) requirement for growth, and growth in media containing thionin, basic fuchsin, and safranin. Furthermore, agglutination with Brucella A and M type monospecific antisera was performed. The isolates also underwent multiplex PCR, specifically the Bruce–Ladder PCR method, for biotyping. The results demonstrated the predominance of Brucella melitensis strains in human brucellosis cases, as identified by both conventional and molecular methods. Specifically, 185 isolates were classified as B. melitensis biovar 3, with the remaining 5 isolates classified as B. melitensis biovar 1. In conclusion, this distribution underscores the significant role of B. melitensis in the epidemiology of human brucellosis in the region. The current study highlights the efficacy of both conventional and molecular methods in Brucella spp. identification, with particular emphasis on the Bruce–Ladder PCR method’s superiority in terms of rapidity and compatibility with traditional techniques. Continued research and surveillance efforts are imperative to deepen our understanding of the epidemiology and dynamics of this zoonotic disease.