The one health perspective is an integrative and holistic approach that recognizes the interconnection and interdependence of human, animal and plant health and aims to improve each sustainably. This perspective has gained particular importance following the coronavirus disease-2019 pandemic and has been acknowledged as a component of public health. Fungal infections also pose significant risks to ecosystems, ranging from crops to animals and humans. These risks partly arise from human and animal mobility and have increased alongside climate change. Therefore, food safety has become an integral part of developing societies. Apples are the most widely consumed fruit worldwide. They are known to have multiple health benefits and have been reported to reduce the risk of chronic diseases such as cancer, diabetes, heart disease and stroke. Previous studies have shown that important human pathogens, including multidrug-resistant Candidozyma auris and Candida parapsilosis were isolated from apple peels. Moreover, although rarely, dematiaceous fungi such as Exophiala dermatitidis and Exophiala phaeomuriformis, which can also be pathogenic for humans and animals, have been identified in apples. The aims of the study were to investigate, the presence of extremotolerant Exophiala species in apples that undergo post-harvest storage processes and are sold in local markets across different regions of Türkiye, as well as the polyaromatic hydrocarbon (PAH) levels in the apples from which these isolates were obtained. Additionally, given their resistance to these molecules, the value of culturing Exophiala species on apples as a biological indicator of PAH pollution and to discuss the findings within the framework of the One Health perspective and to draw attention to this issue were aimed in the study. In the present study, the presence of dematiaceous fungi was investigated in 549 apples collected from local markets in 24 different provinces of Türkiye. Sampling was performed from apple skins using sterile swabs and inoculation was carried out on Sabouraud dextrose agar, Staib agar and Czapek media. Isolates compatible with dematiaceous fungi were subsequently identified by sequencing the rDNA internal transcribed spacer region. Antifungal susceptibility testing against five different triazoles was performed using the CLSI microdilution method. Furthermore, benzo[a]anthracene, benzo[b]fluoranthene, benzo[a] pyrene, and chrysene were measured as indicators to determine the amount of polycyclic aromatic hydrocarbons (PAHs) in the skins of apples from which dematiaceous fungi were recovered. In this study, E.phaeomuriformis was identified in four apples (0.7%). These isolates were detected in the provinces of Ankara, Antalya (Finike district), Kayseri, and Kars (Sarıkamış district). Antifungal susceptibility testing was performed for three isolates, and low MIC values were found for all triazole antifungals except fluconazole.. The levels of the four compounds, considered primary environmental pollutants were determined to be high in the skins of all four apples according to the European Union and Turkish Food Codex limits. This suggests that E.phaeomuriformis, which is known to utilize aromatic hydrocarbons as a carbon source, could be used as a biological indicator of PAH pollution. Additionally, apple skins were considered to represent an oligotrophic habitat. In conclusion, beyond food safety, the need to improve and strengthen public health services is evident.
Rasamsonia species are thermophilic fungi that primarily cause infection in immunocompromised patients. R.argillacea species complex is frequently misidentified as a pathogen due to its morphological similarity to the genera Penicillium and Paecilomyces and its incidence remains undetermined. This situation further complicates the process of timely diagnosis and treatment. Rasamsonia species can be identified using internal transcribed spacer (ITS) sequence analysis, which is considered the primary fungal barcode. Accurate species identification is imperative for the administration of appropriate antifungal treatment. In this report, a case of acute myeloid leukaemia (AML) with R.argillacea growth was presented. A 69-year-old female patient diagnosed with AML who was undergoing chemotherapy was admitted to the hospital due to febrile neutropenia. Despite the administration of appropriate antibiotic therapy, the patient's fever did not respond and her respiratory distress worsened. A subsequent chest computerized tomography scan revealed the presence of bilateral nodular lesions and halo findings in some nodules. The empirical liposomal amphotericin B was initiated at a dosage of 3 mg/kg/day. Following a 17-day course of empirical amphotericin B therapy, the patient exhibited an escalation in respiratory distress and an increase in her blood galactomannan (GM) level (Platelia™ Aspergillus Ag; Bio-Rad, France). Consequently, intravenous (IV) voriconazole was administered at a loading dose of 2x6 mg/kg followed by a maintenance dose of 2x4 mg/kg. Notwithstanding the administration of voriconazole therapy, the patient's blood GM levels persisted at elevated levels on three separate occasions. Consequently, a bronchoalveolar lavage (BAL) sample was obtained for further analysis. However, no growth was detected in the bronchoalveolar lavage (BAL) culture. The BAL GM level was found to be elevated (optic indices: 4.38). The patient developed increasing respiratory distress and confusion and was intubated. A deep tracheal aspirate (DTA) sample was collected. The patient died shortly thereafter. Velvety, beige-colored colonies were observed in the culture media to which the DTA sample inoculated. Microscopic examination of the culture using a lactophenol cotton blue stain revealed cylindrical conidia, rough-walled conidiophores and long, pointed phialides. The isolate was identified as R.argillacea using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (Bruker, Bremen, Germany). This isolate could not be identified based on colony morphology and microscopic appearance; however, it was identified as R. argillacea using the ribosomal DNA ITS region. Its antifungal susceptibility was then assessed using the microdilution method according to the Clinical and Laboratory Standards Institute M38-A2 guidelines. The minimum inhibitory concentrations (MICs) for the antifungal drugs were as follows: fluconazole >64 μg/mL, itraconazole 0.5 μg/mL, voriconazole >16 μg/mL, posaconazole 0.5 μg/ mL, anidulafungin ≤0.015 μg/mL, micafungin 0.03 μg/mL and amphotericin B 1 μg/mL. In this case, the patient died without the causative agent being identified. Although it cannot be definitively stated that R. argillacea was the cause of the patient's mortality due to the lack of an autopsy, this case was presented because it is the first suspected case of R. argillacea isolated and confirmed by molecular methods in Türkiye and to highlight the importance of not neglecting Rasamsonia species which are rare mold fungi.
Abdominal tuberculosis is a form of extrapulmonary tuberculosis that frequently involves the ileocecal region and often mimics conditions such as colorectal cancer or inflammatory bowel disease due to its nonspecific symptoms. While Mycobacterium tuberculosis remains the most common causative agent, rare zoonotic species like Mycobacterium caprae can also lead to human disease. In this case report, a rare case of cecal tuberculosis caused by M.caprae in a 46-year-old woman with a healthy immune system was presented. The patient presented chronic abdominal pain, diarrhea and weight loss for two years. Radiological imaging revealed ileocecal thickening and colonoscopy showed an ulcerovegetative mass raising suspicion of malignancy. Histopathological examination showed chronic granulomatous inflammation with acid-fast bacilli and molecular testing confirmed the presence of M.caprae. The patient was treated with standard anti-tuberculosis therapy including isoniazid, rifampicin, pyrazinamide and ethambutol. However, due to the development of post-treatment intestinal stenosis, surgical intervention was necessary. Human diseases with M.caprae are exceedingly rare and typically associated with occupational or environmental exposure to infected animals or unpasteurized dairy products. In this case, no such exposure was identified. The case highlights the diagnostic challenges posed by intestinal tuberculosis and underscores the importance of considering mycobacterial infections even in immunocompetent hosts. Early recognition and molecular identification are essential for accurate diagnosis and appropriate treatment. Clinicians should remain alert to potential complications such as fibrotic strictures that may require surgical management. This case represents one of the rare reports in the literature of cecal tuberculosis caused by M.caprae. To the best of our knowledge, reports describing similar cases are exceedingly rare.
Onychomycosis is a nail infection most commonly caused by dermatophytes. However in recent years, non-dermatophyte molds have also been increasingly reported as causative agents of onychomycosis. Phoma glomerata is a saprophytic fungus commonly found in nature, which rarely causes infections in humans and to date, only one case has been reported in another country as a causative agent of onychomycosis. In this case report, a case of onychomycosis caused by P.glomerata was presented. A 67-year-old female patient admitted to the dermatology outpatient clinic of our hospital with a oneyear history of discoloration, thickening and fragility of the left big toenail. In the potassium hydroxide microscopic examination of the specimen taken from the nail bed, septate and branched hyphae were observed. Dark brown pigmented, slow-growing mold colonies were observed within 10 days of culture on Sabouraud dextrose agar. Microscopic examination revealed the presence of pycnidial structures. The fungus isolated from the patient was identified as P.glomerata using the VITEK MS Mould Kit with the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (VITEK MS, bioMérieux, France) system and DNA sequencing analysis was performed to confirm the diagnosis. Following genomic DNA extraction, the 28S rRNA gene region was amplified by polymerase chain reaction (PCR) using the NL1 and NL4 primers. After agarose gel electrophoresis of the PCR products, the amplicons were sequenced using the SQK-NBD114.96 kit on the MinION (Oxford Nanopore, United Kingdom) platform. The obtained data were analyzed using the BLAST algorithm in the National Center for Biotechnology Information GenBank database. The sequence was submitted to the NCBI GenBank under the accession number PV975047. The patient was treated with oral terbinafine (250 mg/day) and topical antifungal therapy. Clinical improvement was observed after two months of follow-up. In this study, we present a case of onychomycosis caused by P.glomerata in an elderly diabetic patient living in a rural area. According to our literature review, this is the first case reported from Türkiye and the second worldwide. Current scientific data suggest that Phoma species can cause infections in the skin, subcutaneous tissues or other organs, especially in immunocompromised or debilitated individuals, or following penetrating trauma. Classical phenotypic methods pose significant challenges in identifying this agent and MALDI-TOF MS or molecular methods may be useful for accurate identification.
Hyperemesis gravidarum (HEG) is a pregnancy complication characterized by severe nausea, vomiting more than four times a day and dehydration, especially occurring in the first trimester of pregnancy. In recent years it has been shown that the intestinal bacterial microbiome profile may be associated with a wide range of diseases. The aim of this study was to determine whether the intestinal bacterial microbiome profiles differ between pregnant women diagnosed with hyperemesis gravidarum (HEG) and those with healthy pregnancies. Fresh stool samples were collected from 15 pregnant women diagnosed with HEG and 14 healthy pregnant women who did not have any complaints in the first trimester. After DNA isolation from the samples, 16S rRNA gene-based microbial profiling was performed with next-generation sequencing. The 16S rRNA V3-V4 region was sequenced with paired-end reads (2×250 base pair) on the Illumina MiSeq platform. The average sequence number for each sample was similar (HEG= ~2.54 million, control= ~1.48 million; p> 0.05). After quality filtering, reads obtained from all samples were analyzed by rarefaction at equal depth. Alpha diversity measures were found to be significantly higher in the HEG group compared to the control group (Shannon, ACE, and Chao1 indices; p< 0.05 for all). In the beta diversity analysis, it was observed that the gut microbiome compositions of the two groups were separated; In the Principal Coordinates Analysis plot, the groups were clearly clustered and the group difference was found to be statistically significant by PERMANOVA test (p< 0.01). Significant differences were also found in the comparisons at the taxonomic level. At the class level, the relative abundance of Clostridia was significantly higher in the HEG group (p< 0.05), while the class Bacilli was dominant in the control group (p< 0.05). At the family level, the abundances of Lachnospiraceae and Prevotellaceae were found to be significantly higher in the HEG group than in the control group (p< 0.05). In contrast, at the family level, the rates of Enterobacteriaceae and at the genus level, the rates of Escherichia-Shigella were found to be significantly higher in the control group (p< 0.05). Some bacterial taxa detected only in the HEG group samples were also noteworthy: Collinsella, Blautia, and Dialister genera, which are only found in the intestines of patients with HEG, were not detected in the control group. In conclusion, these findings reveal that there are significant differences between the intestinal microbiome profiles of pregnant women with HEG and healthy pregnant women. The high microbial diversity observed in the HEG group and changes in certain bacterial groups suggest that processes related to lipid and carbohydrate metabolism may play a role in the pathogenesis of HEG. In the future, the clinical significance and possible therapeutic targets of these differences can be evaluated with more comprehensive studies aiming at clarifying causality.
Orf is a zoonotic infection caused by the parapoxvirus belonging to the Poxviridae family. It is usually transmitted to humans from sheep and goats. Human-to-human transmission is quite rare. Shepherds, veterinarians, slaughterhouse workers and people living in rural areas who are in close contact with farm animals constitute the main risk group. It most commonly presents as pustular dermatitis on the hands, usually painless but sometimes associated with tenderness and pain in the early clinical stages. Auricular localization is quite rare, with a few cases involving the ear reported in the literature but earlobe involvement has not been previously reported. In this case report, a 14-year-old female patient who admitted with an erythematous, thick-walled pustular lesion on the right earlobe was presented. In the patient's history, there was close contact with sheep and especially newborn lambs. On physical examination, the lesion was observed to extend to the earring hole and had a fistulized appearance. Total surgical excision was performed under local anesthesia. Histopathological examination revealed proliferative inflammatory features as well as vacuolization and inclusion bodies consistent with viral infection. In molecular analysis, paraffin block-prepared samples were examined and the ORF-RPA gene region encoding the major component (RPO132) of the viral polymerase of the orf virus was amplified by polymerase chain reaction and a definite diagnosis was made. After surgical excision, no additional treatment was applied to the patient and she was followed up for six months with no recurrence or residual disease. Orf is generally a self-limiting infection; however, in atypical localizations it may show a rapidly growing course that mimics malignancy. In the differential diagnosis, especially cutaneous anthrax which is endemic in our country and monkeypox infections which have been reported in recent years, are of importance. In conclusion, it should be kept in mind that orf lesions may occur even in unexpected sites such as the periauricular region, particularly in patients living in rural areas with a history of animal contact. Early diagnosis of orf infection will prevent unnecessary aggressive surgical interventions and will also contribute to the proper follow-up of patients and the prevention of complications.
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.
Pneumocystis pneumonia (PcP) caused by Pneumocystis jirovecii is one of the most common and serious opportunistic infections in immunocompromised patients. People at risk for developing Pneumocystis pneumonia include human immunodeficiency virus positive individuals, cancer patients, people receiving immunosuppressive therapy, organ transplant recipients and people with compromised immune systems. Despite effective treatment and prophylaxis, mortality is reported to be between 15-40%, even in people with immunodeficiency other than acquired immunodeficiency syndrome. Although the number of immunosuppressed patients is increasing, diagnostic and epidemiological studies for this agent are still insufficient. This study aimed to investigate the prevalance and epidemiological characteristics of P.jirovecii isolated from various patient groups. Among the 469 bronchoalveolar lavage fluids or sputum samples sent to the medical microbiology laboratory from various units, 114 samples were selected for indirect fluorescent antibody (IFA) testing and molecular studies based on an examination of the patients' files to determine underlying diseases, use of immunosuppressive drugs, corticosteroid treatments received and the presence of patchy or nodular ground-glass opacity on computed tomography scans and the presence of a cyst-like structure on May-Grunwald Giemsa staining. The presence of P.jirovecii was investigated by IFA and polymerase chain reaction methods and genotyping was performed by sequencing of mtLSU rRNA and internal transcribed spacer (ITS) region. The obtained ITS gene region DNA sequences were aligned and TCS network analysis was performed in the aligned region. As a result, positivity was found in eight samples out of 469 samples by using mtLSU rRNA genotyping, Genotype 1 (n= 3; 37.5%) was found to be the most common genotype in our samples. Genotype 2 (n= 2, 25%), genotype 4 (n= 2, 25%) and genotype 3 were the most frequently detected other genotypes, respectively. When the relationships between the sequences were examined, it was observed that our samples were generally related to the samples originating from Iran. In the present study, the genotyping analysis of the ITS region, constructed using the consensus sequence employed in the study by Lee et al., revealed that the most common genotype was Eh (n=3; 42.85%), followed by Bg (n= 2; 28.57%), Bi (n= 1; 14.28%) and Eg (n=1; 14.28%). Our study is the first genotyping study conducted in our country using the ITS gene region. Different epidemiological findings were found in P.jirovecii genotype frequencies in studies conducted in different geographies. This suggests that genetic variations in P.jirovecii have a geographical component and this may affect the distribution of P.jirovecii strains among humans. According to TCS network analysis, our samples are generally associated with samples originating from Iran. None of our samples are found alongside samples originating from India. However, in certain areas of the analysis, New World and Old-World samples exist together. It can be assumed that globalization and thus the increase in human movement over time has led to the spread of different genotypes to different geographical regions and the formation of genotypic mosaics in certain geographical regions. Man-made destruction of nature and the consequent intertwining of urban and rural boundaries, as well as global warming and climate change have undeniably contributed to these movements.
Dental implants are the most acceptable treatment option for the replacement of missing teeth. Despite the high success rate, the presence of implant complications is increasing. Peri-implant mucositis and peri-implantitis are biologic implant complications induced by a dysbiotic shift in the microbiota. The main goal of the treatment of peri-implant diseases is to remove the bacterial biofilm on the implant surface and restore the ecological balance between the host and oral microbiota. For this purpose, both non-surgical and surgical treatments are applied. Non-surgical approaches based on mechanical debridement focus on biofilm control such as disruption/removal of submucosal biofilm and oral hygiene instructions. Mechanical debridement, non-ionizing radiation sources, antiseptics or antibiotics are included in the non-surgical treatment. Mechanical debridement is applied by the help of the curettes (titanium-coated, carbon fiber, Teflon and plastic), ultrasonic tips, various types of brushes and air-flow devices and allows the removal of soft and hard deposits from the implant surface. However, it remains unclear which treatment is the most effective and predictable for the management of peri-implant diseases. This review article aimed to overview, the non-surgical treatment options of peri-implant diseases and their microbial effectiveness. For this purpose, studies evaluating changes in the peri-implant microbiota before and after treatment using 16S ribosomal RNA (rRNA) sequencing were searched in databases (PubMed and Google Scholar).The literature search covered studies published between 2012 and May 2024 and 1202 of the 1209 articles searched were excluded. Seven studies that met the inclusion criteria were examined; these studies included a total of 107 patients with peri-implant mucositis and 182 patients with peri-implantitis for periods ranging from one to 60 months. Six studies evaluated the effectiveness of mechanical debridement alone or combined with other therapies while one study assessed the hyaluronic acid efficacy. Based on the literature review, it can be inferred that non-surgical treatment demonstrates effectiveness in the short term for managing peri-implant mucositis. However, its impact on the treatment of peri-implantitis appears to be considerably limited. Regarding the treatment of peri-implant mucositis, the application of antimicrobial agents (chlorhexidine or delmopinol) in addition to mechanical treatment (manually or ultrasonic devices) shows both clinical and microbiological effectiveness in the short term. After treatment, the microbial profile tends to shift towards a less dysbiotic form. According to the short-term follow-up findings, the effect of using chlorhexidine in addition to mechanical debridement in peri-implantitis therapy is contradictory. However, additional use of antimicrobial photodynamic therapy also appears to provide short-term benefits. The application of hyaluronic acid may decrease the microbial diversity. However, it is crucial to note that these findings are derived from a limited number of studies, emphasizing the need for future research to provide more comprehensive insights.
This study aimed to determine the serum levels of the LL-37 molecule, associated with the pathophysiology of Brucellosis, in patients diagnosed with Brucellosis and to investigate the relationship between these levels and the clinical course of the disease. The study included 45 acute, 30 subacute, 26 chronic and 19 relapsed patients diagnosed according to clinical, bacteriological and serologic results as Brucellosis, as well as 60 healthy volunteers. Serum LL-37 levels were measured using the enzyme-linked immunosorbent assay method and the results were compared with the clinical data of the patients. Serum LL-37 levels were significantly higher in Brucellosis patients compared to the control group, with variations observed among clinical subgroups. A weak positive correlation was found between serum LL-37 levels and alanine transaminase, C-reactive protein and erythrocyte sedimentation rate values in patients with Brucellosis. Serum LL-37 levels were higher in patients with Brucella spp. growth in blood cultures compared to those without growth. Additionally, patients with complicated Brucellosis involving osteoarticular involvement had significantly higher serum LL-37 levels than those without such complications. Serum LL-37 levels with a cut-off value of 18.26 ng/mL demonstrated a sensitivity of 92% and a specificity of 88% in distinguishing Brucellosis cases from healthy individuals, with a positive predictive value of 82% and a negative predictive value of 91% (area under curve= 0.956, p< 0.001, 95% confidence interval= 0.93-0.98, negative likelihood ratio= 0.09, positive likelihood ratio= 7.66). No previous studies on serum LL-37 levels in Brucellosis were found in the literature. LL-37 appears to have potential as a biomarker for the diagnosis and prognosis of Brucellosis.
Quantitative detection of human immunodeficiency virus-type 1 (HIV-1) and hepatitis C virus (HCV) RNA plays a crucial role in the diagnosis, monitoring of the therapy and evaluation of the treatment response. The ELITe BeGenius® platform (ELITechGroup, Turin, Italy) is a fully automated sample-toresult molecular system integrating extraction, amplification and detection within a single workflow. The HIV-1 ELITe MGB® and HCV ELITe MGB® assays are real-time polymerase chain reaction tests designed for plasma viral-load quantification. This study aimed to verify their analytical performance under routine clinical laboratory conditions. Verification included assessments of accuracy, intra- and inter-assay precision, linearity and method correlation. A total of 70 plasma samples for HIV-1 RNA and 52 for HCV RNA were analyzed using previously tested and stored patient specimens, reference materials, and external quality controls. Results were compared with established reference assays used in accredited laboratories. Statistical analyses included positive, negative, and overall percent agreement (PPA, NPA, OPA), coefficients of variation (CV%), correlation and regression analyses and Bland-Altman bias estimation. For HIV-1 RNA, 19 of 20 positive and all 20 negative plasma samples were correctly identified by the ELITe MGB® assay, yielding a PPA of 95.0%, NPA of 100.0% and OPA of 97.5% (κ= 0.95). Intra-assay precision showed strong repeatability, with CVs of <1-3.9% for low-positive, 0.4-6.4% for medium-positive and <2% for high-positive specimens. Inter-assay reproducibility was consistent with CVs of 12.8% at low, 2.4% at medium, and 1.4% at high viral loads. Correlation analysis showed excellent concordance with the reference assay (p= 0.975, p< 0.001; R²= 0.95) and a mean bias of -0.40 log10 copies/mL in Bland-Altman analysis. Linearity was strong (R²= 0.97), confirming accurate quantification across the dynamic range with minor underestimation at higher dilutions. For HCV RNA, all 14 positive and 14 negative samples were correctly classified (PPA, NPA, and OPA= 100%; κ= 1.00). Intra-assay precision was excellent, with CVs around 2% for both low- and medium-positive samples, confirming consistent repeatability within a single run. Inter-assay reproducibility was equally robust, with CVs of 0.4-3.3% for low positives, 1.0-2.5% for medium and <1.1% for high-titer specimens. Correlation with the comparator method was strong (r= 0.956, p< 0.001; R²= 0.91) with a mean bias of -0.38 log10 IU/mL. Linearity analysis confirmed high proportionality between expected and measured concentrations (R²= 0.96). Deviations were negligible at low titers and slightly elevated at high loads but remained within acceptable limits. The HIV-1 and HCV ELITe MGB® assays on the BeGenius® platform demonstrated high accuracy, reproducibility and linearity, showing excellent correlation with reference methods. These results confirm that the ELITe BeGenius® system provides reliable and clinically valid viral-load measurements suitable for routine diagnostic use. Comprehensive laboratory verification of molecular assays under real-world conditions is crucial to ensure consistent performance, cross-platform comparability and reliable viral-load monitoring.
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.
This study aimed to evaluate the antibiotic resistance profiles, molecular epidemiology, and biofilm formation of Corynebacterium striatum isolated from clinical samples in our hospital. A total of 132 C.striatum isolates were included in the study. Antimicrobial susceptibility testing was performed using the disk diffusion method in accordance with the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Resistance genes were determined using polymerase chain reaction. Biofilm formation was investigated using the microtiter plate method. Clonal relationships in isolates were examined using the Pulsed Field Gel Electrophoresis (PFGE) method. All isolates were found to be susceptible to vancomycin and linezolid. Resistance rates among the isolates were quite high, with resistance to ciprofloxacin, penicillin, clindamycin, rifampin, tetracycline, gentamicin and erythromycin observed in 100.0%, 98.5%, 97.0%, 99.2%, 100.0%, 90.2%, and 74.2% of the isolates, respectively. bla/ampC, ermX, aac(3)-XI, aphA1, gyrA, and tetA genes were detected as 99.2%, 96.2%, 93.2%, 91.7%, 100.0% and 43.8%, respectively. In isolates positive for the aphA1 and aac(3)-XI genes, the gentamicin resistance rate and in isolates positive for the ermX gene, the clindamycin and erythromycin resistance rates were found as significantly higher (p< 0.05). Biofim formation was detected in 28% of the isolates. The similarity ratio of the isolates was determined to be 85%. The four main clusters, A, B, C, and D showed 32 different PFGE patterns. The clustering rate was determined to be 96.0%. In conclusion, the high rates of phenotypic and genotypic antimicrobial resistance among C.striatum strains in our hospital are quite remarkable.
In this report a case of cutaneous Scedosporium apiospermum infection in 75-year-old woman with asthma who was receiving long-term therapy with corticosteroids was presented. She was hospitalized in the department of chest diseases for the follow-up of worsening dyspnea, cor pulmonale and stasis dermatitis. Erythema, localized tenderness and swelling developed on her left foot dorsum during her follow-up in the hospital. A few days later, black-colored papules with an erythematous base were observed on her foot dorsum and anterior surface of the tibia. She was diagnosed with cellulitis. Skin biopsy revealed numerous septated fungal hyphae. Preemptive amphotericin B was added to the antibacterial treatment. Within 48 h of incubation, the Scedosporium colony was isolated based on conventional methods. The fungal ribosomal RNA gene internal transcribed spacer sequence analysis revealed S.apiospermum and deposited into GenBank with accession number OM948685. The minimum inhibition concentration was defined as 1 µg/mL for amphotericin B; 16 µg/mL for fluconazole; 0.25 µg/mL voriconazole, 4 µg/mL for caspofungin, 1 µg/mL for itraconazole and 0.125 µg/mL for posaconazole on 48 h of incubation. The patient was transferred to the intensive care unit due to the deterioration of her general condition with the diagnosis of sepsis. Antimicrobial treatment was modified to caspofungin/ voriconazole combination and imipenem administration. Hepatic failure, bone marrow suppression with severe thrombocytopenia and disseminated intravascular coagulation syndrome developed on the third day of intensive care unit stay. The patient died of severe septic shock and multiorgan failure. We also reviewed the literature presenting similar cutaneous scedosporiosis cases and discussed the results.
Acute gastroenteritis (AGE) is an important public health problem that is very common all over the world. Knowing the causative agents is important for understanding the clinical course of the disease, effective treatment and necessary precautions to be taken. In this study, we aimed to determine the pathogen distribution in AGE cases admitted to our center using multiplex real-time polymerase chain reaction (mRt-PCR) and to demonstrate the clinical and laboratory differences between luminal (type I) and mucosal/invasive (type II) infections. We also aimed to define biomarker thresholds to facilitate decision-making in situations where access to advanced diagnostic tests is limited. Eighty-five patients aged ≥ 18 years were retrospectively analyzed between June and September 2023. Clinical complaints, stool macroscopy and laboratory results recorded at admission including; leukocyte count, neutrophil/ lymphocyte ratio (NLR), hemoglobin, platelet count, C-reactive protein (CRP), renal and hepatic function tests and lactate dehydrogenase (LDH) values were recorded. Stool samples were evaluated by microscopic examination, culture/antigen tests and Bio-Speedy Gastroenteritis mRt-PCR (MX-24L). According to PCR results, the cases were categorized as a pathogen-negative group, a mucosal-type infection group and a luminal-type infection group. Appropriate statistical tests were used, ROC analysis was performed for CRP, NLR and platelet count to predict mucosal type. The median age was 54 years (interquartile range= 38-67) and 56.5% were male. At least one pathogen was detected by PCR in 76% (65/85) of the cases; the most common were Campylobacter spp. (17.3%), enteroinvasive Escherichia coli (12.9%) and norovirus (12.9%). 41.2% of the cases were mucosal type, 35.3% were luminal-type and 23.5% were in the group in which no causative agent was detected. Age was higher in the mucosal type group (p= 0.009). Red color/blood in stool and fever were significantly more common in mucosal type group (both p< 0.001); vomiting was more common in mucosal type group (p= 0.016). CRP and NLR values were significantly higher in mucosal type group (both p≤ 0.001), while platelet count was lower (p= 0.021). ROC analysis revealed CRP as the strongest predictor for mucosal type group. mRt-PCR enables high-rate detection of acute gastroenteritis pathogens, supporting accurate and early treatment and contributing to a reduction in unnecessary antibiotic use. By using this test, the most frequently identified acute gastroenteritis pathogens in our region were detected as Campylobacter, norovirus and EIEC. In settings where these tests are not available, CRP levels ≥ 42.5 mg/L and/or NLR ≥ 3 may serve as indicators in favor of mucosal-type pathogens and thrombocytopenia may further support this clinical profile. The use of simple and easily accessible biomarkers in combination with clinical findings may contribute to more effective field management of AGE cases.
Currently, the increasing isolation rates of New Delhi metallo-beta-lactamase (NDM) positive Klebsiella pneumoniae and the lack of a standard algorithm for the treatment of infections caused by these isolates necessitate the search for effective treatment options. This study aimed to investigate the efficacy of the combination of ceftazidime-avibactam (CZA), frequently used in the treatment of carbapenem-resistant Enterobacterales (CRE) infections in recent years with aztreonam (AZT), which is expected to become available in our country soon and the combination of meropenem (MEM) with colistin (COL), which is frequently preferred in our hospital against NDM-positive K.pneumoniae isolates using in vitro synergy tests and to determine the susceptibility of these isolates to cefiderocol (FDC), which is recommended as an alternative treatment option in CRE infections. A total of 63 K.pneumoniae isolates, isolated from clinical samples in the Bacteriology Laboratory of the Department of Medical Microbiology at Süleyman Demirel University Faculty of Medicine and identified as NDM positive by real-time polymerase chain reaction, were included in the study. The susceptibility of the isolates to CZA, AZT, MEM and COL was tested by broth microdilution method and FDC susceptibility was tested by Kirby-Bauer disk diffusion method according to the European Committee on Antimicrobial Susceptibility Testing criteria. The efficacy of CZA-AZT and MEM-COL combinations against NDM positive K.pneumoniae isolates was tested using the checkerboard method. Time-kill assays were performed to investigate the bactericidal activity of CZA-AZT and MEM-COL combinations at different concentrations and time points in five isolates harboring different carbapenemase genes (two NDM+OXA-48, one NDM, one NDM+OXA-48+KPC, and one NDM+OXA-48/VIM/IMP). All isolates included in our study were found as resistant to CZA, AZT and MEM, while 77.8% were resistant to FDC and 54% were resistant to COL. According to the checkerboard test results, the CZA-AZT combination showed synergistic interaction against all isolates, while the MEM-COL combination exhibited synergistic interaction against 57.1% of the isolates, additive interaction against 25.4% and undefined interaction against 17.5%. In time-kill assays, synergistic activity was observed at various time points in all isolates with the CZA-AZT combination and in four isolates with the MEM-COL combination, while bactericidal activity was detected at certain time points. Although an undefined interaction was determined in the checkerboard test against one isolate (NDM+OXA-48 positive) with the MEM-COL combination, synergistic activity and bactericidal effect were observed at the 12th and 24th hours with the 1xMIC MEM + 1xMIC COL combination in the time-kill assay against the same isolate. In conclusion, the combination of CZA-AZT seems to be a promising treatment option in infections caused by NDM positive K.pneumoniae isolates. In cases where CZA-AZT combination therapy cannot be applied, MEM-COL combination therapy may be considered as an alternative treatment option. In situations where both treatment options cannot be used, cefiderocol monotherapy may be considered as an alternative in selected cases, given the low and heterogeneous susceptibility rates among NDM-positive isolates, provided that close clinical and microbiological monitoring is ensured. However, careful monitoring is required during cefiderocol therapy and treatment modification should be considered in cases of clinical non-response.
Alveolar echinococcosis (AE) caused by Echinococcus multilocularis, is a rare but potentially fatal zoonotic infection. AE most commonly presents with multiple cysts in the liver, may spread to other organs through infiltration or metastasis and can mimic malignancy with fatal consequences if not diagnosed early. Its occurrence in childhood is extremely rare and simultaneous hepatic and pulmonary involvement has been reported only in a few cases. This report aimed to discuss a pediatric AE case with concurrent hepatic and pulmonary involvement, initially misdiagnosed as malignancy, in the light of current literature. The presenting complaints, physical examination findings, diagnostic methods, treatment and follow-up results of a pediatric AE case with hepatic and pulmonary involvement were documented and pediatric AE cases available in the literature were reviewed. A 10-year-old boy presented with a fivemonth history of intermittent fever and weight loss. At admission, multiple cystic lesions were detected in the liver parenchyma, along with widespread cystic foci in both lungs. Laboratory tests revealed marked eosinophilia (44.5%), and E.multilocularis serology (IgG, IHA) together with Western blot (Em70, Em90 positivity) confirmed the diagnosis. According to the "parasitic mass in the liver, neighboring organs involvement and metastasis" classification; the case was staged as P4N0M1. Since surgical resection was not feasible, continuous albendazole therapy (15 mg/kg/day) was initiated. After one year of follow-up, significant radiological regression was observed, without new lesion development or treatment-related toxicity. Pediatric AE with multi-organ involvement may mimic malignancy and cause diagnostic delays. Early diagnosis and appropriate antiparasitic therapy can achieve favorable outcomes even when surgery is not feasible. However, the prolonged duration of therapy and the lack of a well-defined treatment endpoint pose significant challenges in terms of monitoring and potential toxicity. More clinical data are needed to establish optimal treatment duration and follow-up protocols in children.
Cryptococcus neoformans is an encapsulated opportunistic yeast widely distributed in the environment and classified as critical-priority fungal pathogen by the World Health Organisation due to its high mortality and limited access to timely diagnosis and effective treatment. Infection is typically acquired via inhalation, with the primary pulmonary focus often remaining asymptomatic. Particularly in individuals with impaired cell-mediated immunity, it may disseminate hematogenously to central nervous system (CNS), skin and other organs. Cutaneous cryptococcosis is a rare clinical manifestation and in most cases, represents secondary involvement of disseminated disease. Its clinical presentation is highly variable and may mimic cellulitis, abscesses, ulcers or necrotizing soft-tissue infections, posing significant diagnostic challenges. Ruxolitinib is a Janus-kinase inhibitor used to treat myelofibrosis and polycythemia vera. By suppressing interferon-γ and interleukin-12-mediated immune responses, it impairs macrophage activation, reduces T-helper-1 cell responses, suppresses natural-killer cell function, and regulates hematopoietic activity. However, these immunomodulatory effects predispose patients to invasive opportunistic infections, particularly fungal infections. In the literature, cryptococcal infections associated with ruxolitinib have been reported in a limited number of case reports, most commonly involving the pulmonary and/or central nervous system. Cutaneous involvement is exceedingly rare, and to date, no cases from Türkiye have been reported. In this case report, a 67-year-old woman with myelofibrosis who had been receiving ruxolitinib therapy for three-years and developed cutaneous cryptococcosis infection mimicking necrotizing fasciitis, accompanied by asymptomatic pulmonary involvement was presented. Despite broad-spectrum antibacterials, a small papule on the medial thigh rapidly progressed over 25 days, with severe disproportionate pain raising suspicion of necrotizing fasciitis. On admission, physical examination revealed an 8×8 cm ulcerative tissue defect on the left thigh, with surrounding erythema, ecchymosis, desquamation and hemopurulent discharge. Magnetic resonance imaging demonstrated findings suggestive of necrotising soft-tissue infection, prompting urgent surgical intervention. Intraoperatively, diffuse inflammation and patchy necrotic areas were observed and surgical debridement followed by vacuum-assisted wound closure was performed. Microbiological cultures of deep-tissue specimens yielded C.neoformans and the pathogen was confirmed by matrix-assisted laser desorption/ ionisation-time-of-flight-mass spectrometry (MALDI-TOF-MS). Antifungal susceptibility testing showed minimum inhibitory concentrations of 0.5 µg/mL for amphotericin B and 4 µg/mL for fluconazole. Histopathological examination demonstrated yeast cells within a background of suppurative inflammation and focal necrosis. Although the patient had no respiratory symptoms, chest computed tomography revealed a cavitary pulmonary nodule consistent with fungal infection. Bronchoalveolar lavage cultures showed no microbial growth. Evaluation for central nervous system involvement resulted negative for India-ink staining and cerebrospinal fluid multiplex polymerase chain reaction (PCR) test. These findings were considered consistent with systemic cryptococcosis involving the skin and lungs. Antibacterials were discontinued and intravenous liposomal amphotericin-B plus fluconazole was initiated. After central netvous system involvement was excluded, sequential therapy with fluconazole was planned. Ruxolitinib dose was adjusted by haematology. Significant clinical improvement was observed in the early phase of treatment and pain however, the patient died due to acute pulmonary embolism. This case highlights a rare cutaneous presentation of ruxolitinib-associated cryptococcosis and emphasizes the importance of clinical awareness for opportunistic fungal infections in immunosuppressed patients.
Brucellosis and leptospirosis are zoonotic infections with overlapping clinical features, especially in endemic regions. Coinfection of these pathogens is rare and may trigger secondary inflammatory disorders through excessive immune activation. In this report, a rare case of Kikuchi-Fujimoto disease following brucellosis and leptospirosis coinfection with gastrointestinal bleeding was presented. A 31-year-old male presented with fever, malaise, diarrhea and black, foul-smelling stools for three days. Physical examination revealed conjunctival hyperemia, hepatosplenomegaly and diffuse abdominal tenderness. Laboratory findings showed elevated AST, ALT and creatine kinase levels, thrombocytopenia, and prolonged international normalized ratio. Upper gastrointestinal endoscopy demonstrated antral erosions with an active bleeding site. Serologic tests revealed positive Brucella agglutination and Leptospira microscopic agglutination tests with titers of 1/320 and 1/400, respectively. The patient was treated with doxycycline and rifampicin. Three weeks later, he developed painful cervical lymphadenopathy. Excisional biopsy showed necrotizing lymphadenitis consistent with Kikuchi-Fujimoto disease. The patient improved with symptomatic therapy and showed no recurrence at three-month follow-up. Although brucellosis and leptospirosis coinfection is rare, it may induce immune dysregulation leading to secondary inflammatory lymphadenitis. This case highlights the potential link between zoonotic coinfections and Kikuchi-Fujimoto disease and underlines the importance of considering this diagnosis in patients presenting with fever and lymphadenopathy following infectious episodes.
Crimean-Congo hemorrhagic fever (CCHF) is a zoonotic viral hemorrhagic disease with a wide clinical spectrum ranging from mild clinical presentations to fatal outcomes. Reported case-fatality rates vary between 3% and 30%. Therefore, early identification of high-risk patients and referral to appropriate centers are of critical importance in reducing mortality. In this study, we aimed to evaluate the performance of the CURB-65+B score in predicting mortality in patients with CCHF and to compare it with the Acute Physiology and Chronic Health Evaluation II (APACHE II), Sequential Organ Failure Assessment (SOFA), Severity Grading System (SGS) and Severity Scoring Index (SSI) scoring systems. Data from 254 adult CCHF patients who were followed in a tertiary care center and whose diagnosis were confirmed by reverse transcription polymerase chain reaction and/or IgM positivity were retrospectively analyzed. Demographic, clinical and laboratory data were recorded and CURB-65, CURB-65+B, SOFA, APACHE II, SGS and SSI scores were calculated at admission. Survivors and non-survivors were compared; the predictive performance of each scoring system for mortality was assessed using receiver operating characteristic (ROC) analysis and multivariable logistic regression analysis was performed. The overall mortality rate was 2.8% (n= 7). Non-survivors were older and more frequently presented at admission with confusion, hypotension, tachycardia, tachypnea and bleeding. In laboratory analyses, platelet counts and fibrinogen levels were lower in non-survivors compared with survivors, whereas aspartate aminotransferase, alanine transaminase, lactate dehydrogenase, activated partial thromboplastin time, international normalized ratio, D-dimer and C-reactive protein (CRP) levels were higher. In ROC analysis, the most powerful laboratory predictors of mortality were CRP [>14.6 mg/L; area under curve (AUC)= 0.938], prothrombin time (>13.5 s; AUC= 0.996), creatinine (>1.2 mg/dL; AUC= 0.882), and D-dimer (>4770 µg/L; AUC= 0.662). The highest overall accuracy, however was obtained with the CURB-65+B score (AUC= 0.997; 100% sensitivity; 98.8% specificity; p< 0.001). In multivariable analysis, only the CURB-65+B score was identified as an independent predictor of mortality (Odds ratio≈ 14; 95% confidence interval= 2.7-72.6; p= 0.002). Moreover, mortality was markedly higher in patients with a CURB-65+B score ≥3, whereas no deaths were observed among patients with a score <3. With its simple and easily applicable structure, the CURB-65+B score represents a powerful tool for predicting mortality in CCHF. It may facilitate the rapid identification of high-risk patients, recognition of those requiring intensive care and timely referral to appropriate centers in emergency departments and endemic settings. Compared with existing mortality scoring systems, CURB-65+B appears to be more practical, distinctive and to possess a higher predictive accuracy and thus may fill an important gap in the clinical management of CCHF.