Mikrobiyoloji bulteni最新文献

Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) is widely used in microbiology. Composite index (CI) analyses, which involve evaluating spectra obtained fromthe device as well as small peak data, are a crucial method for examining microbial differences. Whenanalysing the impact of external factors on cell composition, the composite correlation index (CCI) facilitates the grouping of spectrum data. In recent years, a significant increase in the isolation of Malasseziafurfur strains from clinical specimens has been observed. Due to its lipid-dependent growth characteristics, this pathogen does not grow on the media typically used in routine mycology, such as Sabouraud’sdextrose agar. It is therefore recommended that each laboratory prepare and use its own appropriatemedia when necessary. However, the contents and their quantities in media used to cultivate Malasseziayeasts can vary considerably. Modified Dixon agar (mDA), modified Leeming & Notman agar (mLNA)and Fast Fung agar (FFA) are widely used as both primary culture media and in research. The variationin the composition of these media may lead to different spectra forming. This study aimed to investigatethe relationship between MALDI-TOF MS spectra obtained from cultivating lipophilic M.furfur strains ondifferent media and to assess their usability in routine practice. Seventeen M.furfur isolates included inthe study were grown on mDA, mLNA and FFA agar. CI analyses of MALDI-TOF MS spectra of the strainswere performed and CCI data were compared. While no difference was found in the CI values of the FFAand mLNA media for the strains included in the study (p> 0.05), the CI values of both media were higherthan those of the mDA media (p< 0.05). Kurtosis values for the media were calculated as 1.83, -0.56, and-1.16, respectively, for FFA, mLNA and mDA. The platykurtic distribution of the mDA medium data in thestudy suggests that, despite its widespread use, it may lead to time-consuming spectroscopic analyses.The high CI values observed in FFA and mLNA media prepared with tween 60 indicate that methods suchas MALDI-TOF MS are more suitable for standardization in the analysis of M.furfur. Differences in tweenwill also affect the efficiency of tween removal protocols in MALDI-TOF MS analyses. The acquisition ofvariable data and the requirement to process minor spectral parameters, such as CI values, underscorethe importance of standardizing culture media protocols. Achieving consistency in media formulationwill further support the generation of comparable data between laboratories.

Candida parapsilosis is an important fungal pathogen that is particularly isolated from blood cultures.In recent years, although there are regional differences between centres, resistance to fluconazole which is the most commonly preferred drug for candidemia, has increased in many regions. This increasecomplicates infection control and adversely affects treatment. In C.parapsilosis, codon 132 Y/F change inERG11 is accepted as the dominant mechanism and it is reported that some amino acid changes in MRR1may also contribute to resistance. In this study, we aimed to elucidate the azole resistance mechanismsof ERG11 and MRR1 in C.parapsilosis sensu stricto isolated in our centre. 30 C.parapsilosis sensu strictoobtained from patients with candidemia in 2018 and 2019 were tested for susceptibility to fluconazoleby broth microdilution method and amplified by colony polymerase chain reaction approach and DNAsequence analysis was performed on selected regions. As a result of the analysis, Y132F mutation wasidentified in one susceptible isolate while Y132F, G307A and K143R mutations were detected in resistantisolates in ERG11; R405K mutation was detected in one susceptible isolate whereas G927C mutation wasobserved in the resistant isolates in MRR1.R398I mutation in ERG11 was detected in dose-dependentsusceptible and sensitive isolates. Although Y132F mutation is the primary mechanism and the most frequently detected mutation, potential mechanisms should not be neglected. In our study, the G307A andG927C mutations detected in resistant isolates were observed as single mutations in some of the samples. Similarly, the R398I mutation in susceptible isolates was identified alone. Studies aimed at elucidatingthese mechanisms will contribute to the proper development of therapeutic strategies.

Sputum is the most commonly used sample in the diagnosis of pulmonary tuberculosis. However,elderly patients, human immunodeficiency virus (HIV) positive patients, patients with neurological deficits and children may not be able to remove sputum easily even if they can produce. Although differentsamples can be taken with invasive methods in patient groups who cannot expectorate, this situation isboth traumatic and costly for the patient. It has been recommended to use stool samples in children andadolescents as a diagnostic sample in pulmonary tuberculosis by using the polymerase chain reaction(PCR) method with Xpert MTB/RIF Ultra by the World Health Organization since 2022. In our study, weaimed to evaluate the potential use of stool samples in adult patients in the diagnosis of pulmonary tuberculosis. Seventeen patients with a pre-diagnosis of tuberculosis who attended the pulmonology clinicof Gaziantep University Şahinbey Research and Application Hospital and 20 volunteers (control group)without tuberculosis symptoms were included in the study. Sputum and stool samples were collectedfrom patients and volunteers. Sputum samples were evaluated by acid-resistant bacilli (AFB) smear microscopy, culture and Xpert MTB/RIF Ultra and stool samples were evaluated only by PCR method withXpert MTB/RIF Ultra. AFB smear microscopy, sputum culture, sputum and stool samples PCR results ofthe control group were all found to be negative. The sputum samples PCR results were found positivein the entire patient group. Forty seven percent (n= 8) of the patients were evaluated as AFB smear microscopy positive, while 100% (n= 17) were evaluated as the sputum culture result positive. The stoolsamples PCR results were found to be positive in 94% (n= 16) of the patients. Although the sputumsample PCR and culture results of one patient were positive, the stool sample PCR result was found tobe negative. When the sputum culture result was considered as a reference, the sensitivity of the stoolsamples PCR test was 94.1%, specificity was 100%, positive predictive value was 100% and negativepredictive value was 95.2%. According to the data obtained in our study, the stool sample may be an alternative sample for the diagnosis of pulmonary tuberculosis in elderly, HIV-positive/immunosuppressivepatients and in patients with neurological deficits who cannot provide a sputum sample or do not havesufficient sputum production.

Lophomonas blattarum is a protozoan that typically infects the lower respiratory tract and causesbronchopulmonary infections. Although its clinical manifestations are nonspecific, they may includesymptoms such as cough, sputum production, fever, chest discomfort, and respiratory distress. Thediagnosis of Lophomonas infection relies on the morphological identification of the parasite in respiratorysecretions using light microscopy. Differentiating the parasite from ciliated bronchial epithelial cells ischallenging and critically important for accurate diagnosis. In this case report a L.blattarum infection inan immunocompetent adult man was presented. A 46-year-old man admitted to our hospital with thecomplaints of hemoptysis, exertional dyspnea, fatigue, night sweats and productive cough. Thoraciccomputed tomography revealed a 2 cm abscess/cyst in the right upper lobe, with adjacent consolidation/atelectasis and ground-glass opacities. Empirical treatment was initiated with a preliminary diagnosisof pneumonia. Due to persistent hemoptysis, fiberoptic bronchoscopy was performed. Sputum andbronchoalveolar lavage (BAL) fluid samples were collected for acid-fast bacilli testing, culture and directmicroscopic examination. Trophozoites morphologically consistent with L.blattarum were observed inthe BAL specimen by direct microscopy and Giemsa staining. A polymerase chain reaction analysis wasperformed to confirm the diagnosis; however, no reliable results specific to the target parasite wereobtained. Therefore, based on compatible microscopic findings, a presumptive diagnosis of Lophomonasinfection was made and nonspecific antibiotic therapies were discontinued in favor of metronidazole.Following the treatment, the patient experienced dramatic clinical and radiological improvementand was discharged in good health. This case highlights that Lophomonas infection can also occur inimmunocompetent individuals and may mimic other bronchopulmonary infections. It underscores thecritical role of microscopic examination in diagnosis, while also pointing to the need for standardizedmolecular diagnostic methods. In clinical practice, the possibility of lophomoniasis should not be ignoredin cases that do not respond to empirical antibiotic therapy and every suspected case should be carefullyevaluated.

There are increasing reports of failure of artemisinin-based combination therapy (ACT) in malariapatients returning from endemic areas. ACT has been used globally as first-line treatment for Plasmodium falciparum malaria. However, with the emergence of artemisinin-resistant strains of P.falciparum andtheir spread across Southeast Asia, there is a risk that these resistant strains could reach areas of highmalaria incidence in Africa and elsewhere. In this case report, two cases of malaria imported from Africa,initially treated with six doses of artemether-lumefantrine (AL) were presented. Two middle-aged menreturning from Gabon and Uganda developed symptoms of malaria in Türkiye and were hospitalizedand diagnosed as P.falciparum malaria. Both patients were treated with AL. After being discharged fromthe hospital with marked improvement, they re-admitted to the hospital with high fever and chills andshowed late signs of clinical failure. One patient was completely cleared of parasites with six doses ofAL treatment and the other after non-ACT antimalarial (quinine and doxycycline) treatment and norecrudescence occurred. AL, an artemisinin-based combination, is a frequently preferred preparation forthe treatment of malaria cases seen in Türkiye. It should be kept in mind that even if parasitemia is clearedin the peripheral blood smear after three days of appropriate AL treatment, treatment failure may be seenin patients and this treatment failure may also include cases of African P.falciparum malaria.

Diabetic foot ulcers (DFUs) are a serious complication of diabetes, leading to high morbidity andmortality rates. Early diagnosis of DFUs is critical for improving patients’ quality of life and reducing theburden on healthcare systems. This study aimed to identify biomarkers that can predict the early development of DFUs and evaluate their potential for clinical applications. The study included three groups:diabetic patients with DFUs, diabetic patients without ulcers and healthy individuals. Serum levels ofhypoxia-inducible factor-1 alpha (HIF-1α), matrix metallopeptidase 9 (MMP-9) and IL-8 were measuredin blood samples and these biomarkers were compared with acute phase reactants such as C-reactiveprotein (CRP), erythrocyte sedimentation rate (ESR) and procalcitonin. The diagnostic values of thesebiomarkers were assessed using receiver operating characteristic (ROC) analysis. HIF-1α levels were foundto be significantly elevated in patients with DFUs and ROC analysis revealed that this biomarker had thehighest diagnostic sensitivity and specificity [area the under curve (AUC= 0.99, p= 0.001)]. The increasein HIF-1α levels suggested that hypoxic responses remain active during the early stages of DFU but decrease in advanced stages due to impaired tissue response to hypoxia. MMP-9 levels were observed toincrease proportionally with Wagner stages and were positively correlated with ESR, indicating its role inchronic inflammation and tissue damage. IL-8 levels were significantly elevated in DFU patients, yet theirlack of correlation with other inflammatory markers suggested that IL-8 might have a more specific rolein the inflammatory process. HIF-1α emerges as a key biomarker in the early detection of DFUs due to itscentral role in hypoxia-driven tissue repair and angiogenesis. Owing to its high specificity and sensitivity(AUC= 0.99), it should be considered a promising biomarker for routine clinical monitoring. The role ofMMP-9 in chronic inflammation and tissue degradation suggests that this biomarker may contribute tothe development of therapies aimed at preventing tissue damage. Similarly, the role of IL-8 in specificinflammatory processes may lead to the development of novel therapeutic approaches targeting neutrophil modulation. Regular monitoring of HIF-1α, MMP-9, and IL-8 could facilitate the early diagnosis andprevention of DFUs. Additionally, the clinical application of these biomarkers may improve patient qualityof life while reducing the economic burden on healthcare systems. Future prospective studies may provide more robust evidence to support the widespread clinical use of these biomarkers.

Ureaplasma parvum and Ureaplasma urealyticum can colonize the urinary and genital tracts and causevarious infections. Due to their fastidious growth requirements, these organisms cannot be identified byroutine laboratory diagnostic methods. Therefore, more detailed studies are needed to investigate theirincidence in the community, resistance characteristics, and clinical manifestations. This study aimed todemonstrate the presence of ureaplasmas in patients with suspected urinary tract infections. As a part ofthe study objectives, a commercial real-time quantitative polymerase chain reaction (qRt-PCR) panel kittargeting U.urealyticum and U.parvum was used and the results were confirmed by sequence analysis. Atotal of 603 midstream urine samples submitted to our laboratory from patients with suspected urinarytract infections were analyzed using a urinary tract infection qRt-PCR panel kit (Bioeksen, Türkiye). Of the195 samples found positive for U.urealyticum and/or U.parvum, 130 with sufficient sample volume weresubjected to next generation sequencing (NGS) using the MinION™ system with a rapid barcoding kit(SQK-RBK110.96), both from Oxford Nanopore Technologies® (UK), according to the manufacturer’s instructions after storage at -20 °C. Of the 195 (32.33%) samples found positive by qRt-PCR, 138 (70.76%)were positive for U.parvum, 46 (23.58%) for U.urealyticum and 11 (5.64%) showed the presence of bothspecies. Sequence analysis was performed on 130 of the 195 qPCR-positive samples that had sufficientvolume. In 17 of these samples, no amplification product was observed during electrophoresis and fiveyielded insufficient sequencing data (< 10 coverage). As a result, sequence analysis data could not beobtained for 22 samples, while valid results were obtained for 108 samples. Among these 108 samples,102 (94.44%) showed concordant results between qPCR and NGS, while six (5.56%) showed discordantresults. One of the six discordant samples was identified as U.urealyticum by qPCR, while it was identified as U.parvum in the sequence analysis. In the remaining five samples, only one of the two speciesdetected by qPCR could be demonstrated by NGS, the other could not be demonstrated. In three of thefive samples, only U.parvum could be demonstrated by sequence analysis and in two, only U.urealyticumcould be demonstrated. In the study, U.parvum and/or U.urealyticum positivity was found at a rate of32.33% in midstream urine samples. In this study, it was aimed to draw attention to the fact that thesemicroorganisms may be a possible cause of urinary tract infections due to their high positivity rates andthey should not be ignored in clinical evaluations.

The human pathogen Cryptococcus neoformans has been isolated from a variety of environmentalsources, including avian excreta, soil, trees, and decaying wood. In addition to the biological characteristics of the yeast, the structure and properties of the external environment play a pivotal role in theprocess of environmental colonization. Peloidotherapy has been used since ancient times in the AegeanRegion (near Denizli, Türkiye) as a treatment or supportive therapy for pathological disorders and musculoskeletal conditions. This therapy involves either immersing patients in natural pools or rehydratingdried mud and applying it directly to the body. Notably, the organic content of these peloids is quitelow. Additionally, commercially packaged peloidotherapy muds undergo high-temperature treatments,which alter their physicochemical properties. While it is possible that sexual reproduction might occurduring environmental colonization by cryptococcal species, even in environments with low organic content, there is currently insufficient data to confirm this phenomenon in peloids. The aim of this studywas to investigate the sexual reproduction of C.neoformans in peloids with low organic content, whichare used in peloidotherapy practices in our country.The aim of this study was to investigate the sexualreproduction of C.neoformans in muds with poor organic content used in peloidotherapy in our country.In this study, commercially packaged peloid samples (1 g/L, filtered in distilled water) from three activesources in the Denizli Basin -Sarayköy, Gölemezli, and Karahayıt- were used to prepare media with varying pH levels, supplemented with 3 g/L CaCO3 and 1 g/L agar. Two reference strains, C.neoformans KN99Aa and KN99 Aα, were tested for their ability to mate on these media. Over the course of a month, theplates were periodically examined for sexual structures, including filaments, hyphae, clamp connections,basidia and basidiospores. Sexual structures were observed in two of the three samples, indicating that,despite their low organic content, reusable and commercially available peloids can support C.neoformans, particularly under conditions of immunosuppression. Moreover, the low organic content and themineral variability of peloids across regions provide a unique environment for studying factors that influence the natural life cycle of significant human pathogens like C.neoformans.