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The aim of this study was to determine the Firmicutes/Bacteroidetes ratio in the gut microbiota and IL-1β, IL-6, IL-8, TLR2, TLR4 and TLR5 gene expression levels in the blood of adult type 2 diabetes (T2D) patients and compare it with that of adult nondiabetic healthy controls (HC).Between May 2016 and April 2017, 99 T2D patients and 99 HCs were enrolled in the study. Bacteroidetes and Firmicutes levels were assessed from stool sample DNA and IL-1β, IL-6, IL-8, TLR2, TLR4, and TLR5 gene expression levels assesed from blood sample RNA via qPCR from both T2D patients and healthy controls.The Firmicutes/Bacteroidetes ratio detected in the stool of type 2 diabetes patients was found to be higher with a statistically significant difference (p0.0001). Gene expression levels of IL-1β, IL-6, IL-8, TLR2, TLR4, and TLR5 were found to be upregulated.The highest upregulation was detected in IL-6 with 11 fold in T2D patients comparing with HCs. F/B ratio and gene expression levels were elevated in T2D patients. Firmicutes were positively correlated with studied gene expressions. A better understanding of the complex interaction between gut microbiota, environment, and diabetes will allow for more effective prevention and treatment strategies for T2D.

Akut gastroenterit (AGE), tüm dünyada yaygın olarak görülen enfeksiyon hastalıkları arasındadır. Campylobacter, Salmonella, Shigella türleri AGE’nin bakteriyel etkenleri arasında ilk sıralarda bulunmaktadır. Bu çalışmada, laboratuvarımıza gönderilen gaita örneklerinde kültür yöntemi ve moleküler yöntemle Campylobacter, Salmonella ve Shigella sıklığını saptamak ve her iki yöntemin kıyaslanması amaçlanmıştır. 2019-2020 yılları arasında Namık Kemal Üniversitesi Tıp Fakültesi Hastanesi’ne ishal yakınması ile başvuran, ayaktan erişkin ve çocuk hasta örnekleri dahil edilmiştir. Dışkı örnekleri Campylobacter, Salmonella ve Shigella türlerinin tespiti için konvansiyonel kültür yöntemleri ve polimeraz zincir reaksiyonu (PZR) yöntemi ile çalışılmıştır. Çalışmamızda 400 (%77 yetişkin, %23 çocuk) hastaya ait dışkı örneği değerlendirilmiştir. Örneklerin kültür ile değerlendirilmesinde 14 örnekte (%3.5) etken saptanmış; 10’u (%2.5) Campylobacter spp., 4’ü (%1) Salmonella spp. olarak tiplendirilmiş, Shigella spp. izole edilememiştir. Kültür yöntemi ile Campylobacter spp. ve Salmonella spp. sıklığı çocuklarda sırasıyla %6.5 ve %2.2, yetişkinlerde %1.3 ve %0.7 olarak saptanmıştır. Örneklerin PZR ile değerlendirilmesinde 38 örnekte (%9.6) etken saptanmış; 33’ünde (%8.3) Campylobacter spp., 5’inde (%1.3) Salmonella spp. varlığı tespit edilmiş, hiçbir örnekte Shigella spp. saptanamamıştır. Kültürde üreme saptanan 14 dışkı örneğinin tamamında PZR yönteminde de aynı etken mikroorganizma tespit edilmiştir. 24 örnekte ise kültürde üreme saptanmayıp sadece PZR’de Campylobacter spp. veya Salmonella spp. saptanmıştır. Gaita kültürü AGE tanısında altın standart yöntem olmasına rağmen araştırmamız sonucunda PZR’nin hem hızlı sonuç vermesi hem de saptama oranının yüksek olması nedeniyle kültüre avantajlı olduğu görülmüştür. Bu nedenle moleküler yöntemlerin rutin tanıda kullanılmasının faydalı olacağı kanaatindeyiz.

PURPOSE: There are conflicting reports regarding the abundance of short-chain fatty acids producing bacteria in the gut microbiota in patients with type 1 and type 2 diabetes. We aimed to determine the amount of Akkermansia muciniphila, Anaerobutyricum hallii, Bifidobacterium adolescentis, Bifidobacterium longum, Collinsella aerofaciens, Faecalibacterium prausnitzii, Lacticaseibacillus rhamnosus, and Parabacteroides distasonis in the gut microbiota in patients with type1 and type2 diabetes, compared with the healthy controls and analyze the correlation between the gene expression levels of two short-chain fatty acids receptors GPR41 and GPR43. METHODS: Forty type 1, 40 type 2 stool and blood samples of diabetes patients, and 40 healthy control samples were studied. DNA and RNA were extracted, and bacteria were detected using a Microbial DNA qPCR Assay kit. Gene expressions were detected with GPR41 and GPR43 primers via in-house qPCR. RESULTS: Compared with healthy controls, B.longum and F.prausnitzii abundance were significantly decreased in patients with type1 and type2 diabetes, A.hallii abundance was increased in patients with type1 and decreased in type2 diabetes contrarily A.muciniphila abundance was decreased in patients with type1 and increased in type2 diabetes. GPR43 gene expression was upregulated in both patients group, however GPR41 was upregulated only in patients with type2 diabetes. CONCLUSIONS: Elevated B. longum and F. prausnitzii abundances were detected in the gut microbiota of patients with type1 and type2 diabetes and compared with healthy controls. B. longum and F.prausnitzii abundances were also correlated with the GPR43 gene expression level in type1 diabetes patients. Extensive studies determining bacteria producing short-chain fatty acids in gut microbiota, and their contribution in the pathogenesis of diabetes, are needed to understand better the mechanism of these diseases.

Introduction: The kidneys are some of the most frequently affected organs during coronavirus disease 2019 (COVID-19). This multicenter study evaluated the incidence of and risk factors for acute kidney injury (AKI) in COVID-19 patients followed up in intensive care unit (ICU) and its association with mortality. Methods: Three hundred twenty-eight patients diagnosed with COVID-19 and hospitalized in ICU were included. Risk factors associated with AKI and mortality were evaluated. Results: Eighty-eight patients (27.9%) were diagnosed with AKI. AKI was significantly associated with older age, higher baseline creatinine level, lower albumin level, and coexistence of cardiovascular disease and chronic obstructive pulmonary disease. Mortality in the entire study group was significantly associated with AKI, older age, requirement of invasive mechanical ventilation, higher neutrophil level, lower lymphocyte, and albumin levels. Conclusion: AKI is frequently seen during the course of COVID-19 and is associated with high mortality. Identifying AKI-related risk factors appears essential in the management of COVID-19 patients. © 2022 International Society for Apheresis and Japanese Society for Apheresis.

Objectives: “Nosocomial infections” or “healthcare-associated infections” are a significant public health problem around the world. This study aimed to assess the rate of laboratory-confirmed healthcare-associated infections, frequency of nosocomial pathogens, and the antimicrobial resistance patterns of bacterial isolates in a University Hospital. Methods: A retrospective evaluation of healthcare-associated infections in a University Hospital, between the years 2015 and 2019 in Tekirdag, Turkey. Results: During the 5 years, the incidence densities of healthcare-associated infections in intensive care units and clinics were 10.31 and 1.70/1000 patient-days, respectively. The rates of ventilator-associated pneumonia, central line–associated bloodstream infections, and catheter-associated urinary tract infections in intensive care units were 11.57, 4.02, and 1.99 per 1000 device-days, respectively. The most common healthcare-associated infections according to the primary sites were bloodstream infections (55.3%) and pneumonia (20.4%). 67.5% of the isolated microorganisms as nosocomial agents were Gram-negative bacteria, 24.9% of Gram-positive bacteria, and 7.6% of Candida. The most frequently isolated causative agents were Escherichia coli (16.7%) and Pseudomonas aeruginosa (15.7%). The rate of extended-spectrum beta-lactamase production among E. coli isolates was 51.1%. Carbapenem resistance was 29.8% among isolates of P. aeruginosa, 95.1% among isolates of Acinetobacter baumannii, and 18.2% among isolates of Klebsiella pneumoniae. Colistin resistance was 2.4% among isolates of A. baumannii. Vancomycin resistance was 5.3% among isolates of Enterococci. Conclusion: Our study results demonstrate that healthcare-associated infections are predominantly originated by intensive care units. The microorganisms isolated from intensive care units are highly resistant to many antimicrobial agents. The rising incidence of multidrug-resistant microorganisms indicates that more interventions are urgently needed to reduce healthcare-associated infections in our intensive care units.

Introduction. The simultaneous use of antifungals with immunosuppressive agents has become a necessity for patients taking immunosuppressive therapy. However, antifungal drugs are problematic because of their limited target. Hypothesis. Scientists have been searching for new antifungals and some compounds with at least additive effects on antifungals. Calcineurin inhibitors used as immunosuppressive agents also attract attention due to their antifungal property. Aim. To evaluate the activity of two calcineurin inhibitors alone and in combination with amphotericin B (AMB), caspofungin (CAS), itraconazole (ITR), voriconazole (VOR) and fluconazole (FLU). Methodology. MICs of AMB, CAS, ITR, VOR, FLU and cyclosporine A (CsA) and tacrolimus (TAC) as calcineurin inhibitors were evaluated by the broth microdilution method against Candida albicans (n=13), C. krusei (n=7) and C. glabrata (n=10). Checkerboard and time-kill methods were performed to investigate the activity of combining calcineurin inhibitors with antifungal drugs. Results. The lowest MIC values were detected with VOR for all Candida isolates tested. Although we did not detect any inhibition for CsA or TAC alone at concentrations tested in this study, the combinations of CAS with CsA showed the highest synergistic activity (36.7%) by the checkerboard method, and CAS with CsA and ITR with TAC combinations exhibited apparent synergistic interaction by the time-kill method. However, the combinations of both CsA and TAC with AMB resulted in antagonistic interactions, especially against C. krusei isolate in time-kill testing. Conclusion. Synergistic interactions in the combinations of TAC or CsA with antifungal drugs, except for AMB, in many concentrations was found to be promising in terms of the treatment of patients with fungal infections.

OBJECTIVE: ‘Nosocomial infections’ or ‘healthcare associated infections’ are a significant public health problem around the world. This study aimed to assess the rate of culture confirmed nosocomial infections (NIs), frequency of nosocomial pathogens and the antimicrobial resistance patterns of bacterial isolates in a University Hospital. METHODS: A retrospective evaluation of NIs in a tertiary hospital, between the years 2015 and 2019 in Tekirdag, Turkey. RESULTS : During the five years, the overall incidence rates (NI/100) and incidence densities (NI/1000 days of stay) of NIs were 2.04% (range 1.76-2.41/100) and 3.50/1000 patients-days (range 2.85-4.64/1000), respectively. 57.4 % of the infections were originated from the Intensive Care Units. The most common NIs according to the primary sites were bloodstream infections (55.3 %) and, pneumonia (20.4%). 67.5% of the isolated microorganisms as nosocomial agents were Gram negative bacteria, 24.9% of Gram positive bacteria and 7.6 % of candida. The most frequently isolated causative agents were Esherichia coli (16.7%) and Pseudomonas aeruginosa (15.7%). The rate of extended spectrum beta-lactamase production among E. coli isolates was 51.1%. Carbapenem resistance was 29.8% among isolates of Pseudomonas aeruginosa; 95.1% among isolates of Acinetobacter baumannii, 18.2% among isolates of Klebsiella pneumoniae. Colistin resistance was 2.4% among isolates of Acinetobacter baumannii. Vancomycin resistance was 5.3% among isolates of Enterococci.CONCLUSION: Our study results demonstrates the microorganisms of isolated from Intensive Care Units demonstrates high level resistance to many antimicrobial agents. The rising in incidence of multidrug-resistant microorganisms indicate that more interventions are urgently needed to reduce NIs in our ICUs.

Background. Burkholderia cepacia complex (Bcc) comprises multi-drug resistant, Gram-negative, motile, and aerobic bacteria. Bcc causes severe nosocomial infections particularly in patients with intravascular catheters and in those with cystic fibrosis. We studied a Bcc outbreak in non-cystic fibrosis patients. Methods. We analyzed data from six patients hospitalized at our center. Blood cultures identified as infectious were incubated onto 5% blood sheep agar, chocolate agar, and eosin methylene blue (EMB) agar. We examined possible sites that could be sources of infection at the clinic. We confirmed isolations with pulsed-field gel electrophoresis (PFGE) tests. Results. The first patient was hospitalized due to left renal agenesis, urinary tract infection, and renal failure. Bcc was isolated in blood cultures obtained due to high fever on the third day of hospitalization. We stopped new patient hospitalizations after detecting Bcc in blood cultures of other five patients. We did not detect further positive specimens obtained from other clinic and the patient rooms. PFGE patterns were similar in all clinical isolates of Bcc indicating that the outbreak had originated from the source. Conclusions. Bcc infection should be considered in cases of nosocomial outbreaks of multi-drug resistant organisms that require hospitalization at intensive care units. Control measures should be taken for prevention of nosocomial infections and required investigations should be done to detect the source of infection.

Objective: Granulomatous mastitis (GM) is a rare chronic inflammatory disease of the breast. The etiological role of bacteria in granulomatous mastitis, which is the most common type of non-lactational mastitis, is not exactly known. Methods: Our study was carried out with tissue and/or abscess cultures of 46 patients who applied to Istanbul University - Cerrahpasa, Cerrahpasa Medical Faculty Hospital, Department of General Surgery, Breast Outpatient Clinic, and Emergency Surgery Service, between January 2015-January 2016 and were diagnosed with GM according to the results of histopathological and clinical examinations. In addition to conventional methods, aerobic bacteria isolated from the samples were identified with the BD Phoenix (Becton, Dickinson Company, Maryland, USA) and anaerobic bacteria with the API 20A (bioMerieux, Marcy l'Etoile, France) kit, and bacterial identification was made by PCR amplification of 16S rRNA from samples in which bacteria were seen in Gram staining but not grow in culture. Antimi-crobial susceptibilities of the bacteria were determined by disc diffusion and gradient test methods. The results were evaluated according to EUCAST 2016 criteria. Results: When the culture results of the patients diagnosed with GM were evaluated, growth was observed in 20 (43.7%) patient materials, and it was not detected in 26 (56.5%) patient materials. Corynebacterium species were detected in 12 (26.1%) of 46 patients. C. kroppenstedtii was isolated in 7 (15.2%), C. urealyticum in 3 (6.5%), and C. amycolatum in 2(4.3%) patients. S. aureus grew in 2 (4.3%) patients, and Klebsiella spp. and Proteus spp. grew in 1 patient each. Peptostreptococcus spp. (3 samples, 6.5%) and B. fragilis (2 samples, 4.3%) were the anaerobic bacteria grown in cultures. Different bacterial species grew together in 6 (30%) of 20 GM patient samples. PCR amplification of 16S rRNA made from pus samples of 19 Gram stain positive but culture-negative cases resulted in C. kroppenstedtii (3 samples), S. epidermidis (3 samples), and anaerobic bacteria such as Peptostreptococcaceae bacterium, Cutibacterium spp., C. acnes, B. breve have been isolated in 1 sample each. Conclusions: We believe that determining aerobic and anaerobic agents that cause granulomatous mastitis and applying specific treatment for the etiological agents rather than using broad-spectrum antibiotics which could lead the antimicrobial resistance, will be beneficial. Antibiotics such as penicillin, gentamicin, vancomycin, and linezolid, which are effective on Gram-positive rods (Corynebacterium species), can be added to the treatment, especially in culture negative cases of granulomatous mastitis.

Background and aim Infections caused by Candida species are significantly increasing today, and invasive Candida infections are generally associated with high mortality. Early diagnosis and identification of Candida spp. is important for the determination of antifungal agents that will be used for treatment. The aim of the present study was to provide a better regimen for Candida infections in the future. Materials and methods TheSensititre YeastOne (SYO) method was compared with The Clinical Laboratory Standards Institute (CLSI) reference broth microdilution (BMD) testing method. Endpoints of minimal inhibitory concentrations (MICs) were determined for both methods. Results By using both methods, MIC values of micafungin, caspofungin, voriconazole, and fluconazole were lower than amphotericin B. The values obtained with the SYO method were in high categorical agreement for ecinocandins and amphotericin B. The results of voriconazole and fluconazole were in low categorical agreement. The categorical agreement between the SYO and the BMD results at 24 h was 82.1% for VORI and 98.4% for AMB. Values obtained with SYO method for all antifungal agents were in high essential agreement with the data of the CLSI reference BMD method. The essential agreement between the SYO and the BMD results at 24 h was 94.0% for MFG and 99.0% for AMB. Conclusions The SYO method was ready-to use, so it appeared to be easier and more efficient for Candida isolates.

Bu calismada hastanemizde izole edilen Candida turlerinin iki farkli yontemle antifungal duyarliliklarinin incelenmesi amaclanmistir. Hastanemizde cesitli departmanlardan gelen klinik orneklerden toplam 200 Candida turu izole edildi. Bu turler geleneksel yontem (germ tup olusturma, corn-meal tween 80 besiyerinde mikroskobik gorunum) ve ticari kit API 20C (Biomerieux, France) ile tanimlandi. Bu turlerin flukonazol (FLU), vorikonazol (VORI), amfoterisin B (AMB) antifungal minimum inhibisyon konsantrasyonu (MIK) degerleri Clinical and Laboratory Standards Institute sivi mikrodilusyon ve disk-difuzyon (DD) yontemine gore degerlendirildi. Izole edilen 200 Candida turu; 100 C. albicans, 25 C. glabrata, 7 C. krusei, 43 C. parapsilosis ve 25 C. tropicalis olarak tanimlandi. Butun Candida izolatlari VORI ‘ye karsi duyarli bulundu. Yuksek direnc (%22,5) orani referans mikrodilusyon yontemi ile AMB antifungaline karsi tespit edilidi. Iki yontem arasinda en iyi kategorik oran sirasi ile VORI (%99), FLU (%84,9) ve AMB (%72,5) olarak hesaplandi.Vorikonazol, flukonazole direncli izolatlarda bile in vitro olarak flukonazolden daha iyi aktivite gostermistir. Ek olarak disk difuzyon yontemi VORI icin alternatif antifungal duyarlilik yontemi olarak degerlendirilebilir.

IntroductionBurkholderia cepacia complex (Bcc) leads to severe nosocomial infections particularly in the patients who have intravascular catheters and cystic fibrosis. The present study aims at investigation of Bcc outbreaks in non-cystic fibrosis patients.Material and MethodsA total of 6 patients who were hospitalized at General Pediatrics Department were included in the study. Blood cultures which yielded positive signals were incubated at 5% blood sheep agar, chocolate agar and Eosin Methylene Blue agar. All fields which could be the source of the infection at the clinic were examined. Isolates confirmation with Pulsed-Field Gel Electrophoresis (PFGE) tests were performed.ResultsThe first patient aged 14.5 years was hospitalized due to left renal agenesis, urinary tract infection and renal failure. Bcc growing was detected in blood culture which was obtained due to high fever at the 3rd day of hospitalization. New patient hospitalizations were stopped due to Bcc growing in blood cultures which was obtained due to high fever in the remaining five patients. No growing was detected in samples obtained from the clinic and the patient rooms. PFGE patterns were similar in all clinical isolates of Bcc indicating that the outbreak had originated from the same origin.ConclusionsBcc infection should always be kept in mind in nosocomial outbreaks due to multi-drug resistance and the need for hospitalization at intensive care unit. Control measures should be taken for prevention of nosocomial infections and required investigations should be done for detection of the source of the infection.

Invasive fungal infections are a leading cause of morbidity and mortality in immunocompromised patients, especially in cases requiring a prolonged stay in the intensive care unit. A total of 99 yeast strains were isolated from 42 postmortem cases. In this study, virulence factors and antifungal susceptibility of these species were evaluated. The isolates were identified as Candida albicans (54), C. tropicalis (15), C. glabrata (12), C. parapsilosis (6), C. lipolytica (3), C. utilis (3), C. krusei (2), C. kefyr (1), and Cryptococcus neoformans (3). The most commonly isolated species was C. albicans, and no resistant species were determined. Despite the equal number of specimens, no secretion of significant virulence factors was associated with the postmortem specimen in the Candida species. Postmortem fungal investigations in forensic autopsies are useful in explaining cause of death in such cases, also may lead to protocols for the treatment of fungal infections and contribute to fungal pathogenesis and epidemiological data.

The aim of this study was to determine and compare the levels of both Bacteroidetes and Firmicutes in the gut microbiota and TLR2/TLR4 gene expression in the blood of patients with type 1 diabetes mellitus (T1DM) and healthy individuals. These results may serve as a preliminary assessment to guide future research.Between January and October 2014, stool and blood samples were collected from 53 adult T1DM patients and 53 age- and gender-matched healthy individuals. Bacteroidetes and Firmicutes levels were assessed from stool sample DNA and TLR2 and TLR4 expression levels were analyzed via qPCR using RNA from EDTA blood samples from both patients and healthy controls.The amounts of Bacteroidetes and Firmicutes were statistically significantly higher and lower, respectively, in the T1DM group than in the healthy control group (p 0.001 and p 0.001, respectively). In addition, the Firmicutes/Bacteroidetes ratios in patients with T1DM were significantly lower than in healthy controls. The TLR4 and TLR2 gene expression levels in T1DM patients were significantly upregulated and downregulated, respectively, compared to those in the control group.Our data are the first to show a relationship between T1DM and gut microbiota in our country. In addition, our results provide information about the connections between T1DM, gut microbiota, and TLR2 and TLR4 expression. We believe that Bacteroidetes and Firmicutes in the gut microbiota may play a role in the autoimmune process of T1DM and that these findings should be further investigated in the future.

Amaç: Aspergillus tu?ru? mantar enfeksiyonları immu?n sistemi baskılanmış hastalarda, yu?ksek mortalite ve morbidite ilesonuçlanan invazif hastalıklara yol açmaktadır. Bu nedenle hızlı ve dog?ru tanı konularak uygun antifungal tedavibaşlanması invazif aspergillozlu hastalar için hayati o?neme sahiptir. Gu?nu?mu?zde daha hızlı, kolay uygulanabilir, yu?ksekduyarlılık ve o?zgu?llu?g?e sahip yeni tanı yo?ntemleri tercih edilmektedir. Bu çalışmada çeşitli klinik o?rneklerden izoleedilen Aspergillus tu?rlerinin; geleneksel yo?ntemler, MALDI-TOF MS sistemi ve DNA dizi analizi yo?ntemi kullanılaraktanımlanması ve bu yo?ntemlerin karşılaştırılması amaçlanmıştır.Yo?ntemler: Bu çalışmada çeşitli klinik o?rneklerden izole edilen toplam 50 Aspergillus izolatı çalışmaya dahil edildi.Aspergillus suşlarından 2 tanesi kontaminasyondan dolayı çalışma dışı bırakıldı.Bulgular: Çalışmamızda referans tanımlama yo?ntemi olarak kullandıg?ımız ITS bo?lgesinin dizi analiziyle, suşların 25tanesi A.fumigatus tu?r kompleksi (%52,08), 17’si A.flavus tu?r kompleksi (%35,42), 3’u?A.niger tu?r kompleksi (%6,25),2’si A.terreus tu?r kompleksi (%4,17), 1’i A.sydowii tu?r kompleksi (%2,08) olarak tanımlandı. Altın standart yo?ntemindizi analizi olduğu ve geleneksel yöntem ile karşılaştırıldığında %97,9 uyum olduğu gözlendi. İki farklı yazılımkullandığımız MALDI-TOF MS sisteminde ise güncel IVD (invitro diagnostik) VITEK MS V.2.0 yazılımı ile doğrutanımlanan köken 37(%77,1) iken SARAMIS 4.12 RUO yazılımı ile doğru tanımlanan köken 42(%87,5) olarakbulundu.Sonuç: Moleküler yöntemler, geleneksel yöntemlerin yetersiz kaldığı ve tür tanımının yapılamadığı durumlardatamamlayıcı yöntem olarak kullanılabilir. Zaman açısından değerlendirildiğinde MALDI-TOF yöntemi hızlı ve duyarlıbir yöntem olmasına rağmen veri tabanının geliştirilmesi amacıyla suş sayısının arttırılarak bu tür çalışmalarıntekrarlanması gerekir. Objective: Fungal infections associated with Aspergillus species cause invasive diseases leading high mortality and morbidity as a result of deficiency of primary defence systems in immunosuppressive patients. Therefore, starting appropriate antifungal treatment after rapid and accurate diagnosis is critically important for invasive aspergillosis patients. Nowadays, more rapid, easily applicable, having high sensitivity and specifity new diagnostic methods are required. In this study, identification of Aspergillus spp. isolated from various clinical samples by using conventional methods, MALDI-TOF MS system and DNA sequence analysis and comparison of the methods are aimed. Methods: Totally 50 Aspergillus strains were included in this study. Two isolates were excluded from the study due to contamination. Results: 25 strains were identified as A.fumigatus species complex (52.08%), 17 strains were identified as A.flavus species complex (35.42%), 3 strains were identified as A.niger species complex (6.25%), 2 strains were A.terreus species complex (4.17%) and 1 strain was A.sydowii species complex (2.08%) byITS sequence analysis method used as reference diagnostic method in this study. The sequence analysis wasthe gold standard method and it was observed that there was 97.9% compliance compared to the conventional method. Two different software programmes were used for MALDI-TOF MS system. 37 strains (77.1%) were accurately defined by current IVD (in vitro diagnostic) VITEK MS V.2.0 whereas 42 strains (87.5%) were accurately defined by SARAMIS 4.12 RUO software programme. Conclusions: Molecular methos are thought to be appropriate to be used as complementary method when conventional methods are insufficient for identification at the species level. Although MALDI-TOF MS method is rapid and sensitive method when evaluated in terms of time, it is concluded that such studies should be repeated with more strains to develop database.

Autism spectrum disorder (ASD) is a general term for a group of complex neurodevelopmental disorders of brain development that limits a person’s ability to function normally. Etiology has not been clearly defined up to date. However, gut microbiota and the bidirectional communication between the gastrointestinal tract and brain, the so-called microbiota–gut–brain axis, are hypothesized, which may be involved in the etiology of several mental disorders. Recent reports suggest that Candida, particularly Candida albicans, growth in intestines may cause lower absorption of carbohydrates and minerals and higher toxin levels which are thought to contribute autistic behaviors. The aim of this study was to identify the 3-year deposited yeasts isolated from stool samples of children with diagnosed or suspected ASD and to determine in vitro activity of nystatin and fluconazole against these isolates using Clinical Laboratory Standards Institute M27-A3 guidelines. A 17-year retrospective assessment was also done using our laboratory records. Among the species identified, intrinsically fluconazole-resistent Candida krusei (19.8 %) and Candida glabrata (14.8 %) with elevated MICs were remarkable. Overall, C. albicans (57.4 %) was the most commonly isolated species in 17 years. The species identification and/or antifungal susceptibility tests have to be performed using the strain isolated from stool sample, to select the appropriate antifungal agent, if antimycotic therapy is needed.

Objective: Candidemia is the fourth most common infection among nosocomial blood circulation infections. Although Candida albicans is the most frequently identified species in invasive candidiasis, incidence of non-albicans Candida species were increased especially among critically ill patients. This reflects the changes in clinical practice. The main objective of the present study is to determine the distribution of the Candida species that causes candidemia in our hospital and contributes to the prevention of nosocomial infections. Methods: In a retrospective study on candidemia, various Candida species isolated from blood cultures were evaluated and their epidemiological, clinical, and microbiological characteristics were determined.Results: A total of 200 species of Candida were identified and the distribution was as follows: 38% C. albicans, 24.5% C. parapsilosis, 16.5% C. tropicalis, 13% C. glabrata, 3% C. krusei, 2% C. sake, 1% C. lusitaniae, 0.5% C. guilliermondii. The highest amounts of (103/200; 51.5%) of Candida species were identified at the adult intensive care unit.Conclusion: Parallel to the increase in the patient population that is as risk for Candida infections, epidemiological studies should be made to identify the species and develop effective treatment protocols, Amaç: Kandidemi, nozokomiyal kan dolaşımı enfeksiyonları arasında dördüncü sırada yer almaktadır. İnvaziv kandidiyazda Candida albicans halen en sık tanımlanan patojen olsa da, albicans dışı kandida türlerine bağlı enfeksiyonlarda dramatik artış dikkati çekmektedir bu durum, klinik uygulamadaki değişimleri yansıtmaktadır. Bu çalışmanın temel amacı kandidemi etkeni Candida türlerinin hastanemizdeki dağılımını belirleyerek hastane enfeksiyonlarının önlenmesine katkıda bulunmaktır.Yöntemler: Retrospektif (2013-2014) bu çalışmada kan kültürlerinden izole edilen Candida türlerinin epidemiyolojik, klinik ve mikrobiyolojik karakteristikleri bildirilmiştir.Bulgular: Toplam 200 Candida spp türü %38 C. albicans, %24,5 C. parapsilosis, %16,5 C. tropicalis, %13 C. glabrata, %3 C. krusei, %2 C. sake, %1 C. lusitaniae, %0,5 C. guilliermondii olarak tanımlanmıştır. Tanımlanan Candida türleri en yüksek oranla (103/200; %51,5) yoğun bakım ünitesinde saptanmıştır.Sonuç: Candida infeksiyonları için risk teşkil eden hasta popülasyonunun artmasına paralel olarak, türlerin tanımlanması ve etkin tedavi protokollerinin geliştirilmesi için epidemiyolojik çalışmaların yapılması gerekmektedir.Anahtar kelimeler: Candida, kandidemi, invaziv kandida infeksiyonu, epidemiyoloji

Bacillus species can be found in air, water, soil, feces, and particularly in the normal flora of patients with a prolonged length of hospitalization. Therefore, isolation of these microorganisms from clinical samples is a common condition and usually regarded as contaminants. Previously, Bacillus cereus has been rarely associated with infections, but in the last few years, it has been reported with increasing frequency as the bacterial pathogen in patients with intravenous drug abuse, trauma, immunodeficiency syndrome, immunosuppressed patients with a history of underlying malignancy and granulocytopenia. In this study, we present a 3-months-old baby girl who was presented to a private health center with a complaint of not sucking well enough. After clinical examination she was diagnosed with neuroblastoma stage 4 S, metastasis was detected in the liver and bone marrow and surrenalectomy and 14 cures of chemotherapy were applied to the patient. Patient was discharged from the hospital with a permanent tunneled catheter, but she returned to the pediatric emergency department with high fever. After laboratory tests she was diagnosed with febrile neutropenia and ceftazidime and amikacin treatment was started. Ceftazidime treatment was stopped after the isolation of B. cereus from peripheral and catheter blood cultures of the patient and teicoplanin treatment was started. Permanent tunneled catheter was removed under anesthesia, and this suggested the case as a catheter-originated bacteremia after reducing fever of the patient. As a result, we suggest that B. cereus isolation in blood cultures could not everytime mean contamination, and B. cereus may cause catheter-related infections in immunosuppressed patients. (JAREM 2015; 5: 75-7)

Background: C. krusei is an opportunistic fungal pathogen that known of its intrinsic fluconazole resistance and its frequency is increasing especially among hematology patients. The increase in the frequency of high mortality fungal infections have accelerated the efforts of new drug development with broad spectrum, low toxicity and the studies including their combination. However, there is no standardized method to evaluate the activity of drug combinations. Aims: To evaluate the activity of caspofungin (CAS) with voriconazole (VOR) and amphotericin B (AMB) alone and in combination and the utility of Etest and disk diffusion methods for antifungal combinations. Methodology: The minimum inhibitory concentrations of VOR, CAS and AMB against 30 clinical C. krusei isolates were determined by using Etest, disk diffusion and reference broth microdilution methods. Combinations of CAS with VOR and CAS with AMB were evaluated using disk diffusion (three different ways) and Etest (two different ways) methods. Original Research Article British Microbiology Research Journal, 4(5): 497-508, 2014 498 Results: All isolates tested were susceptible to VOR and CAS in vitro by all three methods. Categorical agreements of Etest and disk diffusion methods with reference microdilutiontest were 100% for CAS and VOR (for each method), 86.7% and 50% for AMB, respectively. In the all ways of both combination methods, we did not observe distinctly antagonistic or synergic interaction. Conclusion: Etest and disk diffusion could be easy, convenient, and nontime-consuming alternative methods to evaluate the antifungal combinations. The combinations of CAS with VOR and AMB exhibited promising results because of an apparent antagonistic interaction was not detected in this study.

Detection of drug resistance plays a critical role in tuberculosis treatment. The aim of this study was to evaluate the performance of GenoType Mycobacteria Drug Resistance (MTBDR) assay (Hain Lifescience, Germany) and to compare it with radiometric BACTEC 460 TB system (Becton Dickinson, USA) for the detection of rifampicin (RIF) and isoniazid (INH) resistance in 84 Mycobacterium tuberculosis complex (MTBC) isolates. RIF resistance was identified in 6 of 7 (85.7%) isolates and INH resistance was identified in 8 of 14 (57.1%) isolates by the GenoType MTBDR assay. Compared with BACTEC system, the sensitivity, specificity, positive predictive value and negative predictive values were 85.7%, 98.7%, 85.7% and 98.7% for RIF resistance; and 57.1%, 100%, 100% and 92.1% for INH resistance, respectively. GenoType MTBDR assay is reliable when tested specimen is resistant to the tested drugs. Although test was more successful in the detection of RIF resistance, it exhibited low sensitivity for the detection of INH resistance.

Coccidioidomycosis caused by Coccidioides immitis or Coccidioides posadasii is endemic in arid climate zones in America, travel-related cases have been reported. We report the first documented case of coccidioidomycosis in Turkey, overviewing reported cases in Europe and underlying difficulties of differential diagnosis outside endemic regions. The patient was an otherwise healthy 41-year-old man who travelled endemic areas. Laboratory diagnosis was based on direct microscopy of two subsequent subcutaneous biopsy specimens and culture and confirmed molecularly. Laboratory personnel should become aware that BioSafety Level-3 organisms may become more frequent and widespread.

Background Cladophialophora bantiana is a melanised mold with a pronounced tropism for the central nervous system, almost exclusively causing human brain abscesses. Case report We describe a case of cerebral infection by this fungus in an otherwise healthy 28-year-old coal-miner. Environmental occurrence, route of entry, and incubation period of this fungus are unknown, but our case is informative in that the first symptoms occurred about eight weeks after known traumatic inoculation. Lesions were compatible with tuberculous granulomas, and the patient initially received antitubercular treatment. Melanised fungal cells were seen in a brain biopsy and abscess materials. Therapy was switched from empirical antitubercular treatment to amphotericin B (0.5 mg/kg/d), but was changed to voriconazole 200 mg/d, i.v. on the basis of antifungal susceptibility test results. The patient responded clinically, and gradually improved. The isolate was identified by sequencing of the Internal Transcribed Spacer domain of rDNA. Conclusions Given the non-specific clinical manifestations of C. bantiana cerebral abscesses, clinicians and laboratory workers should suspect infections caused by C. bantiana , particularly in immunocompromised patients with a trauma history.

PubMedID: 26857806 The black yeast genus Exophiala is known to cause a wide variety of diseases in severely ill individuals but can also affect immunocompetent individuals. Virulence markers and other physiological parameters were tested in eight clinical and 218 environmental strains, with a specific focus on human-dominated habitats for the latter. Urease and catalase were consistently present in all samples; four strains expressed proteinase and three strains expressed DNase, whereas none of the strains showed phospholipase, haemolysis, or co-haemolysis activities. Biofilm formation was identified in 30 (13.8%) of the environmental isolates, particularly in strains from dishwashers, and was noted in only two (25%) of the clinical strains. These results indicate that virulence factors are inconsistently present in the investigated Exophiala species, suggesting opportunism rather than pathogenicity. © 2016 Blackwell Verlag GmbH.

Invasive aspergillosis usually affects the lungs, and osteomyelitis due to Aspergillus spp. is a rare manifestation of invasive aspergillosis. Generally, there are underlying immunosuppressive conditions such as prolonged granulocytopenia, immunosuppressive therapy, and chronic granulomatous disease. Although amphotericin B is one of the most preferred agents for invasive aspergillosis management, its poor bone penetration and renal toxicity limit its use for the treatment of osteomyelitis, especially in pediatric ages. Case Report / Olgu Sunumu

Background and Design: Dermatophytes, yeasts and some moulds settle on the skin and mucosal surfaces in immunocompetent individuals as commensals. Patients with diabetes mellitus, HIV-positive patients, organ transplant recipients and the patients with malignancies are predisposed to develop superficial fungal infections. We aimed to determine the prevalence, clinical and mycological features of superficial fungal infections in patients with hematologic malignancies in this case-control study.Material and Method: Eighty patients with hematologic malignancies (49 men, 31 women) and 50 healthy individuals (22 men, 28 women) randomly selected at our clinical department as controls were included to this study between 2003 and 2004. The mean age was 52±1.85 years in patients and 41.56±2.04 years in controls. All patients were inspected for superficial fungal infections. Skin scrapings and mucosal swabs were obtained from the toe web, inguinal region, any suspicious lesion and oral mucosa. Nail samples were also collected. All samples were examined by direct microscopy and cultured in Sabouraud dextrose agar (SDA). The yeasts were established in germ-tube production. Results: Fifty-six (70%) of 80 patients with hematologic malignancies had fungal colonization, whereas 21 (42%) of 50 controls had. For both groups, oral mucosa was the predominant area that fungus was mostly isolated from. A rising number of non-dermatophyte moulds (26%) was observed. Candida albicans was the predominant agent isolated from the culture.Conclusion: The prevalence of superficial fungal infection was higher in patients with hematologic malignancies (being immunosuppressed) than in the normal population. Candida albicans was the predominant isolated agent that was found in our study. We observed oral mucosa candidal infection mostly. The rising number of non-dermatophyte moulds is attributed to long-term use of antibiotics, cytotoxic chemotherapies and antifungals.

Aspergillus fumigatus is an opportunistic pathogen responsible for life-threatening infections in immuncompromised patients. Data about the in vitro pharmacodynamics of antifungals against A. fumigatus are limited. In the present study, we investigated the fungicidal activities, at concentrations of 1, 4 and 16 times the minimum inhibitory concentration (MIC), of caspofungin (CAS), amphotericin B (AMB) and voriconazole (VORI) against eight A. fumigatus isolates through the use of time kill and 2,3-Bis [2-methoxy-4-nitro-5-(sulfenylamino) carbonyl-2H-tetrazolium-hydroxide] (XTT) reduction tests. By the conventional time kill test, AMB was fungicidal (≥99.9% reduction in colony forming units; CFU) for all isolates at 4-16 MICs after 48 h incubation. The fungicidal effect for VORI was determined at 4 × MIC for one isolate and at 16 × MIC for four isolates at 48 h of exposure. CAS was also fungicidal at 1 × MIC for one isolate and at 4-16 MICs for two isolates at 48 h. While the percentage of median killing of AMB was found by the time-kill method with XTT as 99% at 4 × MIC and 99.28% at 16 × MIC, that of VORI was 94.5% at 4 × MIC and 92.88% at 16 × MIC after 48 h of incubation. However, a significant increase was observed compared to initial inoculum size with CAS after 48 h. Since the XTT method measures all cellular viability in media, it may give more reliable results about pharmacodynamics of antifungal agents against Aspergillus spp. than the time kill test.

We retrospectively evaluated the distribution of clinical Candida spp. isolated over a 5-year period in our hospital relative to year, specimen types, hospital departments and their antifungal susceptibility patterns. Overall 3,756 Candida spp. were recovered from 10,857 specimens. In vitro antifungal susceptibility tests were conducted with 2,068 isolates against amphotericin B, fluconazole and itraconazole using the Etest method. C. albicans was isolated frequently from non-sterile body specimens while non-C. albicans Candida spp. were commonly recovered from sterile body specimens. Isolation rates of C. albicans were 83%, 61.2% and 49% in non-sterile body specimens, sterile body specimens and blood-sterile body fluids, respectively. C. krusei was an important isolate from specimens of patients in the Haematology and Bone Marrow Transplantation units and its rate of recovery increased in these departments. Amphotericin B resistance was detected in only seven C. krusei isolates, whereas 80% (n = 1,653), 76% (n = 1,572) and 99% (n = 2,061) of all isolates were susceptible to fluconazole, itraconazole and amphotericin B, respectively. In conclusion, the distribution of Candida species was variable among hospital departments and among body sites. These results may be useful in predicting potential fungal pathogens and the choice of antifungal treatment.

Candida glabrata is one of the most frequent organisms isolated from superficial and invasive fungal infections, after Candida albicans. This organism also exhibits intrinsically low susceptibility to azole antifungals and treatment often fails. The microdilution method is not very practical for use in routine susceptibility testing in the clinical laboratory, thus necessitating the use of other methods. In this study, we compared the in vitro activity of five antifungal agents in three different groups (echinocandin, polyene and azole) against 50 C. glabrata isolates by broth microdilution and disk diffusion methods recommended by Clinical Laboratory Standards Institute CLSI M27-A3 and CLSI M44-A, respectively. All the isolates were susceptible to amphotericin B (100%) and 98% of the isolates were susceptible to caspofungin by the broth microdilution method. Within the azole group drugs, voriconazole was the most active followed by fluconazole and itraconazole in vitro. The highest rate of resistance was obtained against itraconazole with a high number of isolates defined as susceptible-dose dependent or resistant. Although the disk diffusion method is easy to use in clinical laboratories, it shows very poor agreement with the reference method for fluconazole and itraconazole against C. glabrata (8% and 14%, respectively).

Contains fulltext : 171933.pdf (Publisher’s version ) (Closed access) Investigations of both virulence factors and antifungal susceptibility profiles are crucial for understanding the pathogenesis and prognosis of ophthalmic mycoses. In this study, we investigated the in vitro antifungal susceptibility of amphotericin B (AMB), voriconazole (VRC), and natamycin (NAT) against a set of 50 fungal isolates obtained from patients with ocular mycoses using the Clinical and Laboratory Standards Institute broth microdilution method. In addition, putative virulence factor, such as secretory phospholipases and proteinases, and biofilm formation activity were analyzed. The geometric means (GMs) of the minimum inhibitory concentrations (MICs) of the antifungals across all isolates were the following (in increasing order): VRC (0.70 mug/mL), AMB (0.81 mug/mL), and NAT (1.05 mug/mL). The highest activity against 14 Aspergillus strains was exhibited by VRC (GM MIC: 0.10 mug/mL), followed by AMB and NAT (GM MICs: 0.21 and 0.27 mug/mL), respectively. However, for 12 Fusarium spp., the GM MIC of VRC (2.66) was higher than those of NAT and AMB (GM MICs 1.3 and 0.8 mug/mL, respectively). Proteinase and phospholipase activity were observed in 30 % and 42 % of the isolates, respectively, whereas only 8 % of the isolates were able to produce biofilms. Phospholipase activity was observed in all Fusarium isolates, but not in any of the Aspergillus isolates. In contrast, biofilm-forming capability was detected in 25 % of the Fusarium isolates, but none of the Aspergillus isolates. The differences in the MICs of AMB, VRC, and NAT, biofilm-forming ability and proteinase and phospholipase activities among the isolates were not significant (p > 0.05). Overall, our study suggests no significant correlation between the antifungal susceptibility profiles and virulence attributes of ocular fungal isolates.

PubMedID: 26612621 Aspergillus species can cause ocular morbidity and blindness, and thus, appropriate antifungal therapy is needed. We investigated the in vitro activity of itraconazole, voriconazole, posaconazole, caspofungin, anidulafungin, and amphotericin B against 14 Aspergillus isolates obtained from patients with ocular mycoses, using the CLSI reference broth microdilution methodology. In addition, time-kill assays were performed, exposing each isolate separately to 1-, 4-, and 16-fold concentrations above the minimum inhibitory concentration (MIC) of each antifungal agent. A sigmoid maximum-effect (Emax) model was used to fit the time-kill curve data. The drug effect was further evaluated by measuring an increase/decrease in the killing rate of the tested isolates. The MICs of amphotericin B, itraconazole, voriconazole, and posaconazole were 0.5–1.0, 1.0, 0.5–1.0, and 0.25 µg/ml for A. brasiliensis, A. niger, and A. tubingensis isolates, respectively, and 2.0–4.0, 0.5, 1.0 for A. flavus, and 0.12–0.25 µg/ml for A. nomius isolates, respectively. A. calidoustus had the highest MIC range for the azoles (4.0–16.0 µg/ml) among all isolates tested. The minimum effective concentrations of caspofungin and anidulafungin were ?0.03–0.5 µg/ml and ?0.03 µg/ml for all isolates, respectively. Posaconazole demonstrated maximal killing rates (Emax = 0.63 h-1, r2 = 0.71) against 14 ocular Aspergillus isolates, followed by amphotericin B (Emax = 0.39 h-1, r2 = 0.87), voriconazole (Emax = 0.35 h-1, r2 = 0.098), and itraconazole (Emax = 0.01 h-1, r2 = 0.98). Overall, the antifungal susceptibility of the non-fumigatusAspergillus isolates tested was species and antifungal agent dependent. Analysis of the kinetic growth assays, along with consideration of the killing rates, revealed that posaconazole was the most effective antifungal against all of the isolates. © 2015, The Author(s). Astellas Pharma Gilead Sciences Seyedmojtaba Seyedmousavi has received research and travel grants from Astellas Pharma B.V. and travel grant from Gilead Sciences. All of the other authors have no competing interests. The authors alone are responsible for the content and composition of the manuscript.

Summary Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour-intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1–D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1–D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis.

Anaerobic bacteria play an important role in eye infections; however, there is limited epidemiologic data based on the the role of these bacteria in the etiology of keratitis and endophthalmitis. The aim of this re- search is to determine the prevalence of anaerobic bacteria in perforated corneal ulcers of patients with keratitis and endophthalmitis and to evaluate their antimicrobial susceptibilities.Corneal scrapings were taken by the ophthalmologist using sterile needles. For the isolation of anaerobic bacteria, samples were inoculated on specific media and were incubated under anaerobic conditions obtained with Anaero-Gen (OxoidMitsubishi Gas Company) in anaerobic jars (Oxoid USA, Inc. Columbia, MD, USA). The molecular identification of anaerobic bacteria was performed by multiplex PCR and the susceptibilities of an- aerobic bacteria to penicillin, chloramphenicol, and clindamycin were determined with the E test (bioMerieux).51 strains of anaerobic bacteria belonging to four different genuses were detected by multiplex PCR and only 46 strains were isolated by culture. All of them were found susceptible to chloramphenicol whereas penicillin resistance was found in 13.3% of P.anaerobius strains, clindamycin resistance was found in 34.8% of P.acnes and 13.3% of P. anaerobius strains. Additionnaly, one strain of P. granulosum was found resistant to clindamycin, one strain of B. fragilis and one strain of P.melaninogenica were found resistant to penicillin and clindamycin.Routine analyses of anaerobes in perforated corneal ulcers is inevitable and usage of appropriate molecular methods, for the detection of bacteria responsible from severe infections which might not be deter- mined by cultivation, may serve for the early decision of the appropriate treatment. Taking into account the in- creasing antimicrobial resistance of anaerobic bacteria, alternative eye specific antibiotics effective against anaer- obes are needed to achieve a successful treatment.

A 5-year-old boy with acute lymphoblastic leukemia and probable pulmonary aspergillosis developed a hard, protuberant, white-yellow and aggressive elongated lesion on the left side of his tongue during a febrile agranulocytopenic episode. Despite the use of broad-spectrum antibiotics and other supportive therapies, the lesion increased to about 2x4 cm in size within two days and became grey-black with an erythemateous, irregular line. Partial excision of the tongue was performed and isolates recovered from the tongue biopsy specimen were identified as Aspergillus flavus. An increase in the systemic dose (7 mg/kg/day) and local intraoral delivery of liposomal amphotericin B was successful in treating the patient and resulted in improved clinical and laboratory findings. Herein, we document the observation of tongue aspergillosis in a leukemic child with probable pulmonary aspergillosis receiving liposomal amphotericin B therapy and the successful treatment of tongue aspergillosis with an increased dose (7mg/kg) of liposomal amphotericin B. To the best of our knowledge, this is the youngest patient with documented intraoral aspergillosis and only the second case of tongue aspergillosis caused by Aspergillus flavus.