Opportunities for pedagogical change in Turkish medical education revealed in the wake of the COVID-19 pandemic.

Phenomenon: As the first stage of a large-scale educational design research (EDR) study focused on the complex problem of providing authentic experiential "hands-on, minds-in" learning opportunities online during a pandemic or other exigency, we conducted a literature review and we interviewed Turkish academic staff and students about their experiences during the first year of the COVID-19 Pandemic. ApproachWe interviewed faculty members, faculty members of medical education departments, and medical students from both public and private medical schools in Türkiye between October 1 and December 31, 2020. Working in pairs, we analyzed the transcripts of 49 interviews using open qualitative coding methods with satisfactory levels of coefficients of agreement. FindingsWe defined six major themes from the qualitative analysis: 1) Fear and concern were the most common reactions when first encountering the pandemic; 2) Teaching methods during the pandemic were primarily unidirectional from faculty to students. This largely one way transmission of information occurred both synchronously and asynchronously; 3) Technological support during the pandemic shutdowns was found to be challenging for both faculties and students; 4) Evaluation of learning during the pandemic was opportunistic and had questionable rigor; 5) Healthy communication was valued by both faculty and students using an array of different tools including social media; and 6) The pandemic had both negative and positive impacts on the educational processes experienced by students and provided by faculty and resulted in recommendations for new approaches to teaching and learning in the future. Medical students were primarily concerned about the susceptibility to COVID-19 of themselves and others, and how the pandemic would affect their progress toward completing their studies. Faculty were primarily concerned about the capacity of online learning to provide clinical learning opportunities and the difficulties of assessing student clinical skills using online modalities. Medical education specialists were primarily concerned about the quality of educational opportunities offered online. InsightsOur findings were similar to other studies conducted in the USA, China, United Kingdom, and other countries. However, the interviews revealed interest among faculty and medical education specialists for further investigation of experiential or active learning models that could be applied in medical education regardless of whether the delivery mode is face-to-face, online, or most likely, blended. In the next stage of our larger scale EDR study, we will design and construct prototype learning environments that incorporate experiential, active, and authentic learning design principles.

Frequency of azole resistance in clinical and environmental strains of Aspergillus fumigatus in Turkey: a multicentre study.

OBJECTIVES: Aspergillus fumigatus causes several diseases in humans and azole resistance in A. fumigatus strains is an important issue. The aim of this multicentre epidemiological study was to investigate the prevalence of azole resistance in clinical and environmental A. fumigatus isolates in Turkey. METHODS: Twenty-one centres participated in this study from 1 May 2018 to 1 October 2019. One participant from each centre was asked to collect environmental and clinical A. fumigatus isolates. Azole resistance was screened for using EUCAST agar screening methodology (EUCAST E.DEF 10.1) and was confirmed by the EUCAST E.DEF 9.3 reference microdilution method. Isolates with a phenotypic resistance pattern were sequenced for the cyp51A gene and microsatellite genotyping was used to determine the genetic relationships between the resistant strains. RESULTS: In total, resistance was found in 1.3% of the strains that were isolated from environmental samples and 3.3% of the strains that were isolated from clinical samples. Mutations in the cyp51A gene were detected in 9 (47.4%) of the 19 azole-resistant isolates, all of which were found to be TR34/L98H mutations. Microsatellite genotyping clearly differentiated the strains with the TR34/L98H mutation in the cyp51A gene from the strains with no mutation in this gene. CONCLUSIONS: The rate of observed azole resistance of A. fumigatus isolates was low in this study, but the fact that more than half of the examined strains had the wild-type cyp51A gene supports the idea that other mechanisms of resistance are gradually increasing.

[Serum Neutrophil Gelatinase-Associated Lipocalin Levels in Acute Brucellosis and Brucellar Spondylodiscitis]. / Akut Brusellozis ve Brusellar Spondilodiskitte Serum Nötrofil Jelatinaz Iliskili Lipokalin Düzeyleri.

Brucellosis is a zoonotic infectious disease caused by Brucella spp., an intracellular bacterium. The complications of acute Brucellosis may affect all organs and systems. The most common complication of the disease is musculoskeletal system involvement. The neutrophil gelatinase-associated lipocalin (NGAL) is a marker of neutrophil formation and acts as a siderophore-binding protein to prevent bacterial iron uptake and its use as a marker in the diagnosis and follow-up of bacterial infections is being investigated. The aim of this study was to measure the serum levels of NGAL in patients with acute Brucellosis and Brucellar spondylodiscitis, and to determine whether there is a correlation between NGAL levels and the progression and complications of the disease. This prospective case control study was conducted with 240 patients and 120 healthy controls. The diagnosis of acute Brucellosis was established when a person was asked to take an STA test due to clinical symptoms within the past eight weeks, and the test result that exceeded 1/160, or a 4-fold titer increase was found in the STA test after an interval of two weeks, and/or there was Brucella spp. growth in the blood culture. A contrasted lumbar magnetic resonance (MR) scan was performed on patients diagnosed with acute Brucellosis who had lower back pain. Presence of spondylodiscitis was assessed radiologically with contrasted lumbar MR images. NGAL levels were determined with ELISA assay. The median NGAL value was found to be 456.67 ng/L (101.41-5804.41 ng/L) in patients with acute Brucellosis and 113.84 ng/L (58.29-542.34 ng/L) in the control group. The median NGAL value was statistically higher in the patients than the control group (p= 0.001). Brucellar spondylodiscitis was detected in 57 (23.7%) of 240 patients diagnosed with acute Brucellosis. The median NGAL value was 1885.62 ng/L (143.21-5804.41 ng/L) in patients with Brucellar spondylodiscitis, and 356.87 ng/L (101.41-1874.07 ng/L) in those who did not have Brucellar spondylodiscitis. This difference was statistically significant (p= 0.001). Erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) values were found to be higher in patients who had Brucellar spondylodiscitis. Blood cultures were drawn from 186 (77.5%) of the 240 patients diagnosed with acute Brucellosis. The blood culture positivity rate was 36.02%. Patients whose blood cultures were positive had higher NGAL levels (p= 0.001). The blood culture positivity rate was higher in patients who were diagnosed with Brucellar spondylodiscitis (p= 0.001). A regression analysis showed that female gender and high levels of NGAL, ESR, and alanine aminotransferase (ALT) could be used as predictors of Brucellar spondylodiscitis. The explanatoriness of the model was 82.3%. Although determination of NGAL levels is seen as a useful marker in the diagnosis of acute Brucellosis and predicting the presence of Brucellar spondylodiscitis, more comprehensive studies are required to be used in clinical practice in regions where Brucellosis is endemic.

Human and animal cystic echinococcosis in Konya, Turkey: molecular identification and the first report of E. equinus from human host in Turkey.

Cystic echinococcosis is a neglected, zoonotic disease in Turkey. The disease is commonly seen in rural areas where the local population is in close contact with livestock and dogs. This research aimed to molecularly identify of hydatid cysts in cattle and human isolates from Konya, Turkey. Following sample collection, direct microscopy was performed. After direct examination, total DNA was extracted, and positive PCR products of cox 1 mitochondrial gene (~ 875 bp) were sequenced. A total of 83 hydatid cysts (cattle n = 57 and human n = 26), 82 were identified as Echinococcus granulosus sensu stricto (G1-G3 genotypes), and one human isolate was characterized as Echinococcus equinus (G4 genotype). Fertility rates of cysts belonging to cattle for liver and lung cysts were 93.3% and 80%, respectively. Out of 26 human originated isolates, 18 (69.2%) of cysts were found to be fertile. To the best of our knowledge, this is the first report of E. equinus from human host in Turkey.

[Investigation of Antibiotic Resistance and Virulence Factors of Enterococcus faecium and Enterococcus faecalis Strains Isolated from Clinical Samples]. / Klinik Örneklerden Izole Edilen Enterococcus faecium ve Enterococcus faecalis Izolatlarinin Antibiyotik Direnci ve Virülans Faktörlerinin Arastirilmasi.

Enterococci, which are commonly found in the environment, cause serious infections despite the absence of well-defined virulence factors and toxins. Knowing the virulence properties of enterococci is important to understand the complex pathogenic structures. In this study, we aimed to investigate the virulence factors (asa1, hyl, cylA, efa, ebp, ace, esp, gelE, sprE, fsrA, fsrB, fsrC genes, gelatinase activity, hemolysin, hydrogen peroxide and biofilm production) and antibiotic resistance of Enterococcus faecium and Enterococcus faecalis strains isolated from clinical specimens. A total of 110 enterococcus isolates which were accepted as infectious agents were included in the study. The polymerase chain reaction method was used to identify the isolates and to detect virulence genes. Characteristics of hemolysis, biofilm formation, hydrogen peroxide production and gelatinase activity were investigated by phenotypic methods. The antibiotic susceptibility test was performed with VITEK 2 automated system. E.faecalis ATCC 29212 standard strain was used as a quality control in all tests. Of the 110 enterococci isolates included in the study, 61 were identified as E.faecium and 49 as E.faecalis. The efa gene was the most frequently detected virulence gene (92.7%), followed by ace (83.6%), esp (66.4%), ebp (60.0%), cylA (50.9%), hyl (46.4%), asa1 (45.5%), gelE, sprE, fsrC (33.6%), fsrA (12.7%) and fsrB (11.8%). All genes except hyl were higher in E.faecalis isolates and the difference was statistically significant (p<0.05). Twenty-five (51%) E.faecalis and 1 (1.6%) E.faecium isolates had beta-hemolysis and the difference was statistically significant (p= 0.000). Seven (11.5%) E.faecium and 4 (8.2%) E.faecalis isolates formed biofilm, but the difference was not statistically significant (p> 0.05). Two (3.3%) E.faecium and 14 (28.6%) E.faecalis isolates exhibited gelatinase activity and the difference between the two species was statistically significant (p= 0.000). Hydrogen peroxide production was not detected in any of the isolates. The highest resistance rate was determined against ciprofloxacin (70.9%). The resistance to ampicillin was 69.1%, high level streptomycin 65.1%, high level gentamicin 39.4%, vancomycin and teicoplanin 4.5%, and linezolid 1.8%. In conclusion, our data indicated that virulence factors except hyl gene and biofilm production were higher in E.faecalis isolates but E.faecium isolates were more resistant to antibiotics. In order to prevent infection of such virulent or resistant isolates in the hospital setting, infection control measures must be followed. In vivo studies are needed for the better understanding of the virulence of enterococci.

Differences of viral panel positive versus negative by real-time PCR in COPD exacerbated patients.

INTRODUCTION: Exacerbations of chronic obstructive pulmonary disease (COPD) are often caused by respiratory tract infections. The aim of this study was to investigate the clinical, laboratory and computed tomography features of patients with hospitalized COPD exacerbations in which respiratory viruses were detected using a real-time polymerase chain reaction (PCR) technique. MATERIALS AND METHODS: This retrospectively planned study included patients hospitalized in the chest diseases clinic due to exacerbation of COPD between November 2018-February 2019. The study included patients who had virus-specific real-time PCR, and computed tomography scans of the chest. RESULT: A total of 110 patients were included in the study. Respiratory viruses were identified in the nasopharyngeal swabs of 50 patients (45.5%) using the real-time PCR method, with rhinovirus (25%), influenza A (13.1%) and coronavirus (11.8%) being the most commonly isolated agents. The mean age of the patients was 68.28 ± 9.59 years in the virus-positive group and 68.20 ± 8.27 years in the virus-negative group (p= 0.963). Gender distribution, rate of smokers, exposure to biofuels, blood leukocyte count, neutrophil percentage, C-reactive protein (CRP) level, FEV1/FVC ratio did not significantly differ between the two groups (p> 0.05). Procalcitonin (PCT) and FEV1 values were significantly lower (p= 0.001 and p= 0.028, respectively) and the number of exacerbations was significantly higher in the virus-positive group (p= 0.001). The length of hospital stay was longer in the virus-positive group than in the virus-negative group (p= 0.012). Among the findings of computed tomography (CT) of the chest, bronchial wall thickening, cystic bronchiectasis, and emphysema did not differ significantly (p> 0.05). The rate of infiltrative lesions (tree-in-bud opacity, ground-glass opacity, atypical pneumonia) was significantly higher in the virus-positive group (p= 0.020). CONCLUSIONS: Viral respiratory tract infections should be considered in hospitalized patients with an exacerbation of COPD who have a history of frequent exacerbations, normal PCT value, and the absence of consolidation in CT scan of the chest. The use of broadspectrum antibiotic therapy should be avoided in patients with these features.

The Prevalence of Mixed Genotype Infections in Turkish Patients with Hepatitis C: a Multicentered Assessment.

BACKGROUND: HCV virus infections are one of the major health problems in the world that can cause cirrhosis and liver cancer at a higher rate than other hepatitis data. The aim of this study was to determine the prevalence of mixed infections with different HCV genotypes in Turkey and also to evaluate the current HCV genotype and sub-type distributions by a multicentered assessment. METHODS: The HCV genotype data of 17,578 hepatitis C patients collected from 23 centers from different geographic regions covering all Turkey were collected. The data included information about the HCV genotypes in the last 10 years (between 2007 and 2016), demographic properties of the patients and the methods/systems used to determine the genotypes. RESULTS: Two hundred twenty-eight of the patients (1.3%) had mixed genotype. The most common mixed genotype combination was 1b + 4 (0.83%) followed by 1a + 1b (0.26%). Genotype distribution varies according to geographical regions. However, genotype 1 (82.92%) was the most common genotype in all regions and all years. This was followed by genotype 3 (7.07%) and genotype 4 (5.43%). A variety of methods were used by the centers including sequencing, pyrosequencing, real-time PCR, in-house RFLP, reverse hybridization (LIPA), and hybridization. CONCLUSIONS: Infection with mixed HCV genotypes in Turkey is uncommon. Genotype distribution varies according to geographic regions; the most common genotype 1 is encountered all over the country, while genotypes 3 and 4 are only in some of the centers. Since there is limited information about mixed HCV infection, further investigations are needed to determine the clinical importance of mixed HCV infection.

First multicentre report of in vitro resistance rates in candidaemia isolates in Turkey.

OBJECTIVES: This study investigated the antifungal resistance rates of isolates from candidaemia patients in 12 tertiary-care centres in Turkey. METHODS: A total of 1991 Candida spp. isolates from 12 centres isolated from 1997-2017 were included in the study. Species/species complex (SC) identification was performed using conventional methods in all centres, occasionally accompanied by MALDI-TOF/MS. Antifungal susceptibility testing was performed for amphotericin B, fluconazole, itraconazole, posaconazole, voriconazole and micafungin (as echinocandin class representative) using the CLSI microdilution method. Resistance rates were determined according to CLSI clinical breakpoints (CBPs). For drugs and species with undetermined CBPs, epidemiological cut-off values were used for wild-type (WT)/non-WT categorisation. RESULTS: No or low rates of resistance were detected in general for tested Candida spp. isolates. Specifically, overall resistance to fluconazole in isolates of Candida parapsilosis SC and Candida glabrata SC were 7.7% and 0.9%, respectively. Resistance rates for C. parapsilosis SC varied extensively from one center to other (0-47.1%). Importantly, no echinocandin resistance was detected. Rates of non-WT isolates were also generally low: fluconazole against Candida lusitaniae, 4.3%; posaconazole against C. parapsilosis SC, 3.5%; posaconazole against Candida krusei, 1.9%; and voriconazole against C. glabrata SC, 0.5%. CONCLUSION: This is the first multicentre report of antifungal resistance rates among candidaemia isolates in Turkey, suggesting low resistance rates in general. Due to varying rates of fluconazole resistance in C. parapsilosis SC isolates that was detected at remarkably high levels in some centres, further studies are warranted to explore the source, clonal relatedness and resistance mechanisms of the isolates.

[Investigation of Streptococcus pyogenes virulence factors and typing by multiple locus variable number tandem repeat fingerprinting (MLVF) method]. / Streptococcus pyogenes izolatlarinin virülans faktörlerinin arastirilmasi ve "multiple locus variable number tandem repeat fingerprinting (MLVF)" yöntemi ile tiplendirilmesi.

Streptococcus pyogenes is an important bacterial pathogen that colonizes the throat and skin of human beings and causes a wide variety of diseases ranging from mild infections like pharyngitis, tonsillitis and impetigo to severe invasive infections such streptococcal toxic shock syndrome, septicemia, and necrotizing fasciitis, and produces a wide variety of virulence factors. The aim of this study was to investigate the antibiotic resistance, virulence genes; [pyrogenic exotoxin genes (speA, C, G, H, I, J, K, L, M, smeZ and ssa), deoxyribonuclease genes (sdaB, spd3, sdc ve sdaD), protease genes (speB, spyCEP ve scpA) and inhibitor genes (mac and sic)] of S.pyogenes strains isolated from throat cultures of patients with symptomatic tonsillo-pharyngitis and typing by multiple locus variable number tandem repeat fingerprinting (MLVF) method. One hundred and fifty S.pyogenes isolates were identified by conventional methods and streptococcus group A latex kit (Biomerieux, France). Antibiotic susceptibility tests were performed by Kirby-Bauer disk diffusion method as recommended by Clinical and Laboratory Standards Institute. DNA isolation was performed by using a commercial DNA isolation kit (Qiagen, Germany) in accordance with manufacturer's recommendations. The virulence genes were determined by multiplex PCR. MLVF method was performed with multiplex PCR using specific primers for repeated sequences within bacterial genome. All of the S.pyogenes isolates were susceptible to penicillin G, cefotaxime, ceftriaxone, chloramphenicol, clindamycin, erythromycin, levofloxacin, vancomycin and linezolid. Among streptococcal pyrogenic exotoxin genes the most frequent gene was smeZ (90.0%) followed by speG (88.0%), speC (58.7%), ssa (42.7%), speA (33.3%), speJ (24.0%), speK (18.7%), speH (14.0%), speI (13.3%), speL and speM (9.3%). Of the DNase genes, sdaB was detected in all strains (100%), spd3, sdc, sdaD genes were determined as 64.7%, 36.0%, 24.7% respectively. Protease genes (speB, spyCEP, scpA) and mac gene from the inhibitor genes were positive in all strains, and sic gene was positive in only 3 (2.0%) of the isolates. Thirty-two different patterns that contained two or more isolates were determined by MLVF analysis. Ninety one isolates were included in any of the 32 different patterns, while 59 isolates were defined as sporadic isolates. In conclusion, S.pyogenes isolates collected from throat cultures of patients with symptomatic tonsillo-pharyngitis in Konya/Turkey were susceptible to all antibiotics studied and have carried a very high rate of virulence factors. However the isolates were mostly clonally unrelated and sporadic. This study is the first report in Turkey, in which S.pyogenes isolates were typed by the MLVF method and a large number of virulence factors were investigated.

[Investigation of various virulence factors of Klebsiella pneumoniae strains isolated from nosocomial infections]. / Hastane enfeksiyonu etkeni Klebsiella pneumoniae izolatlarinda çesitli virülans faktörlerinin arastirilmasi.

Klebsiella pneumoniae is an opportunistic pathogen that commonly affects immunosuppressed patients and causes nosocomial infections. K.pneumoniae has a variety of virulence factors, especially capsule polysaccharide, hypermucoviscosity (HV), fimbriae, toxins and determinants for iron acquisition. The aim of this study was to detect the virulence factors in K.pneumoniae strains isolated from nosocomial infections in two years. Fifty three K.pneumoniae strains isolated from the samples of patients with nosocomial infections in the Medical Microbiology Laboratory of Selcuk University Faculty of Medicine Hospital between 2011 and 2013 were included in the study. Identification and antimicrobial susceptibilities of the isolates were performed by VITEK 2 automatic system. Biofilm formation,α-hemolysin, capsule and HV were investigated by phenotypic methods. Polymerase chain reaction (PCR) was used to detect virulence genes encoding adhesins (fimH-1, mrkD, kpn, ycfM), siderophores (entB: enterobactin, iutA: aerobactin, irp-1, irp-2, ybtS, fyuA: yersiniabactin, iroN: catechols receptor), protectines or invasins (rmpA, magA, traT) and toxins (hlyA, cnf-1). Of the 53 K.pneumoniae isolates,12 (22.6%) were isolated from in patients of reanimation intensive care unit, 8 (15.1%) medical oncology, 7 (13.2%) newborn intensive care unit and 26 (49%) other clinics. The distribution of the isolates according to the samples was as follows: urine (n= 14), blood (n= 13), wound (n= 8), drainage fluid (n= 10), broncho-alveolar lavage (n= 7), and cerebrospinal fluid (n= 1). Isolates which were resistant to meropenem were 5.7% and production of extended spectrum beta-lactamase (ESBL) was 71.7%. The capsule, biofilm formation, and HV were observed in 100%, 79.2%, and 1.9% of the isolates, respectively. Production of α-hemolysin was not detected in any of the isolates. The genes; entB (96.2%), ycfM (86.8%), and mrkD (83.0%) showed high prevalence. The other genes were detected in different ratios: fimH-1 (64.2%), fyuA (54.7%), kpn (49.1%), ybtS (41.5%), irp-1(41.5%), irp-2 (37.7%), traT (11.3%) and iutA (5.7%). Virulence genes; iroN, rmpA, magA, hlyA and cnf-1 were not detected in any of the isolates. Enterobactin had the highest rate among siderophores, and ycfM and mrkD in adhesins. The capsule and biofilm formation were commonly found in the isolates. Hypermucoviscosity was only found in one isolate but associated genes were not detected. Alfa hemolysin production and hlyA gene were not determined. As a result, it seems that the basis of the pathogenicity of K.pneumoniae strains isolated from nosocomial infections are capsule, adhesins, enterobactin and ability of biofilm formation. There is a need for new studies for the continuous monitoring of toxin and invasion ability as well as antibiotic resistance in the control of hospital infection caused by K.pneumoniae.

Assessment of In vitro Antibacterial Activity and Cytotoxicity Effect of Nigella sativa Oil.

BACKGROUND: Methicillin resistance is a serious health concern since it has spread among Staphylococcus aureus and coagulase-negative Staphylococci (CoNS) that are frequent community and nosocomial pathogens worldwide. Methicillin-resistant strains are often resistant to other classes of antibiotics, making their treatment difficult. Nigella sativa oil is known to be active against Gram-positive cocci, yet its in vitro cytotoxicity is rarely investigated, is a proper and powerful candidate for treatment of methicillin-resistant isolates. OBJECTIVES: The aim of this study is to evaluate the in vitro antibacterial activity and cytotoxicity effect of N. sativa oil. MATERIALS AND METHODS: The minimal inhibitory concentrations (MICs) of N. sativa oil were determined by broth microdilution method against four different American Type Culture Collection strains, 45 clinical isolates of methicillin-resistant S. aureus (MRSA), and 77 methicillin-resistant CoNS (MRCoNS). The effects of different dilutions (0.25 µg/mL, 0.5 µg/mL, and 1 µg/mL) of N. sativa oil on the proliferation of gingival fibroblasts were evaluated. RESULTS: The MIC values of N. sativa oil against clinical isolates of Staphylococci were between <0.25 µg/mL and 1.0 µg/mL. Compared to the control group, there was no cytotoxic effect on the proliferation of the gingival fibroblasts. CONCLUSION: In the present study, the oil of N. sativa was very active against MRSA and MRCoNS and had no in vitro cytotoxicity at relevant concentrations. These findings emphasize that there is a requirement for further clinical trials on N. sativa oil for "safe" medical management of infections caused by methicillin-resistant Staphylococci. SUMMARY: The minimal inhibitory concentration (MIC) values of Nigella sativa oil against Staphylococcus aureus American Type Culture Collection (ATCC) 29213, Enterococcus faecalis ATCC 29212, Escherichia coli ATCC 25922, and Pseudomonas aeruginosa ATCC 27853 standard strains were 0.5 µg/mL, 2 µg/mL, 64 µg/mL, and 64 µg/mL, respectivelyThe N. sativa oil showed an excellent antibacterial activity against clinical isolates of methicillin-resistant S. aureus and methicillin-resistant coagulase-negative Staphylococci with very low MIC range of <0.25-1.0 µg/mLThe N. sativa oil exhibited no cytotoxic effect on the proliferation of the gingival fibroblasts. Abbreviation used: ATCC: American Type Culture Collection; CLSI: Clinical and Laboratory Standards Institute; CoNS: Coagulase-negative Staphylococci; DMEM: Dulbecco's modified Eagle's medium; DMSO: Dimethyl sulfoxide; FBS: Fetal bovine serum; HGF: Human gingival fibroblast; MIC: Minimal inhibitory concentration; MRCoNS: Methicillin-resistant CoNS; MRSA: Methicillin-resistant S. aureus.

Identification and antifungal susceptibility of Candida species isolated from bloodstream infections in Konya, Turkey.

BACKGROUND: In this study, our aim was to identify Candida species isolated from bloodstream infections and to determine their susceptibilities to various antifungal agents to demonstrate the local resistance profiles and to guide empirical treatment for clinicians. METHODS: Two hundred Candida isolates (95 Candida albicans, 105 non-albicans Candida strains) were included in the study. Candida species were identified by conventional, biochemical and molecular methods. Antifungal susceptibility tests for amphotericin B, fluconazole, voriconazole, posaconazole, caspofungin and anidulafungin were performed with broth microdilution method according to the Clinical and Laboratory Standards Institute M27-A3 document. RESULTS: Of the 200 Candida strains, the most prevalent species were C. albicans (47.5 %), Candida glabrata (18.0 %) and Candida parapsilosis complex (14.0 %). All Candida species except for three (1.5 %) Candida kefyr strains were susceptible to amphotericin B. Only one (2.8 %) C. glabrata was resistant to fluconazole (MIC ≥ 64 µg/ml), and the others (97.2 %) exhibited dose-dependent susceptibility. All species, but C. glabrata strains, were susceptible to fluconazole. Resistance to voriconazole, posaconazole, caspofungin and anidulafungin was not detected in any strain. CONCLUSION: Candida albicans were susceptible to all antifungal drugs. Three C. kefyr strains were resistant to amphotericin B. Only one C. glabrata was resistant to fluconazole. All the strains were susceptible to voriconazole, posaconazole, caspofungin and anidulafungin. In vitro antifungal susceptibility tests should be performed to select of appropriate and effective antifungal therapy, and monitor the development of resistance.

Screening and genotyping of group B streptococcus in pregnant and non-pregnant women in Turkey.

INTRODUCTION: The purpose of this study was to investigate group B streptococcus (GBS) colonization, to compare the methods, to determine the relationship between GBS carriage and risk factors, and to genotype the GBS isolates. METHODOLOGY: Recto-vaginal swab specimens were obtained from 500 women, and a questionnaire was administered to each to assess their risk factors for GBS carriage. A culture, GBS antigen test, and polymerase chain reaction (PCR) were performed on all samples. Antibiotic susceptibility testing was performed, and the clonal relationship was determined by pulsed-field gel electrophoresis (PFGE) on all viable isolates. RESULTS: Of the 500 women, sixty-eight (13.6%) women were GBS carriers, of whom 9.8% were pregnant and 16.5% not. There was a significant difference between GBS carriage and history of premature rupture of membrane (PROM). GBS was isolated from 65 (13%) samples. GBS was positive in 70 (14%) samples by antigen test and in 62 (12.4%) by PCR. Sixty-eight of the 70 positive antigen tests were confirmed by PCR or culture. Fifty-five isolates were resistant to tetracycline, 16 to erythromycin and clindamycin, and 13 to levofloxacin. Thirteen different pulsotypes and 17 sporadic strains were determined by PFGE. CONCLUSIONS: GBS carriage rate in non-pregnant women was higher than in pregnant women. The GBS antigen test was more sensitive than culture and PCR. GBS isolates did not originate from a single clone and contained sporadic strains. There was a significant difference between GBS carriage and history of PROM. Epidemiologic data obtained in this study will help future studies.

Lack of hepcidin expression attenuates steatosis and causes fibrosis in the liver.

AIM: To investigate the role of key iron-regulatory protein, hepcidin in non-alcoholic fatty liver disease (NAFLD). METHODS: Hepcidin (Hamp1) knockout and floxed control mice were administered a high fat and high sucrose (HFS) or a regular control diet for 3 or 7 mo. Steatosis, triglycerides, fibrosis, protein and gene expression in mice livers were determined by histological and biochemical techniques, western blotting and real-time polymerase chain reaction. RESULTS: Knockout mice exhibited hepatic iron accumulation. Despite similar weight gains, HFS feeding induced hepatomegaly in floxed, but not knockout, mice. The livers of floxed mice exhibited higher levels of steatosis, triglycerides and c-Jun N-terminal kinase (JNK) phosphorylation than knockout mice. In contrast, a significant increase in fibrosis was observed in knockout mice livers within 3 mo of HFS administration. The hepatic gene expression levels of sterol regulatory element-binding protein-1c and fat-specific protein-27, but not peroxisome proliferator-activated receptor-alpha or microsomal triglyceride transfer protein, were attenuated in HFS-fed knockout mice. Knockout mice fed with regular diet displayed increased carnitine palmitoyltransferase-1a and phosphoenolpyruvate carboxykinase-1 but decreased glucose-6-phosphatase expression in the liver. In summary, attenuated steatosis correlated with decreased expression of lipogenic and lipid storage genes, and JNK phosphorylation. Deletion of Hamp1 alleles per se modulated hepatic expression of beta-oxidation and gluconeogenic genes. CONCLUSION: Lack of hepcidin expression inhibits hepatic lipid accumulation and induces early development of fibrosis following high fat intake. Hepcidin and iron may play a role in the regulation of metabolic pathways in the liver, which has implications for NAFLD pathogenesis.

Ceramide Induces Human Hepcidin Gene Transcription through JAK/STAT3 Pathway.

Changes in lipid metabolism and iron content are observed in the livers of patients with fatty liver disease. The expression of hepcidin, an iron-regulatory and acute phase protein synthesized by the liver, is also modulated. The potential interaction of lipid and iron metabolism is largely unknown. We investigated the role of lipid intermediate, ceramide in the regulation of human hepcidin gene, HAMP. Human hepatoma HepG2 cells were treated with cell-permeable ceramide analogs. Ceramide induced significant up-regulation of HAMP mRNA expression in HepG2 cells. The effect of ceramide on HAMP expression was mediated through transcriptional mechanisms because it was completely blocked with actinomycin D treatment. Reporter assays also confirmed the activation of 0.6 kb HAMP promoter by ceramide. HepG2 cells treated with ceramide displayed increased phosphorylation of STAT3, JNK, and NF-κB proteins. However, ceramide induced the binding of STAT3, but not NF-κB or c-Jun, to HAMP promoter, as shown by the chromatin immunoprecipitation assays. The mutation of STAT3 response element within 0.6 kb HAMP promoter region significantly inhibited the stimulatory effect of ceramide on HAMP promoter activity. Similarly, the inhibition of STAT3 with a pan-JAK kinase inhibitor and STAT3 siRNA pool also diminished the induction of both HAMP promoter activity and mRNA expression by ceramide. In conclusion, we have shown a direct role for ceramide in the activation of hepatic HAMP transcription via STAT3. Our findings suggest a crosstalk between lipid and iron metabolism in the liver, which may contribute to the pathogenesis of obesity-related fatty liver disease.

Saturated fatty acids induce post-transcriptional regulation of HAMP mRNA via AU-rich element-binding protein, human antigen R (HuR).

Iron is implicated in fatty liver disease pathogenesis. The human hepcidin gene, HAMP, is the master switch of iron metabolism. The aim of this study is to investigate the regulation of HAMP expression by fatty acids in HepG2 cells. For these studies, both saturated fatty acids (palmitic acid (PA) and stearic acid (SA)) and unsaturated fatty acid (oleic acid (OA)) were used. PA and, to a lesser extent, SA, but not OA, up-regulated HAMP mRNA levels, as determined by real-time PCR. To understand whether PA regulates HAMP mRNA at the transcriptional or post-transcriptional level, the transcription inhibitor actinomycin D was employed. PA-mediated induction of HAMP mRNA expression was not blocked by actinomycin D. Furthermore, PA activated HAMP 3'-UTR, but not promoter, activity, as shown by reporter assays. HAMP 3'-UTR harbors a single AU-rich element (ARE). Mutation of this ARE abolished the effect of PA, suggesting the involvement of ARE-binding proteins. The ARE-binding protein human antigen R (HuR) stabilizes mRNA through direct interaction with AREs on 3'-UTR. HuR is regulated by phosphorylation-mediated nucleo-cytoplasmic shuttling. PA activated this process. The binding of HuR to HAMP mRNA was also induced by PA in HepG2 cells. Silencing of HuR by siRNA abolished PA-mediated up-regulation of HAMP mRNA levels. PKC is known to phosphorylate HuR. Staurosporine, a broad-spectrum PKC inhibitor, inhibited both PA-mediated translocation of HuR and induction of HAMP expression. Similarly, rottlerin, a novel class PKC inhibitor, abrogated PA-mediated up-regulation of HAMP expression. In conclusion, lipids mediate post-transcriptional regulation of HAMP throughPKC- and HuR-dependent mechanisms.

Detection of Methicillin Resistance and Various Virulence Factors in Staphylococcus aureus Strains Isolated from Nasal Carriers.

BACKGROUND: Staphylococus aureus can be found as a commensal on skin and nasal flora or it may cause local and invasive infections. S. aureus has a large number of virulence factors. AIMS: To investigate the methicillin resistance and frequency of various virulence factors in S. aureus nasal isolates. STUDY DESIGN: Descriptive study. METHODS: Nasal samples collected from university students were cultured in media. S. aureus was identified by conventional methods and the Staphyloslide latex test (Becton Dickinson, Sparks, USA). Antibiotic susceptibility tests were conducted, and the methicillin resistance was determined. The mecA, nuc, pvl and staphylococcal toxin genes were examined by polymerase chain reaction (PCR). RESULTS: S. aureus was isolated in 104 of 600 (17.3%) nasal samples. In total, 101 (97.1%) S. aureus isolates were methicillin-sensitive and the remaining 3 (2.9%) were methicillin-resistant. Furthermore, all but five isolates carried at least one staphylococcal enterotoxin gene, with seg being predominant. The tst and eta genes were determined in 29 (27.9%), and 3 (2.9%) isolates, respectively. None of the S. aureus isolates harbored see, etb, and pvl genes. CONCLUSION: A moderate rate of S. aureus carriage and low frequency of MRSA were detected in healthy students. S. aureus isolates had a high prevalence of staphylococcal enterotoxin genes and the tst gene. In this study, a large number of virulence factors were examined in S. aureus nasal isolates, and the data obtained from this study can be used for monitoring the prevalence of virulence genes in S. aureus strains isolated from nasal carriers.

The effect of alcohol and hydrogen peroxide on liver hepcidin gene expression in mice lacking antioxidant enzymes, glutathione peroxidase-1 or catalase.

This study investigates the regulation of hepcidin, the key iron-regulatory molecule, by alcohol and hydrogen peroxide (H2O2) in glutathione peroxidase-1 (gpx-1(-/-)) and catalase (catalase(-/-)) knockout mice. For alcohol studies, 10% ethanol was administered in the drinking water for 7 days. Gpx-1(-/-) displayed significantly higher hepatic H2O2 levels than catalase(-/-) compared to wild-type mice, as measured by 2'-7'-dichlorodihydrofluorescein diacetate (DCFH-DA). The basal level of liver hepcidin expression was attenuated in gpx-1(-/-) mice. Alcohol increased H2O2 production in catalase(-/-) and wild-type, but not gpx-1(-/-), mice. Hepcidin expression was inhibited in alcohol-fed catalase(-/-) and wild-type mice. In contrast, alcohol elevated hepcidin expression in gpx-1(-/-) mice. Gpx-1(-/-) mice also displayed higher level of basal liver CHOP protein expression than catalase(-/-) mice. Alcohol induced CHOP and to a lesser extent GRP78/BiP expression, but not XBP1 splicing or binding of CREBH to hepcidin gene promoter, in gpx-1(-/-) mice. The up-regulation of hepatic ATF4 mRNA levels, which was observed in gpx-1(-/-) mice, was attenuated by alcohol. In conclusion, our findings strongly suggest that H2O2 inhibits hepcidin expression in vivo. Synergistic induction of CHOP by alcohol and H2O2, in the absence of gpx-1, stimulates liver hepcidin gene expression by ER stress independent of CREBH.

Reliability of stool antigen tests: investigation of the diagnostic value of a new immunochromatographic Helicobacter pylori approach in dyspeptic patients.

BACKGROUND: A diagnosis of H. pylori infection can be made by invasive or non-invasive methods. Several noninvasive diagnostic tests based on the detection of H. pylori stool antigen (HpSA) have been developed. The Genx H. pylori stool antigen card test is a new rapid, non-invasive test that is based on monoclonal immunochromatographic assay. The aim of this study was to determine its sensitivity, specificity, and diagnostic accuracy for diagnosing H. pylori infection in adult patients. MATERIALS AND METHODS: A total of 162 patients were included in the study. A gastric biopsy was collected for histopathology and rapid urease testing. Stool specimens for HpSA testing were also collected. Patients were considered H. pylori positive if two invasive tests (histological and rapid urease tests) were positive. RESULTS: Using the reference test, 50.6% of the samples were positive for H. pylori infection. The Genx H. pylori antigen test was positive in 19.7% of patients. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of the Genx H. pylori antigen test were 51.6%, 96.0%, 88.8%, 76.1%, and 79.0%, respectively. CONCLUSIONS: The Genx H. pylori stool antigen card test is a new non-invasive method that is fast and simple to perform but provides less reliable results.

[Investigation of OXA type beta-lactamases and PFGE patterns in Acinetobacter baumannii strains resistant to carbapenems]. / Karbapenemlere dirençli Acinetobacter baumannii suslarinda OXA tipi beta-laktamazlarin arastirilmasi ve PFGE ile genotiplendirilmesi.

Acinetobacter baumannii is an important opportunistic and multidrug-resistant pathogen leading to nosocomial infections. Over the last 10 years, a significant and threatening increase in resistance to carbapenems, mainly due to the dissemination of class D beta-lactamases, has been reported in A.baumannii worldwide. The most common types of beta-lactamases causing carbapenem resistance in A.baumannii are the OXA-23, OXA-24, OXA-40, OXA-58 and OXA-143 type serine beta-lactamases. The aim of this study was to investigate the presence of OXA type beta-lactamases in carbapenem-resistant A.baumannii strains and the clonal relationship between the strains. A total of 105 non-duplicate carbapenem-resistant A.baumannii strains isolated from various clinical samples (68 blood, 18 bronchoalveolar lavage, 13 drainage, 3 urine, 2 cerebrospinal fluid and 1 catheter samples) in the Microbiology Laboratories of Selcuk University, Meram (2009-2012) and Selcuklu (2007-2008) Medical School Hospitals, were included in the study. The isolates were identified by conventional methods and Phoenix 100 BD (BD Diagnostic, USA) and Vitek II (bioMerieux, France) automated systems. Carbapenem susceptibility test was performed by Kirby-Bauer disk diffusion method according to the CLSI standards. bla(OXA 23-like), bla(OXA 24-like), bla(OXA 58-like) and bla(OXA 51-like) genes were amplified by multiplex PCR assay and clonal relatedness was investigated by pulsed-field gel electrophoresis (PFGE) using ApaI enzyme. The bla(OXA 51-like) gene was determined in all carbapenem-resistant A.baumannii isolates, while the bla(OXA 23-like) and bla(OXA 58-like) genes were detected in 46.6% and 53.3% of isolates, respectively. However bla(OXA 24-like) gene was not demonstrated in any isolates. bla(OXA 23-like) gene was determined in both Meram and Selcuklu Medical School hospitals, but bla(OXA 58-like) gene was detected only in Meram Medical School hospital. PFGE analysis of the isolates revealed 32 different groups in bla(OXA 23-like) producing A.baumannii strains and 23 different groups determined in bla(OXA 58-like) producing strains. No common epidemic isolates were detected in the two hospitals, however it was noted that some clones produced small outbreaks in Meram MS hospital. In this study it was shown that bla(OXA 23-like) and bla(OXA 58-like) genes together with bla(OXA 51-like) gene had significant roles in the carbapenem-resistance of A.baumannii strains. Carbapenem-resistant A.baumannii strains producing bla(OXA 23-like) and bla(OXA 58-like) enzymes showed the epidemic potential of this nosocomial pathogen and the requirement of molecular typing methods to identify the epidemiologic relationship of the isolates.