Evaluation of interferon gamma release assay to measure t-cell response in COVID-19 patients from intensive care units and inpatient departments.

BACKGROUND: Interferon gamma release assay (IGRA) is an in vitro blood test to measure interferon gamma (IFN-γ) released from antigen-specific T cells after stimulation with pathogen-specific peptides. In this study, it was aimed to investigate the T-cell response using IGRA and to compare various laboratory values in Coronavirus Disease (COVID-19) patients hospitalized either in hospital inpatient departments or in intensive care units. METHODS: A total of 100 patients (50+50) who were identified as positive for COVID-19 through the molecular method in Selcuk University Faculty of Medicine Infectious Diseases Service and Reanimation Intensive Care Unit were included in the study. IFN-γ levels in blood samples collected from patients were determined using the QuantiFERON Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) (QIAGEN, Germany) kit. The patients' gender, age, c-reactive protein (CRP), aspartate aminotransferase (AST), alanine transaminase (ALT), interleukin (IL)-6, lymphocyte count, procalcitonin, and D-dimer results were obtained from the hospital automation system. RESULTS: Thirty-eight of the IGRA test results were negative, 44 were positive and 18 were inconclusive. The age of patients with negative IGRA test results was significantly higher (p<0.001) compared to patients with positive results. There were no significant differences between patients' IGRA test results and gender, prognosis, IL-6, lymphocyte counts, CRP, AST, and ALT values.Age, death rates, D-dimer, CRP, procalcitonin, AST and ALT values of patients hospitalized in the intensive care unit were significantly higher (p<0.001) compared to the those hospitalized in the inpatient department, while conversely, the lymphocyte values were lower (p<0.001). CONCLUSION: The relatively higher IGRA negative results in the elderly, negative and intermediate results in intensive-care patients, and low lymphocyte levels in intensive-care patients indicate that the cellular immune response is diminished and/or absent. The death rates, D-dimer, CRP, procalcitonin, AST and ALT values of the patients hospitalized in the intensive care unit were higher compared to those from the in-patient department, indicating the severity of inflammation and signaling the development of organ failure. In the light of these findings, we suggest that IGRA tests may serve as a guide in immunomodulatory therapy (Tab. 2, Fig. 2, Ref. 27). Text in PDF www.elis.sk Keywords: COVID-19, interferon gamma release assay test, T cell response.

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.

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.

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.

[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.

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.

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.

Spontaneous pneumomediastinum as a complication in human bocavirus infection.

The most common causes of spontaneous pneumomediastinum (SPM) in children are asthma attack and respiratory tract infection. Here, we describe a case of SPM in a human bocavirus-infected 2-year-old boy with bronchiolitis.

Two outbreaks of ESBL-producing Klebsiella pneumoniae in a neonatal intensive care unit.

BACKGROUND: In the present study, two epidemic episodes of extended spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae in the neonatal intensive care unit (NICU) were evaluated. METHODS: Routine and surveillance culture samples were taken from seven neonates with signs of infection in the NICU of Selcuk University Faculty of Medicine between 10 March and 25 April 2011, and between 11 June and 30 September 2011. RESULTS: ESBL-producing K. pneumoniae strains were isolated in six different samples (one wound, one blood, and four cerebrospinal fluid cultures) of the three neonates in the first episode and in 11 different samples (seven blood and four cerebrospinal fluid cultures) of the four neonates in the second episode. ESBL-producing K. pneumoniae was isolated from inguinal, axillar region, and stool samples of the nine colonized neonates in the second episode. It was determined on pulse field gel electrophoresis that all strains originated from two clones. CONCLUSIONS: The deficiencies in the infection control measures in an NICU may transform into an epidemic rapidly. Therefore, periodic training, observation, and monitoring of compliance are important.

COMMUNITY-ACQUIRED METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS AND GENOTYPES AMONG UNIVERSITY STUDENTS IN TURKEY.

Nasal carriage of Staphylococcus aureus is an important risk factor for nosocomial and community-acquired staphylococcal infections. We investigate the prevalence of community-acquired methicillin-sensitive (CA-MSSA) and -resistant (CA-MRSA), including inducible dormant (ID)-MRSA S. aureus, and genotypes of MRSA strains of nasal cultures from 1,108 university students attending Selcuk University, Turkey. Risk factors were based on replies to a questionnaire. S. aureus was identified using conventional culture methods and a Stapyloslide® latex test. Antibiotic susceptibility and methicillin resistance were determined by a disk diffusion method, and vancomycin susceptibility was performed using an E-test. Identification of mecA and SCCmec types were conducted by PCR and genotypes by pulse field gel-electrophoresis (PFGE). Prevalence of S. aureus was 17%, with 9% being MRSA. Two isolates were SCCmec type III, 11 were SCCmec variant IIIA and one SCCmec type IV. No ID-MRSA was detected. The majority of the isolates were resistant to penicillin and no strain was resistant to vancomycin. Two MRSA strains were PFGE pulsotype A, 9 pulsotype B, 2 pulsotype C, 1 pulso-type D and 3 pulsotype E. Presence of permanent catheter and use of antibiotics in the previous month were risk factors for MSSA colonization and association with medical facilities were risk factors for MRSA carriers. There is a need for multicenter studies in Turkey to investigate CA- and ID-MRSA prevalence and nosocomial infections.

Bacteremia after piezocision.

INTRODUCTION: The aim of this study was to investigate the presence of transient bacteremia after a piezocision procedure. METHODS: The sample consisted of 30 subjects (24 women, 6 men; mean age, 19.6 ± 0.7 years; range, 18.1-22.4 years) with the American Society of Anesthesiologists' physical status I. All patients had Class I skeletal and dental relationships and had fixed orthodontic treatment with the Damon system. The piezocision surgery was performed 1 week after the placement of the orthodontic appliances in all patients. Two 20-mL venous blood samples were collected before and 30 to 60 seconds after the first microincision using an aseptic technique. The samples were inoculated into BACTEC Plus aerobic and anaerobic blood culture bottles and were assessed in the BACTEC blood culture analyzer (Becton Dickinson Diagnostic Instrument Systems, Sparks, Md). The results were analyzed statistically using the McNemar test, with P <0.05 indicating statistical significance. RESULTS: No significant difference between the preoperative and postoperative samples was determined with respect to transient bacteremia (P = 0.250). No bacteremia was detected in the pretreatment samples, although Gemella sanguinis, Streptococcus pluranimalium, and Streptococcus mitis/oralis were detected in 3 postoperative blood samples. CONCLUSIONS: The piezocision procedure might be related to transitory bacteremia. Hence, orthodontists should consider the possibility of bacterial endocarditis in at-risk patients when piezocision is part of the treatment plan.

[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.

[Epidemiology, clinical and microbiological characteristics of invasive streptococcal infections in Turkey, 2010-2011]. / Türkiye'de invazif streptokok enfeksiyonlarinin epidemiyolojisi, klinik ve mikrobiyolojik özellikleri, 2010-2011.

A one-year active surveillance study was conducted to investigate the epidemiological and microbiological characteristics of invasive group A streptococci (GAS) infections in Turkey and to provide data for the establishment of national preventive strategies related to invasive GAS infections. A total of 46 clinical microbiology laboratories from 12 different regions of Turkey (Istanbul; Eastern and Western Marmara; Eastern and Western Blacksea; Aegean; Mediterranean; Western, Central, Northeastern, Middle-eastern and Southeastern Anatolia) participated in the study. Accordingly, GAS strains isolated from sterile body sites (blood, cerebrospinal, synovial, pleural, peritoneal, pericardial fluids) in the study centers between June 2010-June 2011, were sent to Maltepe University Hospital Clinical Microbiology Laboratory for microbiological confirmation and further analysis. The isolates were identified by conventional methods, and for serotyping, opacity factor (OF) and T protein types were investigated. For genotyping GAS lysate preparation, emm gene amplification and sequencing were performed by using the protocols recommended by Centers for Disease Control and Prevention. A total of 65 invasive GAS strains were isolated in 15 of the participant centers, during the study period. The rate of invasive GAS isolation exhibited regional variation, with the highest rates in the Eastern Blacksea (Trabzon, n= 19), followed by Istanbul (n= 17) and Western Anatolia (Ankara, Konya, n= 14). Of the patients with invasive GAS infection 33 were female, 32 were male, with the age range of 0-89 years. GAS strains were most commonly isolated from soft tissue specimens (n= 18), followed by abscess material (n= 10), sterile body fluids (n= 8) and blood (n= 7) samples. Serotyping revealed that 55% (36/65) of the strains were OF positive, and the majority of T protein was polygroup T (n= 20), followed by U (n= 14), B (n= 5), X (n= 3) and Y (n= 2). T protein was not detected in 22 isolates. The strains were found to have 17 different emm types;emm1 (n= 13), emm4 (n= 6), emm6 (n= 6), emm12 (n= 6), emm24 (n= 4), emm14 (n= 3) and emm28 (n= 3). Nine of the strains could not be typed by sequencing. The correlation between emm typing and serotyping was detected as 58%. It was observed that 26-valent vaccines included 70.5% of the invasive GAS strains included in this study. Our study provided initial data concerning the epidemiological properties of invasive GAS infections and characterization of GAS strains in Turkey. The incidence of invasive GAS infections is low in our country. Although immunization programme by 26-valent GAS vaccine is not currently an urgent public health issue for our country, the results of this study indicated that emm types 4 and 24 should better be included in such a vaccine to be used in Turkey. Additionally, since epidemiological features of GAS infections and the microbiological characteristics of the strains can vary by time, for the diagnosis of invasive streptococcal infections and to take the necessary preventive measures, epidemiological studies should be conducted repeatedly.

[MLST types of vancomycin-resistant Enterococcus faecium strains isolated from blood cultures]. / Kan kültürlerinden izole edilen vankomisine dirençli Enterococcus faecium suslarinin MLST tipleri.

Enterococci, particularly vancomycin-resistant enterococci (VRE), are important nosocomial pathogens with limited treatment options. Enterococci have low-level resistance to penicillins and aminoglycosides and are intrinsically resistant to cephalosporins. In addition, they can acquire high-level resistance to beta-lactam antibiotics, aminoglycosides and glycopeptides. The aim of this study was to determine glycopeptide resistance mechanisms and genetic relationships of vancomycin-resistant E.faecium strains isolated from blood cultures between 2003-2009 years by molecular epidemiologic methods. A total of 38 VRE strains isolated from blood cultures were included in this study. The isolates were identified by conventional methods and Phoenix 100 BD automated system (Becton Dickinson Diagnostic Systems, USA) and confirmed by sequence analysis of 16S rRNA amplicons. Antibiotic susceptibility tests were performed by the Kirby-Bauer disk diffusion method accor-ding to the CLSI standards. MIC values of vancomycin were determined in vancomycin resistant strains by E-test (AB Biodisk, Sweden) method. Vancomycin resistance genes included vanA, vanB, vanC, and vanD were investigated by polymerase chain reaction (PCR) method. Clonal relationship between strains was determined by pulsed-field gel electrophoresis (PFGE). Sequence analysis was performed for examples selected for multilocus sequence typing (MLST) of each pulsotype and subtype. Thirty eight strains of enterococci isolated from blood cultures were defined as E.faecium by phenotypic methods and confirmed by 16S rRNA sequence analysis. Vancomycin MIC values of strains were determined as > 256 µg/ml by E test. The vanA gene was detected in all isolates. Clonal relationship of 38 isolates E.faecium carrying the vanA gene was determined by PFGE and MLST methods. PFGE detected four pulsotypes (A-D) and one sporadic isolate. Twenty nine strains belonged to A pulsotype, three strains belonged to B pulsotype, two strains belonged to C pulsotype and three strains belonged to D pulsotype. Out of 29 isolates, eight strains were type A1, nine strains were type A2, six strains were type A3, two strains were type A4 and four strains were type A5. MLST identified four different sequence types (STs). Twenty nine A pulsotype and its subtypes belonged to ST117 (76.3%), three B pulsotype belonged to ST280 (7.9%), two C pulsotype belonged to ST18 (5.2%) and three D pulsotype belonged to ST17 (7.9%). In conclusion, bloodstream infections caused by VRE in our hospital arose from a dominant strain belonged to ST117. However, presence of different pulsotypes of this strain indicated that the strain had been present in the hospital for a long time and had accumulated genetic variations. In addition, infections caused by minor pulsotypes were also detected. Therefore for prevention and control of the spread of nosocomial infections caused by VRE, it is crucial to identify resistance patterns and clonal relationship of these organisms.

[Distribution of emm genotypes and antibiotic susceptibility of Streptococcus pyogenes strains: analogy with the vaccine in development]. / Streptococcus pyogenes suslarinin emm genotiplerinin dagilimi ve antibiyotik duyarliligi: Gelistirilmekte olan asi ile karsilastirma.

Streptococcus pyogenes is the most common bacterial pathogen causing pharyngotonsillitis, and also can lead to diseases such as otitis media, impetigo, necrotizing fasciitis, bacteremia, sepsis and toxic shock-like syndrome. M protein encoded by emm gene is an important virulence factor of S.pyogenes and it is used for genotyping in epidemiological studies. The aims of this study were to determine the M protein types of group A streptococci (GAS) by using emm gene sequence analysis method, to compare the M types in terms of analogy with the vaccine in development and to determine the antibiotic susceptibilities of the isolates. A total of 35 GAS strains isolated from various clinical specimens in our laboratory were included in the study. Strains growing in blood culture were considered as invasive, strains growing in throat and abscess cultures were considered as non-invasive. The isolates have been identified by conventional methods and 16S rRNA sequence analysis at species level. emm genotyping of strains identified as S.pyogenes, was performed by PCR method as proposed by the CDC. Amplicons were obtained and sequenced in 23 out of 35 isolates. The results were compared with CDC emm sequence database. Antibiotic susceptibility of the isolates was performed by agar dilution method and evaluated as recommended by CLSI. Twenty-three out of 35 isolates could be typed and 15 different emm genotypes were detected. The most common emm types were emm1 (22%), emm89 (13%), emm18 (9%) and emm19 (9%). The detection rate of other emm types (emm5, 12, 14, 17, 26, 29, 37, 74, 78, 92, 99) was 47%. Types emm1, 12, 19, 74, 89 and 99 were observed in strains isolated from blood cultures. It was detected that nine of the 15 (60%) emm types are within the contents of 26 valent vaccine (emm 1, 5, 12, 14, 18, 19, 29, 89, 92). It was also observed that 17 (74%) of the 23 cases were infected by vaccine types and the four emm types (emm1, 12, 19, 89) identified in blood samples were among the vaccine types. All of the strains were found susceptible to penicillin, ampicillin, erythromycin, lincomycin, gentamicin, chloramphenicol, vancomycin and linezolid, however six isolates were resistant to levofloxacin (MIC= 4 and 16 µg/ml) and one isolate was resistant to tetracycline (MIC= 16 µg/ml). In conclusion, this preliminary local study with limited number of invasive and non-invasive S.pyogenes isolates, emphasized the need for larger scale multi-center studies to determine the analogy and efficacy of the vaccine in development.