[Investigation of the Clinical Significance of Anti-Dense Fine Speckled 70 (anti-DFS70) Autoantibody and Determination of Accompanying Pathologies]. / Anti-Dense Fine Speckled 70 (anti-DFS70) Otoantikorunun Klinik Öneminin Arastirilmasi ve Eslik Eden Patolojilerin Belirlenmesi.

Autoantibodies targeting nuclear and cytoplasmic autoantigens are used as markers in the diagnosis and classification of systemic autoimmune rheumatic diseases (SARD). The dense fine speckled (DFS) pattern is characterized by the fine-granular fluorescence of the nuclei in the interphase and the metaphase chromatin. DFS70 antibodies have been reported in healthy individuals, various autoimmune disorders, infection, cancer and inflammatory conditions. But there is still lack of information about its clinical significance. This study aimed to investigate the clinical significance of anti-DFS70 autoantibodies and the determination of accompanying pathologies. A total of 5710 serum samples routinely requested for ANA screening were tested between 2017 and 2019. Antinuclear antibody (ANA) and dsDNA were performed by indirect immunofluorescence method (IIF) (Euroimmun, Germany). Immunoblot (IB) method was used for the extractable nuclear antigen profile (ENA) (Euroimmun, Germany). Demographic and clinical data, were investigated from the medical records. Among 5710 samples tested for ANA, 23.7% were ANA positive by IIF. Mean age of the patients were 47.9 and 79.5% were female. Only 8.1% of the study group had SARD. The frequency of DFS pattern by ANA-IIF was 6.0% (342/5710), (mean age ± SD= 44.4 ± 16.7, 88% female). DFS70 pattern-positive patients were sub-grouped according to their diagnosis. SARD were detected 10.8% (mean age ± SD= 55.12 ± 14.10) in DFS70 pattern positive patient group (RA 6.1%, SS 2.6%, SLE 0.9%, SSc 0.6%, UCTD 0.6%). Autoantibodies accompanying anti-DFS70 antibody were determined as Ro-52, SS-A, nucleosome, histone, AMA-M2, dsDNA, respectively. Non-SARD diseases were determined in 89.2% of the patients with positive DFS70 pattern. Non-SARD diseases were detected as musculoskeletal complaints (47.4%), other rheumatic diseases like fibromyalgia (14.3%), dermatological diseases (9.4%), gastrointestinal system diseases (5.6%), hematological disorders (3.8%), thyroid /parathyroid diseases (3.5%), allergic diseases (2.3%), neurological diseases (2.3%) and neoplasia (breast cancer) (0.6%). The anti-DFS70 autoantibody is widely used to exclude the diagnosis of SARD in the absence of concomitant SARD-related autoantibodies. It has been observed that anti-DFS70 autoantibody may be associated with non-SARD rheumatic diseases and in many diseases (dermatological, gastrointestinal system, hematological, thyroid diseases) related to other systems. Therefore it is essential to evaluate these pathologies in patients positive for anti-DFS70 antibodies.

[Determination of cytomegalovirus glycoprotein B genotypes in different geographical regions and different patient groups in Turkey]. / Türkiye'de farkli cografi bölgelerde ve farkli hasta gruplarindaki sitomegalovirus izolatlarinin glikoprotein B genotiplerinin belirlenmesi.

Cytomegalovirus (CMV), a common virus found all around the world, usually causes asymptomatic infections in immunocompetent hosts, however it may lead to serious complications in immunodeficient patients and in the fetus. CMV is divided into four genotypes according to the polymorphisms in UL55 gene that encodes for envelope glycoprotein B. Nucleotide polymorphisms of CMV gB gene can affect the cell tropism of the virus and host immune response and believed to have important changes in the pathogenesis of CMV. The aim of this study was to determine the gB genotypes of CMV isolates from different patient groups selected from different regions of Turkey. A total of 136 clinical specimens from patients (66 female, 70 male; age range: 0-65 years, mean age: 24.03 ± 17.17) who were diagnosed to have CMV infection by polymerase chain reaction (PCR) and/or antigenemia tests, between 2001-2014, in the medical school hospitals of Akdeniz, Ege, Istanbul Cerrahpasa and Erciyes Universities (located at Mediterranean, Aegean, northwest and central Anatolia regions, respectively), were included in the study. The patient group consisted of 80 renal transplant (RT) recipients, 35 stem cell transplant (SCT) recipients, 13 newborns, seven heart transplant (HT) recipients and one pregnant woman. CMV gB genotypes were determined by PCR-RFLP (restriction fragment length polymorphism) method, and DNA sequencing and phylogenetic analysis were performed for the randomly selected 15 isolates with different genotypes. Among 136 (135 plasma, 1 amnion fluid) samples, the most frequent genotype was gB1 (n= 44, 32.4%), followed by gB2 (n= 39, 28.6%), gB3 (n= 36, 26.5%) and gB4 (n= 8, 5.9%); however nine (6.6%) samples could not be genotyped. When analysis were interpreted according to the patient groups, it was determined that the genotypes in RT recipients were gB1 32.3%, gB2 28.7%, gB3 26.5% and gB4 5.9%; in SCT recipients gB1 34.3%, gB2 28.6%, gB3 22.9% and gB4 5.7%; in HT recipients gB3 57.1%, gB1 14.3% and gB2 14.3%; in newborns gB1 38.4%, gB3 30.8%, gB2 15.4% and gB4 7.7%, and gB2 genotype in the pregnant woman. As our study was a descriptive study to determine the genotypes of CMV gB, the relationship between the genotypes and the variants such as viral load, symptomatic disease and prognosis were not analyzed. As a result, the isolation of different gB genotypes in various case groups from four distinctive provinces, underlines the diversity of CMV gB genotypes in Turkey.

Cutaneous Alternaria infectoria infection diagnosed by molecular techniques in a renal transplant patient.

Organ transplant recipients under immunosuppressive therapy have a highly increased risk of opportunistic fungal infections. Cutaneous infection caused by Alternaria species are relatively rare in humans and most cases reported in the literature are in immunocompromised individuals. We report here on a 33-year old male renal transplant patient with diabetes mellitus who presented with cutaneous alternariosis caused by Alternaria infectoria, two years after the transplant. The diagnosis was performed by real-time polymerase chain reaction assay and histopathologic examination. The extension of the lesion under itraconazole treatment required treatment consisting of a combination of surgical excision and liposomal amphotericin B.

Evaluation of a chromogenic medium for detection of extended-spectrum-beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae strains.

BACKGROUND: Because of the emergence and spread of extended-spectrum-beta-lactamase (ESBL)-producing strains which are resistant to many antibiotics, reliable detection of ESBL is very important for infection control. Several chromogenic media have been proposed for the detection of ESBL producers in addition to the conventional phenotypic and genotyping methods. The aim of the present study was to evaluate the performance of Brilliance ESBL agar (Oxoid; Thermo Fisher Scientific, UK), a selective chromogenic agar for the detection of ESBL-producing Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) strains. METHODS: A total of 237 strains (143 ESBL producers (76 isolates of E. coli and 67 isolates of K. pneumoniae) and 94 non-ESBL producers (44 isolates of E. coli and 50 isolates of K. pneumoniae)) isolated from various clinical specimens were included in the study. Isolates were identified by conventional methods, Phoenix system (Becton Dickinson, USA), and mass spectrometry. ESBL confirmation was performed by phenotypical tests. A 10 microL aliquot of each isolate's 0.5 McFarland suspension was streaked onto Brilliance ESBL agar. All plates were incubated at 37 degrees C for 24 hours and then were interpreted for growth and colony color according to the manufacturer's recommendations. Identification and ESBL test results were used to calculate the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the medium evaluated at 24 hours. RESULTS: The sensitivity, specificity, PPV, and NPV of the medium were 97.9%, 100%, 100%, and 96.9%, respectively, when considering only species specific colored colonies of the isolates. CONCLUSIONS: Brilliance ESBL agar could provide a practical alternative to the traditional methods for the identification of ESBL producers.

[Investigation of hepatitis B and hepatitis C virus infections by serological and molecular methods in hemodialysis patients]. / Hemodiyaliz hastalarinda hepatit B ve hepatit C virus enfeksiyonlarinin serolojik ve moleküler yöntemlerle arastirilmasi

Hepatitis B virus (HBV) and hepatitis C virus (HCV) infections are significant causes of morbidity and mortality in hemodialysis patients, since those patients are highly susceptible to infections due to immune suppression. The aims of this study were to investigate the presence of HBV and HCV infections in chronic hemodialysis patients by serological and molecular methods, and to determine the rate of occult HBV infection and the viral genotypes. A total of 201 patients who were under hemodialysis due to end-stage renal disease, were retrospectively evaluated. The study involved the patients at three different centers in Antalya, Turkey during 2006. HBV and HCV markers in the patients' sera were screened by ELISA method, viral nucleic acids were investigated by real-time polymerase chain reaction (PCR) in patients' plasma and viral genotypes were determined by DNA sequence analysis. Detection of at least one of the HBV markers HBsAg, anti-HBc total, and HBV DNA, was accepted as HBV infection, and detection of anti-HCV and/or HCV RNA was accepted as HCV infection. HBsAg positive patients with negative HBV DNA were considered as occult HBV infection. Of the patients 80 (40%) were female, 121 (60%) were male and the mean age was 51.16 ± 16.28 (range 17-93) years. In our study, sole anti-HBs positivity due to HBV vaccination, was detected in 89 (44.3%) patients. One hundred (50%) patients were found positive in terms of HBV infection and 40 (20%) were positive for HCV infection, while 24 (12%) patients had HBV and HCV co-infections. Eighty-five (42.3%) patients had no HBV and HCV infection. Among the 5 (2.5%) patients who were HBsAg positive, four were also HBV DNA positive. Occult HBV infection was detected in 1 (0.5%) patient. Anti-HCV and HCV RNA were found positive in 37 (18.4%) and in 24 (12%) patients, respectively. Among the HCV-RNA positive patients, 3 (12.5%) were anti-HCV negative. ALT and AST levels were found normal in all of the HBV DNA positive patients, and 62.5% (15/24) of HCV RNA positive patients. All of the HBV isolates were identified as genotype D and HCV isolates as genotype 1b. No statistically significant correlation was detected between the HBV infection and patients' age, duration of hemodialysis and elevation of serum transaminase levels (p> 0.05). On the other hand, HCV infection was seen to increase with age (p= 0.047). HCV infection showed a statistically significant increase with the duration of hemodialysis. HCV infection risk was increased in patients who were under hemodialysis for ≥ 25 months (p< 0.001, OR: 0224, 95% CI= 0089-0562). There was also a statistically significant correlation between the presence of HCV infection (anti-HCV and/or HCV RNA positive) and high levels of serum transaminases (p< 0.001). However, in two of the three cases who were anti-HCV negative and HCV RNA positive, serum transaminase levels were normal while the viral loads were high. Therefore to follow-up HCV infection in the hemodialysis patients, anti-HCV and serum transaminase levels may not be sufficient alone and these patients should be evaluated periodically for HCV RNA. In addition, the detection of occult HBV infection in one of the study patients, indicated that HBV DNA should also be investigated at regular intervals in the hemodialysis patients.

Evaluation of vancomycin resistance 3 multiplexed PCR assay for detection of vancomycin-resistant enterococci from rectal swabs.

BACKGROUND: Active screening for vancomycin-resistant enterococci (VRE) using rectal specimens is recommended to limit the spread of antimicrobial resistance within certain high-risk populations. We evaluated the diagnostic performance of Vancomycin Resistance 3 Multiplexed Tandem PCR assay (AusDiagnostics, Australia), a rapid multiplex real-time PCR assay that detects vanA and/or vanB. METHODS: Two-hundred-and-eleven rectal swabs from Hematology and Oncology unit were submitted for VRE surveillance via direct detection of vanA and/or vanB by culture and by using Vancomycin Resistance 3 Multiplexed Tandem PCR assay. Enterococci were identified to the species level by using standard biochemical tests and BD Phoenix Automated Microbiology System (BD Diagnostic Systems, USA). Vancomycin susceptibility of enterococci was determined using Etest (BioMerieux, France). RESULTS: Compared to the culture method, Vancomycin Resistance 3 Multiplexed Tandem PCR assay had a sensitivity of 84.0%, specificity of 98.8%, positive predictive value (PPV) of 91.3%, and negative predictive value (NPV) of 97.6%. The assay failed to detect 18 (8.5%) specimens because of the presence of PCR inhibitors; of the remaining 193 specimens, 25 (12.9%) were positive, 23 for vanA, and 2 for vanB. Although both sensitivity and specificity for vanA VRE was 100% compared to the culture method, all vanB-positive specimens tested negative by VRE culture. CONCLUSIONS: Vancomycin Resistance 3 Multiplexed Tandem PCR assay is a rapid and laborsaving option for VRE surveillance for direct use on rectal swabs. However, the high rate of PCR failure owing to the inhibitors in the specimens and the low specificity for vanB should be considered when interpreting the results.

[Investigation of ESBL types in community acquired urinary Escherichia coli isolates by isoelectric focusing and polymerase chain reaction]. / Toplum kaynakli üriner sistem enfeksiyonu etkeni Escherichia coli suslarinda GSBL enzim tiplerinin izoelektrik odaklama ve polimeraz zincir reaksiyonu yöntemleri ile arastirilmasi

The aim of this study was to determine the extended-spectrum beta-lactamase (ESBL) types by isoelectric focusing (IEF) and polymerase chain reaction (PCR) methods in 56 Escherichia coli strains isolated from urine samples of patients with community-acquired urinary tract infection and determined as ESBL positive with the phenotypic screening tests (E test and combined disk method). IEF revealed that most of the strains produced 1 to 3 different bands, mostly at the isoelectric points 8.2 (n= 44, 79%) compatible with CTX-M. Twenty four (43%) isolates had CTX-M and TEM enzyme bands together, 16 (29%) isolates had only CTX-M enzyme bands, 3 (5%) isolates had CTX-M, TEM, SHV bands, one had CTX-M and SHV enzyme bands together, and one had only TEM band. Eleven E.coli strains did not yield any enzyme bands. PCR analysis revealed that 93% (n= 52) of the isolates had CTX-M, 64% (n= 36) had TEM and 11% (n= 6) had SHV, while 29 (52%) had CTX-M + TEM, three had CTX-M + SHV, and three had CTX-M + TEM + SHV genes together. PER-1 type beta-lactamases were not detected by PCR method. PCR analysis of the eleven strains that yielded no band in IEF showed that 5 strains had CTX-M + TEM, 3 had CTX-M and 3 had TEM enzyme genes. The consistency between IEF and PCR methods for the determination of CTX-M, TEM and SHV enzymes was 85%, 78% and 67%, respectively. Genes encoding ESBL's are usually located on transferrable plasmids that may also carry other resistance determinants. Thus detection of beta-lactamase enzyme types in ESBL positive bacteria is important for the choice of appropriate antimicrobial agents for treatment.

[Shall we report the carbapenem resistance in Pseudomonas aeruginosa and Acinetobacter baumannii strains detected by BD Phoenix system?]. / Pseudomonas aeruginosa ve Acinetobacter baumannii suslarinda BD Phoenix sistemi ile saptanan karbapenem direncini raporlayalim mi?

Imipenem and meropenem are broad spectrum antimicrobial agents that are especially useful in the treatment of nosocomially acquired Pseudomonas aeruginosa and Acinetobacter spp. infections. Previous reports have noted that susceptibility tests could show false resistance to imipenem. For this reason, Centers for Disease Control and Prevention has recommended that all carbapenem resistant or intermediate resistant isolates should be tested with an additional method to verify the results. This study was aimed to evaluate the imipenem and meropenem susceptibilities by disk diffusion, E-test and broth microdilution in P. aeruginosa and Acinetobacter baumannii strains found to be resistant or intermediate to imipenem-meropenem by BD Phoenix automated susceptibility testing system. Between January 2006-January 2007, 85 non-duplicate isolates of A. baumannii and 51 non-duplicate isolates of P. aeruginosa which were determined as resistant or intermediate resistant to imipenem and/or meropenem by BD Phoenix automated identification and susceptibility system (Becton Dickinson, Sparks, MD, USA) were collected in Akdeniz University Hospital Central Laboratory. All strains were tested by E-test (AB Biodisk, Sweden), disk diffusion and reference broth microdilution (BMD) method following CLSI recommendations. All 51 isolates of P. aeruginosa determined as imipenem and/or meropenem resistant or intermediate resistant by BD Phoenix, were found to be imipenem and/or meropenem resistant or intermediate resistant by the reference BMD method. Minor error rates were same for all testing systems (1.9%) except for the meropenem results of BD Phoenix system (5.9%). No major errors were produced by any system. For A. baumannii, only one very major error was detected for meropenem by BD Phoenix system. Number of minor errors determined for meropenem by all testing systems compared to the reference test, ranged from 2 (2.4%) to 3 (3.5%). It was concluded that carbapenem susceptibility test results obtained by BD Phoenix system for P. aeruginosa and A. baumannii isolates, could be reported without an additional susceptibility testing method unless indicated on case basis.

[Investigation of plasmid-mediated AmpC beta-lactamase types in Klebsiella spp. and Escherichia coli isolates resistant or intermediate to cefoxitin]. / Sefoksitine dirençli ya da az duyarli saptanan Klebsiella spp. ve Escherichia coli izolatlarinda plazmid aracili AmpC beta-laktamaz enzim tiplerinin arastirilmasi.

Plasmid mediated AmpC beta-lactamases are reported from Enterobacteriaceae with increasing frequency. There have been reports of treatment failures in patients infected with these organisms and given broad-spectrum cephalosporins. The aim of this study was to investigate the presence of plasmid mediated AmpC beta-lactamases in Escherichia coli and Klebsiella spp. A total of 41 strains of cefoxitin resistant or intermediate E. coli (n= 27) and Klebsiella spp. (n= 14) were collected from january 2005 to January 2006 at Akdeniz University Hospital Central Laboratory. Three-dimensional test was used as a phenotypic confirmatory test. Analytical isoelectric focusing electrophoresis was used to measure the pl values of the beta-lactamases. Plasmid mediated AmpC enzyme genes were amplified using multiplex polymerase chain reaction and sequenced by Beckman Coulter CEQ 8000. AmpC beta-lactamases were only detected in two isolates (7.4%) of E. coli. These isolates produced CMY-2 like enzymes and have either CTX-M or TEM enzyme. Transferable AmpC beta-lactamases are associated with multiple antibiotic resistance. Therefore detection of these enzymes in gram-negative bacteria has a clinical importance, since it can often provide valuable information to clinicians leading to more effective and appropriate use of antimicrobials.