Trends and factors associated with modification or discontinuation of the initial antiretroviral regimen during the first year of treatment in the Turkish HIV-TR Cohort, 2011-2017.

BACKGROUND: There is limited evidence on the modification or stopping of antiretroviral therapy (ART) regimens, including novel antiretroviral drugs. The aim of this study was to evaluate the discontinuation of first ART before and after the availability of better tolerated and less complex regimens by comparing the frequency, reasons and associations with patient characteristics. METHODS: A total of 3019 ART-naive patients registered in the HIV-TR cohort who started ART between Jan 2011 and Feb 2017 were studied. Only the first modification within the first year of treatment for each patient was included in the analyses. Reasons were classified as listed in the coded form in the web-based database. Cumulative incidences were analysed using competing risk function and factors associated with discontinuation of the ART regimen were examined using Cox proportional hazards models and Fine-Gray competing risk regression models. RESULTS: The initial ART regimen was discontinued in 351 out of 3019 eligible patients (11.6%) within the first year. The main reason for discontinuation was intolerance/toxicity (45.0%), followed by treatment simplification (9.7%), patient willingness (7.4%), poor compliance (7.1%), prevention of future toxicities (6.0%), virologic failure (5.4%), and provider preference (5.4%). Non-nucleoside reverse transcriptase inhibitor (NNRTI)-based (aHR = 4.4, [95% CI 3.0-6.4]; p < 0.0001) or protease inhibitor (PI)-based regimens (aHR = 4.3, [95% CI 3.1-6.0]; p < 0.0001) relative to integrase strand transfer inhibitor (InSTI)-based regimens were significantly associated with ART discontinuation. ART initiated at a later period (2015-Feb 2017) (aHR = 0.6, [95% CI 0.4-0.9]; p < 0.0001) was less likely to be discontinued. A lower rate of treatment discontinuation for intolerance/toxicity was observed with InSTI-based regimens (2.0%) than with NNRTI- (6.6%) and PI-based regimens (7.5%) (p < 0.001). The percentage of patients who achieved HIV RNA < 200 copies/mL within 12 months of ART initiation was 91% in the ART discontinued group vs. 94% in the continued group (p > 0.05). CONCLUSION: ART discontinuation due to intolerance/toxicity and virologic failure decreased over time. InSTI-based regimens were less likely to be discontinued than PI- and NNRTI-based ART.

Virulence genes fliC, toxA and phzS are common among Pseudomonas aeruginosa isolates from diabetic foot infections.

BACKGROUND: Outcomes of antibiotic treatment of diabetic foot infections (DFIs) may depend not only on the antimicrobial susceptibility of the aetiologic agents, but also their ability to produce virulence factors. This study aimed to use polymerase chain reaction (PCR) with specific primers to investigate the presence of virulence genes among isolates of Pseudomonas aeruginosa isolates cultured from specimens from diabetic foot and other infections. METHODS: We examined 63 P. aeruginosa isolates from inpatients at two University Hospitals for the presence of 23 known bacterial virulence genes, including lasI, lasR, lasA, lasB, rhll, rhlR, rhlAB, aprA, fliC, toxA, plcH, plcN, ExoS, ExoT, ExoU, ExoY, phzI, phzII, phzM, phzS, pvdA, pilA and pilB. RESULTS: Seven virulence genes (lasl, lasR, lasB, rhll, rhlR, rhlABand Exo T) were present in each isolate. No isolate expressed or presented aprA gene. We found that fliC (p = .01), toxA (p = .041) and phzS (p < .001) were statistically and significantly more common in diabetic foot isolates, while plcH (p < .001) was significantly more common in other infections. CONCLUSIONS: Among clinical isolates of P. aeruginosa from patients with DFIs, three virulence genes that can play important roles in tissue penetration (fliC), tissue damage and survival under anaerobic condition (phzS) and cell death (toxA) were significantly more common than isolates from other infections. The Multilocus sequence typing (MLST) analysis of diabetic foot isolates failed to point/indicate the existence of a specific clone or was not able to characterize/identify a specific clone/clonal complex group. Development of new agents to inhibit the synthesis of these genes may improve outcomes in DFIs treatment.

Epidemiological and molecular characteristics of meticillin-resistant Staphylococcus aureus in Turkey: A multicentre study.

The aim of this study was to investigate the epidemiological and molecular features of clinical meticillin-resistant Staphylococcus aureus (MRSA) isolates in Turkey. MRSA isolates were collected from six regions of Turkey. The mecA and nuc genes were detected by PCR. Antimicrobial susceptibilities were determined by the disk diffusion method. Staphylococcal cassette chromosome mec (SCCmec) and staphylococcal protein A (spa) typing were performed by the sequencing method for 270 randomly selected MRSA isolates. The US Centers for Disease Control and Prevention (CDC) definition was used for epidemiological diagnosis of community-associated MRSA (CA-MRSA). Resistance rates of MRSA to ciprofloxacin, gentamicin, clindamycin, erythromycin, rifampicin, trimethoprim/sulfamethoxazole and tetracycline were 93.4%, 81.2%, 38.5%, 57.8%, 93.9%, 1.1% and 93.1%, respectively. The most frequent SCCmec type was SCCmec III (91.1%). SCCmec type IV was found in 5.2% of the isolates. The most frequent spa type was t030 (81.1%). Five isolates were CA-MRSA if only the epidemiological definition was used (5/725; 0.7%). Two isolates were defined as CA-MRSA both by epidemiological features and SCCmec typing (2/270; 0.7%). Of 14 SCCmec type IV isolates, 12 were not defined as CA-MRSA by epidemiological features. In conclusion, this is the most comprehensive multicentre study in Turkey investigating MRSA using both epidemiological and genotypic features. The CA-MRSA rate is low in Turkey. Combined use of epidemiological and genotypic methods is the most accurate approach for the diagnosis of CA-MRSA.

HIV-1 Transmitted Drug Resistance Mutations in Newly Diagnosed Antiretroviral-Naive Patients in Turkey.

HIV-1 replication is rapid and highly error-prone. Transmission of a drug-resistant HIV-1 strain is possible and occurs within the HIV-1-infected population. In this study, we aimed to determine the prevalence of transmitted drug resistance mutations (TDRMs) in 1,306 newly diagnosed untreated HIV-1-infected patients from 21 cities across six regions of Turkey between 2010 and 2015. TDRMs were identified according to the criteria provided by the World Health Organization's 2009 list of surveillance drug resistance mutations. The HIV-1 TDRM prevalence was 10.1% (133/1,306) in Turkey. Primary drug resistance mutations (K65R, M184V) and thymidine analogue-associated mutations (TAMs) were evaluated together as nucleos(t)ide reverse transcriptase inhibitor (NRTI) mutations. NRTI TDRMs were found in 8.1% (107/1,306) of patients. However, TAMs were divided into three categories and M41L, L210W, and T215Y mutations were found for TAM1 in 97 (7.4%) patients, D67N, K70R, K219E/Q/N/R, T215F, and T215C/D/S mutations were detected for TAM2 in 52 (3.9%) patients, and M41L + K219N and M41L + T215C/D/S mutations were detected for the TAM1 + TAM2 profile in 22 (1.7%) patients, respectively. Nonnucleoside reverse transcriptase inhibitor-associated TDRMs were detected in 3.3% (44/1,306) of patients (L100I, K101E/P, K103N/S, V179F, Y188H/L/M, Y181I/C, and G190A/E/S) and TDRMs to protease inhibitors were detected in 2.3% (30/1,306) of patients (M46L, I50V, I54V, Q58E, L76V, V82A/C/L/T, N83D, I84V, and L90M). In conclusion, long-term and large-scale monitoring of regional levels of HIV-1 TDRMs informs treatment guidelines and provides feedback on the success of HIV-1 prevention and treatment efforts.

Comparison of brucellar and tuberculous spondylodiscitis patients: results of the multicenter "Backbone-1 Study".

BACKGROUND CONTEXT: No direct comparison between brucellar spondylodiscitis (BSD) and tuberculous spondylodiscitis (TSD) exists in the literature. PURPOSE: This study aimed to compare directly the clinical features, laboratory and radiological aspects, treatment, and outcome data of patients diagnosed as BSD and TSD. STUDY DESIGN: A retrospective, multinational, and multicenter study was used. PATIENT SAMPLE: A total of 641 (TSD, 314 and BSD, 327) spondylodiscitis patients from 35 different centers in four countries (Turkey, Egypt, Albania, and Greece) were included. OUTCOME MEASURES: The pre- and peri- or post-treatment spinal deformity and neurologic deficit parameters, and mortality were carried out. METHODS: Brucellar spondylodiscitis and TSD groups were compared for demographics, clinical, laboratory, radiological, surgical interventions, treatment, and outcome data. The Student t test and Mann-Whitney U test were used for group comparisons. Significance was analyzed as two sided and inferred at 0.05 levels. RESULTS: The median baseline laboratory parameters including white blood cell count, C-reactive protein, and erythrocyte sedimentation rate were higher in TSD than BSD (p<.0001). Prevertebral, paravertebral, epidural, and psoas abscess formations along with loss of vertebral corpus height and calcification were significantly more frequent in TSD compared with BSD (p<.01). Surgical interventions and percutaneous sampling or abscess drainage were applied more frequently in TSD (p<.0001). Spinal complications including gibbus deformity, kyphosis, and scoliosis, and the number of spinal neurologic deficits, including loss of sensation, motor weakness, and paralysis were significantly higher in the TSD group (p<.05). Mortality rate was 2.22% (7 patients) in TSD, and it was 0.61% (2 patients) in the BSD group (p=.1). CONCLUSIONS: The results of this study show that TSD is a more suppurative disease with abscess formation requiring surgical intervention and characterized with spinal complications. We propose that using a constellation of constitutional symptoms (fever, back pain, and weight loss), pulmonary involvement, high inflammatory markers, and radiological findings will help to differentiate between TSD and BSD at an early stage before microbiological results are available.

Surgical site infection rates in 16 cities in Turkey: findings of the International Nosocomial Infection Control Consortium (INICC).

BACKGROUND: Surgical site infections (SSIs) are a threat to patient safety; however, there were no available data on SSI rates stratified by surgical procedure (SP) in Turkey. METHODS: Between January 2005 and December 2011, a cohort prospective surveillance study on SSIs was conducted by the International Nosocomial Infection Control Consortium (INICC) in 20 hospitals in 16 Turkish cities. Data from hospitalized patients were registered using the Centers for Disease Control and Prevention (CDC) National Healthcare Safety Network (NHSN) methods and definitions for SSIs. Surgical procedures (SPs) were classified into 22 types according to International Classification of Diseases, Ninth Revision criteria. RESULTS: We recorded 1879 SSIs, associated with 41,563 SPs (4.3%; 95% confidence interval, 4.3-4.7). Among the results, the SSI rate per type of SP compared with rates reported by the INICC and CDC NHSN were 11.9% for ventricular shunt (vs 12.9% vs 5.6%); 5.3% for craniotomy (vs 4.4% vs 2.6%); 4.9% for coronary bypass with chest and donor incision (vs 4.5 vs 2.9); 3.5% for hip prosthesis (vs 2.6% vs 1.3%), and 3.0% for cesarean section (vs 0.7% vs 1.8%). CONCLUSIONS: In most of the 22 types of SP analyzed, our SSI rates were higher than the CDC NHSN rates and similar to the INICC rates. This study advances the knowledge of SSI epidemiology in Turkey, allowing the implementation of targeted interventions.

Transmitted antiretroviral drug resistance mutations in newly diagnosed HIV-1 positive patients in Turkey.

INTRODUCTION: The objective of this study was to determine the transmitted drug resistance mutations (TDRMs) in newly diagnosed HIV-1 positive patients in Turkey. MATERIALS AND METHODS: The study was carried out between 2009 and 2014 and antiretroviral naïve 774 HIV-1 infected patients from 19 Infectious Diseases and Clinical Microbiology Departments in Turkey were included; gender: 664 (86%) male, median age: 37 (range; 1-77), median CD4+T-cell: 360 (range; 1-1320) count/mm(3), median HIV-RNA load: 2.10+E6 (range; 4.2+E2-7.41+E8) IU/mL. HIV-1 drug resistance mutations were detected by population based sequencing of the reverse transcriptase (codon 41-238) and protease (codon 1-99) domains of pol gene of HIV-1, and analyzed according to the criteria by the World Health Organization 2009 list of surveillance drug resistance mutations [1]. RESULTS: The patients had TDRMs to NRTIs (K65R, M184V), NNRTIs (K101E, K103N/S, G190A/E/S, Y181I/C, Y188H/L) and PIs (M46L, I54V, L76V, V82L/T, N83D, I84V, L90M). The prevalence of overall TDRMs was 6.7% (52/774). Resistance mutations were found to be 0.7% (6/774), 4.1% (32/774) and 2.1% (17/774) to NRTIs, NNRTIs and PIs drug groups, respectively. Three patients had NRTIs+NNRTs resistance mutations (M184V+K103N) as multi-class drug resistance. However, thymidine analogue resistance mutations (TAMs) determined two distinct genotypic profiles in the HIV-1 reverse transcriptase: TAM1: M41L, L210W and T215Y, and TAM2: D67N, K70R, K219E/Q, and T215F. The prevalence of TAM1 and TAM2 were 7.7% (60/774) and 4.3% (34/774), respectively. CONCLUSIONS: The TDRMs prevalence of antiretroviral naïve HIV-1 infected patients may be suggested current situation of Turkey. These long-term and large-scale results show that the resistance testing must be an integral part of the management of HIV infection in Turkey.

International Nosocomial Infection Control Consortium (INICC) national report on device-associated infection rates in 19 cities of Turkey, data summary for 2003-2012.

BACKGROUND: Device-associated healthcare-acquired infections (DA-HAI) pose a threat to patient safety, particularly in the intensive care unit (ICU). We report the results of the International Infection Control Consortium (INICC) study conducted in Turkey from August 2003 through October 2012. METHODS: A DA-HAI surveillance study in 63 adult, paediatric ICUs and neonatal ICUs (NICUs) from 29 hospitals, in 19 cities using the methods and definitions of the U.S. NHSN and INICC methods. RESULTS: We collected prospective data from 94,498 ICU patients for 647,316 bed days. Pooled DA-HAI rates for adult and paediatric ICUs were 11.1 central line-associated bloodstream infections (CLABSIs) per 1000 central line (CL)-days, 21.4 ventilator-associated pneumonias (VAPs) per 1000 mechanical ventilator (MV)-days and 7.5 catheter-associated urinary tract infections (CAUTIs) per 1000 urinary catheter-days. Pooled DA-HAI rates for NICUs were 30 CLABSIs per 1000 CL-days, and 15.8 VAPs per 1000 MV-days. Extra length of stay (LOS) in adult and paediatric ICUs was 19.4 for CLABSI, 8.7 for VAP and 10.1 for CAUTI. Extra LOS in NICUs was 13.1 for patients with CLABSI and 16.2 for patients with VAP. Extra crude mortality was 12% for CLABSI, 19.4% for VAP and 10.5% for CAUTI in ICUs, and 15.4% for CLABSI and 10.5% for VAP in NICUs. Pooled device use (DU) ratios for adult and paediatric ICUs were 0.54 for MV, 0.65 for CL and 0.88 for UC, and 0.12 for MV, and 0.09 for CL in NICUs. The CLABSI rate was 8.5 per 1,000 CL days in the Medical Surgical ICUs included in this study, which is higher than the INICC report rate of 4.9, and more than eight times higher than the NHSN rate of 0.9. Similarly, the VAP and CAUTI rates were higher compared with U.S. NHSN (22.3 vs. 1.1 for VAP; 7.9 vs. 1.2 for CAUTI) and with the INICC report (22.3 vs. 16.5 in VAP; 7.9 vs. 5.3 in CAUTI). CONCLUSIONS: DA-HAI rates and DU ratios in our ICUs were higher than those reported in the INICC global report and in the US NHSN report.

Interaction between caspofungin or voriconazole and cefoperazone-sulbactam or piperacillin-tazobactam by in vitro and in vivo methods.

Immunosuppressive patients are at risk of fungal and bacterial infections. Therefore, these patients receive prophylactic, preemptive, empirical or target antifungal and concomitant antibiotic therapy. To this end, caspofungin (CAS) or voriconazole (VRC) antifungals and cefoperazone-sulbactam (CPZ/SAM) or piperacillin-tazobactam (PIP/TAZ) antibiotics may be used. Here, we aimed to investigate the interaction between these antifungals and antibiotics by in vitro and in vivo methods. The interaction was tested by chequerboard analysis and fractional inhibitory concentration index (FICI). It was also tested in a neutropenic mice-invasive candidiasis model and evaluated by fungal burden in kidney tissue of infected animals from the first day to the fifth day of treatment with 24 h intervals. A synergism was detected between CAS and CPZ/SAM (FICI = 0.1) and PIP/TAZ (FICI = 0.3). Fungal burden in tissues of drug-treated mice was reduced compared with controls in a time-dependent manner. In comparison with CAS-alone treated group, there were 1.32 log10 reductions of fungal burden in CAS + CPZ/SAM (p = 0.002) and in CAS + PIP/TAZ group (p = 0.14). The same interactions were not found with VRC and antibiotics. CPZ/SAM had stronger synergistic interaction with CAS than PIP/TAZ. The mechanism of synergism is not well understood. This is most likely due to an increase in the anticandidal effect of CAS plus antibiotics.

Withdrawal of Staphylococcus aureus from intensive care units in Turkey.

BACKGROUND: In the past, Staphylococcus aureus infections have displayed various patterns of epidemiologic curves in hospitals, particularly in intensive care units (ICUs). This study aimed to characterize the current trend in a nationwide survey of ICUs in Turkey. METHODS: A total of 88 ICUs from 36 Turkish tertiary hospitals were included in this retrospective study, which was performed during the first 3 months of both 2008 (period [P] 1) and 2011 (P2). A P value ≤.01 was considered significant. RESULTS: Although overall rates of hospital-acquired infection (HAI) and device-associated infection densities were similar in P1 and P2, the densities of HAIs due to S aureus and methicillin-resistant S aureus (MRSA) were significantly lower in P2 (P < .0001). However, the proportion of HAIs due to Acinetobacter was significantly higher in P2 (P < .0001). CONCLUSIONS: The incidence of S aureus infections is declining rapidly in Turkish ICUs, with potential impacts on empirical treatment strategies in these ICUs.

[Early detection of methicillin resistance by real-time PCR in staphylococci isolated from blood cultures]. / Kan Kültürlerinde Üreyen Stafilokoklarda Metisilin Direncinin Gerçek Zamanli PCR ile Erken Tanisi

Bacteremia caused by methicillin-resistant Staphylococcus aureus (MRSA) has a significant morbidity and mortality. The aim of this study was to evaluate the efficiency of real-time polymerase chain reaction (Rt-PCR) targeting nuc and mec genes in the culture extracts of blood culture systems for the early diagnosis of MRSA. A total of 48 samples that gave positive growth signal in BACTEC 9000 MB (BD, USA) and stained as gram-positive cocci, were included in the study. The samples were collected between 2009 and 2010. VITEC 2 (bioMerieux, France) system was used for the identification and antibiotic susceptibility testing of the isolates. According to the culture results, 15 of the isolates were methicillin-resistant coagulase-negative staphylococci (MRCNS), four were MRSA, 14 were methicillin-susceptible coagulase- negative staphylococci (MSCNS) and 15 were methicillin-susceptible S.aureus (MSSA). However, Rt-PCR yielded 17 MRCNS, eight MRSA, 10 MSCNS and 13 MSSA results. Our findings indicated lack of concordance between blood culture and PCR technique. When the blood culture results were accepted as the gold standard for the determination of methicillin resistance, sensitivity, specificity, positive and negative predictive values of Rt-PCR were found as 73%, 62%, 56% and 78%, respectively. In conclusion, in contrast to the expectations, Rt-PCR was not considered as an appropriate method for the detection of MRSA in routine diagnosis.

[A case of Crimean-Congo hemorrhagic fever with long incubation period in Kocaeli, Turkey]. / Kocaeli'de Uzun Inkübasyon Süreli Sporadik Kirim-Kongo Kanamali Atesi Olgusu.

Crimean-Congo hemorrhagic fever (CCHF) is a viral hemorrhagic disease with high mortality rate. CCHF is endemic in Central Anatolia and East and Central Black Sea parts of Turkey, however sporadic cases have been detected in the other regions. The incubation period of the disease is between 1-3 days (maximum 12 days). In this report, a very rare CCHF case with a long incubation period of 30 days, was reported. A 40-year-old female patient living in a village of Kocaeli, Turkey was admitted to a health center in June 2010 with the complaints of headache, myalgia, nausea, vomiting, fatigue and fever. Since laboratory results revealed severe thrombocytopenia (18.300/mm3), the patient was referred to the university hospital in Kocaeli. It was learned from her history that she had been working in the garden and removed a tick from the skin of gluteal area a month ago without seeking any medical help. Physical examination of the patient revealed that her general condition was well, oriented and cooperative, body temperature was 36.6°C, pulse 82/minute, trombocyte count 69.400/mm3 and liver enzymes were elevated (ALT: 194 U/L, AST: 499 U/L, GGT: 384 U/L, LDH: 1290 U/L). Petecchial lesions were seen on hard palate and extremities and a hyperemic lesion was detected at the gluteal area where the tick had attached. In-house real-time polymerase chain reaction test for CCHF, performed at Refik Saydam National Public Health Agency, Virology Reference and Research Laboratory, revealed positive result. This case was presented to withdraw attention to a long incubation period CCHF and also of its epidemiological importance since it was the first case in Kocaeli province, Turkey.

[Comparison of broth microdilution and E-test methods for the antifungal susceptibility testing of Candida spp. strains isolated from blood cultures]. / Kan kültürlerinden izole edilen Candida spp. suslarinin antifungal ilaçlara karsi duyarliliklarinin belirlenmesinde buyyon mikrodilüsyon ile E-test yöntemlerinin karsilastirilmasi.

The incidence of serious fungal infections, particularly invasive Candida infections exhibit an increasing trend in the last decades since the number of patients receiving immunosuppressive treatment is increasing. This situation eventually results in an increment in resistance to antifungal agents. The aim of this study was to compare the standard broth microdilution (BMD) and E-test methods for antifungal susceptibility testing of Candida species isolated from blood cultures in our hospital, against fluconazole, voriconazole, caspofungin and amphotericin B. A total of 46 Candida strains isolated from the blood cultures by BACTEC 9000 (Becton Dickinson, USA) and identified by conventional techniques and API 20C AUX (BioMerieux, France) during January 2006-December 2007, were included into this study. The identification results of the isolates were as follows: C. albicans (23), C. parapsilosis (10), C. tropicalis (5), C. krusei (3), C. famata (2), C. glabrata (1), C. guilliermondii (1), C. kefyr (1). The antifungal susceptibilities were determined by BMD method described in Clinical and Laboratory Standards Institute M27-A3 document and E-test. Only two isolates (C. albicans and C. globrata) were found to be resistant to fluconazole with E-test but susceptible with BMD. The minimal inhibitory concentration (MIC) values of caspofungin were higher (MIC = 1-2 microg/ml) in C. parapsilosis compared to other Candida species using E-test. Only one C. albicans was resistant to voriconazole by E-test (MIC = 4 microg/ml), but it was susceptible by BMD (MIC = 0.08 microg/ml). Since definite resistance breakpoints do not yet exist for amphotericin B, MIC values were considered for amphotericin B and it was found that all strains had identical low MIC values (< 0.002-0.5). When E-test results were compared with the standard BMD results, MIC values were in agreement 80.4% for fluconazole, 84.7% for amphotericin B, 95.6% for voriconazole and 93.4% for caspofungin. These results indicated that the most frequently isolated Candida species among blood cultures was C. albicans, followed by C. parapsilosis and these isolates had low antifungal resistance rates. When voriconazol and caspofungin susceptibilities were considered, both E-test and BMD susceptibility results were in good aggreement in comparison to fluconazol and amphotericin B. E-test can be considered as a compatible method for the antifungal susceptibility testing of Candida species compared to standard broth microdilution method.

Pseudo-outbreak of Serratia marcescens in a tertiary care hospital.

The aim of this study was to describe a pseudo-outbreak due to Serratia marcescens associated with laboratory contamination, and also the epidemiologic and laboratory methods used to determine the source of contamination. An apparent increase in positive culture results for Serratia marcescens was observed in the Clinical Microbiology Laboratory of Kocaeli University Hospital between September and November 2007. An outbreak investigation including retrospective and prospective studies using chart review, environmental sampling and random arbitrary polymorphic DNA-polymerase chain reaction (RAPD-PCR) of randomly selected isolates were performed by the Infection Control Committee. Nine out of 67 strains belonged to a real infection. S. marcescens was also isolated from saline solution in the specimen processing area of the laboratory. It was recognized that the technician has been using the same stock saline solution for processing specimens without changing the injector. RAPD patterns of the clinical isolates were identical to the pattern of saline strain. The contaminated saline solution was discarded, the technician was trained and no additional cases of suspected contamination have been observed. This pseudo-outbreak emphasize the importance of the observation of specimen processing procedures and the training of laboratory workers.

The relationship between chronic otitis media with effusion and surface and deep flora of hypertrophic adenoids.

OBJECTIVE: The relationship between bacterial flora of the adenoids and middle ear problems is unclear. In this study, superficial and deep aerobic and anaerobic bacterial flora of adenoid tissues were compared in children with and without chronic otitis media with effusion (cOME). PATIENTS AND METHODS: Between 2004 and 2007, family members of children (ages 1-14 years) who were scheduled to undergo adenoidectomy were approached for participation in the study. Of the 180 patients who gave consent, 107 (59%) did not have cOME (Group I), whereas 73 (41%) had had a tympanostomy tube previously due to cOME (Group II). Prior to adenoidectomy, swabs were taken from the surface of the adenoids, and samples of deep tissue for culture were obtained from curetted tissue. All samples were cultured aerobically and anaerobically. Growth of 10 of the bacteria most commonly cultured were evaluated: 5 classified as normal flora (coagulase-negative staphylococci, α-hemolytic streptococci, Neisseria spp., Prevotella spp. ve Peptostreptococci) and 5 potential pathogens (S. aureus, S. pyogenes, S. pneumoniae, H. influenzae ve Moraxella spp.). RESULTS: Isolation rates of potential pathogens including S. pneumoniae,H. influenzae and Moraxella spp. from surface and deep cultures of adenoids were between 5 and 15% (no significant differences between those with and without cOME). While S. aureus was the most frequently isolated bacteria (26%) in children with cOME (Group II), the incidence of S. pyogenes as a potential pathogen was only 1% (p<0.05) in Group II and the anaerobic Prevotella spp. were significantly less common (p<0.05) in children with cOME (Group II). CONCLUSION: Potential pathogens of middle ear colonized in adenoid tissue may not be significant factor for the etiopathogenesis of cOME. Bacterial interference mechanisms may play an important role in pathogenesis of cOME because of Prevotella spp. showed statistically significant decrease children with cOME.

[Analysis of the results of NEQAS international external quality assessment programme for hepatitis B and C virus nucleic acid tests]. / Hepatit B ve C virus nükleik asit testlerinde NEQAS uluslararasi dis kalite kontrol degerlendirme programi sonuçlarinin analizi.

External quality assessment (EQA) has been playing an increasingly important role in the implementation of nucleic acid amplification techniques (PCR) for clinical diagnosis. In this study, the results of HBV-DNA quantification and HCV-RNA detection tests evaluated by United Kingdom National External Quality Assessment Scheme for Microbiology (NEQAS) were analysed and the performance of our laboratory was evaluated. Between April 2006-January 2008, in four different distribution panels including 16 freeze-dried serum and six plasma specimens for HBV-DNA and HCV-RNA testing, respectively, were received. Viral nucleic acids were extracted by magnetic particle technology (NucliSENS-easyMAG, bioMérieux, Boxtel, Holland). HBV-DNA and HCV-RNA tests were performed by Fluorion HBV quantitative v2.0 and Fluorion HCV quantitative v2.1 (lontek AS, Istanbul, Turkey) kits in real-time PCR (iCycler IQ v3.0a - BioRad Laboratories, Hercules, CA, USA) platform. The performance scores of all the quantification tests of HBV-DNA were 2 (completely correct result) and a strong correlation (r= 0.987) between the quantitative HBV data and the target values was found by linear regression analysis. The NEQAS scores of HCV-RNA testing, except for a false negative result (since the viral load in this specimen was very low--79 IU/ml--it was not scored by NEQAS), were 2 in all specimens. The evaluation of the data revealed 100% detection in HBV-DNA and 83.3% detection in HCV-RNA. In conclusion, the results of this study showed high accuracy of HBV quantification in the samples of HBV infected patients under antiviral therapy. However, the analytical sensitivity of HCV-RNA quantitative kit should be improved for the purpose of reliable HCV-RNA results. External quality control panels are important tools for monitoring the quality of diagnostic laboratory tests. Therefore, PCR laboratories should always have EQA in routine procedures.

[Elimination of PCR inhibitors in routine diagnostic real-time PCR assay and results of internal amplification control]. / Rutin gerçek zamanli PCR tani testlerinde PCR inhibitörlerinin eliminasyonu ve internal amplifikasyon kontrol sonuçlari.

Polymerase chain reaction (PCR) inhibitors which can be found in the clinical specimens lead to increased cost of these tests and also cause delay in the results particularly in the routine laboratories. Lysis/dilution methods are effective on the removal of PCR inhibitors and the performance of internal amplification control (IAC). This study was aimed to evaluate the effects of some methods, such as lysis (freezing and thawing) and dilution (1/10) of serum samples, used for the removal of PCR inhibitors, on IAC results. This evaluation was done by investigating the results of 1440 HCV-RNA and 2754 HBV-DNA (Fluorion HCV QNP and HBV QNP; Iontek, Turkey) tests that were performed in our laboratory during January 2005-October 2006 period. The nucleic acid isolation was done by "spin colon" (Qiagen, QIAamp DNA Mini Kit, Germany) and "magnetic particle" (Qiagen, BioRobot EZ1, Germany) technologies and PCR was performed by real-time PCR (iCycler IQ - BioRad Lab., USA). False negative IAC was detected in 211 samples during HCV-RNA tests and correct results were obtained in 66.4% of these when inhibitors were removed by lysis in 121 and by serum dilution in 19 of the samples. For HBV-DNA tests false negative IAC was detected in 15 samples and application of lysis method yielded correct results in 73.3% (11/15) of these. By the application of inhibitor removal methods the rate of false negative IAC decreased from 14.6% to 4.9% (71/1440) in HCV PCR and from 0.5% to 0.1% (4/2754) in HBV PCR. These data indicated that lysis/dilution methods were simple, economical and effective methods that could be used in routine PCR laboratories for the removal of PCR inhibitors and to achieve effective IAC.

Genotyping of Brucella melitensis by rpoB gene analysis and re-evaluation of conventional serotyping method.

In Turkey, where brucellosis is endemic, a comparison of conventional and molecular genotyping methods has not been published to date. In this study, we investigated the efficacy of single nucleotide polymorphism (SNP) analysis of rpoB gene in the genotyping of Brucella melitensis strains by sequencing. In light of the molecular genotyping method available now in Turkey, the adequacy of serological typing alone should be re-evaluated as a tool for epidemiologic studies of B. melitensis.