Five Years' Evaluation of the BD ProbeTec System for the Direct Molecular Detection of Mycobacterium tuberculosis Complex in Respiratory and Nonrespiratory Clinical Samples.

In this study, Mycobacterium tuberculosis complex was detected by BD ProbeTec ET system in 4716 respiratory and 167 nonrespiratory samples [mostly (98%) smear negative). Sensitivity, specificity, positive and negative predictive values were 81.8%, 98.3, 85.1 and 97.9 for respiratory and 100%, 96.2, 64.7 and 100, for nonrespiratory samples, respectively. Among 149 (3.1%) ProbeTec DTB positive and culture negative samples, 72 (65 respiratory and seven nonrespiratory) (48.3%) were recovered from the patients who were evaluated as having TB infection. The system has been found as useful in early diagnosis of tuberculosis infection in association with the clinical, radiological and histopathological findings.

Species level identification and antifungal susceptibility of yeasts isolated from various clinical specimens and evaluation of Integral System Yeasts Plus.

It is essential to use easy, standard, cost-effective and accurate methods for identification and susceptibility testing of yeasts in routine practice. This study aimed to establish the species distribution and antifungal susceptibility of yeast isolates and also to evaluate the performance of the colorimetric and commercially available Integral System Yeasts Plus (ISYP). Yeast isolates (n=116) were identified by conventional methods and ISYP. Antifungal susceptibility testing was performed by the microdilution method according to the standards of CLSI M27-A3 and ISYP. Candida albicans (50%) was the most common species isolated, followed by C. parapsilosis (25%) (mostly in blood samples). According to the CLSI M27-S3 criteria, resistance rates for amphotericin B, flucytosine, fluconazole, itraconazole, and voriconazole were 0%, 0%, 4.6%, 4.5% and 1.8%, respectively. Resistance for miconazole (MIC >1 mg/L) was found as 17.9%. Sixty-two (53.4%) of the isolates which were analyzed by ISYP showed disagreement with those identified by the conventional methods and API ID 32C identification kit or a specific identification code could not be assigned by ISYP. The performance of ISYP could be indicated as low for all antifungal drugs tested according to the ROC analysis (AUC: 0.28-0.56). As the current version of ISYP displays a poor performance, it is recommended to use the other commercial systems whose results are approved as reliable and in agreement with those of the reference methods in identification and susceptibility testing of yeasts.

[Comparison of proportion method in Löwenstein-Jensen medium with the BACTEC 460 TB system for antimycobacterial susceptibility testing of Mycobacterium tuberculosis isolates]. / Mycobacterium tuberculosis Izolatlarinin Antitüberküloz Ilaçlara Duyarliliginin Saptanmasinda Antibiyotikli Löwenstein-Jensen Besiyerinde Proporsiyon Yönteminin BACTEC 460 TB Sistemi ile Karsilastirilmasi

This study was conducted to compare BACTEC 460 TB system and the proportion method in commercially available and ready to use antibiotic added Löweinstein-Jensen (LJ) medium for susceptibility testing of first line drugs in Mycobacterium tuberculosis complex isolates. A total 238 M.tuberculosis strains isolated from clinical samples in our laboratory between 2006-2010 period were included in the study. Susceptibility testing for streptomycin, isoniazid, rifampicin and ethambutol in commercially provided LJ medium (Salubris Inc., Istanbul) was performed by the proportion method as recommended by the manufacturer, and the results were compared with the results of BACTEC 460 TB (Becton Dickinson, USA) system. Resistance rates of M.tuberculosis strains against streptomycin, isoniasid, rifampicin and ethambutol obtained by BACTEC 460 TB system were 19.7%, 42%, 40.8% and 18%, respectively. Those rates were 22.7%, 38.7%, 37% and 15.5%, respectively, by antibiotic added LJ proportion method. There was no statistically significant difference between the two methods in terms of resistance rates (p> 0.05). The rates of consistency between proportion method in LJ medium and BACTEC 460 TB system for streptomycin, isoniasid, rifampicin and ethambutol susceptibility were found as 85.3%, 92.4%, 95.4% and 92.4%, respectively. When comparing the reporting time (interval between beginning of the process to reporting of the results) of the methods, minimal, maximal and average reporting spans for BACTEC 460 TB system were 5, 12 and 8.08 ± 2.65 days, and 15, 42 and 23.89 ± 6.02 days for the proportion method in LJ medium, respectively, being statistically significant (p= 0.001). It was determined that the sensitivity test results of major antimycobacterial drugs in commercial LJ medium were compatible with the BACTEC 460 TB system. Nonetheless, the rate of incompatible results was higher for STR than the other drugs. Although there has been some disadvantages such as longer reporting time, need for experience in manual processing and visual evaluation, standardized LJ media approved for quality can be used for susceptibility testing of M.tuberculosis in the laboratories which do not have eligible conditions for the establishment of automated systems.

Molecular detection and identification of mycobacterium tuberculosis complex and four clinically important nontuberculous mycobacterial species in smear-negative clinical samples by the genotype mycobacteria direct test.

Although the sensitivity and specificity of nucleic acid amplification assays are high with smear-positive samples, the sensitivity with smear-negative and extrapulmonary samples for the diagnosis of tuberculosis in suspicious tuberculosis cases still remains to be investigated. This study evaluates the performance of the GenoType Mycobacteria Direct (GTMD) test for rapid molecular detection and identification of the Mycobacterium tuberculosis complex and four clinically important nontuberculous mycobacteria (M. avium, M. intracellulare, M. kansasii, and M. malmoense) in smear-negative samples. A total of 1,570 samples (1,103 bronchial aspiration, 127 sputum, and 340 extrapulmonary samples) were analyzed. When we evaluated the performance criteria in combination with a positive culture result and/or the clinical outcome of the patients, the overall sensitivity, specificity, and positive and negative predictive values were found to be 62.4, 99.5, 95.9, and 93.9%, respectively, whereas they were 63.2, 99.4, 95.7, and 92.8%, respectively, for pulmonary samples and 52.9, 100, 100, and 97.6%, respectively, for extrapulmonary samples. Among the culture-positive samples which had Mycobacterium species detectable by the GTMD test, three samples were identified to be M. intracellulare and one sample was identified to be M. avium. However, five M. intracellulare samples and an M. kansasii sample could not be identified by the molecular test and were found to be negative. The GTMD test has been a reliable, practical, and easy tool for rapid diagnosis of smear-negative pulmonary and extrapulmonary tuberculosis so that effective precautions may be taken and appropriate treatment may be initiated. However, the low sensitivity level should be considered in the differentiation of suspected tuberculosis and some other clinical condition until the culture result is found to be negative and a true picture of the clinical outcome is obtained.

Nontuberculous mycobacteria isolated from pulmonary specimens between 2004 and 2009: causative agent or not?

Nontuberculous mycobacteria were identified from 45891 samples of 19553 patients with a prediagnosis of pulmonary tuberculosis between November 2004 and January 2009. Among 10041 (21.9%) culture positive samples, 208 (2.1%) pulmonary samples recovered from 77 individual patients were differentiated as mycobacteria other than tuberculosis (MOTT). Proportion of mycobacteria evaluated as causative agent for clinical infection were found as 0.16% (n = 31), mostly M. avium complex, M. abscessus and M. kansasii. Additionally, M. fortuitum-peregrinum complex, M. simiae, M. szulgai / intermedium and M. scrofulaceum were found as causative agent in 2, 2, 2 and 1 patient, respectively. Identification of infections caused by environmental or opportunistic pathogen mycobacteria is required in rapid and accurate diagnosis, infection control and treatment planning of infections caused by M. tuberculosis complex and/or MOTT.

[Identification of atypical mycobacteria isolated from clinical specimens by line probe assay (LIPA)]. / Klinik örneklerden izole edilen atipik mikobakterilerin "line probe assay" (LIPA) yöntemiyle tanimlanmasi.

The aim of this study was the identification of atypical mycobacteria isolated from various samples of patients prediagnosed as tuberculosis between November 2004 and June 2006 by a commercial polymerase chain reaction (PCR) based reverse hybridization kit (INNO-LiPA Mycobacteria v2, Innogenetics NV, Belgium). A total of 21,060 samples obtained from 9660 patients were included to the study. After decontamination and homogenization processes, the samples were cultivated in automated MGIT Bactec 960 system and the diagnosis of atypical mycobacteria was performed in 4532 (21.5%) culture positive samples with NAP test by using Bactec 460 TB system. After DNA isolation, PCR method was performed by using the primers specific for mycobacterial 16S-23S spacer region. PCR products were then hybridized with the probes specific for Mycobacterium species on nitrocellulose strips according to the recommendations of the manufacturer and evaluated. Additionally, two different versions of another commercial Line Probe Assay (LiPA) kit [GenoType Mycobacterium and GenoType Mycobacterium AS (Additional Species), Hain Lifescience, Germany] were used for the detection of unidentified mycobacterial strains. In our study period, 10 different Mycobacterium species were identified from 44 (1%) respiratory tract samples (sputum, bronchial aspiration fluid, bronchoalveolar lavage) belonging to 30 patients. While repeated atypical mycobacterial growth was found in 13 patients on different days, 17 patients showed atypical mycobacterial growth only in one sample or in separate multiple samples taken within the same day. The species distribution among patients were as follows; M. fortuitum-M. peregrinum complex (n=5), M. intracellulare (n=4), M. avium complex (n=4), M. chelonae complex (n=4), M. gordonae (n=4), M. kansasii (n=3), M. szulgailintermedium (n=2), M. simiae (n=1) and M. scrofulaceum (n=1). Two of four samples which were unidentified by INNO-LiPA and GenoType MTBC were identified as M. szulgai/intermedium by GenoType Mycobacterium AS and the other two were found as unidentified atypical mycobacteria (Mycobacterium spp.). As a result, the frequency of atypical mycobacteria isolated in our hospital was thought to be low, however, species-level identification might be useful for the planning of therapy in such patients. In addition, after NAP test, INNO-LiPA and GenoType Mycobacterium were useful tests in microbiological identification of atypical mycobacteria, and GenoType Mycobacterium AS test could be applied in mycobacterial strains which were not identified by the former assays.