[Comparison of Cytomegalovirus Polymerase Chain Reaction Test Results Obtained with Fully Automated Systems: Roche Cobas 6800 and Qiagen NeuMoDx Experience]. / Tam Otomatize Sistemlerde Çalisilan Sitomegalovirüs Polimeraz Zincir Reaksiyonu Test Sonuçlarinin Karsilastirilmasi: Roche Cobas 6800 ile Qiagen NeuMoDx Deneyimi.

Viral load monitoring is important in identifying patients at risk of developing cytomegalovirus (CMV) related complications after transplantation and for this purpose, quantitative real-time polymerase chain reaction (Rt-qPCR) tests are most commonly used. The main problem in CMV DNA Rt-qPCR tests that make quantitative measurements is that there are significant differences in measurements performed with different kits in different laboratories. Comparability of viral load measurements between laboratories has increased with the introduction of quantitative PCR tests calibrated with the CMV International Quantitation Standard (IQS) developed by the World Health Organization (WHO). However, quantitative agreement between measurements made with different kits has still not been fully achieved. In this study, it was aimed to investigate the quantitative compatibility between measurements made with Cobas 6800 (Roche Diagnostics, Mannheim, Germany) and NeuMoDx (Qiagen, Ann Arbor, USA) CMV DNA Rt-qPCR tests, which are fully automated new generation systems calibrated with the WHO CMV IQS. The results of 214 plasma samples, which were studied simultaneously with Cobas 6800 CMV Rt-qPCR and NeuMoDx CMV Rt-qPCR tests were analyzed. In the tests, the extraction, amplification and detection stages were carried out fully automatically. CMV DNA was detected in 144 (67.28%) samples in both tests and was not detected in 53 (24.76%) samples. Incompatible results were obtained in a total of 17 (7.94%) samples. Good agreement was found between the qualitative results of both tests (kappa= 0.80, p< 0.001). When the quantitative results (n= 129) obtained in the dynamic measurement range of both tests were examined, the median viral load values measured by Cobas 6800 CMV Rt-qPCR and NeuMoDx CMV Rt-qPCR tests were 513 IU/mL (range= 35-37000) and 741 IU/mL (range= 68-48978), respectively. According to the correlation analysis, a very strong correlation was found between the results of both tests (r= 0.94, p< 0.001). According to Bland-Altman analysis; the average difference between the results of the NeuMoDx CMV Rt-qPCR test and the Cobas 6800 CMV Rt-qPCR test was found to be -0.14 log10 [standard deviation (SD)= 0.23] IU/mL and it was determined that the Cobas 6800 CMV Rt-qPCR test had lower measurements than the NeuMoDx CMV Rt-qPCR test. In 120 of 129 samples (93%) whose results were within the dynamic measurement range of both tests, the measurement difference was within ± 0.5 log10 IU/mL and in 9 (7%), it was detected as more than ± 0.5 log10 (median 0.54 log10 IU/ml; range= 0.51-0.81). No measurement difference of more than ± 1.0 log10 was detected in any sample. In this study, quantitative agreement was found in the measurements made in plasma samples with the fully automated Cobas 6800 CMV Rt-qPCR and NeuMoDx CMV Rt-qPCR tests calibrated with the CMV IQS. To the best of our knowledge, a study comparing viral load measurements made with Cobas 6800 and NeuMoDx fully automated systems in the detection of CMV DNA has not yet been conducted, and this is the first study on this subject.

Comparison of a novel antigen detection test with reverse transcription polymerase chain reaction assay for laboratory diagnosis of SARS-CoV-2 infection.

Molecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR) in respiratory specimens is considered the gold standard method. This method is highly sensitive and specific but it has some limitations such as being expensive and requiring special laboratory equipment and skilled personnel. RapidFor™ Antigen Rapid Test Kit is a commercially available Ag-RDT which is produced in Turkey and designed to detect the nucleocapsid antigen of SARS-CoV-2 in nasopharyngeal swab samples. The aim of this study was to evaluate the performance of this novel SARS-CoV-2 antigen detection considering the RT-PCR method as the gold standard. Four hundred forty-four nasopharyngeal swab samples which were collected from the patients who met clinical criteria of COVID-19 from ten centers in Turkey between September 2020 and February 2021 were included in the study. All the nasopharyngeal swab samples were tested for SARS-CoV-2 RNA using commercial RT-PCR kits (Bioeksen and A1 Lifesciences, Istanbul, Turkey) according to the manufacturer's instructions. Viral loads were assessed according to the cycle threshold (Ct) values. RapidFor™ SARS-CoV-2 antigen test (Vitrosens Biotechnology, Istanbul, Turkey) was used to investigate the presence of SARS-CoV-2 antigen in all samples following the manufacturer's instructions. Out of 444 nasopharyngeal swab samples tested, 346 (77.9%) were positive and 98 (22.1%) were negative for SARS-CoV-2 RNA by RTPCR. Overall sensitivity of the RapidFor™. Antigen Rapid Test Kit was 80.3% whereas specificity was found to be 87.8%. Positivity rate of rapid antigen test in samples with Ct values over 25 and below 30 was 82.7%, while it increased to 95.7% in samples 20 ≤ Ct < 25 and reached 100% in samples with Ct values below 20. RapidFor™ SARS-CoV-2 Ag test might be a good choice in the screening of symptomatic and asymptomatic patients and their contacts for taking isolation measures early, with advantages over RT-PCR as being rapid, easy and being applicable in every laboratory and even at point of care.

[Investigation of congenital CMV infection with the presence of CMV DNA in saliva samples of new born babies]. / Yenidogan bebeklerin tükürük örneginde CMV DNA varligi ile konjenital CMV enfeksiyonunun arastirilmasi.

Cytomegalovirus (CMV), is the most common cause among congenital infections and is the most seen etiology in long-term sensorineural hearing loss (SNHL) and neurological impairment. Congenital CMV infection (CCMV) was reported in 0.15-2.2% of live-borne neonates in studies from different countries. A significant proportion of infected infants are asymptomatic after birth and might only be detected by routine screening methods during the new born period. The aim of this study was to screen the saliva of live-born neonates with areal-time PCR based method for the detection of CCMV in our hospital. Saliva samples collected in half an hour after birth by dry dacron swabs and were evaluated for CMV DNA (Rt-PCR, Abbott Molecular USA) from 1000 babies born in Ege University Faculty of Medicine Hospital Obstetrics Clinic between October 2015-October 2017. For the confirmation of CCMV, saliva positive newborns were evaluated with the same method for CMV DNA from their urine or blood within 21 days. All newborns were screened for sensorineural hearing tests. Subjects were 497 girls (49.7%) and 503 boys (50.3%), with a mean weight of 3116.8 g and mean of 37.61 birth week. CMV DNA was positive in the saliva of 16 newborns (1.6%). Fourteen newborns were weakly positive for CMV DNA in their saliva and were not confirmed for CCMV infection. Congenital CMV was confirmed in only two (0.2%) with the CMV DNA results in urine and/or blood samples. One of the two newborns with CCMV was symptomatic and had a neurosensorial hearing loss. The other one was asymptomatic. Saliva samples, taken immediately after birth with a noninvasive and easy method for the detection of CMV DNA is very important for diagnosis of CCMV. Positive samples should be confirmed with CMV DNA in urine or blood samples of these newborns. In this study, detection of positivity in saliva samples that were confirmed with other samples of our newborn population for CCMV was 0.2%. The specific diagnosis for CCMV in newborns with a noninvasive and easy collecting sample is important to avoid sequelae and for public health concerns.

Genotype distribution of Mycobacterium tuberculosis in theAegean Region and associated demographic factors

Background/aim: The Aegean Region is the second-ranking region in Turkey according to the Human Development Index and population density and it hosts 1/8 of Turkey's population. Izmir is the largest city of the region, receiving internal migration both from inside and outside the region. The tuberculosis incidence in Izmir is lower than overall in Turkey: 17.7/100,000 in 2011. Our aims were to determine genotypes of Mycobacterium tuberculosis isolates; to explore possible associations between genotypes with case-demographic data, clinical presentation, and antimicrobial susceptibility patterns; and to determine variations in genotype distribution of strains isolated in Ege University Hospital, Izmir. Materials and methods: Forty-nine M. tuberculosis isolates from 49 patients in 1996-2000 and 421 M. tuberculosis isolates from 421 patients in 2009-2014 were spoligotyped. Drug susceptibility testing and demographic data of the 421 isolates were investigated. Chi-square, Student's t, and Mann-Whitney U tests were used for analyses. Results: Among the 470 M. tuberculosis strains, 132 different spoligopatterns were identified and 46 different clusters for 384 strains were determined. The most predominant spoligotypes were ST53 (n = 116; 24.7%) and ST41 (n = 38; 8.1%), followed by ST50 (5.7%), ST284 (4.7%), and ST4 (4.3%), respectively. ST53 was the most predominant type in both sexes. Multidrug resistance (MDR) was determined in 12 isolates, of which six were ST1.Conclusion: As a consequence of worldwide migration and increasing status of HIV-infected hosts, the increasing prevalence of Beijing strains with higher MDR rates may threaten disease control programs. With its increasing trend, ST284 could replace ST41 in the following years in this region.