scholarly journals Comparative performance and cycle threshold values of 10 nucleic acid amplification tests for SARS-CoV-2 on clinical samples

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252757
Author(s):  
Miyuki Mizoguchi ◽  
Sohei Harada ◽  
Koh Okamoto ◽  
Yoshimi Higurashi ◽  
Mahoko Ikeda ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Performance ◽  
Nucleic Acid Amplification ◽  
Clinical Samples ◽  
Nucleic Acid Amplification Tests ◽  
Cycle Threshold ◽  
E Gene ◽  
Viral Copy Number ◽  
Gene Test ◽  
Positive Results

Background A number of nucleic acid amplification tests (NAATs) for SARS-CoV-2 with different reagents have been approved for clinical use in Japan. These include research kits approved under emergency use authorization through simplified process to stabilize the supply of the reagents. Although these research kits have been increasingly used in clinical practice, limited data is available for the diagnostic performance in clinical settings. Methods We compared sensitivity, specificity, and cycle threshold (Ct) values obtained by NAATs using 10 kits approved in Japan including eight kits those receiving emergency use authorization using 69 frozen-stored clinical samples including 23 positive samples with various Ct values and 46 negative samples. Results Viral copy number of the frozen-stored samples determined with LightMix E-gene test ranged from 0.6 to 84521.1 copies/μL. While no false-positive results were obtained by any of these tests (specificity: 100% [95% CI, 88.9%-100%]), sensitivity of the nine tests ranged from 68.2% [95% CI, 45.1%-86.1%] to 95.5% [95% CI, 77.2%-99.9%] using LightMix E-gene test as the gold standard. All tests showed positive results for all samples with ≥100 copies/μL. Significant difference of Ct values even among tests amplifying the same genetic region (N1-CDC, N2) was also observed. Conclusion Difference in the diagnostic performance was observed among NAATs approved in Japan. Regarding diagnostic kits for emerging infectious diseases, a system is needed to ensure both rapidity of reagent supply and accuracy of diagnosis. Ct values, which are sometimes regarded as a marker of infectivity, are not interchangeable when obtained by different assays.

Evaluation of the Luminex xTAG Gastrointestinal Pathogen Panel and the Savyon Diagnostics Gastrointestinal Infection Panel for the detection of enteric pathogens in clinical samples

2014 ◽  
Vol 63 (11) ◽  
pp. 1419-1426 ◽  
Author(s):  
Michael D. Perry ◽  
Sally A. Corden ◽  
Robin A. Howe
Keyword(s):  
Nucleic Acid ◽  
Detection Rate ◽  
Positive Sample ◽  
Nucleic Acid Amplification ◽  
Clinical Samples ◽  
Detection Rates ◽  
Nucleic Acid Amplification Tests ◽  
Gastrointestinal Pathogen ◽  
Conventional Methods ◽  
Culture Positive

Infectious gastrointestinal disease is caused by a diverse array of pathogens, and is a challenging syndrome to correctly diagnose and manage. Conventional laboratory diagnostic methods are often time-consuming and frequently suffer from low detection rates. Two commercial multiplex nucleic acid amplification tests [Luminex xTAG Gastrointestinal Pathogen Panel (GPP) and Savyon Diagnostics Gastrointestinal Infection Panel (GIP)] were applied to 1000 stored diarrhoeal clinical stool samples. The Luminex xTAG GPP and Savyon GIP detected Campylobacter in 42/44 and 44/44 culture-positive samples, Salmonella in 4/4 and 3/4 culture-positive samples, Shigella in 1/1 culture-positive sample, Clostridium difficile toxin in 32/35 ELISA-positive samples, and Giardia in 6/6 wet-preparation-microscopy-positive samples, respectively. When the Luminex GPP assay was used concurrently with conventional methods for 472 clinical samples, it detected Campylobacter in 22/22 culture-positive samples, Salmonella in 1/1 culture-positive sample, Clostridium difficile toxin in 14/14 ELISA-positive samples and Giardia in 4/4 wet-preparation-microscopy-positive samples. The pathogen/toxin detection rate for conventional methods in both sample sets was <10 %. The Luminex xTAG GPP detection rate was 24.8 % in the stored samples and 32.6 % in the concurrently tested samples. The Savyon GIP detection rate was 22.5 %. From stored samples, 2.4 % of Luminex xTAG GPP detections and 3.1 % of Savyon GIP detections could not be confirmed using alternative nucleic acid amplification tests. Enhanced detection rates resulted from increased detection of pathogens routinely sought using conventional methods and were also due to ascertainment of micro-organisms that current testing strategies do not diagnose. Use of multiplex nucleic acid amplification tests will allow clinical laboratories to diagnose infectious gastroenteritis in more patients with diarrhoeal disease by increasing the sensitivity of pathogen detection and by reducing the selective bias of current strategies. The clinical and economic impact of these results warrants further investigation.

scholarly journals Classical and molecular methods for diagnosis of Chlamydia trachomatis infections

2011 ◽  
Vol 64 (9-10) ◽  
pp. 477-480 ◽  
Author(s):  
Snezana Tomanovic ◽  
Slobodanka Djukic
Keyword(s):  
Nucleic Acid ◽  
Chlamydia Trachomatis ◽  
Deoxyribonucleic Acid ◽  
Nucleic Acid Amplification ◽  
Clinical Samples ◽  
Direct Immunofluorescence ◽  
Nucleic Acid Amplification Tests ◽  
Chlamydia Trachomatis Infection ◽  
Culture Cells ◽  
Chlamydial Infections

Introduction. Genital Chlamydia trachomatis infection is the leading cause of bacterial sexually transmitted diseases in industrial countries, particularly among young people. The consequences of chlamydial infections may involve pelvic inflammatory disease, ectopic pregnancy and tubal factor infertility. Methods. Available tests for detection of chlamydia in men and women include culture in tissue culture cells, direct immunofluorescence test, enzyme immune assay, nucelic acid probe hibridization and polymerase chain reaction. Nucleic acid amplification tests use different ribonucleic and deoxyribonucleic acid regions as target molecules for amplifying Chlamydia trachomatis ribonucleic/deoxyribonucleic acid in clinical samples. Nucleic acid amplification tests are more sensitive than non-nucleic acid amplification tests. Conclusion. Although screening programmes exist in a number of countries, the continuously increasing prevalence of chlamydial infections demonstrates the necessity for defining the best method for the diagnosis and the population for screening.

scholarly journals Is it time to move to nucleic acid amplification tests screening for pharyngeal and rectal gonorrhoea in men who have sex with men to improve gonorrhoea control?

Sexual Health ◽  
2011 ◽  
Vol 8 (1) ◽  
pp. 9 ◽  
Author(s):  
Christopher K. Fairley ◽  
Marcus Y. Chen ◽  
Catriona S. Bradshaw ◽  
Sepehr N. Tabrizi
Keyword(s):  
Nucleic Acid ◽  
Antimicrobial Resistance ◽  
Sexual Health ◽  
Nucleic Acid Amplification ◽  
Nucleic Acid Amplification Tests ◽  
Health Clinics ◽  
Sex With Men ◽  
Sexual Health Clinics

The use of nucleic acid amplification tests (NAAT), as well as or in preference to culture for non-genital sites is now recommended both in Australia and overseas because of their greater sensitivity and improved specificity. A survey of 22 Australian sexual health clinics who each year test over 14 500 men who have sex with men (MSM) show that culture remains the predominate method for detecting gonorrhoea at pharyngeal (64%) and rectal (73%) sites. This editorial discusses the potential disadvantages of using culture over NAAT in relation to optimal gonorrhoea control among MSM and advocates that significantly improved control would be achieved by moving to NAAT with the proviso that culture samples are taken wherever possible on NAAT-positive samples and from clients with urethritis to ensure continued surveillance for antimicrobial resistance.

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