Clinical Evaluation of a Rapid Reciprocal-Flow PCR Assay and Real-Time PCR Assay with Quenching Probe for Detection of Complex

Overview

Journal Microorganisms

Date 2025 Jan 25

PMID 39858969

Authors

Kosuke Kosai

Keisuke Matsumoto

Takahisa Ishikawa

Yasuhide Kawamoto

Norihiko Akamatsu

Kenji Ota

Fujiko Mitsumoto-Kaseida

Norihito Kaku

Hiroo Hasegawa

Koichi Izumikawa

Hiroshi Mukae

Katsunori Yanagihara

Affiliations

Soon will be listed here.

Abstract

This study investigated the diagnostic efficiencies of two assays for the detection of complex: (1) the reciprocal-flow real-time polymerase chain reaction (PCR)-based GeneSoC assay and (2) the real-time PCR based GENECUBE MTB assay with quenching probe. These assays were performed for stored clinical samples and results were compared with the confirmed results based on culture and COBAS TaqMan MTB assay. A total of 53 samples (20 confirmed positives and 33 confirmed negatives) were included in the performance analysis. The GeneSoC assay showed concordance in all 53 samples, regardless of specimen type, while the GENECUBE MTB assay showed concordance in 19 of the 20 confirmed positive samples and all 33 confirmed negative samples. The overall agreement was 100.0% for the GeneSoC assay and 98.1% for the GENECUBE MTB assay. Positive and negative percent agreements were 100.0% each for the GeneSoC assay and 95.0% and 100.0%, respectively, for the GENECUBE MTB assay. Both the GeneSoC and GENECUBE MTB assays exhibited excellent performance in detecting complex. The GeneSoC assay is useful for independent assays of individual samples, whereas the GENECUBE MTB assay is suitable for batch assays of multiple samples.

References

Hara T, Suzuki H, Oyanagi T, Koyanagi N, Ushiki A, Kawabata N . Clinical evaluation of a non-purified direct molecular assay for the detection of Clostridioides difficile toxin genes in stool specimens. PLoS One. 2020; 15(6):e0234119. PMC: 7269250. DOI: 10.1371/journal.pone.0234119. View

Ito Y, Iwashima S, Hayano S, Nishio T, Shiozawa R, Yata S . Rapid Detection of the Macrolide Sensitivity of Pneumonia-Causing Mycoplasma pneumoniae Using Quenching Probe Polymerase Chain Reaction (GENECUBE). Mol Diagn Ther. 2018; 22(6):737-747. DOI: 10.1007/s40291-018-0360-x. View

Hida Y, Uemura K, Sugimoto H, Kawashima Y, Koyanagi N, Notake S . Evaluation of performance of the GENECUBE assay for rapid molecular identification of Staphylococcus aureus and methicillin resistance in positive blood culture medium. PLoS One. 2019; 14(7):e0219819. PMC: 6634395. DOI: 10.1371/journal.pone.0219819. View

Park K, Kim J, Lee J, Hwang Y, Jeon K, Koh W . Comparison of the Xpert MTB/RIF and Cobas TaqMan MTB assays for detection of Mycobacterium tuberculosis in respiratory specimens. J Clin Microbiol. 2013; 51(10):3225-7. PMC: 3811628. DOI: 10.1128/JCM.01335-13. View

Yoshida S, Tsuyuguchi K, Kobayashi T, Shimatani Y, Inoue Y . Effect of sputum quality on Mycobacterium avium-intracellulare complex lung disease diagnosis and treatment initiation according to disease type. Diagn Microbiol Infect Dis. 2022; 104(3):115773. DOI: 10.1016/j.diagmicrobio.2022.115773. View

Watanabe R, Asai S, Kakizoe H, Saeki H, Masukawa A, Miyazawa M . Evaluation of the basic assay performance of the GeneSoc® rapid PCR testing system for detection of severe acute respiratory syndrome coronavirus 2. PLoS One. 2021; 16(3):e0248397. PMC: 8009387. DOI: 10.1371/journal.pone.0248397. View

Yang Y, Lu P, Huang S, Jenh Y, Jou R, Chang T . Evaluation of the Cobas TaqMan MTB test for direct detection of Mycobacterium tuberculosis complex in respiratory specimens. J Clin Microbiol. 2010; 49(3):797-801. PMC: 3067742. DOI: 10.1128/JCM.01839-10. View

Ota K, Kurahara R, Tsukamoto C, Kawamoto Y, Akamatsu N, Sasaki D . Performance of the GeneSoC Rapid PCR System in Detection of SARS-CoV-2 from Saliva Specimens. Microbiol Spectr. 2023; :e0325922. PMC: 10101093. DOI: 10.1128/spectrum.03259-22. View

Hida Y, Hisada K, Shimada A, Yamashita M, Kimura H, Yoshida H . Rapid detection of the Mycobacterium tuberculosis complex by use of quenching probe PCR (geneCube). J Clin Microbiol. 2012; 50(11):3604-8. PMC: 3486240. DOI: 10.1128/JCM.01654-12. View

10.

Lee M, Chung K, Wang H, Lin C, Yu C, Lee J . Evaluation of the Cobas TaqMan MTB real-time PCR assay for direct detection of Mycobacterium tuberculosis in respiratory specimens. J Med Microbiol. 2013; 62(Pt 8):1160-1164. DOI: 10.1099/jmm.0.052043-0. View

11.

Takata M, Nakamoto M, Kitaura T, Okada K, Tsuneki-Tokunaga A, Yamasaki A . Rapid Multiplex RT-PCR for Influenza A and B by Genesoc, a Microfluidic PCR System. Yonago Acta Med. 2023; 66(2):223-231. PMC: 10203650. DOI: 10.33160/yam.2023.05.007. View

12.

Kim J, Kim Y, Ki C, Kim J, Lee N . Evaluation of Cobas TaqMan MTB PCR for detection of Mycobacterium tuberculosis. J Clin Microbiol. 2010; 49(1):173-6. PMC: 3020466. DOI: 10.1128/JCM.00694-10. View

13.

Bloemberg G, Voit A, Ritter C, Deggim V, Bottger E . Evaluation of Cobas TaqMan MTB for direct detection of the Mycobacterium tuberculosis complex in comparison with Cobas Amplicor MTB. J Clin Microbiol. 2013; 51(7):2112-7. PMC: 3697670. DOI: 10.1128/JCM.00142-13. View

14.

Park J, Huh H, Koh W, Song D, Ki C, Lee N . Performance evaluation of the Cobas TaqMan MTB assay on respiratory specimens according to clinical application. Int J Infect Dis. 2017; 64:42-46. DOI: 10.1016/j.ijid.2017.08.014. View

15.

Murata M, Kosai K, Akamatsu N, Matsuyama Y, Oda M, Wakamatsu A . Diagnostic Performance of BD Phoenix CPO Detect Panels for Detection and Classification of Carbapenemase-Producing Gram-Negative Bacteria. Microbiol Spectr. 2023; 11(3):e0089723. PMC: 10269800. DOI: 10.1128/spectrum.00897-23. View

16.

Chen J, Lam H, Yip C, Wong S, Chan J, Ma E . Clinical Evaluation of the New High-Throughput Luminex NxTAG Respiratory Pathogen Panel Assay for Multiplex Respiratory Pathogen Detection. J Clin Microbiol. 2016; 54(7):1820-1825. PMC: 4922091. DOI: 10.1128/JCM.00517-16. View

17.

Kosai K, Akamatsu N, Ota K, Mitsumoto-Kaseida F, Sakamoto K, Hasegawa H . BioFire FilmArray Pneumonia Panel enhances detection of pathogens and antimicrobial resistance in lower respiratory tract specimens. Ann Clin Microbiol Antimicrob. 2022; 21(1):24. PMC: 9166201. DOI: 10.1186/s12941-022-00512-8. View

18.

Furutani S, Naruishi N, Hagihara Y, Nagai H . Development of an on-site rapid real-time polymerase chain reaction system and the characterization of suitable DNA polymerases for TaqMan probe technology. Anal Bioanal Chem. 2016; 408(20):5641-9. DOI: 10.1007/s00216-016-9668-8. View

19.

Chin K, Sarmiento M, Norazmi M, Acosta A . DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb). 2018; 113:139-152. DOI: 10.1016/j.tube.2018.09.008. View

20.

Procop G . Laboratory Diagnosis and Susceptibility Testing for Mycobacterium tuberculosis. Microbiol Spectr. 2017; 4(6). DOI: 10.1128/microbiolspec.TNMI7-0022-2016. View