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Ultra-fast, sensitive and quantitative on-chip detection of group B streptococci in clinical samples

(2019) TALANTA. 192. p.220-225
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Abstract
PCR enables sensitive and specific detection of infectious disease agents, but application in point-of-care diagnostic testing remains scarce. A compact tool that runs PCR assays in less than a few minutes and that relies on mass-producible, disposable reactors could revolutionize while-you-wait molecular testing. We here exploit well-established semiconductor manufacturing processes to produce silicon ultra-fast quantitative PCR (UF-qPCR) chips that can run PCR protocols with limited assay optimization. A total of 110 clinical samples were analyzed for the detection of group B streptococci using both a validated benchtop and an on-chip qPCR assay. For the onchip assay, the total reaction time was reduced after optimization to less than 5 min. The standard curve, spanning a concentration range of S log units, yielded a PCR efficiency of 94%. The sensitivity obtained was 96% (96/100; CI: 90-98%) and the specificity 70% (7/10; CI: 40-90%). We show that if melting analyses would be integrated, the obtained sensitivity would drop slightly to 93% (CI: 86-96%), while the specificity would increase to 100% (CI: 72% - 100%). In comparison to the benchtop reference qPCR assay performed on a LightCycler(C)96, the on-chip assay demonstrated a highly significant qualitative (Spearman's rank correlation) and quantitative (linear regression) correlation. Using a mass-producible qPCR chip and limited assay optimization, we were able to develop a validated qPCR protocol that can be carried out in less than five minutes. The analytical performance of the microchip-based UF-qPCR system was shown to match that of a benchtop assay. This is the first report to provide UF-qPCR validation using clinical samples. We demonstrate that qPCR-based while-you-wait testing is feasible without jeopardizing assay performance.
Keywords
Ultra-fast, qPCR, Clinical samples, On-chip, Silicon, Streptococcus agalactiae, POLYMERASE-CHAIN-REACTION, CONTINUOUS-FLOW PCR, DNA AMPLIFICATION, EXTREME PCR, ASSAY, GUIDELINES, AGALACTIAE, AGREEMENT, CARRIAGE, QPCR

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Citation

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Chicago
Cai, Qing, Maarten Fauvart, Rodrigo Sergio Wiederkehr, Benjamin Jones, Piet Cools, Peter Goos, Mario Vaneechoutte, and Tim Stakenborg. 2019. “Ultra-fast, Sensitive and Quantitative On-chip Detection of Group B Streptococci in Clinical Samples.” Talanta 192: 220–225.
APA
Cai, Q., Fauvart, M., Wiederkehr, R. S., Jones, B., Cools, P., Goos, P., Vaneechoutte, M., et al. (2019). Ultra-fast, sensitive and quantitative on-chip detection of group B streptococci in clinical samples. TALANTA, 192, 220–225.
Vancouver
1.
Cai Q, Fauvart M, Wiederkehr RS, Jones B, Cools P, Goos P, et al. Ultra-fast, sensitive and quantitative on-chip detection of group B streptococci in clinical samples. TALANTA. 2019;192:220–5.
MLA
Cai, Qing, Maarten Fauvart, Rodrigo Sergio Wiederkehr, et al. “Ultra-fast, Sensitive and Quantitative On-chip Detection of Group B Streptococci in Clinical Samples.” TALANTA 192 (2019): 220–225. Print.
@article{8577960,
  abstract     = {PCR enables sensitive and specific detection of infectious disease agents, but application in point-of-care diagnostic testing remains scarce. A compact tool that runs PCR assays in less than a few minutes and that relies on mass-producible, disposable reactors could revolutionize while-you-wait molecular testing. We here exploit well-established semiconductor manufacturing processes to produce silicon ultra-fast quantitative PCR (UF-qPCR) chips that can run PCR protocols with limited assay optimization. A total of 110 clinical samples were analyzed for the detection of group B streptococci using both a validated benchtop and an on-chip qPCR assay. For the onchip assay, the total reaction time was reduced after optimization to less than 5 min. The standard curve, spanning a concentration range of S log units, yielded a PCR efficiency of 94\%. The sensitivity obtained was 96\% (96/100; CI: 90-98\%) and the specificity 70\% (7/10; CI: 40-90\%). We show that if melting analyses would be integrated, the obtained sensitivity would drop slightly to 93\% (CI: 86-96\%), while the specificity would increase to 100\% (CI: 72\% - 100\%). In comparison to the benchtop reference qPCR assay performed on a LightCycler(C)96, the on-chip assay demonstrated a highly significant qualitative (Spearman's rank correlation) and quantitative (linear regression) correlation. Using a mass-producible qPCR chip and limited assay optimization, we were able to develop a validated qPCR protocol that can be carried out in less than five minutes. The analytical performance of the microchip-based UF-qPCR system was shown to match that of a benchtop assay. This is the first report to provide UF-qPCR validation using clinical samples. We demonstrate that qPCR-based while-you-wait testing is feasible without jeopardizing assay performance.},
  author       = {Cai, Qing and Fauvart, Maarten and Wiederkehr, Rodrigo Sergio and Jones, Benjamin and Cools, Piet and Goos, Peter and Vaneechoutte, Mario and Stakenborg, Tim},
  issn         = {0039-9140},
  journal      = {TALANTA},
  keyword      = {Ultra-fast,qPCR,Clinical samples,On-chip,Silicon,Streptococcus agalactiae,POLYMERASE-CHAIN-REACTION,CONTINUOUS-FLOW PCR,DNA AMPLIFICATION,EXTREME PCR,ASSAY,GUIDELINES,AGALACTIAE,AGREEMENT,CARRIAGE,QPCR},
  language     = {eng},
  pages        = {220--225},
  title        = {Ultra-fast, sensitive and quantitative on-chip detection of group B streptococci in clinical samples},
  url          = {http://dx.doi.org/10.1016/j.talanta.2018.09.041},
  volume       = {192},
  year         = {2019},
}

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