Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Samples
2.2. Phenotypic Detection and Confirmation by Micro-Array
2.3. Next-Generation Sequencing
2.4. Statistical Methods
3. Results
3.1. DNA Isolation
3.2. Detection of CTX-M-15-ESBL-Producing E. coli
3.3. Statistical Analyses
3.4. Discrepant Results
3.5. Times to Result
4. Discussion
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Phenotypic/Microarray Method | Total | ||
---|---|---|---|
No. (%) Positive | No. (%) Negative | ||
NGS positive | 22 (84.6) | 1 (0.8) | 23 (100) |
NGS negative | 4 (15.4) | 122 (99.2) | 126 (100) |
Total | 26 (100) | 123 (100) | 149 (100) |
Sensitivity (% [No.]) | Specificity (% [No.]) | PPV (% [No.]) | NPV (% [No.]) | |
---|---|---|---|---|
NGS | 85.2 (23) | 100 (122) | 100 (23/23) | 96.8 (122/126) |
Phenotypic/microarray | 96.3 (26) | 100 (122) | 100 (26/26) | 99.2 (122/123) |
Total | 100 (27) | 100 (122) | - | - |
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Peker, N.; Rossen, J.W.A.; Deurenberg, R.H.; Langereis, P.C.; Raangs, E.G.C.; Kluytmans, J.A.; Friedrich, A.W.; Veenemans, J.; Sinha, B. Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis. Microorganisms 2018, 6, 6. https://doi.org/10.3390/microorganisms6010006
Peker N, Rossen JWA, Deurenberg RH, Langereis PC, Raangs EGC, Kluytmans JA, Friedrich AW, Veenemans J, Sinha B. Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis. Microorganisms. 2018; 6(1):6. https://doi.org/10.3390/microorganisms6010006
Chicago/Turabian StylePeker, Nilay, John W. A. Rossen, Ruud H. Deurenberg, Paula C. Langereis, Erwin G. C. Raangs, Jan A. Kluytmans, Alexander W. Friedrich, Jacobien Veenemans, and Bhanu Sinha. 2018. "Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis" Microorganisms 6, no. 1: 6. https://doi.org/10.3390/microorganisms6010006