Table 3.
Total cost per sample by process, accounting for error rates
| Throughput in 2014 (n)* | Total per sample in 2014 (£) | 10% fewer samples per year (£) | 10% more samples per year (£) | ||
|---|---|---|---|---|---|
| WGS and routine clinical workflows | |||||
| MGIT culture | 15 265 | 52·39 | 52·90 | 51·97 | |
| Cepheid Xpert MTB/RIF | 617 | 99·66 | 102·35 | 97·44 | |
| WGS workflow only | |||||
| WGS | 2207 | 118·55 | 120·16 | 117·26 | |
| Routine clinical workflows only | |||||
| Identification assays | 2207 | 55·05 | 55·28 | 54·87 | |
| Hain MTBC | 866 | .. | .. | .. | |
| Hain CM/AS | 1341 | .. | .. | .. | |
| MIRU-VNTR | 866 | 107·75 | 110·89 | 105·18 | |
| First-line DST | 866 | 135·47 | 137·12 | 134·13 | |
| Limited second-line DST† | 62 | 93·01 | 93·24 | 92·83 | |
| Second-line DST‡ | 62 | 101·27 | 104·24 | 98·86 | |
| WGS workflow scenarios | |||||
| MGIT culture and WGS | .. | 170·94 | 173·06 | 169·23 | |
| MGIT culture and WGS and first-line DST | .. | 306·41 | 310·18 | 303·36 | |
| MGIT culture and WGS and first-line DST and full second-line DST | .. | 500·68 | 507·66 | 495·05 | |
| Routine clinical workflow scenarios | |||||
| Culture and identification assays | .. | 107·44 | 108·18 | 106·84 | |
| Culture and identification assays and MIRU-VNTR and first-line DST | .. | 350·66 | 356·19 | 346·15 | |
| Culture and identification assays and MIRU-VNTR and first-line DST and full second-line DST | .. | 544·93 | 553·69 | 537·84 | |
| Total workflow costs | |||||
| WGS-based diagnostics | .. | 480·91 | 486·01 | 476·75 | |
| WGS-based diagnostics and first-line and full second-line DST | .. | 539·53 | 545·37 | 534·73 | |
| Routine clinical workflow-based diagnostics | .. | 518·31 | 524·00 | 513·64 | |
Error rates reported in this study: 1% microscopy, 2% MGIT culture, 10% Cepheid Xpert MTB/RIF, <1% species identification (Hain ID), 13% DNA extraction for WGS, 4% WGS, 1% WGS data analysis, 10% MIRU-VNTR, and <1% DST. WGS=whole-genome sequencing. MGIT=Mycobacteria Growth Indicator Tube. MIRU-VNTR=mycobacterial interspersed repetitive unit-variable-number tandem repeat. DST=drug susceptibility testing.
Number reported in the Birmingham reference laboratory (Birmingham, UK) for 2014. Negative tests not counted for Hain GenoType MTBC (Hain Lifescience, Nehren, Germany), Hain GenoType Mycobacterium CM/AS, second-line DST, Hain GenoType MTBDRplus, or Hain GenoType MTBDRsl.
Done at the Birmingham clinical laboratory.
Done at a second reference laboratory (London, UK). Based on staff time, consumables, and equipment only.