Table 1. Overview of per-sample costs of whole genome sequencing vs conventional methods, by cost type, case studies covering a specified reference period between 2016 and 2019 (n = 8 institutes).
| Case study area | Avian influenza (HPAI) | Influenza A+B | Food-borne pathogensa | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Institution | APHA (UK) | FLI (DE) | EMC (NL) | IZSLER (IT) | INEI-ANLIS (ARG) | MDH (US) | PHAC (CAN) | PHE (UK) | |
| Outbreak or routine surveillance | Outbreak | Outbreak | Routine surveillance | Routine surveillance | Routine surveillance | Routine surveillance | Routine surveillance | Routine surveillance | |
| Number of samples in reference period | 26 | 30 | 630 | 175 | 320 | 1,767 | 8,630 | 15,791 | |
| in 8 months | 3 months | 5 months | 12 months | 12 months | 12 months | 12 months | 12 months | ||
| WGS | |||||||||
| Sequencer used | Illumina MiSeq |
IonTorrent PGM |
Nanopore GridION | Illumina MiSeq | Illumina MiSeq | Illumina MiSeq | Illumina MiSeq | Illumina HiSeq | |
| Batch size for sample processing/sequencing | 1–2 | 6 | 30 | 24 | 12 | 24 | 32 | Processing: 40 | |
| Sequencing: 96 | |||||||||
| Equipment | € 58.53 | € 210.71 | € 2.50 | € 163.49 | € 43.02 | € 29.53 | € 75.90 | € 35.23 | |
| Consumables | € 830.97 | € 254.88 | € 33.52 | € 165.37 | € 104.62 | € 104.40 | € 69.75 | € 53.92 | |
| Staff costs | Professionals | € 39.63 | € 42.60 | € 15.95 | € 52.35 | € 6.85 | € 20.58 | € 61.82 | € 28.30 |
| Technicians | € 87.50 | € 60.19 | € 42.83 | € 13.93 | € 0.00 | € 0.00 | € 7.89 | € 7.15 | |
| Other costs | € 0.00 | € 0.00 | € 3.68b | € 0.00 | € 0.00 | € 0.00 | € 0.00 | € 0.00 | |
| Total per-sample cost WGS | € 1,016.63 | € 568.37 | € 98.48 | € 395.14 | € 154.49 | € 154.51 | € 215.36 | € 124.59 | |
| Conventional methodsc | |||||||||
| Method(s) used | Sanger sequencing (HA/NA analysis) | Sanger sequencing (whole genomed) | PCR; Sanger sequencing (HA/NA); virus isolation; HI; virus neutralisation; NA STAR | Serotyping; PFGE; PCR; MLVA | Biochemical analysis; serotyping; PCR typing; MaldiTOF; PFGE | PFGE; PCR; MaldiTOF | PFGE; biochemical testing; serotyping | PCR; MLVA; MLST; fAFLP; serotyping; phage typing; PFGE; D-tartrate; glucose gas; AMR; biochemistry | |
| Equipment | € 78.55 | (€ 137.35)d | € 2.66 | € 26.04 | n.a. | € 5.84 | € 12.30 | € 7.11 | |
| Consumables | € 21.91 | (€ 360.88)d | € 34.39 | € 20.17 | n.a. | € 32.89 | € 34.95 | € 29.91 | |
| Staff costs | Professionals | € 39.63 | (€ 230.75)d | € 0.38 | € 3.52 | n.a. | € 42.43 | € 6.72 | € 2.92 |
| Technicians | € 150.00 | (€ 107.00)d | € 45.93 | € 25.88 | n.a. | € 0.00 | € 40.32 | € 23.85 | |
| Other costs | € 0.00 | (€ 0.00)d | € 0.00 | € 16.27 | n.a. | n.a. | € 0.00 | € 1.67 | |
| Total per-sample cost conventional methods | € 290.08 | (€ 835.98)d | € 83.36 | € 91.87 | € 46.61 | € 81.16 | € 94.29 | € 65.46 | |
| Cost difference between WGS and conventional methods | |||||||||
| Additional cost WGS | € 726.54 | (− € 267.61)d | € 15.12 | € 303.27 | € 107.88 | € 73.35 | € 121.07 | € 59.13 | |
| Quotient of WGS over conventional methods | 3.5 | 0.7d | 1.2 | 4.3 | 3.3 | 1.9 | 2.3 | 1.9 | |
AMR: antimicrobial resistance; APHA: Animal and Plant Health Agency; ARG: Argentina; CAN: Canada; DE: Germany; EMC: Erasmus Medical Centre; fAFLP: fluorescent amplified fragment length polymorphism; FLI: Friedrich-Loeffler-Institut; HA: haemagglutinin; HI: haemagglutination inhibition; HPAI: highly pathogenic avian influenza; INEI-ANLIS: Instituto Nacional de Enfermedades Infecciosas - Administración Nacional de Laboratorios e Institutos de Salud; IT: Italy; IZSLER: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna; MDH: Maryland Department of Health; MLST: multilocus sequence typing; MLVA: multilocus variable-number tandem repeat analysis; NA: neuraminidase; n.a.: not available; PFGE: pulsed-field gel electrophoresis; PHAC: Public Health Agency Canada; PHE: Public Health England; UK: United Kingdom; US: United States; WGS: whole genome sequencing.
a Salmonella (all), Listeria (IZSLER, PHE, PHAC, MDH), Escherichia coli and Shigella (PHE, INEI-ANLIS, MDH), Campylobacter (PHE, MDH), Vibrio (MDH).
b Costs for supplementary conventional tests that continue to be part of the WGS workflow (virus isolation, HI, virus neutralisation, NA STAR - on a limited number of samples only).
c Note that the cost of conventional methods is a weighted figure which accounts for the use rate of the various methods across the different pathogens.
d Sequencing of a whole genome of a virus using Sanger sequencing – as indicated by FLI as comparator method – is a resource-intensive process that has generally been replaced by next-generation sequencing; Sanger sequencing would typically be used for the (more limited and less resource-intensive) HA/NA analysis (the comparator method used by APHA). The figures from the FLI case study are therefore placed in brackets and are provided for comparison purposes only.