Table 1.
Effect of enrichment methods by metagenomic whole genome sequencing. PJI samples underwent enrichment with either MolYsis or NEBNext microbiome kits prior to metagenomic WGS sequencing. “% of reads indicates” the percentage of all assigned reads attributable to the known pathogen genus as assigned by LMAT relative to the total number of reads. Read numbers are reported in parentheses. “Enrichment factor” indicates the fold increase of percent of assigned reads compared to the unenriched sample.
| No enrichment | NEBNext microbiome DNA enrichment | MolYsis enrichment | |
|---|---|---|---|
| S. aureus PJI | |||
| % of reads | 0.016% (4158 of 25,609,460) | 0.21% (350,625 of 169,981,133) | 7.7% (2,286,890 of 29,530,730) |
| Enrichment factor | 13× | 481× | |
| S. epidermidis PJI | |||
| % of reads | 0.0071% (1682 of 23,606,476) | 0.18% (133,680 of 74,544,475) | 7.0% (2,268,087 of 32,184,381) |
| Enrichment factor | 25× | 986× | |
| E. faecalis PJI | |||
| % of reads | 0.0062% (1671 of 26,949,030) | 0.53% (497,206 of 94,522,959) | 59.4% (16,407,878 of 27,643,294) |
| Enrichment factor | 85× | 9580× |