TABLE 1.
Sonicate fluid samples tested and relative read countsa
| Sample source, sample no. | Site | Microbiology |
No. of reads |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Qiagen REPLI-g single cell kit |
Illustra single cell kit |
Illustra V2 kit |
||||||||||
| Organism in sonicate fluid (concn) | No. of positive tissue cultures | Total | Pathogen reads | Other microbial reads | Total | Pathogen reads | Other microbial reads | Total | Pathogen reads | Other microbial reads | ||
| Culture-positive PJI | ||||||||||||
| 980 | H | Group C Streptococcus (<20) | 1 of 3 | 27,244,012 | 2,694,906 | 103 | 36,576,986 | 286,577 | 556 | 25,754,214 | 3,075,181 | 566 |
| 982 | K | Staphylococcus epidermidis (>100) | 3 of 4 | 28,320,234 | 3,272,895 | 591 | 30,284,116 | 102,934 | 203 | 26,508,366 | 9,539,147 | 17,625 |
| 986 | K | Staphylococcus aureus (<20) | 1 of 5 | 26,835,306 | 26,397 | 77,581 | 28,991,289 | 424 | 308 | 27,391,148 | 168,046 | 240,703 |
| 996 | H | Bacteroides fragilis (>100) | 3 of 3 | 28,388,841 | 155,761 | 4,853 | 28,745,844 | 11,134 | 1,346 | 28,904,638 | 96,154 | 8,140 |
| 1002 | K | Corynebacterium striatum (51–100) | 3 of 3 | 32,165,206 | 536,155 | 2,594 | 27,925,551 | 5,503 | 422 | 32,338,186 | 1,000,810 | 53,019 |
| Culture-negative PJI, 984 | K | Culture negative | 0 of 4 | 31,616,449 | NA | 2,821 | 26,240,307 | NA | 305 | 36,808,230 | NA | 16,974 |
| Aseptic failure | ||||||||||||
| 983 | K | Culture negative | 0 of 3 | 32,924,419 | NA | 278 | 29,076,492 | NA | 522 | 32,128,178 | NA | 45,539 |
| 987 | K | Anaerobic organism (<20) | 1 of 3, Bacillus species | 30,316,155 | NA | 7,628 | 30,587,175 | NA | 265 | 27,955,363 | NA | 655,417 |
| Controls | ||||||||||||
| C. glutamicum | NA | NA | NA | 28,121,822 | 26,912,706 | 2,145 | 28,973,351 | 22,276,446 | 856 | 26,986,400 | 26,149,302 | 1,311 |
| Ringer's solution | NA | NA | NA | 27,488,254 | NA | 24,140 | 29,531,289 | NA | 3,560 | 27,810,322 | NA | 835,014 |
| WGA with no template | NA | NA | NA | 25,669,747 | NA | 6,695 | 53,626,034 | NA | 46,759 | 24,512,662 | NA | 7,818,383 |
Samples are grouped by classification (PJI, prosthetic joint infection). Site indicates the anatomical surgical site (H, hip; K, knee). Microbiology findings include culture results for sonicate fluid as well as accompanying results for intraoperative tissue specimens collected. Sonicate fluid indicates the identified organism as well as the concentration (in number of CFU/10 ml). Total reads were the total number of sequencing reads prior to prefiltering of human reads. Pathogen reads were determined by identifying the number of reads from the identified pathogen's genus, as categorized by LMAT. Other microbial reads were calculated by adding all reads assigned to a genus other than the known pathogen and includes bacterial, viral, fungal, and protozoal reads. NA, not applicable.