TABLE 2.
Microorganisms detected by sonicate fluid culture and metagenomic analysis
| Data set | Subject category (no. of subjects) | Microbiology results (no. of subjects) | Microorganism(s) detected (no. of subjects): |
|
|---|---|---|---|---|
| In sonicate fluid culture | By using metagenomic analysis of sonicate fluid | |||
| Derivation set | Prosthetic joint infection (103) | Positive sonicate fluid culture and metagenomic detection (57) | ||
| Concordance (44) | Staphylococcus epidermidis (20) | S. epidermidis (20) | ||
| Staphylococcus aureus (11) | S. aureus (11) | |||
| Streptococcus agalactiae (2) | S. agalactiae (2) | |||
| Corynebacterium jeikeium (2) | C. jeikeium (2) | |||
| Staphylococcus lugdunensis (1) | S. lugdunensis (1) | |||
| Staphylococcus caprae (1) | S. caprae (1) | |||
| Enterococcus faecalis (1) | E. faecalis (1) | |||
| Citrobacter koseri (1) | C. koseri (1) | |||
| Serratia marcescens (1) | S. marcescens (1) | |||
| Granulicatella adiacens (1) | G. adiacens (1) | |||
| Corynebacterium striatum (1) | C. striatum (1) | |||
| Candida albicans (1) | C. albicans (1) | |||
| E. faecalis + S. epidermidis (1) | E. faecalis + S. epidermidis (1) | |||
| Partial concordance (11) | ||||
| Additional organism(s) found by sonicate fluid culture or metagenomic detection (7) | S. agalactiae + Peptoniphilus indolicus (1) | S. agalactiae + Peptoniphilus harei (1) | ||
| S. aureus + Porphyromonas sp. (1) | S. aureus (1) | |||
| S. aureus (1) | S. aureus + P. harei (1) | |||
| S. epidermidis (1) | S. epidermidis + Finegoldia magna (1) | |||
| S. aureus + S. epidermidis (1) | S. epidermidis (1) | |||
| Viridans group Streptococcus sp. + Klebsiella oxytoca + Corynebacterium sp. (1) | Streptococcus mitis (1) | |||
| Actinomyces odontolyticus + Peptoniphilus sp. + Anaerococcus vaginalis + S. agalactiae + Enterobacter aerogenes (1) | Actinomyces sp. + P. harei + A. vaginalis + S. agalactiae + Anaerococcus obesiensis (1) | |||
| Group- or genus-level identification only by sonicate fluid culture or metagenomic detection (4) | Cutibacterium acnes (1) | Cutibacterium sp. (1) | ||
| Viridans group Streptococcus sp. (1) | Streptococcus sp. (1) | |||
| S. epidermidis (1) | Staphylococcus sp. (1) | |||
| Corynebacterium amycolatum (1) | Corynebacterium sp. (1) | |||
| Discordance (2) | Pseudomonas aeruginosa (2) | S. epidermidis (2) | ||
| Metagenomic detection and negative sonicate fluid culture (15) | S. aureus (3) | |||
| S. epidermidis (2) | ||||
| Staphylococcus sp. (2) | ||||
| Streptococcus dysgalactiae (1) | ||||
| E. faecalis (1) | ||||
|
Clostridium perfringens (1) G. adiacens (1) |
||||
| Enterobacter cloacae (1) | ||||
| Streptococcus equinus + Streptococcus pasteurianus (1) | ||||
| Streptococcus sp. + Staphylococcus sp. (1) | ||||
| Aerococcus urinae + Peptoniphilus sp. (1) | ||||
| No metagenomic detection with positive sonicate fluid culture (3) | C. jeikeium (1) | |||
| C. striatum (1) | ||||
| P. aeruginosa (1) | ||||
| No metagenomic detection with negative sonicate fluid culture (28) | ||||
| Aseptic failure (101) | Metagenomic detection and negative sonicate fluid culture (5) | S. aureus (1) | ||
| Streptococcus thermophilus (1) | ||||
| Bacteroides fragilis (1) | ||||
| Rothia sp. (1) | ||||
| Facklamia sp. (1) | ||||
| No metagenomic detection and negative sonicate fluid culture (96) | ||||
| Validation set | Prosthetic joint infection (110) | Positive sonicate fluid culture and metagenomic detection (52) | ||
| Concordance (39) | S. epidermidis (16) | S. epidermidis (16) | ||
| S. aureus (5) | S. aureus (5) | |||
| S. agalactiae (3) | S. agalactiae (3) | |||
| S. lugdunensis (2) | S. lugdunensis (2) | |||
| G. adiacens (2) | G. adiacens (2) | |||
| Staphylococcus capitis (1) | S. capitis (1) | |||
| Streptococcus salivarius (1) | S. salivarius (1) | |||
| Enterococcus faecium (1) | E. faecium (1) | |||
| E. faecalis (1) | E. faecalis (1) | |||
| Aggregatibacter aphrophilus (1) | A. aphrophilus (1) | |||
| Bacteroides fragilis (1) | B. fragilis (1) | |||
| Cutibacterium avidum (1) | C. avidum (1) | |||
| C. acnes (1) | C. acnes (1) | |||
| Corynebacterium pyruviciproducens (1) | C. pyruviciproducens (1) | |||
| C. striatum (1) | C. striatum (1) | |||
| S. epidermidis + C. amycolatum (1) | S. epidermidis + C. amycolatum (1) | |||
| Partial concordance (12) | ||||
| Additional organism(s) found by sonicate fluid culture or metagenomic detection (7) | S. epidermidis + E. faecalis + Finegoldia magna (1) | E. faecalis (1) | ||
| S. epidermidis + Bacillus sp. (1) | S. epidermidis (1) | |||
| S. aureus (1) | S. aureus + S. epidermidis (1) | |||
| S. aureus (1) | S. mitis + S. aureus (1) | |||
| F. magna + Enterobacter cloacae (1) | F. magna (1) | |||
| Enterococcus gallinarum (1) | E. gallinarum + Enterococcus saccharolyticus (1) | |||
| S. mitis group (1) | F. magna + Streptococcus oralis (1) | |||
| Group- or genus-level identification only by sonicate fluid culture or metagenomic detection (5) | S. epidermidis (2) | Staphylococcus sp. (2) | ||
| Streptococcus anginosus group (1) | Streptococcus intermedius + Streptococcus constellatus (1) | |||
| S. mitis group (1) | Streptococcus sanguinis (1) | |||
| S. mitis group (1) | Streptococcus gordonii (1) | |||
| Discordance (1) | Staphylococcus pseudintermedius + S. epidermidis (1) | S. aureus (1) | ||
| Metagenomic detection and negative sonicate fluid culture (22) | S. aureus (6) | |||
| S. dysgalactiae (3) | ||||
| S. agalactiae (3) | ||||
| S. epidermidis (1) | ||||
| Staphylococcus sp. (1) | ||||
| Pasteurella multocida (1) | ||||
| G. adiacens (1) | ||||
| Corynebacterium glutamicum (1) | ||||
| Burkholderia sp. (1) | ||||
| E. cloacae (1) | ||||
| Mycoplasma salivarium (1) | ||||
| Streptococcus sp. + S. agalactiae (1) | ||||
| Staphylococcus haemolyticus + E. faecalis (1) | ||||
| No metagenomic detection with positive sonicate fluid culture (3) | C. acnes (1) | |||
| Mycobacterium abscessus (1) | ||||
| S. haemolyticus (1) | ||||
| No metagenomic detection and negative sonicate fluid culture (33) | ||||
| Aseptic failure (94) | Metagenomic detection and negative sonicate fluid culture (10) | S. aureus (5) | ||
| S. mitis (1) | ||||
| S. sanguinis (1) | ||||
| Gemella sp. (1) | ||||
| S. mitis + Streptococcus sp. (1) | ||||
| S. sanguinis + S. aureus (1) | ||||
| No metagenomic detection and negative sonicate fluid culture (84) | ||||