TABLE 1.
Interpretation of metagenomic sequencing results by different analytical tools
| Sample | Result(s)a
|
|||||
|---|---|---|---|---|---|---|
| Sonicate fluid culture (CFU/10 ml) | Intraoperative tissue culture | LMAT | CosmosID | One codex | IDbyDNA | |
| Monomicrobial infections | ||||||
| 536 | Corynebacterium jeikeium 20–50 | Cutibacterium acnes 2/4, Staphylococcus saccharolyticus 1/4 | Corynebacterium jeikeium | Corynebacterium jeikeium top hit, did not reach threshold | Corynebacterium jeikeium top hit, did not reach threshold | Corynebacterium jeikeium, Cutibacterium acnes |
| 637 | Aerobic bacterium <20 | Streptococcus viridans group 4/4 | Streptococcus mitis group | Streptococcus species | Streptococcus mitis group; Acinetobacter species | Streptococcus mitis group |
| 656 | Streptococcus agalactiae >100 | 0/4 | Streptococcus agalactiae | Streptococcus agalactiae | Streptococcus agalactiae | Streptococcus agalactiae |
| 782 | Serratia species >100, aerobic bacterium <20 | Serratia species 5/5, Staphylococcus epidermidis 1/5 | Serratia marcescens, Staphylococcus epidermidis | Serratia marcescens | Serratia marcescens, Staphylococcus epidermidis, Aquamicrobium species | Serratia marcescens |
| 814 | Staphylococcus epidermidis 20–50 | Staphylococcus epidermidis 2/4 | Staphylococcus epidermidis | Staphylococcus epidermidis | Staphylococcus epidermidis, Cutibacterium acnes, Streptococcus mitis, Staphylococcus aureus, Staphylococcus warneri, Penicillium citrinum | Staphylococcus epidermidis top hit, did not reach threshold |
| 867 | Staphylococcus aureus >100 | Staphylococcus aureus 5/5, Streptococcus mitis group 1/5, Veillonella species 1/5 | Staphylococcus aureus, Peptoniphilus harei | Staphylococcus aureus, Peptoniphilus harei | Staphylococcus aureus, Peptoniphilus harei | Staphylococcus aureus, Peptoniphilus harei |
| 903 | Staphylococcus epidermidis <20, aerobic bacterium <20 | Staphylococcus epidermidis 2/3 | Staphylococcus epidermidis | Staphylococcus epidermidis top hit, did not reach threshold | Staphylococcus epidermidis, Corynebacterium glutamicum | Staphylococcus epidermidis top hit, did not reach threshold |
| 930 | Streptococcus anginosus >100 | Streptococcus anginosus group 3/3 | Streptococcus anginosus group | Multiple Streptococcus anginosus group species | Multiple Streptococcus anginosus group species | Streptococcus anginosus group |
| 1041 | Mycobacterium abscessus group, not quantified | Mycobacterium abscessus group 2/3 | None identified | None identified | None identified | None identified |
| 1050 | Cutibacterium avidum >100 | Cutibacterium avidum 1/4, small aerobic Gram-positive bacillus 1/4 | Cutibacterium avidum | Cutibacterium avidum, another Propionibacterium species | Cutibacterium avidum | Cutibacterium avidum |
| 1120 | Corynebacterium pyruviciproducens 51–100 | 0/5 | Corynebacterium pyruviciproducens | Corynebacterium pyruviciproducens | Corynebacterium pyruviciproducens, Corynebacterium glutamicum, Acinetobacter junii, Aquamicrobium species, Cutibacterium acnes | Corynebacterium pyruviciproducens |
| Fungal infections | ||||||
| 650 | Candida albicans, not quantified | Candida albicans 3/4, coagulase-negative Staphylococcus species 1/4 | Candida albicans | Candida albicans | Candida albicans top hit, did not reach threshold | Candida albicans |
| 1196 | Candida parapsilosis <20 | Candida parapsilosis 3/3, Cutibacterium acnes 2/3 | Candida parapsilosis | None identified | Candida parapsilosis top hit, did not reach threshold | Candida parapsilosis, Corynebacterium glutamicum |
| Polymicrobial infections | ||||||
| 611 | Streptococcus viridans group >100, Klebsiella oxytoca >100, Gram-positive bacillus resembling Corynebacterium >100 | Klebsiella oxytoca 5/5, Streptococcus viridans group 5/5, Corynebacterium species 5/5, coagulase-negative Staphylococcus species 1/5, Finegoldia magna 1/5, anaerobic Gram-positive coccus 4/5 | Streptococcus viridans group, Klebsiella oxytoca, Corynebacterium species, Staphylococcus epidermidis, Staphylococcus lugdunensis, Finegoldia magna | Streptococcus species, Klebsiella species, Corynebacterium striatum; Finegoldia magna | Streptococcus mitis, Klebsiella oxytoca, Corynebacterium striatum; also Finegoldia magna, Staphylococcus epidermidis, Staphylococcus lugdunensis, Corynebacterium aurimucosum | Streptococcus mitis, Klebsiella oxytoca, Corynebacterium striatum; Staphylococcus epidermidis, Staphylococcus lugdunensis, Finegoldia magna |
| 624 | Finegoldia magna <20, Peptostreptococcus species <20 | Finegoldia magna 5/5, Peptostreptococcus species 1/5 | Finegoldia magna, Anaerococcus prevotii | None identifiedb | Anaerococcus prevotii; Finegoldia magna next top hit, did not reach threshold | Finegoldia magna, Anaerococcus prevotii |
| 863 | Actinomyces odontolyticus >100, Peptoniphilus species >100, Anaerococcus vaginalis >100, Streptococcus agalactiae >100, Enterobacter aerogenes 20–50, small Gram-positive bacillus 20–50, Staphylococcus aureus <20, aerobic bacterium <20 | Actinomyces odontolyticus 3/3, Peptoniphilus species 1/3, Streptococcus agalactiae 3/3, Enterobacter aerogenes 2/3, Staphylococcus aureus 1/3, Trueperella bernardiae 1/3, Pseudomonas aeruginosa 1/3, Corynebacterium striatum 1/3, anaerobic Gram-positive coccus 1/3 | Actinomyces odontolyticus, Peptoniphilus harei, Anaerococcus vaginalis, Streptococcus agalactiae, Enterobacter aerogenes (not Staphylococcus aureus); Anaerococcus obesiensis, Finegoldia magna, Peptoniphilus nanciensis, Varibaculum cambriense | Actinomyces species, Peptoniphilus harei, Anaerococcus vaginalis, Streptococcus agalactiae, Enterobacter aerogenes, Staphylococcus aureus, Anaerococcus obesiensis, Varibaculum cambriense | Actinomyces sp., Peptoniphilus harei, Anaerococcus vaginalis, Streptococcus agalactiae, Staphylococcus aureus, Enterobacter aerogenes, Anaerococcus obesiensis, Varibaculum cambriense, Prevotella nanceiensis, Trueperella bernardiae, Xylanimonas cellulosilytica, Tissierellia bacterium | Actinomyces odontolyticus, Peptoniphilus harei, Anaerococcus vaginalis, Streptococcus agalactiae, Enterobacter aerogenes (not Staphylococcus aureus*), Anaerococcus obesiensis, Trueperella bernardiae, Finegoldia magna, Peptoniphilus nanciensis, Varibaculum cambriense |
| Culture-negative PJIs | ||||||
| 674 | No growth | 0/4 | Aerococcus urinae, Peptoniphilus species, Facklamia languida | Aerococcus urinae, Peptoniphilus species, Clostridiales species | Aerococcus urinae, Peptoniphilus species, Clostridiales species, Cutibacterium acnes, Staphylococcus epidermidis, Acinetobacter baumannii, Lactobacillus iners, Acinetobacter indicus, Actinomyces species | Aerococcus urinae, Peptoniphilus species, Facklamia languida |
| 1094 | No growth | Granulicatella adiacens 1/4 | Granulicatella adiacens | Granulicatella adiacens | Granulicatella adiacens, Cutibacterium acnes, Staphylococcus aureus | Granulicatella adiacens |
| 1116 | No growth | 0/5 | Mycoplasma salivarium | Mycoplasma salivarium | Mycoplasma salivarium | Mycoplasma salivarium |
| 1195 | Corynebacterium tuberculostearicum 1 CFU, aerobic bacterium <20, anaerobic bacterium <20 | Mycobacterium bovis BCG 3/3, Staphylococcus epidermidis 1/3 | Mycobacterium tuberculosis complex | Corynebacterium glutamicumb | Mycobacterium bovis/africanum complex, Corynebacterium glutamicum, Bradyrhizobium species | Mycobacterium tuberculosis complex, Corynebacterium tuberculostearicum |
| Aseptic failures | ||||||
| 641 | No growth | 0/2 | Negative | Negative | Negative | Negative |
| 736 | No growth | 0/3 | Negative | Negative | Negative | Cutibacterium acnes |
| 748 | No growth | 0/3 | Negative | Negative | Bacillus species | Negative |
| 991 | Aerobic bacterium <20 | 0/3 | Negative | Negative | Negative | Staphylococcus epidermidis, Streptococcus mitis |
| Control | ||||||
| LR070516 (Ringer’s) | Not applicable | Not applicable | Negative | Bradyrhizobium 23193 branch | Acinetobacter species | Acinetobacter ursingii, Staphylococcus aureus |
a
Quantitative data reported indicate number of positive cultures/total number collected. Lightface font indicates organisms identified by culture or corroborated by another metagenomic analytical tool. Underlining indicates uncorroborated identifications. Boldface font indicates an organism from culture that was not identified.
b
The indicated organisms (Anaerococcus hydrogenalis for sample 624 and M. bovis for sample 1195) were the organisms detected at the next highest levels in the “unfiltered” results.