TABLE 1.
Clinical and biological data of the 34 positive samples detected positive with Sanger sequencing of the 16S rRNA gene (Sanger 16S) and/or shotgun metagenomics (SMg).
| Suspected type of infection (%;n/N)* | Sample type | Antibiotic therapy** | Identification by SMg | Identification by Sanger 16S | Clinical diagnosis |
| Bone and joint (48.5%; 16/33) | Joint fluid | N | Klebsiella pneumoniae | Negative | Septic arthritis |
| Joint fluid (Knee) | Y | Mycoplasma hominis | Mycoplasma hominis | Septic arthritis | |
| Joint fluid (Knee) | N | Neisseria meningitidis | Neisseria meningitidis | Septic arthritis | |
| Joint fluid | N | Staphylococcus aureus | Staphylococcus aureus | Septic arthritis | |
| Joint fluid | Y | Streptococcus dysgalactiae | Streptococcus dysgalactiae | Septic arthritis | |
| Joint fluid (Knee) | Y | Negative | Streptococcus sp.C Moraxella sp.C | Microcrystalline arthritis | |
| Biopsy (Tissue: sternum) | N | Corynebacterium sp.C | Negative | Non-documented infection | |
| Biopsy (Tissue: hip) | N | Cutibacterium acnes | Negative | Prosthetic joint infection | |
| Biopsy (Tissue: hip) | Y | Escherichia coli | Escherichia coli | Prosthetic joint infection | |
| Biopsy (Tissue: elbow) | Y | Mycobacterium tuberculosis | Negative | Osteoarthritis | |
| Biopsy (Tissue: foot) | Y | Staphylococcus aureus | Staphylococcus aureus | Osteoarthritis | |
| Biopsy (Tissue: spine) | N | Staphylococcus aureus | Staphylococcus aureus | Prosthetic joint infection | |
| Biopsy (Tissue) | Y | Negative | Streptococcus sp. | Septic arthritis | |
| Abscess | N | Cutibacterium acnes | Cutibacterium acnes | Prosthetic joint infection | |
| Abscess (Knee) | Y | Negative | Pseudomonas fluorescens groupC | Non-documented septic arthritis | |
| Abscess (Psoas) | Y | Staphylococcus aureus | Staphylococcus aureus | Vertebral osteomyelitis | |
| Cardiovascular (61.9%; 13/21) | Biopsy (Tissue: aortic aneuvrysm) | Y | Bacteroides fragilis | Bacteroides fragilis | Endocarditis |
| Biopsy (Tissue: vegetation) | N | Bartonella quintana | Bartonella sp. | Endocarditis | |
| Biopsy (Tissue: vegetation) | Y | Enterococcus faecalis | Enterococcus sp. | Endocarditis | |
| Biopsy (Tissue: vegetation) | Y | Staphylococcus aureus | Staphylococcus sp. | Endocarditis | |
| Biopsy (Tissue: aortic valve) | Y | Staphylococcus epidermidis | Negative | Endocarditis | |
| Biopsy (Tissue: valve prosthesis) | N | Streptococcus anginosus | Streptococcus milleri group | Endocarditis | |
| Biopsy (Tissue: vegetation) | Y | Streptococcus dysgalactiae | β-haemolytic Streptococcus | Endocarditis | |
| Biopsy (Tissue: mitral valve) | Y | Streptococcus gordonii | Streptococcus gordonii | Endocarditis | |
| Biopsy (Tissue: vegetation) | Y | Streptococcus mitis group | Streptococcus sp. | Endocarditis | |
| Biopsy (Tissue: carotid) | Y | Streptococcus pneumoniae | α-haemolytic Streptococcus | Aortitis | |
| Biopsy (Tissue) | Y | Streptococcus pyogenes | Streptococcus pyogenes | Endocarditis | |
| Biopsy (Tissue: aortic valve) | Y | Streptococcus sanguinis | Streptococcus mitis group | Endocarditis | |
| Abscess (Mediastinum) | Y | Cutibacterium acnes (associated with cutaneous flora) | Negative | Mediastinitis | |
| Intra-abdominal (100%; 3/3) | Abscess (Liver) | Y | Fusobacterium nucleatum | Fusobacterium nucleatum | Liver abscess |
| Abscess (Liver) | Y | Klebsiella pneumoniae | Negative | Liver abscess | |
| Abscess (Intra-abdominal) | Y | Staphylococcus lugdunensis | Staphylococcus sp. | Abdominal abscess | |
| Genito-urinary (33.3%; 1/3) | Abscess (Kidney) | Y | Enterococcus faecalis | Enterococcus sp. | Kidney graft abscess |
| Skin and soft tissue (50.0%; 1/2) | Granuloma | N | Mycobacterium tuberculosis complex | Negative | Post-BCG infection |
*Percentage of positive samples for each suspected type of infection in at least one method. **One month before and/or at the time of sampling; N, No; Y, Yes;
C, Probable sample contaminant; SMg, Shotgun metagenomics; Sanger 16S, Amplification of the 16S rRNA gene and Sanger sequencing of the PCR products.