TABLE 3.
Microbiota of 41 cases of spontaneous brain abscess as revealed by culture, supplemented by amplicon sequencing of 16S rRNA gene fragments from stored specimensa
| Species group | No. of positive cases |
Mono/poly | ||
|---|---|---|---|---|
| By culture | By 16S | Total | ||
| Streptococcus anginosus group | 17 | 16 | 17 | Both |
| Fusobacterium nucleatum group | 5b | 17 | 17 | Both |
| Aggregatibacter species | 6 | 4 | 6 | Both |
| Parvimonas micra group | 1c | 6 | 6 | Poly |
| Listeria monocytogenes | 3 | 3 | 3 | Mono |
| Prevotella species | 2d | 2 | 3 | Poly |
| Actinomyces species | 2e | 1 | 3 | Poly |
| Nocardia species | 2 | 2 | 2 | Mono |
| Campylobacter species | 2 | 1 | 2 | Poly |
| Aspergillus fumigatus group | 2 | 0 | 2 | Mono |
| Porphyromonas species | 0f | 2 | 2 | Poly |
| Haemophilus influenzae | 1 | 1 | 1 | Mono |
| Streptococcus pneumoniae | 1 | 1 | 1 | Mono |
| Staphylococcus aureus | 1 | 1 | 1 | Mono |
| Escherichia coli | 1 | 1 | 1 | Mono |
| Klebsiella pneumoniae | 1 | 1 | 1 | Mono |
| Anaerobacillus species | 0 | 2 | 2 | NRh |
| Cutibacterium species | 0 | 1 | 1 | NR |
| Flavobacterium species | 0 | 1 | 1 | NR |
| Toxoplasma gondii | 0 | 1g | 1 | Mono |
| Sum | 47 | 64 | 73 | |
Microorganisms are compiled in genera or species groups with the exception of L. monocytogenes, five other bacterial species and Toxoplasma gondii, which were solely detected in monomicrobial infections and identified by standard methods or monoclonal antibodies, respectively. A cutoff value of 5% of aligned reads/sample was used for species group presence by amplicon sequencing, ignoring Bacillus, Bradyrhizobium, Burkholderia, Delftia, Micrococcus, Paracoccus, Ralstonia, Rhizobium, and Sphingomonas.
Eight additional samples were positive after reculture on selective media.
One additional sample (patient 36) was positive after meticulous reculture of stored specimens.
One additional sample (patient 24) was positive after meticulous reculture of stored specimens.
One additional sample (patient 26) was positive after meticulous reculture of stored specimens.
One sample (patient 19) was positive after meticulous reculture of stored specimens.
16S primers amplified a fragment that could be identified as small subunit rRNA located on the 35-kb apicoplast genome of Toxoplasma gondii.
NR, not relevant (only detected in NS samples dominated by negative control species groups [case numbers 2, 6, 8, and 40]).