TABLE 2.
Patient characteristics, microbiota, and outcome of 41 cases of spontaneous brain abscess
| Patient no. | Sex/age | Risk factora | Pre-OP AB | Gram stainc | Culture | 16S sequencing (% of aligned reads) (genus or group level) | Aligned readsd | Outcome at 30 day/1 yre |
|---|---|---|---|---|---|---|---|---|
| 1 | F/5 | HM | No | C+ | S. anginosus group | Fusobacterium (75.7); S. anginosus group (24.1); Campylobacter (0.17) | 844,388 | A/A |
| B− | C. gracilis | |||||||
| 2 | M/53 | L | Yes | Negative | Aspergillus fumigatus | NSf | 764 | A/D |
| 3 | M/50 | UK | Yes | C | S. anginosus group | S. anginosus group (72.3); Fusobacterium (25.2); Parvimonas (2.3) | 60,295 | A/A |
| 4 | F/74 | RA | No | C+ | H. influenzae | Haemophilus (99.7) | 108,926 | A/A |
| 5 | M/26 | A | Yes | ND | Negative | NS | 14,275 | A/A |
| 6 | F/82 | Si | No | ND | Aspergillus fumigatus | NS | 1,091 | A/A |
| 7 | M/18 | BSF | No | C+ | S. anginosus group | S. anginosus group (99.9) | 151,310 | A/A |
| 8 | M/72 | L | Yes | Negative | Negative | NS | 6,840 | A/A |
| 9 | M/49 | UK | No | C+ B− | S. anginosus group | S. anginosus group (61.2); Fusobacterium (37.6); Parvimonas (1.2) | 206,029 | A/A |
| 10 | M/67 | Ca | No | C+ | S. anginosus group | S. anginosus group (99.6) | 126,733 | A/D |
| 11 | M/73 | UK | Yes | C+ | S. anginosus group | S. anginosus group (99.8) | 108,784 | A/A |
| 12 | M/70 | UK | Yes | Negative | S. anginosus group | S. anginosus group (57.9); Parvimonas (20.7); Fusobacterium (16.3); Prevotella (3.5); Campylobacter (1.3); Actinomyces (0.3) | 53,180 | A/A |
| 13 | M/50 | HM | Yes | Negative | S. anginosus group | S. anginosus group (99.9) | 78,806 | A/A |
| 14 | F/54 | Hyd | Yes | C+ | S. anginosus group | S. anginosus group (99.8) | 167,461 | A/A |
| 15 | M/11 | UK | No | C+ | S. pneumoniae | S. mitis group (99.7); Fusobacterium (0.13) | 133,666 | A/A |
| 16 | F/63 | UK | No | Negative | A. aphrophilus | Aggregatibacter (99.7); Fusobacterium (0.09); S. anginosus group (0.06) | 99,756 | A/A |
| 17 | M/58 | UK | Yes | B+ | L. monocytogenes | Listeria (99.7); S. anginosus group (0.22) | 57,691 | A/A |
| 18 | F/39 | A | No | C+ | S. anginosus group | S. anginosus group (61.8); Fusobacterium (20.8); Aggregatibacter (15,5); Actinomyces sp. (1.6) | 438,405 | A/A |
| A. aphrophilus | ||||||||
| 19 | M/48 | UK | No | B− | Fusobacterium sp. | Fusobacterium (81.9); Porphyromonas (11.2); Catonella (2.6); Treponema (2.3); Peptococcus (0.6); Parvimonas (0.6); S. anginosus group (0.4) | 139,604 | A/A |
| B+ | Actinomyces sp. | |||||||
| C+ | Prevotella sp. | |||||||
| 20 | M/63 | UK | No | Negative | Nocardia sp. | Nocardia (94.4); Ralstonia (2.6) | 18,924 | A/A |
| 21 | M/63 | HC | No | cb+ | L. monocytogenes | Listeria (99.2) | 71,476 | A/A |
| 22 | M/69 | UK | No | C+ | S. anginosus group; A. aphrophilus | Fusobacterium (85.5); S. anginosus group (10.9); Porphyromonas (1.2); Parvimonas (1.23); Campylobacter (0.69); Aggregatibacter (0.18) | 128,429 | A/A |
| 23 | F/70 | Ca | No | C+ | S. anginosus group | S. anginosus group (99.9) | 113,208 | A/D |
| 24 | M/75 | UK | No | C+ | S. anginosus group | Fusobacterium (43.8); Prevotella. (26.6); S. anginosus group (26.2); Dialister (3.4) | 128,300 | A/D |
| B− | ||||||||
| 25 | F/57 | A | No | C+ | S. anginosus group | S. anginosus group (99.8) | 195,578 | A/A |
| 26 | M/43 | UK | No | Negative | A. actinomycetemcomitans | Fusobacterium (56.2); Campylobacter (36.4); Actinomyces (7.2) | 213,352 | A/A |
| 27 | F/66 | UK | Yes | Negative | Fusobacterium sp. | Fusobacterium (99.9) | 105,644 | A/A |
| 28 | M/69 | UK | No | Negative | Nocardia sp. | Nocardia (68.5); Ralstonia (17.5); Bradyrhizobium (7.2) | 23,658 | A/A |
| 29 | F/71 | UK | No | C+ | A. aphrophilus; Fusobacterium sp.; Parvimonas sp. | Fusobacterium (68.8); Aggregatibacter (18.0); Parvimonas (12.9) | 119,000 | A/A |
| 30 | M/65 | UK | Yes | C+ | S. anginosus group | S. anginosus group (47.5); Fusobacterium (38.8); Parvimonas (11.5); Actinomyces (1.3) | 280,945 | A/A |
| 31 | M/59 | HC | No | C+ | S. anginosus group | Fusobacterium (89.0); Parvimonas (10.8); Prevotella. (0.14); S. anginosus group (0.01) | 258,253 | A/A |
| B− B+ | Fusobacterium sp. | |||||||
| 32 | F/51 | UK | No | C+ | S. anginosus group | Porphyromonas (50.2); Fusobacterium (27.8); S. anginosus group (8.6); Peptostreptococcus (4.4); Tannerella (3.7); Campylobacter (0.93) | 140,897 | A/A |
| B− | Campylobacter sp. | |||||||
| 33 | M/34 | UK | No | C+ | A. aphrophilus | Parvimonas (37.4); Aggregatibacter (30.9); Fusobacterium (30.2); Actinomyces (1.0) | 118,415 | A/A |
| 34 | M/43 | Bac | Yes | C+ | S. aureus | S. aureus (99.5); Fusobacterium (0.29) | 162,762 | A/A |
| 35 | M/76 | Bac | Yes | B− | K. pneumoniae | Klebsiella (99.7); Streptococcus (0.20) | 93,519 | A/A |
| 36 | F/53 | UK | Yes | B− | Prevotella sp. | Fusobacterium (54.9); Parvimonas (20.8); Prevotella (13.3); Porphyromonas (3.7); Campylobacter (1.5); Treponema (1.2) | 156,010 | A/A |
| C+ | Actinomyces sp. | Mycoplasma (1.0); Actinomyces sp. (0.7) | ||||||
| 37 | F/74 | UK | No | Negative | Fusobacterium sp. | Fusobacterium (99.9) | 145,204 | A/A |
| 38 | M/0 | PB | Yes | B− | E. coli | Escherichia (99.5); Streptococcus (0.30) | 106,631 | A/A |
| 39 | F/30 | Bacb | Yes | Negative | Negative | NS | 17,287 | D/D |
| 40 | F/59 | SS | No | Negative | Negative | NS (identified as the apicoplast genome of T. gondii) | 36,786 | A/D |
| 41 | M/77 | UK | Yes | B+ | L. monocytogenes | Listeria (99.9) | 132,210 | A/A |
a
A, ethanol and/or cannabinoid abuse; Bac, bacteremia with same microorganism <3 months before; BSF, recent basilar skull fracture; Ca, cancer; Hyd, hydrocephalus after previous brain abscess; HC, hepatic cirrhosis; HM, heart malformation; L, leukemia/myeloma; PB, premature birth and E. coli meningitis; RA, rheumatoid arthritis, methotrexate; Si, chronic sinusitis; SS, systemic sclerosis, immune suppression; UK, none detected.
b
Bacteremia with S. aureus <3 months before. Surgical concern whether abscess was correctly aspirated.
c
B−, Gram-negative rods; B+, Gram-positive rods; C, cocci; C+ Gram-positive cocci; cb, coccobacilli; ND, not recorded.
d
Number of reads with >97% similarity to reference sequences in the SILVA database. Underlined numbers stem from 35 PCR amplification cycles.
e
A, alive; D, dead.
f
NS, composition of aligned reads not different from negative controls diagnosed with glioblastoma.