Table 2. Comparison of results obtained by culture, direct sequencing with a single universal primer pair and direct sequencing with the group-specific primer pairs.
| ID | Sample type | Culture* | Universal primer | Group-specific primers | Antibiotic† |
| 1 | Abscess brain | Fusobacterium nucleatum | CX, RI | ||
| Gemella haemolysans/morbillorum | |||||
| Parvimonas sp.‡ | Parvimonas sp. | ||||
| Streptococcus constellatus | Streptococcus intermedius | S. intermedius | |||
| 2 | Abscess brain | F. nucleatum | CX, RI | ||
| S. constellatus | S. intermedius | S. intermedius | |||
| 3 | Abscess brain | Aggregatibacter aphrophilus | CX, MZ | ||
| Eikenella sp. | |||||
| F. nucleatum‡ | F. nucleatum | ||||
| F. nucleatum subsp. polymorphum | |||||
| Neisseria elongata | |||||
| Peptostreptococcus sp. | Parvimonas micra | P. micra | |||
| Streptococcus milleri group | S. intermedius | S. intermedius | |||
| 4 | Abscess brain | No growth | Actinomyces meyeri | CT, MZ | |
| Campylobacter gracilis | |||||
| F. nucleatum‡ | F. nucleatum | ||||
| Prevotella pleuritidis | |||||
| S. intermedius | S. intermedius | ||||
| 5 | Abscess brain | A. meyeri | A. meyeri | – | |
| C. gracilis | C. gracilis | ||||
| Eikenella sp. | |||||
| F. nucleatum | Fusobacterium sp. | Fusobacterium sp. | |||
| Peptostreptococcus sp. | Peptostreptococcus sp. | ||||
| 6 | Abscess liver | E. coli | E. coli/Shigella spp. | E. coli/Shigella spp. | AM |
| Enterococcus faecium | E. faecium/durans | E. faecium/durans | |||
| Klebsiella sp. | |||||
| Lactobacillus rhamnosus | |||||
| Staphylococcus haemolyticus | S. haemolyticus | ||||
| 7 | Abscess liver | G. haemolysans | PT | ||
| Prevotella melaninogenica | P. melaninogenica | ||||
| Streptococcus mitis group | S. mitis group | ||||
| Streptococcus parasanguinis | |||||
| S. haemolyticus | |||||
| 8 | Abscess liver§ | No growth | Clostridium perfringens | C. perfringens | CT |
| E. coli/Shigella spp. | E. coli/Shigella spp. | ||||
| 9 | Abscess muscle | Eikenella corrodens | – | ||
| F. nucleatum‡ | F. nucleatum | ||||
| P. micra | |||||
| Porphyromonas circumdentaria | |||||
| Porphyromonas endodontalis | P. endodontalis | ||||
| Streptococcusmilleri group | S. constellatus/intermedius | ||||
| 10 | Abscess ovarian§ | F. nucleatum | F. nucleatum | F. nucleatum | – |
| Peptostreptococcus sp. | Parvimonas sp. | Parvimonas sp. | |||
| 11 | Abscess pancreas | Bacteroides fragilis | B. fragilis | B. fragilis | IP |
| E. faecium | E. faecium | ||||
| 12 | Abscess pancreas | A. meyeri | IP | ||
| Campylobacter concisus | |||||
| P. melaninogenica | P. melaninogenica/histicola | ||||
| Prevotella histicola | |||||
| CNS | Staphylococcus epidermidis | S. epidermidis | |||
| 13 | Abscess para-aortic | Corynebacterium appendicis | – | ||
| Diphtheroid | Corynebacterium tuberculostearicum | C. tuberculostearicum | |||
| CNS | S. haemolyticus | S. haemolyticus | |||
| 14 | Abscess psoas | No growth | Enterobacter hormaechei | E. hormaechei | MP |
| E. faecium | |||||
| 15 | Abscess spleen | Enterococcus sp. | Enterococcus casseliflavus/gallinarum‡ | E. casseliflavus/gallinarum | Unknown |
| E. coli/Shigella spp. | |||||
| E. faecalis | E. faecalis | ||||
| F. nucleatum | |||||
| S. anginosus | |||||
| Staphylococcus epidermidis | S. epidermidis | ||||
| 16 | Abscess subcut.§ | E. faecium | E. faecium | E. faecium | CI, OX |
| Finegoldia magna | F. magna | F. magna | |||
| 17 | Abscess retro-peritoneal§ | E. faecium | E. faecium/hirae | E. faecium/hirae | CI, MZ, LZ |
| Klebsiella pneumoniae | K. pneumoniae | ||||
| 18 | Bile§ | E. coli | E. coli/Shigella spp. | E. coli/Shigella spp. | CT, MZ |
| F. nucleatum | F. nucleatum | ||||
| 19 | Bile | E. caccae | IP | ||
| Enterococcus sp. | E. casseliflavus/gallinarum | E. casseliflavus/gallinarum | |||
| E. faecalis | |||||
| CNS | S. epidermidis | S. epidermidis | |||
| 20 | Empyema | No growth | P. micra‡ | P. micra | PT |
| Prevotella nigrescens | |||||
| Peptostreptococcus stomatis | P. stomatis | ||||
| S. anginosus | S. anginosus | ||||
| 21 | Empyema§ | C. gracilis | C. gracilis | CT, GE, PC | |
| Fusobacterium sp. | Fusobacterium sp. | ||||
| S. intermedius | S. intermedius | S. intermedius | |||
| 22 | Empyema | F. nucleatum | F. nucleatum | CT, PC | |
| C. gracilis | |||||
| P. micra | P. micra | ||||
| S. intermedius | S. intermedius | S. intermedius | |||
| 23 | Empyema | C. gracilis | CI, CL | ||
| F. nucleatum | |||||
| Haemophilus parainfluenzae | |||||
| P. melaninogenica‡ | P. melaninogenica | ||||
| P. micra | |||||
| S. constellatus | S. constellatus | ||||
| diphtheroid | |||||
| CNS | |||||
| 24 | Empyema | C. gracilis | C. gracilis | PC | |
| E. corrodens | E. corrodens | ||||
| P. micra | |||||
| Prevotella pleuritidis | P. pleuritidis | ||||
| S. intermedius | |||||
| S. parasanguinis | |||||
| 25 | Empyema | Prevotella sp. | P. nigrescens | P. nigrescens | CT |
| Prevotella veroralis | P. veroralis | ||||
| Anaerobic Gram+ve rod | Dialister invisus | ||||
| Dialister micraerophilus | |||||
| P. micra |
*
CNS, coagulase negative Staphylococcus.
†
Antibiotics: –, no treatment; AM, amoxicillin; CI, ciprofloxacin; CL, clindamycin; CT, cefotaxime; CX, ceftriaxone; GE, gentamicin; IP, imipenem; LZ, linezolid; MP, meropenem; MZ, metronidazole; OX, oxacillin; PC, penicillin-G; PT, piperacillin-tazobactam; RI, rifampicin; VA, vancomycin.
‡
Chromatogram too complex to allow for complete analysis. Only dominant peaks included.
§
Samples with identical results for standard direct sequencing and group-specific direct sequencing.