Table 3.
Rare bacterial species identified using molecular identificationa
| Phylum | Genus | Bacterial species confirmed by molecular identification | No. of isolates | No. of isolates identified in the CPI period | No. of isolates identified in the MALDI-TOF MS period | No. of reports in PubMed | 48 rare species by PID | Presence/absence of species in our MALDI-TOF MS database | Presence/absence of species in MALDI-TOF MS database (Brüker) |
|---|---|---|---|---|---|---|---|---|---|
| Actinobacteria | Actinomyces | Actinomyces europaeus | 3 | 1 | 2 | 9 | Yes | Present | Present |
| Actinomyces lingnae | 1 | 0 | 1 | 1 | No | Absent | Absent | ||
| Actinomyces radingae | 5 | 3 | 2 | 10 | Yes | Present | Absent | ||
| Actinomyces urogenitalis | 2 | 0 | 2 | 4 | No | Present | Absent | ||
| Arthrobacter | Arthrobacter cumminsii | 5 | 4 | 1 | 4 | Yes | Present | Absent | |
| Bifidobacterium | Bifidobacterium scardovii | 1 | 1 | 0 | 5 | No | Present | Absent | |
| Brachybacterium | Brachybacterium muris | 1 | 0 | 1 | 3 | No | Present | Absent | |
| Brachybacterium sacelli | 1 | 0 | 1 | 3 | No | Absent | Absent | ||
| Brevibacterium | Brevibacterium massiliense | 1 | 1 | 0 | 2 | Yes | Absent | Absent | |
| Brevibacterium otitidis | 1 | 1 | 0 | 9 | No | Absent | Absent | ||
| Brevibacterium paucivorans | 2 | 1 | 1 | 3 | Yes | Present | Absent | ||
| Brevibacterium ravenspurgense | 1 | 1 | 0 | 0 | Yes | Present | Absent | ||
| Brevibacterium sanguinis | 1 | 1 | 0 | 2 | No | Present | Absent | ||
| Brevibacterium stationis | 1 | 0 | 1 | 10 | No | Present | Absent | ||
| Corynebacterium | Corynebacterium argentoratense | 2 | 0 | 2 | 3 | No | Present | Present | |
| Corynebacterium auriscanis | 3 | 3 | 0 | 5 | Yes | Present | Present | ||
| Corynebacterium confusum | 1 | 0 | 1 | 2 | No | Present | Present | ||
| Corynebacterium coyleae | 4 | 0 | 4 | 7 | Yes | Present | Present | ||
| Corynebacterium durum | 1 | 1 | 0 | 3 | No | Present | Absent | ||
| Corynebacterium fastidiosum | 1 | 0 | 1 | 0 | Yes | Absent | Absent | ||
| Corynebacterium imitans | 1 | 0 | 1 | 2 | Yes | Present | Present | ||
| Corynebacterium kroppenstedtii | 1 | 0 | 1 | 9 | No | Present | Present | ||
| Corynebacterium mucifaciens | 3 | 0 | 3 | 6 | Yes | Present | Present | ||
| Corynebacterium riegelii | 1 | 0 | 1 | 6 | No | Present | Present | ||
| Corynebacterium ureicelerivorans | 1 | 0 | 1 | 3 | No | Present | Present | ||
| Dietzia | Dietzia cinnamea | 1 | 1 | 0 | 10 | No | Present | Absent | |
| Janibacter | Janibacter hoylei | 1 | 0 | 1 | 2 | No | Present | Absent | |
| Microbacterium | Microbacterium aurum | 2 | 1 | 1 | 5 | No | Present | Present | |
| Microbacterium chocolatum | 1 | 1 | 0 | 1 | No | Absent | Absent | ||
| Microbacterium flavum | 1 | 0 | 1 | 5 | No | Present | Absent | ||
| Nesterenkonia | Nesterenkonia lacusekhoensis | 1 | 0 | 1 | 4 | No | Present | Absent | |
| Propionimicrobium | Propionimicrobium lymphophilum | 2 | 1 | 1 | 3 | No | Present | Absent | |
| Trueperella | Trueperella abortisuis | 1 | 1 | 0 | 5 | No | Present | Absent | |
| Zimmermannella | Zimmermannella bifida | 1 | 1 | 0 | 1 | Yes | Absent | Absent | |
| Bacteroidetes | Alistipes | Alistipes finegoldii | 1 | 1 | 0 | 4 | Yes | Present | Absent |
| Bacteroides | Bacteroides dorei | 1 | 1 | 0 | 8 | No | Absent | Absent | |
| Butyricimonas | Butyricimonas virosa | 2 | 0 | 2 | 1 | Yes | Present | Absent | |
| Chryseobacterium | Chryseobacterium hominis | 1 | 0 | 1 | 4 | No | Present | Absent | |
| Chryseobacterium vrystaatense | 1 | 0 | 1 | 3 | No | Absent | Absent | ||
| Peptoniphilus | Candidatus Peptoniphilus massiliensis | 1 | 0 | 1 | 0 | No | Absent | Absent | |
| Porphyromonas | Porphyromonas uenonis | 4 | 4 | 0 | 2 | No | Present | Absent | |
| Prevotella | “Candidatus Prevotella conceptionensis” | 1 | 1 | 0 | 1 | Yes | Present | Absent | |
| Wautersiella | Wautersiella falsenii | 2 | 1 | 1 | 4 | No | Present | Absent | |
| Firmicutes | Aerosphaera | Aerosphaera taetra | 1 | 1 | 0 | 0 | No | Present | Absent |
| Anaerococcus | Anaerococcus octavius | 2 | 2 | 0 | 3 | Yes | Present | Absent | |
| Anaerotruncus | Anaerotruncus colihominis | 2 | 1 | 1 | 2 | No | Present | Absent | |
| Lysinibacillus | Lysinibacillus massiliensis | 1 | 0 | 1 | 8 | No | Absent | Absent | |
| Catabacter | Catabacter hongkongensis | 1 | 1 | 0 | 6 | No | Absent | Absent | |
| Clostridium | Clostridium aldenense | 1 | 0 | 1 | 3 | No | Present | Absent | |
| Dialister | Dialister micraerophilus | 1 | 0 | 1 | 3 | No | Present | Absent | |
| Granulicatella | Granulicatella para-adiacens | 1 | 0 | 1 | 2 | No | Present | Absent | |
| Peptoniphilus | Peptoniphilus harei | 3 | 2 | 1 | 7 | Yes | Present | Absent | |
| Streptococcus | Streptococcus criceti | 3 | 0 | 3 | 10 | No | Present | Present | |
| Streptococcus massiliensis | 2 | 2 | 0 | 1 | Yes | Present | Present | ||
| Streptococcus peroris | 1 | 0 | 1 | 6 | No | Present | Present | ||
| Turicibacter | Turicibacter sanguinis | 1 | 1 | 0 | 3 | Yes | Present | Absent | |
| Fusobacteria | Leptotrichia | Leptotrichia trevisanii | 5 | 4 | 1 | 3 | Yes | Present | Absent |
| Proteobacteria | Acetobacter | Acetobacter indonesiensis | 2 | 2 | 0 | 9 | No | Absent | Absent |
| Acinetobacter | Acinetobacter parvus | 1 | 1 | 0 | 8 | Yes | Present | Present | |
| Acinetobacter septicus | 5 | 4 | 1 | 3 | No | Present | Absent | ||
| Aurantimonas | Aurantimonas altamirensis | 1 | 0 | 1 | 9 | No | Present | Absent | |
| Blastomonas | Blastomonas ursincola | 1 | 1 | 0 | 5 | No | Present | Present | |
| Desulfovibrio | Desulfovibrio intestinalis | 1 | 1 | 0 | 5 | No | Absent | Absent | |
| Enterobacter | Enterobacter kobei | 3 | 0 | 3 | 10 | Yes | Present | Present | |
| Hematobacter | Hematobacter massiliensis | 3 | 1 | 2 | 2 | No | Absent | Absent | |
| Pandoraea | Pandoraea pulmonicola | 3 | 0 | 3 | 7 | Yes | Present | Present | |
| Pantoea | Pantoea brenneri | 1 | 0 | 1 | 1 | No | Absent | Absent | |
| Pantoea eucrina | 1 | 0 | 1 | 2 | No | Present | Absent | ||
| Pseudochrobactrum | Pseudochrobactrum asaccharolyticum | 1 | 0 | 1 | 2 | No | Present | Absent | |
| Pseudomonas | Pseudomonas lurida | 1 | 0 | 1 | 3 | No | Present | Absent | |
| Ralstonia | Ralstonia insidiosa | 1 | 0 | 1 | 5 | No | Present | Absent | |
| Roseomonas | Roseomonas genomospecies 5 | 1 | 1 | 0 | 6 | No | Absent | Absent | |
| Rothia | Rothia aeria | 1 | 1 | 0 | 8 | No | Present | Absent | |
| Serratia | Serratia nematodiphila | 1 | 0 | 1 | 3 | No | Absent | Absent | |
| Sphingomonas | Sphingomonas mucosissima | 1 | 1 | 0 | 2 | No | Present | Absent |
a
List of 75 rare bacterial species identified using molecular identification; 18 of these species were absent from our MALDI-TOF database, and 57 species from the Brüker database. PID, phenotypic identification; CPI, conventional phenotypic identification (Gram staining, API, Vitek 2 system identification).