TABLE 1

Identification results and scores of 108 clinical isolates of Nocardia, Kocuria, Rhodococcus, Gordonia, and Tsukamurella species with the MALDI Bruker Biotyper database (DB 5627)a

Isolate no. by genus (n)Identification results by 16S rRNA sequencingOrganism (best match)ScoreOrganism (second best match)Score
Bacterial speciesGenBank accession no.
Nocardia species (74)
    1N. brasiliensisFJ172109.1Nocardia sp.1.957N. brasiliensis1.856
    2N. brasiliensisFJ172109.1Nocardia sp.1.985N. brasiliensis1.748
    3N. brasiliensisFJ172109.1Nocardia sp.1.904Lactobacillus paracasei (NRI)1.570
    4N. brasiliensisFJ172109.1Nocardia sp.2.041N. brasiliensis1.852
    5N. brasiliensisFJ172109.1Nocardia sp.1.967N. brasiliensis1.773
    6N. brasiliensisFJ172109.1Nocardia sp.2.093N. brasiliensis1.938
    7N. brasiliensisFJ172109.1Nocardia sp.1.97N. brasiliensis1.715
    8N. brasiliensisFJ172109.1Nocardia sp.1.912N. brasiliensis1.754
    9N. brasiliensisFJ172109.1Nocardia sp.2.048N. brasiliensis1.897
    10N. brasiliensisFJ172109.1Nocardia sp.2.019N. brasiliensis (NRI)1.68
    11N. brasiliensisFJ172109.1Nocardia sp.2.009N. brasiliensis1.807
    12N. brasiliensisFJ172109.1Clostridium bifermentans (NRI)b1.455Lactobacillus paracasei (NRI)1.406
    13N. brasiliensisFJ172109.1Nocardia sp.1.867N. brasiliensis1.691
    14N. brasiliensisFJ172109.1N. brasiliensis1.872N. brasiliensis1.845
    15N. brasiliensisFJ172109.1Nocardia sp.2.041N. brasiliensis1.845
    16N. brasiliensisFJ172109.1Nocardia sp.1.995N. brasiliensis1.973
    17N. brasiliensisFJ172109.1Nocardia sp.2.074N. brasiliensis1.923
    18N. brasiliensisFJ172109.1Nocardia sp.2.068N. brasiliensis1.857
    19N. brasiliensisFJ172109.1Nocardia sp.1.971N. brasiliensis1.867
    20N. brasiliensisFJ172109.1Nocardia sp.2.033N. brasiliensis1.858
    21N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.918N. cyriacigeorgica1.908
    22N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.842N. cyriacigeorgica1.841
    23N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.747N. cyriacigeorgica1.722
    24N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.745N. cyriacigeorgica1.719
    25N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.844N. cyriacigeorgica1.839
    26N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica (NRI)1.601N. cyriacigeorgica1.551
    27N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.816N. cyriacigeorgica1.73
    28N. cyriacigeorgicaGQ376180.1Pseudomonas jinjuensis (NRI)1.305Aromatoleum tolulyticus (NRI)1.256
    29N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.712NRI1.611
    30N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.924N. cyriacigeorgica1.862
    31N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.806NRI1.577
    32N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.787NRI1.607
    33N. cyriacigeorgicaGQ376180.1Staphylococcus lutrae (NRI)1.414Lactobacillus fructivorans (NRI)1.412
    34N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.788NRI1.694
    35N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica (NRI)1.661N. cyriacigeorgica (NRI)1.59
    36N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica2.177N. cyriacigeorgica2.165
    37N. cyriacigeorgicaGQ376180.1Staphylococcus epidermidis (NRI)1.404Staphylococcus aureus (NRI)1.387
    38N. cyriacigeorgicaGQ376180.1N. cyriacigeorgica1.784NRI1.562
    39N. farcinicaGQ853065.1N. farcinica2.036N. farcinica1.956
    40N. farcinicaGQ853065.1Lactobacillus paracasei1.447Lactobacillus vini (NRI)1.391
    41N. farcinicaGQ853065.1N. farcinica (NRI)1.632N. farcinica (NRI)1.608
    42N. farcinicaGQ853065.1N. farcinica1.944NRI1.647
    43N. farcinicaGQ853065.1N. farcinica1.943N. farcinica1.929
    44N. farcinicaGQ853065.1N. farcinica1.773NRI1.615
    45N. farcinicaGQ853065.1N. farcinica1.749NRI1.668
    46N. farcinicaGQ853065.1N. farcinica (NRI)1.677N. farcinica (NRI)1.558
    47N. asiaticaGQ217495.1N. cyriacigeorgica2.256N. cyriacigeorgica2.245
    48N. asiaticaGQ217495.1N. cyriacigeorgica1.905N. cyriacigeorgica1.869
    49N. asiaticaGQ217495.1N. asiatica1.843Aeromonas veronii (NRI)1.44
    50N. asiaticaGQ217495.1N. asiatica1.859Lactobacillus paracasei (NRI)1.513
    51N. novaGQ376190.1N. nova2.221NRI1.571
    52N. novaAF430031.1N. nova2.245NRI1.513
    53N. novaGQ376190.1N. nova2.327NRI1.378
    54N. novaGQ376190.1N. nova2.342NRI1.479
    55N. novaGQ376190.1N. nova2.076NRI1.3
    56N. novaFJ172123.1N. nova2.437NRI1.638
    57N. beijingensisGQ217493.1N. asiatica (NRI)1.576Lactobacillus paracasei (NRI)1.552
    58N. beijingensisGQ217493.1N. asiatica (NRI)1.444Nocardia sp. (NRI)1.381
    59N. beijingensisGQ217493.1Nocardia sp. (NRI)1.328N. asiatica (NRI)1.305
    60N. purisGQ217500.1N. cyriacigeorgica (NRI)1.521NRI1.363
    61N. purisGQ217500.1Aromatoleum alkani (NRI)1.393Streptomyces lavendulae (NRI)1.362
    62N. purisGQ217500.1Lactobacillus aviarius (NRI)1.32Streptomyces hirsutus (NRI)1.306
    63N. purisGQ217500.1Rhodococcus equi (NRI)1.42Lactobacillus paracasei (NRI)1.404
    64N. purisAB097453.1Rhizobium radiobacter (NRI)1.418Xenorhabdus ehlersii (NRI)1.281
    65N. otitidiscaviarumGQ376191.1N. otitidiscaviarum2.138N. otitidiscaviarum2.044
    66N. otitidiscaviarumGQ376191.1N. otitidiscaviarum2.132N. otitidiscaviarum1.778
    67N. otitidiscaviarumGQ376191.1N. otitidiscaviarum2.114N. otitidiscaviarum (NRI)1.397
    68N. abscessusGU471235.1Lactobacillus fuchuensis (NRI)1.323Nocardia sp. (NRI)1.294
    69N. abscessusGU471235.1Clostridium tetani (NRI)1.277Lactobacillus amylovorus (NRI)1.274
    70N. rhamnosiphilaEF418604.1Agromyces rhizospherae (NRI)1.325Lactobacillus fructivorans (NRI)1.266
    71N. asteroidesAF430025.1N. asteroides1.777NRI1.580
    72N. elegansGQ376166.1N. nova2.071Lactobacillus paracasei (NRI)1.499
    73N. carneaGU433886.1Staphylococcus equorum (NRI)1.419Lactobacillus amylotrophicus (NRI)1.41
    74N. transvalensisAB084446.1L. paracasei (NRI)1.494Aeromonas salmonicida (NRI)1.416
Kocuria species (15)
    75K. kristinaeEU379300.1K. kristinae1.992K. kristinae1.911
    76K. kristinaeEU379300.1K. kristinae2.115K. kristinae2.085
    77K. kristinaeEU379300.1K. kristinae1.973K. kristinae1.931
    78K. kristinaeEU379300.1K. kristinae2.003K. kristinae1.944
    79K. kristinaeEU379300.1K. kristinae2.005K. kristinae1.808
    80K. kristinaeEU379300.1K. kristinae1.91K. kristinae1.823
    81K. kristinaeEU379300.1K. kristinae1.984K. kristinae1.93
    82K. kristinaeEU379300.1K. kristinae1.756K. kristinae1.747
    83K. kristinaeEU379300.1K. kristinae2.113K. kristinae1.93
    84K. kristinaeEU379300.1K. kristinae1.861NRI1.507
    85K. kristinaeEU379300.1K. kristinae1.95K. kristinae1.81
    86K. kristinaeEU379300.1K. kristinae1.717NRI1.667
    87K. kristinaeEU379300.1K. kristinae1.831NRI1.639
    88K. marinaKF306369.1K. marina1.955NRI1.507
    89K. marinaKF306369.1K. marina1.824NRI1.477
Rhodococcus species (10)
    90R. equiJQ965789.1R. equi2.134R. equi2.010
    91R. equiJQ965789.1R. equi2.240R. equi2.202
    92R. equiJQ965789.1R. equi2.087R. equi2.060
    93R. equiJQ965789.1R. equi2.188R. equi2.073
    94R. equiJQ965789.1R. equi2.255R. equi2.201
    95R. equiJQ965789.1R. equi2.258R. equi2.204
    96R. equiJQ965789.1R. equi2.278R. equi2.175
    97R. equiJQ965789.1R. equi2.192R. equi2.141
    98R. kroppenstedtiiKC346296.1R. kroppenstedtii1.912NRI1.529
    99R. kroppenstedtiiKC346296.1R. kroppenstedtii (NRI)1.595NRI1.519
Gordonia species (7)
    100G. bronchialisHQ316182.1G. bronchialis (NRI)1.662Morganella morganii (NRI)1.543
    101G. bronchialisHQ316182.1Morganella morganii (NRI)1.568Nocardia sp. (NRI)1.302
    102G. bronchialisHQ316182.1G. bronchialis (NRI)1.588Morganella morganii1.482
    103G. amicalisHQ842811.1G. rubripertincta (NRI)1.629G. rubripertincta (NRI)1.593
    104G. amicalisHQ842811.1G. rubripertincta (NRI)1.465G. terrae (NRI)1.404
    105G. amicalisHQ842811.1G. rubripertincta (NRI)1.436Staphylococcus chromogenes (NRI)1.406
    106G. sputiFJ536318.1G. sputi1.984G. sputi (NRI)1.617
Tsukamurella species (2)
    107T. tyrosinosolvensJX154557.1Tsukamurella paurometabola (NRI)1.598Tsukamurella sp. (NRI)1.511
    108T. tyrosinosolvensJX154557.1Tsukamurella sp.1.786T. inchonensis (NRI)1.622
  • a The Bruker Biotyper database (DB 5627) does not include N. beijingensis, N. puris, N. rhamnosiphila, T. tyrosinosolvens, or G. amicalis.

  • b NRI, not a reliable identification.