Bacteriology

Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Nocardia, Rhodococcus, Kocuria, Gordonia, Tsukamurella, and Listeria Species

Po-Ren Hsueh, Tai-Fen Lee, Shin-Hei Du, Shih-Hua Teng, Chun-Hsing Liao, Wang-Hui Sheng, Lee-Jene Teng
R. Patel, Editor
DOI: 10.1128/JCM.00456-14

Article Figures & Data

Figures

  • FIG 1
    FIG 1

    Clustering analysis of spectra generated by the Bruker Biotyper MALDI-TOF MS system for six common Nocardia species with poor identification performance or absence in the Bruker Biotyper database. (A) Six clusters of Nocardia species spectra, i.e., cluster 1, N. cyriacigeorgica; cluster 2, N. brasiliensis; cluster 3, N. farcinica; cluster 4, N. puris; cluster 5, N. asiatica; and cluster 6, N. beijingensis. (B) The six peaks (indicated by numbers and arrows) used to define the six clusters which were generated by ClinProTools with the genetic algorithm are m/z 2,774.477 (cluster 1), m/z 5,389.792 (cluster 2), m/z 6,505.720 (cluster 3), m/z 5,428.795 (cluster 4), m/z 6,525.326 (cluster 5), and m/z 16,085.216 (cluster 6). The absolute intensities of the ions are shown on the y axis, and the masses (m/z) of the ions are shown on the x axis. The m/z values represent the mass-to-charge ratio.

  • FIG 2
    FIG 2

    Clustering analysis of spectra generated by the Bruker Biotyper MALDI-TOF system for three different serotypes of 39 L. monocytogenes isolates. (A) Two clusters of L. monocytogenes spectra, i.e., cluster A (serotype 1/2a) and cluster B (serotypes 1/2b and 4b). Peaks are labeled with arrows. (B) The five peaks (indicated by numbers and arrows) used to define the two clusters that were generated by ClinProTools with the genetic algorithm are m/z 5,594.85, m/z 6,184.39, and m/z 11,187.31 for cluster 1, and m/z 5,601.21 and m/z 11,199.33 for cluster 2. The absolute intensities of the ions are shown on the y axis and the masses (m/z) of the ions are shown on the x axis. The m/z values represent the mass-to-charge ratio.

Tables

  • 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.

  • TABLE 2

    Serotypes, cluster analysis, and score values of MALDI-TOF MS spectra of 39 clinical isolates of L. monocytogenes

    SerotypeNo. of isolatesClusteraNo. of isolates with indicated score values by MALDI-TOF Bruker Biotyper
    <1.71.7–1.999≥2.0
    1/2a10A02 (1.889–1.902)8 (2.058–2.321)
    1/2b17B0017 (2.045–2.375)
    4b12B02 (1.82–1.98)10 (2.069–2.437)

    • ↵a See Fig. 2 for definition of clusters A and B based on cluster analysis by spectra generated by MALDI-TOF Bruker Biotyper.

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