Annals of Laboratory Medicine

Korean Society for Laboratory Medicine (대한진단검사의학회)
권호 표지
DOI QR코드

DOI QR Code

Application of the Whole Genome-Based Bacterial Identification System, TrueBac ID, Using Clinical Isolates That Were Not Identified With Three Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems

  • Received : 2018.10.14
  • Accepted : 2019.05.22
  • Published : 2019.11.01
⟨ Previous Next ⟩

Abstract

Background: Next-generation sequencing is increasingly used for taxonomic identification of pathogenic bacterial isolates. We evaluated the performance of a newly introduced whole genome-based bacterial identification system, TrueBac ID (ChunLab Inc., Seoul, Korea), using clinical isolates that were not identified by three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems and 16S rRNA gene sequencing. Methods: Thirty-six bacterial isolates were selected from a university-affiliated hospital and a commercial clinical laboratory. Species was identified by three MALDI-TOF MS systems: Bruker Biotyper MS (Bruker Daltonics, Billerica, MA, USA), VITEK MS (bioMérieux, Marcy l'Étoile, France), and ASTA MicroIDSys (ASTA Inc., Suwon, Korea). Whole genome sequencing was conducted using the Illumina MiSeq system (Illumina, San Diego, CA, USA), and genome-based identification was performed using the TrueBac ID cloud system (www.truebacid.com). Results: TrueBac ID assigned 94% (34/36) of the isolates to known (N=25) or novel (N=4) species, genomospecies (N=3), or species group (N=2). The remaining two were identified at the genus level. Conclusions: TrueBac ID successfully identified the majority of isolates that MALDI-TOF MS failed to identify. Genome-based identification can be a useful tool in clinical laboratories, with its superior accuracy and database-driven operations.

Keywords

Acknowledgement

This work was supported by the BioNano Health Guard Research Center, funded by the Ministry of Science, ICT and Future Planning (MSIP) of Korea as a Global Frontier Project (Grant Number H-GUARD_2014M3A6B2060509); by the Nano Material Technology Development Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (No.2017M3A7B4039936); and by the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Korea (grant No. HI17C1807). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

References

  1. Vouga M and Greub G. Emerging bacterial pathogens: the past and beyond. Clin Microbiol Infect 2016;22:12-21. https://doi.org/10.1016/j.cmi.2015.10.010
  2. Croxatto A, Prod'hom G, Greub G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 2012;36:380-407. https://doi.org/10.1111/j.1574-6976.2011.00298.x
  3. Van den Abeele AM, Vogelaers D, Vandamme P, Vanlaere E, Houf K. Filling the gaps in clinical proteomics: a do-it-yourself guide for the identification of the emerging pathogen Arcobacter by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Microbiol Methods 2018;152:92-7. https://doi.org/10.1016/j.mimet.2018.07.007
  4. Chun J and Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014;64:316-24. https://doi.org/10.1099/ijs.0.054171-0
  5. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67:1613-7. https://doi.org/10.1099/ijsem.0.001755
  6. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64:346-51. https://doi.org/10.1099/ijs.0.059774-0
  7. Fox GE, Wisotzkey JD, Jurtshuk PJ Jr. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 1992;42:166-70. https://doi.org/10.1099/00207713-42-1-166
  8. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461-6. https://doi.org/10.1099/ijsem.0.002516
  9. Salipante SJ, SenGupta DJ, Cummings LA, Land TA, Hoogestraat DR, Cookson BT. Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology. J Clin Microbiol 2015;53:1072-9. https://doi.org/10.1128/JCM.03385-14
  10. Roach DJ, Burton JN, Lee C, Stackhouse B, Butler-Wu SM, Cookson BT, et al. A year of infection in the Intensive Care Unit: prospective whole genome sequencing of bacterial clinical isolates reveals cryptic transmissions and novel microbiota. PLoS Genet 2015;11:e1005413. https://doi.org/10.1371/journal.pgen.1005413
  11. Mellmann A, Bletz S, Boking T, Kipp F, Becker K, Schultes A, et al. Real-Time Genome sequencing of resistant bacteria provides precision infection control in an institutional setting. J Clin Microbiol 2016;54:2874-81. https://doi.org/10.1128/JCM.00790-16
  12. Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Goker M, Parker CT, et al. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol 2014;12:e1001920. https://doi.org/10.1371/journal.pbio.1001920
  13. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114-20. https://doi.org/10.1093/bioinformatics/btu170
  14. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455-77. https://doi.org/10.1089/cmb.2012.0021
  15. Richter M and Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009;106:19126-31. https://doi.org/10.1073/pnas.0906412106
  16. Murray RG and Stackebrandt E. Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int J Syst Bacteriol 1995;45:186-7. https://doi.org/10.1099/00207713-45-1-186
  17. Fischer S, Mayer-Scholl A, Imholt C, Spierling NG, Heuser E, Schmidt S, et al. Leptospira genomospecies and sequence type prevalence in small mammal populations in Germany. Vector Borne Zoonotic Dis 2018;18:188-99. https://doi.org/10.1089/vbz.2017.2140
  18. Patil PP, Kumar S, Midha S, Gautam V, Patil PB. Taxonogenomics reveal multiple novel genomospecies associated with clinical isolates of Stenotrophomonas maltophilia. Microb Genom 2018;4:e000207.
  19. Salipante SJ, Kalapila A, Pottinger PS, Hoogestraat DR, Cummings L, Duchin JS, et al. Characterization of a multidrug-resistant, novel Bacteroides genomospecies. Emerg Infect Dis 2015;21:95-8. https://doi.org/10.3201/eid2101.140662
  20. Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018;56:280-5. https://doi.org/10.1007/s12275-018-8014-6
  21. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716-21. https://doi.org/10.1099/ijs.0.038075-0
  22. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016;17:132. https://doi.org/10.1186/s13059-016-0997-x
  23. CLSI. Interpretive criteria for identification of bacteria and fungi by DNA target sequencing. Approved guideline MM18-A. Wayne, PA: Clinical and Laboratory Standards Institute, 2008.
  24. Jang KS and Kim YH. Rapid and robust MALDI-TOF MS techniques for microbial identification: a brief overview of their diverse applications. J Microbiol 2018;56:209-16. https://doi.org/10.1007/s12275-018-7457-0
  25. Ndongo S, Andrieu C, Fournier PE, Lagier JC, Raoult D. 'Actinomyces provencensis' sp. nov., 'Corynebacterium bouchesdurhonense' sp. nov., 'Corynebacterium provencense' sp. nov. and 'Xanthomonas massiliensis' sp. nov., 4 new species isolated from fresh stools of obese French patients. New Microbes New Infect 2017;18:24-7. https://doi.org/10.1016/j.nmni.2017.01.013
  26. Kittl S, Brodard I, Rychener L, Jores J, Roosje P, Gobeli Brawand S. Otitis in a cat associated with Corynebacterium provencense. BMC Vet Res 2018;14:200. https://doi.org/10.1186/s12917-018-1526-9
  27. Fonkou MDM, Bilen M, Cadoret F, Fournier PE, Dubourg G, Raoult D. 'Enterococcus timonensis' sp. nov., 'Actinomyces marseillensis' sp. nov., 'Leptotrichia massiliensis' sp. nov., 'Actinomyces pacaensis' sp. nov., 'Actinomyces oralis' sp. nov., 'Actinomyces culturomici' sp. nov. and 'Gemella massiliensis' sp. nov., new bacterial species isolated from the human respiratory microbiome. New Microbes New Infect 2017;22:37-43.
  28. Martiny D, Visscher A, Catry B, Chatellier S, Vandenberg O. Optimization of Campylobacter growth conditions for further identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). J Microbiol Methods 2013;94:221-3. https://doi.org/10.1016/j.mimet.2013.06.018
  29. Mellmann A, Cloud J, Maier T, Keckevoet U, Ramminger I, Iwen P, et al. Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. J Clin Microbiol 2008;46:1946-54. https://doi.org/10.1128/JCM.00157-08

Cited by

  1. Comparative Genomic Analysis of the 2016 Vibrio cholerae Outbreak in South Korea vol.7, 2019, https://doi.org/10.3389/fpubh.2019.00228
  2. Improved Metagenomic Taxonomic Profiling Using a Curated Core Gene-Based Bacterial Database Reveals Unrecognized Species in the Genus Streptococcus vol.9, pp.3, 2019, https://doi.org/10.3390/pathogens9030204
  3. Mechanisms Underlying the Rhizosphere-To-Rhizoplane Enrichment of Cellvibrio Unveiled by Genome-Centric Metagenomics and Metatranscriptomics vol.8, pp.4, 2019, https://doi.org/10.3390/microorganisms8040583
  4. Genome-based reclassification of Paenibacillus jamilae Aguilera et al. 2001 as a later heterotypic synonym of Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994 vol.70, pp.5, 2019, https://doi.org/10.1099/ijsem.0.004140
  5. Isolation of a novel species in the genus Cupriavidus from a patient with sepsis using whole genome sequencing vol.15, pp.5, 2020, https://doi.org/10.1371/journal.pone.0232850
  6. Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans vol.8, pp.6, 2020, https://doi.org/10.3390/microorganisms8060900
  7. Whole-Genome Sequence of Geobacillus thermoleovorans ARTRW1, Isolated from Armutlu Geothermal Spring, Turkey vol.9, pp.24, 2019, https://doi.org/10.1128/mra.00269-20
  8. Phylogenomic characterisation of a novel corynebacterial species pathogenic to animals vol.113, pp.8, 2019, https://doi.org/10.1007/s10482-020-01430-5
  9. Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies vol.10, 2020, https://doi.org/10.1038/s41598-020-68249-y
  10. Genomic characterization of four Escherichia coli strains isolated from oral lichen planus biopsies vol.13, pp.1, 2019, https://doi.org/10.1080/20002297.2021.1905958
  11. Gnotobiotic rainbow trout (Oncorhynchus mykiss) model reveals endogenous bacteria that protect against Flavobacterium columnare infection vol.17, pp.1, 2019, https://doi.org/10.1371/journal.ppat.1009302
  12. Tessaracoccus coleopterorum sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus vol.71, pp.1, 2019, https://doi.org/10.1099/ijsem.0.004588
  13. Factors Associated With MALDI-TOF Mass Spectral Quality of Species Identification in Clinical Routine Diagnostics vol.11, 2019, https://doi.org/10.3389/fcimb.2021.646648
  14. Muricauda brasiliensis sp. nov., isolated from a mat-forming cyanobacterial culture vol.52, pp.1, 2019, https://doi.org/10.1007/s42770-020-00400-3
  15. Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection vol.15, pp.3, 2021, https://doi.org/10.1038/s41396-020-00807-8
  16. Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse vol.71, pp.3, 2019, https://doi.org/10.1099/ijsem.0.004673
  17. Aerophototrophica crusticola gen. nov., sp. nov., isolated from desert biocrusts vol.71, pp.3, 2021, https://doi.org/10.1099/ijsem.0.004677
  18. Arthrobacter terricola sp. nov., isolated from forest soil vol.71, pp.3, 2019, https://doi.org/10.1099/ijsem.0.004686
  19. Brevilactibacter coleopterorum sp. nov., isolated from the intestine of the dark diving beetle Hydrophilus acuminatus, and Weissella coleopterorum sp. nov., isolated from the intestine of the diving b vol.71, pp.4, 2019, https://doi.org/10.1099/ijsem.0.004779
  20. A Novel Species of the Genus Arsenicicoccus Isolated From Human Blood Using Whole-Genome Sequencing vol.41, pp.3, 2019, https://doi.org/10.3343/alm.2021.41.3.323
  21. Genome-guided investigation of secondary metabolites produced by a potential new strain Streptomyces BA2 isolated from an endemic plant rhizosphere in Turkey vol.203, pp.5, 2019, https://doi.org/10.1007/s00203-021-02210-z
  22. Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114 vol.203, pp.6, 2019, https://doi.org/10.1007/s00203-021-02327-1
  23. Comparative Evaluation of Bruker Biotyper and ASTA MicroIDSys for Species Identification in a Clinical Microbiology Laboratory vol.11, pp.9, 2019, https://doi.org/10.3390/diagnostics11091683
  24. Wastewater from the Edible Oil Industry as a Potential Source of Lipase- and Surfactant-Producing Actinobacteria vol.9, pp.9, 2019, https://doi.org/10.3390/microorganisms9091987
  25. Complicated peritoneal dialysis‐associated peritonitis caused by Brevibacterium vol.25, pp.5, 2019, https://doi.org/10.1111/1744-9987.13606
  26. Description of Ornithinimicrobium ciconiae sp. nov., and Ornithinimicrobium avium sp. nov., isolated from the faeces of the endangered and near-threatened birds vol.59, pp.11, 2019, https://doi.org/10.1007/s12275-021-1323-1
  27. Actinomadura graeca sp. nov.: A novel producer of the macrocyclic antibiotic zelkovamycin vol.16, pp.11, 2019, https://doi.org/10.1371/journal.pone.0260413
  28. Heat-killed endophytic bacterium induces robust plant defense responses against important pathogens vol.11, pp.1, 2019, https://doi.org/10.1038/s41598-021-91837-5
  29. Analysis of the Genome of the Heavy Metal Resistant and Hydrocarbon-Degrading Rhizospheric Pseudomonas qingdaonensis ZCR6 Strain and Assessment of Its Plant-Growth-Promoting Traits vol.23, pp.1, 2019, https://doi.org/10.3390/ijms23010214
  30. First Case of Bacteremia and Epididymo-orchitis Caused by Oceanobacillus oncorhynchi subspecies incaldanensis in an Immunocompetent Patient vol.42, pp.2, 2022, https://doi.org/10.3343/alm.2022.42.2.290