Matrix-assisted laser desorption/ionization time-of-flight MS for the accurate identification of complex and in the clinical microbiology laboratory Open Access

Abstract

complex (Bcc) bacteria, currently consisting of 23 closely related species, and , can cause serious and difficult-to-treat infections in people with cystic fibrosis. Identifying bacteria to the species level is considered important for understanding epidemiology and infection control, and predicting clinical outcomes. Matrix-assisted laser desorption/ionization time-of-flight MS (MALDI-TOF) is a rapid method recently introduced in clinical laboratories for bacterial species-level identification. However, reports on the ability of MALDI-TOF to accurately identify Bcc to the species level are mixed.

The aim of this project was to evaluate the accuracy of MALDI-TOF using the Biotyper and VITEK MS systems in identifying isolates from 22 different Bcc species and compared to gene sequencing, which is considered the current gold standard for Bcc.

To capture maximum intra-species variation, phylogenetic trees were constructed from concatenated multi-locus sequence typing alleles and clustered with a novel k-medoids approach. One hundred isolates representing 22 Bcc species, plus , were assessed for bacterial identifications using the two MALDI-TOF systems.

At the genus level, 100 and 97.0 % of isolates were confidently identified as by the Biotyper and VITEK MS systems, respectively; moreover, 26.0 and 67.0 % of the isolates were correctly identified to the species level, respectively. In many, but not all, cases of species misidentification or failed identification, a representative library for that species was lacking.

Currently available MALDI-TOF systems frequently do not accurately identify Bcc bacteria to the species level.

Funding
This study was supported by the:
  • BC Children's Hospital Research Institute (Award Summerstudentship)
    • Principle Award Recipient: Kendrew Wong
  • Cystic Fibrosis Canada (Award Canadian Burkholderia cepacia complex research and referral repository (20R40868))
    • Principle Award Recipient: Mark A Chilvers
  • Cystic Fibrosis Canada (Award Canadian Burkholderia cepacia complex research and referral repository (20R40868))
    • Principle Award Recipient: Manish Sadarangani
  • Cystic Fibrosis Canada (Award Canadian Burkholderia cepacia complex research and referral repository (20R40868))
    • Principle Award Recipient: James Zlosnik
  • Cystic Fibrosis Canada (Award Summer studentship)
    • Principle Award Recipient: Kendrew Wong
Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.001223
2020-06-29
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jmm/69/8/1105.html?itemId=/content/journal/jmm/10.1099/jmm.0.001223&mimeType=html&fmt=ahah

References

  1. Eberl L, Vandamme P. Members of the genus Burkholderia: good and bad guys. F1000Res 2016; 5:1007 [View Article]
    [Google Scholar]
  2. Martina P, Leguizamon M, Prieto CI, Sousa SA, Montanaro P et al. Burkholderia puraquae sp. nov., a novel species of the Burkholderia cepacia complex isolated from hospital settings and agricultural soils. Int J Syst Evol Microbiol 2018; 68:14–20 [View Article]
    [Google Scholar]
  3. Bach E, Sant'Anna FH, Magrich dos Passos JF, Balsanelli E, de Baura VA et al. Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov. Pathog Dis 2017; 75: [View Article]
    [Google Scholar]
  4. De Smet B, Mayo M, Peeters C, Zlosnik JEA, Spilker T et al. Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources. Int J Syst Evol Microbiol 2015; 65:2265–2271 [View Article]
    [Google Scholar]
  5. Mahenthiralingam E, Urban TA, Goldberg JB. The multifarious, multireplicon Burkholderia cepacia complex. Nat Rev Microbiol 2005; 3:144–156 [View Article]
    [Google Scholar]
  6. De Soyza A, Meachery G, Hester KLM, Nicholson A, Parry G et al. Lung transplantation for patients with cystic fibrosis and Burkholderia cepacia complex infection: a single-center experience. The Journal of Heart and Lung Transplantation 2010; 29:1395–1404 [View Article]
    [Google Scholar]
  7. Vandamme P, Dawyndt P. Classification and identification of the Burkholderia cepacia complex: past, present and future. Syst Appl Microbiol 2011; 34:87–95 [View Article]
    [Google Scholar]
  8. van Belkum A, Welker M, Pincus D, Charrier J-P, Girard V. Matrix-Assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiology: what are the current issues?. Ann Lab Med 2017; 37:475–483 [View Article]
    [Google Scholar]
  9. Angeletti S. Matrix assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology. J Microbiol Methods 2017; 138:20–29 [View Article]
    [Google Scholar]
  10. Fehlberg LCC, Andrade LHS, Assis DM, Pereira RHV, Gales AC et al. Performance of MALDI-TOF MS for species identification of Burkholderia cepacia complex clinical isolates. Diagn Microbiol Infect Dis 2013; 77:126–128 [View Article]
    [Google Scholar]
  11. Chakrabarti A. Maldi-Tof. Int J Infect Dis 2016; 45:26 [View Article]
    [Google Scholar]
  12. Singhal N, Kumar M, Kanaujia PK, Virdi JS. Maldi-Tof mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 2015; 6:791 [View Article]
    [Google Scholar]
  13. Wattal C, Oberoi JK, Goel N, Raveendran R, Khanna S. Matrix-Assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) for rapid identification of micro-organisms in the routine clinical microbiology laboratory. Eur J Clin Microbiol 2017; 36:807–812 [View Article]
    [Google Scholar]
  14. De Dios J, Martínez CL, Tato M, Morosini MI, Cobo M et al. Comparison between MALDI-TOF and recA gene sequencing for the identification of Burkholderia cepacia complex species isolated in a cystic fibrosis unit. Journal of Cystic Fibrosis 2016; 15:S75 [View Article]
    [Google Scholar]
  15. Gautam V, Sharma M, Singhal L, Kumar S, Kaur P et al. Maldi-Tof mass spectrometry: an emerging tool for unequivocal identification of non-fermenting gram-negative bacilli. The Indian Journal of Medical Research 2017; 145:665–672
    [Google Scholar]
  16. Alby K, Gilligan PH, Miller MB. Comparison of matrix-assisted laser desorption Ionization–Time of flight (MALDI-TOF) mass spectrometry platforms for the identification of gram-negative rods from patients with cystic fibrosis. J Clin Microbiol 2013; 51:3852–3854 [View Article]
    [Google Scholar]
  17. Kenna DTD, Lilley D, Coward A, Martin K, Perry C et al. Prevalence of Burkholderia species, including members of Burkholderia cepacia complex, among UK cystic and non-cystic fibrosis patients. J Med Microbiol 2017; 66:490–501 [View Article]
    [Google Scholar]
  18. Weber CF, King GM. Volcanic soils as sources of novel CO-oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a member of the Burkholderia cepacia complex. Front Microbiol 2017; 8:207 [View Article]
    [Google Scholar]
  19. Ong KS, Aw YK, Lee LH, Yule CM, Cheow YL et al. Burkholderia paludis sp. nov., an Antibiotic-Siderophore producing novel Burkholderia cepacia complex species, isolated from Malaysian tropical peat swamp soil. Front Microbiol 2016; 7:2046 [View Article]
    [Google Scholar]
  20. Peeters C, Zlosnik JEA, Spilker T, Hird TJ, LiPuma JJ et al. Burkholderia pseudomultivorans sp. nov., a novel Burkholderia cepacia complex species from human respiratory samples and the rhizosphere. Syst Appl Microbiol 2013; 36:483–489 [View Article]
    [Google Scholar]
  21. Mahenthiralingam E, Baldwin A, Dowson CG. Burkholderia cepacia complex bacteria: opportunistic pathogens with important natural biology. J Appl Microbiol 2008; 104:1539–1551 [View Article]
    [Google Scholar]
  22. Jolley KA, Bray JE, Maiden MCJ. Open-Access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Research 2018; 3:124 [View Article]
    [Google Scholar]
  23. Baldwin A, Mahenthiralingam E, Thickett KM, Honeybourne D, Maiden MCJ et al. Multilocus sequence typing scheme that provides both species and strain differentiation for the Burkholderia cepacia complex. J Clin Microbiol 2005; 43:4665–4673 [View Article]
    [Google Scholar]
  24. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article]
    [Google Scholar]
  25. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article]
    [Google Scholar]
  26. Jombart T, Balloux F, Dray S. adephylo: new tools for investigating the phylogenetic signal in biological traits. Bioinformatics 2010; 26:1907–1909 [View Article]
    [Google Scholar]
  27. Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K et al. Cluster. R; 2019
  28. Kassambara A, Mundt F. factoextra; 2017
  29. Yu G, Smith DK, Zhu H, Guan Y, Lam Tommy Tsan‐Yuk. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 2017; 8:28–36 [View Article]
    [Google Scholar]
  30. Coenye T, LiPuma JJ, Henry D, Hoste B, Vandemeulebroecke K et al. Burkholderia cepacia genomovar VI, a new member of the Burkholderia cepacia complex isolated from cystic fibrosis patients. Int J Syst Evol Microbiol 2001; 51:271–279 [View Article]
    [Google Scholar]
  31. Coenye T, Mahenthiralingam E, Henry D, LiPuma JJ, Laevens S et al. Burkholderia ambifaria sp. nov., a novel member of the Burkholderia cepacia complex including biocontrol and cystic fibrosis-related isolates. Int J Syst Evol Microbiol 2001; 51:1481–1490 [View Article]
    [Google Scholar]
  32. Vandamme P, Henry D, Coenye T, Nzula S, Vancanneyt M et al. Burkholderia anthina sp. nov. and Burkholderia pyrrocinia, two additional Burkholderia cepacia complex bacteria, may confound results of new molecular diagnostic tools. FEMS Immunology and Medical Microbiology 2002; 33:143–149 [View Article]
    [Google Scholar]
  33. Vanlaere E, Baldwin A, Gevers D, Henry D, De Brandt E et al. Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov. Int J Syst Evol Microbiol 2009; 59:102–111 [View Article]
    [Google Scholar]
  34. Zlosnik JEA, Zhou G, Brant R, Henry DA, Hird TJ et al. Burkholderia species infections in patients with cystic fibrosis in british Columbia, Canada. 30 Years’ experience. Ann Am Thorac Soc 2015; 12:70–78 [View Article]
    [Google Scholar]
  35. Spilker T, Baldwin A, Bumford A, Dowson CG, Mahenthiralingam E et al. Expanded multilocus sequence typing for Burkholderia species. J Clin Microbiol 2009; 47:2607–2610 [View Article]
    [Google Scholar]
  36. Drevinek P, Mahenthiralingam E. Burkholderia cenocepacia in cystic fibrosis: epidemiology and molecular mechanisms of virulence. Clinical Microbiology and Infection 2010; 16:821–830 [View Article]
    [Google Scholar]
  37. Quon BS, Reid JD, Wong P, Wilcox PG, Javer A et al. Burkholderia gladioli – A predictor of poor outcome in cystic fibrosis patients Who receive lung transplants? A case of locally invasive rhinosinusitis and persistent bacteremia in a 36-year-old lung transplant recipient with cystic fibrosis. Can Respir J 2011; 18:e64–e65 [View Article]
    [Google Scholar]
  38. Murray S, Charbeneau J, Marshall BC, LiPuma JJ. Impact of Burkholderia infection on lung transplantation in cystic fibrosis. Am J Respir Crit Care Med 2008; 178:363–371 [View Article]
    [Google Scholar]
  39. Snell G, Reed A, Stern M, Hadjiliadis D. The evolution of lung transplantation for cystic fibrosis: a 2017 update. J Cyst Fibros 2017; 16:553–564 [View Article]
    [Google Scholar]
  40. Dupont L. Lung transplantation in cystic fibrosis patients with difficult to treat lung infections. Curr Opin Pulm Med 2017; 23:574–579 [View Article]
    [Google Scholar]
  41. Ramos KJ, Smith PJ, McKone EF, Pilewski JM, Lucy A et al. Lung transplant referral for individuals with cystic fibrosis: cystic fibrosis Foundation consensus guidelines. J Cyst Fibros 2019; 18:321–333 [View Article]
    [Google Scholar]
  42. Angeletti S, Ciccozzi M. Matrix-Assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiology: an updating review. Infection, Genetics and Evolution 2019; 76:104063 [View Article]
    [Google Scholar]
  43. Baillie S, Ireland K, Warwick S, Wareham D, Wilks M. Matrix-Assisted laser desorption/ionisation-time of flight mass spectrometry: rapid identification of bacteria isolated from patients with cystic fibrosis. Br J Biomed Sci 2013; 70:144–148 [View Article]
    [Google Scholar]
  44. Florio W, Tavanti A, Barnini S, Ghelardi E, Lupetti A. Recent advances and ongoing challenges in the diagnosis of microbial infections by MALDI-TOF mass spectrometry. Front Microbiol 2018; 9:1097 [View Article]
    [Google Scholar]
  45. Plongla R, Panagea T, Pincus DH, Jones MC, Gilligan PH. Identification of Burkholderia and uncommon glucose-nonfermenting gram-negative bacilli isolated from patients with cystic fibrosis by use of matrix-assisted laser desorption Ionization–Time of flight mass spectrometry (MALDI-TOF MS). J Clin Microbiol 2016; 54:3071–3072 [View Article]
    [Google Scholar]
  46. Vandamme P, Peeters C. Time to revisit polyphasic taxonomy. Antonie van Leeuwenhoek 2014; 106:57–65 [View Article]
    [Google Scholar]
  47. Vijayakumar S, Biswas I, Veeraraghavan B. Accurate identification of clinically important Acinetobacter spp.: an update. Future Sci OA 2019; 5:FSO395 [View Article]
    [Google Scholar]
  48. Papalia M, Steffanowski C, Traglia G, Almuzara M, Martina P et al. Diversity of Achromobacter species recovered from patients with cystic fibrosis, in Argentina. Revista Argentina de Microbiología 2019S0325754119300483
    [Google Scholar]
  49. Šedo O, Radolfová-Křížová L, Nemec A, Zdráhal Z. Limitations of routine MALDI-TOF mass spectrometric identification of Acinetobacter species and remedial actions. J Microbiol Methods 2018; 154:79–85
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.001223
Loading
/content/journal/jmm/10.1099/jmm.0.001223
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed