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Elucidating constraints for differentiation of major human Klebsiella pneumoniae clones using MALDI-TOF MS

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Abstract

The establishment of matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) in routine microbial identification boosted many developments towards high-throughput applications, including bacterial typing. However, results are still controversial for different bacterial species. We aim to evaluate the suitability of MALDI-TOF MS for typing clinically relevant multidrug resistant (MDR) Klebsiella pneumoniae subsp. pneumoniae clones using routine conditions and a previously validated chemometric analysis workflow. Mass spectra of 83 K. pneumoniae clinical isolates representing major human MDR clones [11 sequence types (STs), 22 PFGE-types] recovered in Portugal and Spain during outbreaks and non-outbreak situations (2003–2012) were obtained from cell extracts (CE) and intact cells (IC), and analysed with different chemometric tools. We observed a highly consistent peak pattern among isolates from different clones either with CE or IC, suggesting a high degree of conservation of biomolecules analysed (a large part corresponding to ribosomal proteins). Moreover, the low degree of agreement between MALDI-TOF MS and other methods (from 34.9 % to 43.4 % of correct assignments for CE and from 40.8 % to 70.1 % for IC) corroborates the low discriminatory potential of the technique at infraspecies level. Our results suggest a low discriminatory power of MALDI-TOF MS for clinically relevant MDR K. pneumoniae clones and highlight the need of developing tools for high-resolution typing in this species.

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Author’s contributions

C.R., A.N. and L.P. contributed to the study design. C.R. performed the experimental work related to the acquisition of mass spectra in MALDI-TOF MS, performed chemometric analysis and wrote the manuscript. A.N. participated in data analysis and wrote the manuscript. C.S. and J.A.L. provided expertise in chemometric analysis, participated in the analysis of data, and the revision of the manuscript. H.R. provided access to the MALDI-TOF MS (Bruker Daltonics, Bremen, Germany) equipment, reagents and software, and part of the Portuguese strain collection. T.M.C. and R.C. provided the Spanish strain collection used in this study, expertise and participated in the revision of the manuscript. L.P. contributed for the general conceptualization of the study and methodological approach, the analysis of data and revision of the manuscript. All authors read and approved the final version of this manuscript.

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Authors and Affiliations

  1. UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge de Viterbo Ferreira, n. 228, 4050-313, Porto, Portugal

    C. Rodrigues, Â. Novais & L. Peixe

  2. LAQV-REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal

    C. Sousa

  3. Serviço de Microbiologia, Centro Hospitalar do Porto, Porto, Portugal

    H. Ramos

  4. Servicio de Microbiologia, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain

    T. M. Coque & R. Cantón

  5. CIBER Epidemiología y Salud Pública, Madrid, Spain

    T. M. Coque

  6. Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain

    R. Cantón

  7. Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal

    J. A. Lopes

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  1. C. Rodrigues
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  2. Â. Novais
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  3. C. Sousa
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  4. H. Ramos
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  5. T. M. Coque
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  8. L. Peixe
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Correspondence to L. Peixe.

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Funding

This work received financial support from the European Union (FEDER funds) through Programa Operacional Factores de Competitividade—COMPETE and Portuguese National Funds (FCT, Fundação para a Ciência e Tecnologia) (UID/Multi/04378/2013). Carla Rodrigues and Ângela Novais were supported by fellowships from FCT through Programa Operacional Capital Humano (POCH) (grants number SFRH/BD/84341/2012 and SFRH/BPD/104927/2014, respectively). Spanish isolates were recovered during execution of grants founded by the European Commission (TROCAR-FP7-HEALTH-F3-2008-223031 and, R-GNOSIS-FP7-HEALTH-F3-2011-282512) and the Instituto de Salud Carlos III of Spain (REIPI RD12/0015, Spanish Network for Research in Infectious Diseases) co-financed by the European Development Regional Fund, A Way to Achieve Europe.

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The authors declare that they have no conflict of interest.

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Rodrigues, C., Novais, Â., Sousa, C. et al. Elucidating constraints for differentiation of major human Klebsiella pneumoniae clones using MALDI-TOF MS. Eur J Clin Microbiol Infect Dis 36, 379–386 (2017). https://doi.org/10.1007/s10096-016-2812-8

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  • DOI: https://doi.org/10.1007/s10096-016-2812-8

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