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. 2020 Dec 1;20(1):367.
doi: 10.1186/s12866-020-02052-7.

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae

Sivkheng Kann  1 , Sena Sao  2 , Chanleakhena Phoeung  1 , Youlet By  1   3 , Juliet Bryant  4 , Florence Komurian-Pradel  4 , Vonthanak Saphonn  5 , Monidarin Chou  1 , Paul Turner  6   7
Affiliations

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae

Sivkheng Kann et al. BMC Microbiol. .

Abstract

Background: Serotyping of Streptococcus pneumoniae is important for monitoring of vaccine impact. Unfortunately, conventional and molecular serotyping is expensive and technically demanding. This study aimed to determine the ability of matrix-assisted laser desorption-ionisation time-of-flight (MALDI-TOF) mass spectrometry to discriminate between pneumococcal serotypes and genotypes (defined by global pneumococcal sequence cluster, GPSC). In this study, MALDI-TOF mass spectra were generated for a diverse panel of whole genome sequenced pneumococcal isolates using the bioMerieux VITEK MS in clinical diagnostic (IVD) mode. Discriminatory mass peaks were identified and hierarchical clustering was performed to visually assess discriminatory ability. Random forest and classification and regression tree (CART) algorithms were used to formally determine how well serotypes and genotypes were identified by MALDI-TOF mass spectrum.

Results: One hundred and ninety-nine pneumococci, comprising 16 serotypes and non-typeable isolates from 46 GPSC, were analysed. In the primary experiment, hierarchical clustering revealed poor congruence between MALDI-TOF mass spectrum and serotype. The correct serotype was identified from MALDI-TOF mass spectrum in just 14.6% (random forest) or 35.4% (CART) of 130 isolates. Restricting the dataset to the nine dominant GPSC (61 isolates / 13 serotypes), discriminatory ability improved slightly: the correct serotype was identified in 21.3% (random forest) and 41.0% (CART). Finally, analysis of 69 isolates of three dominant serotype-genotype pairs (6B-GPSC1, 19F-GPSC23, 23F-GPSC624) resulted in the correct serotype identification in 81.1% (random forest) and 94.2% (CART) of isolates.

Conclusions: This work suggests that MALDI-TOF is not a useful technique for determination of pneumococcal serotype. MALDI-TOF mass spectra appear more associated with isolate genotype, which may still have utility for future pneumococcal surveillance activities.

Keywords: Genotype; MALDI-TOF; Mass spectrometry; Serotype; Streptococcus pneumoniae.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
A cluster dendrogram of serotype-organised MALDI-TOF mass spectrum data for 16 serotypes + non-typeable (NT) isolates. The isolate selection includes 130 pneumococcal isolates from 46 global pneumococcal sequence clusters (GPSC). The inner metadata ring denotes GPSC and the outer ring serotype
Fig. 2
Fig. 2
A cluster dendrogram of serotype-organised MALDI-TOF mass spectrum data including only genotypes with ≥ 5 isolates. The isolate selection includes 61 isolates comprising 13 serotypes and nine global pneumococcal sequence clusters (GPSC). The inner metadata ring denotes GPSC and the outer ring serotype
Fig. 3
Fig. 3
A cluster dendrogram of serotype-organised MALDI-TOF mass spectrum data for the three dominant pneumococcal serotype-genotype pairs. The isolate selection comprises 69 pneumococcal isolates. The inner metadata ring denotes global pneumococcal sequence type (GPSC) and the outer ring serotype
See this image and copyright information in PMC

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