Viridans Group Streptococci Clinical Isolates: MALDI-TOF Mass ...

S. pneumoniae identification

The sensitivity of the VITEK MS system for the identification of the 26 S. pneumoniae (25 clinical isolates and 1 ATCC 49619) was 100%, according to optochin susceptibility test, bile solubility test and lytA gene PCR. The specificity of the VITEK MS system for S. pneumoniae identification was 100% because the 132 non pneumococcal isolates (130 clinical isolates and 2 ATCC: S. thermophilus 19258 and S. equi 43079) were never identified as S. pneumoniae (Table 2).

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Table 2. VGS isolates phenotypic and identification results.

https://doi.org/10.1371/journal.pone.0120502.t002

The sensitivity of the MALDI-TOF Biotyper system for the identification of the 26 S. pneumoniae isolates was 100%, according to optochin susceptibility tests, bile solubility test and lytA gene PCR. The specificity of the MALDI-TOF Biotyper system for S. pneumoniae identification was 92.4% (10 non pneumococcal isolates were misidentified as S. pneumoniae) after the last upgrade of the database (January 2014) and 49% with the precedent version (67 non pneumococcal isolates were misidentified as S. pneumoniae) (Table 2).

The VITEK Compact system correctly identified 23/26 (88.5%) S. pneumoniae isolates, these three misidentified S. pneumoniae were in two cases identified as S.pneumoniae/S. mits at the same score and in one case as S. gordonii. The specificity of the VITEK Compact system for S. pneumoniae identification was 100%, the 132 non pneumococcal isolates were never identified as S. pneumoniae (Table 2).

Current phenotypic identification procedures and MALDI-TOF systems were compared to sequence-based identification of three bacterial genes tuf, sodA and rpoB to achieve definitive identification in case of misidentification and to exceed the limited ability of these procedures to differentiate the S. mitis group, as well documented [18,21].

RpoB gene sequencing was the best sequencing method for pneumococcal as well as for viridans non pneumococcal streptococci identification, as reported in Table 2. In fact, rpoB identified S. pneumoniae and non-pneumococcal viridans streptococci concordantly with optochin, bile solubility and lytA amplification than tuf gene sequencing that never identified S. pneumoniae as a single match, but gave always at least two choices at the same score than sodA gene sequencing that identified S. pneumoniae strains with a specificity of 100% but in 21 cases misidentified non pneumococcal streptococci as S. pneumoniae.