Accurate Differentiation of Streptococcus pneumoniae from other Species within the Streptococcus mitis Group by Peak Analysis Using MALDI-TOF MS

Abstract

Despite the benefits of MALDI-TOF MS technology (Matrix-Assisted Laser Desorption-Ionization Time-Of-Flight Mass Spectrometry) reported worldwide and the continuous improving of the available databases, discrimination between Streptococcus pneumoniae and closely related species within the Streptococcus mitis group (SMG) using this methodology has been suboptimal. However, the accurate identification at the species level of this group of microorganisms is important for the appropriate management of infected patients. In this study, 216 SMG isolates -101 S. pneumoniae and 115 corresponding to 7 non-pneumococcal species within this group- were analyzed. All the isolates had been previously identified by conventional methods (optochin and bile solubility tests) and non-pneumococcal isolates were confirmed by sequence analysis (sodA and plys genes) when required. The isolates were also identified with the MALDI Biotyper 3.1 (Bruker Daltonics, Bremen, Germany) using an updated library containing 6,903 Main Spectra Profiles (MSPs). All the analyzed S. pneumoniae were correctly identified with MALDI-TOF MS at species level using the most updated database and all the non-pneumococcal SMG isolates were also identified at the group level. Several peaks (4,964.32, 6,888.90, and 9,516.46 m/z) have been found to be specific of S. pneumoniae, whilst a different set of peaks have proved to be present only in S. mitis (6,839.07 m/z) and S. oralis (5,297.61, 5822.53, and 6,839.07 m/z). Peak analysis allowed correct species assignment of 101/101 S. pneumoniae isolates (100%) and 102/105 S. mitis/oralis isolates (97.1%). Thus, the implementation of MALDI-TOF MS plus peak analysis for the identification of this group of microorganisms may provide precise species-level information that will allow the early implementation of directed antibiotic therapy.

Recent Advances and Ongoing Challenges in the Diagnosis of Microbial Infections by MALDI-TOF Mass Spectrometry

“…In a first evaluation of the accuracy of the Bruker system for routine identification of bacteria, the system correctly identified 95.4% of the 1660 bacterial isolates tested, 84.1% at species level and 11.3% at genus level ( Seng et al, 2009 ). Lack of identification and misidentification were mainly due to insufficient database entries for some bacterial species but these limitations could be overcome by the addition of spectra of successfully identified clinical isolates into commercial databases ( Seng et al, 2009 ; Fernández-Olmos et al, 2012 ; Nomura, 2015 ; Carrasco et al, 2016 ; Marín et al, 2017 ).…”

“…However, for microorganisms with complex cell wall composition such as Mycobacterium spp., the accuracy of identification is often sub-optimal ( Cao et al, 2018 ), and specific pretreatment may be required for protein extraction before MALDI-TOF MS analysis can be effectively performed ( Park et al, 2016 ; Moreno et al, 2018 ). Moreover, identification of some bacterial species may be still problematic, especially for Gram-positive bacteria such as Streptococcus pneumoniae and members of the Streptococcus oralis/mitis group ( Marín et al, 2017 ; Slotved et al, 2017 ), and Listeria spp. ( Farfour et al, 2012 ) but also for some Gram-negative bacteria such as Shigella spp., having low rate of differences in their ribosomal protein sequence with Escherichia coli ( Khot and Fisher, 2013 ), some Enterobacter spp.…”

Strategy using a new antigenic test for rapid diagnosis of Streptococcus pneumoniae infection in respiratory samples from children consulting at hospital

“…The microbiological diagnosis of S. pneumoniae infection is usually based on the semi-quantitative culture of the bacterium from samples of the respiratory tract (usually sputum or rhino-pharyngeal secretions) [4,5]. However, several factors may contribute to make the microbiological confirmation difficult: (i) the differentiation between strains of S. pneumoniae and of alpha haemolytic streptococci (formerly called viridans) that are part of the commensal oral flora may be difficult [6,7]; (ii) the correct identification of S. pneumoniae compared to other Streptococcus species of the mitis group relies usually on the combination of several phenotypic techniques including colony morphology, optochine susceptibility, bile salt lysis and mass spectrometry [6,8,9]; (iii) the culture can be falsely negative when the patient has received early antimicrobial treatment. Therefore, the time to get the result of conventional culture, that is usually 18 h, can be delayed, leading to probabilistic antibiotic treatments that impair antibiotic stewardship [10].…”

A Case of Recurrent Erysipelas Caused by Streptococcus mitis Group

“…Recently, the performance of separating out and identifying S. pneumoniae has been improved by combining a better MALDI Biotyper database with a new algorithm for weighted list (score) [ 20 ]. By assigning specific peak combinations in the mass spectra that are associated with specific species in the S. mitis group, one may further improve species determination [ 21 , 22 ].…”