While numerous studies have attempted to demonstrate equivalence between MALDI-TOF mass spectrometry (MS) and 16S rRNA gene sequencing for bacterial identification, very few studies focus on challenges associated with MALDI-TOF MS reporting when the top two database matches occur at close proximity of scores (difference of less than 0.1 out of 3.0). The purpose of this presentation is to examine the relative limits and strengths of MALDI-TOF MS and 16S rRNA gene sequencing for a cohort of such identification scenarios. The analysis cohort involved nearly 3,250 predominantly environmental bacterial isolates tested over 2 years (March 2014 - March 2016) by MALDI-TOF MS that had top match and second match occurring within 0.1 score difference. Due to lack of adequate separation between the top two matches, these samples were subsequently tested by DNA sequencing of the first 500bp of the 16S rRNA gene for identification. The comparison of results between these technologies highlighted organisms that cannot be unambiguously resolved to species-level by routine MALDI-TOF MS and demonstrated the corresponding performance of 16S rRNA gene sequencing.


  • Prasanna Khot, PhD, Senior Staff Scientist, Charles River