Identifying Bacteria with MALDI-TOF MS Methods

By Caleb Sooknanan


Detecting microbial agents that cause bloodstream infections is a common task in clinical microbiology laboratories. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become one of the most effective bacterial identification methods in recent years, but the corresponding kit for preparing samples is very expensive. This limits the potential use of MALDI-TOF MS in clinical settings. Dr. Shota Yanetani and researchers from Tokyo Medical University and Kyorin University School of Medicine performed a study to evaluate the accuracy of microorganism identification via MALDI-TOF MS for three different culture preparation methods.

The study occurred between December 2013 and June 2014. It compared bacterial identification rates from positive culture bottles prepared using the Sepsityper, centrifugation, and saponin methods. The blood culture specimens were tested for positivity using BacT/ALERT 3D. 228 bottle broths that exhibited positive blood cultures underwent Gram staining. Polymicrobial growth samples were then excluded, and the remaining 195 samples were further analyzed.

For the three sample preparation methods, MALDI-TOF MS analysis procedures were used to directly identify microorganisms from positive blood cultures. The results obtained by MALDI-TOF MS using the three preparation methods were then compared with the results obtained from conventional identification methods. When results between MALDI-TOF MS and conventional methods differed, 16S rRNA gene sequencing was used. Accurate identification via MALDI-TOF MS was defined as results that matched those of conventional methods or results disagreed with conventional methods but matched the results of 16S rRNA gene analysis.

Of the 195 monomicrobial samples included in this study, 92 Gram-positive cocci, 72 Gram-negative rods, 20 Gram-positive rods, and 11 yeast-like fungi were identified by conventional methods or 16S rRNA gene sequencing. 78.5%, 68.7%, and 76.4% of bacteria were appropriately identified from positive blood cultures using the Sepsityper, centrifugation, and saponin methods, respectively. Therefore, the identification rates in samples prepared using the Sepsityper and saponin methods were higher than the rate for the one prepared using the centrifugation method.

Limitations of the study included the infrequent identification of Gram-positive rods, compared to Gram-negative rods and fungi. Also, some polymicrobial samples may have been unintentionally subject to analysis, leading to inaccurate bacterial identifications.

Given how the Saponin method was suggested to be the equivalent of the Sepsitype method in terms of bacterial identification, more research is needed on how these methods can contribute to more accurate and precise practices in identifying pathogens.



  1. Yonetani, et al., Direct identification of microorganisms from positive blood cultures by MALDI-TOF MS using an in-house saponin method. International Journal of Infectious Diseases 52, 37-42 (2016). doi: 10.1016/j.ijid.2016.09.014
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