No identification system is without problems and the same is true with MALDI-TOF MS. A few of the most common issues include the inability to separate certain microorganisms (based on profile similarity), the absence of microorganisms from the database, and the identification of an apparently unusual microorganism that is closely related to a commonly known microorganism (eg, Enterobacter absuriae, a member of the Enterobacter cloacae complex). It is of significant note that erroneous identifications are extremely rare, but caution needs to be exercised and correlation with growth requirements (rate of growth, atmosphere of growth), colony morphology, and Gram stain are strongly recommended.
One common example of the inability to separate certain organisms involves Shigella species and Escherichia coli, which are so closely related that Shigella is not identified by MALDI-TOF MS. To differentiate, colonies should be examined for lactose fermentation, motility, and spot indole should be performed. If positive, an identification of E. coli is appropriate, especially for non-stool specimens. If negative for these tests and particularly for stool isolates, Shigella should be suspected and an alternative method for identification like a phenotypic or immunologic (agglutination) assay performed.
Additionally, using routine database analysis, Streptococcus pneumoniae cannot be distinguished from S. mitis. As such, colony morphology, optochin disc susceptibility (pneumococcus if susceptible), bile solubility (pneumococcus soluble), or a pneumococcus specific agglutination assay (pneumococcus is positive) can be used to differentiate the two bacteria. It is particularly important to identify these bacteria correctly as S. mitis/oralis frequently represents non-pathogenic colonization, while S. pneumoniae is a pathogen capable of causing serious and life-threatening disease. There is now some evidence that MALDI-TOF MS can differentiate these bacteria, which should eliminate the need to rely on optochin disk and bile solubility testing (Manji et al. 2014, Chen et al. 2015).
The ability to definitively identify organisms to genus and species that are unfamiliar to clinicians and laboratorians alike, poses a particular problem. Users of the Bruker system have encountered a number of these, and some have chosen to lump these into a “group” or “complex” of microorganisms with a reporting designation familiar to practitioners. Additionally, reporting by genus designation may also be of more significance than giving a species designation that has no additional clinical impact. Some examples of these are listed in the table on the right.
A description of microorganisms can be found in a number of online databases, including:
List of Prokaryotic Names with Standing in Nomenclature (LPSN) website. Available at: http://www.bacterio.net/
. Accessed September 3, 2019.
Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) website. Available at: http://www.dsmz.de/
. Accessed September 3, 2019.