Data from: Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli

Background: In 2011 northern Germany experienced a large outbreak of
Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent
to microbiology laboratories for epidemiological assessment highlighted
the importance of fast and inexpensive typing procedures. We have
therefore evaluated the applicability of a MALDI-TOF mass spectrometry
based strategy for outbreak strain identification. Methods: Specific peaks
in the outbreak strain’s spectrum were identified by comparative analysis
of archived pre-outbreak spectra that had been acquired for routine
species-level identification. Proteins underlying these discriminatory
peaks were identified by liquid chromatography tandem mass spectrometry
and validated against publicly available databases. The resulting typing
scheme was evaluated against PCR genotyping with 294 E. coli isolates from
clinical samples collected during the outbreak. Results: Comparative
spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z
10883. The underlying proteins were found to be of low prevalence among
genome sequenced E. coli strains. Marker peak detection correctly
classified 292 of 293 study isolates, including all 104 outbreak isolates.
Conclusions: MALDI-TOF mass spectrometry allowed for reliable outbreak
strain identification during a large outbreak of Shiga-Toxigenic E. coli.
The applied typing strategy could probably be adapted to other typing
tasks and might facilitate epidemiological surveys as part of the routine
pathogen identification workflow.