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Comparison of MALDI TOF and MLSA for identification of Pseudomonas and Aeromonas species in environmental samples

The heterogeneity of microbial community in environmental samples can hamper their accurate identification. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has been increasingly applied in clinical microbiology, but still underrated in classification and identification of environmental bacteria. The main reason is software/database used for analysis which is not environmentally-focused. In our study, we evaluate accuracy of MALDI TOF for identification of environmental bacteria from two ubiquitous, widespread genera, Pseudomonas and Aeromonas by comparing it with MLSA (multi locus sequence analysis) method. We used isolates of selected model bacteria (SMB) of Pseudomonas and Aeromonas from different aquaculture, feral and wild aquatic ecosystems, including water column, sediment and aquatic organisms, sampled in 2016 within AQUAHEALTH project. For MLSA analysis three (gyrB, rpoD, rpoB) and four (gyrB, rpoD, recA and dnaJ) housekeping genes of Pseudomonas and Aeromonas species were used for phylogenetic tree construction by MEGA 6 software. For MALDI TOF MS pure cultures of bacteria were grown on selective/TSA plates and then all samples were processed with a MALDI TOF Biotyper (Bruker Daltonik Microflex) commercially at the RBI, Zagreb, Croatia. Concordance with the two methods was 100% at the genus level, but lower at the species level, probably due to the absence of some reference spectra in the database of MALDI TOF. Pseudomonas and Aeromonas are known as very heterogenous genera with taxonomy that has undergone many changes. Our results confirmed the need for the database expansion of MALDI TOF MS for environmental bacteria identification.

Pseudomonas, Aeromonas, MALDI TOF, MLSA, environmental bacteria

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