Bacterial Identification using MALDI-TOF MS

Bacterial species were directly identified from each bacterial colony using matrix-assisted laser desorption ionization-time mass spectrometry (MALDI-TOF MS) (Bruker Daltonics, Bremen, Germany) [58 (link)] following the same protocol as previously described by Seng et al. [59 (link)] with a Microflex spectrometer (Bruker Daltonics, Leipzig, Germany). A score of >2 allowed identification at the species level, and a score of <1.7 was considered as insufficient for the identification at the species level. In this case, 16S rRNA gene was amplified and the amplicon was sequenced. Briefly, DNA extraction was performed using EZ1 DNA kits (Qiagen, Courtaboeuf, France), according to the manufacturer’s protocol. Amplification and sequencing were performed as described in the study by Dahmana et al. [60 (link)] using 16S universal primers [61 (link)]. The obtained electropherograms were assembled and edited using the ChromasPro1.7.7 software (Technelysium Pty Ltd., Tewantin, Australia), and then the sequences obtained were compared with those available in the GenBank database by NCBI BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi).