Quite a mouthful this title! It is in general a bit of an outlier paper for me, but I am very happy to have been involved. I have been interested in MALDI-TOF (matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry) as a tool for bacterial identification for quite some time. Basically (VERY basically), this method involves zapping a colony with a laser, catching the molecules that come flying off and creating a peak chart based on their velocity and charge, see the pic below. (This analysis focuses on the level of proteins, and so is an example of proteomics.) Different bacteria consist of different molecules and produce a different peak pattern. Specific peaks can be compared among strains, or overall peak patterns similarity can be compared by making a dendrogram.
A main reason why I became interested in MALDI-TOF, is that in theory, you could process a large number of samples for little money in little time. The standard way of typing a bacterial isolate is to sequence a marker gene, almost always 16S rRNA (sometimes a different gene, see also here). This approach takes time, as it involves performing a PCR, sending it out by mail for a company to do the actual sequencing, followed by manually checking sequence quality. It is also relatively costly: around £5 per isolate and ususally projects involve at least dozens of isolates. However, MALDI-TOF machines are very expensive, you need a good reference database (i.e. a collection of isolates that have both been sequenced and ‘MALDI’d’ to compare any new isolates with) and in general it might not be quite as quick, cheap and simple as manufacturers would have you believe.
I came in contact with Ondrej Šedo, Zbynek Zdráhal and colleagues in the Czech Republic quite randomly as is usually the case, and they very nicely to offered to type some strain collections for me. (It is in a way weird that you can collaborate and publish with people you have not even met btw.) Using a bit of internal funding from CEITEC (the Central European Institute of Technology) at Masaryk University in Brno, we followed this up by typing Bacillus isolates from two collaborators of mine in Ljubljana, Slovenia, Ines Mandić-Mulec and Polonca Štefanic. (I need to write a post about the work MSc student Anja Pecman from their lab has done in Penryn last year some time soon!) These Bacillus isolates are very closely related ecotypes (see here) and it would be very useful to be able to tell them apart using MALDI-TOF instead of checking a handful mutations in a marker gene or doing loads of phenotypic assays. The experiments done on these isolates suggest that it is indeed possible to delineate different strains belonging to the species level using relatively easy fixes to standard protocols.
Balážová, T, Šedo O, Štefanic P, Mandić-Mulec P, Vos M and Zdráhal Z. Improvement in Staphylococcus and Bacillus strain differentiation by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry profiling by using microwave‐assisted enzymatic digestion.” Rapid Communications in Mass Spectrometry 28.17 (2014): 1855-1861. link to free download