Bacterial Sub-Species Typing Using Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry: What Is Promising?

Round 1

Reviewer 1 Report

This manuscript provides a concise review of the MALDI-TOF technology and how it can be used to identify bacterial sub-species. The manuscript is logically presented with each section focused on an individual bacterium. The manuscript benefited from being well structured. I appreciated that for each of the 13 papers reviewed the same structure was used, the organism typed, the biotyper system used and interpretation methods, the typing method used for comparison, the experimental protocol used to generate the MALDI-TOF peaks, the measurement conditions and software used for processing and finally the outcome. Using this standard approach makes the manuscript easy to read, understand and interpret.

This manuscript is well researched, reported and written and adds to the scientific knowledge of bacterial identification and will be of great benefit for pathology and research laboratories needing to rapidly, reliably and cheaply identify bacterial sub-species.

I have only minor edits to suggest:

1. There are a few inconsistencies on how names are reported. Could these please be fixed so they are consistent?
   1. Line 163 and 174 Axima is in uppercase and Line 282 and 299 it is in lower case
   2. Line 188 and 194 Vitek is in uppercase and Line 239 and 249 is in lower case
2. Are the biotypers presented in Line 188 and Line 239 both bioMérieux Vitek MS instruments? If so, can you please add bioMérieux into the name in Line 188
3. For several of the studies reviewed you were able to report a quantifiable result on the success of the MALDI-TOF typing. For example, Line 88 and 89, a 93% agreement was achieved between MALDI-TOF typing and PFGE as well as spa typing. I understand the value of commenting whether a particular approach was 'successful' or achieved 'poor reproducibility' (for example) however including a figure on the success of each study would add to the weight of your review when reporting the results. Is quantifiable data available for those studies where you do not report it? If so, could you please include.

Author Response

Dear Reviewer

Thank you very much for taking the time to review our manuscript and your kind advice.   I have made the edits according to your suggestions.

Regarding point 3: Many of the studies reviewed do not quantify their success and some put their quantified success in reference to typeability rather than the genotyping methods they used. I have added a table where the level of success is described for each study.

Kind regards
Dr Charlotte Preston-Huber

Reviewer 2 Report

This review reflects well the state of art (published MS) concerning MALDI-TOF MS typing of bacterial isolates. Each article cited is fully described (resuming the most important points, what is very interesting); however sometimes authors do not explain well why they have selected them (the real importance) and how they contribute to the general question. It is not enough to say that they could or not achieve typing by MALDI-TOF MS and if it was or not accurate in a particular case; general conclusions are needed and that is only possible if conditions are similar. For these purpose it might be clarifying include a table that summarizes the relevant data, what also could serve to arise patterns and improve the conclusion achieved in 3 what is a bit abstract.      

Author Response

Dear Reviewer

Thank you very much for taking the time to review our manuscript and the advice given. Regarding the choice of studies, I have added the following sentence to the manuscript:

„The publications were selected based on overall diversity of bacterial species investigated, sample size, and the use of genotyping reference methods for comparison.

 I have also added a table describing shared methods and the levels of success for each study reviewed. Thank you for suggesting this.

From what we have found in the studies reviewed it appears that similar conditions may not be necessary in all cases. One group was able perform successful MALDI typing even when using a different MALDI instrument located in a different laboratory.

With kind regards

Dr Charlotte Preston-Huber