Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Percy Schröttner - , Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty Carl Gustav Carus (Author)
  • Florian Gunzer - , Institute of Medical Microbiology and Virology (Author)
  • Jana Schüppel - , Institute of Medical Microbiology and Virology (Author)
  • Wolfram W Rudolph - , Institute of Medical Microbiology and Virology (Author)

Abstract

There are a number of rare and, therefore, insufficiently described bacterial pathogens which are reported to cause severe infections especially in immunocompromised patients. In most cases only few data, mostly published as case reports, are available which investigate the role of such pathogens as an infectious agent. Therefore, in order to clarify the pathogenic character of such microorganisms, it is necessary to conduct epidemiologic studies which include large numbers of these bacteria. The methods used in such a surveillance study have to meet the following criteria: the identification of the strains has to be accurate according to the valid nomenclature, they should be easy to handle (robustness), economical in routine diagnostics and they have to generate comparable results among different laboratories. Generally, there are three strategies for identifying bacterial strains in a routine setting: 1) phenotypic identification characterizing the biochemical and metabolic properties of the bacteria, 2) molecular techniques such as 16S rRNA gene sequencing and 3) mass spectrometry as a novel proteome based approach. Since mass spectrometry and molecular approaches are the most promising tools for identifying a large variety of bacterial species, these two methods are described. Advances, limitations and potential problems when using these techniques are discussed.

Details

Original languageEnglish
JournalJournal of visualized experiments : JoVE
Issue number113
Publication statusPublished - 11 Jul 2016
Peer-reviewedYes

External IDs

PubMedCentral PMC4993432
Scopus 84979929565

Keywords

Keywords

  • Bacteria/classification, Bacterial Infections/diagnosis, Humans, Proteomics/methods, RNA, Ribosomal, 16S/genetics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization