Bacteria and Bacterial Diagnostics

Diagnostics of bacterial agents is important for health surveillance and to investigate diseases in laboratory rodent colonies. A basic principle of laboratory animal health monitoring is that animals are free from all microorganisms which can interfere with experimental results including their reproducibility. Sentinel animals are usually kept in separate cages supplied with bedding from colony cages to be tested in order to pick up infectious agents in the colonies. To monitor the status of gnotobiotic rodents including those with a defined microbiota, metagenomic techniques have been developed. The most prevalent bacteria reported in both mice and rats have been Helicobacter spp., Rodentibacter pneumotropicus, Rodentibacter heylii or other Rodentibacter spp., Staphylococcus aureus, and beta-hemolytic streptococci of Lancefield type B. For bacteria which can be cultured, MALDI-TOF MS is preferred as a first-line detection method. For Chlamydia spp., DNA sequencing requires some kind of preliminary propagation of the agent in cell culture. A major limitation of 16S rRNA gene sequence-based methods for identification including PCR is that some species cannot be separated, for instance, within Bordetella. The same problem is relevant for MALDI-TOF MS, and in such cases, whole genome sequencing is needed for species-level identification.