Variable genetic element typing: a quick method for epidemiological subtyping of Legionella pneumophila

Abstract

A total of 57 isolates of L. pneumophila were randomly selected from the German National Legionella strain collection and typed by monoclonal antibody subgrouping, seven gene locus sequence-based typing (SBT) scheme and a newly developed variable element typing (VET) system based on the presence or absence of ten variable genetic elements. These elements were detected while screening of a genomic library of strain Corby as well as taken from published data for PAI-1 (pathogenicity island) from strain Philadelphia. Specific primers were designed and used in gel based PCRs. PCR amplification of the mip gene that served as a control. The endpoint was the presence / absence of a PCR product on an ethidiumbromide strained gel. In the present study the index of discrimination was somewhat lower than that of the SBT (0.87 versus 0.97). Nevertheless, the results obtained showed as a 'proof of principle' that this simple and quick typing assay might be useful for the epidemiological characterization of Legionella pneumophila strains.

Real-time investigation of a Legionella pneumophila outbreak using whole genome sequencing

“…Sequence-based typing (SBT) and virulence gene profiling were initially utilized as typing methods as part of the outbreak response but these were not able to discriminate outbreak isolates from non-outbreak isolates, probably due to the clonal nature of L. pneumophila present in the region. Methods such as spoligotyping and variable genetic element typing have been shown to have the potential to discriminate between isolates belonging to the same SBT sequence type [7, 8]; however, these methods can be labour intensive and may still have limited resolution compared to that possible by comparison of the whole genome. Whole genome sequencing of bacteria is becoming increasingly rapid and inexpensive due to advances in next-generation sequencing technology.…”