Epidemiological Genotyping of Legionella pneumophila: from Plasmids to Sequence-Based Typing
Norman K. Fry and Sophie Jarraud
from: Legionellosis Diagnosis and Control in the Genomic Era (Edited by: Jacob Moran-Gilad and Rachel E. Gibbs). Caister Academic Press, U.K. (2020) Pages: 301-320.
Genotyping is used for the identification and differentiation of Legionella types within a species and most often for the species, L. pneumophila, which causes most cases of human infection. Due to the complex nature of Legionella outbreaks and sporadic infections which are often associated with travel, effective genotyping methods must be transportable and accessible with enough resolution to identify closely related strains. This chapter describes each genotyping method developed for the discernment of L. pneumophila including the discovery of diversity within plasmid genomes, restriction endonuclease analysis, pulsed-field gel electrophoresis, restriction fragment length polymorphism analysis and ribotyping, polymerase chain reaction (PCR) typing, amplified fragment length polymorphism analysis and finally sequence-based typing (SBT) which is the recent gold-standard. The shortfalls of each typing method will be discussed and how these flaws lead us into the era of next generation sequencing (NGS) which has already begun to revolutionize typing methodology read more ...