Characterising the methylome ofLegionella longbeachaeserogroup 1 clinical isolates and assessing geo-temporal genetic diversity
Authors: Slow S , Anderson T , Murdoch DR , Bloomfield S , Winter D , Biggs PJ 
Published: September 2020

Legionella longbeachaeis an environmental bacterium that is commonly found in soil and composted plant material. In New Zealand (NZ) it is the most clinically significantLegionellaspecies causing around two-thirds of all notified cases of Legionnaires’ disease. Here we report the sequencing and analysis of the geo-temporal genetic diversity of 54L. longbeachaeserogroup 1 (sg1) clinical isolates that were derived from cases from around NZ over a 22-year period, including one complete genome and its associated methylome.

Our complete genome consisted of a 4.1 Mb chromosome and a 108 kb plasmid. The genome was highly methylated with two known epigenetic modifications, m4C and m6A, occurring in particular sequence motifs within the genome. Phylogenetic analysis demonstrated the 54 sg1 isolates belonged to two main clades that last shared a common ancestor between 108 BCE and 1608 CE. These isolates also showed diversity at the genome-structural level, with large-scale arrangements occurring in some regions of the chromosome and evidence of extensive chromosomal and plasmid recombination. This includes the presence of plasmids derived from recombination and horizontal gene transfer between variousLegionellaspecies, indicating there has been both intra-species and inter-species gene flow. However, because similar plasmids were found among isolates within each clade, plasmid recombination events may pre-empt the emergence of newL. longbeachaestrains.

Our high-quality reference genome and extensive genetic diversity data will serve as a platform for future work linking genetic, epigenetic and functional diversity in this globally important emerging environmental pathogen.

Author Summary

Legionnaires’ disease is a serious, sometimes fatal pneumonia caused by bacteria of the genusLegionella. In New Zealand, the species that causes the majority of disease isLegionella longbeachae. Although the analyses of pathogenic bacterial genomes is an important tool for unravelling evolutionary relationships and identifying genes and pathways that are associated with their disease-causing ability, until recently genomic data forL. longbeachaehas been sparse. Here, we conducted a large-scale genomic analysis of 54L. longbeachaeisolates that had been obtained from people hospitalised with Legionnaires’ disease between 1993 and 2015 from 8 regions around New Zealand. Based on our genome analysis the isolates could be divided into two main groups that persisted over time and last shared a common ancestor up to 1700 years ago. Analysis of the bacterial chromosome revealed areas of high modification through the addition of methyl groups and these were associated with particular DNA sequence motifs. We also found there have been large-scale rearrangements in some regions of the chromosome, producing variability between the differentL. longbeacahestrains, as well as evidence of gene-flow between the variousLegionellaspecies via the exchange of plasmid DNA.