Genomic Analysis of Legionella pneumophila in the Drinking Water System of a Large Building over 25 Years

Abstract

Legionella pneumophila, the causative agent of Legionnaires disease, is often found in the plumbing systems of buildings from where it can be transmitted to humans via inhalation or aspiration of contaminated water drops. Annual routine water sampling from the potable water system of an occupational healthcare building in Basel over 25 years was performed in accordance with national guidelines. Overall, 309 water samples were collected at 38 time points over the period of 25 years. L. pneumophila was recovered from 120 water samples (38.8%) from 26 time points. No clinical infections were recorded during this period. Initial decontamination measures were successful for approximately 12 years, after which an increase in the total number of Legionella colony forming units as well as of L. pneumophila-positive sites was noticed, in 2008. Whole genome sequencing (WGS) analysis of n=123 isolates from n=113 samples showed all L. pneumophila to be sequence type (ST)-45 (Sequence based typing scheme). The isolates are closely related, with only 408 single nucleotide polymorphisms (SNPs) among all isolates after the bioinformatic removal of recombination events. Over the 25 years, a single lineage deriving from a recent common ancestor colonized the water system of this building. The phylogeny of isolate genomes can be interpreted as inferring good water circulation, possible recolonization from a common source after cleaning, with genome evolution and insertion / loss of large elements evident. Regular monitoring of waterlines in healthcare settings helps to identify concentrations of Legionella spp. and WGS is recommended for detailed investigation. Data SummaryAll data is submitted to the ENA under project PRJEB79004 under accession numbers ERR13662450-ERR13662572. Impact StatementThis is the most detailed, long-term study of L. pneumophila in the water system of a single building recorded to date. The L. pneumophila isolates found in the building over the sampling period of 25 years were all closely related, belonging to ST45. SNP analysis suggested that the common ancestor of the cluster was from around 1938 (range 1911 to 1959), and movement of a large genomic island and plasmid transfer were observed. Despite several decontamination measures, it was impossible to completely eradicate Legionella spp. from the water system of the historic building. No infections could be attributed to the presence of L. pneumophila in this building. To mitigate the risk of Legionellosis from such buildings, awareness, regular water testing based on official national guidelines and recommendations, and other control measures, such as the use of sterile water for critical procedures can be recommended.