Evaluation of an optimal epidemiological typing scheme for legionella pneumophila with whole-genome sequence data using validation guidelines

Sophia David*, Massimo Mentasti, Rediat Tewolde, Martin Aslett, Simon R. Harris, Baharak Afshar, Anthony Underwood, Norman Fry, Julian Parkhill, Timothy Harrison

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

39 Citations (Scopus)

Abstract

Sequence-based typing (SBT), analogous to multilocus sequence typing (MLST), is the current gold standard typing method for investigation of legionellosis outbreaks caused by Legionella pneumophila. However, as common sequence types (STs) cause many infections, some investigations remain unresolved. In this study, various whole-genome sequencing (WGS)-based methods were evaluated according to published guidelines, including (i) a single nucleotide polymorphism (SNP)-based method, (ii) extended MLST using different numbers of genes, (iii) determination of gene presence or absence, and (iv) a kmer-based method. L. pneumophila serogroup 1 isolates (n+106) from the standard typing panel, previously used by the European Society for Clinical Microbiology Study Group on Legionella Infections (ESGLI), were tested together with another 229 isolates. Over 98% of isolates were considered typeable using the SNP-and kmer-based methods. Percentages of isolates with complete extended MLST profiles ranged from 99.1% (50 genes) to 86.8% (1,455 genes), while only 41.5% produced a full profile with the gene presence/absence scheme. Replicates demonstrated that all methods offer 100% reproducibility. Indices of discrimination range from 0.972 (ribosomal MLST) to 0.999 (SNP based), and all values were higher than that achieved with SBT (0.940). Epidemiological concordance is generally inversely related to discriminatory power. We propose that an extended MLST scheme with +50 genes provides optimal epidemiological concordance while substantially improving the discrimination offered by SBT and can be used as part of a hierarchical typing scheme that should maintain backwards compatibility and increase discrimination where necessary. This analysis will be useful for the ESGLI to design a scheme that has the potential to become the new gold standard typing method for L. pneumophila.

Original languageEnglish
Pages (from-to)2135-2148
Number of pages14
JournalJournal of Clinical Microbiology
Volume54
Issue number8
DOIs
Publication statusPublished - Aug 2016

Bibliographical note

Funding Information:
INFORMATION This work, including the efforts of Sophia David, Martin Aslett, Simon R. Harris, and Julian Parkhill, was funded by Wellcome Trust (098051).

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