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Study Abstract
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Sequence-based typing (SBT) is the current gold-standard typing method for investigation of legionellosis outbreaks caused by Legionella pneumophila. However, as common sequence types (STs) cause a large number of infections, some investigations remain unresolved by SBT. Here, a number of whole genome sequencing (WGS)-based methods were evaluated as potential typing tools including: i) a SNP-based approach; ii) extended multi-locus sequence typing (MLST) using various numbers of genes; iii) a gene presence/absence-based method; iv) a kmer-based method. They were tested using 106 L. pneumophila serogroup 1 isolates from the standard “typing panel”, as previously used by the European Society for Clinical Microbiology Study Group on Legionella Infections (ESGLI), and an additional 229 isolates.Over 98% isolates were considered typable using the mapping- and kmer-based methods. The percentage of isolates with complete extended MLST profiles ranged from 99.1% (50-gene scheme) to 86.8% (1455-gene scheme) while only 41.5% produced a full profile with the gene presence/absence scheme. Sequencing replicates demonstrated that all WGS-based methods offer 100% reproducibility. When one or more differences yield different types, the methods produce indices of discrimination ranging from 0.972 (ribosomal MLST) to 0.999 (SNP-based method), and all values are higher than that achieved with SBT (0.940). The epidemiological concordance is generally inversely related to the index of discrimination, with the most discriminatory methods failing to provide sufficient epidemiological concordance. Based on these analyses, we propose that an extended MLST scheme with ~50-100 genes maintains good epidemiological concordance while substantially improving on the discrimination offered by SBT, and has the potential to become a new “gold standard” typing method for L. pneumophila.
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