Genomic resolution of outbreak-associated Legionella pneumophila serogroup 1 isolates from New York State.

Raphael BH1, Baker DJ2, Nazarian E2, Lapierre P2, Bopp D2, Kozak-Muiznieks NA1, Morrison SS1, Lucas CE1, Mercante JW1, Musser KA2, Winchell JM3.

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Abstract

A total of 30Legionella pneumophilaserogroup 1 (Lp1) isolates representing 10 separate legionellosis laboratory investigations ("outbreaks") that occurred in New York State between 2004 and 2012 were selected for evaluation of whole genome sequencing (WGS) approaches for molecular subtyping of this organism. Clinical and environmental isolates were available for each outbreak and were initially examined by pulsed-field gel electrophoresis (PFGE). Sequence based typing alleles were extracted from WGS data yielding complete sequence types (ST) for isolates representing 8 out of the 10 outbreaks evaluated in this study. Isolates from separate outbreaks sharing the same ST also contained the fewest differences in core genome single nucleotide polymorphisms (SNPs) and the greatest proportion of identical allele sequences in a whole genome multilocus sequence typing (wgMLST) scheme. Both core SNP and wgMLST analysis distinguished isolates from separate outbreaks including those from two outbreaks sharing indistinguishable PFGE profiles. Isolates from a hospital-associated outbreak spanning multiple years shared indistinguishable PFGE profiles but displayed differences in their genome sequences suggesting the presence of multiple environmental sources. Finally, thertxgene demonstrated differences in the repeat region sequence among ST1 isolates from different outbreaks suggesting that variation in this gene may be useful for targeted molecular subtyping approaches ofL. pneumophila.This study demonstrates the utility of various genome sequence analysis approaches ofL. pneumophilafor environmental source attribution studies while furthering the understanding ofLegionellaecology.

IMPORTANCE:

We demonstrate that whole genome sequencing helps to improve resolution ofLegionella pneumophilaisolated during laboratory investigations of legionellosis compared to traditional subtyping methods. These data can be important in confirming the environmental source of legionellosis outbreaks. Moreover, we evaluated various methods to analyze genome sequence data to help resolve outbreak-related isolates.