title: Genomic Resolution of Outbreak-Associated Legionella pneumophila Serogroup 1 Isolates from New York State.
abstract: A total of 30 Legionella pneumophila serogroup 1 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 analyses 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, the rtx gene 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 for L. pneumophila This study demonstrates the utility of various genome sequence analysis approaches for L. pneumophila for environmental source attribution studies while furthering the understanding of Legionella ecology.
  
  
  
  We demonstrate that whole-genome sequencing helps to improve resolution of Legionella pneumophila isolated during laboratory investigations of legionellosis compared to traditional subtyping methods. These data can be important in confirming the environmental sources of legionellosis outbreaks. Moreover, we evaluated various methods to analyze genome sequence data to help resolve outbreak-related isolates.
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Brian H
authors.initials: BH
authors.lastname: Raphael
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Deborah J
authors.initials: DJ
authors.lastname: Baker
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Nazarian
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Pascal
authors.initials: P
authors.lastname: Lapierre
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Dianna
authors.initials: D
authors.lastname: Bopp
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Natalia A
authors.initials: NA
authors.lastname: Kozak-Muiznieks
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Shatavia S
authors.initials: SS
authors.lastname: Morrison
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Claressa E
authors.initials: CE
authors.lastname: Lucas
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: Mercante
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Kimberlee A
authors.initials: KA
authors.lastname: Musser
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA jwinchell@cdc.gov.
authors.forename: Jonas M
authors.initials: JM
authors.lastname: Winchell
mesh_terms: D004196:Disease Outbreaks; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D005838:Genotype; D006801:Humans; D016952:Legionella pneumophila / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D007877:Legionnaires' Disease / Q000453:epidemiology* / Q000382:microbiology*; D017720:Molecular Epidemiology / Q000379:methods; D058889:Molecular Typing / Q000379:methods*; D009518:New York / Q000453:epidemiology; D065288:Serogroup