Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.

Legionella spp. are the cause of a severe bacterial pneumonia known as Legionnaires' disease (LD). In some cases, current genetic subtyping methods cannot resolve LD outbreaks caused by common, potentially endemic L. pneumophila (Lp) sequence types (ST), which complicates laboratory investigati...

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Main Authors: Jeffrey W Mercante, Jason A Caravas, Maliha K Ishaq, Natalia A Kozak-Muiznieks, Brian H Raphael, Jonas M Winchell
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2018-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC6193728?pdf=render
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spelling doaj-f7e59296acc4443086f35f12606dbe9f2020-11-25T02:32:04ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-011310e020611010.1371/journal.pone.0206110Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.Jeffrey W MercanteJason A CaravasMaliha K IshaqNatalia A Kozak-MuiznieksBrian H RaphaelJonas M WinchellLegionella spp. are the cause of a severe bacterial pneumonia known as Legionnaires' disease (LD). In some cases, current genetic subtyping methods cannot resolve LD outbreaks caused by common, potentially endemic L. pneumophila (Lp) sequence types (ST), which complicates laboratory investigations and environmental source attribution. In the United States (US), ST1 is the most prevalent clinical and environmental Lp sequence type. In order to characterize the ST1 population, we sequenced 289 outbreak and non-outbreak associated clinical and environmental ST1 and ST1-variant Lp strains from the US and, together with international isolate sequences, explored their genetic and geographic diversity. The ST1 population was highly conserved at the nucleotide level; 98% of core nucleotide positions were invariant and environmental isolates unassociated with human disease (n = 99) contained ~65% more nucleotide diversity compared to clinical-sporadic (n = 139) or outbreak-associated (n = 28) ST1 subgroups. The accessory pangenome of environmental isolates was also ~30-60% larger than other subgroups and was enriched for transposition and conjugative transfer-associated elements. Up to ~10% of US ST1 genetic variation could be explained by geographic origin, but considerable genetic conservation existed among strains isolated from geographically distant states and from different decades. These findings provide new insight into the ST1 population structure and establish a foundation for interpreting genetic relationships among ST1 strains; these data may also inform future analyses for improved outbreak investigations.http://europepmc.org/articles/PMC6193728?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Jeffrey W Mercante
Jason A Caravas
Maliha K Ishaq
Natalia A Kozak-Muiznieks
Brian H Raphael
Jonas M Winchell
spellingShingle Jeffrey W Mercante
Jason A Caravas
Maliha K Ishaq
Natalia A Kozak-Muiznieks
Brian H Raphael
Jonas M Winchell
Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.
PLoS ONE
author_facet Jeffrey W Mercante
Jason A Caravas
Maliha K Ishaq
Natalia A Kozak-Muiznieks
Brian H Raphael
Jonas M Winchell
author_sort Jeffrey W Mercante
title Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.
title_short Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.
title_full Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.
title_fullStr Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.
title_full_unstemmed Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.
title_sort genomic heterogeneity differentiates clinical and environmental subgroups of legionella pneumophila sequence type 1.
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2018-01-01
description Legionella spp. are the cause of a severe bacterial pneumonia known as Legionnaires' disease (LD). In some cases, current genetic subtyping methods cannot resolve LD outbreaks caused by common, potentially endemic L. pneumophila (Lp) sequence types (ST), which complicates laboratory investigations and environmental source attribution. In the United States (US), ST1 is the most prevalent clinical and environmental Lp sequence type. In order to characterize the ST1 population, we sequenced 289 outbreak and non-outbreak associated clinical and environmental ST1 and ST1-variant Lp strains from the US and, together with international isolate sequences, explored their genetic and geographic diversity. The ST1 population was highly conserved at the nucleotide level; 98% of core nucleotide positions were invariant and environmental isolates unassociated with human disease (n = 99) contained ~65% more nucleotide diversity compared to clinical-sporadic (n = 139) or outbreak-associated (n = 28) ST1 subgroups. The accessory pangenome of environmental isolates was also ~30-60% larger than other subgroups and was enriched for transposition and conjugative transfer-associated elements. Up to ~10% of US ST1 genetic variation could be explained by geographic origin, but considerable genetic conservation existed among strains isolated from geographically distant states and from different decades. These findings provide new insight into the ST1 population structure and establish a foundation for interpreting genetic relationships among ST1 strains; these data may also inform future analyses for improved outbreak investigations.
url http://europepmc.org/articles/PMC6193728?pdf=render
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