Novel Method To Identify Source-Associated Phylogenetic Clustering Shows that Listeria monocytogenes Includes Niche-Adapted Clonal Groups with Distinct Ecological Preferences

K. K. Nightingale; K. Lyles; M. Ayodele; P. Jalan; Rasmus Nielsen; M. Wiedmann

doi:10.1128/JCM.00618-06

Novel Method To Identify Source-Associated Phylogenetic Clustering Shows that Listeria monocytogenes Includes Niche-Adapted Clonal Groups with Distinct Ecological Preferences

K. K. Nightingale, K. Lyles, M. Ayodele, P. Jalan, Rasmus Nielsen, M. Wiedmann

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

22 Citationer (Scopus)

Abstract

Udgivelsesdato: October 2006

Originalsprog	Engelsk
Tidsskrift	Journal of Clinical Microbiology
Vol/bind	44
Udgave nummer	10
Sider (fra-til)	3742-3751
ISSN	0095-1137
DOI	https://doi.org/10.1128/JCM.00618-06
Status	Udgivet - 2006

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10.1128/JCM.00618-06

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Novel Method To Identify Source-Associated Phylogenetic Clustering Shows that Listeria monocytogenes Includes Niche-Adapted Clonal Groups with Distinct Ecological Preferences. / Nightingale, K. K.; Lyles, K.; Ayodele, M. et al.
I: Journal of Clinical Microbiology, Bind 44, Nr. 10, 2006, s. 3742-3751.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

@article{22175db06c3711dcbee902004c4f4f50,

title = "Novel Method To Identify Source-Associated Phylogenetic Clustering Shows that Listeria monocytogenes Includes Niche-Adapted Clonal Groups with Distinct Ecological Preferences",

abstract = "While phylogenetic and cluster analyses are often used to define clonal groups within bacterial species, the identification of clonal groups that are associated with specific ecological niches or host species remains a challenge. We used Listeria monocytogenes, which causes invasive disease in humans and different animal species and which can be isolated from a number of environments including food, as a model organism to develop and implement a two-step statistical approach to the identification of phylogenetic clades that are significantly associated with different source populations, including humans, animals, and food. If the null hypothesis that the genetic distances for isolates within and between source populations are identical can be rejected (SourceCluster test), then particular clades in the phylogenetic tree with significant overrepresentation of sequences from a given source population are identified (TreeStats test). Analysis of sequence data for 120 L. monocytogenes isolates revealed evidence of clustering between isolates from the same source, based on the phylogenies inferred from actA and inlA (P = 0.02 and P = 0.07, respectively; SourceCluster test). Overall, the TreeStats test identified 10 clades with significant (P < 0.05) or marginally significant (P < 0.10) associations with defined sources, including human-, animal-, and food-associated clusters. Epidemiological and virulence phenotype data supported the fact that the source-associated clonal groups identified here are biologically valid. Overall, our data show that (i) the SourceCluster and TreeStats tests can identify biologically meaningful source-associated phylogenetic clusters and (ii) L. monocytogenes includes clonal groups that have adapted to infect specific host species or colonize nonhost environments. ",

author = "Nightingale, {K. K.} and K. Lyles and M. Ayodele and P. Jalan and Rasmus Nielsen and M. Wiedmann",

year = "2006",

doi = "10.1128/JCM.00618-06",

language = "English",

volume = "44",

pages = "3742--3751",

journal = "Journal of Clinical Microbiology",

issn = "0095-1137",

publisher = "American Society for Microbiology",

number = "10",

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TY - JOUR

T1 - Novel Method To Identify Source-Associated Phylogenetic Clustering Shows that Listeria monocytogenes Includes Niche-Adapted Clonal Groups with Distinct Ecological Preferences

AU - Nightingale, K. K.

AU - Lyles, K.

AU - Ayodele, M.

AU - Jalan, P.

AU - Nielsen, Rasmus

AU - Wiedmann, M.

PY - 2006

Y1 - 2006

N2 - While phylogenetic and cluster analyses are often used to define clonal groups within bacterial species, the identification of clonal groups that are associated with specific ecological niches or host species remains a challenge. We used Listeria monocytogenes, which causes invasive disease in humans and different animal species and which can be isolated from a number of environments including food, as a model organism to develop and implement a two-step statistical approach to the identification of phylogenetic clades that are significantly associated with different source populations, including humans, animals, and food. If the null hypothesis that the genetic distances for isolates within and between source populations are identical can be rejected (SourceCluster test), then particular clades in the phylogenetic tree with significant overrepresentation of sequences from a given source population are identified (TreeStats test). Analysis of sequence data for 120 L. monocytogenes isolates revealed evidence of clustering between isolates from the same source, based on the phylogenies inferred from actA and inlA (P = 0.02 and P = 0.07, respectively; SourceCluster test). Overall, the TreeStats test identified 10 clades with significant (P < 0.05) or marginally significant (P < 0.10) associations with defined sources, including human-, animal-, and food-associated clusters. Epidemiological and virulence phenotype data supported the fact that the source-associated clonal groups identified here are biologically valid. Overall, our data show that (i) the SourceCluster and TreeStats tests can identify biologically meaningful source-associated phylogenetic clusters and (ii) L. monocytogenes includes clonal groups that have adapted to infect specific host species or colonize nonhost environments.

AB - While phylogenetic and cluster analyses are often used to define clonal groups within bacterial species, the identification of clonal groups that are associated with specific ecological niches or host species remains a challenge. We used Listeria monocytogenes, which causes invasive disease in humans and different animal species and which can be isolated from a number of environments including food, as a model organism to develop and implement a two-step statistical approach to the identification of phylogenetic clades that are significantly associated with different source populations, including humans, animals, and food. If the null hypothesis that the genetic distances for isolates within and between source populations are identical can be rejected (SourceCluster test), then particular clades in the phylogenetic tree with significant overrepresentation of sequences from a given source population are identified (TreeStats test). Analysis of sequence data for 120 L. monocytogenes isolates revealed evidence of clustering between isolates from the same source, based on the phylogenies inferred from actA and inlA (P = 0.02 and P = 0.07, respectively; SourceCluster test). Overall, the TreeStats test identified 10 clades with significant (P < 0.05) or marginally significant (P < 0.10) associations with defined sources, including human-, animal-, and food-associated clusters. Epidemiological and virulence phenotype data supported the fact that the source-associated clonal groups identified here are biologically valid. Overall, our data show that (i) the SourceCluster and TreeStats tests can identify biologically meaningful source-associated phylogenetic clusters and (ii) L. monocytogenes includes clonal groups that have adapted to infect specific host species or colonize nonhost environments.

U2 - 10.1128/JCM.00618-06

DO - 10.1128/JCM.00618-06

M3 - Journal article

C2 - 17021104

SN - 0095-1137

VL - 44

SP - 3742

EP - 3751

JO - Journal of Clinical Microbiology

JF - Journal of Clinical Microbiology

IS - 10

ER -