listeria monocytogenes from population structure to genomic epidemiology
TRANSCRIPT
Sylvain Brisse
Institut Pasteur, Microbial Evolutionary Genomics Unit
&
CNRS, UMR 3525, Paris, France
Listeria monocytogenes from population structure
to genomic epidemiology
Listeria monocytogenes is everywhere
• Severity of invasive forms (hospitalization rate around 100%)
• Mortality rate of 20 to 30 % (up to 45% in case of CNS infection)
• Incidence in France
• 4.9 cases / million (2009)
• Around 300 human cases/year
• Last large outbreak in 2003… but numerous small clusters
Listeria monocytogenes infections
• CNS infection
• Bacteremia
• Materno-neonatal infection
• Serotyping, PCR serogrouping
• Pulsed-field gel electrophoresis (PFGE)
• Ribotyping
• Amplified Fragment Length Polymorphism (AFLP)
• Multi-virulence sequence typing (MvLST)
• Multilocus VNTR Analysis (MLVA)
• Multilocus sequence typing (MLST)
ORF2819
lmo0737
1000
800 700 600 500 400 300
M 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
lmo1118
ORF2110
prs
Listeria monocytogenes: ‘classical’ strain typing methods
abcZ bglA cat dapE dat ldh lhkA
3 1 1 1 3 1 3
3 1 1 1 3 1 23
1 2 1 7 22 39 72
3 1 1 1 3 1 31
AllelesSequence type (ST)
1
1
2
3
3
•Allele• Sequence of one gene (lhkA, 480 bp)
MLST: Multilocus Sequence Typing
www.pasteur.fr/mlst
Currently:
~3,500 entries, 993 STs
Konstantinidis & Tiedje 2005
DNA-DNA
ANI
I
II
III
IV
4.99%
5.3%
7.57%
L. monocytogenes lineages ≈ 4 distinct genomic species
Average Nucleotide Identity
• 4 deep phylogenetic lineages
• 2 of them (LI and LII) = 99% of infections
CC7
CC9
CC1
CC6
CC2
CC3
CC4
4b
4b
1/2b
4b
4b
CC59
1/2b
1/2a
1/2a
1/2a
1/2c
CC5
CC87
1/2b
1/2b
L. monocytogenes: a few major clones
LII
LI
I
II
III
IV
Ragon et al. 2008
• Investigate international transmission of Lm strains
• Define population structure at improved resolution
• Enable epidemiological surveillance at global scale
Objectives
Develop a genome-wide MLST typing scheme to:
Core genome MLST
Step 1. Define core genome
Step 2. Define variation at
core genes1
1
2
3
3
Step 3. Define allelic profiles
Strain selection for genome sequencing
Core and pan-genome of L. monocytogenes
958 Lm isolates genome from 4 Public Health Agencies,
N50 > 20,000 nt
CDC, Atlanta 735
Public Health Agency of Canada 36
Statens Serum Institute 83
Institut Pasteur 104
Loci were eliminated if:
• Missing in > 5% genomes (33 loci)
• Paralogous locus > 60% nt identity resulting in wrong locus assignment (6 loci)
• Redundant with 7gMLST (4 loci)
Typeability validated on 650 prospective surveillance genomes from UK and F:
• Locus-level typeability was of 99.7% (1,742 ± 14.4)
Selection of 1,748 cgMLST loci
Robustness of cgMLST genotyping
• EGDe strain, sequenced by Sanger and Illumina (twice):
100% identity of 1,748 allele calls
• Most assemblers converge as long as coverage depth > 30X
core-genome genotyping (cgMLST) process
Contig 1 Contig 3Contig 2
Strain 1
Strain 2
Strain 3
Gene 1 …. Gene 1748
1748 core genes
BLAST
~5 days
~1 hour
914
15
3
9
10
4
1
12
1010
5
75
7
2
7
7
10
1
10
1
13
3
3
12
1
3
14
12
23
12
14
3
1
3
8
10
5
9
10
CC1
CC2
CC3
Lin. I, others
CC9
Lin. II, others
America (n = 77)
Europe (n = 156)
North Africa
(n = 33)
Asia / Middle
East / Oceania
(n = 30)
No significant Fst
MLST clones: Dispersal rate > evolutionary rate
Chenal-Francisque et al., 2011
Everything is Everywhere…at comparable frequency
Longevity of L. monocytogenes MLST clonal groups
Haase et al., Env. Microbiol. 2014
• Most intra-outbreak pairs < 7 mismatches
• 7 : best Dunn’s clustering index
Cut-off value to define cgMLST types (CT) : 7
Defining a threshold for cgMLST ‘types’
International cgMLST ‘types’
• No epidemiological link found upon retrospective analysis
• Long-term stability of CTs
• More precise definition of clustered cases
• More relevant epidemiological investigations
NRC
Core genome MLST discrimination >> PFGE
cgMLST types
• Listeria isolates sent to NRC
• ‘real-time’ genomic sequencing
• Detection of clusters
• Epidemiological investigation
• Remove contaminated productsSingle PFGE type
Listeria monocytogenes population structure
Lineage
Sublineage
cgMLST type
Most sublineages, but not CTs, have been sampled
Sublineages ~ clonal complexes
Transfer of MLST
nomenclature to
sublineages
Nomenclature proposal for L. monocytogenes strains
Lineage - Sublineage – ST – CgMLST type (CT)
LII – SL7 – ST7 – CT932
http://bigsdb.web.pasteur.fr/listeria
Public database for L. monocytogenes cgMLST nomenclature
BIGSdb: Bacterial Genomes Isolates Database
Jolley & Maiden 2010
Databases for genomic epidemiology & population biology
Isolates:
genomes and metadata
Local labs
Reference Centers
Public Private
Strain tracking
Resistome
Virulome
Population biology
Clie
nt
sid
eS
erv
er
sid
e
Public data
Curation
Genotype
nomenclature
database
• cgMLST is a robust approach for L. monocytogenes strain typing
• International transmission demonstrated both at evolutionary and
epidemiological timescales
• cgMLST is more discriminatory than PFGE
• Population structure allows defining nomenclature of sublineages
and CTs
• Public database available for sharing of genome sequences and
nomenclature
• Future needs:
- Ring trials / EQA studies
- Complementary approaches (SNP mapping) for fine scale
resolution
Conclusions
Biology of Infection Unit & National Reference Center for Listeria, Institut Pasteur
Hélène DIEYE, Morgane LAVINA, Pierre THOUVENOT, Alexandre LECLERCQ, Marc LECUIT
Microbial Evolutionary Genomics, Institut Pasteur
Alexandra MOURA, Elise LARSONNEUR, Mylène MAURY, Marie TOUCHON, Alexis CRISCUOLO, Eduardo ROCHA,
Sylvain BRISSE
Center for information Technology, Institut Pasteur
Louis JONES, Emmanuel QUEVILLON
Applied Maths, Belgium
Hannes POUSEELE, Bruno POT
CDC, Atlanta, USA
Peter GERNER-SMIDT, Cheryl TARR
Heather CARLETON, Lee KATZ, Zuzana
KUCEROVA, Steven STROIKA, John
BESSER
SSI, Denmark
Jonas LARSSON, Eva NIELSEN
Public Health England
Tim DALLMAN, Kathie GRANT
PHAC, CanadaAleisha REIMER, Matthew WALKER, Celine NADON
Oxford University, UKKeith JOLLEY
Funding:
Acknowledgements