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Genomic epidemiology of bacterial pathogens
Sylvain Brisse
Institut Pasteur, Microbial Evolutionary Genomics Unit
&
CNRS, UMR 3525, Paris, France
Genotype VirulenceResistance
Microbiological diagnostic
Identification
Epidemiology
Genotype Virulence elementsResistance elements
Genome sequencing: ‘all in one technology’
Sequencing Data analysisSample
DNA extraction
Library preparation
Real-time genome sequencing?
5 days
Microbes know no borders…
• Standardized genotyping strategy
• Sequence databases & common nomenclature
Nomenclature & knowledge
database
Provenance data
& genomes
Isolates
databases
Act locally, think globally
Confidentiality of epi data Standardized approach
Core genome << Pangenome
Touchon et al., 2009
39%UPEC
O157:H7
K12
Escherichia coli
Genomic diversity inside bacterial species
Core genome
~2,000
All genes
(pangenome)
~20,000
families
~11,500
IS excluded
~10,000
Genomic island
Phages
Transposons, IS
ICE
Plasmids
...
Core genome MLST
Step 1. Define core genome
Step 2. Define variation at
core genes1
1
2
3
3
Step 3. Define allelic profiles
Whole-genome genotyping (cgMLST)
Contig 1 Contig 3Contig 2
Gene 1 …. Gene 2000
~ 2000 core genes
BLAST
~5 days
~30 seconds /strain
~ few weeks
~30 seconds /strain
Core-genome based genotyping and classification
Gene 1 …. Gene 2000
Strain A
Strain B
Strain C
time
Expanding clone
Founder
genotype
Ubiquitous
• Human and animal carriage, plants, water, environment
(re)-emergence as a community pathogen
• Severe pneumonia; meningitis: ~20-40% mortality rate
• Pyogenic liver abscess; endophthalmitis (1980’s - )
Hypervirulent K. pneumoniae (hvKP)
Emergence as a multidrug resistant pathogen
• 5 - 8% nosocomial infections Europe / USA
• Urinary, respiratory and bloodstream infections
• Outbreaks
Multidrug resistant (MDR) strains
Klebsiella pneumoniae
Global emergence of Kp carbapenem resistance
Woodford et al., 2011; Nordmann et al., 2011
• KPC
USA 1996; now global
ST258: predominant clone
• NDM-1:
Sweden / India (2008)
Diversity of clones, incl. ST14
Highly MDR (ESBLs; aminoglycosides)
• OXA-48, VIM, …
• Few remaining drugs available
• Death rate > 50%
• ‘urgent threat’ (CDC 2013)
• Colistin, tygecycline resistance
• Need to monitor,
understand and control
emergence
• Local and global levels
MLST-based K. pneumoniae population structure
• Recognition of ST258 as emerging KPC
producer
• Lack of clear-cut clonal structure
ST23
ST258
http://www.pasteur.fr/mlst
> 2200 STs
> 2500 isolates
> 200 submitters
Diancourt et al 2005 JCM
(core-genome MLST, 694 genes)
Genome-wide definition of K. pneumoniae clonal groups
Bialek, Criscuolo et al 2014 EID
• Clear-cut clonal structure
• Cut-off value of 100 mismatches (out of 694) for
delimitation of clonal groups
1000 700CG23
CG258
CG23
Emergence of K. pneumoniae clonal groups
KPC-producing CG258
Israel
Italy
USA
Finland
Poland
Greece
Israel
USA
mainly
Bowers et al 2015 PLoS One
20121994
Virulence factors
known variants
Sequence
database
Toxins
Capsular genes
Adhesins
Secretion systems
…
β-lactams Aminoglycosides Quinolones
Antimicrobial resistance genes
known variants
Sequence
database
β-lactamases
• Class A (TEM, SHV, CTX-M, KPC)
• Class B (NDM, VIM)
• Class C (AmpC)
• Class D (OXA)
• Inactivating enzymes
(AAC, ANT, APH)
• 16S rRNA methylases
(ArmA, Rmt)
• Target changes (GyrAB, ParCE)
• Inactivating enzymes(AAC(6’)-Ib-cr)
• Target protection (Qnr)
• Efflux pumps (OqxAB)
CG23
CG258
Virulence
genes
Gene content breakdown by clonal group
Beta-lactams AminoglycosidesQuinolones
Resistance
genes
blaKPC blaOXA
Bialek, Criscuolo et al., 2014
rmpA
735 genomes
36 genomes
635 genomes
300 genomes
83 genomes
1748 core genes1695 genomes
Listeria global initiative
L. monocytogenes
global population structure
A. Moura;
Listeria NRC &
Lecuit’s unit
• 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’
Listeria monocytogenes population structure
Lineage
Sublineage
cgMLST type
• 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
International cgMLST ‘types’
• No epidemiological link found upon retrospective analysis
• Long-term stability of CTs
• Surveillance at global scale
http://bigsdb.web.pasteur.fr/listeria
Public database for L. monocytogenes cgMLST nomenclature
BIGSdb: Bacterial Genomes Isolates Database
Jolley & Maiden 2010
Acknowledgements: Klebsiella
Microbial Evolutionary Genomics
Suzanne BIALEK, Alexis CRISCUOLO, Virginie PASSET, Marie TOUCHON,
Eduardo ROCHA
Center for information Technology & Communication Center, Institut Pasteur
Louis JONES, Emmanuel QUEVILLON
Paris Hospitals (AP-HP)
Dominique DECRE, Guillaume ARLET, Marie-Hélène NICOLAS-CHANOINE
Enteric Bacterial Pathogens, Institut Pasteur
Simon LE HELLO
MaGe/ MicroScope team, Genoscope, CEA, Evry
Zoé ROUY, Claudine MEDIGUE
Oxford University
Keith JOLLEY, Martin MAIDEN
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, 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: Listeria
Vincent ENOUF