L épidémiologie moléculaire en laboratoire de recherche en bactériologie : l exemple d Escherichia coli

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1 L épidémiologie moléculaire en laboratoire de recherche en bactériologie : l exemple d Escherichia coli Académie Nationale de Pharmacie Paris 15 Mars 2017

2 The various E. coli lifestyles Primary habitat E. coli cells Secondary habitat Digestive tract of vertebrates Among 500 species and bacteria Commensal Soil and sediments Saprophyte Pathogenic Intestinal (InPEC) Extra-intestinal (ExPEC)

3 Habitat primaire Tube digestif des vertébrés Habitat secondaire Eau et sédiments Homme : 10 8 E. coli / g de fèces Commensal, en fait plutôt mutualiste (protège de la colonisation species par les pathogènes, est dans un environnement nutritif, protégé) Pathogè ne Saprophyte The phylogenomics of the

4 A highly variable genome 4,200 to 5,400 genes Core genome: 1,900 genes < 50 % of the genome Pan genome: 18,000 non-orthologous genes Variable genome: Pan Core Touchon et al., PLoS Genet., 2009

5 Core and variable genomes are under distinct selective pressures Variable Core 9,054 strain specific genes deleterious or neutral = transient genes, purged rarely adaptive Touchon et al., PLoS Genet., 2009

6 The recombined fragments on the core genome with their short sizes do not blur the phylogenetic signal A1 A2 A3 A4 A5 B1 B2 B3 B4 C1 C2 C3 Hence, provided enough loci are studied, the topology of the phylogeny is recovered despite quite important recombination Tenaillon et al., Nature Rev Microbiol, 2010

7 E. coli sensu stricto E. albertii A B1 C E D. 13 genes, 9819 bp (Achtman and Pasteur Institute MLST schemes). 7 main phylogroups. Good proxy of the core genome tree F STc95 B2 Clade I E. fergusonii Clermont et al., Environ Microbiol Rep, 2013

8 O18:H7 Subgroup B O1:H1 O25b:H4 O2a:H7 O1:H7 Subgroup C O2a:H4 Subgroup E O1:H7 O2a:H7 Subgroup A Substructure within STc 95 (B2 phylogroup). 105 strains Core genome 35,137 SNPs. ML tree Rooted on ED1a strain O45a:H7 O1:H7 O2a:H4 O1:H7 Subgroup D Gordon et al., Submitted

9 The insertion/deletion events are localised in 133 hot spots 43 asnt trna leux trna

10 A modular organisation of the hot spots of integration: a molecular Lego 64 Strain specific module F Multiple combinations of genetic elements

11 Despite a very high gene flow, genes co-exist in organised genomes exhibiting a robust phylogeny despite numerous gene conversion events

12 Habitat primaire Tube digestif des vertébrés Habitat secondaire Eau et sédiments The molecular epidemiology of Homme : 10 8 E. coli / g de fèces Commensal, en fait plutôt mutualiste (protège de la colonisation par les pathogènes, est dans un environnement nutritif, protégé) Pathogè ne Saprophyte E. coli populations

13 Humans and animals exhibit different E. coli commensal strains % p=0.05 Animals Humans p=0.01 p=0.01 p=0.001 A B1 D B2 Phylogenetic groups 400 animals, 45 species 150 humans >2,500 strains One to 10 randomly selected colonies per subject Escobar-Paramo et al., Environ. Microbiol., 2006 Smati et al., MicrobiologyOpen, 2015

14 Human commensal E. coli populations are geographically structured Prevalence of commensal B2 phylogroup strains (One randomly selected colony per subject) Massot et al., RFL, 2016

15 Human commensal E. coli populations evolve as a function of decades 1980/2000 (n=5+10) 2010 (n=95) Paris area. Same selection of subjects. Same sampling and typing strategies. One randomly selected clone per subject Massot et al., Microbiology, 2016

16 Relative frequency of STc 95 subgroups An epidemic structure within the STc STc 95 strains collected from people living in the Canberra region, Australia Different from USA and France epidemiologies Gordon et al., Submitted

17 An association between the strain phylogeny, the presence of virulence genes and the lifestyle Severe diarrheas (STEC/EHEC, ETEC, Shigella) F F Extra-intestinal diseases Escobar-Paramo et al., Mol Biol Evol, 2004

18 Habitat primaire Habitat secondaire Tube digestif des vertébrés Homme : 10 8 E. coli / g de fèces Commensal, en fait plutôt mutualiste individual level (protège de la colonisation par les pathogènes, est dans un environnement nutritif, protégé) Pathogè ne Eau et sédiments Fine scale molecular Saprophyte epidemiology at the

19 Can we see signs of selection during an infectious process?. 19 patients with deep and closed extra-intestinal infections (UTI, deep abscess, pleurisy, meningitis, peritonitis). 5 to 20 colonies per sample (226 isolates). Genetic diversity (ERIC-PCR, PFGE, MLST, virulence genes). 11 patients were infected by a single clone exhibiting microheterogeneity Levert et al., PLoS Pathog, 2010

20 Cell density (O.D. 600nm) What could explain the within clone diversity? Heritable variations in growth characteristics Time (h) Patient 3, Liver abscess and blood (20 isolates) Levert et al., PLoS Pathog, 2010

21 Bacteria survival (%) Other phenotypic heterogeneities Isolates a b* c d* e* f* g h i* Use No use Exposure to H 2 O 2 (min) Metabolic capacity Biolog plates C sources Motility Resistance to stress H 2 O 2 Strains with impaired growth use fewer substrates, are less motile but more resistant to H 2 O 2.

22 Mouse survival (%) The intrinsic virulence of isolates from a single clone is highly variable , , , 47, Time (h)

23 SDS-PAGE 100 kda ph 4 27 proteins are differentially expressed within the isolates of a single clone Isoelectrofocalisation SecA IleS KatE GyrB SucA Lon ph 7 OmpC ND TolC LamB NmpC RbsK Acs CpsGGadA OmpA AnsB HyaB PoxB RbsA GlmM Cca TdcB TalA FbaB. Central metabolism, membrane, stress associated proteins. Half known as regulated by RpoS RbsB 20 kda WrbA Levert et al., PLoS Pathog, 2010

24 Convergence in inactivating mutations in rpos: a strong sign of selection. Intra-patient and inter-patient convergence in rpos. RpoS, one of the 7 E. coli sigma factors - Regulates a large regulon ( ~ 10% of E. coli genome) - Involved in stationary phase and many stress conditions Different levels of RpoS explain most part of the heterogeneity observed within the patient isolates

25 Habitat primaire Tube digestif des vertébrés Habitat secondaire Eau et sédiments Homme : 10 8 E. coli / g de fèces Commensal, en fait plutôt mutualiste (protège de la colonisation par les pathogènes, est dans un environnement nutritif, protégé) Pathogè ne Saprophyte Take home messages

26 . E. coli is a species with a dynamic genome but a clonal structure of population.. There is an association between the phylogenetic background, the presence of specific traits and the lyfestyle of the strain, indicating epistasis.. There are signs of selection with diversification in vivo during the extra-intestinal infectious process.. The new technologies of sequencing help to decipher the adaptability of E. coli.

27 Mathilde Lescat Maxime Levert Adrien Launay Mounira Smati Tony Le Gall Méril Massot Médéric Diard Ivan Matic Marie Touchon Eduardo Rocha David Gordon University of Sydney Tom Ferenci Patricia Escobar-Paramo Olivier Clermont Bertrand Picard Olivier Tenaillon Pierre Darlu Sören Schubert James Johnson