POPULATION STRUCTURE OF THE PNEUMOCOCCUS IS DRIVEN BY SELECTION ON - - PowerPoint PPT Presentation
FRIDAY , 8 TH JUNE 2018 INSTITUTO DE TECNOLOGIA QUIMICA E BIOLOGICA ( ITQB NOVA ), OEIRAS , PORTUGA L Dr Jos Loureno D EPARTMENTAL L ECTURER IN I NFECTIOUS D ISEASE D EPARTMENT OF Z OOLOGY , U NIVERSITY OF O XFORD POPULATION STRUCTURE OF THE
Dr José Lourenço
DEPARTMENTAL LECTURER IN INFECTIOUS DISEASE DEPARTMENT OF ZOOLOGY, UNIVERSITY OF OXFORD
FRIDAY, 8TH JUNE 2018 INSTITUTO DE TECNOLOGIA QUIMICA E BIOLOGICA (ITQB NOVA), OEIRAS, PORTUGAL
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BSc Software Engineering @IST RESEARCH ASSISTANT @IGC (2005-2008) PhD (PDBC programme) 1y courses @IGC (2008) 3y project @Oxford (2009) POSTDOC @ImperialCollege (2013-2014) POSTDOC @Oxford (2014-2018)
DEPARTMENTAL RESEARCH LECTURER ON INFECTIOUS DISEASE
@Oxford (2018-2022) DENV, CHIKV, YFV, ZIKV FluA, HIV, HCV, HBV Pneumococcus DENV
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Bacteria → also known as the pneumococcus → gram-positive bacterial pathogen → usually found in pairs (diplococci) and does not form spores → presents high levels of recombination and horizontal gene transfer Disease & carriage → commonly carried asymptomatically (nasopharynx) → can cause invasive disease: e.g. pneumonia, meningitis Serotypes → cell capsule dictates antigenic type (serotype) → there are +100 known serotypes → 10 to 15 serotypes are classically responsible for carriage and disease
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Pneumococcal conjugate vaccine (PCV) → contains the capsule sugars → PCV7: 4, 6B, 9V, 14, 18C, 19F and 23F → PCV13: PCV7 + 1, 3, 5, 6A, 7F and 19A PspA CbpA LytB LytA
polysaccharide capsule
Engholm DH et al. FEMS Microbiology Reviews. 2017 POPULATION STRUCTURE OF THE PNEUMOCOCCUS
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pre-vaccination → disease is dominated by a small subset of serotypes (PCV7) → majority of serotypes circulate at low frequency post-vaccination → disease of vaccine types is reduced → disease of non-vaccine types is increased
Waight PA et al. Lancet ID 2015 (England and Wales) POPULATION STRUCTURE OF THE PNEUMOCOCCUS
7 Azarian T et al. PLoS Pathogens 2018 Croucher et al. Nature Genetics 2013 23F, B, A
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Chaos, Persistence, and Evolution of Strain Structure in Antigenically Diverse Infectious
Role of selection in the emergence of lineages and the evolution of virulence in Neisseria
Long-term evolution of antigen repertoires among carried meningococci. Proc. Roy. Soc. B
(2010).
Lineage structure of Streptococcus pneumoniae may be driven by immune selection on the groEL heat-shock protein. Nature Scientific Reports (2017). Identifying Streptococcus pneumoniae genes associated with invasive disease using pangenome-based whole genome sequence typing. Under review (2018). Vaccination can drive an increase in frequencies of antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae. PNAS (2018). Vaccination Drives Changes in Metabolic and Virulence Profiles of Streptococcus pneumoniae.
PLoS Pathogens (2015).
High prevalence of vaccine serotype Streptococcus pneumoniae carriage six years after 13-valent pneumococcal vaccine introduction in Malawi: a prospective serial cross-sectional
vaccine response epidemiological population structure genetic population structure
POPULATION STRUCTURE OF THE PNEUMOCOCCUS
What determines genetic population structure? → which genes determine phylogenetic branching? → which genes determine Sequence cluster (SC)? → which genes determine Serotype (Sero)? → are genes that determine SC the same as those that determine Sero? Dataset → 616 genomes of S. pneumo, Massachusetts (USA, 2001-2007) → full genomes with 2135 genes per sample → known SC and Sero per sample Approach → whole-genome multi-locus sequence typing approach (wgMLST) → machine learning to explore the determinants of SC and Sero
10 Croucher et al. Nature Genetics 2013
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11 reference genome: ATCC700669 serotype 23F
gene A alleles of gene A
discretize and collapse gene's sequence into allele (integers)
1
=
1
=
2
≠ → → →
for all genes
2135 genes
sample 1 sample N
.. .
1 2 1 gene A 3 1 1 1 3 4 1 1 1 1 1 1 3 7 8 1 1 1
.. . .. . .. . .. . .. . .. .
sample 1 sample N
.. .
allelic matrix
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→ Random Forest Algorithm (RFA) - is a collection of Classification Trees (CT) → We set predictor variables (genes) to classify a variable of interest (SC, Sero) Critical outputs → how well it can classify (predict) variables of interest → scores predictor variables according to their importance in getting classification right
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1 2 1 3 1 1 1 3 4 1 1 1 1 1 1 3 7 8 1 1 1
... ... ... ... ... ...
sample 1 sample N
...
2135 predictors variables of interest
10 2 4
6A 19A 19A
SC Sero
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humidity windy golf ok? rainy high false no rainy high true no
high false yes sunny high false yes sunny normal false yes sunny normal true no
normal true yes rainy high false no rainy normal false yes sunny normal false yes rainy normal true yes
high true yes .... .... .... ....
many more samples
OUTLOOK
sunny
rainy
WINDY HUMIDITY
false true high normal
yes yes no no yes go play golf today? importance of predictor
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(... )
bootstra p solutions assembled
→ prediction accuracy → error rates (i.e. false positives) → predictor variable importance → etc. RF increases prediction accuracy and allows for robust error estimations, since the ensemble of slight different classification results adjusts for the instability of individual trees and avoids data overfitting.
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Good classification: lower success for some serotypes was related to varying samples sizes (e.g. N=8 for 16F, N=5 for 17F, N=1 for 21)
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top-scoring genes: → 38% of top genes were placed within 10 genes downstream and upstream of the capsular locus → 62% with compelling support for functional background that mediates competitive interactions or niche specialization
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Perfect classification.
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top-scoring genes: → 75% were randomly distributed along the genome (expectation) → 10 genes were contiguous and within the groESL operon (p-value=1.52×10−06)
Croucher et al. Nature Genetics 2013
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major lineages are determined by variation in the groESL operon (and have been determined
minor lineages are determined by variation in and around the capsular locus (and have been determined more recently and are known to be in constant flux)
Croucher et al. Nature Genetics 2013
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Operon → encodes for groEL (chaperonin) and groES (cofactor) groEL / groES protein complex → 'a nano-cage for protein folding' most of what we know is from E. coli → groEL is a heat-shock protein (stress protein) → at least 50 essential proteins need groESL for folding → groESL is required for cell viability
Hayer-Hartl M et al. Trends in Biochemical Sciences 2016
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23 Wong P et al. Journal of structural biology 2004
groEL is present across bacterial species → only exceptions found are 2 species of mycoplasma (intracellular) groEL is an homolog of HSP60 → HSP60 is present across the kingdoms, including, plants and vertebrates groEL and HSP60 are functionally, structurally and genetically similar
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groEL on the surface of the cell → promotes attachment to epithelial cells of various tissues → various types of shock / stress enhance expression and surface localization → in animal models, increased surface localization can lead to more severe disease (...) Free-form groEL → intracellular bacteria overexport upon macrophage infection → LOX-1 is the macrophage receptor (recognition induces overexpression of LOX-1) → is a potent signal for pro-inflamatory responses (...) Responses (vertebrates) → groEL is highly immunogenic (as are other HSPs) → Immune responses (cell, humoral) to groEL variants can be highly specific → Has been proposed as vaccine candidate for pneumococcus
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capsular locus → determines 'serotype' → under immune selection → locally epistatically linked groESL operon → determines 'lineage' → is under immune selection → necessary for folding of essential proteins implies globally epistatically linked
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PCV-like vaccine with 2 variants → targets particularly successful serotypes → allows for less successful serotypes to expand in the post-vaccination era groEL-based vaccine with 2 variants → targets major lineages → does not allow for less successful serotypes to expand in the post-vaccination era
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What determines (universal) genetic population structure?
Selection acts on multiple loci: such as groESL creating major lineages (Semi-) universal patterns of major & minor lineages emerge in whole-sequence data Strong selection on groEL and the epistatic dependency of the rest of the genome suggest a vaccine would be a promising alternative to vaccines targetting the CPS Selection acts on multiple loci: such as CPS creating minor lineages Patterns (major lineages) have locked in early, while others (minor lineages) are recent & in continuous flux.
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People involved
Sunetra Gupta Uri Obolski Martin C.J. Maiden Eleanor R. Watkins Samuel J. Peacock Callum Morris Neil French Robert S Heyderman Todd D. Swarthout Andrea Gori
Special thanks
Angela Brueggemann Andries van Tonder Richard Moxon EEID website: www.eeid.ox.ac.uk EEID on Twitter: @EEID_oxford JL on Twitter: @LourencoJML
Group contacts Institutions & Programmes
Malawi-Liverpool-Wellcome Trust Clinical Research Programme Liverpool School of Tropical Medicine University College London University of Oxford University of Liverpool
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Funding agencies