Douglas Young
A new horizon for preventive vaccines against tuberculosis Madrid 7th May 2014
Mycobacterium tuberculosis
Evolution of Functional Diversity
844 badgers caught and sampled disease detection by serology 262 captured more than once were test negative on initial capture 22 incident cases
Chambers et al. 2011. Proc Biol Sci B. 278:1913-20 Carter et al. 2012. PLoS One 7:e49833
74% reduction in seropositive disease
79% reductionin IFN g conversion
Field trial of BCG in badgers Gloucestershire 2005-2009
group no of badgers
incident cases
% of total cases
CI F probability
control 82 14 17.1 (10.8-25.9)
vaccinated 179 8 4.5 (2.4-8.2) 0.001
unvaccinated cubs from vaccinated setts had a reduced ESAT6/CFP10 IFNg response
vaccination interrupts onward transmission
Berg et al. 2009. PLoS One 4:e5068 Firdessa et al. 2012. PLoS One 7:e52851
high prevalence > 50%
post-mortem: 67 cultures from 31 animals 67 M. bovis isolates 0 M. tuberculosis isolates
Bovine TB in Ethiopia
30000 carcasses screened in abattoirs1500 lesioned animals, 170 ZN+ cultures
low prevalence 0.5 – 5%
58 M. bovis isolates 8 M. tuberculosis isolates (12%)
A. bovine TB in rural cattle
B. bovine TB in urban intensive farms
M. tuberculosis can cause disease inindividual animals, but it doesn’t establish
an efficient transmission cycle
I want to have a vaccine that interrupts transmission:can I target some layer of species-specific biology that is required for an effective transmission cycle?
THE CONCEPT
I don’t have an experimental model for transmission, so I’m going to try and infer biology by looking at evolution of human isolates
THE STRATEGY
biology involved inmaking a lesion
biology involved ineffective transmission
the ideal vaccine candidate
THE MODEL
Lineage 4
Lineage 3
Lineage 2
Lineage 6 animal strains
Lineage 5
Lineage 1
Lineage 7Global phylogeny of M. tuberculosis
Comas et al. 2013. Nat Genet 45:1176
Rose et al. 2013. Genome Biol Evol 5:1849-62
Do toxin-antitoxin modules regulate “persistence”?
transcription higher in Lineage 1
transcription higher in Lineage 2
in vitro transcription profiling reveals strain variation in transcript abundance
but there’s very little evidence of genomic diversity of TA modules
0 10 20 30 40 50 60 70 80
M. tuberculosis
M. canettii 60008
M. canettii 70010
Mycobacterium sp. JDM601
M. gastri
M. kansasii
M. xenopi
M. yongonense
M. paratuberculosis
M. smegmatis mc2 155
M. avium
M. marinum
M. abscessus
M. ulcerans
M. phleiM. hassiacum
Mycobacterium sp. MCSM. gilvum
M. smegmatis JS623
M. chubuense
Number of TA modules
blue: chromosomered: plasmid
M avium
M. paratuberculosis
M. yongonense
M. kansasii
M. gastri
M. ulcerans
M. marinum
M. canettii 70010
M. tuberculosis
M. canettii 60008
M. xenopi
Mycobacterium sp. JDM601
M. phlei
M. hassiacum
M. smegmatis JS623
M. chubuense
M. gilvum
Mycobacterium sp. MCS
M. smegmatis MC2 155
M. abscessus
100
99
100
100
100
100
100
96
100
57
62
100
88
90
79
76
65
0.02
rpoC sequence, GTR+G+I, Maximum Likelihood phylogeny, 100 bootstrap
high TA mycobacteria (>10 modules) in redTAs and phylogeny
plasmids
lactate dehydrogenaselon protease
ddnnitroreductase
ddnnitroreductase
lactate dehydrogenase
ddnnitroreductase
lactate dehydrogenase
deletion of lon protease
What else is carried on mycobacterial plasmids?
toxin-antitoxin modules
metal ion detox and efflux
cytochrome P450s
adenylate cyclases
diguanylate cyclases
Type VII secretion loci
mce loci
. . .
organism adenylate cyclase domains
M. tuberculosis 16
M. marinum 31
M. ulcerans 15
M. smegmatis mc2 155 7
M. smegmatis JS623 48
MKAN_plasmid 29475 29470 29465 29460 29455 29450 29445 29440 29435 29430 29425 29420
MKAN_chromosome 00155 00160 00195 00200 00205 00210 00215 00220 00225
Rv1783 Rv1784 Rv1792 Rv1793 Rv1794 Rv1795 Rv1796 Rv1797 Rv1798
Rv1785 Rv1786 Rv1787 Rv1789 Rv1790 Rv1791Rv1788
eccB5 eccC5 esxM esxN eccD5 mycP5 eccE5 eccA5
cyp143 PPE25 PE18 PPE26 PPE27 PE19
PE PPE
56% 53% 91% 95% 45% 50% 55% 34% 72%
57% 52% pseudo 94% 45% 48% 57% 31% 72%
Mtb
ESX locus on pMK12478
99% identical sequence in M. yongonense plasmid pMyong1100% identical sequence in M. parascrofulaceum (plasmid?)
yrbE1A mce1A mce1B mce1C mce1D lprK mce1F Rv0175 Rv0176 Rv0177
80%
yrbE1BfadD5 Rv0178mce1R
5787 5785 5784 5783 5782 5781 5780 5779 5778 57775786 5776
60%78% 66% 63% 61% 64% 71% 52% 50% 50% 49%
5788
5775transposase transposaseM. chubuense plasmid pMYCCH01
M. tuberculosis Mce1
MCE locus on pMYCCH01
M. kansasii
M. gastri
M. ulcerans
M. marinum
M. canettii 70010
M. tuberculosis
M. canettii 60008
M. xenopi
no more horizontalgene transfer!
niche isolation?
cobF deletion
cobF
deletion in M. tuberculosis
M. canettii
M. tuberculosis
Deletion of cobF (vitamin B12) in M. tuberculosis
other methyltransferases may(partially?) compensate
Gopinath et al. 2013. Future Microbiol 8:1405
pyruvate kinase SNPalanine dehydrogenase frameshiftPhoR SNPcobL (+MK) deletion (RD9)
The Great M. tuberculosis Schism
more relaxed approachto host restriction?
increasing species adaptation?
M. tuberculosis may have evolved
to rely on vitamin B12 provided by the host?
niche adaptation
• bioavailability of B12 in primates versus ruminants?
• effect of diet – vegetarian versus meat-eating?
• gut microbiome?
homocysteine
methionine propionyl CoA
succinate ribonucleotide
deoxyribonucleotide
MetE MetH
met
hylc
itrat
e(P
rpCD
)m
ethylmalonate
(MutAB)
NrdEF NrdZ
AMINO ACIDBIOSYTHESIS DNA REPLICATION
ENERGY
B12-independentB12-dependent
The optional metabolome of vitamin B12
Lineage 5
Lineage 6
Lineage 4
Lineage 2
Lineage 3
Lineage 7
Lineage 1
22 independentSNPs and frameshiftspredicted to impairfunction of MetH
reduced reliance onB12-dependent
pathways?
post-Neolithic?
human lung
industrial remediation
mycobacteriafreely exchanging
flexible functionality
immunologicalvomiting
nicheadaptation
transmissioncycle
no turning back(no horizontal transfer)
nicheisolation