Why study Pathogen Evolution? pathogen genome diversity

Transcription

1 Evolution of Pathogenic Bacteria: Mycobacterium tuberculosis example Bio 101 Lecture by Seyed E. Hasnain

2 Why study Pathogen Evolution? pathogen genome diversity

3 The composition of the prokaryotic genome. Bacterial genomes consist of a conserved core gene pool and a variable flexible gene pool. The latter consists of accessory and mobile genetic elements (modified after Morschhäuser et al., 2000).

4 Microevolution Development of organisms in days and weeks Macroevolution Development of species and variants in long term intervals 4

5 Genetic mechanism Horizontal gene transfer Plasmid, Phage transfer Micro- evolution Macro- evolution PAI development Genome reduction, Deletions Deletions Development of intracellular pathogens Genetic rearrangements Phase, Antigenic Variation Development of new variants Point mutations Gene expression, Modulation Pathoadaptation 5

6 Why M. tuberculosis 6

7 The Ticking Time Bomb The morbidity and mortality statistics of TB is so extravagant that in the world someone dies of TB every 15 seconds (WHO Report 2003 ) Europe 2.1% US 37.7% Asia 33.3% Africa 9.6% Latin America 17.7% 7 TB Growth Rate

8 Global Scenario of TB Infection 9 Million cases/ year Death 2 Million cases / year 2 Billion people are infected in world Special Feature: Tuberculosis: Nature Medicine : March

9 Despite being completely curable, TB claims the lives of >400,000 people in India every year Magnitude of TB in India 40% of the Indian population is infected with the TB bacillus. Every day, more than 20,000 people become infected with the TB bacillus and about 5000 develop the disease. Every year 18 lakh (or 1.8 million) people in India develop TB, of which nearly 8 lakh (0.8 million) are infectious (sputum-positive). Untreated pulmonary TB cases spread infection to others in the community each infectious patient can infect persons in a year unless effectively treated. RNTPC report

10 Tuberculosis in humans INTRACELLULAR pathogen (facultative extra cellular) Exposed 70% 30% Clearance Infected (2 billion, 8 million new cases per year) 5-10% 80-90% Primary TB Latent TB 5-10% Death (2 million) Reactivation

11 Problems of interventions against TB Lack of Epidemiological Data Several genes with unknown function Problems of Moon lighting Persistence and Immune Evasion Poor understanding of the pathogen-host-environment triangle Emergence of MDR/XDR Emergence of TB-IRIS Emergence of TB-Diabetes synergy Absence of Good Diagnostics: Tuberculin skin test >125 y No new drug for the past 4 decades: 6 months MDT regime No new vaccine (BCG : 75 y; M indicus pranii, a ray of hope) No bio-marker for total sterilization

12 Two major paradigms govern evolution of persistent bacteria Lateral Genome Acquisition Helicobacters Optimization of fitness Mycobacteria Vertical Genome Reduction Emergence of specialist lineages Ahmed et al., 2008 Nature Rev Microbiol 6:

13 Evolution of Genomes Transformation Transduction Conjugation Gene acquisition Plasmids PAIs, Genomic islands (GEIs) Tn, IS, Islets,Integrons Prophages Rearrangements Mutations Deletions Evolved Genome Genome reduction 13

14 Geographic evolution: The concept of Geographic Genomics Genetic changes accumulate in the genome as a repertoire of gene acquisition and loss, on an evolutionary time-scale Many human pathogens have such changes ascribed to rigorous selection against the host defenses and adaptation to different niches Genome wide analysis of such a repertoire in pathogens with different bio-geo-climatic history is a term coined by us as GEOGRAPHIC GENOMICS Majeed et al., Bioinformatics 2004 Hasnain and Ahmed LANCET Infect Dis 2004

15 Reductional polymorphisms are the only major source of lineage diversity in pathogenic Mycobacteria Common ancestor M. africanum M. canettii RD can RD12 RD10 RD8 RD Mic RD7 RD9 RD seal M. tuberculosis (ancestral) TbD1 M. tuberculosis (modern) M. africanum M. pinnipedae decay (pseudogenization) M. leprae M. caprae RD13 RD4 RD1 RD2 RD14 M. microti M. bovis Genotype diversity is otherwise minimum, within the same geographical region M. bovis BCG

16 Reductive Evolution of the Mtb Complex genome Host specificity Effective invasion Survival Genome size Brosch et al., 2002

17 Genomic Features of Ancient strains 1. Fewer than 6 copies of IS Specific signature at MIRU Locus 4 3. Principle genetic group 1 4. Typical spoligotype 5. TbD1 region is intact 17

18 isolate no. origin PGG TbD1 MIRU-VNTR dendrogram spoligotype MIRU-VNTR X T LAM W/Beijing Delhi/CAS EAI Miru 02 VNTR 424 VNTR 577 Miru 04 Miru 40 Miru 10 Miru 16 VNTR1895 Miru 20 VNTR2347 VNTR2401 VNTR2461 Miru 23 Miru 24 Miru 26 Miru 27 VNTR3171 Miru 31 VNTR3690 VNTR4156 Miru 39 Ancestral (40%) Delhi (25%) Beijing (8-10%) Others (15-20%) Single, Double, Triple

19 TbD1/Rd9 analysis in the Indian isolates TbD1 region is present in about 36% isolates - ancient features Q Ahmed et al. J Clin Microbiol :

20 Do ancestral lineages of Mycobacterium tuberculosis predominate in India If yes, does this denotes an ancient focus of tuberculosis in South Asia? Does this provide any advantage for TB management in India?

21 Analysis of samples recovered from Egyptian mummies suggests that the modern lineages of M. tuberculosis diverged from the TbD1+ lineage thousands of years ago. Ancient Hindu scriptures also support the contention that this disease has been present as early as 10, 000 BC in India. Therefore, the predominance of ancestral strains and the relatively poor representation of the most recent lineages in India, as apparent from this study, are consistent with the hypothesis that India is a historically ancient focus of tuberculosis. Isolates from South India have been described to be of low virulence and less disseminating? A careful comparison of the virulence properties of ancient TbD1+ strains with those of the more modern strains, using the variety of animal models currently available, may thus provide novel insights into the evolutionary dynamics of this major pathogen. Gutierrez + Ahmed et al., 2006 Emerging Infect Dis

22 Mycobacterium w genome program Immune related disorders or infections are a result of changing lifestyles and thereby reduced exposure to certain bacteria that have been intricately associated as "old friends" during most of the mammalian evolution. A very important group of bacteria among these organisms, are saprophytic mycobacteria, which are recognized by the innate immune system as biologically harmless. It is hypothesized that these "old friends" might be maintaining levels of regulatory immune cell populations (Rook et al., 2004), such as the cytokine secreting and antigen-presenting cells which are compromised in some allergies (asthma) and chronic infectious diseases (Crohn's disease due to M. avium complex). These concepts are heralding the development of novel probiotic or immunomodulatory therapies for lifestyle diseases based on harmless organisms or their components. One such old friend is Mw!

23 Evolution of Mycobacterial Specialists and Generalists Ahmed N et al., 2007 PLoS ONE

24 Ancestral strains - Old is Gold? India China Russia Of new TB cases, % MDR-TB Of previously treated TB cases, % MDR-TB India is saved of the TB-time bomb (unlike South Africa) despite ~5.7 Million HIV cases Why treatment success reaching ~90%? (Compare -> Russia=58%) Why no institutionalized outbreaks? (Compare -> Kwazulu Natal, SA) India Russia Bestowed with ancestral strains Crippled with Beijing strains Source: WHO Report on TB, 2006, 2007 and 2008

25 OLD is GOLD : Issues to ponder 1. Ancestral lineages are widespread and perhaps do not allow spread of other genogroups Host adaptation? Preferential colonization? Host Genetic resistance? 2. Are ancestral strains really advantageous for the TB control Program? Slow disseminating types? Are these protective: Super infection? Are they less virulent: Less MDR/XDR? Are they more cooperative : Infection burden vs Disease burden? 3. How long this advantage sustains? Diabetes, HIV, Beijing, LAM Ahmed et-al Inf Gen Evol 2009

26 Study of Evolutionary Dynamics and Molecular Epidemiology not only permits tracking of a pathogen but also enables the identification of new antigens of diagnostic potential and also possible drug targets

27 Humans and microbes are not at war. Rather, both parties are engaged in amoral, self interested, co-evolutionary struggle. We need to understand better, and therefore anticipate, the dynamics of that process A J McMichael. Phil. Trans. R. Soc. Lond. B (2004) 359, and Until we Understand These Processes Mtb will Continue to Challenge Human Intelligence!!