Historical intensity of natural selection for resistance to tuberculosis

Gaucher disease protects against tuberculosis

Biallelic mutations in the glucocerebrosidase (GBA1) gene cause Gaucher disease, characterized by lysosomal accumulation of glucosylceramide and glucosylsphingosine in macrophages. Gaucher and other lysosomal diseases occur with high frequency in Ashkenazi Jews. It has been proposed that the underlying mutations confer a selective advantage, in particular conferring protection against tuberculosis. Here, using a zebrafish Gaucher disease model, we find that the mutation GBA1 N370S, predominant among Ashkenazi Jews, increases resistance to tuberculosis through the microbicidal activity of glucosylsphingosine in macrophage lysosomes. Consistent with lysosomal accumulation occurring only in homozygotes, heterozygotes remain susceptible to tuberculosis. Thus, our findings reveal a mechanistic basis for protection against tuberculosis by GBA1 N370S and provide biological plausibility for its selection if the relatively mild deleterious effects in homozygotes were offset by significant protection against tuberculosis, a rampant killer of the young in Europe through the Middle Ages into the 19th century.

Genetic Resistance to Mycobacterium tuberculosis Infection and Disease

Natural history studies of tuberculosis (TB) have revealed a spectrum of clinical outcomes after exposure to Mycobacterium tuberculosis, the cause of TB. Not all individuals exposed to the bacterium will become diseased and depending on the infection pressure, many will remain infection-free. Intriguingly, complete resistance to infection is observed in some individuals (termed resisters) after intense, continuing M. tuberculosis exposure. After successful infection, the majority of individuals will develop latent TB infection (LTBI). This infection state is currently (and perhaps imperfectly) defined by the presence of a positive tuberculin skin test (TST) and/or interferon gamma release assay (IGRA), but no detectable clinical disease symptoms. The majority of healthy individuals with LTBI are resistant to clinical TB, indicating that infection is remarkably well-contained in these non-progressors. The remaining 5-15% of LTBI positive individuals will progress to active TB. Epidemiological investigations have indicated that the host genetic component contributes to these infection and disease phenotypes, influencing both susceptibility and resistance. Elucidating these genetic correlates is therefore a priority as it may translate to new interventions to prevent, diagnose or treat TB. The most successful approaches in resistance/susceptibility investigation have focused on specific infection and disease phenotypes and the resister phenotype may hold the key to the discovery of actionable genetic variants in TB infection and disease. This review will not only discuss lessons from epidemiological studies, but will also focus on the contribution of epidemiology and functional genetics to human genetic resistance to M. tuberculosis infection and disease.

Insights into secular trends of respiratory tuberculosis: The 20th century Maltese experience

Over half a century ago, McKeown and colleagues proposed that economics was a major contributor to the decline of infectious diseases, including respiratory tuberculosis, during the 19^th and 20^th centuries. Since then, there is no consensus among researchers as to the factors responsible for the mortality decline. Using the case study of the islands of Malta and Gozo, we examine the relationship of economics, in particular, the cost of living (Fisher index) and its relationship to the secular trends of tuberculosis mortality. Notwithstanding the criticism that has been directed at McKeown, we present results that improvement in economics is the most parsimonious explanation for the decline of tuberculosis mortality. We reaffirmed that the reproductively aged individuals were most at risk of dying of tuberculosis, seeing that 70 to 90% of all deaths due to tuberculosis occurred between the ages of 15 and 45. There was a clear sex differential in deaths in that, prior to 1930, rates in females were generally higher than males. During times of extreme hardship, the sex differential was exacerbated. Over the course of World War I, the sex gap in tuberculosis rates increased until peaking in 1918 when there was also the influenza pandemic. The heightened differential was most likely a result of gendered roles as opposed to biological differences since female tuberculosis rates again surpassed male rates in 1945 during World War II. Respiratory tuberculosis in both urban and rural settlements (in Malta proper) was significantly influenced by the Fisher index, which explains approximately 61% of the variation in TB death rates (R = 0.78; p<0.0001). In Gozo, there was no significant impact on respiratory tuberculosis (R = 0.23; p = 0.25), most likely a consequence of the island’s isolation, a self-sufficient economy and limited exposure to tuberculosis.

A Multistrain Mathematical Model To Investigate the Role of Pyrazinamide in the Emergence of Extensively Drug-Resistant Tuberculosis

Several infectious diseases of global importance—e.g., HIV infection and tuberculosis (TB)—require prolonged treatment with combination antimicrobial regimens typically involving high-potency core agents coupled with additional companion drugs that protect against the de novo emergence of mutations conferring resistance to the core agents. Often, the most effective (or least toxic) companion agents are reused in sequential (first-line, second-line, etc.) regimens. We used a multistrain model of Mycobacterium tuberculosis transmission in Southeast Asia to investigate how this practice might facilitate the emergence of extensive drug resistance, i.e., resistance to multiple core agents. We calibrated this model to regional TB and drug resistance data using an approximate Bayesian computational approach. We report the proportion of data-consistent simulations in which the prevalence of pre-extensively drug-resistant (pre-XDR) TB—defined as resistance to both first-line and second-line core agents (rifampin and fluoroquinolones)—exceeds predefined acceptability thresholds (1 to 2 cases per 100,000 population by 2035). The use of pyrazinamide (the most effective companion agent) in both first-line and second-line regimens increased the proportion of simulations in which the prevalence exceeded the pre-XDR acceptability threshold by 7-fold compared to a scenario in which patients with pyrazinamide-resistant TB received an alternative drug. Model parameters related to the emergence and transmission of pyrazinamide-resistant TB and resistance amplification were among those that were the most strongly correlated with the projected pre-XDR prevalence, indicating that pyrazinamide resistance acquired during first-line treatment subsequently promotes amplification to pre-XDR TB under pyrazinamide-containing second-line treatment. These findings suggest that the appropriate use of companion drugs may be critical to preventing the emergence of strains resistant to multiple core agents.

The Role of Host Genetics (and Genomics) in Tuberculosis

Familial risk of tuberculosis (TB) has been recognized for centuries. Largely through studies of mono- and dizygotic twin concordance rates, studies of families with Mendelian susceptibility to mycobacterial disease, and candidate gene studies performed in the 20th century, it was recognized that susceptibility to TB disease has a substantial host genetic component. Limitations in candidate gene studies and early linkage studies made the robust identification of specific loci associated with disease challenging, and few loci have been convincingly associated across multiple populations. Genome-wide and transcriptome-wide association studies, based on microarray (commonly known as genechip) technologies, conducted in the past decade have helped shed some light on pathogenesis but only a handful of new pathways have been identified. This apparent paradox, of high heritability but few replicable associations, has spurred a new wave of collaborative global studies. This review aims to comprehensively review the heritability of TB, critically review the host genetic and transcriptomic correlates of disease, and highlight current studies and future prospects in the study of host genomics in TB. An implicit goal of elucidating host genetic correlates of susceptibility to Mycobacterium tuberculosis infection or TB disease is to identify pathophysiological features amenable to translation to new preventive, diagnostic, or therapeutic interventions. The translation of genomic insights into new clinical tools is therefore also discussed.

Rapid mortality transition of Pacific Islands in the 19th century

The depopulation of Pacific islands during the 16th to 19th centuries is a striking example of historical mass mortality due to infectious disease. Pacific Island populations have not been subject to such cataclysmic infectious disease mortality since. Here we explore the processes which could have given rise to this shift in infectious disease mortality patterns. We show, using mathematical models, that the population dynamics exhibited by Pacific Island populations are unlikely to be the result of Darwinian evolution. We propose that extreme mortality during first-contact epidemics is a function of epidemiological isolation, not a lack of previous selection. If, as pathogens become established in populations, extreme mortality is rapidly suppressed by herd immunity, Pacific Island population mortality patterns can be explained with no need to invoke genetic change. We discuss the mechanisms by which this could occur, including (i) a link between the proportion of the population transmitting infectious agents and case-fatality rates, and (ii) the course of infection with pathogens such as measles and smallpox being more severe in adults than in children. Overall, we consider the present-day risk of mass mortality from newly emerging infectious diseases is unlikely to be greater on Pacific islands than in other geographical areas.

Integrative analyses of leprosy susceptibility genes indicate a common autoimmune profile

BACKGROUND

Leprosy is an ancient chronic infection in the skin and peripheral nerves caused by Mycobacterium leprae. The development of leprosy depends on genetic background and the immune status of the host. However, there is no systematic view focusing on the biological pathways, interaction networks and overall expression pattern of leprosy-related immune and genetic factors.

OBJECTIVES

To identify the hub genes in the center of leprosy genetic network and to provide an insight into immune and genetic factors contributing to leprosy.

METHODS

We retrieved all reported leprosy-related genes and performed integrative analyses covering gene expression profiling, pathway analysis, protein-protein interaction network, and evolutionary analyses.

RESULTS

A list of 123 differentially expressed leprosy related genes, which were enriched in activation and regulation of immune response, was obtained in our analyses. Cross-disorder analysis showed that the list of leprosy susceptibility genes was largely shared by typical autoimmune diseases such as lupus erythematosus and arthritis, suggesting that similar pathways might be affected in leprosy and autoimmune diseases. Protein-protein interaction (PPI) and positive selection analyses revealed a co-evolution network of leprosy risk genes.

CONCLUSIONS

Our analyses showed that leprosy associated genes constituted a co-evolution network and might undergo positive selection driven by M. leprae. We suggested that leprosy may be a kind of autoimmune disease and the development of leprosy is a matter of defect or over-activation of body immunity.

Co-evolution of Mycobacterium tuberculosis and Homo sapiens

The causative agent of human tuberculosis (TB), Mycobacterium tuberculosis, is an obligate pathogen that evolved to exclusively persist in human populations. For M. tuberculosis to transmit from person to person, it has to cause pulmonary disease. Therefore, M. tuberculosis virulence has likely been a significant determinant of the association between M. tuberculosis and humans. Indeed, the evolutionary success of some M. tuberculosis genotypes seems at least partially attributable to their increased virulence. The latter possibly evolved as a consequence of human demographic expansions. If co-evolution occurred, humans would have counteracted to minimize the deleterious effects of M. tuberculosis virulence. The fact that human resistance to infection has a strong genetic basis is a likely consequence of such a counter-response. The genetic architecture underlying human resistance to M. tuberculosis remains largely elusive. However, interactions between human genetic polymorphisms and M. tuberculosis genotypes have been reported. Such interactions are consistent with local adaptation and allow for a better understanding of protective immunity in TB. Future 'genome-to-genome' studies, in which locally associated human and M. tuberculosis genotypes are interrogated in conjunction, will help identify new protective antigens for the development of better TB vaccines.

Mouse models of human TB pathology: roles in the analysis of necrosis and the development of host-directed therapies

A key aspect of TB pathogenesis that maintains Mycobacterium tuberculosis in the human population is the ability to cause necrosis in pulmonary lesions. As co-evolution shaped M. tuberculosis (M.tb) and human responses, the complete TB disease profile and lesion manifestation are not fully reproduced by any animal model. However, animal models are absolutely critical to understand how infection with virulent M.tb generates outcomes necessary for the pathogen transmission and evolutionary success. In humans, a wide spectrum of TB outcomes has been recognized based on clinical and epidemiological data. In mice, there is clear genetic basis for susceptibility. Although the spectra of human and mouse TB do not completely overlap, comparison of human TB with mouse lesions across genetically diverse strains firmly establishes points of convergence. By embracing the genetic heterogeneity of the mouse population, we gain tremendous advantage in the quest for suitable in vivo models. Below, we review genetically defined mouse models that recapitulate a key element of M.tb pathogenesis—induction of necrotic TB lesions in the lungs—and discuss how these models may reflect TB stratification and pathogenesis in humans. The approach ensures that roles that mouse models play in basic and translational TB research will continue to increase allowing researchers to address fundamental questions of TB pathogenesis and bacterial physiology in vivo using this well-defined, reproducible, and cost-efficient system. Combination of the new generation mouse models with advanced imaging technologies will also allow rapid and inexpensive assessment of experimental vaccines and therapies prior to testing in larger animals and clinical trials.

Determinants of the Sympatric Host-Pathogen Relationship in Tuberculosis

Major contributions from pathogen genome analysis and host genetics have equated the possibility of Mycobacterium tuberculosis co-evolution with its human host leading to more stable sympatric host–pathogen relationships. However, the attribution to either sympatric or allopatric categories depends on the resolution or grain of genotypic characterization. We explored the influence on the sympatric host-pathogen relationship of clinical (HIV infection and multidrug-resistant tuberculosis [MDRTB]) and demographic (gender and age) factors in regards to the genotypic grain by using spacer oligonucleotide typing (spoligotyping) for classification of M. tuberculosis strains within the Euro-American lineage. We analyzed a total of 547 tuberculosis (TB) cases, from six year consecutive sampling in a setting with high TB-HIV coinfection (32.0%). Of these, 62.0% were caused by major circulating pathogen genotypes. The sympatric relationship was defined according to spoligotype in comparison to the international spoligotype database SpolDB4. While no significant association with Euro-American lineage was observed with any of the factors analyzed, increasing the resolution with spoligotyping evidenced a significant association of MDRTB with sympatric strains, regardless of the HIV status. Furthermore, distribution curves of the prevalence of sympatric and allopatric TB in relation to patients’ age showed an accentuation of the relevance of the age of onset in the allopatric relationship, as reflected in the trimodal distribution. On the contrary, sympatric TB was characterized by the tendency towards a typical (standard) distribution curve. Our results suggest that within the Euro-American lineage a greater degree of genotyping fine-tuning is necessary in modeling the biological processes behind the host-pathogen interplay. Furthermore, prevalence distribution of sympatric TB to age was suggestive of host genetic determinisms driven by more common variants.

Mycobacterium tuberculosis: ecology and evolution of a human bacterium

Some species of the Mycobacterium tuberculosis complex (MTBC), particularly Mycobacterium tuberculosis, which causes human tuberculosis (TB), are the first cause of death linked to a single pathogen worldwide. In the last decades, evolutionary studies have much improved our knowledge on MTBC history and have highlighted its long co-evolution with humans. Its ability to remain latent in humans, the extraordinary proportion of asymptomatic carriers (one-third of the entire human population), the deadly epidemics and the observed increasing level of resistance to antibiotics are proof of its evolutionary success. Many MTBC molecular signatures show not only that these bacteria are a model of adaptation to humans but also that they have influenced human evolution. Owing to the unbalance between the number of asymptomatic carriers and the number of patients with active TB, some authors suggest that infection by MTBC could have a protective role against active TB disease and also against other pathologies. However, it would be inappropriate to consider these infectious pathogens as commensals or symbionts, given the level of morbidity and mortality caused by TB.

Non-clinical factors associated with TB: important for DOTS impact evaluation and disease elimination

Initial optimism that DOTS (Directly Observed Treatment, Short-course) would have a dramatic effect on TB incidence rates in developing countries has not been supported by the evidence accumulated so far. Indeed, where TB incidence rates have decreased, non-clinical socio-economic factors appear to have played at least as great a role. We postulate that in those settings with little or no decrease in TB incidence, there are likely to be common pathway blockages that interfere with the effectiveness of DOTS implementation as socio-economic factors evolve. Measuring socio-economic trends, as well as DOTS implementation, is important for understanding TB control and opens up the opportunity for broader public health engagement.

Year of birth effects in the historical decline of tuberculosis mortality: a reconsideration

Birth cohort patterns in mortality are often used to infer long-lasting impacts of early life conditions. One of the most widely accepted examples of a birth cohort effect is that of tuberculosis mortality before the late 1940s. However the evidential basis for claims of cohort-specific declines in tuberculosis mortality is very slight. Reanalysis of original or enhanced versions of datasets used previously to support claims of cohort effects in tuberculosis mortality indicated that: 1. where the initial decline in tuberculosis mortality occurred within the period of observation, onset of decline occurred simultaneously in many age groups, in a pattern indicative of 'period' not cohort-dependent effects. 2. there was little evidence of 'proportional hazard'-type cohort patterns in tuberculosis mortality for any female population studied. Therefore any mechanisms proposed to underlie this type of cohort pattern in male mortality must be sex-specific. 3. sex ratios of tuberculosis mortality at older ages peaked in cohorts born around 1900, and resembled cohort sex ratios of lung cancer mortality. This analysis indicates that age-specific patterns in the decline in tuberculosis mortality before 1950 are unlikely to reflect improvements in early life conditions. The patterns observed are generally more consistent with the influence of factors that reduced mortality simultaneously in most age groups. Additional influences, possibly smoking habits, impeded the decline of tuberculosis in older adult males, and produced the sex-specific shifts in age distributions of mortality that were previously interpreted as evidence of cohort-dependent mortality decline.

Drosophila melanogaster Selection for Survival of Bacillus cereus Infection: Life History Trait Indirect Responses

To study evolved resistance/tolerance in an insect model, we carried out an experimental evolution study using D. melanogaster and the opportunistic pathogen B. cereus as the agent of selection. The selected lines evolved a 3.0- to 3.3-log increase in the concentration of spores required for 50% mortality after 18–24 generations of selection. In the absence of any treatment, selected lines evolved an increase in egg production and delayed development time. The latter response could be interpreted as a cost of evolution. Alternatively, delayed development might have been a target of selection resulting in increased adult fat body function including production of antimicrobial peptides, and, incidentally, yolk production for oocytes and eggs. When treated with autoclaved spores, the egg production difference between selected and control lines was abolished, and this response was consistent with the hypothesis of a cost of an induced immune response. Treatment with autoclaved spores also reduced life span in some cases and elicited early-age mortality in the selected and wound-control lines both of which were consistent with the hypothesis of a cost associated with induction of immune responses. In general, assays on egg production yielded key outcomes including the negative effect of autoclaved spores on egg production.

Host-pathogen coevolution in human tuberculosis

Tuberculosis (TB) is a disease of antiquity. Yet TB today still causes more adult deaths than any other single infectious disease. Recent studies show that contrary to the common view postulating an animal origin for TB, Mycobacterium tuberculosis complex (MTBC), the causative agent of TB, emerged as a human pathogen in Africa and colonized the world accompanying the Out-of-Africa migrations of modern humans. More recently, evolutionarily 'modern' lineages of MTBC expanded as a consequence of the global human population increase, and spread throughout the world following waves of exploration, trade and conquest. While epidemiological data suggest that the different phylogenetic lineages of MTBC might have adapted to different human populations, overall, the phylogenetically 'modern' MTBC lineages are more successful in terms of their geographical spread compared with the 'ancient' lineages. Interestingly, the global success of 'modern' MTBC correlates with a hypo-inflammatory phenotype in macrophages, possibly reflecting higher virulence, and a shorter latency in humans. Finally, various human genetic variants have been associated with different MTBC lineages, suggesting an interaction between human genetic diversity and MTBC variation. In summary, the biology and the epidemiology of human TB have been shaped by the long-standing association between MTBC and its human host.

Old and new selective pressures on Mycobacterium tuberculosis

Tuberculosis (TB) has been affecting humans for millennia. There is increasing indication that human-adapted Mycobacterium tuberculosis complex (MTBC) has been co-evolving with different human populations. Some of the most important drivers of MTBC evolution have been the host immune response and human demography. These old selective forces have shaped many of the features of human TB we see today. Two new selective pressures have emerged only a few decades ago, namely HIV co-infection and the use of anti-TB drugs. Here we discuss how the emergence of HIV/TB and drug resistance could impact the long-term balance between MTBC and its human host, and how these changes might influence the future evolutionary trajectory of MTBC.

The population dynamics and control of tuberculosis

More than 36 million patients have been successfully treated via the World Health Organization's strategy for tuberculosis (TB) control since 1995. Despite predictions of a decline in global incidence, the number of new cases continues to grow, approaching 10 million in 2010. Here we review the changing relationship between the causative agent, Mycobacterium tuberculosis, and its human host and examine a range of factors that could explain the persistence of TB. Although there are ways to reduce susceptibility to infection and disease, and a high-efficacy vaccine would boost TB prevention, early diagnosis and drug treatment to interrupt transmission remain the top priorities for control. Whatever the technology used, success depends critically on the social, institutional, and epidemiological context in which it is applied.

Kin selection and evolution of infectious disease resistance

Discoveries of mutations conferring resistance to infectious diseases have led to increased interest in the evolutionary dynamics of disease resistance. Several recent papers have estimated the historical strength of selection for mutations conferring disease resistance. These studies are based on simple population genetic models that do not take account of factors such as spatial and family structure. Such factors may have a substantial impact on the strength of natural selection through inclusive fitness effects. That is, people have a strong tendency to live with relatives and therefore have a high probability of transmitting infectious diseases to them. Thus, an allele that protects an individual against disease infection also protects that individual's family members. Because some of these family members are likely to also be carrying the allele, selection for that allele is magnified by family structure. In this paper, I use mathematical modeling techniques to explore the impact of such kin selection on the strength of selection for infectious disease resistance alleles. I show that if the resistance allele has the same proportional effect on both within- and between-family transmission, then the impact of kin selection is relatively minor. Selection coefficients are increased by 5-35%, with a greater benefit for weaker alleles. The reason is that an individual with a strong resistance allele does not need much protection from infection by family members and thus does not benefit much from their alleles. The effect of kin selection can be dramatic, however, if the resistance allele has a larger effect on between-family transmission than within-family transmission (which can occur if between-family infection rates are much smaller than within-family rates), increasing selection coefficients by as much as two- to threefold. These results show conditions when it is important to consider family structure in estimates of the strength of selection for infectious disease resistance alleles.

Introduction: conceptualizing and partitioning the emergence process of zoonotic viruses from wildlife to humans

This introduction provides a telegraphic overview of the processes of zoonotic viral emergence, the intricacies of host-virus interactions, and the distinct role of biological transitions and modifying factors. The process of emergence is conceptualized as two transition stages which are common and required for all disease emergence, (1) human contact with the infectious agent and (2) cross-species transmission of the agent, and two transition stages which are not required for emergence and appear unavailable to many zoonotic pathogens, (3) sustained human-to-human transmission and (4) genetic adaptation to the human host. The latter two transitions are presumably prerequisites for the pandemic emergence of a pathogen. The themes introduced herein are amplified and explored in detail by the contributors to this volume. Each author explores the mechanisms and unique circumstances by which evolution, biology, history, and current context have contrived to drive the emergence of different zoonotic agents by a series of related events; although recognizable similarities exist among the events leading to emergence the details and circumstances are never repetitive.

Host genetics of mycobacterial diseases in mice and men: forward genetic studies of BCG-osis and tuberculosis

In humans, genetic factors have long been suspected to contribute to the onset and outcome of tuberculosis. Such effects are difficult to identify owing to their complex inheritance, and to the confounding impact of environmental factors, notably pathogen-associated virulence determinants. Recently, forward genetic approaches in mouse models and in human populations have been used to elucidate a molecular basis for predisposition to mycobacterial diseases. The genetic dissection of host predisposition to infection with Mycobacterium bovis BCG and M. tuberculosis will help to define the key molecules involved in host antituberculous immunity and should provide new insights into this important infectious disease.

[Robert Koch was right. Towards a new interpretation of tuberculin therapy]

At the centenary of Robert Koch's Nobel Prize award, tuberculosis treatment with tuberculin, which was announced in Berlin in 1890, is still considered a failure. Nevertheless, there is now sufficient information supporting the idea that tuberculin therapy was widely used until the second half of the twentieth century; thus, the impact of this treatment should be studied and related to the decrease in tuberculosis-related mortality recorded in that period. Moreover, tuberculin therapy has inspired at least two new immunotherapies; these, however, were directed toward precisely the opposite effect: suppression of the Koch phenomenon. Thus, inoculation of Mycobacterium vaccae polarizes the immune response towards the Th1 type; and inoculation of RUTI avoids local immunodepression after short-term chemotherapy without inducing toxicity. For this reason, Robert Koch's work on antituberculosis therapy should be reread and proper recognition given to his contribution in this field.

An autosomal dominant major gene confers predisposition to pulmonary tuberculosis in adults

The molecular basis of genetic predisposition to pulmonary tuberculosis in adults remains largely elusive. Few candidate genes have consistently been implicated in tuberculosis susceptibility, and no conclusive linkage was found in two previous genome-wide screens. We report here a genome-wide linkage study in a total sample of 96 Moroccan multiplex families, including 227 siblings with microbiologically and radiologically proven pulmonary tuberculosis. A genome-wide scan conducted in half the sample (48 families) identified five regions providing suggestive evidence (logarithm of the odds [LOD] score >1.17; P < 0.01) for linkage. These regions were then fine-mapped in the total sample of 96 families. A single region of chromosome 8q12-q13 was significantly linked to tuberculosis (LOD score = 3.49; P = 3 × 10⁻⁵), indicating the presence of a major tuberculosis susceptibility gene. Linkage was stronger (LOD score = 3.94; P = 10⁻⁵) in the subsample of 39 families in which one parent was also affected by tuberculosis, whereas it was much lower (LOD score = 0.79) in the 57 remaining families without affected parents, supporting a dominant mode of inheritance of the major susceptibility locus. These results provide direct molecular evidence that human pulmonary tuberculosis has a strong genetic basis, and indicate that the genetic component involves at least one major locus with a dominant susceptibility allele.

Aspartic acid homozygosity at codon 57 of HLA-DQ beta is associated with susceptibility to pulmonary tuberculosis in Cambodia

After infection with Mycobacterium tuberculosis, clinical disease usually remains latent, contained by the host immune response. Although polymorphisms of HLA loci have been hypothesized to play a major role in the breakdown of latency, a functional link has not been established. Molecular-based HLA-typing methods were used to test the association of sets of HLA alleles encoding an aspartic acid at codon 57 of the HLA-DQ beta-chain (HLA-DQ beta57-Asp) with susceptibility to tuberculosis in a cohort of 436 pulmonary tuberculosis patients and 107 healthy controls from Cambodia. HLA class II null cells were transduced with HLA-DQ beta57-Asp or HLA-DQ beta57-Ala and evaluated for their ability to bind peptides from two immunogenic M. tuberculosis specific proteins, ESAT-6 and CFP-10. In this study, we report a highly significant association between progressive pulmonary tuberculosis and homozygosity for HLA-DQ beta57-Asp alleles. The presence of HLA-DQ beta57-Asp resulted in a significantly reduced ability to bind a peptide from the central region of the ESAT-6 protein. Furthermore, when this peptide was presented by an HLA-DQ beta57-Asp allele, Ag-specific IFN-gamma production from CD4+ T cells from tuberculosis patients was significantly less than when this peptide was presented by an HLA-DQ-beta allele encoding an alanine at codon 57. Multiple genetic loci and ethnic-specific factors are likely involved in the human immune response to tuberculosis. The data presented here provide a functional explanation for a highly significant association between an HLA polymorphism and tuberculosis in a highly characterized group of patients with susceptibility to progressive tuberculosis infection in Cambodia.

Promoter variation in the DC-SIGN-encoding gene CD209 is associated with tuberculosis

BACKGROUND

Tuberculosis, which is caused by Mycobacterium tuberculosis, remains one of the leading causes of mortality worldwide. The C-type lectin DC-SIGN is known to be the major M. tuberculosis receptor on human dendritic cells. We reasoned that if DC-SIGN interacts with M. tuberculosis, as well as with other pathogens, variation in this gene might have a broad range of influence in the pathogenesis of a number of infectious diseases, including tuberculosis.

METHODS AND FINDINGS

We tested whether polymorphisms in CD209, the gene encoding DC-SIGN, are associated with susceptibility to tuberculosis through sequencing and genotyping analyses in a South African cohort. After exclusion of significant population stratification in our cohort, we observed an association between two CD209 promoter variants (-871G and -336A) and decreased risk of developing tuberculosis. By looking at the geographical distribution of these variants, we observed that their allelic combination is mainly confined to Eurasian populations.

CONCLUSIONS

Our observations suggest that the two -871G and -336A variants confer protection against tuberculosis. In addition, the geographic distribution of these two alleles, together with their phylogenetic status, suggest that they may have increased in frequency in non-African populations as a result of host genetic adaptation to a longer history of exposure to tuberculosis. Further characterization of the biological consequences of DC-SIGN variation in tuberculosis will be crucial to better appreciate the role of this lectin in interactions between the host immune system and the tubercle bacillus as well as other pathogens.

Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis

The highly successful human pathogen Mycobacterium tuberculosis has an extremely low level of genetic variation, which suggests that the entire population resulted from clonal expansion following an evolutionary bottleneck around 35,000 y ago. Here, we show that this population constitutes just the visible tip of a much broader progenitor species, whose extant representatives are human isolates of tubercle bacilli from East Africa. In these isolates, we detected incongruence among gene phylogenies as well as mosaic gene sequences, whose individual elements are retrieved in classical M. tuberculosis. Therefore, despite its apparent homogeneity, the M. tuberculosis genome appears to be a composite assembly resulting from horizontal gene transfer events predating clonal expansion. The amount of synonymous nucleotide variation in housekeeping genes suggests that tubercle bacilli were contemporaneous with early hominids in East Africa, and have thus been coevolving with their human host much longer than previously thought. These results open novel perspectives for unraveling the molecular bases of M. tuberculosis evolutionary success.

Mycobacterium tuberculosis, the agent of tuberculosis, is a highly successful human pathogen and kills nearly 3 million persons each year. This pathogen and its close relatives sum up in a single and compact clonal group dating back only a few tens of thousands of years. Using genetic data, the researchers have discovered that human tubercle bacilli from East Africa represent extant bacteria of a much broader progenitor species from which the M. tuberculosis clonal group evolved. They estimate that this progenitor species is as old as 3 million years. This suggests that our remote hominid ancestors may well have already suffered from tuberculosis. In addition, the researchers show that tubercle bacilli are able to exchange parts of their genome with other strains, a process that is known to play a crucial role in adaptation of pathogens to their hosts. Thus, the M. tuberculosis genome appears to be a composite assembly, resulting from ancient horizontal DNA exchanges before its clonal expansion. These findings open novel perspectives for unraveling the origin and the molecular bases of M. tuberculosis evolutionary success, and lead to reconsideration of the impact of tuberculosis on human natural selection.

Differential cytokine genotype frequencies among Canadian Aboriginal and Caucasian populations

Genetic diversity related to the human immune response is a key factor in individual and population survival throughout human history. Population diversity in disease susceptibility and resistance have been identified and linked to differences in cytokine mRNA and protein expression levels. Polymorphisms in the regulatory regions of cytokine genes can influence gene transcription levels and they have been associated with susceptibility to, and/or severity of, autoimmune disorders such as rheumatoid arthritis, meningococcus and sepsis. It is reported here that in two study populations, Canadian Aboriginal individuals have a higher frequency of cytokine single-nucleotide polymorphisms favouring a low production of TNFalpha, IFNgamma and IL-10 and high production of IL-6 as compared to a Caucasian population. We postulate that the evolution of this unique cytokine genotype profile may be linked to the Aboriginal adaptation to selection pressures related to an environment in which helminthic, parasitic and fungal infections predominated.

Allelic histories: positive selection on a HIV-resistance allele

The CCR5-Delta32 allele crucially determines the course of HIV infection and appears to be highly protective against the disease. Population genetic studies suggest that the allele has been under positive selection in Europe in the past. In a recent paper, Alison Galvani and Montgomery Slatkin collate the available evidence and use a mathematical model to strongly suggest that smallpox could have exerted sufficient selection pressure to explain the distribution of the allele across Europe. This is a beautiful example of the power of mathematical models in evolutionary genetics.

Mycobacterium tuberculosis pathogenesis and molecular determinants of virulence

Tuberculosis (TB), one of the oldest known human diseases. is still is one of the major causes of mortality, since two million people die each year from this malady. TB has many manifestations, affecting bone, the central nervous system, and many other organ systems, but it is primarily a pulmonary disease that is initiated by the deposition of Mycobacterium tuberculosis, contained in aerosol droplets, onto lung alveolar surfaces. From this point, the progression of the disease can have several outcomes, determined largely by the response of the host immune system. The efficacy of this response is affected by intrinsic factors such as the genetics of the immune system as well as extrinsic factors, e.g., insults to the immune system and the nutritional and physiological state of the host. In addition, the pathogen may play a role in disease progression since some M. tuberculosis strains are reportedly more virulent than others, as defined by increased transmissibility as well as being associated with higher morbidity and mortality in infected individuals. Despite the widespread use of an attenuated live vaccine and several antibiotics, there is more TB than ever before, requiring new vaccines and drugs and more specific and rapid diagnostics. Researchers are utilizing information obtained from the complete sequence of the M. tuberculosis genome and from new genetic and physiological methods to identify targets in M. tuberculosis that will aid in the development of these sorely needed antitubercular agents.