"A re-evaluation of M. prototuberculosis": continuing the debate

Tracking down the White Plague: The skeletal evidence of tuberculous meningitis in the Robert J. Terry Anatomical Skeletal Collection

Paleopathological diagnosis of tuberculosis (TB) essentially relies on the identification of macroscopic lesions in the skeleton that can be related to different manifestations of TB. Among these alterations, granular impressions (GIs) on the inner skull surface have been considered as pathognomonic features of tuberculous meningitis (TBM). GIs may be established by pressure atrophy of the tubercles formed on the outermost meningeal layer during later stages of TBM. Although GIs were used as diagnostic criteria for TBM in the paleopathological practice since the late 20^th century, their diagnostic value has been questioned. To contribute to strengthening the diagnostic value of GIs, a macroscopic investigation–focusing on the macromorphological characteristics and frequency of GIs–was performed on skeletons of known cause of death from the Terry Collection. The χ² analysis of our data revealed that GIs were significantly more common in individuals who died of TB than in individuals who died of non-TB causes. Furthermore, GIs were localized on the inner surface of the skull base and of the lower lateral skull vault. The localization pattern and distribution of GIs on the endocranial surface resemble that of the tubercles observed in the affected meninges during the pathogenesis of TBM. Our results strengthen the tuberculous origin of GIs and imply that they can be considered as specific signs of TBM. Therefore, GIs can be used as diagnostic criteria for TBM in the paleopathological practice, and the diagnosis of TBM can be established with a high certainty when GIs are present in ancient human bone remains.

The Biology and Epidemiology of Mycobacterium canettii

Genome-based insights into the evolution of Mycobacterium tuberculosis and other tuberculosis-causing mycobacteria are constantly increasing. In particular, the recent genomic and functional characterization of several Myocbacterium canettii strains, which are thought to resemble in many aspects the putative common ancestor of the members of the M. tuberculosis complex (MTBC), has consolidated a plausible scenario of the early evolution of tuberculosis-causing mycobacteria, in which the clonal MTBC, comprising numerous key pathogens of mammalian hosts, has evolved from a generalist mycobacterium living in the environment. These studies also have considerably enriched our knowledge on selected molecular events that likely have contributed to the incursion, maintenance and spread of the MTBC members in diverse mammalian hosts. Here, we summarize and discuss recently revealed molecular and evolutionary aspects and emphasize the vast utility of M. canettii strains for identifying the mechanisms that contributed to the global emergence of M. tuberculosis as one of the most important human pathogens.

Mycobacterial Pathogenomics and Evolution

Most mycobacterial species are harmless saprophytes, often found in aquatic environments. A few species seem to have evolved from this pool of environmental mycobacteria into major human pathogens, such as Mycobacterium tuberculosis, the agent of tuberculosis, Mycobacterium leprae, the leprosy bacillus, and Mycobacterium ulcerans, the agent of Buruli ulcer. While the pathogenicity of M. ulcerans relates to the acquisition of a large plasmid encoding a polyketide-derived toxin, the molecular mechanisms by which M. leprae or M. tuberculosis have evolved to cause disease are complex and involve the interaction between the pathogen and the host. Here we focus on M. tuberculosis and closely related mycobacteria and discuss insights gained from recent genomic and functional studies. Comparison of M. tuberculosis genome data with sequences from nontuberculous mycobacteria, such as Mycobacterium marinum or Mycobacterium kansasii, provides a perception of the more distant evolution of M. tuberculosis, while the recently accomplished genome sequences of multiple tubercle bacilli with smooth colony morphology, named Mycobacterium canettii, have allowed the ancestral gene pool of tubercle bacilli to be estimated. The resulting findings are instrumental for our understanding of the pathogenomic evolution of tuberculosis-causing mycobacteria. Comparison of virulent and attenuated members of the M. tuberculosis complex has further contributed to identification of a specific secretion pathway, named ESX or Type VII secretion. The molecular machines involved are key elements for mycobacterial pathogenicity, strongly influencing the ability of M. tuberculosis to cope with the immune defense mounted by the host.

Comparative genomics of mycobacteria: some answers, yet more new questions

Comparative genomic studies permit a genus-level perspective on the distinction between environmental mycobacteria and Mycobacterium tuberculosis, as well as a species-level assessment of genetic variability within M. tuberculosis. Both of these strata of evolutionary analysis serve to generate hypotheses regarding the genomic basis of M. tuberculosis virulence. In contrasting lessons from macroevolutionary study and microevolutionary study, one can form predictions about which segments of the genome are likely to be essential for or dispensable for the pathogenesis of tuberculosis. Although some of these predictions have been experimentally verified, notable exceptions challenge the direct link between these virulence factors and the capacity of M. tuberculosis to successfully cause disease and propagate between human hosts. These unexpected findings serve as the stimulus for further studies, using genomic comparisons and other approaches, to better define the remarkable success of this recalcitrant pathogen.

Diversity and evolution of Mycobacterium tuberculosis: moving to whole-genome-based approaches

Genotyping of clinical Mycobacterium tuberculosis complex (MTBC) strains has become a standard tool for epidemiological tracing and for the investigation of the local and global strain population structure. Of special importance is the analysis of the expansion of multidrug (MDR) and extensively drug-resistant (XDR) strains. Classical genotyping and, more recently, whole-genome sequencing have revealed that the strains of the MTBC are more diverse than previously anticipated. Globally, several phylogenetic lineages can be distinguished whose geographical distribution is markedly variable. Strains of particular (sub)lineages, such as Beijing, seem to be more virulent and associated with enhanced resistance levels and fitness, likely fueling their spread in certain world regions. The upcoming generalization of whole-genome sequencing approaches will expectedly provide more comprehensive insights into the molecular and epidemiological mechanisms involved and lead to better diagnostic and therapeutic tools.

Evolution of smooth tubercle Bacilli PE and PE_PGRS genes: evidence for a prominent role of recombination and imprint of positive selection

BACKGROUND

PE and PE_PGRS are two mycobateria-restricted multigene families encoding membrane associated and secreted proteins that have expanded mainly in the pathogenic species, notably the Mycobacterium tuberculosis complex (MTBC). Several lines of evidence attribute to PE and PE_PGRS genes critical roles in mycobacterial pathogenicity. To get more insight into the nature of these genes, we sought to address their evolutionary trajectories in the group of smooth tubercle bacilli (STB), the putative ancestor of the clonal MTBC.

METHODOLOGY/PRINCIPAL FINDINGS

By focussing on six polymorphic STB PE/PE_PGRS genes, we demonstrate significant incongruence among single gene genealogies and detect strong signals of recombination using various approaches. Coalescent-based estimation of population recombination and mutation rates (ρ and θ, respectively) indicates that the two mechanisms are of roughly equal importance in generating diversity (ρ/θ = 1.457), a finding in a marked contrast to house keeping genes (HKG) whose evolution is chiefly brought about by mutation (ρ/θ = 0.012). In comparison to HKG, we found 15 times higher mean rate of nonsynonymous substitutions, with strong evidence of positive selection acting on PE_PGRS62 (dN/dS = 1.42), a gene that has previously been shown to be essential for mycobacterial survival in macrophages and granulomas. Imprint of positive selection operating on specific amino acid residues or along branches of PE_PGRS62 phylogenetic tree was further demonstrated using maximum likelihood- and covarion-based approaches, respectively. Strikingly, PE_PGR62 proved highly conserved in present-day MTBC strains.

CONCLUSIONS/SIGNIFICANCE

Overall the data indicate that, in STB, PE/PE_PGRS genes have undergone a strong diversification process that is speeded up by recombination, with evidence of positive selection. The finding that positive selection involved an essential PE_PGRS gene whose sequence appears to be driven to fixation in present-day MTBC strains lends further support to the critical role of PE/PE_PGRS genes in the evolution of mycobacterial pathogenicity.

Tuberculosis 2012: biology, pathogenesis and intervention strategies; an update from the city of light

Tuberculosis (TB) remains one of the world's most deadly infectious diseases, with approximately 1.5 million deaths and 9 million new cases of TB in 2010. There is an urgent global need to develop new control tools, with advances necessary in our basic understanding of the pathogen, Mycobacterium tuberculosis, and translation of these findings to public health. It was in this context that the "Tuberculosis 2012: Biology, Pathogenesis, Intervention Strategies" meeting was held in the Institut Pasteur, Paris, France from 11 to 15th Sept 2012. The meeting brought together over 600 delegates from across the globe to hear updates on the latest research findings and how they are underpinning the development of novel vaccines, diagnostics, and drugs.

Importance of the genetic diversity within the Mycobacterium tuberculosis complex for the development of novel antibiotics and diagnostic tests of drug resistance

Despite being genetically monomorphic, the limited genetic diversity within the Mycobacterium tuberculosis complex (MTBC) has practical consequences for molecular methods for drug susceptibility testing and for the use of current antibiotics and those in clinical trials. It renders some representatives of MTBC intrinsically resistant against one or multiple antibiotics and affects the spectrum and consequences of resistance mutations selected for during treatment. Moreover, neutral or silent changes within genes responsible for drug resistance can cause false-positive results with hybridization-based assays, which have been recently introduced to replace slower phenotypic methods. We discuss the consequences of these findings and propose concrete steps to rigorously assess the genetic diversity of MTBC to support ongoing clinical trials.

Origin, spread and demography of the Mycobacterium tuberculosis complex

The evolutionary timing and spread of the Mycobacterium tuberculosis complex (MTBC), one of the most successful groups of bacterial pathogens, remains largely unknown. Here, using mycobacterial tandem repeat sequences as genetic markers, we show that the MTBC consists of two independent clades, one composed exclusively of M. tuberculosis lineages from humans and the other composed of both animal and human isolates. The latter also likely derived from a human pathogenic lineage, supporting the hypothesis of an original human host. Using Bayesian statistics and experimental data on the variability of the mycobacterial markers in infected patients, we estimated the age of the MTBC at 40,000 years, coinciding with the expansion of "modern" human populations out of Africa. Furthermore, coalescence analysis revealed a strong and recent demographic expansion in almost all M. tuberculosis lineages, which coincides with the human population explosion over the last two centuries. These findings thus unveil the dynamic dimension of the association between human host and pathogen populations.

Tuberculosis: evolution in millennia and minutes

Tuberculosis remains a global public health threat: the causative organism, Mycobacterium tuberculosis, was once thought to show little genetic variation, but research in the last 10 years has demonstrated an ability to change in a series of different time frames. Related species of mycobacteria have undergone evolution by deletion of segments of DNA, allowing Mycobacterium bovis and other species to emerge from the M. tuberculosis complex, disproving the previously accepted theories. Deletions also affect the pathogenic potential of different lineages of M. tuberculosis. Over shorter time periods genetic variation is achieved by the movement of insertion sequences such as IS6110. Some lineages identified by this means are over-represented in patient populations, suggesting a genetic advantage, although the mechanism for this is not yet apparent. M. tuberculosis must also adapt to host and antibiotic selection pressure, and this is achieved by point mutations. Almost all antibiotic resistance emerges in this way, and data from clinical and in vitro studies indicate that M. tuberculosis exists with pre-existent mutants that remain as a small proportion of the population because of fitness deficits. Under certain physiological conditions, these rarer mutants may be favoured and, when antibiotic selection pressure is applied, will rise to dominate the bacterial population. M. tuberculosis is a highly effective pathogen that has caused disease in human populations for millennia. We are now starting to understand some of the genetic mechanisms behind this phenomenon.

Application of sensitive and specific molecular methods to uncover global dissemination of the major RDRio Sublineage of the Latin American-Mediterranean Mycobacterium tuberculosis spoligotype family

The Latin American-Mediterranean (LAM) family of Mycobacterium tuberculosis is believed to be the cause of approximately 15% of tuberculosis cases worldwide. Previously, we defined a prevalent sublineage of the LAM family in Brazil by a single characteristic genomic deletion designated RD(Rio). Using the Brazilian strains, we pinpoint an Ag85C(103) single nucleotide polymorphism (SNP) (screened by restriction fragment length polymorphism [RFLP] analysis) that correctly identified all LAM family strains. Importantly, all RD(Rio) strains concomitantly possessed the RD174 deletion. These genetic signatures, along with a newly developed multiplex PCR for rapid differentiation between "wild-type" and RD(Rio) strains, were then used to analyze an international collection of M. tuberculosis strains. RD(Rio) M. tuberculosis was identified from four continents involving 11 countries. Phylogenetic analysis of the IS6110-RFLP patterns from representative RD(Rio) and LAM strains from Brazil, along with all representative clusters from a South African database, confirmed their genetic relatedness and transcontinental transmission. The Ag85C(103) SNP RFLP, as compared to results obtained using a PCR method targeting a LAM-restricted IS6110 element, correctly identified 99.8% of LAM spoligotype strains. Together, these tests were more accurate than spoligotyping at categorizing strains with indefinable spoligotypes and segregated true LAM strains from those with convergent spoligotypes. The fact that RD(Rio) strains were identified worldwide highlights the importance of this LAM family sublineage and suggests that this strain is a global threat that should be specifically targeted by public health resources. Our provision of simple and robust molecular methods will assist the evaluation of the LAM family and the RD(Rio) sublineage.

Genomics and the evolution, pathogenesis, and diagnosis of tuberculosis

Tuberculosis kills nearly 2 million people annually, and current approaches to tuberculosis control are expensive, have limited efficacy, and are vulnerable to being overcome by extensively drug-resistant strains of Mycobacterium tuberculosis. Determination of the genome sequence of M. tuberculosis has revolutionized tuberculosis research, contributed to major advances in the understanding of the evolution and pathogenesis of M. tuberculosis, and facilitated development of new diagnostic tests with increased specificity for tuberculosis. In this review, we describe some of the major progress in tuberculosis research that has resulted from knowledge of the genome sequence and note some of the problems that remain unsolved.

The role of IS6110 in the evolution of Mycobacterium tuberculosis

Members of the Mycobacterium tuberculosis complex contain the transposable element IS6110 which, due to its high numerical and positional polymorphism, has become a widely used marker in epidemiological studies. Here, we review the evidence that IS6110 is not simply a passive or 'junk' DNA sequence, but that, through its transposable activity, it is able to generate genotypic variation that translates into strain-specific phenotypic variation. We also speculate on the role that this variation has played in the evolution of M. tuberculosis and conclude that the presence of a moderate IS6110 copy number within the genome may provide the pathogen with a selective advantage that has aided its virulence.