**6. Acknowledgement**

G.S.B. has a James Bardrick Personal Research Chair and a Royal Society Wolfson Research Merit Award. D.E.M. was a recipient of an Emeritus Fellowship from The Leverhulme Trust, who are also thanked for Project Grant F/00 094/BL (G.S.B., D.E.M., O.Y-C.L.).

#### **7. References**

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the same sample. This is not a static situation, however, as new powerful methods are becoming available for analyses of aDNA and lipids; additionally, the range of lipids

The availability of established aDNA and biomarker protocols and expertise provides avenues into a range of interlocking research areas. As noted above, evolutionary pathways can be verified for tuberculosis, also providing evidence about virulence as the key lipid biomarkers are implicated in this process. The very existence of apparently intact key lipids in ancient samples is also of basic chemical interest; for example, the mycolic acids from the 9,000 year old Atlit-Yam skeletons probably represent the oldest known cyclopropane rings! It is important also to study leprosy, as the evolutionary processes of these two mycobacterial diseases are fatally intertwined with many clear co-infections. The relative prevalence of tuberculosis and leprosy can give clear indications of the prevailing social environment. In tuberculosis/leprosy co-infections it is becoming possible to estimate the relative bacterial load in particular bones and thereby obtain indications regarding which disease was the immediate cause of death. For each disease and co-infections it will be instructive to examine bones throughout particular individual skeletons in order to gain information about dissemination. Evidence of tuberculosis and leprosy can be quite clear in the osteological record, with characteristic bone lesions and deformations and bone loss in the case of leprosy. Biomarker analysis can help illuminate and reinforce the diagnoses of skilled osteologists and compare bacterial loads in bones with and without disease indication. An appealing aspect of lipid biomarker analyses is the possibility of extracting the lipids with neutral solvents, avoiding any chemical or physical damage to particularly valuable bone samples. It must be borne in mind, however, that biomarker analyses for the diagnosis of ancient mycobacterial disease are currently sophisticated procedures, which cannot be easily attempted without time being spent in accumulating the necessary skills

The evolution of life on earth is a complex web of competitive and/or symbiotic interactions. Humans, related primates and all mammals are dependent on a symbiosis with many microorganisms, whose cells outnumber those of the host. From the perspective of the microorganism, the mammalian host provides an ecological niche in which it can multiply and evolve to improve its prospects for survival. In some cases, the interaction of microorganisms with mammals is a rapid, pathogenic process resulting in the demise of the host and the infecting agent passes on to a new subject. Early hominids and humans with a hunter/gatherer lifestyle had a low population density, so an alternative relationship with slow-growing organisms such as the pathogenic mycobacteria, emerged. Such pathogens have a long-term relationship with their host, thus enabling persistence of the organism until transmission is possible. This is likely to occur at the extremes of life, when the host immune response is immature or less effective, and at times of physical or mental stress, often associated with war, famine, poverty or social unrest. This latter scenario is typical of the ancient scourges of tuberculosis and leprosy, caused by *M. tuberculosis* and *M. leprae*,

Several decades ago, it appeared that BCG vaccination and combinations of effective drugs were conquering tuberculosis. However, declining vaccination efficacy, misuse of drug regimens and the rapid spread of HIV/AIDS-related immunodeficiency, together with increased urbanisation and population density, have provided the opportunity for

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**2** 

*Colombia* 

**Genomic Variability of** 

*Corporación CorpoGen, Bogotá D.C.,* 

*Mycobacterium tuberculosis*

Alejandro Reyes and Patricia Del Portillo

María Mercedes Zambrano, Ginna Hernández-Neuta,

Iván Hernández-Neuta, Andrea Sandoval, Andrés Cubillos-Ruiz,

Genomic variability provides the basis for adaptation and evolution and constitutes a fascinating aspect of the metabolically and phylogenetically diverse microbial world. Variability in bacteria has been extensively studied both because it enables inferring evolutionary relationships and because it plays an important role in host-pathogen interactions. Microbiologists, who have long struggled with species classification, have gained a more recent appreciation of the level of genetic diversity in microorganisms that has led to new awareness of what may constitute a bacterial "species" (Doolittle & Zhaxybayeva, 2009). In the clinical setting, genomic variability can represent a significant barrier to treatment. Many pathogens can acquire mutations or foreign genetic material through horizontal gene transfer (HGT) in response to the selective pressure imposed by the host immune system and by chemotherapy (Hawkey & Jones, 2009, Sampson, 2011), resulting in strains that are difficult to eradicate in hospitals as well as during long-term infection. Understanding the extent of genomic variability and its effects on disease in the case of pathogens that display genetic homogeneity and low variability, as is the case for the causative agent of tuberculosis, *Mycobacterium tuberculosis*, is particularly fascinating. The success of *M. tuberculosis* is intimately tied to the infectious process and its interaction with the human host, which is believed to have resulted from a long process of co-evolution (Donoghue, 2009, Gutierrez *et al.*, 2005). As a result, *M. tuberculosis* is capable of subverting the immune response and persisting as a latent form within an individual and for millennia

Despite the availability of chemotherapy and the continued efforts to control the disease, tuberculosis continues to be one of the top ten causes of morbidity and mortality worldwide, with approximately 9 million cases per year, according to the World Health Organization (Lawn & Zumla, 2011). In spite of the growing interest and continued efforts, there are still significant gaps in our knowledge regarding both the pathogen and its interaction with the host that hamper control strategies. The appearance and spread of multi-drug (MDR) as well as extensively drug resistant (XDR) strains of *M. tuberculosis* represent a growing threat worldwide and underscore the importance of effective diagnosis and treatment. Given the

**1. Introduction** 

within the human population.

