Image: Mycobacterium tuberculosis. Credit: © NIAID (CC BY 2.0)



People have inhabited the Andes mountains of South America for more than 9,000 years, adapting to the scarce oxygen available at high altitudes, along with cold temperatures and intense ultraviolet radiation. But a new genomic study led by researchers from Emory University suggests that Indigenous populations in present-day Ecuador also adapted to the tuberculosis bacterium, thousands of years before the arrival of Europeans, as Sophie K Joseph and John Lindo explain.


Profile: Sophie K Joseph


Sophie K Joseph is a PhD student in the Lindo Ancient DNA Lab in the Department of Anthropology at Emory University. She specialises in both the molecular and computational aspects of genomic research, taking an integrative approach to understanding population genetics through whole genome sequencing and statistical modelling.

Her primary research interests are in understanding the effects of different evolutionary pressures on the human genome in the context of important societal and cultural changes, such as agriculture, life at high altitude, and infectious disease. She is particularly interested in understanding how genetic risk factors and the surrounding environment may have influenced disease in past populations.


Profile: John Lindo


John Lindo is an assistant professor at Emory University and is the Principal Investigator of the Lindo Ancient DNA Lab.

His work focuses on the understanding of how humans have adapted to different environments as they moved throughout the Americas before the devastating effects of European colonisation.


Tuberculosis: One of today’s most challenging diseases


Caused by Mycobacterium tuberculosis, a bacterium which primarily infects the lungs, tuberculosis (TB) is easily transmitted between humans via respiratory droplets. These droplets can be spread when an infected person coughs, sneezes, or speaks, and can hang in the air for several hours. Across the world, active TB infections kill millions of people each year, making it one of the deadliest pathogens currently infecting humans today. Moreover, nearly one-third of the world’s population are latent carriers of the bacterium and are at risk for developing active TB.


Image: The Andes of Ecuador by Frederic Edwin Church, circa 1855. Public domain.


The great white plague


Historically, TB was often known in Europe as ‘the consumption’ or ‘the great white plague’. It struck fear in the hearts of everyone, as it did not discriminate among social class or age when claiming its victims – though, poor people in urban areas often had a greater rate of infection due to their crowded living conditions helping to spread the bacteria. TB caused nearly a quarter of all deaths in Europe from the 17th to the 19th centuries. Further back in time, the earliest written mentions of TB infections were in India and China over 2,000 years ago.

Before the isolation of Mycobacterium tuberculosis by German scientist Robert Koch in 1882, there were numerous theories about what caused the debilitating symptoms of TB, including that it was a hereditary illness rather than an infectious one, or that it was caused by damp soil and excess humidity. In the late 18th and early 19th centuries, however, scientists began to recognise the link between crowded living conditions and an increase in TB infections. In 1865, Jean-Antoine Villemin, a surgeon in the French military, infected a rabbit with pus from a human TB skin lesion, providing important documentation about the adaptability of the TB bacterium to infecting other mammals. Several scientists in the 1800s made attempts at isolating Mycobacterium tuberculosis, though the first to be successful was Koch in 1882. Despite this tremendous advancement, it would not be until the mid-20th Century that any effective drug treatments would become available.


Image: Mycobacterium tuberculosis. Credit: © NIAID (CC BY 2.0)

The antibiotic revolution


TB is a persistent pathogen for many reasons, including its cellular structure and ability to escape host immunity. From the beginning of medical treatment of TB using antibiotics, a multi-drug regimen has been necessary. The first combination therapy was approved in 1950 by the Medical Research Council of the United Kingdom. This treatment regimen consisted of the soil bacteria-derived antibiotic streptomycin and a synthetic antimicrobial compound called para-aminosalicylic acid. In 1952, it was discovered that the anticancer drug isoniazid was very effective at curing TB infections, and the so-called ‘triple regimen’ of streptomycin, para-aminosalicylic acid, and isoniazid was best for preventing drug resistance and relapse cases of TB.

However, adherence to drug regimens was a big problem; streptomycin required injections to be given every three days, for example. Beginning in the 1960s, more attention was given to medications that could be administered orally instead. The newly discovered antibiotic rifampin soon replaced streptomycin and para-aminosalicylic acid. Today, isoniazid and rifampin are used in combination to treat people with TB. Typically, this treatment can take 6-12 months, causing major problems in areas of the world that lack the resource availability to support these long treatment regimens. Anything from not being able to access the actual medications to lack of clean water to take them can cause disruptions and failure to complete the treatment. Not only does incomplete TB treatment prolong the suffering of patients, but it can also lead to the development of microbial resistance within their infection.


A drug resistance nightmare:

The last several decades have seen a worrying rise in rates of multidrug-resistant (MDR) TB infections. A TB infection that is resistant to both isoniazid and rifampin, the two most potent TB treatments, is considered MDR.

MTBC lineages:

There are seven main MTBC lineages infecting humans, each having many sub-strains. These lineages generally correlate with a specific geographic distribution. Today, Lineage 4 (L4) of Mycobacterium tuberculosis is most prevalent in Europe and the Americas. L1 and L2 of Mycobacterium tuberculosis are predominantly found in East Asia and the Pacific, L3 in India and East Africa, and L7 in Ethiopia. L5 and L6, the two lineages of the closely related bacterium Mycobacterium africanum, are found in western Africa.

A lineage of tuberculosis spreads to the Americas during European colonisation:

Modelling studies using the genomes of contemporary TB strains show that the L4 lineage left Europe during colonisation and remains the most common type of TB in both Europe and the Americas today.


The tuberculosis bacterium and its spread across the world


Mycobacterium tuberculosis is one member of a group of bacteria called the Mycobacterium tuberculosis complex (MTBC). This group contains lineages of bacteria that are grouped together based on their genetic relatedness. Since genome sequencing techniques have greatly improved over the past several decades, scientists have now sequenced tens of thousands of bacterial genomes and have developed a classification system based on how similar each strain of bacteria is to each other. The MTBC classification system includes all the lineages of Mycobacterium tuberculosis, two types of a closely related human pathogen Mycobacterium africanum, and a clade of animal-infecting mycobacteria like Mycobacterium bovis and Chimpanzee Bacillus.


Tuberculosis co-evolved with humans


Ever since the discovery of TB by Koch in 1882 and subsequent discoveries of other bacteria in the MTBC family, it was thought that human TB first came about as a ‘spill over’ from Mycobacterium bovis from domesticated cattle around 10,000 years ago. However, recent genomic studies of the MTBC lineages suggest that TB infecting other mammals, such as Mycobacterium bovis, instead may have jumped into other animals from humans tens of thousands of years before animal domestication. Modelling using genome sequences from over 250 different MTBC strains from all seven lineages suggests that the MTBC arose at least 70,000 years ago in Africa. One of the first dispersals of L1 happened at the same time as an initial migration of humans out of Africa approximately 67,000 years ago.


Image: Mycobacterium tuberculosis © NIAID. Public domain.

Was Tuberculosis in the Americas before Europeans arrived?


At present, the origin of TB in the Americas is a matter of considerable debate. Until the end of the 20th Century, the almost prevailing assumption was that any bacteria from the MTBC family were not present in the pre-European contact Americas which began approximately 500 years ago. This was based on the devastation of Indigenous populations at the time of colonisation, as recorded in missionary reports. Historians and archaeologists assumed that this pointed to a lack of prior exposure, and therefore lack of immunity, to TB infection. Even before genomic research was available, analyses of human skeletal remains from archaeological sites dated to well before Spanish colonisers arrived showed evidence of bone lesions possibly caused by TB. However, because there is sometimes overlap between lesions caused by TB and other diseases that cause bone degeneration, this alone was not enough to call into question the European-borne TB origin story for the Americas.

A growing body of evidence says ‘yes’: Ancient pathogen genomics


The prevalence and geographic spread of TB in the ancient past is not fully understood, though both genetic and archaeological evidence has suggested its presence within humans in the ancient Americas thousands of years ago. The study of ancient microbes and their evolutionary histories is known as palaeomicrobiology. This field has offered several recent advancements in the understanding of TB in the ancient past of the Americas, particularly in the Andes region of South America. A previous 2014 study by Kirsten Bos and colleagues at the Max Planck Institute for the Science of Human History published three mycobacterial genomes obtained from human skeletal remains in southern Peru, dated to 1,400 years ago. These TB strains were most genetically similar to Mycobacterium pinnipedii, a member of the MTBC found in migratory seals of the southern hemisphere, and closely related to Mycobacterium bovis (found in cows and other bovids), chimpanzee bacillus, and the human L6 Mycobacterium africanum.


Image: I Taita Imbabura; a symbol of ancestry for a number of Indigenous Kichwa tribes in Ecuador. Credit: © Diego Tirira (CC BY-SA 2.0)

Human immunity evolved in the past to fight the bacterium


Alongside colleagues, we recently found some of the first evidence from the human genome that ancient individuals may have adapted to fight TB thousands of years before Europeans arrived in South America. Most of the genetic research in this area of the world has been conducted in collaboration with Indigenous populations from Peru and Bolivia. This new study was one of the first genomic studies partnering with Indigenous peoples from Ecuador and focusing on those living in highland areas ranging from the north and south of the country.

Interestingly, they were not expecting to find anything relating to TB – their initial focus was on identifying how humans adapted to low-oxygen environments in the Andean highlands. When performing statistical scans to look for signals of natural selection in the genomes of these Ecuadorians, they found that the strongest signals actually came from genetic variants related to the anti-TB immune response. Moreover, these genetic variants varied widely in function across the genome, from controlling the immediate immune response of macrophage cells, which engulf and destroy pathogens, to the longer-term and more specific adaptive immune response of T-cells.

While it is interesting to know that Ecuadorian populations might have adapted to fight TB infections, the most important piece of the puzzle came from modelling exactly when these genetic variants first became widespread in the populations ancestral to the living individuals which contributed to the study. The timing of the selection event which caused the TB-related genetic variants to become widespread in the population occurred over 3,000 years ago, well before the arrival of Europeans. This suggests that the MTBC was not only present in the Andes region at this time, but the Indigenous people of Ecuador also adapted to this bacterium in the ancient past. This time period corresponds with the transition from small hunter-gatherer groups to larger agricultural societies. These societies were much more compact and populous, which would have facilitated the spread of respiratory diseases like TB.


Image: The Andes near Quito, Ecuador’s capital city. © David Adam Kess (CC BY-SA 3.0)

If tuberculosis really existed in the Americas before Europeans, how is it possible that the European L4 lineage is so common today?


You may recall that the Mycobacterium tuberculosis L4 lineage left Europe during colonisation and still remains the most common type of TB in the Americas today. So, if there really was some type of TB in the Americas before European colonisers came, perhaps that which Kirsten Bos and colleagues identified in their 2014 study, where did that one go? While we don’t know for certain, one possibility is that it was just outcompeted by the L4 lineage, since the Europeans could have spread the L4 lineage very rapidly as they moved across South America with large armies, often on horseback. Furthermore, recent work suggests that human immunity can be inconsistent among different strains of TB, meaning that even if ancient individuals living in the Andes began adapting to an ancient type of TB thousands of years ago, they may not necessarily have been any better equipped against the European-borne L4 lineage.


Future pieces of the puzzle: why population genetics may hold the key to fighting a public health battle


The origin of TB in the Americas is a matter of considerable debate and uncovering the details of how and when the pathogen first arrived in the Americas is certainly important. But even beyond pathogen evolution in ancient populations, this work has tremendous implications for modern public health, too. As previously discussed, human immune response varies with different TB strains. But people can also have vastly different health outcomes even with infection from the same strain. It is very likely that the gene variants present in a human host play a major role in producing these clinically different responses. We are only just beginning to understand what some of these underlying reasons might be. Inquiry into the genetics of ancient populations and modern populations alike is a crucial avenue of research, as it could eventually reveal potential avenues for personalised treatment beyond typical antibiotics. This will become increasingly crucial in the coming decades, as multi-drug resistant TB infections and resulting deaths are expected to continue their dramatic uptick across the world.


Sophie K Joseph and John Lindo

Department of Anthropology

Emory University

Atlanta, GA,