Saturday, 26 November 2016

In Agra’s slums, community volunteers are visiting the houses one-by-one and asking the occupants a simple question: “Have you been coughing for more than two weeks?”

Of the ten million new cases of TB every year, one-third remain invisible to the public health authorities. India currently holds the dubious title of World’s TB Capital and accounts for one million of those missing patients. Many of those whose TB goes either undiagnosed or unreported are lost somewhere among the muddy streets and flapping fabrics of the poorest urban communities.

Much of India’s TB problem is socioeconomic—poor housing, poor sanitation, overcrowding, and unhealthy populations both at higher risk of developing active TB and with limited access to adequate healthcare. Active case finding among these marginalised and vulnerable populations is part of the solution to ensuring that people receive treatment and do not continue to transmit their infection to others.

A short paper published last week describes the lessons learnt from a pilot project looking for active TB cases among the half-a-million inhabitants of ‘Agra city’. Community volunteers were offered incentives to visit house-to-house and educate the inhabitants on TB, collect demographic details, and ask if anyone had been coughing.

Where the answer was ‘Yes’, potential TB patients were referred to a local health facility for further testing. What surprised me about the results of the study was that only 40% of those referred actually went of their own fruition. The other 60% had to be accompanied by the community volunteers, who returned to the homes of those not self-presenting within one week.

The study also revealed that levels of TB knowledge among the 3,940 households surveyed were actually very high. Ninety-percent of respondents had heard of TB; most of these people knew that coughing was a symptom. Yet the volunteers still managed to find 382 potential TB patients who hadn't sought out a diagnosis.

When questioned, most of the families said they relied on private healthcare providers for medical care. India’s private sector is highly variable, encompassing world-renown TB doctors all the way down to unqualified charlatans. The combination of patients not seeking out medical care and, when they do, turning to someone who won’t necessarily provide them with a correct diagnosis begins to explain why so many cases of TB go undetected.

It was beyond the paper’s scope to discuss why patients don’t seek out a TB diagnosis but, for me, this is one of the most important questions. What are the barriers that stop people living in Agra city—or in any other part of the world, for that matter—from approaching the health services with symptoms of TB?

Because new drugs, vaccines and diagnostics aren’t going to eradicate TB alone; not when millions still don’t receive the existing treatments and people continue to die from what is a curable disease.

Prasad et al. (2016) Lessons learnt from active tuberculosis case finding in an urban slum setting of Agra city, India. Indian J Tuberc. 63(3):119-202

Sunday, 20 November 2016

You know when you drive an unfamiliar car and you have to find your way round all these knobs and buttons to make the car go in the direction you want it to go in? M. tuberculosis has the same problem when it comes to the human immune system. This can make things tricky as it’s a pathogen that practices immune subversion rather than immune evasion—driving the immune response in its own favour rather than hiding.

A lot of the time, specific lineages of TB stick to the human genetic backgrounds that they’ve grown-up infecting. Even as global travel increases and the world gets smaller, these associations between TB lineage and their preferred flavour of human host persist. Over millennia, specific lineages of M. tuberculosis have evolved alongside specific human populations, learning all our secrets and finding ways to navigate our immune systems. Faced with an unfamiliar host, however, the pathogen can struggle.

But some lineages and sub-lineages are better at adapting to new host backgrounds than others. They’re the ‘generalists’ of the TB family. In comparison, the less-adaptable strains are known as ‘specialists’ and more or less stick to geographically restricted populations. They’re the ones who, if they ever go on holiday, demand a hire car exactly like the one they have at home. ‘I can’t be dealing with these fancy Japanese cars’, they say. ‘Give me a nice, British-made Rover.’

This idea of co-evolution and adaption is one I talk about in more detail in my book Catching Breath - The Making and Unmaking of Tuberculosis. The book is basically a scientific biography of TB exploring how M. tuberculosis came to be the world’s biggest infectious disease killer and how science is going to kill it right back. It comes out next summer as part of the Bloomsbury Sigma imprint of popular science books.

Here, though, I wanted to mention a new paper that came out last week from Sebastian Gagneux’s lab in Switzerland. In it, he looks at the success of M. tuberculosis lineage 4. It’s the most adaptable lineage, making its home on every inhabited continent—a generalist lineage that’s found its success thanks to both biological and social phenomena, according to Sebastian’s study. 

The team used SNP-typing and targeted whole genome sequencing to look at the genetic differences between 3,366 lineage 4 strains isolated from 100 different countries. They used the differences to break down lineage 4 into several sub-lineages. Some were generalists found in multiple locations; others, in comparison, were more isolated and rarely strayed outside of small regions of Africa, for example.

Like I said, M. tuberculosis doesn’t hide from the immune system. It wants to be recognised so the bits of the pathogen on the immune system’s watch list don’t tend to vary much at all. But Sebastian’s study showed that the generalists are more immunologically versatile than their specialist counterparts. This is likely because they have evolved to deal with a wider range of host genetic backgrounds and have had to come up with ways to ensure they get their own way no matter who they infect.

The paper was also interested in the sub-lineage known as L4.1/LAM. L4.1/LAM, like Starbucks, is on a mission to take over the entire world. It’s found everywhere from Africa to Australia. The scientists used the genetic differences between members of L4.1/LAM to predict its geographical origin. According to the results, it first emerged in Europe then, as us troublesome Europeans spread around the world, we took our TB with us.

It’s a common story when it comes to TB. The disease is among the world’s oldest and its history is twisted up with that of us humans. The spread of TB around the world tracks with human migrations; explosions in M. tuberculosis populations overlay with human upheavals. Understanding the co-evolution of M. tuberculosis and the human immune system has consequences for, in particular, vaccine design. How do we vaccinate against a pathogen that uses the immune response for its own benefit and how do we make sure any vaccine works in every population where not only the predominant lineage differs but so does the host’s genetic makeup?

Stucki D et al. 2016. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sub-lineages. Nature Genetics.

Yu Y et al. 2015. RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography. Molecular Phylogenetics and Evolution. 87: 46-49