Whole genome sequencing better at tracing TB outbreaks than standard test

Biology News Net ^ | February 13, 2013 | NA

[neverdem]

A new form of genetic testing of the bacteria that causes tuberculosis can provide better information on TB transmission and also trace TB outbreaks more accurately than the current standard test, according to a study from Germany published in this week's PLOS Medicine.

A team of researchers led by Stefan Niemann from Forschungszentrum Borstel, Molecular Mycobacteriology, compared the results of the two types of tests on 86 M. tuberculosis isolates from a TB outbreak in the German states of Hamburg and Schleswig-Holstein between 1997 and 2010, in which 2301 people were diseased in the study period.

They found that the new test (whole genome sequencing) provided more accurate information on clustering and longitudinal spread of the pathogen than the standard test (classical genotyping). Importantly, whole genome sequencing revealed that first outbreak isolates were falsely clustered by classical genotyping and do not belong to one recent transmission chain.

By using whole genome sequencing, the authors estimated that the genetic material of M. tuberculosis evolved at a rate at 0.4 mutations per genome per year, suggesting that the bacterium grows in its natural host (infected people) with a doubling time of 22 hours, or 400 generations per year. This finding about the evolution of M. tuberculosis indicates how information from whole genome sequencing can be used to help trace future outbreaks.

Importantly, as the costs of whole genome sequencing are declining, this test could soon become the standard method for identifying transmission patterns and rates of infectious disease outbreaks.

The authors say: "Our study demonstrates that whole genome sequencing-based typing provides epidemiologically relevant resolution of large, longitudinal [Mycobacterium tuberculosis] outbreaks much more efficiently than classical genotyping."

They continue: "We envision that [whole genome sequencing] progressive effective implementation will be accelerated by the continuously decreasing sequencing costs, broader distribution of so-called bench top genome sequencers, and upcoming bioinformatics developments to facilitate quick and relevant interpretation of the resulting data in public health and medical contexts."

Source : Public Library of Science

[neverdem]

Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

[raybbr]

Just follow the paths of illegal aliens. Do the same for whooping cough. It should be pretty easy to find out where they came from.

[muawiyah]

Not to bust your bubble but around here most TB has two sources ~ junkies and people who've simply been visiting a foreign location where TB is present.

Your community may be different with no junkies and nobody making visits to such places. Others might be in between.

The vector is simple ~ a human being with an active case of TB with whom you come in contact for several hours.

[oh8eleven]

... and people who've simply been visiting a foreign location where TB is present
Sooooo, it's the fault of Americans who go on vacation, NOT the millions of illegals from third world cesspools.

[muawiyah]

Did I say they were Americans?

I live in the Washington DC area. We have a foreign population here composed of the rich and well-born from every country on the planet.

They go home to visit their mommies every now and then.

That's where they pick it up.

The only vector for human beings when it comes to TB is another human being with TB, and you have to stay in close proximity to them for several hours.

Odds are an international air flight is a more likely source than any illegal ~ unless you hang around one of them with TB for several hours.

Let's just say it's a lifestyle choice ~ BTW, we had voluntary TB tests where I worked ~ mostly because we had people who did a lot of international travel working in our headquarters building ~ you could get a test any time you wanted. Over the years several of my friends tested positive for the antibody, but negative to TB. They likely contracted it at work. They'd tell everyone so you'd know to go get a test.

Just like grade school.

[oh8eleven]

We have a foreign population here composed of the rich and well-born from every country on the planet. They go home to visit their mommies every now and then.
You're talking about a sample of one (city) and I seriously doubt if the "rich and well-born" come into contact with TB carriers in their native countries.
And if your explanation was anywhere near cogent, it still wouldn't explain all the dark blue states below.
Gee, I wonder what have in common?

[muawiyah]

The 'city' is DC, but we have about 4.5 million people in the greater SMSA. The foreigners here involved in international relations, trade, banking and a variety of other activities are NUMEROUS.

That's where the TB comes from here if it's not coming from junkies.

I was accused of blaming American tourists for the TB ~ which I didn't. Just relaying to you that the biggest sources are known for this area, and BTW, for most foreigners, when they visit home ~ usually the third world, they all have servants.

Your argument seems to be that uneducated poor people with bad toilet habits are necessarily a prime vector for TB ~ but we already know that transmission depends only on being in close proximity to a person with TB for a number of hours. It's not an instant contact thing, or just encountering the products and byproducts of a sneeze ~ it's breathing the same air over and over.

http://www.lung.org/lung-disease/tuberculosis/tuberculosis-fact-sheet.html