Sequencing traces TB outbreaks
14.02.2013 - EU researchers have prooved next generation sequencing to be more effective in tracing tuberculosis outbreaks than the current gold standard.
A new form of genetic testing of the bacteria that cause tuberculosis (TB) can provide better information on TB transmission and also trace TB outbreaks more accurately than the current gold standard test, according to results from the EU’s €7.8m PathoNGen-Trace project (PLOS Medicine).
A team of researchers led by Stefan Niemann including the SMEs Ridom GmbH (Muenster) and Genoscreen SAS (Lille) compared the results of next-generation sequencing and genotyping on 86 Mycobacterium tuberculosis isolates from a TB outbreak in Germany between 1997 and 2010, in which 2301 people became ill. They found that sequencing provided more accurate information on clustering and longitudinal spread of the pathogen than the standard test (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
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, say the authors. "We envision that progressive effective implementation will be accelerated by the continuously decreasing sequencing costs, broader distribution of so-called bench top next generation sequencers, and upcoming bioinformatics developments to facilitate quick and relevant interpretation of the resulting data in public health and medical contexts." PathoNGen-Trace had been kicked-off in March 2012.