Tracing TB outbreaks and transmission success: Whole genome sequencing better than standard test

February 14, 2013

A new study published in PLOS Medicine revealed that a new form of genetic testing of the bacteria that causes tuberculosis provides better information on TB transmission and also traces TB outbreaks more accurately than the current standard test.

A team of experts from public-health institutions, research institutes and universities in Germany and France led by Stefan Niemann from the Forschungszentrum Borstel compared the results of the two types of tests on 86 M. tuberculosis isolates from a TB outbreak in the German states Hamburg and Schleswig-Holstein (overall 2301 TB cases have been investigated in the study period from 1997 to 2010).

They found that the new test (whole genome sequencing, WGS) provided more accurate information on clustering and longitudinal spread of the pathogen than the standard test (classical genotyping). Importantly, WGS based analyses revealed that first outbreak isolates were falsely clustered by classical genotyping and do not belong to a recent transmission chain.  Indeed, only one clone starts spreading in 1998 indicating that subtle differences in the genome might influence M. tuberculosis transmission success.

"Only genome based investigations allowed us to trace M. tuberculosis spread with the resolution needed to visualize transmission patterns correctly" said Dr. Andreas Roetzer, first author of the study.

Genotyping of M. tuberculosis strains is usually used to guide TB contact tracing, confirm recent transmission chains and detect TB outbreaks. However, as classical genotyping is only approaching a tiny part of the genome, it may not able to distinguish between closely related transmission chains especially over longer time frames. This was confirmed by this study: WGS based typing not only provided a much higher resolution, the genome based cluster results also correlated better with spatio-temporal spread and with contact tracing information.

By using whole genome analysis, 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 can be used to trace future outbreaks.

As a further advantage, whole genome analysis provides much more information than classical genotyping as it allows tracking antibiotic resistance mutations and variations in virulence genes. This is especially powerful for M. tuberculosis since resistance to all antituberculous drugs are encoded in the genome by mutations in particular genes that can be easily accessed by whole genome sequencing.

Importantly, as the costs of whole genome analysis based on Next Generation 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.”

The major obstacle for the general use of Next Generation Sequencing WGS analysis is the complicated data analysis. This is the topic of the EU FP7 Patho-Ngen-Trace project that is coordinated by Dr. Niemann. "We are working on easy to use software solutions that bridge the gap from data to knowledge and open the door for a wide application of Next Generation Sequencing for scientists and clinical microbiologist" explained Dr. Niemann.


Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rüsch-Gerdes S, Supply P, Kalinowski J, Niemann S (2013) Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study. PLoS Med 10(2): e1001387. doi:10.1371/journal.pmed.1001387.




PD Dr. Stefan Niemann
Molecular Mycobacteriology, Forschungszentrum Borstel
Borstel, Germany