Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

BACKGROUND
Understanding Mycobacterium tuberculosis (Mtb) is very important to guide the transmission control strategy efficiently. typing traditional sports do not have enough discriminatory power to overcome the great plague. Here, we examine the potential of using the next-generation genome sequencing to identify the transmission chains associated outbreaks.

RESULTS
Over the long term (1997-2010) prospective, population-based molecular epidemiological surveillance consisting of a total of 2,301 patients, we identified a large outbreak caused by a strain of Mtb lineage Haarlem. The main measure performance results of whole genome sequencing (WGS) is the analysis of the degree of correlation with the analysis WGS contact tracing data and spatio-temporal distribution of plague cases. WGS analysis of 86 isolates revealed 85 single nucleotide polymorphisms (SNPs), grouping plague genome into seven groups (two to 24 isolates each), plus 36 unique SNP profile. WGS Results show that the first outbreak isolates were detected in 1997 were counterfeit clustered by classical genotype.

In 1998, one of the clones (called “Hamburg clone”) began to grow, apparently independently of differences in social environments initial case. genome-based grouping patterns that fit well with contact tracing data and geographic distribution of cases of grouping patterns based on the classic genotype. A maximum of three SNPs identified in the eight confirmed the chain of transmission from human to human, which involved 31 patients. We estimate the Mtb genome evolution rate of 0.4 mutations per genome per year. This level indicates that Mtb grown in natural hosts with a doubling time of about 22 h (400 generations per year). Based on genome variation is found, the emergence of clones Hamburg is dated back to the period between 1993 and 1997, then shortly before the discovery of the outbreak through epidemiological surveillance.

CONCLUSION
Our findings indicate that WGS is superior to conventional genotyping for tracking and investigating Mtb pathogenic micro-epidemics. WGS provides Mtb genome size evolution over time in the context of the natural host.

Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.
Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

Highly multiplexed molecular inversion probe genotyping: SNP targeted more than 10,000 genotypes in a single test tube.

Large-scale genetic studies are very dependent on the multiplex SNP tests efficient and scalable. In this study, we report the development of Molecular Inversion Probe technology with four-color, single-array detection, applied to large scale genotyping of up to 12,000 SNPs per reaction. While generating 38 429 SNPs tests using this technology in a population of 30 trios of the family panel Humain Center d’Etude polymorphisms as part of the International HapMap project, we set up a conversion rate of approximately 90% of SNP with a concordance rate of> 99.6% and the level of completeness of> 98% to test the level of multiplexing up to 12,000plex.

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Furthermore, these individual metrics can be “traded off” and, at the expense of a small portion of the conversion rates, the accuracy can be improved to a very high level. No loss of performance seen when the scale of 6,000plex to 12,000plex the test, it validates the technological capability to suppress cross-reactivity at high multiplex level. These results indicate the suitability of this technology for a comprehensive association study using targeted SNPs in linkage disequilibrium studies indirectly or directly screen for the mutation causes.