Background: In March 2014, a molecular cluster of five multidrug resistant Mycobacterium tuberculosis was detected by the Austrian National Reference Laboratory. An investigation was initiated to determine if transmission had occurred within Austria. Epidemiological links to Germany and Romania prompted a multi-national joint investigation, tracing the outbreak. The results were published by Fiebig and co-workers in 2017.

Methods: CLC Microbial Genomics Module, an extension of CLC Genomics Workbench, contain tools required for typing pathogenic bacteria, tracing outbreaks, and detecting antimicrobial resistance. Preconfigured, but customisable, workflows ensure ease-of-use, allowing users to focus on interpreting analysis results.

Results: Whole genome SNP analysis showed high resolution clustering of isolates. Information on the whole genome further permitted simultaneous detection of resistance causing variants. Using an improved variant detection pipeline, we identified additional variants associated to antimicrobial resistance compared to the original study. Novel variants were explored in the context of 3D protein models to predict and qualify the effect of the variants on antimicrobial susceptibility. 

Conclusion: Using data published by Fiebig at al., 2017, we demonstrate how CLC Microbial Genomics Module can be used to trace pathogen outbreaks and detect resistance causing variants. User-friendly tools and preconfigured workflows ensure ease of use and reproducibility.