Whole genome sequencing of bacterial isolates via next-generation sequencing is becoming a standard approach for clinical microbiology and bio-surveillance labs seeking to conduct outbreak investigations and genomic characterization of isolates. Knowing the identity of a pathogen, subtype, and potential antimicrobial resistance markers it may carry is essential for monitoring pathogens. 

CLC Genomics Workbench, along with the CLC Microbial Genomics Module, provides functionalities for molecular subtyping and epidemiological analyses of bacterial isolates in an easy to use, graphical user interface. In this webinar, we will demonstrate how to carry out taxonomic identification, multi locus sequence typing (MLST), identification of antimicrobial resistance (AMR) markers, and investigation suspect pathogens via SNP based phylogenetic analyses with associated sample metadata. We will also show how such analyses can be streamlined into a preconfigured workflow that ensures ease-of-use, reproducibility, and scalability to any sample throughput.

Learning Objectives: 

1. Assign sequence type and taxonomy
2. Detect antimicrobial resistance genes
3. Perform outbreak analyses