24/05/2017 - 12:00 - Auditori PRBB

Real-time surveillance of antimicrobial resistance using Nanopore sequencing

Scientific sessions, CRG Group Leader Seminars

Stephan Ossowski

Genomic and Epigenomic Variation in Disease Group, Bioinformatics and Genomics Programme, CRG

Talk Abstract:

In this talk Stephan Ossowski will discuss the genetic and epidemiologic analysis of two concurrent long-term outbreaks of extreme drug resistant Pseudomonas aeruginosa and Citrobacter freundii at a university hospital. Whole genome sequencing of hundreds of isolates collected during the outbreak allowed for tracking of bacteria transmission between patients and/or the environment. Using Nanopore sequencing enabled the generation of high quality assemblies and allowed us to identify plasmids carrying multiple resistance genes. Their results suggest that the initial outbreak was driven by a few super-spreaders, but environmental contamination sustained the outbreak for a long period. Furthermore they found that a single plasmid carries all relevant resistance genes and horizontal gene transfer between P. aeruginosa and C. freundii led to the concurrent outbreak.

Short biography:

The Ossowski lab is developing wet-lab and computational methods for medical genomics with a strong focus on NGS applications in clinical diagnostics and precision medicine. The group has implemented protocols and algorithms for variant identification and prioritization in rare and familial diseases as well as in large-scale cancer studies. As part of the International Cancer Genome Consortium (ICGC) the group has developed methods for identification of cancer driver and risk genes, somatic copy number alterations as well as somatic indels. The identification of disease or cancer specific alterations at molecular level is a prerequisite for optimized individual treatment of patients. As complementary field of activity the group is developing techniques for genomic and metagenomic analysis of pathogenic and non-pathogenic bacteria that will provide a better understanding of pathogenicity, host defence, antibiotic resistance and the impact of drugs on the human microbiome.