Workpackage 3

From comparable data to actionable information: Analytical workflows for frontline diagnostics

WP leader: Surbhi Malhotra, UA (14)
co-leaders: Constance Schultsz, AMC, (13) & Anne Pohlmann, FLI (4)

Overall task: To develop an analytical workflow for the use of single isolate and metagenomic NGS in human and veterinary clinical microbiology.

1. To develop general workflows for integration of NGS in clinical laboratory diagnostics.

2. To develop a framework for prediction of phenotypic antimicrobial susceptibility based on the presence or absence of genes and mutations in sequence data.

3. To develop tools for identification of hospital clusters and nosocomial transmission.


Surbhi Malhotra
Universiteit Antwerpen


Anne Pohlmann
Senior Researcher
Friedrich Loeffler Institut - Bundesforschungsinstitut Fuer


Constance Schultsz
Medical Microbiologist
Academic Medical Center of the University of Amsterdam
16 JULY 2024