Pipeline for construction of CRIPSRi libraries and analysis of CRISPRi-seq data: https://www.veeninglab.com/crispri-seq
A Python3 program that counts sequence occurrences in raw FASTQ files. https://veeninglab.com/2fast2q
Microfluidic screening platform
A droplet microfluidic screening platform that can also be run in transmission mode will be published in Nature Protocols (https://www.nature.com/articles/s41596-022-00796-2)
Antimicrobial resistance is a growing problem worldwide. Infections caused by for example staphylococci (S. aureus), pneumococci (S. pneumoniae), E. coli and Pseudomonas are nowadays often difficult to treat due to increasing antimicrobial resistance. Infections caused by these pathogens are particularly problematic if they are associated with biofilms, since the biofilm provides extra protection against antimicrobial compounds.
The aim of the project DISRUPT is to identify new strategies to treat biofilm-associated infections caused by staphylococci, pneumococci, E. coli and Pseudomonas. Targeting and inhibiting bacterial biofilm formation will reduce the chances of infections, and possibly resensitize the bacteria to existing antibiotics. By using state-of-the-art genetic technologies combined with high-throughput screens, the aim is to deliver new anti-biofilm strategies and mechanisms to tackle biofilm-associated infections. Furthermore, the project will generate genetic tools, which will be available for researchers worldwide, working to fight these AMR pathogens.