Mobile Genetic Elements

The research of my group has advanced the detection and analysis of mobile genetic elements (MGEs) such as plasmids, insertion sequences, and phages in complex metagenomic datasets. We identified that metagenomic assembly is the main bottleneck in linking antimicrobial resistance genes to their MGEs, which are critical for understanding the spread of resistance. To address this, we developed MetaMobilePicker, an open-source pipeline that automates the identification and annotation of MGEs and associated resistance genes, making it easier to track the mobilome in diverse environments. This work provides essential tools for studying how MGEs drive the dissemination of antimicrobial resistance, with applications in both environmental and clinical microbiology.

Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements JJ Kerkvliet, A Bossers, JG Kers, R Meneses, R Willems, AC Schürch PeerJ 12, e16695 (2024

Coccidiosis prevention strategies shape the microbiome, resistome and mobilome composition in the broiler gut M Buffoni, JJ Kerkvliet, H Enting, JG Kers, M Rogers, J Visser, et al. Animal microbiome 8 (1), 3 (2026)

Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples. Xu, W., Top, J., Viveen, M.C. et al. BMC Med Genomics 19, 8 (2026).

Software: MetaMobilePicker