Chemoproteomic profiling of adaptive ATP-binding protein activity in Enterococcus faecium in response to host-derived cues

Enterococcus faecium has become a significant nosocomial and opportunistic pathogen, increasingly implicated in severe infections such as urinary tract infections, bacteraemia, and endocarditis. Due to acquired resistance to vancomycin and ampicillin and high intrinsic resistance to other antibiotics, E. faecium infections are often challenging to treat. However, relatively little is known about the molecular factors used by E. faecium during infection. Here, we employed desthiobiotin-ATP as an activity-based probe to investigate the activity profile of ATP-binding proteins in E. faecium upon growth in standard rich laboratory media and in response to host-derived cues. We present a chemoproteomic dataset containing 230 selectively enriched putative ATP-binding proteins. 31 proteins were specifically activated in response to human colonic organoid extract, 19 in response to human serum including the ABC transporter, TcyA, and a sensor histidine kinase, ArlS. Our findings suggest that E. faecium adapts its metabolic and regulatory pathways in response to host-derived signals from human serum and organoid extract, which could be crucial for its survival and pathogenicity in various host tissues. Our study highlights the potential relevance of TcyA and ArlS, that have been implicated in virulence in other pathogens, for further functional characterization in E. faecium.