Target-enriched metagenomic sequencing improves detection and provides consistent resistome characterization across library preparation protocols and DNA inputs
This study evaluated targeted sequencing strategies using fecal microbial communities from multiple host species to determine whether they improve characterization of resistance genes and produce consistent results across different laboratory methods. Target-enriched sequencing detected substantially more resistance genes than conventional shotgun sequencing and produced highly comparable results across library preparation kits and DNA input amounts, even when limited DNA was available.