Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of the Clinically Important Fraction of the β‑Lactam Resistome

High bacterial community diversity and complexity greatly
challenge
the cost-efficient monitoring of clinically prevalent antibiotic-resistant
bacteria, which are usually present as rare and important populations
involved in the environmental dissemination of clinical resistance.
Here, we introduce culture-enriched phenotypic metagenomics that integrates
culture enrichment, phenotypic screening, and metagenomic analyses
as an emerging standardized methodology for targeted resistome monitoring
and apply it to decipher the extended-spectrum β-lactam resistome
in a municipal wastewater treatment plant (WWTP) and its receiving
river. The results showed that clinically prevalent carbapenemase
genes (e.g., the NDM and KPC families) and extended-spectrum β-lactamase
genes (e.g., the CTX-M, TEM, and OXA families) were prevalent in the
WWTP and showed prominent potential in horizontal dissemination. Strikingly,
carbapenem and polymyxin resistance genes co-occurred in the highly
virulent nosocomial pathogens Enterobacter kobei and Citrobacter freundii. Overall,
this study exemplifies phenotypic metagenomics for high-throughput
surveillance of a targeted clinically important fraction of antibiotic
resistomes and substantially expands current knowledge on extended-spectrum
β-lactam resistance in WWTPs.