A Cautionary Case for Host Assignment Based on Broad Environmental bla_OXA Carriers.

Area of Science:

• Environmental microbiology
• Genomics
• Antimicrobial resistance

Background:

• Metagenomic analysis is crucial for studying microbial communities and antibiotic resistance genes (ARGs).
• Reference databases used in metagenomics are often biased towards clinically relevant bacteria, potentially skewing ARG host prediction.
• Accurate identification of ARG hosts in environmental settings is vital for understanding resistance dissemination.

Purpose of the Study:

• To evaluate the accuracy of metagenomic host prediction for ARGs in a wastewater treatment plant.
• To compare metagenomic ARG host assignments with culture-based methods.
• To investigate the role of environmental bacteria in hosting blaOXA genes.

Main Methods:

• Conducted metagenomic screening to identify ARG hosts.
• Employed culture-based methods for validation and broader host identification.
• Performed phenotypic testing to confirm resistance profiles.

Main Results:

• Metagenomic analysis primarily associated blaOXA genes with clinical taxa.
• Culture-based screening revealed a more diverse host range for blaOXA genes, including environmental bacteria.
• Phenotypic tests confirmed resistance patterns consistent with carbapenem-hydrolysing class D β-lactamases.

Conclusions:

• Reference-based metagenomic host prediction can underestimate the diversity of ARG reservoirs in environmental bacteria.
• Environmental bacteria are significant hosts of blaOXA genes.
• Integrating culture-dependent validation with metagenomic approaches is essential for accurate ARG ecology assessment.