Nanopore R10.4 metagenomic detection of bla_CTX-M/bla_DHA antimicrobial resistance genes and their genetic environments in stool.

ABSTRACT: The increasing prevalence of gut colonization with CTX-M extended-spectrum β-lactamase- and/or DHA plasmid-mediated AmpC-producing Escherichia coli is a concern. Here, we evaluate Nanopore-shotgun metagenomic sequencing (Nanopore-SMS) latest V14 chemistry to detect bla_CTX-M and bla_DHA genes from healthy stools. We test 25 paired samples characterized with culture-based methods (native and pre-enriched). Antimicrobial resistant genes (ARGs) are detected from reads and meta-assembled genomes (MAGs) to determine their associated genetic environments (AGEs). Sensitivity and specificity of native Nanopore-SMS are 61.1% and 100%, compared to 81.5% and 75% for pre-enriched Nanopore-SMS, respectively. Native Nanopore-SMS identifies only one sample with an AGE, whereas pre-enr

SUBMITTER: Campos-Madueno EI 

PROVIDER: S-EPMC11358271 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature