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

Author

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  • Edgar I. Campos-Madueno

    (University of Bern
    University of Bern)

  • Claudia Aldeia

    (University of Bern)

  • Andrea Endimiani

    (University of Bern)

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 blaCTX-M and blaDHA 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-enriched Nanopore-SMS recognizes 9/18 plasmids and 5/9 E. coli chromosomes. Pre-enriched Nanopore-SMS identifies more ARGs than native Nanopore-SMS (p

Suggested Citation

  • Edgar I. Campos-Madueno & Claudia Aldeia & Andrea Endimiani, 2024. "Nanopore R10.4 metagenomic detection of blaCTX-M/blaDHA antimicrobial resistance genes and their genetic environments in stool," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51929-y
    DOI: 10.1038/s41467-024-51929-y
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