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Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms

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Abstract

Antimicrobial resistance (AMR) is a public health threat where efficient surveillance is needed to prevent outbreaks. Existing methods for detection of gastrointestinal colonization of multidrug-resistant organisms (MDRO) are limited to specific organisms or resistance mechanisms. Metagenomic next-generation sequencing (mNGS) is a more rapid and agnostic diagnostic approach for microbiome and resistome investigations. We determined if mNGS can detect MDRO from rectal swabs in concordance with standard microbiology results. We performed and compared mNGS performance on short-read Illumina MiSeq (N = 10) and long-read Nanopore MinION (N = 5) platforms directly from rectal swabs to detect vancomycin-resistant enterococci (VRE) and carbapenem-resistant Gram-negative organisms (CRO). We detected Enterococcus faecium (N = 8) and Enterococcus faecalis (N = 2) with associated van genes (9/10) in concordance with VRE culture-based results. We studied the microbiome and identified CRO, Pseudomonas aeruginosa (N = 1), Enterobacter cloacae (N = 1), and KPC-producing Klebsiella pneumoniae (N = 1). Nanopore real-time analysis detected the blaKPC gene in 2.3 min and provided genetic context (blaKPC harbored on pKPC_Kp46 IncF plasmid). Illumina sequencing provided accurate allelic variant determination (i.e., blaKPC-2) and strain typing of the K. pneumoniae (ST-15). We demonstrated an agnostic approach for surveillance of MDRO, examining advantages of both short- and long-read mNGS methods for AMR detection.

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Authors and Affiliations

  1. Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Rebecca Yee, Belita N.A. Opene & Patricia J. Simner

  2. Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA

    Florian P. Breitwieser

  3. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA

    Stephanie Hao, Rachael E. Workman & Winston Timp

  4. Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Pranita D. Tamma

  5. Department of Pathology and Laboratory Medicine, Children’s Hospital of Los Angeles and Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA

    Jennifer Dien-Bard

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  1. Rebecca Yee
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  2. Florian P. Breitwieser
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  3. Stephanie Hao
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  4. Belita N.A. Opene
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  6. Pranita D. Tamma
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  7. Jennifer Dien-Bard
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  8. Winston Timp
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  9. Patricia J. Simner
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Correspondence to Patricia J. Simner.

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Yee, R., Breitwieser, F.P., Hao, S. et al. Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms. Eur J Clin Microbiol Infect Dis 40, 95–102 (2021). https://doi.org/10.1007/s10096-020-03996-4

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  • DOI: https://doi.org/10.1007/s10096-020-03996-4

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