Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms.
Antimicrobial resistance
Metagenomics
Microbiome
Next-generation sequencing
Resistome
Surveillance
Journal
European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology
ISSN: 1435-4373
Titre abrégé: Eur J Clin Microbiol Infect Dis
Pays: Germany
ID NLM: 8804297
Informations de publication
Date de publication:
Jan 2021
Jan 2021
Historique:
received:
16
04
2020
accepted:
23
07
2020
pubmed:
13
8
2020
medline:
2
6
2021
entrez:
13
8
2020
Statut:
ppublish
Résumé
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 bla
Identifiants
pubmed: 32783106
doi: 10.1007/s10096-020-03996-4
pii: 10.1007/s10096-020-03996-4
doi:
Substances chimiques
Carbapenems
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
95-102Références
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