Skip to main content
Top
Published in: European Journal of Clinical Microbiology & Infectious Diseases 1/2021

01-01-2021 | Ertapenem | Original Article

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

Authors: Rebecca Yee, Florian P. Breitwieser, Stephanie Hao, Belita N.A. Opene, Rachael E. Workman, Pranita D. Tamma, Jennifer Dien-Bard, Winston Timp, Patricia J. Simner

Published in: European Journal of Clinical Microbiology & Infectious Diseases | Issue 1/2021

Login to get access

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.
Appendix
Available only for authorised users
Literature
1.
go back to reference Centers for Disease Control and Prevention. (2019) Antibiotic resistance threats in the United States, 2019. CDC Centers for Disease Control and Prevention. (2019) Antibiotic resistance threats in the United States, 2019. CDC
3.
go back to reference Li X, Arias CA, Aitken SL, Galloway Pena J, Panesso D, Chang M, Diaz L, Rios R, Numan Y, Ghaoui S, DebRoy S, Bhatti MM, Simmons DE, Raad I, Hachem R, Folan SA, Sahasarabhojane P, Kalia A, Shelburne SA (2018) Clonal emergence of invasive multidrug-resistant Staphylococcus epidermidis deconvoluted via a combination of whole-genome sequencing and microbiome analyses. Clin Infect Dis. https://doi.org/10.1093/cid/ciy089 Li X, Arias CA, Aitken SL, Galloway Pena J, Panesso D, Chang M, Diaz L, Rios R, Numan Y, Ghaoui S, DebRoy S, Bhatti MM, Simmons DE, Raad I, Hachem R, Folan SA, Sahasarabhojane P, Kalia A, Shelburne SA (2018) Clonal emergence of invasive multidrug-resistant Staphylococcus epidermidis deconvoluted via a combination of whole-genome sequencing and microbiome analyses. Clin Infect Dis. https://​doi.​org/​10.​1093/​cid/​ciy089
4.
go back to reference Clinical and Laboratory Standards Institute. (2019) Performance standards for antimicrobial susceptibility testing; Twenty-Nineth Informational Supplement., vol M100-S29. CLSI, Wayne, PA, USA. Clinical and Laboratory Standards Institute. (2019) Performance standards for antimicrobial susceptibility testing; Twenty-Nineth Informational Supplement., vol M100-S29. CLSI, Wayne, PA, USA.
5.
go back to reference Tamma PD, Fan Y, Bergman Y, Pertea G, Kazmi AQ, Lewis S, Carroll KC, Schatz MC, Timp W, Simner PJ (2019) Applying rapid whole-genome sequencing to predict phenotypic antimicrobial susceptibility testing results among carbapenem-resistant Klebsiella pneumoniae clinical isolates. Antimicrob Agents Chemother 63(1). https://doi.org/10.1128/aac.01923-18 Tamma PD, Fan Y, Bergman Y, Pertea G, Kazmi AQ, Lewis S, Carroll KC, Schatz MC, Timp W, Simner PJ (2019) Applying rapid whole-genome sequencing to predict phenotypic antimicrobial susceptibility testing results among carbapenem-resistant Klebsiella pneumoniae clinical isolates. Antimicrob Agents Chemother 63(1). https://​doi.​org/​10.​1128/​aac.​01923-18
10.
go back to reference Core Team R (2018) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna Core Team R (2018) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
13.
go back to reference Mu A, Kwong JC, Isles NS, Goncalves da Silva A, Schultz MB, Ballard SA, Lane CR, Carter GP, Williamson DA, Seemann T, Stinear TP, Howden BP (2019) Reconstruction of the genomes of drug-resistant pathogens for outbreak investigation through metagenomic sequencing. mSphere 4 (1). doi:https://doi.org/10.1128/mSphere.00529-18 Mu A, Kwong JC, Isles NS, Goncalves da Silva A, Schultz MB, Ballard SA, Lane CR, Carter GP, Williamson DA, Seemann T, Stinear TP, Howden BP (2019) Reconstruction of the genomes of drug-resistant pathogens for outbreak investigation through metagenomic sequencing. mSphere 4 (1). doi:https://​doi.​org/​10.​1128/​mSphere.​00529-18
15.
go back to reference Kafetzopoulou LE, Efthymiadis K, Lewandowski K, Crook A, Carter D, Osborne J, Aarons E, Hewson R, Hiscox JA, Carroll MW, Vipond R, Pullan ST (2018) Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 23 (50). doi:https://doi.org/10.2807/1560-7917.es.2018.23.50.1800228 Kafetzopoulou LE, Efthymiadis K, Lewandowski K, Crook A, Carter D, Osborne J, Aarons E, Hewson R, Hiscox JA, Carroll MW, Vipond R, Pullan ST (2018) Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 23 (50). doi:https://​doi.​org/​10.​2807/​1560-7917.​es.​2018.​23.​50.​1800228
16.
go back to reference Schmidt K, Mwaigwisya S, Crossman LC, Doumith M, Munroe D, Pires C, Khan AM, Woodford N, Saunders NJ, Wain J, O’Grady J, Livermore DM (2017) Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by Nanopore-based metagenomic sequencing. J Antimicrob Chemother 72(1):104–114. https://doi.org/10.1093/jac/dkw397CrossRefPubMed Schmidt K, Mwaigwisya S, Crossman LC, Doumith M, Munroe D, Pires C, Khan AM, Woodford N, Saunders NJ, Wain J, O’Grady J, Livermore DM (2017) Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by Nanopore-based metagenomic sequencing. J Antimicrob Chemother 72(1):104–114. https://​doi.​org/​10.​1093/​jac/​dkw397CrossRefPubMed
Metadata
Title
Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms
Authors
Rebecca Yee
Florian P. Breitwieser
Stephanie Hao
Belita N.A. Opene
Rachael E. Workman
Pranita D. Tamma
Jennifer Dien-Bard
Winston Timp
Patricia J. Simner
Publication date
01-01-2021
Publisher
Springer Berlin Heidelberg
Published in
European Journal of Clinical Microbiology & Infectious Diseases / Issue 1/2021
Print ISSN: 0934-9723
Electronic ISSN: 1435-4373
DOI
https://doi.org/10.1007/s10096-020-03996-4

Other articles of this Issue 1/2021

European Journal of Clinical Microbiology & Infectious Diseases 1/2021 Go to the issue