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Complete and assembled genome sequence of an NDM-9- and CTX-M-15-producing Klebsiella pneumoniae ST147 wastewater isolate from Switzerland


Nüesch-Inderbinen, Magdalena; Zurfluh, Katrin; Stevens, Marc J A; Stephan, Roger (2018). Complete and assembled genome sequence of an NDM-9- and CTX-M-15-producing Klebsiella pneumoniae ST147 wastewater isolate from Switzerland. Journal of Global Antimicrobial Resistance, 13:53-54.

Abstract

OBJECTIVES: Carbapenem-resistant Klebsiella pneumoniae have emerged worldwide and represent a major threat to human health. Here we report the genome sequence of K. pneumoniae 002SK2, an NDM-9- and CTX-M-15-producing strain isolated from wastewater in Switzerland and belonging to the international high-risk clone sequence type 147 (ST147).
METHODS: Whole-genome sequencing of K. pneumoniae 002SK2 was performed using Pacific Biosciences (PacBio) single-molecule, real-time (SMRT) technology RS2 reads (C4/P6 chemistry). De novo assembly was performed using Canu assembler, and sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP).
RESULTS: The genome of K. pneumoniae 002SK2 consists of a 5.4-Mbp chromosome containing blaSHV-11 and fosA6, a 159-kb IncFIB(K) plasmid carrying the heavy metal resistance genes ars and sil, and a 77-kb IncR plasmid containing blaCTX-M-15, blaNDM-9, blaOXA-9 and blaTEM-1.
CONCLUSIONS: Multidrug-resistant K. pneumoniae harbouring blaNDM-9 and blaCTX-M-15 are spreading into the environment, most probably via wastewater from clinical settings.

Abstract

OBJECTIVES: Carbapenem-resistant Klebsiella pneumoniae have emerged worldwide and represent a major threat to human health. Here we report the genome sequence of K. pneumoniae 002SK2, an NDM-9- and CTX-M-15-producing strain isolated from wastewater in Switzerland and belonging to the international high-risk clone sequence type 147 (ST147).
METHODS: Whole-genome sequencing of K. pneumoniae 002SK2 was performed using Pacific Biosciences (PacBio) single-molecule, real-time (SMRT) technology RS2 reads (C4/P6 chemistry). De novo assembly was performed using Canu assembler, and sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP).
RESULTS: The genome of K. pneumoniae 002SK2 consists of a 5.4-Mbp chromosome containing blaSHV-11 and fosA6, a 159-kb IncFIB(K) plasmid carrying the heavy metal resistance genes ars and sil, and a 77-kb IncR plasmid containing blaCTX-M-15, blaNDM-9, blaOXA-9 and blaTEM-1.
CONCLUSIONS: Multidrug-resistant K. pneumoniae harbouring blaNDM-9 and blaCTX-M-15 are spreading into the environment, most probably via wastewater from clinical settings.

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Item Type:Journal Article, refereed, original work
Communities & Collections:05 Vetsuisse Faculty > Institute of Food Safety and Hygiene
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Scopus Subject Areas:Life Sciences > Microbiology
Health Sciences > Immunology and Allergy
Life Sciences > Immunology
Health Sciences > Microbiology (medical)
Uncontrolled Keywords:Genome analysis; Klebsiella pneumoniae; ST147; bla(CTX-M-15); bla(NDM-9)
Language:English
Date:1 June 2018
Deposited On:13 Feb 2019 08:55
Last Modified:29 Jul 2020 10:15
Publisher:Elsevier
ISSN:2213-7165
OA Status:Green
Publisher DOI:https://doi.org/10.1016/j.jgar.2018.03.001
PubMed ID:29551728

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