Magdalena Nüesch-Inderbinen1, Katrin Zurfluh2, Marc J A Stevens2, Roger Stephan2. 1. Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, CH-8057 Zurich, Switzerland. Electronic address: magdalena.nueesch-inderbinen@uzh.ch. 2. Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, CH-8057 Zurich, Switzerland.
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.
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.