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Objectives The global dissemination of vancomycin-resistant enterococci (VRE) has become a serious public-health concern. Although outbreaks are typically caused by nosocomial transmission, contaminated food and water may contribute to the spread of VRE. The aim of this study was to assess the presence of VRE in flowing surface water bodies in Switzerland and to characterise the isolates. Methods Surface water was sampled from rivers, streams and canals throughout Switzerland and was screened for the presence of VRE. Whole-genome sequencing was used to identify antimicrobial resistance genes and the phylogenetic similarity of the obtained isolates. Results VRE were detected in 6 (3.1%) of 191 water samples. The six VRE-containing samples were all collected near treated wastewater discharge sites. The six isolates were identified as Enterococcus faecium sequence type 133 (ST133) and harboured the vancomycin resistance-conferring vanA gene cluster on transposon Tn1546. They showed a close phylogenetic relationship to ST133 swine faecal isolates obtained during a previously reported screening in Switzerland. Conclusion Our results suggest that surface water contributes to the environmental dissemination of VRE. Repeated identification of ST133 clones in geographically distinct water sampling sites and swine faecal samples collected in slaughterhouses may indicate a local dominance of this VRE lineage in Switzerland.

Objectives The objective of this work was to characterise an optrA-carrying Enterococcus faecalis ST16 isolate recovered from a river water sample in Switzerland. Methods Linezolid-resistant E. faecalis F102 was recovered from surface water in Switzerland and was subjected to comprehensive genotypic characterisation and analysis of the genetic environment of the oxazolidinone/phenicol resistance gene optrA. Whole-genome sequencing (WGS) was performed to detect linezolid resistance mechanisms, including mutations in 23S rRNA and ribosomal protein genes as well as acquired resistance genes. The isolate was further characterised by multilocus sequence typing (MLST) and identification of virulence genes. Results WGS detected the presence of optrA identical to the original optrA gene from E. faecalis E349. Analysis of the genetic environment revealed the association of optrA with fexA and a Tn6674-like transposon in co-existence with spc and erm(A) resistance genes. Sequence alignment indicated that the genetic environment of optrA was identical to a Tn6674-like variant from E. faecalis previously isolated from diseased and healthy humans and food-producing animals in the Asia-Pacific region. Enterococcus faecalis F102 did not contain any mutations in 23S rRNA or in genes encoding ribosomal proteins L3, L4 and L22. A total of 14 other resistance genes and 16 virulence genes were detected. Enterococcus faecalis F102 was assigned in silico to ST16. Conclusion The spread of optrA-carrying E. faecalis ST16 with a high pathogenic potential in surface water is a worrisome aspect from a public-health perspective.

Objectives Carbapenem-resistant Escherichia coli have emerged worldwide and represent a major challenge to effective healthcare management. Here we report the genome sequence of an NDM-5- and CTX-M-15-producing E. coli belonging to sequence type 617 isolated from wastewater treatment plant effluent in Switzerland. Methods Whole-genome sequencing of E. coli 657SK2 was performed using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology RS2 reads (C4/P6 chemistry). De novo assembly was carried out using Canu 1.6, and sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Results The genome of E. coli 657SK2 consists of a 4.9-Mbp chromosome containing blaCTX-M-15, genes associated with virulence [fyuA, hlyE, the pyelonephritis-associated pili (pap) gene cluster and the yad gene cluster], the copper resistance gene pco, and genes associated with resistance to quaternary ammonium compound (QAC) disinfectants (emrA, mdfA and sugE). A 173.9-kb multidrug resistance IncFII-FIA-FIB plasmid was detected harbouring aadA2, aadA5, blaNDM-5, blaOXA-1, cat, drfA, drfA17, the mph(A)–mrx–mphR cluster, the tetA–tetC–tetR cluster, and the virulence genes iutA and ylpA. Conclusions The genome sequence of E. coli 657SK2 provides information on resistance mechanisms and virulence characteristics of pathogenic E. coli harbouring blaNDM-5 and blaCTX-M-15 that are spreading into the environment via urban wastewater.

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.