The complete genome sequences of three Listeria monocytogenes serotype 1/2a strains, Lm 3136, Lm 3163, and Lm N1546, which were responsible for listeriosis outbreaks in 2005 and 2011 in Switzerland, are presented here. Copyright © 2016 Tasara et al.
Current methods for the determination of molecular interactions are widely used in the analytical sciences. To identify new methods, we investigated as a model system the hybridisation of a short 7 nt oligonucleotide labelled with, structurally, very similar cyanine dyes CY3 and DY-547, respectively, to a 34 nt oligonucleotide probe immobilised in a zero-mode waveguide (ZMW) nanostructure. Using a modified commercial off-the-shelf DNA sequencer, we established the principles to measure biomolecular interactions at the single-molecule level. Kinetic data were obtained from trains of fluorescence pulses, allowing the calculation of association and dissociation rate constants (k on, k off). For the 7mer labelled with the positively charged CY3 dye, k on and k off are ~3 larger and ~2 times smaller, respectively, compared with the oligonucleotide labelled with negatively charged DY-547 dye. The effect of neighbouring molecules lacking the 7nt binding sequence on single-molecule rate constants is small. The association rate constants is reduced by only 20–35%. Hybrid dissociation is not affected, since as a consequence of the experimental design, rebinding cannot take place. Results of single-molecule experiments were compared with data obtained from surface plasmon resonance (SPR) performed under comparable conditions. A good correlation for the association rate constants within a factor of 1.5 was found. Dissociation rate constants are smaller by a factor of 2–3 which we interpreted as a result of rebinding to neighbouring probes. Results of SPR measurements tend to systematically underestimate dissociation rate constants. The amount of this deviation depends on the association rate constant and the surface probe density. As a consequence, it is recommended to work at low probe densities to keep this effect small.
We present here the full-genome sequence of Escherichia coli K-15KW01, an extended-spectrum-ß-lactamase-producing uropathogenic strain. Assembly and annotation of the draft genome resulted in a 5,154,641-bp chromosome and revealed a chromosomally contained blaCTX-M-15 gene embedded at the right-hand extremity of an ISEcp1 element in a plasmid-like structure (36,907 bp). Copyright © 2016 Zurfluh et al.
Streptococcus tigurinus is responsible for severe invasive infections such as infective endocarditis, spondylodiscitis and meningitis. As described, S. tigurinus isolates AZ_3aT and AZ_14 were highly virulent (HV phenotype) in an experimental model of infective endocarditis and showed enhanced adherence and invasion of human endothelial cells when compared to low virulent S. tigurinus isolate AZ_8 (LV phenotype). Here, we sought whether genetic determinants could explain the higher virulence of AZ_3aT and AZ_14 isolates. Several genetic determinants specific to the HV strains were identified through extensive comparative genomics amongst which some were thought to be highly relevant for the observed HV phenotype. These included i) an iron uptake and metabolism operon, ii) an ascorbate assimilation operon, iii) a newly acquired PI-2-like pilus islets described for the first time in S. tigurinus, iv) a hyaluronate metabolism operon, v) an Entner-Doudoroff pathway of carbohydrates metabolism, and vi) an alternate pathways for indole biosynthesis. We believe that the identified genomic features could largely explain the phenotype of high infectivity of the two HV S. tigurinus strains. Indeed, these features include determinants that could be involved at different stages of the disease such as survival of S. tigurinus in blood (iron uptake and ascorbate metabolism operons), initial attachment of bacterial pathogen to the damaged cardiac tissue and/or vegetation that formed on site (PI-2-like pilus islets), tissue invasion (hyaluronate operon and Entner-Doudoroff pathway) and regulation of pathogenicity (indole biosynthesis pathway).
Here, we present the full sequences of three mcr-1-carrying plasmids isolated from extended-spectrum-ß-lactamase (ESBL)-producing Escherichia coli The plasmids belong to three different replicon types and are 34,640 bp, 209,401 bp, and 247,885 bp in size. We describe for the first time a composite transposon containing mcr-1 localized on a multidrug-resistant (MDR) IncHI2 plasmid harboring additional determinants of resistance to six different classes of antibiotics, including the ESBL gene blaCTX-M-1, and heavy metal resistance. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
The genomes of Pantoea calida DSM 22759T and Pantoea gaviniae DSM 22758T were sequenced using single-molecule real-time sequencing. They consist of a 4.3-Mbp chromosome containing 4,092 genes, of which 3,977 encode proteins, and a 4.5-Mbp chromosome containing 4,236 genes, of which 4,120 encode proteins, respectively. Copyright © 2018 Stevens et al.
The genome of Salmonella enterica subsp. enterica serotype Senftenberg N17-509, a strain isolated from desiccated coconut, was sequenced using single-molecule real-time sequencing. It consists of a 5.1-Mbp chromosome and a 29-kb linear plasmid. Copyright © 2018 Stevens et al.
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).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).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.Multidrug-resistant K. pneumoniae harbouring blaNDM-9 and blaCTX-M-15 are spreading into the environment, most probably via wastewater from clinical settings. Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.
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.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).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.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.Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.
If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.