Kathy E. Raven
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View article: Large-scale characterisation of the nasal microbiome redefines Staphylococcus aureus colonisation status
Large-scale characterisation of the nasal microbiome redefines Staphylococcus aureus colonisation status Open
Staphylococcus aureus colonises the nose in humans, with individuals defined as persistent, intermittent or non-carriers. Unlike the gut microbiome, the nasal microbiome has not been studied in large numbers of people. Here, we define the …
View article: CARRIAGE study - a prospective cohort study of determinants of Staphylococcus aureus nasal colonisation in healthy adults in England.
CARRIAGE study - a prospective cohort study of determinants of Staphylococcus aureus nasal colonisation in healthy adults in England. Open
Background Around 30% of humans carry Staphylococcus aureus in their nose. S. aureus is an important cause of disease, and carriers are at greater risk of bacteraemia than non-carriers. Why some people carry S. aureus while others never do…
View article: The nasal microbiome redefines Staphylococcus aureus colonisation
The nasal microbiome redefines Staphylococcus aureus colonisation Open
Staphylococcus aureus colonises the nose in humans, with individuals defined as persistent, intermittent or non-carriers. Unlike the gut microbiome, the nasal microbiome has not been studied in large numbers of people. Here, we define the …
View article: Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions
Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions Open
Genomic epidemiology enhances the ability to detect and refute methicillin-resistant Staphylococcus aureus (MRSA) outbreaks in healthcare settings, but its routine introduction requires further evidence of benefits for patients and resourc…
View article: Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data
Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data Open
Background: DNA sequencing could become an alternative to in vitro antibiotic susceptibility testing (AST) methods for determining antibiotic resistance by detecting genetic determinants associated with decreased antibiotic susceptibility.…
View article: Impact of a new hospital with close to 100% single-occupancy rooms on environmental contamination and incidence of vancomycin-resistant Enterococcus faecium colonization or infection: a genomic surveillance study
Impact of a new hospital with close to 100% single-occupancy rooms on environmental contamination and incidence of vancomycin-resistant Enterococcus faecium colonization or infection: a genomic surveillance study Open
The use of single-occupancy rooms was associated with reduced environmental contamination with VRE, and lower transmission and isolation of VRE from clinical samples. The cost-effectiveness of single-occupancy room hospitals in reducing he…
View article: Large-Scale Evaluation of a Rapid Fully Automated Analysis Platform to Detect and Refute Outbreaks Based on MRSA Genome Comparisons
Large-Scale Evaluation of a Rapid Fully Automated Analysis Platform to Detect and Refute Outbreaks Based on MRSA Genome Comparisons Open
It has been clearly established that genome sequencing of MRSA improves the accuracy of health care-associated outbreak investigations, including the confirmation and exclusion of outbreaks and identification of patients involved. This cou…
View article: Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents
Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents Open
Enterococcus faecium is a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements …
View article: Exploring the mobilome and resistome of <i>Enterococcus faecium</i> in a One Health context across two continents
Exploring the mobilome and resistome of <i>Enterococcus faecium</i> in a One Health context across two continents Open
Enterococcus faecium is a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements …
View article: Evaluation of methods for whole genome sequencing of <i>Enterococcus faecium</i> in a diagnostic laboratory
Evaluation of methods for whole genome sequencing of <i>Enterococcus faecium</i> in a diagnostic laboratory Open
Enterococcus faecium is an important nosocomial pathogen associated with hospital transmission and outbreaks. Based on growing evidence that bacterial whole genome sequencing enhances hospital outbreak investigation of other bacterial spec…
View article: Defining metrics for whole-genome sequence analysis of MRSA in clinical practice
Defining metrics for whole-genome sequence analysis of MRSA in clinical practice Open
Bacterial sequencing will become increasingly adopted in routine microbiology laboratories. Here, we report the findings of a technical evaluation of almost 800 clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates, in which…
View article: Evaluation of a fully automated bioinformatics tool to predict antibiotic resistance from MRSA genomes
Evaluation of a fully automated bioinformatics tool to predict antibiotic resistance from MRSA genomes Open
Objectives The genetic prediction of phenotypic antibiotic resistance based on analysis of WGS data is becoming increasingly feasible, but a major barrier to its introduction into routine use is the lack of fully automated interpretation t…
View article: Staphylococcus aureus core genome coordintes on the ST22 strain HO 5096 0412
Staphylococcus aureus core genome coordintes on the ST22 strain HO 5096 0412 Open
This file contains the genomic coordinates of the Staphylococcus aureus species core-genome, derived from a collection of 800 S. aureus strains from multiple host species1 using Roary, on the clonal complex 22 S. aureus reference genome (G…
View article: Staphylococcus aureus core genome coordinates on the ST22 strain HO 5096 0412
Staphylococcus aureus core genome coordinates on the ST22 strain HO 5096 0412 Open
This file contains the genomic coordinates of the Staphylococcus aureus species core-genome, derived from a collection of 800 S. aureus strains from multiple host species1 using Roary2, on the clonal complex 22 S. aureus reference genome (…
View article: Staphylococcus aureus core genome coordinates on the ST30 strain MRSA252
Staphylococcus aureus core genome coordinates on the ST30 strain MRSA252 Open
This file contains the genomic coordinates of the Staphylococcus aureus species core-genome, derived from a collection of 800 S. aureus strains from multiple host species1 using Roary2, on the clonal complex 30 Staphylococcus aureus refere…
View article: Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks
Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks Open
Genomic surveillance that combines bacterial sequencing and epidemiological information will become the gold standard for outbreak detection, but its clinical translation is hampered by the lack of automated interpretation tools. We perfor…
View article: Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes
Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes Open
We examined whether genomic surveillance of Escherichia coli in wastewater could capture the dominant E. coli lineages associated with bloodstream infection and livestock in the East of England, together with the antibiotic-resistance gene…
View article: Rapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory
Rapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory Open
Background Routine sequencing of MRSA could bring about significant improvements to outbreak detection and investigation. Sequencing is commonly performed using DNA extracted from a pure culture, but overcoming the delay associated with th…
View article: Methodology for Whole-Genome Sequencing of Methicillin-Resistant <i>Staphylococcus aureus</i> Isolates in a Routine Hospital Microbiology Laboratory
Methodology for Whole-Genome Sequencing of Methicillin-Resistant <i>Staphylococcus aureus</i> Isolates in a Routine Hospital Microbiology Laboratory Open
There is growing evidence for the value of bacterial whole-genome sequencing in hospital outbreak investigations. Our aim was to develop methods that support efficient and accurate low-throughput clinical sequencing of methicillin-resistan…
View article: Detection of vancomycin-resistant <i>Enterococcus faecium</i> hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment
Detection of vancomycin-resistant <i>Enterococcus faecium</i> hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment Open
Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of healthcare-associated infection. Reservoirs of VREfm are largely assumed to be nosocomial although there is a paucity of data on alternative sources. Here, we describe…
View article: One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock
One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock Open
The increasing prevalence of E. coli bloodstream infections is a serious public health problem. We used genomic epidemiology in a One Health study conducted in the East of England to examine putative sources of E. coli associated with seri…
View article: Mobile genetic elements on the ST80 strain 11819-97
Mobile genetic elements on the ST80 strain 11819-97 Open
This file contains the genomic coordinates of mobile genetic elements on the reference genome of clonal complex 80 Staphylococcus aureus 11819-97 strain (Genbank accession number CP003193.1).
View article: Mobile genetic elements on the ST59 strain M013
Mobile genetic elements on the ST59 strain M013 Open
This file contains the genomic coordinates of mobile genetic elements on the reference genome of clonal complex 59 Staphylococcus aureus M013 strain (Genbank accession number CP003166.1).
View article: Mobile genetic elements on the ST8 USA300 FPR3757
Mobile genetic elements on the ST8 USA300 FPR3757 Open
This file contains the genomic coordinates of mobile genetic elements on the reference genome of clonal complex 8 Staphylococcus aureus USA300 FPR3757 strain (Genbank accession number CP000255.1).
View article: Mobile genetic elements on the ST5 strain N315
Mobile genetic elements on the ST5 strain N315 Open
This file contains the genomic coordinates of mobile genetic elements on the reference genome of clonal complex 5 Staphylococcus aureus N315 strain (Genbank accession number BA000018.3).