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View article: Variable rates of SARS-CoV-2 evolution in chronic infections
Variable rates of SARS-CoV-2 evolution in chronic infections Open
An important feature of the evolution of the SARS-CoV-2 virus has been the emergence of highly mutated novel variants, which are characterised by the gain of multiple mutations relative to viruses circulating in the general global populati…
View article: BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies
BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies Open
Microbial genome-wide association study (GWAS) tools often require manual data processing steps, lack comprehensive workflows, and are limited by scalability issues, thus hindering the exploration of bacterial genetic traits. To address th…
View article: Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae
Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae Open
Interpreting the phenotypes of bla SHV alleles in Klebsiella pneumoniae genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal bla S…
View article: Exploiting human immune repertoire transgenic mice for protective monoclonal antibodies against antimicrobial resistant Acinetobacter baumannii
Exploiting human immune repertoire transgenic mice for protective monoclonal antibodies against antimicrobial resistant Acinetobacter baumannii Open
The use of monoclonal antibodies for the control of drug resistant nosocomial bacteria may alleviate a reliance on broad spectrum antimicrobials for treatment of infection. We identify monoclonal antibodies that may prevent infection cause…
View article: Diversity, functional classification and genotyping of SHV β-lactamases in<i>Klebsiella pneumoniae</i>
Diversity, functional classification and genotyping of SHV β-lactamases in<i>Klebsiella pneumoniae</i> Open
Interpreting phenotypes of bla SHV alleles in Klebsiella pneumoniae genomes is complex. While all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal bla SHV al…
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: The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom
The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom Open
Escherichia coli is a ubiquitous component of the human gut microbiome, but is also a common pathogen, causing around 40, 000 bloodstream infections (BSI) in the United Kingdom (UK) annually. The number of E. coli BSI has increased over th…
View article: Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years
Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years Open
Healthcare-associated infections (HCAIs) affect the most vulnerable people in society and are increasingly difficult to treat in the face of mounting antimicrobial resistance (AMR). Routine surveillance represents an effective way of under…
View article: The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom
The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom Open
Escherichia coli is a ubiquitous component of the human gut microbiome, but is also a common pathogen, causing around 40,000 bloodstream infections (BSI) in the UK annually. The number of E. coli BSI has increased over the last decade in t…
View article: Evidence of widespread endemic populations of highly multidrug resistant Klebsiella pneumoniae in hospital settings in Hanoi, Vietnam: a prospective cohort study
Evidence of widespread endemic populations of highly multidrug resistant Klebsiella pneumoniae in hospital settings in Hanoi, Vietnam: a prospective cohort study Open
Medical Research Council Newton Fund, Ministry of Science and Technology, Wellcome Trust, Academy of Medical Sciences, Health Foundation, and National Institute for Health and Care Research Cambridge Biomedical Research Centre.
View article: A qualitative investigation of paediatric intensive care staff attitudes towards the diagnosis of lower respiratory tract infection in the molecular diagnostics era
A qualitative investigation of paediatric intensive care staff attitudes towards the diagnosis of lower respiratory tract infection in the molecular diagnostics era Open
Background In the past decade, molecular diagnostic syndromic arrays incorporating a range of bacterial and viral pathogens have been described. It is unclear how paediatric intensive care unit (PICU) staff diagnose lower respiratory tract…
View article: The rapid detection of respiratory pathogens in critically ill children
The rapid detection of respiratory pathogens in critically ill children Open
Purpose Respiratory infections are the most common reason for admission to Paediatric Intensive Care Units (PICU). Most patients with lower respiratory tract infection (LRTI) receive broad-spectrum antimicrobials, despite low rates of bact…
View article: Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia
Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia Open
Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spect…
View article: Genomic characterisation of multidrug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two intensive care units in Hanoi, Viet Nam: a prospective observational cohort study
Genomic characterisation of multidrug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two intensive care units in Hanoi, Viet Nam: a prospective observational cohort study Open
BACKGROUND: Viet Nam has high rates of antimicrobial resistance (AMR) but little capacity for genomic surveillance. This study used whole genome sequencing to examine the prevalence and transmission of three key AMR pathogens in two intens…
View article: Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia
Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia Open
Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectr…
View article: Low diagnostic yield and time to diagnostic confirmation results in prolonged use of antimicrobials in critically ill children
Low diagnostic yield and time to diagnostic confirmation results in prolonged use of antimicrobials in critically ill children Open
Background: Broad-spectrum antimicrobial therapy is a key driver of antimicrobial resistance. Here, we aimed to review indications for antimicrobial therapy, determine the proportion of suspected bacterial infections that are confirmed by …
View article: Long read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over six years.
Long read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over six years. Open
Background: Healthcare-associated infections (HCAIs) affect the most vulnerable persons in society and are increasingly difficult to treat in the face of mounting antimicrobial resistance (AMR). We used whole-genome sequencing (WGS) to ret…
View article: P48 The limited yield of cultures in the critically ill child
P48 The limited yield of cultures in the critically ill child Open
Background Broad-spectrum antimicrobial therapy is a key driver of antimicrobial resistance. Here, we aimed to review indications for antimicrobial therapy, determine the proportion of suspected bacterial infections that are confirmed by c…
View article: A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events
A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events Open
Identifying linked cases of infection is a critical component of the public health response to viral infectious diseases. In a clinical context, there is a need to make rapid assessments of whether cases of infection have arrived independe…
View article: Rapid Assay for Sick Children with Acute Lung infection Study (RASCALS): diagnostic cohort study protocol
Rapid Assay for Sick Children with Acute Lung infection Study (RASCALS): diagnostic cohort study protocol Open
Introduction Lower respiratory tract infection (LRTI) is the most commonly treated infection in critically ill children. Pathogens are infrequently identified on routine respiratory culture, and this is a time-consuming process. A syndromi…
View article: Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia
Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia Open
Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectr…
View article: Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections
Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections Open
SARS-CoV-2 is notable both for its rapid spread, and for the heterogeneity of its patterns of transmission, with multiple published incidences of superspreading behaviour. Here, we applied a novel network reconstruction algorithm to infer …