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View article: <i>VCAM1</i>-expressing T cells and systemic autoimmunity in Regnase-1 deficiency
<i>VCAM1</i>-expressing T cells and systemic autoimmunity in Regnase-1 deficiency Open
Summary Autoimmunity develops as a result of a breakdown in immune tolerance and activation of autoreactive immune cells. Most of the common autoimmune diseases are polygenic 1 suggesting dysregulation in multiple signalling pathways. By c…
View article: Surveillance of travel-associated isolates elucidates the diversity of non-pandemic Vibrio cholerae
Surveillance of travel-associated isolates elucidates the diversity of non-pandemic Vibrio cholerae Open
Vibrio cholerae is a Gram-negative bacterium found in aquatic environments and is the aetiological agent of cholera, characterized by acute watery diarrhoea and severe dehydration. Cholera presents a significant global health burden of an …
View article: Pulmonary inflammation in severe pneumonia is characterised by compartmentalised and mechanistically distinct sub-phenotypes
Pulmonary inflammation in severe pneumonia is characterised by compartmentalised and mechanistically distinct sub-phenotypes Open
Pneumonia is the leading infectious disease killer worldwide and commonly requires admission to critical care. Despite its prevalence, the underpinning biology of severe pneumonia remains incompletely understood. We performed multifaceted …
View article: Bayesian modelling of antimicrobial resistance in enteric fever in understudied areas
Bayesian modelling of antimicrobial resistance in enteric fever in understudied areas Open
In The Lancet Global Health, Annie J Browne and colleagues1GRAM Typhoid CollaboratorsEstimating the subnational prevalence of antimicrobial resistant Salmonella enterica serovars Typhi and Paratyphi A infections in 75 endemic countries, 19…
View article: Detecting Residual Chronic <i>Salmonella</i> Typhi Carriers on the Road to Typhoid Elimination in Santiago, Chile, 2017–2019
Detecting Residual Chronic <i>Salmonella</i> Typhi Carriers on the Road to Typhoid Elimination in Santiago, Chile, 2017–2019 Open
Background In Santiago, Chile, where typhoid had been hyperendemic (1977–1991), we investigated whether residual chronic carriers could be detected among household contacts of non-travel-related typhoid cases occurring during 2017–2019. Me…
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: Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes Open
Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analys…
View article: Author response: Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes
Author response: Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes Open
Full text Figures and data Side by side Abstract Editor's evaluation eLife digest Introduction Methods Results Discussion Data availability References Decision letter Author response Article and author information Metrics Abstract Backgrou…
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: The rapid detection of respiratory pathogens in critically ill children
The rapid detection of respiratory pathogens in critically ill children Open
View article: Multiplex MinION sequencing suggests enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era
Multiplex MinION sequencing suggests enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era Open
Human adenovirus F41 causes acute gastroenteritis in children, and has recently been associated with an apparent increase in paediatric hepatitis of unknown aetiology in the UK, with further cases reported in multiple countries. Relatively…
View article: Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000<i>Salmonella</i>Typhi genomes
Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000<i>Salmonella</i>Typhi genomes Open
The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which ma…
View article: FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2
FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2 Open
Preventing SARS-CoV-2 infection by modulating viral host receptors, such as angiotensin-converting enzyme 2 (ACE2)1, could represent a new chemoprophylactic approach for COVID-19 that complements vaccination2,3. However, the mechanisms tha…
View article: FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2
FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2 Open
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: Obesity Is Associated with Attenuated Tissue Immunity in COVID-19
Obesity Is Associated with Attenuated Tissue Immunity in COVID-19 Open
Rationale: Obesity affects 40% of U.S. adults, is associated with a proinflammatory state, and presents a significant risk factor for the development of severe coronavirus disease (COVID-19). To date, there is limited information on how ob…
View article: Persistence of Rare Salmonella Typhi Genotypes Susceptible to First-Line Antibiotics in the Remote Islands of Samoa
Persistence of Rare Salmonella Typhi Genotypes Susceptible to First-Line Antibiotics in the Remote Islands of Samoa Open
In this study, we used whole genome sequencing and comparative genomics analyses to characterize the population structure, evolutionary origins, and genomic features of S. Typhi associated with decades of endemic typhoid fever in Samoa.
View article: Enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era: validation of a multiplex amplicon-MinION sequencing method
Enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era: validation of a multiplex amplicon-MinION sequencing method Open
Human adenovirus F41 causes acute gastroenteritis in children, and has recently been associated with an apparent increase in paediatric hepatitis of unknown aetiology in the UK, with further cases reported in multiple countries. Relatively…
View article: Whole genome sequence analysis of Salmonella Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago, Chile in the 1980s and 2010–2016
Whole genome sequence analysis of Salmonella Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago, Chile in the 1980s and 2010–2016 Open
Typhoid fever epidemiology was investigated rigorously in Santiago, Chile during the 1980s, when Salmonella enterica serovar Typhi ( S . Typhi) caused seasonal, hyperendemic disease. Targeted interventions reduced the annual typhoid incide…
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: Persistence of rare<i>Salmonella</i>Typhi genotypes susceptible to first-line antibiotics in the remote islands of Samoa
Persistence of rare<i>Salmonella</i>Typhi genotypes susceptible to first-line antibiotics in the remote islands of Samoa Open
For decades, the remote island nation of Samoa (pop. ~200,000) has faced endemic typhoid fever despite improvements in water quality, sanitation, and economic development. We recently described the epidemiology of typhoid fever in Samoa fr…
View article: Whole genome sequence analysis of <i>Salmonella</i> Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago, Chile in the 1980s and 2010-2016
Whole genome sequence analysis of <i>Salmonella</i> Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago, Chile in the 1980s and 2010-2016 Open
Typhoid fever epidemiology was investigated rigorously in Santiago, Chile during the 1980s, when Salmonella enterica serovar Typhi ( S . Typhi) caused seasonal, hyperendemic disease. Targeted interventions reduced the annual typhoid incide…
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: The Removal of Airborne Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Other Microbial Bioaerosols by Air Filtration on Coronavirus Disease 2019 (COVID-19) Surge Units
The Removal of Airborne Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Other Microbial Bioaerosols by Air Filtration on Coronavirus Disease 2019 (COVID-19) Surge Units Open
Airborne severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected in a coronavirus disease 19 (COVID-19) ward before activation of HEPA-air filtration but not during filter operation; SARS-CoV-2 was again detected followin…
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: The removal of airborne SARS-CoV-2 and other microbial bioaerosols by air filtration on COVID-19 surge units
The removal of airborne SARS-CoV-2 and other microbial bioaerosols by air filtration on COVID-19 surge units Open
Summary Background The COVID-19 pandemic has overwhelmed the respiratory isolation capacity in hospitals; many wards lacking high-frequency air changes have been repurposed for managing patients infected with SARS-CoV-2 requiring either st…
View article: Extended data table 1: Taqman array card results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing.
Extended data table 1: Taqman array card results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing. Open
Data from study, protocol published at 10.5281/zenodo.5081880 Extended Data Table 1: TAC results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing.
View article: Extended data table 1: Taqman array card results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing.
Extended data table 1: Taqman array card results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing. Open
<p>Data from study, protocol published at 10.5281/zenodo.5081880</p>\n\n<p><strong>Extended Data Table 1: TAC results showing all individual target hits with Ct values and whether validated by conventional micr…
View article: A genomic snapshot of Salmonella enterica serovar Typhi in Colombia
A genomic snapshot of Salmonella enterica serovar Typhi in Colombia Open
Little is known about the genetic diversity of Salmonella enterica serovar Typhi ( S . Typhi) circulating in Latin America. It has been observed that typhoid fever is still endemic in this part of the world; however, a lack of standardized…