James E. Bray
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View article: In silico and in vitro analyses for the improved diagnosis of bacterial meningitis
In silico and in vitro analyses for the improved diagnosis of bacterial meningitis Open
Context Diagnosing meningitis remains challenging with etiological agents frequently unidentified. Using both in silico and in vitro approaches, this study evaluated published and novel genetic targets for the detection of common bacterial…
View article: Development of a core genome multilocus sequence typing scheme and life identification number code classification system for Staphylococcus aureus
Development of a core genome multilocus sequence typing scheme and life identification number code classification system for Staphylococcus aureus Open
Staphylococcus aureus infects both humans and animals, and antimicrobial resistance, including multidrug resistance, complicates the treatment of S. aureus infections. Understanding the population structure and distribution of genetic line…
View article: Utilizing large and diverse bacterial genome datasets to improve the detection and identification of Streptococcus pneumoniae via PCR-based diagnostics
Utilizing large and diverse bacterial genome datasets to improve the detection and identification of Streptococcus pneumoniae via PCR-based diagnostics Open
The accurate identification of Streptococcus pneumoniae (pneumococcus) is crucial for diagnostics and surveillance but is complicated by the use of molecular assays that may also detect non-pneumococcal Streptococcus (NPS) species. Therefo…
Origin and Evolution of Bacterial Periplasmic Force Transducers Open
In double-membraned bacteria, non-equilibrium processes that occur at the outer membrane are typically coupled to the chemiosmotically energized inner membrane. TolA and TonB are homologous proteins which energetically couple inner membran…
View article: Understanding the population structure of <i>Moraxella catarrhalis</i> using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system
Understanding the population structure of <i>Moraxella catarrhalis</i> using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system Open
Moraxella catarrhalis is an important cause of infectious exacerbations of chronic obstructive pulmonary disease and otitis media. Previously, seroresistant (SR) and serosensitive (SS) lineages that differed in virulence potential were des…
View article: Development of a core genome multilocus sequence typing (cgMLST) scheme and life identification number (LIN) code classification system for <i>Staphylococcus aureus</i>
Development of a core genome multilocus sequence typing (cgMLST) scheme and life identification number (LIN) code classification system for <i>Staphylococcus aureus</i> Open
Staphylococcus aureus infects both humans and animals, and antimicrobial resistance, including multidrug resistance, complicates treatment of S. aureus infections. Understanding S. aureus population structure and the distribution of geneti…
View article: Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data
Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data Open
Motivation Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high-throughput surveillance and clinical app…
View article: Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure
Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure Open
Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large num…
View article: Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data
Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data Open
Motivation Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high throughput surveillance and clinical app…
View article: Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure
Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure Open
Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonisation, disease, antimicrobial resistance, and vaccine impact. Furthermore, the recent accumulation of large nu…
Phylogenomics of Acinetobacter species and analysis of antimicrobial resistance genes Open
Introduction Non- baumannii Acinetobacter species are increasingly isolated in the clinical setting and the environment. The aim of the present study was to analyze a genome database of 837 Acinetobacter spp. isolates, which included 798 n…
First reported detection of the mobile colistin resistance genes, mcr-8 and mcr-9, in the Irish environment Open
The emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environ…
View article: Association between disease severity and co-detection of respiratory pathogens in infants with RSV infection
Association between disease severity and co-detection of respiratory pathogens in infants with RSV infection Open
BACKGROUND Respiratory syncytial virus (RSV) is the leading cause of hospitalisation associated with acute respiratory infection in infants and young children, with substantial disease burden globally. The impact of additional respiratory …
First reported detection of the mobile colistin resistance genes, <i>mcr</i> -8 and <i>mcr</i> -9, in the Irish environment Open
The emergence and dissemination of mobile colistin resistance ( mcr ) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Envir…
Ribosomal MLST nucleotide identity (rMLST-NI), a rapid bacterial species identification method: application to Klebsiella and Raoultella genomic species validation Open
Bacterial genomics is making an increasing contribution to the fields of medicine and public health microbiology. Consequently, accurate species identification of bacterial genomes is an important task, particularly as the number of genome…
View article: Cardiac Troponin Testing as a Component of Return to Play Cardiac Screening in Young Competitive Athletes Following SARS‐CoV‐2 Infection
Cardiac Troponin Testing as a Component of Return to Play Cardiac Screening in Young Competitive Athletes Following SARS‐CoV‐2 Infection Open
Background Initial protocols for return to play cardiac testing in young competitive athletes following SARS‐CoV‐2 infection recommended cardiac troponin (cTn) to screen for cardiac involvement. This study aimed to define the diagnostic yi…
Effectiveness of Short-Term Heat Acclimation on Intermittent Sprint Performance in the Heat with Moderately Trained Males Open
Purpose: Effectiveness of short-term heat acclimation (STHA), over 5-days (permissive dehydration), on intermittent heat stress test (HST) with males. Methods: Ten, moderately-trained, males (mean [SD]; age 25.6 [8.9] y; stature 180.7 [5.6…
Thiomicrorhabdus heinhorstiae sp. nov. and Thiomicrorhabdus cannonii sp. nov.: novel sulphur-oxidizing chemolithoautotrophs isolated from the chemocline of Hospital Hole, an anchialine sinkhole in Spring Hill, Florida, USA Open
Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phy…
Screening Programs for SARS-CoV-2 Infections on a University Campus — Austin, Texas, September 30–November 30, 2020 Open
Colleges and universities in the United States have relied on various measures during the COVID-19 pandemic to prevent transmission of SARS-CoV-2, the virus that causes COVID-19, including implementing testing programs (1-3). These program…
O09.6 Typing outer membrane vesicle proteins of Neisseria gonorrhoeae provides insight into antimicrobial resistance Open
Background Outer membrane vesicles (OMVs) are known to be produced in significant quantities during gonococcal infection, however, their role remains mostly unknown. In this study, the diversity of gonococcal OMV proteins and their associa…
View article: SARS-CoV-2 Cardiac Involvement in Young Competitive Athletes
SARS-CoV-2 Cardiac Involvement in Young Competitive Athletes Open
Background: Cardiac involvement among hospitalized patients with severe coronavirus disease 2019 (COVID-19) is common and associated with adverse outcomes. This study aimed to determine the prevalence and clinical implications of COVID-19 …
Evolution of Sequence Type 4821 Clonal Complex Hyperinvasive and Quinolone-Resistant Meningococci Open
Expansion of quinolone-resistant Neisseria meningitidis clone ChinaCC4821-R1-C/B from sequence type (ST) 4821 clonal complex (CC4821) caused a serogroup shift from serogroup A to serogroup C invasive meningococcal disease (IMD) in China. T…
Time from Start of Quarantine to SARS-CoV-2 Positive Test Among Quarantined College and University Athletes — 17 States, June–October 2020 Open
To safely resume sports, college and university athletic programs and regional athletic conferences created plans to mitigate transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). Mitigation measures includ…
Evolution of ST-4821 clonal complex hyperinvasive and quinolone-resistant meningococci: the next meningococcal pandemic? Open
The expansion of quinolone-resistant Neisseria meningitidis clone China CC4821-R1-C/B from ST-4821 clonal complex (cc4821) caused a serogroup shift from serogroup A to C in invasive meningococcal disease (IMD) in China. To establish the re…
Distribution of class 1 integrons in historic and contemporary collections of human pathogenic Escherichia coli Open
Integrons play a major role in the evolution and spread of antimicrobial resistance in human pathogens, including Escherichia coli. This study describes the occurrence of class 1 integrons in human pathogenic E. coli, in three isolate coll…