Author: Nicole Stoesser

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Preprints

Changes in paediatric respiratory infections at a UK teaching hospital 2016-2021; impact of the SARS-CoV-2 pandemic.

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Impact of Delta on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK

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Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom

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The impact of SARS-CoV-2 vaccines on antibody responses in the general population in the United Kingdom

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Virus detection and identification in minutes using single-particle imaging and deep learning

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Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

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Increased infections, but not viral burden, with a new SARS-CoV-2 variant

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Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time

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Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing

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SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus

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Genomic diversity affects the accuracy of bacterial SNP calling pipelines

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The duration, dynamics and determinants of SARS-CoV-2 antibody responses in individual healthcare workers

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Stringent thresholds for SARS-CoV-2 IgG assays result in under-detection of cases reporting loss of taste/smell

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The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

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A haemagglutination test for rapid detection of antibodies to SARS-CoV-2

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Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies

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Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli

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Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131

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High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families

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Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

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TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data

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Anti-spike antibody response to natural SARS-CoV-2 infection in the general population

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Flanker: a tool for comparative genomics of gene flanking regions

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Transmission dynamics and between-species interactions of multidrug-resistant Enterobacteriaceae

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Dynamics of mcr-1 prevalence and mcr-1-positive Escherichia coli after the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing based molecular epidemiological study

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Novel blaKPC-carrying species identified in the hospital environment

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Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

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Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

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Genomic epidemiology of a complex, multi-species plasmid-borne blaKPC carbapenemase outbreak in Enterobacterales in the UK, 2009-2014

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The sensitivity improved two-test algorithm "SIT2": a universal optimization strategy for SARS-CoV-2 serology

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Panton-Valentine leukocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial genome-wide association study

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Trends in Escherichia coli bloodstream infection, urinary tract infections and antibiotic susceptibilities in Oxfordshire, 1998-2016: an observational study

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Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries

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The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates

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Molecular epidemiology of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire (UK) 2008-2018

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Genomic network analysis of an environmental and livestock IncF plasmid population

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The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm

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Klebsiella quasipneumonaiae provides a window into carbapenemase gene transfer, plasmid rearrangements and nosocomial acquisition from the hospital environment

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Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399

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Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia

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Transmission patterns of hyper-endemic multi-drug resistant Klebsiella pneumoniae in a Cambodian neonatal unit: a longitudinal study with whole genome sequencing

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Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections

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Antimicrobial resistance surveillance: can we estimate resistance in bloodstream infections from other types of specimen?

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Molecular epidemiology of paediatric bloodstream infections caused by Gram-negative bacteria in Oxfordshire, UK

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