Nicole E Stoesser

Global genomic epidemiology of multi-carbapenemase Enterobacterales

This study analyzes 1501 global genomes of multi-carbapenemase Enterobacterales, identifying common allelic combinations, plasmid distributions, and evolutionary mechanisms.

Benchmarking strain-level profiling of Escherichia coli in short-read gut metagenomes

This study benchmarks six tools for strain-level profiling of E. coli in short-read gut metagenomes, showing significant variation in performance and highlighting StrainR2's high accuracy and PathoScope 2.0/StrainGE's robustness in unknown strain scenarios.

OxBreaker: species-agnostic pipeline for the analysis of outbreaks using nanopore sequencing

OxBreaker is a species-agnostic pipeline for analyzing bacterial and plasmid outbreaks using nanopore sequencing, offering high accuracy and accessibility for real-time genomic surveillance.

Nanopore long-read only genome assembly of clinical Enterobacterales isolates is complete and accurate

This study evaluates Nanopore long-read only genome assembly for clinical Enterobacterales isolates, finding Autocycler with Medaka polishing achieves accuracy comparable to hybrid assemblies.

E. coli phylogeny drives co-amoxiclav resistance through variable expression of blaTEM-1

The paper shows that E. coli phylogeny influences blaTEM-1 expression and co-amoxiclav resistance through lineage-specific regulatory differences.

Global genomic epidemiology of blaGES-5 carbapenemase-associated integrons

The paper analyzes the global genomic diversity of blaGES-5 integrons using a pangenome graph-based workflow, revealing differences between chromosomal and plasmid-associated integrons.

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of Escherichia coli isolates

This paper compares direct cDNA and PCR-cDNA Nanopore sequencing of E. coli isolates, finding PCR-based amplification improves yield but introduces minor GC-content bias.

Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK

The paper investigates plasmid sharing among Enterobacterales in human infections, livestock, wastewater, and waterways in Oxfordshire, finding shared plasmid backbones and rapid accessory gene changes across niches.

Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction

This paper evaluates the performance of new Oxford Nanopore flowcells and chemistries for bacterial genome reconstruction, finding that while R10.4/Kit12 with 'super accuracy' basecalling shows promise, hybrid assembly remains more robust and cost-effective.

High-resolution characterisation of short-term temporal variability in the taxonomic and resistome composition of wastewater influent

This study compares taxonomic and resistome variability between single-timepoint grab and 24H-composite wastewater samples, finding that composites better capture AMR genes and reduce temporal variability.

Evaluation of metagenomic, 16S rRNA gene and ultra-plexed PCR-based sequencing approaches for profiling antimicrobial resistance gene and bacterial taxonomic composition of polymicrobial samples

The paper evaluates metagenomic, 16S rRNA gene, and ultra-plexed PCR-based sequencing methods for taxonomic and AMR gene profiling in polymicrobial samples, finding that AmpliSeq and shotgun metagenomics perform best for resistome profiling.

Flanker: a tool for comparative genomics of gene flanking regions

Flanker clusters gene flanking sequences to identify mobile genetic element patterns associated with antimicrobial resistance genes.

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies

This study optimizes Oxford Nanopore Flowcell usage for hybrid assemblies by reducing sequencing time and cost through washing steps, enabling more isolates per flowcell.

Genomic network analysis of an environmental and livestock IncF plasmid population

The paper analyzes IncF plasmid diversity across environmental and livestock settings using network community analysis, revealing niche-driven partitioning and core gene-defined communities.

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

The paper develops a metagenomic metric to predict antibiotic resistance in Enterobacterales infections using pooled human faecal samples from LMICs and high-income settings.

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

This study evaluates SNP calling pipelines' performance on bacterial data, finding that reference genome selection strongly impacts accuracy, with Snippy performing consistently well across diverse genomes.

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

This study analyzes the genomic epidemiology of a blaKPC carbapenemase outbreak in Enterobacterales in the UK, revealing genetic plasticity and plasmid dynamics across multiple species and lineages.

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

This study compares hybrid assemblies of bacterial genomes using Illumina and long-read sequencing technologies, finding that combining ONT and Illumina reads provides high-quality, low-cost genome reconstruction.

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

The paper tracks K. quasipneumoniae's acquisition of carbapenemase plasmids and environmental persistence in a hospital setting over multiple years.

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

TETyper classifies transposable element variation and genetic contexts from whole-genome sequencing data, revealing high transposition diversity in KPC-associated Tn4401.

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

Bayesian Reconstruction of Transmission within Outbreaks using Genomic Variants

This paper introduces BadTrIP, a Bayesian method to infer host-to-host transmission using genomic variants and epidemiological data, showing improved accuracy over existing approaches.

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

This study investigates the genomic spread of KPC-producing E. coli globally using whole genome sequencing, revealing diverse plasmid and mobile genetic element associations.

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

The paper reports a significant increase in mcr-1-positive multi-drug resistant Enterobacteriaceae in human faecal samples in China, associated with diverse plasmid families and chromosomal integration.

Nested Russian Doll-like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC

This paper tracks the rapid spread of the blaKPC resistance gene in a hospital over five years, revealing nested genetic mobility mechanisms that enable dissemination across species and plasmids.