Nicole E Stoesser

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

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

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

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

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.

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

This paper evaluates the accuracy of bacterial genome reconstruction using Oxford Nanopore R10.4.1 long-read-only sequencing and finds it produces accurate assemblies at 40x depth, competitive with hybrid Illumina-Nanopore assemblies.

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.

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.

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.

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.

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

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

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

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

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.

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.

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.

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

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

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.

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

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.

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.