Samuel Lipworth

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

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.

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.

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.

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.