Rebecca A. Gladstone

The paper identifies invasion-associated genetic variants in pneumococcal lineages by separating serotype and lineage effects, highlighting candidate determinants for experimental investigation.

This study examines capsule switching in Streptococcus pneumoniae using whole-genome sequences, finding that switching is limited to specific capsule-type pairs and influenced by genetic and ecological factors.

This study traces the evolutionary path from ST131-B to ST131-C clades in E. coli by analyzing genomic data from ST131-B0 isolates, revealing genetic changes associated with antibiotic resistance and host adaptation.

The paper identifies antibiotic resistance determinants in oral streptococci using genomic data, revealing high variability and gene exchange, particularly involving tetracycline and macrolide resistance.

This study characterizes the global population structure and genetic diversity of serotype 12F Streptococcus pneumoniae, identifying strand-slippage mutations as a mechanism for capsule variation and vaccine evasion.

This paper uses machine learning to predict the prevalence of ST131-C in UTIs and BSIs using antimicrobial susceptibility data, finding a link between UTI prevalence and BSI burden.

The paper investigates the evolutionary dynamics of colibactin production and resistance in E. coli, showing clonal expansions linked to co-evolution between production and immunity.

The paper estimates the basic reproduction number (R0) for pandemic E. coli clones and finds that ST131-A has an R0 comparable to pandemic influenza viruses.

This study analyzes antibiotic resistance patterns in Streptococcus pneumoniae using global whole-genome sequencing data, identifying trends in multi-drug resistance and serotype distribution.

The paper uses long-read sequencing to analyze plasmids and chromosomes in E. coli over two decades, revealing long-term plasmid-lineage associations and success strategies.

PAN-GWES identifies co-selected and epistatic genomic variations in bacterial genomes using de Bruijn graphs to analyze drug resistance and adaptation traits.

The paper introduces LDWeaver, a method to detect co-selection in bacterial genomes by analyzing both short- and long-range linkage disequilibrium, and validates findings using functional annotation and phenotypic measurements.

The paper introduces a computational pipeline for consistent plasmid typing using long-read sequencing data, enabling classification of novel and known plasmid types.

The paper reconstructs the evolutionary histories of antibiotic-resistant pneumococcal lineages PMEN3 and PMEN9, showing how interspecies recombination contributes to antibiotic resistance and serotype switching.

Panaroo's graph-based pangenome clustering uses gene adjacency across genomes to correct annotation errors, shrinking spurious accessory genomes and enlarging core genomes in simulated and real bacteria.

The paper uses genome-wide association studies to show human and pneumococcal genetic variation influences susceptibility and severity of pneumococcal meningitis.

This paper analyzes pneumococcal carriage genomic data before and after PCV13 introduction, showing reduced vaccine-type strains and limited serotype replacement.

PopPUNK provides fast, scalable clustering of bacterial genomes using k-mer analysis, enabling real-time outbreak detection and stable cluster naming across species and datasets.

SeroBA predicts Streptococcus pneumoniae serotypes from whole genome sequencing data with high concordance and scalability.