Stephanie W. Lo

Identifying candidate genetic determinants associated with invasion in pneumococcal lineages

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

ALLCAPS: a scalable and accurate deep-learning method for in silico pneumococcal serotyping

ALLCAPS is a deep-learning tool for in silico pneumococcal serotyping that outperforms existing methods and identifies novel serotypes.

PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search

PDBe-SIFTS improves residue-level sequence-structure mapping with faster search, better scoring, and accurate alignment, comparable to expert curation.

The global evolutionary dynamics of natural capsule switching in a human-restricted bacterial pathogen

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.

A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions

The paper develops a mathematical model to predict vaccine replacement dynamics in Streptococcus pneumoniae and identifies optimal genomic surveillance strategies.

Niche-specific contribution of the branched-chain amino acid biosynthesis protein IlvD in Streptococcus pneumoniae infection

This study identifies mutations in ilvD, encoding a BCAA biosynthesis protein, as beneficial for pneumococcal survival in blood but detrimental for nasopharyngeal colonization.

Quantifying the mechanisms of vaccine-induced serotype replacement in Streptococcus pneumoniae using genome-informed modelling

The paper quantifies how serotype replacement in Streptococcus pneumoniae is driven by shifts in serotypes within persistent lineages rather than lineage replacement, using genome-informed modeling and longitudinal data.

Global population structure and phase variation of serotype 12F Streptococcus pneumoniae following the introduction of pneumococcal conjugate vaccine

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.

The capsule and genetic background, rather than specific individual loci, strongly influence in vitro pneumococcal growth kinetics

This study shows that pneumococcal growth kinetics are influenced by capsular serotype, lineage, and genetic background rather than specific loci.

SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae

This paper introduces SeroBA(v2.0), a tool for pneumococcal serotyping, and SeroBAnk, a resource for capsular diversity, which accurately identifies 102 serotypes and supports community contributions for updates.

A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline

The paper introduces GPS Pipeline, a scalable and portable genomic analysis tool for Streptococcus pneumoniae, enabling public health outputs with minimal expertise.

Streptococcus pneumoniae vaccine serotype persistence following 13-valent pneumococcal conjugate vaccine introduction in Mongolia: investigating changes in epidemiology, immunology and virulence

The paper examines persistence of vaccine serotypes of Streptococcus pneumoniae in Mongolia after PCV13 introduction, finding changes in lineage composition, virulence, and drug resistance.

Mapping the Phenotypic Landscape of Beta-lactam Resistance in Streptococcus pneumoniae

The paper develops a framework to analyze multivariate beta-lactam resistance in Streptococcus pneumoniae using MIC data from 3,628 isolates, revealing genetic mutations and lineage-specific resistance profiles.

Comparison of gene-by-gene and genome-wide short nucleotide sequence based approaches to define the global population structure of Streptococcus pneumoniae

This paper compares four clustering methods for S. pneumoniae genomes to assess their accuracy in reflecting population structure and highlights the need for standardized nomenclature.

Evidence of virulence and antimicrobial resistance in Streptococcus pneumoniae serotype 16F lineages

This study characterizes serotype 16F Streptococcus pneumoniae lineages and antimicrobial resistance in South African infants and globally, finding associations with disease and resistance.

The role of interspecies recombinations in the evolution of antibiotic resistant pneumococci

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.

Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline

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.

Fast and flexible bacterial genomic epidemiology with PopPUNK

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.