Stephen D. Bentley

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

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

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.

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

This paper trains species-specific transformer models for bacterial genomic surveillance, showing they can cluster genomes, identify emerging lineages, and predict antibiotic resistance gene uptake.

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 study sequenced 4,475 H. influenzae isolates from Thailand and combined them with global data to show pervasive recombination and purifying selection, with MDR lineages widespread and not restricted to disease-causing subpopulations.

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

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.

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

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

The paper uses Hi-C and Pore-C sequencing to compare chromosomal conformation in pneumococcal variants, finding that episomal elements drive differential contact patterns through stochastic replication and excision.

This study characterizes the genomic features of Group B Streptococcus isolates from Argentina, revealing prophage diversity, virulence factors, and antibiotic resistance genes across different clinical sources.

This study quantifies how antibiotic resistance and within-host competition affect pneumococcal strain fitness using longitudinal carriage data.

This paper improves prophage typing for GBS by integrating phylogenetic analysis and integrase typing, identifying 29 prophage types in 615 GBS genomes, including 2 novel integrase subtypes.

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.

TRACS improves transmission inference by accurately estimating SNP-level genetic distances, outperforming existing methods in multiple datasets and revealing species-specific transmission rates between mothers and infants.

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 characterizes multidrug-resistant and ESBL-producing E. coli and K. pneumoniae in maternal and neonatal colonization in a Cameroonian labour ward, finding high prevalence of MDR isolates and blaCTX-M gene.

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

The paper identifies three accessory gene clusters driving host adaptation in Group B Streptococcus across different hosts.

The paper examines changes in bacteriocin prevalence and diversity in pneumococci from Iceland and Kenya before and after vaccine introduction, showing vaccine-induced shifts in bacterial population structure.

This study uses deep sequencing to analyze pneumococcal genetic diversity in infants and mothers, revealing transmission patterns and treatment impacts on resistant strains.

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.

This study traces the evolutionary divergence of Neisseria gonorrhoeae by analyzing global isolates, linking antimicrobial use to the emergence of two distinct lineages with different resistance strategies.

This paper introduces SpydrPick, a model-free method to detect co-selection and epistasis in bacterial genomes, revealing both known and novel targets in human pathogens.

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.

fastbaps provides a fast Bayesian clustering method for genetic data, outperforming existing methods in speed while maintaining comparable accuracy on real and simulated datasets.