Kathryn E. Holt

This study surveys genomic surveillance practices in African labs, finding sufficient capacity but highlighting needs for improved infrastructure and standardization.

A curated Kaptive-compatible database of 88 capsule (K) loci types 97.6% of dereplicated Klebsiella oxytoca species complex genomes, versus 50.3% typed with the existing K. pneumoniae database.

The paper proposes the Life Identification Number (LIN) system as a stable, multilevel strain taxonomy for bacterial pathogens based on core genome MLST to improve epidemiological tracking and nomenclature consistency.

The paper analyzes bacterial diversity and strain dynamics in the infant respiratory microbiome using whole genome sequencing and metagenomics, revealing age-dependent shifts in dominant taxa and expanding reference genomes for airway microbes.

AMRgen is an R package that links antimicrobial resistance genotypes to phenotypes through data harmonization, analysis, and visualization, using surveillance data from priority pathogens.

This study identifies prophage-encoded receptor-binding proteins (RBPs) mediating capsule specificity in Klebsiella pneumoniae, revealing structural diversity and functional activity beyond classical depolymerases.

Verticall detects recombination in bacterial genomic datasets, outperforming existing tools on large and diverse datasets.

Flex-It is a genotyping framework for S. flexneri that rapidly characterizes genotypes and resistance determinants from sequencing data, enabling standardized surveillance of its population structure and antimicrobial resistance.

This study uses metagenomic sequencing to analyze Klebsiella pneumoniae from lung biopsies of Zambian children, identifying genetic sublineages, antimicrobial resistance, and potential vaccine targets.

This study uses whole-genome sequencing to characterize a multidrug-resistant Klebsiella pneumoniae outbreak in a Gambian hospital, identifying the outbreak strain and its environmental sources.

This study maps metabolic diversity in Klebsiella pneumoniae sub-lineages using genomics and metabolic modeling, revealing lineage-specific metabolic profiles that support coexistence through cross-feeding.

This study investigates whether the rmpADC operon alone can increase virulence in classical Klebsiella pneumoniae strains, finding that HMV is necessary but not sufficient for hypervirulence.

This study uses whole-genome sequencing of Vibrio cholerae isolates from Africa to assess genomic diversity and antimicrobial resistance, highlighting the utility of WGS for enhanced surveillance.

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

This study identifies enhanced virulence and stress tolerance as factors contributing to the epidemiological success of Shigella sonnei, using zebrafish models and genomic analysis.

This study identifies simple sequence repeats in rmpA and rmpD/rmpC genes that mediate phase variation of the mucoid phenotype in hypervirulent Klebsiella pneumoniae, enabling adaptation to different infection niches.

The paper investigates the relationship between insertion sequences (IS) and metabolic capacity in four Klebsiella pneumoniae sub-lineages, finding higher IS loads correlate with reduced metabolic gene numbers and substrate utilisation.

Kaptive v3 improves antigen typing accuracy and speed for KpSC genomes by addressing assembly fragmentation issues, enabling efficient in silico serotyping.

The paper introduces TyphiNET, a dashboard for exploring Typhi genomics data to support public health decisions on antimicrobial resistance and vaccine implementation.

This study analyzes KpSC populations across human, animal, and marine sources in Norway, showing distinct yet overlapping populations with limited recent transmission between niches.

EnviroAmpDesigner designs multiplex PCR primer panels for detecting and subtyping specific bacteria in environmental samples, focusing on specificity and minimizing off-target amplification.

The study tracks genomic changes in wMel Wolbachia over six years in three Aedes aegypti populations and finds minimal evolution, supporting its stability as a biocontrol agent.

The paper provides 15 genomically characterized Shigella sonnei isolates representing diverse sub-clades, with complete genome sequences and public availability for research.

AmpliconTyper is a tool for analysing ONT multiplex amplicon sequencing data from environmental samples, using machine learning to classify reads and identify SNPs.

This paper demonstrates that CRISPR-Cas9 enrichment combined with Oxford Nanopore sequencing improves detection of AMR genes and MLST in patient samples compared to unenriched sequencing.

The paper identifies hidden metabolic mutations in Klebsiella pneumoniae cultures grown in rich media, showing how these mutations can persist undetected and affect auxotrophy.

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

The paper updates the EnteroBase platform with new data and tools for genomic epidemiology of bacterial pathogens, including antimicrobial resistance detection and visualization features.

The paper analyzes the genetic diversity and functionality of rmpADC variants in Klebsiella pneumoniae to understand their role in virulence and antimicrobial resistance.

This study sequenced K. pneumoniae isolates from Southern Ghana, identifying genetic diversity, antimicrobial resistance, and virulence traits, highlighting the need for genomic surveillance.