K. E. Holt

Life Identification Numbers: A bacterial strain nomenclature approach

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.

Shigella serotypes associated with carriage in humans establish persistent infection in zebrafish

This paper shows that three Shigella serotypes associated with MSM transmission can establish persistent infection in zebrafish, failing to promote macrophage cell death.

Within-patient and global evolutionary dynamics of Klebsiella pneumoniae ST17

This study investigates the within-host evolution and global spread of Klebsiella pneumoniae ST17, finding limited within-host genetic change and identifying its role in multidrug-resistant hospital infections.

Detection and typing of plasmids in Acinetobacter baumannii using rep genes encoding replication initiation proteins

This paper develops a plasmid typing system for Acinetobacter baumannii using rep genes, identifying 80 distinct types and establishing a database for plasmid classification and detection.

Linear plasmids in Klebsiella and other Enterobacteriaceae

This study identifies and characterizes linear plasmids in Klebsiella pneumoniae and other Enterobacteriaceae, revealing their phylogenetic diversity and potential for horizontal transfer.

Transmission of Klebsiella strains and plasmids within and between Grey-headed flying fox colonies

This study identifies transmission clusters and plasmid exchange among Klebsiella strains in Grey-headed flying foxes, showing gene flow between bat and human-associated isolates.

A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

The paper curates 37 strain-specific genome-scale metabolic models for Klebsiella pneumoniae species complex isolates, revealing strain-specific metabolic differences and gene essentiality.

Novel strains of Klebsiella africana and Klebsiella pneumoniae in Australian Fruit Bats (Pteropus poliocephalus)

This study identifies novel Klebsiella africana and Klebsiella pneumoniae strains in Australian fruit bats, finding low antimicrobial resistance and no hypervirulent or MDR strains.

Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae

The paper identifies hidden transmission of a carbapenemase-producing Klebsiella pneumoniae strain using genomic and metagenomic data from multiple studies.

Five years of GenoTyphi: updates to the global Salmonella Typhi genotyping framework

The paper updates the GenoTyphi framework using 4,632 whole genome sequences, revealing the widespread H58 genotypes and diverse AMR-carrying genotypes in Salmonella Typhi.

Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya

The study investigates typhoid dynamics in Kenya, finding high multidrug-resistant H58 S. Typhi prevalence in both cases and controls, suggesting carriers contribute to community spread.

Detection of plasmid contigs in draft genome assemblies using customized Kraken databases

This paper introduces a method using Kraken with a custom database to detect plasmid contigs in bacterial genome assemblies, showing improved performance over existing tools.

Genomic diversity and antimicrobial resistance of Haemophilus colonising the airways of young children with cystic fibrosis

This study examines Haemophilus colonization and antimicrobial resistance in children with cystic fibrosis, finding high prevalence and diverse AMR mechanisms.

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

The paper develops a genomic framework and genotyping scheme for Shigella sonnei to identify resistance determinants from WGS data, revealing common genotypes linked to antimicrobial resistance and global spread.

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

This study identifies novel marine bacteria capable of mercury methylation, revealing their broader habitat range and oxygen tolerance.

Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs

This paper identifies microorganisms involved in mercury cycling in geothermal springs using metagenomics and geochemical analysis, revealing new insights into microbial mercury speciation and biogeochemical processes.

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

The paper investigates the diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales using comparative genomics across 27,334 genomes, revealing dynamics driven by horizontal gene transfer and selective preservation.

Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive

This paper creates curated databases for Acinetobacter baumannii capsular polysaccharide and outer core loci, compatible with Kaptive, and validates their utility in typing genome assemblies.

Neonatal genetics of gene expression reveal the origins of autoimmune and allergic disease risk

The paper identifies gene expression quantitative trait loci (eQTLs) in neonatal immune cells and links them to autoimmune and allergic disease risk through colocalisation and Mendelian randomisation.

Impact of insertion sequences on convergent evolution of Shigella species

This study examines the role of insertion sequences in the convergent evolution of Shigella species, showing their contribution to gene loss and metabolic streamlining across species.

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia.

This study identifies diverse antimicrobial resistant and hypervirulent Klebsiella pneumoniae strains in South and Southeast Asia, highlighting the convergence of AMR and virulence genes.

Global phylogenomics of multidrug resistant Salmonella enterica serotype Kentucky ST198

This study uses whole-genome sequencing to analyze the global spread and antimicrobial resistance of Salmonella enterica serotype Kentucky ST198, identifying a single clonal lineage responsible for multidrug resistance.

Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers

This study uses whole-genome sequencing of Salmonella Typhi isolates from travelers to analyze genotype distribution and antimicrobial resistance patterns across regions.

Yersiniabactin, Colibactin and Wider Resistome Contribute to Enhanced Virulence and Persistence of KPC-2-Producing Klebsiella pneumoniae CG258 in South America

This study identifies yersiniabactin, colibactin, and an expanded resistome as factors contributing to the enhanced virulence and persistence of KPC-2-producing K. pneumoniae CG258 in South America.

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

The paper compares the evolutionary dynamics of horizontal gene transfer in drug-resistant and virulent Klebsiella pneumoniae clones to assess the risk of gene convergence.

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

The paper tracks the emergence and global spread of a CTX-M-15-producing K. pneumoniae strain ST307, showing it originated in the mid-1990s and is associated with a plasmid containing antimicrobial resistance genes.

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

The paper analyzes the prevalence and evolution of yersiniabactin-encoding mobile elements in Klebsiella pneumoniae using whole genome sequences, identifying diverse lineages and novel dispersal mechanisms.

Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes

Kaptive Web is an online tool for typing Klebsiella K and O loci in genome assemblies, showing extensive diversity in these loci among clinical isolates.

Drivers of antimicrobial resistance amongst intestinal Escherichia coli isolated from children in South Asia and sub-Saharan Africa

This study investigates antimicrobial resistance (AMR) in intestinal Escherichia coli from children in South Asia and sub-Saharan Africa, finding that resistance to newer drugs correlates with usage while older drug resistance persists despite lower usage.

Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital

The paper investigates K. pneumoniae carriage and infection in geriatric wards, finding that most isolates originated from patients' gut microbiomes, while ESBL strains were acquired in the referring hospital.