Microbial Genomics

HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1

Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP

Genomic epidemiology of severe community-onset Acinetobacter baumannii infection

PANINI: Pangenome Neighbour Identification for Bacterial Populations

Genomic analysis of bacteria in the Acute Oak Decline pathobiome

Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria

Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny

An analysis of the IS6/IS26 family of insertion sequences: is it a single family?

EvoMining reveals the origin and fate of natural product biosynthetic enzymes

Domestication of Campylobacter jejuni NCTC 11168

Clonal ST131-H22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids

Assessing the impact, genomics and evolution of type II secretion across a large, medically important genus: the Legionella type II secretion paradigm

Genomics of vancomycin-resistant Enterococcus faecium

Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13

Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia

Genetic affinities of an eradicated European Plasmodium falciparum strain

Using genomics to understand antimicrobial resistance and transmission in Neisseria gonorrhoeae

Quantitative real-time PCR assay for the rapid identification of the intrinsically multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia

Sucrose 6F-phosphate phosphorylase: a novel insight in the human gut microbiome

Phylogenomic analysis of gastroenteritis-associated Clostridium perfringens in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids

O-antigen biosynthesis gene clusters of Escherichia albertii: their diversity and similarity to Escherichia coli gene clusters and the development of an O-genotyping method

Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature

Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame

Endemic fluoroquinolone-resistant Salmonella enterica serovar Kentucky ST198 in northern India

Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group

Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds.

Genome-wide assessment of antimicrobial tolerance in Yersinia pseudotuberculosis under ciprofloxacin stress

A cluster of melioidosis infections in hatchling saltwater crocodiles (Crocodylus porosus) resolved using genome-wide comparison of a common north Australian strain of Burkholderia pseudomallei

Whole-genome sequencing of dog-specific assemblages C and D of Giardia duodenalis from single and pooled cysts indicates host-associated genes

Insertion sequences drive the emergence of a highly adapted human pathogen

Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges

Molecular characterization of respiratory syncytial viruses circulating in a paediatric cohort in Amman, Jordan.

Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni

An in silico survey of Clostridioides difficile extrachromosomal elements\u2009\u2009\u2009

Genomic analysis of carbapenemase-producing Enterobacteriaceae in Queensland reveals widespread transmission of bla IMP-4 on an IncHI2 plasmid

Gauging the epidemic potential of a widely circulating non-invasive meningococcal strain in Africa

In praise of preprints

Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids

Next-generation sequencing of dsRNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO

Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12.

Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics

Genomic differences among carriage and invasive nontypeable pneumococci circulating in South Africa