L. P. Shaw

Adaptation of Pseudomonas aeruginosa to repeated invasion into a commensal competitor

This study examines how Pseudomonas aeruginosa adapts to repeated invasion of Staphylococcus epidermidis, showing divergent evolutionary responses between monoculture and coculture conditions.

Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria

This study shows plasmids avoid restriction-modification system targets, with smaller plasmids adapting via sequence composition and larger ones via protective genes.

Pre-existing chromosomal polymorphisms in pathogenic E. coli potentiate the evolution of antibiotic resistance by MCR-1 plasmid acquisition

The paper shows pre-existing lpxC polymorphisms in E. coli enhance the evolution of colistin resistance via MCR-1 plasmid acquisition through positive epistasis.

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

The paper analyzes the pangenome dynamics of Enterobacteriaceae from environmental sources, finding that plasmids carry more AMR genes and are influenced by niche and geography rather than phylogeny.

Role of the mobilome in the global dissemination of the carbapenem resistance gene blaNDM

This study tracks the global spread of the carbapenem resistance gene blaNDM by analyzing genomic contexts and mobile genetic elements across 6000 bacterial genomes.

Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399

The paper investigates a hospital outbreak of carbapenem-resistant Enterobacteriales, identifying an OXA-48 plasmid in E. coli ST399 as the main driver, with evidence of plasmid conjugation and clonal expansion.

The phylogenetic range of bacterial and viral pathogens of vertebrates

The paper compiles a large host-pathogen association database and analyzes factors influencing host range and zoonotic potential across bacteria and viruses.

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study

This study evaluates the reproducibility of antimicrobial resistance predictions from whole-genome sequencing data across different laboratories and identifies factors contributing to discordant results.

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

This study evaluates how sequencing depth affects taxonomic composition and AMR gene detection in metagenomic samples, finding that higher depth is needed for AMR gene richness.

Modelling microbiome recovery after antibiotics using a stability landscape framework

The paper develops a quantitative stability landscape model to analyze microbiome recovery after antibiotics and finds support for long-term state transitions in gut and salivary microbiomes after ciprofloxacin and clindamycin.

Children with cystic fibrosis are infected with multiple subpopulations of Mycobacterium abscessus with different antimicrobial resistance profiles

This study finds that children with cystic fibrosis have multiple subpopulations of Mycobacterium abscessus with different antimicrobial resistance profiles, not all captured by sputum isolates.