L. P. Shaw

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

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

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.

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

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

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

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.

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.

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.