N. Stoesser

This paper evaluates the accuracy of bacterial genome reconstruction using Oxford Nanopore R10.4.1 long-read-only sequencing and finds it produces accurate assemblies at 40x depth, competitive with hybrid Illumina-Nanopore assemblies.

The paper validates a workflow for detecting antibiotic residues and measuring water chemistry in hospital sink samples, and confirms boric acid preserves microbial and resistome composition for metagenomic sequencing.

The paper identifies a novel MCR-1 variant with low β-lactam co-resistance and shows synthetic peptides from this variant have broad-spectrum antimicrobial activity.

This study evaluates four AMR gene typing methods using simulated and real E. coli data, revealing significant discrepancies and highlighting issues with current bioinformatic approaches.

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 shows that replacing contaminated sink drains with new plumbing increases antimicrobial resistance genes and Enterobacterales abundance due to disrupted biofilms.

The paper shows hospital sink drains are colonized by diverse E. coli and Klebsiella strains, including resistant ones, and may contribute to patient infections.

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.

This study shows that amoxicillin-clavulanate resistance in E. coli is quantitative, not binary, and that WGS-based predictions outperform traditional phenotyping methods.

This study tracks the decline of mcr-1 prevalence and genetic changes in mcr-1-positive Escherichia coli after China banned colistin use in animal feed.

This study evaluates fosfomycin susceptibility testing in KPC-producing Klebsiella pneumoniae isolates and finds that fosA gene presence affects test accuracy, with sodium phosphonoformate improving 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 investigates the evolutionary history of Clostridium difficile RT078, finding that tetracycline resistance genes, particularly tetM, were acquired independently in multiple clonal expansions, contributing to its increased prevalence.

The paper investigates ESC-R-EC and ESC-R-KP colonization in Cambodian children, identifies risk factors, and characterizes resistance gene diversity and genetic contexts.