N. Stoesser

Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing

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.

A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing

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.

Identification of a novel MCR-1 variant displaying low level of co-resistance to β-lactam antibiotics that uncovers a potential novel antimicrobial peptide

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.

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli

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.

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.

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm

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

Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

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

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.

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

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

Dynamics of mcr-1 prevalence and mcr-1-positive Escherichia coli after the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing based molecular epidemiological study

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.

The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates

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.

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.

Klebsiella quasipneumonaiae provides a window into carbapenemase gene transfer, plasmid rearrangements and nosocomial acquisition from the hospital environment

The paper tracks K. quasipneumoniae's acquisition of carbapenemase plasmids and environmental persistence in a hospital setting over multiple years.

A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078

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.

Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia

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.