Publications by authors named "N Stoesser"
Mobile genetic elements are key to the global emergence of antibiotic resistance. We successfully reconstructed the complete bacterial genome and plasmid assemblies of isolates sharing the same carbapenemase gene to understand evolution over time in six confined hospital drains over five years. From 82 isolates we identified 14 unique strains from 10 species with 113 carrying plasmids across 16 distinct replicon types.
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- Antimicrobial resistance (AMR) gene cassettes are genetic segments that can be captured and rearranged by integrons, allowing organisms to adapt to antibiotic pressures, and these integrons exist in both chromosomes and plasmids.
- This study focuses on a specific AMR gene, linked to a class A carbapenemase first detected in Greece, to analyze global patterns of integron diversity using a novel pangenome graph-based method.
- Findings reveal chromosomal integrons are more consistent and conserved in structure, mainly found in a specific strain (ST235), while plasmid-associated integrons display more variability, suggesting that plasmids may facilitate more dynamic genetic recombination.
Article Synopsis
- Whole-transcriptome RNA sequencing using Oxford Nanopore Technologies shows potential for analyzing gene expression in pathogenic bacteria, including antimicrobial resistance genes.
- The study assessed the direct cDNA and PCR-cDNA sequencing kits by analyzing four bacterial isolates from bloodstream infections, utilizing various techniques to minimize bias.
- Results indicated that the PCR-cDNA kit provided higher yield, but users should be cautious of potential bias in genes with very high or low GC content.
Interpreting the phenotypes of alleles in genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal alleles or additional plasmid-borne alleles that have extended-spectrum β-lactamase (ESBL) activity and/or β-lactamase inhibitor (BLI) resistance activity. In addition, the role of individual mutations/a changes is not completely documented or understood.
View Article and Find Full Text PDFBackground: Antimicrobial resistance (AMR) in Escherichia coli is a global problem associated with substantial morbidity and mortality. AMR-associated genes are typically annotated based on similarity to variants in a curated reference database, with the implicit assumption that uncatalogued genetic variation within these is phenotypically unimportant. In this study, we evaluated the performance of the AMRFinder tool and, subsequently, the potential for discovering new AMR-associated gene families and characterising variation within existing ones to improve genotype-to-susceptibility phenotype predictions in E coli.
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