Patrick N. A. Harris

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

Disruption of cAMP Signalling and RNA Regulation Confers Cefiderocol Resistance in Acinetobacter baumannii

This study identifies two mechanisms of cefiderocol resistance in Acinetobacter baumannii: cAMP signalling disruption and Hfq RNA-binding domain truncation, both linked to iron homeostasis and reduced drug activity.

Cross-species convergence of surface polysaccharides shapes the virulence of an atypical carbapenem resistant uropathogenic Escherichia coli clone

The paper identifies a new carbapenem-resistant E. coli clone, ST361, associated with UTI and shows its virulence is linked to surface polysaccharides and mobile genetic elements.

OXA-181 transmission confounded by a stable IncX3 plasmid

This study analyzes the spread of blaOXA-181-producing bacteria in Australia, finding that the IncX3 plasmid is highly stable with minimal genetic variation, suggesting that genomic similarity does not necessarily indicate recent transmission.

Profiling of Burkholderia pseudomallei variants derived from Queensland clinical isolates

The paper profiles Burkholderia pseudomallei variants from clinical isolates to understand colony morphotype variation (CMV) using proteomics and genomics, finding that CMV is driven by regulatory mechanisms rather than genomic mutations.

Co-isolation of genetically distinct Burkholderia pseudomallei strains from a single patient in North Queensland

The paper identifies two genetically distinct Burkholderia pseudomallei strains co-isolated from a single patient and presents their multi-omics characterization.

A simplified, amplicon-based method for whole genome sequencing of human respiratory syncytial viruses

The paper develops a simplified amplicon-based method for whole genome sequencing of RSV viruses, achieving high success rates and coverage with reduced cost and time.

Systematic benchmarking of all-in-one microbial SNP calling pipelines

This paper benchmarks six microbial SNP calling pipelines using multiple datasets, highlighting the variability in performance and the need for standardized benchmarking.

MicroPIPE: An end-to-end solution for high-quality complete bacterial genome construction

MicroPIPE constructs high-quality bacterial genomes using ONT and Illumina sequencing with an automated pipeline.

Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei

The paper uses three whole genome sequencing technologies to analyze a carbapenemase-producing Enterobacter hormaechei outbreak, identifying transmission dynamics and plasmid context.