Klebsiella pneumoniae genomes
75 sequence types. No evidence of patient-to-patient transmission in a 15-month hospital surveillance study.
Microbial Genomics →Microbial genomics · Aotearoa New Zealand
From genome sequence to defensible action.
I use bacterial genomics to resolve transmission, determine how antimicrobial resistance is moving, and define what the evidence supports.
Chromosome + mobile DNA + phylogenyDistinguish clonal transmission from mobile resistance.
mcr-bearing plasmids
Global plasmid context used to resolve how mobile colistin resistance reached and persisted in New Zealand.
IJAA →MRSA genomes
Two decades of AK3 evolution reconstructed alongside the mobile elements acquired and lost through time.
Microbial Genomics →Research
Four connected problems: transmission, mobile resistance, bacterial evolution, and the methods used to infer them.
01 · Transmission
Outbreak or coincidence?
High-resolution genomes can confirm transmission, rule it out, or expose a reservoir routine surveillance did not see.
Genomic surveillance →02 · AMR
Clone or mobile element?
Plasmids and other mobile elements can move resistance across bacterial backgrounds that look unrelated on the chromosome.
Mobile resistance →03 · Evolution
Which changes define the lineage?
Phylogenomics connects bacterial relationships to the genomic changes that accompany emergence, persistence and expansion.
Phylogenomics →04 · Methods
Can the inference be checked?
Focused software makes fragile analytical steps explicit, reproducible and testable.
Research software →Selected studies
Results that changed the interpretation of transmission, resistance or bacterial evolution.
2025
A neonatal outbreak hidden behind wild-type susceptibility
Rapid local sequencing identified Klebsiella variicola, linked four neonatal cases, and placed sink isolates in the same genomic cluster.
Read the study →2025
OXA-48 dissemination at more than one genomic level
Chromosome, plasmid backbone and resistance gene context were analysed together to reconstruct a carbapenem-resistant E. coli ST131 outbreak.
Read the study →2024
Geography inside a pandemic E. coli lineage
Genomic epidemiology revealed geographical clustering within multidrug-resistant ST131 associated with bacteraemia in Wales.
Read the study →2026
Plasmid reservoirs inside a hospital
Nanopore sequencing resolved plasmid-encoded carbapenem resistance dynamics and linked resistance to its genomic reservoirs.
Read the study →Released · Bioconda
NEXCISION
Precise excision of coordinate-labelled genomic sites from transposed NEXUS matrices, with deterministic provenance and SHA-256 checksums.
Bioconda downloads
GitHub stars
OpenAlex citations
# remove reference-defined regions $ nexcise input.nex regions.tsv \ --output filtered.nex \ --report report.json # deterministic output # checksums + counts + warnings
Collaborate
Transmission. AMR. Mobile DNA. Genomic implementation.
I work across clinical microbiology, infection prevention, reference laboratories, bioinformatics and public-health surveillance.
Current interests: outbreak reconstruction · complete bacterial genomes · nanopore sequencing · phylogenomics · reproducible methods.