Mobile DNA as epidemiological engines: lessons from New Zealand

Antimicrobial resistance (AMR) is often framed in terms of the spread of successful bacterial clones. Many clinically important AMR and persistence events, however, are encoded on mobile genetic elements (MGEs) that disseminate across otherwise unrelated bacterial lineages. Many genomic surveillance frameworks define epidemiological relatedness using chromosomal metrics (e.g. single-nucleotide variant- or core-genome multilocus sequence typing-based clustering) and AMR phenotypes, with MGEs typically treated as secondary annotations rather than primary units of analysis. Here, nanopore whole-genome sequencing data from surveillance-linked datasets in New Zealand was explored to examine how MGEs can function as epidemiologically informative units. Leveraging a setting characterised by low background AMR, integrated genomic surveillance for selected high-priority pathogens, and focused nanopore sequencing capacity, three case studies span within-host evolution, ward-level transmission, and long-term lineage success. Genomic analysis identifies: (i) within-host chromosomal integration of a vanB-carrying conjugative transposon in Enterococcus faecium, temporally associated with vancomycin non-susceptibility without strain replacement; (ii) neonatal intensive care unit transmission of Klebsiella variicola associated with an outbreak-specific F-type plasmid encoding toxin-antitoxin, metal-tolerance, and conjugation-associated loci but lacking clinically alarming AMR; and (iii) decades-long persistence of an endemic New Zealand community-associated methicillin-resistant Staphylococcus aureus ‘AK3’ lineage, characterised by stepwise MGE acquisition. These examples illustrate the clinical benefits of resolving MGEs as complete genetic entities using nanopore sequencing, which can reveal epidemiologically relevant signals that may not be captured by chromosome-centred or phenotype-triggered surveillance approaches.