Antimicrobial resistance in livestock is not a future concern. It is a present one, and the UK Animal and Plant Health Agency is tracking it through whole genome sequencing of pathogenic bacteria from diseased animals submitted through the national scanning surveillance programme.

A study published in Frontiers in Microbiology in October 2025, led by Samuel Connelly and colleagues at the APHA, characterised the genomes of 208 pathogenic Escherichia coli isolated from pigs diagnosed with enteric colibacillosis, bowel oedema, and colisepticaemia in England between 2016 and 2020. Sixty-two percent of isolates were multidrug resistant. Two high-risk sequence types, ST90 and ST772, were identified as uniquely associated with diseased juvenile pigs and not previously reported in UK herds.

To understand how resistance genes are being carried and shared between strains, the researchers performed long-read sequencing on a subset of isolates. The PDQeX nucleic acid extractor was the method used for that extraction step. Long-read sequencing demands high-molecular-weight DNA with minimal fragmentation. It is a more exacting requirement than short-read Illumina sequencing, and the sample preparation for it reflects that.

The plasmid analysis that resulted showed MDR plasmids carrying not just antibiotic resistance genes, but also metal and disinfectant resistance genes co-located on the same mobile elements. The question of whether co-location of these resistance genes on the same plasmid might provide a selective advantage is one the authors flag as requiring further investigation.

This is the kind of genomic epidemiology work that underpins the evidence base for antibiotic stewardship in farming. We are glad the extraction step was not the bottleneck.