Using rapid genomics to contain a dangerous hospital outbreak

Researchers at the BRC: Birmingham used rapid DNA sequencing to identify, track and help contain a hospital outbreak of a highly virulent, antibiotic-resistant strain of Klebsiella pneumoniae (hv-CRKP), improving infection control and protecting vulnerable patients.

The challenge

The emergence of hypervirulent, carbapenem-resistant Klebsiella pneumoniae represents a major threat to patient safety. These strains combine high virulence with antibiotic resistance, severely limiting treatment options and increasing the risk of hospital transmission.

In spring 2024, a major regional hospital identified hv-CRKP on a vascular ward, raising concerns about a potential outbreak affecting vulnerable patients. Conventional laboratory methods alone couldn’t rapidly determine whether cases were linked or identify the hypervirulent nature of the strain to guide infection prevention and control (IPC) responses.  

Using genomics to guide action

BRC: Birmingham researchers utilised genomics to guide the IPC measures to control the outbreak. The team deployed real-time Oxford Nanopore sequencing through a collaborative surveillance programme, enabling genomic characterisation of the outbreak strain.

Revealing how the outbreak spread

Sequencing identified the first known UK outbreak of a highly virulent, carbapenem-resistant Klebsiella pneumoniae ST395 strain. Twelve patients were found to be carrying or infected with the bacterium, and 36% had died within six months. Genomic analysis showed that the bacterial samples were very closely related, confirming that transmission had occurred between patients on the vascular ward.

Targeting infection control measures

Importantly, sequencing data directly informed IPC interventions, including targeted ward closure, enhanced environmental cleaning, replacement of toilets and mattresses, sink trap decontamination and intensified screening.   

Uncovering hidden environmental reservoirs

Subsequent investigations showed that hospital plumbing/sinks can act as reservoirs and dissemination points for AMR organisms. Sampling of sink splash zones identified Gram-negative pathogens, including strains carrying resistance plasmids previously associated with patient infections.  

Impact for patients and the NHS

The work demonstrated the real-world value of rapid genomic surveillance in outbreak management. Sequencing enabled earlier identification and precise targeting of IPC measures, helping stop further transmission. This approach strengthened collaboration between microbiology, IPC teams and hospital management, while highlighting the potential for genomics to improve NHS outbreak response capability. This also strengthens the UK’s position in genomic medicine and pathogen surveillance, by demonstrating practical implementation of rapid long-read sequencing in routine healthcare settings.