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Innovative hospital genomic surveillance system detects early outbreak of serious gut infection

21 May 2024

Microbial Genomics
Esr Hospital Photo
Esr Hospital Photo

A team of researchers, including from the Institute of Environmental Science and Research (ESR) and Awanui Labs Wellington, have successfully implemented a Nanopore genomic surveillance system that enabled the early detection and control of a Clostridioides difficile (C. difficile) infection outbreak in a ward of a Wellington-based hospital. The open access findings, described in the journal Infection Control & Hospital Epidemiology, highlight several novel aspects of this approach that could significantly impact future clinical practices.

By prospectively using genomic sequencing, the team was able to identify and manage the C. difficile outbreak at a relatively early stage, demonstrating the potential for such methods to improve patient outcomes and reduce the spread of infections, ultimately making the hospital a safer place for patients. C difficile is a serious bacterial infection of the colon and intestines, which mostly affects people in hospitals.

The study combined a low discrimination genomic typing method for initial identification of strains, with high-quality epidemiological data, proving effective in identifying the outbreak. This dual approach enhanced the accuracy and timeliness of the C. difficile detection.

The researchers employed a simplified bioinformatics approach to analyse sequence data and produce multilocus sequence type (MLST) results, which are used to identify pathogens by analysing the sequences of internal fragments of multiple housekeeping genes. Importantly, this method streamlined the data analysis process, making it more accessible for clinical laboratories.

In a departure from traditional methods, the team used Oxford Nanopore sequencing as their sole sequencing technique. Unlike the commonly used Illumina sequencing technologies, Nanopore sequencing is relatively low-cost and easier to implement. This affordability and simplicity make it feasible for front-line clinical laboratories, even those without prior Next Generation Sequencing experience.

ESR scientist Dr Rhys White, a contributor to the paper, commented on the significance of the study: “Our findings demonstrate that integrating genomic surveillance with simplified bioinformatics and cost-effective sequencing technologies can revolutionize how clinical laboratories detect and manage infectious disease outbreaks. This approach not only enhances our ability to respond swiftly but also makes advanced genomic tools accessible to a broader range of healthcare settings.”