Measuring the effectiveness of genomic sequencing for infection surveillance 

Last year, Awanui Clinical Microbiologist Max Bloomfield discussed how genome sequencing technology developed by Oxford Nanopore, had led to the early detection and containment of an outbreak of Clostridioides difficile infection (CDI) at Wellington Regional Hospital in 2022.  

In the latest stage of their research, Max and the team sought to better understand the outbreak and demonstrate how the early detection and subsequent changes to prevention and control measures prevented further spread of the particular type of C.diffile to other areas of the hospital.  

“CDI is a bacterial infection of the intestines, mostly affecting people in hospital, and can have serious consequences. It can also affect patients who have received antibiotics for other infections, have weakened immune systems, and means they can spend longer in hospital and require more treatment,” says Max,    

“For this reason, scientists at Awanui Labs Wellington have been performing genome sequencing of this bacteria since the beginning of 2022.”  

Max says by matching the sequencing data with patient movements through the hospital, scientists can detect whether the bacteria is spreading between patients, in a way which was not possible before, and put the correct infection prevention and control (IPC) measures in place. 

“During the 2022 outbreak, the genome sequencing technology, called the MinION, identified the type of C. diffile as the ST2 variant which was spreading on one of the wards and was not detected with usual surveillance methods,” says Max. 

“The study demonstrated how the MinION traced what was a sustained outbreak of ST2 over a six-month period on this ward. Because the overall number of patients showing signs of C. diffile infection had not risen above the normal variation to trigger an IPC response, the outbreak would have gone unnoticed without this technology.”  

“The research reaffirmed our position which showed hospitals cannot rely only on standard methods, such as case numbers and epidemiological data, to give an early warning of C. diffile transmission alone.” 

Max says hospitals need support from the laboratories because genome sequencing technology is more effective in detecting the transmission of C. diffile rather than relying on identifying potential cases when symptoms appeared amongst patients. 

“The early detection meant the outbreak in 2022 was contained and there was no further spread of the ST2 variant to other areas of the hospital. Identifying the rise in the ST2 cases led to enhancements in cleaning and prevention measures, making the wards safer for patients. 

“We report all our sequencing data to the hospital and their IPC team. This gives Health NZ – Te Whatu Ora confidence in our scientists to alert them to the threat or presence of C. diffile, and the extent to which the bacteria has been transmitted.  

“This informs and supports the hospital’s preventing and responding to any potential outbreak and minimising any impacts to their patients. This research has clearly demonstrated the effectiveness of genome sequencing in supporting patient health and the value of our labs using the technology further in the future,” says Max. 

The article, titled “Early identification of a ward-based outbreak of Clostridioides difficile using prospective multilocus sequence type-based Oxford Nanopore genomic surveillance” is published on the Cambridge University Press website.  

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