The development will allow public health agencies to identify and respond to outbreaks faster, according to one expert.
Researchers from two Sydney-based universities have developed a new test to uncover the specific strain of bacteria present in whooping cough.
Whooping cough case numbers across the country have spiked to never-before-seen levels in 2024. Identifying the particular strain of Bordetella pertussis bacteria that caused whooping cough used to involve growing the live bacteria in culture, but the shift to PCR testing has made it harder to figure out what strains are circulating in the community – and whether existing vaccines or antibiotics are still targeting the right strains.
Now, a recent study from the University of New South Wales Sydney and the University of Technology Sydney describes a new genomic test that can identify the specific strain of bacteria behind whooping cough using DNA collected for a PCR test. The study findings were published in the Journal of Clinical Microbiology.
“This study paves the way for real-time surveillance of whooping cough strains, overcoming current testing limitations,” said the paper’s lead author Dr Laurence Luu, a chancellor’s research fellow from UTS.
“By knowing what strains are transmitting in the community, this will allow us to spot and respond to outbreaks faster.”
Researchers used 178 diagnostic DNA samples that were collected across the country during the whooping cough outbreaks that occurred in 2010-2012 and 2019 to develop and test their new multiplex PCR approach.
The new testing method, which was found to be effective and sensitive in identifying the specific genetic strain causing the disease, does not require bacteria to be grown in Petri dishes.
“The method we’ve developed… can directly sequence the residual whooping cough DNA leftover from a PCR test and needs as few as four copies of the bacterial DNA to work effectively,” Dr Luu explained.
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Comparing the genetic characteristics of samples taken from the two previous whooping cough outbreaks revealed that while there were up to five different strains of B. pertussis that contributed to the 2010-2012 outbreak, one particular strain had become overwhelmingly dominant during the 2019 outbreak.
“Surprisingly, we also identified a number of cases where the infection wasn’t caused by whooping cough, but by another closely related bacterium called B. holmessi,” said Dr Luu.
“In the clinical laboratories, the two bacteria share the same diagnostic marker, but what we see is that in 2019 there were actually two species that were causing the infection, and even cases where they were co-infected with two different bacteria.
“Having past data is important to understanding how the bacteria may have changed over time, such as whether they are evolving against the vaccines or developing resistance to antibiotics.”
The researchers are currently working with pathology service providers to turn the new approach into a tool that can be used in public health surveillance to identify which strains of whooping cough are currently active in the community.
The latest data from the National Notifiable Disease Surveillance System reports that there have been over 41,000 notifications of whooping cough so far this year, surpassing the previous high of 38,748 in 2011.
