Used to analyse past outbreaks, the new method could be implemented to inform public health policy.
Researchers at UNSW Sydney and the University of Technology Sydney (UTS) have developed a new genomic test that can identify the specific strains of whooping cough (bacterium Bordetella pertussis).
This new technology has provided insights into two previous epidemics of whooping cough in Australia and overseas, with results published today in the Journal of Clinical Microbiology. The team, led by Professor Ruiting Lan from UNSW and Dr Laurence Luu from UTS and UNSW, hope to use the assay to pinpoint the strain responsible for the current outbreak in Australia.
In 2024, all states and territories have reported a rise in whooping cough cases compared to previous years. Detailed information on the strain involved could play a crucial role in improving both the management of the outbreak and future vaccine development.
“This study paves the way for real-time surveillance of whooping cough strains, overcoming current testing limitations,” says UTS Chancellor’s Research Fellow Dr Laurence Luu, who led the study. “Our results provide important baseline data to understand how whooping cough has changed in Australia and could be used to help guide us through the current outbreak.”
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‘The 100-day cough’
Whooping cough is a severe respiratory disease with symptoms that include a persistent cough that can last up to 100 days. The disease is highly infectious, with one infected person potentially spreading it to 17-18 susceptible individuals without vaccination.
“It starts out like all your other cold and flu symptoms – runny nose, mild cough and low-grade fever, but then over time, so within about a week or two, that coughing starts to become more and more intense,” says Dr Luu, also an Adjunct Associate Lecturer in the UNSW School of Biotechnology and Biomolecular Sciences. “It can cause coughing fits followed by a sharp inhalation of breath, which is the noticeable ‘whooping’ noise you hear.”
Vaccination against pertussis is highly recommended for infants and pregnant women, to reduce the risk of infection and complications. Immunisation for pregnant people between 20 to 32 weeks provides important protection for newborns during their most vulnerable early months, before they are eligible for vaccinations.
Outbreak patterns
Previous research from the team suggests that whooping cough may be evolving under vaccine pressure, much like we saw with COVID-19. “Our past research suggests that whooping cough is evolving against the vaccine,” says Dr Luu. “Having said that, the vaccine is still very effective at protecting against serious disease.”
Historical data shows that despite the widespread use of the vaccine, whooping cough cases tend to spike every four to five years.
After an outbreak in 2019, border closures and COVID-19 lockdowns led to a record low in whooping cough cases. However, a recent outbreak in Australia has resulted in approximately 39,000 laboratory confirmed cases – the highest year on record since the introduction of vaccines. Reports indicate that in 2024, there have been more than 10 times the number of cases compared to the whole of 2023, with children aged 9 to 12 accounting for nearly 40% of all notified cases.
The method we've developed, known as mPCR sequencing assay, 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. It doesn’t require us to grow the bacteria.
Developing a sequencing assay for whooping cough
For many years, whooping cough was diagnosed by growing the causative bacteria, before a switch was made over to PCR testing that no longer requires culturing (growing) the live bacteria.
“This change in diagnostic practice means we no longer recover the bacteria for surveillance and can’t monitor what strains are circulating in the community, or whether they are still being targeted by the current vaccine or antibiotics,” says Dr Luu.
To give a clearer insight into the strains causing whooping cough, the team set out to develop a highly sensitive strain test without the need to grow bacteria.
“Usually, to understand what strains are circulating in the community, you need to grow the bacteria, so that you have enough of it to sequence its DNA,” says Dr Luu.
The DNA sequencing on clinical swabs of whooping cough is a cocktail of all sorts of DNA, both from humans and all other bacteria human respiratory tract. “Typically, this makes it really hard to sequence,” says Dr Luu. “But the method we've developed, known as mPCR sequencing assay, 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. It doesn’t require us to grow the bacteria.”
The team tested their assay on 178 leftover diagnostic DNA samples from across Australia from two previous outbreaks, with the samples collected between 2010-2012 and 2019.
Tracking previous epidemics
Analysis of the results provided unprecedented detail on the evolution of the whooping cough strains that had been circulating in Australia prior to the pandemic.
One of the key findings revealed that the 2012 outbreak was characterised by up to five different strains, or lineages, of B. pertussis. “We found that the strains that were associated with the big 2008-2012 epidemic had evolved to no longer produce one of the three components that's targeted by the vaccine.”
By 2019, a single one of these strains had become dominant.
“Surprisingly, we also identified a number of cases where the infection wasn't caused by whooping cough, but by another closely related bacterium called Bordetella holmesii,” says 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.”
Routine surveillance of whooping cough
The gold standard for tracking disease outbreaks is COVID-19, Dr Luu explains. “We knew the exact timing of when Delta and Omicron strains started being circulated which helped us continue to develop the vaccine and respond with appropriate strategies,” he says.
While this latest paper has revealed their assay is effective and sensitive, next steps for Dr Luu and his team involve applying their techniques to the current outbreak.
The team is working with pathology service providers to convert this assay into a tool for routine public health surveillance to determine what strains of whooping cough are circulating in the community. “By knowing what strains are transmitting in the community, this will allow us to spot and respond to outbreaks faster.”
The research team worked closely with Prof Vitali Sintchenko from the NSW Health Pathology Institute of Clinical Pathology and Medical Research and the Sydney Infectious Diseases Institute of the University of Sydney and Dr Jenny Robson from Sullivan Nicolaides Pathology, Queensland.
