Comprehensive molecular diagnostics of respiratory tract infections

By Rob Janssen, Sales and Marketing Manager of PathoFinder

Why it is important to consider all potential pathogens, even during the novel Influenza A H1N1 pandemic.

In 2009, the novel Influenza A (H1N1) pandemic drew a lot of attention to the causes and consequences of respiratory tract infections. Stocks of neuraminidase inhibitors were distributed to key personnel, large scale vaccination campaigns were implemented and many clinical virology laboratories were forced to upscale their services to keep up with the increased demand for influenza tests. Although the effects on morbidity and mortality now appear to be much less dramatic than initially expected, there are still valuable lessons to be learned from this pandemic. One of them is the importance of comprehensive molecular diagnostics.

Once it became clear that a new Influenza A strain had emerged with the potential of rapidly infecting large numbers of individuals on a global scale, many clinical virology laboratories activated their scenarios to cope with large numbers of samples. New diagnostic Real Time RT PCR assays for the novel H1N1 virus, developed by the CDC and other reference centres, were distributed to laboratories worldwide. It almost seemed as if other respiratory pathogens had ceased to exist. Of course this is not true, but many physicians and biologists decided to test only for H1N1 in patients with respiratory symptoms.

To investigate the presence and distribution of other respiratory pathogens during the H1N1 outbreak, the Institute for Medical Microbiology of the University of Basel, Switzerland, tested samples sent to their molecular diagnostics laboratory for H1N1 screening with the RespiFinder plus assay (PathoFinder, Maastricht, the Netherlands). This multiparameter assay can detect and differentiate 19 respiratory pathogens in a single assay, with the same sensitivity as singleplex Real Time PCR.

The initial cohort of 86 suspected H1N1 cases (sampled in May and June 2009) contained 7 H1N1 positive samples (confirmed by a specific Real Time PCR test). These samples yielded a positive signal for Influenza A in the RespiFinder plus assay, showing that the H1N1 infections were detected as well. In 56 of the 86 cases (65%), the RespiFinder plus assay revealed an infection. Apart from the 7 Influenza A cases, 31 cases (36%) of rhinovirus, 5 cases (6%) of adenovirus, 4 cases (5%) of human Metapneumovirus, 3 cases (3%) of Influenza B and 2 cases each (2%) of Coronavirus and Parainfluenza were clearly identified. Finally, also a single case of RSV-B, and a case with a double infection of Mycoplasma pneumoniae and Parainfluenza-1 were detected. Other European laboratories using the RespiFinder technology reported similar observations. Many H1N1 suspected samples turned out to contain other pathogens, some of them (like Legionella pneumophila) even more dangerous than H1N1.

This study demonstrated the limitations of diagnosing the causative pathogen just by looking at the clinical presentation and/or epidemiological prevalence data. The overall detection rate of 65% positives outside of the flu-season indicates that there is a lot of viral activity that remains undiagnosed when labs are testing for a small number of pathogens only. It is clear that there is a big need for comprehensive diagnostics, which test for the presence of many relevant pathogens in a single assay. It is no longer sufficient to ask the question: "is this patient infected with pathogen X or Y?". The question asked should be: "which pathogen is causing this infection?" RespiFinder kits provide the answer to this question in a sensitive, rapid and cost-effective way.

References:

Dumoulin et al, Transplant Infectious Disease 2009: 11: 287-289
Reijans et al, J. Clin. Microbiol. Vol 46, 2008 : 1232-1240