A Survey of Viral-bacterial Co-infection in Respiratory Samples Using Multiplex Real Time-PCR

Influenza and non-Influenza virus related respiratory tract infections are amongst the most common reasons reported for physician visits and hospitalizations, globally. The economic burden associated with these viral infections, within the United States, are upwards of $50 billion annually. Concomitant, or subsequent, co-infections of the respiratory tract by pneumonia-causing pathogenic bacteria, like Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis and Staphylococcus aureus, are often observed in patients suffering from these respiratory viral infections and contribute to significant co-morbidity and mortality. In the present study, respiratory swabs from patients were tested for the presence of viral and bacterial pathogens, by Real-Time PCR, employing the Thermo-Fisher Open Array® platform. Amongst the 5793 samples tested (Dec 2017-Dec 2018), 2357 (40.68%) tested positive for the presence of Influenza and Non-Influenza viral infections. Out of these positive patient samples, 1175 (49.85%) also tested positive for the presence of one or more pneumonia-causing bacterial species. The co-infection data obtained was distributed on the basis of age. Interestingly, nearly 30% of the cases from the younger patient subset (<1 year old and 1-15 years old) were found to be co-infected with S. pneumoniae, H. influenzae and M. catarrhalis within the same sample. In addition, infant (<1 year old) patient viral positive samples, displayed higher than previously reported levels of M. catarrhalis co-infections (72.08%). With the ever-increasing popularity of point of care testing, this study demonstrates the importance and efficacy of a rapid, comprehensive multiplex-PCR, syndromic-panel approach to respiratory disease diagnostics, assisting clinicians to make better, and timely, decisions, potentially leading to improved patient care and outcomes.