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  • Respiratory tract infection testing is not uniform—molecular testing has enabled the simultaneous detection of different pathogens.
  • Differentiating viral and/or bacterial infections is essential for selecting the appropriate treatment.
  • Unnecessary prescribing of antibiotics without knowing the pathogen causing the infection can lead to drug resistance.

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RTI Learning Guide

This comprehensive review of viral, bacterial, fungal, and parasitic RTIs is divided into four chapters: Etiology and Pathophysiology, Clinical Practice, Testing Strategies and Initial Workup, and Public Health Surveillance.

Download guide ›

Testing methods


Accurate testing is needed to distinguish respiratory pathogens, such as SARS-CoV-2 and influenza, from each other

Molecular testing for respiratory pathogens helps laboratories maximize sensitivity for common viruses, including SARS-CoV-2, flu, and RSV. As the pandemic continues to show signs of unpredictability and volatility, we expect SARS-CoV-2 and its variants to remain with us indefinitely. SARS-CoV-2 now joins the list of respiratory pathogens that pathologists will see in the lab, and influenza and COVID-19 share symptoms, making differential diagnosis even more challenging. With the overlap of symptoms, it is helpful for clinical and public health labs to be equipped with molecular tests that can detect genetic material from multiple respiratory viruses.

Multiplex testing assays allow laboratories to test for multiple infectious disease targets in a single reaction. This helps providers rule out multiple respiratory infections with one patient sample. Adoption of multiplex testing assays has grown over the last few years, most notably as a response to the SARS-CoV-2 pandemic.

Looking for a solution for COVID-19, Flu A/B, and RSV? Learn more ›
Looking for more additional respiratory viral targets? Learn more ›


A sample is sent to a lab where experts encourage organisms in the sample to multiply. Then they examine to identify the pathogen.

Antigen (Rapid)

Antigen (Rapid)

Nasal or throat swabs are mixed with liquid on a paper strip to return results within half an hour.

Molecular (PCR) testing

Molecular (PCR)

Genetic material from samples collected on swabs is amplified to detect genetic traces of a specific organism, even in early stages of infection.



Bacterial and viral pathogens chart


Shared symptoms

Bacterial and viral overlap

Differentiating bacteria versus viral infection based on signs and symptoms alone can be challenging. Coughing and sneezing, fever, inflammation, vomiting, diarrhea, fatigue, and cramping can occur in various infections.

Bacterial and viral overlap chart

High-risk patient conditions



  • Asthma
  • Bronchiectasis
  • Bronchopulmonary dysplasia
  • Chronic obstructive pulmonary disease (COPD)
  • Damaged or scarred lung tissue (interstitial lung disease)
  • Pulmonary embolism
  • Pulmonary hypertension
  • Tuberculosis
  • Cancer
  • Chronic Kidney Disease
  • Chronic Liver Disease
  • Cystic Fibrosis
  • Dementia or other neurological conditions
  • Diabetes (type 1 or type 2)
  • HIV infection
  • Heart conditions
  • Immunocompromised state (weakened immune system)
  • Overweight and obesity
  • Physical inactivity
  • Sickle cell disease or thalassemia
  • Solid organ or blood stem cell transplant
  • Stroke or cerebrovascular disease


Benefits of molecular testing


Benefits of molecular testing

Diagnostic PCR testing

Diagnostic PCR (molecular) testing is considered the gold standard for pathogen detection and accuracy of results. The superior sensitivity of a molecular test can detect low pathogen loads. Molecular testing also has the benefit of scalability. Most lab-based PCR tests can accommodate 96 to 384 samples (including controls) simultaneously on a single plate.

Primer set graph

Multiplex testing

Multiplex testing simultaneously differentiates respiratory diseases and helps identify cases of co-infection. Multiplex assay panels can go from two targets to dozens, making it an efficient technique.

Decorative image

The opportunity

The experience of molecular testing during the COVID-19 pandemic has experts looking at using the technology in other disease areas that are the subject of viral and bacterial infections.


Educational resources


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