Karius Medical Case Report: Secondary Infections After Influenza | Karius
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Karius Medical Case Report: Secondary Infections After Influenza

Influenza has significantly altered the course of human history. In the last 100 years, there have been four influenza pandemics, including one in 1918 that killed 50 million people worldwide. For reference, approximately 16 million people were killed in the entirety of World War I. The original cause of the 1918 pandemic was erroneously thought to be the bacteria Haemophilus influenzae, also known as Pfeiffer’s bacillus, because it was found in post-mortem lung tissue analysis.The influenza virus itself was not discovered until 15 years later, in 1933.

We now know that secondary bacterial infections can augment the pathogenesis of influenza, resulting in more severe disease and higher mortality. After the initial influenza infection subsides, damaged respiratory tissues as well as the weakened immune system make the host more vulnerable to secondary infections from both bacteria and fungi.


Common bacterial pathogens that can complicate influenza infection include Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, and Streptococcus pyogenes. Fungal infection with Aspergillus species is also becoming an increasingly well-documented complication.

In secondary infections, it is often difficult to diagnose the specific bacterial agent involved, since blood and respiratory cultures are often negative or obtained after the patient has already been treated with antibiotics. Invasive pulmonary aspergillosis can also emerge as a superinfection in this setting, which may not be on the clinician’s radar.

Recent advances in genomics have enabled development of accurate, comprehensive testing approaches to detect pathogens, which can identify the specific agent complicating influenza and help to guide precise antibiotic or antifungal therapy.

A complete list of more than 1,000 pathogens that the Karius® Test can detect is located here.

We have demonstrated the use of the Karius  Test for the detection of secondary infections in patients who have been infected with influenza. The following is a selected medical case report that illustrates the efficacy and utility of the Karius Test for this patient population.


Clinical Scenario: A three-year-old boy with influenza presented to the hospital with worsening respiratory symptoms: rapid breathing and cough.

A chest x-ray showed a complex pneumonia with a pleural effusion and he was placed on broad empiric antibiotic coverage with Vancomycin and Cefepime.

Blood and respiratory cultures were negative, and a Karius Test was ordered.

Karius Test Result: The Karius Test detected Streptococcus pneumoniae. The antibiotic coverage was narrowed to ampicillin, and the patient improved.

This is part of a series of Karius Medical Case Reports. In this case, the Karius Test was able to accurately identify infection in a clinically actionable timeframe, enabling the clinicians to provide targeted treatment to their patient.

We will discuss additional case reports in future posts.



  1. van der Sluijs et. al. Bench-to-bedside review: Bacterial pneumonia with influenza – pathogenesis and clinical implications. Critical Care (2010) 14(2): 219.
  2. Rynda-Apple et. al. Influenza and Bacterial Superinfection: Illuminating the Immunologic Mechanisms of Disease. Infection and Immunity (2015) 83(10): 3764-3770.
  3. Cunha, BA. Influenza: historical aspects of epidemics and pandemics. Infectious Disease Clinics of North America (2004) 18(1): 141-55.
  4. Taubenberger, JK and Morens, DM. The Pathology of Influenza Virus Infections. Annual Review of Pathology (2008) 3: 499–522.
  5. Crum-Cianflone, NF. Invasive Aspergillosis Associated With Severe Influenza Infections. Open Forum Infectious Diseases (2016) 3(3): ofw171.

DISCLAIMER: Case descriptions have been modified to protect patient privacy and, while every attempt has been made to provide accurate information, errors may occur. This information is provided for educational purposes only, and is not intended to be used as medical advice.