Has SARS‑CoV‑2 infection led to the emergence of new bacterial or fungal strains that cause pneumonia in patients recovering from COVID‑19 pneumonia?

Medical Advisory BoardAll articles are reviewed for accuracy by our Medical Advisory Board
Educational purpose only • Exercise caution as content is pending human review
Article Review Status
Submitted
Under Review
Approved

Last updated: February 20, 2026 • View editorial policy

Personalize

Help us tailor your experience

Which best describes you? Your choice helps us use language that's most understandable for you.

COVID-19 Has Not Created New Strains of Pneumonia-Causing Bacteria or Fungi

COVID-19 has not led to the emergence of new bacterial or fungal strains causing pneumonia; instead, it has been associated with secondary infections from well-established, pre-existing pathogens that commonly cause hospital-acquired and ventilator-associated pneumonia. 1

The Pathogens Remain the Same

The bacterial and fungal organisms identified in COVID-19 patients with secondary pneumonia are the same species that have caused respiratory infections for decades:

Bacterial Pathogens in COVID-19 Secondary Infections

  • Staphylococcus aureus, Haemophilus influenzae, and Streptococcus pneumoniae are the predominant bacterial pathogens in COVID-19 patients with co-infections at hospital admission 1

  • Pseudomonas aeruginosa, Klebsiella species, Escherichia coli, and Stenotrophomonas maltophilia are the most common organisms in secondary bacterial pneumonia developing after hospitalization 2, 3

  • Gram-negative organisms including Enterobacter cloacae, Acinetobacter baumannii, and Enterobacterales species are frequently isolated, particularly in ICU patients 1

  • Mycoplasma pneumoniae has been detected via PCR in some cases, though infrequently 1

Fungal Pathogens in COVID-19 Secondary Infections

  • Aspergillus fumigatus is the most common fungal organism causing secondary pulmonary infections in COVID-19 patients 2

  • Candida species show notably higher abundance in COVID-19 patients compared to non-COVID-19 pneumonia controls 4

What COVID-19 Actually Changed: Frequency, Not Novelty

Incidence of Secondary Infections

  • Bacterial co-infections at hospital admission occur in only 3.5% (95% CI: 0.6-6.1%) of COVID-19 patients 1

  • Secondary bacterial infections after admission develop in 15.5% (95% CI: 10.9-20.1%) of hospitalized COVID-19 patients 1

  • Ventilator-associated pneumonia occurs in 31% of mechanically ventilated COVID-19 patients, with an overall incidence of 5% in all hospitalized COVID-19 patients 1

  • Secondary fungal infections occur in 6.3% (0.9-33.3%) of hospitalized COVID-19 patients, predominantly in critically ill patients 2

Critical Distinction: Severity, Not Novelty

  • COVID-19 patients in the ICU have a 50.5% incidence of ventilator-associated lower respiratory tract infections, significantly higher than influenza pneumonia (30.3%) or non-viral pneumonia (25.3%) 1

  • Non-survivors have a 50% rate of secondary bacterial infections compared to less than 1% in survivors 1

  • The timing of secondary infections averages 10 days (2-21 days) from hospitalization and 9 days (4-18 days) after ICU admission 2

The Real Clinical Problem: Opportunistic Infections, Not New Strains

Why COVID-19 Patients Develop More Secondary Infections

  • Viral-induced immune dysfunction damages respiratory airways and defects both innate and acquired immune responses, creating a favorable environment for bacterial growth and invasion 5

  • Prolonged mechanical ventilation in COVID-19 patients increases exposure time for nosocomial pathogens 1

  • Immunosuppressive therapies including corticosteroids and tocilizumab (IL-6 inhibitors) may increase risk of secondary infection, though evidence is mixed 1

Enrichment of Known Opportunistic Pathogens

  • Acinetobacter baumannii shows notably higher abundance in COVID-19 patients and is positively correlated with inflammation indicators 4

  • Multidrug-resistant organisms are present but actually occur at lower rates in COVID-19 patients (23.3%) compared to influenza or non-viral pneumonia patients 1

  • MRSA accounts for 49.6% of all Staphylococcus aureus isolates in critically ill COVID-19 patients with secondary infections 1

Critical Pitfalls to Avoid

Antibiotic Overuse Without Evidence

  • 60-100% of COVID-19 patients receive antibiotics despite bacterial co-infection rates of only 3.5% at admission 2, 3

  • Prophylactic antibiotic use occurred in 63.7% of SARS-CoV-2 patients and 73.5% of all viral pneumonia cases reviewed, contributing to antimicrobial resistance 3

  • Antibiotics should be discontinued within 48 hours if cultures are negative and clinical improvement occurs 1, 6

Misattributing Mortality to the Virus Alone

  • Mortality rate of 15.2% due to secondary bacterial infections was observed in COVID-19 patients with pneumonia (41 of 268 patients) 3

  • Some patients may die from bacterial co-infection rather than the virus itself, making recognition and appropriate treatment critical 7

The Bottom Line

COVID-19 has not spawned new bacterial or fungal strains. The pathogens causing pneumonia in COVID-19 patients are identical to those causing hospital-acquired pneumonia, ventilator-associated pneumonia, and healthcare-associated infections for decades. What has changed is the frequency of these secondary infections in critically ill patients and the widespread inappropriate use of empirical antibiotics. 1, 2, 3

References

1
Guideline

Guideline Directed Topic Overview

Dr.Oracle Medical Advisory Board & Editors, 2025

6
Guideline

Treatment and Diagnosis of Pneumonia

Praxis Medical Insights: Practical Summaries of Clinical Guidelines, 2025

Related Questions

Can a respiratory infection produce secondary bacteremia?
At what point during a viral illness should a persistent fever raise concern for a secondary bacterial infection?
What is the treatment for viral pneumonia?
What is the recommended treatment for viral or bacterial infections?
How can a viral illness lead to pneumonia that requires treatment with antibiotics, particularly in patients with risk factors such as age over 65 or underlying health conditions?
How should I manage an 11‑month‑old infant presenting with fever and vomiting?
What does a sinusoidal pattern on a cardiotocogram indicate and how should it be managed during labor?
My 11‑month‑old infant with fever and prior non‑bilious vomiting is now vomiting yellow (bilious) material—what immediate steps should be taken?
What is the appropriate ciprofloxacin dosing and treatment duration for an otherwise healthy adult woman with uncomplicated cystitis?
What is the recommended follow‑up plan and anticoagulation duration for a patient after a pulmonary embolism, including timing of visits, choice of anticoagulant, monitoring of renal function, and criteria for stopping or continuing therapy?
Can an adult patient be safely treated with clonidine 0.2 mg, desvenlafaxine (Pristiq) 100 mg, mirtazapine 7.5 mg, and quetiapine XR (Seroquel) 50 mg together?

Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

Have a follow-up question?

Our Medical A.I. is used by practicing medical doctors at top research institutions around the world. Ask any follow up question and get world-class guideline-backed answers instantly.

Ask Question