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Data suggests that since the onset of the COVID-19 pandemic, there has been an increased prevalence of antimicrobial resistant infections and increases in healthcare-associated infections (HAIs). A recent study shows an alarming incidence of multidrug-resistant candidiasis in COVID-19 patients, which carries high morbidity and mortality rates. With this increasing prevalence of resistant infections, the utilization of  surveillance tools such as whole genome sequencing (WGS) are critical in preventing the spread of these infections.


COVID-19 Associated Candidiasis (CAC) Risk Factors and Treatment

Candidiasis is an infection caused by Candida, a type of fungi. COVID-19 associated candidiasis (CAC) is defined as “a secondary infection or super-infection of candidiasis occurring after the event of COVID-19.”

 In a systematic review analyzing fungal isolates from 2018-2020 in 48 hospitals worldwide, it is indicated that : “[T]he prevalence of C. auris infections increased to 14% in COVID-19 patients, particularly those with diabetes mellitus (42.7%), hypertension (32.9%), and obesity (14.6%); and those with central venous catheter insertion (76.8%); stay in the intensive care unit (ICU) (75.6%), and broad-spectrum antibiotic usage (74.3%).”

Presumptive factors have been identified as contributors which may have led to the increase in C. auris infections among COVID-19 patients. A patient’s weakened immune system, the use of anti-viral or immunosuppressant drugs, and direct damage from the SARS-CoV-2 virus are suspected contributors. Healthcare setting related factors such as a shortage of personal protective equipment (PPE) and poor hand hygiene, which occurred with the rapid onset and accelerated pace of the pandemic, may have also been factors.

In addition to an increased prevalence of candidiasis infections, studies are also noting an increase in multidrug-resistant strains. Resistant infections can be more difficult and sometimes impossible to treat, due to limited options for effective antimicrobial therapy. Treatment for fungal infections commonly includes the utilization of anti-fungal drugs such as fluconazole, voriconazole, or amphotericin B. However, as noted in this study, only echinocandins are effective in treating multidrug-resistant C. auris infections.


Surveillance Tools Can Help Combat COVID-19 Associated Candidiasis

With limited treatment options, early recognition is key—as emphasized by the study authors, “early detection and appropriate therapy is generally believed to be critical to improve the outcome of C. auris infections in the era of COVID-19.”  However, clinical diagnosis of Candida infections in patients with COVID-19 is difficult and relies heavily on clinicians’ alertness to infection symptoms. Due to that challenge, infection prevention and surveillance using tools such as whole genome sequencing could help “to disclose the epidemiology of healthcare-associated infection and to better control and prevent these infections.

Whole Genome Sequencing is an advanced infection surveillance tool that can be used to provide insights into the genetic basis of resistance mechanisms. WGS helps to combat the spread of antimicrobial resistance (AMR) by enhancing surveillance and giving researchers the information needed to identify the pathogen and track its spread and evolution.

WGS is more often utilized in high-income countries given its high cost and complexity. However, as exhibited with the COVID-19 pandemic, global accessibility to diagnostic tools and surveillance plays a critical role in effective disease mitigation.  

With the high prevalence of resistant CAC infections, as well as other types of healthcare-associated infections, accessibility to diagnostic tools and surveillance to support better patient outcomes is vital. A collaborative and comprehensive approach consisting of rapid diagnostics combined with global disease surveillance can help mitigate the rise and spread of COVID-19 associated candidiasis (CAC) and other resistant infections.




  • Infectious Diseases