Opportunistic Fungal Infections and how mNGS can Help

What are opportunistic fungi?

Opportunistic fungi are a group of fungi that cause secondary infections in those vulnerable individuals whose immune system is compromised by a pathogen that caused some primary infection. These fungi usually don’t cause diseases in normal healthy individuals and target immunocompromised people only, often causing some serious even life-threatening secondary infections. Many groups of opportunistic fungi are part of normal respiratory flora and cause respiratory infections in people with damaged immune system such as Human Immunodeficiency Virus (HIV) positive individuals or patients taking drugs that suppress immune. For instance, acquired immunodeficiency syndrome (AIDS) results in severe T-cell depletion therefore, chances of developing serious; even life-threatening opportunistic fungal infections are higher. Fungi like Aspergillus, Candida, Cryptococcus, Histoplasma and Mucormycosis are responsible for early mortality in AIDS patients.

Patients with viral respiratory infections are also known to be exceptionally susceptible to fungal infections. Recent studies have identified several opportunistic infections in COVID-19 patients (Figure 1) and the co-infections contributed to the death of significant number of Covid-19 positive patients in many countries severely hit by corona virus pandemic. Covid-19 induced immunosuppression is a major risk factor for developing opportunistic fungal infection. A marked increase in Mucormycosis / black fungus infections was observed in Covid-19 positive intensive care patients in India during second wave of the pandemic. It’s a common co-infection in people suffering from severe Covid-19. Ayşenur Sümer Coşkun, Şenay Öztürk Durmaz (2021) investigated the records of 627 patients admitted to intense care unit with a diagnosis of Covid-19. Thirty-two patients were found positive of opportunistic fungal infection of which 25 patients died. Most of the patients had developed Candida parapsilosis infection during their lifetime. They concluded that opportunistic fungal infections play a role in increasing the mortality rate of Covid-19 positive patients. According to Kinal Bhatt, Arjola Agolli et al (2021), the following opportunistic fungal infections were more commonly associated with Covid-19 pandemic in India:

  1. Mucormycosis
  2. Candida auris
  3. Pneumocystis pneumonia
  4. Pulmonary aspergillosis

 Fig1 Percentage of variation of cases of covid-19 patients with opportunistic fungal infections 

Detection of opportunistic fungal infections and role of mNGS:

Fast and timely detection of opportunistic fungal infections is important in saving the lives of immunocompromised patients. Traditional techniques of diagnosing fungal infections have many shortcomings and not always accurate and fast. Many diagnosis methods are time-consuming, lack sensitivity and specificity. For example, diagnosis of Candida by culturing takes 24 to 48 hours and positive detection rate is also low [8]. There is always a chance of misdiagnoses with traditional histopathological, direct microscopic and serologic examinations. Speed and cost effectiveness also are also two factors that play important role in determining the best diagnostic methods. Many current diagnostic methods lack these two important factors.

Metagenomic Next Generation Sequencing offers fast and accurate detection of fungal or any microbial infection. Although it comes with certain limitations, it has great potential to replace traditional fungal detection techniques such as culturing and histopathological examination of specimens in clinical microbiology laboratories. Jiejun Shi et al (2021) conducted a case study to determine the effectiveness of metagenomic Next Generation Sequencing in diagnosis of Talaromycosis of an individual with healthy immune system. The patient was a 79-years-old man and presented with symptoms of cough and recurrent fever. They made a diagnosis of bacterial pneumonia after routine examination and put him on antibiotics therapy. The patient received meropenem injection and then tigecycline injection successively but felt no improvement in symptoms. Then they tried metagenomic Next Generation Sequencing and Talaromyces marneffei was detected. The patient was treated with Voriconazole which resulted in marked alleviation of symptoms.

Conclusion: They concluded from the case study of Talaromycosis that mNGS is often faster than traditional techniques in detecting opportunistic fungal or any microbial infection when exact pathogenic cause is not known.

Dan Xie, Wen Xu et al (2021) conducted a similar study to assess the value of metagenomic Next Generation Sequencing in diagnosing pneumonia caused by Pneumocystis jirovecii (P.jirovecii). Pneumocystis pneumonia usually follows renal transplantation and not easy to diagnose.  Seven patients who suffered from Pneumocystis pneumonia after kidney transplant were   enrolled and all of them underwent metagenomic Next Generation Sequencing (mNGS). Sequence of Pneumocystis jirovecii was identified in blood or bronco-alveolar lavage fluid (BALF). All the patients were given Trimethoprim-sulfamethoxazole combined with caspofungin for pneumonia treatment that resulted in improvement of symptoms and eradication of infection. They concluded that mNGS is a powerful tool that could be used for fast and early diagnosis of Pneumocystis jirovecii pneumonia in renal transplantation recipients.

Sometimes, routine microbiologic testing fails to detect rare and uncommon fungal infections. Such pathogens can be easily diagnosed within a few hours by applying next-generation sequencing. It is cost effective and fast diagnostic technique as compared to traditional culturing and serology and would be of great help in early diagnosis and treatment of life-threatening opportunistic fungal infections. Application of next generation sequencing in clinical microbiology laboratories to detect opportunistic infections in covid-19 positive patients admitted to intensive care units will greatly help save the lives of many immunocompromised patients.