The stealth superbug, decoded

A team of scientists in Bengaluru is behind the genome sequencing of Candida auris, a fungus that has caused disease outbreaks in five continents this year

November 27, 2016 12:02 am | Updated 12:02 am IST

EMERGING THREAT: “A paper by the scientists has shown that many cases have been misdiagnosed in India.” Picture shows the structure of the fungus. Photo: Special Arrangement

EMERGING THREAT: “A paper by the scientists has shown that many cases have been misdiagnosed in India.” Picture shows the structure of the fungus. Photo: Special Arrangement

On November 4, the Centers for Disease Control and Prevention, a leading public health institute in Atlanta, U.S., reported 13 cases of infection by the deadly fungus Candida auris in several parts of the country. Apart from the U.S., outbreaks have been reported this year in eight countries across four continents — India, Pakistan, South Korea, Kuwait, South Africa, Colombia, Venezuela and United Kingdom.

A paper by scientists from the Indian Institute of Science (IISc) in Bengaluru has shown that many cases of Candida auris have been misdiagnosed in the country. In 2015, a team led by Utpal Tatu, professor of biochemistry, IISc, completed the genotype sequencing of Candida auris , widely considered an emerging superbug fungus as it does not respond to conventional antifungal drugs. The genome data were submitted to the National Center for Biotechnology Information, U.S. and is now considered as the reference genome across the globe.

India, an epicentre

Candidiasis is a fungal infection caused by Candida species, often seen in patients whose immune system is compromised, such as AIDS patients or in case of transplants, malignancies and the use of catheters. Most of the infections are hospital-acquired, especially in ICU settings.

The first case reported was in Japan in an external ear canal infection in a patient in 2009. Since then, most cases have been invasive in nature and India has one of the highest number of infections caused by this superbug, says PhD student Sharanya Chatterjee, a member of the IISc team who studied isolates of Candida from a private hospital in Bengaluru. She found that in many cases, the fungus had been misidentified with another Candida species, Candida haemulonii .

Dr. Tatu’s team was among the first to report the high rate of misdiagnosis of Candida auris . “Current diagnostic procedures to detect fungal infections cannot detect Candida auris , which is resistant to common antifungal treatment. In several patients, by the time we had made the correct diagnosis, it was too late,” says Ms. Chatterjee.

The team of scientists has developed a diagnostic tool to detect Candida auris using polymerase chain reactions. “The rise of more virulent forms is connected to the indiscriminate use of antibiotics,” says Dr. Tatu, adding, “The strain found in the United States was resistant to even the third class of antifungal treatment.”

Highly resistant fungus

One reason for the high resistance to existing drugs is that this species has a higher number of drug efflux pumps compared to other species, says Ms. Chatterjee. Drug efflux pumps are proteins that prevent other drugs from crossing the cell membrane. The IISc team’s research was published in the September 2015 issue of BMC Genomics .

Sudarshan Ballal, director, Manipal Hospitals, which provided the isolates for the study, says the research highlighted the need for clinical-academic collaboration. “We have been able to dissect a fungus found commonly in hospitals and study it at the genome level. Some fungi look alike at macroscopic level, but their genotype could be very different, sort of like twins,” he says, adding, “If you know it is Candida auris from day one, you could start off with treatment which it is sensitive to.” Dr. Ballal agrees with Dr. Tatu about indiscriminate use of antibiotics as a possible cause: “Killing all kinds of bacteria gives space for fungi to grow.”

Dr. Tatu and his team of researchers feel that it is high time officials took note of the situation. “It is very difficult to establish how many cases have been misdiagnosed in India as very little study has been done on this, and since most patients who acquire Candida are already quite ill, a delayed diagnosis could be fatal,” he says.

Echoing Dr. Ballal, Dr. Tatu says the emergence of superbugs is a small example of the lacunae between academic research that studies the current disease scenario and current clinical practices, and shows the need for greater collaboration between the two. Apart from Candida auris , Dr. Tatu’s team is also studying numerous other infections, their evolutionary origins, diagnosis and treatment, with a view to filling this gap.

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