3.6% of hospitalised Covid patients in India had fungal, bacterial infections: ICMR study

Just as cases of black fungus are being reported in coronavirus disease (Covid-19) patients during the second wave of the pandemic, secondary bacterial and fungal infections affected at least 3.6% (ranging from 1.7% to 28% between hospitals) of patients hospitalised with Covid-19 during the last wave, found a study by the Indian Council of Medical Research (ICMR) published on Monday.

The mortality in patients with these secondary infections increased to 56.7% as against 10.6% among hospitalised patients in the ten hospitals from where data was collected. The mortality in those with secondary infections was as high as 78.9% in one of the hospitals, the data shows.

"What we found was that most of these secondary infections, 78% of them, were acquired at the hospital; the indication for infections started two days after hospitalisation and most of the samples had gram negative bacteria showing that they were hospital-based infection. This could be because infection control policies at the hospitals went for a toss amid the pandemic.

Hand hygiene wasn't as good because of double gloving and use of PPE kits in the hot weather also added to that," said Dr Kamini Walia, corresponding author of the paper and a scientist with the epidemiology and communicable diseases department at ICMR.

She added, "The most common pathogens causing the infection were Klebsiella pneumonia and Acinetobacter baumannii; usually E coli is the most common pathogen found as per previous ICMR reports. Both the infections are very difficult to treat because they have acquired lot of resistant genes over time.

The treatment will further become difficult post-Covid. Hospitals must invest in infection control and rationalise antimicrobial prescriptions."

Interestingly, the hospitals did not report cases of the fungal infection mucormycosis, cases of which have shot up during the second wave.

"[This is] a double whammy; Covid-19, along with the secondary infections, increases mortality significantly... Mucormycosis cases reported after the second wave are largely with the overuse of steroids. At the peak [of the second wave], steroids had vanished from the market. This has never happened before; It is one of the most common medicines available," said Dr Chand Wattal, head of the department of microbiology at Sir Ganga Ram hospital, one of the ten centres that were included in the study.

More importantly, the study cautions against the increase in antimicrobial resistance in the coming years due to excessive use of stronger medicines. Around 74.4% of the total antimicrobials prescribed in the hospitals were from the Watch and Reserve category of the World Health Organization (WHO).

The WHO classifies all antibiotics in three categories – Access drugs that can treat commonly encountered pathogens and have lower resistance potential, Watch drugs that have higher resistance potential and are critical for treatment, and Reserve drugs that need to be saved as last resort for drug-resistant microbes and given only once an infection is confirmed.

"Around 47% of the infections were found to be multi-drug resistant; but more than 74% of the antimicrobials prescribed were from the Watch and Reserve category. And, the ten hospitals from where we have collected data are in the ICMR network; they have been trained in infection control and antimicrobial stewardship. We can only imagine what is happening in other hospitals," said Dr Walia.

"These hospitals are backed by good lab facilities and many of these antibiotics should be prescribed only after the culture test comes positive. However, a very low number of samples were collected for microbial culture," she said.

Of the 17,534 patients with Covid-19 admitted to the ten hospitals between 1 June, 2020, and August 30, 2020, only 7,163 samples were sent for microbial culture – with multiple samples belonging to the same patients. The low sampling, doctors said was because of the practical problems; not many healthcare workers wanted to collect these samples during the first wave when not much was known about the disease.

"The sample size decreased considerably because people were scared to take the samples; especially those that generate aerosols such as lavage (a procedure where lower respiratory tract is flushed with fluid which is collected for diagnosis). The sampling has increased now that people are aware of how to protect themselves," said Dr Wattal.

There are no guidelines on rational use of antimicrobial in Covid-19 patients by ICMR.