Covid-19: disinfectants and sanitisers are changing microbiomes

The acceleration of antimicrobial resistance in covid-19 is genuinely alarming.1 It has added to the prevailing large scale and indiscriminate use of antibiotics, not only for treatment of human and animal diseases but also in animal food production systems.

Fortunately, the tools exist for studying emergence and spread of antibiotic resistance and making “resistome” informed predictions.23 In addition, global and country specific action plans are in place for mitigation of antibiotic resistance threats.

One more concern is the immeasurable effect of the large scale use of disinfectants and sanitisers in the covid-19 pandemic on the microbiomes of various ecological niches in humans, animals, and environments. Dysbiosis in host-commensal interactions is a likely outcome of such practices, thereby affecting the host’s immune functioning, metabolism, physiological parameters, and susceptibility to infectious and non-infectious diseases.4

Probiotics, immunobiotics, synbiotics, and so on are promising correctives for dysbiosis.5 But the problems caused by excessive use of disinfectants and sanitisers globally extend beyond dysbiosis—for example, emergence of alcohol resistance in Enterococcus faecium, a nosocomial pathogen, and its vancomycin resistant strains (as superbugs) has recently been reported.6 The dilemma is that by using disinfectants, sanitisers, and antibiotics for containment of covid-19, we are causing immeasurable collateral damage to microbiomes, “wiping” several commensals in various niches and possibly creating “mines” for newer threats.

We need to use the available tools and technologies and develop new ones that allow assessment of damage to microbial ecosystems, closely examine human-animal-microbial relationships, enable forecasting of newer threats, and reveal checkpoints to contain such threats. Hopefully, every lesson learnt from the prevailing wisdom of (judicious) use of antibiotics, sanitisers, and disinfectants for containment of covid-19 will guide us into a better equipped future with containable threats.