Mycology lab of the future-slants to sequencing

ABSTRACT

As the world enters the third decade of the 21st century, infectious diseases continue to pose major challenges to the survival and well-being of human kind.The COVID-19 pandemic demonstrated how indispensable technological advances and innovations are in our fight against the vast legion of bugs;also, it a fascinating living pro of of the adage 'Necessity is the mother of invention' to witness at what stupendous pace not only diagnostics but therapies and even vaccines were developed, approved, validated, distributed and utilized. All fueled by the overwhelming and unprecedented health emergency that was the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic.Many more infectious pathogens, presumably viral, are believed to be waiting in the wings;Monkeypox did not waste much time in proving us right! In our country, India, the foresight of our best scientific brains and scientific policymakers led to the establishment of a network of Viral Research and Diagnostic Laboratories (VRDL) at the medical college, state, and regional levels with the premier institutes like National Institute of Virology (NIV), Pune, acting as an able mentor, under the aegis of the Indian Council of Medical Research (ICMR). The VRDL Network proved its worth and played an extremely important role in monitoring and managing the pandemic as, wave after wave, swept across our nation. Moreover, our indigenous drug makers jumped into the fray and excelled on par with our western counterparts in the timely development of effective vaccines. In a country like India, we are faced with additional challenges in the form of certain infectious diseases whose burden is borne mainly by the socio-economically disadvantaged, mainly in the tropics. These diseases and strategies for their mitigation have been taken up by the World Health Organization (WHO) in a big way by means of the Initiative for Control of Neglected Tropical Diseases (NTDs). Besides bacterial and viral diseases, Eukaryotic organisms are also important entities as etiological agents of NTDs. Eukaryotic medical microbiology (EMM) comprising medical mycology, medical protistology, medical helminthology, and medical entomology needs greater attention in India. Except malaria which has been at the forefront owing to the huge disease burden and associated mortality, several other parasitic infestations have indeed been neglected-an issue which the WHO rightly highlighted as part of its NTD elimination initiative. Though Mycetoma, chromoblastomycosis, and other deep mycoses are the only fungal diseases to find a place on the list of NTDs, many other fungal diseases continue to plague our communities. Mucocutaneous candidiasis and dermatophytosis may neither be commoner in the tropics nor are they neglected (rather, dermatophytosis tends to be overtreated in many cases!) but they merit attention simply because of the discomfort and disruption to daily life that they cause. We propose that a network of Medical eukaryotic microbiology (MEM) Laboratories be set up with special emphasis on the NTDs on a regional and national scale in our country to effectively deal with these infectious diseases prevalent in our communities. The diagnostic services offered by these 'MEM-NTDLs' can comprise of Microscopy, including fluorescent microscopy and special stains Microarrays MALDI-T OF Multiplex PCR NGS, including handy DNA sequencing technologies exemplified by the Nanopore MinION For dealing with these eukaryotic diseases, we believe that we need to adopt advanced techniques like MALDI and NGS in a big way. Culture, which continues to be the gold standard for bacteriological diagnoses, may now be termed to have historical significance at best in the case of fungal diseases because of the slow turnaround time and by the ubiquitous presence of fungal spores behaving as lab contaminants.Similarly, serological techniques may have a very limited role in the workup of eukaryotic infections owing to the complex antigenic profile of these organisms and the chronicity of the disease condition . Microscopy can be retained for the relative procedural simplicity and rapidity of results. The 'advanced' diagnostic techniques mentioned above have been around for quite some time now and have been widely applied in the microbiology diagnostic laboratory as well.With requisite training and provision of equipment and appropriately trained technical staff, a MEM-NTDL can be operated successfully at the district level in a planned manner.This would greatly enhance the quality of health services available to our population and enable our country to reach the goal of Health for All in the near future. Following identification, comes the very important aspect of antimicrobial chemotherapy susceptibility testing.Even here, alternatives to the growth-based, culture-dependent systems should be sought-the role of Biomarkers related to the growth and metabolism of eukaryotic organisms should be explored and incorporated in practical diagnostics as an aid to infectious diseases therapy and patient management. This can be part of the scope of the MEM-NTDL of the future.