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 Table of Contents  
Year : 2022  |  Volume : 66  |  Issue : 2  |  Page : 230-233  

Challenges in setting up a diagnostic microbiology laboratory during coronavirus disease 2019 crisis and impact on the diagnosis of communicable diseases

1 Assistant Professor, Department of Microbiology, National Cancer Institute-All India Institute of Medical Sciences, New Delhi, India
2 Professor and Head, Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India

Date of Submission10-Sep-2021
Date of Decision26-Oct-2021
Date of Acceptance05-Nov-2021
Date of Web Publication12-Jul-2022

Correspondence Address:
Arghya Das
Department of Microbiology, National Cancer Institute and All India Institute of Medical Sciences, New Delhi
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/ijph.ijph_1774_21

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The coronavirus disease 2019 (COVID-19) pandemic has left the health-care workers exhausted and the system dwindling. The challenges have been immense everywhere and even worse in developing countries. Despite the Indian Government's forethought and active investment in various national programs, the pandemic has brought unconceivable repercussions on the management and notification of several other lethal infectious diseases including human immunodeficiency virus (HIV) and tuberculosis. Although the phenomenal capacity building for COVID-19 testing and diagnosis over a short time is admirable, the journey has been arduous. From convincing the hospital managements to create the recommended infrastructure, to the procurement of necessary equipment and consumables on an urgent basis, and providing services round the clock with limited workforce, the laboratory personnel throughout the country have done a remarkable job in their quest to combat the pandemic. However, the work needs to be pursued further in apprehension and preparedness for any emerging agents.

Keywords: Challenges, coronavirus disease 2019, diagnosis, laboratory, preparedness, strengthening

How to cite this article:
Vidyarthi AJ, Das A, Chaudhry R. Challenges in setting up a diagnostic microbiology laboratory during coronavirus disease 2019 crisis and impact on the diagnosis of communicable diseases. Indian J Public Health 2022;66:230-3

How to cite this URL:
Vidyarthi AJ, Das A, Chaudhry R. Challenges in setting up a diagnostic microbiology laboratory during coronavirus disease 2019 crisis and impact on the diagnosis of communicable diseases. Indian J Public Health [serial online] 2022 [cited 2022 Aug 13];66:230-3. Available from:

   Introduction Top

Health-care organizations across the globe are recently fighting their most exhausting battle in modern times against infectious disease. The coronavirus disease 2019 (COVID-19) pandemic has made us witness an unprecedented scale of social and economic breakdown. The challenges faced have ranged from people being deprived of necessities to a shortage of workforce and supplies in the health-care industry.[1] The testing, contact tracing, and isolation strategy are premiering among the array of measures to mitigate the pandemic.[2] The ability to scale up laboratory services may be easier for those countries which have entered the pandemic with sustained investment in health infrastructure, including laboratory equipment, logistics systems, technicians, and information technology, but not for developing nations like India.[3]

   Efforts in Laboratory Capacity Building for Diagnosis of Communicable Diseases in India before Coronavirus Disease 2019 Top

Over the past decades, the Government of India has invested generously through its various programs in laboratory capacity building. The National Tuberculosis Elimination Programme (NTEP), National AIDS Control Programme, and National Vector Borne Disease Control Programme have set the bar high for other developing nations. The Integrated Disease Surveillance Programme is focused on developing laboratory capacity across the country for surveillance of epidemic-prone diseases such as typhoid, cholera, dengue, hepatitis, measles, diphtheria, and leptospirosis in a decentralized manner.[4] Some international organizations such as the U. S. Centers for Disease Control and Prevention are also supporting different institutions in India by strengthening laboratory-based surveillance and specimen referral systems.[5] Unfortunately, the efforts have seemed to be not enough to meet the demand of laboratory investigations from a rapidly growing health delivery system catering to the need of 1.4 billion individuals.

   State of the Major Communicable Diseases during Coronavirus Disease 2019 Pandemic in India Top

The long battles against the age-old infectious diseases came to a halt during the COVID-19 crisis. As the focus was directed to COVID-19, the access to screening, diagnosis, and treatment of the existing infections became extremely restricted. The most evident impact was notably the worldwide decline in the number of newly diagnosed cases of tuberculosis (TB), the top-ranked in the list of mortality by a single infectious agent before the COVID-19 pandemic.[6] Not surprisingly, India ranked first by contributing 41% of the worldwide decline in the notification of TB cases.[6] The data of NTEP depicted an overall 25% decrease in the notification of cases in 2020 than the preceding year.[7]

There was also a decrease in the new cases of two vector-borne diseases, malaria, and dengue by 45% and 75%, respectively, in 2020 than in 2019.[8] Besides the possibility of low vector-borne transmission, underreporting in the setting of already overburdened health-care facilities in the country during the pandemic emerged as the likely cause behind the decrease in the incident cases of these diseases [Figure 1].[9]
Figure 1: Trend in malaria and dengue cases and deaths in India (The estimates of the cases are in thousands and the mortality estimates are in absolute numbers). Credit note: The figure is created with the statistics mentioned in the website of National Vector Borne Disease Control Programme, Directorate General of Health Services, Ministry of Health and Family Welfare, Government of India. Source: National Vector Borne Disease Control Programme. Diseases. New Delhi: National Vector Borne Disease Control Programme; 2021. Available from: 4.php?lang = 1&level = 0&linkid = 407&lid = 3683. [Last accessed on 2021 Oct 24].

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India experienced a steady decline in adult (15–49 years) HIV prevalence since the beginning of this millennium. In 2019, the estimated adult prevalence was reported to be 0.22%.[10] Although the figure seems to be smaller in comparison with that of the middle-income countries, its huge population makes India the third-worst affected nation by the HIV epidemic in the world. There was growing evidence on increased susceptibility of people living with HIV to COVID-19.[11] However, this risk was inevitably overlooked, as the services for HIV detection and management were disrupted in our country.[12] In a survey conducted in India and other nine countries in collaboration with the AIDS Society of India, a decrease in undergoing HIV confirmatory tests by 46% of the at-risk population in the year 2020 was reported.[13]

Infections with resistant bugs also emerged as the physician's worst nightmare in the inpatient care setting, especially intensive care units.[14] The situation was further complicated with COVID-19 pneumonia which itself may resemble bacterial pneumonia or secondary bacterial pneumonia may set in the COVID-19-affected patients.[15] However, the lack of robust diagnostic tests which can distinguish between the viral and bacterial infections with less turnaround time became an impediment in deciding the antibiotic treatment. Coinfections of respiratory pathogens such as Klebsiella pneumoniae, Staphylococcus aureus, and Legionella pneumophila Scientific Name Search  in COVID-19 patients were reported in the literature.[16]

   Challenges for the Diagnostic Microbiology Laboratories during the Pandemic Top

The herculean task to initiate or scale up diagnostic microbiology services including severe acute respiratory syndrome coronavirus 2 testing is posed with many challenges.

First and foremost is the laboratory construction and designing itself in the available space following the recommendations, which may involve building a new structure or dismantling and renovating the existing infrastructure. The Indian Council of Medical Research has mandated the availability of a Biosafety level 2 (BSL-2) laboratory including a molecular biology setup for viral detection for COVID-19 testing.[17] While the approvals from the competent authority in an institution are extensive and tedious, the workforce available for the construction works is also limited, especially during the time of imposed restrictions when the majority of the construction workers have returned to their homes.

Secondly, the procurement of the equipment and required consumables is another impediment to the task. The hospital staffs involved in procurement are overburdened and exhausted after hours of over shift fulfilling the requirement of essential supplies (medicines, personal protective equipment, etc.) resulting from a sudden surge of patients. The vendors and manufacturing executives are also reluctant to visit the hospitals for equipment installation, demonstration, and maintenance. The rules and regulations of procurement in government organizations are also dynamic. The Government of India in 2016 has launched the Government e-Market portal to facilitate substantial reduction of product prices in comparison to the tender, rate contract, and direct purchases.[18] While the former aims at transparency and ease of buying, the officials are still not well versed with the regulations of this relatively new system which results in undue delay in the supply chain. Furthermore, the necessary technical committee meetings for any equipment are being postponed frequently and the physical files for approvals are also being circumvented in the process. Everything is carried out online including the meetings and hospital information system. However, the system ceases to function in case of an Internet breakdown.

Thirdly, even if the equipment is available, the availability of trained workforce remains a challenge. At the time when the health-care delivery capacity in a hospital is already saturated, a significant proportion of laboratory personnel (residents, technicians, laboratory attendant, and multitasking staff) are being summoned and posted to perform their duties at patient sides. Thus, all activities including sample collection, transportation, and processing are being affected. The hands-on training of recruits is also hindered and the entire training process has become dependent on technology, i.e., computers and the Internet. Although the online mode of learning is simple and secure, the lack of practical training may compromise personnel safety and the quality of tests in a diagnostic laboratory.

Last but not least is the allocation of funds which is largely being diverted to the treatment of COVID-19 patients. Looking at the present crisis, the focus of expenditure exclusively on treatment-related activities in a hospital may be considered pertinent but at the cost of compromising building new or strengthening already existing laboratory capacity.

   Public Health Implications, Opportunities, and Recommendations Top

The hurdles in scaling up laboratory capacities at the institutional level may seem to be insignificant but have grave consequences from a public health perspective. We have witnessed how shifting the focus away from an infectious agent has reversed years of advancement in the management of a communicable disease leading to increased mortality [Table 1]. Nevertheless, scaling up the diagnostic facilities from scratch for the diagnosis of COVID-19 in India will remain an undisputed success story for a long time. India displayed a tremendous potential in building laboratory capacity even at the time of an ongoing pandemic with the increase in the number of COVID-19 testing laboratories from 14 to 1596 over a short period (February to August in 2020) despite multiple issues related to infrastructure, skilled human resource, data monitoring, and supply chain constraints.[19] Technological innovations, collaboration with private sectors, and institution of robust supply chain besides leveraging the testing abilities of the scientific and technical institutions are among the key measures to make COVID-19 diagnosis affordable and accessible to all from the rough terrains of Ladakh to the islands of Lakshadweep and Andaman and Nicobar.[19] While the experience gained will help to further strengthen the ability of laboratory diagnosis for multiple infectious diseases in the country, we should be vigilant against the emerging and reemerging threats and work toward the laboratory preparedness for a prompt response simultaneously continuing our effort in diagnosis and testing of the existing infectious diseases.
Table 1: Trend in year-wise tuberculosis mortality from 2014-2020

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The current pandemic provided us with a unique opportunity to think wisely and act smart. Accreditation of the laboratories to ensure quality and reliability, training of laboratory workforce, building networks of reference laboratories, strong regulatory systems for testing kits and reagents alongside the equitable distribution of resources, and uninterrupted funding from government and international agencies will ensure our preparedness before an emerging or reemerging pathogen may unleash itself to begin the next pandemic.

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Conflicts of interest

There are no conflicts of interest.

   References Top

Shadmi E, Chen Y, Dourado I, Faran-Perach I, Furler J, Hangoma P, et al. Health equity and COVID-19: Global perspectives. Int J Equity Health 2020;19:104.  Back to cited text no. 1
Contreras S, Dehning J, Loidolt M, Zierenberg J, Spitzner FP, Urrea-Quintero JH, et al. The challenges of containing SARS-CoV-2 via test-trace-and-isolate. Nat Commun 2021;12:378.  Back to cited text no. 2
Rajan S, Cylus J, Mckee M. Successful find-test-trace-isolate-support systems: How to win at snakes and ladder. Eurohealth 2020;26: 34-9.  Back to cited text no. 3
Integrated Disease Surveillance Programme. Laboratory Strengthening. New Delhi: National Centre for Disease Control; 2021. Available from: [Last accessed on 2021 Oct 24].  Back to cited text no. 4
University of Iowa Division of Sponsored Programs. CDC in India: Strengthening Laboratory Systems, Surveillance for Priority Infectious Diseases. Iowa: The University of Iowa; 2020. Available from: [Last accessed 2021 Oct 24].  Back to cited text no. 5
WHO Global Tuberculosis Programme. Global Tuberculosis Report 2021. Geneva: World Health Organization; 2021. Available from: [Last accessed on 2021 Oct 24].  Back to cited text no. 6
National Tuberculosis Elimination Programme. India TB Report 2021. New Delhi: Central TB Division; 2021. Available from: [Last accessed on 2021 Oct 24].  Back to cited text no. 7
National Vector Borne Disease Control Programme. Diseases. New Delhi: National Vector Borne Disease Control Programme; 2021. Available from: [Last accessed on 2021 Oct 24].  Back to cited text no. 8
Mohan A, Wara UU, Amjad SW, Rackimuthu S, Hunain R, Khan H, et al. Malaria amidst COVID-19 in India: Challenges, efforts, and recommendations. Clin Epidemiol Glob Health 2021;12:100867.  Back to cited text no. 9
NACO Surveillance & Epidemiology-Strategic Information Division. India HIV Estimates 2019 Report. New Delhi: National AIDS Control Organisation; 2019. Available from: [Last accessed on 2021 Oct 24].  Back to cited text no. 10
WHO Newsroom. Coronavirus Disease (COVID-19): HIV and Antiretrovirals. World Health Organization; November 2020. Available from: [Last accessed on 2021 Oct 24].  Back to cited text no. 11
Kumar S. AIDS and COVID-19 infections: Impact on vulnerable Indian population. New Microbes New Infect 2021;42:100903.  Back to cited text no. 12
Gilead, AIDS Society of India Reveals Impact of COVID-19 on Delivery of HIV Care. BioSpectrum; December 01, 2020. Available from: [Last acessed on 2021 Oct 24].  Back to cited text no. 13
Vidyarthi AJ, Das A, Chaudhry R. Antimicrobial resistance and COVID-19 syndemic: Impact on public health. Drug Discov Ther 2021;15:124-9.  Back to cited text no. 14
Knight GM, Glover RE, McQuaid CF, Olaru ID, Gallandat K, Leclerc QJ, et al. Antimicrobial resistance and COVID-19: Intersections and implications. Elife 2021;10:e64139.  Back to cited text no. 15
Sreenath K, Batra P, Vinayaraj EV, Bhatia R, SaiKiran K, Singh V, et al. Coinfections with other respiratory pathogens among patients with COVID-19. Microbiol Spectr 2021;9:e0016321.  Back to cited text no. 16
Indian Council of Medical Research. Information for Testing Laboratories. New Delhi: Published by Ministry of Health and Family Welfare (MoHFW), Government of India; 2020. Available from: [Last accessed on 2021 Sep 30].  Back to cited text no. 17
National Portal of India. Government e-Marketplace (GeM): Procurement Made Smart. Available from: [Last accessed on 2021 Sep 30].  Back to cited text no. 18
WHO News. How India Scaled up its Laboratory Testing Capacity for COVID19. World Health Organization: August 2020. Available from: [Last accessed on 2021 Oct 24].  Back to cited text no. 19


  [Figure 1]

  [Table 1]


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