The Department of Microbiology came in to existence as an independent department in the year 1987 with bifurcation of the combined departments of Pathology and Bacteriology, under the Headship of Prof. U. C. Chaturvedi till March 1999. Thereafter, Prof. S. K. Agarwal headed the department till December 2008. After his retirement, Prof. Mastan Singh took over the reins and after his superannuation on October 16th 2016, Prof. Amita Jain took over as the current Head of the Department. The department has contributed immensely to the teaching, training, patient care and research in Microbiology. This is one of the most developed departments in the state of Uttar Pradesh and recognized nationally for quality testing, research and training. Currently the department handles more than 4 Lac specimens annually for various diagnostic tests. The department comprises ten independent divisions, ten faculty positions, six MD seats and three PDCC seats. The divisions are Bacteriology, Virology, Mycology, Parasitology, Serology, HIV and ICTC, Hospital infection surveillance, Covid-19 lab, Tuberculosis lab and Trauma emergency lab. We are NABL accredited laboratories with all TB and HIV tests. Virology lab based on its outstanding performance since inception in 2010, supported by the Indian council of Medical Research/ Department of Health Research (DHR) and Ministry of Health and Family Welfare Government of India, it was selected as one of the 13 labs from throughout India for initially conducting SARS CoV-2 testing. Covid -19 Lab of our department are mentoring all state labs for Covid testing and Nodal lab of UP. By July 2021, lab tested more than 23 lac Covid-19 samples by RTPCR; which is highest number of covid-19 samples RTPCR tested in India by any single lab. ICMR has declared KGMU as a Centre of Excellence for Covid-19 testing. HIV and ICTC lab has the status of State Reference Laboratory. In our department RTI/STI state reference centre running since 2010 and WHO surveillance centre for diphtheria and Pertussis since 2016. ICMR funded antimicrobial resistance surveillance centre since year 2018. TB lab is recognized as Intermediate Reference Laboratory since 2006. Department received a grant from ICMR to develop Advanced Mycology Diagnostic and Research Centre at KGMU in 2021. Department gets students registered in the University for PhD and MD-PhD courses. The Department has a very vibrant academic bent and often organizes CMEs/ hands on workshops and Faculty of the department is awarded many Honours, awards and prizes. Few retired faculty members have received several honours like FNA and S.S. Bhatnagar awards. Research work done by the faculty is recognized nationally as well as internationally. Several research projects are conducted by the faculty regularly and papers are published in various scientific journal of repute by the faculty of the department.
The department has following functionally independent divisions:
COVID milestones:
By July 2021, lab tested > 21 lac COVID-19 samples by RTPCR; which is HIGHEST NUMBER OF COVID-19 SAMPLES RTPCR TESTED IN INDIA. It was untiring journey of a year 2020 from 72 samples/day to 7200 samples /day. Other COVID-19 testing platforms available at KGMU are Gene-Xpert and Truenat, Abbott RealTime SARS-C0V-2 assay, Ag detection-RDT and Antibody detection- both RDT and ELISA. Lab are mentoring all state labs for COVID testing and Nodal lab (State Reference Lab) of UP- which is a huge task considering UP is the state with the highest number of RT-PCR labs in the country. Developing existing lab space and design in terms of equipment specifications and procurement, reagent specifications and ensuring quality.There is ongoing training task to hand-hold and troubleshooting state’s manpower for RTPCR testing and biomedical safety measures related to COVID-19. Till date we trained all BSL-2 labs performing RT-PCR testing including 10 new BSL-2 labs, 7 new district hospital labs, 25 RT-PCR labs in Public sectors and all the pvt sector medical college labs. Several SOPs, power point presentations and videos have also been prepared those are available on the University website and can be freely accessed by anyone for guidance. KGMU is also running an ICMR-Inter Laboratory Quality Control (ILQC) program for all COVID-19 RT-PCR labs both public and private in UP. The lab’s efforts have been recognized nationwide and ICMR has declared KGMU as a Centre of Excellence for COVID-19 testing. KGMU is given the Centre of Excellence for validation of new diagnostics kits by ICMR: Till date around 40 test kits have been validated by KGMU. Kits manufactured under MAKE IN INDIA were promoted and supported by us. KGMU identified UK/South African COVID mutant COVID strains in UP state by S gene sequencing. KGMU worked efficiently in managing surplus COVID-19 online ICMR-U.P. state portal data and incorporated newer technologies to integrate ICMR and UP state online portal. We are collaborating in various National and international COVID-19 scientific projects.
1.VIROLOGY MILESTONES (OTHER THAN COVID)
Virology laboratory is a high end diagnostic center, which offers a range of endorsed quality assured testing services for diagnosis of viral diseases. Laboratory is supported by ICMR and DHR in which most of the test are offered free of cost not only indoor/outdoor patients of our large tertiary hospitals in UP.
Besides COVID-19 testing, the lab also enjoys the title of "national center for quality assurance of scrub typhus testing by serological and molecular methods" and one of the centers for "National Hepatitis control program". It is also one of the state level laboratories of DHR that has always been on the forefront for conducting outbreak investigations, be it Dengue, Chikungunya, swine flu (Influenza A, H1N1) or Acute Encephalitis Syndrome besides providing diagnostic services for in and out patients visiting hospitals attached to KGMU. The facility provides accurate diagnosis within 24-48 hours of receipt of samples thereby facilitating patient tailored treatment.
Till date more than 200,000 samples have been referred from throughout UP and adjoining states like Bihar and Uttarakhand. The lab has State of the Art BSL- 2 and BSL- 3 facilities armed with latest technology diagnostic equipment like Next Gen Sequencer, capillary sequencers, tissue culture instruments, fluorescent microscope, Real time PCR machine, conventional PCR machine, ELISA and chemiluminescence assay systems etc. It has the technical expertise to diagnose more than 31 human pathogenic viruses using serological, molecular methods, immunofluorescence or cell culture techniques. The lab is well recognized by the national and International agencies viz. Centre for Disease Control and Prevention, Atlanta, NIMHANS, Bangalore, NIV, Pune for clinical diagnosis and genomic research on pathogenic viruses. VRDL is also actively involved in training of post-graduate candidates in MD, MD-PhD and PhD courses and offering training to other laboratories and hospitals in the state. In last 5 yrs, it has published more than 80 research papers in esteemed national and international journals having good citations. More than a thousand sequences have been submitted in the GenBank of National centre for biotechnology, USA and 8 patents are filled in Indian patent agency.
Test offered by laboratory in the form of serological (ELISA) and molecular (PCR) assays are as follows-Test for AES/AFI panel (Japanese Encephalitis virus, dengue virus, Chickungunya virus, Herpes simplex virus-1 & 2, Scrub, Enterovirus, VZV, Rabies, West Nile virus, Zika virus, Rhino, BK, JC and Adenovirus ), Test for SARI/ILI panel(Influenza A, B,Parainfluenza,Respiratory syncytial virus, Measles, Human Boca virus, Human meta-pnuemo virus), Test panel for PUO pyrexia of unknown origin( ParvoB-19 virus, EBV-Epstein barr virus and CMV- Cytomegalo virus)Test for TORCH panel (IgM antibodies ELISA for anti-CMV, anti- Rubella, anti-HSV),Test for acute and chronic viral hepatitis (Acute Hepatitis A, B, E and chronic hepatitis C with viral load and sequencing & hepatitis B with its markers- HBsAg, HBeAg, HBeAb, antiHBc and antiHBs titer along with viral load) Laboratory is also performing different test for COVID-19 diagnosis which includes RT-PCR, Rapid antigen test, truenat, CBNAAT and Antibody testing. Most of the virology tests are interlinked with NIV Pune and IAMM-EQAS program for quality assurance.
2.Bacteriology:
Clinical Bacteriology diagnostic laboratory is involved in isolation and identification of wide range of bacterial pathogens from different clinical samples. Bacterial antibiotic susceptibility testing is performed to identify antibiotic-resistant bacteria and determine optimal therapeutic options by latest Clinical Laboratory Standard Guidelines (CLSI). More than 40,000 samples are processed annually and division ensures accurate identification and timely reporting and prevention of infections. Other activities include culture media preparation, media & glass ware sterilization, etc. A large number of locally isolated and standard bacterial cultures are maintained in stock vials and by lyophilization. Serotyping of bacteria including Salmonella, Vibrio and Shigella is also done. Standard CLSI guidelines are followed in reporting and laboratory SOP is also available. Extensive work is being done on isolation and identification of fastidious bacteria including Pneumococcus, C. diphtheriae, H. influenzae, Gonococcus, etc. National Shigella Centre laboratory is a referral centre and has expertise in Shigella culture and identication. The laboratory is equipped with state-of-the-art instruments and assays which makes it possible to diagnose infectious diseases by conventional and automated methods. The laboratory is well equipment and keeps incorporating latest technology for rapid pathogen identification. It has VITEK 2 Compact System automated ID/AST for fast and accurate identification of pathogens. Automated culture machines are available for blood and sterile body fluid cultures (Bactec and BacT alert).MALDI-TOF mass spectrometer for bacterial identification is now available in arsenal of diagnostic tools. MALDI-TOF stands for Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry, an instrument that allows our microbiologists to quickly identify bacteria based on the organism's protein composition. The MALDI-TOF uses a unique "protein fingerprint", or spectra, from the bacteria of interest, which is then compared to a library of known spectra to produce an identification. Thanks to this technology the bacteriology lab can identify bacteria as early as one day after the specimen arrives at the laboratory. Once the microorganism is isolated it can be accurately identified within minutes rather than 2-7 days using traditional testing methods. This allows Bacteriology lab to produce accurate and molecular-based results faster than ever.This division is also involved in patient driven research related activities. Research work on Pneumococcus, C.diphtheriae, MRSA, VRE, CONS, Uropathogenic E.coli, recurrent UTI, childhood infections including pneumonias, neonatal meningitis neonatal septicaemia is being carried out currently. Since year 2012, we have been identified as regional centre for laboratory diagnosis of reproductive tract infections/sexually transmitted diseases. As part of this program we participate in EQAS for serological tests for syphilis and IAMM EQAS for baceriology. Extensive work on epidemiology of Rickettsial diseases in also been done. We have been recently identified as regional center for WHO sponsored "Diphtheria surveillance project" an ambitious country wide project. PCR for methicillin resistant Staphylococcus aureus (MRSA), M. tuberculosis, Chlamydia trachomatis and Chlamydia pneumoniae are being done for research purposes.
3.Tuberculosis laboratory:
Tuberculosis (TB) laboratory is one of the most technologically advanced laboratories in State that provides highest quality and consultative diagnostic services for Tuberculosis. The laboratory is proud to be recognized as "Intermediate Reference Laboratory" and it supports the State TB Control Programme with its diagnostic services, training, supervisory and external quality assurance services (to district/ peripheral laboratories) and advisory services since 2006.
Over time, TB laboratory has expanded its facility, services and capacity. Currently with capacity of about 120 tests per day, the laboratory offers a range of microbiological tests (liquid and solid culture drug susceptibility test, Cartridge based nucleic acid amplification test, Line Probe Assay, Fluorescent microscopy) endorsed by WHO. The continued commitment of laboratory to excellence is demonstrated through technically advanced equipments (GeneXpert, MGIT 960, GT Blot, LED-FM etc), specialized lab facilities (like BSL-3 and LPA Labs), LIMS for better patient care and laboratory operation, accreditation from highest accreditation body in India (NABL) and trusted service delivery by professional and highly trained staff. A feather in the cap has been the recent installment of 16 moduleGeneXpert machine that has further increased the testing capacity of the lab. All laboratory services are supported by State TB Cell, U.P., Central TB Division, MoHFW, New Delhi and other International NGOs(like FIND, PATH, USAID etc.)
TB Laboratory undertakes basic, epidemiological as well as operational research studies and the momentum and quality of scientific work is always kept up. The laboratory also provides training and research opportunity to MD students and Ph.D Scholars; and conducts CME / workshops time-to time for clinicians, scientist and laboratory professionals
4.Serology Lab
Various serological tests including VDRL, RPR, TPHA, WIDAL, ASO titres, CRP and Rh factor are being done routinely in this laboratory. Numerous ELISAs are carried out including for Scrub typhus, Brucellosis, Typhi dot, Leptospirosis. Immunofluorescent microscopy, Dark field microscopy for spirochaetes is also done for diagnosis of various pathogens. Procalcitonin a sepsis marker is also done.
5.Mycology Lab
The clinical mycology laboratory helps in the diagnosis of various fungal infections in patients coming from Uttar Pradesh, its adjoining states and neighbouring countries such as Nepal and Bangladesh. This laboratory very efficiently helps in the diagnosis of deep, systemic, superficial and subcutaneous mycosis. Identification of fungi is done both by conventional and the latest MALDI-ToF based Vitek MS. This laboratory also caters antifungal susceptibility of yeast such as Candida spp, Cryptococcus spp. and filamentous fungi such as Aspergillus spp., Fusarium spp. Zygomycetes and Dermatophytes both by disk diffusion and gold standard broth micro dilution method (BMD). Besides identification and antifungal susceptibility, antigen based tests such as Aspergillus Galactomannan antigen both from serum and BAL; and Cryptococcal antigen both from CSF and serum are also available. This division is also involved in various research activities such as molecular identification of fungi from blood in cancer patients, Fungal rhinosinusitis, Fungal infections in HIV patients, Ventilator associated fungal infections and Eumycetoma. To keep a check on the quality of work, mycology lab also participates in the medical mycology EQAS.
6.HIV lab and ICTC:
This lab enjoys the status of State Reference Laboratory and is also NABL accredited. The lab is equipped with all the modern equipment and has facilities for performing pre and post test counseling, rapid tests, CD4 counts, HIV viral loads etc. The machine has now also been approved for COVID-19 testing and will be used for the same also.
7.Hospital Infection surveillance:
There is an active hospital Infection Surveillance team. Samples are collected from various Operation theatres/wards etc. Quantitative air sampling of surgical OT's is done by air sampler. Laboratory participates in active bacteriological surveillance in Operation theatres and various wards of the hospital. Hospital infection control lab is also responsible for preparation of antibiogram for the associated hospitals half yearly. Research work is carried out on antimicrobial resistance in bacterial pathogens at phenotypic and genotypic level and molecular typing of bacterial isolates is also done for hospital acquired infections.
8.Parasitology:
The clinical diagnostic parasitology laboratory is well-equipped laboratory, which offers service for the identification of a wide range of human parasites from various clinical specimens. Routine diagnostic services are available for malaria, filarial, intestinal parasites, stool examination, etc. Rapid diagnostic tests (RDTs) are available for Malaria, filarial, Kala azar, etc. Newer tests have been introduced to detect Entamoeba, Crytosporidium, Echinococcus, Cysticercosis, etc by ELISA test. Studies on pathogenesis of visceral leishmaniasisare also conducted.
