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Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals (BJGMC), Pune, India

Facility

The Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals (BJGMC) Campus facilities are centrally located in the city of Pune (population 4 million) in the state of Maharashtra. It has 375 faculty and 2020 staff, supports a 1500-bed tertiary care facility, which cares for >60,000 inpatients and >525,000 outpatients annually. The hospital has 14 clinical departments and 3 laboratory departments. The BJGMC Medical School is AC-NIELSEN ranked as one of the top 10 medical colleges in India. BJGMC/Sassoon is a public hospital, administered by the Ministry of Health of the State of Maharashtra. It has one of India’s largest HIV public sector HIV care centers that is funded by the National AIDS Control Organization of India and the Maharashtra State AIDS Control Society. Over 60,000 patients have been registered since 2005. First-line and second-line HIV treatment is provided for free, along with routine HIV monitoring labs. It also has an Indian Government Revised National TB Control Program (RNTCP) center where over 4000 patients are evaluated for TB each year. The TB/Chest Department has an outpatient facility and a 65-bed inpatient ward; there are 4 full-time and 2 part-time faculty, 15 residents and 6-8 clinical nurses. They evaluate 75-100 outpatients and 10-15 inpatients admissions daily. TB patients are screened daily Mondays through Saturdays in both inpatient and outpatient facilities. BJGMC also has Department of Psychiatry that has 6 full time faculty including 2 psychologists and 10 residents. It has daily OPD of 120-150 patients and 60 bed inpatient facility. It is well equipped to provide psycho-diagnostic and psychotherapeutic services for deaddiction and mental health illness.

Pharmacy

The BJGMC-JHU CRS Central Research Pharmacy is located on the 2nd floor of the Infosys building on the BJGMC campus. Study products will be received, stored, and prepared for dispensing in the Central Research Pharmacy. Research participants are not seen in the Central Research Pharmacy. The 216 square feet pharmacy has a lockable window, a secured door, and a sink. The pharmacy has floor-to-ceiling fixed open shelves built in the wall near the drug preparation table and also on the wall above the sink, and a drug preparation counter made of granite marble stone with marble shelving to store pharmacy supplies. There is

additional shelving on the wall above the computer desks for storage. In addition, there is a large locked metal shelved storage cabinet, one open shelved metal rack, a large glass-door file cabinet, two single glass-door refrigerators, an air conditioner system comprised of two alternating air conditioners to control the room temperature, three laptops, printer/copier machine, fax machine, a pharmacy-dedicated mobile phone, two work desks, a Hitex temperature monitoring device with a dedicated phone number, and digital min/max thermometers. This integrated temperature monitoring system has calling facility using a SIM card. It sends text messages to all four pharmacists on a daily basis at a particular time of day. If there is deviation then it sends text messages at first to all the pharmacists and then gives calls to all. It continues to call until a pharmacist physically acknowledges the alarm in-pharmacy. It can be plugged into a power supply and also has battery backup connected to support the equipment when there is no power. The temperature data is downloaded twice monthly and is stored electronically in the computer. The data is printed, reviewed, initialed, and kept in a pharmacy file. The temperature is also documented twice manually in the Central Research Pharmacy on working days by the pharmacists. The Central Research Pharmacy is equipped with a strong battery backup system, which has 16 batteries to support the power system in case of power failure. Key access to the Central Research Pharmacy room is limited to the study pharmacists only.Outpatient study participants are seen in the Pediatric Clinic Pharmacy, Antenatal Clinic Pharmacy, and HIV ART clinic (dedicated clinic for study patients). Participant-specific study products are prepared and labeled in the Central Research Pharmacy and are brought to the outpatient clinic pharmacies by the CRS Pharmacist on the day of the scheduled participant study visit. The chain of custody document is maintained for all the study products transported to respective clinics. The study products are kept in a cooling incubator (maintained at 23-25°C) or refrigerated until dispensed to the study participants by the CRS Pharmacist. Any un-dispensed participant-specific study products are brought back to the Central Research Pharmacy for storage.

Inpatient study participants are admitted to the maternity ward or the inpatient ward. Participant-specific study products are prepared and labeled in the Central Research Pharmacy and are brought to the inpatient unit by the CRS Pharmacist. The study products are kept in a cooling incubator or refrigerator if required and administered to the participant by the study nurse or study clinician. Any unused participant-specific study product is brought back to the Central Research Pharmacy. These areas are described in more detail below:

Pediatric Clinic Pharmacy – is located on the ground floor of the Pediatric Building of the hospital. This pharmacy room is in the Pediatric Clinic where the pediatric patients are seen for study visits. This 100 square feet area is equipped with continuous air conditioning with two air conditioners, one locked cooling incubator, one locked refrigerator, continuous temperature monitoring device, min/max thermometers in the refrigerator and incubator, two metal open-shelved racks, one small closed metal cabinet, and a sink. The data from the temperature monitoring device are downloaded twice monthly and the temperature from the min/max thermometer is documented manually on work days by the pharmacists. This pharmacy can be used for long-term storage of the study products and can serve as backup for Central Research Pharmacy if required. The Pediatric Clinic Pharmacy is always locked and key access to the incubator, refrigerator, and pharmacy room is limited to the study pharmacists only.

Antenatal Clinic (ANC) Dispensary Pharmacy – is located in the Antenatal clinic of the hospital on the first floor of the main hospital building. The total area is about 93 square feet. There are wooden cabinets for storage and one locked cooling incubator, which is monitored by a continuous temperature data logger and a min/max thermometer. The temperature data from the data logger are downloaded weekly and the temperatures from the min/max thermometer are documented daily manually by the pharmacists. The ANC Dispensary Pharmacy is always locked when not in use. Key access to the ANC Dispensary Pharmacy is limited to the study pharmacists only.

Labor and Delivery Room Incubator – a cooling incubator is located in the Labor and Delivery Room on the third floor of the hospital. This incubator will be used for participant-specific study product storage for the perinatal studies. The continuous temperature data logger and continuous digital min/max thermometer are placed in the incubator to monitor the temperature. The temperature data from data logger are downloaded weekly and the temperatures from the min/max thermometer are documented on work days manually by the pharmacists. The incubator is always locked and key access to the incubator is limited to study pharmacists and study nurses only.

Ward No. 15 Inpatient Dispensing Area – is used for dispensing inpatient study drugs for adult patients. It is located on the 2nd floor of the main hospital building. This 40 square foot room has been used for DAIDS studies A5225 for a cryptococcal meningitis trial and is available for future inpatient studies. There is one cooling incubator and a refrigerator. The biosafety cabinet that was installed in this room to prepare sterile products has been dismantled; however, a new space is available to re-install the biosafety cabinet for any future studies. The incubator and refrigerator temperatures will be monitored by a temperature data logger and temperature data will be downloaded weekly and min/max thermometers will be used to record the temperature manually on work days by study pharmacists once this area is in use for any future study. The incubator and refrigerator are always locked. Key access to the incubator and the refrigerator is limited to the study pharmacists and study nurses.

The clinics and wards of the hospital are not air-conditioned and the ambient temperature exceeds the temperature range required for study product. As a result the BJGMC-JHU CRS centralizes drug storage in the Central CRS Pharmacy and Pediatric Clinic Pharmacy, which meet all requirements for primary and backup air conditioners, backup power generators, and out-of-temperature-range notification. Combined with dispensary locations in the Pediatric Clinic, ANC, maternity ward, and inpatient unit, which are well equipped with temporary drug storage, temperature monitoring capabilities, and full time study pharmacist services for all Network studies, the BJGMC-JHU CRS Pharmacy is able to provide support to a varied participant population in pediatric, maternal health, HIV treatment and prevention, and opportunistic infection protocols. The BJGMC-JHU CRS Pharmacy has successfully managed DAIDS research activities by following GCP and adhering to India’s regulatory requirements for research.

Laboratory

The BJGMC lab has established laboratory infrastructure for various testing. It has the capacity to perform more than 50 lab analyses required by the NIH trials networks and other studies. All protocol-related lab activities (phlebotomy, sample receiving, processing, specimen management) are done in Laboratory Data Management System (LDMS) and others (FreezerPRO, Nautilus, hematology, cytology PAP staining, PBS and microscopy, chemistry, thyroid hormone testing,HemoglobinA1c, rapid tests for HIV, malaria, chikungunya, serology, CD4, viral load HIV,HPV, Xpert CT/NG, HPV, cytokines, chemokines and diabetic panels on BioPlex-Multiple immunoassay system, ELISAs for HIV, HBV, HCV, Dengue and cytokines, flow cytometry immunology assays, IGRAs like QFT Plus assay etc.) are performed at the central Clinical Research Site (CRS) lab. The lab also performs processing for specialty immunological assays. Furthermore, the site has capacity to store biorepository at -80C and in Liquid nitrogen and can store samples long term if required. Appropriate temperature monitoring system and electricity backup are installed. The site also has separate set up for PBMC processing and cryopreservation and has IQA certification by Duke Human Vaccine Institute. The laboratory also performs Cytometric bead array (CBA), ADCC, ADCP and Mtb antigen specific ELISAs assays.

Fig 1: Safety lab testing Fig 2: Safety lab testing

Currently, several projects have ongoing like diagnostic studies in TB and TB/HIV, including TB in pregnant women and children, TB meningitis in children, minimal TB in children, as well as, a TB and household contact

cohort study with specimen biobanking. Studies in neonatal sepsis, maternal colonization, antimicrobial resistance, Dengue, Chikungunya and Zika diagnosis in pregnant women have also recently been conducted.

Fig 3: PBMC processing lab Fig 4: Sample processing lab

The BJGMC Clinical Research (CRS) Lab is set up in the Infosys Building at the BJ Government Medical College(BJGMC) and Sassoon General Hospitals(SGH). Approximately 1500 square feet is used for sample collection, processing, safety labs, serology, immunology, PBMC cryopreservation and repository with LDMS. There is a separate virology area of 300 sq ft at BJGMC. The Research Lab facility includes facilities like readers(2) and washers(2) for ELISA testing, biosafety cabinets (6) for sample handling for BSL-2 lab, water baths (2), centrifuges (3), refrigerated centrifuges (5), refrigerators (7), -20C freezers(2), -80C freezers (15) and Liquid Nitrogen canisters (6) for long term specimen storage PBMCs. The Virology Lab has an Abbott m2000RT PCR and ABI 7500DX instruments with minispin, multi pipettes, BSC-2, dry heat block for HIV-1 RealTime assay for HIV confirmation and RealTime High Risk HPV assay and other PCRs like HSV, Dengue, Chikungunya and Zika.

Specimen Collection and TransportThe specimens are collected at the TB and other clinics and are transported to the CRS laboratory using transport carriers with biohazard labels and at appropriate temperatures. The samples are received in lab, accepted as per standard procedures. The appropriate testing is performed in the CRS lab and results are generated and data files are completed for specified research studies.

External Quality Assurance ProgramThe CRS laboratory has participated in OneWorld Accuracy (OWA) and College of American Pathologists (CAP) programs for external quality assurance of safety, microbiology, serology testing. The following survey panels are received either 2 or 3 times in a year. There is CAP EQA for hematology, blood gas, hemoglobin A1c, and OWA EQA for bacteriology, chemistry, urine pregnancy testing, cryptococcus antigen testing, body fluids, mycology, anti-HIV ELISA and rapid testing, hepatitis ELISA, and urinalysis. The CRS laboratory also participates in Immunology Quality Assurance (IQA) program run by Duke University for PBMC Cryopreservation, 4x/year, UKNEQAS for Lymphocyte subset 6x/year, and for Interferon gamma release assay 6x/year, Virology Quality Assurance (VQA) Program 4x/year, run by Rush University for viral load. The evaluations are overseen by Patient Safety Monitoring and International Laboratory Evaluation (pSMILE).

NIH-sponsored auditsThe CRS laboratory is evaluated annually by NIH-sponsored safety and quality auditors including Pharmaceutical Product Development (PPD) and Westat/Family Health International. All reports are assessed by Patient Safety Monitoring in International Laboratories (pSMILE) to ensure the integrity and reliability of tests.

Laboratory safety and trainingLaboratory and clinical staff that handle human specimens are required to undergo safety training. Training includes instruction on handwashing, use of personal protective equipment, safe handling of sharps,

transportation of clinical specimens, exposure to blood or body fluids, and use of emergency personal protective equipment and occupational health and safety. Written policies exist for testing of exposed healthcare workers, testing of source patients, and post-exposure prophylaxis. Training also includes chemical, mechanical, electrical, and fire safety. Policies exist for the investigation of incidents with corrective action and reporting. Training for comprehensive waste management is also included. A TB-specific infection control procedure is in place mandated by the NIH ACTG and IMPAACT Network trials.

CRS Repository FacilityThe CRS repository has 15 -800 C freezers of approx. 500L capacity, 2 -200 C freezers, and 6 LN2 canisters including 1 automatic filling LN2 freezer. The study specimens from numerous studies have been well stored for long-term storage. The repository includes serum, plasma, PBMCs, cell pellets, body fluids, breast milk, saliva, urine, hair, dried blood spots, stimulated blood, stimulated plasma, sputum, and Mtb and bacterial culture isolates. There are approximately 300,000 specimens currently banked in freezers from several studies.

Temperature Monitoring System (TMS)There are 3 Temperature Monitoring Systems with 32, 16 and 8 probes available at the BJGMC CRS repository, safety and PBMC laboratories. These monitor and record the temperature at specific intervals and are active 24hoursx7days/week. The TMS system gives audio visual indication when temperature is out of limits and also indicates which channel temperature is out of limit. The TMS is provided with battery backup up to 3 hours and is connected to a computer. TMS software allows the data from TMS to be routinely downloaded into the PC for analysis. Automatic report generation is done and observed in Excel and has the following systems: 1) Alerts are received via SMS mentioning the channel that goes out of limit and blank calls from the TMS. Also on a daily basis, SMS with the status of each channel is sent to the concerned lab staff; 2) Alerts are received via calls from the TMS, which mention the channel that goes out of limit.

Laboratory Data Management System (LDMS) Currently LDMS version 13.0.0.23 is uploaded on the system. The BJGMC Laboratory currently uses LDMS, a comprehensive program designed by NIH-contracted Frontier Science and Technology Research Foundation, Inc. (FSTRF) for laboratories conducting medical research. We use LDMS to log and view specimen data; keep an accurate inventory of specimens by allocating locations in the freezer, create shipping manifests for specimens that need to be shipped to other laboratories; run assays and retrieve result data and create reports on specimen data for some assays. The specimens are entered with the details like PID, collection date/time, primary specimen type, additives, derivatives number of aliquots and quantity. The specimen has been allocated and tracked by unique global ID. All the specimen details appear on the self-adhesive label using Brady BP PR300PLUS printers (3) available at site lab. Other specimen management systems like FreezerPRO, Global trace and Nautilus are available at site and used for specific studies.

CRS Repository Freezers

CRS Repository LN2 Canisters

Cytokine analysis facility: We have the Bioplex 200- Multiplex Immunoassay system (Biorad), available on leased basis, to run protein cytokine analysis. We have leased this before for our various publications.

Offices and Computers: All clinical faculty have desktop computers that are connected to the internet and the campus email server. There is a centralized printer, scanner and photocopy facility in the data center. Research staff hired under BJGMC have access to the BJGMC CRS office resources (located in the Pathology Museum and the Data Center on the BJGMC Campus), which include >10 HP desktop computers that are connected to a T-LAN line for high speed internet, a centralized HP laser printer, scanner and photocopier. All Project staff, working under the JHU India Pune office, have laptop computers connected via wireless internet to the central server through which they get access to high speed internet and network printers. In addition, CRS laboratory key staff has HP laptops (14) and desktops (08), internet facility, scanners, printers and xerox facilities available.

Fig 5: Molecular virology facility

BJ Government Medical College - Pathology/Histopathology LaboratoryThe Histopathology laboratory is located at first floor of BJGMC and comprises approximately1500 square feet of space equipped with penta-head microscopes, paraffin embedding automated tissue processor, microtome and paraffin dispensing station. Special staining procedures are performed including PAS, SM, reticulin, Gram, and AFB. In Cytology, body fluid cytology and fine needle aspiration cytology (FNAC) with Leishman staining and PAP staining for cervical cytology is done. There is set up for clinical pathology in the hospital lab. The hematology testing is performed using 5 parts-diff hematology analyzers-SysmexXS800i in BJGMC research lab.

BJ Government Medical College - Bacteriology Laboratory (under Clinical Microbiology Department)The Bacteriology Laboratory is located on the first floor of BJGMC and comprises approximately 1000 square feet of space. It is equipped for manual and automated laboratory methods for bacteriological testing. There is a separate 400 square foot media preparation room to perform sterilization of media with two autoclaves for sterile work and one for discard used media. The conventional microscopic methods using various stains, wet mount, and culture methods, drug susceptibility testing are used for routine testing along with serological tests like VDRL, TPHA and RPR whereas facility like BD BACTEC™ 9120 Blood Culture System, BD Phoenix™ Automated Microbiology System are shared with CRS laboratory and used for research purpose. The Vitek2-Biomerieux bacterial culture identification and antibiotic susceptibility system has recently installed and in use. There are autoclaves, incubators, Vortex, microscopes to support testing. The laboratory is NABL accredited.

BJGMC Mycobacteriology LaboratoryWe have established TB microbiology laboratories (BSL-2+ as well as a BSL-3) with the help of BJGMC administration and the NIH-funded AIDS Clinical Trials Network (ACTG) and IMPAACT networks. This is a shared space between the BJGMC clinical microbiology department as well as the TB research team. Approximately 800 square feet of space was given by BJGMC and renovated to accommodate the BSL-3 and BSL 2+ laboratories. The BSL -3 laboratory is equipped with 2 biosafety hoods & 2 MGIT(Mycobacterial Growth Indicator Tube) 960 machines. The BSL 2+ is equipped with 3 biosafety hoods ,2 Refrigerated centrifuges, and an unsterile refrigerator,& 1-MGIT 960.The smear staining area is also accommodated in the BSL-2 + laboratory along with the eyewash station. The Bactec MGIT 960 machine is an automated liquid bacterial culture machine. The Drug sensitivity testing for first-line as well as second-line TB drugs is also performed by liquid culture using the MGIT.

The laboratory is validated and approved for the following tests:1) AFB smear microscopy- (ZN & FM)2) MGIT- liquid culture3) MGIT-First line Drug Susceptibility Testing4) MGIT- Second line Drug Susceptibility Testing5) Gene Xpert6) Gene Xpert Ultra7) LJ-Solid Culture.8) Line Probe Assay.( For 1st Line as well as 2nd Line)

The ante room of the BSL 2+ lab has a sterile fridge and a Sample receiving area. All the samples received are checked in this area against lab requisition forms and then transported inside the BSL 2+ for processing

The third room in TB area houses a walk in Incubator in one part of the room. The other part of the room is used for Microscopy and LJ readings An oil immersion microscope as well as a fluorescent reading microscope is available A walk In Cold Room is also present near the laboratory.

The fourth room is a Molecular room which has two DAIDS funded Cepheid–Gene Xpert IV/IV and XVIII/VIII installed. The molecular room also has a dedicated LPA area where cabins are built as required by the LPA protocol.

BSL-3 lab

BSL-2+

Microscopy

A separate area has been built behind the laboratory, which houses the media preparation room, room temperature storage of required material as well as one sterile and one discarding autoclave.

Specimen collection, storage and transportOur lab has worked to optimize the quality of patient specimens for TB diagnostics. We have developed SOPs and have ongoing assessments of collection procedures, transport times and transport conditions. We have standardized checklists for research clinicians and our TB lab staff who undergo scheduled QA/QC review. Samples are collected at various locations in the hospital and are transported to the laboratory within an hour by the attendant ensuring the maintenance of a cold chain.

BiosafetyWe have a BSL-3 and a BSL-2+ laboratory. All the necessary personal protection equipment have been provided and are being used by the staff. All of our staff have been trained and implement infection control and laboratory safety procedures.  We also assess the tuberculin skin test status, X- rays and basic hemogram of all staff yearly. We restrict access to the Lab allowing only trained lab staff to enter the area. We have yearly safety re-trainings as well as safety audits conducted by our Safety Officer.

Temperature Monitoring SystemThe laboratory has a temperature monitoring system, which is used to monitor the temperature of the key equipment’s in the laboratory.

Data ManagementA small area above the TB Lab has been converted into a Lab Data Management Center. The data from all the studies carried out the TB laboratory is managed in this place. The completion of all source documents, report completion as well as uploading the data in the respective software is completed here. All the source documents from the laboratory are also stored and maintained in this area.

Current Mycobaceriology workloadAnnually, our CRS TB research laboratory processes approximately 3500 sputum samples for AFB smear, Gene xpert, culture DST and LPA. The Research laboratory processes samples for the network as well as the non-network protocols including pediatric and woman oriented protocols. Along with sputum, the laboratory also has the capacity to process gastric aspirate/lavage as well as extrapulmonary samples.

Sassoon Hospital is also part of India’s Revised National TB Control Program (RNTCP) and a separate clinical staff processes an additional 8000 samples for AFB smear in another area of the hospital. The Routine TB microbiology laboratory also processes approximately 2000 – 2500 samples, which include pulmonary as well as extrapulmonary samples from the patients visiting the hospital.

External Quality Assurance (EQA) statusSince 2009, BJGMC Mycobacteriology Laboratory has participated in EQA. Initially, samples were received from in the College of American Pathologist (CAP) EQA program (E-A, B/ Five simulated clinical isolates and one specimen for performing an acid-fast bacillus smear, DST and ID shipments twice a year). Currently, the TB lab performs the INSTAND EQA for Smear, Culture Identification & first Line as well as second line DST. The lab receives 6 slides for staining & 5 samples for decontamination and culture detection of Mycobacteria, along with 5 other samples for drug susceptibility testing (DST). The panels are received for each of the above tests twice a year. EQA is also performed for Gene Xpert from NHLS-South Africa. These consist of 4 dried spots/panel 3 times a year.

The lab is also enrolled for LPA EQA with NHLS-South Africa with 3 panels / year for first-line as well as second-line LPA. The laboratory also performs EQA evaluation for Qualitative testing from pSMILE twice a year.

Data Management

The TB laboratory is NABL accredited as well as certified by National Mycobacteriology Certification System of Central TB division- Ministry of Health, Government of India for Tuberculosis Culture and Drug Susceptibility testing by conventional culture based DST for first line anti Tb drugs.

The BJGMC CRS Study Laboratory Information Management System (SLIMS)Additionally, the site is equipped with SLIMS (Study Laboratory Information Management System) designed by CTIS Inc, USA. The purpose of this software application is to digitally implement: specimen collections, processing, testing and lab result reporting. The scope of SLIMs includes, but not limited to, importation of patient demographic information from parallel data management program, patient registration, specimen collection, transport of specimens, processing of specimens, and result reporting. The digital system has reduced manual efforts and space constraints.

The BJGMC CRS Data Management CenterThe BJGMC CRS Data Management Center has two data servers (HP ProLiant ML 110 G6) and 8 computers of which 4 are exclusively used for data entry and the remaining are used by key data management personnel. The data management also has two Sony laptops used as a back-up and for staff trainings. In addition, the CRS has 44 workspaces in various clinic locations for CRS staff to access study-related documents (i.e., participant visit logs, study protocols) stored on the server. All the computers are password protected and connected via a LAN and have wired high speed, uninterrupted Internet connection. In addition to the central internet connection the data management team and key personnel have USB internet connection as a back-up. The BJGMC CRS has 6 printers (3 network and 3 non-network) and 2 Cannon photocopy machines. All equipment are on annual maintenance contract and are serviced once every 3 months.

BJGMC Community Outreach Mobile Van The Van is available to provide study outreach for cohort and trial participants. In addition, the van has a mobile chest Xray machine, a Gene Xpert machine for TB testing, a refrigerator to keep samples collected in the field, a clinical bed and a counseling room to deliver services and educate and inform people in the community.

Laboratory Testing CapacityChemistry XHistology XToxicology NAHematology XImmunology XCD4 XImmunology/Serology XVirology X

HIV Viral Load XHIV DNA or Total Nucleic Acid X

HIV Resistance Genotyping  Metabolic tests XMicrobiology XPharmacology Cytology XSpecimen processing XTB XUrinalysis X

X: capacity on-site, NA: not applicable