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FACILITIES & RESOURCES

Johns Hopkins University School of Medicine

Johns Hopkins Center for Clinical Global Health Education Research (CCGHE)

The Johns Hopkins Center for Clinical Global Health Education (CCGHE) is a center of excellence supporting clinical care, clinical research, and research training in resource-limited settings that complements and builds upon the extensive ongoing international, collaborative research and training programs at the Johns Hopkins School of Medicine and the Johns Hopkins Bloomberg School of Public Health. The Center has a large IndoUS clinical research program where clinical trials and observational cohorts on HIV and TB are conducted in Pune, Chennai, Mumbai and other sites in India. The Center also uses innovative technology including telemedicine and elearning to bring the expertise of Johns Hopkins faculty, from both laboratory and clinic, to the world’s neediest countries and people.

Office Space. The CCGHE space encompasses approximately 2100 square feet with private offices, shared office space and a conference room/classroom which seats 20 people. The shared office space area is equipped with computers, telephones, fax and photocopy machine, and will serve as “a home base office” to the trainees where they will be provided with workstation space during their time at Hopkins.

Computers. All staff have Pentium processor Dell computer systems with 2 monitors, HP Laserjet 2420 printer, and appropriate software. The PCs are running Windows 2013 and are connected to the University’s local area network (LAN) and can access the school’s UNIX server by TCP/IP protocol. This provides software compatibility and access to e-mail both internally and externally. In addition, faculty have laptop computers with a Pentium processor and Windows supported by the JHU SOM’s network service.

Conferencing Capabilities. All staff are equipped with hardware and computer software to conduct GoToMeeting® and Skype® conference calling with international partners to reduce costs while maintaining active and frequent communication. The CCGHE also has a conference service to handle multi-point calls for those partners without internet and Skype® capability.

Videoconferencing and Multimedia. The CCGHE has a conference meeting room and a fully-equipped, state-of-the art Polycom video conference studio located on the 5th floor of the Phipps building. These rooms are capable of both videoconferencing and multimedia capture and online streaming of training content and support of clinical trial and research training meetings.

Johns Hopkins Pune, India Office

Johns Hopkins has a dedicated team of research staff and office space in Pune, India to coordinate India-based research activities in collaboration with the Byramjee Jeejeebhoy Government Medical College (BJGMC) and other Indian institutions. Our Pune site has a large active clinical trials unit that conducts clinical trials and observational cohort studies funded by the NIH, CDC, Indian government and foundations. We have a NICHD funded RO1 clinical trial for pediatric TB meningitis (TMB KIDS), a NICHD RO1 prospective cohort study of immune changes of pregnancy and impact on TB-specific responses in HIV+ and HIV-negative pregnant women and their infants. We have a NIH-funded TREAT ASIA cohort of HIV-infected adults and children seeking care in the public sector HIV care program at Pune. We have two large NIH-and Indian government funded TB cohort studies (C-TRIUMPh: Cohort for TB Research by the Indo-US Medical Partnership and RePORT India: Common Protocol for Collecting Data and Specimens from Participants in the Regional Prospective Observational Research for Tuberculosis) where TB cases and household contacts are being prospectively funded. We also have 8 NIH-funded clinical trials that are being conducted as part of the International Maternal Pediatric Adolescent AIDS Clinical Trials Group (IMPAACT) and Adult AIDS Clinical

Trials Group (ACTG), including 4 related to TB. In addition, the Johns Hopkins India office manages and provides collaborative oversight of these studies with BJGMC, Pune, NIRT, and our other collaborators. There is approximately 700 square feet of office space and 400 square feet of space for the BJGMC Clinical Trials Unit (CTU) and Indo-US studies data management center. There is also approximately 700 square feet of space off-site for data archiving. The data management space is for data entry and storage (approximately 200 square feet of space is used for data storage). There are 6 workstations for data entry, plus 2 servers and 2 workstations for data managers. In addition, there are 2 HP laptops in the data center. All staff have computers, and the 8 team leaders (clinical research site leader, statistician, regulatory coordinator, study coordinator, data manager, lead pharmacist, laboratory manager, budget director) each have an HP laptop. In total, there are 30 computers at various locations. There is a networked 2 Mbps Internet service and a separate broadband speed videoconferencing line dedicated for research and training discussions for Indo-US collaborations. There are, currently 20 research staff employed under the JHU Pune India affiliate office to support Indo-US research studies. Additional staff are hired by the Indian institutions via subcontracts and our JHU group provides all necessary technical support and training for GCP, GCLP, clinical trials conduct and cohort management.

Byramjee Jeejeebhoy Government Medical College, Pune, India

Clinical InfrastructureThe 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 1450-bed tertiary care facility which cares for >60,000 inpatients and >525,000 outpatients annually. The hospital has 14 clinical departments and three laboratory departments. The BJGMC Medical School is AC-NIELSEN ranked as one of the top 10 medical colleges in India. 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 4,000 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.

Laboratory FacilitiesThe BJGMC lab has established laboratory infrastructure for multiple assays. It has the capacity to perform more than 30 lab analyses required by the NIH trials networks. All protocol-related lab activities (sample collection, receiving, processing, Laboratory Data Management Systems (LDMS) entry, specimen storage, hematology, cervical cytology and histology, chemistry, serology, bacteriology, immunology-lymphocyte subsets and cytokines, HIV, HPV, HBV RT PCR, HIV qualitative assay etc.) are performed at the central CRS lab. The lab also performs processing for specialty immunological assays, and can store samples if required. The CRS lab also performs cytokine assays using flow cytometry and Luminex platform. Appropriate temperature monitoring system with electricity backup are installed. The site has also set up PBMC processing (chemicals, reagents and liquid nitrogen storage facility are available) and is IQA certified for PBMC cryopreservation. The laboratory also performs interferon gamma release assays (IGRA) such as Quantiferon Gold in tube assay (QGIT) and Cytometric bead array (CBA) assays.

TB and Bacteriology LaboratoryBJGMC has established a microbiology laboratory (BSL-2 plus) through private donations and a public-private partnership between Becton Dickenson (BD) and the BJGMC CTU. A thousand square feet of space was

given by BJGMC and renovated to accommodate two Bactec MGIT 960 machines, an automated BACTEC bacterial culture and Phoenix system, and a new area to perform AFB smear and culture processing. The site also has a DAIDS funded Cepheid –Gene Xpert instruments in place. An area with approximately two thousand square feet has been allotted for TB lab expansion. Currently the site has diagnostic studies ongoing in TB, including a TB active and household contact cohort study, Tuberculosis with Diabetes study,TB in pregnant women and children; Antimicrobial resistance and TB, H1N1, dengue and Chikungunya studies have also recently been conducted and ongoing.

The BJGMC Research Lab is set up in the Infosys Building at the BJ Government Medical College and Sassoon General Hospital. Approximately 1200 square feet is used for sample collection, processing, safetylabs, serology, immunology, and repository with LDMS. There is a separate Molecular virology area of 500 square feet. The Research Lab has a Sysmex automated cell analyzers, Roche Cobas automated chemistry analyzers, BioRad ELISA readers and washers, BD FACS Canto II, BD FACS count,D-10 HbA1c,Roche electrolyte analyzers, BSL-2, water bath, refrigerated centrifuges, refrigerators, Lab data management system (LDMS), UPS backups, Temp. Monitoring system (TMS), -80 freezers and LN2 freezers for specimen and PBMC storage. The additional 400 square feet space has been developed as new PBMC processing lab which is equipped with BSL-2, refrigerated centrifuges, microscopes and automated cell counter for cell Viability Analyzer.

The Molecular Virology Lab has an Abbott m2000RT PCR and ABI 7500 fast DX RealTime PCR instruments with minispin, multi pipettes, BSC-2, dry heat block for HIV confirmation and RealTime High Risk HPV assay with other PCR assays like Dengue and Zika viruses.

Bacteriology Laboratory (under Microbiology Department)The Bacteriology Laboratory is located on the first floor of BJ Government Medical College and comprises approximately1000 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 BD BACTEC™ 9120 Blood Culture System, BD Phoenix™ Automated Microbiology System are used for research purpose. There are autoclaves, incubators, Vortex, microscopes to support testing. All of the equipment is present in the Microbiology laboratory.

Pathology/Histopathology LaboratoryThe Histopathology laboratory is located at first floor of BJ Government Medical College 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 also 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 the BJGMC research lab.

BJGMC Mycobacteriology LaboratoryBJGMC has established a microbiology laboratory (BSL-2) through private donations and a public-private partnership between Becton Dickenson (BD) and the BJGMC CTU. A new BSL-3 TB laboratory is under construction and completion is expected in Q3 2017. Funding was provided by the NIH, the RNTCP and philanthropic donations.

A thousand square feet of space was given by the BJGMC and renovated to accommodate two Bactec MGIT 960 machines, an automated BACTEC bacterial culture and Phoenix system, and a new area to perform AFB smear and TB culture methods. The lab is approved for AFB smear, manual LJ and DST. The TB lab is fully accredited to perform TB AFB microscopy, culture, DST and other infectious diseases diagnostics. The validation of Bactec MGIT is complete. Our lab has a DAIDS funded Cepheid–Gene Xperts installed and are used for rapid molecular TB detection and drug resistance testing. Also, BSL-3 facility and Hain Genotype Line Probe assay (LPA) will be installed soon at TB lab.  We also have a training room linked with high speed internet and videoconferencing which can be used for training Lab staff.

Specimen Collection, Storage and Transport Our 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 which are periodically monitored for quality control and quality assurance. 

The Cepheid GeneXpert System for rapid detection of M. tuberculosis and rifampicin resistance using molecular diagnostics is onsite. Validation plans have been developed for detection, identification and rifampicin susceptibility testing as compared to current methodologies. The site is enrolled in the recently established DAIDS EQA program managed by NHL South Africa.

BJGMC CRS TB/Microbiology Laboratory- BD MGIT machines for AFB Culture

BJGMC CRS Specimen Storage Facility – Sensaphone Temperature Monitoring System, Voltage stabilizers and generators for backup electricity are in place

BiosafetyWe currently have a BSL-2 lab (BSL-3 is under construction).  All of our staff have been trained and implement infection control and laboratory safety procedures.  We now assess the tuberculin skin test status of all staff on a regular basis and to date there have been no new seroconversions. We restrict access to the Lab allowing only trained lab staff to enter the area.

External Quality Assurance (EQA) StatusSince 2009, our Mycobacteriology Laboratory has participated in the INSTAND EQA program includes 2 surveys for performing an acid-fast bacillus smear, DST and ID shipments in a year). Described below are the completed validations and approvals and currently has switched to INSTAND EQA survey. Mycobacterial Culture ValidationManual solid Lowenstein Jenson (LJ) culture method validation: Our Laboratory performed LJ culture validation from August 2010 to 5 November 2010. A total of 153 (140 positive and 13 negative) cultures were processed with serial dilutions of 3 ATCC and 8 strains from CAP EQA specimens using autoclaved patient sputa as the matrix. The validation study was reviewed and approved by SMILE. BD Mycobacterial Growth In Tube (MGIT) liquid culture system validation: Our Laboratory has performed MGIT validation between July 2011 to March 2012 on patient samples, ATCC cultures and EQA strains. The validation plan was reviewed and approved by SMILE. The laboratory has maintained EQA certification for NIH TB trials.

RepositoryOur Laboratory has 8 large -800 C freezers, two -200 C freezer, and three LN2 freezer. The four -800 C, two LN2, 2 temp. Monitoring systems of 32 and 8 channels and UPS for power back up will be added in the facility soon. The study specimens from numerous studies have been well stored for long-term storage without any problems, including from TB studies in children and pregnant women (e.g. serum, plasma, whole blood, saliva, hair, PBMCs, sputum and TB isolates from adult and pediatric TB cases and QGIT supernatant from adult, pediatric and pregnant women).

Temperature Monitoring System (TMS)Temperature Monitoring System with 8 and 32 probes are available at BJGMC repository and monitors and records the temperature at specific intervals. It 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 4 hours and is connected to a computer. TMS software allows the data from TMS to be downloaded into 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

BJGMC CRS Core Laboratory- Sample Processing in Sterile Biosafety hood

BJGMC CRS TB/Microbiology Laboratory- Specimen processing for AFB under Sterile Biosafety Hood

calls from the TMS which mention the channel that goes out of limit.

Laboratory Data Management System (LDMS) current version 12.1.0.16Our BJGMC Laboratory currently uses LDMS, a comprehensive program designed by 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 disks and manifests for specimens that need to be sent to other laboratories; run assays and retrieve result data and create reports on specimen data. The specimens are entered with the details like PID, collection date/time, primary specimen type, 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. There is 1 server and 3 clients LDMS stations are available in CRS and TB lab for specimen entries and to maintain repository.

Offices and ComputersAll 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 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 liaison office, have laptop computers connected via wireless internet to the central server through which they get access to high speed internet and network printers.

The 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 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.