Research, Research Training and Training Grants
Houston Methodist Hospital offers excellent research opportunities in infectious diseases, mentored research training, training grants and scholarships with > $ 20 million in direct costs of NIH funding for the division. Projects involve a variety of topics including molecular mechanisms of resistance, microbiome science in immunocompromised and critically ill patients, VRE bacteremia, resistance to novel agents in Gram-negative organisms, genomics and bioinformatics in infectious diseases, phage therapies, treatment of LVAD infections, artificial intelligence and nanotechnology in infectious diseases and animal models.
The Houston Methodist Center for Infectious Diseases: As a result of major investments during the COVID-19 pandemic, Houston Methodist has launched a new Center for Infectious Diseases. James Musser, MD, PhD, Chair of the Department of Pathology and Genomic Medicine and Cesar Arias MD PhD, Chief of the ID division, serve as Center Director and co-Director, respectively. The Center will leverage the outstanding initiatives launched during the pandemic with faculty in the Departments of Medicine (Division of Infectious Diseases and Critical care), Pathology and Genomic Medicine, Infection Prevention and Control, Pharmacy, the Center for Outcomes Research, and the Cockrell Center for Advanced Therapeutics.
The current laboratories include:
Genomics and Bioinformatics at the Houston Methodist Center for Infectious Diseases: The Houston Methodist Center for Infectious Diseases has established a robust infrastructure for whole genome sequencing, which plays a crucial role in the routine workflow for studying SARS-COV-2 and antimicrobial resistant pathogens in the ICU. The center's Genomics and Bioinformatics division operates a cutting-edge BSL-2 laboratory with specialized rooms for various tasks, including sample accessioning, RNA and DNA extraction, sequencing library preparation, and sample quality control. The facility houses an impressive range of sequencing platforms, such as the Illumina NovaSeq 6000, NextSeq 2000, MiSeqDX, Oxford Nanopore GridION X5, MinION machines, and a Promethion 2 solo sequencer, enabling comprehensive genomics and transcriptomics analysis of both infectious disease pathogens and hosts. To handle a large volume of samples efficiently, the laboratory employs advanced robotic liquid handlers from Hamilton, Eppendorf, and Raining, enhancing the precision and reliability of the assays.
For bioinformatics analysis, the center has access to the Research Institute high-performance computer (RI HPC). The HPC system features Dell 6400 servers with Intel Xeon Gold 6240 CPUs (36 cores, 376 GB memory) and a private network connection for compute nodes. The head node comprises Lenovo ThinkSystem SR650 servers equipped with Intel Xeon Gold 6348 CPUs (112 cores, 256 GB memory) and high availability for enhanced performance. Additionally, a GPU node utilizes Lenovo ThinkSystem SR650 servers with Intel Xeon Gold 6326 CPUs (64 cores, 256 GB memory) and NVIDIA A100 GPUs to accelerate computationally intensive tasks. Moreover, a big memory node incorporates Lenovo SR650 servers with Intel Xeon Gold 6348 CPUs (112 cores, 2 TB memory) and an NVIDIA A10 GPU, providing ample resources for memory-intensive operations. The HPC system is efficiently managed using Bright/NVIDIA Cluster Manager and SLURM, while storage needs are catered to by an Infinidat F6260 system. With this state-of-the-art infrastructure, the center can perform advanced genomics and bioinformatics analysis to further the understanding of infectious diseases.
The Academy of Physician-Scientists: This program was selected as one of only ten medical schools in the nation to receive a highly prestigious Burroughs Wellcome Fund (BWF) Physician-Scientist Institutional Award to catalyze highly innovative programs for training non-PhD physicians for successful academic careers as physician-scientists. In partnership with Texas A&M University Health Science Center, College of Medicine, and College of Engineering, and the Texas Medical Center, the Houston Methodist Academic Institute (HMAI) is part of the Burroughs Wellcome Fund Academy of Physician Scientists, which serves as a pipeline for attracting and nurturing medical students, residents and fellows to pursue successful research careers as physician scientists. This initiative provides funding for intensely mentored research training and a robust curriculum within a community of physician scientists and engineers and is expected to foster and expedite opportunities to progress from student to resident to fellows and develop a new generation of physician-scientists who are highly competitive for independent research careers.
NIH T32 Training Program on Antimicrobial Resistance (TP-AMR) hosted by the Gulf Coast Consortia: Antimicrobial resistance (AMR) has become one of the top public health priorities worldwide. Our new, innovative, inter-disciplinary and multi-institutional AMR program will train the next generation of physicians, physician-scientists, PharmDs and PhD researchers on the complex, multifaceted and challenging problems that AMR presents. Trainees will be immersed in the rich and fertile environment of the Houston Texas Medical Center and will interact at the interface of clinical practice, basic science, drug discovery, public health and hospital epidemiology. Our world-class AMR researchers, existing resources, institutional support, administrative organization and a collaborative, cross-disciplinary environment already in place offer the perfect platform for a high-quality training program encompassing 8 major biomedical research institutions. The goal is to provide the training, skills, and tools needed to translate research findings into actionable items in the clinic and to translate patient-based observations back into the laboratory to counteract AMR in patients across the medical spectrum.
Houston Methodist Academic Institute (HMAI): The Houston Methodist Academic Institute is the cornerstone of Houston Methodist’s position as a nationally recognized academic medical center. The Academic Institute’s two components, the Research Institute and Education Institute, include 775 faculty, 2,047 credentialed researchers, 41,344 learners, 900 active clinical studies, and $64.1 million in total extramural funding. Annual research expenditures of $158.5 million and education expenditures of $37.8 million support the Houston Methodist mission of leading medicine. The Academic Institute facilitates the interchange of ideas among the clinical, research, and education pillars of Houston Methodist while coordinating academic strategy for the system. The Research Institute provides critical research programs and infrastructure to bring new scientific discoveries to patients as rapidly as possible through translational medicine. Its research goals are closely aligned with the academic resources for Houston Methodist Hospital’s Centers of Excellence. The Education Institute coordinates Graduate Medical Education and Continuing Medical Education. The Academic Institute has primary affiliations with Weill Cornell Medicine, New York Presbyterian Hospital, and Texas A&M Health Science Center. In 2021, the Weill Cornell Graduate School of Medical Sciences expanded its PhD program in Physiology, Biophysics & Systems Biology to the Houston Methodist Academic Institute. This allows accepted students to complete their research studies in Houston while being jointly mentored by faculty from both sites.
Houston Methodist Research Institute: Established in 2004 as part of the Academic Institute, the Houston Methodist Research Institute (HMRI) is the research enterprise of Houston Methodist. HMRI supports research and education programs at Houston Methodist by providing the platform technologies, research programs, administrative support, staff, and facilities needed to rapidly translate laboratory discoveries into new diagnostics, therapies, and treatments. This groundwork mission of leading medicine is founded in a commitment to bring medical breakthroughs to patients by investing in clinical, research, and education innovation. HMRI has 775 faculty and 2,047 credentialed researchers with a portfolio of $153.8 million annual investment in research. HMRI is housed in the Research Institute Building (RIB), a modern 440,000-sq. ft. building adjacent to the main hospital, and it hosts the laboratories of many faculty members as well as outstanding facilities for basic and clinical research. HMRI strives to drive innovative research through participation in several collaborative centers and consortia, including 19 interdisciplinary departments, 19 various research programs, and 6691 worldwide collaborations in 136 countries. Also maintaining formal affiliations with Texas A&M University, Weill Cornell Medical College, Weill Cornell Medicine Graduate School of Medical Sciences, and the University of Houston, the vertically integrated laboratories together with technological resources provide investigators, physician scientists, and their collaborators rapid and seamless progression from ideas to improving patient experiences at the bedside.
Research training structure during the ID fellowship
- The goal of research training is to provide the fellows with the skills to be effective and efficient in doing research, in the context of a specific research project. The expectation will be that the fellow has a presentation at a regional or national conference and a manuscript prepared ready for publication toward the end of the 2nd year of ID fellowship.
- Early in the fellowship there will be dedicated seminars where the fellow can learn about research methods, the different research faculty and their areas of research. This will be followed by one-on-one opportunities to interact with each of the faculty in the first few months of the fellowship to identify the right mentors based on the fellows’ interests and fit.
- Once the research project and mentors are identified, the fellow and their mentors are responsible for presenting their progress at research in progress meetings every three months. Research faculty from different areas of expertise in the Texas Medical Center will be invited to these meetings and will give useful feedback to the presenter.
- A RRC (Research Review Committee) will critically review the progress and evaluate the research project every three months, and give actionable feedback.
- After completion of the research project there will be a final presentation towards the end of the 2nd year.
- By the end of the first year or early in the 2nd year of fellowship the fellow can let the program director and the RRC know if he desires to pursue the 3rd year clinical investigator track. The RRC will review the progress and determine eligibility for the 3rd year of research.
Current research
The Houston Methodist Center for Infectious Diseases: As a result of major investments during the COVID-19 pandemic, Houston Methodist has launched a new Center for Infectious Diseases. James Musser, MD, PhD, Chair of the Department of Pathology and Genomic Medicine and Cesar Arias MD PhD, Chief of the ID division, serve as Center Director and co-Director, respectively. The Center will leverage the outstanding initiatives launched during the pandemic with faculty in the Departments of Medicine (Division of Infectious Diseases and Critical care), Pathology and Genomic Medicine, Infection Prevention and Control, Pharmacy, the Center for Outcomes Research, and the Cockrell Center for Advanced Therapeutics.
The current laboratories include:
Laboratory for Antimicrobial Research (PI: Cesar Arias): The laboratory is focused on a multidisciplinary approach to combat antimicrobial-resistant pathogens. Projects span from basic molecular mechanism of resistance including microbial biochemistry, genomics, microbiome science to clinical trials that are conducted within the Division of infectious diseases. Specific projects mostly funded by grants from the NIH include molecular mechanisms of daptomycin resistance in enterococci, clinical and genomic epidemiology of enterococcal infections, the clinical impact and molecular basis of the cefazolin inoculum effect in methicillin-susceptible Staphylococcus aureus, dynamics of colonization and infection by multidrug-resistant organisms in critically ill and immunocompromised patients, resistance to cefiderocol in Pseudomonas aeruginosa, artificial intelligence for susceptibility testing, Candida colonization in liver transplant patients, novel approaches in diagnostic microbiology. - Laboratory for Molecular and Translational Human Infectious Diseases Research (PI: James Musser): Investigators in this laboratory are interested in many areas of contemporary infectious disease research, including molecular mechanisms of pathogenesis, human genetics of susceptibility to infectious agents, and vaccinology. We are interested in a diverse range of pathogens and the diseases they cause, including but not limited to group A Streptococcus, group B Streptococcus, Mycobacterium tuberculosis, and Staphylococcus aureus.
- Laboratory of Antibody Discovery & Accelerated Protein Therapeutics (ADAPT) (PI: Jimmy Gollihar, PhD): The work in ADAPT encompasses a broad range of engineering biology, from the design of simple genetic “parts” and circuits to protein engineering and industrial biomanufacturing. Dr. Gollihar uses synthetic biology applications to domesticate non-model organisms and engineer proteins or biosynthetic pathways with therapeutic and industrial potential. He applies a holistic approach to protein engineering by integrating concepts from directed evolution, rational design, and artificial intelligence to create biological countermeasures, diagnostics, and vaccine candidates. Recently, ADAPT has contributed to the genomic surveillance and characterization of SARS-CoV-2, B-cell repertoire mining for neutralization and protection assays, and the engineering of enzymes intended for mRNA vaccine manufacturing
Genomics and Bioinformatics at the Houston Methodist Center for Infectious Diseases: The Houston Methodist Center for Infectious Diseases has established a robust infrastructure for whole genome sequencing, which plays a crucial role in the routine workflow for studying SARS-COV-2 and antimicrobial resistant pathogens in the ICU. The center's Genomics and Bioinformatics division operates a cutting-edge BSL-2 laboratory with specialized rooms for various tasks, including sample accessioning, RNA and DNA extraction, sequencing library preparation, and sample quality control. The facility houses an impressive range of sequencing platforms, such as the Illumina NovaSeq 6000, NextSeq 2000, MiSeqDX, Oxford Nanopore GridION X5, MinION machines, and a Promethion 2 solo sequencer, enabling comprehensive genomics and transcriptomics analysis of both infectious disease pathogens and hosts. To handle a large volume of samples efficiently, the laboratory employs advanced robotic liquid handlers from Hamilton, Eppendorf, and Raining, enhancing the precision and reliability of the assays.
For bioinformatics analysis, the center has access to the Research Institute high-performance computer (RI HPC). The HPC system features Dell 6400 servers with Intel Xeon Gold 6240 CPUs (36 cores, 376 GB memory) and a private network connection for compute nodes. The head node comprises Lenovo ThinkSystem SR650 servers equipped with Intel Xeon Gold 6348 CPUs (112 cores, 256 GB memory) and high availability for enhanced performance. Additionally, a GPU node utilizes Lenovo ThinkSystem SR650 servers with Intel Xeon Gold 6326 CPUs (64 cores, 256 GB memory) and NVIDIA A100 GPUs to accelerate computationally intensive tasks. Moreover, a big memory node incorporates Lenovo SR650 servers with Intel Xeon Gold 6348 CPUs (112 cores, 2 TB memory) and an NVIDIA A10 GPU, providing ample resources for memory-intensive operations. The HPC system is efficiently managed using Bright/NVIDIA Cluster Manager and SLURM, while storage needs are catered to by an Infinidat F6260 system. With this state-of-the-art infrastructure, the center can perform advanced genomics and bioinformatics analysis to further the understanding of infectious diseases.
Training grants and support for trainee research
The Academy of Physician-Scientists: This program was selected as one of only ten medical schools in the nation to receive a highly prestigious Burroughs Wellcome Fund (BWF) Physician-Scientist Institutional Award to catalyze highly innovative programs for training non-PhD physicians for successful academic careers as physician-scientists. In partnership with Texas A&M University Health Science Center, College of Medicine, and College of Engineering, and the Texas Medical Center, the Houston Methodist Academic Institute (HMAI) is part of the Burroughs Wellcome Fund Academy of Physician Scientists, which serves as a pipeline for attracting and nurturing medical students, residents and fellows to pursue successful research careers as physician scientists. This initiative provides funding for intensely mentored research training and a robust curriculum within a community of physician scientists and engineers and is expected to foster and expedite opportunities to progress from student to resident to fellows and develop a new generation of physician-scientists who are highly competitive for independent research careers.
NIH T32 Training Program on Antimicrobial Resistance (TP-AMR) hosted by the Gulf Coast Consortia: Antimicrobial resistance (AMR) has become one of the top public health priorities worldwide. Our new, innovative, inter-disciplinary and multi-institutional AMR program will train the next generation of physicians, physician-scientists, PharmDs and PhD researchers on the complex, multifaceted and challenging problems that AMR presents. Trainees will be immersed in the rich and fertile environment of the Houston Texas Medical Center and will interact at the interface of clinical practice, basic science, drug discovery, public health and hospital epidemiology. Our world-class AMR researchers, existing resources, institutional support, administrative organization and a collaborative, cross-disciplinary environment already in place offer the perfect platform for a high-quality training program encompassing 8 major biomedical research institutions. The goal is to provide the training, skills, and tools needed to translate research findings into actionable items in the clinic and to translate patient-based observations back into the laboratory to counteract AMR in patients across the medical spectrum.
Houston Methodist Academic Institute (HMAI): The Houston Methodist Academic Institute is the cornerstone of Houston Methodist’s position as a nationally recognized academic medical center. The Academic Institute’s two components, the Research Institute and Education Institute, include 775 faculty, 2,047 credentialed researchers, 41,344 learners, 900 active clinical studies, and $64.1 million in total extramural funding. Annual research expenditures of $158.5 million and education expenditures of $37.8 million support the Houston Methodist mission of leading medicine. The Academic Institute facilitates the interchange of ideas among the clinical, research, and education pillars of Houston Methodist while coordinating academic strategy for the system. The Research Institute provides critical research programs and infrastructure to bring new scientific discoveries to patients as rapidly as possible through translational medicine. Its research goals are closely aligned with the academic resources for Houston Methodist Hospital’s Centers of Excellence. The Education Institute coordinates Graduate Medical Education and Continuing Medical Education. The Academic Institute has primary affiliations with Weill Cornell Medicine, New York Presbyterian Hospital, and Texas A&M Health Science Center. In 2021, the Weill Cornell Graduate School of Medical Sciences expanded its PhD program in Physiology, Biophysics & Systems Biology to the Houston Methodist Academic Institute. This allows accepted students to complete their research studies in Houston while being jointly mentored by faculty from both sites.
Houston Methodist Research Institute: Established in 2004 as part of the Academic Institute, the Houston Methodist Research Institute (HMRI) is the research enterprise of Houston Methodist. HMRI supports research and education programs at Houston Methodist by providing the platform technologies, research programs, administrative support, staff, and facilities needed to rapidly translate laboratory discoveries into new diagnostics, therapies, and treatments. This groundwork mission of leading medicine is founded in a commitment to bring medical breakthroughs to patients by investing in clinical, research, and education innovation. HMRI has 775 faculty and 2,047 credentialed researchers with a portfolio of $153.8 million annual investment in research. HMRI is housed in the Research Institute Building (RIB), a modern 440,000-sq. ft. building adjacent to the main hospital, and it hosts the laboratories of many faculty members as well as outstanding facilities for basic and clinical research. HMRI strives to drive innovative research through participation in several collaborative centers and consortia, including 19 interdisciplinary departments, 19 various research programs, and 6691 worldwide collaborations in 136 countries. Also maintaining formal affiliations with Texas A&M University, Weill Cornell Medical College, Weill Cornell Medicine Graduate School of Medical Sciences, and the University of Houston, the vertically integrated laboratories together with technological resources provide investigators, physician scientists, and their collaborators rapid and seamless progression from ideas to improving patient experiences at the bedside.