Cesar Arias, MD, PhD
Cesar A. Arias MD PhD (project 1 lead; Co-PI, communicating PI, Administrative Core Lead). Dr, Arias is Professor of Medicine and Molecular Genetics specializing as an infectious diseases physician-scientist with more than 28 years of experience in the AMR field focused on Gram-positive organisms (particularly working on VRE) and genomics of antimicrobial resistant pathogens (>170 publications in the field). He is currently director of CARMiG and Chair of GCC-AMR and also directs the Center for Infectious Diseases at UTHealth School of Public Health. Work from his laboratory has resulted in high-impact publications describing novel mechanisms of resistance. His laboratory has recently focused on the genetic and biochemical bases of daptomycin and antimicrobial peptide resistance in enterococci resulting, among other applications, in the change in the clinical breakpoint of daptomycin. Additionally, he has robust genomics expertise studying the population genetics of multi-drug resistant pathogens both in the USA and abroad and serves actively within the NIH-funded Antimicrobial resistance Leadership Group (ARLG; leading one of the two sequencing facilities and as PI of the international component), and serves as editor of Antimicrobial Agents and Chemotherapy.
Kevin Garey, PharmD
Kevin W. Garey, PharmD, MS, FASHP (Co-I Projects 1 and 3). Dr. Garey is Chair, Department of Pharmacy Practice and Translational Research, Professor of Pharmacy Practice at the School of Pharmacy, University of Houston and is an internationally recognized expert on clinical aspects related to C. difficile and infection caused by other priority antibiotic-resistant pathogens. Dr. Garey is a member of the Infectious Diseases Society of American (IDSA) Committee and will advise on diagnostic aspects and statistical development of the infectious disease risk algorithms for use in its application in assessing infection risk to C. difficile, VRE and ESBL/CRE pathogens. Dr. Garey’ role on the project will be to advise on clinical infectious disease biomarkers for patient classification, as well as identify patients with pathogen colonization.
Rosa Gonzales, MBA
Rosa Gonzales, MBA (Fiscal Oversight). Ms. Gonzalez' career has focused on business administration aspects, with special emphasis in the health care industry. I am currently a Senior Administrative Manager at The University of Texas – McGovern Medical School, Division of Infectious Diseases, Center for Antimicrobial Resistance and Microbial Genomics (CARMiG), supporting Dr. Cesar A. Arias, Professor of Medicine, Microbiology and Molecular Genetics. I obtained a Bachelor's Degree in Public Relations in 1994 at the Universidad de Costa Rica in San Jose, Costa Rica, a Bachelor's Degree in Human Resources Management in 2005 at the American Intercontinental University in Chicago, Illinois, and a Master’s Degree in Business Administration in 2007 with concentration in Operations Management at the American Intercontinental University in Chicago, Illinois. Before working in the health care industry, I had the opportunity to work in different international organizations such as the Deutsche Gesellschaft für Technische Zusammenarbeit-Cooperation in the Forestry and Timber Sectors (GTZ-COSEFORMA) as Chief of Public Relations, and the Inter-American Institute for Cooperation on Agriculture of the Organization of American States (IICA-OAS) as Office Manager for the General Directorate where I helped with negotiating agreements with the Secretaries of State of the governing bodies that consisted of 34 member states in different countries of Latin American, the Caribbean and Spain. Additionally, I was selected to work with the Organization of American States as an international observer during the electoral process of Nicaragua, Guatemala and Mexico.
Tony Haag, PhD
Anthony Haag PhD (Functional genomics core co-lead). Dr. Haag is Assistant Professor at Baylor College of Medicine and Director of the Metabolomics and Proteomics laboratory at Texas Children’s Microbiome Center. His primary research focus is on applying mass spectrometry to understand the metabolic functions and pathways of the human gut microbiome and its signaling mechanisms. Dr. Haag has assembled a core group of staff experienced in the field of mass spectrometry (MS) and specializes in metabolite and protein identification, quantification, and biomarker discovery. His laboratory is proficient in performing both targeted and untargeted metabolomics analysis using a variety of instrumentation and personal expertise. Due to the emergence of multi-drug resistant microorganisms, his lab specializes in developing new assays that allow for the rapid monitoring of antibiotic-resistant organisms. He currently engages in direct collaboration with other institutions in devising rapid antibiotic susceptibility assays for clinical bacterial isolates.
Blake Hanson, PhD
Blake Hanson PhD (Functional genomics core co-lead). Assistant Professor and Associate Director of Microbial Genomics at CARMiG. Dr. Hanson is an expert in infectious disease transmission and colonization dynamics, microbial genomics, and bioinformatics. As a postdoctoral associate, he focused on the study of the human microbiome and AMR, developing and applying the latest generation sequencing technologies to the study of how the bacteria and viruses within the human microbiome impact the development of disease. Within CARMiG, Dr. Hanson has built extensive sequencing and analysis capabilities, including a high-performance analysis cluster, an Illumina HiSeq 4000, and an Oxford Nanopore GridION X5. His laboratory has developed a research platform focusing on elucidating complex antimicrobial resistance mechanisms from clinically relevant bacteria using next- and third-generation DNA and RNA sequencing, and applying those same methods and techniques to the detection of antimicrobial resistance determinants in microbial communities and the study of how those mechanisms move throughout the microbial communities. As the co-lead of the Functional Genomics Core, Dr. Hanson will assist Dr. Haag by applying his robust expertise with high-throughput DNA and RNA sequencing techniques, and application of bioinformatics to microbial genomics and molecular epidemiology.
Tor Savidge, PhD
Tor Savidge PhD (project 3 lead; Co-PI). Dr. Savidge is Associate Professor at BCM, Associate Director of the Texas Children’s Microbiome Center and a Full Member of the NIDDK-funded Texas Medical Center Digestive Diseases Center. His NIH-funded research has focused on emerging research concepts, including the involvement of the host-microbiome interactions in the induction of intestinal infectious disease. As PI of an independently NIH-funded gut microbiome research laboratory focusing on neuroimmune-microbe interactions, his U01, R01, R21 and CTSA-funded research efforts have focused on C. difficile pathogenesis, with recent investigative efforts including the discovery of novel small molecule modulators of host susceptibility to infection. Through his work, identification and quantification of metabolites and proteins in patient fecal specimens have been facilitated by targeted and global mass spectrometry techniques developed as functional biomarker technology with several patents issued. Dr. Savidge has authored >100 primary manuscripts, 6 patent filings, and edited 1 book on microbial imaging for the Methods in Microbiology series. He currently serves as Chair of the Microbiome and Microbial Diseases Section of the American Gastroenterology Association Institute Council; he is also an expert microbiome panel adviser for several NIH academic and small business study sections, as well as for the 2035 NASA Mars Mission, and serves on the editorial board for the American Journal of Physiology.
Sam Shelburne, MD, PhD
Samuel Shelburne, MD PhD (project 2 lead; Co-PI). Dr. Shelburne is an infectious diseases physician-scientist and a Professor in the Departments of Infectious Diseases and Genomic Medicine at MDACC. Leader of the Microbiome Working Group at MDACC, he has published extensively on leveraging the microbiome to predict infections in immunocompromised patients. His laboratory also has an active AMR research program which encompasses a broad array of pathogens impacting immunocompromised persons. For example, he has defined mechanisms and risk factors for the development of tetracycline, fluoroquinolone, and β-lactam resistance amongst streptococci in additional to leveraging genomics techniques to study the proliferation of multi-drug resistant Acinetobacter baumannii and Staphylococcus epidermidis. His stature in the AMR field is evidenced by his recent appointment to the steering committee of the Antibiotic Resistant Leadership Group with a mandate to expand work on highly susceptible patients. Moreover, he is the primary mentor on a K01 Mentored Scientist Career Development Award form NIAID that merges microbiome and AMR investigation. His laboratory has developed exciting new automated tools to identify and predict AMR mechanisms in gram-negative bacteria using whole genome sequencing data including working with Dr. Arias on how accessory gene amplification impacts carbapenem resistance.
Suzanne Tomlinson, PhD, MBA
Suzanne Tomlinson PhD, MBA (Administrative Core). Dr. Tomlinson is the Director of Research Programs for the Gulf Coast Consortia (GCC) and also coordinates all academic and research activities of CARMiG and GCC-AMR. She has > 20 years of project management experience of both small (5+ members) and large (>500 members) teams not only in scientific research, but also in small businesses, nonprofit organizations, and various boards and advisory committees. Her primary responsibilities include direction of the 10 GCC research consortia and clusters. She has played a crucial role from the inception of the GCC-AMR cluster through the development of inter-institutional agreements and operations for shared resources, providing a platform for seamless cross-institutional collaboration that has led to large annual conferences and monthly seminars focused on AMR research, and grants (funded and/or submitted) to support AMR projects and training programs. In addition, she co-developed and directs the award-winning GCC Rigor and Reproducibility certificate program and manages the John S. Dunn Foundation Collaborative Research Award Pilot Grant Program.
Todd Treangen, PhD
Todd Treangen PhD (FUSE core, Co-I) is an Assistant Professor of Computer Science at Rice University, and faculty member of the Institute for Biosciences and Bioengineering (IBB) faculty member and Systems, Synthetic, and Physical Biology (SSPB) graduate program at Rice University. He has over 15 years of experience in Computational Biology and Bioinformatics. Dr. Treangen is also the co-founder of the COVID-19 International Research Team (COV-IRT, www.cov-irt.org), Maryland Bioinformatics Lab (MarBL, https://github.com/marbl/), and MidAtlantic Microbiome Meetup (M3, http://blog.umd.edu/m3/).
Dr. Treangen’s research group at Rice University is primarily focused on developing computational tools for microbial comparative genomics, computational microbial forensics, and metagenomics (www.treangenlab.com). Examples of published computational tools Dr. Treangen has helped develop include: (i) Mash: a MinHash based global distance estimate that allows for rapid all-versus-all global sequence comparison, (ii) MetaCarvel: a graph-based approach for teasing out biologically-relevant variation from metagenomic samples, and (iii) ParSNP: a multiple genome alignment tool designed for closely related bacterial genomes, capable of aligning thousands of intraspecific bacterial genomes in frugal computational environments. Dr. Treangen will assist Dr. Hanson and Dr. Haag by bringing his bioinformatics experience specific to microbial genomics and metagenomics to bear to the FUSE core, and focus on the development of novel computational tools and methodology to help ignite the FUSE core in support of the three DYNAMITE P01 projects.