In February 2011, Texas Children’s Microbiome Center successfully relocated to the 9th floor of the hospital’s main research facility, the Feigin Center.
In February 2011, Texas Children’s Microbiome Center successfully relocated to the 9th floor of the hospital’s main research facility, the Feigin Center. Since the move, extensive effort has been made to standardize uni-directional workflow (a requirement for molecular laboratories) and designate areas in the laboratory as required (“clean” areas for reagents, “dirty” areas for samples and nucleic acid manipulation). TCMC is now fully-operational with dedicated efforts in core functions (including the DNA sequencing core), research and bioinformatics.
While transitioning the project to TCMC, recruitment of new research assistants and faculty members has been crucial. The newly assembled team has a vast amount of experience and current expertise in the field of clinical molecular diagnostics, metagenomics, next-generation sequencing and bioinformatics. With a fully-staffed and trained group of researchers, TCMC is well poised to move rapidly through the next few years of the research plan.
Year one milestones and measurable outcomes encompassed both the discovery and development phases of the project.
Transition from DNA chips to DNA sequencing methodologies: This milestone has been accomplished with a fully-functional next-generation sequencing pipeline (454 technology) housed within TCMC.
selection of optimal nucleic acid (DNA and RNA) extraction for blood culture, stool, spinal fluid, respiratory, blood and tissue samples (Year one- One optimal extraction method per specimen type): The optimal DNA extraction method has been determined and continues to be refined in a series of progressive steps. Currently, TCMC has developed DNA extraction methods suitable for downstream sequencing for stool samples, tissue samples and cultured bacterial samples. Initial development work is being pursued on sputum and blood samples. A sample stability agent is also being investigated as a resource for the preservation of nucleic acids (DNA and RNA) in a variety of specimen types. Both DNA and RNA isolation method optimization from those samples is in progress.
Development of sequencing methods for important bacteria/viruses in blood culture, stool, spinal fluid, respiratory, blood and tissue samples (Year one- One optimal sequencing protocol per specimen type): Next-generation sequencing methodology (using 454 technology) is currently undergoing standardization within TCMC. Two targets important in bacterial identification are currently in use for bacterial culture, stool and tissue samples. These targets will also be useful in the sequencing of sputum and blood samples.
Submission and Internal Review Board (IRB) approval of human studies protocols: Several pilot studies involving bacterial identification in the pediatric population have been approved by the IRB. Additional protocols regarding specific specimen types (ie, sputum) are in progress and will be submitted soon.
Discover candidate pathogens or new human microbes/viruses: With the new broader approach to pathogen identification by next-generation sequencing, more baseline data must be generated before novel/candidate pathogens can be identified. TCMC core is ready to generate primary sequencing data and now has the bioinformatics resources to perform the necessary data mining and downstream analyses to identify candidate pathogens.
Research and development pertaining to many aspects of pediatric infectious disease have been made possible thanks to the generous support of the Grant-A-Starr Foundation. These efforts are allowing us to remain on the cutting-edge of diagnostic development. Molecular epidemiology research related to antibiotic-resistant bacteria was presented at the Association for Molecular Pathology (AMP) Annual Meeting in November 2010 and resulted in Dr. Ruth Ann Luna receiving the AMP Young Investigator Award. Additional work related to real-time sequencing for bacterial identification in clinical samples has been submitted for presentation at this year’s meeting. In addition, an article titled “Rapid stool-based diagnosis of Clostridium difficile infection by real-time PCR in a children’s hospital” was published in the Journal of Clinical Microbiology in March 2011.
The donation received from the Grant-A-Starr Foundation continues to provide salary support for research and development personnel and is allowing us to obtain the reagents and consumables needed for our ongoing development. The Division of Molecular Pathology was pleased to welcome Jessica Runge and Yue Shang, two new research assistants within TCMC with responsibilities pertaining to Texas Children’s Diagnostic Research Project. Jessica is a clinically certified molecular technologist, and Yue has many years of experience in metagenomics and is simultaneously pursuing her Ph.D. in public health.