Evaluation of MiSeq for Microbial Identification in Specimens

Blood Stream Infections

Sequence Technique, Infectious Disease, Pathogen Detection, Diagnostic, Natural History

Background: Researchers are testing a new way to find out what causes infections in people in hospitals. Current techniques use chemical or biological tests on a person s samples. Samples are blood, tissue, stool, saliva, urine, etc. Researchers are testing new techniques that use a device called MiSeq. It can sequence all of the DNA (genetic material) in a sample. This may show microorganisms, such as bacteria, fungi, and viruses that cause infection. Researchers want to know if the new test works as well or better than current tests. They will do this by looking at about 250 samples. Objective: To test if MiSeq works as well as or better than current tests to identify microorganisms that cause infection. Eligibility: NIH patients whose samples have been sent to the Microbiology Service s lab for routine microbiologic testing. Design: Participants will consent to have samples they gave as part of their routine medical care used in the study. For those under age 18, a parent or legal guardian will consent.

The purpose of this study is to evaluate and optimize testing that uses a next-generation DNA sequencing instrument, Illumina MiSeq, along with the associated computer infrastructure and bioinformatics software required for sequence analysis. This system is ultimately intended for use by the NIH Clinical Center Department of Laboratory Medicine to identify infectious agents in primary patient specimens. Next generation sequencing techniques based on sequencing of total DNA from primary specimens are expected to have many advantages over classical microbiological approaches. These include the detection of pathogens directly from primary specimens that may be difficult or impossible to culture. In this study, discarded patient samples and autopsy material will be tested with the MiSeq system to identify and classify bacteria, viruses, and other pathogens. For the purpose of this study, the term samples will refer to any sample such as swabs, tissue biopsies, blood, feces, saliva, urine, wound, etc. The investigators analyzing the sequencing results will be blinded to the microbiology culture results for a validation subset of specimens to be tested with the MiSeq system. The results of the MiSeq analysis will be converted into a form that can be compared with the Microbiology Services official culture results that are stored in the laboratory information system (software from SCC SOFT Computer \[Clearwater, FL, USA\]).

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