CDC Expands MicrobeNet Pathogen Library With Help From Industry

By Lori Solomon, Editor, Diagnostic Testing & Emerging Technologies

The U.S. Centers for Disease Control and Prevention (CDC) recently announced another new partnership with industry to expand the utility of its MicrobeNet library of more than 2,400 rare and emerging infectious bacteria and fungi. In May, the CDC announced a partnership with Bruker (Boston) to add a new module based on bacterial protein signatures generated from the company’s MALDI Biotyper system. Now, the CDC has announced yet another partnership with Thermo Fisher Scientific (Carlsbad, Calif.) to connect Sanger sequencing results from its Applied Biosystems Capillary Electrophoresis instruments to the MicrobeNet database. The additional species coverage will improve infectious disease diagnosis and surveillance.

MicrobeNet launched in 2013 as a way to help U.S. public health and clinical laboratories rapidly identify rare and emerging infections. Prior to MicrobeNet, laboratorians needing to identify a rare bacteria or fungi, or to confirm a diagnosis, sent a sample to CDC for testing. MicrobeNet speeds time to diagnosis and treatment by offering a library of pathogens searchable by DNA sequence or biochemical tests. While CDC has been adding to the library on a monthly basis, these two industry partnerships will further expand the library and speed the ability for diagnoses of rare and emerging pathogens.

The latest collaboration with Thermo Fisher’s MicrobeBridge software platform connects Sanger sequencing results to the MicrobeNet online reference database. This enables speedier identification of microbial pathogens that has implications for individual treatment and global outbreak investigation, Thermo Fisher says. MicrobeBridge integrates with all Applied Biosystems capillary electrophoresis instruments and automates the assembly and quality control of raw Sanger sequencing data into a searchable format in the MicrobeNet database. Thermo Fisher said in a statement that it plans to develop compatible software for its next-generation sequencing and mass spectrometry platforms as well.

The new module developed in collaboration with Bruker, allows laboratories to search the protein signatures of the bacteria and compare them to the rare pathogens in CDC’s MicrobeNet library through Bruker’s MALDI Biotyper systems. Bruker announced the results of this collaboration in June at the American Society for Microbiology (ASM) Microbe 2016 conference. The MALDI Biotyper uses high-throughput MALDI-time-of-flight (TOF) mass spectrometry and is being rapidly adopted in microbiology laboratories. Bruker says its advantages are its speed, accuracy, and extensive species coverage. This coverage is further enhanced with the CDC MicrobeNet MALDI-TOF library module. The MALDI-TOF reference library adds an additional 800 species to the microorganism reference library, which will grow with the open-library feature that enables users to generate and contribute customer-defined and validated libraries. Additionally, Bruker says, the MALDI module in MicrobeNet offers “dramatic” cost savings for clinical and public health laboratories because they no longer will need to develop their own pathogen libraries.