The Infectious Diseases Institute’s Applied Microbiology Services Laboratory (AMSL) has undergone a lot of change over the past two years. The lab was established early in 2020 in partnership with the Department of Microbiology to support collaborative and contract research with external partners with a goal of creating a unique training environment for students. Learn more about the AMSL origin story here >>
Soon after, to assist Ohio State’s Covid-19 response, AMSL assumed responsibility for SARS-CoV-2 testing across campus, allowing the university to remain as open and as functional as possible in the ‘new normal.’ Over the course of the pandemic, AMSL conducted 848,666 PCR diagnostic tests from saliva samples with an average turnaround time of under nine hours. During this time, AMSL employed a team of almost 90 lab workers, including undergraduate, graduate, and professional students as well as full-time staff. Many of those workers have since gone on to apply the skills they gained with AMSL in graduate or professional school, research, clinical work, or industry. Learn more about SARS-CoV-2 testing in AMSL here >>
Alongside these testing and training activities, ASML conducted genomic sequencing of SARS-CoV-2 saliva samples to identify variants of concern and understand better the virus’s evolution throughout the course of the pandemic. The lab purchased two Illumina NextSeq2000 instruments, conducted 150 sequencing runs, generated over 15 terabytes of data, and submitted 5,619 SARS-CoV-2 genomic sequences to the global public health database, GISAID. AMSL was the first to identify the Delta and BA.2 variants in Ohio. In addition to human samples, AMSL conducted genomic sequencing on over 1,800 wastewater samples and developed novel bioinformatics for wastewater sequencing (manuscript in review). The lab was also instrumental in the genomic sequencing of samples from white-tailed deer in Ohio, establishing their role as a reservoir for the virus. Check out this Nature article on SARS-CoV-2 in deer >>
AMSL’s Pivot to Strategic Growth Areas
This summer, AMSL pivoted away from managing a human diagnostic SARS-CoV-2 test lab to focus on developing its other microbiology- and infectious disease-related projects and services in support of IDI strategic priorities. With Ohio State’s SARS-CoV-2 human testing transitioning to the College of Medicine, AMSL is now able to build on its successes during the height of the pandemic and grow into new areas.
Genomic Sequencing Services
Building on its SARS-CoV-2 sequencing activities, AMSL now offers broader sequencing services to the microbiology and infectious disease community at Ohio State. The lab already has a dozen internal clients including IDI faculty Drs. Matthew Anderson, Andrew Bowman, Patrick Bradley, Karen Dannemiller, Greg Habing, Vanessa Hale, Jonathan Jacobs, Jiyoung Lee, Zelalem Mekuria, Michael Oglesbee, Richard Robinson, Daniel Spakowitz, Matthew Sullivan, Thomas Wittum, and Daniel Wozniak. The depth and breadth of this group highlights AMSL’s interdisciplinary focus.
In addition, AMSL has facilitated industry needs through contracts with Procter & Gamble, Abbott Nutrition, and local biotechnology company Flexsus.
In partnership with the Center of Microbiome Science (CoMS), AMSL is developing a microbiome platform to provide low-cost whole genome analysis of complex samples from humans, animals, plants, and the environment. These bioinformatic services will be run through the Ohio Supercomputer Center (OSC). AMSL has hired a full-time bioinformatician for this growing project.
AMSL offers pathogen genome characterization for bacteria, viruses, and fungi. In partnership with the Global One Health initiative (GOHi), the lab is supporting Gates Foundation work by studying Campylobacter transmission between children and poultry in Ethiopia. AMSL is also deepening its partnerships with CDC, the Air Force Research Laboratory (AFRL), the United Nations Food and Agriculture Organization (UNFAO), and many other stakeholders through sequencing services.
Tick-Borne Pathogen Testing Coming Soon!
For over a year, AMSL has been working with Risa Pesapane, PhD, Assistant Professor in the Department of Veterinary Preventive Medicine and the School of Environment and Natural Resources, to develop Buckeye Bug Bite, a tick identification and tick-borne pathogen testing service for the public. People will be able to submit ticks they find on themselves or their animals and find out the ticks’ species as well as whether the ticks are carrying common tick-borne pathogens. This service will include four tick species and over 20 pathogens of human and animal concern. Buckeye Bug Bite users will then be able to take these results to their doctors or veterinarians to inform diagnostic and care needs.
As part of this project, AMSL has partnered with the Centers for Disease Control and Prevention (CDC), the Ohio Department of Health (ODH), Zoetis, and several local health departments. AMSL also partnered with local company Wavefront Software to build the Laboratory Information Management System (LIMS). The lab is evaluating next-generation sequencing approaches and is interested in building a special vector-borne disease panel that will include both ticks and mosquitoes. This project will help train students, provide critical public health and research data, promote additional extension activities, and generate revenue for AMSL.
Dust & Wastewater: Genomic Analysis of Environmental Samples
In partnership with Karen Dannemiller, PhD, Associate Professor in the Department of Civil, Environmental, and Geodetic Engineering and the Division of Environmental Health Sciences, AMSL will continue to monitor dust samples for the presence of viral pathogens with an additional year of financial support from the university. The lab analyzes 75 campus dust samples per week – PCR testing to determine how much SARS-CoV-2 is in each sample and genomic sequencing to identify which SARS-CoV-2 variant(s) are present. AMSL is working on expanding this dust testing approach (i.e., both PCR and genomic sequencing) - the lab recently completed a study showing that influenza virus can be identified with these techniques and is also part of a pilot project with CDC focused on detection of norovirus.
Alongside dust, AMSL also conducts significant wastewater testing activities and recently was awarded a $700k project to perform sequence analysis for pathogen characterization for the state of Ohio. This project will include 150 wastewater samples per week from ten universities across Ohio. The lab is also a pilot site for the CDC National Wastewater Surveillance System (NWSS) for sequencing data, and all of AMSL’s data will go through this system to be shared nationally.
Continued dust and wastewater testing will provide key indicator data for the pandemic management team on campus. High levels of detection in dust and wastewater might indicate the need for additional surveillance testing in students, staff, and faculty. Outside of the university, wastewater data will be one of the key indicators for ODH to manage the pandemic, and they are planning to expand beyond SARS-CoV-2 into other pathogens. AMSL is hoping to partner with ODH for this expansion.
Bacillus Genetic Stock Center (BGSC)
As part of AMSL’s shift from SARS-CoV-2 saliva testing to other strategic areas, the lab is assuming management of the BGSC, an earnings operation in the Department of Microbiology that was initiated about 30 years ago as part of a National Science Foundation award. BGSC’s primary mission is to maintain genetically characterized strains, cloning vectors, and bacteriophages for the genus Bacillus and related organisms and to distribute these materials without prejudice to qualified scientists and educators throughout the world. With an established and growing domestic and international customer base, AMSL will use FY23 as a year to analyze and assess additional growth opportunities in this space.
AMSL’s Home—The Biological Sciences Building
Through AMSL’s strong partnership with the Department of Microbiology and with the support of department chair and professor Dr. Kurt Fredrick, AMSL will have a permanent home in rooms 405 and 411 in the Biological Sciences Building. Renovations are in the planning stage now as part of a larger renovation plan involving other space within the Department of Microbiology. The renovated lab space will facilitate AMSL’s strategic mission.
Research
AMSL submitted an application to the Strategic Ohio Council for Higher Education (SOCHE) for a microbiome research program with AFRL. If funded, this program would support 1-2 students and focus on the effects of microgravity on the gut microbiome using a gut-on-a-chip technology from the Air Force. AMSL would be responsible for the sequencing and analysis portions of this study.
Education
AMSL will have its first microbiology graduate student this fall and the lab is partnering with the Department of Microbiology to offer undergraduate and graduate-level training focused on research problems from external collaborators. They are considering adding a virology lab or a diagnostics lab section to this microbiology curriculum.
AMSL Technical Director and IDI Strategic Alliance Officer, Dr. Seth Faith, gave lectures as part of the GOHi One Health Summer Institute this year and the lab is planning to hold its own genomics workshop next summer. Looking to the future, AMSL is evaluating the possibility of offering certificates in Microbiome Science (in partnership with CoMS) and in Biotechnology (in partnership with the College of Arts & Sciences).
IDI is proud of the important work that AMSL has accomplished and we continue to support AMSL in these in these future initiatives.