Source: CORNELL UNIVERSITY submitted to
NAHLN - NATIONAL ANIMAL HEALTH DIAGNOSTIC LABORATORY
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
Reporting Frequency
Annual
Accession No.
1017718
Grant No.
2018-37620-28832
Project No.
NYCV474586
Proposal No.
2018-06005
Multistate No.
(N/A)
Program Code
AA-G
Project Start Date
Sep 1, 2018
Project End Date
Aug 31, 2019
Grant Year
2018
Project Director
Elvinger, F.
Recipient Organization
CORNELL UNIVERSITY
(N/A)
ITHACA,NY 14853
Performing Department
Dept. of Population Medicine
Non Technical Summary
The Animal Health Diagnostic Center (AHDC) and New York State Veterinary Diagnostic Laboratory (NYSVDL) at Cornell University, established by law (New York Code - AGM - Article 5 §73-b) to support "the health of food and fiber producing animals, companion animals, sport and recreational animals, exotic animals and wildlife," is a comprehensive veterinary diagnostic laboratory, offering services in anatomic and clinical pathology; microbiology (sections of bacteriology, virology, parasitology, molecular diagnostics, and serology); toxicology; endocrinology, and comparative coagulation. Faculty in the Veterinary Support Services group provide consultation and assistance to clients on test selection, sampling and testing strategies, interpretation of results and incorporation of diagnostics in disease prevention, surveillance and control programs. The AHDC includes the Quality Milk Production Services (QMPS) with laboratories in Canton, Cobleskill, Ithaca and Warsaw; the Avian Health Program including the Duck Research Laboratory on Long Island, and the Wildlife Health Program. One quarter of the $30+ Million annual operational budget of the AHDC is funded through a contract with the NYS Department of Agriculture and Markets, close to two thirds are generated from testing fee revenues, and the remainder is covered by additional state, federal, and industry contracts. The AHDC plans to leverage this funding to effectively support the proposed project.This project is to study and support the responsiveness and readiness of the AHDC in a regional or national high impact disease outbreak in livestock and poultry. Such outbreaks affect the economic viability of animal and food industries and public health. It is imperative that a national system be in place to not only detect a first instance of foreign animal or emerging disease, but also provide the capacity to scale up testing activities to provide the testing backbone for all disease control, eradication and post outbreak surveillance, and to enhance and/or develop tests and work processes to effectively respond to such emergencies. With more than 200 faculty and staff who in fiscal year 2018, processed more than 220,000 accessions for more than 7,000 veterinary accounts from all states and territories of the Union and from abroad the AHDC has the expertise and infrastructure to be a Level 1 laboratory in the National Animal Health Laboratory Network (NAHLN).
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3113299000120%
3113499000130%
3113699000110%
3113899000140%
Keywords
Goals / Objectives
Goals and objectives of this project include providing and maintaining expertise and infrastructure for detection of high impact animal disease and disease agents. The AHDC has been designated a Level 1 laboratory in the NAHLN based on its accreditation status, infrastructure and functional laboratory information management system, its high level of emergency preparedness, surveillance capabilities and continuous surveillance output, the value and level of animal commodities in its service areas, and its active organizational contribution to the network.The AHDC has 1,586 ft2 BSL-3 functional space that is fully commissioned and has proficiency tested personnel and capability to test for many disease agents, including several select agents and diseases under NAHLN scope including avian influenza and exotic Newcastle disease, classical swine fever, chronic wasting disease and scrapie, foot and mouth disease, and swine influenza. As new NAHLN-sanctioned assays are approved for use, the AHDC is prepared to bring these tests on-line according to NAHLN prescribed protocols and time lines. The AHDC is to provide NAHLN testing not only for New York State, but for other states in the Northeast and the United States as needed and is set up to provide reserve testing capacity for other NAHLN laboratories as determined by Veterinary Services, maintaining surge capacity for FAD testing of 1,128 tests per 8-hour shift, and working to expand this capacity through improved use of technology.
Project Methods
The AHDC offers a comprehensive array of assays and platforms in all diagnostic domains under AAVLD accreditation and for select assays in virology, bacteriology, serology and molecular diagnostics under A2LA ISO 17025 accreditation to test for animal disease agents and disease. In particular for this project the AHDC molecular diagnostics, virology and histopathology laboratories have implemented the NAHLN standardized tests for diseases that affect or have the potential to affect livestock and poultry in the Northeast including influenza and exotic Newcastle disease, classical swine fever, chronic wasting disease and scrapie, foot and mouth disease, and swine influenza. The AHDC in addition is expanding its whole genome sequencing capabilities for detection of emerging diseases and support of epidemiologic investigations. The AHDC furthermore, in the past and in the context of this current project is actively pursuing enhanced electronic communication tools to message testing data to its federal partners in Veterinary Services.

Progress 09/01/18 to 08/31/19

Outputs
Target Audience:NAHLN funding to the AHDC is to enhance federal and state capabilities for early detection of high impact livestock and poultry disease, ramp up testing capacity during outbreaks to support control and eradication efforts, and maintain disease surveillance to confirm successful eradication and freedom from disease. The targeted audience are all animal health regulatory state and federal agencies, but in particular livestock and poultry industries, as well as all stakeholders in animal and public health. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Bacterial whole genome sequencing PT administered jointly by FDA and CDC Additional staff members were able to participate in proficiency testing for FADs Two analysts attended ASM NGS to stay current on bioinformatics approaches for infectious disease discovery and detection Our lead bioinformatics analyst, Patrick Mitchell, took a Cornell course in computer science and is registered for a machine learning short course to being in August Our bioinformatics team attended training on pathogen transcriptomics held by the IBM Research - Artificial Intelligence unit François Elvinger attended training on ICS-300 - Intermediate ICS for Expanding Incidents and ASF Tabletop exercise at Plum Island for NAHLN labs Roopa Venugopalan assisted in the NDV outbreak at UC Davis in a two-week deployment Jasminka Alikalfic attended Avian Influenza NPIP training How have the results been disseminated to communities of interest?Laboratory representation at the 2018 AAVLD Conference in Kansas City, MO; numerous travel award winners presenting on work performed Laura Goodman participated in the NAHLN MTWG WGS subcommittee Laura Goodman participated in the APHIS monthly Asian long-horned tick stakeholder call The AHDC participated in NAHLN Exercises and Drills and provided feedback during calls Various members presented on the following topics: "One Health WGS: Genomic Surveillance of Zoonotic and Animal Pathogens" at the Microbial genomics and public health session at the Northeast regional ASM meeting in Albany, NY. "Genomic AMR Surveillance of Zoonotic and Animal Pathogens" invited talk at Arizona Infectious Disease Training, Phoenix, AZ. Presented on animal health AMR surveillance at the National Institute for Animal Agriculture Antibiotics Symposium in Overland Park, KS. "One Health Data Reporting, Sharing, and Collaborating," Address to the Presidential Advisory Council on Combating Antibiotic-Resistant Bacteria (PACCARB), Washington DC. "Practical applications of NGS in swine diagnostics and surveillance," Invited talk at the American Association of Swine Veterinarian (AASV) annual meeting, Orlando, FL. "One Health Pathogen Surveillance with Advanced Molecular Detection," University of New Hampshire "Genetic AMR Predictions and Big Data-Implications for One Health," American Association of Veterinary Laboratory Diagnosticians (AAVLD) Bacteriology symposium, Kansas City, MO. What do you plan to do during the next reporting period to accomplish the goals? The AHDC will continue to take the necessary actions to conduct the requested activities to meet the responsibilities of a Level 1 laboratory, in particular, to provide support for IT personnel, the AHDC Quality System, and laboratory and administrative personnel in all NAHLN related activities. Information Technology Support Quality System Support Technical and Administrative Personnel Support Electronic Messaging and NAHLN related IT enhancements Quality Management Support Increase of FAD and emerging disease diagnostics capabilities and capacities

Impacts
What was accomplished under these goals? Participation in NAHLN exercises Received approval for messaging of APMV-1, IAV-S, ASF, CSF Proficiency testing completed Passed NVSL/NPIP Salmonella serotyping PT exclusively by whole genome sequencing Maintained bacterial WGS on Illumina platforms under the auspices of AAVLD and ISO/IEC 17025 accreditation and mentored other labs seeking accreditation for WGS Worked with NARMS at FDA to integrate animal health AMR surveillance data into their reporting, resulting in a recent publication

Publications