THE OFFICIAL NEWSLETTER OF THE NATIONAL ANIMAL HEALTH LABORATORY NETWORK (NAHLN)

A STATE AND FEDERAL PARTNERSHIP TO SAFEGUARD ANIMAL HEALTH  

NAHLN rapidly responded to the threat of COVID-19 by developing the capability to test for SARS-CoV-2 and working together to build capacity.

We are very proud that the NAHLN labs were the first to identify COVID-19 in an animal species. Nadia, a tiger from the Bronx Zoo, was sampled for testing at the University of Illinois Veterinary Diagnostic Laboratory (IL VDL) and the Cornell University Animal Health Diagnostic Center. The samples in both NAHLN labs tested presumptive-positive; Dr. Frederickson, IL VDL, drove the samples to the NVSL for confirmatory testing. Samples were taken from Nadia the afternoon of April 2 ^nd , NAHLN lab testing occurred on April 3 ^rd , and the confirmatory testing was completed on April 4 ^th . The importance and effectiveness of our Network is apparent to our Federal partners.

Currently there are 28 NAHLN laboratories testing for SARS-CoV-2. Testing animal samples in NAHLN laboratories is typically completed at the request of the State Animal Health Officials in collaboration with the State Public Health Veterinarian. The majority of NAHLN laboratories are using a real-time PCR assay based on the CDC protocol, although some laboratories use different assays identifying different viral targets. Any presumptive positives identified in NAHLN laboratories will be sent to NVSL for confirmatory testing. Currently, the only positive animals tested at NAHLN laboratories and confirmed by NVSL are the tigers and lions from Bronx zoo. The capacity for testing has been affected by shortages in reagents, supplies, and equipment. Many of the NAHLN laboratories have been asked to support their state’s COVID-19 response by sharing equipment, reagents, and even analysts with their public health laboratories. Shortages not only affect our capacity for SARS-CoV-2 testing in NAHLN laboratories, but may also affect capacity to test for other NAHLN scope diseases.

We have 9 NAHLN laboratories with the capability to test human samples for SARS-CoV-2. Eight of these   laboratories are animal testing laboratories and one is a public health laboratory that is also approved as a NAHLN laboratory to test animal samples for several diseases of high consequence (Influenza A virus in avian and swine, Foot and Mouth Disease, Classical Swine Fever, and African swine fever). Animal testing numbers remain low in NAHLN laboratories based on guidance collaboratively developed by CDC, USDA, FDA, and others using a One Health approach. Routine testing of animals for SARS-CoV-2 is not recommended. Decision to test an animal should be agreed upon using a One Health approach between appropriate local, state, and/or federal public health and animal health officials. Veterinarians are strongly encouraged to rule out other, more common causes of illness in animals before considering SARS-CoV-2 testing. NAHLN laboratories provide their animal testing numbers weekly. As of May 15, 2020 approximately 195 animals have been tested. Dogs, cats and ferrets make up 79% of those tested. Other animals tested are: armadillo, bat, bobcat, camel, chimpanzee, civet, gorilla, hamster, lemur, leopard, lion, orangutan, parrot, pig, tamandua, tamarin and tiger.

NAHLN laboratories doing SARS-CoV-2 testing meet weekly with NVSL to discuss technical issues associated with the assays and concerns over availability of needed reagents and supplies. To address supply issues, we have remained in communication with vendors to update them on specific needs and shared with the NAHLN laboratories any helpful hints for ordering or availability of alternative products. Several NAHLN laboratories have voiced needs to the group and other laboratories have stepped up to help provide temporary help to fill the needs. It has been a wonderful opportunity to see how a successful network functions!

NAHLN is participating in three working groups focused on different areas related to COVID-19 testing in animals. These are:

USG Interagency COVID-19 Working Group- CDC, USDA, FDA, DOD, DHS

Integrated Consortium of Laboratory Networks (ICLN)

NAHLN/NVSL COVID-19 Working Group

 

Article submitted by Christina Loiacono, Coordinator, M.S., PhD., NAHLN Program Office, USDA APHIS VS D & B, NVSL, Ames, IA.

Dr. Suelee Robbe-Austerman has been selected to serve as the Director of the National Veterinary Services Laboratories (NVSL), effective April 26. As the NVSL Director, Dr. Robbe-Austerman will be responsible for the scientific leadership of the NVSL, as well as being ultimately responsible for the overall planning, coordination, evaluation, and program/administrative direction of the NVSL.  

 

Dr. Robbe-Austerman has served as the Director of the NVSL Diagnostic Bacteriology and Pathology Laboratory since 2017. From 2011-2017, she served as the Mycobacteria and Brucella Section Head after starting her career with NVSL as a veterinary medical officer in 2007. During her tenure at NVSL, she has overseen the incorporation of next generation sequencing technologies and led the incorporation of several new assays into our USDA programs to assist with disease confirmation, characterization, and traceability. Dr. Robbe-Austerman has collaborated extensively with international partners and public health to characterize bacterial pathogens within North America and throughout the world. As NVSL Director, she hopes to continue to enhance NVSL’s partnerships with laboratory networks and international institutions to advance diagnostics and disease response. Dr. Robbe-Austerman received her DVM from Colorado State and a MS in Production Animal Medicine and PhD in Veterinary Microbiology from Iowa State.

 

Article submitted by Traci Imlau, Program Assistant, NAHLN Program Office, USDA APHIS VS D & B, NVSL, Ames, IA.

In 2019 the NAHLN program office received 57 proposals for projects that will enhance animal agriculture emergency preparedness and response capabilities specifically by addressing needs within NAHLN laboratories in the following areas:

APHIS Veterinary Services staff and MRP IT staff reviewed all applications against evaluation criteria and ranked the proposals within each proposal and again across priorities. Both internal and external subject-matter experts were asked for input as appropriate. This process was completed in 30 days. Following presentation to the Office of the Secretary and approval, all awards were executed in March of 2020. This process from announcement to execution of funding was completed in just over 6 months!

2020 NAHLN Farm Bill Priorities

( Information will be inserted from the APHIS announcement if it’s available prior to newsletter distribution. or below )

The NAHLN Priorities recommended by the Council and approved by the NAHLN Executive Committee will be sent to the Office of the Secretary of Agriculture to be reviewed/approved in the next two weeks. Those priorities are:

The list of 2020 NAHLN Farm Bill priorities will again be provided to the Office of the Secretary for review and approval. An opportunity announcement for a competitive evaluation process should be provided in June of 2020, with proposals due back 60 days after the announcement.  

Article submitted by Traci Imlau, Program Assistant, NAHLN Program Office, USDA APHIS VS D & B, NVSL, Ames, IA and by Christina Loiacono, Coordinator, M.S., PhD., NAHLN Program Office, USDA APHIS VS D & B, NVSL, Ames, IA.

Article submitted by Jennifer Rodriguez, Management and Program Analyist , NAHLN Program Office, USDA APHIS VS D & B, NVSL, Ames, IA.

The NAHLN Program Office is updating all messaging guides to conform with current reporting needs for outbreak and surveillance animal disease testing across Veterinary Services, and to capture changes made in the HL7 format or schema. The messaging guides provide instructions and standards for the NAHLN labs on what information needs to be included and how to format that data in their lab’s HL7 electronic message. NAHLN has messaging guides available for the following diseases; virulent Newcastle Disease (APMV-1), African swine fever, classical swine fever, foot-and-mouth disease, avian influenza, swine influenza, pseudorabies, and vesicular stomatitis.

 

The main changes for this current round of updates are:

·          Modifying the order in which the message segments are listed within the guide to improve readability

·          Providing information on obx.21, the unique observation ID field. Currently this is an optional field, but will be required when the NAHLN schema 2.1 is implemented. (A schema defines the structure and contents that are to be included in the message)

·          Including more examples of the HL7 coding or formatting for specific data points.

·          Identifying fields that have changed or been modified since the last guide was issued. An example of this is changes to the acknowledgement message.

 

The process for updating messaging guides starts in the NAHLN program office by editing the document to include any known changes from the last version. The guide is then provided to the IT core working group (which includes IT subject matter experts from our NAHLN laboratories), the NVSL reference laboratories and the appropriate VS commodity group(s) for review and input. Once the messaging guides are finalized, they are posted on the Veterinary Terminology Services Laboratory site ( VTSL site ) and the APHIS Laboratory Portal in the document library. The NAHLN laboratories approved to message for that disease are then notified that the new version of the guide is available.

 

As of May 2020, the FMD messaging guide has been updated and posted to the VTSL site and the APHIS Laboratory Portal. Labs will be notified as the other messaging guides updates are available.

Article submitted by Jennifer Rodriguez, Management and Program Analyist , NAHLN Program Office, USDA APHIS VS D & B, NVSL, Ames, IA.

Article submitted by Traci Imlau, Program Assistant, NAHLN Program Office, USDA APHIS VS D & B, NVSL, Ames, IA and Kelly Burkhart, Microbiologist, NAHLN Program Office   USDA APHIS VS D & B, NVSL, Ames, IA  

In May, a “Drills & Survey” module was added to the APHIS Laboratory Portal. This module, which includes a date stamp feature, provides an online platform for laboratory members to provide responses to NAHLN related drills and surveys, and will reduce or eliminate the need for such requests to be sent via email. All laboratory members, with a Portal account that includes access to the Lab Directory, have access to this module and can submit a response on behalf of the lab as needed. The module’s history section allows each laboratory to view responses submitted by their lab for past events. This module has been successfully utilized for multiple surveys since its implementation.



Article submitted by Cindy Chard-Bergstrom, Microbiologist, NAHLN Program Office   USDA APHIS VS D & B, NVSL, Ames, IA  

Year two of the NAHLN AMR pilot project was completed in December of 2019. The primary objective of this pilot is to demonstrate the viability of implementing a sampling stream for monitoring AMR profiles in animal pathogens routinely isolated by veterinary clinics and diagnostic laboratories across the U.S. and to provide AMR profiles for livestock and production animals (cattle, swine and poultry), as well as companion animals (horses, dogs and cats) that are clinically ill.

The year two report describes AMR data collected and funded through USDA, covering January 1 – December 31, 2019. Twenty-four laboratories participated in the 2 ^nd year, an increase of 20.8% from the initial year of this pilot. Twenty-three of these laboratories were members of the NAHLN and one laboratory outside of the NAHLN was associated with a U.S. college of veterinary medicine. Bacterial isolates were selected to represent both pathogens of veterinary importance and zoonotic bacteria monitored through other national food-borne pathogen surveillance systems. Overall, 5430 isolates were submitted in 2019, a 41% increase over 2018. Isolates surveyed in 2019 were; Escherichia coli (E. coli) (2743 isolates across all animal species) , Salmonella enterica spp. (850 isolates from cattle), Mannheimia haemolytica (612 isolates from cattle), Streptococcus suis (167 isolates from swine), Pasteurella multocida (51 isolates from poultry), Streptococcus equi (57 isolates from horses, S. equi ssp. zooepidemicus (359 isolates from horses) and Staphylococcus intermedius group (1061 isolates from dogs and cats).

Antimicrobial resistance was evaluated for antibiotics with animal and bacterial-specific breakpoints given in the most recent version of the Clinical Laboratory Standards Institute’s (CLSI’s) Vet08 document ( Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated from Animals) (CLSI, 2018) . 

Results for 2019 show that oxacillin resistance (OX ^R ) in S. intermedius group isolates continues to increase in dogs. These OX ^R isolates also continue to exhibit high resistance rates of 60% - 100% to all other antimicrobial classes for which CLSI canine breakpoints are available. Additionally, 62.3% of the OX ^R isolates were also categorized as multi-drug resistant (MDR), the highest MDR rate of all animal/bacterial categories. This is an increase from 2018, where 56.9% of isolates in this category were classified as MDR. 

Across production animals, resistance rates for M. haemolytica in cattle showed a slight decreasing trend, with over 75% of isolates being pan-susceptible to all antimicrobials. Antimicrobial resistance in swine S. suis isolates was at or below 15%, with the exception of tetracycline which had a resistance rate of 98%. Veterinary clinical breakpoints are not available for the other bacterial pathogens monitored in cattle, swine and poultry, so evaluation of resistance trends for these bacteria is not possible. 

F or companion animals, a slight overall downward trend in E. coli antimicrobial resistance was observed in dogs. More bacteria were identified in 2019 as candidates for screening for extended beta lactamase resistance over 2018 for both dogs and cats. Isolates of S. equi and S. equi ssp. zooepidemicus in horses showed extremely low resistance to penicillin and cephalosporins at ~1% resistance or lower, but conversely were highly resistant to fluoroquinolones, tetracyclines and aminoglycosides (84%-100% resistance).



Article submitted by Beth Harris, Associate Coordinator, NAHLN Program Office USDA APHIS VS D & B, NVSL, Ames, IA  

ASF Outbreak Laboratory Response Course

-Incident Command System (ICS) 300 training

On July 28 - August 2, 2019, the NAHLN Exercises and Drills committee hosted the ASF Outbreak Laboratory Response Course – Incident Command System (ICS) 300 training in conjunction with Plum Island Animal Disease Center. Approximately 50 participants from NAHLN Laboratories attended the course and received training on ASF clinical signs, diagnosis, outbreak response, and industry impacts. This course included ICS 300 lectures, ASF clinical case demonstrations, ASF tabletop exercises, ASF necropsy, and updates on the ASF outbreak in China. This course was critical to improving the performance of participants during a potential ASF outbreak.  

National ASF Swine Fever Exercise for Agriculture Response (SFEAR)

On September 23-26, 2019, the United States Department of Agriculture’s (USDA) Animal and Plant Health Inspection Service (APHIS) led a series of functional exercises. 

This exercise was a part of APHIS’s overall African swine fever preparedness effort. APHIS notified the World Animal Health Organization (OIE) about this exercise in advance. OIE shared this information with its member countries.

APHIS staff, representatives from 14 states and the swine industry, participated in the exercises. They were designed to be unique activities targeting key areas of ASF response and mitigation. 

16 NAHLN Laboratories participated in SFEAR.

The general focus of each day’s play was:

Gaps identified during this exercise will be incorporated in the planning for future exercises. The next exercise was planned for Southeastern Region FADSAFE 2020 – FMD to be held in November 2020; however, due to the COVID-19 situation it is now postponed to November 2021. 

NAHLN ASF Exercise

On September 24 – 25, 2019, the NAHLN coordinated an exercise to piggyback on the National ASF SFEAR exercise. This exercise took advantage of the SFEAR awareness infrastructure and provided an opportunity to invite additional labs beyond the 14 participating in SFEAR states. In all, 35 NAHLN labs participated in the exercise.

These exercises provided a good opportunity to work through the entire process!

Article submitted by Traci Imlau, Program Assistant, NAHLN Program Office, USDA APHIS VS D & B, NVSL, Ames, IA

The NAHLN program staff is a small but dedicated staff with a wide range of responsibilities that support the mission of the NAHLN, including the ability to provide this country with early detection, rapid response, and appropriate recovery from an adverse animal health event. The majority of what the NAHLN program staff do on a day to day basis is in support of our f ounding principles  . We require laboratories to implement a quality management system. To accomplish this, most labs are accredited by a third party. Laboratories that are not accredited are visited by NAHLN program staff to confirm a quality system exists. NAHLN program staff also leads working groups that ensure protocols and equipment are standardized, communication from laboratories is secure, and that laboratories maintain a high level of preparedness. Finally, the NAHLN supports other VS priorities, including outbreak response for high consequence animal diseases, and surveillance for high consequence animal diseases in both livestock and wildlife.

Our Staff

 

Article submitted by Christina Loiacono, Coordinator, M.S., PhD., NAHLN Program Office, USDA APHIS VS D & B, NVSL, Ames, IA.

The current number of NAHLN laboratories at each level in 2020 is as follows:

25 Level 1 Laboratories (includes 6 branch labs)

27 Level 2 Laboratories (includes 1 branch lab)

6 Level 3 Laboratories

1 Affiliate Laboratory

Welcome to the new members of the Coordinating Council:

NAHLN Laboratory Level 1:

Dr. Beate Crossley – California Animal Health & Food Safety Laboratory

NAHLN Laboratory Level 2:

Dr. Debbie Reed – Murray State University, Breathitt Veterinary Center

Dr. Udeni Balasuriya – Louisiana Animal Disease Diagnostic Laboratory

NAHLN Laboratory Level 3:

Dr. Louise Dufour Zavala – Georgia Poultry Laboratory Network

Thank you to the members rotating off the Coordinating Council:

NAHLN Laboratory Level 1:

Dr. Keith Bailey – formerly of the Oklahoma Animal Disease Diagnostic Laboratory

NAHLN Laboratory Level 2:

Dr. Timothy Hanosh – New Mexico Department of Agriculture Veterinary Diagnostic Services

Dr. William Laegried – Wyoming State Veterinary Laboratory

Welcome to the new members of the Methods Technical Working Group

Dr. Laura Goodman, New York, Animal Health Diagnostic Center at Cornell

Mr. Jeremy Snyder, New Jersey Department of Agriculture, Animal Health Diagnostic Laboratory

Dr. Binu Velayudhan, North Carolina, Rollins Animal Disease Diagnostic Laboratory

Dr. Lifang Yan, Mississippi Veterinary Research and Diagnostic Laboratory

Thank you to the members rotating off the Methods Technical Working Group

Dr. Beate Crossley – California Animal Health & Food Safety Laboratory

Mr. Dan Bradway - Washington Animal Disease Diagnostic Laboratory

Dr. David Wilson - Utah Veterinary Diagnostic Laboratory

 

Article submitted by Traci Imlau, Program Assistant, NAHLN Program Office, USDA APHIS VS D & B, NVSL, Ames, IA.

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