The Challenges and Future of Diagnostics in Poultry Medicine

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1 The Challenges and Future of Diagnostics in Poultry Medicine Frederic J. Hoerr, DVM, PhD Western Poultry Disease Conference March 20, 2017 Sacramento, California

2 The future is already here it's just not very evenly distributed. William Gibson, 1993

3 Where poultry diagnostics are performed (USA) USDA NVSL, NPRC State laboratories University-based laboratories Hybrid State-University labs Production company laboratories Cooperative laboratories Corporate and independently-owned laboratories Biological and Pharmaceutical Companies

4 Academic Infrastructure Concerns for the future of poultry diagnostics

30,0000 acres for each congressional district Stipulated military training (later - ROTC) Justin S.

5 Morrill Act: Land-Grant College Act of 1862 Land-Grant College Act of 1862, or Morrill Act Grants of land to states to finance the establishment of colleges specializing in agriculture and the mechanic arts. 30,0000 acres for each congressional district Stipulated military training (later - ROTC) Justin S. Morrill, Land-Grant Act of 1898 supported African American and American Indian Colleges Many poultry diagnosticians today received some, if not all, of their academic/residency training at an 1862 Land-Grant University.

6 2017: Three Land-Grant College Strategic Plans Agriculture and the mechanic arts is variously rephrased as Instruction, research and community engagement Conservation and enhancement of. intellectual, cultural, and environmental heritage...increasing and disseminating scientific, humanistic and social knowledge for the benefit of the larger society The sustainability of poultry diagnostics and component disciplines is subject to administrative shifts. Without involvement by poultry producers, programs can deteriorate and disappear.

Poultry States State government support of

and extension are under pressure. http://www.

7 Poultry States State government support of higher education is decreasing. Land-grant universities are affected. Poultry resources for diagnostics, research, and extension are under pressure.

8 State Diagnostic Infrastructure Issues Concerns for the future of poultry diagnostics

9 The Dilution (or Enhancement) of Poultry Diagnostic Resources Poultry Percentage of resources allocated to poultry Poultry Livestock Tension in Resource Allocation Poultry Livestock (Swine, Cattle, Sheep, Goats) Aquatic species Honeybees Dogs & Cats Pet birds Horses Zoos and Wildlife (CWD, TB, AI, Arbovirus) Public Health Rabies, Arboviruses, etc. Food Safety Total resources available to poultry: expertise, equipment, capacity

10 Corporate and independentlyowned poultry diagnostic services Incorporation and capitalization Accounting and business development Licensing and permits Quality system implementation and accreditation Diversity of services, some unique, but less likely for comprehensive services to be under one roof Networking and subcontracting Interstate and international clientele

11 Sustaining infrastructure in poultry diagnostics National Poultry Improvement Plan Methodology Model partnership of regulatory diagnostics poultry production Federal laboratories NVSL, SERPRL, ADOL (new NPRC) Definitive diagnostic and research support in poultry disease crises AAAP reference publications, with ongoing updates Diseases of Poultry, Isolation and Identification of Avian Pathogens, Avian Histopathology USAHA, AAAP, AAVLD and other forums of policy, position and priority development

12 Proposed cuts in 2018 USDA budget Sonny Perdue USDA Secretary Nominee

13 Funding Never waste a crisis! Toxic fat contamination of feed Exotic Newcastle disease 911 and the threat of agrobioterrorism Bovine spongiform encephalopathy Chronic wasting disease and tuberculosis in wild Cervidae Avian Influenza Crisis Crisis?? Years Catastrophic poultry or animal disease is a political driver in the cyclical investment in diagnostic infrastructure.

14 Technical advancements in my career Personal computer Word processor and dictation software Spreadsheet and Power Point SAS, Prism, analytical programs Laboratory administrative software Monoclonal antibodies Antigen-capture ELISA ELISA serology and robotics Digital photography GPS analysis Database information retrieval Immunohistochemistry, in situ detection GC-Mass-spectral analysis Bacterial rapid identification Polymerase chain reaction - PCR/RT PCR Single agent, multiplex Restriction endonuclease fragment analysis General awareness of BSL 1, 2, 3, 4 Genomic sequence analysis Quantitative PCR Next-generation, metagenomic sequencing Gut, respiratory, skin, urogenital biome analysis

15 Technology s future Agent detection More information, quicker turnaround, possibly done by fewer labs and fewer persons Robotics and other equipment advances Obsolescence of standard equipment, i.e. microscopes The only certain prediction is that technological advances will continue.

16 Helpful advances that will continue NAHLN National Animal Health Laboratory Network Standardized and multiplied response capability to catastrophic disease Forced the implementation of quality management into noncompliant poultry laboratories Quality system implementation and accreditation AAVLD, 17025, A2LA, ISO 9001 Improved the quality and consistency of laboratory data Reduced inter-laboratory variation Global language Investment of time and resources Improved laboratory safety

17 Communication Barriers to Diagnostic Success Poultry diagnostics is a blend of two disciplines Science of the diagnostic discipline that generates a result Interpreting the result to poultry production systems Laboratory scientists may fall short in understanding the application of data to poultry production Poultry speak can intimidate capable diagnosticians Filtering the flow of diagnostic information based on interpersonal comfort may lose important details Effective communication between diagnostician and producer requires ongoing effort and dialogue.

18 Poultry Diagnostics: Generation of Knowledge Diagnostic labs - the point of the spear in generating new disease information Linkage with the research community Data harvesting and mining for retrospective studies Microbial arching for research and development, and new vaccines Diagnostic labs should spin off research ideas, isolates, and perspective to the research community.

19 Poultry Diagnostics Three approaches to defining disease interactions for large production systems Retrospective Studies Production- Integrated Diagnostics Metagenomic Analysis

20 Broiler Viral Enteritis Runting Stunting Syndrome Bursa Atrophy Thymus Atrophy

21 No. Cases No. Cases Max Bursa Score (Mean) Max Thymus Score (Mean) Viral enteritis diagnosis: Retrospective PCR and Immune System Histopathology Broilers: Intestinal Virus Detection by Age Astrovirus Rotavirus Reovirus N=258 Cases Broilers: Cases by Enteric Viruses Detected N=258 Cases Virus Positive Broilers <20 days: Maximum Bursa Depletion Score N=134 Cases Virus Positive Broilers <20 days: Maximum Thymus Depletion Score N=131 Cases Normal 1 Normal Age - Days Astrovirus Rotavirus Reovirus AstroRota AstroReo Virus RotaReo AstroRotaReo 0 RSS Astrovirus Rotavirus Reovirus AstroRota Virus AstroReo RotaReo AstroRotaReo 0 RSS Astrovirus Rotavirus Reovirus AstroRota AstroReo RotaReo Virus AstroRotaReo

22 Production- Integrated Diagnostics Sampling the flock to define the temporal onset and severity of disease

23 Anticipated Broiler Health Challenges by Age Rickets Adenovirus - vertical Adenovirus - immunosuppression Ascites/Synovitis/Tendonosis/DPM Gangrenous Dermatitis/Cellulitis E. coli, Salmonella E. coli, Ornithobacterium, Enterobacter CAV Blue Wing Coccidia Vx or challenge Bursal Dis / B-Cell CAV Thymus Atrophy/T-Cell Necrotic enteritis E. maxima IBV/PMV Vx Reaction Harsh Immuno/cycling Bronchitis, PMV, LT Challenge Viral Enteritis Viral Proventriculitis Omphalitis, Aspergillus, Dehydration, Ammonia Feed manufacture and management, water, lights, ventilation, daily care 1 7 Feed change

24 Role of Diagnostician in Poultry Traditional Morbidity and Mortality Diagnosis Identification of major disease(s) Diagnostics integrated with production. Disease erodes genetic potential and leads to nutrient wastage and partitioning away from growth or egg production Onset and severity 1% 100%

25 Defined Ages Tissue collection Lesion scoring Morphometrics Integrated histopathology to define disease onset and focus agent detection

26 Broilers, 14 days normal vs. affected Jejunum Duodenum Pancreas Veterinary Diagnostic Pathology, LLC 26

27 ???????

Case 25910 25911 25912 25913 25914 Reference M16-001 M16-002 M16-003 M16-004 M16-005 Species

Company Tyson Foods Tyson Foods Tyson Foods Tyson Foods Tyson Foods Complex Oglethorpe, GA

Vincent Sections 9 10 10 10 10 Slides 2 2 2 2 2 Organ 1 2 3 4 5 6 Mean Comment 1 2 3 4 5 6 Mean

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 4 4 4 4 3.5 3.

6 1 1 1 1 1 1 Villus atr 1 1 1 1 1 1 3 1 2 1 1.6 1 3 1 1 1 1.4 1 2 1 1 1 1.2 1 1 1 1 2 1.

4 LP/GALT 1 1 1 1 1 1 1 1 2 1 1.2 1 1 1 1 1 1 2 1 1 1 1 1.

2 1 1 1 1 1 1 1 1 1 1 1 1 cysts 1 3 2 1 1.75 1 1 1 3 1 1.

28 Case Reference M M M M M Species Broilers Broilers Broilers Broilers Broilers Age Units days days days days days Company Tyson Foods Tyson Foods Tyson Foods Tyson Foods Tyson Foods Complex Oglethorpe, GA Oglethorpe, GA Oglethorpe, GA Oglethorpe, GA Oglethorpe, GA Farm/Group C&K Woodville Joseph Rocky Vincent Sections Slides Organ Mean Comment Mean Comment Mean Comment Mean Comment Mean Comment Bursa score Acute Mid Intestine m m m Coccidia Villus atr Crypt HP LP/GALT Bacteria/dysbact cysts other Bursa mean score Coccidia Index Enteritis Index Total Gut Lesion Index Basic Methodology of Toxicologic Pathology Veterinary Diagnostic Pathology, LLC

29 Broilers days -- Bursa, duodenum, pancreas, midgut, cecum Ongoing viral enteritis to 35+ days with two species of coccidia challenge

Units days days days days days days days Company Koch Foods Koch Foods Koch Foods Koch Foods Koch Foods Koch Foods Koch Foods Complex Morristown Morristown Morristown Morristown Morristown Morristown

York Sections 19 22 20 20 20 20 21 Slides 4 4 4 4 4 4 4 Organ 1 2 3 4 5 Mean Comment 1 2 3 4 5 6 Mean Comment 1 2 3 4 5 Mean Comment 1 2 3 4 5 Mean Comment 1 2 3 4 5 Mean Comment 1 2 3 4 5 Mean

30 Units days days days days days days days Company Koch Foods Koch Foods Koch Foods Koch Foods Koch Foods Koch Foods Koch Foods Complex Morristown Morristown Morristown Morristown Morristown Morristown Morristown Farm/Group Corbin Necis Kevin Naig McConnel Adam York Mark Evans Chucked Fork B.J. York Sections Slides Organ Mean Comment Mean Comment Mean Comment Mean Comment Mean Comment Mean Comment Mean Comment Broilers days Bursa score cryptosporidium Duodenum a a a m a a m m a a a a a a a/m Coccidia Villus atr Crypt HP LP/GALT Bacteria/dysbact cysts cystic ent cystic ent cystic ent cystic ent other Pancreas Lymphocytic HP Other Mid Intestine m m m m m m m m m m m m m m m m Coccidia Villus atr Crypt HP LP/GALT Bacteria/dysbact cysts cystic ent cystic ent cystic ent cystic ent other Cecum Coccidia LP/GALT Bacteria/dysbact Other Bursa mean score Coccidia Index Enteritis Index days Total Gut Lesion Index Veterinary Diagnostic Pathology, LLC 30

31 High indices Veterinary Diagnostic Pathology, LLC

32 R a tio Morphometrics D u o d e n u m a n d J e ju n u m V :C R a tio D u o d e n u m ~ :1 J e ju n u m ~ 4-5 :1 A g e in D a y s Veterinary Diagnostic Pathology, LLC

33 Disease Progression Summary Bursal disease E. maxima E. acervulina Cystic Enteritis Survey Ages Veterinary Diagnostic Pathology, LLC CF RptBursaMidgutPowerPntTemplate.FJH

34 Routine scheduled mortality surveys using database to record basic information: Location Breed Age Body weight Cause of death Production-integrated gross pathology to define a disease

35 Prolapse and Tetany All Complexes

36 Prolapse and Tetany by Breed

37 Prolapse and Tetany by Age: 2016 to 2017

38 T o ta l S e rto li C e lls Production-integrated diagnostics: Testicular morphometrics a T o ta l S e r to li C e lls in 1 0, 4 0 x F ie ld s a B y A g e 4 0 b b c d b c 2 0 c d e d e e w 2 2 w 2 5 w 4 8 w T K G d 4 9 w 5 3 w G o o d 5 3 w P o o r 5 4 T & K P o o r A g e in W e e k s D. Johnson F. Wilson, and F.J. Hoerr 2016

Enteric Virome Metagenomic Analysis: SPF Sentinels

L (2015) Comparative Analysis of the Intestinal

Birds Placed on Selected Broiler Chicken Farms.

39 Enteric Virome Metagenomic Analysis: SPF Sentinels on 6 broiler farms Day JM, Oakley BB, Seal BS, Zsak L (2015) Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms. PLoS ONE 10(1): e doi: /journal. pone

40 The (great) metagenomic - microbiome awakening Bacterial, viral, fungal, protozoal populations Gut Also Respiratory Skin Urinary Genital

41 The causative relationship between a microbe and a disease Koch s postulates Applicable for some classic infectious diseases Problematic for some/many diseases Fredricks and Relman modified Koch s postulates for 21 st century Bradford Hill criteria Molecular pathological epidemiology (MPE) Single pathogen significance will continue, but microbial community analysis and correlation with disease production parameters will become important.

42 Poultry Disease Definition elastic if not elusive Classic diseases meeting Koch s postulates Diseases of Poultry table of contents Emerging diseases Diseases of complex or unknown etiology Infections, carrier states, and residues of food safety and public health concern Dysbacteriosis Production-eroding risk factors Viral and bacterial communities, and their associations Metabolic disorders, antinutritional factors, and nutritional imbalances Influenced by: Genetics Nutrition Management

43 Summary Challenge and Future of Diagnostics in Poultry Medicine University and state diagnostics experience cyclical support Federal funding may be pressured Corporate and independent diagnostic opportunities exist Expanding option for employment and services. Interstate and international services Poultry diagnostics has a role in knowledge advancement Data capture and retrospective studies Production integrated diagnostics are resource intensive but provide temporal information for intervention and mitigation Metagenomic microbiome analysis provides remarkable opportunities and some new paradigms

44 Thank you

Interaction of Gumboro and other Immunosuppressive Diseases on Respiratory Disease

Interaction of Gumboro and other Immunosuppressive Diseases on Respiratory Disease FREDERIC J. HOERR II SEMINARIO INTERNACIONAL AVICOLA MERIAL PANAMA CITY, PANAMA JULY 10, 2014 Broiler Disease by Age Rickets