Visualization and application of disease diagnosis codes for population health management using porcine diseases as a model

Accurate and timely results of diagnostic investigations and laboratory testing guide clinical interventions for the continuous improvement of animal health and welfare. Infectious diseases can severely limit the health, welfare, and productivity of populations of animals. Livestock veterinarians submit thousands of samples daily to veterinary diagnostic laboratories (VDLs) for disease diagnosis, pathogen monitoring, and surveillance. Individual diagnostic laboratory reports are immediately useful; however, aggregated historical laboratory data are increasingly valued by clinicians and decision-makers to identify changes in the health status of various animal populations over time and geographical space. The value of this historical information is enhanced by visualization of trends of agent detection, disease diagnosis, or both, which helps focus time and resources on the most significant pathogens and fosters more effective communication between livestock producers, veterinarians, and VDL professionals. Advances in data visualization tools allow quick, efficient, and often real-time scanning and analysis of databases to inform, guide, and modify animal health intervention algorithms. Value is derived at the farm, production system, or regional level. Visualization tools allow client-specific analyses, benchmarking, formulation of research questions, and monitoring the effects of disease management and precision farming practices. We present here the approach taken to visualize trends of disease occurrence using porcine disease diagnostic code data for the period 2010 to 2019. Our semi-automatic standardized creation of a visualization platform allowed the transformation of diagnostic report data into aggregated information to visualize and monitor disease diagnosis.     

ASVCP quality assurance guidelines: control of general analytical factors in veterinary laboratories

Owing to lack of governmental regulation of veterinary laboratory performance, veterinarians ideally should demonstrate a commitment to self-monitoring and regulation of laboratory performance from within the profession. In response to member concerns about quality management in veterinary laboratories, the American Society for Veterinary Clinical Pathology (ASVCP) formed a Quality Assurance and Laboratory Standards (QAS) committee in 1996. This committee recently published updated and peer-reviewed Quality Assurance Guidelines on the ASVCP website. The Quality Assurance Guidelines are intended for use by veterinary diagnostic laboratories and veterinary research laboratories that are not covered by the US Food and Drug Administration Good Laboratory Practice standards (Code of Federal Regulations Title 21, Chapter 58). The guidelines have been divided into 3 reports on 1) general analytic factors for veterinary laboratory performance and comparisons, 2) hematology and hemostasis, and 3) clinical chemistry, endocrine assessment, and urinalysis. This report documents recommendations for control of general analytical factors within veterinary clinical laboratories and is based on section 2.1 (Analytical Factors Important In Veterinary Clinical Pathology, General) of the newly revised ASVCP QAS Guidelines. These guidelines are not intended to be all-inclusive; rather, they provide minimum guidelines for quality assurance and quality control for veterinary laboratory testing. It is hoped that these guidelines will provide a basis for laboratories to assess their current practices, determine areas for improvement, and guide continuing professional development and education efforts.     

ASVCP quality assurance guidelines: control of preanalytical and analytical factors for hematology for mammalian and nonmammalian species, hemostasis, and crossmatching in veterinary laboratories

In December 2009, the American Society for Veterinary Clinical Pathology (ASVCP) Quality Assurance and Laboratory Standards committee published the updated and peer-reviewed ASVCP Quality Assurance Guidelines on the Society's website. These guidelines are intended for use by veterinary diagnostic laboratories and veterinary research laboratories that are not covered by the US Food and Drug Administration Good Laboratory Practice standards (Code of Federal Regulations Title 21, Chapter 58). The guidelines have been divided into 3 reports: (1) general analytical factors for veterinary laboratory performance and comparisons; (2) hematology, hemostasis, and crossmatching; and (3) clinical chemistry, cytology, and urinalysis. This particular report is one of 3 reports and provides recommendations for control of preanalytical and analytical factors related to hematology for mammalian and nonmammalian species, hemostasis testing, and crossmatching and is adapted from sections 1.1 and 2.3 (mammalian hematology), 1.2 and 2.4 (nonmammalian hematology), 1.5 and 2.7 (hemostasis testing), and 1.6 and 2.8 (crossmatching) of the complete guidelines. These guidelines are not intended to be all-inclusive; rather, they provide minimal guidelines for quality assurance and quality control for veterinary laboratory testing and a basis for laboratories to assess their current practices, determine areas for improvement, and guide continuing professional development and education efforts.     

Survey of antimicrobial susceptibility testing practices of veterinary diagnostic laboratories in the United States

OBJECTIVE: To describe antimicrobial susceptibility testing practices of veterinary diagnostic laboratories in the United States and evaluate the feasibility of collating this information for the purpose of monitoring antimicrobial resistance in bacterial isolates from animals. DESIGN: Cross-sectional study. PROCEDURES: A questionnaire was mailed to veterinary diagnostic laboratories throughout the United States to identify those laboratories that conduct susceptibility testing. Nonrespondent laboratories were followed up through telephone contact and additional mailings. Data were gathered regarding methods of susceptibility testing, standardization of methods, data management, and types of isolates tested. RESULTS: Eighty-six of 113 (76%) laboratories responded to the survey, and 64 of the 86 (74%) routinely performed susceptibility testing on bacterial isolates from animals. Thirty-four of the 36 (94%) laboratories accredited by the American Association of Veterinary Laboratory Diagnosticians responded to the survey. Laboratories reported testing > 160,000 bacterial isolates/y. Fifty-one (88%) laboratories reported using the Kirby-Bauer disk diffusion test to evaluate antimicrobial susceptibility; this accounted for 65% of the isolates tested. Most (87%) laboratories used the NCCLS (National Committee for Clinical Laboratory Standards) documents for test interpretation. Seventy-five percent of the laboratories performed susceptibility testing on bacterial isolates only when they were potential pathogens. CONCLUSIONS: The veterinary diagnostic laboratories represent a comprehensive source of data that is not easily accessible in the United States. Variability in testing methods and data storage would present challenges for data aggregation, summary, and interpretation.     

A proposal to leverage high-quality veterinary diagnostic laboratory large data streams for animal health,public health,and One Health

Test data generated by ~60 accredited member laboratories of the American Association of Veterinary Laboratory Diagnosticians (AAVLD) is of exceptional quality. These data are captured by 1 of 13 laboratory information management systems (LIMSs) developed specifically for veterinary diagnostic laboratories (VDLs). Beginning ~2000, the National Animal Health Laboratory Network (NAHLN) developed an electronic messaging system for LIMS to automatically send standardized data streams for 14 select agents to a national repository. This messaging enables the U.S. Department of Agriculture to track and respond to high-consequence animal disease outbreaks such as highly pathogenic avian influenza. Because of the lack of standardized data collection in the LIMSs used at VDLs, there is, to date, no means of summarizing VDL large data streams for multi-state and national animal health studies or for providing near-real-time tracking for hundreds of other important animal diseases in the United States that are detected routinely by VDLs. Further, VDLs are the only state and federal resources that can provide early detection and identification of endemic and emerging zoonotic diseases. Zoonotic diseases are estimated to be responsible for 2.5 billion cases of human illness and 2.7 million deaths worldwide every year. The economic and health impact of the SARS-CoV-2 pandemic is self-evident. We review here the history and progress of data management in VDLs and discuss ways of seizing unexplored opportunities to advance data leveraging to better serve animal health, public health, and One Health.     

ASVCP quality assurance guidelines: control of preanalytical, analytical, and postanalytical factors for urinalysis, cytology, and clinical chemistry in veterinary laboratories

In December 2009, the American Society for Veterinary Clinical Pathology (ASVCP) Quality Assurance and Laboratory Standards committee published the updated and peer-reviewed ASVCP Quality Assurance Guidelines on the Society's website. These guidelines are intended for use by veterinary diagnostic laboratories and veterinary research laboratories that are not covered by the US Food and Drug Administration Good Laboratory Practice standards (Code of Federal Regulations Title 21, Chapter 58). The guidelines have been divided into 3 reports: (1) general analytical factors for veterinary laboratory performance and comparisons; (2) hematology, hemostasis, and crossmatching; and (3) clinical chemistry, cytology, and urinalysis. This particular report is one of 3 reports and documents recommendations for control of preanalytical, analytical, and postanalytical factors related to urinalysis, cytology, and clinical chemistry in veterinary laboratories and is adapted from sections 1.1 and 2.2 (clinical chemistry), 1.3 and 2.5 (urinalysis), 1.4 and 2.6 (cytology), and 3 (postanalytical factors important in veterinary clinical pathology) of these guidelines. These guidelines are not intended to be all-inclusive; rather, they provide minimal guidelines for quality assurance and quality control for veterinary laboratory testing and a basis for laboratories to assess their current practices, determine areas for improvement, and guide continuing professional development and education efforts.     

ASVCP quality assurance guidelines: external quality assessment and comparative testing for reference and in‐clinic laboratories

The purpose of this document is to educate providers of veterinary laboratory diagnostic testing in any setting about comparative testing. These guidelines will define, explain, and illustrate the importance of a multi‐faceted laboratory quality management program which includes comparative testing. The guidelines will provide suggestions for implementation of such testing, including which samples should be tested, frequency of testing, and recommendations for result interpretation. Examples and a list of vendors and manufacturers supplying control materials and services to veterinary laboratories are also included.     

Clinical hematology practices at veterinary teaching hospitals and private diagnostic laboratories

The clinical hematology practices utilized at veterinary teaching hospitals and private veterinary diagnostic laboratories were surveyed using a questionnaire. The hematology caseload at private diagnostic laboratories was larger, and comprised predominantly of canine and feline submissions. The Coulter S Plus IV and Serono Baker 9000 were the hematology analyzers used most frequently at veterinary medical laboratories. The Abbott Cell-Dyn 3500, a multispecies analyzer capable of leukocyte differential counting, was utilized more by private laboratories. Commercial hematology control reagents were used at all laboratories; teaching hospital laboratories more often used reagents supplied by the manufacturer of the analyzer. A greater percentage of private diagnostic laboratories participated in the external quality assurance programs offered by Veterinary Laboratory Association and College of American Pathologists. While private diagnostic laboratories retained the EDTA blood specimens longer after initial testing, the teaching hospital laboratories retained blood smears and complete blood count reports longer. The complete blood count reports at veterinary teaching laboratories more often included red blood cell volume distribution width, mean platelet volume, manual hematocrit, plasma protein, and leukocyte differentials as absolute concentrations. The laboratory practices utilized by these veterinary medical laboratories were generally similar, and differences were attributed to divergent emphasis on economic accountability and clinical investigation.     

Veterinary syndromic surveillance: Current initiatives and potential for development

This paper reviews recent progress in the development of syndromic surveillance systems for veterinary medicine. Peer-reviewed and grey literature were searched in order to identify surveillance systems that explicitly address outbreak detection based on systematic monitoring of animal population data, in any phase of implementation. The review found that developments in veterinary syndromic surveillance are focused not only on animal health, but also on the use of animals as sentinels for public health, representing a further step towards One Medicine. The main sources of information are clinical data from practitioners and laboratory data, but a number of other sources are being explored. Due to limitations inherent in the way data on animal health is collected, the development of veterinary syndromic surveillance initially focused on animal health data collection strategies, analyzing historical data for their potential to support systematic monitoring, or solving problems of data classification and integration. Systems based on passive notification or data transfers are now dealing with sustainability issues. Given the ongoing barriers in availability of data, diagnostic laboratories appear to provide the most readily available data sources for syndromic surveillance in animal health. As the bottlenecks around data source availability are overcome, the next challenge is consolidating data standards for data classification, promoting the integration of different animal health surveillance systems, and also the integration to public health surveillance. Moreover, the outputs of systems for systematic monitoring of animal health data must be directly connected to real-time decision support systems which are increasingly being used for disease management and control.     

The laboratory network in Australia and New Zealand – an evolving system

This paper discusses the network of government, private and university veterinary laboratories in Australia and New Zealand and how it is adapting and evolving to meet the challenges it faces. It includes the mechanisms for standardisation of procedures, quality assurance, and the role of national reference laboratories hosted by state government laboratories. It also highlights the crisis in supply of veterinary diagnosticians, especially the declining numbers of veterinary pathologists. Recent positive changes include the setting up of the National Animal Health Laboratory Strategy and an initiative to empower State and Territory government laboratories to test for exotic diseases. The ideal outcome for Australia and New Zealand is a laboratory service that remains the gold standard around the world.     

The quality assurance of proficiency testing programs for animal disease diagnostic laboratories.

Laboratory data credibility has 3 major components: 1) valid methods, 2) proficiency testing (PT) to verify that the analyst can conduct the method and to compare results of other laboratories using the same method, and 3) third-party accreditation to verify that the laboratory is competent to conduct testing and that the method validation has been done within the environment and requirements of an effective quality-management system. Participation in external PT programs by a laboratory is strongly recommended in International Organization for Standardization/International Electrotechnical Commission International Standard 17025. Most laboratory accreditation bodies using this standard require that laboratories participate in such programs to be accredited. Internal PT is also recommended for each analyst. Benchmarking, or comparison between laboratories using PT or reference materials, is also recommended as part of the validation and evaluation of test methods. These requirements emphasize the need for proficiency test providers to demonstrate their competence. Requirements for competence are documented in national and international standards and guidelines, and accreditation is available for providers. This article discusses the activities and the components that are necessary and recommended for PT projects and programs for animal disease diagnostic testing. These are based on the requirements of the national and international standards, which address this subject, and on the experience of the author. The accreditation of external PT programs is also discussed. Organizations that accredit PT providers or that provide PT programs are listed. Existing references, guidelines, and standards that are relevant to PT in veterinary diagnostic laboratories are discussed.     

Suggested guidelines for immunohistochemical techniques in veterinary diagnostic laboratories

This document is the consensus of the American Association of Veterinary Laboratory Diagnosticians (AAVLD) Subcommittee on Standardization of Immunohistochemistry on a set of guidelines for immunohistochemistry (IHC) testing in veterinary laboratories. Immunohistochemistry is a powerful ancillary methodology frequently used in many veterinary laboratories for both diagnostic and research purposes. However, neither standardization nor validation of IHC tests has been completely achieved in veterinary medicine. This document addresses both issues. Topics covered include antibody selection, fixation, antigen retrieval, antibody incubation, antibody dilutions, tissue and reagent controls, buffers, and detection systems. The validation of an IHC test is addressed for both infectious diseases and neoplastic processes. In addition, storage and handling of IHC reagents, interpretation, quality control and assurance, and troubleshooting are also discussed. Proper standardization and validation of IHC will improve the quality of diagnostics in veterinary laboratories.     

ASVCP reference interval guidelines: determination of de novo reference intervals in veterinary species and other related topics

Reference intervals (RI) are an integral component of laboratory diagnostic testing and clinical decision‐making and represent estimated distributions of reference values (RV) from healthy populations of comparable individuals. Because decisions to pursue diagnoses or initiate treatment are often based on values falling outside RI, the collection and analysis of RV should be approached with diligence. This report is a condensation of the ASVCP 2011 consensus guidelines for determination of de novo RI in veterinary species, which mirror the 2008 Clinical Laboratory and Standards Institute (CLSI) recommendations, but with language and examples specific to veterinary species. Newer topics include robust methods for calculating RI from small sample sizes and procedures for outlier detection adapted to data quality. Because collecting sufficient reference samples is challenging, this document also provides recommendations for determining multicenter RI and for transference and validation of RI from other sources (eg, manufacturers). Advice for use and interpretation of subject‐based RI is included, as these RI are an alternative to population‐based RI when sample size or inter‐individual variation is high. Finally, generation of decision limits, which distinguish between populations according to a predefined query (eg, diseased or non‐diseased), is described. Adoption of these guidelines by the entire veterinary community will improve communication and dissemination of expected clinical laboratory values in a variety of animal species and will provide a template for publications on RI. This and other reports from the Quality Assurance and Laboratory Standards (QALS) committee are intended to promote quality laboratory practices in laboratories serving both clinical and research veterinarians.     

Laboratory procedures.

The main foundation to veterinary medicine is the availability of laboratory tests. These tests may be performed in-clinic or at diagnostic laboratories. In-clinic testing is advantageous in producing quick results, but demands sound technical ability, basic equipment,and access to some routine and special reagents. Laboratory-based testing can back up those routine techniques that mayor may not be available at the clinic level as well as provide specialized testing. The knowledge of commercially available diagnostic services is important as well as preparation and proper shipping of samples for accurate determinations.     

Utilizing technology to enhance laboratory–client interaction while encouraging best behavior

As client interactions with veterinary diagnostic laboratories have evolved, so have client expectations: faster results, enhanced accessibility to cases, and more seamless data transfer from the laboratory database; all of these factors have encouraged the evolution of diagnostic laboratory systems. This evolution started with 24-h access to laboratory results via the web, yet data quality remained at the mercy of the person filling out the form. If bad (incomplete) information was flowing in, then the data coming out was equally bad (incomplete or inconsistent). By designing a web-based system integrated into our existing reporting platform, the Iowa State University Veterinary Diagnostic Laboratory (ISU-VDL) set out to improve the quality of submission data by including the premises identification number (PIN) and obtaining consistent location data, all while presenting to the client an easy-to-use interface. Efforts continued by incentivizing the use of this tool and client submission practices. As clients transitioned, data have become more complete, resulting in easier queries and an improved ability to leverage the diagnostic data. To further enhance the client experience, a streamlined daily reporting summary was designed to communicate laboratory results succinctly. The use of these web-based tools had a positive impact on the quality and consistency of the diagnostic data. As new ideas develop, the ISU-VDL strives to foster continuous improvement and positively impact the clients’ experience.     

社会需求与兽医系统实验室能力提升

兽医系统实验室在指导动物疫病防控、维护公共卫生安全等方面占有举足轻重的地位。随着动物疫病防控工作的不断深化,加强兽医系统实验室能力建设显得尤为紧迫。本文着重介绍了近年来重庆市兽医实验室体系建设的一些实践措施,以期为其他省份兽医系统实验室的进一步发展提供参考。     

Effective use of analytical laboratories for the diagnosis of toxicologic problems in small animal practice

The increasing sophistication of toxicologic analyses offered by veterinary diagnostic laboratories provides the practitioner with a valuable resource for the diagnosis of companion and exotic animal toxicoses. The availability of such testing is a valuable service that can be offered to veterinary clientele. Appropriate and timely toxicologic testing may permit more successful treatment of affected patients and protect animals and humans from hazardous exposure that might occur if a responsible toxicant goes unrecognized. Perhaps the most critical point to keep in mind, however, is that no matter how sophisticated the toxicologic laboratory is, a correct diagnosis is dependent upon the submission of appropriate biologic and environmental samples.     

Data standardization implementation and applications within and among diagnostic laboratories: integrating and monitoring enteric coronaviruses

Every day, thousands of samples from diverse populations of animals are submitted to veterinary diagnostic laboratories (VDLs) for testing. Each VDL has its own laboratory information management system (LIMS), with processes and procedures to capture submission information, perform laboratory tests, define the boundaries of test results (i.e., positive or negative), and report results, in addition to internal business and accounting applications. Enormous quantities of data are accumulated and stored within VDL LIMSs. There is a need for platforms that allow VDLs to exchange and share portions of laboratory data using standardized, reliable, and sustainable information technology processes. Here we report concepts and applications for standardization and aggregation of data from swine submissions to multiple VDLs to detect and monitor porcine enteric coronaviruses by RT-PCR. Oral fluids, feces, and fecal swabs were the specimens submitted most frequently for enteric coronavirus testing. Statistical algorithms were used successfully to scan and monitor the overall and state-specific percentage of positive submissions. Major findings revealed a consistently recurrent seasonal pattern, with the highest percentage of positive submissions detected during December–February for porcine epidemic diarrhea virus, porcine deltacoronavirus, and transmissible gastroenteritis virus (TGEV). After 2014, very few submissions tested positive for TGEV. Monitoring VDL data proactively has the potential to signal and alert stakeholders early of significant changes from expected detection. We demonstrate the importance of, and applications for, data organized and aggregated by using LOINC and SNOMED CTs, as well as the use of customized messaging to allow inter-VDL exchange of information.     

2021年江苏省兽医系统实验室检测能力比对结果统计与思考

为进一步增强江苏省兽医系统实验室对动物疫病的监测预警能力,本文对江苏疫控中心2021年10月组织的全省兽医系统（12个市级、65个县级）实验室比对结果进行了统计,样品正确率为97.81%（1115/1140）,实验室正确率为84.42%（65/77）。比对结果表明,77个实验室均具备开展主要动物疫病监测预警的技术能力,但少数实验室的个别比对项目检测结果存在一定偏差。提示仍然需要加强实验室建设,包括扩充专业人才队伍、增加资金投入、及时更新检测设备等,不断提高检测业务能力。