UK DIAGNOSTIC ROUNDS
The University of Kentucky Veterinary Diagnostic Laboratory (UKVDL) announces a Next-Generation Sequencing Service
The UKVDL is excited to offer Next-Generation Se- quencing (NGS). NGS allows for the genetic identifi-
cation of infectious disease agents in clinical samples by utilizing unbiased, massive, parallel sequencing of all nu- cleic acids in any given sample. Sequencing will enhance diagnostic service and research capabilities as an extension of our existing microbiology sections to help identify po- tential pathogens, both endemic and emerging, that may cause morbidity and mortality in animals.
In many infectious diseases involving one or more body systems, it can be difficult to reach a definitive diagnosis. Identification of potential pathogens in these cases could include viral, bacterial, protozoal, fungal, or various com- binations, of pathogens, which may require complex an- cillary testing that may take several days, if not weeks to detect. In addition, many pathogens cannot be cultured or are difficult to grow from clinical specimens using rou- tine laboratory methodologies. Te implementation of NGS and leading-edge bioinformatic analysis at the UK- VDL will assist practitioners, farm and animal owners, and university researchers in the discovery and identifi- cation of novel and known pathogens. It will also enable innovative disease surveillance methods for endemic and emerging diseases of animals and allow detection of patho- gens of veterinary and human concern from insect vectors.
Te following NGS services are now available to practi- tioners and researchers:
Shotgun Metagenomics Sequencing Shotgun metagenomics (next-generation sequencing) is typically used in undiagnosed cases or outbreak situ- ations. Tis method allows genetic identification of in- fectious disease agents in clinical samples by unbiased amplification of all nucleic acids within the sample. Te UKVDL has implemented a Miseq (Illumina) next gen- eration sequencer, which can generate around 1 million nucleic acid reads per sample. Tose reads are then com- pared to published libraries to identify the population of organisms within the sample. However, in some cases the number of reads for a pathogen of interest may not be suf- ficient to produce a full or partial genome due to compe- tition with host nucleic acids, low bacterial or viral titers, degraded nucleic acids, or a low number of total reads. When sufficient reads are available, the identification of one or more pathogen and full or partial draft genomes will be reported. Days tested: As needed. Turnaround time: 1-3 weeks
24 KVMA News
Specimen Requirements: At least 10 g of tissue or fecal material, 5 ml of whole blood, urine or other body fluid, or swabs Shipping info: Sterile blood tubes, plastic tubes with se- cure caps, and/or whirl-pak bags can be used. Samples should be placed in an insulated box containing ice packs or dry-ice. Improper handling of samples may affect the quality of the NGS results. Fee: $400.00 per sample
Bacterial or Viral Whole Genome Sequencing: Tis method allows sequencing of bacterial or viral ge- nomes using the Miseq (Illumina) sequencer. Analysis may include species identification, de novo assembly, dif- ferentiation of vaccine from wild-type strains, screening for antibiotic resistance genes, pangenome comparison, and phylogenetic analysis. If a clinical sample is submit- ted, a culture will first be performed (with a separate fee) and then sequencing will be performed on the isolate. Days tested: As needed Turnaround time: 1-3 weeks Specimen Requirements: At least 1 ml of freshly grown viral or bacterial culture in liquid media or bacteria sub- mitted on a solid agar medium. Shipping info: Isolates should be in sterile plastic tubes with secure cap or on agar plates.
Samples should be
placed in an insulated box containing ice packs or dry- ice. Improper handling of samples may affect the quality of the NGS results. Fee: $200.00 per sample
Next Generation Sequencing Analysis Only
(includes viral and bacterial WGS) Te analysis of whole genome sequences of bacteria or viruses can be performed on fastq files (a specific com- puter file format that includes the nucleic acid sequence) from samples sequenced at other facilities. Bacterial and/ or viral analysis may include species identification, de novo assembly, differentiation of vaccine from wild-type strains, screening for antibiotic resistance genes, pange- nome comparison, and phylogenetic analysis. Days tested: As needed. Turnaround time: 1-3 weeks Specimen Requirements: fastq file Fee: $100.00 per sample
For more information please contact the UKVDL (859-
257-8283) and discuss with Drs. Erdal Erol or Litty Paul.
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