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Whole Genome Sequencing Lab Service

Category Press Release
Publish Date 9/26/2018
Author Sergey Balashov, Ph.D.
Title Microbial Source Tracking and Outbreak Investigation by Whole Genome Sequencing
Introduction EMSL is expanding now to areas of high resolution microbial strain typing, source tracking and outbreak surveillance based on whole genome sequencing (WGS).

Cinnaminson, NJ,  September 26th , 2018

EMSL Analytical Inc. has been at the forefront of microbial source tracking for many years. Until recently, the menu of molecular source tracking methods has been limited to qPCR assays for fecal biomarkers: Bacteroides species specific for warm blooded animals and Bacteroides species of human origin. With acquisition of advanced molecular instrumentation and bioinformatic capabilities, EMSL is expanding now to areas of high resolution microbial strain typing, source tracking and outbreak surveillance based on whole genome sequencing (WGS).

WGS provides the maximum possible discriminatory level in typing closely related bacterial isolates and establishing genetic relatedness between them. It is rapidly becoming a gold standard in characterization of foodborne and environmental pathogens by far surpassing other biological techniques for strain identification and subtyping such as restriction-fragment length polymorphism typing (RFLP) or pulsed-field gel electrophoresis (PFGE). The power of WGS is in unambiguous and comprehensive definition of the complete bacterial genome which can be used for more than one purpose: identification, subtyping, detection of virulence and antimicrobial resistance markers. WGS-based epidemiological surveillance and source tracking deliver ultimate resolution for tracing contamination routes and sources of infections. In cases of disease outbreak, WGS makes possible the precise identification of a source, determination of transmission events and description of the outbreak dynamics.

Applied as a research tool and outbreak investigation technology by Centers for Disease Control and Prevention (CDC), Food and Drug Administration (FDA) and National Antimicrobial Resistance Surveillance System (NARMS), WGS is now becoming a method available to EMSL customers. We use high throughput Illumina sequencing platform for generation of genomic data and combination of bioinformatic approaches for data processing. Core-genome multi locus sequence typing (cgMLST), a technique used for genomic data analysis, generates individual allelic profiles and performs phylogenetic clustering of genomes displaying a relatedness of bacterial strains under examination. This high-resolution analysis enables the efficient identification of closely related isolates and aids source tracking and internal outbreak investigations. All the sequencing information is stored securely and delivered along with test report comprising cluster analysis results.

WGS-based subtyping and strain typing is a valuable addition to molecular tools used for foodborne disease management and investigation of outbreaks caused by environmental microorganisms. EMSL has already successfully applied the platform for investigations of Legionella outbreak and Listeria food plant contamination. Predefined cgMLST profiles for Brucella, Campylobacter, Enterococcus, Klebsiella, Salmonella, Staphylococcus and many other bacterial species can also be applied for epidemiological surveillance of corresponding pathogens. Our private genomic database is expanding as more food and environmental isolates get sequenced. With new WGS services, EMSL is becoming a first response provider to many food safety and environmental challenges. Our customers will benefit from advanced genomic testing options, in-depth microbial analysis, and confidentiality of test results.

To learn more about WGS and other EMSL laboratory testing services, please visit For assistance, please call 1-800-220-3675 or email

About EMSL Analytical, Inc.
EMSL Analytical is one of the leading testing laboratories with over 45 locations throughout the United States and Canada. EMSL is a nationally recognized and locally focused provider specializing in fast laboratory results for mold, bacteria, Legionella, USP <797>, pathogens, asbestos, lead, soot, char & ash from fires, VOC’s, odors, radon, formaldehyde, indoor air quality, microbiology, environmental, industrial hygiene, radiological, food, beverage & consumer products and material testing services for the identification of unknown substances. EMSL services both professionals and the general public. EMSL maintains an extensive list of accreditations from leading organizations as well as state and federal regulating bodies including, but not limited to A2LA, AIHA LAP, LLC. (AIHA EMLAP, AIHA IHLAP, AIHA ELLAP), NVLAP, CDC ELITE, CPSC, CA ELAP, NY ELAP, TX DOH, NJDEP and multiple other state accrediting agencies. Please visit our website at for a complete listing of accreditations. In addition, EMSL carries a wide range of Sampling Equipment and Investigative Products for environmental professionals.

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