WGS in Microbial Molecular Identification

Whole genome sequencing (WGS), developed from the expansion of human genomics, is becoming available as a routine tool for clinical microbiology. WGS improved the identification of bacteria in culture, with the almost perfect agreement between phenotype and predicted antimicrobial susceptibility. Creative Biolabs has expertise and capabilities in providing high-quality WGS solutions for microbial identification.

About WGS

WGS, also known as full genome sequencing, complete genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a single time. It is a laboratory process that determines the complete genome sequence of an organism under study providing significantly more information than routine molecular diagnostic tools. As the cost of WGS has steadily declined, more and more microbiology laboratories have started WGS projects.

WGS is an important tool for the study of organisms, both human and microbial. Unlike 16S rRNA gene sequencing, WGS provides a clear-cut criterion for bacterial classification. Furthermore, bacterial species is now defined by the relatedness of genome sequences. WGS has considerable potential in clinical diagnosis because it can provide accurate species identification and can achieve the resolution of different strains.

Whole genome sequencing workflow.Fig.1 Whole genome sequencing workflow. (Kwong, 2015)

WGS in Microbiology

At present, the potential application of WGS in the identification of bacterial pathogens in diagnostic microbiology laboratories mainly includes four aspects: identification, typing, drug resistance detection, and virulence gene detection

  • Identification

WGS may play a key role in organisms that cannot be identified by conventional methods. This includes organisms that often undergo methods such as 16S rDNA sequencing or specific nucleic acid probes to confirm identification.

  • Typing

Typing is organism-specific and requires constant validation. In contrast, WGS can replace traditional typing methods, either in silicon typing, or superior differentiation capabilities.

  • Resistance Detection

WGS also has potential applications to assist in antimicrobial resistance detection. Current analyses using WGS data can readily detect acquired resistance such as beta-lactamases and aminoglycoside modifying enzymes.

  • Virulence Profiling

Another major potential use of WGS data for biometrics is to detect genetic markers for toxicity.

Advantages of Whole-Genome Sequencing

  • Provide a high-resolution, base-by-base view of the genome
  • Capture large and small variables that might be missed by targeted approaches
  • Potential pathogenic variants are identified for further follow-up studies on gene expression and regulatory mechanisms
  • Provide a large amount of data in a short time to support the assembly of new genomes

Creative Biolabs is a complete live biotherapeutic probiotic (LBP) development solutions provider. We deliver services of unparalleled quality. We are happy to discuss your goals so that we can determine which methods and techniques can best be used to get the most reliable answers and most effectively manner. If you are interested in our WGS services, please contact us for more information.

Reference

  1. Kwong J C, McCallum N, Sintchenko V, et al. Whole genome sequencing in clinical and public health microbiology. Pathology. 2015, 47(3): 199-210.

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