Protein-Coding Gene Sequencing with AccuGENX-ID® ProSeq
Occasionally, there are organisms that are too closely related and have a high degree of conservation in the ribosomal RNA regions such that 16S sequencing is not able to separate them (our “Species*” confidence level, which indicates that the unknown matches two or more closely related species).
in the Pharmaceutical Industry
Bacterial Identification service with AccuGENX-ID® ProSeq is a highly discriminatory and accurate sequence-based method that can be used to distinguish between very closely related microorganisms to the species level. Resolution is achieved by analyzing protein-coding genes.
If the AccuGENX-ID® report contains a species* confidence level (indicating the identification resolution is to the group or complex level), and we have determined the target gene that can distinguish between the different species in that group of organisms, customers can request our identification with ProSeq service.
Eligible bacterial species include Burkholderia cepacia complex (BCC) among others. Please contact us for a full list of available closely related microorganism groups for species-level identification.
Bacterial ID Service: AccuGENX-ID® BacSeq
For many organisms, traditional phenotypic identification is problematic, takes a great amount of time, and can result in subjective interpretation of bacterial identification results. Not all strains within a given bacterial species consistently exhibit a particular characteristic, thereby limiting phenotypic identification methods. Additionally, library databases utilized in support of phenotypic identification are limited.
Our AccuGENX-ID® BacSeq bacterial identification service process adheres to the reference method used by taxonomists because it delivers the most accurate and reliable sequence data for identifications. When this process is combined with the full coverage, validated Accugenix® library, the resulting phylogenic analysis is unparalleled.
Charles River AccuGENX-ID® BacSeq identifies microogranisms through comparative sequencing of the 16S ribosomal RNA (rRNA) gene in bacteria. The bacterial DNA sequence is assessed for quality, assembled, and compared to the validated Accugenix® library. A phylogenetic tree is interpreted by trained data analysts in order to make the bacterial characterization and identification.
Our microbial phylogeneticists use a combination of the genetic variability, branching order of the neighbor joining tree, and knowledge of the interspecies variation when interpreting the bacterial identification reports and assigning the taxonomic confidence level.
The proprietary methods employed by Charles River's bacterial identification service compare sample sequences against full-coverage proprietary libraries, result in conclusive data interpretation, and make identifications with assigned confidence levels based on phylogenetic analyses.
Utilizing this scientifically proven method and our validated, continuously curated, proprietary bacterial library provides the most accurate bacterial identifications. Outsourcing bacterial identifications to our cGMP-compliant, ISO 17025-accredited contract testing laboratories can help save time and resources for other important QC tasks.
Frequently Asked Questions (FAQs) about Bacterial identification Services
What techniques are used to identify bacteria?
16s rRNA sequencing is known as the gold standard for bacterial identification. Comparative sequencing of the 16S ribosomal RNA (rRNA) gene in bacteria has been proven to be the most accurate and reproducible method for identifying unknown organisms. The technology is inherently stable, which allows for reproducible data for identification. Another suitable identification method for bacterial identification is matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The MALDI-TOF testing process yields a unique protein spectral fingerprint that can be compared to a bacterial database for identification. A variety of phenotypic identification methods are also available for bacterial identification, however, these biochemical and metabolic tests are subjective by nature and do not provide enough discrimination to offer accurate and reproducible identification results. Our bacterial identification services offer 16s rRNA sequencing and MALDI-TOF options because they are the most reliable methods.
Why is accurate bacterial identification important?
Accurate bacterial identification is critical for environmental monitoring (EM) programs in pharmaceutical and other regulated product manufacturing industries. Identification of unknown isolates is an essential first step in understanding the risk that microorganisms have on the manufacturing environment, final product, and subsequently the patients. Accurate bacterial identification services that provide EM data tracking and trending solutions help maintain a clear baseline view of the facility’s microbial flora so that unusual activity is recognized early and there is time for remediation.
What are the critical elements of accurate bacterial identification?
The organism reference library is an essential part of the bacterial identification process. A bacterial isolate cannot be accurately identified without a matching species entry in the database. Therefore, a relevant and validated reference library is equally as important as the technology and methodology used to identify bacteria. Aside from library comparison, interpretation of the sequence and report generation are also critical parts of the bacterial identification process.
What microbial samples require identification?
Any isolates detected during environmental monitoring testing, bioburden testing, or sterility testing should be submitted for identification.