SLST and MLST Sequence-based Strain Typing

AccuGENX-ST® is a microbial characterization process used to distinguish members of the same species to the strain level by utilizing the well-established, highly accurate sequencing methods of SLST and MLST (single and multilocus sequence typing).

We perform DNA sequencing of targets outside of the standard regions sequenced for microbial identification (16S, D2, or ITS2) to provide you with data to prove differences and/or similarities at the strain level. Determination to the strain level using SLST and MLST allows you to definitively track the source of contamination or simply verify your known production strains.


Is Your Organism of Interest
on the AccuGENX-ST® Validated Method List?

pippets assay tips used to verify species

From Acholeplasma laidlawii to Yarrowia lipolytica, each species investigated by our Accugenix® R&D team is validated and listed. New species may be developed and validated on request.

Download the List


Given the increased reproducibility of SLST and MLST sequence-based strain typing, they can help determine if your probiotic strains are the same or if the isolates recovered from one area are the same or different as another isolate—an important trait that allows for high resolution and greater confidence in your tracking and trending projects over time compared to methods utilizing fragment-based analysis.

  • Why Outsource Sequence Typing Services Using Accugenix®
    • The foundation is built upon DNA sequencing results.
    • SLST and MLST data serve as primary resources for tracking and documenting the genetic relationship of bacteria at a global scale.
    • SLST and MLST sequence-based stain typing results are easily cataloged and referenced for future comparisons.
    • SLST and MLST techniques are highly reproducible, unambiguous, and scalable.
    • Gain access to relevant organism library and bioinformatics experts
    • Short turnaround times

Specific Species

In order to achieve a higher degree of resolution, each species is researched by our R&D team to determine the gene targets outside of the region used for identification that will most definitively resolve them at the subspecies or strain level. The number and identity of these loci vary for each species, due to the level of relatedness and rate of evolution within each group.


Would You Like E. coli with That?

gloved microbiological lab technician holding media plate streaked with E.coli

Read about how AccuGENX-ST® was used to facilitate a contamination investigation at a dietary supplement and beverage manufacturing company.

Download the case study


Tracking Sources of Contamination

If a sterility failure occurs, customers can send samples to us, and we can assist in determining the root cause. We will first identify the isolates by 16S rDNA sequencing. If the 16S sequence is different, you can be sure that the isolates are different strains. Further characterization is necessary for those isolates that have identical 16S sequences and can be done using SLST or MLST (single and multilocus sequence typing). This strain typing technology is designed to deliver the most informative data and have the ability to obtain an unambiguous result from all strains within a species.

Our SLST and MLST sequence-based strain typing can help you map your microbial environment. We can create a library database of sequences from the microorganisms found in your manufacturing environment. When a contaminant is encountered, you can quickly pinpoint where you have seen that particular strain before. This greatly reduces the time and cost associated with identifying the source of contamination.

  • Methods for Sequence-based Strain Typing

    Microbial identification using the rRNA regions is a robust technology. There are times, however, when additional information is needed and it is essential to be able to differentiate organisms below the species level. Increased discrimination at the strain level can be achieved by sequencing, analyzing and comparing highly variable loci (regions) in the organism's genome. MLST and SLST (single and multilocus sequence typing) analyze essential protein coding genes, or housekeeping genes, that encode for proteins necessary for the normal cellular functions of the bacterium all of which contain more variability in their sequences.

    After extracting DNA from the sample, which can be viable or non-viable, the first step in this process is an accurate ID to the species level. This must be performed before starting MLST or SLST to determine appropriate targets and primer sets as the target genes will not be the same for each species being characterized.

    The target genes are PCR amplified using the gene-specific primers and subjected to comparative DNA sequence analysis. All the sequences from each gene target are aligned and compared to the other organisms' sequence data and the level of divergence or conservation between the organisms is calculated and displayed with a phylogenetic tree. We will interpret the data for you and state whether the isolates are indistinguishable by the sequencing of the particular gene targets or whether the isolates are different sequence types.

  • SPECIFICATIONS

    Order Code

    Turnaround Time (TAT) Test Code
    5 days AccuGENX-ST-5
    5 days AccuGENX-XGST-5

How to Interpret an AccuGENX-ST® Strain Typing Report

pippets being used for strain typing

This guide details how to interpret S/MLST results generated by AccuGENX-ST®.

Download the Guide



Frequently Asked Questions (FAQs) About SLST and MLST

  • What is the difference between microbial identification and strain typing?

    Genotypic microbial identification is performed by DNA sequencing of the conserved 16S rRNA in bacteria and IT2 region in fungi. The identification is made based on phylogenetic analysis and can only resolve down to the species level. Because members of the same species can still have genetic diversity, strain typing can be achieved by sequencing other highly variable genetic loci. The resulting data will convey whether isolates are different from each other or indistinguishable.

  • What is the difference between AccuGENX-ST® and AccuGENX-XGST®?

    While both tests are used for strain typing, AccuGENX-XGST® can be used for specific organisms that have a published MLST scheme with defined alleles. The comparison report will include the allelic number for each gene sequenced and the strain type of the sample (if previously defined).

  • What are strain typing methods such as SLST and MLST used for?

    Strain typing is a microbial characterization process that is used to distinguish members of the same species at the strain level. This technique is often used in contamination investigations to help find the root cause or source of a sterility failure or product contamination. Strain typing can also be used to confirm microbial production strain identities and to differentiate them from environmental contaminants.