High-resolution, reproducible MLST analysis for bacterial strain typing across research, clinical, and industrial applications, using standardized and validated workflows.
MLST is a sequence-based method used to characterize bacterial isolates by analyzing internal fragments of multiple housekeeping genes. Typically, 6 to 8 conserved genes are sequenced to detect nucleotide variations that define unique alleles. Each allele is assigned a number, and the combination of alleles across loci forms an allelic profile known as a sequence type (ST), enabling precise and reproducible strain typing. BaseClear provides MLST services to generate standardized strain-level identification based on validated gene sequencing and database comparison.
MLST is used by organizations that require high-resolution and reproducible bacterial strain identification. BaseClear supports clients across research, clinical, and industrial microbiology, including: Academic and research institutions studying bacterial diversity and evolution; Public health and surveillance laboratoriesmonitoringoutbreaks and transmission; Biopharmaceutical and biotechnology companies performing strain verification or contamination tracking; Food, environmental, and agricultural laboratories conducting microbial source tracing; Contract research and testing organizations supporting diverse microbiology workflows. Typical use cases include strain differentiation, epidemiological tracking, phylogenetic analysis, and comparative microbial studies.
BaseClear performs MLST analysis using established housekeeping gene schemes specific to the target bacterial species. Genomic DNA is extracted from cultured isolates, followed by PCR amplification of selected loci (typically 6–8 genes). The resulting amplicons are sequenced using Sanger sequencing to ensure high accuracy across both strands.
The sequencing data is processed through a standardized pipeline:
This workflow ensures reproducible strain typing and compatibility with global MLST reference frameworks.
Clients receive a structured MLST report containing all analytical outputs in a clear and standardized format suitable for research or operational use.
The report typically includes:
All results are delivered in a format suitable for documentation, downstream analysis, or integration into laboratory information systems.
You share your sample details, and our specialists define the most suitable MLST approach for your application.
You submit your bacterial isolate or DNA sample following our clear guidelines to ensure smooth processing.
We perform targeted sequencing of housekeeping genes and analyze the data to assign allele profiles and sequence types (ST) with fast turnaround times.
Your results are reviewed against established MLST databases to confirm strain identity.
You receive a clear, structured report with all results and interpretation, ready to support your research or decision-making.
Aligned with EFSA guidance on toxigenicity and pathogenicity
Combined with WGS and literature study
Use of established mammalian cell-based assays
Results translated into regulatory conclusions
MLST is a nucleotide sequence-based method for characterising bacterial isolates using internal fragments of multiple housekeeping genes. Each unique sequence at a locus is assigned an allele number, and the combination of alleles across loci defines the sequence type (ST). This provides a portable and unambiguous approach for comparing isolates between laboratories and studies.
MLST loci are internal fragments of housekeeping genes selected for their presence in all isolates of a species and their ability to accumulate slowly evolving sequence variation. Each locus is treated as an independent genetic marker within the MLST scheme. The set of loci used is defined by the species-specific MLST database.
A sequence type is assigned by determining the allelic profile of an isolate across all MLST loci and comparing it to profiles stored in a curated MLST database. If the allelic profile matches an existing entry, the corresponding ST is assigned. Novel combinations of alleles are designated as new STs subject to curation.
MLST data is generated by PCR amplification and sequencing of internal fragments of each housekeeping gene included in the scheme. High-quality sequence reads are used to determine exact nucleotide sequences for each locus. These sequences are then queried against allele databases for allele number assignment.
MLST data is analyzed by assigning allele numbers to each locus and combining them into an allelic profile. This profile is then used to query the MLST database to determine the corresponding sequence type. The resulting profiles can be used for isolate comparison and population structure analysis.
MLST can identify potentially novel alleles or sequence types when an isolate contains previously unrecorded sequence variation at one or more loci. Such findings are verified through sequence quality assessment and comparison with existing database entries. Validated novel alleles and STs may be submitted for inclusion in the reference database.
MLST provides a defined, gene-by-gene framework for strain characterization based on a fixed set of loci, whereas whole genome sequencing analyses variation across the entire genome. MLST is optimized for standardized inter-laboratory comparison using curated allele and ST databases, while WGS offers higher resolution for fine-scale genomic analysis.
Rapid DNA fingerprinting method for comparing microbial isolates and assessing genetic relatedness in routine strain typing studies.
High-resolution genomic analysis for in-depth strain comparison, outbreak investigation, and detailed microbial characterization.
Support regulatory-focused strain characterization using genomic analysis and interpretation for compliance and documentation purposes.
Speak with an MLST specialist in a free consultation to review your samples, define the most appropriate typing scheme, and understand expected deliverables before starting. You will receive clear guidance on workflow, turnaround time, and suitability for your project, with no obligation to proceed.
