Variant Analysis Service

Bacterial Isolate Typing

Our Bacterial Isolate Typing services focus on generating insights into the genetic variations of microbial isolates. You can choose whether this is performed using Multi-Locus Sequence Typing (MLST) and Core Genome MLST (cgMLST) or if single nucleotide polymorphisms should be used.

Bacterial Isolate Typing Service (based on SNP profiles)

The data analysis service focuses on utilizing single nucleotide polymorphisms (SNPs) to generate insights into the genetic variations of microbial isolates. SNP profiles are created by analyzing core genome across the samples, enabling the grouping of isolates based on genetic relationships and evolutionary history.

The service is designed to support researchers and institutions engaged in bacterial genomic research, epidemiological studies, and microbial strain comparison.

Service components

Data Preprocessing: Quality control and preprocessing of raw sequencing data (e.g., trimming, filtering, error correction).
Reference Genome Mapping: Sequencing reads are aligned to a reference genome using specialized bioinformatics tools like BWA, Bowtie2, or STAR to ensure precise positioning. Following alignment, duplicate reads, mapping errors, and low-confidence alignments are filtered out to enhance accuracy.
Core Genome Identification: This step identifies the core genome across all samples, focusing on high-quality genomic regions that are shared among them. Variants such as SNPs, insertions, and deletions are then identified by comparing the mapped reads to the reference genome in these regions.
Pairwise SNP Distance Calculation: Based on core genome SNPs, pairwise SNP distances are calculated to facilitate comparative analysis.
Phylogenetic Clustering: Samples are clustered phylogenetically, providing insights into their evolutionary relationships and aiding in comparative genomic analysis.

Deliverables

Raw Sequence Reads: Provided in fastq.gz format for further analysis.
SNP Distance Matrix: Delivered in TSV format, allowing for easy integration into various analytical tools.
Comprehensive Analysis Report: An HTML report summarizing the findings, methodologies, and insights derived from the analysis.

Requirements

The service requires the complete genome of the bacterial strain of interest in FASTA format or accession ID from the public databases such as Genbank, Ensembl, etc.,

Minimum Sample Requirement: A minimum of 3 samples is required for analysis.

Multi-Locus Sequence Typing (MLST) and Core Genome MLST (cgMLST) Profiling

The data analysis service focuses on utilizing Multi-Locus Sequence Typing (MLST) and Core Genome MLST (cgMLST) techniques to generate insights into the genetic variations of microbial isolates. MLST and cgMLST profiles are created by analyzing multiple loci across the genome, enabling the grouping of isolates based on genetic relationships and evolutionary history.

These methods are essential for tracking microbial outbreaks, identifying transmission patterns, and understanding genetic diversity within a species. By analyzing the sequences of conserved genes or core genome regions, highly accurate phylogenetic relationships are generated, contributing to epidemiological studies, strain characterization, and antibiotic resistance surveillance.

Service components

Data Preprocessing: Quality control and preprocessing of raw sequencing data (e.g., trimming, filtering, error correction).
Locus Selection: Identification and extraction of appropriate loci for MLST or cgMLST, based on the species or group under investigation.
Allele Calling: Determination of unique alleles for each locus based on genetic variation.
Profile Generation: Construction of MLST or cgMLST profiles for each isolate, consisting of allele numbers or sequence types (STs).
Clustering & Phylogenetic Analysis: Clustering of isolates based on genetic profiles and generating a phylogenetic tree to reflect evolutionary relationships.
Epidemiological Inferences: Assessment of genetic diversity and relatedness of isolates, identifying potential transmission pathways or clonal clusters.

Deliverables

Methodology Report: A comprehensive document detailing the methods used for sequence analysis, profile generation, and any assumptions made during the process.
- MLST/cgMLST Profiles: A table or report listing the sequence type (ST) for each isolate, including allele numbers or profiles for each analyzed locus.
- Phylogenetic Tree: A graphical representation of evolutionary relationships between isolates, based on genetic similarities, often produced using methods like Neighbor-Joining method.
- Allele and Locus Information: A detailed report showing the alleles identified for each locus across all isolates, including any new or rare allele types identified.
Clustering Metrics: Cluster analysis results grouping isolates based on genetic similarity (distance matrix).
Raw Data: Access to raw sequencing data (in FASTQ format)