ID Genomics offers Multilocus Sequence Typing (MLST) and 16sRNA sequencing services for a broad range of Gram-negative and Gram-positive pathogens. Whether you are studying the characteristics of microbes, monitoring them for food safety, or tracking them for environmental or epidemiological studies, accurate and timely identification of your microbes and their DNA markers is critical to your success.
Multi-locus Sequence Type (MLST) provides a finer resolution of microbial identification than 16S identification for applications that require discrimination or organisms within species. The MLST Sequence Type (ST) identity of your samples is determined by sequencing the DNA at 5-10 select and standardized loci in your specimen, determining the allele identity of the sequences and assembling the allelic profile to determine the unique Sequence Type. MLST typing is available for up to 100 bacterial species.
The small set of loci sequenced provide a fast and economical way to type your organisms, yet they are selected to represent the whole genome in terms of strain identity and evolution. MLST’s DNA sequence-based typing provides an unambiguous and reproducible identification system that is the common language in microbial identification. MLST is suitable for applications requiring highly discriminatory microbial identification such as epidemiology, contamination detection and tracking, and basic research. Information on origin, pathogenicity, serotype, etc. of isolates of a particular sequence type or neighboring sequence types is also available from public MLST databases.
The MLST Process:
• Single colony samples can be submitted in culture or DNA format.
• DNA is isolated from culture samples if required
• PCR amplification of the MLST target loci
• The PCR amplicons are sequenced
• Sequence data is viewed and analyzed
• For each specimen, allele numbers are assigned for each loci
• For Full and Extended MLST samples, the assembled sequence types (ST) are assigned.
• Your samples are plotted in a tree diagram which shows their relationship and proximity to each other.
Report and analysis results:
Your analysis results are returned to you as the following package.
• MLST Alleles and Sequence Types (STs)
An Excel file showing the assigned alleles for each of your samples. Sequence type information is shown for Full and Extended MLST samples.
• Tree diagram
One or more tree diagrams are provided to show the relationship between your samples as determined from the MLST typing.
• Novel allele sequences
Any new allele sequences encountered in typing your samples are provided to you for future reference.
Please contact us for a quote.
Staphylococcus aureus is a major human pathogen causing skin and tissue infections, pneumonia, septicemia, and device-associated infections. The emergence of strains resistant to methicillin (MRSA) and other antibacterial agents has become a major concern, especially in the hospital environment, because of the high mortality of the infections caused by these strains. Single locus DNA-sequencing of the polymorphic VNTR in the 3' coding region of the Staphylococcus protein A gene (spa) can be used for reliable, accurate and discriminatory typing of MRSA. Repeats are assigned a numerical code and the spa-type is deduced from the order of specific repeats.
SPA typing has been shown to be highly concordant with MLST and some studies suggest that it is suitable for macroepidemiology and evolutionary investigations based on studies of European and international isolates.
Our service includes:
The sequence of the variable region of the 16S rRNA ribosomal gene from your submitted microbes is analyzed to identify their taxonomy, usually to the species level. Compared to phenotype-based approaches, the 16S-based identification approach is fast, accurate, convenient and reproducible, well suited for identifying and tracking unknown samples.
The 16S-based identification process:
• Single colony samples can be submitted in different formats from live cultures to just DNA.
• DNA is isolated from live samples if required.
• PCR amplification of the target region of the 16S rRNA gene.
• The PCR amplicon is sequenced using the 1492R primer. Request a Quote for sequencing from the forward primer or both forward and reverse primers.
• Sequence data is viewed and analyzed.
• Phylogenetic analysis identifies the closest neighbors in the Ribosomal Database Project (RDP) reference database.
• Taxonomic information is derived from proximity to the nearest reference.
Your analysis results are returned to as a package containing the following information:
• Taxonomic Classifications
An Excel file listing the taxonomic classification of each of your samples based on the nearest neighbors in the RDB database.
• Phylogenetic Tree
A combined phylogenetic tree showing all of your strains in relation to each other and to the nearest known neighbors
• Sequence information
A file of all your 16S sequences in FASTA format
Please contact us for a quote.
Antimicrobial resistance (AMR) is the ability of bacteria to stop an antimicrobial (antibiotics) from working against it. As a result, standard treatments become ineffective, infections persist and may spread to others.
Antibiotic susceptibility testing can be used in the context of identification, screening, or species description.
We offer disc-diffusion antibiotic susceptibility testing performed according to the CLSI M100S 26th Edition (2016) recommendations for any bacterial sample up to biosafety level 2 (BSL-2).
Disc-diffusion method uses antibiotic-containing wafers or disks to test whether particular bacteria are susceptible to specific antibiotics. First, a pure culture of bacteria should be isolated from the sample. Then, a known quantity of bacteria are grown overnight on agar (solid growth media) plates in the presence of a thin wafer that contains a known amount of a relevant antibiotic. If the bacteria are susceptible to the particular antibiotic from a wafer, an area of clear media where bacteria are not able to grow surrounds the wafer, which is known as the zone of inhibition. A larger zone of inhibition around an antibiotic-containing disk indicates that the bacteria are more sensitive to the antibiotic in the disk.
Our service includes:
Metagenomics is a next-generation sequencing (NGS) based method. Unlike PCR-based approaches, it is a culture-free method that enables genetic analysis of an entire microbial communities’ genomes in a complex sample. This creates a biodiversity profile that can be further associated with functional composition analysis of known and unknown organism lineages (ie, genera or taxa).
Metagenomic studies are commonly performed by analyzing the prokaryotic 16S ribosomal RNA gene (16S rRNA), which is approximately 1,500 bp long and contains nine variable regions interspersed between conserved regions. Variable regions of 16S rRNA are frequently used in phylogenetic classifications such as genus or species in diverse microbial populations. Our service is based on sequencing the variable V3, V4 and V5 regions of the 16S rRNA gene.
Our service includes:
QIIME Preprocessing and QIIME Visualizations
Quantitative Insights into Microbial Ecology (QIIME) is designed to take users from raw sequencing data to publication quality graphics and statistics.
We can provide ISO17025 certified results.
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