DNA analysis of the 16S ribosomal gene DNA is a time tested method to identify the taxonomic identity of unknown microbes, often to the species level. You send us live or inactive bacteria or their isolated DNA and we extract, amplify, and sequence the 16S rRNA gene variable region. Sequence information is analyzed and compared to a reference library of microbial sequences to determine the nearest matching neighbors in the library. Phylogenetic and distance analysis of each microbe presents the most likely genus or species taxonomy and a graphical representation of the proximity to nearest reference neighbors.
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.
The 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.
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.
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.