Rapid Microbial Identification (RMID) with NGS

Ion AmpliSeq Rapid Microbial Identification (RMID) Research Panel

The Ion AmpliSeq Rapid Microbial Identification (RMID) Research Panel is a pre-designed custom targeted next-generation sequencing (NGS) research panel that is available to order on AmpliSeq.com as a made-to-order community panel product. It uses Ion AmpliSeq technology for targeted NGS to research bacterial 16S rRNA, fungal rRNA, and rpoB regions, allowing for pan-bacterial and pan-fungal metagenomic detection, along with species-specific identification of 88 microbial species in a single assay.

 

The panel supports DNA extracted and purified from various research sample types, including FFPE tissue, bronchoalveolar lavage (BAL), cerebrospinal fluid (CSF), blood, joint fluid, and stool. This analysis can be completed in as little as 24 hours with automated NGS.

Complete list of species-specific targets identified by the Ion AmpliSeq RMID Panel

 

 

Targets for species-specific identification​

 

Gram-negative bacteria​

 

Desulfovibrio alaskensis​

 

Prevotella histicola​

 

Enterococcus faecium​

 

Ruminococcus gnavus​

 

Acinetobacter baumannii​

 

Enterobacter cloacae​

 

Proteus mirabilis​

 

Enterococcus gallinarum​

 

Slackia exigua​

 

Bacteroides fragilis​

 

Escherichia coli​

 

Pseudomonas aeruginosa​

 

Enterococcus hirae​

 

Staphylococcus aureus​

 

Bacteroides nordii​

 

Fusobacterium nucleatum​

 

Serratia marcescens​

 

Eubacterium limosum​

 

Staphylococcus epidermidis​

 

Bacteroides thetaiotaomicron​

 

Gardnerella vaginalis​

 

Veillonella parvula​

 

Eubacterium rectale​

 

Staphylococcus haemolyticus​

 

Bacteroides vulgatus​

 

Gemmiger formicilis​

 

Gram-positive bacteria​

 

Faecalibacterium prausnitzii​

 

Streptococcus gallolyticus​

 

Barnesiella intestinihominis​

 

Haemophilus influenzae​

 

Anaerococcus vaginalis​

 

Holdemania filiformis​

 

Streptococcus infantarius​

 

Borrelia burgdorferi​

 

Helicobacter bilis​

 

Atopobium parvulum​

 

Lactobacillus acidophilus​

 

Streptococcus pneumoniae​

 

Campylobacter concisus​

 

Helicobacter bizzozeronii​

 

Bifidobacterium adolescentis​

 

Lactobacillus delbrueckii​

 

Streptococcus pyogenes​

 

Campylobacter curvus​

 

Helicobacter hepaticus​

 

Bifidobacterium animalis​

 

Lactobacillus johnsonii​

 

Streptococcus salivarius​

 

Campylobacter gracilis​

 

Helicobacter pylori​

 

Bifidobacterium bifidum​

 

Lactobacillus murinus​

 

Streptococcus sanguinis​

 

Campylobacter hominis​

 

Klebsiella oxytoca​

 

Bifidobacterium longum​

 

Lactobacillus reuteri​

 

Mycobacteria​

 

Campylobacter jejuni​

 

Klebsiella pneumoniae​

 

Blautia obeum​

 

Lactobacillus rhamnosus​

 

Mycoplasma fermentans ​

 

Campylobacter rectus​

 

Neisseria meningitidis​

 

Clostridium difficile​

 

Lactococcus lactis​

 

Mycoplasma penetrans ​

 

Chlamydia pneumoniae​

 

Parabacteroides distasonis​

 

Collinsella aerofaciens​

 

Parvimonas micra​

 

Fungi​

 

Chlamydia trachomatis​

 

Parabacteroides merdae​

 

Collinsella stercoris​

 

Peptostreptococcus anaerobius​

 

Candida albicans​

 

Citrobacter freundii​

 

Phascolarctobacterium faecium​

 

Cutibacterium acnes​

 

Peptostreptococcus stomatis​

 

​

 

 

Citrobacter rodentium​

 

Porphyromonas gingivalis​

 

Dorea formicigenerans​

 

Roseburia intestinalis​

 

​

 

 

Cloacibacillus porcorum​

 

Prevotella copri​

 

Enterococcus faecalis​

 

Ruminococcus bromii​

 

 

 

Webinar: Rapid microbial detection and ID with NGS

Learn how rapid NGS is advancing detection and identification of microbial pathogens

Dr. Jennifer Dien Bard discusses her experience using an automated targeted NGS method to rapidly detect and identify bacteria and fungi directly from specimens.

Jennifer Dien Bard, PhD

Chief Clinical Operations Director

Clinical Microbiology and Virology

Department of Pathology and Laboratory Medicine

Children's Hospital Los Angeles

 

Rapid microbial identification with NGS workflow

Figure from Osborn LJ et al. J Clin Microbiol. 2024 May 8;62(5):e0174923, used with permission.

 

  • Low input requirements—requires as little as 5 ng of input DNA
  • Highly automated NGS workflow—easier adoption, lower user intervention, and improved lab efficiency
  • Rapid turnaround time—go from nucleic acid to results in as little as 24 hours, with only ~10 minutes of hands-on time for NGS library prep through sequencing and analysis
  • Comprehensive microbial detection—NGS-based detection and identification of bacteria, mycobacteria, and fungi in a single assay

NGS solutions for RMID research

The Ion AmpliSeq RMID Research Panel is a custom targeted NGS community panel. You can use the pre-designed panel as-is or customize to adapt to your unique NGS testing needs. Ion AmpliSeq panels are based on ultrahigh-multiplex PCR, enabling clinical microbiology researchers to rapidly and easily detect and identify bacterial and fungal species in samples.

Ion AmpliSeq NGS panels

Get ultimate flexibility and speed for pivotal results with Ion AmpliSeq panels

When navigating through the complexities of infectious disease and microbiology research, you need a discovery tool that is both flexible and rapid for analyzing microbes of interest. Ion AmpliSeq technology can help. It is globally recognized as a widely adopted amplicon-based enrichment method for targeted NGS. Clinical and translational researchers worldwide choose Ion AmpliSeq technology for a fast, simple, and scalable NGS solution.

Custom gene panel

Need a custom panel? Use Ion AmpliSeq Designer.

Ion AmpliSeq Designer is an online primer design tool that lets you create custom panels for Ion Torrent NGS. Available in ready-to-use, made-to-order, and on-demand formats, Ion AmpliSeq panels consist of a pool of oligonucleotide primer pairs, with each pair designed to amplify a specified genomic region. Each panel can be designed to interrogate entire microbial genomes or all bases across a gene, or it can be focused on specific regions to study microbial variants or mutation hotspots.

Ion Torrent NGS systems for RMID research

The Ion AmpliSeq RMID Research Panel is compatible with both the Ion GeneStudio S5 systems and the Genexus System to deliver ease of use, automation capabilities, and rapid NGS test results in as little as 24 hours.

Genexus System

Through a combination of workflow automation, sequencing performance, and automated data analysis and reporting, the Ion Torrent Genexus System  brings the power of in-house NGS to microbiology labs worldwide without the need for extensive sequencing and bioinformatics expertise.

  • Simply load and go—the Genexus Integrated Sequencer  and Genexus Purification System  combine to automate your NGS workflow. With just two touchpoints and only twenty minutes of hands-on time, you can obtain reliable NGS reports in as little as 24 hours.

  • Learn more, faster, with an integrated NGS system—efficiently go from sample to report with automated sample prep and sequencing instruments joined together by powerful Genexus Software

  • Move quickly and confidently—built-in features like onboard sample tracking and barcoding are engineered to increase productivity while helping reduce errors

  • Obtain insights from a wide range of clinical research sample types—includes lysates (FFPE, fresh-frozen tissue, bone marrow), plasma, whole blood, and peripheral blood leukocytes (PBLs)

Ion GeneStudio S5 systems

Helping clinical microbiology researchers achieve deeper insights through fast, efficient, and cost-effective generation of large sequencing datasets, the Ion GeneStudio S5 systems enable scalable, high-throughput NGS for a broad range of applications.

  • Get insights fast—with sequencing and analysis complete in as little as three hours, you can go from sample to analyzed data in a single day

  • Save hands-on time—combine the Ion GeneStudio S5 systems with the Ion Chef System for a fully automated targeted NGS workflow, from library preparation to sequence analysis and reporting
    • Spend less than 45 minutes of hands-on time for library preparation to chip loading
    • Complete sequencing runs in as little as 2.5 hours
       
  • Automate report generation—transform data to insight with analysis, QC reporting, and variant calling on Thermo Fisher Connect or an in-house Ion Reporter Server

Ready to speak to a Thermo Fisher Scientific representative?

We will be happy to answer your questions and provide a demo of our rapid microbial identification (RMID) NGS solutions.

For Research Use Only. Not for use in diagnostic procedures.

CN: 62894