Enhancing and Improving Diagnostic Microbiology with qPCR + NGS

Expand clinical impact through enhanced diagnostic power

At Dr. James Snyder’s mycology laboratory at the University of Louisville Hospital, a mold would not sporulate using conventional methods despite repeated attempts. A sample was submitted to MicroGenDX for qPCR+NGS, which identified the isolate as a rare fungus in just four days, and the patient’s symptoms resolved with an appropriate antifungal therapy. View Dr. Snyder video

In another example of NGS diagnostic efficacy, a landmark 15-center study demonstrated 68.6% of revision failures following two-stage exchange were due to untreated or undertreated pathogens missed by culture, but detected by NGS at the time of initial resection. Only 8.6% of failures had negative NGS results at the time of revision surgery. Read about study

13 years of 16S/ITS NGS testing quality and reliability

With over 750,000 qPCR+NGS samples processed, referencing against a validated microbial database of 57,000+ microbes, MicroGenDX ensures representation of a comprehensive and growing library of infective organisms. This precise and expanding identification has been consistently confirmed by a 99% CAP proficiency average from more than 1,000 blinded specimens. MicroGenDX has also been a trusted research partnership lab for the FDA, NASA, and the CDC. View CAP data

Attentive customer service

MicroGenDX accepts the largest selection of media and specimen types, offers a 3.5 day turnaround time for NGS reports and a 24-48 hour turnaround for identification of antimicrobial resistance genes, and provides custom capabilities and validation of lab developed tests in collaboration with customers.

Industry leader in reference laboratory affordability

• $100 for direct colony identification

• Competitively priced specimen identification (please contact MicroGenDX or your representative for pricing)

NGS supports physicians with culture-negative infection management

Originally described in 1982, it is now believed that any environmental stressor could send a community into this non-culturable but still viable state (VNBC). Known human pathogens such as E. coli, .E faecalis, P. aeruginosa and S. aureus are all capable of entering and resuscitating from a VBNC state without losing their virulence. During the VBNC state, the microbes maintain their cellular structure and biology (allowing detection with molecular testing) along with significant gene expression, but they are non-culturable by ‘standard’ laboratory methods.

NGS supports direct colony identification from culture

MicroGenDX offers direct colony identification from agar and broth media for bacteria, mycobacteria and fungi using a curated database of 57,000+ microbes. MicroGenDX NGS results have demonstrated 96% concordance with traditional culture based on a study by Dr. Javad Parvizi at Thomas Jefferson University and published in the Bone and Joint Journal, 2018.

qPCR + 16S/ITS NGS testing

When laboratory methods fail to identify fastidious or slow growth organisms, NGS direct identification is the gold standard. This includes:

• Direct colony identification from agar and broth media (including positive blood cultures) for bacteria, mycobacteria, and fungi

• Direct identification of bacteria, mycobacteria and fungi from specimens

• Identification of up to 17 clinically significant antimicrobial resistance genes in Gram-positive and Gram-negative organisms

Widest selection of specimen types

MicroGenDX accepts the following:

• Synovial fluid

• Hardware/heart valve

• Blood

• Urine

• Cerebrospinal fluid (CSF)

• Sputum and saliva

• Respiratory swabs

• Bronchoalveolar lavage (BAL)

• Tissue drainage

• FFPE

Microbiology Lab Services from MicroGenDX

Precision DNA testing for patients with nontuberculous mycobacteria (NTM)

Rapidly speciate mycobacteria in 24 hrs (qPCR)

• Rapidly identify NTM species Mycobacterium avium complex (MAC) and Mycobacterium abscessus complex (MABSC) — differentiating them from Mycobacterium tuberculosis complex — along with these related genera: Nocardia, Rhodococcus, Gordona, Tsukamurella, Streptomyces, and Actinomyces

Differentiate and quantify all bacteria (NGS)

• Differentiate among 120 mycobacterial species and 20K+ bacterial species

• Quantify overall bacterial burden and identify dominant species

Convenience of sample submission

• Sample collection materials provided, shipping cost to lab covered

• Sputum, swab and BAL accepted

• Solid and liquid media accepted

Direct colony identification

Use of next-generation DNA sequencing for the direct identification of bacterial and fungal isolates from multiple microbiological agars. This is intended for those organisms that cannot be identified by current laboratory methods. Turnaround time is 3.5 days.

Rapid PCR STI testing

For more information about MicroGenDX as a reference laboratory for STIs please click here

Acceptance of Diverse Test Samples

NGS brings comprehensive, precise analysis to an array of samples types, such as:

• Bacteria: Blood agar, Chocolate agar, MacConkey Agar, Tryptic Soy Agar/Broth, Thioglycolate Broth, and Positive Blood Culture Bottle

• Fungi: Yeast Malt (YM) Agar and Sabouraud Dextrose Agar

• AFB: Algae Slant and BD-MGIT™ or equivalent

• Mycobacteria: Löwenstein–Jensen medium

• Patient Remnant Samples: Cardiac valve tissue, spinal abscess, synovial fluid, etc.

Antimicrobial resistance genes

Next-Gen comprehensive DNA sequencing for detection of bacteria and qPCR rapid screening for resistance genes, including methicillin, vancomycin, beta lactam, carbapenem, macrolide, aminoglycoside, tetracycline, quinolone, bactrim, and extended spectrum beta lactamase.

Direct colony identification

Identification of:

• Bacterial (Gram positive and Gram negative) colony

• Mycobacteria (rapid and slow growing) colony

• Partially acid-fast colony

• Yeast colony

• Mold

Accepted transport media:

• Blood/chocolate /TSA/Sabouraud slants

• Blood/chocolate /MacConkey/TSA /Sabouraud plates

• Positive blood culture (aliquote broth)

Direct sample is also acceptable and recommended in cases where discrepancies are seen between a positive microscopic examination (Gram stain) and negative growth after 24 hours.

Direct sample is strongly recommended in cases where atypical, fastidious or nutritionally deficient bacteria is observed and for rapid identification of molds and AFB seen on direct examination (AFB fluorescent stain, etc.).