Specialty testing for Molecular Microbiology

Founded in 2001, the UW Molecular Microbiology laboratory provides real-time PCR and DNA sequence-based testing for hospitals and clinics from all over the world. Our approaches provide highly accurate, rapid and sensitive capture of genomic information which, when integrated with the traditional discipline of clinical microbiology, enables robust diagnoses and provides accurate descriptions of new and emerging microbial pathogens. The molecular microbiology division offers a wide range of testing for detection and identification of specific microorganisms and gene products, as well as microbial DNA directly from clinical samples.

More information regarding submission of samples can be obtained viewing individual test pages below.

• Molecular Microbiology Order Form
• Molecular Microbiology Specimen Submission: Additional information regarding specimen submission.
• Molecular Microbiology Acceptable Specimens: Full list of acceptable specimens.
• Contact us: molmicdx@uw.edu

Direct detection of microbial DNA from tissues

DNA is isolated from specimen and amplified by conventional PCR using a battery of broad-range primers dependent on the test type requested. Amplified products are sequenced and the organism(s) identified on the basis of sequence data. Select a test type below to learn more.

• Bacterial PCR reflex NGS [BCTDNA], Bacterial detection by 16S NGS [NGS16S]
• Bacterial DNA Detection by PCR (without reflex to NGS) [NRBDNA]
• Nontuberculous Mycobacteria DNA Detection [NTMDNA]
• M. tuberculosis complex DNA Detection [TBCDNA]
• Fungal PCR reflex NGS [FUNDNA], Fungal DNA Detection by ITS Next Gen Seq [NGSITS]
• Fungal DNA Detection by PCR (without reflex to NGS) [NRFDNA]

Detection and identification of specific pathogens

DNA is isolated from a cultured organism or direct patient specimen and amplified using primers developed specifically to detect a particular organism. Amplifications are performed either as conventional or real-time PCR. Select a test type below to learn more.

Bacteria

• Bartonella DNA detection by PCR [BRTDNA]
• Enterobacterales DNA Detection [ENBDNA]
• Legionella DNA detection by PCR [LEGDNA]
• Mycoplasma and Ureaplasma DNA Detection by PCR [MPLDNA]
• Tropheryma whipplei DNA detection by PCR [TWHDNA]
• Treponema pallidum DNA detection by NAAT [TPLDNA]
• Treponema Pallidum DNA detection, Mucocutaneous [TPLSWB]

Mycobacteria

• M. tuberculosis complex DNA Detection [TBCDNA]
• Nontuberculous Mycobacteria DNA Detection [NTMDNA]

Fungi

• Aspergillus fumigatus DNA detection by PCR [ASPDNA]
• Coccidioides DNA detection by PCR [COCDNA]
• Cryptococcus DNA detection by PCR [CRYDNA]
• Histoplasma DNA detection by PCR [HISDNA]
• Mucorales DNA detection by PCR [MUCDNA]
• Pneumocystis DNA detection by PCR [PNEDNA]

Parasite

• Acanthamoeba and Balamuthia species PCR [AMBPCR]
• Leishmania species DNA detection by PCR [LSHDNA]
• Toxoplasma DNA detection by PCR [TOXDNA]

Identification of cultured organisms by DNA sequence based methods

• AFB ID by Sequence Analysis [ASEQID]
• Bacteria ID by Sequence Analysis [BSEQID]
• Mold ID by Sequence Analysis [MSEQID]
• Yeast ID by Sequence Analysis [YSEQID]
• Bacterial ID by Whole Genome Sequencing [BWGSID]

Specific gene detection in cultured organisms

• mecA by PCR [MECPCR]
• MTB Resistance by Whole Genome Sequencing [MTBWGR]

Organism typing

• Bacterial Strain Typing by Whole Genome Sequencing [NGSTYP]

Broad range PCR

Broad range PCR to aid in diagnosing infection

• Hauser N, Werzen A, and Rapaka RR. The Brief Case: Streptococcus intermedius Brain Abscesses in an Otherwise Healthy Young Man Diagnosed by 16S rRNA Gene Sequencing. J Clin Microbiol 2022, 60:e0197020. 35045273
• Wood BR, et al. Mycobacterium avium Complex Osteomyelitis in Persons With Human Immunodeficiency Virus: Case Series and Literature Review. Open Forum Infect Dis 2015, 2:ofv090. 26180837
• Basein T, et al. Microbial Identification Using DNA Target Amplification and Sequencing: Clinical Utility and Impact on Patient Management. Open Forum Infect Dis 2018, 5:ofy257. 30539032
• Robinson LA, Smith P, Sengupta DJ, Prentice JL, and Sandin RL. Molecular analysis of sarcoidosis lymph nodes for microorganisms: a case-control study with clinical correlates. BMJ Open 2013, 3:e004065. 24366580
• Sivagnanam S, et al. Seasonal clustering of sinopulmonary mucormycosis in patients with hematologic malignancies at a large comprehensive cancer center. Antimicrob Resist Infect Control 2017, 6:123. 29225797
• Malakzai MO, et al. Multifocal but non-disseminated phaeohyphomycosis in a healthy man via a unique mechanism: Ejection from motor vehicle accident into a vegetable field in Afghanistan resulting in multiple contaminated skin wounds. J Cutan Pathol 2017, 44:620-624. 28349548

Unusual Causes of infection

Identify unusual causes of infection

• Austin MC, et al. Rhodococcus fascians infection after haematopoietic cell transplantation: not just a plant pathogen? JMM Case Rep 2016, 3:e005025. 28348752
• Harrington SM, et al. Novel fastidious, partially acid-fast, anaerobic Gram-positive bacillus associated with abscess formation and recovered from multiple medical centers. J Clin Microbiol 2013, 51:3903-7. 24025902
• Westley BP, Horazdovsky RD, Michaels DL, and Brown DR. Identification of a Novel Mycoplasma Species in a Patient With Septic Arthritis of the Hip and Seal Finger. Clin Infect Dis 2016, 62:491-3. 26449564
• Navas ME, et al. Can anaerobes be acid fast? A novel, clinically relevant acid fast anaerobe. JMM Case Rep 2016, 3:e005036. 28348766
• Teixeira L, et al. Mycobacterium llatzerense lung infection in a liver transplant recipient: case report and review of the literature. Am J Transplant 2013, 13:2198-200. 23763545

Identify unusual causes of infection (parasites)

• Konnick EQ, et al. Incidental identification of Strongyloides stercoralis infection by broad-range 28S rDNA gene sequencing in a patient with a hematolymphoid malignancy. Diagn Microbiol Infect Dis 2016, 86:362-364. 27645607
• Conrady CD, et al. The First Case of Trypanosoma cruzi-Associated Retinitis in an Immunocompromised Host Diagnosed With Pan-Organism Polymerase Chain Reaction. Clin Infect Dis 2018, 67:141-143. 29385482

NGS

Clinical application of whole genome sequencing

• Werth BJ, et al. Emergence of dalbavancin non-susceptible, vancomycin-intermediate Staphylococcus aureus (VISA) after treatment of MRSA central line-associated bloodstream infection with a dalbavancin- and vancomycin-containing regimen. Clin Microbiol Infect 2018, 24:429.e1-429.e5. 28782651
• Butler-Wu SM, Sengupta DJ, Kittichotirat W, Matsen FA 3rd, and Bumgarner RE. Genome sequence of a novel species, Propionibacterium humerusii. J Bacteriol 2011, 193:3678. 21571999