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.
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
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
DNA of the cultured organism is isolated and amplified using broad-range primers and conventional PCR conditions. Amplified products are then sequenced and the organism is identified on the basis of the sequence data. Select a test type below to learn more.
- 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
DNA of a cultured organism is isolated and amplified using primers developed specifically to detect a particular gene. Amplifications are performed under real-time PCR conditions and results are based on the presence or absence of amplification. Select a test type below to learn more.
Organism typing
References
- Stephen J. Salipante, Dhruba J. SenGupta, Lisa A. Cummings, Tyler A. Land, Daniel R. Hoogestraat, Brad T. Cookson
Application of Whole-Genome Sequencing for Bacterial Strain Typing in Molecular Epidemiology.
J. Clin. Microbiol. April 2015 vol. 53 no. 4 1072-1079 - Stephen J. Salipante, Toana Kawashima, Christopher Rosenthal, Daniel R. Hoogestraat, Lisa A. Cummings, Dhruba J. Sengupta, Timothy T. Harkins, Brad T. Cookson, Noah G. Hoffman
Performance Comparison of Illumina and Ion Torrent NextGeneration Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling.
Appl. Environ. Microbiol. December 2014 vol. 80 no. 24 7583-7591 - SenGupta DJ, Cummings LA, Hoogestraat DR, Butler-Wu SM, Shendure J, Cookson BT, Salipante SJ.
Whole-Genome Sequencing for High-Resolution Investigation of Methicillin-Resistant Staphylococcus aureus Epidemiology and Genome Plasticity.
J Clin Microbiol. 2014 Aug;52(8):2787-96. doi: 10.1128/JCM.00759-14. Epub 2014 May 21. - Stephen J. Salipante, Dhruba J. Sengupta, Lisa A. Cummings, Aaron Robinson, Kyoko Kurosawa, Daniel R. Hoogestraat, Brad T. Cookson
Whole genome sequencing indicates Corynebacterium jeikeium comprises 4 separate genomospecies and identifies a dominant genomospecies among clinical isolates.
International Journal of Medical Microbiology, In Press. - SenGupta DJ, Cummings LA, Hoogestraat DR, Butler-Wu SM, Shendure J, Cookson BT, Salipante SJ.
Whole-Genome Sequencing for High-Resolution Investigation of Methicillin-Resistant Staphylococcus aureus Epidemiology and Genome Plasticity.
J Clin Microbiol. 2014 Aug;52(8):2787-96. doi: 10.1128/JCM.00759-14. Epub 2014 May 21. - Salipante SJ, Hoogestraat DR, Abbott AN, SenGupta DJ, Cummings LA, Butler-Wu SM, Stephens K, Cookson BT, Hoffman NG.
Coinfection of Fusobacterium nucleatum and Actinomyces israelii in mastoiditis diagnosed by next-generation DNA sequencing.
J Clin Microbiol. 2014 May;52(5):1789-92. doi: 10.1128/JCM.03133-13. Epub 2014 Feb 26. - Salipante SJ, Sengupta DJ, Hoogestraat DR, Cummings LA, Bryant BH, Natividad C, Thielges S, Monsaas PW, Chau M, Barbee LA, Rosenthal C, Cookson BT, Hoffman NG.
Molecular diagnosis of Actinomadura madurae infection by 16S rRNA deep sequencing.
J Clin Microbiol. 2013 Dec;51(12):4262-5. doi: 10.1128/JCM.02227-13. Epub 2013 Oct 9. - Stephen J. Salipante, Dhruba J. Sengupta, Christopher Rosenthal, Gina Costa, Jessica Spangler, Elizabeth H. Sims, Michael A. Jacobs, Samuel I. Miller, Daniel R. Hoogestraat, Brad T. Cookson, Connor McCoy, Frederick A. Matsen, Jay Shendure, Clarence C. Lee, Timothy T. Harkins, Noah G. Hoffman
Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections
PLoS ONE 8(5): e65226. doi:10.1371 / journal.pone.0065226 Published: May 29, 2013. - Desiree Marshall, MD; Dhruba J. SenGupta, PhD; Daniel R. Hoogestraat, MB(ASCP); Karen Stephens, PhD; Brad T. Cookson, MD, PhD; Cecilia C.S. Yeung, MD
Multilocus Sequencing for Rapid Identification of Molds
CAP Today Feature Story, February 2013. - Salipante SJ, Hoogestraat DR, Sengupta DJ, Murphey D, Panayides K, Hamilton E, Castaneda-Sanchez I, Kennedy J, Monsaas PW, Mendoza L, Stephens K, Dunn JJ, Cookson BT
Molecular Diagnosis of Subcutaneous Pythium insidiosum Infection by Use of PCR Screening and DNA Sequencing
J Clin Microbiol. 2012 Apr;50(4):1480-3. Epub 2012 Jan 11. PMID: 22205808 - Murphy SC, Hoogestraat DR, Sengupta DJ, Prentice J, Chakrapani A, Cookson BT
Molecular diagnosis of cystoisosporiasis using extended-range PCR screening
J. Mol Diagn. 2011 May;13(3):359-62. Epub 2011 Mar 31. PubMed PMID: 21458380; PubMed Central PMCID: PMC3077734. - Stockinger DE, Roellich KM, Vogel KW, Eiffert KL, Torrence AE, Prentice JL, Stephens KG, Wallis CK, Hotchkiss CE, Murnane RD.
Primary hepatic Mycobacterium tuberculosis complex infection with terminal dissemination in a pig-tailed macaque (Macaca nemestrina).
J Am Assoc Lab Anim Sci. 2011 Mar;50(2):258-62. PMID: 21439222 - Yager JE, Ford ES, Boas ZP, Haseley LA, Cookson BT, Sengupta DJ, Fang FC, Gottlieb GS
Ureaplasma urealyticum continuous ambulatory peritonealdialysis-associated peritonitis diagnosed by 16S rRNA gene PCR
J Clin Microbiol. 2010 Nov;48(11):4310-2. Epub 2010 Aug 25. PubMed PMID: 20739488; PubMed Central PMCID: PMC3020887. - Dhruba J. SenGupta and Brad T. Cookson
SeqSharp | A General Approach for Improving Cycle-Sequencing That Facilitates a Robust One-Step Combined Amplification and Sequencing Method
Journal of Molecular Diagnostics, Vol. 12, No. 3, May 2010 - de Sanctis, Jorgelina T. MD; Carpenter, Christopher F. MD; Sims, Matthew D. MD, PhD; SenGupta, Dhruba J. PhD; Prentice, Jennifer L. MS, MT (ASCP); Cookson, Brad T. MD, PhD; Boyanton, Bobby L. Jr MD, MT (ASCP)
Culture-Negative Endocarditis and the Use of Molecular Diagnostics: A Case Report
Infectious Diseases in Clinical Practice, March 2010 , Volume 18, Issue 2, pp 120-123 - Woodward JF, Sengupta DJ, Cookson BT, Park JO, Dellinger EP
Disseminated Community-Acquired USA300 Methicillin-Resistant Staphylococcus aureus Pyomyositis and Septic Pulmonary Emboli in an Immunocompetent Adult
Surg Infections 2009 Nov 4 | PMID: 19888867 - Harrington AT, Creutzfeldt CJ, Sengupta DJ, Hoogestraat DR, Zunt JR, Cookson BT
Diagnosis of Neurocysticercosis by Detection of Taenia solium DNA Using a Global DNA Screening Platform.
Clinical Infectious Diseases 2009;48:Nov 24 | PMID: 19025499 - Hoffman N. G. and Cookson B. T.
Case 8-2007: A Man with Chest Pain Followed by Cardiac Arrest. N. Engl. J. Med. 2007 365(25) 2652 - Nichols, W. G., J. Prentice, Y. Houze, L. Carlson, and B. T. Cookson
Fatal pulmonary infection associated with a novel organism Parastreptomyces abscessus. J. Clin. Microbiol. 2005 43(10): 5376-79. - Rakeman, J. L., U. Bui, K. LaFe, M. B. Coyle, and B. T. Cookson
Multilocus DNA sequence comparisons rapidly identify pathogenic molds. J. Clin. Microbiol. 2005 43(7): 3324-3333. - Pottumarthy, S., J. M. Schapiro, J. L. Prentice, Y. B. Houze, S. R. Swanzy, F. C. Fang, and B. T. Cookson
Clinical isolates of Staphylococcus intermedius masquerading as Methicillin-resistant Staphlococcus aureus. J. Clin. Microbiol. 2004 42(12): 5881-5884. - Panackal, A. A., Y. B. Houze, J. Prentice, S. S. Leopold, B. T. Cookson, W. C. Liles, and A. P. Limaye
Prosthetic joint infection due to Helcococcus pyogenes. J. Clin. Microbiol. 2004 42(6): 2872-4. - Selvarangan, R., W-K. Wu, T. T. Nguyen, L. C. Carlson, C. K. Wallis, S. K. Stiglich, Y-C. Chen, K. C. Jost, Jr., J. L. Prentice, R. J. Wallace, S. L. Rassoulian Barrett, B. T. Cookson, and M. B. Coyle
Characterization of a novel group of mycobacteria: Proposal of Mycobacterium sherrisii sp.. J. Clin. Microbiol. 2004 42: 90-98. - Selvarangan, R., U. Bui, A. P. Limaye, and B. T. Cookson
Rapid Identification of Commonly Encountered Candida Species Directly from Blood Culture Bottles. J. Clin. Microbiol. 2003 41: 5660-5664. - Novicki, T. J., K. LaFe, L. Bui, U. Bui, R. Geise, K. Marr, B. T. Cookson
Genetic diversity among clinical isolates of Acremonium strictum determined during an investigation of a fatal mycosis.. J. Clin. Microbiiol. 2003 41: 2623-2628. - Pottumarthy, S., A. P. Limaye, J. L. Prentice, Y. B. Houze, S. R. Swanzy, and B. T. Cookson
Nocardia veterana, a New Emerging Pathogen. J. Clin. Microbiol. 2003 41: 1705-1709. - Selvarangan, R., A. P. Limaye, and B.T. Cookson
Rapid identification and differentiation of Candida albicans and C. dubliniensis by capillary-based amplification and fluorescent probe hybridization. J Clin. Microbiol. 2002 40: 4308-4312. - Lingappa, J., W. Lawrence, S. West-Keefe, R. Gautom, and B. T. Cookson
Diagnosis of community-acquired Pertussis infection: Comparison of both culture and fluorescent-antibody assays with PCR detection using electrophoresis and dot blot hybridization. J. Clin. Microbiol. 2002 40: 2908-2912. - Chen,Y-C, J. D. Eisner, M. M. Kattar, S. L. Rassoulian-Barrett, K. Lafe, A. P. Limaye, and B. T. Cookson
Polymorphic Internal Transcribed Spacer Region 1 DNA Sequences Identify Medically Important Yeasts. J. Clin. Microbiol. 2001 39: 4042-4051. - Kattar, M. M., B. T. Cookson, L. C. Carlson, S. Stiglich, M. Schwartz, T. Nguyen, R. Daza, C. K. Wallis, S. L. Yarfitz, and M. B. Coyle
Tsukamurella strandjordae sp. nov., a Proposed New Species Causing Sepsis . J. Clin. Microbiol. 2001 39: 1467-1476. - Rassoulian-Barrett, S. L., B. T. Cookson, L. C. Carlson, K.A. Bernard, and M. B. Coyle
Diversity within Reference Strains of Corynebacterium matruchotii Includes Corynebacterium durum and a Novel Organism. J. Clin. Microbiol. 2001 39: 943-948. - Limaye A. P., Connolly P. A., Sagar M., Fritsche T. R., Cookson B. T., Wheat L. J., Stamm W. E.
Transmission of Histoplasma capsulatum by Organ Transplantation. N Engl J Med. 2000, 343 (16): 1163-1166 - Chen, Y-C, J. D. Eisner, M. M. Kattar, S. L. Rassoulian-Barrett, K. LaFe, S. L. Yarfitz, A. P. Limaye, and B. T. Cookson
Identification of Medically Important Yeasts Using PCR-Based Detection of DNA Sequence Polymorphisms in the Internal Transcribed Spacer 2 Region of the rRNA Genes . J. Clin. Microbiol. 2000 38: 2302-2310. - Limaye, A. P., D. K. Turgeon, B. T. Cookson, and T. R. Fritsche
Pseudomembranous Colitis Caused by a Toxin A B+ Strain of Clostridium difficile. J. Clin. Microbiol. 2000 38: 1696-1697. - M. M. Kattar, J. F. Chavez, A. P. Limaye, S. L. Rassoulian-Barrett, S. L. Yarfitz, L. C. Carlson, Y. Houze, S. Swanzy, B. L. Wood, and B. T. Cookson
Application of 16S rRNA Gene Sequencing To Identify Bordetella hinzii as the Causative Agent of Fatal Septicemia. J. Clin. Microbiol. 2000 38: 789-794.
Associated Tests
| Code | Name | Specimen | Comments |
|---|---|---|---|
| ASEQID | AFB ID by Sequence Analysis | Pure Culture | |
| ASPDNA | Aspergillus fumigatus DNA detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| BSEQID | Bacteria ID by Sequence Analysis | Pure Culture | |
| NGS16S | Bacterial detection by 16S NGS | This only available as a reflexive test,... | |
| NRBDNA | Bacterial DNA Detection by PCR (without reflex to NGS) | Tissue (Fresh frozen or paraffin-embedde... | |
| BWGSID | Bacterial ID by Whole Genome Sequencing | Pure Culture | |
| BCTDNA | Bacterial PCR reflex NGS | Tissue (Fresh frozen or paraffin-embedde... | |
| NGSTYP | Bacterial Strain Typing by Whole Genome Sequencing | Pure culture of bacterial organisms | |
| BRTDNA | Bartonella DNA detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| COCDNA | Coccidioides DNA detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| CRYDNA | Cryptococcus DNA detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| ENBDNA | Enterobacterales DNA Detection | This only available as a reflexive test,... | |
| NGSITS | Fungal DNA Detection by ITS Next Gen Seq | This only available as a reflexive test,... | |
| NRFDNA | Fungal DNA Detection by PCR (without reflex to NGS) | Tissue (Fresh frozen or paraffin-embedde... | |
| FUNDNA | Fungal PCR reflex NGS | Tissue (Fresh frozen or paraffin-embedde... | |
| HISDNA | Histoplasma DNA detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| LEGDNA | Legionella DNA detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| LSHDNA | Leishmania species DNA detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| MECPCR | mecA by PCR | Pure culture | |
| MSEQID | Mold ID by Sequence Analysis | Pure Culture | |
| MTBWGR | MTB Resistance by Whole Genome Sequencing | Pure Culture | |
| TBCDNA | M. tuberculosis complex DNA Detection | Tissue (Fresh frozen or paraffin-embedde... | |
| MAVDNA | Mycobacterium avium complex DNA Detection | Tissue (Fresh frozen or paraffin-embedde... | |
| MCHDNA | Mycobacterium chimaera DNA detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| MPLDNA | Mycoplasma and Ureaplasma DNA Detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| NTMDNA | Nontuberculous Mycobacteria DNA Detection | Tissue (Fresh frozen or paraffin-embedde... | |
| PNEDNA | Pneumocystis DNA detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| TOXDNA | Toxoplasma DNA detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| TPLDNA | Treponema pallidum DNA detection by NAAT | Tissue (Fresh frozen or paraffin-embedde... | |
| TPLSWB | Treponema Pallidum DNA detection, Mucocutaneous | UTM Swab | |
| TWHDNA | Tropheryma whipplei DNA detection by PCR | Tissue (Fresh frozen or paraffin-embedde... | |
| YSEQID | Yeast ID by Sequence Analysis | Pure Culture |
Last updated 2025-03-11T17:37:38.897166+00:00