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Molecular Detection of Filamentous Fungi in Formalin-Fixed Paraffin-Embedded Specimens in Invasive Fungal Wound Infections Is Feasible with High Specificity.
J Clin Microbiol 2019; 58(1)JC

Abstract

Trauma-related invasive fungal wound infections (IFIs) are associated with significant morbidity and mortality. Early identification and treatment are critical. Traditional identification methods (e.g., fungal cultures and histopathology) can be delayed and insensitive. We assessed a PCR-based sequencing assay for rapid identification of filamentous fungi in formalin-fixed paraffin-embedded (FFPE) specimens obtained from combat casualties injured in Afghanistan. Blinded FFPE specimens from cases (specimens positive on histopathology) and controls (specimens negative on histopathology) were submitted for evaluation with a panfungal PCR. The internal transcribed spacer 2 (ITS2) region of the fungal ribosomal repeat was amplified and sequenced. The PCR results were compared with findings from histopathology and/or culture. If injury sites contributed multiple specimens, findings for the site were collapsed to the site level. We included 64 case subjects (contributing 95 sites) and 102 controls (contributing 118 sites). Compared to histopathology, panfungal PCR was specific (99%), but not as sensitive (63%); however, sensitivity improved to 83% in specimens from sites with angioinvasion. Panfungal PCR identified fungi of the order Mucorales in 33 of 44 sites with angioinvasion (75%), whereas fungal culture was positive in 20 of 44 sites (45%). Saksenaea spp. were the dominant fungi identified by PCR in specimens from angioinvasion sites (57%). Panfungal PCR is specific, albeit with lower sensitivity, and performs better at identifying fungi of the order Mucorales than culture. DNA sequencing offers significant promise for the rapid identification of fungal infection in trauma-related injuries, leading to more timely and accurate diagnoses.

Authors+Show Affiliations

Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA anuradha.ganesan.ctr@mail.mil. Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA. Walter Reed National Military Medical Center, Bethesda, Maryland, USA.Walter Reed National Military Medical Center, Bethesda, Maryland, USA.Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA.Walter Reed National Military Medical Center, Bethesda, Maryland, USA.Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA. Brooke Army Medical Center, JBSA Fort Sam Houston, Texas, USA.Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA.Landstuhl Regional Medical Center, Landstuhl, Germany.Joint Pathology Center, Silver Spring, Maryland, USA.U.S. Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, USA.Landstuhl Regional Medical Center, Landstuhl, Germany.LADR GmbH Medizinisches Versorgungszentrum Dr. Kramer und Kollegen, Geesthacht, Germany.Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA.University of Texas Health Sciences Center at San Antonio, San Antonio, Texas, USA.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31619528

Citation

Ganesan, Anuradha, et al. "Molecular Detection of Filamentous Fungi in Formalin-Fixed Paraffin-Embedded Specimens in Invasive Fungal Wound Infections Is Feasible With High Specificity." Journal of Clinical Microbiology, vol. 58, no. 1, 2019.
Ganesan A, Wells J, Shaikh F, et al. Molecular Detection of Filamentous Fungi in Formalin-Fixed Paraffin-Embedded Specimens in Invasive Fungal Wound Infections Is Feasible with High Specificity. J Clin Microbiol. 2019;58(1).
Ganesan, A., Wells, J., Shaikh, F., Peterson, P., Bradley, W., Carson, M. L., ... Wickes, B. L. (2019). Molecular Detection of Filamentous Fungi in Formalin-Fixed Paraffin-Embedded Specimens in Invasive Fungal Wound Infections Is Feasible with High Specificity. Journal of Clinical Microbiology, 58(1), doi:10.1128/JCM.01259-19.
Ganesan A, et al. Molecular Detection of Filamentous Fungi in Formalin-Fixed Paraffin-Embedded Specimens in Invasive Fungal Wound Infections Is Feasible With High Specificity. J Clin Microbiol. 2019 Dec 23;58(1) PubMed PMID: 31619528.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Molecular Detection of Filamentous Fungi in Formalin-Fixed Paraffin-Embedded Specimens in Invasive Fungal Wound Infections Is Feasible with High Specificity. AU - Ganesan,Anuradha, AU - Wells,Justin, AU - Shaikh,Faraz, AU - Peterson,Philip, AU - Bradley,William, AU - Carson,M Leigh, AU - Petfield,Joseph L, AU - Klassen-Fischer,Mary, AU - Akers,Kevin S, AU - Downing,Kevin, AU - Bialek,Ralf, AU - Tribble,David R, AU - Wickes,Brian L, Y1 - 2019/12/23/ PY - 2019/07/31/received PY - 2019/10/10/accepted PY - 2020/06/23/pmc-release PY - 2019/10/18/pubmed PY - 2019/10/18/medline PY - 2019/10/18/entrez KW - PCR KW - PCR-based assay KW - combat KW - invasive fungal infection KW - invasive fungal wound infection KW - mucormycosis KW - trauma JF - Journal of clinical microbiology JO - J. Clin. Microbiol. VL - 58 IS - 1 N2 - Trauma-related invasive fungal wound infections (IFIs) are associated with significant morbidity and mortality. Early identification and treatment are critical. Traditional identification methods (e.g., fungal cultures and histopathology) can be delayed and insensitive. We assessed a PCR-based sequencing assay for rapid identification of filamentous fungi in formalin-fixed paraffin-embedded (FFPE) specimens obtained from combat casualties injured in Afghanistan. Blinded FFPE specimens from cases (specimens positive on histopathology) and controls (specimens negative on histopathology) were submitted for evaluation with a panfungal PCR. The internal transcribed spacer 2 (ITS2) region of the fungal ribosomal repeat was amplified and sequenced. The PCR results were compared with findings from histopathology and/or culture. If injury sites contributed multiple specimens, findings for the site were collapsed to the site level. We included 64 case subjects (contributing 95 sites) and 102 controls (contributing 118 sites). Compared to histopathology, panfungal PCR was specific (99%), but not as sensitive (63%); however, sensitivity improved to 83% in specimens from sites with angioinvasion. Panfungal PCR identified fungi of the order Mucorales in 33 of 44 sites with angioinvasion (75%), whereas fungal culture was positive in 20 of 44 sites (45%). Saksenaea spp. were the dominant fungi identified by PCR in specimens from angioinvasion sites (57%). Panfungal PCR is specific, albeit with lower sensitivity, and performs better at identifying fungi of the order Mucorales than culture. DNA sequencing offers significant promise for the rapid identification of fungal infection in trauma-related injuries, leading to more timely and accurate diagnoses. SN - 1098-660X UR - https://www.unboundmedicine.com/medline/citation/31619528/Molecular_Detection_of_Filamentous_Fungi_in_Formalin-Fixed_Paraffin-Embedded_Specimens_in_Invasive_Fungal_Wound_Infections_is_Feasible_with_High_Specificity L2 - http://jcm.asm.org/cgi/pmidlookup?view=long&pmid=31619528 DB - PRIME DP - Unbound Medicine ER -