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Ellis GC, Shaikh F, Carson ML, Sercy E, Stewart L, Andrews JM, Campbell WR, Mende K, Yabes JM, Tribble DR, Bialek R, Wickes BL, Ganesan A. A Seminested PCR Method for the Diagnosis of Invasive Fungal Infections in Combat Injured. Open Forum Infect Dis 2024; 11:ofae078. [PMID: 38887475 PMCID: PMC11181181 DOI: 10.1093/ofid/ofae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/09/2024] [Indexed: 06/20/2024] Open
Abstract
Background Among combat injured, invasive fungal infections (IFIs) result in significant morbidity. Cultures and histopathology are the primary diagnostic methods for IFIs, but they have limitations. We previously evaluated a panfungal polymerase chain reaction assay, which was 83% sensitive and 99% specific for angioinvasive IFIs. Here, we evaluated 3 less resource-intensive seminested assays targeting clinically relevant fungi in the order Mucorales and genera Aspergillus and Fusarium. Methods Formalin-fixed paraffin-embedded tissue specimens from a multicenter trauma IFI cohort (2009-2014) were used. Cases were US military personnel injured in Afghanistan with histopathologic IFI evidence. Controls were patients with similar injury patterns and no laboratory IFI evidence (negative culture and histopathology). Seminested assays specific to Mucorales (V4/V5 regions of 18S rDNA), Aspergillus (mitochondrial tRNA), and Fusarium (internal transcribed spacer [ITS]/28A regions of DNA) were compared with a panfungal assay amplifying the internal transcribed spacer 2 region of rDNA and to histopathology. Results Specimens from 92 injury sites (62 subjects) were compared with control specimens from 117 injuries (101 subjects). We observed substantial agreement between the seminested and panfungal assays overall, especially for the order Mucorales. Moderate agreement was observed at the genus level for Aspergillus and Fusarium. When compared with histopathology, sensitivity and specificity of seminested assays were 67.4% and 96.6%, respectively (sensitivity increased to 91.7% when restricted to sites with angioinvasion). Conclusions Prior studies of seminested molecular diagnostics have focused on culture-negative samples from immunocompromised patients. Our findings underscore the utility of the seminested approach in diagnosing soft-tissue IFIs using formalin-fixed paraffin-embedded tissue samples, especially with angioinvasion.
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Affiliation(s)
- Graham C Ellis
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Faraz Shaikh
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - M Leigh Carson
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Erica Sercy
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Laveta Stewart
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | | | - Wesley R Campbell
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Katrin Mende
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Brooke Army Medical Center, JBSA Fort Sam Houston, Houston, Texas, USA
| | - Joseph M Yabes
- Brooke Army Medical Center, JBSA Fort Sam Houston, Houston, Texas, USA
| | - David R Tribble
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Ralf Bialek
- LADR GmbH MVZ Dr, Kramer & Kollegen, Geesthacht, Germany
| | - Brian L Wickes
- The Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Anuradha Ganesan
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
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Sajeer Paramabth M, Varma M. Demystifying PCR tests, challenges, alternatives, and future: A quick review focusing on COVID and fungal infections. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:719-728. [PMID: 37485773 DOI: 10.1002/bmb.21771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023]
Abstract
The polymerase chain reaction (PCR) technique is one of the most potent tools in molecular biology. It is extensively used for various applications ranging from medical diagnostics to forensic science and food quality testing. This technique has facilitated to survive COVID-19 pandemic by identifying the virus-infected individuals effortlessly and effectively. This review explores the principles, recent advancements, challenges, and alternatives of PCR technique in the context of COVID-19 and fungal infections. The introduction of PCR technique for anyone new to this field is the primary aim of this review and thereby equips them to understand the science of COVID-19 and related fungal infections in a simplistic manner.
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Affiliation(s)
| | - Manoj Varma
- Center for Nano Science and Engineering (CeNSE), Indian Institute of Science, Bangalore, India
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Liu X, Song Y, Li R. The use of combined PCR, fluorescence in situ hybridisation and immunohistochemical staining to diagnose mucormycosis from formalin-fixed paraffin-embedded tissues. Mycoses 2021; 64:1460-1470. [PMID: 34674327 DOI: 10.1111/myc.13382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To develop a comprehensive diagnostic system for mucormycosis from formalin-fixed paraffin-embedded tissues, consisting of own-designed real-time polymerase chain reaction (PCR) assays, fluorescence in situ hybridisation, and immunohistochemical staining. METHODS We designed 11 primers and probes for specific real-time PCR assays based on genome sequences, and validated the specificity by Aspergillus, Fusarium, Scedosporium, Lomentospora, Cryptococcus and Candida species. Formalin-fixed paraffin-embedded (FFPE) tissues from forty-four mouse model infected by above fungi were collected and extracted DNA by laser capture microdissection (LCM) and direct extraction methods for real-time PCR assays. In addition, seventeen clinical specimens histopathologically proven for mucormycosis were included for specific detection with the new diagnostic system. RESULTS The real-time PCR assays allowed detection of a minimum of 10 CFU/ml equivalent gDNA of each species. No cross-reaction with gDNA among species was noted. From mouse model specimens, the sensitivity of real-time PCR in samples extracted with LCM versus direct extraction method was 100% versus 91.43% at Mucorales level and 80% versus 45.71% at species level, respectively. The specificity was 100%. From clinical samples, LCM combined with real-time PCR can test 88.24% (15/17) of Mucorales. Sensitivities of fluorescence in situ hybridisation (FISH) and immunohistochemical staining (IHC) were 70.59% and 41.18%, respectively. Combined LCM-RT-PCR, FISH and IHC yielded positive results in all samples. CONCLUSIONS The combination diagnostic system we developed is a culture-independent and robust method which enables rapid species identification from FFPE tissues for timely diagnosis of mucormycosis.
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Affiliation(s)
- Xiao Liu
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Peking University First Hospital, Beijing, China
| | - Yinggai Song
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Peking University First Hospital, Beijing, China
| | - Ruoyu Li
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Peking University First Hospital, Beijing, China
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Lackner N, Posch W, Lass-Flörl C. Microbiological and Molecular Diagnosis of Mucormycosis: From Old to New. Microorganisms 2021; 9:microorganisms9071518. [PMID: 34361953 PMCID: PMC8304313 DOI: 10.3390/microorganisms9071518] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 12/12/2022] Open
Abstract
Members of the order Mucorales may cause severe invasive fungal infections (mucormycosis) in immune-compromised and otherwise ill patients. Diagnosis of Mucorales infections and discrimination from other filamentous fungi are crucial for correct management. Here, we present an overview of current state-of-the-art mucormycosis diagnoses, with a focus on recent developments in the molecular field. Classical diagnostic methods comprise histology/microscopy as well as culture and are still the gold standard. Newer molecular methods are evolving quickly and display great potential in early diagnosis, although standardization is still missing. Among them, quantitative PCR assays with or without melt curve analysis are most widely used to detect fungal DNA in clinical samples. Depending on the respective assay, sequencing of the resulting PCR product can be necessary for genus or even species identification. Further, DNA-based methods include microarrays and PCR-ESI-MS. However, general laboratory standards are still in development, meaning that molecular methods are currently limited to add-on analytics to culture and microscopy.
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Kerezoudis P, Watts CR, Bydon M, Dababneh AS, Deyo CN, Frye JM, Kelley PC, Kemp AM, Palraj BV, Pupillo GT. Diagnosis and Treatment of Isolated Cerebral Mucormycosis: Patient-Level Data Meta-Analysis and Mayo Clinic Experience. World Neurosurg 2018; 123:425-434.e5. [PMID: 30415043 DOI: 10.1016/j.wneu.2018.10.218] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Isolated cerebral mucormycosis is a rare and serious infection associated with intravenous drug abuse. METHODS We performed a comprehensive meta-analysis of cases reported in studies and have included an unreported case from our institution. We searched PubMed/Medline, EMBASE, Scopus, Cochrane Databases, and our institution's electronic medical health records from inception through March 31, 2018. The cases were considered isolated (only affecting the cerebrum, cerebellum, or brainstem) if the absence of other primary sources of infection had been documented. Continuous variables were summarized using the median and interquartile range and categorical variables using frequencies and proportions. The relationships between variables were tested using the Wilcoxon rank sum and Pearson χ2 tests. RESULTS A total of 130 studies (141 patients) met the eligibility requirements and were screened; 68 patients were included. The median age was 28 years (interquartile range, 24-38); 57% were men. Most patients had a history of intravenous drug abuse (82%), and 20% had positive human immunodeficiency virus findings. The lesion location was mostly supratentorial (91%), especially in the basal ganglia (71.2%). The cultures were positive in 38%, with Rhizopus the most common organism (59%). The mortality rate was 65%. The survivors were significantly more likely to have received amphotericin B (92% vs. 43%; P < 0.001) or to have undergone stereotactic aspiration (58% vs. 25%; P < 0.01). CONCLUSIONS Isolated cerebral mucormycosis has a pooled mortality rate of 65%. The presence of lesions in the basal ganglia, rapidly progressive symptoms, and a history of intravenous drug abuse should raise suspicion for the early initiation of amphotericin B and stereotactic aspiration.
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Affiliation(s)
| | - Charles R Watts
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA; Department of Neurosurgery, Mayo Clinic Health System-Franciscan Healthcare, La Crosse, Wisconsin, USA.
| | - Mohamad Bydon
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Ala S Dababneh
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA; Department of Infectious Diseases, Mayo Clinic Health System-Franciscan Healthcare, La Crosse, Wisconsin, USA
| | - Christopher N Deyo
- Department of Hospital Medicine, Mayo Clinic Health System-Franciscan Healthcare, La Crosse, Wisconsin, USA
| | - Judson M Frye
- Department of Radiology, Mayo Clinic Health System-Franciscan Healthcare, La Crosse, Wisconsin, USA
| | - Parker C Kelley
- Department of Neurosurgery, Mayo Clinic Health System-Franciscan Healthcare, La Crosse, Wisconsin, USA
| | - Anna M Kemp
- Department of Pathology, Mayo Clinic Health System-Franciscan Healthcare, La Crosse, Wisconsin, USA
| | - Bharath V Palraj
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA; Department of Infectious Diseases, Mayo Clinic Health System-Franciscan Healthcare, La Crosse, Wisconsin, USA
| | - Gregory T Pupillo
- Department of Neurology, Mayo Clinic Health System-Franciscan Healthcare, La Crosse, Wisconsin, USA
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Farid S, AbuSaleh O, Liesman R, Sohail MR. Isolated cerebral mucormycosis caused by Rhizomucor pusillus. BMJ Case Rep 2017; 2017:bcr-2017-221473. [PMID: 28978601 DOI: 10.1136/bcr-2017-221473] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
A 61-year-old man with relapsing chronic lymphocytic leukaemia, status post allogeneic stem cell transplant and multiple chemotherapy regimens presented to the emergency room after suffering a grand mal seizure. His evaluation revealed a 1.5-2 cm ring-enhancing left temporal lobe brain lesion on the CT scan. This brain lesion was resected and the histopathology revealed an invasive fungal organism resembling mucormycosis. Amplification and sequencing of the 28S ribosomal RNA gene identified the organism as Rhizomucor pusillus The patient was treated with liposomal amphotericin B 5 mg/kg every 24 hours for 4 weeks, and then was transitioned to oral posaconazole. Serial brain imaging at 1 and 3 months, while on therapy, showed significant improvement.
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Affiliation(s)
- Saira Farid
- Department of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Omar AbuSaleh
- Department of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Rachael Liesman
- Department of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
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Increasing incidence of mucormycosis in a large Spanish hospital from 2007 to 2015: Epidemiology and microbiological characterization of the isolates. PLoS One 2017; 12:e0179136. [PMID: 28591186 PMCID: PMC5462442 DOI: 10.1371/journal.pone.0179136] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 05/24/2017] [Indexed: 11/19/2022] Open
Abstract
We studied 19 cases of proven/probable mucormycosis diagnosed from 2007 to 2015 in our hospital and assessed the microbiological characteristics of the isolates. We recorded the incidence of mucormycosis and clinical and microbiological data of infected patients. Isolates were identified to molecular level and tested for their antifungal susceptibility to azoles, amphotericin B, and liposomal amphotericin B according to the CLSI M-38 A2 procedure. The incidence of mucormycosis in cases/100,000 hospital admissions during 2007–2015 increased significantly with respect to that reported in 1988–2006 (3.3 vs. 1.2; P<0.05). Patients mainly had hematological malignancies (52.6%) and/or trauma/surgical wounds (52.6%) and had received antifungal agents before the diagnosis of mucormycosis in 68% of cases. Diagnosis was by isolation (n = 17/19) and/or direct staining (n = 17/18) of Mucorales fungi in clinical samples. Identification was by panfungal PCR in patients with negative results in culture and in direct staining. The microorganisms identified were Lichtheimia spp. (42%), Rhizopus spp. (21%), Cunninghamella bertholletiae (16%), and others (21%). Liposomal amphotericin B was always more active than the other drugs against all the microorganisms except C. bertholletiae. All patients received antifungal treatment with 1 or more antifungal agents, mainly liposomal amphotericin B (17/19). Mortality was 47.4%, although this was significantly lower in the 11 patients in whom debridement was performed (18% vs. 87.5%) (P = 0.015). The incidence of mucormycosis has risen in recent years. The proportion of cases with soft tissue involvement was high, and Lichtheimia was the most frequently involved species. The highest antifungal activity was observed with liposomal amphotericin B.
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