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Kushner LE, Schwenk HT, Qin F, Boothroyd D, Aftandilian C. Application of cell-free DNA fungal polymerase chain reaction for invasive fungal disease evaluation in pediatric oncology and stem cell transplant patients. Pediatr Blood Cancer 2024:e31133. [PMID: 38943234 DOI: 10.1002/pbc.31133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 04/19/2024] [Accepted: 05/21/2024] [Indexed: 07/01/2024]
Abstract
BACKGROUND Molecular diagnostics may enable early, noninvasive detection of invasive fungal disease (IFD) in immunocompromised patients. Cell-free deoxyribonucleic acid (cfDNA) fungal polymerase chain reaction (PCR) assays were recently incorporated into institutional prolonged febrile neutropenia pathways. We aimed to evaluate the performance of plasma cfDNA PCR panels (mold and Candida panels) in pediatric oncology and hematopoietic stem cell transplant (HSCT) patients with clinical concern for IFD. METHODS This single-center, observational study assessed plasma cfDNA fungal PCR performance for noninvasive IFD detection in hospitalized pediatric oncology and HSCT patients. The primary outcome was IFD diagnosis per published consensus definitions within 1 month. Positive and negative agreement between plasma cfDNA fungal PCR and consensus definitions were calculated. We also described test turnaround time and patient survival. RESULTS From October 2021 to 2022, 54 patients underwent 60 evaluations with 11 proven/probable IFD cases. Comparing plasma cfDNA fungal PCRs to consensus definitions for proven/probable IFD, there was 73% positive agreement and 96% negative agreement. Two proven/probable cases with negative PCRs were caused by organisms not included on either panel. Median time to cfDNA fungal PCR result was 35 hours (interquartile range: 19-69) in eight proven/probable cases detected by cfDNA fungal PCR. There were 17 deaths among 54 patients, and IFD contributed to 45% of deaths in patients with proven/probable IFD. CONCLUSIONS Plasma cfDNA fungal PCRs detected relevant molds or yeast in most cases classified as proven/probable IFD. However, this targeted approach missed some cases. More studies are required to determine optimal utilization of molecular diagnostics in pediatric patients.
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Affiliation(s)
- Lauren E Kushner
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Stanford University School of Medicine, Palo Alto, California, USA
| | - Hayden T Schwenk
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Stanford University School of Medicine, Palo Alto, California, USA
| | - FeiFei Qin
- Quantitative Sciences Unit, Stanford University, Palo Alto, California, USA
| | - Derek Boothroyd
- Quantitative Sciences Unit, Stanford University, Palo Alto, California, USA
| | - Catherine Aftandilian
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplant and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, California, USA
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Neoh CF, Chen SCA, Lanternier F, Tio SY, Halliday CL, Kidd SE, Kong DCM, Meyer W, Hoenigl M, Slavin MA. Scedosporiosis and lomentosporiosis: modern perspectives on these difficult-to-treat rare mold infections. Clin Microbiol Rev 2024; 37:e0000423. [PMID: 38551323 PMCID: PMC11237582 DOI: 10.1128/cmr.00004-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
SUMMARYAlthough Scedosporium species and Lomentospora prolificans are uncommon causes of invasive fungal diseases (IFDs), these infections are associated with high mortality and are costly to treat with a limited armamentarium of antifungal drugs. In light of recent advances, including in the area of new antifungals, the present review provides a timely and updated overview of these IFDs, with a focus on the taxonomy, clinical epidemiology, pathogenesis and host immune response, disease manifestations, diagnosis, antifungal susceptibility, and treatment. An expansion of hosts at risk for these difficult-to-treat infections has emerged over the last two decades given the increased use of, and broader population treated with, immunomodulatory and targeted molecular agents as well as wider adoption of antifungal prophylaxis. Clinical presentations differ not only between genera but also across the different Scedosporium species. L. prolificans is intrinsically resistant to most currently available antifungal agents, and the prognosis of immunocompromised patients with lomentosporiosis is poor. Development of, and improved access to, diagnostic modalities for early detection of these rare mold infections is paramount for timely targeted antifungal therapy and surgery if indicated. New antifungal agents (e.g., olorofim, fosmanogepix) with novel mechanisms of action and less cross-resistance to existing classes, availability of formulations for oral administration, and fewer drug-drug interactions are now in late-stage clinical trials, and soon, could extend options to treat scedosporiosis/lomentosporiosis. Much work remains to increase our understanding of these infections, especially in the pediatric setting. Knowledge gaps for future research are highlighted in the review.
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Affiliation(s)
- Chin Fen Neoh
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Westmead Hospital, Sydney, Australia
- The University of Sydney, Sydney, Australia
- Department of Infectious Diseases, Westmead Hospital, Sydney, Australia
| | - Fanny Lanternier
- Service de Maladies Infectieuses et Tropicales, Hôpital universitaire Necker-Enfants malades, Paris, France
- National Reference Center for Invasive Mycoses and Antifungals, Translational Mycology research group, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
| | - Shio Yen Tio
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Catriona L Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Westmead Hospital, Sydney, Australia
| | - Sarah E Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, Australia
| | - David C M Kong
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Australia
- The National Centre for Antimicrobial Stewardship, The Peter Doherty Institute for Infections and Immunity, Melbourne, Australia
- Centre for Medicine Use and Safety, Monash Institute of Pharmaceutical Sciences, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Melbourne, Australia
- School of Medicine, Deakin University, Waurn Ponds, Geelong, Australia
| | - Wieland Meyer
- The University of Sydney, Sydney, Australia
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Translational Medical Mycology Research Group, ECMM Excellence Center for Clinical Mycology, Medical University of Graz, Graz, Austria
| | - Monica A Slavin
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
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Cao Y, Li Y, Wang M, Wang L, Fang Y, Wu Y, Liu Y, Liu Y, Hao Z, Kang H, Gao H. INTERPRETABLE MACHINE LEARNING FOR PREDICTING RISK OF INVASIVE FUNGAL INFECTION IN CRITICALLY ILL PATIENTS IN THE INTENSIVE CARE UNIT: A RETROSPECTIVE COHORT STUDY BASED ON MIMIC-IV DATABASE. Shock 2024; 61:817-827. [PMID: 38407989 DOI: 10.1097/shk.0000000000002312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
ABSTRACT The delayed diagnosis of invasive fungal infection (IFI) is highly correlated with poor prognosis in patients. Early identification of high-risk patients with invasive fungal infections and timely implementation of targeted measures is beneficial for patients. The objective of this study was to develop a machine learning-based predictive model for invasive fungal infection in patients during their intensive care unit (ICU) stay. Retrospective data was extracted from adult patients in the MIMIC-IV database who spent a minimum of 48 h in the ICU. Feature selection was performed using LASSO regression, and the dataset was balanced using the BL-SMOTE approach. Predictive models were built using six machine learning algorithms. The Shapley additive explanation algorithm was used to assess the impact of various clinical features in the optimal model, enhancing interpretability. The study included 26,346 ICU patients, of whom 379 (1.44%) were diagnosed with invasive fungal infection. The predictive model was developed using 20 risk factors, and the dataset was balanced using the borderline-SMOTE (BL-SMOTE) algorithm. The BL-SMOTE random forest model demonstrated the highest predictive performance (area under curve = 0.88, 95% CI = 0.84-0.91). Shapley additive explanation analysis revealed that the three most influential clinical features in the BL-SMOTE random forest model were dialysis treatment, APSIII scores, and liver disease. The machine learning model provides a reliable tool for predicting the occurrence of IFI in ICU patients. The BL-SMOTE random forest model, based on 20 risk factors, exhibited superior predictive performance and can assist clinicians in early assessment of IFI occurrence in ICU patients. Importance: Invasive fungal infections are characterized by high incidence and high mortality rates characteristics. In this study, we developed a clinical prediction model for invasive fungal infections in critically ill patients based on machine learning algorithms. The results show that the machine learning model based on 20 clinical features has good predictive value.
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Affiliation(s)
- Yuan Cao
- Emergency Department, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | | | | | | | - Yuan Fang
- Department of Critical Care Medicine, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | | | | | - Yixuan Liu
- Emergency Department, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ziqian Hao
- Emergency Department, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hongjun Kang
- Department of Critical Care Medicine, the First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Hengbo Gao
- Emergency Department, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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Alza-Arcila J, Ramírez-Sánchez IC, Diaz-Sanabria RA. Histoplasma capsulatum tenosynovitis: An unusual presentation in a kidney transplant recipient. Transpl Infect Dis 2024; 26:e14269. [PMID: 38501790 DOI: 10.1111/tid.14269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
Histoplasmosis is an expected endemic mycosis in solid organ transplant recipients and occurs as a primary infection, reactivation, or, rarely, acquired from an infected allograft. Reactivation is favored by maintenance immunosuppression or anti-rejection therapy, which facilitates the appearance of disseminated forms as well as unusual presentations. We present the case of a 66-year-old woman with isolated tenosynovitis due to Histoplasma capsulatum 25 years after a kidney transplant.
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Affiliation(s)
- Jhongert Alza-Arcila
- Internal Medicine Department, Infectious Diseases Section, Medical School, Universidad de Antioquia, Medellin, Colombia
| | - Isabel Cristina Ramírez-Sánchez
- Internal Medicine Department, Infectious Diseases Section, Medical School, Universidad de Antioquia, Medellin, Colombia
- Internal Medicine Department, Infectious Diseases Section, Hospital Pablo Tobón Uribe, Medical School, Medellin, Colombia
| | - Ricardo Augusto Diaz-Sanabria
- Internal Medicine Department, Infectious Diseases Section, Medical School, Universidad de Antioquia, Medellin, Colombia
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Moreno A, Mah J, Budvytiene I, Ho DY, Schwenk HT, Banaei N. Dynamics and prognostic value of plasma cell-free DNA PCR in patients with invasive aspergillosis and mucormycosis. J Clin Microbiol 2024; 62:e0039424. [PMID: 38602412 PMCID: PMC11237630 DOI: 10.1128/jcm.00394-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Aspergillus species and Mucorales agents are the primary etiologies of invasive fungal disease (IFD). Biomarkers that predict outcomes are needed to improve care. Patients diagnosed with invasive aspergillosis and mucormycosis using plasma cell-free DNA (cfDNA) PCR were retested weekly for 4 weeks. The primary outcome included all-cause mortality at 6 weeks and 6 months based on baseline cycle threshold (CT) values and results of follow-up cfDNA PCR testing. Forty-five patients with Aspergillus and 30 with invasive Mucorales infection were retested weekly for a total of 197 tests. Using the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium (EORTC/MSG) criteria, 30.7% (23/75), 25.3% (19/75), and 38.7% (29/75) had proven, probable, and possible IFD, respectively. In addition, 97.3% (73/75) were immunocompromised. Baseline CT increased significantly starting at week 1 for Mucorales and week 2 for Aspergillus. Aspergillosis and mucormycosis patients with higher baseline CT (CT >40 and >35, respectively) had a nonsignificantly higher survival rate at 6 weeks, compared with patients with lower baseline CT. Mucormycosis patients with higher baseline CT had a significantly higher survival rate at 6 months. Mucormycosis, but not aspergillosis patients, with repeat positive cfDNA PCR results had a nonsignificantly lower survival rate at 6 weeks and 6 months compared with patients who reverted to negative. Aspergillosis patients with baseline serum Aspergillus galactomannan index <0.5 and <1.0 had significantly higher survival rates at 6 weeks when compared with those with index ≥0.5 and ≥1.0, respectively. Baseline plasma cfDNA PCR CT can potentially be used to prognosticate survival in patients with invasive Aspergillus and Mucorales infections. IMPORTANCE We show that Aspergillus and Mucorales plasma cell-free DNA PCR can be used not only to noninvasively diagnose patients with invasive fungal disease but also to correlate the baseline cycle threshold with survival outcomes, thus potentially allowing the identification of patients at risk for poor outcomes, who may benefit from more targeted therapies.
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Affiliation(s)
- Angel Moreno
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Jordan Mah
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Indre Budvytiene
- Clinical Microbiology Laboratory, Stanford Health Care, Palo Alto, California, USA
| | - Dora Y. Ho
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - Hayden T. Schwenk
- Division of Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Clinical Microbiology Laboratory, Stanford Health Care, Palo Alto, California, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
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Lamoth F, Kontoyiannis DP. PCR diagnostic platforms for non- Aspergillus mold infections: ready for routine implementation in the clinic? Expert Rev Mol Diagn 2024; 24:273-282. [PMID: 38501431 DOI: 10.1080/14737159.2024.2326474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/29/2024] [Indexed: 03/20/2024]
Abstract
INTRODUCTION While Aspergillus spp. remain the predominant cause of invasive mold infections, non-Aspergillus molds, such as the Mucorales or Fusarium spp., account for an increasing proportion of cases. The diagnosis of non-Aspergillus invasive mold infections (NAIMI) is challenging because of the low sensitivity and delay of conventional microbiological tests. Therefore, there is a particular interest to develop molecular tools for their early detection in blood or other clinical samples. AREAS COVERED This extensive review of the literature discusses the performance of Mucorales-specific PCR and other genus-specific or broad-range fungal PCR that can be used for the diagnosis of NAIMI in diverse clinical samples, with a focus on novel technologies. EXPERT OPINION PCR currently represents the most promising approach, combining good sensitivity/specificity and ability to detect NAIMI in clinical samples before diagnosis by conventional cultures and histopathology. Several PCR assays have been designed for the detection of Mucorales in particular, but also Fusarium spp. or Scedosporium/Lomentospora spp. Some commercial Mucorales PCRs are now available. While efforts are still needed for standardized protocols and the development of more rapid and simpler techniques, PCR is on the way to becoming an essential test for the early diagnosis of mucormycosis and possibly other NAIMIs.
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Affiliation(s)
- Frederic Lamoth
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Institute of Microbiology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dimitrios P Kontoyiannis
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Misra A, Powell EA. Preanalytical Challenges of Molecular Microbiology Tests. Clin Lab Med 2024; 44:33-43. [PMID: 38280796 DOI: 10.1016/j.cll.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
As infectious disease diagnostics increasingly incorporates molecular techniques, there are unique preanalytical concerns that must be considered. First, noninvasive specimen types that may be inadequate for culture-based diagnostics may be acceptable when using molecular tests. Second, specimen containers must be evaluated for the presence of substances that may interfere with amplification or sequencing reactions. Finally, the capacity of transport, storage, and processing conditions to maintain nucleic acid integrity and avoid contamination must be assessed. This review explores these issues and the effects they may have on result quality.
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Affiliation(s)
- Anisha Misra
- Department of Laboratory Medicine, Cleveland Clinic, Robert J. Tomsich Pathology and Laboratory Medicine Institute, 10300 Carnegie Avenue LL-1, Cleveland, OH 44195, USA
| | - Eleanor A Powell
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, 3188 Bellevue Avenue, Cincinnati, OH 45219, USA.
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García-Rodríguez G, Duque-Molina C, Kondo-Padilla I, Zaragoza-Jiménez CA, González-Cortés VB, Flores-Antonio R, Villa-Reyes T, Vargas-Rubalcava A, Ruano-Calderon LÁ, Tinoco-Favila JC, Sánchez-Salazar HC, Rivas-Ruiz R, Castro-Escamilla O, Martínez-Gamboa RA, González-Lara F, López-Martínez I, Chiller TM, Pelayo R, Bonifaz LC, Robledo-Aburto Z, Alcocer-Varela J. Outbreak of Fusarium solani Meningitis in Immunocompetent Persons Associated With Neuraxial Blockade in Durango, Mexico, 2022-2023. Open Forum Infect Dis 2024; 11:ofad690. [PMID: 38370296 PMCID: PMC10873708 DOI: 10.1093/ofid/ofad690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/02/2024] [Indexed: 02/20/2024] Open
Abstract
Background Fungal meningitis can be associated with epidural anesthesia procedures. Fusariosis is a rare infection typically affecting immunocompromised patients and rarely causes meningitis. During 2022-2023, public health officials responded to a large outbreak of Fusarium solani meningitis associated with epidural anesthesia in Durango, Mexico. Methods The public health response and epidemiological and clinical features of patients affected by this outbreak were described. Coordinated actions were addressed to identify the etiological agent, determine its drug susceptibility, develop diagnostic tests, and implement clinical and epidemiological protocols. Retrospective analyses of clinical variables and outcomes were performed to determine association with better patient survival. Results A total of 1801 persons exposed to epidural anesthesia were identified, of whom 80 developed meningitis. Fusarium solani was found in 3 brain biopsies and showed susceptibility to voriconazole and amphotericin B. After F solani polymerase chain reaction (PCR) implementation, 57 patients with meningitis were PCR-screened, and 31 (38.8%) had a positive result. Most patients were female (95%), and cesarean section was the most common surgical procedure (76.3%). The case fatality rate was 51.3% (41 patients) and the median hospitalization duration was 39.5 days (interquartile range, 18-86 days). Seventy-one patients (88.8%) received voriconazole/amphotericin B and 64 subjects (80%) additionally received steroids. Cox regression analysis showed an increased lethality risk in patients who received antifungal treatment after 5 days (hazard ratio, 2.1 [95% confidence interval, 1.01-4.48], P < .05). Conclusions The F solani meningitis outbreak in Durango was an unprecedented medical challenge. Timely treatment and effective healthcare management were associated with better survival outcomes.
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Affiliation(s)
| | - Célida Duque-Molina
- Dirección de Prestaciones Médicas, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Irasema Kondo-Padilla
- Dirección de los Servicios de Salud del Estado de Durango, Secretaría de Salud, Durango, Mexico
| | | | - Vladimir Brian González-Cortés
- Coordinación de la Red Hospitalaria de Vigilancia Epidemiológica, Dirección de Información Epidemiológica, Secretaría de Salud, Mexico City, Mexico
| | - Rocio Flores-Antonio
- Coordinación de la Red Hospitalaria de Vigilancia Epidemiológica, Dirección de Información Epidemiológica, Secretaría de Salud, Mexico City, Mexico
| | - Tania Villa-Reyes
- Coordinación de la Red Hospitalaria de Vigilancia Epidemiológica, Dirección de Información Epidemiológica, Secretaría de Salud, Mexico City, Mexico
| | - Adriana Vargas-Rubalcava
- Coordinación de la Red Hospitalaria de Vigilancia Epidemiológica, Dirección de Información Epidemiológica, Secretaría de Salud, Mexico City, Mexico
| | - Luis Ángel Ruano-Calderon
- Servicio de Neurología, Hospital General 450, Servicios de Salud del Estado de Durango, Secretaría de Salud, Durango, Mexico
| | - Juan Carlos Tinoco-Favila
- Clínica de Infectología, Hospital General 450, Servicios de Salud del Estado de Durango, Secretaría de Salud, Durango, Mexico
| | | | - Rodolfo Rivas-Ruiz
- División de Investigación Clínica, Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Octavio Castro-Escamilla
- División de Investigación Clínica, Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Rosa Areli Martínez-Gamboa
- Laboratorio de Microbiología Clínica, Servicio de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Fernanda González-Lara
- Laboratorio de Microbiología Clínica, Servicio de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Irma López-Martínez
- Dirección de Diagnóstico y Referencia, Instituto de Diagnóstico y Referencia Epidemiológicos, Secretaría de Salud, Mexico City, Mexico
| | - Tom M Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rosana Pelayo
- Unidad de Educación e Investigación, Dirección de Prestaciones Médicas, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Laura C Bonifaz
- Coordinación de Investigación en Salud, Dirección de Prestaciones Médicas, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Zoe Robledo-Aburto
- Dirección General, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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A J, S S S, K S, T S M. Extracellular vesicles in bacterial and fungal diseases - Pathogenesis to diagnostic biomarkers. Virulence 2023; 14:2180934. [PMID: 36794396 PMCID: PMC10012962 DOI: 10.1080/21505594.2023.2180934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Intercellular communication among microbes plays an important role in disease exacerbation. Recent advances have described small vesicles, termed as "extracellular vesicles" (EVs), previously disregarded as "cellular dust" to be vital in the intracellular and intercellular communication in host-microbe interactions. These signals have been known to initiate host damage and transfer of a variety of cargo including proteins, lipid particles, DNA, mRNA, and miRNAs. Microbial EVs, referred to generally as "membrane vesicles" (MVs), play a key role in disease exacerbation suggesting their importance in pathogenicity. Host EVs help coordinate antimicrobial responses and prime the immune cells for pathogen attack. Hence EVs with their central role in microbe-host communication, may serve as important diagnostic biomarkers of microbial pathogenesis. In this review, we summarize current research regarding the roles of EVs as markers of microbial pathogenesis with specific focus on their interaction with host immune defence and their potential as diagnostic biomarkers in disease conditions.
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Affiliation(s)
- Jnana A
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sadiya S S
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Satyamoorthy K
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Murali T S
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
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Castillo Almeida NE, Cichon CJ, Gomez CA. How I approach diarrhea in hematological transplant patients: A practical tool. Transpl Infect Dis 2023; 25 Suppl 1:e14184. [PMID: 37910586 DOI: 10.1111/tid.14184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/15/2023] [Indexed: 11/03/2023]
Abstract
Diarrhea in hematopoietic stem-cell transplantation (HSCT) remains a multifactorial challenge that demands a nuanced diagnostic approach. The causes of infectious diarrhea in HSCT recipients are diverse and influenced by patient-specific risk factors, the post-transplant timeline, and local epidemiology. During the past decade, our understanding of diarrhea in HSCT has witnessed a transformative shift through the incorporation of gastrointestinal (GI) multiplex polymerase chain reaction (PCR) panels. However, the judicious application of these panels is imperative to avoid overtesting and prevent adverse outcomes. The challenge lies in distinguishing between the diverse causes of diarrhea, ascertaining the clinical significance of detected pathogens, and navigating the diagnostic uncertainty presented by several non-infectious conditions such as mucositis, intestinal dysbiosis, and acute graft-versus-host disease (aGvHD), all of which mimic infection. This review examines the landscape of infectious diarrhea in the HSCT population, encompassing both established (e.g., Cytomegalovirus, Clostridioides difficile, and norovirus) and emerging pathogens (e.g., sapoviruses, astroviruses). We propose a multifaceted diagnostic algorithm that combines clinical assessment, risk stratification, and tailored utilization of molecular platforms. While multiplex GI panels present invaluable opportunities for rapid and comprehensive pathogen detection, their judicious use is pivotal in preserving diagnostic stewardship. Customization of diagnostic algorithms tailored to local epidemiology ensures optimal patient care and resource utilization.
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Affiliation(s)
- Natalia E Castillo Almeida
- Department of Internal Medicine, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Catherine J Cichon
- Department of Internal Medicine, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Carlos A Gomez
- Department of Internal Medicine, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
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11
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Roland LT, Humphreys IM, Le CH, Babik JM, Bailey CE, Ediriwickrema LS, Fung M, Lieberman JA, Magliocca KR, Nam HH, Teo NW, Thomas PC, Winegar BA, Birkenbeuel JL, David AP, Goshtasbi K, Johnson PG, Martin EC, Nguyen TV, Patel NN, Qureshi HA, Tay K, Vasudev M, Abuzeid WM, Hwang PH, Jafari A, Russell MS, Turner JH, Wise SK, Kuan EC. Diagnosis, Prognosticators, and Management of Acute Invasive Fungal Rhinosinusitis: Multidisciplinary Consensus Statement and Evidence-Based Review with Recommendations. Int Forum Allergy Rhinol 2023; 13:1615-1714. [PMID: 36680469 DOI: 10.1002/alr.23132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/28/2022] [Accepted: 12/31/2022] [Indexed: 01/22/2023]
Abstract
BACKGROUND Acute invasive fungal sinusitis (AIFS) is an aggressive disease that requires prompt diagnosis and multidisciplinary treatment given its rapid progression. However, there is currently no consensus on diagnosis, prognosis, and management strategies for AIFS, with multiple modalities routinely employed. The purpose of this multi-institutional and multidisciplinary evidence-based review with recommendations (EBRR) is to thoroughly review the literature on AIFS, summarize the existing evidence, and provide recommendations on the management of AIFS. METHODS The PubMed, EMBASE, and Cochrane databases were systematically reviewed from inception through January 2022. Studies evaluating management for orbital, non-sinonasal head and neck, and intracranial manifestations of AIFS were included. An iterative review process was utilized in accordance with EBRR guidelines. Levels of evidence and recommendations on management principles for AIFS were generated. RESULTS A review and evaluation of published literature was performed on 12 topics surrounding AIFS (signs and symptoms, laboratory and microbiology diagnostics, endoscopy, imaging, pathology, surgery, medical therapy, management of extrasinus extension, reversing immunosuppression, and outcomes and survival). The aggregate quality of evidence was varied across reviewed domains. CONCLUSION Based on the currently available evidence, judicious utilization of a combination of history and physical examination, laboratory and histopathologic techniques, and endoscopy provide the cornerstone for accurate diagnosis of AIFS. In addition, AIFS is optimally managed by a multidisciplinary team via a combination of surgery (including resection whenever possible), antifungal therapy, and correcting sources of immunosuppression. Higher quality (i.e., prospective) studies are needed to better define the roles of each modality and determine diagnosis and treatment algorithms.
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Affiliation(s)
- Lauren T Roland
- Department of Otolaryngology-Head and Neck Surgery, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Ian M Humphreys
- Department of Otolaryngology-Head and Neck Surgery, University of Washington, Seattle, Washington, USA
| | - Christopher H Le
- Department of Otolaryngology-Head and Neck Surgery, University of Arizona College of Medicine, Tucson, Arizona, USA
| | - Jennifer M Babik
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Christopher E Bailey
- Department of Otolaryngology-Head and Neck Surgery, West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - Lilangi S Ediriwickrema
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, Irvine, California, USA
| | - Monica Fung
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Joshua A Lieberman
- Department of Pathology and Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Kelly R Magliocca
- Department of Pathology and Laboratory Medicine, Emory University Medical Center, Atlanta, Georgia, USA
| | - Hannah H Nam
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, Orange, California, USA
| | - Neville W Teo
- Department of Otorhinolaryngology, Head and Neck Surgery, Singapore General Hospital, Singapore
| | - Penelope C Thomas
- Department of Radiology, University of Washington Medical Center, Seattle, Washington, USA
| | - Blair A Winegar
- Department of Radiology and Imaging Sciences, University of Utah Hospital, Salt Lake City, Utah, USA
| | - Jack L Birkenbeuel
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, California, USA
| | - Abel P David
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Khodayar Goshtasbi
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, California, USA
| | - Patricia G Johnson
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Allegheny Health Network, Pittsburgh, Pennsylvania, USA
| | - Elaine C Martin
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, California, USA
| | - Theodore V Nguyen
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, California, USA
| | - Neil N Patel
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Hannan A Qureshi
- Department of Otolaryngology-Head and Neck Surgery, University of Washington, Seattle, Washington, USA
| | - Kaijun Tay
- Department of Otorhinolaryngology, Head and Neck Surgery, Singapore General Hospital, Singapore
| | - Milind Vasudev
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, California, USA
| | - Waleed M Abuzeid
- Department of Otolaryngology-Head and Neck Surgery, University of Washington, Seattle, Washington, USA
| | - Peter H Hwang
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, California, USA
| | - Aria Jafari
- Department of Otolaryngology-Head and Neck Surgery, University of Washington, Seattle, Washington, USA
| | - Matthew S Russell
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Justin H Turner
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt School of Medicine, Nashville, Tennessee, USA
| | - Sarah K Wise
- Department of Otolaryngology-Head and Neck Surgery, Emory University Medical Center, Atlanta, Georgia, USA
| | - Edward C Kuan
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, California, USA
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12
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Sparks R, Halliday CL, Green W, Chen SCA. Panfungal PCR on formalin-fixed, paraffin-embedded tissue: to proceed or not proceed? Pathology 2023:S0031-3025(23)00126-5. [PMID: 37316383 DOI: 10.1016/j.pathol.2023.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/09/2023] [Accepted: 03/28/2023] [Indexed: 06/16/2023]
Abstract
Performance of panfungal PCR-DNA sequencing assays for diagnosis of invasive fungal disease on formalin-fixed, paraffin-embedded tissue (FFPE) is influenced by many variables. Interpretation of a positive result can be challenging due to the need to differentiate colonisers and contaminants from clinically significant pathogens. We conducted a retrospective audit on FFPE tissue specimens that underwent panfungal PCR from January 2021 to August 2022. Panfungal PCR results from samples where fungal elements were visualised on histopathology were compared with results from samples where no fungal elements were visualised. The cost per clinically significant positive sample in each group was calculated. Of the 248 FFPE tissues sampled, 18.1% (45/248) had fungal forms seen on histopathology. Panfungal PCR was positive in 22/45 samples (48.9%), with 16 (35.6%) results deemed clinically significant. For the remaining 203 specimens, panfungal PCR was positive in 19 (9.4%) samples with only six (3.0%) clinically significant. The average cost per clinically significant result was AUD 258.13 in the histopathology positive group and AUD 3,105.22 in the histopathology negative group. Our data suggest panfungal PCR has limited clinical utility in FFPE tissue when no fungal elements are seen. Restricting the assay to only those samples that are positive on histopathological examination aids interpretation of PCR positive results and conserves laboratory resources.
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Affiliation(s)
- Rebecca Sparks
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Catriona L Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia.
| | - Wendy Green
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia; Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
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13
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Xu Y, Gu F, Hu S, Wu Y, Wu C, Deng Y, Gu B, Chen Z, Yang Y. A cell wall-targeted organic-inorganic hybrid nano-catcher for ultrafast capture and SERS detection of invasive fungi. Biosens Bioelectron 2023; 228:115173. [PMID: 36878067 DOI: 10.1016/j.bios.2023.115173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/28/2022] [Accepted: 02/18/2023] [Indexed: 02/25/2023]
Abstract
Due to the extended culture period and various inconveniences in vitro culture, the detection of invasive fungi is rather difficult, leading to high mortality rates of the diseases caused by them. It is, however, crucial for clinical therapy and lowering patient mortality to quickly identify invasive fungus from clinical specimens. A promising non-destructive method for finding fungi is surface-enhanced Raman scattering (SERS), however, its substrate has a low level of selectivity. Clinical sample components can obstruct the target fungi's SERS signal on account of their complexity. Herein, an MNP@PNIPAMAA hybrid organic-inorganic nano-catcher was created by using ultrasonic-initiated polymerization. The caspofungin (CAS), a fungus cell wall-targeting drug, is used in this study. We investigated MNP@PNIPAMAA-CAS as a technique to rapidly extract fungus from complex samples under 3 s. SERS could subsequently be used to instantly identify the fungi that were successfully isolated with an efficacy rate of about 75%. The entire process took just 10 min. This method is an important breakthrough that might be advantageous in terms of the rapid detection of invasive fungi.
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Affiliation(s)
- Yu Xu
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, China; College of Intelligent Science and Control Engineering, Jinling Institute of Technology, Nanjing, 211169, China
| | - Feng Gu
- Department of Laboratory Medicine, Xuzhou Central Hospital, Xuzhou, 221000, China
| | - Shan Hu
- Department of Laboratory Medicine, Xuzhou Tumor Hospital, Xuzhou, 221005, China
| | - Yunjian Wu
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, China
| | - Changyu Wu
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yaling Deng
- College of Intelligent Science and Control Engineering, Jinling Institute of Technology, Nanjing, 211169, China
| | - Bing Gu
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510000, China.
| | - Zheng Chen
- School of Material Science and Engineering, China University of Mining and Technology, Xuzhou, 221116, China.
| | - Ying Yang
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, China.
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14
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Trecourt A, Rabodonirina M, Mauduit C, Traverse-Glehen A, Devouassoux-Shisheboran M, Meyronet D, Dijoud F, Ginevra C, Chapey-Picq E, Josse E, Martins-Simoes P, Bentaher A, Dupont D, Miossec C, Persat F, Wallon M, Ferry T, Pham F, Simon B, Menotti J. Fungal Integrated Histomolecular Diagnosis Using Targeted Next-Generation Sequencing on Formalin-Fixed Paraffin-Embedded Tissues. J Clin Microbiol 2023; 61:e0152022. [PMID: 36809009 PMCID: PMC10035294 DOI: 10.1128/jcm.01520-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Histopathology is the gold standard for fungal infection (FI) diagnosis, but it does not provide a genus and/or species identification. The objective of the present study was to develop targeted next-generation sequencing (NGS) on formalin-fixed tissue samples (FTs) to achieve a fungal integrated histomolecular diagnosis. Nucleic acid extraction was optimized on a first group of 30 FTs with Aspergillus fumigatus or Mucorales infection by macrodissecting the microscopically identified fungal-rich area and comparing Qiagen and Promega extraction methods through DNA amplification by A. fumigatus and Mucorales primers. Targeted NGS was developed on a second group of 74 FTs using three primer pairs (ITS-3/ITS-4, MITS-2A/MITS-2B, and 28S-12-F/28S-13-R) and two databases (UNITE and RefSeq). A prior fungal identification of this group was established on fresh tissues. Targeted NGS and Sanger sequencing results on FTs were compared. To be valid, the molecular identifications had to be compatible with the histopathological analysis. In the first group, the Qiagen method yielded a better extraction efficiency than the Promega method (100% and 86.7% of positive PCRs, respectively). In the second group, targeted NGS allowed fungal identification in 82.4% (61/74) of FTs using all primer pairs, in 73% (54/74) using ITS-3/ITS-4, in 68.9% (51/74) using MITS-2A/MITS-2B, and in 23% (17/74) using 28S-12-F/28S-13-R. The sensitivity varied according to the database used (81% [60/74] using UNITE compared to 50% [37/74] using RefSeq [P = 0.000002]). The sensitivity of targeted NGS (82.4%) was higher than that of Sanger sequencing (45.9%; P < 0.00001). To conclude, fungal integrated histomolecular diagnosis using targeted NGS is suitable on FTs and improves fungal detection and identification.
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Affiliation(s)
- Alexis Trecourt
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
| | - Meja Rabodonirina
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Claire Mauduit
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
- Centre Méditerranéen de Médecine Moléculaire (C3M), Unité 1065, Institut National de la Santé et de la Recherche Médicale, Nice, France
| | - Alexandra Traverse-Glehen
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Mojgan Devouassoux-Shisheboran
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - David Meyronet
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Pathologie Multi-site—Site Est, Hospices Civils de Lyon, Centre Hospitalier Lyon Est, Lyon, France
| | - Frédérique Dijoud
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Pathologie Multi-site—Site Est, Hospices Civils de Lyon, Centre Hospitalier Lyon Est, Lyon, France
| | - Christophe Ginevra
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Légionelles, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Emmanuelle Chapey-Picq
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Emilie Josse
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Patricia Martins-Simoes
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Staphyloccoques, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Abderrazzak Bentaher
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Dupont
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - Charline Miossec
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Florence Persat
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - Martine Wallon
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Tristan Ferry
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Maladies Infectieuses et Tropicales, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Félix Pham
- Service de Dermatologie, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
| | - Bruno Simon
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Service de Virologie, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Jean Menotti
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
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15
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Osman NA, Anwar MM, Singh B, Gupta GK, Rabie AM. A peek behind the curtain in the diagnosis and management of COVID‑19‑Associated Mucormycosis (CAM). J Egypt Public Health Assoc 2023; 98:4. [PMID: 36859556 PMCID: PMC9977480 DOI: 10.1186/s42506-022-00125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/28/2022] [Indexed: 06/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19)-associated mucormycosis (CAM) is responsible for a high mortality rate due to its unique and severe host-pathogen interactions. Critically ill or immunocompromised COVID-19 patients are more prone to suffer from aggressive mycoses. Probable victims include those with uncontrolled diabetes mellitus (DM), metabolic acidosis, prolonged neutropenia, increased ferritin levels, hypoxia, and prolonged hospitalization with/without mechanical ventilators and corticosteroids administration. The current review aims to outline the journey of patients with CAM as well as the advantages and disadvantages of the currently available diagnostic techniques. It also discussed the current status of treatment options and caveats in the management of mucormycosis. Multidisciplinary team, early diagnosis, controlling the predisposing condition(s), complete surgical debridement, effective antifungal therapies (e.g., amphotericin B, isavuconazole, and posaconazole), and implementing antifungal stewardship programs are imperative in CAM cases.
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Affiliation(s)
- Nermin A. Osman
- Biomedical Informatics and Medical Statistics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Mohammed Moustapha Anwar
- Department of Biotechnology, Institute of Graduate Studies and Research (IGSR), Alexandria University, Alexandria, Egypt
| | | | - Girish K. Gupta
- Department of Pharmaceutical Chemistry, Sri Sai College of Pharmacy, Badhani, Pathankot, 145001 Punjab India
| | - Amgad M. Rabie
- Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City, 35744 Dikernis, Dakahlia Governorate Egypt
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16
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Pulmonary Histoplasmosis: A Clinical Update. J Fungi (Basel) 2023; 9:jof9020236. [PMID: 36836350 PMCID: PMC9964986 DOI: 10.3390/jof9020236] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Histoplasma capsulatum, the etiological agent for histoplasmosis, is a dimorphic fungus that grows as a mold in the environment and as a yeast in human tissues. The areas of highest endemicity lie within the Mississippi and Ohio River Valleys of North America and parts of Central and South America. The most common clinical presentations include pulmonary histoplasmosis, which can resemble community-acquired pneumonia, tuberculosis, sarcoidosis, or malignancy; however, certain patients can develop mediastinal involvement or progression to disseminated disease. Understanding the epidemiology, pathology, clinical presentation, and diagnostic testing performance is pivotal for a successful diagnosis. While most immunocompetent patients with mild acute or subacute pulmonary histoplasmosis should receive therapy, all immunocompromised patients and those with chronic pulmonary disease or progressive disseminated disease should also receive therapy. Liposomal amphotericin B is the agent of choice for severe or disseminated disease, and itraconazole is recommended in milder cases or as "step-down" therapy after initial improvement with amphotericin B. In this review, we discuss the current epidemiology, pathology, diagnosis, clinical presentations, and management of pulmonary histoplasmosis.
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17
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Molecular Diagnosis of Endemic Mycoses. J Fungi (Basel) 2022; 9:jof9010059. [PMID: 36675880 PMCID: PMC9866865 DOI: 10.3390/jof9010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023] Open
Abstract
Diagnosis of endemic mycoses is still challenging. The moderated availability of reliable diagnostic methods, the lack of clinical suspicion out of endemic areas and the limitations of conventional techniques result in a late diagnosis that, in turn, delays the implementation of the correct antifungal therapy. In recent years, molecular methods have emerged as promising tools for the rapid diagnosis of endemic mycoses. However, the absence of a consensus among laboratories and the reduced availability of commercial tests compromises the diagnostic effectiveness of these methods. In this review, we summarize the advantages and limitations of molecular methods for the diagnosis of endemic mycoses.
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18
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Hilt EE, Ferrieri P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel) 2022; 13:genes13091566. [PMID: 36140733 PMCID: PMC9498426 DOI: 10.3390/genes13091566] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.
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19
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West PT, Brooks EF, Costales C, Moreno A, Jensen TD, Budvytiene I, Khan A, Pham THM, Schwenk HT, Bhatt AS, Banaei N. Near-fatal Legionella pneumonia in a neonate linked to home humidifier by metagenomic next generation sequencing. MED 2022; 3:565-567. [PMID: 35863347 PMCID: PMC9769437 DOI: 10.1016/j.medj.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/31/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Patrick T West
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Erin F Brooks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Cristina Costales
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Angel Moreno
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tanner Dean Jensen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Indre Budvytiene
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - Aslam Khan
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Trung H M Pham
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Hayden T Schwenk
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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20
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Skin Biopsy in Pediatric Oncology/Hematopoietic Stem Cell Transplantation Patients. Am J Dermatopathol 2022; 44:728-733. [PMID: 35925552 DOI: 10.1097/dad.0000000000002200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
ABSTRACT The aim of this study was to review the dermatopathological findings in skin biopsy specimens from pediatric oncology and hematopoietic stem cell transplantation patients over a 20-year period. Three hundred fifty-two skin biopsies from 240 patients were reviewed, and the findings were grouped into 6 categories: index neoplasms, nonindex neoplasms, infections, graft-versus-host disease, other treatment complications, and others. Among the index neoplasms identified on skin biopsy, the most common conditions were Langerhans cell histiocytosis (14 patients) and melanoma (7 patients), with other hematological malignancies and an array of soft-tissue tumors accounting for the bulk of the remainder. Neoplastic conditions common in general dermatopathological practice such as basal cell carcinoma and squamous cell carcinoma were uncommon, each being identified in only 1 patient younger than the age of 18, although basal cell carcinomas developing subsequently in young adult life were identified in 7 patients. Infections were common, with infectious agents or viral cytopathic effects (not including human papillomavirus) identified in 34 biopsies. A significant proportion (74%) represented invasive fungal infections, which are of very significant clinical importance. Biopsies performed for a clinical suspicion of graft-versus-host seldom showed histological features to suggest an alternative diagnosis, with only a single case suggesting a diagnosis of toxic erythema of chemotherapy identified.
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21
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The Evolving Landscape of Diagnostics for Invasive Fungal Infections in Lung Transplant Recipients. CURRENT FUNGAL INFECTION REPORTS 2022. [DOI: 10.1007/s12281-022-00433-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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Sabino R, Wiederhold N. Diagnosis from Tissue: Histology and Identification. J Fungi (Basel) 2022; 8:jof8050505. [PMID: 35628760 PMCID: PMC9144216 DOI: 10.3390/jof8050505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/22/2022] Open
Abstract
The diagnosis and initiation of appropriate treatment against invasive fungal infections depend upon accurate identification of pathogens by pathologists and clinical microbiologists. Histopathology is often critical in providing diagnostic insight in patients with suspected fungal infections, and such findings are incorporated into the definitions of proven or probable disease caused by certain pathogens. Such examinations can offer provisional identifications of fungal organisms, which can help guide initial therapy while laboratory results are pending. Common etiologic agents of invasive mycoses may be recognized based on morphologic characteristics observed in tissue and biologic fluids, such as those obtained from bronchoalveolar lavage and bronchial washings. However, care should be taken in the interpretation of these findings, as there may be a false sense of the ability to correctly categorize fungal organisms to the genus or species level by morphologic features alone. Studies have demonstrated discordant results between histopathology and laboratory results due to overlapping morphologic features, morphologic mimics, and sampling errors. Thus, histopathology plays an integral role in providing a differential of potential fungal pathogens but must be combined with results from laboratory studies, including cultures, antigen tests, serology, and molecular assays, in order to improve accuracy in the identification of etiologic agents of fungal infections. Inaccurate identification of the infecting organism can lead to inappropriate antifungal therapy and possibly poor clinical outcomes.
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Affiliation(s)
- Raquel Sabino
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Correspondence: ; Tel.: +351-217519247
| | - Nathan Wiederhold
- Fungus Testing Laboratory, Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA;
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23
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Development and evaluation of a novel fast broad-range PCR and sequencing assay (FBR-PCR/S) using dual priming oligonucleotides targeting the ITS/LSU gene regions for rapid diagnosis of invasive fungal diseases: multi-year experience in a large Canadian healthcare zone. BMC Infect Dis 2022; 22:375. [PMID: 35418032 PMCID: PMC9008905 DOI: 10.1186/s12879-022-07356-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
Background This study evaluated the performance of a novel fast broad range PCR and sequencing (FBR-PCR/S) assay for the improved diagnosis of invasive fungal disease (IFD) in high-risk patients in a large Canadian healthcare region.
Methods A total of 114 clinical specimens (CS) including bronchoalveolar lavages (BALs) were prospectively tested from 107 patients over a 2-year period. Contrived BALs (n = 33) inoculated with known fungi pathogens were also tested to increase diversity. Patient characteristics, fungal stain and culture results were collected from the laboratory information system. Dual-priming oligonucleotide (DPO) primers targeted to the internal transcribed spacer (ITS) (~ 350 bp) and large subunit (LSU) (~ 550 bp) gene regions were used to perform FBR-PCR/S assays on extracted BALs/CS. The performance of the molecular test was evaluated against standard microbiological methods and clinical review for the presence of IFD.
Results The 107 patients were predominantly male (67, 62.6%) with a mean age of 59 years (range = 0–85 years): 74 (69.2%) patients had at least one underlying comorbidity: 19 (34.5%) had confirmed and 12 (21.8%) had probable IFD. Culture recovered 66 fungal isolates from 55 BALs/CS with Candida spp. and Aspergillus spp. being most common. For BALs, the molecular assay vs. standard methods had sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV), and efficiency of 88.5% vs.100%, 100% vs. 61.1%, 100% vs. 88.5%, 61.1% vs. 100%, and 90.2% for both. For other CS, the molecular assay had similar performance to standard methods with sensitivity, specificity, PPV, NPV and efficiency of 66.7%, 87.0%, 66.7%, 87.0% and 81.3% for both methods. Both methods also performed similarly, regardless of whether CS stain/microscopy showed yeast/fungal elements. FBR-PCR/S assays results were reported in ~ 8 h compared to fungal cultures that took between 4 and 6 weeks.
Conclusions Rapid molecular testing compared to standard methods have equivalent diagnostic efficiency but improves clinical utility by reporting a rapid species-level identification the same dayshift (~ 8 h).
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24
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Breakthrough Trichosporon asahii in a Patient With New Diagnosis B-ALL on Echinocandin Prophylaxis: A Case Report. J Pediatr Hematol Oncol 2022; 44:e514-e517. [PMID: 35200226 DOI: 10.1097/mph.0000000000002339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/24/2021] [Indexed: 11/27/2022]
Abstract
Invasive fungal disease is a difficult to diagnose complication of therapy in patients with hematologic malignancy. Antifungal prophylaxis is recommended in high-risk populations, but its use in other populations is less clear. This brief report describes a patient with Trisomy 21 on caspofungin prophylaxis who died of disseminated Trichosporon asahii during induction therapy for new diagnosis low-risk B-cell acute lymphoblastic leukemia, accompanied by a review of similar cases in the literature. Her case highlights the utility of relatively novel diagnostic modalities and reinforces the need for caution in placing patients on antifungal prophylaxis.
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25
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Quintero O, Allard L, Ho D. Invasive mold infection of the gastrointestinal tract - A case series of 22 immunocompromised patients from a single academic center. Med Mycol 2022; 60:6517313. [PMID: 35092429 PMCID: PMC8896981 DOI: 10.1093/mmy/myac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/24/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Invasive mold infection (IMI) of the gastrointestinal (GI) tract is a rare complication in immunocompromised patients that carries a high mortality rate. It is most often described in the setting of disseminated disease. Early diagnosis and treatment are critical in its management, but this is rarely obtained, leading to delayed therapy. To describe the clinical characteristics, treatment and outcomes of this infection, we reviewed all the cases of adult patients with histopathological findings from autopsy or surgical specimens that demonstrated fungal invasion into the GI tract at Stanford Hospital & Clinics from January 1997 to August 2020. Twenty-two patients that met criteria were identified and they were all immunocompromised, either due to their underlying medical conditions or the treatments that they received. The most common underlying disease was hematological malignancies (63.6%) and the most common symptoms were abdominal pain, GI bleeding and diarrhea. A majority of patients (72.7%) had disseminated invasive mold infection, while the rest had isolated GI tract involvement. In 2/3 of our cases, the fungal genus or species was confirmed based on culture or PCR results. Given the very high mortality associated with GI mold infection, this diagnosis should be considered when evaluating immunocompromised patients with concerning GI signs and symptoms. A timely recognition of the infection, prompt initiation of appropriate antifungal therapy as well as surgical intervention if feasible, are key to improve survival from this devastating infection.
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Affiliation(s)
- Orlando Quintero
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine 300 Pasteur Drive, Lane Building L-135, Stanford, CA 94305- 5107, USA
| | - Libby Allard
- Department of Pathology, Stanford University School of Medicine 300 Pasteur Drive, Stanford, CA 94305- 5107, USA
| | - Dora Ho
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine 300 Pasteur Drive, Lane Building L-135, Stanford, CA 94305- 5107, USA
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26
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Glasgow HL, Cruz K, Murphy SC. Reverse-transcription PCR increases sensitivity of broad-range fungal detection in bronchoalveolar lavage fluid. Med Mycol 2021; 60:6433194. [PMID: 34878120 DOI: 10.1093/mmy/myab061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Broad-range PCR targeting 28S D1-D2 ribosomal DNA (rDNA) identifies numerous fungi but has limited sensitivity in clinical specimens. Ribosomal RNA (rRNA) vastly outnumbers rDNA, suggesting reverse transcription (RT)-PCR could improve detection. Among contrived samples, RT-PCR decreased 28S PCR cycle threshold values by 10--12 cycles and lowered the limit of detection > 2000-fold. Among 32 bronchoalveolar lavage specimens, RT-PCR detected 12/15 (80%) fungal PCR- or culture-positive specimens, versus 6/12 (50%) by 28S PCR, 9/12 (75%) by any fungal PCR, and 13/15 (87%) by culture. RT-PCR newly identified fungi in 4/17 (24%) PCR- and culture-negative specimens. RT substantially increased 28S PCR sensitivity overall. LAY SUMMARY Fungal infection remains difficult to diagnose in the laboratory. Here, we have shown that detecting ribosomal RNA and DNA, rather than only ribosomal DNA, in a broad range fungal assay results in a significant enhancement in the ability to detect and identify fungal pathogens in clinical samples.
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Affiliation(s)
- Heather L Glasgow
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, USA
| | - Kurtis Cruz
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, USA
| | - Sean C Murphy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, USA.,Department of Microbiology, University of Washington, Seattle, Washington, 98195, USA
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27
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Zhu A, Zembower T, Qi C. Molecular detection, not extended culture incubation, contributes to diagnosis of fungal infection. BMC Infect Dis 2021; 21:1159. [PMID: 34781879 PMCID: PMC8591865 DOI: 10.1186/s12879-021-06838-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/02/2021] [Indexed: 02/07/2023] Open
Abstract
Background Despite its low sensitivity, fungal culture remains one of the key methods for diagnosis and treatment of fungal infections, as it identifies the etiology at the genus and species level and affords the opportunity for susceptibility testing. The Manual of Clinical Microbiology recommends that fungal culture screening for all pathogens should routinely be held for 4 weeks to maximize the recovery of slow-growing species. Information on the optimal fungal culture time in this era of expansion of immunocompromised populations and availability of molecular diagnostics is lacking. We reviewed our experience with fungal culture to determine the optimal culture incubation time. In addition, our experience of broad-range ITS PCR for diagnosis of culture-negative fungal infections was also reviewed. Methods Fungal culture and ITS PCR results from January 1, 2013, to December 31, 2017, were reviewed. Results This study included 4234 non-duplicated positive cultures. Ninety-six percent (4058) of the positive cultures were detected in the first 7 days of incubation. During the second week of incubation, 111 (2.8%) positives were detected from day 8 to day 10, and 71 (1.7%) were detected from day 11 to day 14. Only 6 (0.1%) positive cultures were detected in the third week of incubation, and no positive culture was detected in the fourth week of incubation. No clinically significant fungal isolates were recovered after 14 days. Clinically significant pathogens were detected in 16 (0.2%) culture-negative samples by ITS PCR. Conclusion Extending culture incubation beyond 2 weeks did not generate clinically relevant results. When culture failed to make a laboratory diagnosis, broad-range internal transcribed spacer (ITS) rRNA gene PCR followed by sequencing produced clinically significant results.
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Affiliation(s)
- Alex Zhu
- Northwestern University, IL, Evanston, USA
| | - Teresa Zembower
- Department of Pathology, Clinical Microbiology Laboratory, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, 303 E. Chicago Ave., Chicago, IL, 60611, USA.,Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chao Qi
- Department of Pathology, Clinical Microbiology Laboratory, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, 303 E. Chicago Ave., Chicago, IL, 60611, USA.
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28
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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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29
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High Clinical Impact of Broad-Range Fungal PCR in Suspected Fungal Sinusitis. J Clin Microbiol 2021; 59:e0095521. [PMID: 34406798 DOI: 10.1128/jcm.00955-21] [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] [Indexed: 02/05/2023] Open
Abstract
Broad-range fungal PCR is a powerful tool for identifying pathogens directly from patient specimens; however, reported estimates of clinical utility vary and costs discourage universal testing. We investigated the diagnostic and clinical utility of broad-range fungal PCR by examining 9 years of results from sinonasal specimens, hypothesizing that this anatomic location would identify immunocompromised patients at high risk for invasive fungal disease. We retrospectively identified 644 PCRs and 1,446 fungal cultures from sinus sites. To determine the relative performance of each testing modality, we performed chart review on 52 patients having specimens submitted for culture and PCR on the same day. Positivity rates were significantly higher for PCR (37.1%) than culture (13.7%) but similar for formalin-fixed and fresh tissues (42.3% versus 34.6%). Relative to culture, PCR had significantly faster turnaround time to both preliminary (94.5 versus 108.8 h) and final positive (137.9 versus 278.5 h) results. Among chart-reviewed patients, 88% were immunocompromised, 65% had proven or probable fungal disease, and testing sensitivities for culture and PCR (67.5% and 85.0%) were not statistically different. Nevertheless, PCR identified pathogens not recovered by culture in 14.9% of cases and informed clinical decision-making in 16.7% of all reviewed cases, and sensitivity of PCR combined with culture (90.0%) was higher than that of culture alone. We conclude that broad-range fungal PCR is frequently informative for patients at risk of serious fungal disease and is complementary to and has faster turnaround time than culture. Formalin-fixed tissue does not adversely affect diagnostic yield, but anatomic site may impact assay positivity rates.
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30
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Srinivas S, Kumari P, Gupta DK. Utility of Panfungal PCR in the diagnosis of invasive fungal infections in febrile neutropenia. J Family Med Prim Care 2021; 10:2533-2540. [PMID: 34568132 PMCID: PMC8415693 DOI: 10.4103/jfmpc.jfmpc_2325_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/02/2020] [Accepted: 03/01/2021] [Indexed: 11/26/2022] Open
Abstract
Background: The prevalence of invasive fungal infections (IFIs) is increasing due to the increasing population of immunocompromised patients. Fungal culture is the gold standard for diagnosis but not sensitive and the turnaround time is long. Samples for histopathology are difficult to obtain because of profound cytopenias. We conducted this study with the aim to evaluate panfungal PCR for the diagnosis of IFIs in patients of febrile neutropenia. Methods: This was a single-centre, cross-sectional observational study. Patients of febrile neutropenia suspected of having IFI were included in the study. Panfungal PCR was performed on the blood of included patients along with other investigations for diagnosis of IFI. The sensitivity, specificity, positive predictive value, and negative predictive value of panfungal PCR were calculated using EORTC/MSG 2008 criteria as the gold standard. Results: Fifty patients of febrile neutropenia were included in the study, of which 52% were diagnosed positive by panfungal PCR assay. The sensitivity, specificity, positive predictive value, and negative predictive value of panfungal PCR assay was found to be 82.76%, 90.48%, 92.31% and 79.17% respectively. Conclusion: Panfungal PCR is a promising and highly sensitive diagnostic test for screening at-risk patients suspected to have IFIs. The use of panfungal PCR assay in combination with other diagnostic modalities and clinical judgment can be very helpful in the early diagnosis of IFI.
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Affiliation(s)
- Sujay Srinivas
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Pushpa Kumari
- Department of Medicine, VMMC and Safdarjung Hospital, New Delhi, India
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31
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Waris RS, Ballard M, Hong D, Seddik TB. Meningitis due to Roseomonas in an immunocompetent adolescent. Access Microbiol 2021; 3:000213. [PMID: 34151165 PMCID: PMC8209696 DOI: 10.1099/acmi.0.000213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/21/2021] [Indexed: 11/29/2022] Open
Abstract
Both bacterial and aseptic meningitis can complicate neurosurgery, but they are often difficult to distinguish clinically or by cerebrospinal fluid (CSF) analysis. We present an adolescent with subacute meningitis after neurosurgery, eventually diagnosed with meningitis caused by Roseomonas mucosa via 16S rRNA gene sequencing after two negative CSF cultures. He was treated successfully with intravenous meropenem with full recovery. This case shows that distinguishing bacterial from aseptic meningitis is important to allow directed antibiotic therapy. We recommend considering bacterial meningitis in the differential diagnosis of aseptic meningitis complicating neurosurgery, and to perform molecular diagnostics such as bacterial sequencing if the suspicion of bacterial meningitis is high.
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Affiliation(s)
- Rabbia S Waris
- Pediatric Hospital Medicine, Stanford University, Stanford, CA, USA
| | - Melissa Ballard
- Pediatric Neurosurgery, Lucile Packard Children's Hospital, Stanford, CA, USA
| | - David Hong
- Pediatric Neurosurgery, Stanford University, Stanford, CA, USA
| | - Talal B Seddik
- Pediatric Infectious Diseases, Stanford University, Stanford, CA, USA
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32
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Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC). J Clin Microbiol 2021; 59:e0178420. [PMID: 33504591 DOI: 10.1128/jcm.01784-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fungal infections are a rising threat to our immunocompromised patient population, as well as other nonimmunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics. To jointly address this diagnostic challenge, the Fungal Diagnostics Laboratory Consortium (FDLC) was recently created. The FDLC consists of 26 laboratories from the United States and Canada that routinely provide fungal diagnostic services for patient care. A survey of fungal diagnostic capacity among the 26 members of the FDLC was recently completed, identifying the following diagnostic gaps: lack of molecular detection of mucormycosis; lack of an optimal diagnostic algorithm incorporating fungal biomarkers and molecular tools for early and accurate diagnosis of Pneumocystis pneumonia, aspergillosis, candidemia, and endemic mycoses; lack of a standardized molecular approach to identify fungal pathogens directly in formalin-fixed paraffin-embedded tissues; lack of robust databases to enhance mold identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; suboptimal diagnostic approaches for mold blood cultures, tissue culture processing for Mucorales, and fungal respiratory cultures for cystic fibrosis patients; inadequate capacity for fungal point-of-care testing to detect and identify new, emerging or underrecognized, rare, or uncommon fungal pathogens; and performance of antifungal susceptibility testing. In this commentary, the FDLC delineates the most pressing unmet diagnostic needs and provides expert opinion on how to fulfill them. Most importantly, the FDLC provides a robust laboratory network to tackle these diagnostic gaps and ultimately to improve and enhance the clinical laboratory's capability to rapidly and accurately diagnose fungal infections.
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33
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Sunagawa K, Nakamura S, Sato Y, Iida S, Miyazaki Y, Suzuki T, Katano H. Morphological and genetic identification of fungal genus/species in formalin-fixed, paraffin-embedded specimens obtained from patients with histologically proven fungal infection. Mycoses 2021; 64:851-859. [PMID: 34028893 DOI: 10.1111/myc.13325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Although fungi are found relatively easily by microscopic examination of pathological samples, identification of fungal genus and species in pathological samples is not easy because the morphological features of fungi are similar among genera and species. OBJECTIVES A multiple real-time PCR was developed for identification of fungal genus/species, and morphological characterizations of fungi were analysed in pathological samples. PATIENTS/METHODS Seventy-five formalin-fixed paraffin-embedded (FFPE) samples morphologically proven to contain any fungus were examined. A multiple real-time PCR system was developed to identify 25 fungal genus/species in pathological samples. Morphology of fungus in the specimens was re-reviewed retrospectively based on the results of real-time PCR. RESULTS Real-time PCR identified fungal genus/species in 56 of 75 (74.6%) specimens with histologically proven fungal infection. In 53 specimens of filamentous fungi, Aspergillus spp. (22 specimens), Cladosporium (8), Scedosporium apiospermum (4), Malassezia sympodialis (1) and Candida albicans (1) were identified. Pseudohyphae of Candida were confused with filamentous fungus in a case. Morphological observation suggested differences in the presence of septated or non-septated hyphae, the filament size, and the branch angle among genus/species of filamentous fungi; however, genus/species was not able to be determined by their morphological features. In 22 specimens of yeasts, real-time PCR allowed for the identification of Candida albicans (12 specimens), Candida glabrata (2), Cladosporium (2), Scedosporium apiospermum (2), Pichia kudriavzevii (1) and Aspergillus sydowii (1). CONCLUSIONS These data suggest that it is difficult to identify fungal genus/species by morphological features alone. Real-time PCR is useful to identify fungal genus/species in pathological samples.
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Affiliation(s)
- Keishin Sunagawa
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.,Clinical Pathology and Laboratory Medicine, Anatomic Pathology, Saitama Cooperative Hospital, Saitama, Japan
| | - Shigeki Nakamura
- Department of Microbiology, Tokyo Medical University, Tokyo, Japan
| | - Yuko Sato
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.,Division of Infectious Diseases Pathology, Department of Global Infectious Diseases, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yoshitsugu Miyazaki
- Department of Chemotherapy and Mycoses, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Harutaka Katano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
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34
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Wilmes D, Coche E, Rodriguez-Villalobos H, Kanaan N. Fungal pneumonia in kidney transplant recipients. Respir Med 2021; 185:106492. [PMID: 34139578 DOI: 10.1016/j.rmed.2021.106492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
Fungal pneumonia is a dreaded complication encountered after kidney transplantation, complicated by increased mortality and often associated with graft failure. Diagnosis can be challenging because the clinical presentation is non-specific and diagnostic tools have limited sensitivity and specificity in kidney transplant recipients and must be interpreted in the context of the clinical setting. Management is difficult due to the increased risk of dissemination and severity, multiple comorbidities, drug interactions and reduced immunosuppression which should be applied as an important adjunct to therapy. This review will focus on the main causes of fungal pneumonia in kidney transplant recipients including Pneumocystis, Aspergillus, Cryptococcus, mucormycetes and Histoplasma. Epidemiology, clinical presentation, laboratory and radiographic features, specific characteristics will be discussed with an update on diagnostic procedures and treatment.
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Affiliation(s)
- D Wilmes
- Division of Internal Medicine, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - E Coche
- Division of Radiology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - H Rodriguez-Villalobos
- Division of Microbiology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - N Kanaan
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium.
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35
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Li XQ, Yuan JP, Fu AS, Wu HL, Liu R, Liu TG, Sun SR, Chen C. New Insights of Corynebacterium kroppenstedtii in Granulomatous Lobular Mastitis based on Nanopore Sequencing. J INVEST SURG 2021; 35:639-646. [PMID: 34036894 DOI: 10.1080/08941939.2021.1921082] [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] [Indexed: 10/21/2022]
Abstract
BACKGROUND The etiology of granulomatous lobular mastitis (GLM) remains unknown. This study aimed to detect bacteria in GLM using Nanopore sequencing and identify the relationship between GLM and Corynebacterium kroppenstedtii. METHODS AND MATERIALS The bacterial detection on fresh samples (including breast pus and tissue) of 50 GLM patients using nanopore sequencing and culture methods. The bacterial detection rate of participants with different stages were compared and analyzed. Formalin-fixed and paraffin-embedded (FFPE) tissues from 39 patients were performed on Gram staining to identify Gram-positive bacilli (GPB) within lipid vacuoles. Moreover, the clinicopathological characteristics of GLM patients in different bacterial subgroups were also conducted. RESULTS In 50 GLM patients, the detection rate of bacteria was 78% using nanopore sequencing method, especially in the early stage of GLM (over 80%), which was significantly higher than that using culture methods (24%, p < 0.001). The dominant bacteria were Corynebacterium species (64%), especially for the Corynebacterium kroppenstedtii. The detection rate of C. kroppenstedtii in nanopore sequencing method (56%) was higher than that in culture methods (16%, p < 0.001). Gram staining positive of bacteria in 7 patients, and 5 of them were C. kroppenstedtii. Thirty-one patients (31/39, 79.5%) exhibited typical histological structure of cystic neutrophilic granulomatous mastitis (CNGM), and eighteen patients detected with C. kroppenstedtii. CONCLUSION Nanopore sequencing showed rapid and accurate bacteria detection over culture method in GLM patients. GLM is not sterile inflammation and closely related to C. kroppenstedtii. CNGM was associated with Corynebacterium infection, especially for C. kroppenstedtii.
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Affiliation(s)
- Xin-Qian Li
- Renmin Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Jing-Ping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Ai-Si Fu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Hong-Li Wu
- Department of Breast Surgery, People's Hospital of Ningxia Autonomous Region, Yinchuan, Ningxia, PR China
| | - Ran Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Tian-Gang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Sheng-Rong Sun
- Renmin Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Chuang Chen
- Renmin Hospital of Wuhan University, Wuhan, Hubei, PR China
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36
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Lockhart SR, Bialek R, Kibbler CC, Cuenca-Estrella M, Jensen HE, Kontoyiannis DP. Molecular Techniques for Genus and Species Determination of Fungi From Fresh and Paraffin-Embedded Formalin-Fixed Tissue in the Revised EORTC/MSGERC Definitions of Invasive Fungal Infection. Clin Infect Dis 2021; 72:S109-S113. [PMID: 33709128 DOI: 10.1093/cid/ciaa1836] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The EORTC/MSGERC have revised the definitions for proven, probable, and possible fungal diseases. The tissue diagnosis subcommittee was tasked with determining how and when species can be determined from tissue in the absence of culture. The subcommittee reached a consensus decision that polymerase chain reaction (PCR) from tissue, but not immunohistochemistry or in situ hybridization, can be used for genus or species determination under the new EORTC/MSGERC guidelines, but only when fungal elements are identified by histology. Fungal elements seen in tissue samples by histopathology and identified by PCR followed by sequencing should fulfill the definition of a proven fungal infection, identified to genus/species, even in the absence of culture. This summary discusses the issues that were deliberated by the subcommittee to reach the consensus decision and outlines the criteria a laboratory should follow in order to produce data that meet the EORTC/MSGERC definitions.
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Affiliation(s)
- Shawn R Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ralf Bialek
- LADR GmbH MVZ Dr. Kramer und Kollegen, Geesthacht, Germany
| | | | - Manuel Cuenca-Estrella
- Laboratorio de referencia e investigación en Micología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Spain
| | - Henrik E Jensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Dimitrios P Kontoyiannis
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
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37
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Scedosporium and Lomentospora infections in lung transplant recipients. CURRENT FUNGAL INFECTION REPORTS 2021. [DOI: 10.1007/s12281-021-00416-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Senchyna F, Hogan CA, Murugesan K, Moreno A, Ho DY, Subramanian A, Schwenk HT, Budvytiene I, Costa HA, Gombar S, Banaei N. Clinical Accuracy and Impact of Plasma Cell-Free DNA Fungal PCR Panel for Non-Invasive Diagnosis of Fungal Infection. Clin Infect Dis 2021; 73:1677-1684. [PMID: 33606010 DOI: 10.1093/cid/ciab158] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Invasive fungal infection (IFI) is a growing cause of morbidity and mortality in oncology and transplant patients. Diagnosis of IFI is often delayed due to need for invasive biopsy and low sensitivity of conventional diagnostic methods. Fungal cell-free DNA (cfDNA) detection in plasma is a novel testing modality for the non-invasive diagnosis of IFI. METHODS A novel bioinformatic pipeline was created to interrogate fungal genomes and identify multicopy sequences for cfDNA PCR targeting. A real-time PCR panel was developed for 12 genera and species most commonly causing IFI. Sensitivity and specificity of the fungal PCR panel were determined using plasma samples from patients with IFI and non-IFI controls. Clinical impact of fungal PCR panel was evaluated prospectively based on the treating team's interpretation of the results. RESULTS Overall, the sensitivity and specificity were 56.5% (65/115, 95% confidence interval [CI], 47.4%-65.2%) and 99.5% (2064/2075; 95% CI, 99.0%-99.7%), respectively. In the subset of patients with an optimized plasma volume (2mL), sensitivity was 69.6% (48/69; 95% CI, 57.9%-79.2%). Sensitivity was 91.7% (11/12; 95% CI, 62.5%-100%) for detection of Mucorales agents, 56.3% (9/16; 95% CI, 33.2%-76.9%) for Aspergillus species, and 84.6% (11/13; 95% CI, 56.5%-96.9%) for Candida albicans. In a prospective evaluation of 226 patients with suspected IFI, cfDNA testing was positive in 47 (20.8%) patients and resulted in a positive impact on clinical management in 20/47 (42.6%). CONCLUSIONS The fungal cfDNA PCR panel offers a non-invasive approach to early diagnosis of IFI, providing actionable results for personalized care.
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Affiliation(s)
- Fiona Senchyna
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - Kanagavel Murugesan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Angel Moreno
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dora Y Ho
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aruna Subramanian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Hayden T Schwenk
- Division of Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Indre Budvytiene
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - Helio A Costa
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Saurabh Gombar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
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39
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Lysen C, Silva-Flannery L, Zaki SR, Gary JM, Lockhart SR. Performance evaluation of fungal DNA PCR amplification from formalin-fixed paraffin-embedded tissue for diagnosis: Experience of a tertiary reference laboratory. Mycoses 2021; 64:603-611. [PMID: 33527526 DOI: 10.1111/myc.13249] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Diagnosis of invasive fungal infections from formalin-fixed paraffin-embedded (FFPE) tissues by PCR amplification is a developing technology. One of the difficulties of establishing a validated protocol for this testing is that the gold standard, culture, is much less sensitive than the test being validated. OBJECTIVES To validate FFPE PCR as a refence laboratory identification methodology in the absence of abundant gold standard specimens. METHODS In this validation, PCR from FFPE tissue was compared to other diagnostic methods for genus/species identification. Four different groups of correlative data from FFPE tissues were used to validate this procedure. Thirteen specimens had culture or serology results and FFPE PCR results, 49 specimens had both immunohistochemistry (IHC) identification and FFPE PCR results, 118 specimens had histological evidence of fungal elements, 64 of which also had FFPE PCR results, and 36 fungal mock tissues or fungal negative tissues were used. RESULTS The sensitivity determined from the tissues with positive fungal histopathology was 54%. The specificity of the cases for which there were both culture and FFPE PCR results was 100%. For the correlation with IHC, the specificity was 98%. For the mock tissues and fungal negative tissues, the calculated analytical sensitivity was 94%, specificity was 95%, and accuracy was 94%. CONCLUSIONS By uniquely combining various data sources, this study provides a comprehensive framework for how validation can be achieved in the absence of a gold standard and outlines the excellent performance of PCR from FFPE tissue, despite relatively the low sensitivity when compared to histopathology.
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Affiliation(s)
- Colleen Lysen
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Luciana Silva-Flannery
- Infectious Disease Pathology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sherif R Zaki
- Infectious Disease Pathology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joy M Gary
- Infectious Disease Pathology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shawn R Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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40
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Freeman Weiss Z, Leon A, Koo S. The Evolving Landscape of Fungal Diagnostics, Current and Emerging Microbiological Approaches. J Fungi (Basel) 2021; 7:jof7020127. [PMID: 33572400 PMCID: PMC7916227 DOI: 10.3390/jof7020127] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/27/2021] [Accepted: 02/04/2021] [Indexed: 12/17/2022] Open
Abstract
Invasive fungal infections are increasingly recognized in immunocompromised hosts. Current diagnostic techniques are limited by low sensitivity and prolonged turnaround times. We review emerging diagnostic technologies and platforms for diagnosing the clinically invasive disease caused by Candida, Aspergillus, and Mucorales.
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Affiliation(s)
- Zoe Freeman Weiss
- Brigham and Women’s Hospital, Division of Infectious Diseases, Boston, MA 02115, USA; (A.L.); (S.K.)
- Massachusetts General Hospital, Division of Infectious Diseases, Boston, MA 02115, USA
- Correspondence:
| | - Armando Leon
- Brigham and Women’s Hospital, Division of Infectious Diseases, Boston, MA 02115, USA; (A.L.); (S.K.)
| | - Sophia Koo
- Brigham and Women’s Hospital, Division of Infectious Diseases, Boston, MA 02115, USA; (A.L.); (S.K.)
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41
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Czech MM, Nayak AK, Subramanian K, Suarez JF, Ferguson J, Jacobson KB, Montgomery SP, Chang M, Bae GH, Raghavan SS, Wang H, Miranti E, Budvytiene I, Shoor SM, Banaei N, Rieger K, Deresinski S, Holubar M, Blackburn BG. Reactivation of Chagas Disease in a Patient With an Autoimmune Rheumatic Disease: Case Report and Review of the Literature. Open Forum Infect Dis 2021; 8:ofaa642. [PMID: 33575423 PMCID: PMC7863873 DOI: 10.1093/ofid/ofaa642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
Reactivation of Chagas disease has been described in immunosuppressed patients, but there is a paucity of literature describing reactivation in patients on immunosuppressive therapies for the treatment of autoimmune rheumatic diseases. We describe a case of Chagas disease reactivation in a woman taking azathioprine and prednisone for limited cutaneous systemic sclerosis (lcSSc). Reactivation manifested as indurated and erythematous cutaneous nodules. Sequencing of a skin biopsy specimen confirmed the diagnosis of Chagas disease. She was treated with benznidazole with clinical improvement in the cutaneous lesions. However, her clinical course was complicated and included disseminated CMV disease and subsequent septic shock due to bacteremia. Our case and review of the literature highlight that screening for Chagas disease should be strongly considered for patients who will undergo immunosuppression for treatment of autoimmune disease if epidemiologically indicated.
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Affiliation(s)
- Mary M Czech
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Ashwin K Nayak
- Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Kavitha Subramanian
- Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jose F Suarez
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jessica Ferguson
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Karen Blake Jacobson
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Susan P Montgomery
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Gordon H Bae
- Department of Dermatology, Stanford University School of Medicine, Redwood City, California, USA
| | - Shyam S Raghavan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Hannah Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Eugenia Miranti
- Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Indre Budvytiene
- Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA
| | - Stanford Mervyn Shoor
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California, USA
| | - Niaz Banaei
- Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA
| | - Kerri Rieger
- Department of Dermatology, Stanford University School of Medicine, Redwood City, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Stan Deresinski
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Marisa Holubar
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Brian G Blackburn
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
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Chen SCA, Halliday CL, Hoenigl M, Cornely OA, Meyer W. Scedosporium and Lomentospora Infections: Contemporary Microbiological Tools for the Diagnosis of Invasive Disease. J Fungi (Basel) 2021; 7:23. [PMID: 33406673 PMCID: PMC7823285 DOI: 10.3390/jof7010023] [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: 11/26/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022] Open
Abstract
Scedosporium/Lomentospora fungi are increasingly recognized pathogens. As these fungi are resistant to many antifungal agents, early diagnosis is essential for initiating targeted drug therapy. Here, we review the microbiological tools for the detection and diagnosis of invasive scedosporiosis and lomentosporiosis. Of over 10 species, Lomentospora prolificans, Scedosporium apiospermum, S. boydii and S. aurantiacum cause the majority of infections. Definitive diagnosis relies on one or more of visualization, isolation or detection of the fungus from clinical specimens by microscopy techniques, culture and molecular methods such as panfungal PCR or genus-/species-specific multiplex PCR. For isolation from respiratory tract specimens, selective media have shown improved isolation rates. Species identification is achieved by macroscopic and microscopic examination of colonies, but species should be confirmed by ITS with or without β-tubulin gene sequencing or other molecular methods. Matrix-assisted laser desorption ionization-time of flight mass spectrometry databases are improving but may need supplementation by in-house spectra for species identification. Reference broth microdilution methods is preferred for antifungal susceptibility testing. Next-generation sequencing technologies have good potential for characterization of these pathogens. Diagnosis of Scedosporium/Lomentospora infections relies on multiple approaches encompassing both phenotypic- and molecular-based methods.
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Affiliation(s)
- Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia;
- Marie Bashir Institute for Infectious Diseases & Biosecurity, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia;
- Marie Bashir Institute for Infectious Diseases & Biosecurity, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Martin Hoenigl
- Division of Infectious Diseases and Global Health, University of California San Diego, San Diego, CA 92103, USA;
- Clinical and Translational Fungal-Working Group, University of California San Diego, San Diego, CA 92103, USA
- Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Oliver A. Cornely
- Department of Internal Medicine, Excellence Centre for Medical Mycology (ECMM), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50923 Cologne, Germany;
- Translational Research Cologne Excellence Cluster on Cellular Responses in Aging-associated Diseases (CECAD), 50923 Cologne, Germany
- Clinical Trials Centre Cologne (ZKS Koln), 50923 Cologne, Germany
| | - Wieland Meyer
- Marie Bashir Institute for Infectious Diseases & Biosecurity, The University of Sydney, Sydney, NSW 2006, Australia;
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW 2006, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW 2145, Australia
- Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
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43
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Flaherty BR, Barratt J, Lane M, Talundzic E, Bradbury RS. Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing. MICROBIOME 2021; 9:1. [PMID: 33388088 PMCID: PMC7778815 DOI: 10.1186/s40168-020-00939-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/14/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Targeted amplicon deep sequencing (TADS) has enabled characterization of diverse bacterial communities, yet the application of TADS to communities of parasites has been relatively slow to advance. The greatest obstacle to this has been the genetic diversity of parasitic agents, which include helminths, protozoa, arthropods, and some acanthocephalans. Meanwhile, universal amplification of conserved loci from all parasites without amplifying host DNA has proven challenging. Pan-eukaryotic PCRs preferentially amplify the more abundant host DNA, obscuring parasite-derived reads following TADS. Flaherty et al. (2018) described a pan-parasitic TADS method involving amplification of eukaryotic 18S rDNA regions possessing restriction sites only in vertebrates. Using this method, host DNA in total DNA extracts could be selectively digested prior to PCR using restriction enzymes, thereby increasing the number of parasite-derived reads obtained following NGS. This approach showed promise though was only as sensitive as conventional PCR. RESULTS Here, we expand on this work by designing a second set of pan-eukaryotic primers flanking the priming sites already described, enabling nested PCR amplification of the established 18S rDNA target. This nested approach facilitated introduction of a second restriction digestion between the first and second PCR, reducing the proportional mass of amplifiable host-derived DNA while increasing the number of PCR amplification cycles. We applied this method to blood specimens containing Babesia, Plasmodium, various kinetoplastids, and filarial nematodes and confirmed its limit of detection (LOD) to be approximately 10-fold lower than previously described, falling within the range of most qPCR methods. CONCLUSIONS The assay detects and differentiates the major malaria parasites of humans, along with several other clinically important blood parasites. This represents an important step towards a TADS-based universal parasite diagnostic (UPDx) test with a sufficient LOD for routine applications. Video Abstract.
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Affiliation(s)
- Briana R Flaherty
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Joel Barratt
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA.
| | - Meredith Lane
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Synergy America Inc., Duluth, GA, USA
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Richard S Bradbury
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
- School of Health and Life Sciences, Federation University, Ballarat, Australia.
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44
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de la Mata Navazo S, Slöcker Barrio M, García-Morín M, Beléndez C, Escobar Fernández L, Rincón-López EM, Aguilera Alonso D, Guinea J, Marín M, Butragueño-Laiseca L, López-Herce Cid J. Case Report: Severe ARDS in a Pediatric Hematopoietic Stem-Cell Transplantation Recipient Caused by Disseminated Toxoplasmosis. Front Pediatr 2021; 9:810718. [PMID: 35155320 PMCID: PMC8826680 DOI: 10.3389/fped.2021.810718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022] Open
Abstract
Toxoplasma gondii infection is a severe complication of hematopoietic stem-cell transplantation (HSCT) recipients that can remain unnoticed without a high clinical suspicion. We present the case of a 6-year-old patient with acute lymphoblastic leukemia and HSCT recipient who was admitted to the Pediatric Intensive Care Unit (PICU) on post-transplantation day +39 with fever, hypotension, severe respiratory distress and appearance of a lumbar subcutaneous node. She developed severe Acute Respiratory Distress Syndrome (ARDS) and underwent endotracheal intubation and early mechanical ventilation. Subsequently, she required prone ventilation, inhaled nitric oxide therapy and high-frequency oscillatory ventilation (HFOV). An etiologic study was performed, being blood, urine, bronchoalveolar lavage and biopsy of the subcutaneous node positive for Toxoplasma gondii by Polymerase Chain Reaction (PCR). Diagnosis of disseminated toxoplasmosis was established and treatment with pyrimethamine, sulfadiazine and folinic acid started. The patient showed clinical improvement, allowing weaning of mechanical ventilation and transfer to the hospitalization ward after 40 days in the PICU. It is important to consider toxoplasmosis infection in immunocompromised patients with sepsis and, in cases of severe respiratory distress, early mechanical ventilation should be started using the open lung approach. In Toxoplasma IgG positive patients, close monitoring and appropriate anti-infectious prophylaxis is needed after HSCT.
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Affiliation(s)
- Sara de la Mata Navazo
- Pediatric Intensive Care Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Research Network on Maternal and Child Health and Development (RedSAMID), Hospital Universitario Gregorio Marañón, Madrid, Spain.,Department of Maternal and Child Public Health, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - María Slöcker Barrio
- Pediatric Intensive Care Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Research Network on Maternal and Child Health and Development (RedSAMID), Hospital Universitario Gregorio Marañón, Madrid, Spain.,Department of Maternal and Child Public Health, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Marina García-Morín
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Department of Maternal and Child Public Health, School of Medicine, Complutense University of Madrid, Madrid, Spain.,Pediatric Hematology and Oncology Unit, Department of Pediatrics, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Cristina Beléndez
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Department of Maternal and Child Public Health, School of Medicine, Complutense University of Madrid, Madrid, Spain.,Pediatric Hematology and Oncology Unit, Department of Pediatrics, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Laura Escobar Fernández
- Pediatric Hematology and Oncology Unit, Department of Pediatrics, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Elena María Rincón-López
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Department of Maternal and Child Public Health, School of Medicine, Complutense University of Madrid, Madrid, Spain.,Pediatric Infectious Diseases Unit, Department of Pediatrics, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - David Aguilera Alonso
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Department of Maternal and Child Public Health, School of Medicine, Complutense University of Madrid, Madrid, Spain.,Pediatric Infectious Diseases Unit, Department of Pediatrics, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Jesús Guinea
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Mercedes Marín
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Laura Butragueño-Laiseca
- Pediatric Intensive Care Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Research Network on Maternal and Child Health and Development (RedSAMID), Hospital Universitario Gregorio Marañón, Madrid, Spain.,Department of Maternal and Child Public Health, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Jesús López-Herce Cid
- Pediatric Intensive Care Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Research Network on Maternal and Child Health and Development (RedSAMID), Hospital Universitario Gregorio Marañón, Madrid, Spain.,Department of Maternal and Child Public Health, School of Medicine, Complutense University of Madrid, Madrid, Spain
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45
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Abstract
Anatomic pathology is an important resource for detection and exclusion of infectious diseases in tissue specimens. Detection of a microorganism (i.e. bacteria, fungi, parasite) in tissue sections is frequently the beginning of a work-up and occasionally sufficient for definitive microbiologic identification. Close correlation with cultures and ancillary testing in the microbiology laboratory is of paramount importance in arriving at a diagnosis and identify with certitude causative pathogen(s). This review will discuss the adequacy and limitations of histopathology in the diagnosis of infectious diseases, describe potential pitfalls, and discuss the appropriate use of molecular diagnostics in formalin-fixed, paraffin embedded tissues.
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Affiliation(s)
- Alvaro C Laga
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Amory-3, Boston, MA 02115, USA.
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46
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Epstein DJ, Thompson LDR, Saleem A, Kao CS, Epstein JI. Fungal prostatitis due to endemic mycoses and Cryptococcus: A multicenter case series. Prostate 2020; 80:1006-1011. [PMID: 32572997 DOI: 10.1002/pros.24034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/05/2020] [Indexed: 11/11/2022]
Abstract
BACKGROUND Fungal prostatitis is exceedingly rare with mostly case reports. METHODS Electronic medical records at three medical centers were searched for cases of fungal prostatitis due to endemic mycoses and Cryptococcus over the preceding 10 years. RESULTS Seven cases were identified from 105 600 prostate biopsies within the Southern California Permanente Medical Group for an incidence of 0.0066%. An additional eight cases were identified from two other health care systems. Excluding four patients without available clinical data, 11 patients were reviewed, most of whom underwent biopsy due to elevated prostate-specific antigen. Four were asymptomatic and the remainder had nonspecific signs or symptoms. All biopsies revealed granulomatous inflammation and fungal organisms. Seven patients had coccidioidomycosis, three patients had cryptococcosis (confirmed in two cases and suspected by organism morphology in the other), and one patient had likely histoplasmosis based on organism morphology. Prolonged antifungal treatment was standard; outcomes were favorable. CONCLUSION Fungal prostatitis due to endemic mycoses and Cryptococcus is uncommon and associated with favorable outcomes but generally involves prolonged therapy.
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Affiliation(s)
- David J Epstein
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Lester D R Thompson
- Department of Pathology, Southern California Permanente Medical Group, Pasadena, California
| | - Atif Saleem
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Chia-Sui Kao
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Jonathan I Epstein
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
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47
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Cartier N, Chesnay A, N'diaye D, Thorey C, Ferreira M, Haillot O, Bailly É, Desoubeaux G. Candida nivariensis: Identification strategy in mycological laboratories. J Mycol Med 2020; 30:101042. [PMID: 32919860 DOI: 10.1016/j.mycmed.2020.101042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 10/23/2022]
Abstract
Candida nivariensis is a cryptic fungal species classified within the Candida glabrata complex. It was described for the first time in 2005 by the means of DNA sequencing. We report a rare case of C. nivariensis deep-seated infection occurring in a 77-year-old man hospitalized for cysto-prostatectomy. Phenotypic testing based on the direct examination and the macroscopic features of the in vitro culture initially suggested C. glabrata species, while MALDI-TOF mass spectrometry enables correct identification. The isolate was found resistant to fluconazole, like in almost 20% of the reported cases. Herein, we present our practical strategy to reliably characterize this rare cryptic species. To date, MALDI-TOF mass spectrometry-based analysis showed very good results for such a purpose.
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Affiliation(s)
- N Cartier
- Parasitologie - mycologie - médecine tropicale, CHRU de Tours, 37044 Tours, France
| | - A Chesnay
- Parasitologie - mycologie - médecine tropicale, CHRU de Tours, 37044 Tours, France; CEPR - Inserm U1100/équipe 3, faculté de médecine, université de Tours, 37032 Tours, France
| | - D N'diaye
- Médecine interne et maladies infectieuses, CHRU de Tours, 37044 Tours, France
| | - C Thorey
- Médecine interne et maladies infectieuses, CHRU de Tours, 37044 Tours, France
| | - M Ferreira
- CEPR - Inserm U1100/équipe 3, faculté de médecine, université de Tours, 37032 Tours, France; Pneumologie, CHRU de Tours, 37044 Tours, France
| | - O Haillot
- Urologie, CHRU de Tours, 37044 Tours, France
| | - É Bailly
- Parasitologie - mycologie - médecine tropicale, CHRU de Tours, 37044 Tours, France
| | - G Desoubeaux
- Parasitologie - mycologie - médecine tropicale, CHRU de Tours, 37044 Tours, France; CEPR - Inserm U1100/équipe 3, faculté de médecine, université de Tours, 37032 Tours, France.
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48
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Editorial: Diagnosis of infection in immunocompromised patients: from microscopy to next generation sequencing and host gene signatures. Curr Opin Infect Dis 2020; 32:295-299. [PMID: 31169551 DOI: 10.1097/qco.0000000000000567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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49
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Knowledge at what cost? An audit of the utility of panfungal PCR performed on bronchoalveolar lavage fluid specimens at a tertiary mycology laboratory. Pathology 2020; 52:584-588. [PMID: 32576387 DOI: 10.1016/j.pathol.2020.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/23/2020] [Accepted: 03/31/2020] [Indexed: 11/21/2022]
Abstract
The diagnostic utility and costs of panfungal PCR assays for invasive fungal disease (IFD) from bronchoalveolar lavage fluid (BALF) specimens are incompletely defined. In a retrospective audit, panfungal PCR results from 2014-2018 were matched with information on request forms and the registrar/microbiologist diary of clinical liaison. Identification of a single fungus other than a commensal was considered potentially clinically significant, and assessed for clinical relevance. Of 1002 specimens tested, an estimated 90% were requested in patients without clinical suspicion of IFD. There were 530 (52.9%) PCR-positive results of which 485/530 (91.5%) identified multiple fungal species or commensal fungi; 45 (8.5%) were clinically significant but only in 12 (1.2%) was panfungal PCR the sole diagnostic test leading to IFD diagnosis, all in immunocompromised patients with clinical suspicion of IFD. Costs of panfungal PCR tests averaged AUD 133 per test, or AUD 26,767/annum. However, the average cost-per-diagnosis achieved was AUD 15,978/annum. Limiting testing to patients at risk and with clinical suspicion of IFD, may save over AUD 13,383/annum (assuming 50-90% reduction in testing). The value-added utility of panfungal PCR on BALF is 1.2% (12/1002). We have since introduced pre-analytical stewardship limiting routine panfungal PCR testing of BALF to high-risk patients in our hospital.
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50
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Abstract
Appropriate diagnosis of invasive fungal infections (IFIs) is critical due to the high rates of morbidity and mortality, as well as the substantial economic burden, associated with the management of these diseases. The recognition of IFI and differentiation from other infections with similar clinical presentations can be challenging, which can lead to diagnostic error that not only has an impact on individual patient health outcomes but also on antimicrobial drug usage and the growing threat of antimicrobial resistance in bacteria. Therefore, there is a significant need for improved stewardship related to diagnostic testing for and treatment of IFIs. The purpose of this review is to highlight recent advances related to current fungal diagnostics, as well as explore some of the most innovative technology that has emerged with the potential to shift the paradigm of clinical mycology. In general, this review will discuss research related to enhanced fungal culture utilization and identification techniques, expanded applications of fungal antigen testing, and recently developed molecular assays and other novel nonculture fungal diagnostic approaches. Specifically, the application of mass spectrometry, novel glycobiomarker detection, and detection of fungal-specific volatile organic compounds will be reviewed, along with other key updates, to provide the reader with an updated review that extends beyond the basics of IFI laboratory diagnostics. Where appropriate, the reader will be directed to more comprehensive reviews of certain aspects of clinical mycology laboratory testing to provide a broader context for the critical consideration of these updates.
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