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Li Y, Qu L, Wang J, Chen P, Jiang A, Liu H. Predictors of breakthrough invasive fungal infections (BIFI) in pediatric acute leukemia: a retrospective analysis and predictive model development. Front Med (Lausanne) 2024; 11:1488514. [PMID: 39720656 PMCID: PMC11666376 DOI: 10.3389/fmed.2024.1488514] [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: 08/30/2024] [Accepted: 11/25/2024] [Indexed: 12/26/2024] Open
Abstract
Objective This study aims to identify key risk factors associated with the development of breakthrough invasive fungal infections (BIFI) in pediatric acute leukemia patients to improve early detection and intervention strategies. Method A retrospective analysis was conducted on 160 pediatric patients with acute leukemia admitted to Anhui Provincial Children's Hospital between October 2018 and June 2022. The study evaluated the impact of various clinical parameters on BIFI risk using univariate and multivariable analyses, with data including patient demographics, treatment regimens, and infection outcomes. The predictive model was assessed using receiver operating characteristic (ROC) curve analysis, calibration plots, and decision curve analysis (DCA). Result Among the 160 pediatric acute leukemia patients, 34 (22.22%) developed BIFI. Univariate analysis identified longer durations of neutrophil deficiency (P < 0.001), broad-spectrum antibiotic use (P < 0.001), higher volumes of red blood cell transfusions (P = 0.001), and elevated C-reactive protein (CRP) levels (P < 0.001) as significant factors associated with BIFI. Multivariable analysis confirmed these as significant predictors, with odds ratios for neutrophil deficiency (OR = 1.38, 95% CI [1.15, 1.69]), antibiotic use (OR = 1.41, 95% CI [1.10, 1.84]), transfusions (OR = 2.54, 95% CI [1.39, 5.13]), and CRP levels (OR = 1.10, 95% CI [1.04, 1.17]). The model validation showed strong predictive performance with an AUC of 0.890 (95% CI: 0.828-0.952), good calibration (Brier score = 0.099), and demonstrated clinical utility across a range of risk thresholds. Conclusion The study highlights the importance of considering these key predictors in the management of pediatric acute leukemia patients to mitigate the risk of BIFI. Incorporating these factors into personalized treatment strategies could enhance early intervention, reduce infection rates, and improve overall patient outcomes.
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Affiliation(s)
| | | | | | | | | | - Hongjun Liu
- Department of Hematology and Oncology, Anhui Provincial Children's Hospital (Anhui Hospital, Pediatric Hospital of Fudan University), Hefei, China
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Cotter A, Dracatos P, Beddoe T, Johnson K. Isothermal Detection Methods for Fungal Pathogens in Closed Environment Agriculture. J Fungi (Basel) 2024; 10:851. [PMID: 39728347 DOI: 10.3390/jof10120851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 12/05/2024] [Accepted: 12/07/2024] [Indexed: 12/28/2024] Open
Abstract
Closed environment agriculture (CEA) is rapidly gaining traction as a sustainable option to meet global food demands while mitigating the impacts of climate change. Fungal pathogens represent a significant threat to crop productivity in CEA, where the controlled conditions can inadvertently foster their growth. Historically, the detection of pathogens has largely relied on the manual observation of signs and symptoms of disease in the crops. These approaches are challenging at large scale, time consuming, and often too late to limit crop loss. The emergence of fungicide resistance further complicates management strategies, necessitating the development of more effective diagnostic tools. Recent advancements in technology, particularly in molecular and isothermal diagnostics, offer promising tools for the early detection and management of fungal pathogens. Innovative detection methods have the potential to provide real-time results and enhance pathogen management in CEA systems. This review explores isothermal amplification and other new technologies in detection of fungal pathogens that occur in CEA.
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Affiliation(s)
- Aylwen Cotter
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Bundoora 3083, Australia
| | - Peter Dracatos
- La Trobe Institute for Sustainable Agriculture and Food, Department of Ecological, Plant and Animal Sciences, La Trobe University, Bundoora 3083, Australia
| | - Travis Beddoe
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Bundoora 3083, Australia
- La Trobe Institute for Sustainable Agriculture and Food, Department of Ecological, Plant and Animal Sciences, La Trobe University, Bundoora 3083, Australia
| | - Kim Johnson
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Bundoora 3083, Australia
- La Trobe Institute for Sustainable Agriculture and Food, Department of Ecological, Plant and Animal Sciences, La Trobe University, Bundoora 3083, Australia
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Jeyaraaj JR, Ragunathan L, Kanniyan K, Subramanian P, Shebeena S, Asarudeen M, Robin JR. Fungal nasal polyposis - A rare case report. Indian J Med Microbiol 2024; 53:100768. [PMID: 39613299 DOI: 10.1016/j.ijmmb.2024.100768] [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: 05/23/2024] [Revised: 10/18/2024] [Accepted: 11/27/2024] [Indexed: 12/01/2024]
Abstract
Aspergillus peyronelii is an emerging and rare pathogen causing chronic rhinosinusitis with fungal nasal polyposis among immunocompetent individuals. Usual fungal aetiologies are Aspergillus spp, Mucor spp and Cladosporium spp, among which Aspergillus flavus being the most common in India. We present a case of 28-year-old woman with unilateral nasal obstruction with 15 years history of allergy, diagnosed as nasal polyposis, uncovered an uncommon pathogen A.peyronelii. Being a saprophytic and endophytic fungus, meticulously diagnostic approaches were employed for the precise identification. Further researches are needed to optimize diagnostic strategies and therapeutic intervention of this species.
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Affiliation(s)
- Jaishma Rajni Jeyaraaj
- Department of Microbiology, Aarupadai Veedu Medical College and Hospital, Vinayaka Missions Research Foundation (Deemed to be University), Kirumampakkam, Puducherry, 607403, India.
| | - Latha Ragunathan
- Department of Microbiology, Aarupadai Veedu Medical College and Hospital, Vinayaka Missions Research Foundation (Deemed to be University), Kirumampakkam, Puducherry, 607403, India.
| | - Kavitha Kanniyan
- Department of Microbiology, Aarupadai Veedu Medical College and Hospital, Vinayaka Missions Research Foundation (Deemed to be University), Kirumampakkam, Puducherry, 607403, India.
| | - Pramodhini Subramanian
- Department of Microbiology, Aarupadai Veedu Medical College and Hospital, Vinayaka Missions Research Foundation (Deemed to be University), Kirumampakkam, Puducherry, 607403, India.
| | - Sherief Shebeena
- Department of Microbiology, Aarupadai Veedu Medical College and Hospital, Vinayaka Missions Research Foundation (Deemed to be University), Kirumampakkam, Puducherry, 607403, India.
| | - Mohamed Asarudeen
- Department of Microbiology, Aarupadai Veedu Medical College and Hospital, Vinayaka Missions Research Foundation (Deemed to be University), Kirumampakkam, Puducherry, 607403, India.
| | - Jenifer Raj Robin
- Department of Microbiology, Aarupadai Veedu Medical College and Hospital, Vinayaka Missions Research Foundation (Deemed to be University), Kirumampakkam, Puducherry, 607403, India.
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4
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Liu Q, Yang X, Zhao J, Wang C, Lu B. Comparison of performances of laboratory methods in diagnosing pulmonary cryptococcosis in 1508 patients having lung biopsy tissues collected: a 6-year retrospective study. Eur J Clin Microbiol Infect Dis 2024; 43:2301-2309. [PMID: 39307849 DOI: 10.1007/s10096-024-04946-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 09/10/2024] [Indexed: 12/01/2024]
Abstract
PURPOSE The diagnosis of pulmonary cryptococcosis (PC) remains challenging, particularly in patients presenting with lobar or patchy consolidation on chest radiographs. Biopsies are sometimes performed for histopathologic examination and microbiological culture to differentiate infections, including PC, from lung cancers. However, to date, the clinical value of small biopsy samples and their reasonable processing methods for detecting Cryptococcus are rarely evaluated. Furthermore, the cryptococcal antigen (CrAg) test has been widely used in cryptococcosis diagnosis due to its high specificity. This 6-year retrospective study aimed to assess the efficacy of four tests commonly used for detecting Cryptococcus in the diagnosis of pulmonary cryptococcosis, and reveal that the combination of 2 or 3 methods would raise diagnosis sensitivity. METHODS The results of CrAg test, histopathologic examination and routine cryptococcal culture of sputum/bronchoalveolar lavage fluid (BALF) were collected from hospitalized patients between June 2019 to May 2024. Additionally, the results of 4 above-mentioned methods were analyzed to compare their effectiveness in PC diagnosis. RESULTS Among 1508 patients whose biopsy specimens were sent for pathogen detection, 63 PC cases were diagnosed, and 24 C. neoformans strains were cultivated using the Myco/F Lytic culture, which was more than those by sputum/BALF culture (9 strains). CrAg was positive in 82.5% (52/63) PC patients and remained the most sensitive method. The combination of CrAg and biopsy culture will increase the overall diagnostic yield to 95.2% (60/63). CONCLUSIONS In summary, for those having biopsy tissue collected, the combination of CrAg and biopsy culture using Myco/F could effectively identify most PC cases.
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Affiliation(s)
- Qi Liu
- China-Japan Friendship Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, China
| | - Xinrui Yang
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiankang Zhao
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and MultimorbidityNational Clinical Research Center for Respiratory DiseasesCenter of Respiratory Medicine, Beijing, People's Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Chunlei Wang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and MultimorbidityNational Clinical Research Center for Respiratory DiseasesCenter of Respiratory Medicine, Beijing, People's Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Binghuai Lu
- China-Japan Friendship Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, China.
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and MultimorbidityNational Clinical Research Center for Respiratory DiseasesCenter of Respiratory Medicine, Beijing, People's Republic of China.
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
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Charoonrochana N, Jinawath N, Santanirand P, Jiaranaikulwanich A, Taweewongsounton A, Setthaudom C, Tanpaibule T, Surin D, Damronglerd P, Limvorapitak W, Rungwittayatiwat S, Pinsai S, Niparuck P, Rotjanapan P. A pilot study on nasal wash galactomannan as a surrogate marker for invasive aspergillosis among hematology patients in Thailand. Sci Rep 2024; 14:29383. [PMID: 39592659 PMCID: PMC11599846 DOI: 10.1038/s41598-024-80374-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 11/18/2024] [Indexed: 11/28/2024] Open
Abstract
Universal antifungal treatment has been recommended among hematology patients during chemotherapy to prevent invasive aspergillosis (IA) in developed countries, but it remains a significant challenge in resource-limited settings. Identifying at-risk individuals could enhance clinical outcomes. A prospective pilot study was conducted at four Thai tertiary care hospitals from April 2021 to January 2023, aiming to assess the correlation and the potential of nasal wash galactomannan (GM) as an IA predictor in hematology patients. It enrolled all patients with acute myeloid leukemia (AML) requiring induction chemotherapy and those admitted for stem cell transplantation (SCT). Nasal wash fluid samples were collected for galactomannan testing and fungal culture to assess Aspergillus spp. colonization before chemotherapy. The study included 34 AML and SCT patients. Among them, 3/34 tested positive for Aspergillus spp. colonization via nasal wash fungal culture. After six months, 18 (52.9%) patients were diagnosed with IA-15/25 patients with AML and 3/9 SCT recipients. The traditional culture did not predict IA, whereas nasal wash fluid galactomannan cutoff value of 0.46 yielded a sensitivity of 40% and a specificity of 80% for predicting probable and possible IA in patients with AML. However, in the subgroup analysis, the test did not reveal any correlation with IA development. More extensive studies are needed to validate the optimal IA risk prediction strategy.
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Affiliation(s)
- Natnai Charoonrochana
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Faculty of Medicine Ramathibodi Hospital, Chakri Naruebodindra Medical Institute, Mahidol University, Samut Prakan, Thailand
- Integrative Computational Biosciences Center, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Division of Clinical Microbiology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Atisak Jiaranaikulwanich
- Division of Clinical Microbiology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | - Chavachol Setthaudom
- Division of Immunology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Bangkok, Thailand
| | - Tananun Tanpaibule
- Department of Medicine, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Dootsadeephorn Surin
- Department of Medicine, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Pansachee Damronglerd
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Thammasat University, Pathum Thani, Thailand
| | - Wasithep Limvorapitak
- Division of Hematology, Department of Medicine, Faculty of Medicine, Thammasat University, Pathum Thani, Thailand
| | | | - Subencha Pinsai
- Department of Medicine, Chao Phraya Abhaibhubejhr Hospital, Prachin Buri, Thailand
| | - Pimjai Niparuck
- Division of Hematology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Porpon Rotjanapan
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 270 Rama VI Rd, Bangkok, 10400, Thailand.
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Posadas-Cantera S, Mehrbarzin N, Wetzel S, Goelz H, Kousoulas L, Utzolino S, Häcker G, Badr MT. Enhancing ascitic fungal infection diagnosis through next-generation sequencing: a pilot study in surgical ICU patients. Front Cell Infect Microbiol 2024; 14:1441805. [PMID: 39554813 PMCID: PMC11564152 DOI: 10.3389/fcimb.2024.1441805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 10/03/2024] [Indexed: 11/19/2024] Open
Abstract
Objectives Ascites, often associated with critical pathologies such as liver cirrhosis or bowel perforation, can be complicated by fungal infection, increasing mortality especially in intensive care settings and demanding rapid diagnosis and adequate treatment. Traditional microbiological diagnostic methods have limited sensitivity in accurately identifying fungal pathogens in ascitic fluid. Alternative diagnostic methods may offer important insights to enable guiding of antifungal therapy and refining empirical treatment strategies. The objective of this study was to evaluate the potential of next-generation sequencing methods to identify specific fungal pathogens responsible for ascitic fluid infections. Methods We prospectively collected 50 ascitic fluid samples from ICU patients with suspected ascites infection. In addition to standard culture-based microbiological testing, an ascitic fluid aliquot underwent fungal DNA isolation and was analyzed by next-generation sequencing (NGS) methods for identification of fungal species. Results Of 50 ascitic samples collected, five samples showed growth of Candida spp. in culture. After DNA isolation and ITS2 PCR, detectable amplification was achieved in 10 samples. Sequencing of the 50 patients' samples identified facultative pathogenic fungi in 19 patients. In 15 cases, culture alone would not have permitted the identification of all facultative pathogenic fungi. The identification of fungal DNA by sequencing was significantly associated with poor patient outcome and a number of clinical parameters. Conclusions Our results show a higher sensitivity for NGS-based diagnostic methods in the identification of ascitic fluid fungal infections compared to culture-based diagnostics. This may be beneficial especially for patients in a critical care setting, who have an increased prevalence of comorbidities and high mortality. The implementation of such methods in standard diagnosis will require increased standardization of the workflows and interpretation of the sequencing results with respect to patients' clinical picture.
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Affiliation(s)
- Sara Posadas-Cantera
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Negin Mehrbarzin
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Simon Wetzel
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- Centre for Inherited Metabolic Diseases (CMMS), Karolinska University Hospital, Solna, Sweden
| | - Hanna Goelz
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Lampros Kousoulas
- Department of General and Visceral Surgery, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Stefan Utzolino
- Department of General and Visceral Surgery, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- IMM-PACT-Program, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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Shen S, Wang W, Ma Y, Wang S, Zhang S, Cai X, Chen L, Zhang J, Li Y, Wu X, Wei J, Zhao Y, Huang A, Niu S, Wang D. Affinity molecular assay for detecting Candida albicans using chitin affinity and RPA-CRISPR/Cas12a. Nat Commun 2024; 15:9304. [PMID: 39468064 PMCID: PMC11519397 DOI: 10.1038/s41467-024-53693-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 10/18/2024] [Indexed: 10/30/2024] Open
Abstract
Invasive fungal infections (IFIs) pose a significant threat to immunocompromised individuals, leading to considerable morbidity and mortality. Prompt and accurate diagnosis is essential for effective treatment. Here we develop a rapid molecular diagnostic method that involves three steps: fungal enrichment using affinity-magnetic separation (AMS), genomic DNA extraction with silicon hydroxyl magnetic beads, and detection through a one-pot system. This method, optimized to detect 30 CFU/mL of C. albicans in blood and bronchoalveolar lavage (BAL) samples within 2.5 h, is approximately 100 times more sensitive than microscopy-based staining. Initial validation using clinical samples showed 93.93% sensitivity, 100% specificity, and high predictive values, while simulated tests demonstrated 95% sensitivity and 100% specificity. This cost-effective, highly sensitive technique offers potential for use in resource-limited clinical settings and can be easily adapted to differentiate between fungal species and detect drug resistance.
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Affiliation(s)
- Shimei Shen
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Dermatology and Cosmetology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- Department of Clinical Laboratory Medicine, Chongqing Red Cross Hospital (Jiangbei District People's Hospital), Chongqing, China
| | - Wen Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chengdu Medical College (Nuclear Industry 416 Hospital), Chengdu, China
| | - Yuanyan Ma
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Shilei Wang
- Department of Dermatology and Cosmetology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Shaocheng Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chengdu Medical College (Nuclear Industry 416 Hospital), Chengdu, China
- School of Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Xuefei Cai
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Liang Chen
- Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jin Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yalan Li
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Xiaoli Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Jie Wei
- Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Yanan Zhao
- Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA.
| | - Ailong Huang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
| | - Siqiang Niu
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Deqiang Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China.
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
- Western (Chongqing) Collaborative Innovation Center for Intelligent Diagnostics and Digital Medicine, Chongqing National Biomedicine Industry Park, Chongqing, China.
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Ismadi YKM, Mohamad S, Harun A. Development of multiplex real-time PCR for simultaneous detection of common fungal pathogens in invasive mycoses. PeerJ 2024; 12:e18238. [PMID: 39430554 PMCID: PMC11491059 DOI: 10.7717/peerj.18238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 09/15/2024] [Indexed: 10/22/2024] Open
Abstract
Background Fungi are common opportunistic pathogens that pose a significant threat to immunocompromised patients, particularly when late detection occurs. Methods In this study a multiplex real-time PCR has been developed for simultaneous detection of common fungal pathogens associated with invasive mycoses in a diagnostic setting. Results The specificity of the assay was rigorously tested on 40 types of organisms (n = 65), demonstrating 100% specificity. The limit of detection was determined to be 100 pg/μl (106 copies/μl), achievable within a rapid 3-h timeframe. The PCR assay efficiency exhibited a range between 89.77% and 104.30% for each target organism, with linearity falling between 0.9780 and 0.9983. Conclusion This multiplex real-time PCR assay holds promise for enhancing the timely and accurate diagnosis of invasive mycoses, particularly in immunocompromised patient populations.
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Affiliation(s)
- Yasmin Khairani Muhammad Ismadi
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Suharni Mohamad
- School of Dental Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
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9
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Ortiz B, Varela D, Fontecha G, Torres K, Cornely OA, Salmanton-García J. Strengthening Fungal Infection Diagnosis and Treatment: An In-depth Analysis of Capabilities in Honduras. Open Forum Infect Dis 2024; 11:ofae578. [PMID: 39421702 PMCID: PMC11483579 DOI: 10.1093/ofid/ofae578] [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: 07/11/2024] [Accepted: 09/30/2024] [Indexed: 10/19/2024] Open
Abstract
Background Invasive fungal infections (IFIs) are a major public health concern in low- and middle-income countries (LMICs) due to limited diagnostic and treatment resources, leading to high morbidity and mortality. Despite their significant global burden, IFIs are underrecognized and underdiagnosed in LMICs. This study evaluates the diagnostic and therapeutic capacities for managing IFI in Honduras, a country with unique health care challenges. Methods From March to December 2023, a comprehensive survey was conducted across multiple health care centers in Honduras. The survey, reviewed for content and clarity by local medical institutions, targeted medical microbiologists and clinicians to assess various aspects of fungal disease diagnosis and treatment. Data included the availability and use of diagnostic tools and antifungal therapies, identifying gaps and limitations in current practices. Results The survey revealed that Candida spp (97.4%) and Aspergillus spp (35.9%) were the most concerning pathogens. Although microscopy and culture methods were available in most institutions, their application in suspected IFI cases was inconsistent, and antifungal susceptibility testing was rarely performed. Advanced diagnostic techniques, such as antigen detection, were available in only a few institutions, while antibody detection and polymerase chain reaction testing were entirely absent. All hospitals had access to at least 1 triazole antifungal, typically fluconazole, but there was a notable scarcity of more potent antifungals, including amphotericin B formulations and echinocandins. The limited use of available diagnostic tools and the restricted availability of essential antifungals were identified as major barriers to effective IFI management. Conclusions This study highlights significant gaps in the diagnostic and therapeutic capabilities for managing IFI in Honduras. The underutilization of basic diagnostic tools, the inaccessibility of advanced testing methods, and the limited availability of essential antifungal medications underscore the urgent need for capacity-building initiatives, infrastructure improvements, and policy reforms. Addressing these deficiencies is critical for enhancing the management of IFI in Honduras, with broader implications for similar LMIC settings. These findings can inform targeted interventions and resource allocation to improve outcomes for patients with IFI.
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Affiliation(s)
- Bryan Ortiz
- Instituto de Investigaciones en Microbiología, Facultad de Ciencias, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Diana Varela
- Servicio de Infectología, Servicio de Atención Integral de Pacientes con VIH, Hospital Escuela, Tegucigalpa, Honduras
- Instituto de Enfermedades Infecciosas y Parasitarias Antonio Vidal, Tegucigalpa, Honduras
| | - Gustavo Fontecha
- Instituto de Investigaciones en Microbiología, Facultad de Ciencias, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Karla Torres
- Agrupación de Microbiólogos Propietarios de Laboratorios Privados de Honduras, Tegucigalpa, Honduras
- Departamento de Química y Biología, Centro Universitario Regional de Occidente, Santa Rosa de Copán, Honduras
| | - Oliver A Cornely
- Faculty of Medicine and University Hospital Cologne, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf and Excellence Center for Medical Mycology, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Clinical Trials Centre Cologne, University of Cologne, Cologne, Germany
| | - Jon Salmanton-García
- Faculty of Medicine and University Hospital Cologne, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf and Excellence Center for Medical Mycology, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
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10
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Takoutsing BD, Ooi SZY, Egu C, Gillespie CS, Dalle DU, Erhabor J, Ciuculete AC, Kesici Ö, Awad AK, Dokponou YCH, Khan M, Ikwuegbuenyi CA, Dada OE, Bandyopadhyay S, Bankole NDA. Management and outcome of intracranial fungal infections in children and adults in Africa: a scoping review. BMC Infect Dis 2024; 24:789. [PMID: 39107727 PMCID: PMC11301832 DOI: 10.1186/s12879-024-09694-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
INTRODUCTION Intracranial fungal infections' (IcFIs) varying clinical manifestations lead to difficulties in diagnosis and treatment. African populations are disproportionately affected by the high burden of the disease. There is a lack of clarity as to the diagnostic and treatment modalities employed across the continent. In this review, we aim to detail the management, and outcome of IcFIs across Africa. METHODS This scoping review was conducted using the Arksey and O'Malley framework. MEDLINE, EMBASE, Cochrane Library, African Index Medicus, and African Journals Online were searched for relevant articles from database inception to August 10th, 2021. The Preferred Reporting Items for Systematic Review and Meta-Analysis extension for Scoping Reviews guidelines were used to report the findings of the review. RESULTS Of the 5,779 records identified, 131 articles were included. The mean age was 35.6 years, and the majority (56.4%) were males. The majority (n = 8,433/8,693, 97.0%) of IcFIs presented as a meningitis, the most common communicable predisposing factor of IcFIs was HIV/AIDS (n = 7,815/8,693, 89.9%), and the most common non-communicable risk factor was diabetes mellitus (n = 32/8,693, 0.4%). Cryptococcus species was the most common (n = 8,428/8,693, 97.0%) causative organism. The most commonly used diagnostic modality was cerebrospinal (CSF) cultures (n = 4,390/6,830, 64.3%) for diffuse IcFIs, and MRI imaging (n = 12/30, 40%) for focal IcFIs. The most common treatment modality was medical management with antifungals only (n = 4,481/8,693, 51.6%). The most commonly used antifungal agent in paediatric, and adult patients was amphotericin B and fluconazole dual therapy (51.5% vs 44.9%). The overall mortality rate was high (n = 3,475/7,493, 46.3%), and similar for both adult and paediatric patients (47.8% vs 42.1%). CONCLUSION Most IcFIs occurred in immunosuppressed individuals, and despite the new diagnostic techniques, CSF culture was mostly used in Africa. Antifungals regimens used was similar between children and adults. The outcome of IcFIs in Africa was poor for both paediatric and adult patients.
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Affiliation(s)
| | | | - Chinedu Egu
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | - Conor S Gillespie
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | - David Ulrich Dalle
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | - Joshua Erhabor
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | | | - Özgür Kesici
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | - Ahmed K Awad
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | | | - Mehdi Khan
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | | | | | - Soham Bandyopadhyay
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
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11
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Jan HE, Tsai CS, Cia CT, Lee CC, Chen YW, Lee NY, Li CW, Li MC, Syue LS, Lo CL, Chang TC, Wu CJ, Ko WC, Chen PL. PCR-Based Microarray Enhances Diagnosis of Culture-Negative Biopsied Tissue in Patients with Invasive Mold Infections: Real-World Experience in a Tertiary Medical Center. J Fungi (Basel) 2024; 10:530. [PMID: 39194856 DOI: 10.3390/jof10080530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/17/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
A fungal polymerase chain reaction (PCR) amplifies conserved genes across diverse species, combined with the subsequent hybridization of amplicons using a specific oligonucleotide microarray, allowing for the rapid detection of pathogens at the species level. However, the performance of microarrays in diagnosing invasive mold infections (IMI) from infected tissue samples is rarely reported. During the 4-year study period, all biopsied tissue samples from patients with a suspected IMI sent for microarray assays were analyzed. A partial segment of the internal transcribed spacer (ITS) region was amplified by nested PCR after DNA extraction. Amplicons were hybridized with specific probes for a variety of mold species using an in-house oligonucleotide microarray. A total of 80 clinical samples from 74 patients were tested. A diagnosis of an IMI was made in 10 patients (4 proven, 1 probable, 3 possible, 2 clinical suspicion). The PCR/microarray test was positive for three out of four proven IMIs, one probable IMI, and one out of three possible IMIs. Two patients with positive PCR/microarray findings were considered to have clinical suspicion of an IMI, and their responsible physicians initiated antifungal therapy despite the absence of supporting microbiological and histological evidence. Clinical diagnoses were categorized into non-IMI and IMI groups (including proven, probable, possible, and clinical suspicion). The sensitivity and specificity of the microarray in diagnosing the IMIs were 70% and 95.7%, respectively, while the sensitivity and specificity of the culture and histological findings were 10%/96.3% and 40.0%/100%, respectively. PCR-based methods provide supportive microbiological evidence when culture results are inconclusive. The combination of a microarray with fungal culture and histology promotes the precise diagnosis of IMIs in difficult-to-diagnose patients.
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Affiliation(s)
- Hao-En Jan
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Chin-Shiang Tsai
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Department of Internal Medicine, National Cheng Kung University Hospital Douliu Branch, College of Medicine, National Cheng Kung University, Yunlin 640, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Cong-Tat Cia
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Ching-Chi Lee
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
- Clinical Medical Research Center, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Ying-Wen Chen
- Department of Internal Medicine, National Cheng Kung University Hospital Douliu Branch, College of Medicine, National Cheng Kung University, Yunlin 640, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Nan-Yao Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Chia-Wen Li
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Ming-Chi Li
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Ling-Shan Syue
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Ching-Lung Lo
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Tsung-Chain Chang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi-Jung Wu
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 704, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Po-Lin Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, Tainan 704, Taiwan
- Diagnostic Microbiology and Antimicrobial Resistance Laboratory, National Cheng Kung University Hospital, Tainan 704, Taiwan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
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12
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Arendrup MC, Armstrong-James D, Borman AM, Denning DW, Fisher MC, Gorton R, Maertens J, Martin-Loeches I, Mehra V, Mercier T, Price J, Rautemaa-Richardson R, Wake R, Andrews N, White PL. The Impact of the Fungal Priority Pathogens List on Medical Mycology: A Northern European Perspective. Open Forum Infect Dis 2024; 11:ofae372. [PMID: 39045012 PMCID: PMC11263880 DOI: 10.1093/ofid/ofae372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/28/2024] [Indexed: 07/25/2024] Open
Abstract
Fungal diseases represent a considerable global health concern, affecting >1 billion people annually. In response to this growing challenge, the World Health Organization introduced the pivotal fungal priority pathogens list (FPPL) in late 2022. The FPPL highlights the challenges in estimating the global burden of fungal diseases and antifungal resistance (AFR), as well as limited surveillance capabilities and lack of routine AFR testing. Furthermore, training programs should incorporate sufficient information on fungal diseases, necessitating global advocacy to educate health care professionals and scientists. Established international guidelines and the FPPL are vital in strengthening local guidance on tackling fungal diseases. Future iterations of the FPPL have the potential to refine the list further, addressing its limitations and advancing our collective ability to combat fungal diseases effectively. Napp Pharmaceuticals Limited (Mundipharma UK) organized a workshop with key experts from Northern Europe to discuss the impact of the FPPL on regional clinical practice.
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Affiliation(s)
- Maiken Cavling Arendrup
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Andrew M Borman
- Mycology Reference Laboratory, UK Health Security Agency, Bristol, UK
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - David W Denning
- Manchester Fungal Infection Group, The University of Manchester, Manchester, UK
- Global Action For Fungal Infections, Geneva, Switzerland
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Rebecca Gorton
- Department of Infection Sciences, Health Services Laboratories, London, UK
| | - Johan Maertens
- Department of Hematology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Ignacio Martin-Loeches
- Department of Intensive Care Medicine, St. James's Hospital, Dublin, Ireland
- Hospital Clinic, IDIBAPS, Universidad de Barcelona, Spain
- CIBERes, Barcelona, Spain
| | - Varun Mehra
- Department of Haematological Medicine, Kings College Hospital NHS Foundation Trust, London, UK
| | - Toine Mercier
- Department of Oncology-Hematology, AZ Sint-Maarten, Mechelen, Belgium
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Jessica Price
- Public Health Wales Mycology Reference Laboratory, UHW, Cardiff, UK
| | - Riina Rautemaa-Richardson
- Department of Infectious Diseases, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, NIHR Manchester Biomedical Research Centre (BRC) at the Manchester Academic Health Science Centre, The University of Manchester and Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
- Mycology Reference Centre Manchester (MRCM), ECMM Excellence Centre of Medical Mycology, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
| | - Rachel Wake
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Natalie Andrews
- Napp Pharmaceuticals Limited, a member of the Mundipharma network of independent associated companies, Cambridge, UK
| | - P Lewis White
- Public Health Wales Mycology Reference Laboratory, UHW, Cardiff, UK
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13
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Turanoglu OF, Talay Cevlik E, Vural C. Investigation of adhesion status of Candida species to the surface of resin materials produced at different angles with additive manufacturing. BMC Oral Health 2024; 24:738. [PMID: 38937749 PMCID: PMC11209985 DOI: 10.1186/s12903-024-04505-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND The aim of this study was to evaluate the adhesion of Candida glabrata, Candida albicans, Candida krusei, Candida parapsilosis and Candida tropicalis yeasts to disk-shaped resin materials produced from resin which used in the production of surgical guide with 0, 45 and 90-degrees printing orientations by Liquid Crystal Display additive manufacturing technology. METHODS Disk-shaped specimens were printed with surgical guide resin using the Liquid Crystal Display production technique in 3 printing orientations (0, 45 and 90-degrees). Surface roughness and contact angle values were evaluated. Real-Time PCR analysis was performed to evaluate Candida adhesion (C. glabrata, C. albicans, C. krusei, C. parapsilosis and C. tropicalis) Field emission scanning electron microscope (FESEM) images of the materials were obtained. RESULTS Specimens oriented at 45-degrees demonstrated higher surface roughness (P < .05) and lower contact angle values than other groups. No significant difference was found in the adhesion of C. glabrata, C. albicans, and C. parapsilosis among specimens printed at 0, 45, and 90-degrees orientations (P > .05). A higher proportion of C. krusei and C. tropicalis was found in the specimens printed at orientation degrees of 45 = 90 < 0 with statistical significance. Analyzing the adhesion of all Candida species reveals no statistical disparity among the printing orientations. CONCLUSIONS The surface roughness, contact angle, and adhesion of certain Candida species are affected by printing orientations. Hence, careful consideration of the printing orientation is crucial for fabricating products with desirable properties. In 45-degree production, roughness increases due to the layered production forming steps, whereas in 0-degree production, certain Candida species exhibit high adhesion due to the formation of porous structures. Consequently, considering these factors, it is advisable to opt for production at 90-degrees, while also considering other anticipated characteristics.
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Affiliation(s)
- Omer F Turanoglu
- Department of Prosthodontics, Faculty of Dentistry, Aydın Adnan Menderes University, Aydın, Efeler, 09100, Turkey
| | - Esra Talay Cevlik
- Department of Prosthodontics, Faculty of Dentistry, Aydın Adnan Menderes University, Aydın, Efeler, 09100, Turkey.
| | - Caner Vural
- Department of Biology, Molecular Biology Section, Faculty of Science, Pamukkale University, Denizli, Pamukkale, 20160, Turkey
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14
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Goshia T, Aralar A, Wiederhold N, Jenks JD, Mehta SR, Karmakar A, E S M, Sharma A, Sun H, Kebadireng R, White PL, Sinha M, Hoenigl M, Fraley SI. Universal digital high-resolution melting for the detection of pulmonary mold infections. J Clin Microbiol 2024; 62:e0147623. [PMID: 38695528 PMCID: PMC11237519 DOI: 10.1128/jcm.01476-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/21/2024] [Indexed: 05/14/2024] Open
Abstract
Invasive mold infections (IMIs) are associated with high morbidity, particularly in immunocompromised patients, with mortality rates between 40% and 80%. Early initiation of appropriate antifungal therapy can substantially improve outcomes, yet early diagnosis remains difficult to establish and often requires multidisciplinary teams evaluating clinical and radiological findings plus supportive mycological findings. Universal digital high-resolution melting (U-dHRM) analysis may enable rapid and robust diagnoses of IMI. A universal fungal assay was developed for U-dHRM and used to generate a database of melt curve signatures for 19 clinically relevant fungal pathogens. A machine learning algorithm (ML) was trained to automatically classify these pathogen curves and detect novel melt curves. Performance was assessed on 73 clinical bronchoalveolar lavage samples from patients suspected of IMI. Novel curves were identified by micropipetting U-dHRM reactions and Sanger sequencing amplicons. U-dHRM achieved 97% overall fungal organism identification accuracy and a turnaround time of ~4 hrs. U-dHRM detected pathogenic molds (Aspergillus, Mucorales, Lomentospora, and Fusarium) in 73% of 30 samples classified as IMI, including mixed infections. Specificity was optimized by requiring the number of pathogenic mold curves detected in a sample to be >8 and a sample volume to be 1 mL, which resulted in 100% specificity in 21 at-risk patients without IMI. U-dHRM showed promise as a separate or combination diagnostic approach to standard mycological tests. U-dHRM's speed, ability to simultaneously identify and quantify clinically relevant mold pathogens in polymicrobial samples, and detect emerging opportunistic pathogens may aid treatment decisions, improving patient outcomes. IMPORTANCE Improvements in diagnostics for invasive mold infections are urgently needed. This work presents a new molecular detection approach that addresses technical and workflow challenges to provide fast pathogen detection, identification, and quantification that could inform treatment to improve patient outcomes.
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Affiliation(s)
- Tyler Goshia
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
| | - April Aralar
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
| | - Nathan Wiederhold
- Department of Pathology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Jeffrey D Jenks
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Durham County Department of Public Health, Durham, North Carolina, USA
| | - Sanjay R Mehta
- Department of Medicine, University of California San Diego, San Diego, California, USA
- San Diego Veterans Administration Medical Center, San Diego, California, USA
| | | | - Monish E S
- MelioLabs Inc., Santa Clara, California, USA
| | | | - Haoxiang Sun
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
| | - Refilwe Kebadireng
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
| | - P Lewis White
- Public Health Wales Microbiology Cardiff, Cardiff University, UHW, Cardiff, United Kingdom
- Centre for Trials Research, Division of Infection and Immunity, Cardiff University, UHW, Cardiff, United Kingdom
| | - Mridu Sinha
- MelioLabs Inc., Santa Clara, California, USA
| | - Martin Hoenigl
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- ECMM Excellence Center for Medical Mycology, Medical University of Graz, Graz, Austria
| | - Stephanie I Fraley
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
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15
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Tang Z, Wang H, Liu Y, Wang C, Li X, Yang Q. Current status and new experimental diagnostic methods of invasive fungal infections after hematopoietic stem cell transplantation. Arch Microbiol 2024; 206:237. [PMID: 38678508 DOI: 10.1007/s00203-024-03905-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 02/19/2024] [Indexed: 05/01/2024]
Abstract
Invasive fungal infections (IFIs) are common and life-threatening complications in post-hematopoietic stem cell transplantation (post-HSCT) recipients, Severe IFIs can lead to systemic infection and organ damage, which results in high mortality in HSCT recipients. With the development of the field of fungal infection diagnosis, more and more advanced non-culture diagnostic tools have been developed, such as glip biosensors, metagenomic next-generation sequencing, Magnetic Nanoparticles and Identified Using SERS via AgNPs+ , and artificial intelligence-assisted diagnosis. The advanced diagnostic approaches contribute to the success of HSCT and improve the overall survival of post-HSCT leukemia patients by supporting therapeutical decisions. This review provides an overview of the characteristics of two high-incidence IFIs in post-HSCT recipients and discusses some of the recently developed IFI detection technologies. Additionally, it explores the potential application of cationic conjugated polymer fluorescence resonance energy transfer (CCP-FRET) technology for IFI detection. The aim is to offer insights into selecting appropriate IFI detection methods and gaining an understanding of novel fungal diagnostic approaches in laboratory settings.
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Affiliation(s)
- Zhenhua Tang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - HaiTao Wang
- Department of Hematology, The Fifth Medical Center of Chinese, PLA General Hospital, Beijing, 100071, China
| | - Yuankai Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Chen Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xinye Li
- Lanzhou Petrochemical General Hospital (The Fourth Affiliated Hospital of Gansu University of Chinese Medicine), Gansu, 730060, China.
| | - Qiong Yang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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16
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Acosta-Mosquera Y, Tapia JC, Armas-González R, Cáceres-Valdiviezo MJ, Fernández-Cadena JC, Andrade-Molina D. Prevalence and Species Distribution of Candida Clinical Isolates in a Tertiary Care Hospital in Ecuador Tested from January 2019 to February 2020. J Fungi (Basel) 2024; 10:304. [PMID: 38786659 PMCID: PMC11122525 DOI: 10.3390/jof10050304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 05/25/2024] Open
Abstract
The incidence of candidemia in healthcare centers is associated with high morbidity and mortality. Frequency varies significantly among regions, with some species being more prevalent than others in Latin America. In this study, 191 clinical Candida isolates were collected from a major hospital in Ecuador from January 2019 to February 2020 aiming to assess their prevalence and distribution. After data processing, 168 isolates characterized by the VITEK 2 system were subsequently identified by ITS sequencing. Results showed diverse Candida species distributions, with C. albicans and C. tropicalis being the most prevalent across different clinical sources. In hospitalized individuals, C. tropicalis (38%) and C. albicans (37%) were the most prevalent, followed by, C. parapsilosis (16%), C. glabrata (5%), and other non-Candida albicans (NCA) species (6%). Conversely, C. parapsilosis (48%), C. albicans (20%), and C. glabrata (14%), associated with candidemia, were the most common in blood and CSF. Additionally, uncommon NCA species such as C. haemulonii, C. kefyr, and C. pelliculosa were identified in Ecuador for the first time. Discrepancies in species identification were observed between the VITEK 2 system and ITS sequencing, coinciding at 85%. This highlights the need for ongoing surveillance and identification efforts in Ecuador's clinical and epidemiological settings.
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Affiliation(s)
| | - Juan Carlos Tapia
- Omics Science Laboratory, Faculty of Health Science, Universidad Espíritu Santo, Samborondon 092301, Ecuador; (J.C.T.); (M.J.C.-V.)
| | - Rubén Armas-González
- Instituto Interamericano de Cooperación para la Agricultura (IICA), Representación Ecuador-Proyecto-5CN-1RBT, Quito 170518, Ecuador;
- Faculty of Health Science, Universidad Espíritu Santo, Samborondon 092301, Ecuador
| | - María José Cáceres-Valdiviezo
- Omics Science Laboratory, Faculty of Health Science, Universidad Espíritu Santo, Samborondon 092301, Ecuador; (J.C.T.); (M.J.C.-V.)
| | - Juan Carlos Fernández-Cadena
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Derly Andrade-Molina
- Omics Science Laboratory, Faculty of Health Science, Universidad Espíritu Santo, Samborondon 092301, Ecuador; (J.C.T.); (M.J.C.-V.)
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17
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Foglia F, Greco G, Zannella C, Chianese A, Ambrosino A, Conzo A, Conzo G, De Filippis A, Finamore E, Docimo L, Galdiero M. A case of Magnusiomyces capitatus isolated during monitoring in an antimicrobial diagnostic stewardship context. IDCases 2024; 36:e01959. [PMID: 38681078 PMCID: PMC11046207 DOI: 10.1016/j.idcr.2024.e01959] [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: 11/17/2023] [Revised: 03/12/2024] [Accepted: 04/14/2024] [Indexed: 05/01/2024] Open
Abstract
Magnusiomyces capitatus (M. capitatus) is an emerging opportunistic yeast in the Mediterranean region typically isolated from immunocompromised patients, usually affected by blood malignancies. We reported a rare case of M. capitatus infection, isolated from a drainage fluid in a patient affected by lung cancer recovered in the University Hospital of Campania "Luigi Vanvitelli", Naples, Italy. The isolate was identified by phenotypic methods, i.e., Gram and Lactophenol cotton blue (LCB) staining, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. We identified M. capitatus on the third day from Sabouraud Dextrose Agar supplemented with chloramphenicol and gentamicin. Antifungal susceptibility test revealed that 5-fluorocytosine was the most active drug against M. capitatus, followed by itraconazole and voriconazole, micafungin, amphotericin B and fluconazole, posaconazole, anidulafungin, and caspofungin. Our data showed the importance of an early cultural and fast microbiology diagnosis based on the characteristic morphologic features observed in Gram-stained smears of blood culture positive bottles, and the validation via MALDI-TOF MS. This dual approach has significant impact in the clinical management of infectious diseases and antibiotic stewardship, by integrating sample processing, fluid handling, and detection for rapid bacterial diagnosis.
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Affiliation(s)
- Francesco Foglia
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Giuseppe Greco
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Carla Zannella
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Annalisa Chianese
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Annalisa Ambrosino
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Alessandra Conzo
- Division of General and Oncologic Surgery, Department of Cardiothoracic Sciences, University of Campania "Luigi Vanvitelli", Via Pansini 1, 80131 Naples, Italy
| | - Giovanni Conzo
- Division of General and Oncologic Surgery, Department of Cardiothoracic Sciences, University of Campania "Luigi Vanvitelli", Via Pansini 1, 80131 Naples, Italy
| | - Anna De Filippis
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Emiliana Finamore
- Complex Operative Unity of Virology and Microbiology, University Hospital of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Ludovico Docimo
- Division of General and Oncologic Surgery, Department of Cardiothoracic Sciences, University of Campania "Luigi Vanvitelli", Via Pansini 1, 80131 Naples, Italy
| | - Massimiliano Galdiero
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
- Complex Operative Unity of Virology and Microbiology, University Hospital of Campania "Luigi Vanvitelli", 80138 Naples, Italy
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18
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Chavez MA, Munigala S, Burnham CAD, Yarbrough ML, Squires C, Fox J, Gasama H, Hsueh K, Warren DK. Impact of diagnostic stewardship interventions in the collection process of fungal blood cultures. Infect Control Hosp Epidemiol 2024; 45:384-386. [PMID: 37800346 PMCID: PMC10933497 DOI: 10.1017/ice.2023.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/03/2023] [Accepted: 07/08/2023] [Indexed: 10/07/2023]
Abstract
We implemented 2 interventions to improve utilization and contamination at our institution: kits to improve appropriate sample collection and an electronic order alert displaying appropriate indications of fungal blood cultures. An electronic order alert when ordering fungal blood cultures was associated with decreased utilization without decrease in positivity rate.
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Affiliation(s)
- Miguel A. Chavez
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Satish Munigala
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Carey-Ann D. Burnham
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Melanie L. Yarbrough
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Crystal Squires
- Department of Laboratories, Barnes-Jewish Hospital, St. Louis, Missouri
| | - Josephine Fox
- Department of Hospital Epidemiology and Infection Prevention, Barnes Jewish Hospital, St. Louis, Missouri
| | - Heather Gasama
- Department of Hospital Epidemiology and Infection Prevention, Barnes Jewish Hospital, St. Louis, Missouri
| | - Kevin Hsueh
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - David K. Warren
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
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19
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Chatterjee K, Taneja J, Agarwal C, Sasidharan J, Das A, Pandey A. Utility of galactomannan diagnostic assay in rhino-orbito-cerebral mycosis in COVID-19 patients. Indian J Med Microbiol 2024; 48:100557. [PMID: 38447858 DOI: 10.1016/j.ijmmb.2024.100557] [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: 07/15/2023] [Revised: 02/21/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
An increasing number of fungal infections were reported post COVID-19 and many of them were caused by fungi of mixed aetiologies. This study was carried out to assess the utility of serum galactomannan (GM) assay in establishing the etiology of acute rhino-orbito-cerebral mycosis caused by Aspergillus spp. Two serum samples were obtained from 41 suspected post COVID-19 rhino-orbito-cerebral mycosis patients to perform GM assay. Serum GM assay was positive in 68.7% of the cases of proven aspergillosis at cut off OD = 1.0. Serum GM assay can be used as a supplementary test in the diagnosis of rhino-orbito-cerebral mycosis caused by Aspergillus spp.
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Affiliation(s)
- Kuhu Chatterjee
- Department of Microbiology, ESIC Medical College and Hospital, Faridabad, Haryana, India.
| | - Juhi Taneja
- Department of Microbiology, ESIC Medical College and Hospital, Faridabad, Haryana, India.
| | - Charu Agarwal
- Department of Pathology, ESIC Medical College and Hospital, Faridabad, Haryana, India.
| | - Jaseetha Sasidharan
- Department of Otorhinolaryngology, ESIC Medical College and Hospital, Faridabad, Haryana, India.
| | - Asim Das
- ESIC Medical College and Hospital, Faridabad, Haryana, India.
| | - Aparna Pandey
- Department of Microbiology, ESIC Medical College and Hospital, Faridabad, Haryana, India.
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20
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Zacharioudakis IM, Zervou FN, Marsh K, Siegfried J, Yang J, Decano A, Dubrovskaya Y, Mazo D, Aguero-Rosenfeld M. Utility of incorporation of beta-D-glucan and T2Candida testing for diagnosis and treatment of candidemia. Diagn Microbiol Infect Dis 2024; 108:116107. [PMID: 38071859 DOI: 10.1016/j.diagmicrobio.2023.116107] [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: 05/20/2022] [Revised: 09/20/2023] [Accepted: 10/12/2023] [Indexed: 01/22/2024]
Abstract
The additive role of non-culture-based methods for the diagnosis of candidemia remains unknown. We evaluated 2 clinical practices followed in our hospitals for the diagnosis of candidemia, namely practice#1 including a combination of blood cultures and T2Candida, and practice#2 that also included Beta-D-glucan (BDG). Three out of 96 patients testing positive with practice#1 received a complete antifungal course. Of the 120 patients evaluated with practice#2, 29 were positive. Only 55.2% of those received a complete course. We observed significant differences in antifungal utilization, with 268.5 antifungal days/1000 patient-days for practice#1, as opposed to 371.9 days for practice#2, a nearly 40% difference. However, we found similar rates of antifungal discontinuation among negative patients at 3 days of testing (36.8% and 37.0% respectively). No differences were detected in death and/or subsequent diagnosis of candidemia. In summary, addition of BDG was interpreted variably by clinicians, was associated with an increase in antifungal utilization, and did not correlate with measurable clinical benefits for patients.
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Affiliation(s)
- Ioannis M Zacharioudakis
- Division of Infectious Diseases and Immunology, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA.
| | - Fainareti N Zervou
- Division of Infectious Diseases and Immunology, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Kassandra Marsh
- Department of Pharmacy, NYU Langone Health, New York, NY, USA
| | | | - Jenny Yang
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Arnold Decano
- Division of Infectious Diseases and Immunology, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA; Department of Pharmacy, NYU Langone Health, New York, NY, USA
| | - Yanina Dubrovskaya
- Division of Infectious Diseases and Immunology, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA; Department of Pharmacy, NYU Langone Health, New York, NY, USA
| | - Dana Mazo
- Division of Infectious Diseases and Immunology, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Maria Aguero-Rosenfeld
- Division of Infectious Diseases and Immunology, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA; Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
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21
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Schemiko Almeida K, Rossi SA, Alves LR. RNA-containing extracellular vesicles in infection. RNA Biol 2024; 21:37-51. [PMID: 39589334 PMCID: PMC11601058 DOI: 10.1080/15476286.2024.2431781] [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] [Revised: 11/07/2024] [Accepted: 11/15/2024] [Indexed: 11/27/2024] Open
Abstract
Extracellular vesicles (EVs) are membrane-bound particles released by cells that play vital roles in intercellular communication by transporting diverse biologically active molecules, including RNA molecules, including mRNA, miRNA, lncRNA, and other regulatory RNAs. These RNA types are protected within the lipid bilayer of EVs, ensuring their stability and enabling long-distance cellular interactions. Notably, EVs play roles in infection, where pathogens and host cells use EV-mediated RNA transfer to influence immune responses and disease outcomes. For example, bacterial EVs play a crucial role in infection by modulating host immune responses and facilitating pathogen invasion. This review explores the complex interactions between EV-associated RNA and host-pathogen dynamics in bacteria, parasites, and fungi, aiming to uncover molecular mechanisms in infectious diseases and potential therapeutic targets.
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Affiliation(s)
- Kayo Schemiko Almeida
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ, Curitiba, PR, Brazil
| | - Suélen Andreia Rossi
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ, Curitiba, PR, Brazil
| | - Lysangela Ronalte Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ, Curitiba, PR, Brazil
- National Institute of Science and Technology in Human Pathogenic Fungi, São Paulo, Brazil
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22
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Goshia T, Aralar A, Wiederhold N, Jenks JD, Mehta SR, Sinha M, Karmakar A, Sharma A, Shrivastava R, Sun H, White PL, Hoenigl M, Fraley SI. Universal Digital High Resolution Melt for the detection of pulmonary mold infections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566457. [PMID: 37986859 PMCID: PMC10659414 DOI: 10.1101/2023.11.09.566457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Invasive mold infections (IMIs) such as aspergillosis, mucormycosis, fusariosis, and lomentosporiosis are associated with high morbidity and mortality, particularly in immunocompromised patients, with mortality rates as high as 40% to 80%. Outcomes could be substantially improved with early initiation of appropriate antifungal therapy, yet early diagnosis remains difficult to establish and often requires multidisciplinary teams evaluating clinical and radiological findings plus supportive mycological findings. Universal digital high resolution melting analysis (U-dHRM) may enable rapid and robust diagnosis of IMI. This technology aims to accomplish timely pathogen detection at the single genome level by conducting broad-based amplification of microbial barcoding genes in a digital polymerase chain reaction (dPCR) format, followed by high-resolution melting of the DNA amplicons in each digital reaction to generate organism-specific melt curve signatures that are identified by machine learning. Methods A universal fungal assay was developed for U-dHRM and used to generate a database of melt curve signatures for 19 clinically relevant fungal pathogens. A machine learning algorithm (ML) was trained to automatically classify these 19 fungal melt curves and detect novel melt curves. Performance was assessed on 73 clinical bronchoalveolar lavage (BAL) samples from patients suspected of IMI. Novel curves were identified by micropipetting U-dHRM reactions and Sanger sequencing amplicons. Results U-dHRM achieved an average of 97% fungal organism identification accuracy and a turn-around-time of 4hrs. Pathogenic molds (Aspergillus, Mucorales, Lomentospora and Fusarium) were detected by U-dHRM in 73% of BALF samples suspected of IMI. Mixtures of pathogenic molds were detected in 19%. U-dHRM demonstrated good sensitivity for IMI, as defined by current diagnostic criteria, when clinical findings were also considered. Conclusions U-dHRM showed promising performance as a separate or combination diagnostic approach to standard mycological tests. The speed of U-dHRM and its ability to simultaneously identify and quantify clinically relevant mold pathogens in polymicrobial samples as well as detect emerging opportunistic pathogens may provide information that could aid in treatment decisions and improve patient outcomes.
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Affiliation(s)
- Tyler Goshia
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - April Aralar
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Nathan Wiederhold
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Jeffrey D. Jenks
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham County Department of Public Health, Durham, NC, USA
| | - Sanjay R. Mehta
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- San Diego Veterans Administration Medical Center, San Diego, CA, USA
| | | | | | | | | | - Haoxiang Sun
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - P. Lewis White
- Public Health Wales Microbiology Cardiff, and Cardiff University Centre for Trials Research/Division of Infection/Immunity, University Hospital of Wales, Cardiff, United Kingdom
| | - Martin Hoenigl
- Department of Medicine, Medical University of Graz, Graz, Austria
| | - Stephanie I. Fraley
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
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23
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Nenciarini S, Cavalieri D. Immunomodulatory Potential of Fungal Extracellular Vesicles: Insights for Therapeutic Applications. Biomolecules 2023; 13:1487. [PMID: 37892168 PMCID: PMC10605264 DOI: 10.3390/biom13101487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Extracellular vesicles (EVs) are membranous vesicular organelles that perform a variety of biological functions including cell communication across different biological kingdoms. EVs of mammals and, to a lesser extent, bacteria have been deeply studied over the years, whereas investigations of fungal EVs are still in their infancy. Fungi, encompassing both yeast and filamentous forms, are increasingly recognized for their production of extracellular vesicles (EVs) containing a wealth of proteins, lipids, and nucleic acids. These EVs play pivotal roles in orchestrating fungal communities, bolstering pathogenicity, and mediating interactions with the environment. Fungal EVs have emerged as promising candidates for innovative applications, not only in the management of mycoses but also as carriers for therapeutic molecules. Yet, numerous questions persist regarding fungal EVs, including their mechanisms of generation, release, cargo regulation, and discharge. This comprehensive review delves into the present state of knowledge regarding fungal EVs and provides fresh insights into the most recent hypotheses on the mechanisms driving their immunomodulatory properties. Furthermore, we explore the considerable potential of fungal EVs in the realms of medicine and biotechnology. In the foreseeable future, engineered fungal cells may serve as vehicles for tailoring cargo- and antigen-specific EVs, positioning them as invaluable biotechnological tools for diverse medical applications, such as vaccines and drug delivery.
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Affiliation(s)
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy;
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24
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Yoo IY, Park YJ. Culture-independent diagnostic approaches for invasive aspergillosis in solid organ transplant recipients. KOREAN JOURNAL OF TRANSPLANTATION 2023; 37:155-164. [PMID: 37751964 PMCID: PMC10583980 DOI: 10.4285/kjt.23.0043] [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: 07/31/2023] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023] Open
Abstract
Prompt and accurate diagnosis of invasive aspergillosis (IA) is crucial for immunocompromised patients, including those who have received a solid organ transplant (SOT). Despite their low sensitivity, microscopic detection and conventional culture are considered the 'gold standard' methods. In conjunction with conventional culture, culture-independent assays such as serum galactomannan testing and Aspergillus polymerase chain reaction (PCR) have been incorporated into the diagnostic process for IA. The recently revised consensus definitions from the European Organization for Research and Treatment of Cancer and the Mycosis Study Group have adjusted the threshold for positive galactomannan testing based on the sample type, and have excluded 1,3-β-D-glucan testing as a mycological criterion. Following extensive standardization efforts, positive Aspergillus PCR tests using serum, plasma, or bronchoalveolar lavage fluid have been added. However, there are limited studies evaluating the clinical utility of these culture-independent assays for the early diagnosis of IA in SOT recipients. Therefore, further research is required to determine whether these assays could aid in the early diagnosis of IA in SOT recipients, particularly in relation to the organ transplanted. In this review, we examine the culture-independent diagnostic methods for IA in SOT recipients, as well as the clinical utility of these assays.
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Affiliation(s)
- In Young Yoo
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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25
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Shafiee F, Soltani R, Meidani M. Invasive fungal infections in hematologic malignancies: Incidence, management, and antifungal therapy. JOURNAL OF RESEARCH IN MEDICAL SCIENCES : THE OFFICIAL JOURNAL OF ISFAHAN UNIVERSITY OF MEDICAL SCIENCES 2023; 28:73. [PMID: 38116484 PMCID: PMC10729687 DOI: 10.4103/jrms.jrms_1072_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 06/25/2023] [Accepted: 07/17/2023] [Indexed: 12/21/2023]
Abstract
The incidence of invasive fungal infections (IFIs) has increased in recent years as a result of increasing the incidence of hematologic malignancies (HMs). IFIs, as the opportunistic diseases, are the most important concern in these patients with a high mortality rate. These infections are one of the leading causes of morbidity and mortality in HM patients and an important factor in increasing the costs of patients' management because of the prolonged hospitalization and the inevitable need to use antifungal agents. Due to the changes in the pattern of organisms causing IFIs, unavailability of effective and safe antifungal drugs, and high rate of drug resistance as well as lack of fast and accurate diagnostic methods, these infections have become a serious and life-threatening problem necessitating effective prevention and treatment strategies using suitable antifungal agents, especially in high-risk patients. The aim of the present study was to review the pathogens causing various types of IFIs, diagnostic methods, and novel prophylactic and therapeutic antifungal regimens in HM patients according to the new published studies and clinical trials.
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Affiliation(s)
- Fatemeh Shafiee
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasool Soltani
- Department of Clinical Pharmacy and Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohsen Meidani
- Department of Infectious Diseases, Imam Khomeini Hospital, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
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26
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Lusida M, Arifijanto MV, Rachman BE, Alkaff FF. Difficulty in management of acute invasive fungal rhinosinusitis in Indonesia during the COVID-19 pandemic: A case report. Respir Med Case Rep 2023; 46:101916. [PMID: 38046461 PMCID: PMC10689262 DOI: 10.1016/j.rmcr.2023.101916] [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: 04/20/2023] [Revised: 08/22/2023] [Accepted: 09/06/2023] [Indexed: 12/05/2023] Open
Abstract
Invasive fungal rhinosinusitis is a rare disease with a high morbidity and mortality rate. Lately, COVID-19 has been associated with an increased incidence of this disease. We present the first case of COVID-19-associated acute invasive fungal rhinosinusitis found in Indonesia. The risk factors for the disease include corticosteroid use and antibiotic use. The case was complicated with left orbital cellulitis and cerebral abscess. Difficulty of management in Indonesia during the COVID-19 pandemic includes hesitancy of the patient to seek medical care and the availability of surgical team for COVID-19-positive patients. Monitoring of corticosteroid and antibiotic use must be emphasized during the pandemic. Awareness of the disease needs to be increased in Indonesia.
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Affiliation(s)
- Michael Lusida
- Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga-Dr. Soetomo General Hospital, Surabaya, 60286, Indonesia
| | - M. Vitanata Arifijanto
- Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga-Dr. Soetomo General Hospital, Surabaya, 60286, Indonesia
- Division of Tropical Medicine and Infectious Disease, Faculty of Medicine, Universitas Airlangga-Dr. Soetomo General Hospital, Surabaya, 60286, Indonesia
| | - Brian Eka Rachman
- Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga-Dr. Soetomo General Hospital, Surabaya, 60286, Indonesia
- Division of Tropical Medicine and Infectious Disease, Faculty of Medicine, Universitas Airlangga-Dr. Soetomo General Hospital, Surabaya, 60286, Indonesia
| | - Firas Farisi Alkaff
- Division of Pharmacology and Therapy, Department of Anatomy, Histology, And Pharmacology, Faculty of Medicine Universitas Airlangga, Surabaya, East Java 60132, Indonesia
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, the Netherlands
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27
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Al Hajri H, Al-Salmi W, Al Hinai K, Al-Housni S, Al-Harrasi A, Al Hashami H, Al-Hatmi AM. Invasive fungal infections in children with leukemia in a tertiary hospital in Oman: An eight-year review. Curr Med Mycol 2023; 9:16-22. [PMID: 38361957 PMCID: PMC10864744 DOI: 10.22034/cmm.2023.345108.1447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/11/2023] [Accepted: 12/02/2023] [Indexed: 02/17/2024] Open
Abstract
Background and Purpose Invasive fungal disease (IFD) is a common and serious consequence of leukemia in children and the incidence of these infections has increased due to chemotherapy. This study aimed to present the epidemiology of IFD in a cohort of children with leukemia from a tertiary reference institution in Oman. Materials and Methods A retrospective study of IFDs in pediatric patients below 13 years of age with newly diagnosed or relapsed leukemia was conducted at the Royal Hospital in Muscat, Oman. From 2010 to 2017, IFD episodes in children with leukemia were evaluated retrospectively, considering age, gender, type of leukemia, chemotherapy regimen, IFD detection phase, neutropenia, prevention, diagnostic method, and treatment. Results Between 2010 and 2017, 198 children with leukemia were admitted and treated at Royal Hospital. Invasive fungal infection (IFI) was diagnosed in 32 patients out of 198 (16.1%), and IFI was defined as probable and proven in 53% (n=17) and 47% (n=15) of the cases, respectively. At 1.1:1, the male-to-female ratio was roughly equal. According to chest computed tomography scans, 65.6% of patients had radiological features of fungal infections. Positive fungal cultures were found in the bronchoalveolar lavage of three patients, 37.5% of whom had positive blood cultures, and 3% had positive urine cultures as a neonatal invasive candidiasis. In three patients, invasive aspergillosis caused pulmonary IFD, accounting for 9.3% of all infection sites. Candidaemia was found in 28% of IFD patients, and the most common organism was Candida tropicalis (15.6%), followed by Candida parapsilosis (6.25%). Furthermore, the major risk factor was febrile neutropenia. Conclusion In children with leukemia, invasive fungal infection is common and serious. Despite aggressive treatment, mortality among these high-risk patients remains high.
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Affiliation(s)
| | | | - Karima Al Hinai
- Department of Paediatric Haematology and Oncology, Royal Hospital, Muscat, Oman
| | - Saif Al-Housni
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
| | - Hilal Al Hashami
- Department of Paediatrics Infectious Disease, Royal Hospital, Muscat, Oman
| | - Abdullah M.S. Al-Hatmi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
- Center of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
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28
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AlMaghrabi RS, Al-Musawi T, Albaksami O, Subhi AL, Fakih RE, Stone NR. Challenges in the Management of Invasive Fungal Infections in the Middle East: Expert Opinion to Optimize Management Using a Multidisciplinary Approach. Cureus 2023; 15:e44356. [PMID: 37779746 PMCID: PMC10539715 DOI: 10.7759/cureus.44356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2023] [Indexed: 10/03/2023] Open
Abstract
Invasive fungal infection (IFI) is a significant global healthcare concern among critically ill and immunocompromised patients. In Middle Eastern countries, IFI has been steadily increasing among hospitalized patients in the past two decades. Diagnosis of IFI at an early stage is crucial for efficient management. Invasive fungal infection management is complex and requires the involvement of physicians from different specialties. There are several challenges associated with IFI management in the countries in the Middle East. This review aims to understand the key challenges associated with IFI management in the Middle East, encompassing epidemiology, diagnosis, therapeutic options, and optimizing a multidisciplinary approach. In addition, this review aims to incorporate expert opinions from multidisciplinary fields for optimizing IFI management in different Middle Eastern countries by addressing key decision points throughout the patient's journey. Lack of epidemiological data on fungal infections, slow and poorly sensitive conventional culture-based diagnostic tests, limited availability of biomarker testing, lack of awareness of clinical symptoms of the disease, limited knowledge on fungal infections, lack of local practice guidelines, and complicated disease management are the major challenges associated with IFI diagnosis and management in the Middle Eastern countries. Implementation of a multidisciplinary approach, antifungal stewardship, improved knowledge of fungal infections, the use of rapid diagnostic tests, and enhanced epidemiological research are warranted to lower the IFI burden in the Middle East.
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Affiliation(s)
- Reem S AlMaghrabi
- Department of Medicine, Organ Transplant Center, King Faisal Specialist Hospital and Research Centre, Riyadh, SAU
| | - Tariq Al-Musawi
- Department of Critical Care Medicine, Al Salam Hospital, Al-Khobar, SAU
- Department of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, BHR
| | - Osama Albaksami
- Department of Infectious Diseases, Infectious Disease Hospital, Kuwait City, KWT
| | - Ahmad L Subhi
- Department of Infectious Diseases, Al-Qassimi Hospital, Sharjah, ARE
| | - Riad E Fakih
- Department of Hematology, King Faisal Specialist Hospital and Research Centre, Riyadh, SAU
- Department of Clinical Research, Alfaisal University, Riyadh, SAU
| | - Neil R Stone
- Department of Microbiology, Hospital for Tropical Diseases, London, GBR
- Department of Microbiology, University College London Hospitals, London, GBR
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29
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Jabrodini A, Sohrabizdeh M, Aboutalebian S, Hashemi SB, Zomorodian K, Alirezaie A, Rasti Jahromi M, Shamsdin SN, Motamedi M. Molecular strategy for the direct detection and identification of the most common fungal community in cerumen specimens by multiplex PCR. J Med Microbiol 2023; 72. [PMID: 37624031 DOI: 10.1099/jmm.0.001746] [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: 08/26/2023] Open
Abstract
Introduction. Otomycosis is a superficial fungal infection that is responsible for approximately 9-27 % of otitis externa. However, fungal communities in otomycosis are varied, but Aspergillus spp. and Candida spp. are the most common causes of this infection.Hypothesis Statement. The multiplex PCR assay is postulated to be able to directly detect more than one fungal genus in cerumen specimens.Aim. This study aimed to develop and evaluate the role of the multiplex PCR assay in detecting the most common genus of fungi that cause otomycosis directly from the cerumen specimens.Methodology. To detect Candida and Aspergillus/Penicillium genera, three pairs of primers, including pan-fungal, pan-Candida, and pan-Aspergillus/Penicillium, were used in a multiplex PCR. In order to evaluate the performance and reproducibility of the multiplex PCR. the cerumen of 140 patients suspected of otomycosis were investigated.Results. Pan-Candida and pan-Aspergillus/Penicillium primers were designed to amplify the ITS1-5.8S-ITS2 region and the β-tubulin gene, respectively. In the multiplex PCR assay, 64 (47.40 %) and 118 (87.40 %) specimens were positive with pan-Candida and pan-Aspergillus/Penicillium primers, respectively. Double amplicon bands of Candida and Aspergillus were obtained in 51 (37.77 %) specimens. In the culture method, yeast (n=18, 13.33 %) and mould (n=117, 86.66 %) were isolated from 135 cerumen specimens. The sensitivity, specificity, and positive and negative predictive values of the multiplex PCR assays using culture method results as the gold standard were determined to be 94, 33, 97, and 22 %, respectively.Conclusion. In our study, multiplex PCR assays enabled simultaneous detection of two common genera of the causative agent of otomycosis in a cerumen specimen. Regarding the high sensitivity of the first step of the multiplex PCR assay, this assay may be used for the direct detection of Candida and Aspergillus genera in other clinical specimens.
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Affiliation(s)
- Ahmad Jabrodini
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Sohrabizdeh
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Aboutalebian
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Basir Hashemi
- Otolaryngology Research Center, Department of Otolaryngology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamiar Zomorodian
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arefeh Alirezaie
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mona Rasti Jahromi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyedeh Neda Shamsdin
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Marjan Motamedi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Kianipour S, Dehghan P, Emami Ardestani M. Detection of Opportunistic Fungi from the Bronchoalveolar Lavage Specimens of Patients with Pulmonary Diseases. Adv Biomed Res 2023; 12:176. [PMID: 37694245 PMCID: PMC10492593 DOI: 10.4103/abr.abr_297_22] [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: 09/05/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 09/12/2023] Open
Abstract
Background Opportunistic fungi are a constantly evolving group of pathogens that become active when the immune system is compromised, begin to multiply, and soon overwhelm the weakened immune system. This study was performed to evaluate the number of opportunistic fungi in bronchoalveolar lavage (BAL) samples of patients with pulmonary diseases. Materials and Methods After receiving patients' consent and demographic forms, a total of 120 BAL samples were taken by a pulmonary physician. The etiologic agents were identified by standard morphological and molecular methods. Yeast cells were counted on culture media, and direct smears were precisely examined for the presence of yeasts elements, Pneumocystis, and filamentous fungi. Results In this study, 29 (24.1%) patients showed positive direct smears for yeast elements in their BAL samples. The mean colony count of yeasts was 42,000 (CFU/mL) on culture media. Six (5%) species of filamentous fungi, including three (2.5%) isolates of Penicillium species (P. variabile, P. glabrum, and P. thomii), two (1.67%) Aspergillus species (A. flavus and A. fumigatus), 1 case (0.83%) Pseudallescheria boydii were detected. Seven cases (5.83%) of Pneumocystis cysts were observed in the direct smears stained with Giemsa. Identification of all fungi confirmed by molecular or sequencing methods. Conclusions Due to the presence of a large number of fungi in the BAL samples and possible physical interference with the selected drugs for treatment, we draw the attention of pulmonologists to this important issue. Rapid diagnosis of fungal infections is essential to optimize treatments and outcomes.
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Affiliation(s)
- Sahar Kianipour
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Parvin Dehghan
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Emami Ardestani
- Department of Internal Medicine, School of Medicine, Al-Zahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
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Fang W, Wu J, Cheng M, Zhu X, Du M, Chen C, Liao W, Zhi K, Pan W. Diagnosis of invasive fungal infections: challenges and recent developments. J Biomed Sci 2023; 30:42. [PMID: 37337179 DOI: 10.1186/s12929-023-00926-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/13/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. MAIN TEXT A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. CONCLUSION The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.
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Affiliation(s)
- Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Mingrong Cheng
- Department of Anorectal Surgery, The Third Affiliated Hospital of Guizhou Medical University, Guizhou, 558000, China
| | - Xinlin Zhu
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Mingwei Du
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Kangkang Zhi
- Department of Vascular and Endovascular Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
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Felix GN, de Freitas VLT, da Silva Junior AR, Magri MMC, Rossi F, Sejas ONE, Abdala E, Malbouisson LMS, Guimarães T, Benard G, Del Negro GMB. Performance of a Real-Time PCR Assay for the Detection of Five Candida Species in Blood Samples from ICU Patients at Risk of Candidemia. J Fungi (Basel) 2023; 9:635. [PMID: 37367571 DOI: 10.3390/jof9060635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/22/2023] [Accepted: 05/13/2023] [Indexed: 06/28/2023] Open
Abstract
The gold standard for diagnosing invasive candidiasis still relies on blood cultures, which are inefficient and time-consuming to analyze. We developed an in-house qPCR assay to identify the 5 major Candida species in 78 peripheral blood (PB) samples from ICU patients at risk of candidemia. Blood cultures and (1,3)-β-D-glucan (BDG) testing were performed concurrently to evaluate the performance of the qPCR. The qPCR was positive for DNA samples from all 20 patients with proven candidemia (positive PB cultures), showing complete concordance with Candida species identification in blood cultures, except for detection of dual candidemia in 4 patients, which was missed by blood cultures. Additionally, the qPCR detected Candida species in six DNA samples from patients with positive central venous catheters blood (CB) but negative PB cultures. BDG values were similarly high in these six samples and the ones with proven candidemia, strongly suggesting the diagnosis of a true candidemia episode despite the negative PB cultures. Samples from patients neither infected nor colonized yielded negative results in both the qPCR and BDG testing. Our qPCR assay was at least as sensitive as blood cultures, but with a shorter turnaround time. Furthermore, negative results from the qPCR provided strong evidence for the absence of candidemia caused by the five major Candida species.
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Affiliation(s)
- Gabriel N Felix
- Laboratory of Medical Mycology (LIM 53), Instituto de Medicina Tropical, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-000, Brazil
| | - Vera L T de Freitas
- Laboratório de Investigação Médica em Imunologia (LIM 48), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-000, Brazil
| | - Afonso R da Silva Junior
- Central Laboratory Division (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-010, Brazil
| | - Marcello M C Magri
- Central Laboratory Division (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-010, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Flavia Rossi
- Central Laboratory Division (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-010, Brazil
| | - Odeli N E Sejas
- Cancer Institute of São Paulo State (ICESP), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 01246-000, Brazil
| | - Edson Abdala
- Cancer Institute of São Paulo State (ICESP), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 01246-000, Brazil
| | - Luiz M S Malbouisson
- Discipline of Anesthesiology, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Thais Guimarães
- Infectious Diseases Department, Hospital do Servidor Público Estadual de São Paulo (IAMSPE), São Paulo 04029-000, Brazil
| | - Gil Benard
- Laboratory of Medical Mycology (LIM 53), Instituto de Medicina Tropical, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-000, Brazil
| | - Gilda M B Del Negro
- Laboratory of Medical Mycology (LIM 53), Instituto de Medicina Tropical, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP), São Paulo 05403-000, Brazil
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Lionakis MS. Exploiting antifungal immunity in the clinical context. Semin Immunol 2023; 67:101752. [PMID: 37001464 PMCID: PMC10192293 DOI: 10.1016/j.smim.2023.101752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Indexed: 03/31/2023]
Abstract
The continuous expansion of immunocompromised patient populations at-risk for developing life-threatening opportunistic fungal infections in recent decades has helped develop a deeper understanding of antifungal host defenses, which has provided the foundation for eventually devising immune-based targeted interventions in the clinic. This review outlines how genetic variation in certain immune pathway-related genes may contribute to the observed clinical variability in the risk of acquisition and/or severity of fungal infections and how immunogenetic-based patient stratification may enable the eventual development of personalized strategies for antifungal prophylaxis and/or vaccination. Moreover, this review synthesizes the emerging cytokine-based, cell-based, and other immunotherapeutic strategies that have shown promise as adjunctive therapies for boosting or modulating tissue-specific antifungal immune responses in the context of opportunistic fungal infections.
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Affiliation(s)
- Michail S Lionakis
- From the Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Xie S, Lai Z, Xia H, Tang M, Lai J, Liu Q, Lu Z, He D, Qi J, Liu X. A case report of brainstem hemorrhage due to Rhizopus delemar-induced encephalitis diagnosed by metagenomic next-generation sequencing (mNGS). BMC Infect Dis 2023; 23:235. [PMID: 37069515 PMCID: PMC10107577 DOI: 10.1186/s12879-023-08192-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/23/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Rhizopus delemar is an invasive fungal pathogen that can cause fatal mucormycosis in immunodeficient individuals. Encephalitis caused by R. delemar is rare and difficult to diagnose early. Clinical detection methods for R. delemar include blood fungal culture, direct microscopic examination, and histopathological examination, but the detection is often inadequate for clinical diagnosis and can easily lead to missed diagnosis with delayed treatment. CASE PRESENTATION We report a case of a 47-year-old male with brainstem hemorrhage caused by encephalitis due to R. delemar. The patient had a history of hypertension, type 2 diabetes, and irregular medication. No pathogens were detected in cerebrospinal fluid (CSF) and nasopharyngeal secretion cultures. R. delemar was identified by metagenomic next-generation sequencing (mNGS) in CSF, and in combination with the patient's clinical characteristics, encephalitis caused by R. delemar was diagnosed. Antibiotic treatment using amphotericin B liposome in combination with posaconazole was given immediately. However, due to progressive aggravation of the patient's symptoms, he later died due to brainstem hemorrhage after giving up treatment. CONCLUSIONS mNGS technique is a potential approach for the early diagnosis of infections, which can help clinicians provide appropriate antibiotic treatments, thus reducing the mortality and disability rate of patients.
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Affiliation(s)
- Shuhua Xie
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Zhaohui Lai
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd, Beijing, 100176, China
| | - Mingze Tang
- Department of Scientific Affairs, Hugobiotech Co., Ltd, Beijing, 100176, China
| | - Jinxing Lai
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Qing Liu
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Zhijuan Lu
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Dehai He
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Jiangli Qi
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China
| | - Xianghong Liu
- Department of Neurology, Ganzhou People's Hospital, Jiangxi, 341000, China.
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He B, Yang Q. Updates in Laboratory Identification of Invasive Fungal Infection in Neonates. Microorganisms 2023; 11:1001. [PMID: 37110424 PMCID: PMC10145787 DOI: 10.3390/microorganisms11041001] [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: 03/10/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Invasive fungal infection (IFI) in immunocompromised neonates is significantly associated with high morbidity and mortality and has become the third most common infection in Neonatal Intensive Care Units. The early diagnosis of IFI for neonatal patients is difficult because of the lack of specific symptoms. The traditional blood culture remains the gold standard in clinical diagnosis for neonatal patients but it requires a long duration, which delays treatment initiation. Detections of fungal cell-wall components are developed for early diagnosis but the diagnostic accuracy in neonates needs to be improved. PCR-based laboratory methods, such as real-time PCR, droplet digital PCR, and the cationic conjugated polymer fluorescence resonance energy transfer (CCP-FRET) system, distinguish the infected fungal species by their specific nucleic acids and show a high sensitivity and specificity. Particularly, the CCP-FRET system, which contains a cationic conjugated polymer (CCP) fluorescent probe and pathogen-specific DNA labeled with fluorescent dyes, could identify multiple infections simultaneously. In the CCP-FRET system, the CCP and fungal DNA fragments can self-assemble into a complex with an electrostatic interaction and the CCP triggers the FRET effect under ultraviolet light to make the infection visible. Here, we summarize the recent laboratory methods for neonatal IFI identification and provide a new perspective for early clinical fungal diagnosis.
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Affiliation(s)
| | - Qiong Yang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China;
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Codreanu SI, Ciurea CN. Candida spp. DNA Extraction in the Age of Molecular Diagnosis. Microorganisms 2023; 11:microorganisms11040818. [PMID: 37110241 PMCID: PMC10143247 DOI: 10.3390/microorganisms11040818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
The standard procedure for the detection of candidemia is blood culture, a method that might require 3-5 days for a positive result. Compared with culturing, molecular diagnosis techniques can provide faster diagnosis. The current paper aimed to present the main strengths and constraints of current molecular techniques for Candida spp. DNA extraction, analyzing their efficiency from a time, price, and ease of usage point of view. A comprehensive search was conducted using the PubMed NIH database for peer-reviewed full-text articles published before October 2022. The studies provided adequate data on the diagnosis of the infection with the Candida spp. DNA extraction is a relevant step in yielding pure qualitative DNA to be amplified in molecular diagnostic techniques. The most used fungal DNA extraction strategies are: mechanical (bead beating, ultrasonication, steel-bullet beating), enzymatic (proteinase K, lysozyme, lyticase), and chemical extraction (formic acid, liquid nitrogen, ammonium chloride). More clinical studies are needed to formulate adequate guidelines for fungal DNA extraction as the current paper highlighted discrepancies in the reported outcome.
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Affiliation(s)
- Smaranda Ioana Codreanu
- Faculty of Medicine, "George Emil Palade" University of Medicine, Pharmacy, Sciences and Technology of Târgu Mures, 38 Gheorghe Marinescu Street, 540139 Târgu Mures, Romania
| | - Cristina Nicoleta Ciurea
- Department of Microbiology, Faculty of Medicine, "George Emil Palade" University of Medicine, Pharmacy, Sciences and Technology of Târgu Mures, 38 Gheorghe Marinescu Street, 540139 Târgu Mures, Romania
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Loubet D, Sarton B, Lelièvre L, Grouteau G, Iriart X, Chauvin P, Fillaux J, Valentin A, Berry A, Silva S, Bonneville F, Cassaing S, Guemas E. Fatal mucormycosis and aspergillosis coinfection associated with haemophagocytic lymphohistiocytosis: A case report and literature review. J Mycol Med 2023; 33:101325. [PMID: 36270214 DOI: 10.1016/j.mycmed.2022.101325] [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: 01/24/2022] [Revised: 07/08/2022] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
Invasive mould infections are life-threatening and mainly occur in immunocompromised patients. Whereas aspergillosis is described during haemophagocytic lymphohistiocytosis (HLH), only a few cases of concomitant mucormycosis with HLH have been reported. Here, we present an uncommon coinfection of mucormycosis and aspergillosis associated with HLH probably due to a varicella zoster virus (VZV) viraemia which was unresponsive to triple antifungal therapy (liposomal amphotericin B combined with isavuconazole and caspofungin). A review of the cases of mucormycosis with HLH showed that this uncommon association was always lethal and underscored the relevance of screening for mould infections in patients with HLH.
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Affiliation(s)
- Dorian Loubet
- Department of Parasitology and Mycology, CHU Toulouse, Toulouse, France
| | - Benjamine Sarton
- Critical Care Unit, University Hospital of Purpan, Toulouse, France; Toulouse NeuroImaging Center, Unité Mixte de Recherche 1214, Institut National de la Santé et de la Recherche Médicale, Université Paul Sabatier, Toulouse, France
| | - Lucie Lelièvre
- Department of Infectious and Tropical Diseases, CHU Toulouse, Toulouse, France
| | - Gaspard Grouteau
- Department of Infectious and Tropical Diseases, CHU Toulouse, Toulouse, France
| | - Xavier Iriart
- Department of Parasitology and Mycology, CHU Toulouse, Toulouse, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse, CNRS UMR5051, INSERM UMR1291, UPS, Toulouse, France
| | - Pamela Chauvin
- Department of Parasitology and Mycology, CHU Toulouse, Toulouse, France
| | - Judith Fillaux
- Department of Parasitology and Mycology, CHU Toulouse, Toulouse, France
| | - Alexis Valentin
- Department of Parasitology and Mycology, CHU Toulouse, Toulouse, France; PHARMA-Dev, UMR 152 IRD-UPS, Université Toulouse, France
| | - Antoine Berry
- Department of Parasitology and Mycology, CHU Toulouse, Toulouse, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse, CNRS UMR5051, INSERM UMR1291, UPS, Toulouse, France
| | - Stein Silva
- Critical Care Unit, University Hospital of Purpan, Toulouse, France; Toulouse NeuroImaging Center, Unité Mixte de Recherche 1214, Institut National de la Santé et de la Recherche Médicale, Université Paul Sabatier, Toulouse, France
| | - Fabrice Bonneville
- Neuroradiology Department, Pierre-Paul-Riquet/Purpan University Hospital, Toulouse, France
| | - Sophie Cassaing
- Department of Parasitology and Mycology, CHU Toulouse, Toulouse, France; RESTORE Institute, UMR 1301-Inserm 5070-CNRS EFS Univ. P. Sabatier, Toulouse, France
| | - Emilie Guemas
- Department of Parasitology and Mycology, CHU Toulouse, Toulouse, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse, CNRS UMR5051, INSERM UMR1291, UPS, Toulouse, France.
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Polymer-based particles against pathogenic fungi: A non-uptake delivery of compounds. BIOMATERIALS ADVANCES 2023; 146:213300. [PMID: 36708684 DOI: 10.1016/j.bioadv.2023.213300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/14/2022] [Accepted: 01/13/2023] [Indexed: 01/22/2023]
Abstract
The therapy of life-threatening fungal infections is limited and needs urgent improvement. This is in part due to toxic side effects of clinically used antifungal compounds or their limited delivery to fungal structures. Until today, it is a matter of debate how drugs or drug-delivery systems can efficiently reach the intracellular lumen of fungal cells and how this can be improved. Here, we addressed both questions by applying two different polymeric particles for delivery of compounds. Their formulation was based on two biocompatible polymers, i.e., poly(lactic-co-glycolic acid)50:50 and poly(methyl methacrylate-stat-methacrylic acid)90:10 yielding particles with hydrodynamic diameters ranging from 100 to 300 nm. The polymers were covalently labeled with the fluorescent dye DY-550 to monitor the interaction between particles and fungi by confocal laser scanning microscopy. Furthermore, the fluorescent dye coumarin-6 and the antifungal drug itraconazole were successfully encapsulated in particles to study the fate of both the cargo and the particle when interacting with the clinically most important human-pathogenic fungi Aspergillus fumigatus, A. terreus, Candida albicans, and Cryptococcus neoformans. While the polymers were exclusively located on the fungal surface, the encapsulated cargo was efficiently transported into fungal hyphae, indicated by increased intracellular fluorescence signals due to coumarin-6. In accordance with this finding, compared to the pristine drug a reduced minimal inhibitory concentration for itraconazole was determined, when it was encapsulated. Together, the herein used polymeric particles were not internalized by pathogenic fungi but were able to efficiently deliver hydrophobic cargos into fungal cells.
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Rozova V, Khanina A, Teng JC, Teh JSK, Worth LJ, Slavin MA, Thursky KA, Verspoor K. Detecting evidence of invasive fungal infections in cytology and histopathology reports enriched with concept-level annotations. J Biomed Inform 2023; 139:104293. [PMID: 36682389 DOI: 10.1016/j.jbi.2023.104293] [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: 07/04/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
Invasive fungal infections (IFIs) are particularly dangerous to high-risk patients with haematological malignancies and are responsible for excessive mortality and delays in cancer therapy. Surveillance of IFI in clinical settings offers an opportunity to identify potential risk factors and evaluate new therapeutic strategies. However, manual surveillance is both time- and resource-intensive. As part of a broader project aimed to develop a system for automated IFI surveillance by leveraging electronic medical records, we present our approach to detecting evidence of IFI in the key diagnostic domain of histopathology. Using natural language processing (NLP), we analysed cytology and histopathology reports to identify IFI-positive reports. We compared a conventional bag-of-words classification model to a method that relies on concept-level annotations. Although the investment to prepare data supporting concept annotations is substantial, extracting targeted information specific to IFI as a pre-processing step increased the performance of the classifier from the PR AUC of 0.84 to 0.92 and enabled model interpretability. We have made publicly available the annotated dataset of 283 reports, the Cytology and Histopathology IFI Reports corpus (CHIFIR), to allow the clinical NLP research community to further build on our results.
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Affiliation(s)
- Vlada Rozova
- School of Computing Technologies, RMIT University, Melbourne, Australia; School of Computing and Information Systems, University of Melbourne, Melbourne, Australia; National Centre for Infections in Cancer, Peter MacCallum, Cancer Centre, Melbourne, Australia.
| | - Anna Khanina
- 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, University of Melbourne, Melbourne, Australia
| | - Jasmine C Teng
- National Centre for Infections in Cancer, Peter MacCallum, Cancer Centre, Melbourne, Australia; Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Joanne S K Teh
- National Centre for Infections in Cancer, Peter MacCallum, Cancer Centre, Melbourne, Australia; Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Leon J Worth
- 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, University of Melbourne, Melbourne, Australia
| | - 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, University of Melbourne, Melbourne, Australia
| | - Karin A Thursky
- 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, University of Melbourne, Melbourne, Australia; National Centre for Antimicrobial Stewardship, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Karin Verspoor
- School of Computing Technologies, RMIT University, Melbourne, Australia; School of Computing and Information Systems, University of Melbourne, Melbourne, Australia.
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Marino A, Calvo M, Trovato L, Scalia G, Gussio M, Consoli U, Ceccarelli M, Nunnari G, Cacopardo B. Mucorales/ Fusarium Mixed Infection in Hematologic Patient with COVID-19 Complications: An Unfortunate Combination. Pathogens 2023; 12:pathogens12020304. [PMID: 36839576 PMCID: PMC9964160 DOI: 10.3390/pathogens12020304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/25/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Hematological diseases, especially those causing severe neutropenia, represent the main factor in the development of invasive fungal infections (IFIs). Furthermore, COVID-19 has been considerably associated with IFIs due to immunological dysregulation, prolonged hospitalization in intensive care units, and immunomodulatory therapies. Opportunistic molds are correlated with elevated morbidity and mortality rates in these patients, due to immune impairment, diagnostic complexity, and therapeutic challenges. Among opportunistic fungal infections, the Mucorales and Fusarium species are considered particularly aggressive, especially during severe neutropenia. A mixed Mucorales/Fusarium infection has been rarely described in scientific literature. Herein, we report a case of Mucorales and Fusarium co-infection in a patient with acute leukemia whose clinical history was also complicated by COVID-19. Herein, we report a challenging case in order to encourage the clinical suspicion of combined fungal infections in immunosuppressed patients, performing a punctual microbiological diagnosis, and promptly administering the correct empiric and targeted antifungal therapy.
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Affiliation(s)
- Andrea Marino
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, ARNAS Garibaldi Hospital, University of Catania, 95122 Catania, Italy
| | - Maddalena Calvo
- U.O.C. Laboratory Analysis Unit, A.O.U. “Policlinico-Vittorio Emanuele”, Via S. Sofia 78, 95123 Catania, Italy
- Correspondence:
| | - Laura Trovato
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
- U.O.C. Laboratory Analysis Unit, A.O.U. “Policlinico-Vittorio Emanuele”, Via S. Sofia 78, 95123 Catania, Italy
| | - Guido Scalia
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
- U.O.C. Laboratory Analysis Unit, A.O.U. “Policlinico-Vittorio Emanuele”, Via S. Sofia 78, 95123 Catania, Italy
| | - Maria Gussio
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, ARNAS Garibaldi Hospital, University of Catania, 95122 Catania, Italy
| | - Ugo Consoli
- Unità Operativa Complessa (UOC) di Ematologia, ARNAS Garibaldi Hospital, 95122 Catania, Italy
| | - Manuela Ceccarelli
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, ARNAS Garibaldi Hospital, University of Catania, 95122 Catania, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Bruno Cacopardo
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, ARNAS Garibaldi Hospital, University of Catania, 95122 Catania, Italy
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Takoutsing BD, Ooi SZY, Egu CB, Gillespie CS, Bandyopadhyay S, Dada OE, Dokponou YCH, Dalle DU, Ciuculete AC, Awad AK, Khan M, Erhabor J, Ikwuegbuenyi CA, Kesici Ö, Bankole NDA. Management and outcomes of intracranial fungal infections in children and adults in Africa: a scoping review protocol. BMJ Open 2023; 13:e065943. [PMID: 36731932 PMCID: PMC9896247 DOI: 10.1136/bmjopen-2022-065943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION The protocol presents the methodology of a scoping review that aims to synthesise contemporary evidence on the management and outcomes of intracranial fungal infections in Africa. METHODS AND ANALYSIS The scoping review will be conducted in accordance with the Arksey and O'Malley's framework. The research question, inclusion and exclusion criteria and search strategy were developed based on the Population, Intervention, Comparator, Outcome framework. A search will be conducted in electronic bibliographic databases (Medline (OVID), Embase, African Journals Online, Cochrane Library and African Index Medicus). No restrictions on language or date of publication will be made. Quantitative and qualitative data extracted from included articles will be presented through descriptive statistics and a narrative description. ETHICS AND DISSEMINATION This study protocol does not require ethical approval. Findings will be reported in a peer-reviewed medical journal and presented at local, regional, national and international conferences.
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Affiliation(s)
| | | | - Chinedu Brian Egu
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | - Conor S Gillespie
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | - Soham Bandyopadhyay
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | | | | | - David Ulrich Dalle
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | | | - Ahmed K Awad
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | - Mehdi Khan
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | - Joshua Erhabor
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
| | | | - Özgür Kesici
- Research Department, Association of Future African Neurosurgeons, Yaounde, Cameroon
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Crintea A, Carpa R, Mitre AO, Petho RI, Chelaru VF, Nădășan SM, Neamti L, Dutu AG. Nanotechnology Involved in Treating Urinary Tract Infections: An Overview. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:555. [PMID: 36770516 PMCID: PMC9919202 DOI: 10.3390/nano13030555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Considered as the most frequent contaminations that do not require hospitalization, urinary tract infections (UTIs) are largely known to cause significant personal burdens on patients. Although UTIs overall are highly preventable health issues, the recourse to antibiotics as drug treatments for these infections is a worryingly spread approach that should be addressed and gradually overcome in a contemporary, modernized healthcare system. With a virtually alarming global rise of antibiotic resistance overall, nanotechnologies may prove to be the much-needed 'lifebuoy' that will eventually suppress this prejudicial phenomenon. This review aims to present the most promising, currently known nano-solutions, with glimpses on clinical and epidemiological aspects of the UTIs, prospective diagnostic instruments, and non-antibiotic treatments, all of these engulfed in a comprehensive overview.
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Affiliation(s)
- Andreea Crintea
- Department of Medical Biochemistry, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania
| | - Rahela Carpa
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University, 400084 Cluj-Napoca, Romania
| | - Andrei-Otto Mitre
- Department of Pathophysiology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania
| | - Robert Istvan Petho
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania
| | - Vlad-Florin Chelaru
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania
| | - Sebastian-Mihail Nădășan
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania
| | - Lidia Neamti
- Department of Medical Biochemistry, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania
| | - Alina Gabriela Dutu
- Department of Medical Biochemistry, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania
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Wang J, Meng S, Lin K, Yi X, Sun Y, Xu X, He N, Zhang Z, Hu H, Qie X, Zhang D, Tang Y, Huang WE, He J, Song Y. Leveraging single-cell Raman spectroscopy and single-cell sorting for the detection and identification of yeast infections. Anal Chim Acta 2023; 1239:340658. [PMID: 36628751 DOI: 10.1016/j.aca.2022.340658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022]
Abstract
Invasive fungal infection serves as a great threat to human health. Discrimination between fungal and bacterial infections at the earliest stage is vital for effective clinic practice; however, traditional culture-dependent microscopic diagnosis of fungal infection usually requires several days, meanwhile, culture-independent immunological and molecular methods are limited by the detectable type of pathogens and the issues with high false-positive rates. In this study, we proposed a novel culture-independent phenotyping method based on single-cell Raman spectroscopy for the rapid discrimination between fungal and bacterial infections. Three Raman biomarkers, including cytochrome c, peptidoglycan, and nucleic acid, were identified through hierarchical clustering analysis of Raman spectra across 12 types of most common yeast and bacterial pathogens. Compared to those of bacterial pathogens, the single cells of yeast pathogens demonstrated significantly stronger Raman peaks for cytochrome c, but weaker signals for peptidoglycan and nucleic acid. A two-step protocol combining the three biomarkers was established and able to differentiate fungal infections from bacterial infections with an overall accuracy of 94.9%. Our approach was also used to detect ten raw urinary tract infection samples. Successful identification of fungi was achieved within half an hour after sample obtainment. We further demonstrated the accurate fungal species taxonomy achieved with Raman-assisted cell ejection. Our findings demonstrate that Raman-based fungal identification is a novel, facile, reliable, and with a breadth of coverage approach, that has a great potential to be adopted in routine clinical practice to reduce the turn-around time of invasive fungal disease (IFD) diagnostics.
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Affiliation(s)
- Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Kaicheng Lin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xiaofei Yi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 20040, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yixiang Sun
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 20040, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Na He
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhiqiang Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Huijie Hu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China
| | - Xingwang Qie
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Jian He
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China.
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Jiang S, Yan H, Lu X, Wei R, Chen H, Zhang A, Shi W, Xia L. How to improve the outcomes of elderly acute myeloid leukemia patients through allogeneic hematopoietic stem cell transplantation. Front Immunol 2023; 14:1102966. [PMID: 37207218 PMCID: PMC10189056 DOI: 10.3389/fimmu.2023.1102966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 04/19/2023] [Indexed: 05/21/2023] Open
Abstract
In recent years, with the gradual advancement of haploidentical transplantation technology, the availability of donors has increased significantly, along with the widespread use of reduced-intensity conditioning and the improvement of nursing techniques, giving more elderly acute myeloid leukemia (AML) patients the chance to receive allogeneic hematopoietic stem cell transplantation. We have summarized the classic and recently proposed pre-transplant assessment methods and assessed the various sources of donors, conditioning regimens, and post-transplant complication management based on the outcomes of large-scale clinical studies for elderly AML patients.
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Affiliation(s)
| | | | | | | | | | | | - Wei Shi
- *Correspondence: Linghui Xia, ; Wei Shi,
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45
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Malhotra S, Ranjan V, Suman C, Patil S, Malhotra A, Bhatia NK. Advanced Microbiological Diagnostic Techniques in Fungal Infections of the Central Nervous System. VIRAL AND FUNGAL INFECTIONS OF THE CENTRAL NERVOUS SYSTEM: A MICROBIOLOGICAL PERSPECTIVE 2023:419-463. [DOI: 10.1007/978-981-99-6445-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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Hounchonou FH, Runge J, Ganser A, Hartmann C, Raab P, Krauss JK. Stereotactic biopsy of a brain lesion caused by hormographiella aspergillata. Surg Neurol Int 2022; 13:596. [PMID: 36761261 PMCID: PMC9899447 DOI: 10.25259/sni_576_2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/30/2022] [Indexed: 01/01/2023] Open
Abstract
Background Invasive fungal infections are an increasing problem in immunosuppressed patients. In patients with the central nervous system involvement, there is a high case fatality rate. There is a very limited experience with infections caused by Hormographiella aspergillata (HA) in such cases and most often diagnosis is only confirmed postmortem. Case Description We report the case of a 53-year-old woman with acute myeloid leukemia. After primary therapy with daunorubicin, cytarabine, and gemtuzumab ozogamicin, the patient developed pneumonia and later neurological symptoms caused by multiple gadolinium-enhancing brain lesions in magnetic resonance imaging (MRI). Stereotactic biopsy of a frontal precentral lesion was performed and revealed HA infection. The patient died in the further course secondary to cardiopulmonary problems. Conclusion Stereotactic biopsy is a safe way to establish the diagnosis of unclear lesions such as HA infection. We recommend to perform stereotactic biopsy early in immunocompromised patients with brain lesions to guide further treatment.
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Affiliation(s)
- F. H. Hounchonou
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany.,Corresponding author: F. H. Hounchonou, Department of Neurosurgery, Hannover Medical School, Hannover, Germany.
| | - Joachim Runge
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
| | - Arnold Ganser
- Department of Haematology, Haemostaseology, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Christian Hartmann
- Department of Neuropathology, Hannover Medical School, Hannover, Germany
| | - Peter Raab
- Department of Institute for Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | - Joachim K. Krauss
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
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Lopes JP, Lionakis MS. Pathogenesis and virulence of Candida albicans. Virulence 2022; 13:89-121. [PMID: 34964702 PMCID: PMC9728475 DOI: 10.1080/21505594.2021.2019950] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 12/18/2022] Open
Abstract
Candida albicans is a commensal yeast fungus of the human oral, gastrointestinal, and genital mucosal surfaces, and skin. Antibiotic-induced dysbiosis, iatrogenic immunosuppression, and/or medical interventions that impair the integrity of the mucocutaneous barrier and/or perturb protective host defense mechanisms enable C. albicans to become an opportunistic pathogen and cause debilitating mucocutaneous disease and/or life-threatening systemic infections. In this review, we synthesize our current knowledge of the tissue-specific determinants of C. albicans pathogenicity and host immune defense mechanisms.
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Affiliation(s)
- José Pedro Lopes
- From the Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD, USA
| | - Michail S. Lionakis
- From the Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD, USA
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48
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Matzko ME, Sephton-Clark PCS, Young EL, Jhaveri TA, Martinsen MA, Mojica E, Boykin R, Pierce VM, Cuomo CA, Bhattacharyya RP. A novel rRNA hybridization-based approach to rapid, accurate Candida identification directly from blood culture. Med Mycol 2022; 60:6674770. [PMID: 36002024 PMCID: PMC9989835 DOI: 10.1093/mmy/myac065] [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: 06/21/2022] [Revised: 08/03/2022] [Accepted: 08/22/2022] [Indexed: 01/24/2023] Open
Abstract
Invasive fungal infections are increasingly common and carry high morbidity and mortality, yet fungal diagnostics lag behind bacterial diagnostics in rapidly identifying the causal pathogen. We previously devised a fluorescent hybridization-based assay to identify bacteria within hours directly from blood culture bottles without subculture, called phylogeny-informed rRNA-based strain identification (Phirst-ID). Here, we adapt this approach to unambiguously identify 11 common pathogenic Candida species, including C. auris, with 100% accuracy from laboratory culture (33 of 33 strains in a reference panel, plus 33 of 33 additional isolates tested in a validation panel). In a pilot study on 62 consecutive positive clinical blood cultures from two hospitals that showed yeast on Gram stain, Candida Phirst-ID matched the clinical laboratory result for 58 of 59 specimens represented in the 11-species reference panel, without misclassifying the 3 off-panel species. It also detected mixed Candida species in 2 of these 62 specimens, including the one discordant classification, that were not identified by standard clinical microbiology workflows; in each case the presence of both species was validated by both clinical and experimental data. Finally, in three specimens that grew both bacteria and yeast, we paired our prior bacterial probeset with this new Candida probeset to detect both pathogen types using Phirst-ID. This simple, robust assay can provide accurate Candida identification within hours directly from blood culture bottles, and the conceptual approach holds promise for pan-microbial identification in a single workflow. LAY SUMMARY Candida bloodstream infections cause considerable morbidity and mortality, yet slow diagnostics delay recognition, worsening patient outcomes. We develop and validate a novel molecular approach to accurately identify Candida species directly from blood culture one day faster than standard workflows.
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Affiliation(s)
- Michelle E Matzko
- Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Poppy C S Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Eleanor L Young
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Tulip A Jhaveri
- Microbiology Laboratory, Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Melanie A Martinsen
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Evan Mojica
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rich Boykin
- NanoString Technologies, Inc., Seattle, WA 98109, USA
| | - Virginia M Pierce
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Roby P Bhattacharyya
- Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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Mendonça A, Carvalho-Pereira J, Franco-Duarte R, Sampaio P. Optimization of a Quantitative PCR Methodology for Detection of Aspergillus spp. and Rhizopus arrhizus. Mol Diagn Ther 2022; 26:511-525. [PMID: 35710958 PMCID: PMC9202985 DOI: 10.1007/s40291-022-00595-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2022] [Indexed: 11/25/2022]
Abstract
Introduction Multiplex quantitative polymerase chain reaction (qPCR) methods for the detection of Aspergillus spp. based only on SYBR Green and melting curve analysis of PCR products are difficult to develop because most targets are located within ITS regions. The aim of this study was to adapt our previously developed methodology based on a multiplex PCR assay coupled with GeneScan analysis to provide a qPCR method. Methods A SYBR Green-based real-time PCR assay was optimized to detect A. fumigatus, A. flavus, A. niger, A. terreus, and R. arrhizus in a multiplex assay and applied to cultured fungi and spiked plasma. Results Different melting temperatures allowed identification of all five pathogens and discrimination between them, even in samples with low amounts of fungal gDNA (from 1.3 to 33.0 pg/μL), which has been reported previously as problematic. No false-positive results were obtained for non-target species, including bacteria and human DNA. This method allowed detection of fungal pathogens in human plasma spiked with fungal DNA and in coinfections of A. niger/R. arrhizus. Discussion This work provides evidence for the use of a qPCR multiplex method based on SYBR Green and melting curve analysis of PCR products for the detection of A. fumigatus, A. flavus, A. niger, A. terreus, and R. arrhizus. The proposed method is simpler and less expensive than available kits based on fluorescent probes and can be used for aiding diagnosis of the most relevant invasive filamentous fungi, particularly in low-income health care institutions. Supplementary Information The online version contains supplementary material available at 10.1007/s40291-022-00595-1.
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Affiliation(s)
- Alexandre Mendonça
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
| | - Joana Carvalho-Pereira
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.
| | - Paula Sampaio
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
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50
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Proceedings of the Clinical Microbiology Open 2018 and 2019 - a Discussion about Emerging Trends, Challenges, and the Future of Clinical Microbiology. J Clin Microbiol 2022; 60:e0009222. [PMID: 35638361 DOI: 10.1128/jcm.00092-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clinical Microbiology Open (CMO), a meeting supported by the American Society for Microbiology's Clinical and Public Health Microbiology Committee (CPHMC) and Corporate Council, provides a unique interactive platform for leaders from diagnostic microbiology laboratories, industry, and federal agencies to discuss the current and future state of the clinical microbiology laboratory. The purpose is to leverage the group's diverse views and expertise to address critical challenges, and discuss potential collaborative opportunities for diagnostic microbiology, through the utilization of varied resources. The first and second CMO meetings were held in 2018 and 2019, respectively. Discussions were focused on the diagnostic potential of innovative technologies and laboratory diagnostic stewardship, including expansion of next-generation sequencing into clinical diagnostics, improvement and advancement of molecular diagnostics, emerging diagnostics, including rapid antimicrobial susceptibility and point of care testing (POCT), harnessing big data through artificial intelligence, and staffing in the clinical microbiology laboratory. Shortly after CMO 2019, the coronavirus disease 2019 (COVID-19) pandemic further highlighted the need for the diagnostic microbiology community to work together to utilize and expand on resources to respond to the pandemic. The issues, challenges, and potential collaborative efforts discussed during the past two CMO meetings proved critical in addressing the COVID-19 response by diagnostic laboratories, industry partners, and federal organizations. Planning for a third CMO (CMO 2022) is underway and will transition from a discussion-based meeting to an action-based meeting. The primary focus will be to reflect on the lessons learned from the COVID-19 pandemic and better prepare for future pandemics.
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