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Hamburger FG, Gales AC, Colombo AL. Systematic Review of Candidemia in Brazil: Unlocking Historical Trends and Challenges in Conducting Surveys in Middle-Income Countries. Mycopathologia 2024; 189:60. [PMID: 38940953 DOI: 10.1007/s11046-024-00867-w] [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: 04/02/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024]
Abstract
INTRODUCTION Candidemia, a bloodstream infection predominantly affecting critically ill patients, poses a significant global health threat especially with the emergence of non-albicans Candida species, including drug-resistant strains. In Brazil, limited access to advanced diagnostic tools and trained microbiologists hampers accurate identification of Candida species and susceptibility to antifungals testing hindering surveillance efforts. METHODS We conducted a systematic review spanning publications from 2017 to 2023 addressing Candida species distribution and antifungal susceptibility among Brazilian patients with candidemia. RESULTS Despite initially identifying 7075 records, only 16 met inclusion criteria providing accurate information of 2305 episodes of candidemia. The predominant species were C. albicans, C. parapsilosis, and C. tropicalis, followed by notable proportions of Nakaseomyces glabratus. Limited access to diagnostic tests was evident as only 5 out of 16 studies on candidemia were able to report antifungal susceptibility testing results. In vitro resistance to echinocandins was rare (only 6/396 isolates, 1,5%). In counterpart, fluconazole exhibited resistance rates ranging from 0 to 43%, with great heterogeneity among different studies and species of Candida considered. CONCLUSION Our review underscores the critical need for enhanced surveillance and research efforts to address the evolving landscape of candidemia and antifungal resistance in Brazil. Despite some limitations, available data suggest that while resistance to echinocandins and amphotericin B remains rare, there is a growing concern regarding resistance to fluconazole among Candida species.
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Affiliation(s)
- Flávio Guinsburg Hamburger
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Ana Cristina Gales
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Antimicrobial Resistance Institute of São Paulo (Aries), São Paulo, Brazil
| | - Arnaldo Lopes Colombo
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil.
- Antimicrobial Resistance Institute of São Paulo (Aries), São Paulo, Brazil.
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Ionescu S, Luchian I, Damian C, Goriuc A, Porumb-Andrese E, Popa CG, Cobzaru RG, Ripa C, Ursu RG. Candida auris Updates: Outbreak Evaluation through Molecular Assays and Antifungal Stewardship-A Narrative Review. Curr Issues Mol Biol 2024; 46:6069-6084. [PMID: 38921033 PMCID: PMC11202268 DOI: 10.3390/cimb46060362] [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: 04/27/2024] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Candida auris was reported by the WHO as second to Cryptococcus neoformans, in the list of nineteen fungal priority pathogens, along with two species with a new nomenclature, Nakaseomyces glabrata (Candida glabrata) and Pichia kudriavzevii (Candida krusei). This novel classification was based on antifungal resistance, the number of deaths, evidence-based treatment, access to diagnostics, annual incidence, and complications and sequelae. We assessed which molecular assays have been used to diagnose Candida auris outbreaks in the last five years. Using "Candida auris; outbreak; molecular detection" as keywords, our search in PubMed revealed 32 results, from which we selected 23 original papers published in 2019-2024. The analyzed studies revealed that the detection methods were very different: from the VITEK® 2 System to MALDI TOF (Matrix-Assisted Laser Desorption Ionization-Time of Flight), NGS (Next-Generation Sequencing), WGS (Whole Genome Sequencing), and commercially available real-time PCR (Polymerase Chain Reaction) assays. Moreover, we identified studies that detected antifungal resistance genes (e.g., FKS for echinocandins and ERG11 for azoles). The analyzed outbreaks were from all continents, which confirms the capability of this yeast to spread between humans and to contaminate the environment. It is important that real-time PCR assays were developed for accurate and affordable detection by all laboratories, including the detection of antifungal resistance genes. This will allow the fast and efficient implementation of stewardship programs in hospitals.
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Affiliation(s)
- Silvia Ionescu
- Department of Preventive Medicine and Interdisciplinarity (IX), Microbiology, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania (R.G.U.)
| | - Ionut Luchian
- Department of Periodontology, Faculty of Dental Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
| | - Costin Damian
- Department of Preventive Medicine and Interdisciplinarity (IX), Microbiology, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania (R.G.U.)
| | - Ancuta Goriuc
- Department of Biochemistry, Faculty of Dental Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Elena Porumb-Andrese
- Department of Medical Specialties (III)—Discipline of Dermatology, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Cosmin Gabriel Popa
- Department of Anatomy, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Roxana Gabriela Cobzaru
- Department of Preventive Medicine and Interdisciplinarity (IX), Microbiology, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania (R.G.U.)
| | - Carmen Ripa
- Department of Preventive Medicine and Interdisciplinarity (IX), Microbiology, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania (R.G.U.)
| | - Ramona Gabriela Ursu
- Department of Preventive Medicine and Interdisciplinarity (IX), Microbiology, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania (R.G.U.)
- Microbiology Department, Gynecology and Obstetrics Hospital-Cuza Voda, 700038 Iasi, Romania
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Góralska K, Szybka M, Karuga FF, Pastuszak-Lewandoska D, Brzeziańska-Lasota E. Acquired resistance or tolerance? - in search of mechanisms underlying changes in the resistance profile of Candida albicans and Candida parapsilosis as a result of exposure to methotrexate. J Mycol Med 2024; 34:101476. [PMID: 38507825 DOI: 10.1016/j.mycmed.2024.101476] [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: 01/11/2024] [Revised: 02/29/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
The increasing prevalence of fungal strains showing acquired resistance and multidrug resistance is an increasing therapeutic problem, especially in patients with a severely weakened immune system and undergoing chemotherapy. What is also extremely disturbing is the similarity of the resistance mechanisms of fungal cells and other eukaryotic cells, including human cells, which may contribute to the development of cross-resistance in fungi in response to substances used in e.g. anticancer treatment. An example of such a drug is methotrexate, which is pumped out of eukaryotic cells by ABC transmembrane transporters - in fungi, used to remove azoles from fungal cells. For this reason, the aim of the study was to analyze the expression levels of genes: ERG11, MDR1 and CDR1, potentially responsible for the occurrence of cross-resistance in Candida albicans and Candida parapsilosis as a result of fungal exposure to methotrexate (MTX). In vitro exposure of C. albicans and C. parapsilosis strains to methotrexate showed a high increase in resistance to fluconazole and a partial increase in resistance to voriconazole. Analysis of the expression of resistance genes showed varied responses of the tested strains depending on the species. In the case of C. albicans, an increase in the expression of the MDR1 gene was observed, and a decrease in ERG11 and CDR1. However, for C. parapsilosis there was an increase in the expression of the CDR1 gene and a decrease in ERG11 and MDR1. We noted the relationship between the level of resistance to voriconazole and the level of ERG11 gene expression in C. albicans. This indicates that this type of relationship is different for each species. Our research confirms that the mechanisms by which fungi acquire resistance and develop cross-resistance are highly complex and most likely involve several pathways simultaneously. The emergence of multidrug resistance may be related to the possibility of developing tolerance to antimycotics by fungi.
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Affiliation(s)
- Katarzyna Góralska
- Department of Biology and Parasitology, Chair of Biology and Medical Microbiology, Medical University of Lodz. Żeligowskiego Street 7/9 90-752 Lodz, Poland.
| | - Małgorzata Szybka
- Department of Microbiology and Medical Laboratory Immunology, Chair of Biology and Medical Microbiology, Medical University of Lodz. Pomorska Street 251 (Building C5) 92-213 Lodz, Poland
| | - Filip Franciszek Karuga
- Department of Biology and Parasitology, Chair of Biology and Medical Microbiology, Medical University of Lodz. Żeligowskiego Street 7/9 90-752 Lodz, Poland; Department of Sleep Medicine and Metabolic Disorders, Medical University of Lodz, 90-419 Lodz, Poland
| | - Dorota Pastuszak-Lewandoska
- Department of Microbiology and Medical Laboratory Immunology, Chair of Biology and Medical Microbiology, Medical University of Lodz. Pomorska Street 251 (Building C5) 92-213 Lodz, Poland
| | - Ewa Brzeziańska-Lasota
- Department of Biomedicine and Genetics, Chair of Biology and Medical Microbiology, Medical University of Lodz. Mazowiecka Street 5 (Building A6) 92-215 Lodz, Poland
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Shahabudin S, Azmi NS, Lani MN, Mukhtar M, Hossain MS. Candida albicans skin infection in diabetic patients: An updated review of pathogenesis and management. Mycoses 2024; 67:e13753. [PMID: 38877612 DOI: 10.1111/myc.13753] [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: 03/15/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024]
Abstract
Candida species, commensal residents of human skin, are recognized as the cause of cutaneous candidiasis across various body surfaces. Individuals with weakened immune systems, particularly those with immunosuppressive conditions, are significantly more susceptible to this infection. Diabetes mellitus, a major metabolic disorder, has emerged as a critical factor inducing immunosuppression, thereby facilitating Candida colonization and subsequent skin infections. This comprehensive review examines the prevalence of different types of Candida albicans-induced cutaneous candidiasis in diabetic patients. It explores the underlying mechanisms of pathogenicity and offers insights into recommended preventive measures and treatment strategies. Diabetes notably increases vulnerability to oral and oesophageal candidiasis. Additionally, it can precipitate vulvovaginal candidiasis in females, Candida balanitis in males, and diaper candidiasis in young children with diabetes. Diabetic individuals may also experience candidal infections on their nails, hands and feet. Notably, diabetes appears to be a risk factor for intertrigo syndrome in obese individuals and periodontal disorders in denture wearers. In conclusion, the intricate relationship between diabetes and cutaneous candidiasis necessitates a comprehensive understanding to strategize effective management planning. Further investigation and interdisciplinary collaborative efforts are crucial to address this multifaceted challenge and uncover novel approaches for the treatment, management and prevention of both health conditions, including the development of safer and more effective antifungal agents.
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Affiliation(s)
- Sakina Shahabudin
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Pahang, Malaysia
| | - Nina Suhaity Azmi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Pahang, Malaysia
| | - Mohd Nizam Lani
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | | | - Md Sanower Hossain
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Pahang, Malaysia
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5
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Nie Y, Yin Y, Zhao H, Liu X, Huang B. Unveiling species diversity within the family Conidiobolaceae (Entomophthorales) in China: Descriptions of two new species and reassessment of the taxonomic position of Conidioboluspolyspermus. MycoKeys 2024; 105:203-216. [PMID: 38818111 PMCID: PMC11137373 DOI: 10.3897/mycokeys.105.117871] [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: 12/27/2023] [Accepted: 04/30/2024] [Indexed: 06/01/2024] Open
Abstract
In the present study, two new Conidiobolus s.s. species were described relying on the morphological studies and phylogenetic analysis utilizing nuclear large subunit of rDNA (nucLSU), mitochondrial small subunit of rDNA (mtSSU), and elongation-factor-like gene (EFL) sequences. Conidiobolusjiangxiensissp. nov. is distinguished by its short primary conidiophores, a feature not commonly observed in other Conidiobolus s.s. species. Conversely, Conidiobolusmarcoconidiussp. nov. is characterized by larger primary conidia and the emergence of 2-5 secondary conidia from each branched secondary conidiophores. Additionally, the taxonomic reassessment of C.polyspermus confirms its distinct status within the genus Conidiobolus s.s. Moreover, molecular analyses, incorporating the nucLSU, mtSSU, and EFL sequences, provide robust support for the phylogenetic placement of the two newly described species and the taxonomic identity of C.polyspermus. This investigation contributes valuable insights into the species diversity of Conidiobolaceae in China, enhancing our understanding of the taxonomy within this fungal family.
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Affiliation(s)
- Yong Nie
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei 230036, ChinaAnhui University of TechnologyHefeiChina
| | - Ying Yin
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma,anshan 243002, ChinaAnhui Agricultural UniversityHefeiChina
| | - Heng Zhao
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - XiaoYong Liu
- College of Life Sciences, Shandong Normal University, Jinan 250014, ChinaShandong Normal UniversityJinanChina
| | - Bo Huang
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma,anshan 243002, ChinaAnhui Agricultural UniversityHefeiChina
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El Ghalid M, Chiarelli A, Brisse S, Betsou F, Garcia-Hermoso D. Stability and Qualification of a Legacy Fungal Collection. Biopreserv Biobank 2024. [PMID: 38686572 DOI: 10.1089/bio.2023.0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
Background: Microbial culture collections are valuable repositories for qualified and diverse microorganisms, playing a pivotal role in research, education, innovation, as well as in our response to current and emerging public health and societal challenges. However, such precious holdings, when not integrated in professional biobank infrastructures, may be vulnerable to major risks such as staff retirement, changes in the institutional strategy, or natural disasters. The process of preserving and rescuing "historical" collections can be long and treacherous with a loss of a part of the collection. At the Biological Resource Center of Institut Pasteur, we undertook the challenge of rescuing the dormant legacy fungal collection. Materials and Methods: A total of 64 freeze-dried strains, including yeasts and filamentous fungi, were characterized by using a polyphasic approach combining morphological features and molecular data. We assessed the viability, purity, and authenticity of selected strains isolated from multiple sources and stored for more than 20 years. Results: Our preliminary results show long-term stability of the selected strains and successful qualification in terms of purity and authentication. Moreover, based on the most recent taxonomic revisions, we updated and revised the nomenclature, where applicable. Conclusion: Our findings demonstrated the potential value of reviving historical microbial collections for biobanking and research activities and reassure us about the collection's future reopening.
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Affiliation(s)
- Mennat El Ghalid
- Institut Pasteur, Université Paris Cité, Biological Resource Center of the Institut Pasteur, Paris, France
| | - Adriana Chiarelli
- Institut Pasteur, Université Paris Cité, Biological Resource Center of the Institut Pasteur, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biological Resource Center of the Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Fay Betsou
- Institut Pasteur, Université Paris Cité, Biological Resource Center of the Institut Pasteur, Paris, France
| | - Dea Garcia-Hermoso
- Institut Pasteur, Université Paris Cité, Biological Resource Center of the Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, National Reference Center for Invasive Mycoses and Antifungals, Translational Mycology research group, Mycology Department, Paris, France
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Bras G, Satala D, Juszczak M, Kulig K, Wronowska E, Bednarek A, Zawrotniak M, Rapala-Kozik M, Karkowska-Kuleta J. Secreted Aspartic Proteinases: Key Factors in Candida Infections and Host-Pathogen Interactions. Int J Mol Sci 2024; 25:4775. [PMID: 38731993 PMCID: PMC11084781 DOI: 10.3390/ijms25094775] [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: 03/15/2024] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Extracellular proteases are key factors contributing to the virulence of pathogenic fungi from the genus Candida. Their proteolytic activities are crucial for extracting nutrients from the external environment, degrading host defenses, and destabilizing the internal balance of the human organism. Currently, the enzymes most frequently described in this context are secreted aspartic proteases (Saps). This review comprehensively explores the multifaceted roles of Saps, highlighting their importance in biofilm formation, tissue invasion through the degradation of extracellular matrix proteins and components of the coagulation cascade, modulation of host immune responses via impairment of neutrophil and monocyte/macrophage functions, and their contribution to antifungal resistance. Additionally, the diagnostic challenges associated with Candida infections and the potential of Saps as biomarkers were discussed. Furthermore, we examined the prospects of developing vaccines based on Saps and the use of protease inhibitors as adjunctive therapies for candidiasis. Given the complex biology of Saps and their central role in Candida pathogenicity, a multidisciplinary approach may pave the way for innovative diagnostic strategies and open new opportunities for innovative clinical interventions against candidiasis.
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Affiliation(s)
- Grazyna Bras
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland (M.Z.); (J.K.-K.)
| | - Dorota Satala
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland (M.Z.); (J.K.-K.)
| | - Magdalena Juszczak
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland (M.Z.); (J.K.-K.)
- Doctoral School of Exact and Natural Sciences, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Kamila Kulig
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland (M.Z.); (J.K.-K.)
| | - Ewelina Wronowska
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland (M.Z.); (J.K.-K.)
| | - Aneta Bednarek
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland (M.Z.); (J.K.-K.)
- Doctoral School of Exact and Natural Sciences, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Marcin Zawrotniak
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland (M.Z.); (J.K.-K.)
| | - Maria Rapala-Kozik
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland (M.Z.); (J.K.-K.)
| | - Justyna Karkowska-Kuleta
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland (M.Z.); (J.K.-K.)
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Arastehfar A, Daneshnia F, Floyd DJ, Jeffries NE, Salehi M, Perlin DS, Ilkit M, Lass-Flöerl C, Mansour MK. Echinocandin persistence directly impacts the evolution of resistance and survival of the pathogenic fungus Candida glabrata. mBio 2024; 15:e0007224. [PMID: 38501869 PMCID: PMC11005346 DOI: 10.1128/mbio.00072-24] [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: 01/17/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Recent epidemiological studies documented an alarming increase in the prevalence of echinocandin-resistant (ECR) Candida glabrata blood isolates. ECR isolates are known to arise from a minor subpopulation of a clonal population, termed echinocandin persisters. Although it is believed that isolates with a higher echinocandin persistence (ECP) are more likely to develop ECR, the implication of ECP needs to be better understood. Moreover, replacing laborious and time-consuming traditional approaches to determine ECP levels with rapid, convenient, and reliable tools is imperative to advance our understanding of this emerging concept in clinical practice. Herein, using extensive ex vivo and in vivo systemic infection models, we showed that high ECP isolates are less effectively cleared by micafungin treatment and exclusively give rise to ECR colonies. Additionally, we developed a flow cytometry-based tool that takes advantage of a SYTOX-based assay for the stratification of ECP levels. Once challenged with various collections of echinocandin-susceptible blood isolates, our assay reliably differentiated ECP levels in vitro and predicted ECP levels in real time under ex vivo and in vivo conditions when compared to traditional methods relying on colony-forming unit counting. Given the high and low ECP predictive values of 92.3% and 82.3%, respectively, our assay showed a high agreement with traditional approach. Collectively, our study supports the concept of ECP level determination in clinical settings and provides a robust tool scalable for high-throughput settings. Application of this tool facilitates the interrogation of mutant and drug libraries to further our understanding of persister biology and designing anti-persister therapeutics. IMPORTANCE Candida glabrata is a prevalent fungal pathogen able to replicate inside macrophages and rapidly develop resistance against frontline antifungal echinocandins. Multiple studies have shown that echinocandin resistance is fueled by the survival of a small subpopulation of susceptible cells surviving lethal concentrations of echinocandins. Importantly, bacterial pathogens that exhibit high antibiotic persistence also impose a high burden and generate more antibiotic-resistant colonies. Nonetheless, the implications of echinocandin persistence (ECP) among the clinical isolates of C. glabrata have not been defined. Additionally, ECP level determination relies on a laborious and time-consuming method, which is prone to high variation. By exploiting in vivo systemic infection and ex vivo models, we showed that C. glabrata isolates with a higher ECP are associated with a higher burden and more likely develop echinocandin resistance upon micafungin treatment. Additionally, we developed an assay that reliably determines ECP levels in real time. Therefore, our study identified C. glabrata isolates displaying high ECP levels as important entities and provided a reliable and convenient tool for measuring echinocandin persistence, which is extendable to other fungal and bacterial pathogens.
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Affiliation(s)
- Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Farnaz Daneshnia
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel J. Floyd
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Mostafa Salehi
- Department Industrial Engineering Faculty of K.N., Toosi University of Technology, Tehran, Iran
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, District of Columbia, USA
| | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, University of Çukurova, Adana, Türkiye
| | - Cornelia Lass-Flöerl
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Innsbruck, Austria
| | - Michael K. Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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9
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Kidd SE, Hagen F, Halliday CL, Abdolrasouli A, Boekhout T, Crous PW, Ellis DH, Elvy J, Forrest GN, Groenewald M, Hahn RC, Houbraken J, Rodrigues AM, Scott J, Sorrell TC, Summerbell RC, Tsui CKM, Yurkov A, Chen SCA. Inconsistencies within the proposed framework for stabilizing fungal nomenclature risk further confusion. J Clin Microbiol 2024; 62:e0157023. [PMID: 38441055 PMCID: PMC11005369 DOI: 10.1128/jcm.01570-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Affiliation(s)
- Sarah E. Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, South Australia, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Alireza Abdolrasouli
- Department of Medical Microbiology, King’s College Hospital, London, United Kingdom
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Teun Boekhout
- College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Pedro W. Crous
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Department of Biology, Molecular Microbiology, Utrecht University, Utrecht, the Netherlands
| | - David H. Ellis
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Juliet Elvy
- Awanui Labs, Dunedin Hospital, Dunedin, New Zealand
| | | | | | - Rosane C. Hahn
- Medical Mycology Laboratory/Investigation, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
- Júlio Muller Hospital, EBSERH, Cuiabá, Mato Grosso, Brazil
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Anderson M. Rodrigues
- Department of Microbiology, Immunology and Parasitology, Laboratory of Emerging Fungal Pathogens, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - James Scott
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Sporometrics, Toronto, Ontario, Canada
| | - Tania C. Sorrell
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Richard C. Summerbell
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Sporometrics, Toronto, Ontario, Canada
| | - Clement K. M. Tsui
- Infectious Diseases Research Laboratory, National Center for Infectious Diseases, Singapore, Singapore
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Andrey Yurkov
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
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10
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Murphy CR, Teoh Z, Whitehurst D, Brammer C, Perkins K, Paulsen G, Miller-Handley H, Danziger-Isakov L, Otto WR. Disseminated Disease After Candidemia in Children and Young Adults: Epidemiology, Diagnostic Evaluation and Risk Factors. Pediatr Infect Dis J 2024; 43:328-332. [PMID: 38091489 DOI: 10.1097/inf.0000000000004212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
BACKGROUND Treatment of candidemia may be complicated by hematogenous dissemination. Limited data exist to guide decision-making regarding the evaluation for disseminated disease. We sought to describe the epidemiology of invasive disease after candidemia, report the diagnostic evaluations performed and identify risk factors for disseminated disease. METHODS We performed a retrospective single-center study of candidemia from January 1, 2012 to December 31, 2022. Disseminated candidiasis was defined as radiologic findings consistent with end-organ disease, abnormal ophthalmologic exam or growth of Candida spp. from a sterile site after an episode of candidemia. A multilevel regression model was used to identify risk factors for dissemination. RESULTS The cohort included 124 patients with 144 episodes of candidemia. Twelve patients died before an evaluation for dissemination occurred. Only 107/132 patients underwent evaluation for dissemination. Tests obtained included abdominal imaging (93/132), echocardiography (91/132), neuroimaging (45/132) and chest imaging (38/132). A retinal examination was performed in 90/132 patients. Overall, 27/107 patients (25%) had disseminated disease. Frequently identified sites of dissemination were lungs and abdominal organs. Regression modeling identified prematurity [adjusted odds ratio (aOR): 11.88; 95% confidence interval (CI): 1.72-81.90] and mitochondrial and genetic disease (aOR: 5.66; 95% CI: 1.06-30.17) as risk factors for disseminated candidiasis. Each additional day of candidemia increased the odds of dissemination (aOR: 1.36; 95% CI: 1.12-1.66). DISCUSSION In a heterogeneous cohort of patients, disseminated candidiasis was common. Evaluation for disseminated disease was variable. Those with persistent candidemia had significantly increased risk of dissemination and should undergo a standardized evaluation for disseminated disease.
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Affiliation(s)
- Catherine R Murphy
- From the Department of Pediatrics, University of Cincinnati
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Zheyi Teoh
- From the Department of Pediatrics, University of Cincinnati
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Caitlin Brammer
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kerrigan Perkins
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Grant Paulsen
- From the Department of Pediatrics, University of Cincinnati
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Hilary Miller-Handley
- From the Department of Pediatrics, University of Cincinnati
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lara Danziger-Isakov
- From the Department of Pediatrics, University of Cincinnati
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - William R Otto
- From the Department of Pediatrics, University of Cincinnati
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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11
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Ettadili H, Vural C. Current global status of Candida auris an emerging multidrug-resistant fungal pathogen: bibliometric analysis and network visualization. Braz J Microbiol 2024; 55:391-402. [PMID: 38261261 PMCID: PMC10920528 DOI: 10.1007/s42770-023-01239-0] [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: 10/29/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Candida auris is an emerging multidrug-resistant fungal pathogen associated with nosocomial infections and hospital outbreaks worldwide, presenting a serious global health threat. There has been a rapid emergence of scientific research publications focusing on therapeutic compounds, diagnostic techniques, control strategies, prevention, and understanding the epidemiology related to C. auris. OBJECTIVE This study aims to provide the most up-to-date comprehensive and integrated examination of C. auris research subject and demonstrate that C. auris is indeed a topic of increasing interest. METHODS The search query "candida-auris" was used as a topic term to find and retrieve relevant data published between 2009 and 15 June 2023, from the Web of Science Core Collection (WoSCC) database. In this work, the bibliometric analysis and network visualization were conducted using VOSviewer software, and Biblioshiny interface accessible through the Bibliometrix R-package on RStudio software. RESULTS The yearly growth rate percentage (37.91%), along with the strong positive correlations between publications and citations (r = 0.981; p < 0.001), suggests heightened scholarly engagement in this topic. The USA, India, China, and the UK have emerged as pivotal contributors, with the Centers for Disease Control and Prevention (CDC) in the USA being the most productive institution. Current research hotspots in this field mainly focused on identifying and limiting transmission of the clonal strains, epidemiology, antifungal resistance, and in vitro antifungal susceptibility testing. CONCLUSION This detailed bibliometric analysis in C. auris topic shows that this fungal pathogen has garnered growing attention and attracted progressively more scholars. This paper will help researchers to find without difficulty the relevant articles, research hotspots, influential authors, institutions, and countries related to the topic.
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Affiliation(s)
- Hamza Ettadili
- Faculty of Science, Department of Biology, Molecular Biology Section, Pamukkale University, 20160, Denizli, Turkey
| | - Caner Vural
- Faculty of Science, Department of Biology, Molecular Biology Section, Pamukkale University, 20160, Denizli, Turkey.
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12
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Yazdy GM, Mitchell C, Sobel JD, Tuddenham S. Recurrent Infectious Vaginitis: A Practical Approach for the Primary Care Clinician. Med Clin North Am 2024; 108:373-392. [PMID: 38331486 DOI: 10.1016/j.mcna.2023.08.017] [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: 02/10/2024]
Abstract
Recurrent infectious vaginitis can lead to significant morbidity, patient frustration, and health care costs. The most common causes are bacterial vaginosis (BV) and vulvovaginal candidiasis (VVC); however, other infectious and noninfectious etiologies should be considered in patients with recurrent symptoms. A detailed history and physical examination with appropriate testing at the time of symptoms is critical to establishing a correct diagnosis. Management options for recurrent BV and VVC are limited. Complex cases including those with atypical symptoms, negative testing for common causes, refractory symptoms despite appropriate therapy or recurrences during suppressive therapy will require referral to specialist care.
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Affiliation(s)
- Golsa M Yazdy
- Department of Gynecology & Obstetrics, Johns Hopkins University, 4940 Eastern Avenue, Baltimore, MD 21224, USA
| | - Caroline Mitchell
- Department of Obstetrics and Gynecology, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA
| | - Jack D Sobel
- Department of Medicine, Division of Infectious Diseases, Wayne State University, 3901 Chrysler Drive Suite 4A, Detroit, MI 48201, USA
| | - Susan Tuddenham
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University, 5200 Eastern Avenue, MFL Center Tower, Suite 381, Baltimore, MD 21224, USA.
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13
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Gudisa R, Harchand R, Rudramurthy SM. Nucleic-Acid-Based Molecular Fungal Diagnostics: A Way to a Better Future. Diagnostics (Basel) 2024; 14:520. [PMID: 38472992 DOI: 10.3390/diagnostics14050520] [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: 01/03/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
The world has seen a tremendous increase in the number of fungal infections during the past two decades. Recently, the World Health Organisation released the pathogen priority list for fungal infections, signifying the importance of these infections in the fields of research and public health. Microbiology laboratories demand an upgrade in the diagnostic system to keep up with the increased burden of these infections. Diagnosis of fungal infections using conventional techniques has always faced limitations in terms of specificity, sensitivity, and turnaround time. Although these methods are the core pillars of the diagnosis, there is an increased need for molecular approaches. Molecular techniques have revolutionised the field of fungal diagnostics. The diverse array of molecular techniques, including techniques like Polymerase Chain Reaction (PCR), have emerged as a cornerstone in fungal diagnostics. Molecular techniques have transformed fungal diagnostics, providing powerful tools for the rapid and accurate identification of pathogens. As these technologies continue to evolve, their integration into routine clinical practice holds the promise of improving patient outcomes through timely and targeted antifungal interventions. This review will cover the molecular approaches involved in fungal diagnostics, moving from the basic techniques to the advanced-level nucleic-acid-based molecular approaches providing a high throughput and decreased turnaround time for the diagnosis of serious fungal infections.
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Affiliation(s)
- Rajendra Gudisa
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Ritika Harchand
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
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14
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Barrs VR, Beczkowski PM, Talbot JJ, Hobi S, Teoh SN, Hernandez Muguiro D, Shubitz LF, Sandy J. Invasive Fungal Infections and Oomycoses in Cats: 1. Diagnostic approach. J Feline Med Surg 2024; 26:1098612X231219696. [PMID: 38189288 PMCID: PMC10949879 DOI: 10.1177/1098612x231219696] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
CLINICAL RELEVANCE In contrast to superficial fungal infections, such as dermatophytosis, invasive fungal infections (IFIs) are characterised by penetration of tissues by fungal elements. Disease can spread locally within a region or can disseminate haematogenously or via the lymphatics. The environment is the most common reservoir of infection. Since fungal spores are airborne, indoor cats are also susceptible to IFIs. Some environmental fungi are ubiquitous and present globally, while others are endemic or hyperendemic within specific geographic regions. Zoonotic pathogens include Microsporum canis, Sporothrix schenckii and Sporothrix brasiliensis. AIM In the first of a two-part article series, the approach to the investigation of feline IFIs and oomycoses is reviewed. As well as tips for diagnosis, and information on the ecological niche and distribution of fungal pathogens, the review covers clinical presentation of the most common IFIs, including cryptococcosis, histoplasmosis, blastomycosis, coccidioidomycosis, sporotrichosis, phaeohyphomycosis, aspergillosis and dermatophytic pseudomycetoma, as well as the oomycoses pythiosis, lagenidiosis and paralagenidiosis. In Part 2, the spectrum of activity, mechanisms of action, pharmacokinetic and pharmacodynamic properties and adverse effects of antifungal drugs are reviewed, and the treatment and prognosis for specific IFIs and oomycoses are discussed. EVIDENCE BASE The review draws on published evidence and the authors' combined expertise in feline medicine, mycology, dermatology, clinical pathology and anatomical pathology.
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Affiliation(s)
- Vanessa R Barrs
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR China
- Centre for Animal Health and Welfare, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR China
| | - Paweł M Beczkowski
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR China
| | | | - Stefan Hobi
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR China
| | - Shu Ning Teoh
- Veterinary Specialists Aotearoa, Henderson, Auckland, New Zealand
| | | | - Lisa F Shubitz
- Valley Fever Center for Excellence, The University of Arizona, AZ, USA
| | - Jeanine Sandy
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR China
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15
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Peçanha-Pietrobom PM, Truda VSS, Fernández-Ruiz M, Gutiérrez MG, Sukiennik TCT, Santos DWDCL, Valerio M, Gioia F, Rodríguez-Goncer I, Giacobbe DR, Vena A, Machado M, Bassetti M, Muñoz P, Aguado JM, Tedesco-Silva H, Colombo AL. Natural history and prognostic factors of candidemia in kidney transplant recipients: A retrospective, multinational study. Mycoses 2024; 67:e13669. [PMID: 37946667 DOI: 10.1111/myc.13669] [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: 05/23/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND The natural history of candidemia in kidney transplant recipients (KTR) remains poorly understood. This study aimed to evaluate mortality, prognostic factors and overall graft loss after candidemia in KTRs. METHODS This is a retrospective multicentre study enrolling all KTRs ≥15 years old with candidemia diagnosed at hospitals in Brazil, Spain and Italy from 2010 to 2020. Primary endpoints were mortality rates at 14 and 30 days. Secondary endpoints were prognostic factors of 14-day mortality and overall graft loss. RESULTS We enrolled 93 KTRs of which 75 were from Brazil. The mean time interval from transplantation to the onset of candidemia was 45.2 ± 61.5 months. 42% of all patients were on haemodialysis, 31.3% had an episode of sepsis and 39% underwent surgery within 30 days before fungemia. European patients were more likely to receive echinocandin (32 vs. 72%, p < .001). 22.7% of Brazilian patients did not receive any antifungal before death. All-cause mortality at 14 days was higher in Brazil (41.3 vs. 11.1%, p = .016). Candida colonisation (OR 6.91 [95% CI: 1.08-44.3], p = .042) and hypotension (OR 4.87 [95% CI: 1.62-14.66], p = .005) were associated with 14-day mortality. Echinocandin treatment had a protective effect (OR 0.19 [95% CI: 0.05-0.73], p = .015). Graft loss at 90 days occurred in 48% of patients (70.7 in Brazil vs. 22.2% in Europe, p < .01). CONCLUSIONS Candidemia in KTR is usually documented late after engraftment in patients requiring HD, surgical procedures and dysbiosis secondary to antibiotic use. Mortality was higher in Brazil. Echinocandin therapy was associated with improved survival.
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Affiliation(s)
- Paula M Peçanha-Pietrobom
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vanessa S S Truda
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario '12 de Octubre', Instituto de Investigación Sanitaria Hospital '12 de Octubre' (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Medicine, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Manuel García Gutiérrez
- Unit of Infectious Diseases, Hospital Universitario Reina Sofía-IMIBIC-Universidad de Cordoba, Cordoba, Spain
| | | | - Daniel Wagner De C L Santos
- Department of Infectious Diseases and Infection Control, Universidade Federal do Maranhão, Ebserh-UFMA, São Luis, Brazil
- Instituto D'Or de Pesquisa e Ensino, IDOR, Hospital UDI, São Luis, Brazil
| | - Maricela Valerio
- Department of Medicine, Facultad de Medicina, Universidad Complutense, Madrid, Spain
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
| | - Francesca Gioia
- Department of Infectious Disease, University Hospital Ramon y Cajal, Madrid, Spain
- IRYCIS-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBER-Consorcio Centro de Investigación Biomédica en Red-(CB21/13/00084), Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación, Madrid, Spain
| | - Isabel Rodríguez-Goncer
- Unit of Infectious Diseases, Hospital Universitario '12 de Octubre', Instituto de Investigación Sanitaria Hospital '12 de Octubre' (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Daniele Roberto Giacobbe
- Infectious Diseases Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Antonio Vena
- Infectious Diseases Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Marina Machado
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Matteo Bassetti
- Infectious Diseases Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Patricia Muñoz
- Department of Medicine, Facultad de Medicina, Universidad Complutense, Madrid, Spain
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
| | - José María Aguado
- Unit of Infectious Diseases, Hospital Universitario '12 de Octubre', Instituto de Investigación Sanitaria Hospital '12 de Octubre' (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Medicine, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Helio Tedesco-Silva
- Hospital do Rim-Fundação Oswaldo Ramos, São Paulo, Brazil
- Department of Medicine, Division of Nephrology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Arnaldo Lopes Colombo
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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16
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Borman AM, Johnson EM. Changes in fungal taxonomy: mycological rationale and clinical implications. Clin Microbiol Rev 2023; 36:e0009922. [PMID: 37930182 PMCID: PMC10732072 DOI: 10.1128/cmr.00099-22] [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: 05/22/2023] [Accepted: 07/13/2023] [Indexed: 11/07/2023] Open
Abstract
Numerous fungal species of medical importance have been recently subjected to and will likely continue to undergo nomenclatural changes as a result of the application of molecular approaches to fungal classification together with abandonment of dual nomenclature. Here, we summarize those changes affecting key groups of fungi of medical importance, explaining the mycological (taxonomic) rationale that underpinned the changes and the clinical relevance/importance (where such exists) of the key nomenclatural revisions. Potential mechanisms to mitigate unnecessary taxonomic instability are suggested, together with approaches to raise awareness of important changes to minimize potential clinical confusion.
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Affiliation(s)
- Andrew M. Borman
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
| | - Elizabeth M. Johnson
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
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17
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Lass-Flörl C, Steixner S. The changing epidemiology of fungal infections. Mol Aspects Med 2023; 94:101215. [PMID: 37804792 DOI: 10.1016/j.mam.2023.101215] [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: 01/04/2023] [Revised: 06/19/2023] [Accepted: 09/21/2023] [Indexed: 10/09/2023]
Abstract
Invasive fungal diseases are common complications in critically ill patients and in those with significant underlying imbalanced immune systems. Fungal co-, and/or super-infections are emerging and have become a rising concern within the last few years. In Europe, cases of candidiasis and aspergillosis dominate, followed by mucormycosis in India. Epidemiological studies show an increasing trend in the incidence of all three entities. Parallel to this, a shift within the underlying fungal pathogens is observed. More non-albicans Candida infections and aspergillosis with cryptic species are on the rise; cryptic species may cover intrinsic resistance to azoles and other antifungal drugs. The recent COVID-19 pandemic led to a significantly increasing incidence of invasive fungal diseases among hospitalized patients.
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Affiliation(s)
- Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, A-6020, Innsbruck, Austria.
| | - Stephan Steixner
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, A-6020, Innsbruck, Austria
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18
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Hernández Solis A, Rabadan Armenta SJ, Araiza Santibáñez J, Bonifaz A, Serna Valle FJ, Mojica Jaimes E. Necrotizing pneumonia due to Saprochaete capitata in a patient with diabetes mellitus. Case report. Med Mycol Case Rep 2023; 42:100603. [PMID: 37701416 PMCID: PMC10494254 DOI: 10.1016/j.mmcr.2023.08.006] [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: 06/13/2023] [Revised: 08/08/2023] [Accepted: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
Saprochaete capitata is a yeast-like fungus of the Dipodascaceae family, capable of colonizing the skin and the respiratory and gastrointestinal tracts. We present a 56-year-old man with diabetes mellitus who was admitted to the hospital presenting with fever, cough and hemoptysis. The diagnosis of necrotizing pneumonia was made by direct microscopy of the bronchoalveolar lavage fluid showed and Saprochaete capitata was identified by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-TOF MS®). Treatment consisted of itraconazole 200 mg every 12 hours orally for 30 days, leading to clinical and radiological improvement. Saprochaete capitata infection is a rare cause of pulmonary mycoses.
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Affiliation(s)
- Alejandro Hernández Solis
- Servicio de Neumología y Cirugía de Tórax, Hospital General de México, “Dr. Eduardo Liceaga”, Ciudad de México, Código postal: 06720, Mexico
| | - Saul Javier Rabadan Armenta
- Servicio de Neumología y Cirugía de Tórax, Hospital General de México, “Dr. Eduardo Liceaga”, Ciudad de México, Código postal: 06720, Mexico
| | - Javier Araiza Santibáñez
- Laboratorio de Micología, Hospital General de México, “Dr. Eduardo Liceaga”, Ciudad de México, Código postal: 06720, Mexico
| | - Alexandro Bonifaz
- Laboratorio de Micología, Hospital General de México, “Dr. Eduardo Liceaga”, Ciudad de México, Código postal: 06720, Mexico
| | | | - Eliasib Mojica Jaimes
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Estado de México. Código postal: 54075, Mexico
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19
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Menu E, Filori Q, Dufour JC, Ranque S, L’Ollivier C. A Repertoire of the Less Common Clinical Yeasts. J Fungi (Basel) 2023; 9:1099. [PMID: 37998905 PMCID: PMC10671991 DOI: 10.3390/jof9111099] [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: 10/09/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Invasive fungal diseases are a public health problem. They affect a constantly increasing number of at-risk patients, and their incidence has risen in recent years. These opportunistic infections are mainly due to Candida sp. but less common or rare yeast infections should not be underestimated. These so-called "less common" yeasts include Ascomycota of the genera Candida (excluding the five major Candida species), Magnusiomyces/Saprochaete, Malassezia, and Saccharomyces, and Basidiomycota of the genera Cryptococcus (excluding the Cryptococcus neoformans/gattii complex members), Rhodotorula, and Trichosporon. The aim of this review is to (i) inventory the less common yeasts isolated in humans, (ii) provide details regarding the specific anatomical locations where they have been detected and the clinical characteristics of the resulting infections, and (iii) provide an update on yeast taxonomy. Of the total of 239,890 fungal taxa and their associated synonyms sourced from the MycoBank and NCBI Taxonomy databases, we successfully identified 192 yeasts, including 127 Ascomycota and 65 Basidiomycota. This repertoire allows us to highlight rare yeasts and their tropism for certain anatomical sites and will provide an additional tool for diagnostic management.
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Affiliation(s)
- Estelle Menu
- Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France; (S.R.); (C.L.)
- Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, Aix Marseille Université, 13385 Marseille, France
| | - Quentin Filori
- INSERM, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, ISSPAM, Aix Marseille University, 13385 Marseille, France; (Q.F.); (J.-C.D.)
| | - Jean-Charles Dufour
- INSERM, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, ISSPAM, Aix Marseille University, 13385 Marseille, France; (Q.F.); (J.-C.D.)
- APHM, Hôpital de la Timone, Service Biostatistique et Technologies de l’Information et de la Communication, 13385 Marseille, France
| | - Stéphane Ranque
- Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France; (S.R.); (C.L.)
- Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, Aix Marseille Université, 13385 Marseille, France
| | - Coralie L’Ollivier
- Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France; (S.R.); (C.L.)
- Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, Aix Marseille Université, 13385 Marseille, France
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20
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Rúa-Giraldo ÁL. Fungal taxonomy: A puzzle with many missing pieces. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:288-311. [PMID: 37721899 PMCID: PMC10588969 DOI: 10.7705/biomedica.7052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/24/2023] [Indexed: 09/20/2023]
Abstract
Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.
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Kidd SE, Abdolrasouli A, Hagen F. Reply to "Re: Fungal Nomenclature: Managing Change Is the Name of the Game". Open Forum Infect Dis 2023; 10:ofad394. [PMID: 37547849 PMCID: PMC10404001 DOI: 10.1093/ofid/ofad394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/08/2023] Open
Affiliation(s)
- Sarah E Kidd
- National Mycology Reference Centre, Microbiology & Infectious Diseases, SA Pathology, South Australia, Australia
| | - Alireza Abdolrasouli
- Department of Medical Microbiology, King’s College Hospital, London, UK
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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Hennequin C, Coste A, Imbert C. WITHDRAWN: Changes in the fungal nomenclature: Why and how to manage? J Mycol Med 2023; 33:101387. [PMID: 37104987 DOI: 10.1016/j.mycmed.2023.101387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- C Hennequin
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Service de Parasitologie-Mycologie, F-75012 Paris, France
| | - A Coste
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - C Imbert
- Laboratoire Ecologie et Biologie des Interactions (EBI), University Poitiers, UMR CNRS 7267, F-86000 Poitiers, France
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Jenks JD, White PL, Kidd SE, Goshia T, Fraley SI, Hoenigl M, Thompson GR. An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections. Expert Rev Mol Diagn 2023; 23:1135-1152. [PMID: 37801397 PMCID: PMC10842420 DOI: 10.1080/14737159.2023.2267977] [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: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens. AREAS COVERED We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS). EXPERT OPINION PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.
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Affiliation(s)
- Jeffrey D Jenks
- Durham County Department of Public Health, Durham, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - P Lewis White
- Public Health Wales Microbiology Cardiff, UHW, United Kingdom and Centre for trials research/Division of Infection/Immunity, Cardiff University, Cardiff, UK
| | - Sarah E Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, Australia
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - George R Thompson
- University of California Davis Center for Valley Fever, Sacramento, CA, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, CA, USA
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
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Pieta A, Venetsanopoulou AI, Kittas C, Christaki E, Voulgari PV. Recurrent Scedosporium apiospermum Cutaneous Infection in a Patient with Rheumatoid Arthritis: The Potent Role of IL-6 Signaling Pathway Blockade: A Case-Based Review. J Fungi (Basel) 2023; 9:683. [PMID: 37367619 DOI: 10.3390/jof9060683] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023] Open
Abstract
Rheumatoid arthritis (RA) patients deal with a higher risk of bacterial and fungal infections compared to the general population because of their dysregulated immune system as well as the immunosuppressive therapy they usually receive. Scedosporium spp. is a fungal pathogen responsible for cutaneous, lung, central nervous system, and eye infections, mostly in immunocompromised patients, leading to death in disseminated cases. We report the case of an 81-year-old woman with rheumatoid arthritis treated with steroids and an IL-6 inhibitor who was diagnosed with scedosporiosis of the upper limb. She was treated with voriconazole for one month, which was discontinued due to adverse events, and when scedosporiosis relapsed, she switched to itraconazole. We also reviewed the current literature on RA patients presenting with Scedosporium infections. Early and accurate diagnosis of scedosporiosis has therapeutic and prognostic implications, as traditionally this fungus is resistant to commonly used antifungals. Clinical alertness regarding uncommon infections, including fungal, in patients with autoimmune diseases on immunomodulatory agents is essential for effective treatment.
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Affiliation(s)
- Antigone Pieta
- Department of Rheumatology, School of Health Sciences, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Aliki I Venetsanopoulou
- Department of Rheumatology, School of Health Sciences, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Christos Kittas
- Microbiology Laboratory, School of Health Sciences, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Eirini Christaki
- 1st Division of Internal Medicine & Infectious Diseases Unit, University General Hospital of Ioannina, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Paraskevi V Voulgari
- Department of Rheumatology, School of Health Sciences, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
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Spruijtenburg B, Rudramurthy SM, Meijer EFJ, van Haren MHI, Kaur H, Chakrabarti A, Meis JF, de Groot T. Application of Novel Short Tandem Repeat Typing for Wickerhamomyces anomalus Reveals Simultaneous Outbreaks within a Single Hospital. Microorganisms 2023; 11:1525. [PMID: 37375027 DOI: 10.3390/microorganisms11061525] [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: 05/04/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Wickerhamomyces anomalus, previously known as Candida pelliculosa, occasionally causes candidemia in humans, primarily infecting neonates, and infants. The mortality rate of these invasive infections is high, and isolates with a reduced susceptibility to fluconazole have been reported. W. anomalus outbreaks are regularly reported in healthcare facilities, especially in neonatal intensive care units (NICUs). In order to rapidly genotype isolates with a high-resolution, we developed and applied a short tandem repeat (STR) typing scheme for W. anomalus. Six STR markers were selected and amplified in two multiplex PCRs, M3 and M6, respectively. In total, 90 W. anomalus isolates were typed, leading to the identification of 38 different genotypes. Four large clusters were found, unveiling simultaneous outbreak events spread across multiple units within the same hospital. STR typing results of 11 isolates were compared to whole-genome sequencing (WGS) single nucleotide polymorphism (SNP) calling, and the identified genotypic relationships were highly concordant. We performed antifungal susceptibility testing of these isolates, and a reduced susceptibility to fluconazole was found for two (2.3%) isolates. ERG11 genes of these two isolates were examined using WGS data, which revealed a novel I469L substitution in one isolate. By constructing a homology model for W. anomalus ERG11p, the substitution was found in close proximity to the fluconazole binding site. In summary, we showed multiple W. anomalus outbreak events by applying a novel STR genotyping scheme.
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Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Eelco F J Meijer
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Merlijn H I van Haren
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Harsimran Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, 50931 Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
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Hennequin C, Coste A, Imbert C. Changes in the fungal nomenclature: Why and how to manage? J Mycol Med 2023; 33:101404. [PMID: 37163874 DOI: 10.1016/j.mycmed.2023.101404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- C Hennequin
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Service de Parasitologie-Mycologie, F-75012 Paris, France.
| | - A Coste
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - C Imbert
- Laboratoire Ecologie et Biologie des Interactions (EBI), University Poitiers, UMR CNRS 7267, F-86000 Poitiers, France
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Pinheiro BG, Pôssa AP, Ricci G, Nishikaku AS, Hagen F, Hahn RC, de Camargo ZP, Rodrigues AM. Development of a Multiplex qPCR Assay for Fast Detection and Differentiation of Paracoccidioidomycosis Agents. J Fungi (Basel) 2023; 9:jof9030358. [PMID: 36983526 PMCID: PMC10057483 DOI: 10.3390/jof9030358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Classic paracoccidioidomycosis (PCM) is a potentially deadly neglected tropical systemic mycosis caused by members of the Paracoccidioides brasiliensis complex (P. brasiliensis s. str., P. americana, P. restrepiensis, and P. venezuelensis) and P. lutzii. The laboratorial diagnosis of PCM relies on observing pathognomonic structures such as the “steering wheel” or “Mickey Mouse” shape in the direct mycological examination, fresh biopsied tissue in 10% KOH, histopathological analysis, and/or the isolation of the fungus in culture. However, these procedures are time-consuming and do not allow for the speciation of Paracoccidioides due to overlapping morphologies. Here, we propose a new one-tube multiplex probe-based qPCR assay to detect and recognize agents of the P. brasiliensis complex and P. lutzii. Primers (Paracoco-F and Paracoco-R) and TaqMan probes (PbraCx-Fam, Plu-Ned, and Paracoco-Vic) were developed to target the rDNA (ITS2/28S) in the Paracoccidioides genome. A panel of 77 Paracoccidioides isolates revealed a 100% specificity (AUC = 1.0, 95% CI 0.964–1.000, p < 0.0001) without cross-reacting with other medically relevant fungi or human and murine DNA. The lower limit of detection was 10 fg of gDNA and three copies of the partial rDNA amplicon. Speciation using qPCR was in perfect agreement with AFLP and TUB1-RFLP markers (kappa = 1.0). As a proof of concept, we assessed a panel of 16 formalin-fixed and paraffin-embedded specimens from histopathologically confirmed PCM patients to reveal a significant sensitivity of 81.25% and specificity of 100% (AUC = 0.906 ± 0.05, 95% CI = 0.756–0.979, p < 0.0001, Youden index J = 0.8125). Our assay achieved maximum sensitivity (100%) and specificity (100%) using fresh clinical samples (n = 9) such as sputum, bronchoalveolar lavage, and tissue fragments from PCM patients (AUC = 1.0, 95% CI 0.872–1.000, p < 0.0001, Youden index J = 1.0). Overall, our qPCR assay simplifies the molecular diagnosis of PCM and can be easily implemented in any routine laboratory, decreasing a critical bottleneck for the early treatment of PCM patients across a vast area of the Americas.
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Affiliation(s)
- Breno Gonçalves Pinheiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Ana Paula Pôssa
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Giannina Ricci
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr. Ivo Ricci, São Carlos 13561-020, Brazil
| | - Angela Satie Nishikaku
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr. Ivo Ricci, São Carlos 13561-020, Brazil
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Rosane Christine Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá 78060-900, Brazil
- Júlio Muller University Hospital, Federal University of Mato Grosso, Cuiabá 78048-902, Brazil
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Correspondence: ; Tel.: +55-1155764551 (ext. 1540)
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Fan X, Dai RC, Kudinha T, Gu L. A pseudo-outbreak of Cyberlindnera fabianii funguria: Implication from whole genome sequencing assay. Front Cell Infect Microbiol 2023; 13:1130645. [PMID: 36960046 PMCID: PMC10030058 DOI: 10.3389/fcimb.2023.1130645] [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: 12/23/2022] [Accepted: 02/21/2023] [Indexed: 03/09/2023] Open
Abstract
Background Although the yeast Cyberlindnera fabianii (C. fabianii) has been rarely reported in human infections, nosocomial outbreaks caused by this organism have been documented. Here we report a pseudo-outbreak of C. fabianii in a urology department of a Chinese hospital over a two-week period. Methods Three patients were admitted to the urology department of a tertiary teaching hospital in Beijing, China, from Nov to Dec 2018, for different medical intervention demands. During the period Nov 28 to Dec 5, funguria occurred in these three patients, and two of them had positive urine cultures multiple times. Sequencing of rDNA internal transcribed spacer (ITS) region and MALDI-TOF MS were applied for strain identification. Further, sequencing of rDNA non-transcribed spacer (NTS) region and whole genome sequencing approaches were used for outbreak investigation purpose. Results All the cultured yeast strains were identified as C. fabianii by sequencing of ITS region, and were 100% identical to the C. fabianii type strain CBS 5640T. However, the MALDI-TOF MS system failed to correctly identify this yeast pathogen. Moreover, isolates from these three clustered cases shared 99.91%-100% identical NTS region sequences, which could not rule out the possibility of an outbreak. However, whole genome sequencing results revealed that only two of the C. fabianii cases were genetically-related with a pairwise SNP of 192 nt, whilst the third case had over 26,000 SNPs on its genome, suggesting a different origin. Furthermore, the genomes of the first three case strains were phylogenetically even more diverged when compared to a C. fabianii strain identified from another patient, who was admitted to a general surgical department of the same hospital 7 months later. One of the first three patients eventually passed away due to poor general conditions, one was asymptomatic, and other clinically improved. Conclusion In conclusion, nosocomial outbreaks caused by emerging and uncommon fungal species are increasingly being reported, hence awareness must be raised. Genotyping with commonly used universal gene targets may have limited discriminatory power in tracing the sources of infection for these organisms, requiring use of whole genome sequencing to confirm outbreak events.
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Affiliation(s)
- Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Rong-Chen Dai
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Timothy Kudinha
- School of Dentistry and Medical Sciences, Charles Sturt University, Leeds Parade, Oranges, NSW, Australia
- NSW Health Pathology, Regional and Rural, Orange hospital, Orange, NSW, Australia
| | - Li Gu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- *Correspondence: Li Gu,
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