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Daneshnia F, Floyd DJ, Ryan AP, Ghahfarokhy PM, Ebadati A, Jusuf S, Munoz J, Jeffries NE, Elizabeth Yvanovich E, Apostolopoulou A, Perry AM, Lass-Flörl C, Birinci A, Hilmioğlu-Polat S, Ilkit M, Butler G, Nobile CJ, Arastehfar A, Mansour MK. Evaluation of outbreak persistence caused by multidrug-resistant and echinocandin-resistant Candida parapsilosis using multidimensional experimental and epidemiological approaches. Emerg Microbes Infect 2024; 13:2322655. [PMID: 38380673 PMCID: PMC10916928 DOI: 10.1080/22221751.2024.2322655] [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: 01/09/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
Candida parapsilosis is known to cause severe and persistent outbreaks in clinical settings. Patients infected with multidrug-resistant C. parapsilosis (MDR Cp) isolates were identified in a large Turkish hospital from 2017-2020. We subsequently identified three additional patients infected with MDR Cp isolates in 2022 from the same hospital and two echinocandin-resistant (ECR) isolates from a single patient in another hospital. The increasing number of MDR and ECR isolates contradicts the general principle that the severe fitness cost associated with these phenotypes could prevent their dominance in clinical settings. Here, we employed a multidimensional approach to systematically assess the fitness costs of MDR and ECR C. parapsilosis isolates. Whole-genome sequencing revealed a novel MDR genotype infecting two patients in 2022. Despite severe in vitro defects, the levels and tolerances of the biofilms of our ECR and MDR isolates were generally comparable to those of susceptible wild-type isolates. Surprisingly, the MDR and ECR isolates showed major alterations in their cell wall components, and some of the MDR isolates consistently displayed increased tolerance to the fungicidal activities of primary human neutrophils and were more immunoevasive during exposure to primary human macrophages. Our systemic infection mouse model showed that MDR and ECR C. parapsilosis isolates had comparable fungal burden in most organs relative to susceptible isolates. Overall, we observed a notable increase in the genotypic diversity and frequency of MDR isolates and identified MDR and ECR isolates potentially capable of causing persistent outbreaks in the future.
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Affiliation(s)
- Farnaz Daneshnia
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel J. Floyd
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Adam P. Ryan
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Pegah Mosharaf Ghahfarokhy
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
- Health Sciences Research Institute, University of California – Merced, Merced, CA, USA
| | - Arefeh Ebadati
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | - Sebastian Jusuf
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Julieta Munoz
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | | | | | - Anna Apostolopoulou
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Austin M. Perry
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | - Cornelia Lass-Flörl
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Innsbruck, Austria
| | - Asuman Birinci
- Department of Medical Microbiology, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Türkiye
| | | | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, Türkiye
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
- Health Sciences Research Institute, University of California – Merced, Merced, CA, USA
| | - Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael K. Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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2
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Siopi M, Georgiou PC, Paranos P, Beredaki MI, Tarpatzi A, Kalogeropoulou E, Damianidou S, Vasilakopoulou A, Karakosta P, Pournaras S, Meletiadis J. Increase in candidemia cases and emergence of fluconazole-resistant Candida parapsilosis and C. auris isolates in a tertiary care academic hospital during the COVID-19 pandemic, Greece, 2020 to 2023. Euro Surveill 2024; 29:2300661. [PMID: 39027938 PMCID: PMC11258949 DOI: 10.2807/1560-7917.es.2024.29.29.2300661] [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: 11/21/2023] [Accepted: 05/04/2024] [Indexed: 07/20/2024] Open
Abstract
BackgroundThe COVID-19 pandemic and the emergence of Candida auris have changed the epidemiological landscape of candidaemia worldwide.AimWe compared the epidemiological trends of candidaemia in a Greek tertiary academic hospital before (2009-2018) and during the early COVID-19 (2020-2021) and late COVID-19/early post-pandemic (2022-2023) era.MethodsIncidence rates, species distribution, antifungal susceptibility profile and antifungal consumption were recorded, and one-way ANOVA or Fisher's exact test performed. Species were identified by MALDI-ToF MS, and in vitro susceptibility determined with CLSI M27-Ed4 for C. auris and the EUCAST-E.DEF 7.3.2 for other Candida spp.ResultsIn total, 370 candidaemia episodes were recorded during the COVID-19 pandemic. Infection incidence (2.0 episodes/10,000 hospital bed days before, 3.9 during the early and 5.1 during the late COVID-19 era, p < 0.0001), C. auris (0%, 9% and 33%, p < 0.0001) and fluconazole-resistant C. parapsilosis species complex (SC) (20%, 24% and 33%, p = 0.06) infections increased over time, with the latter not associated with increase in fluconazole/voriconazole consumption. A significant increase over time was observed in fluconazole-resistant isolates regardless of species (8%, 17% and 41%, p < 0.0001). Resistance to amphotericin B or echinocandins was not recorded, with the exception of a single pan-echinocandin-resistant C. auris strain.ConclusionCandidaemia incidence nearly tripled during the COVID-19 era, with C. auris among the major causative agents and increasing fluconazole resistance in C. parapsilosis SC. Almost half of Candida isolates were fluconazole-resistant, underscoring the need for increased awareness and strict implementation of infection control measures.
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Affiliation(s)
- Maria Siopi
- Clinical Microbiology Laboratory, "Attikon" University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiota-Christina Georgiou
- Clinical Microbiology Laboratory, "Attikon" University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Paschalis Paranos
- Clinical Microbiology Laboratory, "Attikon" University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria-Ioanna Beredaki
- Clinical Microbiology Laboratory, "Attikon" University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Aikaterini Tarpatzi
- Clinical Microbiology Laboratory, "Attikon" University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Eleni Kalogeropoulou
- Clinical Microbiology Laboratory, "Attikon" University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Sofia Damianidou
- Clinical Microbiology Laboratory, "Attikon" University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandra Vasilakopoulou
- Clinical Microbiology Laboratory, "Attikon" University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Polyxeni Karakosta
- Clinical Microbiology Laboratory, "Attikon" University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Spyros Pournaras
- Clinical Microbiology Laboratory, "Attikon" University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Joseph Meletiadis
- Clinical Microbiology Laboratory, "Attikon" University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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3
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Bergin S, Doorley LA, Rybak JM, Wolfe KH, Butler G, Cuomo CA, Rogers PD. Analysis of clinical Candida parapsilosis isolates reveals copy number variation in key fluconazole resistance genes. Antimicrob Agents Chemother 2024:e0161923. [PMID: 38712935 DOI: 10.1128/aac.01619-23] [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: 12/08/2023] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
We used whole-genome sequencing to analyze a collection of 35 fluconazole-resistant and 7 susceptible Candida parapsilosis isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. Phylogenetic analysis shows that although the collection is diverse, two persistent clinical lineages were identified. We identified copy number variation (CNV) of two genes, ERG11 and CDR1B, in resistant isolates. Two strains have a CNV at the ERG11 locus; the entire ORF is amplified in one, and only the promoter region is amplified in the other. We show that the annotated telomeric gene CDR1B is actually an artifactual in silico fusion of two highly similar neighboring CDR genes due to an assembly error in the C. parapsilosis CDC317 reference genome. We report highly variable copy numbers of the CDR1B region across the collection. Several strains have increased the expansion of the two genes into a tandem array of new chimeric genes. Other strains have experienced a deletion between the two genes creating a single gene with a reciprocal chimerism. We find translocations, duplications, and gene conversion across the CDR gene family in the C. parapsilosis species complex, showing that it is a highly dynamic family.
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Affiliation(s)
- Sean Bergin
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Laura A Doorley
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jeffrey M Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kenneth H Wolfe
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, USA
| | - P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Çaklovica Küçükkaya I, Orhun G, Çağatay AA, Kalaycı S, Esen F, Şahin F, Ağaçfidan A, Erturan Z. Comparison of Candida colonization in intensive care unit patients with and without COVID-19: First prospective cohort study from Turkey. Med Mycol 2024; 62:myae035. [PMID: 38592959 DOI: 10.1093/mmy/myae035] [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: 01/17/2024] [Revised: 03/15/2024] [Accepted: 04/08/2024] [Indexed: 04/11/2024] Open
Abstract
Candida species are the primary cause of fungal infections in intensive care units (ICUs). Despite the increasing prevalence of Candida-related infections, monitoring the progression of these infections from colonization in COVID-19 ICU patients lacks sufficient information. This study aims prospectively to compare 62 COVID-19 and 60 non-COVID-19 ICU patients from admission to discharge in terms of colonization development, rates, isolated Candida species, risk factors, and Candida infections during hospitalization. A total of 1464 samples were collected at specific time intervals from various body sites [mouth, skin (axilla), rectal, and urine]. All samples were inoculated onto CHROMagar Candida and CHROMagar Candida Plus media, and isolates identified using MALDI-TOF MS. COVID-19 patients exhibited significantly higher colonization rates in oral, rectal, and urine samples compared to non-COVID-19 patients, (p < 0.05). Among the Candida species, non-albicans Candida was more frequently detected in COVID-19 patients, particularly in oral (75.8%-25%; p < 0.001) and rectal regions (74.19% - 46.66%; p < 0.05). Colonization with mixed Candida species was also more prevalent in the oropharyngeal region (p < 0.05). Mechanical ventilation and corticosteroid use emerged as elevated risk factors among COVID-19 patients (p < 0.05). Despite the colonization prevalence, both COVID-19-positive and negative patients exhibited low incidences of Candida infections, with rates of 9.67% (n = 6/62) and 6.67% (n = 3/60), respectively. Consequently, although Candida colonization rates were higher in COVID-19 ICU patients, there was no significant difference in Candida infection development compared to the non-COVID-19 group. However, the elevated rate of non-albicans Candida isolates highlights potential future infections, particularly given their intrinsic resistance in prophylactic or empirical treatments if needed. Additionally, the high rate of mixed colonization emphasizes the importance of using chromogenic media for routine evaluation.
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Affiliation(s)
- Ilvana Çaklovica Küçükkaya
- Istanbul University Istanbul Faculty of Medicine, Department of Medical Microbiology, 34093, Istanbul, Turkey
| | - Günseli Orhun
- Istanbul University Istanbul Faculty of Medicine, Department of Anesthesiology and Reanimation, 34093, Istanbul, Turkey
| | - Arif Atahan Çağatay
- Istanbul University Istanbul Faculty of Medicine, Department of Infectious Diseases and Clinical Microbiology, 34093, Istanbul, Turkey
| | - Sadık Kalaycı
- Yeditepe University Faculty of Engineering, Department of Genetics and Bioengineering, 34755, Istanbul, Turkey
| | - Figen Esen
- Istanbul University Istanbul Faculty of Medicine, Department of Anesthesiology and Reanimation, 34093, Istanbul, Turkey
| | - Fikrettin Şahin
- Istanbul University Istanbul Faculty of Medicine, Department of Infectious Diseases and Clinical Microbiology, 34093, Istanbul, Turkey
| | - Ali Ağaçfidan
- Istanbul University Istanbul Faculty of Medicine, Department of Medical Microbiology, 34093, Istanbul, Turkey
| | - Zayre Erturan
- Istanbul University Istanbul Faculty of Medicine, Department of Medical Microbiology, 34093, Istanbul, Turkey
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5
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Zuniga-Moya JC, Papadopoulos B, Mansoor AER, Mazi PB, Rauseo AM, Spec A. Incidence and Mortality of COVID-19-Associated Invasive Fungal Infections Among Critically Ill Intubated Patients: A Multicenter Retrospective Cohort Analysis. Open Forum Infect Dis 2024; 11:ofae108. [PMID: 38567199 PMCID: PMC10986750 DOI: 10.1093/ofid/ofae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/21/2024] [Indexed: 04/04/2024] Open
Abstract
Background An association between coronavirus disease 2019 (COVID-19)-associated invasive fungal infections (CAIFIs) and high mortality among intubated patients has been suggested in previous research. However, some of the current evidence was derived from small case series and multicenter studies conducted during different waves of the COVID-19 pandemic. We examined the incidence of CAIFIs and their associated mortality using a large, multicenter COVID-19 database built throughout the pandemic. Methods We conducted a retrospective analysis of the National COVID Cohort Collaborative (N3C) database collected from 76 medical centers in the United States between January 2020 and August 2022. Patients were 18 years or older and intubated after severe acute respiratory syndrome coronavirus 2 infection. The primary outcomes were incidence and all-cause mortality at 90 days. To assess all-cause mortality, we fitted Cox proportional hazard models after adjusting for confounders via inverse probability weighting. Results Out of the 4 916 229 patients with COVID-19 diagnosed during the study period, 68 383 (1.4%) met our cohort definition. The overall incidence of CAIFI was 2.80% (n = 1934/68 383). Aspergillus (48.2%; n = 933/1934) and Candida (41.0%; n = 793/1934) were the most common causative organisms. The incidence of CAIFIs associated with Aspergillus among patients who underwent BAL was 6.2% (n = 83/1328). Following inverse probability weighting, CAIFIs caused by Aspergillus (hazard ratio [HR], 2.0; 95% CI, 1.8-2.2) and Candida (HR, 1.7; 95% CI, 1.5-1.9) were associated with increased all-cause mortality. Systemic antifungals reduced mortality in 17% of patients with CAIFI with Aspergillus and 24% of patients with CAIFI with Candida. Conclusions The incidence of CAIFI was modest but associated with higher 90-day all-cause mortality among intubated patients. Systemic antifungals modified mortality.
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Affiliation(s)
| | | | | | - Patrick B Mazi
- St Louis School of Medicine, Washington University, St Louis, Missouri, USA
| | - Adriana M Rauseo
- St Louis School of Medicine, Washington University, St Louis, Missouri, USA
| | - Andrej Spec
- St Louis School of Medicine, Washington University, St Louis, Missouri, USA
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6
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Karakoyun AS, Spruijtenburg B, Unal N, Meijer EFJ, Sucu M, Hilmioğlu-Polat S, Meis JF, de Groot T, Ilkit M. Molecular typing and antifungal susceptibility profile of Candida krusei bloodstream isolates from Türkiye. Med Mycol 2024; 62:myae005. [PMID: 38289726 DOI: 10.1093/mmy/myae005] [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: 11/29/2023] [Revised: 01/05/2024] [Accepted: 01/29/2024] [Indexed: 02/01/2024] Open
Abstract
Candida krusei also known as Pichia kudriavzevii is a potentially multidrug-resistant yeast because it is intrinsically resistant to fluconazole and develops acquired resistance to echinocandins and polyenes. Here, we aim to provide a better understanding of the epidemiology and transmission modes of C. krusei infections by comparing invasive bloodstream (n = 35) and non-invasive vaginal (n = 20) C. krusei isolates. The genetic relatedness of the isolates was assessed using a newly described short tandem repeat (STR) analysis and their sensitivity to eight antifungal compounds was evaluated by antifungal susceptibility testing using the CLSI microbroth dilution method. All C. krusei isolates revealed unique STR genotypes, indicating the absence of clonal transmission in the study group. Furthermore, no drug-resistant or non-wild-type isolates were identified. Our findings demonstrated high resolution of STR genotyping for the detection and simultaneous genetic analysis of multiple C. krusei strains in clinical samples and excellent in vitro activity of common antifungal agents against invasive strains.
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Affiliation(s)
- Ayşe Sultan Karakoyun
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, Adana, Türkiye
| | - Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Disease, Canisius-Wilhelmina Hospital (CWZ)/Dicoon, SZ Nijmegen, The Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Nevzat Unal
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, Adana, Türkiye
- University of Health Sciences, Adana City Training and Research Hospital, Laboratory of Medical Microbiology, Adana, Türkiye
| | - Eelco F J Meijer
- Department of Medical Microbiology and Infectious Disease, Canisius-Wilhelmina Hospital (CWZ)/Dicoon, SZ Nijmegen, The Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Mete Sucu
- Division of Perinatology, Department of Obstetrics and Gynecology, Faculty of Medicine, Çukurova University, Adana, Türkiye
| | - Süleyha Hilmioğlu-Polat
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Ege University, Izmir, Türkiye
| | - Jacques F Meis
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Disease, Canisius-Wilhelmina Hospital (CWZ)/Dicoon, SZ Nijmegen, The Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, Adana, Türkiye
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7
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Govrins M, Lass-Flörl C. Candida parapsilosis complex in the clinical setting. Nat Rev Microbiol 2024; 22:46-59. [PMID: 37674021 DOI: 10.1038/s41579-023-00961-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
Representatives of the Candida parapsilosis complex are important yeast species causing human infections, including candidaemia as one of the leading diseases. This complex comprises C. parapsilosis, Candida orthopsilosis and Candida metapsilosis, and causes a wide range of clinical presentations from colonization to superficial and disseminated infections with a high prevalence in preterm-born infants and the potential to cause outbreaks in hospital settings. Compared with other Candida species, the C. parapsilosis complex shows high minimal inhibitory concentrations for echinocandin drugs due to a naturally occurring FKS1 polymorphism. The emergence of clonal outbreaks of strains with resistance to commonly used antifungals, such as fluconazole, is causing concern. In this Review, we present the latest medical data covering epidemiology, diagnosis, resistance and current treatment approaches for the C. parapsilosis complex. We describe its main clinical manifestations in adults and children and highlight new treatment options. We compare the three sister species, examining key elements of microbiology and clinical characteristics, including the population at risk, disease manifestation and colonization status. Finally, we provide a comprehensive resource for clinicians and researchers focusing on Candida species infections and the C. parapsilosis complex, aiming to bridge the emerging translational knowledge and future therapeutic challenges associated with this human pathogen.
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Affiliation(s)
- Miriam Govrins
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.
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8
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Bergin S, Doorley LA, Rybak JM, Wolfe KH, Butler G, Cuomo CA, Rogers PD. Analysis of clinical Candida parapsilosis isolates reveals copy number variation in key fluconazole resistance genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571446. [PMID: 38168157 PMCID: PMC10760152 DOI: 10.1101/2023.12.13.571446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
We used whole-genome sequencing to analyse a collection of 35 fluconazole resistant and 7 susceptible Candida parapsilosis isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. Phylogenetic analysis shows that although the collection is diverse, two probable outbreak groups were identified. We identified copy number variation of two genes, ERG11 and CDR1B, in resistant isolates. Two strains have a CNV at the ERG11 locus; the entire ORF is amplified in one, and only the promoter region is amplified in the other. We show the annotated telomeric gene CDR1B is actually an artefactual in silico fusion of two highly similar neighbouring CDR genes due to an assembly error in the C. parapsilosis CDC317 reference genome. We report highly variable copy numbers of the CDR1B region across the collection. Several strains have increased expansion of the two genes into a tandem array of new chimeric genes. Other strains have experienced a deletion between the two genes creating a single gene with a reciprocal chimerism. We find translocations, duplications, and gene conversion across the CDR gene family in the C. parapsilosis species complex, showing that it is a highly dynamic family.
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Affiliation(s)
- Sean Bergin
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Laura A Doorley
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey M Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kenneth H Wolfe
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI, USA
| | - P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
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9
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Pallotta F, Brescini L, Ianovitz A, Luchetti I, Franca L, Canovari B, Cerutti E, Barchiesi F. The Clinical Characteristics of Bloodstream Infections Due to Candida spp. in Patients Hospitalized in Intensive Care Units during the SARS-CoV-2 Pandemic: The Results of a Multicenter Study. J Fungi (Basel) 2023; 9:642. [PMID: 37367578 DOI: 10.3390/jof9060642] [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: 05/15/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
Candidemia is a serious health threat. Whether this infection has a greater incidence and a higher mortality rate in patients with COVID-19 is still debated. In this multicenter, retrospective, observational study, we aimed to identify the clinical characteristics associated with the 30-day mortality in critically ill patients with candidemia and to define the differences in candidemic patients with and without COVID-19. Over a three-year period (2019-2021), we identified 53 critically ill patients with candidemia, 18 of whom (34%) had COVID-19 and were hospitalized in four ICUs. The most frequent comorbidities were cardiovascular (42%), neurological (17%), chronic pulmonary diseases, chronic kidney failure, and solid tumors (13% each). A significantly higher proportion of COVID-19 patients had pneumonia, ARDS, septic shock, and were undergoing an ECMO procedure. On the contrary, non-COVID-19 patients had undergone previous surgeries and had used TPN more frequently. The mortality rate in the overall population was 43%: 39% and 46% in the COVID-19 and non-COVID-19 patients, respectively. The independent risk factors associated with a higher mortality were CVVH (HR 29.08 [CI 95% 3.37-250]) and a Charlson's score of > 3 (HR 9.346 [CI 95% 1.054-82.861]). In conclusion, we demonstrated that candidemia still has a high mortality rate in patients admitted to ICUs, irrespective of infection due to SARS-CoV-2.
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Affiliation(s)
- Francesco Pallotta
- Dipartimento di Scienze Biomediche e Sanità Pubblica, Università Politecnica delle Marche, 60126 Ancona, Italy
- Clinica Malattie Infettive, Azienda Ospedaliera Universitaria Ospedali Riuniti Umberto I-Lancisi-Salesi, 60126 Ancona, Italy
| | - Lucia Brescini
- Dipartimento di Scienze Biomediche e Sanità Pubblica, Università Politecnica delle Marche, 60126 Ancona, Italy
- Clinica Malattie Infettive, Azienda Ospedaliera Universitaria Ospedali Riuniti Umberto I-Lancisi-Salesi, 60126 Ancona, Italy
| | - Arianna Ianovitz
- Dipartimento di Scienze Biomediche e Sanità Pubblica, Università Politecnica delle Marche, 60126 Ancona, Italy
- Clinica Malattie Infettive, Azienda Ospedaliera Universitaria Ospedali Riuniti Umberto I-Lancisi-Salesi, 60126 Ancona, Italy
| | - Ilenia Luchetti
- Dipartimento di Scienze Biomediche e Sanità Pubblica, Università Politecnica delle Marche, 60126 Ancona, Italy
- Clinica Malattie Infettive, Azienda Ospedaliera Universitaria Ospedali Riuniti Umberto I-Lancisi-Salesi, 60126 Ancona, Italy
| | - Lucia Franca
- Dipartimento di Scienze Biomediche e Sanità Pubblica, Università Politecnica delle Marche, 60126 Ancona, Italy
- Malattie Infettive, Azienda Sanitaria Territoriale Pesaro-Urbino, 61029 Pesaro, Italy
| | - Benedetta Canovari
- Malattie Infettive, Azienda Sanitaria Territoriale Pesaro-Urbino, 61029 Pesaro, Italy
| | - Elisabetta Cerutti
- Anestesia e Rianimazione dei Trapianti e Chirurgia Maggiore, Azienda Ospedaliera Universitaria Ospedali Riuniti Umberto I-Lancisi-Salesi, 60126 Ancona, Italy
| | - Francesco Barchiesi
- Dipartimento di Scienze Biomediche e Sanità Pubblica, Università Politecnica delle Marche, 60126 Ancona, Italy
- Malattie Infettive, Azienda Sanitaria Territoriale Pesaro-Urbino, 61029 Pesaro, Italy
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10
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Daneshnia F, de Almeida Júnior JN, Ilkit M, Lombardi L, Perry AM, Gao M, Nobile CJ, Egger M, Perlin DS, Zhai B, Hohl TM, Gabaldón T, Colombo AL, Hoenigl M, Arastehfar A. Worldwide emergence of fluconazole-resistant Candida parapsilosis: current framework and future research roadmap. THE LANCET. MICROBE 2023; 4:e470-e480. [PMID: 37121240 PMCID: PMC10634418 DOI: 10.1016/s2666-5247(23)00067-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 05/02/2023]
Abstract
Candida parapsilosis is one of the most commen causes of life-threatening candidaemia, particularly in premature neonates, individuals with cancer of the haematopoietic system, and recipients of organ transplants. Historically, drug-susceptible strains have been linked to clonal outbreaks. However, worldwide studies started since 2018 have reported severe outbreaks among adults caused by fluconazole-resistant strains. Outbreaks caused by fluconazole-resistant strains are associated with high mortality rates and can persist despite strict infection control strategies. The emergence of resistance threatens the efficacy of azoles, which is the most widely used class of antifungals and the only available oral treatment option for candidaemia. The fact that most patients infected with fluconazole-resistant strains are azole-naive underscores the high potential adaptability of fluconazole-resistant strains to diverse hosts, environmental niches, and reservoirs. Another concern is the multidrug-resistant and echinocandin-tolerant C parapsilosis isolates, which emerged in 2020. Raising awareness, establishing effective clinical interventions, and understanding the biology and pathogenesis of fluconazole-resistant C parapsilosis are urgently needed to improve treatment strategies and outcomes.
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Affiliation(s)
- Farnaz Daneshnia
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - João N de Almeida Júnior
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil; Clinical Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, University of Çukurova, Adana, Türkiye
| | - Lisa Lombardi
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Austin M Perry
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, USA; Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
| | - Marilyn Gao
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, USA; Health Sciences Research Institute, University of California Merced, Merced, CA, USA
| | - Matthias Egger
- Division of Infectious Diseases, ECMM Excellence Center, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA; Department of Medical Sciences, Hackensack School of Medicine, Nutley, NJ, USA; Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Bing Zhai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tobias M Hohl
- Infectious Disease Service, Department of Medicine and Human Oncology, and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Toni Gabaldón
- Life Sciences Programme, Supercomputing Center, Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain; Catalan Institution for Research and Advanced Studies, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Barcelona, Spain
| | - Arnaldo Lopes Colombo
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Martin Hoenigl
- Division of Infectious Diseases, ECMM Excellence Center, Department of Internal Medicine, Medical University of Graz, Graz, Austria; Bio TechMed, Graz, Austria; Translational Medical Mycology Research Group, Medical University of Graz, Graz, Austria.
| | - Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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11
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Daneshnia F, Hilmioğlu-Polat S, Ilkit M, Fuentes D, Lombardi L, Binder U, Scheler J, Hagen F, Mansour MK, Butler G, Lass-Flörl C, Gabaldon T, Arastehfar A. Whole-genome sequencing confirms a persistent candidaemia clonal outbreak due to multidrug-resistant Candida parapsilosis. J Antimicrob Chemother 2023:7143692. [PMID: 37100456 DOI: 10.1093/jac/dkad112] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/24/2023] [Indexed: 04/28/2023] Open
Abstract
OBJECTIVES Although perceived as a rare clinical entity, recent studies have noted the emergence of MDR C. parapsilosis (MDR-Cp) isolates from single patients (resistant to both azole and echinocandins). We previously reported a case series of MDR-Cp isolates carrying a novel FKS1R658G mutation. Herein, we identified an echinocandin-naive patient infected with MDR-Cp a few months after the previously described isolates. WGS and CRISPR-Cas9 editing were used to explore the origin of the new MDR-Cp isolates, and to determine if the novel mutation confers echinocandin resistance. METHODS WGS was applied to assess the clonality of these isolates and CRISPR-Cas9 editing and a Galleria mellonella model were used to examine whether FKS1R658G confers echinocandin resistance. RESULTS Fluconazole treatment failed, and the patient was successfully treated with liposomal amphotericin B (LAMB). WGS proved that all historical and novel MDR-Cp strains were clonal and distant from the fluconazole-resistant outbreak cluster in the same hospital. CRISPR-Cas9 editing and G. mellonella virulence assays confirmed that FKS1R658G confers echinocandin resistance in vitro and in vivo. Interestingly, the FKS1R658G mutant showed a very modest fitness cost compared with the parental WT strain, consistent with the persistence of the MDR-Cp cluster in our hospital. CONCLUSIONS Our study showcases the emergence of MDR-Cp isolates as a novel threat in clinical settings, which undermines the efficacy of the two most widely used antifungal drugs against candidiasis, leaving only LAMB as a last resort. Additionally, surveillance studies and WGS are warranted to effectively establish infection control and antifungal stewardship strategies.
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Affiliation(s)
- Farnaz Daneshnia
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114USA
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, 1012 WX, The Netherlands
| | | | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Diego Fuentes
- Comparative Genomics group, Life Sciences department, Barcelona Supercomputing Center (BSC-CNS), Carrer de Jordi Girona, 29, 31, 08034 Barcelona, Spain
- Comparative Genomics group, Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), Carrer Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Lisa Lombardi
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Ulrike Binder
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Jakob Scheler
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Ferry Hagen
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, 1012 WX, The Netherlands
- Westerdijk Fungal Biodiversity Institute, Utrecht, 3584CT, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, 3584CX, The Netherlands
| | - Michael K Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115USA
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Cornelia Lass-Flörl
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Toni Gabaldon
- Comparative Genomics group, Life Sciences department, Barcelona Supercomputing Center (BSC-CNS), Carrer de Jordi Girona, 29, 31, 08034 Barcelona, Spain
- Comparative Genomics group, Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), Carrer Baldiri Reixac 10, 08028, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115USA
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12
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Bauer KA, Yu K, Moise PA, Finelli L, Ai C, Watts J, Ye G, Gupta V. Morbidity and mortality of hospitalised patients with candidemia during the various severe acute respiratory syndrome coronavirus 2 pandemic waves: A multicentre evaluation of 248 US hospitals. Mycoses 2023; 66:483-487. [PMID: 36740751 DOI: 10.1111/myc.13573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/07/2023]
Abstract
BACKGROUND Studies evaluating outcomes of COVID-19 patients with candidemia are limited and have only evaluated a single timepoint during the pandemic. OBJECTIVES To compare the prevalence and outcomes associated with candidemia in patients based on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) status and through the various pandemic waves (1 March 2020-5 March 2022). PATIENTS/METHODS Multicentre, retrospective cohort analysis of data from 248 US medical facilities using the BD Insights Research Database (Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA). Eligible patients were adults aged ≥18 years who were hospitalised for >1 day, had a SARS-CoV-2 test and a positive blood culture for Candida spp. RESULTS During the study time frame, there were 2,402,879 hospital admissions; 234,903 (9.7%) and 2,167,976 (90.3%) patients were SARS-CoV-2 positive and negative, respectively. A significantly higher rate of candidemia/1000 admissions was observed in SARS-CoV-2-positive patients compared to SARS-CoV-2-negative patients (3.18 vs. 0.99; p < .001). The highest candidemia rate for SARS-CoV-2-positive patients was observed during the Alpha SARS-CoV-2 wave (June 2020-August 2020) with the lowest candidemia rate during the Omicron wave. Hospital mortality was significantly higher in SARS-CoV-2-positive patients compared to SARS-CoV-2-negative patients with candidemia (59.6% vs. 30.8%; p < .001). When evaluating the mortality rate through the various pandemic waves, the rate for the overall population did not change. CONCLUSIONS Our study indicates high morbidity and mortality for hospitalised patients with COVID-19 and candidemia which was consistent throughout the pandemic. Patients with COVID-19 are at an increased risk for candidemia; importantly, the magnitude of which may differ based on the circulating variant.
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Affiliation(s)
| | - Kalvin Yu
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | | | | | - ChinEn Ai
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Janet Watts
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Gang Ye
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Vikas Gupta
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
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13
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Witt LS, Howard-Anderson JR, Jacob JT, Gottlieb LB. The impact of COVID-19 on multidrug-resistant organisms causing healthcare-associated infections: a narrative review. JAC Antimicrob Resist 2022; 5:dlac130. [PMID: 36601548 PMCID: PMC9798082 DOI: 10.1093/jacamr/dlac130] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) changed healthcare across the world. With this change came an increase in healthcare-associated infections (HAIs) and a concerning concurrent proliferation of MDR organisms (MDROs). In this narrative review, we describe the impact of COVID-19 on HAIs and MDROs, describe potential causes of these changes, and discuss future directions to combat the observed rise in rates of HAIs and MDRO infections.
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Affiliation(s)
- Lucy S Witt
- Corresponding author. E-mail: ; @drwittID, @JessH_A, @jestjac
| | - Jessica R Howard-Anderson
- Division of Infection Diseases, Emory University School of Medicine, Atlanta, GA, USA,Emory Antibiotic Resistance Group, Emory University, Atlanta, GA, USA
| | - Jesse T Jacob
- Division of Infection Diseases, Emory University School of Medicine, Atlanta, GA, USA,Emory Antibiotic Resistance Group, Emory University, Atlanta, GA, USA
| | - Lindsey B Gottlieb
- Division of Infection Diseases, Emory University School of Medicine, Atlanta, GA, USA,Emory Antibiotic Resistance Group, Emory University, Atlanta, GA, USA
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14
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Daneshnia F, de Almeida Júnior JN, Arastehfar A, Lombardi L, Shor E, Moreno L, Mendes AV, Barberino MG, Yamamoto DT, Butler G, Perlin DS, Colombo AL. Determinants of fluconazole resistance and echinocandin tolerance in C. parapsilosis isolates causing a large clonal candidemia outbreak among COVID-19 patients in a Brazilian ICU. Emerg Microbes Infect 2022; 11:2264-2274. [PMID: 36066554 PMCID: PMC9542950 DOI: 10.1080/22221751.2022.2117093] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Patients presenting with severe COVID-19 are predisposed to acquire secondary fungal infections such as COVID-19-associated candidemia (CAC), which are associated with poor clinical outcomes despite antifungal treatment. The extreme burden imposed on clinical facilities during the COVID-19 pandemic has provided a permissive environment for the emergence of clonal outbreaks of multiple Candida species, including C. auris and C. parapsilosis. Here we report the largest clonal CAC outbreak to date caused by fluconazole resistant (FLZR) and echinocandin tolerant (ECT) C. parapsilosis. Sixty C. parapsilosis strains were obtained from 57 patients at a tertiary care hospital in Brazil, 90% of them were FLZR and ECT. Although only 35.8% of FLZR isolates contained an ERG11 mutation, all of them contained the TAC1L518F mutation and significantly overexpressed CDR1. Introduction of TAC1L518F into a susceptible background increased the MIC of fluconazole and voriconazole 8-fold and resulted in significant basal overexpression of CDR1. Additionally, FLZR isolates exclusively harbored E1939G outside of Fks1 hotspot-2, which did not confer echinocandin resistance, but significantly increased ECT. Multilocus microsatellite typing showed that 51/60 (85%) of the FLZR isolates belonged to the same cluster, while the susceptible isolates each represented a distinct lineage. Finally, biofilm production in FLZR isolates was significantly lower than in susceptible counterparts Suggesting that it may not be an outbreak determinant. In summary, we show that TAC1L518F and FKS1E1393G confer FLZR and ECT, respectively, in CAC-associated C. parapsilosis. Our study underscores the importance of antifungal stewardship and effective infection control strategies to mitigate clonal C. parapsilosis outbreaks.
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Affiliation(s)
- Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - João N de Almeida Júnior
- Special Mycology Laboratory, Federal University of São Paulo, Brazil.,Clinical Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Lisa Lombardi
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Erika Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA.,Hackensack Meridian School of Medicine, Nutley NJ 07710, USA
| | - Lis Moreno
- Hospital São Rafael, Salvador, Brazil.,Instituto D'OR de Pesquisa e Ensino (IDOR)
| | - Ana Verena Mendes
- Hospital São Rafael, Salvador, Brazil.,Instituto D'OR de Pesquisa e Ensino (IDOR)
| | | | | | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA.,Hackensack Meridian School of Medicine, Nutley NJ 07710, USA.,Georgetown University Lombardi Comprehensive Cancer Center, Washington DC 20057, USA
| | - Arnaldo Lopes Colombo
- Special Mycology Laboratory, Federal University of São Paulo, Brazil.,Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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15
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Kakehi A, Hagiya H, Iio K, Nakano Y, Ihoriya H, Taira Y, Nakamoto K, Hasegawa K, Higashikage A, Otsuka F. Candida dubliniensis fungemia in a patient with severe COVID-19: A case report. J Infect Chemother 2022; 28:1433-1435. [PMID: 35863730 PMCID: PMC9293379 DOI: 10.1016/j.jiac.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/27/2022] [Accepted: 07/12/2022] [Indexed: 10/30/2022]
Abstract
Candida dubliniensis phenotypically mimics Candida albicans in its microbiological features; thus, its clinical characteristics have yet to be fully elucidated. Here we report the case of a 68-year-old Japanese man who developed C. dubliniensis fungemia during treatment for severe coronavirus disease 2019 (COVID-19). The patient was intubated and received a combination of immunosuppressants, including high-dose methylprednisolone and two doses of tocilizumab, as well as remdesivir, intravenous heparin, and ceftriaxone. A blood culture on admission day 11 revealed Candida species, which was confirmed as C. dubliniensis by mass spectrometry. An additional sequencing analysis of the 26S rDNA and ITS regions confirmed that the organism was 100% identical to the reference strain of C. dubliniensis (ATCC MYA-646). Considering the simultaneous isolation of C. dubliniensis from a sputum sample, the lower respiratory tract could be an entry point for candidemia. Although treatment with micafungin successfully eradicated the C. dubliniensis fungemia, the patient died of COVID-19 progression. In this case, aggressive immunosuppressive therapy could have caused the C. dubliniensis fungemia. Due to insufficient clinical reports on C. dubliniensis infection based on definitive diagnosis, the whole picture of the cryptic organism is still unknown. Further accumulation of clinical and microbiological data of the pathogen is needed to elucidate their clinical significance.
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Affiliation(s)
- Ayaka Kakehi
- Microbiology Division, Clinical Laboratory, Okayama University Hospital, Okayama, 700-8558, Japan
| | - Hideharu Hagiya
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan.
| | - Koji Iio
- Microbiology Division, Clinical Laboratory, Okayama University Hospital, Okayama, 700-8558, Japan
| | - Yasuhiro Nakano
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Hiromi Ihoriya
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Yuki Taira
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Kenta Nakamoto
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Kou Hasegawa
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Akihito Higashikage
- Microbiology Division, Clinical Laboratory, Okayama University Hospital, Okayama, 700-8558, Japan
| | - Fumio Otsuka
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
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16
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Papadimitriou-Olivgeris M, Kolonitsiou F, Kefala S, Spiliopoulou A, Aretha D, Bartzavali C, Siapika A, Marangos M, Fligou F. Increased incidence of candidemia in critically ill patients during the Coronavirus Disease 2019 (COVID-19) pandemic. Braz J Infect Dis 2022; 26:102353. [PMID: 35500645 PMCID: PMC9035354 DOI: 10.1016/j.bjid.2022.102353] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/05/2022] [Accepted: 04/11/2022] [Indexed: 12/15/2022] Open
Abstract
Background Patients with severe Coronavirus Disease 2019 (COVID-19) are treated with corticosteroids. Aim We aimed to evaluate the role of corticosteroid treatment in candidemia development during the COVID-19 pandemic. Methods This retrospective study was conducted in a Greek ICU, from 2010 to August 2021, encompassing a pre-pandemic and a pandemic period (pandemic period: April 2020 to August 2021). All adult patients with candidemia were included. Results During the study period, 3,572 patients were admitted to the ICU, 339 patients during the pandemic period, of whom 196 were SARS-CoV-2-positive. In total, 281 candidemia episodes were observed in 239 patients, 114 in the pandemic period. The majority of candidemias in both periods were catheter-related (161; 50.4%). The incidence of candidemia in the pre-pandemic period was 5.2 episodes per 100 admissions, while in the pandemic period was 33.6 (p < 0.001). In the pandemic period, the incidence among COVID-19 patients was 38.8 episodes per 100 admissions, while in patients without COVID-19 incidence was 26.6 (p = 0.019). Corticosteroid administration in both periods was not associated with increased candidemia incidence. Conclusions A significant increase of candidemia incidence was observed during the pandemic period in patients with and without COVID-19. This increase cannot be solely attributed to immunosuppression (corticosteroids, tocilizumab) of severe COVID-19 patients, but also to increased workload of medical and nursing staff.
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