1
|
Narayanan A, Selvakumar P, Siddharthan R, Sanyal K. Identification of C. auris clade 5 isolates using claID. Med Mycol 2024; 62:myae018. [PMID: 38414264 DOI: 10.1093/mmy/myae018] [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: 12/09/2023] [Revised: 02/05/2024] [Accepted: 02/26/2024] [Indexed: 02/29/2024] Open
Abstract
Candida auris poses threats to the global medical community due to its multidrug resistance, ability to cause nosocomial outbreaks and resistance to common sterilization agents. Different variants that emerged at different geographical zones were classified as clades. Clade-typing becomes necessary to track its spread, possible emergence of new clades, and to predict the properties that exhibit a clade bias. We previously reported a colony-Polymerase Chain Reaction-based, clade-identification method employing whole genome alignments and identification of clade-specific sequences of four major geographical clades. Here, we expand the panel by identifying clade 5 which was later isolated in Iran, using specific primers designed through in silico analyses.
Collapse
Affiliation(s)
- Aswathy Narayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,560064, India
| | - Pavitra Selvakumar
- Computational Biology, The Institute of Mathematical Sciences, Chennai, 600113, India
- Homi Bhabha National Institute, Mumbai, 400094, India
| | - Rahul Siddharthan
- Computational Biology, The Institute of Mathematical Sciences, Chennai, 600113, India
- Homi Bhabha National Institute, Mumbai, 400094, India
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,560064, India
| |
Collapse
|
2
|
Giacobbe DR, Mikulska M, Vena A, Di Pilato V, Magnasco L, Marchese A, Bassetti M. Challenges in the diagnosis and treatment of candidemia due to multidrug-resistant Candida auris. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1061150. [PMID: 37746122 PMCID: PMC10512377 DOI: 10.3389/ffunb.2023.1061150] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/16/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Daniele Roberto Giacobbe
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Malgorzata Mikulska
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Antonio Vena
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Laura Magnasco
- Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Anna Marchese
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- Unità di Microbiologia, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Matteo Bassetti
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| |
Collapse
|
3
|
Functional Expression of Recombinant Candida auris Proteins in Saccharomyces cerevisiae Enables Azole Susceptibility Evaluation and Drug Discovery. J Fungi (Basel) 2023; 9:jof9020168. [PMID: 36836283 PMCID: PMC9960696 DOI: 10.3390/jof9020168] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Candida auris infections are difficult to treat due to acquired drug resistance against one or multiple antifungal drug classes. The most prominent resistance mechanisms in C. auris are overexpression and point mutations in Erg11, and the overexpression of efflux pump genes CDR1 and MDR1. We report the establishment of a novel platform for molecular analysis and drug screening based on acquired azole-resistance mechanisms found in C. auris. Constitutive functional overexpression of wild-type C. auris Erg11, Erg11 with amino acid substitutions Y132F or K143R and the recombinant efflux pumps Cdr1 and Mdr1 has been achieved in Saccharomyces cerevisiae. Phenotypes were evaluated for standard azoles and the tetrazole VT-1161. Overexpression of CauErg11 Y132F, CauErg11 K143R, and CauMdr1 conferred resistance exclusively to the short-tailed azoles Fluconazole and Voriconazole. Strains overexpressing the Cdr1 protein were pan-azole resistant. While CauErg11 Y132F increased VT-1161 resistance, K143R had no impact. Type II binding spectra showed tight azole binding to the affinity-purified recombinant CauErg11 protein. The Nile Red assay confirmed the efflux functions of CauMdr1 and CauCdr1, which were specifically inhibited by MCC1189 and Beauvericin, respectively. CauCdr1 exhibited ATPase activity that was inhibited by Oligomycin. The S. cerevisiae overexpression platform enables evaluation of the interaction of existing and novel azole drugs with their primary target CauErg11 and their susceptibility to drug efflux.
Collapse
|
4
|
Gómez-Gaviria M, Martínez-Álvarez JA, Chávez-Santiago JO, Mora-Montes HM. Candida haemulonii Complex and Candida auris: Biology, Virulence Factors, Immune Response, and Multidrug Resistance. Infect Drug Resist 2023; 16:1455-1470. [PMID: 36942024 PMCID: PMC10024503 DOI: 10.2147/idr.s402754] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
There is worldwide concern about the constant increase in infections caused by Candida species that are multiresistant to antifungal drugs. The most common candidiasis is caused by Candida albicans, however, the species of the Candida haemulonii complex and Candida auris are emerging opportunistic pathogens, which isolation from clinical samples has significantly increased in the past years. The special interest in the study of these species lies in their ability to evade the action of antifungal drugs, such as amphotericin B, azoles, and echinocandins. In addition, the phenotypic changes of these species have given them the ability to easily adapt to environmental changes, including the host milieu and immunity. In this paper, a detailed review of the current literature on the C. haemulonii complex and C. auris is shown, analyzing aspects such as biology, immune response, putative virulence factors, infection, treatment, and the current strategies for diagnosis.
Collapse
Affiliation(s)
- Manuela Gómez-Gaviria
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Guanajuato, Gto, México
- Correspondence: Manuela Gómez-Gaviria; Héctor M Mora-Montes, Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, Col. Noria Alta, Guanajuato, Gto, C. P. 36050, México, Tel +52 473-7320006 Ext. 8193, Fax +52 473-7320006 Ext. 8153, Email ;
| | - José A Martínez-Álvarez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Guanajuato, Gto, México
| | - Joaquín O Chávez-Santiago
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Guanajuato, Gto, México
| | - Héctor M Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Guanajuato, Gto, México
| |
Collapse
|
5
|
ClaID: a Rapid Method of Clade-Level Identification of the Multidrug Resistant Human Fungal Pathogen Candida auris. Microbiol Spectr 2022; 10:e0063422. [PMID: 35343775 PMCID: PMC9045239 DOI: 10.1128/spectrum.00634-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Candida auris, the multidrug-resistant human fungal pathogen, emerged as four major distinct geographical clades (clade 1–clade 4) in the past decade. Though isolates of the same species, C. auris clinical strains exhibit clade-specific properties associated with virulence and drug resistance. In this study, we report the identification of unique DNA sequence junctions by mapping clade-specific regions through comparative analysis of whole-genome sequences of strains belonging to different clades. These unique DNA sequence stretches are used to identify C. auris isolates at the clade level in subsequent in silico and experimental analyses. We develop a colony PCR-based clade-identification system (ClaID), which is rapid and specific. In summary, we demonstrate a proof-of-concept for using unique DNA sequence junctions conserved in a clade-specific manner for the rapid identification of each of the four major clades of C. auris. IMPORTANCEC. auris was first isolated in Japan in 2009 as an antifungal drug-susceptible pathogen causing localized infections. Within a decade, it simultaneously evolved in different parts of the world as distinct clades exhibiting resistance to antifungal drugs at varying levels. Recent studies hinted the mixing of isolates belonging to different geographical clades in a single location, suggesting that the area of isolation alone may not indicate the clade status of an isolate. In this study, we compared the genomes of representative strains of the four major clades to identify clade-specific sequences, which were then used to design clade-specific primers. We propose the utilization of whole genome sequence data to extract clade-specific sequences for clade-typing. The colony PCR-based method employed can rapidly distinguish between the four major clades of C. auris, with scope for expanding the panel by adding more primer pairs.
Collapse
|
6
|
Vitale RG. Role of Antifungal Combinations in Difficult to Treat Candida Infections. J Fungi (Basel) 2021; 7:731. [PMID: 34575770 PMCID: PMC8468556 DOI: 10.3390/jof7090731] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/27/2021] [Accepted: 09/02/2021] [Indexed: 01/23/2023] Open
Abstract
Candida infections are varied and, depending on the immune status of the patient, a life-threatening form may develop. C. albicans is the most prevalent species isolated, however, a significant shift towards other Candida species has been noted. Monotherapy is frequently indicated, but the patient's evolution is not always favorable. Drug combinations are a suitable option in specific situations. The aim of this review is to address this problem and to discuss the role of drug combinations in difficult to treat Candida infections. A search for eligible studies in PubMed and Google Scholar databases was performed. An analysis of the data was carried out to define in which cases a combination therapy is the most appropriate. Combination therapy may be used for refractory candidiasis, endocarditis, meningitis, eye infections and osteomyelitis, among others. The role of the drug combination would be to increase efficacy, reduce toxicity and improve the prognosis of the patient in infections that are difficult to treat. More clinical studies and reporting of cases in which drug combinations are used are needed in order to have more data that support the use of this therapeutic strategy.
Collapse
Affiliation(s)
- Roxana G. Vitale
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina;
- Unidad de Parasitología, Sector Micología, Hospital J. M. Ramos Mejía, Buenos Aires, Argentina
| |
Collapse
|
7
|
[AmBisome, three challenges: Candida auris infection, central nervous system infection, and biofilm-associated infection]. Rev Iberoam Micol 2021; 38:84-90. [PMID: 34144836 DOI: 10.1016/j.riam.2021.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/21/2021] [Accepted: 03/31/2021] [Indexed: 12/17/2022] Open
Abstract
The treatment of invasive fungal infections remains a challenge, both for the diagnosis and for the need of providing the appropriate antifungal therapy. Candida auris is a pathogenic yeast that is responsible for hospital outbreaks, especially in intensive care units; it is characterized by a high resistance to the antifungal agents and can become multidrug-resistant. At present, the recommended antifungal agents for the invasive infections with this pathogen are echinocandins, always after carrying out an antifungal susceptibility testing. In case of no clinical response or persistent candidemia, the addition of liposomal amphotericin B or isavuconazole may be considered. Both fungal infection of the central nervous system and that associated with biomedical devices remain rare entities affecting mainly immunocompromised patients. However, an increase in their incidence in recent years, along with high morbidity and mortality, has been shown. The treatment of these infections is conditioned by the limited knowledge of the pharmacokinetic properties of antifungals. A better understanding of the pharmacokinetic and pharmacodynamic parameters of the different antifungals is essential to determine the efficacy of the antifungal agents in the treatment of these infections.
Collapse
|
8
|
Černáková L, Roudbary M, Brás S, Tafaj S, Rodrigues CF. Candida auris: A Quick Review on Identification, Current Treatments, and Challenges. Int J Mol Sci 2021; 22:4470. [PMID: 33922907 PMCID: PMC8123192 DOI: 10.3390/ijms22094470] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 02/07/2023] Open
Abstract
Candida auris is a novel and major fungal pathogen that has triggered several outbreaks in the last decade. The few drugs available to treat fungal diseases, the fact that this yeast has a high rate of multidrug resistance and the occurrence of misleading identifications, and the ability of forming biofilms (naturally more resistant to drugs) has made treatments of C. auris infections highly difficult. This review intends to quickly illustrate the main issues in C. auris identification, available treatments and the associated mechanisms of resistance, and the novel and alternative treatment and drugs (natural and synthetic) that have been recently reported.
Collapse
Affiliation(s)
- Lucia Černáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia;
| | - Maryam Roudbary
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran;
| | - Susana Brás
- Centre of Biological Engineering, LIBRO—‘Laboratório de Investigação em Biofilmes Rosário Oliveira’, University of Minho, 4710-057 Braga, Portugal;
| | - Silva Tafaj
- Microbiology Department, University Hospital “Shefqet Ndroqi”, 1044 Tirana, Albania;
| | - Célia F. Rodrigues
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal
| |
Collapse
|
9
|
Ahmad S, Alfouzan W. Candida auris: Epidemiology, Diagnosis, Pathogenesis, Antifungal Susceptibility, and Infection Control Measures to Combat the Spread of Infections in Healthcare Facilities. Microorganisms 2021; 9:microorganisms9040807. [PMID: 33920482 PMCID: PMC8069182 DOI: 10.3390/microorganisms9040807] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/21/2022] Open
Abstract
Candida auris, a recently recognized, often multidrug-resistant yeast, has become a significant fungal pathogen due to its ability to cause invasive infections and outbreaks in healthcare facilities which have been difficult to control and treat. The extraordinary abilities of C. auris to easily contaminate the environment around colonized patients and persist for long periods have recently resulted in major outbreaks in many countries. C. auris resists elimination by robust cleaning and other decontamination procedures, likely due to the formation of 'dry' biofilms. Susceptible hospitalized patients, particularly those with multiple comorbidities in intensive care settings, acquire C. auris rather easily from close contact with C. auris-infected patients, their environment, or the equipment used on colonized patients, often with fatal consequences. This review highlights the lessons learned from recent studies on the epidemiology, diagnosis, pathogenesis, susceptibility, and molecular basis of resistance to antifungal drugs and infection control measures to combat the spread of C. auris infections in healthcare facilities. Particular emphasis is given to interventions aiming to prevent new infections in healthcare facilities, including the screening of susceptible patients for colonization; the cleaning and decontamination of the environment, equipment, and colonized patients; and successful approaches to identify and treat infected patients, particularly during outbreaks.
Collapse
|
10
|
Alfouzan W, Ahmad S, Dhar R, Asadzadeh M, Almerdasi N, Abdo NM, Joseph L, de Groot T, Alali WQ, Khan Z, Meis JF, Al-Rashidi MR. Molecular Epidemiology of Candida Auris Outbreak in a Major Secondary-Care Hospital in Kuwait. J Fungi (Basel) 2020; 6:E307. [PMID: 33233388 PMCID: PMC7712429 DOI: 10.3390/jof6040307] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/11/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
The emerging, often multidrug-resistant Candida auris is increasingly being associated with outbreaks in healthcare facilities. Here we describe the molecular epidemiology of a C. auris outbreak during 18 months, which started in 2018 in the high dependency unit (HDU) of a secondary-care hospital in Kuwait. Demographic and clinical data for candidemia and colonized patients were prospectively recorded. Clinical and environmental isolates were subjected to phenotypic and molecular identification; antifungal susceptibility testing by broth microdilution method; PCR-sequencing of ERG11 and FKS1 for resistance mechanisms to triazoles and echinocandins, respectively; and molecular fingerprinting by short tandem repeat (STR) analyses. Seventy-one (17 candidemic and 54 colonized) patients including 26 with candiduria and seven environmental samples yielded C. auris. All isolates were identified as C. auris by Vitek2, MALDI-TOF MS, PCR amplification and/or PCR-sequencing of rDNA. Twelve candidemia and 26 colonized patients were admitted or exposed to HDU. Following outbreak recognition, an intensive screening program was instituted for new patients. Despite treatment of all candidemia and 36 colonized patients, 9 of 17 candidemia and 27 of 54 colonized patients died with an overall crude mortality rate of ~50%. Nearly all isolates were resistant to fluconazole and contained the Y132F mutation in ERG11 except one patient's isolates, which were also distinct by STR typing. Only urine isolates from two patients developed echinocandin resistance with concomitant FKS1 mutations. The transmission of C. auris in this outbreak was linked to infected/colonized patients and the hospital environment. However, despite continuous surveillance and enforcement of infection control measures, sporadic new cases continued to occur, challenging the containment efforts.
Collapse
Affiliation(s)
- Wadha Alfouzan
- Microbiology Unit, Department of Laboratories, Farwaniya Hospital, P.O. Box 13373, Farwaniya 81004, Kuwait; (R.D.); (N.A.)
- Department of Microbiology, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait; (S.A.); (M.A.); (L.J.); (Z.K.)
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait; (S.A.); (M.A.); (L.J.); (Z.K.)
| | - Rita Dhar
- Microbiology Unit, Department of Laboratories, Farwaniya Hospital, P.O. Box 13373, Farwaniya 81004, Kuwait; (R.D.); (N.A.)
| | - Mohammad Asadzadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait; (S.A.); (M.A.); (L.J.); (Z.K.)
| | - Noura Almerdasi
- Microbiology Unit, Department of Laboratories, Farwaniya Hospital, P.O. Box 13373, Farwaniya 81004, Kuwait; (R.D.); (N.A.)
| | - Naglaa M. Abdo
- Department of Infection Control, Farwaniya Hospital, P.O. Box 13373, Farwaniya 81004, Kuwait;
- Department of Community, Environmental and Occupational Medicine, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Leena Joseph
- Department of Microbiology, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait; (S.A.); (M.A.); (L.J.); (Z.K.)
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; (T.d.G.); (J.F.M.)
| | - Walid Q. Alali
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait;
| | - Ziauddin Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait; (S.A.); (M.A.); (L.J.); (Z.K.)
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; (T.d.G.); (J.F.M.)
- Center of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, Curitiba 80060-000, Brazil
| | | |
Collapse
|