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Politi L, Vrioni G, Hatzianastasiou S, Lada M, Martsoukou M, Sipsas NV, Chini M, Baka V, Kafkoula E, Masgala A, Pirounaki M, Michailidis C, Chrysos G, Zarkotou O, Mamali V, Papastamopoulos V, Saroglou G, Pournaras S, Meletiadis J, Karakasiliotis I, Karachalios S, Smilakou S, Skandami V, Orfanidou M, Argyropoulou A, Tsakris A, Kontopidou F. Candida auris in Greek healthcare facilities: Active surveillance results on first cases and outbreaks from eleven hospitals within Attica region. J Mycol Med 2024; 34:101477. [PMID: 38574412 DOI: 10.1016/j.mycmed.2024.101477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Candida auris was sporadically detected in Greece until 2019. Thereupon, there has been an increase in isolations among inpatients of healthcare facilities. AIM We aim to report active surveillance data on MALDI-TOF confirmed Candida auris cases and outbreaks, from November 2019 to September 2021. METHODS A retrospective study on hospital-based Candida auris data, over a 23-month period was conducted, involving 11 hospitals within Attica region. Antifungal susceptibility testing and genotyping were conducted. Case mortality and fatality rates were calculated and p-values less than 0.05 were considered statistically significant. Infection control measures were enforced and enhanced. RESULTS Twenty cases with invasive infection and 25 colonized were identified (median age: 72 years), all admitted to hospitals for reasons other than fungal infections. Median hospitalisation time until diagnosis was 26 days. Common risk factors among cases were the presence of indwelling devices (91.1 %), concurrent bacterial infections during hospitalisation (60.0 %), multiple antimicrobial drug treatment courses prior to hospitalisation (57.8 %), and admission in the ICU (44.4 %). Overall mortality rate was 53 %, after a median of 41.5 hospitalisation days. Resistance to fluconazole and amphotericin B was identified in 100 % and 3 % of tested clinical isolates, respectively. All isolates belonged to South Asian clade I. Outbreaks were identified in six hospitals, while remaining hospitals detected sporadic C. auris cases. CONCLUSION Candida auris has proven its ability to rapidly spread and persist among inpatients and environment of healthcare facilities. Surveillance focused on the presence of risk factors and local epidemiology, and implementation of strict infection control measures remain the most useful interventions.
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Affiliation(s)
- Lida Politi
- ECDC Fellowship Programme, Field Epidemiology Path (EPIET), European Centre for Disease Prevention and Control (ECDC), Department of Microbial Resistance and Infections in Health Care Settings, Directorate of Surveillance and Prevention of Infectious Diseases, National Public Health Organization, Athens, Greece.
| | - Georgia Vrioni
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Greece
| | - Sofia Hatzianastasiou
- Department of Microbial Resistance and Infections in Health Care Settings, Directorate of Surveillance and Prevention of Infectious Diseases, National Public Health Organization, Athens, Greece
| | - Malvina Lada
- Second Department of Internal Medicine, "Sismanogleio" General Hospital of Athens, Athens, Greece
| | - Maria Martsoukou
- Department of Microbiology, "Sismanogleio" General Hospital, Athens, Greece
| | - Nikolaos V Sipsas
- Infectious Diseases Unit, "Laikon" General Hospital, and Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Chini
- 3rd Department of Internal Medicine and Infectious Diseases Unit, "Korgialeneion-Benakeion" General Hospital, Athens, Greece
| | - Vasiliki Baka
- Microbiology Department, "Korgialeneion-Benakeion" General Hospital, Athens, Greece
| | - Eleni Kafkoula
- Microbiology Department, "Korgialeneion-Benakeion" General Hospital, Athens, Greece
| | - Aikaterini Masgala
- 2nd Department of Internal Medicine, "Konstantopouleio" General Hospital, Athens, Greece
| | - Maria Pirounaki
- Department of Medicine and Laboratory, National and Kapodistrian University of Athens Medical School, "Hippokration" General Hospital, Athens, Greece
| | - Christos Michailidis
- 1st Department of Internal Medicine, "Georgios Gennimatas" General Hospital of Athens, Athens, Greece
| | - Georgios Chrysos
- 2nd Department of Medicine and Infectious Diseases Unit, Tzaneio Hospital, Piraeus, Greece
| | | | - Vasiliki Mamali
- Department of Microbiology, Tzaneio Hospital, Piraeus, Greece
| | - Vasileios Papastamopoulos
- 5th Department of Internal Medicine and Infectious Diseases Unit, "Evaggelismos" General Hospital, Athens, Greece
| | - Georgios Saroglou
- Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - Spyros Pournaras
- Department of Clinical Microbiology, ATTIKON University Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Joseph Meletiadis
- Department of Clinical Microbiology, ATTIKON University Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Stefanos Karachalios
- Department of Microbiology, "Agioi Anargyroi" General Oncology Hospital, Athens, Greece
| | | | - Vasiliki Skandami
- Department of Microbiology, "Hippokration" Athens General Hospital, Athens, Greece
| | - Maria Orfanidou
- Microbiology Department, "Georgios Gennimatas" General Hospital, Athens, Greece
| | - Athina Argyropoulou
- Department of Clinical Microbiology, "Evaggelismos" General Hospital, Athens, Greece
| | - Athanassios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Greece
| | - Flora Kontopidou
- Directorate of Surveillance and Prevention of Infectious Diseases, National Public Health Organization, Athens, Greece
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2
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Izumi H, Nafie LA, Dukor RK. Effect of Conformational Variability on the Drug Resistance of Candida auris ERG11p and FKS1. ACS OMEGA 2024; 9:19816-19823. [PMID: 38737078 PMCID: PMC11080008 DOI: 10.1021/acsomega.3c08134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 05/14/2024]
Abstract
Candida auris infection has been recognized as an urgent threat to antifungal drug resistance, and the Eagle effect of C. auris FKS1 (1,3-β-d-glucan synthase) wild-type isolates has also been noted. The Eagle effect, namely, where higher concentrations of antifungals reduce fungicidal activity relative to lower concentrations, is a confounding factor of apparent antifungal resistance, but the detailed mechanism remains unclear. Here, we present the conformational variability of mutation sites for ERG11p (lanosterol 14α-demethylase) and FKS1 from deep neural network-based prediction along with the reported X-ray crystallographic and cryo-electron microscopy (cryo-EM) structures of antifungals. The sequence variability maps provide valuable insights into the inconsistent correlation between azole resistance and the mysterious Eagle effect with the dispersion of minimal inhibitory concentration (MIC) for echinocandin resistance. The conformational variability prediction supports the hypothesis that mutations K143R of clade I, VF125AL of clade III, and Y132F of clade IV for C. auris ERG11p make the corresponding site variable and that an increased population of invisible variable conformations potentially contributes to triazole resistance. In contrast, the predicted rigid conformation by the S639F mutation of hot spot region 1 (HS1) for FKS1 suggests that caspofungin (CAS) is involved in an uncompetitive inhibition, and a decreased population of the CAS-bound state of FKS1 with Rho1 leads to drug resistance. The predicted variable HS1 region for FKS1 WT isolates and the rigid one for FKS1 S639F mutants support the in vivo drug response and the in vitro MIC dispersion. A plausible mechanism of the Eagle effect is hereby proposed, namely, that a high concentration of CAS with a high membrane affinity reduces the population of the CAS-bound state of FKS1 with Rho1, as well as accompanying events such as aggregation or association depending on the conformational variability of HS1.
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Affiliation(s)
- Hiroshi Izumi
- National
Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba West, Tsukuba Ibaraki 305-8569, Japan
| | - Laurence A. Nafie
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244-4100, United
States
- BioTools
Inc., Bee Line Hwy, Jupiter, Florida 33458, United States
| | - Rina K. Dukor
- BioTools
Inc., Bee Line Hwy, Jupiter, Florida 33458, United States
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3
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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.
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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
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4
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Bohner F, Papp C, Takacs T, Varga M, Szekeres A, Nosanchuk JD, Vágvölgyi C, Tóth R, Gacser A. Acquired Triazole Resistance Alters Pathogenicity-Associated Features in Candida auris in an Isolate-Dependent Manner. J Fungi (Basel) 2023; 9:1148. [PMID: 38132749 PMCID: PMC10744493 DOI: 10.3390/jof9121148] [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: 09/13/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Fluconazole resistance is commonly encountered in Candida auris, and the yeast frequently displays resistance to other standard drugs, which severely limits the number of effective therapeutic agents against this emerging pathogen. In this study, we aimed to investigate the effect of acquired azole resistance on the viability, stress response, and virulence of this species. Fluconazole-, posaconazole-, and voriconazole- resistant strains were generated from two susceptible C. auris clinical isolates (0381, 0387) and compared under various conditions. Several evolved strains became pan-azole-resistant, as well as echinocandin-cross-resistant. While being pan-azole-resistant, the 0381-derived posaconazole-evolved strain colonized brain tissue more efficiently than any other strain, suggesting that fitness cost is not necessarily a consequence of resistance development in C. auris. All 0387-derived evolved strains carried a loss of function mutation (R160S) in BCY1, an inhibitor of the PKA pathway. Sequencing data also revealed that posaconazole treatment can result in ERG3 mutation in C. auris. Despite using the same mechanisms to generate the evolved strains, both genotype and phenotype analysis highlighted that the development of resistance was unique for each strain. Our data suggest that C. auris triazole resistance development is a highly complex process, initiated by several pleiotropic factors.
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Affiliation(s)
- Flora Bohner
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Csaba Papp
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Tamas Takacs
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Mónika Varga
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - András Szekeres
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Joshua D. Nosanchuk
- Department of Medicine (Infectious Diseases), Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA;
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Csaba Vágvölgyi
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Renáta Tóth
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Attila Gacser
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
- HCEMM-USZ Fungal Pathogens Research Group, Department of Microbiology, University of Szeged, 6726 Szeged, Hungary
- HUN-REN-USZ Pathomechanisms of Fungal Infections Research Group, University of Szeged, 6726 Szeged, Hungary
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5
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Byun SA, Kwon YJ, Lee GY, Choi MJ, Jeong SH, Kim D, Choi MH, Kee SJ, Kim SH, Shin MG, Won EJ, Shin JH. Virulence Traits and Azole Resistance in Korean Candida auris Isolates. J Fungi (Basel) 2023; 9:979. [PMID: 37888235 PMCID: PMC10607439 DOI: 10.3390/jof9100979] [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: 09/12/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
Abstract
We analyzed the virulence traits and azole resistance mechanisms of 104 Candida auris isolates collected from 13 Korean hospitals from 1996 to 2022. Of these 104 isolates, 96 (5 blood and 91 ear isolates) belonged to clade II, and 8 (6 blood and 2 other isolates) belonged to clade I. Fluconazole resistance (minimum inhibitory concentration ≥32 mg/L) was observed in 68.8% of clade II and 25.0% of clade I isolates. All 104 isolates were susceptible to amphotericin B and three echinocandins. In 2022, six clade I isolates indicated the first nosocomial C. auris cluster in Korea. Clade II C. auris isolates exhibited reduced thermotolerance at 42 °C, with diminished in vitro competitive growth and lower virulence in the Galleria mellonella model compared to non-clade II isolates. Of the 66 fluconazole-resistant clade II isolates, several amino acid substitutions were identified: Erg11p in 14 (21.2%), Tac1Ap in 2 (3.0%), Tac1Bp in 62 (93.9%), and Tac1Bp F214S in 33 (50.0%). Although there were a limited number of non-clade II isolates studied, our results suggest that clade II C. auris isolates from Korean hospitals might display lower virulence traits than non-clade II isolates, and their primary fluconazole resistance mechanism is linked to Tac1Bp mutations.
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Affiliation(s)
- Seung A Byun
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
| | - Yong Jun Kwon
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
| | - Ga Yeong Lee
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
| | - Min Ji Choi
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Dokyun Kim
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Min Hyuk Choi
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Seung-Jung Kee
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
| | - Soo Hyun Kim
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
| | - Myung Geun Shin
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
| | - Eun Jeong Won
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
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6
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Biran R, Cohen R, Finn T, Brosh-Nissimov T, Rahav G, Yahav D, Amit S, Shachor-Meyouhas Y, Atamna A, Bishara J, Ashkenazi-Hoffnung L, Ben Zvi H, Hershman-Sarafov M, Maayan S, Maor Y, Schwartz O, Zimhony O, Lellouche J, Elbaz M, Burdelova E, Mizrahi N, Novikov A, Henig O, Ben-Ami R. Nationwide Outbreak of Candida auris Infections Driven by COVID-19 Hospitalizations, Israel, 2021-2022. Emerg Infect Dis 2023; 29:1297-1301. [PMID: 37347492 PMCID: PMC10310389 DOI: 10.3201/eid2907.221888] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
We report an outbreak of Candida auris across multiple healthcare facilities in Israel. For the period of May 2014-May 2022, a total of 209 patients with C. auris infection or colonization were identified. The C. auris incidence rate increased 30-fold in 2021 (p = 0.00015), corresponding in time with surges of COVID-19-related hospitalization. Multilocus sequence typing revealed hospital-level outbreaks with distinct clones. A clade III clone, imported into Israel in 2016, accounted for 48.8% of typed isolates after January 2021 and was more frequently resistant to fluconazole (100% vs. 63%; p = 0.00017) and voriconazole (74% vs. 5.2%; p<0.0001) than were non-clade III isolates. A total of 23% of patients had COVID-19, and 78% received mechanical ventilation. At the hospital level, outbreaks initially involved mechanically ventilated patients in specialized COVID-19 units and then spread sequentially to ventilated non-COVID-19 patients and nonventilated patients.
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7
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Brandt P, Mirhakkak MH, Wagner L, Driesch D, Möslinger A, Fänder P, Schäuble S, Panagiotou G, Vylkova S. High-Throughput Profiling of Candida auris Isolates Reveals Clade-Specific Metabolic Differences. Microbiol Spectr 2023; 11:e0049823. [PMID: 37097196 PMCID: PMC10269459 DOI: 10.1128/spectrum.00498-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/04/2023] [Indexed: 04/26/2023] Open
Abstract
Candida auris, a multidrug-resistant human fungal pathogen that causes outbreaks of invasive infections, emerged as four distinct geographical clades. Previous studies identified genomic and proteomic differences in nutrient utilization on comparison to Candida albicans, suggesting that certain metabolic features may contribute to C. auris emergence. Since no high-throughput clade-specific metabolic characterization has been described yet, we performed a phenotypic screening of C. auris strains from all 4 clades on 664 nutrients, 120 chemicals, and 24 stressors. We identified common and clade- or strain-specific responses, including the preferred utilization of various dipeptides as nitrogen source and the inability of the clade II isolate AR 0381 to withstand chemical stress. Further analysis of the metabolic properties of C. auris isolates showed robust growth on intermediates of the tricarboxylic acid cycle, such as citrate and succinic and malic acids. However, there was reduced or no growth on pyruvate, lactic acid, or acetate, likely due to the lack of the monocarboxylic acid transporter Jen1, which is conserved in most pathogenic Candida species. Comparison of C. auris and C. albicans transcriptomes of cells grown on alternative carbon sources and dipeptides as a nitrogen source revealed common as well as species-unique responses. C. auris induced a significant number of genes with no ortholog in C. albicans, e.g., genes similar to the nicotinic acid transporter TNA1 (alternative carbon sources) and to the oligopeptide transporter (OPT) family (dipeptides). Thus, C. auris possesses unique metabolic features which could have contributed to its emergence as a pathogen. IMPORTANCE Four main clades of the emerging, multidrug-resistant human pathogen Candida auris have been identified, and they differ in their susceptibilities to antifungals and disinfectants. Moreover, clade- and strain-specific metabolic differences have been identified, but a comprehensive overview of nutritional characteristics and resistance to various stressors is missing. Here, we performed high-throughput phenotypic characterization of C. auris on various nutrients, stressors, and chemicals and obtained transcriptomes of cells grown on selected nutrients. The generated data sets identified multiple clade- and strain-specific phenotypes and induction of C. auris-specific metabolic genes, showing unique metabolic properties. The presented work provides a large amount of information for further investigations that could explain the role of metabolism in emergence and pathogenicity of this multidrug-resistant fungus.
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Affiliation(s)
- Philipp Brandt
- Septomics Research Center, Friedrich Schiller University, and Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Mohammad H. Mirhakkak
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Lysett Wagner
- Septomics Research Center, Friedrich Schiller University, and Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | | | - Anna Möslinger
- Septomics Research Center, Friedrich Schiller University, and Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
- Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Pauline Fänder
- Septomics Research Center, Friedrich Schiller University, and Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Sascha Schäuble
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Slavena Vylkova
- Septomics Research Center, Friedrich Schiller University, and Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
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8
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Sathi FA, Aung MS, Paul SK, Nasreen SA, Haque N, Roy S, Ahmed S, Alam MM, Khan S, Rabbany MA, Biswas JP, Kobayashi N. Clonal Diversity of Candida auris, Candida blankii, and Kodamaea ohmeri Isolated from Septicemia and Otomycosis in Bangladesh as Determined by Multilocus Sequence Typing. J Fungi (Basel) 2023; 9:658. [PMID: 37367594 DOI: 10.3390/jof9060658] [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: 05/05/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023] Open
Abstract
Candida auris, Candida blankii, and Kodamaea ohmeri have been regarded as emerging fungal pathogens that can cause infections with high mortality. For genotyping of C. auris, a multilocus sequence typing (MLST) scheme based on four locus sequences has been reported, while there is no typing scheme for C. blankii and K. ohmeri. In the present study, the existing MLST scheme of C. auris was modified by adding more locus types deduced from sequence data available in the GenBank database. Furthermore, MLST schemes of C. blankii and K. ohmeri were developed using the four cognate loci (ITS, RPB1, RPB2, D1/D2) and similar sequence regions to those of C. auris. These MLST schemes were applied to identify the ST (sequence type) of clinical isolates of C. auris (n = 7), C. blankii (n = 9), and K. ohmeri (n = 6), derived from septicemia or otomycosis in Bangladesh in 2021. All the C. auris isolates were classified into a single ST (ST5) and clade I, having a Y132F substitution in ERG11p, which is associated with azole resistance. Similarly, all the C. blankii isolates belonged to a single type (ST1). In contrast, six K. ohmeri isolates were assigned to five types (ST1-ST5), suggesting its higher genetic diversity. These findings revealed the availability of MLST schemes for these three fungal species for understanding their clonal diversity among clinical isolates.
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Affiliation(s)
- Fardousi Akter Sathi
- Department of Microbiology, Mymensingh Medical College, Mymensingh 2200, Bangladesh
| | - Meiji Soe Aung
- Department of Hygiene, School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
| | | | | | - Nazia Haque
- Department of Microbiology, Mymensingh Medical College, Mymensingh 2200, Bangladesh
| | - Sangjukta Roy
- Department of Microbiology, Mymensingh Medical College, Mymensingh 2200, Bangladesh
| | - Salma Ahmed
- Mugda Medical College, Dhaka 1214, Bangladesh
| | | | - Shahed Khan
- Department of Oral Microbiology, Mymensingh Medical College Hospital, Mymensingh 2200, Bangladesh
| | - Mohammad Arif Rabbany
- Department of Neonatology, Mymensingh Medical College Hospital, Mymensingh 2200, Bangladesh
| | - Joy Prokas Biswas
- Department of Pathology, Netrokona Medical College, Netrokona 2400, Bangladesh
| | - Nobumichi Kobayashi
- Department of Hygiene, School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
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9
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Katsiari M, Mavroidi A, Kesesidis N, Palla E, Zourla K, Ntorlis K, Konstantinidis K, Laskou M, Strigklis K, Sakkalis A, Nikolaou C, Platsouka ED, Karakasiliotis I, Vrioni G, Tsakris A. Emergence of Clonally-Related South Asian Clade I Clinical Isolates of Candida auris in a Greek COVID-19 Intensive Care Unit. J Fungi (Basel) 2023; 9:jof9020243. [PMID: 36836357 PMCID: PMC9964037 DOI: 10.3390/jof9020243] [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: 01/03/2023] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Candida auris has recently emerged as a multidrug-resistant yeast implicated in various healthcare-associated invasive infections and hospital outbreaks. In the current study, we report the first five intensive care unit (ICU) cases affected by C. auris isolates in Greece, during October 2020-January 2022. The ICU of the hospital was converted to a COVID-19 unit on 25 February 2021, during the third wave of COVID-19 in Greece. Identification of the isolates was confirmed by Matrix Assisted Laser Desorption Ionization Time of Flight mass spectroscopy (MALDI-TOF]. Antifungal susceptibility testing was performed by the EUCAST broth microdilution method. Based on the tentative CDC MIC breakpoints, all five C. auris isolates were resistant to fluconazole (≥32 μg/mL), while three of them exhibited resistance to amphotericin B (≥2 μg/mL). The environmental screening also revealed the dissemination of C. auris in the ICU. Molecular characterization of C. auris clinical and environmental isolates was performed by MultiLocus Sequence Typing (MLST) of a set of four genetic loci, namely ITS, D1/D2, RPB1 and RPB2, encoding for the internal transcribed spacer region (ITS) of the ribosomal subunit, the large ribosomal subunit region and the RNA polymerase II largest subunit, respectively. MLST analysis showed that all isolates possessed identical sequences in the four genetic loci and clustered with the South Asian clade I strains. Additionally, PCR amplification and sequencing of the CJJ09_001802 genetic locus, encoding for the "nucleolar protein 58" that contains clade-specific repeats was performed. Sanger sequence analysis of the TCCTTCTTC repeats within CJJ09_001802 locus also assigned the C. auris isolates to the South Asian clade I. Our study confirms that C. auris is an emerging yeast pathogen in our region, especially in the setting of the ongoing COVID-19 worldwide pandemic. Adherence to strict infection control is needed to restrain further spread of the pathogen.
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Affiliation(s)
- Maria Katsiari
- Intensive Care Unit, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Angeliki Mavroidi
- Department of Microbiology, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Nikolaos Kesesidis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Eleftheria Palla
- Department of Microbiology, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Konstantina Zourla
- Department of Microbiology, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Kyriakos Ntorlis
- Intensive Care Unit, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Konstantinos Konstantinidis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Maria Laskou
- Intensive Care Unit, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | | | - Anastasios Sakkalis
- Intensive Care Unit, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Charikleia Nikolaou
- Intensive Care Unit, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Evangelia D. Platsouka
- Department of Microbiology, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Georgia Vrioni
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 75 MikrasAsias Street, 11527 Athens, Greece
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 75 MikrasAsias Street, 11527 Athens, Greece
- Correspondence: ; Tel.: +30-210-7462011
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Martins-Santana L, Rezende CP, Rossi A, Martinez-Rossi NM, Almeida F. Addressing Microbial Resistance Worldwide: Challenges over Controlling Life-Threatening Fungal Infections. Pathogens 2023; 12:pathogens12020293. [PMID: 36839565 PMCID: PMC9961291 DOI: 10.3390/pathogens12020293] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Fungal infections are a serious global concern because of their ability to spread and colonize host tissues in immunocompromised individuals. Such infections have been frequently reported worldwide and are currently gaining clinical research relevance owing to their resistant character, representing a bottleneck in treating affected people. Resistant fungi are an emergent public health threat. The upsurge of such pathogens has led to new research toward unraveling the destructive potential evoked by these species. Some fungi-grouped into Candida, Aspergillus, and Cryptococcus-are causative agents of severe and systemic infections. They are associated with high mortality rates and have recently been described as sources of coinfection in COVID-hospitalized patients. Despite the efforts to elucidate the challenges of colonization, dissemination, and infection severity, the immunopathogenesis of fungal diseases remains a pivotal characteristic in fungal burden elimination. The struggle between the host immune system and the physiological strategies of the fungi to maintain cellular viability is complex. In this brief review, we highlight the relevance of drug resistance phenotypes in fungi of clinical significance, taking into consideration their physiopathology and how the scientific community could orchestrate their efforts to avoid fungal infection dissemination and deaths.
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Affiliation(s)
- Leonardo Martins-Santana
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Caroline Patini Rezende
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Antonio Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Nilce Maria Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
- Correspondence:
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Usefulness of Chromogenic Media with Fluconazole Supplementation for Presumptive Identification of Candida auris. Diagnostics (Basel) 2023; 13:diagnostics13020231. [PMID: 36673041 PMCID: PMC9857578 DOI: 10.3390/diagnostics13020231] [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: 10/31/2022] [Revised: 12/23/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Introduction:Candida auris is a major threat to public health. Rapid detection is essential for early treatment and transmission control. The use of chromogenic media allows the presumptive identification of this new species. The aim of this study is to describe the morphological characteristics of C. auris colonies on three commercial chromogenic media. Methods: Nineteen C. auris isolates from different countries/clades and 18 isolates of other species were cultivated in CHROMagarTM Candida Plus, HiCromeTM Candida, CHROMagar-Candida, and fluconazole-supplemented (32 mg/L) CHROMagar-Candida media. Results: On CHROMagarTM Candida Plus and HiCromeTM Candida, C. auris isolates from Colombia, Venezuela, India, Korea, and Japan displayed blue-shaded colonies, while isolates from Spain and Germany exhibited light pink shades with a bluish halo. All isolates showed white to pink colonies on CHROMagar-Candida. On CHROMagar Candida supplemented with fluconazole, whilst C. auris, C. glabrata, or C. krusei showed a similar pink color at 48 h incubation, phenotypic differentiation was possible by the rough, paraffin-like texture or the intense purple color acquired by C. krusei and C. glabrata, respectively. Moreover, in this medium, the presence of C. auris in combination with other species of similar color was not limiting for its early identification, due to this medium selecting only strains resistant to this antifungal. Conclusions: The use of chromogenic media such as CHROMagarTM Candida Plus facilitates a presumptive identification of C. auris. However, this identification can be difficult in the presence of mixed cultures. In these cases, the use of CHROMagarTM Candida medium with 32 mg/L fluconazole offers better performance for the identification of C. auris by inhibiting fluconazole-susceptible strains and selecting rare or high fluconazole MIC (>32 mg/L) isolates.
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Shahi G, Kumar M, Skwarecki AS, Edmondson M, Banerjee A, Usher J, Gow NA, Milewski S, Prasad R. Fluconazole resistant Candida auris clinical isolates have increased levels of cell wall chitin and increased susceptibility to a glucosamine-6-phosphate synthase inhibitor. Cell Surf 2022; 8:100076. [PMID: 35252632 PMCID: PMC8891998 DOI: 10.1016/j.tcsw.2022.100076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 11/22/2022] Open
Abstract
In 2009 Candida auris was first isolated as fungal pathogen of human disease from ear canal of a patient in Japan. In less than a decade, this pathogen has rapidly spread around the world and has now become a major health challenge that is of particular concern because many strains are resistant to multiple class of antifungal drugs. The lack of available antifungals and rapid increase of this fungal pathogen provides an incentive for the development of new and more potent anticandidal drugs and drug combinatorial treatments. Here we have explored the growth inhibitory activity against C. auris of a synthetic dipeptide glutamine analogue, L-norvalyl-N 3-(4-methoxyfumaroyl)-L-2,3- diaminopropanoic acid (Nva-FMDP), that acts as an inhibitor of glucosamine-6-phosphate (GlcN-6-P) synthase - a key enzyme in the synthesis of cell wall chitin. We observed that in contrast to FLC susceptible isolates of C. auris, FLC resistant isolates had elevated cell wall chitin and were susceptible to inhibition by Nva-FMDP. The growth kinetics of C. auris in RPMI-1640 medium revealed that the growth of FLC resistant isolates were 50-60% more inhibited by Nva-FMDP (8 μ g/ml) compared to a FLC susceptible isolate. Fluconazole resistant strains displayed increased transcription of CHS1, CHS2 and CHS3, and the chitin content of the fluconazole resistant strains was reduced following the Nva-FMDP treatment. Therefore, the higher chitin content in FLC resistant C. auris isolates may make the strain more susceptible to inhibition of the antifungal activity of the Nva-FMDP peptide conjugate.
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Affiliation(s)
- Garima Shahi
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana 122413, India
| | - Mohit Kumar
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana 122413, India
| | - Andrzej S. Skwarecki
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, 11/12 Narutowicza Street, 80-952 Gdansk, Poland
| | - Matt Edmondson
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Atanu Banerjee
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana 122413, India
| | - Jane Usher
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Neil A.R. Gow
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Sławomir Milewski
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, 11/12 Narutowicza Street, 80-952 Gdansk, Poland
| | - Rajendra Prasad
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana 122413, India
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13
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Deshkar S, Patil N, Amberkar S, Lad A, Siddiqui F, Sharan S. Identification and Antifungal Drug Susceptibility Pattern of Candida auris in India. J Glob Infect Dis 2022; 14:131-135. [PMID: 36636301 PMCID: PMC9831210 DOI: 10.4103/jgid.jgid_44_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 11/05/2022] Open
Abstract
Introduction Candida auris has turned up as a multidrug-resistant nosocomial agent with outbreaks reported worldwide. The present study was conducted to evaluate the antifungal drug susceptibility pattern of C. auris. Methods Isolates of C. auris were obtained from clinically suspected cases of candidemia from January 2019 to June 2021. Identification was done with matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) and panfungal DNA polymerase chain reaction (PCR), followed by sequencing. Antifungal susceptibility testing was performed with broth microdilution method. Results Out of 50 isolates C. auris, 49 were identified by MALDI-TOF and one isolate was identified with panfungal DNA PCR followed by sequencing. For fluconazole, 84% (n = 42) isolates were found to be resistant and 16% (n = 8) isolates were susceptible (minimum inhibitory concentrations [MICs] range 0.5-16). Posaconazole exhibited potent activity, followed by itraconazole. For amphotericin B, only 6% (n = 3) isolates were resistant with MICs ≥2 μg/mL. Only 4% (n = 2) isolates exhibited resistance to caspofungin. No resistance was noted for micafungin and anidulafungin. One (2%) isolate was found to be panazole resistant. One (2%) isolate was resistant to fluconazole, amphotericin B, and caspofungin. Conclusion Correct identification of C. auris can be obtained with the use of MALDI-TOF and sequencing methods. A small percentage of fluconazole-sensitive isolates are present. Although elevated MICs for amphotericin B and echinocandins are not generally observed, the possibility of resistance with the irrational use of these antifungal drugs cannot be denied. Pan azole-resistant and pan drug-resistant strains of C. auris are on rise.
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Affiliation(s)
- Smita Deshkar
- Department of Infectious Diseases, Metropolis Healthcare Limited, Global Reference Laboratory, Mumbai, Maharashtra, India,Address for correspondence: Dr. Smita Deshkar, Department of Infectious Diseases, Metropolis Healthcare Limited, Kohinoor City, Commercial Bldg. - A, 4th Floor, Off-L.B.S. Road, Vidyavihar (West), Mumbai - 400 070, Maharashtra, India. E-mail:
| | - Niranjan Patil
- Department of Infectious Diseases, Metropolis Healthcare Limited, Global Reference Laboratory, Mumbai, Maharashtra, India
| | - Shraddha Amberkar
- Department of Infectious Diseases, Metropolis Healthcare Limited, Global Reference Laboratory, Mumbai, Maharashtra, India
| | - Ashish Lad
- Department of Infectious Diseases, Metropolis Healthcare Limited, Global Reference Laboratory, Mumbai, Maharashtra, India
| | - Farozan Siddiqui
- Department of Microbiology, Metropolis Healthcare Limited, Global Reference Laboratory, Mumbai, Maharashtra, India
| | - Swati Sharan
- Department of Molecular Biology, Metropolis Healthcare Limited, Global Reference Laboratory, Mumbai, Maharashtra, India
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14
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Spruijtenburg B, Badali H, Abastabar M, Mirhendi H, Khodavaisy S, Sharifisooraki J, Armaki MT, de Groot T, Meis JF. Confirmation of fifth Candida auris clade by whole genome sequencing. Emerg Microbes Infect 2022; 11:2405-2411. [PMID: 36154919 PMCID: PMC9586689 DOI: 10.1080/22221751.2022.2125349] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Candida auris has emerged globally as a multidrug-resistant pathogen causing outbreaks in health care facilities. Whole genome sequencing (WGS) analysis has identified four major clades, while earlier WGS data from a single Iranian isolate suggested the existence of a potential fifth clade. Here, we confirm the existence of this fifth clade by providing WGS data of another four Iranian isolates. These clade V isolates differed less than 100 single-nucleotide polymorphisms (SNPs) between each other, while they were separated from the other clades by more than 200,000 SNPs. Two of these isolates were resistant to fluconazole and were found to harbour mutations in the TAC1b and ERG11 genes.
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Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands .,Centre of Expertise in Mycology Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Hamid Badali
- Department of Molecular Microbiology & Immunology, South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Mahdi Abastabar
- Invasive Fungi Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, Faculty of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Joobin Sharifisooraki
- Health Reproductive Research Center, Sari Branch, Islamic Azad University, Sari, Mazandaran, Iran
| | - Mojtaba Taghizadeh Armaki
- Department of Medical Mycology and Parasitology, School of Medicine, Babol University of Medical Sciences, Babol, Iran.
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands .,Centre of Expertise in Mycology Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands .,Centre of Expertise in Mycology Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands .,Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
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15
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Sarvestani HK, Ramandi A, Getso MI, Razavyoon T, Javidnia J, Golrizi MB, Saboor-Yaraghi AA, Ansari S. Mass spectrometry in research laboratories and clinical diagnostic: a new era in medical mycology. Braz J Microbiol 2022; 53:689-707. [PMID: 35344203 PMCID: PMC9151960 DOI: 10.1007/s42770-022-00715-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Diagnosis by clinical mycology laboratory plays a critical role in patient care by providing definitive knowledge of the cause of infection and antimicrobial susceptibility data to physicians. Rapid diagnostic methods are likely to improve patient. Aggressive resuscitation bundles, adequate source control, and appropriate antibiotic therapy are cornerstones for success in the treatment of patients. Routine methods for identifying clinical specimen fungal pathogen are based on the cultivation on different media with the subsequent examination of its phenotypic characteristics comprising a combination of microscopic and colony morphologies. As some fungi cannot be readily identified using these methods, molecular diagnostic methods may be required. These methods are fast, but it can cost a lot. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs. It can be considered an alternative for conventional biochemical and molecular identification systems in a microbiological laboratory. The reliability and accuracy of this method have been scrutinized in many surveys and have been compared with several methods including sequencing and molecular methods. According to these findings, the reliability and accuracy of this method are very high and can be trusted. With all the benefits of this technique, the libraries of MALDI-TOF MS need to be strengthened to enhance its performance. This review provides an overview of the most recent research literature that has investigated the applications and usage of MT-MS to the identification of microorganisms, mycotoxins, antifungal susceptibility examination, and mycobiome research.
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Affiliation(s)
- Hasti Kamali Sarvestani
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Ramandi
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Muhammad Ibrahim Getso
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Bayero University, PMB, Kano, 3011, Nigeria
| | - Taraneh Razavyoon
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Javidnia
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Miaad Banay Golrizi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ali-Akbar Saboor-Yaraghi
- Department of Nutrition and Biochemistry, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Saham Ansari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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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.
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Reslan L, Araj GF, Finianos M, El Asmar R, Hrabak J, Dbaibo G, Bitar I. Molecular Characterization of Candida auris Isolates at a Major Tertiary Care Center in Lebanon. Front Microbiol 2022; 12:770635. [PMID: 35145489 PMCID: PMC8822126 DOI: 10.3389/fmicb.2021.770635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 11/23/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The globally emerging Candida auris pathogens poses heavy burden to the healthcare system. Their molecular analyses assist in understanding their epidemiology, dissemination, treatment, and control. This study was warranted to describe the genomic features and drug resistance profiles using whole genome sequencing (WGS) among C. auris isolates from Lebanon. METHODS A total of 28 C. auris clinical isolates, from different hospital units, were phenotypically identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and tested for antifungal resistance using Vitek-2 system and E test. The complete genomes were determined by WGS using long reads sequencing (PacBio) to reveal the clade distribution and antifungal resistance genes. RESULTS Candida auris revealed uniform resistance to fluconazole and amphotericin B, with full susceptibility to echinocandins. Among key resistance genes studied, only two mutations were detected: Y132F in ERG11 gene and a novel mutation, D709E, found in CDR1 gene encoding for an ABC efflux pump. Phylogenetically, C. auris genomes belonged to South Asian clade I and showed limited genetic diversity, suggesting person to person transmission. CONCLUSION This characterization of C. auris isolates from Lebanon revealed the exclusivity of clade I lineage together with uniform resistance to fluconazole and amphotericin B. The control of such highly resistant pathogen necessitates an appropriate and rapid recovery and identification to contain spread and outbreaks.
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Affiliation(s)
- Lina Reslan
- American University of Beirut, Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, Beirut, Lebanon
| | - George F. Araj
- American University of Beirut, Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, Beirut, Lebanon
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Marc Finianos
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzeň, Czechia
| | - Rima El Asmar
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzeň, Czechia
| | - Ghassan Dbaibo
- American University of Beirut, Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzeň, Czechia
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Abstract
Candida auris is an emerging yeast species that has the unique characteristics of patient skin colonization and rapid transmission within healthcare facilities and the ability to rapidly develop antifungal resistance. When C. auris first started appearing in clinical microbiology laboratories, it could only be identified using DNA sequencing. In the decade since its first identification outside of Japan there have been many improvements in the detection of C. auris. These include the expansion of MALDI-TOF databases to include C. auris, the development of both laboratory-developed tests and commercially available kits for its detection, and special CHROMagar for identification from laboratory specimens. Here we discuss the current tools and resources that are available for C. auris identification and detection.
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Yadav A, Singh A, Chowdhary A. Isolation of Candida auris in Clinical Specimens. Methods Mol Biol 2022; 2517:3-20. [PMID: 35674941 DOI: 10.1007/978-1-0716-2417-3_1] [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: 06/15/2023]
Abstract
Candida auris is a multidrug-resistant yeast causing healthcare-associated outbreaks of blood stream infections worldwide. Currently, C. auris isolation and identification is complicated by issues such as misidentification and long turnaround time associated with application of commonly used diagnostic tools. Based on phenotypic characteristics, differentiation of C. auris from related Candida haemulonii complex spp. is problematic. Candida auris can be misidentified using biochemical-based systems such as VITEK 2 YST, API 20C, BD Phoenix yeast identification system, and MicroScan. C. auris growth at 42 °C and in the presence of 10% NaCl helps in presumptive identification of this yeast from related Candida haemulonii complex spp. A new CHROMagar™ Candida Plus agar is an excellent alternative to current conventional mycological media for the screening of patients colonized/infected with Candida auris. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) can differentiate C. auris from other Candida species, but not all the reference databases included in MALDI-TOF devices allow for detection. Currently, accurate identification of C. auris can be performed using the updated FDA-approved libraries or "research use-only" libraries. Molecular techniques have greatly enhanced the diagnosis of C. auris. Sequencing of rDNA genetic loci, namely, internal transcribed spacer and D1/D2 region of large subunit (LSU), and PCR/qPCR assays has successfully been applied for identification of C. auris. Real-time PCR assays bear incomparable potential of being the most efficient tool for high-throughput screening of surveillance samples. If properly validated, they can deliver the diagnostic result within several hours, since the DNA can be isolated directly from the patient specimen without the need of obtaining a colony. In this chapter we detailed the isolation of Candida auris from various clinical specimens and its currently available identification methods and hitches.
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Affiliation(s)
- Anamika Yadav
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
| | - Ashutosh Singh
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India.
| | - Anuradha Chowdhary
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
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Abdolrasouli A, Fraser MA. Candida auris Identification and Profiling by MALDI-ToF Mass Spectrometry. Methods Mol Biol 2022; 2517:21-32. [PMID: 35674942 DOI: 10.1007/978-1-0716-2417-3_2] [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: 06/15/2023]
Abstract
MALDI-ToF MS has become the standard method for routine identification of most medically important yeasts in clinical and public health laboratories and has largely replaced phenotypic identification methods as a first-line identification tool. Fungal identification is based on extensive and well-curated mass spectra libraries usually provided by the manufacturer of the MALDI-ToF MS platform; however, many centers do create specialized or in-house database collections to aid analysis. Most MALDI-ToF MS systems offer simple and standardized workflows for the identification of clinically relevant yeasts to species level with a high throughput, high accuracy, and a low overall cost per test. This makes MALDI-ToF MS an ideal platform for use in routine clinical, diagnostic, and research microbiology laboratories which may lack experience or expertise in the identification of pathogenic fungi.In this chapter we review three standard protocols for the proteomic-based identification of Candida auris isolated from cultures of clinical or environmental surveillance samples in diagnostic and research laboratories.
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Affiliation(s)
- Alireza Abdolrasouli
- Department of Medical Microbiology, King's College Hospital , London, UK.
- Department of Infectious Diseases, Imperial College London, London, UK.
| | - Mark A Fraser
- National Mycology Reference Laboratory, UK Health Security Agency, Bristol, UK
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21
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A Chronic Autochthonous Fifth Clade Case of Candida auris Otomycosis in Iran. Mycopathologia 2021; 187:121-127. [PMID: 34855102 DOI: 10.1007/s11046-021-00605-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/30/2021] [Indexed: 10/19/2022]
Abstract
Candida auris, a multidrug-resistant nosocomial pathogen, has emerged globally with high morbidity and mortality among immunocompromised individuals and COVID19 hospitalized patients. Five major clades of C. auris have been previously described. The fifth clade is exclusively found in Iran where C. auris isolates are genetically distinct from other clades by > 200,000 single-nucleotide polymorphisms. The origin of C. auris remains unclear, and limited clinical data are available at present regarding clade V infection or colonization. Herein, another case of otomycosis in Iran caused by an isolate of C. auris belonging to the fifth clade is reported. Genotyping revealed that the obtained C. auris isolate from Isfahan clustered with earlier clade V isolates from Babol, cities around 600 km separated, which indicates that C. auris clade V is established in Iran. C. auris is thought to exist more commonly in Iran, given that limited diagnostic capacity in the country has probably curbed the identification of more C. auris cases. Therefore, surveillance of the environment, patients and healthcare facilities in different geographical regions in Iran is urgently required.
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Dennis EK, Chaturvedi S, Chaturvedi V. So Many Diagnostic Tests, So Little Time: Review and Preview of Candida auris Testing in Clinical and Public Health Laboratories. Front Microbiol 2021; 12:757835. [PMID: 34691009 PMCID: PMC8529189 DOI: 10.3389/fmicb.2021.757835] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/13/2021] [Indexed: 01/13/2023] Open
Abstract
The recognition of a new yeast, Candida auris, in 2009 in East Asia, and its rapid global spread, was a reminder of the threats posed by multidrug-resistant fungal pathogens. C. auris had likely remained unrecognized for a long time as accurate tests were not available. The laboratory community responded to the C. auris challenge by publishing 35 new or revised diagnostic methods between 2014 and early 2021. The commercial sector also modified existing diagnostic devices. These C. auris diagnostic tests run the gamut from traditional culture-based differential and selective media, biochemical assimilations, and rapid protein profiles, as well as culture-independent DNA-based diagnostics. We provide an overview of these developments, especially the tests with validation data that were subsequently adopted for common use. We share a workflow developed in our laboratory to process over 37,000 C. auris surveillance samples and 5,000 C. auris isolates from the outbreak in the New York metropolitan area. Our preview covers new devices and diagnostic approaches on the horizon based on microfluidics, optics, and nanotechnology. Frontline laboratories need rapid, cheap, stable, and easy-to-implement tests to improve C. auris diagnosis, surveillance, patient isolation, admission screening, and environmental control. Among the urgent needs is a lateral flow assay or similar device for presumptive C. auris identification. All laboratories will benefit from devices that allow rapid antifungal susceptibility testing, including detection of mutations conferring drug resistance. Hopefully, multiplex test panels are on the horizon for synergy of C. auris testing with ongoing surveillance of other healthcare-associated infections. C. auris genome analysis has a proven role for outbreak investigations, and diagnostic laboratories need quick access to regional and national genome analysis networks.
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Affiliation(s)
- Emily K Dennis
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, United States.,Department of Biomedical Sciences, University at Albany, Albany, NY, United States
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, United States
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Carolus H, Jacobs S, Lobo Romero C, Deparis Q, Cuomo CA, Meis JF, Van Dijck P. Diagnostic Allele-Specific PCR for the Identification of Candida auris Clades. J Fungi (Basel) 2021; 7:754. [PMID: 34575792 PMCID: PMC8471779 DOI: 10.3390/jof7090754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/19/2022] Open
Abstract
Candida auris is an opportunistic pathogenic yeast that emerged worldwide during the past decade. This fungal pathogen poses a significant public health threat due to common multidrug resistance (MDR), alarming hospital outbreaks, and frequent misidentification. Genomic analyses have identified five distinct clades that are linked to five geographic areas of origin and characterized by differences in several phenotypic traits such as virulence and drug resistance. Typing of C. auris strains and the identification of clades can be a powerful tool in molecular epidemiology and might be of clinical importance by estimating outbreak and MDR potential. As C. auris has caused global outbreaks, including in low-income countries, typing C. auris strains quickly and inexpensively is highly valuable. We report five allele-specific polymerase chain reaction (AS-PCR) assays for the identification of C. auris and each of the five described clades of C. auris based on conserved mutations in the internal transcribed spacer (ITS) rDNA region and a clade-specific gene cluster. This PCR method provides a fast, cheap, sequencing-free diagnostic tool for the identification of C. auris, C. auris clades, and potentially, the discovery of new clades.
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Affiliation(s)
- Hans Carolus
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, 3001 Leuven, Belgium; (H.C.); (S.J.); (C.L.R.)
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium;
| | - Stef Jacobs
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, 3001 Leuven, Belgium; (H.C.); (S.J.); (C.L.R.)
| | - Celia Lobo Romero
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, 3001 Leuven, Belgium; (H.C.); (S.J.); (C.L.R.)
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium;
| | - Quinten Deparis
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium;
- Laboratory for Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| | | | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 Nijmegen, The Netherlands;
- Centre of Expertise in Mycology Radboudumc/CWZ, 6532 Nijmegen, The Netherlands
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, 3001 Leuven, Belgium; (H.C.); (S.J.); (C.L.R.)
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium;
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Ayhan K, Coşansu S, Orhan-Yanıkan E, Gülseren G. Advance methods for the qualitative and quantitative determination of microorganisms. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Xu X, Lv H, Zhang F, Zhu H, Cai L. A Comparison of Candida Detection in Sputum by the Conventional Culture and Fluorescent Polymerase Chain Reaction Methods. Med Sci Monit 2021; 27:e930293. [PMID: 34158468 PMCID: PMC8237698 DOI: 10.12659/msm.930293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Candida is a pathogenic fungus. In recent years, the increase in immunosuppressive diseases has led to an increase in Candida infections, with the lungs being the most common site. Therefore, the aim of this study was to compare the positive detection rates of Candida in sputum samples by Candida culture and fluorescent polymerase chain reaction (PCR), and to explore a new method for rapid, accurate, and effective detection of Candida in sputum, providing swift evidence of clinical fungal infection. Material/Methods From October 2016 to March 2017, 300 sputum samples were collected and detected by the conventional culture method and fluorescent PCR method. The positive rate of Candida detection was compared between the 2 methods. Results In the 300 sputum samples, the positive detection rate of Candida was 50% by the culture method and 65.67% by the fluorescent PCR method (P<0.001). Therefore, the positive detection rate of Candida was higher by the fluorescent PCR method. Conclusions The conventional culture method for Candida needs a longer duration (24 h to 48 h) and the positive detection rate is low. However, it takes only 3 h to detect Candida in sputum by the fluorescent PCR method, the positive detection rate is high, and can be used as a screening method for Candida in sputum samples. Additional large-scale clinical trials need to be completed to assess the correlation between fluorescent PCR and pulmonary Candida infection.
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Affiliation(s)
- Xiaoqun Xu
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China (mainland).,Clinical Laboratory Center, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China (mainland)
| | - Huoyang Lv
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, The Affiliated People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China (mainland)
| | - Fengwei Zhang
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China (mainland).,Clinical Laboratory Center, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China (mainland)
| | - Houyong Zhu
- Department of Cardiology, Hangzhou Traditional Chinese Medicine (TCM) Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China (mainland)
| | - Long Cai
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China (mainland).,Clinical Laboratory Center, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China (mainland)
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MALDI-TOF MS in a Medical Mycology Laboratory: On Stage and Backstage. Microorganisms 2021; 9:microorganisms9061283. [PMID: 34204665 PMCID: PMC8231132 DOI: 10.3390/microorganisms9061283] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
The implementation of MALDI-TOF MS in medical microbiology laboratories has revolutionized practices and significantly reduced turnaround times of identification processes. However, although bacteriology quickly benefited from the contributions of this technique, adjustments were necessary to accommodate the specific characteristics of fungi. MALDI-TOF MS is now an indispensable tool in clinical mycology laboratories, both for the identification of yeasts and filamentous fungi, and other innovative uses are gradually emerging. Based on the practical experience of our medical mycology laboratory, this review will present the current uses of MALDI-TOF MS and the adaptations we implemented, to allow their practical execution in a daily routine. We will also introduce some less mainstream applications, like those for fungemia, or even still under development, as is the case for the determination of sensitivity to antifungal agents or typing methods.
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27
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Narayanan A, Vadnala RN, Ganguly P, Selvakumar P, Rudramurthy SM, Prasad R, Chakrabarti A, Siddharthan R, Sanyal K. Functional and Comparative Analysis of Centromeres Reveals Clade-Specific Genome Rearrangements in Candida auris and a Chromosome Number Change in Related Species. mBio 2021; 12:e00905-21. [PMID: 33975937 PMCID: PMC8262905 DOI: 10.1128/mbio.00905-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/22/2022] Open
Abstract
The thermotolerant multidrug-resistant ascomycete Candida auris rapidly emerged since 2009 causing systemic infections worldwide and simultaneously evolved in different geographical zones. The molecular events that orchestrated this sudden emergence of the killer fungus remain mostly elusive. Here, we identify centromeres in C. auris and related species, using a combined approach of chromatin immunoprecipitation and comparative genomic analyses. We find that C. auris and multiple other species in the Clavispora/Candida clade shared a conserved small regional GC-poor centromere landscape lacking pericentromeres or repeats. Further, a centromere inactivation event led to karyotypic alterations in this species complex. Interspecies genome analysis identified several structural chromosomal changes around centromeres. In addition, centromeres are found to be rapidly evolving loci among the different geographical clades of the same species of C. auris Finally, we reveal an evolutionary trajectory of the unique karyotype associated with clade 2 that consists of the drug-susceptible isolates of C. aurisIMPORTANCECandida auris, the killer fungus, emerged as different geographical clades, exhibiting multidrug resistance and high karyotype plasticity. Chromosomal rearrangements are known to play key roles in the emergence of new species, virulence, and drug resistance in pathogenic fungi. Centromeres, the genomic loci where microtubules attach to separate the sister chromatids during cell division, are known to be hot spots of breaks and downstream rearrangements. We identified the centromeres in C. auris and related species to study their involvement in the evolution and karyotype diversity reported in C. auris We report conserved centromere features in 10 related species and trace the events that occurred at the centromeres during evolution. We reveal a centromere inactivation-mediated chromosome number change in these closely related species. We also observe that one of the geographical clades, the East Asian clade, evolved along a unique trajectory, compared to the other clades and related species.
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Affiliation(s)
- Aswathy Narayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Rakesh Netha Vadnala
- Computational Biology, The Institute of Mathematical Sciences/HBNI, Chennai, India
| | - Promit Ganguly
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Pavitra Selvakumar
- Computational Biology, The Institute of Mathematical Sciences/HBNI, Chennai, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rajendra Prasad
- Amity Institute of Biotechnology, Amity University Haryana, Haryana, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rahul Siddharthan
- Computational Biology, The Institute of Mathematical Sciences/HBNI, Chennai, India
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- Osaka University, Suita, Japan
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Performance of Two Novel Chromogenic Media for the Identification of Multidrug-Resistant Candida auris Compared with Other Commercially Available Formulations. J Clin Microbiol 2021; 59:JCM.03220-20. [PMID: 33536293 DOI: 10.1128/jcm.03220-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/25/2021] [Indexed: 12/22/2022] Open
Abstract
Non-albicans Candida species are emerging in the nosocomial environment, with the multidrug-resistant (MDR) species Candida auris being the most notorious example. Consequently, rapid and accurate species identification has become essential. The objective of this study was to evaluate five commercially available chromogenic media for the presumptive identification of C. auris Two novel chromogenic formulations, CHROMagar Candida Plus (CHROMagar) and HiCrome C. auris MDR selective agar (HiMedia), and three reference media, CandiSelect (Bio-Rad), CHROMagar Candida (CHROMagar), and Chromatic Candida (Liofilchem), were inoculated with a collection of 9 genetically diverse C. auris strains and 35 strains from closely related comparator species. After 48 h of incubation, the media were evaluated for their ability to detect and identify C. auris All media had the same limitations in the differentiation of the more common species Candida dubliniensis and Candida glabrata Only on CHROMagar Candida Plus did C. auris colonies develop a species-specific coloration. Nevertheless, the closely related pathogenic species Candida pseudohaemulonii and Candida vulturna developed a similar appearance as C. auris on this medium. CHROMagar Candida Plus was shown to be superior in the detection and identification of C. auris, with 100% inclusivity for C. auris compared to 0% and 33% for the reference media and HiCrome C. auris MDR selective agar, respectively. Although C. vulturna and C. pseudohaemulonii can cause false positives, CHROMagar Candida Plus was shown to be a valuable addition to the plethora of mostly molecular methods for C. auris detection and identification.
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Evaluation of Synergistic Activity of Isavuconazole or Voriconazole plus Anidulafungin and the Occurrence and Genetic Characterization of Candida auris Detected in a Surveillance Program. Antimicrob Agents Chemother 2021; 65:AAC.02031-20. [PMID: 33431416 DOI: 10.1128/aac.02031-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/19/2020] [Indexed: 12/27/2022] Open
Abstract
A total of 15 Candida auris isolates from the SENTRY antimicrobial surveillance program between 2006 and 2019 were combined with 21 isolates from other collections for the evaluation of antifungal susceptibility and synergy against anidulafungin plus voriconazole or isavuconazole using the checkerboard method. Surveillance isolates were analyzed for genetic relatedness and resistance mechanisms. Applying the tentative statistical epidemiological cutoff values and the Centers for Disease Control tentative breakpoints, 32/36 isolates were resistant to fluconazole, 5/36 were resistant to amphotericin B, 5/36 were non-wild-type (NWT) to anidulafungin, 3/36 were NWT to micafungin, and 1/36 and 10/36 were NWT to isavuconazole and voriconazole, respectively. Of these, 10 isolates were multidrug resistant, which means that these isolates were resistant to 2 antifungal classes. Synergy or partial synergy was noted in 5/36 and 22/36, respectively, of the isolates with the combination of anidulafungin plus voriconazole, and 11/36 and 19/36 isolates, respectively, for the combination of anidulafungin plus isavuconazole. Multilocus sequence type (MLST) analysis of the 15 SENTRY isolates demonstrated that the isolates from the US were genetically related to, but different from, isolates from Latin America (Panama and Colombia) and Germany. Single nucleotide polymorphism (SNP) analysis showed that the 15 SENTRY isolates belonged to the described international clades and had associated Erg11 alterations, including 11 isolates displaying K143R, one displaying F126L, and one displaying Y501H alterations and a fluconazole MIC result of ≥64 mg/liter. Resistance mechanisms were not observed in the two isolates displaying fluconazole MIC values at 4 and 16 mg/liter. Isavuconazole displayed activity and greater synergy when tested with anidulafungin than seen with anidulafungin plus voriconazole against the C. auris clinical isolates that displayed resistance phenotypes.
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Abstract
Candida auris is a recently emerged multidrug-resistant fungal pathogen capable of causing severe infections in hospitalized patients. Despite its recognition as a human pathogen a decade ago, so far the natural ecological niche(s) of C. auris remains enigmatic. Candida auris is a multidrug resistant pathogen that presents a serious global threat to human health. As C. auris is a newly emerged pathogen, several questions regarding its ecological niche remain unexplored. While species closely related to C. auris have been detected in different environmental habitats, little is known about the natural habitat(s) of C. auris. Here, we explored the virgin habitats around the very isolated Andaman Islands in the Indian Ocean for evidence of C. auris. We sampled coastal wetlands, including rocky shores, sandy beaches, tidal marshes, and mangrove swamps, around the Andaman group of the Andaman & Nicobar Islands, Union Territory, in India. Forty-eight samples of sediment soil and seawater were collected from eight sampling sites representing the heterogeneity of intertidal habitats across the east and west coast of South Andaman district. C. auris was isolated from two of the eight sampling sites, a salt marsh and a sandy beach. Interestingly, both multidrug-susceptible and multidrug-resistant C. auris isolates were found in the sample. Whole-genome sequencing analysis clustered the C. auris isolates into clade I, showing close similarity to other isolates from South Asia. Isolation of C. auris from the tropical coastal environment suggests its association with the marine ecosystem. The fact that viable C. auris was detected in the marine habitat confirms C. auris survival in harsh wetlands. However, the ecological significance of C. auris in salt marsh wetland and sandy beaches to human infections remains to be explored.
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de Groot T, Janssen T, Faro D, Cremers NAJ, Chowdhary A, Meis JF. Antifungal Activity of a Medical-Grade Honey Formulation against Candida auris. J Fungi (Basel) 2021; 7:jof7010050. [PMID: 33450974 PMCID: PMC7828376 DOI: 10.3390/jof7010050] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 02/06/2023] Open
Abstract
Candida auris is a pathogenic yeast causing outbreaks in intensive care units with high mortality rates. The treatment of C. auris colonization is challenging due to high resistance rates. A potential alternative antifungal treatment is medical-grade honey. In this study the susceptibility of C. auris and other Candida species to the medical-grade honey-based formulation L-Mesitran® Soft was investigated. The medical-grade honey formulation reduced the growth of C. auris and other Candida species in a dose-dependent manner. This inhibition was not only due to the honey component, as treatment with an identical concentration of this component only was less effective and even stimulated the growth of C. albicans and C. glabrata, supporting the interpretation that supplements in the medical-grade honey formulation enhanced the antimicrobial activity. Increasing the concentration of the honey component to 40%, as is also present in an undiluted medical-grade honey formulation, lead to a 1- to 4-log inhibition of all Candida species. Unprocessed local honey reduced the growth of nearly all Candida species more strongly than medical-grade honey. C. auris' susceptibility to the medical-grade honey formulation did not depend on geographic origin or resistance profile, although the multiresistant isolates tended to be more susceptible. Altogether, medical-grade honey formulation has a strong antifungal activity against C. auris and other Candida species. Future studies should demonstrate whether the treatment of open wounds or skin colonized with C. auris is feasible and effective in the clinical setting.
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Affiliation(s)
- Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands; (T.J.); (D.F.); (J.F.M.)
- Correspondence: ; Tel.: +31-24-365-8677
| | - Tom Janssen
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands; (T.J.); (D.F.); (J.F.M.)
| | - Dirk Faro
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands; (T.J.); (D.F.); (J.F.M.)
| | | | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India;
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands; (T.J.); (D.F.); (J.F.M.)
- Centre of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
- Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, Curitiba 80060-000, Brazil
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Pla L, Santiago-Felipe S, Tormo-Mas MÁ, Ruiz-Gaitán A, Pemán J, Valentín E, Sancenón F, Aznar E, Martínez-Máñez R. Oligonucleotide-capped nanoporous anodic alumina biosensor as diagnostic tool for rapid and accurate detection of Candida auris in clinical samples. Emerg Microbes Infect 2020; 10:407-415. [PMID: 33372852 PMCID: PMC7954474 DOI: 10.1080/22221751.2020.1870411] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Candida auris has arisen as an important multidrug-resistant fungus because of several nosocomial outbreaks and elevated rates of mortality. Accurate and rapid diagnosis of C. auris is highly desired; nevertheless, current methods often present severe limitations and produce misidentification. Herein a sensitive, selective, and time-competitive biosensor based on oligonucleotide-gated nanomaterials for effective detection of C. auris is presented. In the proposed design, a nanoporous anodic alumina scaffold is filled with the fluorescent indicator rhodamine B and the pores blocked with different oligonucleotides capable of specifically recognize C. auris genomic DNA. Gate opening modulation and cargo delivery is controlled by successful DNA recognition. C. auris is detected at a concentration as low as 6 CFU/mL allowing obtaining a diagnostic result in clinical samples in one hour with no prior DNA extraction or amplification steps.
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Affiliation(s)
- Luis Pla
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València Valencia, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.,Unidad Mixta de Investigación en Nanomedicina y Sensores, Universitat Politècnica de València, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain
| | - Sara Santiago-Felipe
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València Valencia, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.,Unidad Mixta de Investigación en Nanomedicina y Sensores, Universitat Politècnica de València, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain
| | - María Ángeles Tormo-Mas
- Grupo de Investigación Infección Grave, Instituto de Investigación Sanitaria La Fe (IISLAFE), Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Alba Ruiz-Gaitán
- Grupo de Investigación Infección Grave, Instituto de Investigación Sanitaria La Fe (IISLAFE), Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Javier Pemán
- Grupo de Investigación Infección Grave, Instituto de Investigación Sanitaria La Fe (IISLAFE), Hospital Universitari i Politècnic La Fe, Valencia, Spain.,Servicio de Microbiología, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Eulogio Valentín
- Grupo de Investigación Infección Grave, Instituto de Investigación Sanitaria La Fe (IISLAFE), Hospital Universitari i Politècnic La Fe, Valencia, Spain.,GMCA Research Unit, Departamento de Microbiología y Ecología, Universitat de Valencia, Valencia, Spain
| | - Félix Sancenón
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València Valencia, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.,Unidad Mixta de Investigación en Nanomedicina y Sensores, Universitat Politècnica de València, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain.,Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Elena Aznar
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València Valencia, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.,Unidad Mixta de Investigación en Nanomedicina y Sensores, Universitat Politècnica de València, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain.,Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Ramón Martínez-Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València Valencia, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.,Unidad Mixta de Investigación en Nanomedicina y Sensores, Universitat Politècnica de València, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain.,Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain
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Čmoková A, Kolařík M, Dobiáš R, Hoyer LL, Janouškovcová H, Kano R, Kuklová I, Lysková P, Machová L, Maier T, Mallátová N, Man M, Mencl K, Nenoff P, Peano A, Prausová H, Stubbe D, Uhrlaß S, Větrovský T, Wiegand C, Hubka V. Resolving the taxonomy of emerging zoonotic pathogens in the Trichophyton benhamiae complex. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00465-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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dos Santos Ramos MA, dos Santos KC, da Silva PB, de Toledo LG, Marena GD, Rodero CF, de Camargo BAF, Fortunato GC, Bauab TM, Chorilli M. Nanotechnological strategies for systemic microbial infections treatment: A review. Int J Pharm 2020; 589:119780. [PMID: 32860856 PMCID: PMC7449125 DOI: 10.1016/j.ijpharm.2020.119780] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/27/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Abstract
Systemic infections is one of the major causes of mortality worldwide, and a shortage of drug approaches applied for the rapid and necessary treatment contribute to increase the levels of death in affected patients. Several drug delivery systems based in nanotechnology such as metallic nanoparticles, liposomes, nanoemulsion, microemulsion, polymeric nanoparticles, solid lipid nanoparticles, dendrimers, hydrogels and liquid crystals can contribute in the biological performance of active substances for the treatment of microbial diseases triggered by fungi, bacteria, virus and parasites. In the presentation of these statements, this review article present and demonstrate the effectiveness of these drug delivery systems for the treatment of systemic diseases caused by several microorganisms, through a review of studies on scientific literature worldwide that contributes to better information for the most diverse professionals from the areas of health sciences. The studies demonstrated that the drug delivery systems described can contribute to the therapeutic scenario of these diseases, being classified as safe, active platforms and with therapeutic versatility.
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Affiliation(s)
- Matheus Aparecido dos Santos Ramos
- Department of Drugs and Medicines, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil,Corresponding authors
| | - Karen Cristina dos Santos
- Department of Drugs and Medicines, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Patrícia Bento da Silva
- Department of Genetic and Morphology, Brasília University (UNB), Institute of Biological Sciences, Zip Code: 70735100, Brazil
| | - Luciani Gaspar de Toledo
- Department of Biological Sciences, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Gabriel Davi Marena
- Department of Drugs and Medicines, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Camila Fernanda Rodero
- Department of Drugs and Medicines, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Bruna Almeida Furquim de Camargo
- Department of Biological Sciences, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Giovanna Capaldi Fortunato
- Department of Biological Sciences, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Taís Maria Bauab
- Department of Biological Sciences, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Marlus Chorilli
- Department of Drugs and Medicines, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil.
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Agnew-Francis KA, Tang Y, Lin X, Low YS, Wun SJ, Kuo A, Elias SMASI, Lonhienne T, Condon ND, Pimentel BNAS, Vergani CE, Smith MT, Fraser JA, Williams CM, Guddat LW. Herbicides That Target Acetohydroxyacid Synthase Are Potent Inhibitors of the Growth of Drug-Resistant Candida auris. ACS Infect Dis 2020; 6:2901-2912. [PMID: 32986949 DOI: 10.1021/acsinfecdis.0c00229] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Acetohydroxyacid synthase (AHAS, EC 2.2.1.6), the first enzyme in the branched chain amino acid biosynthesis pathway, is the target for more than 50 commercially available herbicides, and is a promising target for antimicrobial drug discovery. Herein, we have expressed and purified AHAS from Candida auris, a newly identified human invasive fungal pathogen. Thirteen AHAS inhibiting herbicides have Ki values of <2 μM for this enzyme, with the most potent having Ki values of <32 nM. Six of these compounds exhibited MIC50 values of <1 μM against C. auris (CBS10913 strain) grown in culture, with bensulfuron methyl (BSM) being fungicidal and the most potent (MIC50 of 0.090 μM) in defined minimal media. The MIC50 value increases to 0.90 μM in media enriched by the addition of branched-chain amino acids at the expected concentration in the blood serum. The sessile MIC50 for BSM is 0.6 μM. Thus, it is also an excellent inhibitor of the growth of C. auris biofilms. BSM is nontoxic in HEK-293 cells at concentrations >100 μM and thus possesses a therapeutic index of >100. These data suggest that targeting AHAS is a viable strategy for treating C. auris infections.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Bruna N. A. S. Pimentel
- School of Dentistry, São Paulo State University (UNESP), Araraquara, Rua Humaita, 1680, 14801-903 Araraquara, SP Brazil
| | - Carlos E. Vergani
- School of Dentistry, São Paulo State University (UNESP), Araraquara, Rua Humaita, 1680, 14801-903 Araraquara, SP Brazil
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Chen J, Tian S, Han X, Chu Y, Wang Q, Zhou B, Shang H. Is the superbug fungus really so scary? A systematic review and meta-analysis of global epidemiology and mortality of Candida auris. BMC Infect Dis 2020; 20:827. [PMID: 33176724 PMCID: PMC7656719 DOI: 10.1186/s12879-020-05543-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Candida auris is a new pathogen called "superbug fungus" which caused panic worldwide. There are no large-scale epidemiology studies by now, therefore a systematic review and meta-analysis was undertaken to determine the epidemic situation, drug resistance patterns and mortality of C. auris. METHODS We systematically searched studies on the clinical report of Candida auris in Pubmed, Embase and Cochrane databases until October 6, 2019. A standardized form was used for data collection, and then statics was performed with STATA11.0. RESULTS It showed that more than 4733 cases of C. auris were reported in over 33 countries, with more cases in South Africa, United States of America, India, Spain, United Kingdom, South Korea, Colombia and Pakistan. C. auirs exhibited a decrease in case count after 2016. Clade I and III were the most prevalent clades with more cases reported and wider geographical distribution. Blood stream infection was observed in 32% of the cases, which varied depending on the clades. Resistance to fluconazole, amphotericin B, caspofungin, micafungin and anidulafungin in C. auris were 91, 12, 12.1, 0.8 and 1.1%. The overall mortality of C. auris infection was 39%. Furthermore, subgroup analyses showed that mortality was higher in bloodstream infections (45%), and lower in Europe (20%). CONCLUSIONS Over 4000 cases of C. auris were reported in at least 33 countries, which showed high resistance to fluconazole, moderate resistance to amphotericin B and caspofungin, high sensitivity to micafungin and anidulafungin. The crude mortality for BSI of C. auris was 45% which was similar to some drug-resistant bacteria previously reported. In conclusion, C. auris displayed similar characteristics to some drug resistance organisms. This study depicts several issues of C. auris that are most concerned, and is of great significance for the clinical management.
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Affiliation(s)
- Jingjing Chen
- Department of Laboratory Medicine, the First Affiliated Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China
- National Clinical Research Center for Laboratory Medicine, the First Affiliated Hospital of China Medical University, Shenyang, 110001, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Sufei Tian
- Department of Laboratory Medicine, the First Affiliated Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China
- National Clinical Research Center for Laboratory Medicine, the First Affiliated Hospital of China Medical University, Shenyang, 110001, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Xiaoxu Han
- Department of Laboratory Medicine, the First Affiliated Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China
- National Clinical Research Center for Laboratory Medicine, the First Affiliated Hospital of China Medical University, Shenyang, 110001, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Yunzhuo Chu
- Department of Laboratory Medicine, the First Affiliated Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China
- National Clinical Research Center for Laboratory Medicine, the First Affiliated Hospital of China Medical University, Shenyang, 110001, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Qihui Wang
- Department of Laboratory Medicine, the First Affiliated Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China
- National Clinical Research Center for Laboratory Medicine, the First Affiliated Hospital of China Medical University, Shenyang, 110001, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Baosen Zhou
- Department of Clinical Epidemiology and Center of Evidence-Based Medicine, the First Hospital of China Medical University, Shenyang, 110001, China
| | - Hong Shang
- Department of Laboratory Medicine, the First Affiliated Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.
- National Clinical Research Center for Laboratory Medicine, the First Affiliated Hospital of China Medical University, Shenyang, 110001, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China.
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37
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Candida auris: An Overview of How to Screen, Detect, Test and Control This Emerging Pathogen. Antibiotics (Basel) 2020; 9:antibiotics9110778. [PMID: 33167419 PMCID: PMC7694398 DOI: 10.3390/antibiotics9110778] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022] Open
Abstract
The multidrug-resistant yeast Candida auris is associated with invasive infections in critically ill patients and has been isolated in different countries worldwide. Ease of spread, prolonged persistence in the environment and antifungal drug resistance pose a significant concern for the prevention of transmission and management of patients with C. auris infections. Early and correct identification of patients colonized with C. auris is critical in containing its spread. However, this may be complicated by C. auris strains being misidentified as other phylogenetically related pathogens. In this review, we offer a brief overview highlighting some of the critical aspects of sample collection, laboratory culture-dependent and independent identification and the susceptibility profile of C. auris.
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Vatanshenassan M, Boekhout T, Mauder N, Robert V, Maier T, Meis JF, Berman J, Then E, Kostrzewa M, Hagen F. Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris. J Fungi (Basel) 2020; 6:jof6030146. [PMID: 32854308 PMCID: PMC7576496 DOI: 10.3390/jof6030146] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022] Open
Abstract
Candida auris is an emerging opportunistic yeast species causing nosocomial outbreaks at a global scale. A few studies have focused on the C. auris genotypic structure. Here, we compared five epidemiological typing tools using a set of 96 C. auris isolates from 14 geographical areas. Isolates were analyzed by microsatellite typing, ITS sequencing, amplified fragment length polymorphism (AFLP) fingerprint analysis, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and Fourier-transform infrared (FTIR) spectroscopy methods. Microsatellite typing grouped the isolates into four main clusters, corresponding to the four known clades in concordance with whole genome sequencing studies. The other investigated typing tools showed poor performance compared with microsatellite typing. A comparison between the five methods showed the highest agreement between microsatellite typing and ITS sequencing with 45% similarity, followed by microsatellite typing and the FTIR method with 33% similarity. The lowest agreement was observed between FTIR spectroscopy, MALDI-TOF MS, and ITS sequencing. This study indicates that microsatellite typing is the tool of choice for C. auris outbreak investigations. Additionally, FTIR spectroscopy requires further optimization and evaluation before it can be used as an epidemiological typing method, comparable with microsatellite typing, as a rapid method for tracing nosocomial fungal outbreaks.
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Affiliation(s)
- Mansoureh Vatanshenassan
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX Amsterdam, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX Amsterdam, The Netherlands
| | - Norman Mauder
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- BioAware, B-4280 Hannut, Belgium
| | - Thomas Maier
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands;
- Center of Expertise in Mycology Radboudumc, Canisius Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands
- Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, 80060-000 Curitiba, Brazil
| | - Judith Berman
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, 6997801 Tel Aviv, Israel;
| | - Euníce Then
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, 28359 Bremen, Germany; (M.V.); (N.M.); (T.M.)
- Correspondence: (M.K.); (F.H.); Tel.: +49-421-2205-1258 (M.K.); +31-30-2122-600 (F.H.)
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands; (T.B.); (V.R.); (E.T.)
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Correspondence: (M.K.); (F.H.); Tel.: +49-421-2205-1258 (M.K.); +31-30-2122-600 (F.H.)
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付 雷, 乐 婷, 王 玲, 郭 辉, 刘 志, 杨 钧, 陈 清, 胡 静. [Study on growth characteristics of Candida auris under different conditions in vitro and its in vivo toxicity]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:1049-1055. [PMID: 32895165 PMCID: PMC7386228 DOI: 10.12122/j.issn.1673-4254.2020.07.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To investigate the characteristics of growth and metabolism and the in vivo toxicity of Candida auris under different conditions. METHODS We observed the growth of Candida auris and Candida albicans under routine culture conditions and in different pH and salt concentrations, and compared their activities of sugar fermentation using microbiochemical reaction tubes. Four-week-old nude mice were randomized into Candida auris infection group (n=5), Candida albicans infection group (n=5) and control group (n=5) for intragastric administration of 0.3 mL suspension the two Candida species (5×109 cfu/mL) or 0.3 mL normal saline. Samples of the liver, kidney, intestine, feces and blood were taken for analysis of the in vivo distribution and toxicity of Candida albicans by fungal culture and histopathological examination. RESULTS Candida auris exhibited logarithmic growth at 8-24 h after inoculation and showed stable growth after 24 h. Candida auris showed optimal growth within the pH value range of 5-7 with a growth pattern identical to that of Candida albicans. Candida auris grew better than Candida albicans in media containing 5% and 10% NaCl, and could ferment glucose, sucrose, trehalose and sorbitol. Candida auris could be isolated from the feces, blood, liver and kidney of infected nude mice, and the liver had the highest fungal load (5.7 log10 cfu/g). Candida auris could cause pathological changes in the liver and intestine of the mice, but with a lesser severity as compared with Candida albicans. CONCLUSIONS Candida auris exhibits optimal growth in mildly acidic or neutral conditions with a high salt tolerance, and can potentially penetrate the intestinal barrier into blood and lead to tissue injuries in hosts with immunosuppression.
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Affiliation(s)
- 雷雯 付
- 南方医科大学珠江医院医院感染管理科,广东 广州 510280Department of Nosocomial Infection Administration, Zhujiang Hospital, Southern Medical University, Guangzhou, China, 510280
- 南方医科大学公共卫生学 院流行病学系,广东 广州 510515Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - 婷婷 乐
- 南方医科大学珠江医院医院感染管理科,广东 广州 510280Department of Nosocomial Infection Administration, Zhujiang Hospital, Southern Medical University, Guangzhou, China, 510280
| | - 玲 王
- 南方医科大学珠江医院医院感染管理科,广东 广州 510280Department of Nosocomial Infection Administration, Zhujiang Hospital, Southern Medical University, Guangzhou, China, 510280
| | - 辉杰 郭
- 南方医科大学公共卫生学 院流行病学系,广东 广州 510515Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - 志华 刘
- 南方医科大学南方医院感染内科,广东 广州 510515Department of Infectious Disease, Nanfang Hospital, Guangzhou 510515, China
| | - 钧 杨
- 南方医科大学公共卫生学 院流行病学系,广东 广州 510515Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - 清 陈
- 南方医科大学公共卫生学 院流行病学系,广东 广州 510515Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - 静 胡
- 南方医科大学珠江医院医院感染管理科,广东 广州 510280Department of Nosocomial Infection Administration, Zhujiang Hospital, Southern Medical University, Guangzhou, China, 510280
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40
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Arastehfar A, Daneshnia F, Najafzadeh MJ, Hagen F, Mahmoudi S, Salehi M, Zarrinfar H, Namvar Z, Zareshahrabadi Z, Khodavaisy S, Zomorodian K, Pan W, Theelen B, Kostrzewa M, Boekhout T, Lass-Flörl C. Evaluation of Molecular Epidemiology, Clinical Characteristics, Antifungal Susceptibility Profiles, and Molecular Mechanisms of Antifungal Resistance of Iranian Candida parapsilosis Species Complex Blood Isolates. Front Cell Infect Microbiol 2020; 10:206. [PMID: 32509592 PMCID: PMC7253641 DOI: 10.3389/fcimb.2020.00206] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/16/2020] [Indexed: 11/13/2022] Open
Abstract
Clonal expansion of fluconazole resistant (FLZ-R) Candida parapsilosis isolates is increasingly being identified in many countries, while there is no study exploring the antifungal susceptibility pattern, genetic diversity, and clinical information for Iranian C. parapsilosis blood isolates. Candida parapsilosis species complex blood isolates (n = 98) were recovered from nine hospitals located in three major cities, identified by MALDI-TOF MS, and their genetic relatedness was examined by AFLP fingerprinting. Antifungal susceptibility testing followed CLSI-M27-A3 and ERG11, MRR1 and hotspots 1/2 (HS1/2) of FKS1 were sequenced to assess the azole and echinocandin resistance mechanisms, respectively. Ninety-four C. parapsilosis and four Candida orthopsilosis isolates were identified from 90 patients. Only 43 patients received systemic antifungal drugs with fluconazole as the main antifungal used. The overall mortality rate was 46.6% (42/90) and death mostly occurred for those receiving systemic antifungals (25/43) relative to those not treated (17/47). Although, antifungal-resistance was rare, one isolate was multidrug-resistant (FLZ = 16 μg/ml and micafungin = 8 μg/ml) and the infected patient showed therapeutic failure to FLZ prophylaxis. Mutations causing azole and echinocandin resistance were not found in the genes studied. AFLP revealed five genotypes (G) and G1 was the main one (59/94; 62.7%). Clinical outcome was significantly associated with city (P = 0.02, α <0.05) and Mashhad was significantly associated with mortality (P = 0.03, α <0.05). Overall, we found a low level of antifungal resistance for Iranian C. parapsilosis blood isolates, but the noted MDR strain can potentially become the source of future infections and challenge the antifungal therapy in antifungal-naïve patients. AFLP typing results warrants confirmation using other resolutive typing methods.
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Affiliation(s)
- Amir Arastehfar
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Farnaz Daneshnia
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ferry Hagen
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Shahram Mahmoudi
- Department of Medical Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Salehi
- Department of Infectious Diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Namvar
- Department of Microbiology, School of Biological Sciences, Islamic Azad University, Tehran, Iran
| | - Zahra Zareshahrabadi
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamiar Zomorodian
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Weihua Pan
- Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Bart Theelen
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | | | - Teun Boekhout
- Yeast Biodiversity Department, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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Tan J, Tay J, Hedrick J, Yang YY. Synthetic macromolecules as therapeutics that overcome resistance in cancer and microbial infection. Biomaterials 2020; 252:120078. [PMID: 32417653 DOI: 10.1016/j.biomaterials.2020.120078] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
Synthetic macromolecular antimicrobials have shown efficacy in the treatment of multidrug resistant (MDR) pathogens. These synthetic macromolecules, inspired by Nature's antimicrobial peptides (AMPs), mitigate resistance by disrupting microbial cell membrane or targeting multiple intracellular proteins or genes. Unlike AMPs, these polymers are less prone to degradation by proteases and are easier to synthesize on a large scale. Recently, various studies have revealed that cancer cell membrane, like that of microbes, is negatively charged, and AMPs can be used as anticancer agents. Nevertheless, efforts in developing polymers as anticancer agents has remained limited. This review highlights the recent advancement in the development of synthetic biodegradable antimicrobial polymers (e.g. polycarbonates, polyesters and polypeptides) and anticancer macromolecules including peptides and polymers. Additionally, strategies to improve their in vivo bioavailability and selectivity towards bacteria and cancer cells are examined. Lastly, future perspectives, including use of artificial intelligence or machine learning, in the development of antimicrobial and anticancer macromolecules are discussed.
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Affiliation(s)
- Jason Tan
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Singapore, 138669, Singapore; Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Joyce Tay
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Singapore, 138669, Singapore; Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - James Hedrick
- IBM Almaden Research Center, 650 Harry Road, San Jose, CA, 95120, United States
| | - Yi Yan Yang
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Singapore, 138669, Singapore.
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Ademe M, Girma F. Candida auris: From Multidrug Resistance to Pan-Resistant Strains. Infect Drug Resist 2020; 13:1287-1294. [PMID: 32440165 PMCID: PMC7211321 DOI: 10.2147/idr.s249864] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/19/2020] [Indexed: 11/23/2022] Open
Abstract
Candida auris is an emerging multidrug-resistant fungus that is rapidly spreading worldwide. Currently, C. auris cases have been reported globally from >30 countries. Most reported infections involve critically ill patients in hospitals, mainly in intensive care unit settings. Infection with C. auris is associated with high mortality rates, and it is often resistant to multiple classes of antifungal drugs. Despite the rapid global spread, it is difficult to predict the actual burden of the infection as the standard laboratory methods fail to correctly identify the fungi. Longer stays in healthcare facilities, use of tracheostomies and percutaneous endoscopic gastrostomy tubes, ventilators in clinical care units and mobile equipment in healthcare settings are shown as major risk factors of C. auris infection. Due to its propensity to cause outbreaks and its antifungal resistance, C. auris poses a risk for patients in healthcare facilities. The emergence of pan-resistant C. auris strains in some areas is an alarming signal for the disease with limited treatment options, high mortality rates, and the ability of the pathogen to spread easily in healthcare settings. In this regard, susceptibility testing on clinical isolates, mainly for patients treated with echinocandins, is needed. Increasing awareness about C. auris infection and advancing the diagnostic methods are also essential for early detection and control of the deadly fungal infection.
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Affiliation(s)
- Muluneh Ademe
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Friehiwot Girma
- Department of Pediatrics and Child Health Nursing, School of Health Sciences, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
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ElBaradei A. A decade after the emergence of Candida auris: what do we know? Eur J Clin Microbiol Infect Dis 2020; 39:1617-1627. [PMID: 32297040 DOI: 10.1007/s10096-020-03886-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/30/2020] [Indexed: 12/18/2022]
Abstract
Candida auris is a remarkable emerging pathogen. It has emerged separately, yet simultaneously in different parts of the world, establishing four phylogenetic and geographic distinct clades with a potential fifth clade that was recently reported. C. auris is often perceived as a pathogen in disguise, due to its frequent misidentification and its immune evasion. On the other hand, many of the recovered isolates are multidrug-resistant. In fact, some of these isolates are resistant to the three main antifungal classes: echinocandins, azoles, and polyenes. Moreover, C. auris has the ability to persist and survive on different objects for a long time, aided by different adhering mechanisms including aggregation and biofilm formation, thereby causing outbreaks of invasive infections in hospital settings. However, C. auris ability to maintain its pathogenicity at high temperatures remains among its most unique properties. This is why C. auris represents a challenging threat, and more studies are needed to meet this challenge. This review highlights different characteristics of this emerging yeast with emphasis on its antifungal resistance, its ability to persistent on different surfaces, and its immune evasion capability.
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Affiliation(s)
- Amira ElBaradei
- Department of Microbiology and Immunology, Faculty of Pharmacy and Drug Manufacturing, Pharos University in Alexandria, Alexandria, Egypt. .,Alexandria University Hospital, Alexandria University, Alexandria, Egypt.
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Abstract
Neonates and immunosuppressed/immunocompromised pediatric patients are at high risk of invasive fungal diseases. Appropriate antifungal selection and optimized dosing are imperative to the successful prevention and treatment of these life-threatening infections. Conventional amphotericin B was the mainstay of antifungal therapy for many decades, but dose-limiting nephrotoxicity and infusion-related adverse events impeded its use. Despite the development of several new antifungal classes and agents in the past 20 years, and their now routine use in at-risk pediatric populations, data to guide the optimal dosing of antifungals in children are limited. This paper reviews the spectra of activity for approved antifungal agents and summarizes the current literature specific to pediatric patients regarding pharmacokinetic/pharmacodynamic data, dosing, and therapeutic drug monitoring.
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Affiliation(s)
- Kevin J Downes
- Division of Infectious Diseases, Children's Hospital of Philadelphia, 2716 South Street, Suite 10360, Philadelphia, PA, 19146, USA.
- Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Center for Clinical Pharmacology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, USA.
| | - Brian T Fisher
- Division of Infectious Diseases, Children's Hospital of Philadelphia, 2716 South Street, Suite 10360, Philadelphia, PA, 19146, USA
- Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, USA
| | - Nicole R Zane
- Center for Clinical Pharmacology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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Magobo R, Mhlanga M, Corcoran C, Govender NP. Multilocus sequence typing of azole-resistant Candida auris strains, South Africa. S Afr J Infect Dis 2020; 35:116. [PMID: 34485470 PMCID: PMC8378186 DOI: 10.4102/sajid.v35i1.116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/16/2020] [Indexed: 11/25/2022] Open
Abstract
Background Candida auris is an emerging multidrug-resistant fungal pathogen associated with high mortality. Methods We investigated the genetic relatedness of clinical C. auris isolates from patients admitted to either public- or private-sector hospitals, which were submitted to a reference laboratory from 2012 to 2015. Patient demographics and clinical details were recorded. We performed antifungal susceptibility testing, sequencing of the hotspot 1 and 2 regions of the FKS1 and FKS2 genes for all isolates with an echinocandin minimum inhibitory concentration (MIC) of ≥1 µg/mL and cluster analysis using multilocus sequence typing. Results Eighty-five isolates were confirmed as C. auris. The median patient age was 59 years [inter-quartile range (IQR): 48–68 years], with male patients accounting for 68% of cases. Specimen types included urine (29%), blood (27%), central venous catheter tips (25%), irrigation fluid (7%), tissue (5%), respiratory tract specimens (4%) and other (3%). Ninety-seven per cent of isolates were resistant to fluconazole, 7% were resistant to both fluconazole and voriconazole, 8% were resistant to both fluconazole and echinocandins (considered multidrug resistant) and all were susceptible to amphotericin B. Of the 15 randomly selected fluconazole-resistant isolates, 14 isolates had an isavuconazole MIC ≤ 1 µg/mL. No FKS mutations were detected. Multilocus sequence typing (MLST) analysis grouped isolates into two clusters: cluster 1 and cluster 2 comprising 83 and 2 isolates, respectively. Conclusions Azole-resistant C. auris strains circulating in South African hospitals were related by MLST, but the possibility of nosocomial transmission should be explored using a more discriminatory technique, for example, whole genome sequencing.
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Affiliation(s)
- Rindidzani Magobo
- Centre for Healthcare-associated Infections, Antimicrobial Resistance and Mycoses, Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa.,Ampath National Reference Laboratory, Pretoria, South Africa
| | - Mabatho Mhlanga
- Centre for Healthcare-associated Infections, Antimicrobial Resistance and Mycoses, Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Craig Corcoran
- Ampath National Reference Laboratory, Pretoria, South Africa
| | - Nelesh P Govender
- Centre for Healthcare-associated Infections, Antimicrobial Resistance and Mycoses, Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa
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Lo Cascio G, Vincenzi M, Soldani F, De Carolis E, Maccacaro L, Sorrentino A, Nadali G, Cesaro S, Sommavilla M, Niero V, Naso L, Grancini A, Azzini AM, Sanguinetti M, Tacconelli E, Cornaglia G. Outbreak of Saprochaete clavata Sepsis in Hematology Patients: Combined Use of MALDI-TOF and Sequencing Strategy to Identify and Correlate the Episodes. Front Microbiol 2020; 11:84. [PMID: 32082293 PMCID: PMC7004961 DOI: 10.3389/fmicb.2020.00084] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Introduction New fungal species are increasingly reported in immunocompromised patients. Saprochaete clavata (S. clavata), an ascomycetous fungus formerly called Geotrichum clavatum, is intrinsically resistant to echinocandins and is often misidentified. Objective We describe a cluster of seven S. clavata infections in hospitalized hematology patients who developed this rare fungemia within a span of 11 months. Three of the seven patients died. Identification of the isolates was determined only with the Saramis database of VitekMS system and sequencing of the internal transcribed spacer (ITS) region. Clonal relatedness of the isolates was determined by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF) analysis; clonal correlation between the strains was investigated by means of phylogenetic analysis, based on single-nucleotide variants (SNPs). Clinical presentation, 1–3 β-D-glucan (BG) and galactomannan (GM) antigen results and analysis of possible sources of contamination are also described with a prospective case–control study of the outbreak. Results MALDI-TOF MS-Vitek (bioMerieux, Marcy l’Etoile, France) failed to identify the six isolates, while SARAMIS (bioMerieux, Marcy l’Etoile, France) identified the isolates as S. clavata. Initially, Vitek 2 identified the strains as Geotrichum capitatum in two of the seven cases. Molecular identification gave 99% homology with S. clavata. BG was positive in three out of six patients (range 159 to >523 pg/ml), GM results were always negative. All the isolates were resistant to echinocandins (anidulafungin, micafungin, and caspofungin) and Fluconazole, but susceptible to Flucytosine and Voriconazole. One isolate showed acquired resistance to Flucytosine and Amphotericin B during treatment. Both the correlation-based dendrograms obtained by MALDI-TOF MS (Bruker Daltonics) and MS-Vitek not only clustered six of the seven bloodstream infection (BSI) isolates in the same group, but also showed their strong relatedness. Phylogenetic analysis using SNPrelate showed that the seven samples recorded during the investigation period clustered together. We observed a split between one case and the remainder with a node supported by a z-score of 2.3 (p-value = 0.021) and 16 mutations unique to each branch. Conclusion The use of proteomics for identification and evaluation of strain clonality in outbreaks of rare pathogens is a promising alternative to laborious and time-consuming molecular methods, even if molecular whole-genome sequencing (WGS) typing will still remain the reference method for rare emergent pathogens.
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Affiliation(s)
- Giuliana Lo Cascio
- Microbiology and Virology Unit, Department of Pathology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Marcello Vincenzi
- Infectious Disease Unit, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Fabio Soldani
- Infectious Disease Unit, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elena De Carolis
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Laura Maccacaro
- Microbiology and Virology Unit, Department of Pathology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Annarita Sorrentino
- Microbiology and Virology Unit, Department of Pathology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Gianpaolo Nadali
- Haematology Unit, Department of Medicine, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Simone Cesaro
- Division of Pediatric Oncohaematology, Department of Pediatrics, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Michele Sommavilla
- Direzione Medica Ospedaliera, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Valentina Niero
- Sezione di Igiene e Medicina Preventiva, Ambientale e Occupazionale, Dipartimento Diagnostica e Sanità Pubblica, Università di Verona, Verona, Italy
| | - Laura Naso
- Microbiology and Virology Unit, Department of Pathology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
| | - Anna Grancini
- Laboratorio di Analisi Chimico - Cliniche e Microbiologia, Fondazione IRCCS Cà Granda O. Maggiore Policlinico, Milan, Italy
| | - Anna Maria Azzini
- Infectious Disease Unit, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - E Tacconelli
- Infectious Disease Unit, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Giuseppe Cornaglia
- Microbiology and Virology Unit, Department of Pathology, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy
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Sabino R, Veríssimo C, Pereira ÁA, Antunes F. Candida auris, an Agent of Hospital-Associated Outbreaks: Which Challenging Issues Do We Need to Have in Mind? Microorganisms 2020; 8:E181. [PMID: 32012865 PMCID: PMC7074697 DOI: 10.3390/microorganisms8020181] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/28/2022] Open
Abstract
The emergence of Candida auris is considered as one of the most serious problems associated with nosocomial transmission and with infection control practices in hospital environment. This multidrug resistant species is rapidly spreading worldwide, with several described outbreaks. Until now, this species has been isolated from different hospital surfaces, where it can survive for long periods. There are multiple unanswered questions regarding C. auris, such as prevalence in population, environmental contamination, effectiveness of infection prevention and control, and impact on patient mortality. In order to understand how it spreads and discover possible reservoirs, it is essential to know the ecology, natural environment, and distribution of this species. It is also important to explore possible reasons to this recent emergence, namely the environmental presence of azoles or the possible effect of climate change on this sudden emergence. This review aims to discuss some of the most challenging issues that we need to have in mind in the management of C. auris and to raise the awareness to its presence in specific indoor environments as hospital settings.
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Affiliation(s)
- Raquel Sabino
- Reference Unit for Parasitic and Fungal Infections, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge. Avenida Padre Cruz, 1649-016 Lisbon, Portugal;
- Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, Ed. Egas Moniz, 1649-028 Lisboa, Portugal; (Á.A.P.); (F.A.)
| | - Cristina Veríssimo
- Reference Unit for Parasitic and Fungal Infections, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge. Avenida Padre Cruz, 1649-016 Lisbon, Portugal;
- Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, Ed. Egas Moniz, 1649-028 Lisboa, Portugal; (Á.A.P.); (F.A.)
| | - Álvaro Ayres Pereira
- Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, Ed. Egas Moniz, 1649-028 Lisboa, Portugal; (Á.A.P.); (F.A.)
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário Lisboa Norte/Hospital de Santa Maria, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Francisco Antunes
- Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, Ed. Egas Moniz, 1649-028 Lisboa, Portugal; (Á.A.P.); (F.A.)
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Development of Candida auris Short Tandem Repeat Typing and Its Application to a Global Collection of Isolates. mBio 2020; 11:mBio.02971-19. [PMID: 31911492 PMCID: PMC6946803 DOI: 10.1128/mbio.02971-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Candida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and causes mainly hospital-associated outbreaks. To track and trace outbreaks and to relate them to new introductions from elsewhere, whole-genome sequencing and amplified fragment length polymorphism (AFLP) have been used for molecular typing. Whole-genome sequencing is costly and available only at a few centers, and AFLP is a complicated technique and hard to interpret. We describe a novel simple STR genotyping technique based on short tandem repeats in the C. auris genome. We also show that the performance of this STR-based genotyping technique has proven comparable to that of WGS. Overall, this work provides a novel, rapid, reliable, and cost-effective method of molecular outbreak investigations of C. auris. Candida auris is a pathogenic yeast that causes invasive infections with high mortality. Infections most often occur in intensive care units of health care facilities. It is crucial to trace the source and prevent further spread of C. auris during an outbreak setting; therefore, genotyping of C. auris is required. To enable fast and cost-effective genotyping, we developed a short tandem repeat (STR) typing assay for C. auris. STRs in C. auris were identified, and from an initial selection of 23 STRs, 12 were used to develop a STR typing assay. Having shown that the STR typing assay was reproducible and specific, a robust set of 444 C. auris isolates was investigated to identify genotypic diversity. In concordance with whole-genome sequencing (WGS) analysis, we identified five major different C. auris clusters of South American, South Asian, African, East Asian, and Iranian origin. Overall, a total of 40 distinct genotypes were identified, with the largest variety in the South Asian clade. Comparison with WGS demonstrated that isolates with <20 single nucleotide polymorphisms (SNPs) are mostly not differentiated by STR analysis, while isolates with 30 or more SNPs usually have differences in one or more STR markers. Altogether, a highly reproducible and specific STR typing assay for C. auris was developed; this assay distinguishes the five different C. auris clades in identical fashion to WGS, while most isolates differing by >30 SNPs, as determined via WGS, are also separated. This new C. auris-specific genotyping technique is a rapid, reliable, and cost-effective alternative to WGS analysis to investigate outbreaks.
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Global epidemiology of emerging Candida auris. Curr Opin Microbiol 2019; 52:84-89. [DOI: 10.1016/j.mib.2019.05.008] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/23/2019] [Accepted: 05/30/2019] [Indexed: 11/18/2022]
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50
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Alastruey-Izquierdo A, Asensio A, Besoli A, Calabuig E, Fernández-Ruiz M, Garcia-Vidal C, Gasch O, Guinea J, Martín-Gomez MT, Paño JR, Ramirez P, Ruiz-Gaitán A, Salavert M, Tasias M, Viñuela L, Pemán J. [GEMICOMED/GEIRAS-SEIMC recommendations for the management of Candida auris infection and colonization]. Rev Iberoam Micol 2019; 36:109-114. [PMID: 31694788 DOI: 10.1016/j.riam.2019.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/25/2019] [Accepted: 06/05/2019] [Indexed: 11/19/2022] Open
Abstract
Candida auris is a new species of Candida that causes nosocomial outbreaks in several countries around the world, including Spain. C.auris is resistant to fluconazole and multi- and pan-resistant strains have been described. It is highly transmissible and can survive long term in the hospital environment, causing long-lasting outbreaks that are difficult to detect in early stages, and making it difficult to control and eradicate. It is currently an emerging threat to global health. This document provides a set of guidelines, developed by a multidisciplinary team, to limit the impact and facilitate the control of C.auris infection based on the experiences gathered in the Spanish and English outbreaks. The implementation of early and strict surveillance and control measures is essential to prevent the spread of the outbreak, which can spread over time, posing a significant risk to complex, critical and immunocompromised surgical patients. Immediate notification of C.auris isolation to clinical and infection control teams, as well as to health authorities and institutions, is essential to implement infection control measures at all levels in a timely manner, to prevent internal and inter-centre transmission, and to ensure a proper surveillance and prevention to patients who are already colonized and can develop an infection.
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Affiliation(s)
- Ana Alastruey-Izquierdo
- Laboratorio de Referencia e Investigación en Micología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, España.
| | - Angel Asensio
- Hospital Universitario Puerta de Hierro, Majadahonda, Madrid, España
| | - Anna Besoli
- Hospital Universitario de Vic, Vic, Barcelona, España
| | - Eva Calabuig
- Unidad de Enfermedades Infecciosas (Área Clínica Médica), Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Mario Fernández-Ruiz
- Unidad de Enfermedades Infecciosas, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), Madrid, España
| | - Carolina Garcia-Vidal
- Unidad de Enfermedades Infecciosas, Hospital Clínic-IDIBAPS, Universidad de Barcelona, Barcelona, España
| | - Oriol Gasch
- Servicio de Enfermedades Infecciosas, Hospital Universitari Parc Taulí, Sabadell, Barcelona, España
| | - Jesús Guinea
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón. Instituto de Investigación Sanitaria Gregorio Marañón. CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, España
| | | | - Jose Ramón Paño
- Hospital Clínico Universitario Lozano Blesa, Zaragoza, España
| | - Paula Ramirez
- Servicio de Medicina Intensiva, Hospital Universitari i Politécnic La Fe, Valencia, España
| | - Alba Ruiz-Gaitán
- Servicio de Microbiología, Hospital Universitari i Politécnic La Fe, Valencia, España
| | - Miguel Salavert
- Unidad de Enfermedades Infecciosas (Área Clínica Médica), Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Mariona Tasias
- Unidad de Enfermedades Infecciosas (Área Clínica Médica), Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Lourdes Viñuela
- Servicio de Microbiología, Hospital Universitario Río Hortega, Valladolid, España
| | - Javier Pemán
- Servicio de Microbiología, Hospital Universitari i Politécnic La Fe, Valencia, España
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