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McTaggart LR, Eshaghi A, Hota S, Poutanen SM, Johnstone J, De Luca DG, Bharat A, Patel SN, Kus JV. First Canadian report of transmission of fluconazole-resistant Candida parapsilosis within two hospital networks confirmed by genomic analysis. J Clin Microbiol 2024; 62:e0116123. [PMID: 38112529 PMCID: PMC10793253 DOI: 10.1128/jcm.01161-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/06/2023] [Indexed: 12/21/2023] Open
Abstract
Candida parapsilosis is a common cause of non-albicans candidemia. It can be transmitted in healthcare settings resulting in serious healthcare-associated infections and can develop drug resistance to commonly used antifungal agents. Following a significant increase in the percentage of fluconazole (FLU)-nonsusceptible isolates from sterile site specimens of patients in two Ontario acute care hospital networks, we used whole genome sequence (WGS) analysis to retrospectively investigate the genetic relatedness of isolates and to assess potential in-hospital spread. Phylogenomic analysis was conducted on all 19 FLU-resistant and seven susceptible-dose dependent (SDD) isolates from the two hospital networks, as well as 13 FLU susceptible C. parapsilosis isolates from the same facilities and 20 isolates from patients not related to the investigation. Twenty-five of 26 FLU-nonsusceptible isolates (resistant or SDD) and two susceptible isolates from the two hospital networks formed a phylogenomic cluster that was highly similar genetically and distinct from other isolates. The results suggest the presence of a persistent strain of FLU-nonsusceptible C. parapsilosis causing infections over a 5.5-year period. Results from WGS were largely comparable to microsatellite typing. Twenty-seven of 28 cluster isolates had a K143R substitution in lanosterol 14-α-demethylase (ERG11) associated with azole resistance. As the first report of a healthcare-associated outbreak of FLU-nonsusceptible C. parapsilosis in Canada, this study underscores the importance of monitoring local antimicrobial resistance trends and demonstrates the value of WGS analysis to detect and characterize clusters and outbreaks. Timely access to genomic epidemiological information can inform targeted infection control measures.
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Affiliation(s)
| | | | - Susy Hota
- Infection Prevention and Control Department, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Susan M. Poutanen
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, University Health Network/Sinai Health, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jennie Johnstone
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Infection Prevention and Control Department, Sinai Health, Toronto, Ontario, Canada
| | - Domenica G. De Luca
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Samir N. Patel
- Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Julianne V. Kus
- Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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Luo Z, Ning Y, Yu S, Xiao M, Dai R, Chen X, Wang Y, Kang W, Jiang Y, Yu H, Liang H, Xu Y, Sun T, Zhang L. The first established microsatellite markers to distinguish Candida orthopsilosis isolates and detection of a nosocomial outbreak in China. J Clin Microbiol 2023; 61:e0080623. [PMID: 37877725 PMCID: PMC10662339 DOI: 10.1128/jcm.00806-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/11/2023] [Indexed: 10/26/2023] Open
Abstract
The infection proportion of Candida orthopsilosis, a member of the C. parapsilosis complex, has increased globally in recent years, and nosocomial outbreaks have been reported in several countries. This study aimed to establish microsatellite loci-based typing method that was able to effectively distinguish among C. orthopsilosis isolates. Three reference C. orthopsilosis genome sequences were analyzed to identify repeat loci. DNA sequences containing over eight bi- or more nucleotide repeats were selected. A total of 51 loci were initially identified, and locus-specific primers were designed and tested with 20 epidemiologically unrelated isolates. Four loci with excellent reproducibility, specificity, and resolution for molecular typing purposes were identified, and the combined discriminatory power (DP, based on 20 epidemiologically unrelated isolates) of these four loci was 1.0. Reproducibility was demonstrated by consistently testing three strains each in triplicate, and stability, demonstrated by testing 10 successive passages. Then, we collected 48 C. orthopsilosis non-duplicate clinical isolates from the China Hospital Invasive Fungal Surveillance Net study to compare the DP of the microsatellite-based typing with internal transcribed spacer (ITS) and amplified fragment length polymorphism (AFLP) typing analyses, using ATCC 96139 as a reference strain. These 49 isolates were subdivided into 12 microsatellite types (COMT1-12), six AFLP types, and three ITS types, while all the isolates with the same COMT belonged to consistent AFLP and ITS type, demonstrating the high DP of our microsatellite-type method. According to our results, COMT12 was found to be the predominant type in China, and COMT5 was the second largest and responsible for causing a nosocomial outbreak. This microsatellite-type method is a valuable tool for the differentiation of C. orthopsilosis and could be vital for epidemiological studies to determine strain relatedness and monitor transmission.
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Affiliation(s)
- Zhengyu Luo
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yating Ning
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Shuying Yu
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Rongchen Dai
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinfei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yao Wang
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Wei Kang
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yan Jiang
- Department of Microbiology and Immunology, Guizhou Medical University Affiliated Hospital, Guiyang, China
| | - Hua Yu
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Hongjie Liang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, The First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Yingchun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Tianshu Sun
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Clinical Biobank, Medical Research Center, National Science and Technology Key Infrastructure on Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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3
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Lin H, Guo J, Li Y, Xiao C, Hu L, Chen H, Lu X, Wu W. In vitro antifungal susceptibility profile and genotypic characterization of clinical Aspergillus isolates in Eastern China on behalf of Eastern China Invasive Fungi Infection Group. Med Mycol 2023; 61:myad082. [PMID: 37580143 DOI: 10.1093/mmy/myad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/27/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023] Open
Abstract
Aspergillus species is a widespread environmental mould that can cause aspergillosis. The purpose of this study was to investigate the antifungal susceptibility profile and genotypic characterization of clinical Aspergillus isolates from different provinces in Eastern China. The data included the antifungal susceptibility distributions with eight common antifungal drugs, cyp51A gene mutations of triazole-resistant Aspergillus fumigatus sensu stricto, and the genotypic relationships among the A. fumigatus sensu stricto isolates based on microsatellite typing. A. fumigatus sensu lato was the most common clinical Aspergillus species (n = 252), followed by A. flavus (n = 169), A. terreus (n = 37), A. niger (n = 29), and A. nidulans (n = 4). The modal minimum effective concentration values of micafungin and anidulafungin were lower than those of caspofungin for all Aspergillus species. The in vitro efficacy of isavuconazole was similar to that of voriconazole against most Aspergillus species. Sequencing revealed cyp51A gene mutations TR34/L98H, TR34/L98H/S297T/F495I, and TR46/Y121F/T289A in four triazole-resistant A. fumigatus sensu stricto. Phylogenetic analyses using microsatellite markers of A. fumigatus sensu stricto revealed that 211 unique genotypes clustered into two clades. The data demonstrate the diversity of clinically relevant Aspergillus species in Eastern China. Routine antifungal susceptibility testing should be performed to monitor the antifungal resistance and guide clinical therapy.
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Affiliation(s)
- Huiping Lin
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Yueting Li
- Department of Laboratory Medicine, Jiangxi provincial People's Hospital Affiliated to Nanchang University, Nanchang 330006, China
| | - Chenlu Xiao
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Liang Hu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Hui Chen
- Department of Laboratory Medicine, Jiangxi provincial People's Hospital Affiliated to Nanchang University, Nanchang 330006, China
| | - Xiuhai Lu
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, 250000, China
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
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Kim TY, Huh HJ, Lee GY, Choi MJ, Yu HJ, Cho SY, Chang YS, Kim YJ, Shin JH, Lee NY. Evolution of Fluconazole Resistance Mechanisms and Clonal Types of Candida parapsilosis Isolates from a Tertiary Care Hospital in South Korea. Antimicrob Agents Chemother 2022;:e0088922. [PMID: 36226945 DOI: 10.1128/aac.00889-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the evolution of fluconazole resistance mechanisms and clonal types of Candida parapsilosis isolates from a tertiary care hospital in South Korea. A total of 45 clinical isolates, including 42 collected between 2017 and 2021 and 3 collected between 2012 and 2013, were subjected to antifungal susceptibility testing, sequencing of fluconazole resistance genes (ERG11, CDR1, TAC1, and MRR1), and microsatellite typing. Twenty-two isolates carried Y132F (n = 21; fluconazole MIC = 2 to >256 mg/L) or Y132F+R398I (n = 1; fluconazole MIC = 64 mg/L) in ERG11 and four isolates harbored N1132D in CDR1 (fluconazole MIC = 16 to 64 mg/L). All 21 Y132F isolates exhibited similar microsatellite profiles and formed a distinct group in the dendrogram. All four N1132D isolates displayed identical microsatellite profiles. Fluconazole MIC values of the Y132F isolates varied depending on their MRR1 mutation status (number of isolates, year of isolation, and MIC): K177N (n = 8, 2012 to 2020, 2 to 8 mg/L); K177N + heterozygous G982R (n = 1, 2017, 64 mg/L); K177N + heterozygous S614P (n = 2, 2019 to 2020, 16 mg/L); and K177N + homozygous S614P (n = 10, 2020 to 2021, 64 to > 256 mg/L). Our study revealed that Y132F in ERG11 and N1132D in CDR1 were the major mechanisms of fluconazole resistance in C. parapsilosis isolates. Furthermore, our results suggested that the clonal evolution of Y132F isolates persisting and spreading in hospital settings for several years occurred with the acquisition of heterozygous or homozygous MRR1 mutations associated with a gradual increase in fluconazole resistance.
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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: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Čmoková A, Kolařík M, Guillot J, Risco-Castillo V, Cabañes F, Nenoff P, Uhrlaß S, Dobiáš R, Mallátová N, Yaguchi T, Kano R, Kuklová I, Lysková P, Mencl K, Hamal P, Peano A, Hubka V. Host-driven subspeciation in the hedgehog fungus, Trichophyton erinacei, an emerging cause of human dermatophytosis. Persoonia 2022; 48:203-218. [PMID: 38234687 PMCID: PMC10792284 DOI: 10.3767/persoonia.2023.48.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/20/2022] [Indexed: 01/19/2024]
Abstract
Trichophyton erinacei is a main cause of dermatophytosis in hedgehogs and is increasingly reported from human infections worldwide. This pathogen was originally described in the European hedgehog (Erinaceus europaeus) but is also frequently found in the African four-toed hedgehog (Atelerix albiventris), a popular pet animal worldwide. Little is known about the taxonomy and population genetics of this pathogen despite its increasing importance in clinical practice. Notably, whether there are different populations or even cryptic species associated with different hosts or geographic regions is not known. To answer these questions, we collected 161 isolates, performed phylogenetic and population-genetic analyses, determined mating-type, and characterised morphology and physiology. Multigene phylogeny and microsatellite analysis supported T. erinacei as a monophyletic species, in contrast to highly incongruent single-gene phylogenies. Two main subpopulations, one specific mainly to Atelerix and second to Erinaceus hosts, were identified inside T. erinacei, and slight differences in the size of microconidia and antifungal susceptibilities were observed among them. Although the process of speciation into two lineages is ongoing in T. erinacei, there is still gene flow between these populations. Thus, we present T. erinacei as a single species, with notable intraspecies variability in genotype and phenotype. The data from wild hedgehogs indicated that sexual reproduction in T. erinacei and de novo infection of hedgehogs from soil are probably rare events and that clonal horizontal spread strongly dominates. The molecular typing approach used in this study represents a suitable tool for further epidemiological surveillance of this emerging pathogen in both animals and humans. The results of this study also highlighted the need to use a multigene phylogeny ideally in combination with other independent molecular markers to understand the species boundaries of dermatophytes. Citation: Čmoková A, Kolařík M, Guillot J, et al. 2022. Host-driven subspeciation in the hedgehog fungus, Trichophyton erinacei, an emerging cause of human dermatophytosis. Persoonia 48: 203-218. https://doi.org/10.3767/persoonia.2022.48.06.
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Affiliation(s)
- A. Čmoková
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - M. Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - J. Guillot
- Dynamyc Research Group EA 7380, Ecole Nationale Vétérinaire d’Alfort, UPEC, USC ANSES, Maisons-Alfort, France
- Department of Dermatology, Parasitology, Mycology, Ecole Nationale Vétérinaire, Agroalimentaire et de l’Alimentation, Oniris, Nantes, France
| | - V. Risco-Castillo
- Dynamyc Research Group EA 7380, Ecole Nationale Vétérinaire d’Alfort, UPEC, USC ANSES, Maisons-Alfort, France
- Ecole Nationale Vétérinaire d’Alfort, Biopole Alfort, Service de Parasitologie-Mycologie, Maisons-Alfort, France
| | - F.J. Cabañes
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Autonomous University of Barcelona, Barcelona, Spain
| | - P. Nenoff
- Laboratory of Medical Microbiology, Mölbis, Germany
| | - S. Uhrlaß
- Laboratory of Medical Microbiology, Mölbis, Germany
| | - R. Dobiáš
- Public Health Institute in Ostrava, Ostrava, Czech Republic
- Institute of Laboratory Medicine, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - N. Mallátová
- Laboratory of Medical Parasitology and Mycology, Hospital České Budějovice, České Budějovice, Czech Republic
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - R. Kano
- Teikyo University Institute of Medical Mycology (TIMM), Tokyo, Japan
| | - I. Kuklová
- Department of Dermatology and Venereology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - P. Lysková
- Laboratory of Mycology, Department of Medical Microbiology Prague and Kladno, Prague, Czech Republic
| | - K. Mencl
- Pardubice Regional Hospital, Pardubice, Czech Republic
| | - P. Hamal
- Department of Microbiology, Palacký University and University hospital, Olomouc, Czech Republic
| | - A. Peano
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
- Medical Mycology Research Center, Chiba University, Chiba, Japan
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Kirchhoff L, Braun L, Schmidt D, Dittmer S, Dedy J, Herbstreit F, Stauf R, Steckel NK, Buer J, Rath PM, Steinmann J, Verhasselt HL. COVID-19-associated pulmonary aspergillosis in ICU patients in a German reference centre: phenotypic and molecular characterization of Aspergillus fumigatus isolates. Mycoses 2022; 65:458-465. [PMID: 35138651 PMCID: PMC9115305 DOI: 10.1111/myc.13430] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 01/08/2023]
Abstract
Background COVID‐19‐associated invasive pulmonary aspergillosis (CAPA) is associated with increased mortality. Cases of CAPA caused by azole‐resistant Aspergillus fumigatus strains have been reported. Objectives To analyse the twelve‐month CAPA prevalence in a German tertiary care hospital and to characterise clinical A. fumigatus isolates from two German hospitals by antifungal susceptibility testing and microsatellite genotyping. Patients/Methods. Retrospective observational study in critically ill adults from intensive care units with COVID‐19 from 17 February 2020 until 16 February 2021 and collection of A. fumigatus isolates from two German centres. EUCAST broth microdilution for four azole compounds and microsatellite PCR with nine markers were performed for each collected isolate (N = 27) and additional for three non‐COVID A. fumigatus isolates. Results welve‐month CAPA prevalence was 7.2% (30/414), and the rate of azole‐resistant A. fumigatus isolates from patients with CAPA was 3.7% with detection of one TR34/L98H mutation. The microsatellite analysis revealed no major clustering of the isolates. Sequential isolates mainly showed the same genotype over time. Conclusions Our findings demonstrate similar CAPA prevalence to other reports and a low azole‐resistance rate. Genotyping of A. fumigatus showed polyclonal distribution except for sequential isolates.
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Affiliation(s)
- Lisa Kirchhoff
- Institute of Medical Microbiology, University Hospital Essen, ECMM Centre of Excellence in Mycology, Germany
| | - Lukas Braun
- Institute of Medical Microbiology, University Hospital Essen, ECMM Centre of Excellence in Mycology, Germany
| | - Dirk Schmidt
- Institute of Medical Microbiology, University Hospital Essen, ECMM Centre of Excellence in Mycology, Germany
| | - Silke Dittmer
- Institute of Medical Microbiology, University Hospital Essen, ECMM Centre of Excellence in Mycology, Germany
| | - Jutta Dedy
- University Hospital Essen, Pharmacy, Germany
| | - Frank Herbstreit
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital Essen, Germany
| | - Raphael Stauf
- Institute of Hospital Hygiene and Clinical Microbiology, Klinikum Dortmund gGmbH, Dortmund, Germany
| | - Nina Kristin Steckel
- Department of Bone Marrow Transplantation, West German Cancer Centre, University Hospital Essen, Essen, Germany
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, ECMM Centre of Excellence in Mycology, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Hospital Essen, ECMM Centre of Excellence in Mycology, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University Hospital Essen, ECMM Centre of Excellence in Mycology, Germany.,Institute of Clinical Hygiene, Medical Microbiology and Infectiology, General Hospital Nürnberg, Paracelsus Medical University, Nuremberg, Germany
| | - Hedda Luise Verhasselt
- Institute of Medical Microbiology, University Hospital Essen, ECMM Centre of Excellence in Mycology, Germany
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Aneke CI, Čmoková A, Hubka V, Rhimi W, Otranto D, Cafarchia C. Subtyping Options for Microsporum canis Using Microsatellites and MLST: A Case Study from Southern Italy. Pathogens 2021; 11:4. [PMID: 35055952 PMCID: PMC8780581 DOI: 10.3390/pathogens11010004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
Microsporum canis is considered one of the most common zoophilic dermatophyte species causing infections in animals and humans worldwide. However, molecular epidemiological studies on this dermatophyte are still rare. In this study, we aimed to analyse the population structure and relationships between M. canis strains (n = 66) collected in southern Italy and those isolated from symptomatic and asymptomatic animals (cats, dogs and rabbits) and humans. For subtyping purposes, using multilocus sequence typing (MLST) and multilocus microsatellite typing (MLMT), we first used a limited set of strains to screen for variability. No intraspecies variability was detected in six out of the eight reference genes tested and only the ITS and IGS regions showed two and three sequence genotypes, respectively, resulting in five MLST genotypes. All of eight genes were, however, useful for discrimination among M. canis, M. audouinii and M. ferrugineum. In total, eighteen microsatellite genotypes (A-R) were recognized using MLMT based on six loci, allowing a subdivision of strains into two clusters based on the Bayesian iterative algorithm. Six MLMT genotypes were from multiple host species, while 12 genotypes were found only in one host. There were no statistically significant differences between clusters in terms of host spectrum and the presence or absence of lesions. Our results confirmed that the MLST approach is not useful for detailed subtyping and examining the population structure of M. canis, while microsatellite analysis is a powerful tool for conducting surveillance studies and gaining insight into the epidemiology of infections due to this pathogen.
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Affiliation(s)
- Chioma Inyang Aneke
- Dipartimento di Medicina Veterinaria, Università degli Studi Aldo Moro, 70010 Bari, Italy; (C.I.A.); (D.O.)
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka 410001, Nigeria
| | - Adéla Čmoková
- Department of Botany, Faculty of Science, Charles University, 12801 Prague, Czech Republic;
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Vít Hubka
- Department of Botany, Faculty of Science, Charles University, 12801 Prague, Czech Republic;
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Wafa Rhimi
- Faculty of Veterinary Sciences, Bu-Ali Sina University, Hamedan 6517658978, Iran;
| | - Domenico Otranto
- Dipartimento di Medicina Veterinaria, Università degli Studi Aldo Moro, 70010 Bari, Italy; (C.I.A.); (D.O.)
- Faculty of Veterinary Sciences, Bu-Ali Sina University, Hamedan 6517658978, Iran;
| | - Claudia Cafarchia
- Dipartimento di Medicina Veterinaria, Università degli Studi Aldo Moro, 70010 Bari, Italy; (C.I.A.); (D.O.)
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9
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Thomaz DY, de Almeida JN, Sejas ONE, Del Negro GMB, Carvalho GOMH, Gimenes VMF, de Souza MEB, Arastehfar A, Camargo CH, Motta AL, Rossi F, Perlin DS, Freire MP, Abdala E, Benard G. Environmental Clonal Spread of Azole-Resistant Candida parapsilosis with Erg11-Y132F Mutation Causing a Large Candidemia Outbreak in a Brazilian Cancer Referral Center. J Fungi (Basel) 2021; 7:259. [PMID: 33808442 PMCID: PMC8066986 DOI: 10.3390/jof7040259] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/17/2021] [Accepted: 03/25/2021] [Indexed: 12/27/2022] Open
Abstract
Clonal outbreaks due to azole-resistant Candida parapsilosis (ARCP) isolates have been reported in numerous studies, but the environmental niche of such isolates has yet to be defined. Herein, we aimed to identify the environmental niche of ARCP isolates causing unremitting clonal outbreaks in an adult ICU from a Brazilian cancer referral center. C. parapsilosis sensu stricto isolates recovered from blood cultures, pericatheter skins, healthcare workers (HCW), and nosocomial surfaces were genotyped by multilocus microsatellite typing (MLMT). Antifungal susceptibility testing was performed by the EUCAST (European Committee for Antimicrobial Susceptibility Testing) broth microdilution reference method and ERG11 was sequenced to determine the azole resistance mechanism. Approximately 68% of isolates were fluconazole-resistant (76/112), including pericatheter skins (3/3, 100%), blood cultures (63/70, 90%), nosocomial surfaces (6/11, 54.5%), and HCW's hands (4/28, 14.2%). MLMT revealed five clusters: the major cluster contained 88.2% of ARCP isolates (67/76) collected from blood (57/70), bed (2/2), pericatheter skin (2/3), from carts (3/7), and HCW's hands (3/27). ARCP isolates were associated with a higher 30 day crude mortality rate (63.8%) than non-ARCP ones (20%, p = 0.008), and resisted two environmental decontamination attempts using quaternary ammonium. This study for the first time identified ARCP isolates harboring the Erg11-Y132F mutation from nosocomial surfaces and HCW's hands, which were genetically identical to ARCP blood isolates. Therefore, it is likely that persisting clonal outbreak due to ARCP isolates was fueled by environmental sources. The resistance of Y132F ARCP isolates to disinfectants, and their potential association with a high mortality rate, warrant vigilant source control using effective environmental decontamination.
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Affiliation(s)
- Danilo Y. Thomaz
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
| | - João N. de Almeida
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
- Central Laboratory Division (LIM-03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil; (A.L.M.); (F.R.)
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA; (A.A.); (D.S.P.)
| | - Odeli N. E. Sejas
- Cancer Institute of São Paulo State, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brazil; (O.N.E.S.); (M.E.B.d.S.); (M.P.F.); (E.A.)
| | - Gilda M. B. Del Negro
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
| | - Gabrielle O. M. H. Carvalho
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
| | - Viviane M. F. Gimenes
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
| | - Maria Emilia B. de Souza
- Cancer Institute of São Paulo State, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brazil; (O.N.E.S.); (M.E.B.d.S.); (M.P.F.); (E.A.)
| | - Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA; (A.A.); (D.S.P.)
| | - Carlos H. Camargo
- Bacteriology Center, Instituto Adolfo Lutz, São Paulo 01246-000, Brazil;
| | - Adriana L. Motta
- Central Laboratory Division (LIM-03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil; (A.L.M.); (F.R.)
| | - Flávia Rossi
- Central Laboratory Division (LIM-03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil; (A.L.M.); (F.R.)
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA; (A.A.); (D.S.P.)
| | - Maristela P. Freire
- Cancer Institute of São Paulo State, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brazil; (O.N.E.S.); (M.E.B.d.S.); (M.P.F.); (E.A.)
| | - Edson Abdala
- Cancer Institute of São Paulo State, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brazil; (O.N.E.S.); (M.E.B.d.S.); (M.P.F.); (E.A.)
| | - Gil Benard
- Laboratory of Medical Mycology (LIM-53), Instituto de Medicina Tropical e Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.Y.T.); (G.M.B.D.N.); (G.O.M.H.C.); (V.M.F.G.)
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10
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Cao D, Wang F, Yu S, Dong S, Wu R, Cui N, Ren J, Xu T, Wang S, Wang M, Fang H, Yu Y. Prevalence of Azole-Resistant Aspergillus fumigatus is Highly Associated with Azole Fungicide Residues in the Fields. Environ Sci Technol 2021; 55:3041-3049. [PMID: 33544588 DOI: 10.1021/acs.est.0c03958] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Triazole resistance in Aspergillus fumigatus is a growing public health concern. In addition to its emergence in the therapy of invasive aspergillosis by triazole medicines, it has been frequently detected in agricultural fields all over the world. Here, we explore the potential link between residues of azole fungicides with similar chemical structure to triazole medicines in soil and the emergence of resistant A. fumigatus (RAF) through 855 500 km2 monitoring survey in Eastern China covering 6 provinces. In total, 67.3%, 15.2%, 12.3%, 2.9%, 1.5%, 0.4%, and 0.3% of the soil samples contained these five fungicides (tebuconazole, difenoconazole, propiconazole, hexaconazole, and prochloraz) of 0-100, 100-200, 200-400, 400-600, 600-800, 800-1000, and >1000 ng/g, respectively. The fractions of samples containing RAF isolates were 2.4%, 5.2%, 6.4%, 7.7%, 7.4%, 14.3%, and 20.0% of the samples with total azole fungicide residues of 0-100, 100-200, 200-400, 400-600, 600-800, 800-1000, and >1000 ng/g, respectively. We find that the prevalence of RAFs is positively (P < 0.0001) correlated with residual levels of azole fungicides in soils. Our results suggest that the use of azole fungicides in agriculture should be minimized and the intervals between treatments expanded to reduce the selective pressure toward the development of resistance in A. fumigatus in agricultural fields.
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11
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Yadav A, Singh A, Wang Y, van Haren MHI, Singh A, de Groot T, Meis JF, Xu J, Chowdhary A. Colonisation and Transmission Dynamics of Candida auris among Chronic Respiratory Diseases Patients Hospitalised in a Chest Hospital, Delhi, India: A Comparative Analysis of Whole Genome Sequencing and Microsatellite Typing. J Fungi (Basel) 2021; 7:jof7020081. [PMID: 33530297 PMCID: PMC7910912 DOI: 10.3390/jof7020081] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/07/2021] [Accepted: 01/16/2021] [Indexed: 01/23/2023] Open
Abstract
Candida auris is a nosocomial pathogen responsible for an expanding global public health threat. This ascomycete yeast has been frequently isolated from hospital environments, representing a significant reservoir for transmission in healthcare settings. Here, we investigated the relationships among C. auris isolates from patients with chronic respiratory diseases admitted in a chest hospital and from their fomites, using whole-genome sequencing (WGS) and multilocus microsatellite genotyping. Overall, 37.5% (n = 12/32) patients developed colonisation by C. auris including 9.3% of the screened patients that were colonised at the time of admission and 75% remained colonised till discharge. Furthermore, 10% of fomite samples contained C. auris in rooms about 8.5 days after C. auris colonised patients were admitted. WGS and microsatellite typing revealed that multiple strains contaminated the fomites and colonised different body sites of patients. Notably, 37% of C. auris isolates were resistant to amphotericin B and a novel amino acid substitution, G145D in ERG2 gene, was detected in all amphotericin B resistant isolates. In addition, 55% of C. auris isolates had two copies of the MDR1 gene. Our results suggest significant genetic and ecological diversities of C. auris in healthcare setting. The WGS and microsatellite genotyping methods provided complementary results in genotype identification.
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Affiliation(s)
- Anamika Yadav
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India; (A.Y.); (A.S.); (A.S.)
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
| | - Anubhav Singh
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India; (A.Y.); (A.S.); (A.S.)
| | - Yue Wang
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada; (Y.W.); (J.X.)
| | - Merlijn HI van Haren
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; (M.H.v.H.); (T.d.G.); (J.F.M.)
| | - Ashutosh Singh
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India; (A.Y.); (A.S.); (A.S.)
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; (M.H.v.H.); (T.d.G.); (J.F.M.)
- Centre of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; (M.H.v.H.); (T.d.G.); (J.F.M.)
- Centre of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada; (Y.W.); (J.X.)
| | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India; (A.Y.); (A.S.); (A.S.)
- Correspondence:
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12
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Cao D, Wu R, Dong S, Wang F, Ju C, Yu S, Xu S, Fang H, Yu Y. Five-Year Survey (2014 to 2018) of Azole Resistance in Environmental Aspergillus fumigatus Isolates from China. Antimicrob Agents Chemother 2020; 64:e00904-20. [PMID: 32718960 DOI: 10.1128/AAC.00904-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/19/2020] [Indexed: 01/05/2023] Open
Abstract
A total of 191 soil samples from Hangzhou, China, were submitted to detect non-wild-type (non-WT) Aspergillus fumigatus and its associated mechanisms. There were 2 (4.7%), 13 (12.4%), and 31 (23.1%) isolates identified as non-WT in 2014, 2016, and 2018, respectively. The resistant mutations of TR34/L98H, TR46/Y121F/T289A, and TR34/L98H/S297T/F495I were found in 3, 5, and 5 non-WT isolates. The G448S mutation, previously only found in clinical settings, was detected in A. fumigatus from soil samples.
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13
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Zhang L, Yu SY, Chen SCA, Xiao M, Kong F, Wang H, Ning YT, Lu MY, Sun TS, Hou X, Zhou ML, Kang W, Zhang G, Duan SM, Xu YC. Molecular Characterization of Candida parapsilosis by Microsatellite Typing and Emergence of Clonal Antifungal Drug Resistant Strains in a Multicenter Surveillance in China. Front Microbiol 2020; 11:1320. [PMID: 32612597 PMCID: PMC7309193 DOI: 10.3389/fmicb.2020.01320] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 05/25/2020] [Indexed: 12/22/2022] Open
Abstract
Candida parapsilosis is an important species causing invasive candidiasis (IC) in China. The present survey was a national multicenter study of the molecular epidemiology and antifungal susceptibility profiles of C. parapsilosis. Non-duplicate C. parapsilosis isolates were collected from 10 hospitals across China in the CHIF-NET program 2016–2017. Isolates were genotyped using four highly polymorphic microsatellite markers, and susceptibility profiles determined using Sensititre YeastOneTM YO10. A total of 319 C. parapsilosis from separate patients with IC were studied; 49.2, 17.9, and 10.3% isolates were from patients in surgical departments, general intensive care units (ICUs) and neonatal ICUs (NICU), respectively. C. parapsilosis showed good susceptibility to nine antifungal drugs. Microsatellite analysis identified 122 microsatellite (MT) types. Most MT types had sporadic distribution. However, we identified 32 clusters across 10 hospitals; seven clusters were caused by seven endemic genotypes involving five or more isolates in hospitals designated as H01, H02, H06, and H10. These clusters mainly affected surgical departments and ICUs, except for genotype MT42 which was seen in 22 patients from NICU (hospital H06). Of 16 fluconazole-resistant isolates, seven from hospital H02 shared the same genotype MT70, and three from hospital H04 were of genotype MT47. For 37 isolates with non-wild type MICs to 5-flucytosine, 29 were from hospital H01 (genotype MT48). Here we present the first nationwide molecular epidemiology study of C. parapsilosis in China, identified several previously unrecognized clusters, which included antifungal drug resistant isolates. These findings provide important data for control of IC in China.
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Affiliation(s)
- Li Zhang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Shu-Ying Yu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, University of Sydney, Westmead, NSW, Australia
| | - Meng Xiao
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, University of Sydney, Westmead, NSW, Australia
| | - He Wang
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ya-Ting Ning
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Min-Ya Lu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Tian-Shu Sun
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Hou
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Kang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ge Zhang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Si-Meng Duan
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
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14
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Herkert PF, Meis JF, Lucca de Oliveira Salvador G, Rodrigues Gomes R, Aparecida Vicente V, Dominguez Muro M, Lameira Pinheiro R, Lopes Colombo A, Vargas Schwarzbold A, Sakuma de Oliveira C, Simão Ferreira M, Queiroz-Telles F, Hagen F. Molecular characterization and antifungal susceptibility testing of Cryptococcus neoformans sensu stricto from southern Brazil. J Med Microbiol 2018; 67:560-569. [PMID: 29461182 DOI: 10.1099/jmm.0.000698] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Cryptococcosis is acquired from the environment by the inhalation of Cryptococcus cells and may establish from an asymptomatic latent infection into pneumonia or meningoencephalitis. The genetic diversity of a Cryptococcus neoformans species complex has been investigated by several molecular tools, such as multi-locus sequence typing, amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism and microsatellite analysis. This study aimed to investigate the genotype distributions and antifungal susceptibility profiles of C. neoformans sensu lato isolates from southern Brazil. METHODOLOGY We studied 219 C. neoformans sensu lato isolates with mating- and serotyping, AFLP fingerprinting, microsatellite typing and antifungal susceptibility testing.Results/Key findings. Among the isolates, 136 (69 %) were from HIV-positive patients. Only C. neoformans mating-type α and serotype A were observed. AFLP fingerprinting analysis divided the isolates into AFLP1/VNI (n=172; 78.5 %), AFLP1A/VNII (n=19; 8.7 %), AFLP1B/VNII (n=4; 1.8 %) and a new AFLP pattern AFLP1C (n=23; 10.5 %). All isolates were susceptible to tested antifungals and no correlation between antifungal susceptibility and genotypes was observed. Through microsatellite analysis, most isolates clustered in a major microsatellite complex and Simpson's diversity index of this population was D=0.9856. CONCLUSION The majority of C. neoformans sensu stricto infections occurred in HIV-positive patients. C. neoformans AFLP1/VNI was the most frequent genotype and all antifungal drugs had high in vitro activity against this species. Microsatellite analyses showed a high genetic diversity within the regional C. neoformans sensu stricto population, and correlation between environmental and clinical isolates, as well as a temporal and geographic relationship.
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Affiliation(s)
- Patricia Fernanda Herkert
- Postgraduate Program in Microbiology, Parasitology and Pathology, Biological Sciences, Department of Basic Pathology, Federal University of Parana, Curitiba, Brazil.,Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands.,CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands.,Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | | | - Renata Rodrigues Gomes
- Postgraduate Program in Microbiology, Parasitology and Pathology, Biological Sciences, Department of Basic Pathology, Federal University of Parana, Curitiba, Brazil.,Department of Biological Science, State University of Parana/Campus Paranaguá, Paranaguá, PR, Brazil
| | - Vania Aparecida Vicente
- Postgraduate Program in Microbiology, Parasitology and Pathology, Biological Sciences, Department of Basic Pathology, Federal University of Parana, Curitiba, Brazil
| | - Marisol Dominguez Muro
- Laboratory of Mycology, Hospital de Clínicas, Federal University of Parana, Curitiba, Brazil
| | | | | | | | - Carla Sakuma de Oliveira
- Hospital Universitário do Oeste do Paraná, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | | | - Flávio Queiroz-Telles
- Comunnitarian Health Department, Hospital de Clínicas, Federal University of Parana, Curitiba, Brazil
| | - Ferry Hagen
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands.,Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
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15
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Viel A, Legras JL, Nadai C, Carlot M, Lombardi A, Crespan M, Migliaro D, Giacomini A, Corich V. The Geographic Distribution of Saccharomyces cerevisiae Isolates within three Italian Neighboring Winemaking Regions Reveals Strong Differences in Yeast Abundance, Genetic Diversity and Industrial Strain Dissemination. Front Microbiol 2017; 8:1595. [PMID: 28883812 PMCID: PMC5573751 DOI: 10.3389/fmicb.2017.01595] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/04/2017] [Indexed: 11/30/2022] Open
Abstract
In recent years the interest for natural fermentations has been re-evaluated in terms of increasing the wine terroir and managing more sustainable winemaking practices. Therefore, the level of yeast genetic variability and the abundance of Saccharomyces cerevisiae native populations in vineyard are becoming more and more crucial at both ecological and technological level. Among the factors that can influence the strain diversity, the commercial starter release that accidentally occur in the environment around the winery, has to be considered. In this study we led a wide scale investigation of S. cerevisiae genetic diversity and population structure in the vineyards of three neighboring winemaking regions of Protected Appellation of Origin, in North-East of Italy. Combining mtDNA RFLP and microsatellite markers analyses we evaluated 634 grape samples collected over 3 years. We could detect major differences in the presence of S. cerevisiae yeasts, according to the winemaking region. The population structures revealed specificities of yeast microbiota at vineyard scale, with a relative Appellation of Origin area homogeneity, and transition zones suggesting a geographic differentiation. Surprisingly, we found a widespread industrial yeast dissemination that was very high in the areas where the native yeast abundance was low. Although geographical distance is a key element involved in strain distribution, the high presence of industrial strains in vineyard reduced the differences between populations. This finding indicates that industrial yeast diffusion it is a real emergency and their presence strongly interferes with the natural yeast microbiota.
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Affiliation(s)
- Alessia Viel
- Interdepartmental Centre for Research in Viticulture and Enology, University of PadovaConegliano, Italy
| | - Jean-Luc Legras
- SPO, INRA, SupAgro, Université de MontpellierMontpellier, France
| | - Chiara Nadai
- Interdepartmental Centre for Research in Viticulture and Enology, University of PadovaConegliano, Italy
| | - Milena Carlot
- Interdepartmental Centre for Research in Viticulture and Enology, University of PadovaConegliano, Italy
| | - Angiolella Lombardi
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of PadovaLegnaro, Italy
| | - Manna Crespan
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia Agraria-Centro di Ricerca per la Viticoltura e l'enologiaConegliano, Italy
| | - Daniele Migliaro
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia Agraria-Centro di Ricerca per la Viticoltura e l'enologiaConegliano, Italy
| | - Alessio Giacomini
- Interdepartmental Centre for Research in Viticulture and Enology, University of PadovaConegliano, Italy.,Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of PadovaLegnaro, Italy
| | - Viviana Corich
- Interdepartmental Centre for Research in Viticulture and Enology, University of PadovaConegliano, Italy.,Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of PadovaLegnaro, Italy
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16
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Khodavaisy S, Badali H, Rezaie S, Nabili M, Moghadam KG, Afhami S, Hagen F, Aala F, Hashemi SJ, Meis JF. Genotyping of clinical and environmental Aspergillus flavus isolates from Iran using microsatellites. Mycoses 2016; 59:220-225. [PMID: 26756650 DOI: 10.1111/myc.12451] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 11/25/2015] [Accepted: 11/27/2015] [Indexed: 11/27/2022]
Abstract
Aspergillus flavus is the second most important Aspergillus species causing human infections in tropical countries. Despite an increasing number of infections of A. flavus in Iran, the molecular epidemiology of clinical and environmental strains has not been well studied. We used a panel of nine microsatellite markers to analyse the genetic relatedness of A. flavus. Microsatellite typing of 143 (n = 119 clinical and n = 24 environmental) isolates demonstrated 118 different genotypes. A possible outbreak at a pulmonary ward was discovered. The discriminatory power for the individual markers ranged from 0.4812 to 0.9457 and the panel of all nine markers combined yielded a diversity index of 0.9948. This high-resolution typing method assists in better understanding of the molecular epidemiology of A. flavus.
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Affiliation(s)
- Sadegh Khodavaisy
- Department of Medical Mycology and Parasitology, Tehran University of Medical Science, Tehran, Iran.,Department of Medical Mycology and Parasitology, Kurdistan University of Medical Science, Sanandaj, Iran
| | - Hamid Badali
- Department of Medical Mycology and Parasitology, Mazandaran University of Medical Science, Sari, Iran
| | - Sassan Rezaie
- Department of Medical Mycology and Parasitology, Tehran University of Medical Science, Tehran, Iran
| | - Mojtaba Nabili
- Department of Medical Mycology and Parasitology, Mazandaran University of Medical Science, Sari, Iran
| | - Keivan G Moghadam
- Department of Pulmonary Diseases, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirin Afhami
- Department of Infectious Diseases, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Farzad Aala
- Department of Medical Mycology and Parasitology, Kurdistan University of Medical Science, Sanandaj, Iran
| | - Sayed-Jamal Hashemi
- Department of Medical Mycology and Parasitology, Tehran University of Medical Science, Tehran, Iran
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands.,Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands
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17
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Chowdhary A, Sharma C, Kathuria S, Hagen F, Meis JF. Prevalence and mechanism of triazole resistance in Aspergillus fumigatus in a referral chest hospital in Delhi, India and an update of the situation in Asia. Front Microbiol 2015; 6:428. [PMID: 26005442 PMCID: PMC4424976 DOI: 10.3389/fmicb.2015.00428] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/22/2015] [Indexed: 01/23/2023] Open
Abstract
Aspergillus fumigatus causes varied clinical syndromes ranging from colonization to deep infections. The mainstay of therapy of Aspergillus diseases is triazoles but several studies globally highlighted variable prevalence of triazole resistance, which hampers the management of aspergillosis. We studied the prevalence of resistance in clinical A. fumigatus isolates during 4 years in a referral Chest Hospital in Delhi, India and reviewed the scenario in Asia and the Middle East. Aspergillus species (n = 2117) were screened with selective plates for azole resistance. The isolates included 45.4% A. flavus, followed by 32.4% A. fumigatus, 15.6% Aspergillus species and 6.6% A. terreus. Azole resistance was found in only 12 (1.7%) A. fumigatus isolates. These triazole resistant A. fumigatus (TRAF) isolates were subjected to (a) calmodulin and β tubulin gene sequencing (b) in vitro antifungal susceptibility testing against triazoles using CLSI M38-A2 (c) sequencing of cyp51A gene and real-time PCR assay for detection of mutations and (d) microsatellite typing of the resistant isolates. TRAF harbored TR34/L98H mutation in 10 (83.3%) isolates with a pan-azole resistant phenotype. Among the remaining two TRAF isolates, one had G54E and the other had three non-synonymous point mutations. The majority of patients were diagnosed as invasive aspergillosis followed by allergic bronchopulmonary aspergillosis and chronic pulmonary aspergillosis. The Indian TR34/L98H isolates had a unique genotype and were distinct from the Chinese, Middle East, and European TR34/L98H strains. This resistance mechanism has been linked to the use of fungicide azoles in agricultural practices in Europe as it has been mainly reported from azole naïve patients. Reports published from Asia demonstrate the same environmental resistance mechanism in A. fumigatus isolates from two highly populated countries in Asia, i.e., China and India and also from the neighboring Middle East.
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Affiliation(s)
- Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi Delhi, India
| | - Cheshta Sharma
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi Delhi, India
| | - Shallu Kathuria
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi Delhi, India
| | - Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital Nijmegen, Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital Nijmegen, Netherlands ; Department of Medical Microbiology, Radboud University Medical Center Nijmegen, Netherlands
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18
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Dhieb C, Normand AC, L'Ollivier C, Gautier M, Vranckx K, El Euch D, Chaker E, Hendrickx M, Dalle F, Sadfi N, Piarroux R, Ranque S. Comparison of MALDI-TOF mass spectra with microsatellite length polymorphisms in Candida albicans. J Mass Spectrom 2015; 50:371-377. [PMID: 25800019 DOI: 10.1002/jms.3538] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/30/2014] [Accepted: 11/02/2014] [Indexed: 06/04/2023]
Abstract
Candida albicans is the most frequent yeast involved in human infections. Its population structure can be divided into several genetic clades, some of which have been associated with antifungal susceptibility. Therefore, detecting and monitoring fungal clones in a routine laboratory setting would be a major epidemiological advance. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra results are now widely used as bar codes to identify microorganisms in clinical microbiology laboratories. This study aimed at testing MALDI-TOF mass spectra bar codes to identify clades among a set of C. albicans isolates. Accordingly, 102 clinical strains were genotyped using 10 microsatellite markers and analyzed via MALDI-TOF mass spectrometry. The mass spectra were compared with a reference spectral library including 33 well-characterized collection strains, using a Microflex(TM) system and Biotyper(TM) software, to test the capacity of the spectrum of a given isolate to match with the reference mass spectrum of an isolate from the same genetic clade. Despite high confidence species identification, the spectra failed to significantly match with the corresponding clade (p = 0.74). This was confirmed with the MALDI-TOF spectra similarity dendrogram, in which the strains were dispersed irrespective of their genetic clade. Various attempts to improve intra-clade spectra recognition were unsuccessful. In conclusion, MALDI-TOF mass spectra bar code analysis failed to reliably recognize genetically related C. albicans isolates. Further studies are warranted to develop alternative MALDI-TOF mass spectra analytical approaches to identify and monitor C. albicans clades in the routine clinical laboratory.
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Affiliation(s)
- C Dhieb
- Laboratoire de Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, 2092, Tunis, Tunisia
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19
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Chowdhary A, Sharma C, Kathuria S, Hagen F, Meis JF. Azole-resistant Aspergillus fumigatus with the environmental TR46/Y121F/T289A mutation in India. J Antimicrob Chemother 2013; 69:555-7. [PMID: 24084639 DOI: 10.1093/jac/dkt397] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
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