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Chen YZ, Tseng KY, Wang SC, Huang CL, Lin CC, Zhou ZL, Tsai DJ, Lin CM, Chen YL, Chen KT, Liao YC, Chen FJ, Sytwu HK, Lan CY, Lo HJ. Fruits are vehicles of drug-resistant pathogenic Candida tropicalis. Microbiol Spectr 2023; 11:e0147123. [PMID: 37905800 PMCID: PMC10714812 DOI: 10.1128/spectrum.01471-23] [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: 05/24/2023] [Accepted: 09/03/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Of 123 identified isolates from the fruit surface, C. tropicalis was the most frequently found species, followed by Meyerozyma caribbica and Candida krusei. All three fluconazole-resistant C. tropicalis were non-susceptible to voriconazole and belonged to the same predominant genotype of azole-resistant C. tropicalis causing candidemia in patients in Taiwan. Our findings provide evidence that fruit should be washed before eaten not only to remove chemicals but also potential drug-resistant pathogenic microbes, especially for immunocompromised individuals. To keep precious treatment options in patients, we not only continuously implement antimicrobial stewardship in hospitals but also reducing/stopping the use of agricultural fungicide classes used in human medicine.
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Affiliation(s)
- Yin-Zhi Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Kuo-Yun Tseng
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Si-Chong Wang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Ciao-Lin Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Chih-Chao Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Zi-Li Zhou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - De-Jiun Tsai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Chiao-Mei Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Yu-Lian Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Kai-Ting Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Huey-Kang Sytwu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Chung-Yu Lan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsiu-Jung Lo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- School of Dentistry, China Medical University, Taichung, Taiwan
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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] [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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Douglas AP, Stewart AG, Halliday CL, Chen SCA. Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management. J Fungi (Basel) 2023; 9:1059. [PMID: 37998865 PMCID: PMC10672668 DOI: 10.3390/jof9111059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.
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Affiliation(s)
- Abby P. Douglas
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Adam G. Stewart
- Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women’s Hospital Campus, The University of Queensland, Herston, QLD 4006, Australia;
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
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Mesquida A, Machado M, Dávila-Cherres L, Vicente T, Sánchez-Carrillo C, Alcalá L, Reigadas E, Muñoz P, Guinea J, Escribano P. The Gastrointestinal Tract Is Pinpointed as a Reservoir of Candida albicans, Candida parapsilosis, and Candida tropicalis Genotypes Found in Blood and Intra-Abdominal Samples. J Fungi (Basel) 2023; 9:732. [PMID: 37504721 PMCID: PMC10381600 DOI: 10.3390/jof9070732] [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: 04/18/2023] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023] Open
Abstract
BACKGROUND Candida spp., as part of the microbiota, can colonise the gastrointestinal tract. We hypothesised that genotyping Candida spp. isolates from the gastrointestinal tract could help spot genotypes able to cause invasive infections. MATERIALS/METHODS A total of 816 isolates of C. albicans (n = 595), C. parapsilosis (n = 118), and C. tropicalis (n = 103) from rectal swabs (n = 754 patients) were studied. Genotyping was conducted using species-specific microsatellite markers. Rectal swab genotypes were compared with previously studied blood (n = 814) and intra-abdominal (n = 202) genotypes. RESULTS A total of 36/754 patients had the same Candida spp. isolated from blood cultures, intra-abdominal samples, or both; these patients had candidemia (n = 18), intra-abdominal candidiasis (n = 11), both clinical forms (n = 1), and non-significant isolation (n = 6). Genotypes matching the rectal swab and their blood cultures (84.2%) or their intra-abdominal samples (92.3%) were found in most of the significant patients. We detected 656 genotypes from rectal swabs, 88.4% of which were singletons and 11.6% were clusters. Of these 656 rectal swab genotypes, 94 (14.3%) were also detected in blood cultures and 34 (5.2%) in intra-abdominal samples. Of the rectal swab clusters, 62.7% were previously defined as a widespread genotype. CONCLUSIONS Our study pinpoints the gastrointestinal tract as a potential reservoir of potentially invasive Candida spp. genotypes.
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Affiliation(s)
- Aina Mesquida
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo, 46, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Marina Machado
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo, 46, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Lorena Dávila-Cherres
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo, 46, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Teresa Vicente
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo, 46, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Carlos Sánchez-Carrillo
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo, 46, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Luis Alcalá
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo, 46, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Elena Reigadas
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo, 46, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo, 46, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Jesús Guinea
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo, 46, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Pilar Escribano
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo, 46, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- School of Health Sciences-HM Hospitals, Camilo José Cela University, 28692 Madrid, Spain
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Spruijtenburg B, Baqueiro CCSZ, Colombo AL, Meijer EFJ, de Almeida JN, Berrio I, Fernández NB, Chaves GM, Meis JF, de Groot T. Short Tandem Repeat Genotyping and Antifungal Susceptibility Testing of Latin American Candida tropicalis Isolates. J Fungi (Basel) 2023; 9:jof9020207. [PMID: 36836321 PMCID: PMC9958743 DOI: 10.3390/jof9020207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
Candida tropicalis is emerging as one of the most common Candida species causing opportunistic infections in Latin America. Outbreak events caused by C. tropicalis were reported, and antifungal resistant isolates are on the rise. In order to investigate population genomics and look into antifungal resistance, we applied a short tandem repeat (STR) genotyping scheme and antifungal susceptibility testing (AFST) to 230 clinical and environmental C. tropicalis isolates from Latin American countries. STR genotyping identified 164 genotypes, including 11 clusters comprised of three to seven isolates, indicating outbreak events. AFST identified one isolate as anidulafungin-resistant and harboring a FKS1 S659P substitution. Moreover, we identified 24 clinical and environmental isolates with intermediate susceptibility or resistance to one or more azoles. ERG11 sequencing revealed each of these isolates harboring a Y132F and/or Y257H/N substitution. All of these isolates, except one, were clustered together in two groups of closely related STR genotypes, with each group harboring distinct ERG11 substitutions. The ancestral C. tropicalis strain of these isolates likely acquired the azole resistance-associated substitutions and subsequently spread across vast distances within Brazil. Altogether, this STR genotyping scheme for C. tropicalis proved to be useful for identifying unrecognized outbreak events and better understanding population genomics, including the spread of antifungal-resistant isolates.
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Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Cynthea C. S. Z. Baqueiro
- Disciplina de Infectologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04021-001, SP, Brazil
| | - Arnaldo L. Colombo
- Disciplina de Infectologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04021-001, SP, Brazil
| | - Eelco F. J. Meijer
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - João N. de Almeida
- Disciplina de Infectologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04021-001, SP, Brazil
- Hospital Israelita Albert Einstein, São Paulo 05652-900, SP, Brazil
| | - Indira Berrio
- Hospital General de Medellín Luz Castro de Gutiérrez ESE, Medellín 050015, Colombia
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín 050015, Colombia
| | - Norma B. Fernández
- Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires 2351, Argentina
| | - Guilherme M. Chaves
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, Curitiba 80060-000, PR, Brazil
- Department I of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Excellence Center for Medical Mycology, 50931 Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Correspondence:
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Spruijtenburg B, van Haren MHI, Chowdhary A, Meis JF, de Groot T. Development and Application of a Short Tandem Repeat Multiplex Typing Assay for Candida tropicalis. Microbiol Spectr 2023; 11:e0461822. [PMID: 36715547 PMCID: PMC10100945 DOI: 10.1128/spectrum.04618-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Candida tropicalis is a clinically important yeast that causes candidemia in humans with a high mortality rate. The yeast primarily infects immunocompromised patients, and causes outbreaks in health care facilities. Antifungal resistant isolates have been reported. We developed a short tandem repeat (STR) typing scheme for C. tropicalis to enable fast, cost-effective, and high-resolution genotyping. For the development of the typing scheme, 6 novel STR markers were selected, combined into 2 multiplex PCRs. In total, 117 C. tropicalis isolates were typed, resulting in the identification of 104 different genotypes. Subsequently, the outcome of STR typing of 10 isolates was compared to single nucleotide polymorphism (SNP) calling from whole-genome sequencing (WGS). Isolates with more than 111 SNPs were differentiated by the typing assay. Two isolates, which were identical according to SNP analysis, were separated by STR typing in 1 marker. To test specificity, the STR typing was applied to 15 related yeast species, and we found no amplification of these targets. For reproducibility testing, 2 isolates were independently typed five times, which showed identical results in each experiment. In summary, we developed a reliable and multiplex STR genotyping for C. tropicalis, which was found to correlate well to SNP calling by WGS. WGS analysis from and extensive collection of isolates is required to establish the precise resolution of this STR assay. IMPORTANCE Candida tropicalis frequently causes candidemia in immunocompromised patients. C. tropicalis infections have a high mortality rate, and the yeast is able to cause outbreaks in health care facilities. Further, antifungal resistant isolates are on the rise. Genotyping is necessary to investigate potential outbreaks. Here, we developed and applied a STR genotyping scheme in order to rapidly genotype isolates with a high-resolution. WGS SNP outcomes were highly comparable with STR typing results. Altogether, we developed a rapid, high-resolution, and specific STR genotyping scheme for C. tropicalis.
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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
| | - Merlijn H. I. van Haren
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Anuradha Chowdhary
- Medical Mycology Unit, Department of Medical Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - 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 I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany
| | - 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
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7
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Díaz-García J, Gómez A, Machado M, Alcalá L, Reigadas E, Sánchez-Carrillo C, Pérez-Ayala A, de la Pedrosa EGG, González-Romo F, Cuétara MS, García-Esteban C, Quiles-Melero I, Zurita ND, Algarra MM, Durán-Valle MT, Sánchez-García A, Muñoz P, Escribano P, Guinea J. Candida Genotyping of Blood Culture Isolates from Patients Admitted to 16 Hospitals in Madrid: Genotype Spreading during the COVID-19 Pandemic Driven by Fluconazole-Resistant C. parapsilosis. J Fungi (Basel) 2022; 8:jof8111228. [PMID: 36422050 PMCID: PMC9698610 DOI: 10.3390/jof8111228] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/07/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Candidaemia and invasive candidiasis are typically hospital-acquired. Genotyping isolates from patients admitted to different hospitals may be helpful in tracking clones spreading across hospitals, especially those showing antifungal resistance. METHODS We characterized Candida clusters by studying Candida isolates (C. albicans, n = 1041; C. parapsilosis, n = 354, and C. tropicalis, n = 125) from blood cultures (53.8%) and intra-abdominal samples (46.2%) collected as part of the CANDIMAD (Candida in Madrid) study in Madrid (2019-2021). Species-specific microsatellite markers were used to define the genotypes of Candida spp. found in a single patient (singleton) or several patients (cluster) from a single hospital (intra-hospital cluster) or different hospitals (widespread cluster). RESULTS We found 83 clusters, of which 20 were intra-hospital, 49 were widespread, and 14 were intra-hospital and widespread. Some intra-hospital clusters were first detected before the onset of the COVID-19 pandemic, but the number of clusters increased during the pandemic, especially for C. parapsilosis. The proportion of widespread clusters was significantly higher for genotypes found in both compartments than those exclusively found in either the blood cultures or intra-abdominal samples. Most C. albicans- and C. tropicalis-resistant genotypes were singleton and presented exclusively in either blood cultures or intra-abdominal samples. Fluconazole-resistant C. parapsilosis isolates belonged to intra-hospital clusters harboring either the Y132F or G458S ERG11p substitutions; the dominant genotype was also widespread. CONCLUSIONS the number of clusters-and patients involved-increased during the COVID-19 pandemic mainly due to the emergence of fluconazole-resistant C. parapsilosis genotypes.
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Affiliation(s)
- Judith Díaz-García
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Ana Gómez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Marina Machado
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Luis Alcalá
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Elena Reigadas
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Carlos Sánchez-Carrillo
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Ana Pérez-Ayala
- Clinical Microbiology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital 12 de Octubre, 28041 Madrid, Spain
| | - Elia Gómez-García de la Pedrosa
- Clinical Microbiology Department, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Fernando González-Romo
- Clinical Microbiology Department, Hospital Universitario Clínico San Carlos, 28040 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos IdISSC, 28040 Madrid, Spain
| | - María Soledad Cuétara
- Clinical Microbiology Department, Hospital Universitario Severo Ochoa, 28914 Leganés, Spain
| | - Coral García-Esteban
- Clinical Microbiology Department, Hospital Universitario de Getafe, 28901 Madrid, Spain
| | | | - Nelly Daniela Zurita
- Clinical Microbiology Department, Hospital Universitario de La Princesa, 28006 Madrid, Spain
| | - María Muñoz Algarra
- Clinical Microbiology Department, Hospital Universitario Puerta de Hierro Majadahonda, 28220 Madrid, Spain
| | - María Teresa Durán-Valle
- Clinical Microbiology Department, Hospital Universitario de Móstoles, Móstoles, 28935 Madrid, Spain
| | - Aída Sánchez-García
- Laboratorio Central de la CAM-URSalud-Hospital Infanta Sofía, San Sebastián de los Reyes, 28703 Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Pilar Escribano
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Jesús Guinea
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-915-868-453; Fax: +34-915-044-906
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8
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Jafarian H, Hardani AK, Asnafi AA, Mahmoudabadi AZ. Population structure, susceptibility profile, phenotypic and mating properties of Candida tropicalis isolated from pediatric patients. Microb Pathog 2022; 170:105690. [PMID: 35917988 DOI: 10.1016/j.micpath.2022.105690] [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: 05/28/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 10/16/2022]
Abstract
BACKGROUND Candida tropicalis is one of the most frequently isolated species and is commonly associated with nosocomial infections, hematological malignancy, neutropenia, and urinary tract infections. AIMS This study aims to genotype C. tropicalis strains isolated from pediatric patients admitted to two hospitals in Ahvaz, Iran. We provide a vision of the genotypes, mating types, enzymatic activity, phenotypes, and antifungal susceptibility profile of these isolates. METHODS Candida tropicalis isolates were collected from various clinical (Oral, urine, wound, and bronchoalveolar lavage) and environmental sources between November 2020 and November 2021. Primitively, samples were cultured on CHROMagar Candida. All isolates were identified by sequencing the Internal Transcribed Spacer (ITS) region for precise identification. Isolates were genotyped by six microsatellite markers specific for C. tropicalis. Antifungal susceptibility profiles were determined against eight antifungal agents according to CLSI M27 standards. The phenotype of each C. tropicalis isolate was assessed using yeast peptone dextrose agar supplemented with phloxine B. Mating types of C. tropicalis isolates were determined using MTLa1 and MTL2 specific primers. RESULTS Species identification revealed 46 C. tropicalis strains. Among them, 39 different genotypes were detected that have split into 34 singletons and five clusters. Twenty isolates were the non-wild type for itraconazole and posaconazole. Four isolates were multidrug-resistant. The activity of hemolysin and esterase enzyme was very strong among all isolates. Mating type and phenotype were not significantly correlated with genotypes (p = 0.721 and p = 0.135, respectively). CONCLUSIONS To conclude, tested populations were moderately differentiated with high gene flow. One cluster of isolates among different hospitals was identified, and three clusters were from different cities.
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Affiliation(s)
- Hadis Jafarian
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Amir Kamal Hardani
- Department of Pediatrics, School of Medicine, Abuzar Children Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Amin Asnafi
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Zarei Mahmoudabadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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9
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The Interplay Between Neutral and Adaptive Processes Shapes Genetic Variation During Candida Species Evolution. CURRENT CLINICAL MICROBIOLOGY REPORTS 2021. [DOI: 10.1007/s40588-021-00171-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Arastehfar A, Daneshnia F, Hafez A, Khodavaisy S, Najafzadeh MJ, Charsizadeh A, Zarrinfar H, Salehi M, Shahrabadi ZZ, Sasani E, Zomorodian K, Pan W, Hagen F, Ilkit M, Kostrzewa M, Boekhout T. Antifungal susceptibility, genotyping, resistance mechanism, and clinical profile of Candida tropicalis blood isolates. Med Mycol 2021; 58:766-773. [PMID: 31828316 PMCID: PMC7398758 DOI: 10.1093/mmy/myz124] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/14/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Candida tropicalis is one of the major candidaemia agents, associated with the highest mortality rates among Candida species, and developing resistance to azoles. Little is known about the molecular mechanisms of azole resistance, genotypic diversity, and the clinical background of C. tropicalis infections. Consequently, this study was designed to address those questions. Sixty-four C. tropicalis bloodstream isolates from 62 patients from three cities in Iran (2014–2019) were analyzed. Strain identification, antifungal susceptibility testing, and genotypic diversity analysis were performed by MALDI-TOF MS, CLSI-M27 A3/S4 protocol, and amplified fragment length polymorphism (AFLP) fingerprinting, respectively. Genes related to drug resistance (ERG11, MRR1, TAC1, UPC2, and FKS1 hotspot9s) were sequenced. The overall mortality rate was 59.6% (37/62). Strains were resistant to micafungin [minimum inhibitory concentration (MIC) ≥1 μg/ml, 2/64], itraconazole (MIC > 0.5 μg/ml, 2/64), fluconazole (FLZ; MIC ≥ 8 μg/ml, 4/64), and voriconazole (MIC ≥ 1 μg/ml, 7/64). Pan-azole and FLZ + VRZ resistance were observed in one and two isolates, respectively, while none of the patients were exposed to azoles. MRR1 (T255P, 647S), TAC1 (N164I, R47Q), and UPC2 (T241A, Q340H, T381S) mutations were exclusively identified in FLZ-resistant isolates. AFLP fingerprinting revealed five major and seven minor genotypes; genotype G4 was predominant in all centers. The increasing number of FLZ-R C. tropicalis blood isolates and acquiring FLZ-R in FLZ-naive patients limit the efficiency of FLZ, especially in developing countries. The high mortality rate warrants reaching a consensus regarding the nosocomial mode of C. tropicalis transmission.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | | | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arezoo Charsizadeh
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammadreza Salehi
- Department of infectious diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Zare Shahrabadi
- Department of Medical Mycology and Parasitology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elahe Sasani
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, 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 200003, China
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | | | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam1012 WX, The Netherlands
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11
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Mehta N, Baghela A. Quorum sensing-mediated inter-specific conidial anastomosis tube fusion between Colletotrichum gloeosporioides and C. siamense. IMA Fungus 2021; 12:7. [PMID: 33789776 PMCID: PMC8015167 DOI: 10.1186/s43008-021-00058-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/21/2021] [Indexed: 02/07/2023] Open
Abstract
Many plant pathogenic filamentous fungi undergo fusion of conidia through conidial anastomosis tubes (CATs), which is believed to facilitate horizontal gene transfer between species. We discovered a remarkable inter-specific CAT fusion between two important plant fungal pathogens Colletotrichum gloeosporioides and C. siamense. In an invitro assay, under no selection pressure, the inter-specific CAT fusion was preferred with higher frequency (25% ± 5%) than intra-specific CAT fusion (11% ± 3.6%). Different stages of CAT fusion viz. CAT induction, homing, and fusion were observed during this inter-specific CAT fusion. The CAT fusion was found to be higher in absence of nutrients and under physiological stresses. This CAT fusion involved a quorum sensing phenomenon, wherein the CAT induction was dependent on conidial density and the putative quorum sensing molecule was extractable in chloroform. Movement of nuclei, mitochondria, and lipid droplets were observed during the CAT fusion. Post CAT fusion, the resulting conidia gave rise to putative heterokaryotic progenies with variable colony characteristics as compared to their parental strains. Few heterokaryons showed variable AFLP banding pattern compared to their parental strains, thereby suggesting a possible genetic exchange between the two species through CAT fusion. The heterokaryotic progenies exhibited varied fitness under different stress conditions. Our study illustrated a possible role of inter-specific CAT fusion in generation of genetic and phenotypic diversity in these fungal pathogens.
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Affiliation(s)
- Nikita Mehta
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology Group, MACS-Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, India.,Savitribai Phule Pune University, Pune, 411007, India
| | - Abhishek Baghela
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology Group, MACS-Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, India. .,Savitribai Phule Pune University, Pune, 411007, India.
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12
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O’Brien CE, Oliveira-Pacheco J, Ó Cinnéide E, Haase MAB, Hittinger CT, Rogers TR, Zaragoza O, Bond U, Butler G. Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples. PLoS Pathog 2021; 17:e1009138. [PMID: 33788904 PMCID: PMC8041210 DOI: 10.1371/journal.ppat.1009138] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/12/2021] [Accepted: 03/15/2021] [Indexed: 01/02/2023] Open
Abstract
Candida tropicalis is a human pathogen that primarily infects the immunocompromised. Whereas the genome of one isolate, C. tropicalis MYA-3404, was originally sequenced in 2009, there have been no large-scale, multi-isolate studies of the genetic and phenotypic diversity of this species. Here, we used whole genome sequencing and phenotyping to characterize 77 isolates of C. tropicalis from clinical and environmental sources from a variety of locations. We show that most C. tropicalis isolates are diploids with approximately 2-6 heterozygous variants per kilobase. The genomes are relatively stable, with few aneuploidies. However, we identified one highly homozygous isolate and six isolates of C. tropicalis with much higher heterozygosity levels ranging from 36-49 heterozygous variants per kilobase. Our analyses show that the heterozygous isolates represent two different hybrid lineages, where the hybrids share one parent (A) with most other C. tropicalis isolates, but the second parent (B or C) differs by at least 4% at the genome level. Four of the sequenced isolates descend from an AB hybridization, and two from an AC hybridization. The hybrids are MTLa/α heterozygotes. Hybridization, or mating, between different parents is therefore common in the evolutionary history of C. tropicalis. The new hybrids were predominantly found in environmental niches, including from soil. Hybridization is therefore unlikely to be associated with virulence. In addition, we used genotype-phenotype correlation and CRISPR-Cas9 editing to identify a genome variant that results in the inability of one isolate to utilize certain branched-chain amino acids as a sole nitrogen source.
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Affiliation(s)
- Caoimhe E. O’Brien
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - João Oliveira-Pacheco
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Eoin Ó Cinnéide
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Max A. B. Haase
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thomas R. Rogers
- Department of Clinical Microbiology, Trinity College Dublin, Dublin, Ireland; Department of Microbiology, St James’s Hospital, Dublin, Ireland
| | - Oscar Zaragoza
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, Km2, Majadahonda, Madrid, Spain
| | - Ursula Bond
- Department of Microbiology, School of Genetics and Microbiology, Trinity College Dublin, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
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13
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Arastehfar A, Hilmioğlu-Polat S, Daneshnia F, Hafez A, Salehi M, Polat F, Yaşar M, Arslan N, Hoşbul T, Ünal N, Metin DY, Gürcan Ş, Birinci A, Koç AN, Pan W, Ilkit M, Perlin DS, Lass-Flörl C. Recent Increase in the Prevalence of Fluconazole-Non-susceptible Candida tropicalis Blood Isolates in Turkey: Clinical Implication of Azole-Non-susceptible and Fluconazole Tolerant Phenotypes and Genotyping. Front Microbiol 2020; 11:587278. [PMID: 33123116 PMCID: PMC7573116 DOI: 10.3389/fmicb.2020.587278] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/07/2020] [Indexed: 12/18/2022] Open
Abstract
Candida tropicalis is the fourth leading cause of candidemia in Turkey. Although C. tropicalis isolates from 1997 to 2017 were characterized as fully susceptible to antifungals, the increasing global prevalence of azole-non-susceptible (ANS) C. tropicalis and the association between high fluconazole tolerance (HFT) and fluconazole therapeutic failure (FTF) prompted us to re-evaluate azole susceptibility of C. tropicalis in Turkey. In this study, 161 C. tropicalis blood isolates from seven clinical centers were identified by ITS rDNA sequencing, genotyped by multilocus microsatellite typing, and tested for susceptibility to five azoles, two echinocandins, and amphotericin B (AMB); antifungal resistance mechanisms were assessed by sequencing of ERG11 and FKS1 genes. The results indicated that C. tropicalis isolates, which belonged to 125 genotypes grouped into 11 clusters, were fully susceptible to echinocandins and AMB; however, 18.6% of them had the ANS phenotype but only two carried the ANS-conferring mutation (Y132F). HFT was recorded in 52 isolates, 10 of which were also ANS. Large proportions of patients infected with ANS and HFT isolates (89 and 40.7%, respectively) showed FTF. Patients infected with azole-susceptible or ANS isolates did not differ in mortality, which, however, was significantly lower for those infected with HFT isolates (P = 0.007). There were significant differences in mortality (P = 0.02), ANS (P = 0.012), and HFT (P = 0.007) among genotype clusters. The alarming increase in the prevalence of C. tropicalis blood isolates with ANS and HFT in Turkey and the notable FTF rate should be a matter of public health concern.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | | | | | | | - Mohammadreza Salehi
- Department of Infectious Diseases and Tropical Medicine, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Furkan Polat
- Department of Microbiology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Melike Yaşar
- Department of Microbiology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Nazlı Arslan
- Department of Microbiology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Tuğrul Hoşbul
- Department of Microbiology, Gulhane Training and Research Hospital, University of Health Sciences, Ankara, Turkey
| | - Nevzat Ünal
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, Turkey.,Department of Microbiology, Adana City Hospital, University of Health Sciences, Adana, Turkey
| | - Dilek Yeşim Metin
- Department of Microbiology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Şaban Gürcan
- Department of Microbiology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Asuman Birinci
- Department of Microbiology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Ayşe Nedret Koç
- Department of Microbiology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Weihua Pan
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, China
| | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, Turkey
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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14
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Díaz-García J, Arendrup MC, Cantón R, García-Rodríguez J, Gómez A, Gómez E, Orden B, Parisi G, Pemán J, Posteraro B, Sanguinetti M, Da Matta DA, Colombo AL, Muñoz P, Sánchez-Carrillo C, Guinea J, Escribano P. Candidemia Candida albicans clusters have higher tendency to form biofilms than singleton genotypes†. Med Mycol 2020; 58:887-895. [PMID: 32022851 DOI: 10.1093/mmy/myaa002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/30/2019] [Accepted: 01/13/2020] [Indexed: 12/15/2022] Open
Abstract
The capacity of Candida spp. to form biofilms allows them to attach either to living or inert surfaces, promoting their persistence in hospital environments. In a previous study, we reported strain-to-strain variations in Candida spp. biofilm development, suggesting that some genotypes may be greater biofilm formers than others. In this study, we hypothesize that isolates pertaining to clusters may be found more frequently in the environment due to their ability to form biofilms compared to singleton genotypes. Two hundred and thirty-nine Candida spp. isolates (78 clusters) from candidemia patients admitted to 16 hospitals located in different cities and countries-and the same number of singleton genotypes used as controls-were tested in terms of biofilm formation using the crystal violet and the XTT reduction assays. Candida albicans clusters showed higher biofilm formation in comparison to singleton genotypes (P < .01). The biofilms formed by intra-hospital C. albicans clusters showed higher metabolic activity (P < .05). Furthermore, marked variability was found among species and type of cluster. We observed that the higher the number of isolates, the higher the variability of biofilm production by isolates within the cluster, suggesting that the production of biofilm by isolates of the same genotype is quite diverse and does not depend on the type of cluster studied. In conclusion, candidemia Candida spp. clusters-particularly in the case of C. albicans-show significantly more biomass production and metabolic activity than singleton genotypes.
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Affiliation(s)
- Judith Díaz-García
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Maiken C Arendrup
- Unit of Mycology Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rafael Cantón
- Servicio de Microbiología. Hospital Ramón y Cajal, Madrid and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Ana Gómez
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Elia Gómez
- Servicio de Microbiología. Hospital Ramón y Cajal, Madrid and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Beatriz Orden
- Hospital Puerta del Hierro-Majadahonda, Madrid, Spain
| | | | - Javier Pemán
- Instituto de Investigación Sanitaria La Fe, Valencia, Spain
- Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Brunella Posteraro
- Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A; Gemelli IRCCS, Rome, Italy
| | | | - Arnaldo L Colombo
- Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, Spain
| | - Carlos Sánchez-Carrillo
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
| | - Jesús Guinea
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
| | - Pilar Escribano
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
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15
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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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Megri Y, Arastehfar A, Boekhout T, Daneshnia F, Hörtnagl C, Sartori B, Hafez A, Pan W, Lass-Flörl C, Hamrioui B. Candida tropicalis is the most prevalent yeast species causing candidemia in Algeria: the urgent need for antifungal stewardship and infection control measures. Antimicrob Resist Infect Control 2020; 9:50. [PMID: 32264966 PMCID: PMC7140370 DOI: 10.1186/s13756-020-00710-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/24/2020] [Indexed: 12/29/2022] Open
Abstract
Background Despite being associated with a high mortality and economic burden, data regarding candidemia are scant in Algeria. The aim of this study was to unveil the epidemiology of candidemia in Algeria, evaluate the antifungal susceptibility pattern of causative agents and understand the molecular mechanisms of antifungal resistance where applicable. Furthermore, by performing environmental screening and microsatellite typing we sought to identify the source of infection. Methods We performed a retrospective epidemiological-based surveillance study and collected available blood yeast isolates recovered from the seven hospitals in Algiers. To identify the source of infection, we performed environmental screening from the hands of healthcare workers (HCWs) and high touch areas. Species identification was performed by API Auxa-Color and MALDI-TOF MS and ITS sequencing was performed for species not reliably identified by MALDI-TOF MS. Antifungal susceptibility testing followed CLSI M27-A3/S4 and included all blood and environmental yeast isolates. ERG11 sequencing was performed for azole-resistant Candida isolates. Microsatellite typing was performed for blood and environmental Candida species, where applicable. Results Candida tropicalis (19/66) was the main cause of candidemia in these seven hospitals, followed by Candida parapsilosis (18/66), Candida albicans (18/66), and Candida glabrata (7/66). The overall mortality rate was 68.6% (35/51) and was 81.2% for C. tropicalis-infected patients (13/16). Fluconazole was the main antifungal drug used (12/51); 41% of the patients (21/51) did not receive any systemic treatment. Candida parapsilosis was isolated mainly from the hands of HCWs (7/28), and various yeasts were collected from high-touch areas (11/47), including Naganishia albida, C. parapsilosis and C. glabrata. Typing data revealed interhospital transmission on two occasions for C. parapsilosis and C. glabrata, and the same clone of C. parapsilosis infected two patients within the same hospital. Resistance was only noted for C. tropicalis against azoles (6/19) and fluconazole-resistant C. tropicalis isolates (≥8 μg/ml) (6/19) contained a novel P56S (5/6) amino acid substitution and a previously reported one (V234F; 1/6) in Erg11p. Conclusions Collectively, our data suggest an urgent need for antifungal stewardship and infection control strategies to improve the clinical outcome of Algerian patients with candidemia. The high prevalence of C. tropicalis joined by fluconazole-resistance may hamper the therapeutic efficacy of fluconazole, the frontline antifungal drug used in Algeria.
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Affiliation(s)
- Youcef Megri
- Parasitology and Mycology Department, Mustapha University Hospital, 16000, Algiers, Algeria
| | - Amir Arastehfar
- Yeast Department, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands. .,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands.
| | - Teun Boekhout
- Yeast Department, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Farnaz Daneshnia
- Yeast Department, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Caroline Hörtnagl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Bettina Sartori
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ahmed Hafez
- Biotechvana, 46980, Paterna, Valencia, Spain
| | - Weihua Pan
- Shanghai Key Laboratory Molecular Medical Mycology, Shanghai, 200003, China.
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Boussad Hamrioui
- Parasitology and Mycology Department, Mustapha University Hospital, 16000, Algiers, Algeria
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Prakash A, Sundar G, Sharma B, Hagen F, Meis JF, Chowdhary A. Genotypic diversity in clinical and environmental isolates of Cryptococcus neoformans from India using multilocus microsatellite and multilocus sequence typing. Mycoses 2020; 63:284-293. [PMID: 31820495 DOI: 10.1111/myc.13041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND Cryptococcus neoformans is the leading cause of cryptococcal meningitis in HIV/AIDS patients. As infections in humans are predominantly caused by the inhalation of basidiospores from environmental sources, therefore, analysing the population structure of both clinical and environmental populations of C neoformans can increase our understanding of the molecular epidemiology of cryptococcosis. OBJECTIVE To investigate the genotypic diversity and antifungal susceptibility profile of a large collection of C neoformans isolates (n = 523) from clinical and environmental sources in India between 2001 and 2014. MATERIALS AND METHODS Cryptococcus neoformans isolates were genotyped by AFLP, microsatellite typing (MLMT) and MLST. In vitro antifungal susceptibility for standard antifungals was undertaken using CLSI M27-A3. RESULTS All isolates were C neoformans, AFLP1/VNI and exhibited mating-type MATα. MLMT revealed that the majority of isolates belonged to microsatellite cluster (MC) MC3 (49%), followed by MC1 (35%), and the remaining isolates fell in 11 other MC types. Interestingly, two-thirds of clinical isolates were genotype MC3 and only 17% of them were MC1, whereas majority of environmental strains were MC1 (54%) followed by MC3 (16%). Overall, MLST assigned 5 sequence types (STs) among all isolates and ST93 was the most common (n = 76.7%), which was equally distributed in both HIV-positive and HIV-negative patients. Geometric mean MICs revealed that isolates in MC1 were significantly less (P < .05) susceptible to amphotericin B, 5-flucytosine, itraconazole, posaconazole and isavuconazole than isolates in MC3. CONCLUSIONS The study shows a good correlation between MLMT and MLST genotyping methods. Further, environmental isolates were genetically more diverse than clinical isolates.
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Affiliation(s)
- Anupam Prakash
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Gandhi Sundar
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Brijesh Sharma
- Department of Medicine, PGIMER & Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Jacques F Meis
- Center of Expertise in Mycology, Radboud University Medical Centre/Canisius Wilhelmina Hospital and Excellence Center for Medical Mycology of the European Confederation of Medical Mycology (ECMM), Nijmegen, The Netherlands.,Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, Netherlands
| | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
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Guinea J, Arendrup MC, Cantón R, Cantón E, García-Rodríguez J, Gómez A, de la Pedrosa EGG, Hare RK, Orden B, Sanguinetti M, Pemán J, Posteraro B, Ruiz-Gaitán A, Parisi G, Da Matta DA, Colombo AL, Sánchez-Carrillo C, Reigadas E, Muñoz P, Escribano P. Genotyping Reveals High Clonal Diversity and Widespread Genotypes of Candida Causing Candidemia at Distant Geographical Areas. Front Cell Infect Microbiol 2020; 10:166. [PMID: 32432048 PMCID: PMC7214738 DOI: 10.3389/fcimb.2020.00166] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/30/2020] [Indexed: 12/16/2022] Open
Abstract
The objectives of this study were to gain further insight on Candida genotype distribution and percentage of clustered isolates between hospitals and to identify potential clusters involving different hospitals and cities. We aim to genotype Candida spp. isolates causing candidemia in patients admitted to 16 hospitals in Spain, Italy, Denmark, and Brazil. Eight hundred and eighty-four isolates (Candida albicans, n = 534; C. parapsilosis, n = 282; and C. tropicalis, n = 68) were genotyped using species-specific microsatellite markers. CDC3, EF3, HIS3, CAI, CAIII, and CAVI were used for C. albicans, Ctrm1, Ctrm10, Ctrm12, Ctrm21, Ctrm24, and Ctrm28 for C. tropicalis, and CP1, CP4a, CP6, and B for C. parapsilosis. Genotypes were classified as singletons (genotype only found once) or clusters (same genotype infecting two or more patients). Clusters were defined as intra-hospital (involving patients admitted to a single hospital), intra-ward (involving patients admitted to the same hospital ward) or widespread (involving patients admitted to different hospitals). The percentage of clusters and the proportion of patients involved in clusters among species, genotypic diversity and distribution of genetic diversity were assessed. Seven hundred and twenty-three genotypes were detected, 78 (11%) being clusters, most of which (57.7%; n = 45/78) were intra-hospital clusters including intra-ward ones (42.2%; n = 19/45). The proportion of clusters was not statistically different between species, but the percentage of patients in clusters varied among hospitals. A number of genotypes (7.2%; 52/723) were widespread (found at different hospitals), comprising 66.7% (52/78) of clusters, and involved patients at hospitals in the same city (n = 21) or in different cities (n = 31). Only one C. parapsilosis cluster was a widespread genotype found in all four countries. Around 11% of C. albicans and C. parapsilosis isolates causing candidemia are clusters that may result from patient-to-patient transmission, widespread genotypes commonly found in unrelated patients, or insufficient microsatellite typing genetic discrimination.
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Affiliation(s)
- Jesús Guinea
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
- *Correspondence: Jesús Guinea
| | - Maiken C. Arendrup
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rafael Cantón
- Servicio de Microbiología. Hospital Ramón y Cajal, Madrid and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Emilia Cantón
- Instituto de Investigación Sanitaria La Fe, Universidad de Valencia, Valencia, Spain
| | | | - Ana Gómez
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
| | - Elia Gómez G. de la Pedrosa
- Servicio de Microbiología. Hospital Ramón y Cajal, Madrid and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Rasmus K. Hare
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
| | - Beatriz Orden
- Department of Clinical Microbiology, Hospital Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Javier Pemán
- Instituto de Investigación Sanitaria La Fe, Universidad de Valencia, Valencia, Spain
- Department of Clinical Microbiology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Brunella Posteraro
- Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alba Ruiz-Gaitán
- Instituto de Investigación Sanitaria La Fe, Universidad de Valencia, Valencia, Spain
| | - Gabriella Parisi
- Department of Clinical Microbiology, Azienda Ospedaliera San Camillo-Forlanini, Rome, Italy
| | | | - Arnaldo L. Colombo
- Special Mycology Laboratory, Universida de Federalde São Paulo, São Paulo, Brazil
| | - Carlos Sánchez-Carrillo
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
| | - Elena Reigadas
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Pilar Escribano
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
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Candida tropicalis geographic population structure maintenance and dispersion in the coastal environment may be influenced by the climatic season and anthropogenic action. Microb Pathog 2018; 128:63-68. [PMID: 30550843 DOI: 10.1016/j.micpath.2018.12.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 11/24/2022]
Abstract
Candida tropicalis is a pathogenic yeast with worldwide recognition as the second or third more frequently isolated species in Latin America, for both superficial and systemic infections. Because of its high prevalence, and growing clinical interest, it is essential to understand genetic variability patterns of this important Candida species in the tropics. Besides belonging to the human normal microbiota, C. tropicalis may be found in other warm blood animals and in the environment, including water and sand of beaches. The aims of the present study were to evaluate genotypic and phenotypic variability of 62 isolates of C. tropicalis obtained from the coastal environment in Northeast Brazil using microsatellite and MALDI-TOF/MS comparisons. There was a relatively low correspondence between these typing techniques employed. Therefore, further studies are needed to consolidate the use of MALDI-TOF/MS as a yeast typing tool. Nevertheless, the two methods employed demonstrated the heterogeneity of C. tropicalis in a coastal environment. We also found relative maintenance of the population structure within the same season, which may reinforce the idea that this species presents the potential to remain in the environment for a long period of time. In addition, highly related strains were found within different geographic points of collection, demonstrating that this strain may be dispersed at long distances, probably influenced by anthropogenic actions and driven by the sea tides and wind.
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Microsatellite Length Polymorphism for DNA-Based Typing of Candida albicans Isolated from HIV Positive Patients in Tehran, Iran. Jundishapur J Microbiol 2018. [DOI: 10.5812/jjm.64041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Abstract
The availability of complete fungal genomes is expanding rapidly and is offering an extensive and accurate view of this "kingdom." The scientific milestone of free access to more than 1000 fungal genomes of different species was reached, and new and stimulating projects have meanwhile been released. The "1000 Fungal Genomes Project" represents one of the largest sequencing initiative regarding fungal organisms trying to fill some gaps on fungal genomics. Presently, there are 329 fungal families with at least one representative genome sequenced, but there is still a large number of fungal families without a single sequenced genome. In addition, additional sequencing projects helped to understand the genetic diversity within some fungal species. The availability of multiple genomes per species allows to support taxonomic organization, brings new insights for fungal evolution in short-time scales, clarifies geographical and dispersion patterns, elucidates outbreaks and transmission routes, among other objectives. Genotyping methodologies analyze only a small fraction of an individual's genome but facilitate the comparison of hundreds or thousands of isolates in a small fraction of the time and at low cost. The integration of whole genome strategies and improved genotyping panels targeting specific and relevant SNPs and/or repeated regions can represent fast and practical strategies for studying local, regional, and global epidemiology of fungi.
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Affiliation(s)
- Ricardo Araujo
- University of Porto, Porto, Portugal; School of Medicine and Health Sciences, Flinders University, Adelaide, SA, Australia.
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22
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Mehta N, Hagen F, Aamir S, Singh SK, Baghela A. Development of a High-Resolution Multi-Locus Microsatellite Typing Method for Colletotrichum gloeosporioides. MYCOBIOLOGY 2017; 45:401-408. [PMID: 29371809 PMCID: PMC5780373 DOI: 10.5941/myco.2017.45.4.401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 06/07/2023]
Abstract
Colletotrichum gloeosporioides is an economically important fungal pathogen causing substantial yield losses indifferent host plants. To understand the genetic diversity and molecular epidemiology of this fungus, we have developed a novel, high-resolution multi-locus microsatellite typing (MLMT) method. Bioinformatic analysis of C. gloeosporioides unannotated genome sequence yielded eight potential microsatellite loci, of which five, CG1 (GT)n, CG2 (GT1)n, CG3 (TC)n, CG4 (CT)n, and CG5 (CT1)n were selected for further study based on their universal amplification potential, reproducibility, and repeat number polymorphism. The selected microsatellites were used to analyze 31 strains of C. gloeosporioides isolated from 20 different host plants from India. All microsatellite loci were found to be polymorphic, and the approximate fragment sizes of microsatellite loci CG1, CG2, CG3, CG4, and CG5 were in ranges of 213-241, 197-227, 231-265, 209-275, and 132-188, respectively. Among the 31 isolates, 55 different genotypes were identified. The Simpson's index of diversity (D) values for the individual locus ranged from 0.79 to 0.92, with the D value of all combined five microsatellite loci being 0.99. Microsatellite data analysis revealed that isolates from Ocimum sanctum, Capsicum annuum (chili pepper), and Mangifera indica (mango) formed distinct clusters, therefore exhibited some level of correlation between certain genotypes and host. The developed MLMT method would be a powerful tool for studying the genetic diversity and any possible genotype-host correlation in C. gloeosporioides.
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Affiliation(s)
- Nikita Mehta
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology Group, MACS-Agharkar Research Institute, Pune 411004, India
- Savitribai Phule Pune University, Pune 411007, India
| | - Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen 6532 SZ, The Netherlands
| | - Sadaf Aamir
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology Group, MACS-Agharkar Research Institute, Pune 411004, India
- Savitribai Phule Pune University, Pune 411007, India
| | - Sanjay K Singh
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology Group, MACS-Agharkar Research Institute, Pune 411004, India
- Savitribai Phule Pune University, Pune 411007, India
| | - Abhishek Baghela
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology Group, MACS-Agharkar Research Institute, Pune 411004, India
- Savitribai Phule Pune University, Pune 411007, India
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Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How? Clin Microbiol Rev 2017; 30:671-707. [PMID: 28490578 DOI: 10.1128/cmr.00043-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes. STR polymorphisms are based on the number of repeats of short DNA fragments, mostly outside coding regions, and thus are expected to be more polymorphic and more rapidly evolving than MLST markers. There is no consensus on a universal typing system. Either one or both of these approaches are now available for Candida spp., Aspergillus spp., Fusarium spp., Scedosporium spp., Cryptococcus neoformans, Pneumocystis jirovecii, and endemic mycoses. The choice of the method and the number of loci to be tested depend on the clinical question being addressed. Next-generation sequencing is becoming the most appropriate method for fungi with no MLP or MLST typing available. Whatever the molecular tool used, collection of clinical data (e.g., time of hospitalization and sharing of similar rooms) is mandatory for investigating outbreaks and nosocomial transmission.
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Zuza-Alves DL, Silva-Rocha WP, Chaves GM. An Update on Candida tropicalis Based on Basic and Clinical Approaches. Front Microbiol 2017; 8:1927. [PMID: 29081766 PMCID: PMC5645804 DOI: 10.3389/fmicb.2017.01927] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/21/2017] [Indexed: 01/12/2023] Open
Abstract
Candida tropicalis has emerged as one of the most important Candida species. It has been widely considered the second most virulent Candida species, only preceded by C. albicans. Besides, this species has been recognized as a very strong biofilm producer, surpassing C. albicans in most of the studies. In addition, it produces a wide range of other virulence factors, including: adhesion to buccal epithelial and endothelial cells; the secretion of lytic enzymes, such as proteinases, phospholipases, and hemolysins, bud-to-hyphae transition (also called morphogenesis) and the phenomenon called phenotypic switching. This is a species very closely related to C. albicans and has been easily identified with both phenotypic and molecular methods. In addition, no cryptic sibling species were yet described in the literature, what is contradictory to some other medically important Candida species. C. tropicalis is a clinically relevant species and may be the second or third etiological agent of candidemia, specifically in Latin American countries and Asia. Antifungal resistance to the azoles, polyenes, and echinocandins has already been described. Apart from all these characteristics, C. tropicalis has been considered an osmotolerant microorganism and this ability to survive to high salt concentration may be important for fungal persistence in saline environments. This physiological characteristic makes this species suitable for use in biotechnology processes. Here we describe an update of C. tropicalis, focusing on all these previously mentioned subjects.
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Affiliation(s)
| | | | - Guilherme M. Chaves
- Laboratory of Medical and Molecular Mycology, Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, Brazil
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Al-Obaid K, Asadzadeh M, Ahmad S, Khan Z. Population structure and molecular genetic characterization of clinical Candida tropicalis isolates from a tertiary-care hospital in Kuwait reveal infections with unique strains. PLoS One 2017; 12:e0182292. [PMID: 28854190 PMCID: PMC5576731 DOI: 10.1371/journal.pone.0182292] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/15/2017] [Indexed: 11/19/2022] Open
Abstract
Candida tropicalis is a frequently isolated yeast species causing bloodstream, urinary tract and other infections particularly in patients admitted to intensive care units (ICUs) and those requiring prolonged urinary catheterization (UC) or receiving broad-spectrum antibiotics (BSA). This study investigated clinical characteristics and genetic relatedness among C. tropicalis strains isolated from patients at Al-Amiri Hospital in Kuwait. C. tropicalis strains (n = 63) isolated from blood, genito-urinary, respiratory (RT) and digestive (GIT) tracts and wound sites from 54 patients were used. All isolates were phenotypically identified and tested against six antifungal drugs by using Vitek 2 system. Molecular identification was performed by PCR amplification of rDNA. Fingerprinting was achieved by 6-loci-based multilocus sequence typing (MLST) and data were analyzed by BioNumerics software for phylogenetic relationships. Patients mean age was >65 years and >20% patients were hospitalized in ICUs. Most patients had underlying conditions that included UC, BSA, diabetes and RT/GIT abnormalities. Most candiduria cases had UC, ureteric stent or suprapubic catheters. All isolates were identified as C. tropicalis by Vitek 2 and by species-specific PCR. Sixty-two isolates were susceptible to all tested antifungal drugs. MLST identified 59 diploid sequence types (DSTs) including 54 newly-identified DSTs. C. tropicalis isolates from multiple sites of same patient usually belonged to different DSTs. Interestingly, 56 of 57 isolates from 48 patients belonged to unique genotypes. Only six isolates from six patients belonged to three DSTs (clusters), however, C. tropicalis strains in each cluster were isolated >3 months apart. Our data show diverse origins of C. tropicalis infections in Kuwait as most isolates were unique strains. There was no obvious correlation between cluster isolates with time of isolation and/or hospital ward of their origin. This study presents the first MLST analysis of C. tropicalis isolates from Middle East and may be useful for studying genetic relationships among global C. tropicalis strains.
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Affiliation(s)
- Khaled Al-Obaid
- Microbiology, Department of Medical Laboratories, Al-Amiri Hospital, Sharq, Kuwait
| | - Mohammad Asadzadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- * E-mail:
| | - Ziauddin Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
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26
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Novel Polymorphic Multilocus Microsatellite Markers to Distinguish Candida tropicalis Isolates. PLoS One 2016; 11:e0166156. [PMID: 27820850 PMCID: PMC5098789 DOI: 10.1371/journal.pone.0166156] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/18/2016] [Indexed: 11/19/2022] Open
Abstract
Candida tropicalis is an important pathogen. Here we developed and evaluated a polymorphic multilocus microsatellite scheme employing novel genetic markers for genotyping of C. tropicalis. Using 10 isolates from 10 unique (separate) patients to screen over 4000 tandem repeats from the C. tropicalis genome (strain MYA-3404), six new candidate microsatellite loci (ctm1, ctm3, ctm8, ctm18, ctm24 and ctm26) were selected according to amplification success, observed polymorphisms and stability of flanking regions by preliminary testing. Two known microsatellite loci CT14 and URA3 were also studied. The 6-locus scheme was then tested against a set of 82 different isolates from 32 patients. Microsatellite genotypes of isolates from the same patient (two to five isolates per patient) were identical. The six loci produced eight to 17 allele types and identified 11 to 24 genotypes amongst 32 patients’ isolates, achieving a discriminatory power (DP) of 0.76 to 0.97 (versus 0.78 for both CT14 and URA3 loci, respectively). Testing of a combination of only three loci, ctm1, ctm3 and ctm24, also achieved maximum typing efficiency (DP = 0.99, 29 genotypes). The microsatellite typing scheme had good correlation compared with pulsed-field gel electrophoresis, although was slightly less discriminatory. The new six-locus microsatellite typing scheme is a potentially valuable tool for genotyping and investigating microevolution of C. tropicalis.
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Marcos-Zambrano LJ, Escribano P, Sánchez-Carrillo C, Bouza E, Guinea J. Scope and frequency of fluconazole trailing assessed using EUCAST in invasive Candida spp. isolates. Med Mycol 2016; 54:733-9. [PMID: 27161788 DOI: 10.1093/mmy/myw033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/23/2016] [Indexed: 11/14/2022] Open
Abstract
Trailing is a well-known phenomenon that is defined as reduced but persistent visible growth of Candida spp. at fluconazole concentrations above the MIC. Trailing is commonly detected using the CLSI M27-A3 method, although little is known about its frequency when investigated with EUCAST. We assessed the frequency and scope of fluconazole trailing after using EUCAST EDef 7.2. against a large number of Candida spp. isolates from patients with candidemia. We studied 639 fluconazole-susceptible non-krusei Candida spp. isolates from 570 patients admitted to Gregorio Marañón Hospital. Isolates were tested in vitro for fluconazole susceptibility according to the EUCAST EDef 7.2 procedure; trailing was defined as the presence of any residual growth in wells containing fluconazole concentrations above the MIC. According to the mean percentage of trailing observed, isolates were classified as residual trailers (0.1-5%), slight trailers (6%-10%), moderate trailers (11%-15%), and heavy trailers (>15%). The relationship between trailing and genotyping was assessed. The mean overall percentage of trailing was 6.8%, with C. albicans and C. tropicalis showing the highest percentages (9.75% and 9.29%, respectively; P < .001). C. albicans and C. tropicalis had the highest percentage of heavy trailers (>15%). Trailing was not genotype-specific. Fluconazole trailing was observed frequently when EUCAST was used for antifungal susceptibility testing, particularly in isolates of C. albicans and C. tropicalis The cut-off proposed enabled us to classify the isolates according to the degree of trailing and can be used as the basis for future studies to evaluate the clinical impact of this phenomenon.
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Affiliation(s)
- Laura Judith Marcos-Zambrano
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Pilar Escribano
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
| | - Carlos Sánchez-Carrillo
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
| | - Emilio Bouza
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Jesús Guinea
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
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Yu M, Yu J, Li H, Wang Y, Yin X, Bo H, Ding H, Zhou Y, Liu Y. Survey and analysis of simple sequence repeats in the Ustilaginoidea virens genome and the development of microsatellite markers. Gene 2016; 585:28-34. [PMID: 26992636 DOI: 10.1016/j.gene.2016.03.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 11/15/2022]
Abstract
Ustilaginoidea virens is the causal agent of rice false smut, causing quantitative and qualitative losses in rice industry. However, the development and application of simple sequence repeat (SSR) markers for genetic diversity studies in U. virens were limited. This study is the first to perform large-scale development of SSR markers of this pathogen at the genome level, to (1) compare these SSR markers with those of other fungi, (2) analyze the pattern of the SSRs, and (3) obtain more informative genetic markers. U. virens is rich in SSRs, and 13,778 SSRs were identified with a relative abundance of 349.7SSRs/Mb. The most common motifs in the genome or in noncoding regions were mononucleotides, whereas trinucleotides in coding sequences. A total of 6 out of 127 primers were randomly selected to be used to analyze 115 isolates, and these 6 primers showed high polymorphism in U. virens. This study may serve as an important resource for molecular genetic studies in U. virens.
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Affiliation(s)
- Mina Yu
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Junjie Yu
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Huanhuan Li
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Yahui Wang
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Xiaole Yin
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Huiwen Bo
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Life Sciences College of Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Ding
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Life Sciences College of Nanjing Agricultural University, Nanjing 210095, China
| | - Yuxin Zhou
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Yongfeng Liu
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
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29
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Li Z, Jiang C, Dong D, Zhang L, Tian Y, Ni Q, Mao E, Peng Y. The Correlation Between Candida Colonization of Distinct Body Sites and Invasive Candidiasis in Emergency Intensive Care Units: Statistical and Molecular Biological Analysis. Mycopathologia 2016; 181:475-84. [PMID: 26886444 DOI: 10.1007/s11046-016-9991-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/01/2016] [Indexed: 10/22/2022]
Abstract
Both statistical and molecular biological methods were used to evaluate the association between Candida colonization of different body sites and invasive candidiasis (IC) and analyse the potential infection sources of IC. Candida surveillance cultures from the urine, sputum, rectum and skin were performed on patients admitted to an emergency intensive care units (EICU) of a tertiary care hospital in Shanghai, China, from February 2014 to January 2015. Specimens were collected once a week at admission and thereafter. The patients' clinical data were collected, and Candida isolates were genotyped using polymorphic microsatellite markers. A total of 111 patients were enrolled. Patients with positive urine (23.3 vs. 2.5 %, p = 0.001) and rectal swab (13.6 vs. 0 %, p = 0.010) cultures were more likely to develop IC. However, the risk for IC was not significantly different among patients with and without respiratory (10.0 vs. 5.8 %, p = 0.503) and skin (33.3 vs. 6.5 %, p = 0.056) colonization. Gene microevolution frequently occurred at rectal swab and urine sites, and IC with possible source of infection was caused by rectal isolates (2/7), urine isolates (4/7) and sputum isolate (1/7).The colonization of gut and urinary tract maybe more relevant indicators of IC, which should be taken into consideration when selecting practical body sites for Candida surveillance cultures.
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Affiliation(s)
- Zhen Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China
| | - Cen Jiang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China
| | - Danfeng Dong
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China
| | - Lihua Zhang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China
| | - Yuan Tian
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China
| | - Qi Ni
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China
| | - Enqiang Mao
- Department of Emergency Intensive Care Unit, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China.
| | - Yibing Peng
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China.
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