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Multicenter evaluation of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy-based method for rapid identification of clinically relevant yeasts. J Clin Microbiol 2021; 60:e0139821. [PMID: 34669460 DOI: 10.1128/jcm.01398-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fourier transform infrared (FTIR) spectroscopy has demonstrated applicability as a reagent-free whole-organism fingerprinting technique for both microbial identification and strain typing. For routine application of this technique in microbiology laboratories, acquisition of FTIR spectra in the attenuated total reflectance (ATR) mode simplifies the FTIR spectroscopy workflow, providing results within minutes after initial culture without prior sample preparation. In our previous central work, 99.7% correct species identification of clinically relevant yeasts was achieved by employing an ATR-FTIR-based method and spectral database developed by our group. In this study, ATR-FTIR spectrometers were placed in 6 clinical microbiology laboratories over a 16-month period and were used to collect spectra of routine yeast isolates for on-site identification to the species level. The identification results were compared to those obtained from conventional biochemical tests and/or matrix-assisted laser desorption/ionization time of flight mass spectrometry. Isolates producing discordant results were reanalyzed by routine identification methods, ATR-FTIR spectroscopy and PCR gene sequencing of the D1/D2 and ITS regions. Among the 573 routine clinical yeast isolates collected and identified by the ATR-FTIR-based method, 564 isolates (98.4%) were correctly identified at the species level while the remaining isolates were inconclusive with no misidentifications. Due to the low prevalence of Candida auris in routine isolates, additional randomly selected C. auris (n = 24) isolates were obtained for evaluation and resulted in 100% correct identification. Overall, the data obtained in our multicenter evaluation study using multiple spectrometers and system operators indicate that ATR-FTIR spectroscopy is a reliable, cost-effective yeast identification technique that provides accurate and timely (∼3 minutes/sample) species identification promptly after the initial culture.
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2
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Keller B, Kuder H, Visscher C, Siesenop U, Kamphues J. Yeasts in Liquid Swine Diets: Identification Methods, Growth Temperatures and Gas-Formation Potential. J Fungi (Basel) 2020; 6:E337. [PMID: 33291632 PMCID: PMC7761980 DOI: 10.3390/jof6040337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/19/2020] [Accepted: 12/02/2020] [Indexed: 12/30/2022] Open
Abstract
Liquid feed is susceptible to microbiological growth. Yeasts are said to cause sudden death in swine due to intestinal gas formation. As not all animals given high yeast content feed fall ill, growth and gas formation potential at body temperature were investigated as possible causally required properties. The best identification method for these environmental yeasts should be tested beforehand. Yeasts derived from liquid diets without (LD - S) and liquid diets with maize silage (LD + S) were examined biochemically (ID32C-test) and with MALDI-TOF with direct smear (DS) and an extraction method (EX). Growth temperature and gas-forming potential were measured. With MALDI-EX, most yeast isolates were identified: Candida krusei most often in LD - S, and C. lambica most often in LD + S, significantly more than in LD - S. Larger colonies, 58.75% of all yeast isolates, were formed at 25 °C rather than at 37 °C; 17.5% of all isolates did not grow at 37 °C at all. Most C. krusei isolates formed high gas amounts within 24 h, whereas none of the C. lambica, C. holmii and most other isolates did. The gas pressure formed by yeast isolates varied more than tenfold. Only a minority of the yeasts were able to produce gas at temperatures common in the pig gut.
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Affiliation(s)
- Birgit Keller
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany; (H.K.); (C.V.); (J.K.)
| | - Henrike Kuder
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany; (H.K.); (C.V.); (J.K.)
| | - Christian Visscher
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany; (H.K.); (C.V.); (J.K.)
| | - Ute Siesenop
- Institute for Microbiology, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany;
| | - Josef Kamphues
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany; (H.K.); (C.V.); (J.K.)
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Kumar A, Nair R, Kumar M, Banerjee A, Chakrabarti A, Rudramurthy SM, Bagga R, Gaur NA, Mondal AK, Prasad R. Assessment of antifungal resistance and associated molecular mechanism in Candida albicans isolates from different cohorts of patients in North Indian state of Haryana. Folia Microbiol (Praha) 2020; 65:747-754. [PMID: 32219719 DOI: 10.1007/s12223-020-00785-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/10/2020] [Indexed: 01/04/2023]
Abstract
The present study examines the trend in distribution of Candida species and their antifungal resistance patterns in hospitals across Haryana, a North Indian state with poorly addressed epidemiology of fungal infections. In our collection of 228 Candida isolates, Candida albicans dominated in both high vaginal swab (HVS) and urine samples while Candida glabrata and Candida tropicalis were the second-highest non-albicans Candida species (NAC), respectively. Of note, in blood samples, C. tropicalis and C. albicans were present in equal numbers. All 228 isolates were subjected to antifungal susceptibility tests, whereby 51% of C. albicans recovered from HVS samples displayed fluconazole resistance. To understand its mechanistic basis, expression profiling of efflux pump genes CDR1, CDR2, MDR1 and azole drug target, ERG11 was performed in 20 randomly selected resistant isolates, wherein many isolates elicited higher expression. Further, ERG11 gene sequencing suggested that most of the isolates harbored mutations, which are not reported with azole resistance. However, one isolate, RPCA9 (MIC 64 μg/mL) harbored triple mutation (Y132C, F145L, A114V), wherein Y132 and F145 sites were previously implicated in azole resistance. Interestingly, one isolate, (RPCA61) having MIC > 128 μg/mL harbored a novel mutation, G129R. Of note, HVS isolates RPCA 21, RPCA 22, and RPCA 44 (MICs 64 to > 128 μg/mL) did not show any change in alteration in ERG11 or overexpression of efflux pump genes. Together, this study presents a first report of Candida infections in selected hospitals of Haryana State.
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Affiliation(s)
- Ashok Kumar
- Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Amity Education Valley, Gurugram, 122413, India
| | - Remya Nair
- Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Amity Education Valley, Gurugram, 122413, India
| | - Mohit Kumar
- Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Amity Education Valley, Gurugram, 122413, India.,International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Atanu Banerjee
- Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Amity Education Valley, Gurugram, 122413, India
| | - Arunaloke Chakrabarti
- The Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | | | - Ruchika Bagga
- Fortis Memorial Research Institute (FMRI), Gurugram, India
| | - Naseem A Gaur
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Alok K Mondal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rajendra Prasad
- Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Amity Education Valley, Gurugram, 122413, India.
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Lacerda MPF, Marcelino MY, Lourencetti NMS, Neto ÁB, Gattas EA, Mendes-Giannini MJS, Fusco-Almeida AM. Methodologies and Applications of Proteomics for Study of Yeast Strains: An Update. Curr Protein Pept Sci 2019; 20:893-906. [PMID: 31322071 DOI: 10.2174/1389203720666190715145131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022]
Abstract
Yeasts are one of the mostly used microorganisms as models in several studies. A wide range of applications in different processes can be attributed to their intrinsic characteristics. They are eukaryotes and therefore valuable expression hosts that require elaborate post-translational modifications. Their arsenal of proteins has become a valuable biochemical tool for the catalysis of several reactions of great value to the food (beverages), pharmaceutical and energy industries. Currently, the main challenge in systemic yeast biology is the understanding of the expression, function and regulation of the protein pool encoded by such microorganisms. In this review, we will provide an overview of the proteomic methodologies used in the analysis of yeasts. This research focuses on the advantages and improvements in their most recent applications with an understanding of the functionality of the proteins of these microorganisms, as well as an update of the advances of methodologies employed in mass spectrometry.
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Affiliation(s)
- Maria Priscila F Lacerda
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Mônica Yonashiro Marcelino
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Natália M S Lourencetti
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Álvaro Baptista Neto
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | - Edwil A Gattas
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | | | - Ana Marisa Fusco-Almeida
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
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Yu SY, Zhang L, Chen S, Kong F, Xiao M, Wang H, Hou X, Zhou ML, Zhang G, Zhang JJ, Duan SM, Kang W, Xu YC. Candida isolates causing refractory or recurrent oropharyngeal candidiasis in 11 hospitals in China. Infect Drug Resist 2019; 12:865-875. [PMID: 31114266 PMCID: PMC6489570 DOI: 10.2147/idr.s199359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 03/19/2019] [Indexed: 12/24/2022] Open
Abstract
Introduction: We studied the species distribution and antifungal susceptibilities of Candida isolates causing refractory or recurrent oropharyngeal candidiasis (OPC) in a multicenter study in China (2013–2016). Methods: Species identification was performed using the Bruker Biotyper (Bruker Daltonics, Germany) matrix-assisted laser desorption/ionization time of flight mass spectrometry system supplemented by internal transcribed spacer sequencing as required. Antifungal susceptibilities were determined by the Clinical and Laboratory Standards Institute document (CLSI) M27-A3 broth microdilution methodology. Results: A total of 558 non-duplicate Candida isolates comprising 10 species were obtained from 535 patients. Candida albicans was the most common species (89.6%), followed by C. glabrata (5.2%), C. tropicalis (2.9%), and C. parapsilosis (0.7%). Azoles were active against C. albicans with susceptibility rates of 96% and 95.8% for fluconazole and voriconazole, respectively. MIC50 values of C. albicans to fluconazole, voriconazole, itraconazole, and miconazole were 1, 0.03, 0.25 and 0.12 μg/mL, respectively, higher than those in previous studies of which OPC patients (corresponding MIC50 values of 0.25 , 0.015 , 0.06 , and 0.03 μg/mL). Except for itraconazole, the MIC50 and MIC90 values of 58 non-C. albicans to other azoles were two to threefold higher than C. albicans. Miconazole, amphotericin B, nystatin, and 5-flucytosine had good in vitro antifungal activity for all isolates. Conclusion: The study provides valuable data on the species distribution and antifungal susceptibility of oropharyngeal Candida isolates from geographically diverse areas of China. C. albicans remains the most common species but with increasing rates of azoles resistance.
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Affiliation(s)
- Shu-Ying Yu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People's Republic of China
| | - Li Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People's Republic of China
| | - Sharon Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR -New South Wales Health Pathology, The University of Sydney, Westmead, New South Wales, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR -New South Wales Health Pathology, The University of Sydney, Westmead, New South Wales, Australia
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People's Republic of China
| | - He Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People's Republic of China
| | - Xin Hou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People's Republic of China
| | - Meng-Lan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People's Republic of China
| | - Ge Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People's Republic of China
| | - Jing-Jia Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People's Republic of China
| | - Si-Meng Duan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People's Republic of China
| | - Wei Kang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People's Republic of China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People's Republic of China
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Zhao Y, Tsang CC, Xiao M, Chan JFW, Lau SKP, Kong F, Xu Y, Woo PCY. Yeast identification by sequencing, biochemical kits, MALDI-TOF MS and rep-PCR DNA fingerprinting. Med Mycol 2018; 56:816-827. [PMID: 29228397 DOI: 10.1093/mmy/myx118] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 10/12/2017] [Indexed: 01/14/2023] Open
Abstract
No study has comprehensively evaluated the performance of 28S nrDNA and ITS sequencing, commercial biochemical test kits, MALDI-TOF MS platforms, and the emerging rep-PCR DNA fingerprinting technology using a cohort of yeast strains collected from a clinical microbiology laboratory. In this study, using 71 clinically important yeast isolates (excluding Candida albicans) collected from a single centre, we determined the concordance of 28S nrDNA and ITS sequencing and evaluated the performance of two commercial test kits, two MALDI-TOF MS platforms, and rep-PCR DNA fingerprinting. 28S nrDNA and ITS sequencing showed complete agreement on the identities of the 71 isolates. Using sequencing results as the standard, 78.9% and 71.8% isolates were correctly identified using the API 20C AUX and Vitek 2 YST ID Card systems, respectively; and 90.1% and 80.3% isolates were correctly identified using the Bruker and Vitek MALDI-TOF MS platforms, respectively. Of the 18 strains belonging to the Candida parapsilosis species complex tested by DiversiLab automated rep-PCR DNA fingerprinting, all were identified only as Candida parapsilosis with similarities ≥93.2%, indicating the misidentification of Candida metapsilosis and Candida orthopsilosis. However, hierarchical cluster analysis of the rep-PCR DNA fingerprints of these three species within this species complex formed three different discrete clusters, indicating that this technology can potentially differentiate the three species. To achieve higher accuracies of identification, the databases of commercial biochemical test kits, MALDI-TOF MS platforms, and DiversiLab automated rep-PCR DNA fingerprinting needs further enrichment, particularly for uncommonly encountered yeast species.
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Affiliation(s)
- Ying Zhao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Chi-Ching Tsang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jasper F W Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
| | - Susanna K P Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.,Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research - Pathology West, Westmead Hospital, Westmead, New South Wales, Australia
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Patrick C Y Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.,Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
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7
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Hu Z, Zhang J, Chen Z, Jin Z, Leng P, Zhou J, Xie X. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric identification and antifungal susceptibility analysis of Candida species isolated from patients with invasive yeast infections in five university hospitals. Braz J Microbiol 2018; 50:99-105. [PMID: 30637643 DOI: 10.1007/s42770-018-0027-0] [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: 07/25/2018] [Accepted: 10/15/2018] [Indexed: 11/29/2022] Open
Abstract
In this multicenter study, we compared the performance of the Bruker Biotyper MS system and VITEK 2 YST systems for invasive yeast identification, investigated the distribution of isolated species, and evaluated the antifungal susceptibility profiles of Candida albicans, Candida parapsilosis, and Candida tropicalis. In cases of discrepant results lack of identification with either method, molecular identification techniques were employed. We tested 216 clinical isolates, and concordance between the two methods was observed for 192/216 isolates (88.9%). For five unidentified strains (2.3%), an internal transcribed spacer (ITS) sequencing approach was used. In brief, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) provided short turnaround times and more reliable results than those of Vitek 2 YST. In Wuhan, C. albicans, C. parapsilosis, Candida glabrata, and C. tropicalis were the most common pathogens (93.0%) in patients with candidemia. Cryptococcus neoformans was mainly detected in cerebrospinal fluid samples (88.9%). Trichosporon asahii were all isolated from drainage fluids in the Surgery. Candida albicans was clearly susceptible to azoles, while C. parapsilosis and C. tropicalis displayed differences in susceptibility to azoles. Our findings provide a basis for the practical application of MALDI-ToF MS for identification and for the use of ATB FUNGUS 3 to characterize the susceptibility of Candida spp., thereby providing significant data for therapeutic decisions.
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Affiliation(s)
- Zhimin Hu
- Department of Clinical Microbiology Laboratory, Wuhan No. 1 Hospital of Tongji Medical College, Huazhong University of Science and Technology, No. 215 Zhongshan Ave., Wuhan, 430022, China.
| | - Juling Zhang
- Department of Clinical Laboratory, PLA 302 Hospital, No. 100 West Fourth Ring Road, Peking, 100166, China
| | - Zhongju Chen
- Department of Clinical Microbiology Laboratory, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Liberation Ave., Wuhan, 430030, China
| | - Zhengjiang Jin
- Department of Clinical Microbiology Laboratory, Hubei Women and Children's Hospital, No. 745 Wuluo Road, Wuhan, 430070, China
| | - Pei Leng
- Department of Clinical Laboratory, Wuhan Women and Children Medical Care Center, No. 100 Xianggang Road, Wuhan, 430015, China
| | - Junying Zhou
- Department of Clinical Microbiology Laboratory, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuhan, 430071, China
| | - Xiaofang Xie
- Department of Clinical Microbiology Laboratory, The First Affiliated Hospital of Soochow University, No. 188 Shizi Street, Soochow, 215006, China
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8
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Ko JH, Jung DS, Lee JY, Kim HA, Ryu SY, Jung SI, Joo EJ, Cheon S, Kim YS, Kim SW, Cho SY, Kang CI, Chung DR, Lee NY, Peck KR. Changing epidemiology of non-albicans candidemia in Korea. J Infect Chemother 2018; 25:388-391. [PMID: 30482698 DOI: 10.1016/j.jiac.2018.09.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/28/2018] [Accepted: 09/30/2018] [Indexed: 10/28/2022]
Abstract
An epidemiologic surveillance of non-albicans candidemia for a 6-year period was conducted in Korea. Compared to the published epidemiologic data for the previous 6 years, an increase of C. glabrata (from 21.3% to 28.5%) and a decrease of C. parapsilosis (from 36.5% to 24.7%) were noticed. During the study period, C. tropicalis (36.4%) was most frequently isolated non-albicans Candida, followed by C. glabrata (28.5%), C. parapsilosis (24.7%), and C. krusei (2.6%). Replacement of primary amphotericin B treatment with echinocandins (P < 0.001) eliminated amphotericin B resistance (from 7.8% in 2011 to 0% in 2014).
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Affiliation(s)
- Jae-Hoon Ko
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dong Sik Jung
- Division of Infectious Diseases, Dong-A University College of Medicine, Busan, Republic of Korea
| | - Ji Yeon Lee
- Division of Infectious Diseases, Keimyung University Dongsan Medical Center, Daegu, Republic of Korea
| | - Hyun Ah Kim
- Division of Infectious Diseases, Keimyung University Dongsan Medical Center, Daegu, Republic of Korea
| | - Seong Yeol Ryu
- Division of Infectious Diseases, Keimyung University Dongsan Medical Center, Daegu, Republic of Korea
| | - Sook-In Jung
- Division of Infectious Diseases, Chonnam National University Hospital, Gwangju, Republic of Korea
| | - Eun-Jeong Joo
- Division of Infectious Diseases, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Shinhye Cheon
- Division of Infectious Diseases, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Yeon-Sook Kim
- Division of Infectious Diseases, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Shin-Woo Kim
- Division of Infectious Diseases, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Sun Young Cho
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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9
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Stefaniuk EM. The Usefulness of Chromogenic Media for Qualitative and Semi-Quantitative Diagnostic of Urinary Tract Infections. Pol J Microbiol 2018; 67:213-218. [PMID: 30015459 PMCID: PMC7256849 DOI: 10.21307/pjm-2018-031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2018] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to evaluate the usefulness of chromogenic media for isolation of bacteria from urine and direct identification of UTI pathogens. A total of 100 urine specimens were inoculated on blood agar and MacConkey agar as a reference method and on the following media to be tested: chromID® CPS® Elite (CPSE, bioMérieux), CHROMagar™ Orientation (BioMaxima), BD CHROMagar Orientation Medium (ORI, Becton Dickinson), CHROMagar™ Orientation (ORIE, Graso) and Brillance UTI Clarity Agar (UTI C, Oxoid). After a 24-hour incubation period, 47 Gram-positive cocci and 62 Gram-negative rods were observed. The specificity and sensitivity of all chromogenic media was 97.3% and 93.5% respectively for qualitative diagnostic; and 81.9% and 81.3% respectively for semi-quantitative diagnostic. The mean PPV and NPV of the chromogenic media were 98.7% and 87.7% for qualitative UTI diagnostic, and 90.9% and 71.9% respectively for semi-quantitative diagnostic.
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Affiliation(s)
- Elżbieta M Stefaniuk
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute,Warsaw,Poland
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10
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Berrio I, Maldonado N, De Bedout C, Arango K, Cano LE, Valencia Y, Jiménez-Ortigosa C, Perlin DS, Gómez BL, Robledo C, Robledo J. Comparative study of Candida spp. isolates: Identification and echinocandin susceptibility in isolates obtained from blood cultures in 15 hospitals in Medellín, Colombia. J Glob Antimicrob Resist 2017; 13:254-260. [PMID: 29183771 DOI: 10.1016/j.jgar.2017.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 10/04/2017] [Accepted: 11/20/2017] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES Invasive candidiasis has a high impact on morbidity and mortality in hospitalised patients. Accurate and timely methods for identification of Candida spp. and determination of echinocandin susceptibility have become a priority for clinical microbiology laboratories. METHODS This study was performed to compare matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS) identification with sequencing of the D1/D2 region of the rRNA gene complex 28 subunit in 147 Candida spp. isolates obtained from patients with candidaemia. Antimicrobial susceptibility testing was performed by broth microdilution (BMD) and Etest. Sequencing of the FKS1 and FKS2 genes was performed. RESULTS The most common species isolated were Candida albicans (40.8%), followed by Candida parapsilosis (23.1%) and Candida tropicalis (17.0%). Overall agreement between the results of identification by MALDI-TOF/MS and molecular identification was 99.3%. Anidulafungin and caspofungin susceptibility by the BMD method was 98.0% and 88.4%, respectively. Susceptibility to anidulafungin and caspofungin by Etest was 93.9% and 98.6%, respectively. Categorical agreement between Etest and BMD was 91.8% for anidulafungin and 89.8% for caspofungin, with lower agreements in C. parapsilosis for anidulafungin (76.5%) and C. glabrata for caspofungin (40.0%). No mutations related to resistance were found in the FKS genes, although 54 isolates presented synonymous polymorphisms in the hotspots sequenced. CONCLUSIONS MALDI-TOF/MS is a good alternative for routine identification of Candida spp. isolates. DNA sequencing of the FKS genes suggested that the isolates analysed were susceptible to echinocandins; alternatively, unknown resistance mechanisms or limitations related to antifungal susceptibility tests may explain the resistance found in a few isolates.
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Affiliation(s)
- Indira Berrio
- Clínica El Rosario, Carrera 41 #62-5, Medellín, Colombia; Corporación para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia; Hospital general de Medellín "Luz Castro de Gutierrez" ESE, Carrera 48 # 32-102, Medellín, Colombia
| | - Natalia Maldonado
- Laboratorio Médico de Referencia, Calle 63 No. 41-27, Medellín, Colombia.
| | - Catalina De Bedout
- Corporación para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia
| | - Karen Arango
- Corporación para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia
| | - Luz Elena Cano
- Corporación para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia; Microbiology School, Universidad de Antioquia (UdeA), Cl. 67 #53-108, Medellín, Colombia
| | - Yorlady Valencia
- Corporación para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia
| | - Cristina Jiménez-Ortigosa
- Public Health Research Institute, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, USA
| | - David S Perlin
- Public Health Research Institute, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, USA
| | - Beatriz L Gómez
- Corporación para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia; School of Medicine and Health Sciences, Universidad Rosario, Calle 12C No. 6-25, Bogotá, Colombia
| | - Carlos Robledo
- Laboratorio Médico de Referencia, Calle 63 No. 41-27, Medellín, Colombia
| | - Jaime Robledo
- Corporación para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia; Laboratorio Médico de Referencia, Calle 63 No. 41-27, Medellín, Colombia; School of Health Sciences, Universidad Pontificia Bolivariana (UPB), Calle 78b No. 72a-109, Medellín, Colombia
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11
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A Comprehensive Analysis of MALDI-TOF MS and Ribosomal DNA Sequencing for Identification of Clinical Yeasts. CURRENT FUNGAL INFECTION REPORTS 2017. [DOI: 10.1007/s12281-017-0297-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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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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13
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Hirota K, Yumoto H, Sapaar B, Matsuo T, Ichikawa T, Miyake Y. Pathogenic factors in Candida biofilm-related infectious diseases. J Appl Microbiol 2016; 122:321-330. [PMID: 27770500 DOI: 10.1111/jam.13330] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/11/2016] [Accepted: 10/15/2016] [Indexed: 01/07/2023]
Abstract
Candida albicans is a commonly found member of the human microflora and is a major human opportunistic fungal pathogen. A perturbation of the microbiome can lead to infectious diseases caused by various micro-organisms, including C. albicans. Moreover, the interactions between C. albicans and bacteria are considered to play critical roles in human health. The major biological feature of C. albicans, which impacts human health, resides in its ability to form biofilms. In particular, the extracellular matrix (ECM) of Candida biofilm plays a multifaceted role and therefore may be considered as a highly attractive target to combat biofilm-related infectious diseases. In addition, extracellular DNA (eDNA) also plays a crucial role in Candida biofilm formation and its structural integrity and induces the morphological transition from yeast to the hyphal growth form during C. albicans biofilm development. This review focuses on pathogenic factors such as eDNA in Candida biofilm formation and its ECM production and provides meaningful information for future studies to develop a novel strategy to battle infectious diseases elicited by Candida-formed biofilm.
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Affiliation(s)
- K Hirota
- Department of Oral Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - H Yumoto
- Department of Conservative Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - B Sapaar
- Department of Oral and Maxillofacial Prosthodontics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - T Matsuo
- Department of Conservative Dentistry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - T Ichikawa
- Department of Oral and Maxillofacial Prosthodontics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Y Miyake
- Department of Oral Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
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