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Koc Ö, Kessler HH, Hoenigl M, Wagener J, Suerbaum S, Schubert S, Dichtl K. Performance of Multiplex PCR and β-1,3-D-Glucan Testing for the Diagnosis of Candidemia. J Fungi (Basel) 2022; 8:jof8090972. [PMID: 36135696 PMCID: PMC9504845 DOI: 10.3390/jof8090972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022] Open
Abstract
Bloodstream infections caused by Candida yeasts (candidemia) are associated with high morbidity and mortality. Diagnosis remains challenging, with the current gold standard—isolation from blood culture (BC)—being limited by low sensitivity and long turnaround time. This study evaluated the performance of two nonculture methods: PCR and β-1,3-D-glucan (BDG) testing. The sera of 103 patients with BC-proven candidemia and of 46 controls were analyzed with the Fungiplex Candida Real-Time PCR and the Wako β-Glucan Test. The BDG assay demonstrated higher sensitivity than the multiplex PCR (58% vs. 33%). This was particularly evident in ICU patients (60% vs. 28%) and in C. albicans candidemia (57% vs. 37%). The earlier prior to BC sampling the sera were obtained, the more the PCR sensitivity decreased (46% to 18% in the periods of 0−2 and 3−5 days before BC, respectively), while BDG testing was independent of the sampling date. No positive PCR results were obtained in sera sampled more than five days before BC. Specificities were 89% for BDG and 93% for PCR testing. In conclusion, BDG testing demonstrated several advantages over PCR testing for the diagnosis of candidemia, including higher sensitivity and earlier diagnosis. However, BC remains essential, as BDG does not allow for species differentiation.
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Affiliation(s)
- Özlem Koc
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
| | - Harald H. Kessler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Johannes Wagener
- Microbiology Department, St. James’s Hospital, D08 RX0X Dublin, Ireland
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, The University of Dublin, St. James’s Hospital Campus, D08 RX0X Dublin, Ireland
| | - Sebastian Suerbaum
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
| | - Sören Schubert
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
- Correspondence: (S.S.); (K.D.)
| | - Karl Dichtl
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, 80336 Munich, Germany
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
- Correspondence: (S.S.); (K.D.)
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Taher OMEA, Othman HBEA, Gedawy SABG, Elarab HE, Elkhatib WF, El-Razzaz MK. Evaluation of Pan-fungal PCR in Early Detection of Invasive Fungal Infection in Egyptian Patients with Hematological Malignancies. Jpn J Infect Dis 2022; 75:543-548. [PMID: 35768275 DOI: 10.7883/yoken.jjid.2022.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Incidence of invasive fungal infections (IFI) has increased due to the rising influx of patients suffering from immunodeficiency. A case-control analysis was performed at Ain Shams University Hospitals, Cairo, Egypt. The cases group (n = 80) included eighty patients diagnosed with hematological malignancies and the control group (n = 20) included twenty patients. All patients were tested for the detection of fungal species using blood culture, pan-fungal Real Time PCR. Fungal species differentiation was made by High Resolution Melting (HRM) PCR. The clinical cases suspected to have IFD were 39 cases out of the 80 patients. Pan-fungal PCR detection rate was 41/80 (51.3 %). HRM-PCR identified the fungal species to be 51.2% Candida albicans, 44% Non-Candida albicans, and 4.9% Mucor. Blood culture was positive in 2 patients with acute myeloid leukaemia (AML). There was a highly significant rate of fungal detection using pan-fungal Real Time PCR technique compared to blood culture technique (p <0.001). Real Time PCR using pan-fungal marker is a sensitive, rapid, and superior to blood culture in detection of IFI and HRM-PCR is a specific test for species identification.
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Affiliation(s)
| | | | | | - Hoda Ezz Elarab
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Egypt
| | - Walid Faisal Elkhatib
- Microbiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, Egypt.,Department of Microbiology & Immunology, Faculty of Pharmacy, Galala University, Egypt
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Keighley C, Cooley L, Morris AJ, Ritchie D, Clark JE, Boan P, Worth LJ. Consensus guidelines for the diagnosis and management of invasive candidiasis in haematology, oncology and intensive care settings, 2021. Intern Med J 2021; 51 Suppl 7:89-117. [DOI: 10.1111/imj.15589] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Caitlin Keighley
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Camperdown New South Wales Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology Westmead New South Wales Australia
- Southern IML Pathology, Sonic Healthcare Coniston New South Wales Australia
| | - Louise Cooley
- Department of Microbiology and Infectious Diseases Royal Hobart Hospital Hobart Tasmania Australia
- University of Tasmania Hobart Tasmania Australia
| | - Arthur J. Morris
- LabPLUS, Clinical Microbiology Laboratory Auckland City Hospital Auckland New Zealand
| | - David Ritchie
- Department of Clinical Haematology Peter MacCallum Cancer Centre and Royal Melbourne Hospital Melbourne Victoria Australia
| | - Julia E. Clark
- Department of Infection Management Queensland Children's Hospital, Children's Health Queensland Brisbane Queensland Australia
- Child Health Research Centre The University of Queensland Brisbane Queensland Australia
| | - Peter Boan
- PathWest Laboratory Medicine WA, Department of Microbiology Fiona Stanley Fremantle Hospitals Group Murdoch Western Australia Australia
- Department of Infectious Diseases Fiona Stanley Fremantle Hospitals Group Murdoch Western Australia Australia
| | - Leon J. Worth
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre Melbourne Victoria Australia
- Department of Infectious Diseases Peter MacCallum Cancer Centre Melbourne Victoria Australia
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Scharf S, Bartels A, Kondakci M, Haas R, Pfeffer K, Henrich B. fuPCR as diagnostic method for the detection of rare fungal pathogens, such as Trichosporon, Cryptococcus and Fusarium. Med Mycol 2021; 59:1101-1113. [PMID: 34379780 DOI: 10.1093/mmy/myab045] [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: 03/02/2021] [Revised: 07/21/2021] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Fungal respiratory tract colonisation is a common finding in patients with hematologic neoplasms due to immunosuppression inherent in the diseases and exacerbated by therapy. This greatly increases the risk of fungal infections of the lungs, which is associated with significant mortality. Therefore, reliable diagnostic methods with rapidly available results are needed to administer adequate antifungal therapy.We have established an improved method for fungal DNA extraction and amplification that allows simultaneous detection of fungal families based on a set of multiplexed real time PCR reactions (fuPCR). We analysed respiratory rinses and blood of 94 patients with haematological systemic diseases by fuPCR and compared it with the results of culture and serological diagnostic methods. 40 healthy subjects served as controls.Regarding Candida species, the highest prevalence resulted from microbiological culture of respiratory rinses and from detection of antibodies in blood serum in patients (61% and 47%, respectively) and in the control group (29% and 51%, respectively). Detection of other pathogenic yeasts, such as Cryptococcus and Trichosporon, and moulds, such as Fusarium, was only possible in patients by fuPCR from both respiratory rinses and whole blood and serum. These fungal species were found statistically significantly more frequent in respiratory rinses collected from patients after myeloablative therapy for stem cell transplantation compared to samples collected before treatment (p<<0.05i>).The results show that fuPCR is a valuable complement to culturing and its inclusion in routine mycological diagnostics might be helpful for early detection of pathophysiologically relevant respiratory colonisation for patients with hematologic neoplasms. LAY ABSTRACT We validated a set of PCR reactions (fuPCR) for use in routine diagnostic. In contrast to culture and serological methods, only by fuPCR pathogenic yeasts (Cryptococcus and Trichosporon) and moulds (Aspergillus and Fusarium) were detected in respiratory rinses and blood of haematological patients.
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Affiliation(s)
- Sebastian Scharf
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich-Heine University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Anna Bartels
- Department of Haematology, Oncology and Clinical Immunology, Heinrich-Heine University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Mustafa Kondakci
- Department of Haematology, Oncology and Clinical Immunology, Heinrich-Heine University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Rainer Haas
- Department of Haematology, Oncology and Clinical Immunology, Heinrich-Heine University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich-Heine University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich-Heine University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
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He X, Ma Y, Xie H, Rao G, Yang Z, Zhang J, Feng Z. Biomimetic Nanostructure Platform for Cancer Diagnosis Based on Tumor Biomarkers. Front Bioeng Biotechnol 2021; 9:687664. [PMID: 34336803 PMCID: PMC8320534 DOI: 10.3389/fbioe.2021.687664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
Biomarker discovery and its clinical use have attracted considerable attention since early cancer diagnosis can significantly decrease mortality. Cancer biomarkers include a wide range of biomolecules, such as nucleic acids, proteins, metabolites, sugars, and cytogenetic substances present in human biofluids. Except for free-circulating biomarkers, tumor-extracellular vesicles (tEVs) and circulating tumor cells (CTCs) can serve as biomarkers for the diagnosis and prognosis of various cancers. Considering the potential of tumor biomarkers in clinical settings, several bioinspired detection systems based on nanotechnologies are in the spotlight for detection. However, tremendous challenges remain in detection because of massive contamination, unstable signal-to-noise ratios due to heterogeneity, nonspecific bindings, or a lack of efficient amplification. To date, many approaches are under development to improve the sensitivity and specificity of tumor biomarker isolation and detection. Particularly, the exploration of natural materials in biological frames has encouraged researchers to develop new bioinspired and biomimetic nanostructures, which can mimic the natural processes to facilitate biomarker capture and detection in clinical settings. These platforms have substantial influence in biomedical applications, owing to their capture ability, significant contrast increase, high sensitivity, and specificity. In this review, we first describe the potential of tumor biomarkers in a liquid biopsy and then provide an overview of the progress of biomimetic nanostructure platforms to isolate and detect tumor biomarkers, including in vitro and in vivo studies. Capture efficiency, scale, amplification, sensitivity, and specificity are the criteria that will be further discussed for evaluating the capability of platforms. Bioinspired and biomimetic systems appear to have a bright future to settle obstacles encountered in tumor biomarker detection, thus enhancing effective cancer diagnosis.
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Affiliation(s)
- Xiping He
- Department of Rehabilitation Medicine, The Affiliated Wenling Hospital of Wenzhou Medical University, Wenling, China
| | - Yifan Ma
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, United States
| | - Haotian Xie
- Department of Mathematics, The Ohio State University, Columbus, OH, United States
| | - Gaofeng Rao
- Department of Rehabilitation Medicine, The Affiliated Wenling Hospital of Wenzhou Medical University, Wenling, China
| | - Zhaogang Yang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jingjing Zhang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, United States
| | - Zhong Feng
- Department of Neurology, The Affiliated Wenling Hospital of Wenzhou Medical University, Wenling, China
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Menu E, Landier J, Prudent E, Ranque S, L’Ollivier C. Evaluation of 11 DNA Automated Extraction Protocols for the Detection of the 5 Mains Candida Species from Artificially Spiked Blood. J Fungi (Basel) 2021; 7:jof7030228. [PMID: 33808911 PMCID: PMC8003619 DOI: 10.3390/jof7030228] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 01/08/2023] Open
Abstract
The molecular detection of Candida plays an important role in the diagnosis of candidaemia, a major cause of morbidity and mortality. The sensitivity of this diagnosis is partly related to the efficiency of yeast DNA extraction. In this monocentric study, we investigated the suitability of 11 recent automated procedures for the extraction of low and high amounts of Candida DNA from spiked blood. The efficacy of the DNA extraction procedures to detect Candida spp. in blood samples ranged from 31.4% to 80.6%. The NucliSENSTM easyMAGTM procedure was the most efficient, for each species and each inoculum. It significantly outperformed the other procedures at the lower Candida inocula mimicking the clinical setting. This study highlighted a heterogeneity in DNA extraction efficacy between the five main Candida species (Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis and Candida krusei). Up to five automated procedures were appropriate for C. krusei DNA extraction, whereas only one method yielded an appropriate detection of low amount of C. tropicalis. In the era of the syndromic approach to bloodstream infection diagnosis, this evaluation of 11 automated DNA extraction methods for the PCR diagnosis of candidaemia, puts the choice of an appropriate method in routine diagnosis within the reach of laboratories.
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Affiliation(s)
- Estelle Menu
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs—Infections Tropicales et Méditerranéennes, 13385 Marseille, France; (S.R.); (C.L.)
- IHU Méditerranée Infection, 13385 Marseille, France;
- Correspondence:
| | - Jordi Landier
- Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, Institut de Recherche pour le Développement, Institut National de Santé et de Recherche Médicale, Aix Marseille Université, 13385 Marseille, France;
| | - Elsa Prudent
- IHU Méditerranée Infection, 13385 Marseille, France;
| | - Stéphane Ranque
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs—Infections Tropicales et Méditerranéennes, 13385 Marseille, France; (S.R.); (C.L.)
- IHU Méditerranée Infection, 13385 Marseille, France;
| | - Coralie L’Ollivier
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs—Infections Tropicales et Méditerranéennes, 13385 Marseille, France; (S.R.); (C.L.)
- IHU Méditerranée Infection, 13385 Marseille, France;
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7
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Zhang S, Zhao Q, Xue W, Li Y, Guo Y, Wu X, Huo S, Li Y, Li C. The isolation and identification of Candida glabrata from avian species and a study of the antibacterial activities of Chinese herbal medicine in vitro. Poult Sci 2021; 100:101003. [PMID: 33676095 PMCID: PMC8046950 DOI: 10.1016/j.psj.2021.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 11/13/2022] Open
Abstract
Previously, a fungus was isolated from a diseased pigeon group clinically suspected of being infected with Candida. The fungus was subsequently identified as Candida glabrata using morphology, physiology, biochemistry, and molecular biology testing methods. In the present study, to determine the controlling effects of Chinese herbal medicine for C. glabrata, the bacteriostatic effects of the ethanol extracts Acorus gramineus, Sophora flavescens, Polygonum hydropiper, Cassia obtusifolia, Pulsatilla chinensis, Dandelion, and Cortex phellodendri on C. glabrata in vitro were analyzed. The results showed that the minimum inhibitory concentrations (MIC80) of Cortex phellodendri was 0.25 μg/μL. Meanwhile, that of S. flavescens was 32 μg/μL; C. obtusifolia was 56 μg/μL; A. gramineus and Polygonum hydropiper was 64 μg/μL; and P. chinensis was 112 μg/μL. However, MIC80 for Dandelion was undetectable. In addition, improved drug sensitivity tests revealed that colonies had grown after 24 h in the blank group, as well as the Polygonum hydropiper, P. chinensis, Dandelion, and ethanol groups. The colonies first appeared at the 48-hour point in the other drug-sensitive medium of Chinese herbal medicine. However, no colony growth was found in Cortex phellodendri medium, and the formation of the maximum colony diameter in that group was later than the blank group (e.g., 96 h in the blank group and 120 h in the Chinese herbal medicine group). It was observed that only 17 colony-forming units had grown in 125 μg/μL of the S. flavescens medium, which was significantly different from other groups. Also, the final colony diameter was significantly smaller than that of the other experimental groups. Therefore, it was determined that the A. gramineus, S. flavescens, Polygonum hydropiper, Cassia obtusifolia, P. chinensis, and Cortex phellodendri had certain inhibitory effects on the growth of the C. glabrata. Among those, it was observed that the Cortex phellodendri had the strongest inhibitory effects, followed by the S. flavescens. In the future, these Chinese herbal medicines are expected to be used to treat the fungal infections related to C. glabrata in poultry to improve production performance.
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Affiliation(s)
- Shuang Zhang
- The College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China
| | - Qianhui Zhao
- The College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China
| | - Wenhui Xue
- The College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China
| | - Yurong Li
- The College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China
| | - Yu Guo
- The College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China
| | - Xianjun Wu
- The College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China
| | - Shuying Huo
- The College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China.
| | - Yong Li
- The Dingnong Corporation of Hebei, Dingzhou County, Hebei 073000, China
| | - Chenyao Li
- The Dingnong Corporation of Hebei, Dingzhou County, Hebei 073000, China
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He ZX, Zhao HH, Wang FK. PCR-detectable Candida DNA exists a short period in the blood of systemic candidiasis murine model. Open Life Sci 2020; 15:677-682. [PMID: 33817256 PMCID: PMC7747513 DOI: 10.1515/biol-2020-0075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/21/2020] [Accepted: 07/11/2020] [Indexed: 12/15/2022] Open
Abstract
Invasive candidiasis is a major challenge to clinical medicine today. However, traditional fungal diagnostic techniques and empirical treatments have shown great limitations. Although efforts are necessarily needed in methodology standardization and multicenter validation, polymerase chain reaction (PCR) is a very promising assay in detecting fungal pathogens. Using a "heat-shock" DNA preparation method, a rapid and simple PCR protocol for quantification of the Candida albicans (C. albicans) ribosomal DNA was established. The PCR assay could detect Candida DNA as low as 10 CFU/mL in samples prepared by the heat-shock protocol, without any cross-reaction with DNA prepared from other Candida spp. and bacterial pathogens. For simulated blood samples, the PCR test sensitivity of whole blood samples was better than that of plasma and blood cells. In the systemic candidiasis murine model, detectable DNA was only observed within 24 h after C. albicans SC5314 injection, which is much shorter than that observed in the kidney.
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Affiliation(s)
- Zheng-Xin He
- Department of Clinical Laboratory, The 980th Hospital of PLA Joint Logistical Support Force (Bethune International Peace Hospital), 398 Zhongshan Road, Shijiazhuang, Hebei, 050082, People's Republic of China
| | - Hui-Hai Zhao
- Department of Clinical Laboratory, The 980th Hospital of PLA Joint Logistical Support Force (Bethune International Peace Hospital), 398 Zhongshan Road, Shijiazhuang, Hebei, 050082, People's Republic of China
| | - Fu-Kun Wang
- Department of Clinical Laboratory, The 980th Hospital of PLA Joint Logistical Support Force (Bethune International Peace Hospital), 398 Zhongshan Road, Shijiazhuang, Hebei, 050082, People's Republic of China
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Scharf S, Bartels A, Kondakci M, Pfeffer K, Henrich B, Haas R. Introduction of a bead beating step improves fungal DNA extraction from selected patient specimens. Int J Med Microbiol 2020; 310:151443. [PMID: 32862838 DOI: 10.1016/j.ijmm.2020.151443] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/25/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022] Open
Abstract
In immunocompromised patients a colonisation with fungi carries the risk to develop serious invasive fungal infection. An early detection is therefore important, but not optimal hitherto. Fortunately, molecular genetic methods have increased the sensitivity of fungal detection and limited the time, until results are available. However, their success depends on an efficient extraction of genomic DNA from the fungal cell in the given diagnostic specimen. To improve the routine DNA preparation method for yeasts and moulds, the impact of bead beating on fungal DNA release was evaluated. PBS, blood and respiratory rinse were spiked with Candida glabrata or Aspergillus fumigatus. DNA was extracted by mechanical bead beating in addition to the different steps of the DNA preparation protocol, which comprised liquid nitrogen treatment, proteinase K digestion and DNA isolation using the EZ1 DNA Tissue Kit and Workstation. In every method variant tested, treatment with liquid nitrogen did not improve the DNA release. Bead beating once followed by proteinase K digestion and EZ1-work-up led to the highest DNA release from fungus, spiked in PBS, and increased the extracted DNA amount of C. glabrata about 100-fold and of A. fumigatus about 10-fold in relation to sole EZ1-work-up. In fungus-spiked respiratory rinse and blood, highest increase in DNA release was measured after triple bead beating with simultaneous proteinase K digestion. Fungal DNA release of C. glabrata increased for >100-fold in respiratory rinse and for >1000-fold in blood and of A. fumigatus for >10-fold in respiratory rinse and about 5- to 10-fold in blood. The data of this study clearly demonstrate that preparation of fungal DNA from human specimens is optimized by introduction of a bead beating step to the conventional DNA-preparation method without the necessity of a liquid nitrogen step.
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Affiliation(s)
- Sebastian Scharf
- Institute of Medical Microbiology and Hospital Hygiene, University of Duesseldorf, Germany; Department of Haematology, Oncology and Clinical Immunology, University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Anna Bartels
- Department of Haematology, Oncology and Clinical Immunology, University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Mustafa Kondakci
- Department of Haematology, Oncology and Clinical Immunology, University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, University of Duesseldorf, Germany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, University of Duesseldorf, Germany.
| | - Rainer Haas
- Department of Haematology, Oncology and Clinical Immunology, University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
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10
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Sensitivity and reproducibility improvements in a human plasma immunoassay with removal of clotting factors. Anal Biochem 2019; 585:113410. [PMID: 31473245 DOI: 10.1016/j.ab.2019.113410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/07/2019] [Accepted: 08/28/2019] [Indexed: 11/22/2022]
Abstract
Interferences in human plasma immunoassay are severe challenge that affects the sensitivity and reproducibility of the assay. The clotting factor fibrinogen is a negatively charged protein and is one of the most common sources of interference in immunoassays, and its removal increases the sensitivity and reproducibility. Here, we present a highly sensitive and reproducible method for the detection of prostate specific antigen (PSA) in human plasma immunoassays. Protamine sulfate, a highly positively charged protein, was used to precipitate fibrinogen via ionic interaction to improve the sensitivity and reproducibility of human plasma immunoassay. In a sandwich ELISA for PSA using plasma and protamine-treated plasma samples, the limit of detection was improved from 413 pg/mL in plasma to 235 pg/mL in protamine-treated plasma samples, and the coefficient of variation known as a measure of reproducibility was significantly lowered by protamine treatment. The use of protamine sulfate in human plasma immunoassays for detection of PSA using quartz crystal microbalance (QCM) biosensors resulted in increased sensitivity and reproducibility by about 2-fold and 3-fold, respectively, relative to when not using protamine sulfate. Based on these results, protamine sulfate was the best choice to increase the sensitivity and reproducibility in immunoassays using plasma samples.
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11
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Detection of Coxiella burnetii Using Silicon Microring Resonator in Patient Blood Plasma. MICROMACHINES 2019; 10:mi10070427. [PMID: 31252533 PMCID: PMC6680664 DOI: 10.3390/mi10070427] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 11/16/2022]
Abstract
Blood plasma from patients is a powerful resource for diagnosing infectious disease due to it having many genetic materials as well as being relatively easy to obtain. Thus, various biosensors have been investigated for diagnosing diseases in blood plasma. However, there are no optimized and validated sensors for clinical use due to the low sensitivity, complexity, and difficulties of removing the inhibitors from plasma samples. In this study, we described a silicon microring resonator sensor used to detect Coxiella burnetii from the blood plasma of Q-fever patients in a label-free, real-time manner. Q-fever is an infectious disease caused by Coxiella burnetii via direct contact or inhalation aerosols. We validated this biosensor in the blood plasma of 35 clinical samples (including 16 Q fever samples infected with Coxiella burnetii and 19 samples infected with other febrile diseases. The biosensors are capable of rapid (10 min), highly sensitive (87.5%), and specific (89.5%) detection in plasma samples compared to the use of the conventional method.
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12
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Chandra S, Smith K, Alanazi AD, Alyousif MS, Emery D, Slapeta J. Rhipicephalus sanguineus sensu lato from dogs and dromedary camels in Riyadh, Saudi Arabia: low prevalence of vector-borne pathogens in dogs detected using multiplexed tandem PCR panel. Folia Parasitol (Praha) 2019; 66. [PMID: 31332102 DOI: 10.14411/fp.2019.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 05/09/2019] [Indexed: 11/19/2022]
Abstract
Despite the global distribution of the brown dog tick, Rhipicephalus sanguineus (Latreille, 1806) sensu lato (s.l.), limited information exists about their identity from the Arabian Peninsula. Ticks from free roaming urban dogs and dromedary camels in Riyadh, Saudi Arabia were morphologically identified, confirmed with scanning electron microscopy and characterised at mitochondrial DNA (cox1, 12S rDNA and 16S rDNA). A total of 186 ticks were collected from 65 free roaming dogs (n = 73) and 84 dromedary camels (n = 113). Morphologically, 5.9% (11/186) were R. sanguineus s.l. and Hyalomma spp. (93.5%, 174/186). From within R. sanguineus s.l., the presence of Rhipicephalus cf. camicasi Morel, Mouchet et Rodhain, 1976 (1 dog, 2 camels) and Rhipicephalus turanicus Pomerantsev, 1936 (1 camel) is reported. The examined R. cf. camicasi form a sister group to R. sanguineus s.l. tropical lineage at all DNA markers. Dogs were parasitised by Hyalomma dromedarii Koch, 1844 (n = 59), Hyalomma impeltatum Schulze et Schlottke, 1930 (n = 1), Hyalomma excavatum Koch, 1844 (n = 2), Hyalomma turanicum Pomerantsev, 1946 (n = 1) and Hyalomma rufipes Koch,1844 (n = 1). DNA from dog blood (n = 53) from Riyadh confirmed a low prevalence of canine vector-borne pathogens that does not exceed 5.7% for Babesia spp., Mycoplasma spp., Anaplasma platys, Hepatozoon canis and Ehrlichia canis using multiplexed tandem PCR (MT-PCR) and diagnostic PCR. Low prevalence of R. sanguineus s.l. on dogs likely contributed to the low level of canine vector-borne pathogens in Saudi Arabia. We demonstrate that dogs in the central Arabian Peninsula are more commonly parasitised by Hyalomma spp. than R. sanguineus s.l.
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Affiliation(s)
- Shona Chandra
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Karen Smith
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Abdullah D Alanazi
- Department of Biological Sciences, Faculty of Science and Humanities, Shaqra University, Ad-Dawadimi, Saudi Arabia
| | - Mohamed S Alyousif
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - David Emery
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jan Slapeta
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
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Turgut M, Challa S, Akhaddar A. Histopathology. FUNGAL INFECTIONS OF THE CENTRAL NERVOUS SYSTEM 2019. [PMCID: PMC7123394 DOI: 10.1007/978-3-030-06088-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
During the last 30 years, advances in intensive and critical care units, organ transplantation, concomitant use of immunosuppressive drugs, and increasing prevalence of chronic diseases, malnutrition, and other debilitating conditions, as well as the human immunodeficiency virus pandemic, have increased the incidence of systemic mycotic diseases, the most serious form of fungal diseases are the ones that comprise the central nervous system, representing the most dangerous clinical situations. In those cases, starting an adequate therapy through a rapid and assertive diagnosis is absolutely necessary. Considering the fastidious microbiological nature of some fungi (longtime requirement, specific culture conditions, and biohazard issues), as well as the lack of alternative testing availability, a rapid diagnosis is always challenging. When a tissue or liquid specimen is available, its pathological analysis constitutes a rapid and cost-effective way to provide a presumptive or definitive diagnosis of an invasive fungal infection; however, microbiologists, pathologists, and clinicians need to be aware of the limitations of microscopical diagnosis. In this chapter, we review the usual histological presentation of the most frequent central nervous system fungal infections.
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Affiliation(s)
- Mehmet Turgut
- Department of Neurosurgery, Aydın Adnan Menderes University, School of Medicine, Aydın, Turkey
| | - Sundaram Challa
- Department of Pathology, Basavatarakam Indo-American Hospital & Research Institute, Hyderabad, Telangana India
| | - Ali Akhaddar
- Department of Neurosurgery, Avicenne Military Hospital, Mohammed V University in Rabat, Marrakech, Morocco
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Abstract
Diagnosing fungal infections poses a number of unique problems, including a decline in expertise needed for identifying fungi, and a reduced number of instruments and assays specific for fungal identification compared to that of bacteria and viruses.These problems are exacerbated by the fact that patients with fungal infections are often immunosuppressed, which predisposes to infections from both commonly and rarely seen fungi. In this review, we discuss current and future molecular technologies used for fungal identification, and some of the problems associated with development and implementation of these technologies in today’s clinical microbiology laboratories. Diagnosing fungal infections poses a number of unique problems. In this Review, Wickes and Wiederhold discuss molecular technologies used for fungal identification, and the problems associated with their development and implementation in today’s clinical microbiology laboratories.
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Kashiha A, Setayesh N, Panahi Y, Ahmadi A, Soltany-Rezaee-Rad M, Najafi A, Rouini MR, Namipashaki A, Sahebkar A, Mojtahedzadeh M. Prevalence of candidemia and associated candida subtypes following severe sepsis in non-neutropenic critically ill patients. ACTA BIO-MEDICA : ATENEI PARMENSIS 2018; 89:193-202. [PMID: 29957751 PMCID: PMC6179014 DOI: 10.23750/abm.v89i2.5385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 05/25/2016] [Indexed: 11/23/2022]
Abstract
Background: Invasive candidiasis management through the rapid initiation of appropriate antifungal therapy has been shown to be associated with the better prognosis, improved clinical outcome and reduced mortality in critically ill patients. Therefore, selection of an appropriate antifungal therapy should be based on the distribution of candida species and the pattern of antifungal resistance. This study aimed to assess the prevalence of candidemia and associated subtypes following severe sepsis in non-neutropenic critically ill patients. Methods: This study was a cross-sectional study that was conducted on severe sepsis patients stayed at least seven days in intensive care unit. Patients less than 18 years old, pregnant and breastfeeding patients, immunocompromised patients, neutropenic patients, patients with concurrent use of antifungal medicines and cytotoxic agents were excluded.To asses the candidemia, one mililiter of patients’ blood sample was collected. Sample analysis was performed by Real-Time PCR and high resolution melting curve analysis method. Results: Thirty-one critically ill patients were recruited in this study over 12-month period. Candidemia with a detection limit of 100 pg per 0.2 ml blood sample was not recognized in any of the included patients. Conclusion: The present result indicates low incidence of candidemia in the targeted intensive care units, but other factors such as small sample size, exclusion of patients with compromised immune system and the low fungal load at the time of sampling may also account for our observation. (www.actabiomedica.it)
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Affiliation(s)
- Arefeh Kashiha
- Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Neda Setayesh
- Department of Pharmaceutical Biotechnology and Pharmaceutical Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | | | - Arezoo Ahmadi
- Department of Anesthesiology and Critical Care Medicine, Faculty of Medicine, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohammad Soltany-Rezaee-Rad
- Department of Pharmaceutical Biotechnology and Pharmaceutical Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Atabak Najafi
- Department of Anesthesiology and Critical Care Medicine, Faculty of Medicine, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Rouini
- epartment of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences.
| | - Atefeh Namipashaki
- Department of Medical Biotechology, Faculty of Advanced Technologies in Medicine, Tehran University of Medical Sciences. Tehran, Iran.
| | | | - Mojtaba Mojtahedzadeh
- Clinical Pharmacy Department, Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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Abstract
PURPOSE OF REVIEW Bloodstream infections are a major cause of hospital and ICU admission with high morbidity and mortality; however, early and targeted antimicrobial therapy reduces mortality in high-risk patients. This article focuses on the diagnosis of bloodstream infections by PCR-based approaches at an early stage to enable prompt treatment and prevent organ dysfunction. RECENT FINDINGS PCR systems offering highly multiplexed targeting of bacterial and/or fungal pathogens (in whole blood) offer the best opportunity for clinical impact, as informed decisions can be made within 4-8 h of the blood draw. Although more rapid, these systems are typically associated with lower sensitivity and specificity than postculture detection methods which rely on microbial growth. Additionally, unlike postculture methods, detection directly from blood is not prone to misleading results because of concurrent (or previous) therapy, which limit clinical relevance. SUMMARY Rapid and accurate identification of the cause of sepsis is essential in improving patient outcomes. Early identification of these pathogens by nucleic acid detection assays directly from blood samples remains key to achieving this, particularly if taken at the time of presentation. Selection of the most suitable PCR system is typically influenced by local epidemiology and by the resources of the testing laboratory.
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T2 Magnetic Resonance Assay: Overview of Available Data and Clinical Implications. J Fungi (Basel) 2018; 4:jof4020045. [PMID: 29617284 PMCID: PMC6023470 DOI: 10.3390/jof4020045] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 01/05/2023] Open
Abstract
Invasive candidiasis is a common healthcare-associated infection with a high mortality rate that can exceed 60% in cases of septic shock. Blood culture performance is far from ideal, due to the long time to positivity and suppression by antifungal agents. The T2 Magnetic Resonance (T2MR) assay is an FDA-approved qualitative molecular diagnostic method that can detect and speciate the 5 most common Candida spp.; namely, Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, and Candida krusei, in approximately 5 h. In a multicenter clinical trial that included both a prospective and a contrived arm to represent the full range of clinically relevant concentrations of Candida spp., T2MR demonstrated a sensitivity and specificity of 91.1% and 98.1%, respectively. The utility of T2MR in candidemia depends on the prevalence of disease in each clinical setting. In intensive care units and other high-prevalence settings, the incorporation of T2MR in diagnostic algorithms is very appealing. T2MR is expected to allow timely initiation of antifungal therapy and help with anti-fungal stewardship. In low-prevalence settings, the positive predictive value of T2MR might not be enough to justify initiation of antifungal treatment in itself. The performance of T2MR has not been studied in cases of deep-seated candidiasis. Despite some promising evidence in published clinical trials, further studies are needed to determine the performance of T2MR in invasive candidiasis without candidemia. Overall, experience with T2MR in everyday clinical practice is evolving but, in the right setting, this technology is expected to provide “actionable information” for the management of patients evaluated for candidemia.
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Asadzadeh M, Ahmad S, Al-Sweih N, Khan Z. Rapid and Accurate Identification of Candida albicans and Candida dubliniensis by Real-Time PCR and Melting Curve Analysis. Med Princ Pract 2018; 27:543-548. [PMID: 30176672 PMCID: PMC6422113 DOI: 10.1159/000493426] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 09/03/2018] [Indexed: 01/14/2023] Open
Abstract
OBJECTIVE Candida albicans and Candida dubliniensis are germ tube-positive pathogenic yeast species. Accurate identification of these two species is warranted since C. albicans is a highly pathogenic species while C. dubliniensis exhibits increased adherence to buccal epithelial cells, reduced susceptibility to azoles and resistance to flucytosine. We have developed a duplex real-time PCR assay for rapid detection and differentiation between clinical C. albicans and C. dubliniensis isolates. MATERIALS AND METHODS A duplex real-time PCR assay was developed by using two species-specific primer pairs and SYBR Green dye to differentiate C. albicans and C. dubliniensis isolates via melting curve analysis of real-time PCR amplicons. Amplification products were also analyzed by agarose gel electrophoresis to confirm real-time PCR results. RESULTS Melting temperatures (Tm) for reference strains of C. albicans and C. dubliniensis were 86.55 and 82.75°C, respectively. No amplicon was obtained with DNA from reference strains of 8 other common Candida spp. When real-time PCR was applied on 226 clinical isolates previously identified by the Vitek 2 system and/or PCR sequencing of rDNA, Tm values for C. albicans (n = 113) and C. dubliniensis (n = 98) were 86.68 ± 0.529 and 82.616 ± 0.535°C, respectively. The results were confirmed by agarose gel electrophoresis. No amplicon was obtained from 15 isolates belonging to 9 other Candida spp. CONCLUSIONS The real-time PCR assay described here does not require prior identification of clinical yeast isolates as C. albicans/C. dubliniensis by germ tube formation and accurately reports results within 2 h. Detection of amplicons by agarose gel electrophoresis is also suitable for resource-poor settings devoid of real-time PCR facilities.
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Affiliation(s)
- Mohammad Asadzadeh
- *Mohammad Asadzadeh, Department of Microbiology, Faculty of Medicine, Kuwait University, PO Box 24923, Safat 13110 (Kuwait), E-Mail
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Parin U, Erbas G, Kirkan S, Savasan S, Tugba Yuksel H, Balat G. Detection of Candida species by nested PCR method in one-humped camels (Camelus dromedarius). Trop Anim Health Prod 2017; 50:421-425. [PMID: 29080936 DOI: 10.1007/s11250-017-1452-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 10/19/2017] [Indexed: 01/05/2023]
Abstract
Systemic fungal diseases are the infections caused by false treatment protocols and generally are not taken into consideration especially in the veterinary field. One-humped camels are found in the western side of the Aegean region of our country and bred for wrestling. The aim of this study is the application of diagnosing systemic fungi infection from camel blood samples by the PCR method. In this study, specific primers for DNA topoisomerase II gene sequences were used. As a result, a systemic fungal infection was detected by the nested PCR method from 10 (20%) out of 50 DNA samples taken from camels located on the western side of the Aegean region. In this study, 3 (30%) samples were identified as Candida albicans, 3 (30%) samples were identified as C. glabrata, and 4 (40%) samples were identified as C. parapsilosis. In conclusion, the 20% positive systemic fungal infection rate in one-humped camels observed in the present study showed that the systemic fungal infections are not taken into considerations in veterinary medicine. Further studies are suggested in order to obtain and to maintain extensive data for systemic fungal diseases in our country for one-humped camels.
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Affiliation(s)
- Ugur Parin
- Department of Microbiology, Veterinary Faculty, University of Adnan Menderes, 09016, Aydın, Turkey
| | - Goksel Erbas
- Department of Microbiology, Veterinary Faculty, University of Adnan Menderes, 09016, Aydın, Turkey.
| | - Sukru Kirkan
- Department of Microbiology, Veterinary Faculty, University of Adnan Menderes, 09016, Aydın, Turkey
| | - Serap Savasan
- Department of Microbiology, Veterinary Faculty, University of Adnan Menderes, 09016, Aydın, Turkey
| | - H Tugba Yuksel
- Department of Microbiology, Veterinary Faculty, University of Adnan Menderes, 09016, Aydın, Turkey
| | - Gamze Balat
- Department of Microbiology, Veterinary Faculty, University of Adnan Menderes, 09016, Aydın, Turkey
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Yoo YK, Kim J, Kim G, Kim YS, Kim HY, Lee S, Cho WW, Kim S, Lee SM, Lee BC, Lee JH, Hwang KS. A highly sensitive plasma-based amyloid-β detection system through medium-changing and noise cancellation system for early diagnosis of the Alzheimer's disease. Sci Rep 2017; 7:8882. [PMID: 28827785 PMCID: PMC5567090 DOI: 10.1038/s41598-017-09370-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/24/2017] [Indexed: 01/17/2023] Open
Abstract
We developed an interdigitated microelectrode (IME) sensor system for blood-based Alzheimer's disease (AD) diagnosis based on impedimetric detection of amyloid-β (Aβ) protein, which is a representative candidate biomarker for AD. The IME sensing device was fabricated using a surface micromachining process. For highly sensitive detection of several tens to hundreds of picogram/mL of Aβ in blood, medium change from plasma to PBS buffer was utilized with signal cancellation and amplification processing (SCAP) system. The system demonstrated approximately 100-folds higher sensitivity according to the concentrations. A robust antibody-immobilization process was used for stability during medium change. Selectivity of the reaction due to the affinity of Aβ to the antibody and the sensitivity according to the concentration of Aβ were also demonstrated. Considering these basic characteristics of the IME sensor system, the medium change was optimized in relation to the absolute value of impedance change and differentiated impedance changes for real plasma based Aβ detection. Finally, the detection of Aβ levels in transgenic and wild-type mouse plasma samples was accomplished with the designed sensor system and the medium-changing method. The results confirmed the potential of this system to discriminate between patients and healthy controls, which would enable blood-based AD diagnosis.
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Affiliation(s)
- Yong Kyoung Yoo
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, Korea
- Department of Electrical Engineering, Kwangwoon University, Seoul, 139-701, South Korea
| | - Jinsik Kim
- Department of Medical Biotechnology, College of Life Science and Biotechnology, Dongguk University, Seoul, Korea
| | - Gangeun Kim
- Center for BioMicrosystems, Korea Institute of Science and Technology (KIST), Seoul, 136-791, South Korea
| | - Young Soo Kim
- Department of Pharmacy & Integrated Science and Engineering Division, Yonsei University, Incheon, 21983, South Korea
| | - Hye Yun Kim
- Department of Pharmacy & Integrated Science and Engineering Division, Yonsei University, Incheon, 21983, South Korea
| | - Sejin Lee
- Department of Pharmacy & Integrated Science and Engineering Division, Yonsei University, Incheon, 21983, South Korea
| | - Won Woo Cho
- CANTIS.co, Sangnok-gu, Ansan-si, Gyeonggi-do, 426-901, South Korea
| | - Seongsoo Kim
- Department of Chemical Engineering, Kangwon National University, Gangwon-do, 200-701, South Korea
| | - Sang-Myung Lee
- Department of Chemical Engineering, Kangwon National University, Gangwon-do, 200-701, South Korea
| | - Byung Chul Lee
- Center for BioMicrosystems, Korea Institute of Science and Technology (KIST), Seoul, 136-791, South Korea
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul, 139-701, South Korea
| | - Kyo Seon Hwang
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, Korea.
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Yeasts. Microbiol Spectr 2017; 4. [PMID: 27726781 DOI: 10.1128/microbiolspec.dmih2-0030-2016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeasts are unicellular organisms that reproduce mostly by budding and less often by fission. Most medically important yeasts originate from Ascomycota or Basidiomycota. Here, we review taxonomy, epidemiology, disease spectrum, antifungal drug susceptibility patterns of medically important yeast, laboratory diagnosis, and diagnostic strategies.
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Abstract
The discovery of HIV was largely due to the presence of Pneumocystis pneumonia (PCP) in young patients that did not have the usual known causes of immune deficiencies in the early 1980s. Currently, treatment with highly active anti-retroviral therapy (HAART) and the use of prophylaxis for PCP have lowered the frequency of fungal infections; however, these infections continue to cause morbidity and mortality in those patients that fall out or are not in care. The frequency of specific fungal diseases in HIV patients will depend on the prevalence of fungi in the particular geographic location. Nowadays, superficial and invasive Candida infections, PCP, and cryptococci are the most frequent fungal infections seen in HIV positive patients worldwide. The role of pathology in diagnosing fungal infections is crucial because a lesion may be biopsied without obtaining mycology cultures, certain organisms may take several weeks to grow, or the sample sent to the mycology laboratory may not have the organism. Following we will describe fungal infections that are particularly frequent in HIV infected patients and their key pathological features.
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Affiliation(s)
- Jeannette Guarner
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States.
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Abstract
PCR can aid in the diagnosis of invasive fungal disease (IFD). While the large number of "in-house" methodologies drives technological diversity, providing robustness, they make it difficult to identify optimal strategies, limiting standardization, and widespread acceptance. No matter how efficient, PCR utility will be limited by the quality of extracted nucleic acid. This chapter highlights benefits and limitations affecting the nucleic acid extraction process, before focusing on recent recommendations that through multicenter evaluation have provided optimal and standardized methodology.
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Affiliation(s)
- P Lewis White
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK.
| | - Rosemary A Barnes
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK.,Department of Infection and Immunity, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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Rahn S, Schuck A, Kondakci M, Haas R, Neuhausen N, Pfeffer K, Henrich B. A novel comprehensive set of fungal Real time PCR assays (fuPCR) for the detection of fungi in immunocompromised haematological patients—A pilot study. Int J Med Microbiol 2016; 306:611-623. [DOI: 10.1016/j.ijmm.2016.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/12/2016] [Indexed: 01/04/2023] Open
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Evaluation of Fluorescent Capillary Electrophoresis for Rapid Identification of Candida Fungal Infections. J Clin Microbiol 2016; 54:1295-303. [PMID: 26935732 DOI: 10.1128/jcm.00118-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022] Open
Abstract
Early diagnosis of fungal infection is critical for initiating antifungal therapy and reducing the high mortality rate in immunocompromised patients. In this study, we focused on rapid and sensitive identification of clinically important Candida species, utilizing the variability in the length of the ITS2 rRNA gene and fluorescent capillary electrophoresis (f-ITS2-PCR-CE). The method was developed and optimized on 29 various Candida reference strains from which 26 Candida species were clearly identified, while Candida guilliermondii, C. fermentati, and C. carpophila, which are closely related, could not be distinguished. The method was subsequently validated on 143 blinded monofungal clinical isolates (comprising 26 species) and was able to identify 88% of species unambiguously. This indicated a higher resolution power than the classical phenotypic approach which correctly identified 73%. Finally, the culture-independent potential of this technique was addressed by the analysis of 55 retrospective DNA samples extracted directly from clinical material. The method showed 100% sensitivity and specificity compared to those of the combined results of cultivation and panfungal PCR followed by sequencing used as a gold standard. In conclusion, this newly developed f-ITS2-PCR-CE analytical approach was shown to be a fast, sensitive, and highly reproducible tool for both culture-dependent and culture-independent identification of clinically important Candida strains, including species of the "psilosis" complex.
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Guo Y, Yang JX, Liang GW. A Real-Time PCR Assay Based on 5.8S rRNA Gene (5.8S rDNA) for Rapid Detection of Candida from Whole Blood Samples. Mycopathologia 2015; 181:405-13. [PMID: 26687075 DOI: 10.1007/s11046-015-9977-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/10/2015] [Indexed: 11/29/2022]
Abstract
The prevalence of Candida in bloodstream infections (BSIs) has increased. To date, the identification of Candida in BSIs still mainly relies on blood culture and serological tests, but they have various limitations. Therefore, a real-time PCR assay for the detection of Candida from whole blood is presented. The unique primers/probe system was designed on 5.8S rRNA gene (5.8S rDNA) of Candida genus. The analytical sensitivity was determined by numbers of positive PCRs in 12 repetitions. At the concentration of 10(1) CFU/ml blood, positive PCR rates of 100 % were obtained for C. albicans, C. parapsilosis, C. tropicalis, and C. krusei. The detection rate for C. glabrata was 75 % at 10(1) CFU/ml blood. The reaction specificity was 100 % when evaluating the assay using DNA samples from clinical isolates and human blood. The maximum CVs of intra-assay and inter-assay for the detection limit were 1.22 and 2.22 %, respectively. To assess the clinical applicability, 328 blood samples from 82 patients were prospectively tested and real-time PCR results were compared with results from blood culture. Diagnostic sensitivity of the PCR was 100 % using as gold standard blood culture, and specificity was 98.4 %. Our data suggest that the developed assay can be used in clinical laboratories as an accurate and rapid screening test for the Candida from whole blood. Although further evaluation is warranted, our assay holds promise for earlier diagnosis of candidemia.
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Affiliation(s)
- Yi Guo
- Department of Clinical Laboratory, Peking University Aerospace School of Clinical Medicine, No. 15 Yuquan Road, Haidian District, Beijing, 100049, China
| | - Jing-Xian Yang
- Department of Clinical Laboratory, Peking University Aerospace School of Clinical Medicine, No. 15 Yuquan Road, Haidian District, Beijing, 100049, China
| | - Guo-Wei Liang
- Department of Clinical Laboratory, Peking University Aerospace School of Clinical Medicine, No. 15 Yuquan Road, Haidian District, Beijing, 100049, China.
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Abstract
Rapid, accurate diagnostic laboratory tests are needed to improve clinical outcomes of invasive fungal disease (IFD). Traditional direct microscopy, culture and histological techniques constitute the 'gold standard' against which newer tests are judged. Molecular diagnostic methods, whether broad-range or fungal-specific, have great potential to enhance sensitivity and speed of IFD diagnosis, but have varying specificities. The use of PCR-based assays, DNA sequencing, and other molecular methods including those incorporating proteomic approaches such as matrix-assisted laser desorption ionisation-time of flight mass spectroscopy (MALDI-TOF MS) have shown promising results. These are used mainly to complement conventional methods since they require standardisation before widespread implementation can be recommended. None are incorporated into diagnostic criteria for defining IFD. Commercial assays may assist standardisation. This review provides an update of molecular-based diagnostic approaches applicable to biological specimens and fungal cultures in microbiology laboratories. We focus on the most common pathogens, Candida and Aspergillus, and the mucormycetes. The position of molecular-based approaches in the detection of azole and echinocandin antifungal resistance is also discussed.
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Lu S, Li X, Calderone R, Zhang J, Ma J, Cai W, Xi L. Whole blood Nested PCR and Real-time PCR amplification ofTalaromyces marneffeispecific DNA for diagnosis. Med Mycol 2015; 54:162-8. [DOI: 10.1093/mmy/myv068] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 07/03/2015] [Indexed: 11/12/2022] Open
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Loeffler J, Mengoli C, Springer J, Bretagne S, Cuenca-Estrella M, Klingspor L, Lagrou K, Melchers WJG, Morton CO, Barnes RA, Donnelly JP, White PL. Analytical Comparison of In Vitro-Spiked Human Serum and Plasma for PCR-Based Detection of Aspergillus fumigatus DNA: a Study by the European Aspergillus PCR Initiative. J Clin Microbiol 2015; 53:2838-45. [PMID: 26085614 PMCID: PMC4540929 DOI: 10.1128/jcm.00906-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/12/2015] [Indexed: 12/04/2022] Open
Abstract
The use of serum or plasma for Aspergillus PCR testing facilitates automated and standardized technology. Recommendations for serum testing are available, and while serum and plasma are regularly considered interchangeable for use in fungal diagnostics, differences in galactomannan enzyme immunoassay (GM-EIA) performance have been reported and are attributed to clot formation. Therefore, it is important to assess plasma PCR testing to determine if previous recommendations for serum are applicable and also to compare analytical performance with that of serum PCR. Molecular methods testing serum and plasma were compared through multicenter distribution of quality control panels, with additional studies to investigate the effect of clot formation and blood fractionation on DNA availability. Analytical sensitivity and time to positivity (TTP) were compared, and a regression analysis was performed to identify variables that enhanced plasma PCR performance. When testing plasma, sample volume, preextraction-to-postextraction volume ratio, PCR volume, duplicate testing, and the use of an internal control for PCR were positively associated with performance. When whole-blood samples were spiked and then fractionated, the analytical sensitivity and TTP were superior when testing plasma. Centrifugation had no effect on DNA availability, whereas the presence of clot material significantly lowered the concentration (P = 0.028). Technically, there are no major differences in the molecular processing of serum and plasma, but the formation of clot material potentially reduces available DNA in serum. During disease, Aspergillus DNA burdens in blood are often at the limits of PCR performance. Using plasma might improve performance while maintaining the methodological simplicity of serum testing.
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Affiliation(s)
| | | | | | | | | | | | - Katrien Lagrou
- National Reference Center for Mycosis, University Hospitals Leuven, Leuven, Belgium Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | | | | | | | | | - P Lewis White
- Public Health Wales Microbiology Cardiff, Cardiff, United Kingdom
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Chen SC, Sorrell TC, Chang CC, Paige EK, Bryant PA, Slavin MA. Consensus guidelines for the treatment of yeast infections in the haematology, oncology and intensive care setting, 2014. Intern Med J 2015; 44:1315-32. [PMID: 25482743 DOI: 10.1111/imj.12597] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pathogenic yeast forms are commonly associated with invasive fungal disease in the immunocompromised host, including patients with haematological malignancies and patients of haemopoietic stem cell transplants. Yeasts include the Candida spp., Cryptococcus spp., Pneumocystis jirovecii and some lesser-known pathogens. Candida species remain the most common cause of invasive yeast infections (and the most common human pathogenic fungi). These guidelines present evidence-based recommendations for the antifungal management of established, invasive yeast infections in adult and paediatric patients in the haematology/oncology setting. Consideration is also given to the critically ill patient in intensive care units, including the neonatal intensive care unit. Evidence for 'pre-emptive' or 'diagnostic-driven antifungal therapy' is also discussed. For the purposes of this paper, invasive yeast diseases are categorised under the headings of invasive candidiasis, cryptococcosis and uncommon yeast infections. Specific recommendations for the management of Pneumocystis jirovecii are presented in an accompanying article (see consensus guidelines by Cooley et al. appearing elsewhere in this supplement).
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Affiliation(s)
- S C Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead, New South Wales; Department of Infectious Diseases, Westmead Hospital, Westmead, New South Wales; Sydney Medical School, The University of Sydney, Sydney, New South Wales
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Detection of multiple fungal species in blood samples by real-time PCR: an interpretative challenge. J Clin Microbiol 2015; 52:3515-6. [PMID: 25143424 DOI: 10.1128/jcm.01685-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Multicenter evaluation of Candida QuickFISH BC for identification of Candida species directly from blood culture bottles. J Clin Microbiol 2015; 53:1672-6. [PMID: 25762766 DOI: 10.1128/jcm.00549-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 03/02/2015] [Indexed: 12/31/2022] Open
Abstract
Candida species are common causes of bloodstream infections (BSI), with high mortality. Four species cause >90% of Candida BSI: C. albicans, C. glabrata, C. parapsilosis, and C. tropicalis. Differentiation of Candida spp. is important because of differences in virulence and antimicrobial susceptibility. Candida QuickFISH BC, a multicolor, qualitative nucleic acid hybridization assay for the identification of C. albicans (green fluorescence), C. glabrata (red fluorescence), and C. parapsilosis (yellow fluorescence), was tested on Bactec and BacT/Alert blood culture bottles which signaled positive on automated blood culture devices and were positive for yeast by Gram stain at seven study sites. The results were compared to conventional identification. A total of 419 yeast-positive blood culture bottles were studied, consisting of 258 clinical samples (89 C. glabrata, 79 C. albicans, 23 C. parapsilosis, 18 C. tropicalis, and 49 other species) and 161 contrived samples inoculated with clinical isolates (40 C. glabrata, 46 C. albicans, 36 C. parapsilosis, 19 C. tropicalis, and 20 other species). A total of 415 samples contained a single fungal species, with C. glabrata (n = 129; 30.8%) being the most common isolate, followed by C. albicans (n = 125; 29.8%), C. parapsilosis (n = 59; 14.1%), C. tropicalis (n = 37; 8.8%), and C. krusei (n = 17; 4.1%). The overall agreement (with range for the three major Candida species) between the two methods was 99.3% (98.3 to 100%), with a sensitivity of 99.7% (98.3 to 100%) and a specificity of 98.0% (99.4 to 100%). This study showed that Candida QuickFISH BC is a rapid and accurate method for identifying C. albicans, C. glabrata, and C. parapsilosis, the three most common Candida species causing BSI, directly from blood culture bottles.
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Molecular Diagnosis in Fungal Infection Control. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2015. [DOI: 10.1007/s40506-015-0040-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Molecular and nonmolecular diagnostic methods for invasive fungal infections. Clin Microbiol Rev 2015; 27:490-526. [PMID: 24982319 DOI: 10.1128/cmr.00091-13] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Invasive fungal infections constitute a serious threat to an ever-growing population of immunocompromised individuals and other individuals at risk. Traditional diagnostic methods, such as histopathology and culture, which are still considered the gold standards, have low sensitivity, which underscores the need for the development of new means of detecting fungal infectious agents. Indeed, novel serologic and molecular techniques have been developed and are currently under clinical evaluation. Tests like the galactomannan antigen test for aspergillosis and the β-glucan test for invasive Candida spp. and molds, as well as other antigen and antibody tests, for Cryptococcus spp., Pneumocystis spp., and dimorphic fungi, have already been established as important diagnostic approaches and are implemented in routine clinical practice. On the other hand, PCR and other molecular approaches, such as matrix-assisted laser desorption ionization (MALDI) and fluorescence in situ hybridization (FISH), have proved promising in clinical trials but still need to undergo standardization before their clinical use can become widespread. The purpose of this review is to highlight the different diagnostic approaches that are currently utilized or under development for invasive fungal infections and to identify their performance characteristics and the challenges associated with their use.
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Candida colonization as a risk marker for invasive candidiasis in mixed medical-surgical intensive care units: development and evaluation of a simple, standard protocol. J Clin Microbiol 2015; 53:1324-30. [PMID: 25673797 DOI: 10.1128/jcm.03239-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Colonization with Candida species is an independent risk factor for invasive candidiasis (IC), but the minimum and most practicable parameters for prediction of IC have not been optimized. We evaluated Candida colonization in a prospective cohort of 6,015 nonneutropenic, critically ill patients. Throat, perineum, and urine were sampled 72 h post-intensive care unit (ICU) admission and twice weekly until discharge or death. Specimens were cultured onto chromogenic agar, and a subset underwent molecular characterization. Sixty-three (86%) patients who developed IC were colonized prior to infection; 61 (97%) tested positive within the first two time points. The median time from colonization to IC was 7 days (range, 0 to 35). Colonization at any site was predictive of IC, with the risk of infection highest for urine colonization (relative risk [RR]=2.25) but with the sensitivity highest (98%) for throat and/or perineum colonization. Colonization of ≥2 sites and heavy colonization of ≥1 site were significant independent risk factors for IC (RR=2.25 and RR=3.7, respectively), increasing specificity to 71% to 74% but decreasing sensitivity to 48% to 58%. Molecular testing would have prompted a resistance-driven decision to switch from fluconazole treatment in only 11% of patients infected with C. glabrata, based upon species-level identification alone. Positive predictive values (PPVs) were low (2% to 4%) and negative predictive values (NPVs) high (99% to 100%) regardless of which parameters were applied. In the Australian ICU setting, culture of throat and perineum within the first two time points after ICU admission captures 84% (61/73 patients) of subsequent IC cases. These optimized parameters, in combination with clinical risk factors, should strengthen development of a setting-specific risk-predictive model for IC.
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Semiquantitative multiplexed tandem PCR for detection and differentiation of four Theileria orientalis genotypes in cattle. J Clin Microbiol 2014; 53:79-87. [PMID: 25339402 DOI: 10.1128/jcm.02536-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oriental theileriosis is an emerging, tick-borne disease of bovines in the Asia-Pacific region and is caused by one or more genotypes of the Theileria orientalis complex. This study aimed to establish and validate a multiplexed tandem PCR (MT-PCR) assay using three distinct markers (major piroplasm surface protein, 23-kDa piroplasm membrane protein, and the first internal transcribed spacer of nuclear DNA), for the simultaneous detection and semiquantification of four genotypes (Buffeli, Chitose, Ikeda, and type 5) of the T. orientalis complex. Analytical specificity, analytical sensitivity, and repeatability of the established MT-PCR assay were assessed in a series of experiments. Subsequently, the assay was evaluated using 200 genomic DNA samples collected from cattle from farms on which oriental theileriosis outbreaks had occurred, and 110 samples from a region where no outbreaks had been reported. The results showed the MT-PCR assay specifically and reproducibly detected the expected genotypes (i.e., genotypes Buffeli, Chitose, Ikeda, and type 5) of the T. orientalis complex, reliably differentiated them, and was able to detect as little as 1 fg of genomic DNA from each genotype. The diagnostic specificity and sensitivity of the MT-PCR were estimated at 94.0% and 98.8%, respectively. The MT-PCR assay established here is a practical and effective diagnostic tool for the four main genotypes of T. orientalis complex in Australia and should assist studies of the epidemiology and pathophysiology of oriental theileriosis in the Asia-Pacific region.
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Gavaldà J, Meije Y, Fortún J, Roilides E, Saliba F, Lortholary O, Muñoz P, Grossi P, Cuenca-Estrella M. Invasive fungal infections in solid organ transplant recipients. Clin Microbiol Infect 2014; 20 Suppl 7:27-48. [DOI: 10.1111/1469-0691.12660] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Taira CL, Okay TS, Delgado AF, Ceccon MEJR, de Almeida MTG, Del Negro GMB. A multiplex nested PCR for the detection and identification of Candida species in blood samples of critically ill paediatric patients. BMC Infect Dis 2014; 14:406. [PMID: 25047415 PMCID: PMC4223582 DOI: 10.1186/1471-2334-14-406] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/10/2014] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Nosocomial candidaemia is associated with high mortality rates in critically ill paediatric patients; thus, the early detection and identification of the infectious agent is crucial for successful medical intervention. The PCR-based techniques have significantly increased the detection of Candida species in bloodstream infections. In this study, a multiplex nested PCR approach was developed for candidaemia detection in neonatal and paediatric intensive care patients. METHODS DNA samples from the blood of 54 neonates and children hospitalised in intensive care units with suspected candidaemia were evaluated by multiplex nested PCR with specific primers designed to identify seven Candida species, and the results were compared with those obtained from blood cultures. RESULTS The multiplex nested PCR had a detection limit of four Candida genomes/mL of blood for all Candida species. Blood cultures were positive in 14.8% of patients, whereas the multiplex nested PCR was positive in 24.0% of patients, including all culture-positive patients. The results obtained with the molecular technique were available within 24 hours, and the assay was able to identify Candida species with 100% of concordance with blood cultures. Additionally, the multiplex nested PCR detected dual candidaemia in three patients. CONCLUSIONS Our proposed PCR method may represent an effective tool for the detection and identification of Candida species in the context of candidaemia diagnosis in children, showing highly sensitive detection and the ability to identify the major species involved in this infection.
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Affiliation(s)
| | | | | | | | | | - Gilda Maria Barbaro Del Negro
- Laboratory of Medical Mycology (LIM-53), Clinical Dermartology Division, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP) and Instituto de Medicina Tropical da Universidade de São Paulo (IMT-USP), Av, Dr, Enéas Carvalho de Aguiar, 500, Andar térreo, Predio 2, CEP, 05403-900 São Paulo, SP, Brazil.
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Fortun J, Meije Y, Buitrago MJ, Gago S, Bernal-Martinez L, Peman J, Perez M, Gomez-G Pedrosa E, Madrid N, Pintado V, Martin-Davila P, Cobo J, Fresco G, Moreno S, Cuenca-Estrella M. Clinical validation of a multiplex real-time PCR assay for detection of invasive candidiasis in intensive care unit patients. J Antimicrob Chemother 2014; 69:3134-41. [DOI: 10.1093/jac/dku225] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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40
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Alanio A, Bretagne S. Difficulties with molecular diagnostic tests for mould and yeast infections: where do we stand? Clin Microbiol Infect 2014; 20 Suppl 6:36-41. [DOI: 10.1111/1469-0691.12617] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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41
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Aitken SL, Beyda ND, Shah DN, Palmer HR, Lasco TM, Koo H, Garey KW. Clinical Practice Patterns in Hospitalized Patients at Risk for Invasive Candidiasis. Ann Pharmacother 2014; 48:683-90. [DOI: 10.1177/1060028014529928] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Rapid diagnostic tests for Candida are becoming available that may supplement traditional microbiological identification. Objective: Assess clinical practice patterns in patients with or at risk of candidiasis who may benefit from the use of rapid diagnostic tests. Methods: This was a prospective cohort study of patients with candidemia or receiving systemic antifungals conducted at a university-affiliated tertiary care hospital. Time to initiation of therapy, Candida species, time to identification, and indications for antifungal use were assessed. Results: A total of 162 patients with candidemia aged 58 ± 17 years were identified. Average time to yeast identification yeast was 2.2 ± 1.3 days and varied by Candida species (range = 0.6-7.9 days). Average time for patient to start antifungal therapy was 3.5 ± 2.1 days. In Monte Carlo simulations, average time to initiation of antifungal therapy was 0.6 ± 0.2 days for T2Candida, 2.6 ± 1.3 days for PNA-FISH (fluorescence in situ hybridization using peptide nucleic acid probes), and 2.5 ± 1.4 days for MALDI-TOF (matrix-assisted laser desorption/ionization time of flight). Use of T2Candida on the day of the blood culture collection resulted in 3136 to 6078 fewer doses of echinocandins annually per 5000 patients. Conclusion: Many interventions are possible for antifungal stewardship programs to improve care of patients at risk for systemic candidiasis, including rapid identification of yeast species and limiting unnecessary antifungal agents. Technology enabling rapid diagnosis of Candida will be paramount to appropriate, cost-effective treatment of patients with or at risk for candidiasis.
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Affiliation(s)
- Samuel L. Aitken
- University of Houston College of Pharmacy, Houston, TX, USA
- St Luke’s Hospital, Texas Medical Center, Houston, TX, USA
| | | | - Dhara N. Shah
- University of Houston College of Pharmacy, Houston, TX, USA
| | | | - Todd M. Lasco
- St Luke’s Hospital, Texas Medical Center, Houston, TX, USA
| | - Hoonmo Koo
- St Luke’s Hospital, Texas Medical Center, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - Kevin W. Garey
- University of Houston College of Pharmacy, Houston, TX, USA
- St Luke’s Hospital, Texas Medical Center, Houston, TX, USA
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A multiplex real-time PCR assay for identification of Pneumocystis jirovecii, Histoplasma capsulatum, and Cryptococcus neoformans/Cryptococcus gattii in samples from AIDS patients with opportunistic pneumonia. J Clin Microbiol 2014; 52:1168-76. [PMID: 24478409 DOI: 10.1128/jcm.02895-13] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A molecular diagnostic technique based on real-time PCR was developed for the simultaneous detection of three of the most frequent causative agents of fungal opportunistic pneumonia in AIDS patients: Pneumocystis jirovecii, Histoplasma capsulatum, and Cryptococcus neoformans/Cryptococcus gattii. This technique was tested in cultured strains and in clinical samples from HIV-positive patients. The methodology used involved species-specific molecular beacon probes targeted to the internal transcribed spacer regions of the rDNA. An internal control was also included in each assay. The multiplex real-time PCR assay was tested in 24 clinical strains and 43 clinical samples from AIDS patients with proven fungal infection. The technique developed showed high reproducibility (r(2) of >0.98) and specificity (100%). For H. capsulatum and Cryptococcus spp., the detection limits of the method were 20 and 2 fg of genomic DNA/20 μl reaction mixture, respectively, while for P. jirovecii the detection limit was 2.92 log10 copies/20 μl reaction mixture. The sensitivity in vitro was 100% for clinical strains and 90.7% for clinical samples. The assay was positive for 92.5% of the patients. For one of the patients with proven histoplasmosis, P. jirovecii was also detected in a bronchoalveolar lavage sample. No PCR inhibition was detected. This multiplex real-time PCR technique is fast, sensitive, and specific and may have clinical applications.
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Yurdakul P, Colakoglu S. Molecular methods for detection of invasive fungal infections and mycobacteria and their clinical significance in hematopoietic stem cell transplantation. Methods Mol Biol 2014; 1109:239-70. [PMID: 24473787 DOI: 10.1007/978-1-4614-9437-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Infection remains an important source of morbidity and mortality in patients who undergo hematopoietic stem cell transplantation (HSCT). In the immune reconstitution period after transplantation, HSCT recipients are most likely to have bacterial or fungal infections. Invasive fungal infections (IFIs) and mycobacterial infections (MBIs) are among the complications of HSCT, with high morbidity and mortality rates. Early diagnosis of both is crucial in order to manipulate the disease and to avoid fulminant outcomes. This chapter reviews the current knowledge on the molecular diagnosis of IFIs and MBIs in HSCT recipients, describing two different polymerase chain reaction (PCR)-based methods, one commercial (qPCR, Roche) and one in-house IS6110-based protocol.
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Affiliation(s)
- Pinar Yurdakul
- Ankara University Faculty of Medicine, Cord Blood Bank, Ankara, Turkey
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Jeddi F, Piarroux R, Mary C. Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases. ACTA ACUST UNITED AC 2013; 20:52. [PMID: 24331004 PMCID: PMC3859032 DOI: 10.1051/parasite/2013051] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 11/28/2013] [Indexed: 01/29/2023]
Abstract
During the last 20 years, molecular biology techniques have propelled the diagnosis of parasitic diseases into a new era, as regards assay speed, sensitivity, and parasite characterization. However, DNA extraction remains a critical step and should be adapted for diagnostic and epidemiological studies. The aim of this report was to document the constraints associated with DNA extraction for the diagnosis of parasitic diseases and illustrate the adaptation of an automated extraction system, NucliSENS easyMAG, to these constraints, with a critical analysis of system performance. Proteinase K digestion of samples is unnecessary with the exception of solid tissue preparation. Mechanically grinding samples prior to cell lysis enhances the DNA extraction rate of fungal cells. The effect of host-derived nucleic acids on the extraction efficiency of parasite DNA varies with sample host cell density. The optimal cell number for precise parasite quantification ranges from 10 to 100,000 cells. Using the NucliSENS easyMAG technique, the co-extraction of inhibitors is reduced, with an exception for whole blood, which requires supplementary extraction steps to eliminate inhibitors.
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Affiliation(s)
- Fakhri Jeddi
- Aix-Marseille Université, Faculté de Médecine, UMR MD3, 13284 Marseille, France - APHM, Hôpital de la Timone, Laboratoire de Parasitologie-Mycologie, 13385 Marseille, France
| | - Renaud Piarroux
- Aix-Marseille Université, Faculté de Médecine, UMR MD3, 13284 Marseille, France - APHM, Hôpital de la Timone, Laboratoire de Parasitologie-Mycologie, 13385 Marseille, France
| | - Charles Mary
- Aix-Marseille Université, Faculté de Médecine, UMR MD3, 13284 Marseille, France - APHM, Hôpital de la Timone, Laboratoire de Parasitologie-Mycologie, 13385 Marseille, France
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45
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Zhang SX. Enhancing molecular approaches for diagnosis of fungal infections. Future Microbiol 2013; 8:1599-611. [DOI: 10.2217/fmb.13.120] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Molecular tests can improve the diagnosis of fungal infections. Despite the increasing application for fungal detection, molecular tests are still not accepted as a diagnostic criterion to define invasive fungal diseases. This limitation is largely due to a lack of a standardized method. Method standardization can be achieved by following a consensus protocol developed by a working group, by performing a molecular test in a centralized laboratory or by using a commercial assay that provides a standardized method and quality-controlled reagents. Forming a consortium or a working group consisting of large-scale diagnostic mycology laboratories can accelerate the process of validating and implementing a commercial molecular assay for clinical use through a joint effort between industry partners and clinicians. Development of molecular tests not only for the detection of fungi but also for the identification of antifungal drug resistance directly in blood, bronchoalveolar lavage fluid, cerebrospinal fluid, and formalin-fixed and paraffin-embedded tissues greatly enhances fungal diagnostic capacities. Advances of developing quantitative assays and RNA detection platforms may provide another avenue to further improve fungal diagnostics.
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Affiliation(s)
- Sean X Zhang
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, 600 Wolfe Street, Meyer B1-193, Baltimore 21287, MD, USA
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Xafranski H, Melo ASA, Machado AM, Briones MRS, Colombo AL. A quick and low-cost PCR-based assay for Candida spp. identification in positive blood culture bottles. BMC Infect Dis 2013; 13:467. [PMID: 24099320 PMCID: PMC3851980 DOI: 10.1186/1471-2334-13-467] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 09/26/2013] [Indexed: 12/26/2022] Open
Abstract
Background Differences in the susceptibility of Candida species to antifungal drugs make identification to the species level important for clinical management of candidemia. Molecular tests are not yet standardized or available in most clinical laboratories, although such tests can reduce the time required for species identification, as compared to the conventional culture-based methods. To decrease laboratory costs and improve diagnostic accuracy, different molecular methods have been proposed, including DNA extraction protocols to produce pure DNA free of PCR inhibitors. The objective of this study was to validate a new format of molecular method, based on the internal transcribed spacer (ITS) of the rDNA gene amplification followed by sequencing, to identify common and cryptic Candida species causing candidemia by analyzing DNA in blood culture bottles positive for yeasts. Methods For DNA extraction, an “in-house” protocol based on organic solvent extraction was tested. Additional steps of liquid nitrogen incubation followed by mechanical disruption ensured complete cell lysis, and highly pure DNA. One hundred sixty blood culture bottles positive for yeasts were processed. PCR assays amplified the ITS region. The DNA fragments of 152 samples were sequenced and these sequences were identified using the GenBank database (NCBI). Molecular yeast identification was compared to results attained by conventional method. Results The organic solvent extraction protocol showed high reproducibility in regards to DNA quantity, as well as high PCR sensitivity (10 pg of C. albicans DNA and 95% amplification on PCR). The identification of species at the molecular level showed 97% concordance with the conventional culturing method. The molecular method tested in the present study also allowed identification of species not commonly implicated in human infections. Conclusions This study demonstrated that our molecular method presents significant advantages over the conventional yeast culture identification method by providing accurate results within 24 hours, in contrast to at least 72 hours required by the automated conventional culture method. Additionally, our molecular method allowed the identification of mixed infections, as well as infections due to emergent fungal pathogens. This economical DNA extraction method developed in our laboratory provided high-quality DNA and 60% cost savings compared to commercial methods.
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Affiliation(s)
- Hemílio Xafranski
- Laboratório Especial de Micologia, Departamento de Medicina, Universidade Federal de São Paulo, Rua Pedro de Toledo 669 5 andar, São Paulo, SP, Brazil.
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Huttunen R, Syrjänen J, Vuento R, Aittoniemi J. Current concepts in the diagnosis of blood stream infections. Are novel molecular methods useful in clinical practice? Int J Infect Dis 2013; 17:e934-8. [PMID: 23871281 DOI: 10.1016/j.ijid.2013.04.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 04/02/2013] [Accepted: 04/04/2013] [Indexed: 12/21/2022] Open
Abstract
The decision on the right empirical treatment in bacteremia places particular demands on the clinician. As long as no microbiological diagnosis can be immediately drawn, the clinical diagnosis together with knowledge of local antimicrobial resistance must determine the antimicrobial choice. The use of several amplification, hybridization, and mass spectrometry methods has been studied in patient cohorts in comparison with blood culture-based conventional techniques. However, no clinical outcome trials have been conducted in which the use of these novel methods would guide antimicrobial therapy. Local differences in bacterial antimicrobial resistance cause differences in the regional need for molecular methods for the early detection of resistance mechanisms. The implementation of novel methods in clinical use requires active discussion between laboratory experts and clinicians. Providing rapid susceptibility results using conventional methods can lead to timely changes to appropriate antimicrobial therapy and the costs are lower than with the molecular methods. Gram-stain information in combination with clinical data is an underestimated, underused, rapid, and economical means of assessing the etiology of blood stream infection.
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Affiliation(s)
- Reetta Huttunen
- Department of Internal Medicine, Tampere University Hospital, Box 2000, FI-33521 Tampere, Finland; University of Tampere Medical School, University of Tampere, Tampere, Finland.
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Colombo AL, Cortes JA, Zurita J, Guzman-Blanco M, Alvarado Matute T, de Queiroz Telles F, Santolaya ME, Tiraboschi IN, Echevarría J, Sifuentes J, Thompson-Moya L, Nucci M. [Recommendations for the diagnosis of candidemia in Latin America. Grupo Proyecto Épico]. Rev Iberoam Micol 2013; 30:150-7. [PMID: 23764553 DOI: 10.1016/j.riam.2013.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 05/16/2013] [Indexed: 11/20/2022] Open
Abstract
Candidemia is one of the most frequent opportunistic mycoses worldwide. Limited epidemiological studies in Latin America indicate that incidence rates are higher in this region than in the Northern Hemisphere. Diagnosis is often made late in the infection, affecting the initiation of antifungal therapy. A more scientific approach, based on specific parameters, for diagnosis and management of candidemia in Latin America is warranted. 'Recommendations for the diagnosis and management of candidemia' are a series of manuscripts that have been developed by members of the Latin America Invasive Mycosis Network. They aim to provide a set of best-evidence recommendations for the diagnosis and management of candidemia. This publication, 'Recommendations for the diagnosis of candidemia in Latin America', was written to provide guidance to healthcare professionals on the diagnosis of candidemia, as well as on the usefulness and application of susceptibility testing in patients who have a confirmed diagnosis of candidemia. Computerized searches of existing literature were performed by PubMed. The data were extensively reviewed and analyzed by members of the group. The group also met on two occasions to pose questions, discuss conflicting views, and deliberate on a series of management recommendations. 'Recommendations for the diagnosis of candidemia in Latin America' includes diagnostic methods used to detect candidemia, Candida species identification, and susceptibility testing. The availability of methods, their costs and treatment settings are considered. This manuscript is the first of this series that deals with diagnosis and treatment of invasive candidiasis. Other publications in this series include: 'Recommendations for the management of candidemia in adults in Latin America', 'Recommendations for the management of candidemia in children in Latin America', and 'Recommendations for the management of candidemia in neonates in Latin America'.
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Affiliation(s)
- Arnaldo Lopes Colombo
- Federal University of São Paulo, São Paulo, Brasil; Latin America Invasive Mycosis Network.
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Pemán J, Zaragoza R. Combined use of nonculture-based lab techniques in the diagnosis and management of critically ill patients with invasive fungal infections. Expert Rev Anti Infect Ther 2013; 10:1321-30. [PMID: 23241189 DOI: 10.1586/eri.12.128] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Invasive fungal infections are associated with high morbidity and mortality in critically ill patients due, in part, to diagnostic difficulties in the early stages. Nonculture-based techniques such as (1,3)-β-d-glucan, galactomannan, mannan and antimannan antibodies, Candida albicans germ tube-specific antibodies or fungal DNA are required for earlier diagnosis, prognostic information and monitoring outcome. A decision-tree algorithm based on the combination of nonculture-based techniques is suggested to optimize the diagnosis and evolution of critically ill patients at risk of invasive mycoses. The use of (1,3)-β-d-glucan and blood cultures twice a week is proposed; if positive, treatment initiation is recommended alongside the performance of the nonculture-based microbiological tool depending on suspected mycoses and the availability of techniques.
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Affiliation(s)
- Javier Pemán
- Servicio de Microbiología, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
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