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He B, Yang Q. Updates in Laboratory Identification of Invasive Fungal Infection in Neonates. Microorganisms 2023; 11:1001. [PMID: 37110424 PMCID: PMC10145787 DOI: 10.3390/microorganisms11041001] [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: 03/10/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Invasive fungal infection (IFI) in immunocompromised neonates is significantly associated with high morbidity and mortality and has become the third most common infection in Neonatal Intensive Care Units. The early diagnosis of IFI for neonatal patients is difficult because of the lack of specific symptoms. The traditional blood culture remains the gold standard in clinical diagnosis for neonatal patients but it requires a long duration, which delays treatment initiation. Detections of fungal cell-wall components are developed for early diagnosis but the diagnostic accuracy in neonates needs to be improved. PCR-based laboratory methods, such as real-time PCR, droplet digital PCR, and the cationic conjugated polymer fluorescence resonance energy transfer (CCP-FRET) system, distinguish the infected fungal species by their specific nucleic acids and show a high sensitivity and specificity. Particularly, the CCP-FRET system, which contains a cationic conjugated polymer (CCP) fluorescent probe and pathogen-specific DNA labeled with fluorescent dyes, could identify multiple infections simultaneously. In the CCP-FRET system, the CCP and fungal DNA fragments can self-assemble into a complex with an electrostatic interaction and the CCP triggers the FRET effect under ultraviolet light to make the infection visible. Here, we summarize the recent laboratory methods for neonatal IFI identification and provide a new perspective for early clinical fungal diagnosis.
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Affiliation(s)
| | - Qiong Yang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China;
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He Z, Huo X, Piao J. Rapid preparation of Candida genomic DNA: combined use of enzymatic digestion and thermal disruption. AMB Express 2023; 13:1. [PMID: 36592236 PMCID: PMC9807692 DOI: 10.1186/s13568-022-01500-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 12/07/2022] [Indexed: 01/03/2023] Open
Abstract
Nucleic acid based molecular technologies are the most promising tools for the early diagnosis of Candida infection. A simple and effective DNA preparation method is of critical for standardizing and applying molecular diagnostics in clinic laboratories. The goal of this study was to develop a Candida DNA preparation method that was quick to do, easy to perform, and bio-safe. Snailase and lyticase were screened and combined in this work to enhance the lysis of Candida cells. The lysis solution composition and metal bath were optimized to boost amplification efficiency and biosafety. A duplex real-time PCR was established to evaluate the sensitivity and specificity of the preparation method. Using the supernatant from the rapid preparation method as templates, the duplex PCR sensitivities for five common Candida species were determined to be as low as 100 CFUs. When compared to conventional preparation methods, the samples prepared by our method showed higher PCR detection sensitivity. PCR identification and ITS sequencing were 100% consistent, which was better than biochemical identification. This study demonstrates a rapid method for Candida DNA preparation that has the potential to be used in clinical laboratories. Meanwhile, the practical application of the method for clinical samples needs to be proven in future investigations.
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Affiliation(s)
- Zhengxin He
- grid.452440.30000 0000 8727 6165Basic Medical Laboratory, The 980th Hospital of PLA Joint Logistical Support Force (Bethune International Peace Hospital), 398 Zhongshan Road, Shijiazhuang, 050082 Hebei People’s Republic of China
| | - Xiaosai Huo
- grid.452440.30000 0000 8727 6165Basic Medical Laboratory, The 980th Hospital of PLA Joint Logistical Support Force (Bethune International Peace Hospital), 398 Zhongshan Road, Shijiazhuang, 050082 Hebei People’s Republic of China
| | - Jingzi Piao
- grid.412557.00000 0000 9886 8131College of Plant Protection, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866 Liaoning People’s Republic of China
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Aboutalebian S, Mahmoudi S, Charsizadeh A, Nikmanesh B, Hosseini M, Mirhendi H. Multiplex size marker (YEAST PLEX) for rapid and accurate identification of pathogenic yeasts. J Clin Lab Anal 2022; 36:e24370. [PMID: 35318737 PMCID: PMC9102616 DOI: 10.1002/jcla.24370] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/26/2022] [Accepted: 02/10/2022] [Indexed: 11/18/2022] Open
Abstract
Background Multiple yeast species can cause human disease, involving superficial to deep‐seated infections. Treatment of these infections depends on the accurate identification of causative agents; however, reliable methods are not available in many laboratories, especially not in resource‐limited settings. Here, a new multiplex assay for rapid and low‐cost identification of pathogenic yeasts is described. Methods A two‐step multiplex assay named YEAST PLEX that comprises of four tubes and identifies 17 clinically important common to rare yeasts was designed and evaluated. The set also provides PCR amplicon of unidentified species for direct sequencing. The specificity of YEAST PLEX was tested using 28 reference strains belonging to 17 species and 101 DNA samples of clinically important non‐target bacteria, parasites, and fungi as well as human genomic DNA. The method was further analyzed using 203 previously identified and 89 unknown clinical yeast isolates. Moreover, the method was tested for its ability to identify mixed yeast colonies by using 18 mixed suspensions of two or three species. Results YEAST PLEX was able to identify all the target species without any non‐specific PCR products. When compared to PCR‐sequencing/MALDI‐TOF, the results of YEAST PLEX were in 100% agreement. Regarding the 89 unknown clinical isolates, random isolates were selected and subjected to PCR‐sequencing. The results of sequencing were in agreement with those of YEAST PLEX. Furthermore, this method was able to correctly identify all yeasts in mixed suspensions. Conclusion YEAST PLEX is an accurate, low‐cost, and rapid method for identification of yeasts, with applicability, especially in developing countries.
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Affiliation(s)
- Shima Aboutalebian
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Mycology Reference Laboratory, Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shahram Mahmoudi
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Arezoo Charsizadeh
- Immunology, Asthma, and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahram Nikmanesh
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahnaz Hosseini
- Mycology Reference Laboratory, Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Mycology Reference Laboratory, Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
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Khodadadi H, Karimi L, Jalalizand N, Adin H, Mirhendi H. Utilization of size polymorphism in ITS1 and ITS2 regions for identification of pathogenic yeast species. J Med Microbiol 2017; 66:126-133. [PMID: 28260588 DOI: 10.1099/jmm.0.000426] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Despite the existence of a variety of available yeast-identification strategies, easier and more cost-effective methods are required for routine use in clinical laboratories. The internal transcribed spacer (ITS) regions of fungal rRNA genes exhibit variable sizes depending on the yeast species. In the present study, fragment size polymorphism (FSP) analysis of the ITS1 and ITS2 regions for identification of the clinically most important yeast species was assessed. METHODOLOGY The ITS1 and ITS2 regions of 190 strains, including isolates of 31 standard strains and 159 clinical isolates, were separately PCR amplified with two primer sets: ITS1-ITS2 and ITS3-ITS4. PCR products were mixed and the two-band electrophoretic pattern of each sample was analysed according to the size of the ITS regions as predicted from the GenBank database. RESULTS Using this method and avoiding expensive tools such as sequencing or capillary electrophoresis, we were able to differentiate nearly all pathogenic yeast species, including Candida albicans, Candida tropicalis, Candida glabrata, Candida parapsilosis, Candida krusei, Candida guilliermondii, Candida kefyr, Candida lusitaniae, Candida rugosa, Cryptococcus neoformans and Saccharomyces cerevisiae. The method showed limited discriminatory power to differentiate species of the Candida parapsilosis complex. Differentiation of Candida albicans and Candida tropicalis needs already identified controls. CONCLUSION FSP method benefits from advantages such as lower cost, higher speed and wider range of species than some commercial yeast-identification methods. We consider this method as one of the easiest molecular approaches for identifying a wide range of human pathogenic yeast species, applicable to both diagnostic and epidemiological purposes.
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Affiliation(s)
- Hossein Khodadadi
- Department of Medical Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ladan Karimi
- Dr. Beheshti Hospital, Social Security Organization, Shiraz, Iran
| | - Nilufar Jalalizand
- Department of Medical Parasitology and Mycology, School of Public Health, National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Adin
- Department of Medical Parasitology and Mycology, School of Public Health, National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Noguchi H, Iwase T, Omagari D, Asano M, Nakamura R, Ueki K, Shinozuka K, Kaneko T, Tonogi M, Ohki H. Rapid detection of Candida albicans in oral exfoliative cytology samples by loop-mediated isothermal amplification. J Oral Sci 2017; 59:541-547. [DOI: 10.2334/josnusd.16-0717] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Hiroyasu Noguchi
- Division of Oral Structural and Functional Biology, Nihon University Graduate School of Dentistry
| | - Takashi Iwase
- Department of Pathology, Nihon University School of Dentistry
| | - Daisuke Omagari
- Department of Pathology, Nihon University School of Dentistry
| | - Masatake Asano
- Department of Pathology, Nihon University School of Dentistry
| | - Ryota Nakamura
- Division of Oral Structural and Functional Biology, Nihon University Graduate School of Dentistry
| | - Kosuke Ueki
- Division of Oral Structural and Functional Biology, Nihon University Graduate School of Dentistry
| | - Keiji Shinozuka
- Department of Oral and Maxillofacial Surgery, Nihon University School of Dentistry
| | - Tadayoshi Kaneko
- Department of Oral and Maxillofacial Surgery, Nihon University School of Dentistry
| | - Morio Tonogi
- Department of Oral and Maxillofacial Surgery, Nihon University School of Dentistry
| | - Hiderou Ohki
- Department of Oral and Maxillofacial Surgery, Nihon University School of Dentistry
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Recent Progress in the Diagnosis of Pathogenic Candida Species in Blood Culture. Mycopathologia 2016; 181:363-9. [PMID: 27003437 DOI: 10.1007/s11046-016-0003-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/13/2016] [Indexed: 01/23/2023]
Abstract
Candidemia has become an emerging invasive fungal disease. Prompt treatment with appropriate antifungal agent is crucial to reduce the mortality of candidemia. The conventional blood culture method, which is considered the gold standard for candidemia diagnosis, has a low sensitivity and is time-consuming to perform. Recently, several novel advanced diagnostic methods that have a higher sensitivity and a shorter turnaround time than the conventional blood culture method have been developed for the early detection of Candida in blood samples or in blood culture broth. Most of these newer methods were developed using various molecular techniques, such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, peptide nucleic acid fluorescence in situ hybridization, and a number of DNA-based techniques including in-house and commercial polymerase chain reactions. In this article, we review and summarize the novel molecular methods that have been recently used for the detection and identification of Candida organisms in blood specimens.
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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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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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