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Trippa D, Scalenghe R, Basso MF, Panno S, Davino S, Morone C, Giovino A, Oufensou S, Luchi N, Yousefi S, Martinelli F. Next-generation methods for early disease detection in crops. PEST MANAGEMENT SCIENCE 2024; 80:245-261. [PMID: 37599270 DOI: 10.1002/ps.7733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/21/2023] [Indexed: 08/22/2023]
Abstract
Plant pathogens are commonly identified in the field by the typical disease symptoms that they can cause. The efficient early detection and identification of pathogens are essential procedures to adopt effective management practices that reduce or prevent their spread in order to mitigate the negative impacts of the disease. In this review, the traditional and innovative methods for early detection of the plant pathogens highlighting their major advantages and limitations are presented and discussed. Traditional techniques of diagnosis used for plant pathogen identification are focused typically on the DNA, RNA (when molecular methods), and proteins or peptides (when serological methods) of the pathogens. Serological methods based on mainly enzyme-linked immunosorbent assay (ELISA) are the most common method used for pathogen detection due to their high-throughput potential and low cost. This technique is not particularly reliable and sufficiently sensitive for many pathogens detection during the asymptomatic stage of infection. For non-cultivable pathogens in the laboratory, nucleic acid-based technology is the best choice for consistent pathogen detection or identification. Lateral flow systems are innovative tools that allow fast and accurate results even in field conditions, but they have sensitivity issues to be overcome. PCR assays performed on last-generation portable thermocyclers may provide rapid detection results in situ. The advent of portable instruments can speed pathogen detection, reduce commercial costs, and potentially revolutionize plant pathology. This review provides information on current methodologies and procedures for the effective detection of different plant pathogens. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Daniela Trippa
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Riccardo Scalenghe
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | | | - Stefano Panno
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Salvatore Davino
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Chiara Morone
- Regione Piemonte - Phytosanitary Division, Torino, Italy
| | - Antonio Giovino
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Palermo, Italy
| | - Safa Oufensou
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Nicola Luchi
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Florence, Italy
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Federico Martinelli
- Department of Biology, University of Florence, Florence, Italy
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Florence, Italy
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Chen F, Chen Y, Chi Y, Gao T, Zhao Y, Shao H. Diagnosis of invasive pulmonary fungal infections by a real-time panfungal PCR assay in non-neutropenic patients. Medicine (Baltimore) 2023; 102:e36385. [PMID: 38134111 PMCID: PMC10735100 DOI: 10.1097/md.0000000000036385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/09/2023] [Indexed: 12/24/2023] Open
Abstract
This study explored the utility of quantitative real-time panfungal PCR assay in diagnosing invasive pulmonary fungal diseases (IPFD) in non-neutropenic patients. Panfungal PCR assay was performed on respiratory tract specimens from patients whose clinical signs could not exclude fungal infection. At the same time, the samples were subjected to bacterial and fungal culture, microscopic examination and galactomannan antigen (GM) test in order to find the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the 4 diagnostic methods in proven and probable cases. 518 specimens were collected while 63 respiratory tract specimens tested by PCR had positive results. According to diagnostic criteria, 40 patients were diagnosed with IPFD, with 12 proven, 20 probable and 8 possible cases. Among these, 33 patients of PCR results were positive, most of which were from BALF samples (44.12%). 23 cases were caused by Aspergillus species, with Aspergillus fumigatus was the major cause. Other Aspergillus species, including Aspergillus flavus, Aspergillus terreus and Aspergillus nidulans were found in 1 sample respectively. Candida species were found in 5 samples, Pneumocystis jeroveci pneumonia (PJP) in 4 samples and Mucormycosis in 1 sample. An analysis of proven/probable diagnosis showed a sensitivity of 78.13%, specificity of 92.18%, PPV of 39.68% and NPV of 98.46% for PCR and 50%, 85.27%, 35.7%, 95.65% for GM test respectively. The Ct value difference between proven/probable and possible cases had no statistical significance (P = .824). Fungal culture showed a sensitivity of 17.5% while microscopic examination sensitivity of 32.5%. Through stratified analysis, no apparent correlation was found between the Ct value of the PCR assay and GM value (r: 0.223, P = .294). But a conjunction of the 2 tests raised the PPV of Aspergillus to 90%. As shown in this study, the panfungal RT-PCR assay has high sensitivity and consistency with serological test and culture. Its high PPV in the detection of Aspergillus and PJP were also evident.
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Affiliation(s)
- Feifei Chen
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yubao Chen
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yin Chi
- NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, China
| | - Tianyi Gao
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Youcai Zhao
- Department of Pathology Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hongtao Shao
- Department of Gerontology Medicine, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
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3
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Zhao M, Wang X, Wang K, Li Y, Wang Y, Zhou P, Wang L, Zhu W. Recombinant polymerase amplification combined with lateral flow strips for the detection of deep-seated Candida krusei infections. Front Cell Infect Microbiol 2022; 12:958858. [PMID: 36004333 PMCID: PMC9394440 DOI: 10.3389/fcimb.2022.958858] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
The incidence of Candida infections in intensive care units (ICU) has significantly increased in recent years, and these infections have become one of the most serious complications threatening the lives of ICU patients. The proportion of non-Candida albicans infections, such as Candida krusei and Candida glabrata infections, which are resistant to fluconazole, is increasing each year. Early identification of the strains causing Candida infections is important for the timely implementation of targeted treatments to save patients’ lives. However, the current methods of direct microscopy, culture, and histopathology, as well as other diagnostic methods, have many shortcomings, such as their low sensitivity and long assay times; therefore, they cannot meet the needs for early clinical diagnosis. Recombinant polymerase amplification (RPA) is a promising isothermal amplification technique that can be performed without sophisticated instruments and equipment, and is suitable for use in resource-poor areas. RPA combined with lateral flow strips (LFS) can be used to rapidly amplify and visualize target genes within 20 min. In this study, RPA-LFS was used to amplify the internal transcribed spacer 2 (ITS2) region of C. krusei. The primer-probe design was optimized by introduction of base mismatches (probe modification of five bases) to obtain a specific and sensitive primer-probe combination for the detection of clinical specimens. Thirty-five common clinical pathogens were tested with RPA-LFS to determine the specificity of the detection system. The RPA-LFS system specifically detected C. krusei without cross-reaction with other fungi or bacteria. A gradient dilution of the template was tested to explore the lower limit of detection and sensitivity of the assay. The sensitivity was 10 CFU/50 µL per reaction, without interference from genomic DNA of other species. The RPA-LFS and qPCR assays were performed on 189 clinical specimens to evaluate the detection performance of the RPA-LFS system. Seventy-six specimens were identified as C. krusei, indicating a detection rate of 40.2%. The results were consistent with those of qPCR and conventional culture methods. The RPA-LFS system established in our study provides a reliable molecular diagnostic method for the detection of C. krusei, thus meeting the urgent need for rapid, specific, sensitive, and portable clinical field testing.
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Affiliation(s)
- Mengdi Zhao
- Department of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Xizhen Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Kun Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yuanyuan Li
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yan Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Ping Zhou
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
- *Correspondence: Ping Zhou, ; Lei Wang, ; Wenjun Zhu,
| | - Lei Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- *Correspondence: Ping Zhou, ; Lei Wang, ; Wenjun Zhu,
| | - Wenjun Zhu
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
- *Correspondence: Ping Zhou, ; Lei Wang, ; Wenjun Zhu,
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Foo PC, Nurul Najian AB, Muhamad NA, Ahamad M, Mohamed M, Yean Yean C, Lim BH. Loop-mediated isothermal amplification (LAMP) reaction as viable PCR substitute for diagnostic applications: a comparative analysis study of LAMP, conventional PCR, nested PCR (nPCR) and real-time PCR (qPCR) based on Entamoeba histolytica DNA derived from faecal sample. BMC Biotechnol 2020; 20:34. [PMID: 32571286 PMCID: PMC7310076 DOI: 10.1186/s12896-020-00629-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background This study reports the analytical sensitivity and specificity of a Loop-mediated isothermal amplification (LAMP) and compares its amplification performance with conventional PCR, nested PCR (nPCR) and real-time PCR (qPCR). All the assays demonstrated in this study were developed based on Serine-rich Entamoeba histolytica protein (SREHP) gene as study model. Results A set of SREHP gene specific LAMP primers were designed for the specific detection of Entamoeba histolytica. This set of primers recorded 100% specificity when it was evaluated against 3 medically important Entamoeba species and 75 other pathogenic microorganisms. These primers were later modified for conventional PCR, nPCR and qPCR applications. Besides, 3 different post-LAMP analyses including agarose gel electrophoresis, nucleic acid lateral flow immunoassay and calcein-manganese dye techniques were used to compare their limit of detection (LoD). One E. histolytica trophozoite was recorded as the LoD for all the 3 post-LAMP analysis methods when tested with E. histolytica DNA extracted from spiked stool samples. In contrast, none of the PCR method outperformed LAMP as both qPCR and nPCR recorded LoD of 100 trophozoites while the LoD of conventional PCR was 1000 trophozoites. Conclusions The analytical sensitivity comparison among the conventional PCR, nPCR, qPCR and LAMP reveals that the LAMP outperformed the others in terms of LoD and amplification time. Hence, LAMP is a relevant alternative DNA-based amplification platform for sensitive and specific detection of pathogens.
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Affiliation(s)
- Phiaw Chong Foo
- Acarology Unit, Infectious Disease Research Centre, Institute for Medical Research, Ministry of Health Malaysia, National Institutes of Health Complex, Bandar Setia Alam, 40170, Shah Alam, Selangor, Malaysia. .,Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - A B Nurul Najian
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.,Bacteriology Unit, Infectious Disease Research Centre, Institute for Medical Research, Ministry of Health Malaysia, National Institutes of Health Complex, Bandar Setia Alam, 40170, Shah Alam, Selangor, Malaysia
| | - Nuramin A Muhamad
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Mariana Ahamad
- Acarology Unit, Infectious Disease Research Centre, Institute for Medical Research, Ministry of Health Malaysia, National Institutes of Health Complex, Bandar Setia Alam, 40170, Shah Alam, Selangor, Malaysia
| | - Maizan Mohamed
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, City Campus, Pengkalan Chepa, Locked bag 36, 16100, Kota Bharu, Kelantan, Malaysia
| | - Chan Yean Yean
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.,Hospital USM, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Boon Huat Lim
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
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Tsai MH, Lin LC, Hsu JF, Lai MY, Huang HR, Chiang MC, Lu JJ. Rapid identification of invasive fungal species using sensitive universal primers-based PCR and restriction endonuclease digestions coupled with high-resolution melting analysis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 52:728-735. [PMID: 31302087 DOI: 10.1016/j.jmii.2019.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/25/2019] [Accepted: 06/06/2019] [Indexed: 10/26/2022]
Abstract
BACKGOUND Conventional diagnosis of invasive fungal disease from blood cultures is often notoriously delayed and inadequately sensitive. We aimed to develop a universal primers-based polymerase chain reaction (PCR) assay and restriction fragment length polymorphisms (RFLP) for rapid identification of invasive fungal disease (IFD). METHODS We evaluated 16 clinical fungal species using a combination of PCR assays with 3 different restriction endonucleases targeting various internal transcribed spacer (ITS) regions and high resolution melting analysis (HRMA). Serial samples from 75 patients suspected to have IFD were analyzed for clinical verification. RESULTS We have designed a universal PCR capable of amplifying a portion of the 18S rRNA gene of 16 clinically important fungal species. The restriction patterns of most PCR products generated by EcoRI or double digested by ClaI and AvaI were different, except Aspergillus niger and Aspergillus flavus had a similar pattern, and Aspergillus fumigatus and Aspergillus terreus had a similar pattern. All these species had a unique melting curve shape using the HRMA. Both HRMA and universal PCR had adequate sensitivity, and all sixteen reference fungal species can be clearly distinguished by the universal PCR-RFLP-HRMA assay. With a reference library of 176 clinically relevant fungal strains, and 75 clinical samples from patients with suspicious IFD were tested, our assay identified 100% and 61.1% of isolates from the reference library and clinical samples, respectively. CONCLUSIONS Universal PCR and RFLP coupled with HRMA could be a highly discriminative and useful molecular diagnostic that could enhance the current diagnostic, treatment, and surveillance methods of invasive fungal disease.
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Affiliation(s)
- Ming-Horng Tsai
- Division of Neonatology and Pediatric Hematology/Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, Yunlin, Taiwan; College of Medicine, Chang Gung University, Taiwan; Graduate Institute of Clinical Medical Science, College of Medicine, Chang Gung University, Taiwan
| | - Lee-Chung Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Jen-Fu Hsu
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taiwan
| | - Mei-Yin Lai
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taiwan
| | - Hsuan-Rong Huang
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taiwan
| | - Ming-Chou Chiang
- Division of Pediatric Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan.
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6
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Dunbar S, Das S. Amplification chemistries in clinical virology. J Clin Virol 2019; 115:18-31. [PMID: 30953805 PMCID: PMC7106405 DOI: 10.1016/j.jcv.2019.03.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/19/2019] [Accepted: 03/25/2019] [Indexed: 01/04/2023]
Abstract
Molecular diagnostic methods have evolved and matured considerably over the last several decades and are constantly being evaluated and adopted by clinical laboratories for the identification of infectious pathogens. Advancement in other technologies such as fluorescence, electronics, instrumentation, automation, and sensors have made the overall diagnostic process more accurate, sensitive, and rapid. Nucleic acid based detection procedures, which rely on the fundamental principles of DNA replication have emerged as a popular and standard diagnostic method, and several commercial assays are currently available based on different nucleic acid amplification techniques. This review focuses on the major amplification chemistries that are used for developing commercial assays and discusses their application in the clinical virology laboratory.
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Hwa CZR, Tsai SP, Yee JL, Van Rompay KK, Roberts JA. Evidence of simian retrovirus type D by polymerase chain reaction. J Med Primatol 2017; 46:79-86. [PMID: 28370081 DOI: 10.1111/jmp.12266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND Over the past few years, there have been reports of finding Simian retrovirus type D (SRV) in macaque colonies where some animals were characterized as antibody positive but virus negative raising questions about how SRV was transmitted or whether there is a variant strain detected by antibody but not polymerase chain reaction (PCR) in current use. METHODS We developed a three-round nested PCR assay using degenerate primers targeting the pol gene to detect for SRV serotypes 1-5 and applied this newly validated PCR assay to test macaque DNA samples collected in China from 2010 to 2015. RESULTS Using the nested PCR assay validated in this study, we found 0.15% of the samples archived on FTA® cards were positive. CONCLUSIONS The source of SRV infection identified within domestic colonies might have originated from imported macaques. The multiplex nested PCR assay developed here may supplement the current assays for SRV.
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Affiliation(s)
- Christian Z R Hwa
- Pathogen Detection Laboratory (PDL), California National Primate Research Center (CNPRC), University of California, Davis, CA, USA
| | - Sheung Pun Tsai
- Pathogen Detection Laboratory (PDL), California National Primate Research Center (CNPRC), University of California, Davis, CA, USA
| | - JoAnn L Yee
- Pathogen Detection Laboratory (PDL), California National Primate Research Center (CNPRC), University of California, Davis, CA, USA
| | - Koen K Van Rompay
- Pathogen Detection Laboratory (PDL), California National Primate Research Center (CNPRC), University of California, Davis, CA, USA
| | - Jeffrey A Roberts
- Pathogen Detection Laboratory (PDL), California National Primate Research Center (CNPRC), University of California, Davis, CA, USA
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8
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Identification of food and beverage spoilage yeasts from DNA sequence analyses. Int J Food Microbiol 2015; 213:71-8. [DOI: 10.1016/j.ijfoodmicro.2015.05.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 05/18/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
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9
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Sensitive and rapid RT-qPCR quantification of pathogenic Candida species in human blood. J Microbiol Methods 2015; 117:128-35. [PMID: 26232708 DOI: 10.1016/j.mimet.2015.07.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/27/2015] [Accepted: 07/27/2015] [Indexed: 12/23/2022]
Abstract
For accurate diagnosis and appropriate treatment of candidiasis, we developed a highly sensitive quantitative RT-PCR (RT-qPCR) system for five Candida species that have been reported to be the major causes of bloodstream fungal infection (Candida albicans, Candida glabrata, Candida tropicalis, Candida parapsilosis, and Candida krusei), together with a system for all pathogenic Candida species. Cells of each fungal species spiked into human peripheral blood (PB) were specifically detected at a lower detection limit of 10(0) cell/1 mL PB by this system using the newly developed specific primer sets targeting 18S or 26S rRNA of the five Candida species, together with the existing group primer set. The total count of the five Candida spp. as the sum of those obtained by using the five species primer sets was equivalent to the count obtained by using the group primer set, indicating that the group set covered the major five Candida spp. in human blood with the same degree of accuracy as the species primer sets. The RT-qPCR counts of the Candida species were in good agreement with CFU counts obtained by their culture on CHROMagar™, with a lower detection limit of 10(0)cell/mL of PB. Candida rRNA molecules were stably stored for at least 7 days at 4°C by keeping the blood specimens in an RNA stabilizing reagent. These results strongly suggest that this sensitive system is useful for accurate and rapid diagnosis of Candida bloodstream infections.
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10
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Kurtzman CP, Mateo RQ, Kolecka A, Theelen B, Robert V, Boekhout T. Advances in yeast systematics and phylogeny and their use as predictors of biotechnologically important metabolic pathways. FEMS Yeast Res 2015; 15:fov050. [PMID: 26136514 DOI: 10.1093/femsyr/fov050] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2015] [Indexed: 01/02/2023] Open
Abstract
Detection, identification and classification of yeasts have undergone a major transformation in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of the nuclear large subunit rRNA gene and from ITS now permits many laboratories to identify species quickly and accurately, thus replacing the laborious and often inaccurate phenotypic tests previously used. Phylogenetic analysis of gene sequences is leading to a major revision of yeast systematics that will result in redefinition of nearly all genera. This new understanding of species relationships has prompted a change of rules for naming and classifying yeasts and other fungi, and these new rules are presented in the recently implemented International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). The use of molecular methods for species identification and the impact of Code changes on classification will be discussed, as will use of phylogeny for prediction of biotechnological applications.
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Affiliation(s)
- Cletus P Kurtzman
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Raquel Quintilla Mateo
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven, Belgium Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Anna Kolecka
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Bart Theelen
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Vincent Robert
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Teun Boekhout
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
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11
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Kelly MS, Benjamin DK, Smith PB. The epidemiology and diagnosis of invasive candidiasis among premature infants. Clin Perinatol 2015; 42:105-17, viii-ix. [PMID: 25677999 PMCID: PMC4328135 DOI: 10.1016/j.clp.2014.10.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Invasive candidiasis is a leading infectious cause of morbidity and mortality in premature infants. Improved recognition of modifiable risk factors and antifungal prophylaxis has contributed to the recent decline in the incidence of this infection among infants. Invasive candidiasis typically occurs in the first 6 weeks of life and presents with nonspecific signs of sepsis. Definitive diagnosis relies on the growth of Candida in blood culture or cultures from other normally sterile sites, but this may identify fewer than half of cases. Improved diagnostics are needed to guide the initiation of antifungal therapy in premature infants.
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Affiliation(s)
- Matthew S. Kelly
- Duke Clinical Research Institute, Durham, North Carolina
- Department of Pediatrics, Duke University, Durham, North Carolina
| | - Daniel K. Benjamin
- Duke Clinical Research Institute, Durham, North Carolina
- Department of Pediatrics, Duke University, Durham, North Carolina
| | - P. Brian Smith
- Duke Clinical Research Institute, Durham, North Carolina
- Department of Pediatrics, Duke University, Durham, North Carolina
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12
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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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Chun K, Syndergaard C, Damas C, Trubey R, Mukindaraj A, Qian S, Jin X, Breslow S, Niemz A. Sepsis Pathogen Identification. ACTA ACUST UNITED AC 2015; 20:539-61. [PMID: 25631157 DOI: 10.1177/2211068214567345] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Indexed: 12/29/2022]
Abstract
Sepsis is a rapidly progressing, severe inflammatory response to infection, causing more than 200,000 deaths per year. Rapid, specific pathogen identification is important to guide sepsis treatment. In this review, we describe and compare currently available commercial products for sepsis diagnosis and pathogen identification, based on microbiological, molecular, and mass spectrometric technologies. Microbiological techniques, the current "gold standard" in sepsis pathogen identification, include blood culture followed by subculturing and pathogen identification via biochemical or microscopic means. These methods have been automated but nevertheless require several days to generate results. Alternative technologies, including highly multiplexed PCR-based methods and mass spectrometric approaches, can decrease the required turnaround time. Matrix-assisted laser-desorption ionization time-of-flight-based systems have recently become an attractive option to rapidly identify a broad spectrum of sepsis pathogens with good sensitivity and specificity. Effectively integrating rapid sepsis pathogen identification into the hospital workflow can improve patient outcomes and can reduce the length of hospitalization and cost per patient.
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Affiliation(s)
- Katy Chun
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Chas Syndergaard
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Carlos Damas
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Richard Trubey
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | | | - Shenyu Qian
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Xin Jin
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Scott Breslow
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
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Duclos G, Dumont JC, Ranque S, Zieleskiewicz L, Bruder N. [Meningitis to Candida albicans at the adult, use of the new diagnosis methods]. ACTA ACUST UNITED AC 2014; 33:533-5. [PMID: 25127852 DOI: 10.1016/j.annfar.2014.07.002] [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: 03/26/2014] [Accepted: 07/09/2014] [Indexed: 11/15/2022]
Abstract
Candida albicans or non-albicans are a frequent source of infection but seldom displayed in cerebrospinal fluid although responsible of an important number of nosocomial meningitis. Diagnosis is difficult which often delays treatment, which in turn hinders prognostic. This clinical case shows a patient afflicted with a deadly C. albicans meningitis and allows us to focus on new diagnostic tools and advice against this infection.
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Affiliation(s)
- G Duclos
- Département d'anesthésie-réanimation, hôpital Nord, chemin des Bourrelly, 13015 Marseille, France.
| | - J-C Dumont
- Département d'anesthésie-réanimation, hôpital de la Timone, 264, rue Saint-Pierre, 13005 Marseille, France
| | - S Ranque
- Laboratoire de mycologie médicale, hôpital de la Timone, université Aix-Marseille - Timone, 264, rue Saint-Pierre, 13005 Marseille, France
| | - L Zieleskiewicz
- Département d'anesthésie-réanimation, hôpital Nord, chemin des Bourrelly, 13015 Marseille, France
| | - N Bruder
- Département d'anesthésie-réanimation, hôpital de la Timone, 264, rue Saint-Pierre, 13005 Marseille, France
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15
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Oz Y, Kiraz N. Diagnostic methods for fungal infections in pediatric patients: microbiological, serological and molecular methods. Expert Rev Anti Infect Ther 2014; 9:289-98. [DOI: 10.1586/eri.10.168] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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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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Mallus F, Martis S, Serra C, Loi G, Camboni T, Manzin A. Usefulness of capillary electrophoresis-based multiplex PCR assay for species-specific identification of Candida spp. J Microbiol Methods 2012; 92:150-2. [PMID: 23220101 DOI: 10.1016/j.mimet.2012.11.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 11/30/2012] [Accepted: 11/30/2012] [Indexed: 10/27/2022]
Abstract
The study evaluated the performances of a commercial multiplex PCR assay, the Seegene Seeplex STI Master Panel 3, for Candida spp. identification. Eighty clinical strains of Candida spp. were identified with this system and a homemade multiplex PCR assay. The results were also compared with those obtained with two phenotypic methods. The study provided a preliminary evaluation of a multiplex assay from Seegene that uses capillary electrophoresis as the detection of amplified products. The Seeplex assay was found to be a rapid and useful method for identifying large numbers of yeast isolates in the clinical laboratory context.
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Affiliation(s)
- F Mallus
- Department of Biomedical Sciences, Microbiology and Virology Unit, University of Cagliari, Italy
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18
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Ahmad S, Khan Z. Invasive candidiasis: A review of nonculture-based laboratory diagnostic methods. Indian J Med Microbiol 2012; 30:264-9. [DOI: 10.4103/0255-0857.99482] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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19
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Pathak E, El-Borai FE, Campos-Herrera R, Johnson EG, Stuart RJ, Graham JH, Duncan LW. Use of real-time PCR to discriminate parasitic and saprophagous behaviour by nematophagous fungi. Fungal Biol 2012; 116:563-73. [DOI: 10.1016/j.funbio.2012.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 01/06/2012] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
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Bousbia S, Papazian L, Saux P, Forel JM, Auffray JP, Martin C, Raoult D, La Scola B. Repertoire of intensive care unit pneumonia microbiota. PLoS One 2012; 7:e32486. [PMID: 22389704 PMCID: PMC3289664 DOI: 10.1371/journal.pone.0032486] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 01/31/2012] [Indexed: 12/14/2022] Open
Abstract
Despite the considerable number of studies reported to date, the causative agents of pneumonia are not completely identified. We comprehensively applied modern and traditional laboratory diagnostic techniques to identify microbiota in patients who were admitted to or developed pneumonia in intensive care units (ICUs). During a three-year period, we tested the bronchoalveolar lavage (BAL) of patients with ventilator-associated pneumonia, community-acquired pneumonia, non-ventilator ICU pneumonia and aspiration pneumonia, and compared the results with those from patients without pneumonia (controls). Samples were tested by amplification of 16S rDNA, 18S rDNA genes followed by cloning and sequencing and by PCR to target specific pathogens. We also included culture, amoeba co-culture, detection of antibodies to selected agents and urinary antigen tests. Based on molecular testing, we identified a wide repertoire of 160 bacterial species of which 73 have not been previously reported in pneumonia. Moreover, we found 37 putative new bacterial phylotypes with a 16S rDNA gene divergence ≥ 98% from known phylotypes. We also identified 24 fungal species of which 6 have not been previously reported in pneumonia and 7 viruses. Patients can present up to 16 different microorganisms in a single BAL (mean ± SD; 3.77 ± 2.93). Some pathogens considered to be typical for ICU pneumonia such as Pseudomonas aeruginosa and Streptococcus species can be detected as commonly in controls as in pneumonia patients which strikingly highlights the existence of a core pulmonary microbiota. Differences in the microbiota of different forms of pneumonia were documented.
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Affiliation(s)
- Sabri Bousbia
- URMITE, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine, CNRS-IRD UMR 6236, Marseille, France
| | - Laurent Papazian
- Service de Réanimation Médicale, Hôpital Nord, Marseille, France
| | - Pierre Saux
- Département d'Anesthésie-Réanimation, Hôpital la Timone, Marseille, France
| | - Jean Marie Forel
- Service de Réanimation Médicale, Hôpital Nord, Marseille, France
| | | | - Claude Martin
- Département d'Anesthésie-Réanimation, Hôpital Nord, Marseille, France
| | - Didier Raoult
- URMITE, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine, CNRS-IRD UMR 6236, Marseille, France
| | - Bernard La Scola
- URMITE, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine, CNRS-IRD UMR 6236, Marseille, France
- * E-mail:
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21
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Kourkoumpetis TK, Fuchs BB, Coleman JJ, Desalermos A, Mylonakis E. Polymerase chain reaction-based assays for the diagnosis of invasive fungal infections. Clin Infect Dis 2012; 54:1322-31. [PMID: 22362884 DOI: 10.1093/cid/cis132] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Currently accepted fungal diagnostic techniques, such as culture, biopsy, and serology, lack rapidity and efficiency. Newer diagnostic methods, such as polymerase chain reaction (PCR)-based assays, have the potential to improve fungal diagnostics in a faster, more sensitive, and specific manner. Preliminary data indicate that, when PCR-based fungal diagnostic assays guide antifungal therapy, they may lower patient mortality and decrease unnecessary antifungal treatment, improving treatment-associated costs and avoiding toxicity. Moreover, newer PCR techniques can identify antifungal resistance DNA loci, but the clinical correlation between those loci and clinical failure has to be studied further. In addition, future studies need to focus on the implementation of PCR techniques in clinical decision making and on combining them with other diagnostic tests. A consensus on the standardization of PCR techniques, along with validation from large prospective studies, is necessary to allow widespread adoption of these assays.
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Affiliation(s)
- Themistoklis K Kourkoumpetis
- Department of Medicine, Infectious Disease Division, Massachusetts General Hospital, Harvard Medical School, Boston 02214, USA
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22
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Reichard U, Buchheidt D, Lass-Flörl C, Loeffler J, Lugert R, Ruhnke M, Tintelnot K, Weig M, Groß U. Interlaboratory comparison of PCR-based identification of Candida and Aspergillus DNA in spiked blood samples. Mycoses 2012; 55:426-34. [PMID: 22248125 DOI: 10.1111/j.1439-0507.2011.02167.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Despite PCR per se being a powerful and sensitive technique, regarding the detection of fungi in patients' blood, no consensus for a standardised PCR protocol yet exists. To complement other ongoing or accomplished studies which tackle this problem, the German Reference Center for Systemic Mycoses conducted an interlaboratory comparison starting with blood samples spiked with fungal cell elements. Altogether, six laboratories using in-house PCR-protocols from Germany and Austria participated in the trial. Blood samples were spiked with vital cells of Candida albicans or Aspergillus fumigatus. Candida was used in the yeast form, whereas Aspergillus cells were either spiked as conidia or as very young germlings, also known as smoo cells. Spiked blood samples contained between 10 and 10 000 cells ml(-1). Depending on the techniques used for fungal cell disruption and DNA-amplification, detection quality was variable between laboratories, but also differed within single laboratories in different trials particularly for samples spiked with less than 100 cells ml(-1). Altogether, at least regarding the detection of A. fumigatus, two of six laboratories showed constant reliable test results also with low fungal cell number spiked samples. Protocols used by these labs do not differ substantially from others. However, as particularities, one protocol included a conventional phenol chloroform extraction during the DNA preparation process and the other included a real time PCR-protocol based on FRET probes. Other laboratory comparisons on the basis of clinical samples should follow to further evaluate the procedures. The difficulties and problems of such trials in general are discussed.
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Affiliation(s)
- Utz Reichard
- Department of Medical Microbiology and National Reference Center for Systemic Mycoses, University Hospital of Goettingen, Germany.
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Mokaddas E, Khan ZU, Ahmad S, Nampoory MRN, Burhamah M. Value of (1-3)-β-d-glucan, Candida mannan and Candida DNA detection in the diagnosis of candidaemia. Clin Microbiol Infect 2011; 17:1549-53. [PMID: 21883664 DOI: 10.1111/j.1469-0691.2011.03608.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study determined the value of (1,3)-β-d-glucan (BDG), Candida mannan (MN) and Candida species-specific DNA as surrogates for diagnosis of candidaemia. Thirty-nine patients yielding Candida species in blood cultures were investigated for presence of BDG, MN and Candida species-specific DNA in serum samples. The Candida spp. bloodstream isolates included C. albicans (n = 16), C. tropicalis (n = 10), C. parapsilosis (n = 7), C. glabrata (n = 3) and C. dubliniensis (n = 3). Positivity of the three markers was as follows: Candida DNA for corresponding Candida species, 100%; BDG, 87%; MN, 59%. Despite varying sensitivities of these biomarkers, they provided a useful adjunct to the diagnosis of candidaemia.
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Affiliation(s)
- E Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University
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Figueras C, Díaz de Heredia C, García JJ, Navarro M, Ruiz-Contreras J, Rossich R, Rumbao J, Frick MA, Roselló EM. [The Spanish Society of Paediatric Infectious Diseases (SEIP) recommendations on the diagnosis and management of invasive candidiasis]. An Pediatr (Barc) 2011; 74:337.e1-337.e17. [PMID: 21396895 DOI: 10.1016/j.anpedi.2010.12.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 02/02/2023] Open
Abstract
Candida yeasts are ubiquitous commensals, which can cause opportunistic infection in any location of the body. The source of infection may be both endogenous and exogenous. Invasive candidiasis encompasses different entities ranging from invasive candidiasis to disseminated multiorgan infection. Invasive candidiasis is the third leading cause of nosocomial bloodstream infection and the fourth of all nosocomial infections. It is also the most common invasive fungal infection in non-neutropenic critically ill patients, with a remarkable increase in the last 20 years owing to the increased survival of these patients and to more complex diagnostic, therapeutic and surgical procedures. Its incidence in infants, according to recent reviews, stands at 38.8 cases/100,000 children younger than 1 year. Candida albicans remains the most frequent isolate in invasive infections, although infections caused by other species have risen in the last years, such as C. kruzsei, C. glabrata and C. parapsilosis; the latter causing invasive candidiasis mainly associated with central venous catheter management, especially in neonatal units. The overall mortality of invasive candidiasis is high, with 30-day mortality reaching 20-44% in some series involving paediatric patients. This report provides an update on incidence, epidemiology, clinical presentation, diagnosis, treatment and outcome of invasive infection by Candida spp. in the paediatric patient.
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Affiliation(s)
- C Figueras
- Unidad de Patología Infecciosa e Inmunodeficiencias de Pediatría, Hospital Vall d'Hebron, Barcelona, España. Coordinadora del Grupo de estudio de la IFI de la SEIP
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25
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Focke M, Stumpf F, Roth G, Zengerle R, von Stetten F. Centrifugal microfluidic system for primary amplification and secondary real-time PCR. LAB ON A CHIP 2010; 10:3210-2. [PMID: 20938554 DOI: 10.1039/c0lc00161a] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Pre-amplification is a basis for numerous polymerase chain reaction (PCR) protocols but bears severe contamination risks due to handling of high-copy DNA samples. Therefore we developed a self-contained centrifugal microfluidic system comprising pre-stored reagents; it enables pre-amplification of specific DNA sequences prior to automated aliquoting and real-time PCR in a modified commercial thermocycler.
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Affiliation(s)
- Maximilian Focke
- Laboratory for MEMS Applications, Department of Microsystems Engineering (IMTEK), University of Freiburg, Georges-Koehler-Allee 106, 79110, Freiburg, Germany
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26
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PCR diagnosis of invasive candidiasis: systematic review and meta-analysis. J Clin Microbiol 2010; 49:665-70. [PMID: 21106797 DOI: 10.1128/jcm.01602-10] [Citation(s) in RCA: 267] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Invasive candidiasis (IC) is a significant cause of morbidity and mortality. Diagnosis relies on culture-based methods, which lack sensitivity and delay diagnosis. We conducted a systematic review assessing the diagnostic accuracy of PCR-based methods to detect Candida spp. directly in blood samples. We searched electronic databases for prospective or retrospective cohort and case-control studies. Two reviewers abstracted data independently. Meta-analysis was performed using a hierarchical logistic regression model. Random-effects metaregression was performed to assess the effects of study methods and infection characteristics on sensitivity or specificity values. We included 54 studies with 4,694 patients, 963 of whom had proven/probable or possible IC. Perfect (100%) sensitivity and specificity for PCR in whole-blood samples was observed when patients with cases had candidemia and controls were healthy people. When PCR was performed to evaluate patients with suspected invasive candidiasis, the pooled sensitivity for the diagnosis of candidemia was 0.95 (confidence interval, 0.88 to 0.98) and the pooled specificity was 0.92 (0.88 to 0.95). A specificity of >90% was maintained in several analyses considering different control groups. The use of whole-blood samples, rRNA, or P450 gene targets and a PCR detection limit of ≤ 10 CFU/ml were associated with improved test performance. PCR positivity rates among patients with proven or probable IC were 85% (78 to 91%), while blood cultures were positive for 38% (29 to 46%). We conclude that direct PCR using blood samples had good sensitivity and specificity for the diagnosis of IC and offers an attractive method for early diagnosis of specific Candida spp. Its effects on clinical outcomes should be investigated.
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Bousbia S, Papazian L, La Scola B, Raoult D. Detection of plant DNA in the bronchoalveolar lavage of patients with ventilator-associated pneumonia. PLoS One 2010; 5:e11298. [PMID: 20585574 PMCID: PMC2891989 DOI: 10.1371/journal.pone.0011298] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 06/06/2010] [Indexed: 01/01/2023] Open
Abstract
Background Hospital-acquired infections such as nosocomial pneumonia are a serious cause of mortality for hospitalized patients, especially for those admitted to intensive care units (ICUs). Despite the number of the studies reported to date, the causative agents of pneumonia are not completely known. Herein, we found by molecular technique that vegetable and tobacco DNA may be detected in the bronchoalveolar lavage from patients with ventilator-associated pneumonia (VAP). Methodology/Principal Findings In the present study, we studied bronchoalveolar lavage (BAL) from patients admitted to ICUs with ventilator-associated pneumonia. BAL fluids were assessed with molecular tests, culture and blood culture. We successfully identified plant DNA in six patients out of 106 (6%) with ventilator-associated pneumonia. Inhalation was confirmed in four cases and suspected in the other two cases. Inhalation was significantly frequent in patients with plant DNA (four out of six patients) than those without plant DNA (three out of 100 patients) (P<0.001). Nicotiana tabacum chloroplast DNA was identified in three patients who were smokers (cases 2, 3 and 6). Cucurbita pepo, Morus bombycis and Triticum aestivum DNA were identified in cases 1, 4 and 5 respectively. Twenty-three different bacterial species, two viruses and five fungal species were identified from among these six patients by using molecular and culture techniques. Several of the pathogenic microorganisms identified are reported to be food-borne or tobacco plant-associated pathogens. Conclusions/Significance Our study shows that plants DNA may be identified in the BAL fluid of pneumonia patients, especially when exploring aspiration pneumonia, but the significance of the presence of plant DNA and its role in the pathogenesis of pneumonia is unknown and remains to be investigated. However, the identification of these plants may be a potential marker of aspiration in patients with pneumonia.
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Affiliation(s)
- Sabri Bousbia
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, Faculté de Médecine, CNRS-IRD UMR 6236-198, Marseille, France
| | - Laurent Papazian
- Service de Réanimation Médicale, Hôpitaux Sud, Marseille, France
| | - Bernard La Scola
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, Faculté de Médecine, CNRS-IRD UMR 6236-198, Marseille, France
| | - Didier Raoult
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, Faculté de Médecine, CNRS-IRD UMR 6236-198, Marseille, France
- * E-mail:
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The era of molecular and other non-culture-based methods in diagnosis of sepsis. Clin Microbiol Rev 2010; 23:235-51. [PMID: 20065332 DOI: 10.1128/cmr.00043-09] [Citation(s) in RCA: 256] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Sepsis, a leading cause of morbidity and mortality throughout the world, is a clinical syndrome with signs and symptoms relating to an infectious event and the consequent important inflammatory response. From a clinical point of view, sepsis is a continuous process ranging from systemic inflammatory response syndrome (SIRS) to multiple-organ-dysfunction syndrome (MODS). Blood cultures are the current "gold standard" for diagnosis, and they are based on the detection of viable microorganisms present in blood. However, on some occasions, blood cultures have intrinsic limitations in terms of sensitivity and rapidity, and it is not expected that these drawbacks will be overcome by significant improvements in the near future. For these principal reasons, other approaches are therefore needed in association with blood culture to improve the overall diagnostic yield for septic patients. These considerations have represented the rationale for the development of highly sensitive and fast laboratory methods. This review addresses non-culture-based techniques for the diagnosis of sepsis, including molecular and other non-culture-based methods. In particular, the potential clinical role for the sensitive and rapid detection of bacterial and fungal DNA in the development of new diagnostic algorithms is discussed.
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Abstract
Neonatal candidiasis is serious and often fatal. Blood culture, the standard for diagnosis, has a sensitivity of 50% or less, and isolate speciation and susceptibility takes several days. This review explores recent advances in Candida detection using various diagnostic strategies.
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Vemulapalli R, Gulani J, Santrich C. A real-time TaqMan RT-PCR assay with an internal amplification control for rapid detection of transmissible gastroenteritis virus in swine fecal samples. J Virol Methods 2009; 162:231-5. [PMID: 19729039 PMCID: PMC7112873 DOI: 10.1016/j.jviromet.2009.08.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Revised: 08/16/2009] [Accepted: 08/25/2009] [Indexed: 01/22/2023]
Abstract
A TaqMan probe-based real-time RT-PCR assay was developed for simultaneous detection of RNA of transmissible gastroenteritis virus (TGEV) in pig fecal samples and RNA of enhanced green fluorescent protein (EGFP) added exogenously as an internal amplification control. The TGEV primers and probe were designed to be specific to a portion of the S gene sequence conserved in all TGEV isolates, but absent in the closely related porcine respiratory coronaviruses. The optimized TaqMan assay detected a minimum of 2.8 copies of in vitro transcribed RNA of the target S gene and RNA extracted from 1 TCID50/ml of TGEV. Using 113 clinical samples received at our diagnostic laboratory over a 4-year period, the performance of the assay was tested and compared with that of a previously described nested RT-PCR assay. All the fecal samples which tested positive for TGEV by the nested RT-PCR assay also tested positive by the TaqMan assay. However, approximately 9% of the samples that tested negative by the nested RT-PCR assay tested positive by the TaqMan assay. These results indicate that the developed TaqMan assay is a highly sensitive diagnostic test for rapid detection of TGEV in pig fecal samples.
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Affiliation(s)
- Ramesh Vemulapalli
- Molecular Diagnostics Section, Animal Disease Diagnostic Laboratory, Purdue University, West Lafayette, IN 47907, USA.
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