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Abstract
The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.
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Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg Lluís Companys 23, 08010 Barcelona, Spain
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Schroers HJ, O’Donnell K, Lamprecht SC, Kammeyer PL, Johnson S, Sutton DA, Rinaldi MG, Geiser DM, Summerbell RC. Taxonomy and phylogeny of theFusarium dimerumspecies group. Mycologia 2017; 101:44-70. [DOI: 10.3852/08-002] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Kerry O’Donnell
- National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, Illinois 61604
| | | | | | - Stuart Johnson
- Loyola University Medical Center, Maywood, Illinois 60153
| | | | - Michael G. Rinaldi
- Fungus Testing Laboratory, University of Texas Health Science Center at San Antonio, Texas 78229
| | - David M. Geiser
- Department of Plant Pathology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Richard C. Summerbell
- Sporometrics Inc., 219 Dufferin Street, Suite 20C, Toronto, Ontario, M6K 1Y9, Canada; CBS Fungal Biodiversity Centre, Utrecht, The Netherlands
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Chin VK, Foong KJ, Maha A, Rusliza B, Norhafizah M, Chong PP. Early expression of local cytokines during systemic Candida albicans infection in a murine intravenous challenge model. Biomed Rep 2014; 2:869-874. [PMID: 25279161 DOI: 10.3892/br.2014.365] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 08/13/2014] [Indexed: 12/22/2022] Open
Abstract
Local cytokine production is a significant indicator for disease pathogenesis or progression. Previous studies on cytokine production during systemic Candida albicans (C. albicans) infection were solely on kidney or single cell type interaction with C. albicans. Therefore, the present study aimed to assess the early cytokine expression of various target organs (kidney, spleen and brain) over a 72-h time course during systemic C. albicans infection. The local cytokine profiles of the target organs during systemic C. albicans infection were measured by cytometric bead array and ELISA analysis. The results demonstrated that interleukin-6 (IL-6) and IL-2 were statistically significant (P<0.05) in the spleen at 24 and 72 h post-infection, whereas in the kidney, IL-6 and tumor necrosis factor-α (TNF-α) were statistically significant (P<0.05) at 24 and 72 h post-infection and CXCL-1 and transforming growth factor-β (TGF-β) were statistically significant (P<0.05) at 72 h post-infection. In the brain, IL-6 and TNF-α were statistically significant (P<0.05) at 24 and 72 h post-infection, whereas TGF-β was statistically significant (P<0.05) at 72 h post-infection. These findings demonstrate that host immune responses were varied among target organs during systemic C. albicans infection. This could be important for designing targeted immunotherapy against this pathogen through immunomodulatory approaches in future exploratory research.
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Affiliation(s)
- Voon Kin Chin
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Kuan Jeang Foong
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Abdullah Maha
- Department of Pathology, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Basir Rusliza
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Mohtarrudin Norhafizah
- Department of Pathology, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Pei Pei Chong
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang, Selangor 43400, Malaysia ; Translational Infectious Diseases Program, Centre for Translational Medicine, Department of Microbiology, National University of Singapore, Singapore 117597, Republic of Singapore
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Liao MH, Lin JF, Li SY. Application of a multiplex suspension array for rapid and simultaneous identification of clinically important mold pathogens. Mol Cell Probes 2012; 26:188-93. [DOI: 10.1016/j.mcp.2012.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 06/14/2012] [Accepted: 06/25/2012] [Indexed: 11/29/2022]
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Gaitanis G, Magiatis P, Hantschke M, Bassukas ID, Velegraki A. The Malassezia genus in skin and systemic diseases. Clin Microbiol Rev 2012; 25:106-41. [PMID: 22232373 DOI: 10.1128/CMR.00021-11] [Citation(s) in RCA: 353] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the last 15 years, the genus Malassezia has been a topic of intense basic research on taxonomy, physiology, biochemistry, ecology, immunology, and metabolomics. Currently, the genus encompasses 14 species. The 1996 revision of the genus resulted in seven accepted taxa: M. furfur, M. pachydermatis, M. sympodialis, M. globosa, M. obtusa, M. restricta, and M. slooffiae. In the last decade, seven new taxa isolated from healthy and lesional human and animal skin have been accepted: M. dermatis, M. japonica, M. yamatoensis, M. nana, M. caprae, M. equina, and M. cuniculi. However, forthcoming multidisciplinary research is expected to show the etiopathological relationships between these new species and skin diseases. Hitherto, basic and clinical research has established etiological links between Malassezia yeasts, pityriasis versicolor, and sepsis of neonates and immunocompromised individuals. Their role in aggravating seborrheic dermatitis, dandruff, folliculitis, and onychomycosis, though often supported by histopathological evidence and favorable antifungal therapeutic outcomes, remains under investigation. A close association between skin and Malassezia IgE binding allergens in atopic eczema has been shown, while laboratory data support a role in psoriasis exacerbations. Finally, metabolomic research resulted in the proposal of a hypothesis on the contribution of Malassezia-synthesized aryl hydrocarbon receptor (AhR) ligands to basal cell carcinoma through UV radiation-induced carcinogenesis.
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Ando A, Shigenari A, Ota M, Sada M, Kawata H, Azuma F, Kojima-Shibata C, Nakajoh M, Suzuki K, Uenishi H, Kulski JK, Inoko H. SLA-DRB1 and -DQB1 genotyping by the PCR-SSOP-Luminex method. ACTA ACUST UNITED AC 2011; 78:49-55. [PMID: 21506937 DOI: 10.1111/j.1399-0039.2011.01669.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A simple and novel genotyping method was developed to detect alleles at the swine leukocyte antigen (SLA)-DRB1 and -DQB1 class II loci by using polymerase chain reaction (PCR)-fluorescently labeled sequence-specific oligonucleotide probes (SSOPs) and Luminex 100 xMAP detection. The PCR-SSOP-Luminex method exhibited accuracy of 95% for both SLA-DRB1 and -DQB1 in 6 homozygous and 16 heterozygous pig samples as confirmed by sequencing the PCR products of the same samples. In addition, 12 low-resolution SLA class II haplotypes consisting of 7 and 9 DRB1 and DQB1 alleles were identified, respectively, in one population of 283 Landrace pigs. This genotyping method facilitates the rapid and accurate identification of two- or four-digit alleles at the SLA-DRB1 and -DQB1 loci.
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Affiliation(s)
- A Ando
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
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Clotilde LM, Bernard C, Hartman GL, Lau DK, Carter JM. Microbead-based immunoassay for simultaneous detection of Shiga toxins and isolation of Escherichia coli O157 in foods. J Food Prot 2011; 74:373-9. [PMID: 21375872 DOI: 10.4315/0362-028x.jfp-10-344] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a significant foodborne pathogen with great economic consequences. There has been an increased food safety concern with this organism since outbreaks of human illnesses caused by this pathogen were first reported in 1982. Therefore, developing a reliable, sensitive, and rapid assay capable of detecting E. coli O157 and the main toxins produced by STEC (i.e., Shiga toxins 1 [Stx(1)] and 2 [Stx(2)]) will directly benefit regulatory agencies by minimizing analysis time. Here, we use Luminex technology to detect multiple analytes in a single 50-ml sample. Using commercially available monoclonal antibodies coupled to carboxylated magnetic microbeads, we developed an immunoassay capable of simultaneously serotyping E. coli O157 and detecting Stx(1) and/or Stx(2). The specificity and sensitivity of this immunoassay was tested against a collection of 34 E. coli isolates belonging to various O serogroups phenotypically different for Stx. The results were compared with microplate sandwich enzyme-linked immunosorbent assay (ELISA), and no cross-reactivity was observed for any of the monoclonal antibodies used. An increased sensitivity up to 1,000 times was observed in the microbead-based immunoassay when compared with the microplate sandwich ELISA. The results indicate that Luminex technology has the potential to simultaneously detect multiple targets without loss of specificity and/or sensitivity. A blind experiment was conducted with 48 samples of ground beef, lettuce, and milk spiked with ≤2 CFU/g E. coli. All the samples were correctly identified, with no false positives or false negatives. This microbead-based immunoassay could be extended to simultaneously detect additional foodborne pathogens and their toxic markers.
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Affiliation(s)
- Laurie M Clotilde
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA 94710, USA
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Pfrender M, Hawkins C, Bagley M, Courtney G, Creutzburg B, Epler J, Fend S, Ferrington L, Hartzell P, Jackson S, Larsen D, Lévesque C, Morse J, Petersen M, Ruiter D, Schindel D, Whiting M. Assessing Macroinvertebrate Biodiversity in Freshwater Ecosystems: Advances and Challenges in DNA-based Approaches. The Quarterly Review of Biology 2010; 85:319-40. [DOI: 10.1086/655118] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Deak E, Etienne KA, Lockhart SR, Gade L, Chiller T, Balajee SA. Utility of a Luminex-based assay for multiplexed, rapid species identification of Candida isolates from an ongoing candidemia surveillance. Can J Microbiol 2010; 56:348-51. [PMID: 20453902 DOI: 10.1139/w10-003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A Candida-specific Luminex-based assay with 11 probes was employed for multiplexed, rapid identification of 1182 Candida sp. isolates that were received as part of an ongoing population-based surveillance. All the Candida isolates were previously identified by a combination of methods, including phenotype and sequence analysis. Results showed that the Luminex assay was an attractive alternative to reference methods, as it is rapid, yields correct species identification, and is user friendly.
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Affiliation(s)
- Eszter Deak
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Mayali X, Palenik B, Burton RS. Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology. Environ Microbiol 2010; 12:975-89. [DOI: 10.1111/j.1462-2920.2004.02142.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nishigaki Y, Ueno H, Coku J, Koga Y, Fujii T, Sahashi K, Nakano K, Yoneda M, Nonaka M, Tang L, Liou CW, Paquis-Flucklinger V, Harigaya Y, Ibi T, Goto Y, Hosoya H, DiMauro S, Hirano M, Tanaka M. Extensive screening system using suspension array technology to detect mitochondrial DNA point mutations. Mitochondrion 2010; 10:300-8. [PMID: 20064630 DOI: 10.1016/j.mito.2010.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 11/25/2009] [Accepted: 01/05/2010] [Indexed: 11/21/2022]
Abstract
We established an extensive and rapid system using suspension array to detect 61 representative mitochondrial DNA (mtDNA) heteroplasmic or homoplasmic point mutations (29 for Series A and 32 for Series B) in 22 genes: 1 each in MT-RNR1, -TV, -ND1, -TQ, -TW, -TC, and -TH genes; 2 each in MT-TN, -TG, -ND4, -TL2, -TE, and -CYB genes; 3 each in MT-ATP6, -ND3, and -ND5 genes; 4 each in MT-CO1 and -TK genes; 5 each in MT-TI, -TS1, and -ND6 genes; and 10 in the MT-TL1 gene. We carefully selected 5'-biotinylated primers and pooled primers for use in two sets of multiplex-PCR amplifications. To detect both mutant and wild-type mtDNA, even when polymorphisms were present near the target mutation sites, we designed specific oligonucleotide probes. By using the mtDNA point mutation detection system of Series A (29 mutations) and Series B (32 mutations), we screened a total of 3103 mutant sites in 107 DNA samples for Series A and 13,101 mutant sites in 397 DNA samples for Series B. We succeeded in determining 99.4% (Series A) and 99.6% (Series B) of the targeted mutant sites by use of the system. The 22 samples with the m.3243A>G heteroplasmic mutation revealed positive signals with both mutant- and wild-type-specific probes in this detection system with a detection limit of approximately 2%. This genetic screening platform is useful to reach a definitive diagnosis for mitochondrial diseases.
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Wang J, Yang Y, Zhou L, Wang J, Jiang Y, Hu K, Sun X, Hou Y, Zhu Z, Guo Z, Ding Y, Yang R. Simultaneous detection of five biothreat agents in powder samples by a multiplexed suspension array. Immunopharmacol Immunotoxicol 2010; 31:417-27. [PMID: 19555207 DOI: 10.1080/08923970902740837] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A suspension array-based multiplexed immunoassay was developed for rapid, sensitive, specific, and simultaneous detection of multiple biothreat-associated agents in powder samples. The 5-plexed immunoassays using sets of 9-plexed coupled fluorescent beads were employed to simultaneously detect five representative biothreat agents, including B. anthracis spore, Y. pestis, SARS-CoV, staphylococcal enterotoxin B (SEB) and ricin from a single powder sample and the feasibility for field samples was demonstrated by both blinded and standard laboratory trials. The detection sensitivity and dynamic range for the five biothreat agents from different powders might be varied depending on the nature of the powder and the feature of the contaminating agent. The limit of detection for Y. pestis, B. anthracis spores, SEB, ricin, SARS-CoV N protein in milk powder was 20 cfu, 111 cfu, 110pg, 5.4 ng and 2 ng per test respectively. Compared to conventional ELISA method, the suspension array has a higher sensitive ability, and can detect five biothreat agents simultaneously with high reproducibility.
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Affiliation(s)
- Jing Wang
- Institute of Health Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, People's Republic of China
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Lau A, Chen S, Sleiman S, Sorrell T. Current status and future perspectives on molecular and serological methods in diagnostic mycology. Future Microbiol 2009; 4:1185-222. [DOI: 10.2217/fmb.09.70] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.
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Affiliation(s)
- Anna Lau
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia
| | - Sharon Chen
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia and Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sue Sleiman
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Tania Sorrell
- Centre for Infectious Diseases & Microbiology, Westmead Hospital, Darcy and Hawkesbury Roads, Westmead, NSW 2145, Australia
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Etienne KA, Kano R, Balajee SA. Development and validation of a microsphere-based Luminex assay for rapid identification of clinically relevant aspergilli. J Clin Microbiol 2009; 47:1096-100. [PMID: 19244469 DOI: 10.1128/JCM.01899-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Luminex-based assay for the rapid identification of Aspergillus species was designed, optimized, and validated with 131 clinical isolates of Aspergillus fumigatus, A. flavus, A. niger, A. terreus, A. ustus, and A. versicolor. The six species-specific probes were directed toward the internal transcribed spacer 1 (ITS-1) region and tested in a multiplex format with results generated within 6 h. Species identifications generated by the Aspergillus Luminex assay were 100% concordant with results from comparative sequence analyses of the ITS-1 region and showed excellent specificity. The Aspergillus Luminex assay is a rapid, relatively simple method that may prove to be a useful diagnostic tool for rapid Aspergillus identification in clinical laboratory settings.
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Chaturvedi V. The role of flow cytometry in medical mycology. Curr Fungal Infect Rep 2008. [DOI: 10.1007/s12281-008-0021-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
Culture-based methods used for microbial detection and identification are simple to use, relatively inexpensive, and sensitive. However, culture-based methods are too time-consuming for high-throughput testing and too tedious for analysis of samples with multiple organisms and provide little clinical information regarding the pathogen (e.g., antibiotic resistance genes, virulence factors, or strain subtype). DNA-based methods, such as polymerase chain reaction (PCR), overcome some these limitations since they are generally faster and can provide more information than culture-based methods. One limitation of traditional PCR-based methods is that they are normally limited to the analysis of a single pathogen, a small group of related pathogens, or a small number of relevant genes. Microarray technology enables a significant expansion of the capability of DNA-based methods in terms of the number of DNA sequences that can be analyzed simultaneously, enabling molecular identification and characterization of multiple pathogens and many genes in a single array assay. Microarray analysis of microbial pathogens has potential uses in research, food safety, medical, agricultural, regulatory, public health, and industrial settings. In this article, we describe the main technical elements of microarray technology and the application and potential use of DNA microarrays for food microbial analysis.
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Affiliation(s)
- Avraham Rasooly
- U.S. Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, Maryland, USA.
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Affiliation(s)
- Mara R. Diaz
- University of Miami, Rosenstiel School of Marine and Atmospheric Science Miami Florida
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Zhang H, Yang X, Wang K, Tan W, Zhou L, Zuo X, Wen J, Chen Y. Detection of single-base mutations using 1-D microfluidic beads array. Electrophoresis 2008; 28:4668-78. [PMID: 18072213 DOI: 10.1002/elps.200700048] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The application of a 1-D microfluidic beads array that is composed of individually addressable functionalized SiO2 beads has been demonstrated for detection of single-base mutations based on "sandwich" hybridization assay without additional sample labeling and PCR amplification. We concentrated on detection of mutations in the human p53 tumor suppressor gene with more than 50% mutation frequency in the known human cancers. Using a microinjection system, functionalized beads could be selectively and linearly arrayed in a single microfluidic channel comprising many periodic chambers. This 1-D microfluidic beads array was sufficiently sensitive to identify single-nucleotide mutations in 40 pM quantities of DNA targets and could discriminate the mutated alleles in an excess of nonmutated alleles at a level of one mutant in 100 wild-type sequences. The surface of beads was regenerated and rehybridized up to six times without obvious loss of signal. The entire reaction process was done at room temperature within minutes, and only 2-10 microL sample solution was needed to complete the whole detection process. The p53 genotypes of A549, CNE2, and SKBr-3 cell lines were also correctly evaluated by using mRNA extracts as target without need for sample labeling and amplification. Thus, this platform enabled rapid and exact discrimination of gene mutations with the advantages of reusability, simple handling of liquid, low cost, and little reagent consumption.
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Affiliation(s)
- He Zhang
- State Key Laboratory of Chemo/Biosensing & Chemometrics, Biomedical Engineering Center, College of Chemistry & Chemical Engineering, Hunan University, Changsha, Hunan, PR China
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Wang QM, Li J, Wang SA, Bai FY. Rapid differentiation of phenotypically similar yeast species by single-strand conformation polymorphism analysis of ribosomal DNA. Appl Environ Microbiol 2008; 74:2604-11. [PMID: 18344345 DOI: 10.1128/AEM.02223-07] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Single-strand conformation polymorphism (SSCP) analysis of ribosomal DNA (rDNA) was investigated for rapid differentiation of phenotypically similar yeast species. Sensitive tests indicated that some yeast strains with one, most strains with two, and all strains with three or more nucleotide differences in the internal transcribed spacer 1 (ITS1) or ITS2 region could be distinguished by PCR SSCP analysis. The discriminative power of SSCP in yeast species differentiation was demonstrated by comparative studies of representative groups of yeast species from ascomycetes and basidiomycetes, including Saccharomyces species, medically important Candida species, and phylloplane basidiomycetous yeast species. Though the species within each group selected are closely related and have relatively similar rDNA sequences, they were clearly differentiated by PCR-SSCP analysis of the ITS1 region, given the amplified fragments were less than 350 bp in sizes. By using SSCP analysis for rapid screening of yeast strains with different rDNA sequences, species diversity existing in a large collection of yeast strains from natural sources was effectively and thoroughly investigated with substantially reduced time and cost in subsequent DNA sequencing.
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Young SH, Antonini JM, Roberts JR, Erdely AD, Zeidler-Erdely PC. Performance evaluation of cytometric bead assays for the measurement of lung cytokines in two rodent models. J Immunol Methods 2008; 331:59-68. [DOI: 10.1016/j.jim.2007.11.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Accepted: 11/14/2007] [Indexed: 11/16/2022]
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Li J, Zhong W. A two-dimensional suspension array system by coupling field flow fractionation to flow cytometry. J Chromatogr A 2008; 1183:143-9. [PMID: 18243223 DOI: 10.1016/j.chroma.2008.01.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 01/08/2008] [Accepted: 01/14/2008] [Indexed: 10/22/2022]
Abstract
Flow field flow fractionation (Fl-FFF) was coupled to flow cytometry to improve the performance of suspension arrays. Size-based separation of the protein-conjugated microspheres by Fl-FFF was performed and the results demonstrated that, the separation could tolerate a wide range of carrier fluid conditions (pH values, salt concentrations, and buffer compositions) favorable for immunoassays. The immuno-complex remained intact during Fl-FFF, as revealed by fluorescence measurements before and after the Fl-FFF separation, and SDS-PAGE of the eluted proteins. The sample throughput of the suspension array can be increased several folds by using particles of different sizes and separating them with Fl-FFF before flow cytometric measurement. Moreover, the gel result hinted that the continuous wash inside the Fl-FFF system may lower the assay background, another possible advantage of the two-dimensional suspension array system.
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Affiliation(s)
- Jishan Li
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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Spiess B, Seifarth W, Hummel M, Frank O, Fabarius A, Zheng C, Mörz H, Hehlmann R, Buchheidt D. DNA microarray-based detection and identification of fungal pathogens in clinical samples from neutropenic patients. J Clin Microbiol 2007; 45:3743-53. [PMID: 17715373 PMCID: PMC2168469 DOI: 10.1128/jcm.00942-07] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing incidence of invasive fungal infections (IFI) in immunocompromised patients emphasizes the need to improve diagnostic tools. We established a DNA microarray to detect and identify DNA from 14 fungal pathogens (Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus, Candida albicans, Candida dubliniensis, Candida glabrata, Candida lusitaniae, Candida tropicalis, Fusarium oxysporum, Fusarium solani, Mucor racemosus, Rhizopus microsporus, Scedosporium prolificans, and Trichosporon asahii) in blood, bronchoalveolar lavage, and tissue samples from high-risk patients. The assay combines multiplex PCR and consecutive DNA microarray hybridization. PCR primers and capture probes were derived from unique sequences of the 18S, 5.8S, and internal transcribed spacer 1 regions of the fungal rRNA genes. Hybridization with genomic DNA of fungal species resulted in species-specific hybridization patterns. By testing clinical samples from 46 neutropenic patients with proven, probable, or possible IFI or without IFI, we detected A. flavus, A. fumigatus, C. albicans, C. dubliniensis, C. glabrata, F. oxysporum, F. solani, R. microsporus, S. prolificans, and T. asahii. For 22 of 22 patients (5 without IFI and 17 with possible IFI), negative diagnostic results corresponded with negative microarray data. For 11 patients with proven (n = 4), probable (n = 2), and possible IFI (n = 5), data for results positive by microarray were validated by other diagnostic findings. For 11 of 11 patients with possible IFI, the microarray results provided additional information. For two patients with proven and probable invasive aspergillosis, respectively, microarray results were negative. The assay detected genomic DNA from 14 fungal pathogens from the clinical samples, pointing to a high significance for improving the diagnosis of IFI.
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Affiliation(s)
- Birgit Spiess
- III Medizinische Universitätsklinik, Medizinische Fakultät Mannheim der Universität Heidelberg, Theodor-Kutzer-Ufer 1-3, D-68167, Mannheim, Germany
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Dunbar SA, Jacobson JW. Parallel processing in microbiology: Detection of infectious pathogens by Luminex xMAP multiplexed suspension array technology. ACTA ACUST UNITED AC 2007; 29:79-86. [DOI: 10.1016/j.clinmicnews.2007.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Bovers M, Diaz MR, Hagen F, Spanjaard L, Duim B, Visser CE, Hoogveld HL, Scharringa J, Hoepelman IM, Fell JW, Boekhout T. Identification of genotypically diverse Cryptococcus neoformans and Cryptococcus gattii isolates by Luminex xMAP technology. J Clin Microbiol 2007; 45:1874-83. [PMID: 17442792 PMCID: PMC1933031 DOI: 10.1128/jcm.00223-07] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 03/05/2007] [Accepted: 04/11/2007] [Indexed: 11/20/2022] Open
Abstract
A Luminex suspension array, which had been developed for identification of Cryptococcus neoformans and Cryptococcus gattii isolates, was tested by genotyping a set of 58 mostly clinical isolates. All genotypes of C. neoformans and C. gattii were included. In addition, cerebrospinal fluid (CSF) obtained from patients with cryptococcal meningitis was used to investigate the feasibility of the technique for identification of the infecting strain. The suspension array correctly identified haploid isolates in all cases. Furthermore, hybrid isolates possessing two alleles of the Luminex probe region could be identified as hybrids. In CSF specimens, the genotype of the cryptococcal strains responsible for infection could be identified after optimization of the PCR conditions. However, further optimization of the DNA extraction protocol is needed to enhance the usability of the method in clinical practice.
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Affiliation(s)
- M Bovers
- CBS-Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584CT Utrecht, The Netherlands
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Baums IB, Goodwin KD, Kiesling T, Wanless D, Fell JW. Luminex detection of fecal indicators in river samples, marine recreational water, and beach sand. Mar Pollut Bull 2007; 54:521-36. [PMID: 17350051 PMCID: PMC1950674 DOI: 10.1016/j.marpolbul.2006.12.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 12/14/2006] [Accepted: 12/19/2006] [Indexed: 05/06/2023]
Abstract
Research to understand and remediate coastal pollution is moving toward a multitiered approach in which traditional enumeration of fecal indicators is accompanied by molecular analysis of a variety of targets. Technology that rapidly detects multiple microbial contaminants would benefit from such an approach. The Luminex 100 system is a suspension array that assays multiple analytes rapidly in a single well of a microtiter plate. The ability of the system to simultaneously detect multiple fecal indicating bacteria in environmental samples was tested. Primer/probe sets were designed to simultaneously detect the following fecal indicators: the Bacteroides fragilis group, Enterococcus spp., Escherichia coli and Shigella spp., Bacteroides distasonis, and Ent. faecalis. Specificity and sensitivity of the Luminex probes was tested against laboratory cultures. In addition, sequencing, culture plate testing, and specificity testing with environmental isolates were steps taken to validate the function of the assay with environmental samples. Luminex response to cultures and to environmental samples was consistent with sequencing results, suggesting that the technology has the potential to simultaneously detect multiple targets for coastal water quality applications, particularly as progress is made to efficiently extract DNA from water and sediment matrices.
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Affiliation(s)
- Iliana B. Baums
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Kelly D. Goodwin
- National Oceanographic and Atmospheric Administration, Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry Division, Miami, FL 33149, USA
- * Corresponding author. NOAA/AOML/Ocean Chemistry Division, 4301 Rickenbacker Causeway, Miami, FL 33149, USA. Tel.: +1 305 361 4384; fax:+1 305 361 4447. E-mail address:
| | - Traci Kiesling
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - David Wanless
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Jack W. Fell
- Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
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Abstract
Malassezia yeasts are commensals of normal human skin, but also cause pityriasis versicolor, seborrhoeic dermatitis and evidence is accumulating that they play a significant role in atopic eczema/dermatitis syndrome (AEDS; formerly atopic dermatitis). The taxonomy of the genus has changed considerably and is likely to change more in the future. Our understanding of the interaction between Malassezia and the host demonstrates that it has the paradoxical ability to both stimulate and suppress the immune response directed against it and there is a fine balance in its existence at the interface between commensalism and pathogenicity.
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Affiliation(s)
- H R Ashbee
- Mycology Reference Centre, Department of Microbiology, Leeds General Infirmary, Leeds, UK.
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Abstract
Human pathogenic aspergilli are identified in the clinical diagnostic laboratory predominantly by macro- and micro-morphology. Such phenotypic characteristics are largely subjective and unstable, as they are influenced by environmental factors, including media and temperature of incubation. Recent advances in molecular biology have impacted the field of mycology; multiple studies have noted new genetically distinct species that are not easily distinguished by phenotypic characteristics. Strengths of molecular typing methods include objectivity and the ability to identify nonsporulating or slowly growing fungi. As such, molecular methods provide powerful tools for the study of the epidemiology, evolution and population biology of fungal pathogens. This review focuses on current and future methods of identifying aspergilli, and implications regarding Aspergillus species/strain identification.
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Affiliation(s)
- S Arunmozhi Balajee
- Centers for Disease Control and Prevention, Mycotic Diseases Branch, Atlanta, GA 30333, USA.
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