Pub Date : 2015-01-01Epub Date: 2015-05-14DOI: 10.1016/bs.mim.2015.04.002
Steve Miller, Ulas Karaoz, Eoin Brodie, Sherry Dunbar
Advancements in molecular technologies have provided new platforms that are being increasingly adopted for use in the clinical microbiology laboratory. Among these, microarray methods are particularly well suited for diagnostics as they allow multiplexing, or the ability to test for multiple targets simultaneously from the same specimen. Microarray technologies commonly used for the detection and identification of microbial targets include solid-state microarrays, electronic microarrays and bead suspension microarrays. Microarray methods have been applied to microbial detection, genotyping and antimicrobial resistance gene detection. Microarrays can offer a panel approach to diagnose specific patient presentations, such as respiratory or gastrointestinal infections, and can discriminate isolates by genotype for tracking epidemiology and outbreak investigations. And, as more information has become available on specific genes and pathways involved in antimicrobial resistance, we are beginning to be able to predict susceptibility patterns based on sequence detection for particular organisms. With further advances in automated microarray processing methods and genotype-phenotype prediction algorithms, these tests will become even more useful as an adjunct or replacement for conventional antimicrobial susceptibility testing, allowing for more rapid selection of targeted therapy for infectious diseases.
{"title":"Solid and Suspension Microarrays for Microbial Diagnostics.","authors":"Steve Miller, Ulas Karaoz, Eoin Brodie, Sherry Dunbar","doi":"10.1016/bs.mim.2015.04.002","DOIUrl":"10.1016/bs.mim.2015.04.002","url":null,"abstract":"<p><p>Advancements in molecular technologies have provided new platforms that are being increasingly adopted for use in the clinical microbiology laboratory. Among these, microarray methods are particularly well suited for diagnostics as they allow multiplexing, or the ability to test for multiple targets simultaneously from the same specimen. Microarray technologies commonly used for the detection and identification of microbial targets include solid-state microarrays, electronic microarrays and bead suspension microarrays. Microarray methods have been applied to microbial detection, genotyping and antimicrobial resistance gene detection. Microarrays can offer a panel approach to diagnose specific patient presentations, such as respiratory or gastrointestinal infections, and can discriminate isolates by genotype for tracking epidemiology and outbreak investigations. And, as more information has become available on specific genes and pathways involved in antimicrobial resistance, we are beginning to be able to predict susceptibility patterns based on sequence detection for particular organisms. With further advances in automated microarray processing methods and genotype-phenotype prediction algorithms, these tests will become even more useful as an adjunct or replacement for conventional antimicrobial susceptibility testing, allowing for more rapid selection of targeted therapy for infectious diseases.</p>","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54117845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-01-01DOI: 10.1016/BS.MIM.2015.09.001
R. White, J. Cardenas, R. Hayden
{"title":"Virology: The Next Generation from Digital PCR to Single Virion Genomics","authors":"R. White, J. Cardenas, R. Hayden","doi":"10.1016/BS.MIM.2015.09.001","DOIUrl":"https://doi.org/10.1016/BS.MIM.2015.09.001","url":null,"abstract":"","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/BS.MIM.2015.09.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54117749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-01-01DOI: 10.1016/BS.MIM.2015.05.003
A. Singer, Yi-Wei Tang
{"title":"Chapter 17 - Artificial Nucleic Acid Probes and Their Applications in Clinical Microbiology","authors":"A. Singer, Yi-Wei Tang","doi":"10.1016/BS.MIM.2015.05.003","DOIUrl":"https://doi.org/10.1016/BS.MIM.2015.05.003","url":null,"abstract":"","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/BS.MIM.2015.05.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54117502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-01-01Epub Date: 2015-07-07DOI: 10.1016/bs.mim.2015.04.005
Julia Engstrom-Melnyk, Pedro L Rodriguez, Olivier Peraud, Raymond C Hein
Since the invention of the polymerase chain reaction (PCR) and discovery of Taq polymerase, PCR has become a staple in both research and clinical molecular laboratories. As clinical and diagnostic needs have evolved over the last few decades, demanding greater levels of sensitivity and accuracy, so too has PCR performance. Through optimisation, the present-day uses of real-time PCR and quantitative real-time PCR are enumerable. The technique, combined with adoption of automated processes and reduced sample volume requirements, makes it an ideal method in a broad range of clinical applications, especially in virology. Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. All of these serve vital roles in the continuum of care to enhance patient management. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats.
{"title":"Clinical Applications of Quantitative Real-Time PCR in Virology.","authors":"Julia Engstrom-Melnyk, Pedro L Rodriguez, Olivier Peraud, Raymond C Hein","doi":"10.1016/bs.mim.2015.04.005","DOIUrl":"10.1016/bs.mim.2015.04.005","url":null,"abstract":"<p><p>Since the invention of the polymerase chain reaction (PCR) and discovery of <i>Taq</i> polymerase, PCR has become a staple in both research and clinical molecular laboratories. As clinical and diagnostic needs have evolved over the last few decades, demanding greater levels of sensitivity and accuracy, so too has PCR performance. Through optimisation, the present-day uses of real-time PCR and quantitative real-time PCR are enumerable. The technique, combined with adoption of automated processes and reduced sample volume requirements, makes it an ideal method in a broad range of clinical applications, especially in virology. Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. All of these serve vital roles in the continuum of care to enhance patient management. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats.</p>","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54117437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-01-01DOI: 10.1016/BS.MIM.2015.04.001
H. Pouseele, P. Supply
{"title":"Chapter 10 - Accurate Whole-Genome Sequencing-Based Epidemiological Surveillance of Mycobacterium Tuberculosis","authors":"H. Pouseele, P. Supply","doi":"10.1016/BS.MIM.2015.04.001","DOIUrl":"https://doi.org/10.1016/BS.MIM.2015.04.001","url":null,"abstract":"","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/BS.MIM.2015.04.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54117811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-01-01DOI: 10.1016/BS.MIM.2015.05.001
B. Pritt
{"title":"Molecular diagnostics in the diagnosis of parasitic infection","authors":"B. Pritt","doi":"10.1016/BS.MIM.2015.05.001","DOIUrl":"https://doi.org/10.1016/BS.MIM.2015.05.001","url":null,"abstract":"","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/BS.MIM.2015.05.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54117449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-08-28DOI: 10.1016/BS.MIM.2014.07.001
V. Sangal, L. Nieminen, N. Tucker, P. Hoskisson
{"title":"Revolutionizing Prokaryotic Systematics Through Next-Generation Sequencing","authors":"V. Sangal, L. Nieminen, N. Tucker, P. Hoskisson","doi":"10.1016/BS.MIM.2014.07.001","DOIUrl":"https://doi.org/10.1016/BS.MIM.2014.07.001","url":null,"abstract":"","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/BS.MIM.2014.07.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54117381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-01-01DOI: 10.1016/BS.MIM.2014.05.001
Thomas Williams, S. Heaps
{"title":"An introduction to phylogenetics and the tree of life","authors":"Thomas Williams, S. Heaps","doi":"10.1016/BS.MIM.2014.05.001","DOIUrl":"https://doi.org/10.1016/BS.MIM.2014.05.001","url":null,"abstract":"","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/BS.MIM.2014.05.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54117361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-01-01DOI: 10.1016/BS.MIM.2014.05.003
Radhey S. Gupta
{"title":"Chapter 8 – Identification of Conserved Indels that are Useful for Classification and Evolutionary Studies","authors":"Radhey S. Gupta","doi":"10.1016/BS.MIM.2014.05.003","DOIUrl":"https://doi.org/10.1016/BS.MIM.2014.05.003","url":null,"abstract":"","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/BS.MIM.2014.05.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54117365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-01-01DOI: 10.1016/BS.MIM.2014.08.004
O. Kamneva, N. Ward
{"title":"Chapter 9 - Reconciliation Approaches to Determining HGT, Duplications, and Losses in Gene Trees","authors":"O. Kamneva, N. Ward","doi":"10.1016/BS.MIM.2014.08.004","DOIUrl":"https://doi.org/10.1016/BS.MIM.2014.08.004","url":null,"abstract":"","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/BS.MIM.2014.08.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54117800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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