Emerging Technologies for the Clinical Microbiology Laboratory

Buchan, Blake W.; Ledeboer, Nathan A.

doi:10.1128/cmr.00003-14

Cited by 248 publications

(170 citation statements)

References 256 publications

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“…Matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry (MS) has emerged as a useful technique for rapid and precise pathogen identification in clinical laboratories (7). Recent studies analyzing the performance of MALDI-TOF MS for the identification of more than 1,000 yeast isolates (Ͼ95% Candida) describe successful species identification ranging from 95 to 98% compared to DNAbased gold-standard techniques (8,9).…”

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confidence: 99%

Evaluating and Improving Vitek MS for Identification of Clinically Relevant Species of Trichosporon and the Closely Related Genera Cutaneotrichosporon and Apiotrichum

et al. 2017

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Trichosporon species are relevant etiologic agents of hospital-acquired infections. High mortality rates are attributed to Trichosporon deep-seated infections in immunocompromised individuals, making fast and accurate species identification relevant for hastening the discovery of best-targeted therapy. Recently, Trichosporon taxonomy has been reassessed, and three genera have been proposed for the pathogenic species: Trichosporon, Cutaneotrichosporon, and Apiotrichum. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has replaced old phenotypic methods for microorganism identification in clinical laboratories, but spectral profile databases have to be evaluated and improved for optimal species identification performance. Vitek MS (bioMérieux) is one of the commercially available MALDI-TOF MS platforms for pathogen identification, and its spectral profile databases remain poorly evaluated for Trichosporon, Cutaneotrichosporon, and Apiotrichum species identification. We herein evaluated and improved Vitek MS for the identification of the main clinical relevant species of Trichosporon, Cutaneotrichosporon, and Apiotrichum using a large set of strains and isolates belonging to different yeast collections in Brazil and France.KEYWORDS Trichosporon, Cutaneotrichosporon, Apiotrichum, Vitek M, MALDI-TOF mass spectrometry O pportunistic non-Candida yeasts, including Trichosporon spp., are emerging pathogens of deep-seated infections in the context of immunodepression and/or invasive procedures (1, 2). In addition, outbreaks of catheter-related fungemia by these pathogens have been described in neonatal intensive care units (3).Based on molecular phylogenetic analysis, Trichosporon pathogenic species were initially subdivided into three clades: clade Porosum, which included the species

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confidence: 99%

Evaluating and Improving Vitek MS for Identification of Clinically Relevant Species of Trichosporon and the Closely Related Genera Cutaneotrichosporon and Apiotrichum

et al. 2017

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“…Better knowledge of sequences should improve interpretation by medical biologists and, thus, the information that they provide to clinicians. Among emerging technologies for a clinical microbiology laboratory, microarray methods (chips) are more and more attractive for the detection of resistance genes (9).…”

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A Structure-Based Classification of Class A β-Lactamases, a Broadly Diverse Family of Enzymes

Slama²,

et al. 2016

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SUMMARYFor medical biologists, sequencing has become a commonplace technique to support diagnosis. Rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. This is particularly true for data concerning class A β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. Many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. We analyzed several hundred amino acid sequences of class A β-lactamase enzymes for phylogenic relationships, the presence of specific residues, and cluster patterns. A clear distinction was first made between dd-peptidases and class A enzymes based on a small number of residues (S70, K73, P107, 130SDN132, G144, E166, 234K/R, 235T/S, and 236G [Ambler numbering]). Other residues clearly separated two main branches, which we named subclasses A1 and A2. Various clusters were identified on the major branch (subclass A1) on the basis of signature residues associated with catalytic properties (e.g., limited-spectrum β-lactamases, extended-spectrum β-lactamases, and carbapenemases). For subclass A2 enzymes (e.g., CfxA, CIA-1, CME-1, PER-1, and VEB-1), 43 conserved residues were characterized, and several significant insertions were detected. This diversity in the amino acid sequences of β-lactamases must be taken into account to ensure that new enzymes are accurately identified. However, with the exception of PER types, this diversity is poorly represented in existing X-ray crystallographic data.

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“…Przedmiotem niniejszego opracowania jest charakterystyka ważniej-szych spośród nich. Omawiane techniki genetyczne, coraz częściej i szerzej zastępują testy opierające się na ocenie właściwościach fenotypowych drobnoustrojów i reakcjach antygen-przeciwciało (3,6,23,24). Dotychczas opracowano wiele technik wykrywania i analizy materiału genetycznego bakterii i wirusów, z których najbardziej istotnymi wydają się: łańcuchowa reakcja polimerazy (polymerase chain reaction -PCR) (25,26,36) wraz z jej pochodnymi modyfikacjami oraz techniki amplifikacji DNA w warunkach stałej temperatury (29,40).…”

Section: Artykuł Przeglądowy Reviewunclassified

Increasing importance of genomics in recognition of infectious animal diseases taking into account OIE requirements

Grzegorz.¹,

Truszczyński²,

Zygmunt³

2017

Medycyna Weterynaryjna

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Currently, the diagnosis methods applied in bacteriology and virology are frequently focused at modern molecular methods such as polymerase chain reaction (PCR), real-time PCR, loop-mediated isothermal amplification (LAMP) or confirmatory methods for already identified infectious agents of animals such as high throughput sequencing- HTS, or next-generation sequencing (NGS). A number of these methods are officially recommended by the World Organisation for Animal Health (OIE) for the routine diagnosis of major animal diseases with the greatest economical impact. The aim of this paper is to provide to a reader an overview on recent genomic methods used in diagnosis of infectious animal diseases along with their advantages and limitations. These methods facilitate efficient and reliable identification of animal pathogens and allow to characterize and sometimes to identify a newly recognized species of bacteria and viruses.

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Emerging Technologies for the Clinical Microbiology Laboratory

Cited by 248 publications

References 256 publications

Evaluating and Improving Vitek MS for Identification of Clinically Relevant Species of Trichosporon and the Closely Related Genera Cutaneotrichosporon and Apiotrichum

Evaluating and Improving Vitek MS for Identification of Clinically Relevant Species of Trichosporon and the Closely Related Genera Cutaneotrichosporon and Apiotrichum

A Structure-Based Classification of Class A β-Lactamases, a Broadly Diverse Family of Enzymes

Increasing importance of genomics in recognition of infectious animal diseases taking into account OIE requirements

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