A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS

Veloo, Alida; Jean-Pierre, Hélène; Justesen, Ulrik Stenz; Morris, Trefor; Urban, E.; Wybo, Ingrid; Shah, Haroun N.; Friedrich, Alex; Nagy, Elisabeth; Kostrzewa, Markus

doi:10.1016/j.anaerobe.2017.07.004

Cited by 12 publications

(10 citation statements)

References 13 publications

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“…The introduction of molecular methods, array-based systems and novel technological advancements in clinical microbiology, such as whole-genome sequencing (WGS) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (which utilizes the spectra of conserved ribosomal proteins for identification) has revolutionised the detection and correct identification of anaerobic bacteria. Although the development of databases containing bacterial spectra, required for identification is still underway (with projects like the ‘European Network for Rapid Identification of Anaerobes’ [ENRIA] leading the charge), MALDI-TOF MS changed the face of diagnostic bacteriology in the last decade, both in the case of aerobes and anaerobes [ 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 ]. Whole-genome sequencing is a novel technology used for culture-independent diagnostic testing (CIDT).…”

Section: Cultivation and Identification Of Anaerobesmentioning

confidence: 99%

Identification and Antimicrobial Susceptibility Testing of Anaerobic Bacteria: Rubik’s Cube of Clinical Microbiology?

2017

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Anaerobic bacteria have pivotal roles in the microbiota of humans and they are significant infectious agents involved in many pathological processes, both in immunocompetent and immunocompromised individuals. Their isolation, cultivation and correct identification differs significantly from the workup of aerobic species, although the use of new technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, whole genome sequencing) changed anaerobic diagnostics dramatically. In the past, antimicrobial susceptibility of these microorganisms showed predictable patterns and empirical therapy could be safely administered but recently a steady and clear increase in the resistance for several important drugs (β-lactams, clindamycin) has been observed worldwide. For this reason, antimicrobial susceptibility testing of anaerobic isolates for surveillance purposes or otherwise is of paramount importance but the availability of these testing methods is usually limited. In this present review, our aim was to give an overview of the methods currently available for the identification (using phenotypic characteristics, biochemical testing, gas-liquid chromatography, MALDI-TOF MS and WGS) and antimicrobial susceptibility testing (agar dilution, broth microdilution, disk diffusion, gradient tests, automated systems, phenotypic and molecular resistance detection techniques) of anaerobes, when should these methods be used and what are the recent developments in resistance patterns of anaerobic bacteria.

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Section: Cultivation and Identification Of Anaerobesmentioning

confidence: 99%

Identification and Antimicrobial Susceptibility Testing of Anaerobic Bacteria: Rubik’s Cube of Clinical Microbiology?

2017

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“…A review evaluating the performance of MALDI-TOF MS systems for identification of anaerobes comparing results published between 2010 and 2012 showed that correct species-level identification varied between 55% and 93.8% depending on the number of tested isolates and the number of different anaerobic species and genera investigated in the different studies [51]. This underlined the need for further development of databases for a broader applicability in a clinical routine which was also shown by a European ring trial with participants using different databases and yielding different performances based on the coverage of the databases [49]. In addition, an increasing number of publications about less frequently isolated or even newly described anaerobic species (e.g.…”

Section: Anaerobic Bacteriamentioning

confidence: 90%

“…High-quality spectra for anaerobes can be acquired after 24-48 h of incubation, and direct spotting of biomass from suitable colonies followed by an ontarget extraction with 70% formic acid is usually sufficient. Full extraction may only be important in routine for some groups such as GPAC and Actinomyces spp [48,49]. As intensive sporulation may cause deviations in fingerprint patterns, extended incubation time may deteriorate species identification of clostridia [43,50].…”

Section: Anaerobic Bacteriamentioning

confidence: 99%

How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria – the rare and the unknown

Kostrzewa

Nagy

Schröttner

et al. 2019

Expert Review of Molecular Diagnostics

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Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.

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“…A multicenter, multicountry clinical trial showed replicability in identification of microbiological strains. [ 115 ] This resulted in the development of MALDI‐TOF MS for clinical use in diagnostic microbiology [ 110,116,125,117–124 ] and in 2013, the Bruker MALDI Biotyper CA [ 126 ] and the bioMérieux VITEK MS [ 127 ] were approved by the FDA for clinical mass spectrometry micro‐organism identification and differentiation.…”

Section: Mass Spectrometrymentioning

confidence: 99%

Increasing Complexity to Simplify Clinical Care: High Resolution Mass Spectrometry as an Enabler of AI Guided Clinical and Therapeutic Monitoring

Yee

Drum

2020

Advanced Therapeutics

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Clinical care increasingly relies on individualized, highly multidimensional data for patient phenotyping. This review focusses on two technologies which are contributing to this trend and, in their mutual overlap, may provide a novel and powerful contribution to future clinical care. Artificial intelligence (AI), in particular the technique of deep learning, is steadily making inroads to clinical care and has demonstrated the ability to extract clinically relevant features from complex datasets. Likewise, mass spectrometry (MS), in particular high-resolution MS, is gaining the ability to provide highly multidimensional datasets from patient samples with the quality necessary for clinical decision making. The convergence of these trends has resulted in the nascent application of deep learning analytics to high resolution mass spectra. Due to the large volumes of content provided by high resolution mass spectra and the ability of multilayer neural networks to extract subtle features from complex datasets, future integration of their mutual application is identified as a research area of high priority for clinical care. Factors are identified that have contributed to historical progress for each technology and recommendations are provided to accelerate the mutual application of deep learning and mass spectrometry techniques to patient care.

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A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS

Cited by 12 publications

References 13 publications

Identification and Antimicrobial Susceptibility Testing of Anaerobic Bacteria: Rubik’s Cube of Clinical Microbiology?

Identification and Antimicrobial Susceptibility Testing of Anaerobic Bacteria: Rubik’s Cube of Clinical Microbiology?

How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria – the rare and the unknown

Increasing Complexity to Simplify Clinical Care: High Resolution Mass Spectrometry as an Enabler of AI Guided Clinical and Therapeutic Monitoring

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