Detection of Escherichia coli sequence type 131 by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: implications for infection control policies?

Lafolie, J.; Sauget, Marlène; Cabrolier, Nadège; Hocquet, Didier; Bertrand, Xavier

doi:10.1016/j.jhin.2014.12.022

Cited by 22 publications

(16 citation statements)

References 16 publications

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“…Their potential to serve as MALDI-TOF MS biomarkers has been applied to clinically relevant phylogenetic groups (Hotta et al, 2010;Ziegler et al, 2015;Rothen et al, 2019), and multiple databases using marker masses predicted from genomic data are now available (Kassim et al, 2017;Ojima-Kato et al, 2017;Tomachewski et al, 2018). A ribosomal marker based approach has successfully been applied to distinguish between subspecies and clonal complexes within species such as Streptococcus agalactiae and Escherichia coli (Matsumura et al, 2014;Lafolie et al, 2015;Rothen et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Factors Associated With MALDI-TOF Mass Spectral Quality of Species Identification in Clinical Routine Diagnostics

Cuénod

Foucault²,

Pflüger³

et al. 2021

Front. Cell. Infect. Microbiol.

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BackgroundAn accurate and timely identification of bacterial species is critical in clinical diagnostics. Species identification allows a potential first adaptation of empiric antibiotic treatments before the resistance profile is available. Matrix assisted Laser Desorption Ionization Time of Flight mass spectrometry (MALDI-TOF MS) is a widely used method for bacterial species identification. However, important challenges in species identification remain. These arise from (i) incomplete databases, (ii) close relatedness of species of interest, and (iii) spectral quality, which is currently vaguely defined.MethodsWe selected 47 clinically relevant bacterial isolates from 39 species, which can be challenging to identify by MALDI-TOF MS. We measured these isolates under various analytical conditions on two MALDI-TOF MS systems. First, we identified spectral features, which were associated with correct species identification in three different databases. Considering these features, we then systematically compared spectra produced with three different sample preparation protocols. In addition, we varied quantities of bacterial colony material applied and bacterial colony age.ResultsWe identified (i) the number of ribosomal marker peaks detected, (ii) the median relative intensity of ribosomal marker peaks, (iii) the sum of the intensity of all detected peaks, (iv) a high measurement precision, and (v) reproducibility of peaks to act as good proxies of spectral quality. We found that using formic acid, measuring bacterial colonies at a young age, and frequently calibrating the MALDI-TOF MS device increase mass spectral quality. We further observed significant differences in spectral quality between different bacterial taxa and optimal measurement conditions vary per taxon.ConclusionWe identified and applied quality measures for MALDI-TOF MS and optimized spectral quality in routine settings. Phylogenetic marker peaks can be reproducibly detected and provide an increased resolution and the ability to distinguish between challenging species such as those within the Enterobacter cloacae complex, Burkholderia cepacia complex, or viridans streptococci.

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Section: Introductionmentioning

confidence: 99%

Factors Associated With MALDI-TOF Mass Spectral Quality of Species Identification in Clinical Routine Diagnostics

Cuénod

Foucault²,

Pflüger³

et al. 2021

Front. Cell. Infect. Microbiol.

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“…Also, in a study using 109 ESBL-producing E . coli collected from clinical settings and the environment in France, the peak was identified as m/z 9713 15 . Moreover, in a study using 73 E .…”

Section: Discussionmentioning

confidence: 99%

Identification of specific protein amino acid substitutions of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli ST131: a proteomics approach using mass spectrometry

Nakamura

Komatsu

Ohno

et al. 2019

Sci Rep

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The global pandemic of ESBL-producing Escherichia coli is associated with sequence type 131 (ST131). However, mechanisms of ST131 spread remain unclear. This study searched for proteins with amino acid substitutions specific for ST131 and used proteomics analysis to clarify ST131 characteristics. Five proteins had ST131-specific amino acid substitutions: uncharacterized protein YahO with E34A ( m/z 7655); UPF0337 protein YjbJ with V59D, D60S and T63K ( m/z 8351); uncharacterized protein YnfD with S106T ( m/z 8448); and acid stress chaperone HdeA with Q92K and N94S ( m/z 9714). Soluble cytochrome b562 ( m/z 11783) showed seven amino acid substitutions, and the sequence differed between clade C of the pandemic clade and non-C. In silico analysis showed YahO protein-protein interaction with YjbJ, possibly related to biofilm formation. Although the function of soluble cytochrome b562 is electron transport of unknown function, its involvement in biofilm formation was predicted. HdeA was a gastric acid resistance-related protein. The function of YnfD was completely unclear. In conclusion, ST131-specific protein amino acid substitutions consisted mainly of a gastric acid resistance protein and proteins of unknown function (possibly involved in biofilm formation), which might be mechanisms for long-term colonization in the human intestinal tract.

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“…Esta hidrólisis es seguida por una descarboxilación del producto hidrolizado, lo que resulta en un desplazamiento del pico de -44 Da más de la forma hidrolizada, cambios en los espectros que son fácilmente detectados por MALDI-TOF MS. Mediante este principio, y empleando diferentes agentes inhibidores de β-lactamasas como ácido clavulánico, tazobactam o ácido 3-aminofenilborónico (APBA), los mismos autores describieron la detección de resistencia a ampicilina en E. coli, de cefotaxima y ceftazidima en E. coli y K. pneumoniae, así como la hidrolisis de carbapenémicos por K. pneumoniae a través del uso de la tecnología MALDI-TOF MS. Adicional a los procedimientos basados en la hidrólisis, recientemente se ha reportado la utilidad de esta tecnología para la detección de cepas de E. coli pertenecientes al grupo clonal ST131, productoras de Betalactamasas de Espectro Extendido (BLEE), mediante la visualización de un pico específi-co en el espectro de masas 53,54 .…”

Section: Identificación De Marcadores De Resistencia a Los Antimicrobunclassified

La espectrometría de masas MALDI-TOF en el laboratorio de microbiología clínica

Maldonado

Robledo

2017

Infect

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ResumenLos métodos fenotípicos empleados para la identificación de microorganismos dependen de procesos metabólicos que requieren de tiempos de incubación mínimos para alcanzar resultados confiables. La espectrometría de masas MALDI-TOF (desorción/ionización láser asistida por una matriz con detección de masas por tiempo de vuelo) se ha instaurado como una metodología relevante para la identificación de microorganismos mediante el análisis de proteínas, a través de la creación de un espectro de masas específico de género y especie. En esta revisión, se presenta MALDI-TOF MS como una tecnología precisa para la identificación de bacterias, levaduras, mohos, en incluso de virus, que además, permite la reducción del tiempo para obtener un resultado de identificación, que puede impactar los costos de atención y duración de la estancia hospitalaria. La identificación de microorganismos directamente de muestras biológicas y la detección de mecanismos de resistencia a antimicrobianos, prometen un mayor impacto clínico y epidemiológico con el desarrollo e implementación de esta tecnología en los laboratorios de microbiología clínica.Palabras clave: MALDI-TOF MS, espectrometría de masas, diagnóstico microbiológico, identificación de patógenos, proteómica, infección del torrente sanguíneo, infección del tracto urinario. MALDI-TOF mass spectrometry in clinical microbiology laboratories. AbstractPhenotypic methods used for the identification of microorganisms depend on metabolic processes that require minimum incubation times to achieve reliable results. For this reason, MALDI-TOF MS (Matrix Assisted Laser Desorption/Ionization Mass Spectrometry) has been established as a relevant methodology for the identification of microorganisms using analysis of proteins, through the creation of a mass spectrum specific for genus and species. In the present review, MALDI-TOF MS is presented as an accurate technology for identifying bacteria, yeasts, molds and viruses; Its use allows reduction of the time to obtain an identification result, which may impact the costs of care and length of hospital stay. The identification of microorganisms directly from biological samples and the detection of mechanisms of antimicrobial resistance, promise an additional clinical and epidemiological impact with the development and implementation of this technology in clinical microbiology laboratories.Keywords: MALDI-TOF MS, mass spectrometry, microbiological diagnostic, pathogen identification, proteomics, blood stream infection, urinary tract infection. REVISIÓN IntroducciónLa identificación de microorganismos se ha realizado tradicionalmente por métodos basados en tinciones que permiten la clasificación de la morfología microscópica con el fin de apoyar decisiones diagnósticas y terapéuticas tempranas; así como en pruebas in vitro basadas en reacciones bioquímicas utilizadas por sistemas manuales o automatizados, que integran pruebas con diferentes sustratos, incrementando la rapidez y simplicidad de la identificación. Sin embargo, estos métodos fenotí...

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Detection of Escherichia coli sequence type 131 by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: implications for infection control policies?

Cited by 22 publications

References 16 publications

Factors Associated With MALDI-TOF Mass Spectral Quality of Species Identification in Clinical Routine Diagnostics

Factors Associated With MALDI-TOF Mass Spectral Quality of Species Identification in Clinical Routine Diagnostics

Identification of specific protein amino acid substitutions of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli ST131: a proteomics approach using mass spectrometry

La espectrometría de masas MALDI-TOF en el laboratorio de microbiología clínica

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