MALDI-TOF Mass Spectrometry Is a Fast and Reliable Platform for Identification and Ecological Studies of Species from Family Rhizobiaceae

Ferreira, Laura; Sánchez-Juanes, Fernando; García‐Fraile, Paula; Rivas, Raúl; Mateos, Pedro F.; Martínez‐Molina, Eustoquio; González-Buitrago, José Manuel; Velázquez, Encarna

doi:10.1371/journal.pone.0020223

Cited by 102 publications

(75 citation statements)

References 82 publications

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“…These advantages, along with the proven accuracy of MALDI-TOF MS-based identification of bacteria, have revolutionized the routine identification of microorganisms to species and subspecies level in clinical diagnostic and food microbiological laboratories (Croxatto et al 2012;Mazzeo et al 2006). MALDI-TOF MS has also been shown to be an excellent tool for identification of diverse rhizobial species of Bradyrhizobium, Ensifer, Shinella, and Rhizobium applicable to large populations of isolates in ecological and taxonomic studies (Ferreira et al 2011;Sánchez-Juanes et al 2013). …”

Section: Discussionmentioning

confidence: 99%

“…Our results showed that MALDI-TOF MS analysis using the rhizobia-specific database grouped RNB strains into genera and species congruent with the phylogenies obtained using marker gene sequences (16S rRNA, MLSA) and consistent with classifications previously obtained for cluster analysis of MALDI-TOF spectra of Ensifer and Rhizobium spp. (Ferreira et al 2011). The database also provided an accurate and highly resolved analysis of strain diversity at the species and often subspecies level.…”

Section: Discussionmentioning

confidence: 99%

“…MALDI-TOF MS offers the possibility of accurately resolving bacterial identity to the genus, species, and subspecies levels in some taxa and has successfully been applied to diverse rhizobial strains grown on solid media (Ferreira et al 2011;Sánchez-Juanes et al 2013;Ziegler et al 2012) and found inside legume nodules (Ziegler et al 2012). In most direct MALDI-TOF MS analyses, bacterial cells are lysed to release the intracellular proteins, which are then ionized and separated according to their mass-to-charge ratio (m/z) and recorded as distinct peaks, generating a complex spectrum, or fingerprint that is characteristic of a bacterial sample.…”

Section: Introductionmentioning

confidence: 99%

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Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Ziegler

Pothier

Ardley

et al. 2015

Appl Microbiol Biotechnol

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Accurate identification of soil bacteria that form nitrogen-fixing associations with legume crops is challenging given the phylogenetic diversity of root nodule bacteria (RNB). The labor-intensive and time-consuming 16S ribosomal RNA (rRNA) sequencing and/or multilocus sequence analysis (MLSA) of conserved genes so far remain the favored molecular tools to characterize symbiotic bacteria. With the development of mass spectrometry (MS) as an alternative method to rapidly identify bacterial isolates, we recently showed that matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) can accurately characterize RNB found inside plant nodules or grown in cultures. Here, we report on the development of a MALDI-TOF RNB-specific spectral database built on whole cell MS fingerprints of 116 strains representing the major rhizobial genera. In addition to this RNB-specific module, which was successfully tested on unknown field isolates, a subset of 13 ribosomal proteins extracted from genome data was found to be sufficient for the reliable identification of nodule isolates to rhizobial species as shown in the putatively ascribed ribosomal protein masses (PARPM) database. These results reveal that data gathered from genome sequences can be used to expand spectral libraries to aid the accurate identification of bacterial species by MALDI-TOF MS.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Ziegler

Pothier

Ardley

et al. 2015

Appl Microbiol Biotechnol

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“…By generating unique whole-cell protein-based fingerprints for each colony, the Biotyper permits highly reproducible identification of bacterial colonies to the genus or species level. Because of its reproducibility, ease of use, and cost effectiveness, the Biotyper is used extensively in clinical and public health microbiological laboratories (53) and is finding increased use in ecological studies (54)(55)(56). To standardize growth prior to analysis, individual colonies were tooth-picked onto a one-third TSA plate and grown overnight.…”

Section: Methodsmentioning

confidence: 99%

Gut Microbiota Colonization and Transmission in the Burying Beetle Nicrophorus vespilloides throughout Development

Wang

Rozen

2017

Appl Environ Microbiol

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Carrion beetles in the genus Nicrophorus rear their offspring on decomposing carcasses where larvae are exposed to a diverse community of decomposer bacteria. Parents coat the carcass with antimicrobial secretions prior to egg hatch (defined as prehatch care) and also feed regurgitated food, and potentially bacteria, to larvae throughout development (defined as full care). Here, we partition the roles of prehatch and posthatch parental care in the transmission and persistence of culturable symbiotic bacteria to larvae. Using three treatment groups (full care, prehatch care only, and no care), we found that larvae receiving full care are predominantly colonized by bacteria resident in the maternal gut while larvae receiving no care are colonized with bacteria from the carcass. More importantly, larvae receiving only prehatch care were also predominantly colonized by maternal bacteria; this result indicates that parental treatment of the carcass, including application of bacteria to the carcass surface, is sufficient to ensure symbiont transfer even in the absence of direct larval feeding. Later in development, we found striking evidence that pupae undergo an aposymbiotic stage, after which they are recolonized at eclosion with bacteria similar to those found on the molted larval cuticle and on the wall of the pupal chamber. Our results clarify the importance of prehatch parental care for symbiont transmission in Nicrophorus vespilloides and suggest that these bacteria successfully outcompete decomposer bacteria during larval and pupal gut colonization.IMPORTANCE Here, we examine the origin and persistence of the culturable gut microbiota of larvae in the burying beetle Nicrophorus vespilloides. This insect is particularly interesting for this study because larvae are reared on decomposing vertebrate carcasses, where they are exposed to high densities of carrion-decomposing microbes. Larvae also receive extensive parental care in the form of carcass preservation and direct larval feeding. We find that parents transmit their gut bacteria to larvae both directly, through regurgitation, and indirectly via their effects on the carcass. In addition, we find that larvae become aposymbiotic during pupation but are recolonized apparently from bacteria shed onto the insect cuticle before adult eclosion. Our results highlight the diverse interactions between insect behavior and development on microbiota composition. They further suggest that competitive interactions mediate the bacterial composition of Nicrophorus larvae together with or apart from the influence of beetle immunity, suggesting that the bacterial communities of these insects may be highly coevolved with those of their host species.KEYWORDS Nicrophorus, parental care, symbiosis, microbiota, transmission A nimals are colonized by a diverse community of bacterial symbionts that play crucial roles in their ecology and evolution (1-3). This has been especially well studied in insects, whose bacterial symbionts can influence traits ranging from mate

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“…La rapidez y relativa sencillez del uso de la espectrometría de masas ya ha demostrado su utilidad en comparación con otros sistemas diagnósticos en el laboratorio de microbiología (18)(19)(20)(21). El diagnós-tico del agente etiológico productor de la bacteriemia requiere el cultivo previo del microorganismo en medio sólido desde los frascos de hemocultivo positivo, lo que supone un retraso de al menos 8-24 horas.…”

Section: Discussionunclassified

Sepsityper® for rapid identification of microorganisms from positive blood cultures

Camacho-Luque¹,

Peña-Monje²,

Álvarez-Estévez³

et al. 2014

Actual. Med.

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Nuestro estudio ha evaluado las ventajas de la utilización del kit Sepsityper® para la identificación rápida de microorganismos a partir de hemocultivos positivos, acompañado de la tecnología de espectrometría de masas MALDITOF MS®, en comparación con los métodos tradicionales empleados para el diagnóstico de bacteriemia. Para la identificación del microorganismo en 379 hemocultivos positivos en el Departamento de Microbiología del Hospital Universitario San Cecilio, se aplicó la espectrometría de masas MALDITOF MS® utilizando el sistema Sepsityper® (Bruker) y se comparó con la identificación mediante métodos convencionales (Wider, Vitek II, Api). La correlación de resultados de los dos esquemas diagnósticos fue determinada estadísticamente por el coeficiente de correlación kappa. La distribución de los aislamientos fue de un 24,7 % de Bacilos Gram negativos (BGN) y 75,3 % de microorganismos Cocos Gram positivos (CGP). La concordancia global de resultados fue del 95,8 % en la especie (k = 0,928) y del 98,7 % en el género (k = 0,977), siendo el porcentaje de identificaciones fallidas del 1,3%. Para BGN hubo una concordancia de resultados del 95,2 % (k = 0,928, especie), y 100 % (k = 1, género). Respecto a los CGP, la concordancia fue del 98,2 % en género (k = 0,931), y del 82,5 % (k = 0,627) a nivel de especie. En nuestra experiencia se ha observado una ganancia de al menos 13-23h en la identificación a nivel de especie. La utilización del kit Sepsityper® para la identificación rápida de microorganismos a partir de hemocultivos positivos, acompañado de MALDITOF MS®, muestra una excelente correlación respecto a la identificación realizada a través de la metodología convencional, con una importante disminución del tiempo hasta la identificación. AbstractOur study has evaluated the advantages of using Sepsityper® kit for a fast identification of microorganisms from positive blood cultures, along with the mass spectrometry technology MALDITOF-MS®, compared to traditional methods used for diagnosis of bacteremia. To identify the microorganism isolated from the 379 positive blood cultures (BC +) the Department of Microbiology, University Hospital San Cecilio, MALDITOF-MS® mass spectrometry along with Sepsityper® (Bruker) were applied and it was compared to the conventional methods for the identification of this organism. The correlation of results between these two diagnostic schemes was statistically determined by kappa correlation coefficient. The distribution of the isolates was 24.7% for Gram negative bacilli (GNB) and 75.3% for Gram-positive cocci (GPC). The overall concordance of results was 95.8% within the species (k = 0.928) and 98.7% within the genus (k = 0.977), with a failed-identification percentage of 1.3%. For GNB there was a concordance of results of 95.2% (k = 0.928, species), and 100% (k = 1, genus). Regarding the GPC, the concordance was 98.2% within the genus (k = 0.931), and 82.5% (k = 0.627) at the species level. According to our experience there was a gain of at least 13-23 hours in the identific...

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MALDI-TOF Mass Spectrometry Is a Fast and Reliable Platform for Identification and Ecological Studies of Species from Family Rhizobiaceae

Cited by 102 publications

References 82 publications

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Gut Microbiota Colonization and Transmission in the Burying Beetle Nicrophorus vespilloides throughout Development

Sepsityper® for rapid identification of microorganisms from positive blood cultures

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