Development of a Custom MALDI-TOF MS Database for Species-Level Identification of Bacterial Isolates Collected From Spacecraft and Associated Surfaces

Objective:To evaluate the performance of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) by using 190 Catalase-negative Gram-Positive Cocci (GPC) clinical isolates.Methods:All isolates were identified by conventional phenotypic tests following the proposed scheme by Ruoff and Christensen and MALDI-TOF MS (Bruker Daltonics, BD, Bremen, Germany). Two different extraction methods (direct transfer formic acid method on spot and ethanol formic acid extraction method) and different cut-offs for genus/specie level identification were used. The score cut-offs recommended by the manufacturer (≥ 2.000 for species-level, 1.700 to 1.999 for genus level and <1.700 no reliable identification) and lower cut-off scores (≥1.500 for genus level, ≥ 1.700 for species-level and score <1.500 no reliable identification) were considered for identification. A minimum difference of 10% between the top and next closest score was required for a different genus or species.MALDI-TOF MS identification was considered correct when the result obtained from MS database agreed with the phenotypic identification result.When both methods gave discordant results, the 16S rDNA orsodAgenes sequencing was considered as the gold standard identification method. The results obtained by MS concordant with genes sequencing, although discordant with conventional phenotyping, were considered correct. MS results discordant with 16S orsodA identification were considered incorrect.Results:Using the score cut-offs recommended by the manufacturer, 97.37% and 81.05% were correctly identified to genus and species level, respectively. On the other hand, using lower cut-off scores for identification, 97.89% and 94.21% isolates were correctly identified to genus and species level respectively by MALDI-TOF MS and no significant differences between the results obtained with two extraction methods were obtained.Conclusion:The results obtained suggest that MALDI-TOF MS has the potential of being an accurate tool for Catalase-negative GPC identification even for those species with difficult diagnosis asHelcococcus,Abiotrophia,Granulicatella, among others. Nevertheless, expansion of the library, especially including more strains with different spectra on the same species might overcome potential “intraspecies” variability problems. Moreover, a decrease of the identification scores for species and genus-level identification must be considered since it may improve the MALDI-TOF MS accuracy.

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A MALDI-TOF MS database with broad genus coverage for species-level identification of Brucella

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0006874 ◽

2018 ◽

Vol 12 (10) ◽

pp. e0006874 ◽

Cited By ~ 14

Author(s):

Jennifer Mesureur ◽

Sandrine Arend ◽

Béatrice Cellière ◽

Priscillia Courault ◽

Pierre-Jean Cotte-Pattat ◽

...

Keyword(s):

Species Level ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Level Identification ◽

Tof Ms

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Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing

BMC Microbiology ◽

10.1186/s12866-014-0312-5 ◽

2014 ◽

Vol 14 (1) ◽

Cited By ~ 34

Author(s):

Annette Carola Anderson ◽

Mohamed Sanunu ◽

Christian Schneider ◽

Andreas Clad ◽

Lamprini Karygianni ◽

...

Keyword(s):

16S Rdna ◽

Species Level ◽

16S Rdna Sequencing ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Ms Analysis ◽

Rdna Sequencing ◽

Level Identification ◽

Tof Ms

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Multicenter Evaluation of Rapid BACpro® II for the Accurate Identification of Microorganisms Directly from Blood Cultures Using MALDI-TOF MS

Diagnostics ◽

10.3390/diagnostics11122251 ◽

2021 ◽

Vol 11 (12) ◽

pp. 2251

Author(s):

Marina Oviaño ◽

André Ingebretsen ◽

Anne K. Steffensen ◽

Antony Croxatto ◽

Guy Prod’hom ◽

...

Keyword(s):

Blood Cultures ◽

Species Level ◽

Correct Identification ◽

Gram Positive ◽

Gram Negative ◽

Maldi Tof Ms ◽

Gram Positive Bacteria ◽

Maldi Tof ◽

Level Identification ◽

Tof Ms

The identification of microorganisms directly from blood cultures using MALDI-TOF MS has been shown to be the most impacting application of this methodology. In this study, a novel commercial method was evaluated in four clinical microbiology laboratories. Positive blood culture samples (n = 801) were processed using a rapid BACpro® II kit and then compared with the routine gold standard. A subset of monomicrobial BCs (n = 560) were analyzed in parallel with a Sepsityper® Kit (Bruker Daltonics, Bremen, Germany) and compared with the rapid BACpro® II kit. In addition, this kit was also compared with two different in-house methods. Overall, 80.0% of the monomicrobial isolates (609/761; 95% CI 71.5–88.5) were correctly identified by the rapid BACpro® II kit at the species level (92.3% of the Gram negative and 72.4% of the Gram positive bacteria). The comparison with the Sepsityper® Kit showed that the rapid BACpro® II kit generated higher rates of correct species-level identification for all categories (p > 0.0001), except for yeasts identified with score values > 1.7. It also proved superior to the ammonium chloride method (p > 0.0001), but the differential centrifugation method allowed for higher rates of correct identification for Gram negative bacteria (p > 0.1). The percentage of accurate species-level identification of Gram positive bacteria was particularly noteworthy in comparison with other commercial and in-house methods.

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Isolation of Candida auris from cystic fibrosis patient, Greece, April 2019

Eurosurveillance ◽

10.2807/1560-7917.es.2019.24.29.1900400 ◽

2019 ◽

Vol 24 (29) ◽

Cited By ~ 3

Author(s):

Angeliki Stathi ◽

Ioanna Loukou ◽

Helen Kirikou ◽

Argyri Petrocheilou ◽

Maria Moustaki ◽

...

Keyword(s):

Cystic Fibrosis ◽

Fungal Infection ◽

Cystic Fibrosis Patient ◽

Species Level ◽

Sputum Culture ◽

Candida Auris ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Level Identification ◽

Tof Ms

We report the first isolation of Candida auris in Greece from a sputum culture of a cystic fibrosis patient in their 20s under posaconazole treatment. The pathogen was identified as C. duobushaemulonii by VITEK2YST, but as C. auris by MALDI-TOF MS. This case underscores the need for species-level identification of all non-albicans Candida (NAC) isolates from cystic fibrosis patients and patients with predisposing factors to fungal infection.

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Evaluation of the rapidBACpro® II kit for the rapid identification of microorganisms directly from blood cultures using MALDI-TOF MS

10.1101/2021.01.25.428200 ◽

2021 ◽

Author(s):

Marina Oviaño ◽

André Ingebretsen ◽

Anne K Steffensen ◽

Antony Croxatto ◽

Guy Prod’hom ◽

...

Keyword(s):

Blood Cultures ◽

Species Level ◽

Correct Identification ◽

Gram Positive ◽

Gram Negative ◽

Maldi Tof Ms ◽

Gram Positive Bacteria ◽

Maldi Tof ◽

Level Identification ◽

Tof Ms

AbstractObjectivesIdentification of microorganisms directly from blood cultures (BCs) using MALDI-TOF MS has shown to be the application with most impact in this methodology. In this study, a novel commercial method, the rapidBACpro® II, was evaluated in four clinical microbiology laboratories.MethodsPositive blood culture samples (n=801) were processed using the rapidBACpro® II kit and then compared with routine gold standard. A subset of monomicrobial BCs (n=560) were analyzed in parallel with the Sepsityper® kit (Bruker Daltonics, Bremen, Germany) and compared with the rapidBACpro® II kit. In addition, the rapidBACpro® II kit was also compared with two different in-house methods.ResultsOverall, 80.0% of the monomicrobial isolates (609/761) were correctly identified by the rapidBACpro® II kit at the species level (92.3% of the Gram negative and 72.4% of the Gram positive bacteria). The comparison with the Sepsityper® kit yielded higher rates of correct species-level identification provided by the rapidBACpro® II kit for all categories (p>0.0001) except for yeasts identified with score values >1.7. It also proved superior to the ammonium chloride method (p>0.0001) but the differential centrifugation method allowed higher rates of correct identification for Gram negative bacteria (p>0.1).ConclusionsThe rapidBACpro® II kit allowed a high rate of microorganisms correctly identified. The percentage of accurate species-level identification of Gram positive bacteria was particularly noteworthy in comparison with other commercial and in-house methods. This fact was especially interesting in the case of Staphylococcus sp. and Streptococcus sp. in order to elucidate their clinical impact, for example in device-associated bacteremia.

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Rapid species level identification of fish eggs by proteome fingerprinting using MALDI-TOF MS

Journal of Proteomics ◽

10.1016/j.jprot.2020.103993 ◽

2021 ◽

Vol 231 ◽

pp. 103993

Author(s):

Sven Rossel ◽

Andrea Barco ◽

Matthias Kloppmann ◽

Pedro Martínez Arbizu ◽

Bastian Huwer ◽

...

Keyword(s):

Species Level ◽

Fish Eggs ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Level Identification ◽

Tof Ms

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Integrative Description of Cryptic Tigriopus Species From Korea Using MALDI-TOF MS and DNA Barcoding

Frontiers in Marine Science ◽

10.3389/fmars.2021.648197 ◽

2021 ◽

Vol 8 ◽

Author(s):

Jisu Yeom ◽

Nayeon Park ◽

Raehyuk Jeong ◽

Wonchoel Lee

Keyword(s):

Species Identification ◽

Species Level ◽

Morphological Comparison ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Low Costs ◽

A New Species ◽

Level Identification ◽

Tof Ms

MALDI Time-of-Flight Mass Spectrometry (MALDI-TOF MS) provides a fast and reliable alternative method for species-level identification of pathogens and various metazoans. Compared to the commonly used mitochondrial cytochrome c oxidase subunit I (mtCOI) barcoding, advantages of MALDI-TOF MS are rapid species identifications and low costs. In this study, we used MALDI-TOF MS to determine whether spectra patterns of different species can be used for species identification. We obtained a total of 138 spectra from individual specimens of Tigriopus, which were subsequently used for various cluster analyses. Our findings revealed these spectra form three clear clusters with high AU value support. This study validates the viability of MALDI-TOF MS as a methodology for higher-resolution species identification, allowing detection of cryptic species of harpacticoida. In addition, we propose a new species, Tigriopus koreanus sp. nov. by utilizing integrative methods such as morphological comparison, mtCOI barcoding, and MALDI-TOF MS.

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An analysis of the population of Cryptococcus neoformans strains isolated from animals in Poland, in the years 2015–2019

Scientific Reports ◽

10.1038/s41598-021-86169-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Magdalena Florek ◽

Urszula Nawrot ◽

Agnieszka Korzeniowska-Kowal ◽

Katarzyna Włodarczyk ◽

Anna Wzorek ◽

...

Keyword(s):

Cryptococcus Neoformans ◽

Species Level ◽

Molecular Type ◽

Animal Group ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Severe Infections ◽

Resistant Strains ◽

World Distribution ◽

Tof Ms

AbstractFungi belonging to the Cryptococcus neoformans/C. gattii species complex (CNGSC) are pathogens causing severe infections in humans and animals, that for humans may result in a mortality rate ranging up to 70%. The CNGSC is divided into eight major molecular types, that may differ in their virulence and susceptibility. In order to fully understand the epidemiology of cryptococcosis, it is important to study the world distribution and population structure of these pathogens. The present study is the first presenting a population of strains isolated in Poland and one of the few using a multi-species animal group as a source of the specimen. The pathogen was present in 2.375% of the tested animals. The URA5-RFLP and MALDI-TOF MS analyses have revealed that the population consisted exclusively of C. neoformans strains, with a predominance of major molecular type VNIV (C. neoformans var. neoformans). The MALDI-TOF MS was used to perform the CNGSC strains identification on both the species and sub-species level. Despite the fact that the animals providing the specimens were not treated with 5-fluorocytosine, around 10% of the tested population presented MIC values exceeding 64 mg/L, indicating the existence of the 5-fluorocytosine-resistant strains in the environment.

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Performance of Five Commercial Identification Platforms for Identification of Staphylococcus delphini

Journal of Clinical Microbiology ◽

10.1128/jcm.00721-19 ◽

2019 ◽

Vol 57 (11) ◽

Cited By ~ 2

Author(s):

Matthew C. Canver ◽

Tsigereda Tekle ◽

Samantha T. Compton ◽

Katrina Callan ◽

Eileen M. Burd ◽

...

Keyword(s):

Distinct Species ◽

Human Infection ◽

Species Level ◽

Accurate Identification ◽

Content Type ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Staphylococcus Intermedius ◽

Animal Pathogens ◽

Tof Ms

ABSTRACT The Staphylococcus intermedius group (SIG) is a collection of coagulase-positive staphylococci consisting of four distinct species, namely, Staphylococcus cornubiensis, Staphylococcus delphini, Staphylococcus intermedius, and Staphylococcus pseudintermedius. SIG members are animal pathogens and rare causes of human infection. Accurate identification of S. pseudintermedius has important implications for interpretation of antimicrobial susceptibility testing data and may be important for other members of the group. Therefore, we sought to evaluate the performance of five commercially available identification platforms with 21 S. delphini isolates obtained from a variety of animal and geographic sources. Here, we show that automated biochemical platforms were unable to identify S. delphini to the species level, a function of its omission from their databases, but could identify isolates to the SIG level with various degrees of success. However, all automated systems misidentified at least one isolate as Staphylococcus aureus. One matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system was able to identify S. delphini to the species level, suggesting that MALDI-TOF MS is the best option for distinguishing members of the SIG. With the exception of S. pseudintermedius, it is unclear if other SIG members should be routinely identified to the species level; however, as our understanding of their role in animal and human diseases increases, it may be necessary and important to do so.

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