A comparison of Api 20A vs MALDI-TOF MS for routine identification of clinically significant anaerobic bacterial strains to the species level

Objective: The aim of this study was to determine the capacity of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) to identify 155 HACEK clinical isolates and other fastidious or infrequently isolated Gram-negative rods (e.g., Actinobacillus, Capnocytophaga, Pasteurella, Neisseria, Moraxella, Dysgonomonas, among others). Methods: All the isolates were identified by standard biochemical tests and MALDI-TOF MS. 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. MALDI-TOF MS identification was considered correct when the result obtained from the MS database agreed with the phenotypic identification result. When both the methods gave discordant results, the 16S rDNA gene sequencing was considered as the gold standard identification method. Results: Employing the score cut-offs suggested by the manufacturer, 93.55% and 69.03% isolates were correctly identified at the genus and species level, respectively. On the contrary , employing lower cut-off scores for identification, 98.06% and 92.09% isolates were properly identified at the genus and species level respectively and no significant differences between the results obtained with two extraction methods were observed . Conclusion: The accurate identification of 14 genera showed the reliability of MALDI-TOF MS as an optional methodology to the routine identification methods currently used in laboratories.

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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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Identification of the ‘Streptococcus anginosus group’ by matrix-assisted laser desorption ionization – time-of-flight mass spectrometry

Journal of Medical Microbiology ◽

10.1099/jmm.0.076653-0 ◽

2014 ◽

Vol 63 (9) ◽

pp. 1143-1147 ◽

Cited By ~ 12

Author(s):

Katherine Woods ◽

David Beighton ◽

John L. Klein

Keyword(s):

Species Level ◽

Direct Transfer ◽

Laser Desorption Ionization ◽

Ionization Time ◽

Maldi Tof Ms ◽

Streptococcus Anginosus ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Transfer Method ◽

Tof Ms

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) provides rapid, accurate and cost-effective identification of a range of bacteria and is rapidly changing the face of routine diagnostic microbiology. However, certain groups of bacteria, for example streptococci (in particular viridans or non-haemolytic streptococci), are less reliably identified by this method. We studied the performance of MALDI-TOF MS for identification of the ‘Streptococcus anginosus group’ (SAG) to species level. In total, 116 stored bacteraemia isolates identified by conventional methods as belonging to the SAG were analysed by MALDI-TOF MS. Partial 16S rRNA gene sequencing, supplemented with sialidase activity testing, was performed on all isolates to provide ‘gold standard’ identification against which to compare MALDI-TOF MS performance. Overall, 100 % of isolates were correctly identified to the genus level and 93.1 % to the species level by MALDI-TOF MS. However, only 77.6 % were correctly identified to the genus level and 59.5 % to the species level by a MALDI-TOF MS direct transfer method alone. Use of a rapid in situ extraction method significantly improved identification rates when compared with the direct transfer method (P<0.001). We recommend routine use of this method to reduce the number of time-consuming full extractions required for identification of this group of bacteria by MALDI-TOF MS in the routine diagnostic laboratory. Only 22 % (1/9) of Streptococcus intermedius isolates were reliably identified by MALDI-TOF MS to the species level, even after full extraction. MALDI-TOF MS reliably identifies S. anginosus and Streptococcus constellatus to the species level but does not reliably identify S. intermedius.

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Matrix-assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a Reliable Tool to Identify Species of Catalase-negative Gram-positive Cocci not Belonging to the Streptococcus Genus

The Open Microbiology Journal ◽

10.2174/1874285801610010202 ◽

2016 ◽

Vol 10 (1) ◽

pp. 202-208 ◽

Cited By ~ 7

Author(s):

Marisa Almuzara ◽

Claudia Barberis ◽

Viviana Rojas Velázquez ◽

Maria Soledad Ramirez ◽

Angela Famiglietti ◽

...

Keyword(s):

Extraction Methods ◽

Species Level ◽

Ionization Time ◽

Maldi Tof Ms ◽

Genus Level ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Level Identification ◽

Gram Positive Cocci ◽

Tof Ms

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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The use of Principle Component Analysis and MALDI-TOF MS for the differentiation of mineral forming Virgibacillus and Bacillus species isolated from Sabkhas

University of the Future: Re-Imagining Research and Higher Education ◽

10.29117/quarfe.2020.0069 ◽

2020 ◽

Author(s):

Rim Abdel Samad ◽

Zulfa Al Disi ◽

Mohammad Ashfaq ◽

Nabil Zouari

Keyword(s):

Clustering Analysis ◽

Potential Role ◽

Protein Profiling ◽

Bacillus Species ◽

Pca Analysis ◽

Bacterial Strains ◽

Protein Biomarkers ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Tof Ms

Occurrence of mineral forming and other bacteria in mats is well demonstrated. However, their high diversity shown by ribotyping was not explained, although it could explain the diversity of formed minerals. Common biomarkers as well as phylogenic relationships are useful tools to clustering the isolates and predict their potential role in the natural niche. In this study, combination of MALDI-TOF MS with PCA was shown a powerful tool to categorize 35 mineral forming bacterial strains isolated from Dohat Fshaikh sabkha, at northwest of Qatar (23 from decaying mats and 12 from living ones). 23 strains from decaying mats belong to Virgibacillus genus as identified by ribotyping and are shown highly involved in formation of protodolomite and a diversity of minerals. They were used as internal references in categorization of sabkha bacteria. Combination of isolation of bacteria on selective mineral forming media, their MALDI TOF MS protein profiling and PCA analysis established their relationship in a phyloproteomic based on protein biomarkers including m/z 4905, 3265, 5240, 6430, 7765, and 9815. PCA analysis clustered the studied strains into 3 major clusters, showing strong correspondence to the 3 phyloproteiomic groups that were established by the dendrogram. Both clustering analysis means have evidently demonstrated a relationship between known Virgibacillus strains and other related bacteria based on profiling of their synthesized proteins. Thus, larger populations of bacteria in mats can be easily screened for their potential to exhibit certain activities, which is of ecological, environmental and biotechnological significance.

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Establishment and Application of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for Detection of Shewanella Genus

Frontiers in Microbiology ◽

10.3389/fmicb.2021.625821 ◽

2021 ◽

Vol 12 ◽

Author(s):

Keyi Yu ◽

Zhenzhou Huang ◽

Ying Li ◽

Qingbo Fu ◽

Lirong Lin ◽

...

Keyword(s):

Laser Desorption ◽

Rapid Identification ◽

Species Level ◽

Laser Desorption Ionization ◽

Ionization Time ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Type Strains ◽

Tof Ms

Shewanella species are widely distributed in the aquatic environment and aquatic organisms. They are opportunistic human pathogens with increasing clinical infections reported in recent years. However, there is a lack of a rapid and accurate method to identify Shewanella species. We evaluated here matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of Shewanella. A peptide mass reference spectra (PMRS) database was constructed for the type strains of 36 Shewanella species. The main spectrum projection (MSP) cluster dendrogram showed that the type strains of Shewanella species can be effectively distinguished according to the different MS fingerprinting. The PMRS database was validated using 125 Shewanella test strains isolated from various sources and periods; 92.8% (n = 116) of the strains were correctly identified at the species level, compared with the results of multilocus sequence analysis (MLSA), which was previously shown to be a method for identifying Shewanella at the species level. The misidentified strains (n = 9) by MALDI-TOF MS involved five species of two groups, i.e., Shewanella algae–Shewanella chilikensis–Shewanella indica and Shewanella seohaensis–Shewanella xiamenensis. We then identified and defined species-specific biomarker peaks of the 36 species using the type strains and validated these selected biomarkers using 125 test strains. Our study demonstrated that MALDI-TOF MS was a reliable and powerful tool for the rapid identification of Shewanella strains at the species level.

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Evaluation of ID Fungi Plates Medium for Identification of Molds by MALDI Biotyper

Journal of Clinical Microbiology ◽

10.1128/jcm.01687-19 ◽

2020 ◽

Vol 58 (5) ◽

Cited By ~ 2

Author(s):

Marie Gladys Robert ◽

Charlotte Romero ◽

Céline Dard ◽

Cécile Garnaud ◽

Odile Cognet ◽

...

Keyword(s):

Filamentous Fungi ◽

Susceptibility Testing ◽

Antifungal Susceptibility ◽

Antifungal Susceptibility Testing ◽

Maldi Tof Ms ◽

Extraction Protocol ◽

Maldi Tof ◽

Morphological Aspects ◽

Routine Identification ◽

Tof Ms

ABSTRACT MALDI-TOF mass spectrometry (MS) identification of pathogenic filamentous fungi is often impaired by difficulties in harvesting hyphae embedded in the medium and long extraction protocols. The ID Fungi Plate (IDFP) is a novel culture method developed to address such difficulties and improve the identification of filamentous fungi by MALDI-TOF MS. We cultured 64 strains and 11 clinical samples on IDFP, Sabouraud agar-chloramphenicol (SAB), and ChromID Candida agar (CAN2). We then compared the three media for growth, ease of harvest, amount of material picked, and MALDI-TOF identification scores after either rapid direct transfer (DT) or a long ethanol-acetonitrile (EA) extraction protocol. Antifungal susceptibility testing and microscopic morphology after subculture on SAB and IDFP were also compared for ten molds. Growth rates and morphological aspects were similar for the three media. With IDFP, harvesting of fungal material for the extraction procedure was rapid and easy in 92.4% of cases, whereas it was tedious on SAB or CAN2 in 65.2% and 80.3% of cases, respectively. The proportion of scores above 1.7 (defined as acceptable identification) were comparable for both extraction protocols using IDFP (P = 0.256). Moreover, rates of acceptable identification after DT performed on IDFP (93.9%) were significantly higher than those obtained after EA extraction with SAB (69.7%) or CAN2 (71.2%) (P = <0.001 and P = 0.001, respectively). Morphological aspects and antifungal susceptibility testing were similar between IDFP and SAB. IDFP is a culture plate that facilitates and improves the identification of filamentous fungi, allowing accurate routine identification of molds with MALDI-TOF-MS using a rapid-extraction protocol.

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Modulation of the Discriminatory Power of MALDI-TOF MS Profiling for Distinguishing Between Closely Related Bacterial Strains

Applications of Mass Spectrometry in Microbiology ◽

10.1007/978-3-319-26070-9_7 ◽

2016 ◽

pp. 185-202 ◽

Cited By ~ 1

Author(s):

Ondrej Šedo ◽

Zbyněk Zdráhal

Keyword(s):

Discriminatory Power ◽

Bacterial Strains ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Tof Ms

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Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry in diagnosis of clinical Nocardia species

Journal of Laboratory Medicine ◽

10.1515/labmed-2018-0180 ◽

2019 ◽

Vol 43 (3) ◽

pp. 157-162

Author(s):

Gülşen Hasçelik ◽

Markus Kostrzewa ◽

Hamit Kaan Müştak ◽

Celalettin Uner ◽

Kadir Serdar Diker

Keyword(s):

Species Level ◽

Rrna Gene ◽

Laser Desorption Ionization ◽

Ionization Time ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Maldi Biotyper ◽

Rrna Gene Sequencing ◽

Tof Ms

Abstract Background The routine identification to the species level of Nocardia genus by conventional methods is a fastidious and time-consuming process owing to the limited biochemical reactivity of these microorganisms, often requiring 1 or more days to complete identification. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a new technology for definitive and rapid species identification. Methods We evaluated the MALDI-TOF MS for the identification of 44 clinical isolates of Nocardia species in comparison to 16S ribosomal RNA (rRNA) gene sequencing. Nocardia isolates were identified by microbiological examination, phenotypical tests and MALDI-TOF MS and the results were compared by 16S rRNA gene sequencing. Results Of the 44 Nocardia strains, the identification of 28 isolates was determined with MALDI Biotyper database. According to this, 16 isolates (57.1%) of the strain log scores were ≥2. Two (7.1%) were identified to the species level (log scores of ≥2) as Nocardia otitidiscaviarum. The addition of a newly established Nocardia database (16 new Nocardia strains included to the original database) did significantly improve the scores. The results were 43 (97.7%) correct identification to the species level (log scores of ≥2). Conclusions This study showed that the identification of clinical Nocardia isolates by the Bruker MALDI Biotyper is highly reliable, whereas identification rates are generally lower than those for some Gram-negative bacteria and Gram-positive cocci. Based on our data, the identification rates can be improved by validated new database entries and the results can be confirmed with nucleic acid sequence analysis.

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