scholarly journals Performance of MALDI–TOF Mass Spectrometry in the Philippines

2021 ◽  
Vol 6 (3) ◽  
pp. 112
Author(s):  
Morichika Osa ◽  
Maria Cecilia Belo ◽  
Zita Dela Merced ◽  
Annavi Marie G. Villanueva ◽  
Jaira Mauhay ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
The Philippines ◽  
Species Level ◽  
Middle Income ◽  
Maldi Tof Ms ◽  
Middle Income Countries ◽  
Biochemical Methods ◽  
Maldi Tof ◽  
Fungal Isolates ◽  
Tof Ms

Identification of the causative pathogen in infectious diseases is important for surveillance and to guide treatment. In low- and middle-income countries (LMIC), conventional culture and identification methods, including biochemical methods, are reference-standard. Biochemical methods can lack sensitivity and specificity and have slow turnaround times, causing delays in definitive therapy. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI–TOF MS) is a rapid and accurate diagnostic method. Most studies comparing MALDI–TOF MS and biochemical methods are from high-income countries, with few reports from LMIC with tropical climates. The aim of this study was to assess the performance of MALDI–TOF MS compared to conventional methods in the Philippines. Clinical bacterial or fungal isolates were identified by both MALDI–TOF MS and automated (VITEK2) or manual biochemical methods in the San Lazaro Hospital, Metro Manila, the Philippines. The concordance between MALDI­–TOF MS and automated (VITEK2) or manual biochemical methods was analyzed at the species and genus levels. In total, 3530 bacterial or fungal isolates were analyzed. The concordance rate between MALDI–TOF MS and biochemical methods was 96.2% at the species level and 99.9% at the genus level. Twenty-three isolates could not be identified by MALDI–TOF MS. In this setting, MALDI–TOF MS was accurate compared with biochemical methods, at both the genus and the species level. Additionally, MALDI–TOF MS improved the turnaround time for results. These advantages could lead to improved infection management and infection control in low- and middle-income countries, even though the initial cost is high.

scholarly journals Rapid identification of Legionella species by mass spectrometry

2010 ◽  
Vol 59 (3) ◽  
pp. 273-284 ◽  
Author(s):  
Claire Moliner ◽  
Christophe Ginevra ◽  
Sophie Jarraud ◽  
Christophe Flaudrops ◽  
Marielle Bedotto ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Bacterial Species ◽  
Rapid Identification ◽  
Species Level ◽  
Blind Test ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tract Infections ◽  
Pcr Targeting ◽  
Tof Ms

Legionella species are facultative, intracellular bacteria that infect macrophages and protozoa, with the latter acting as transmission vectors to humans. These fastidious bacteria mostly cause pulmonary tract infections and are routinely identified by various molecular methods, mainly PCR targeting the mip gene and sequencing, which are expensive and time-consuming. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has emerged as a rapid and inexpensive method for identification of bacterial species. This study evaluated the use of MALDI-TOF-MS for rapid species and serogroup identification of 21 Legionella species recognized as human pathogens. To this end, a reference MS database was developed including 59 Legionella type strains, and a blind test was performed using 237 strains from various species. Two hundred and twenty-three of the 237 strains (94.1 %) were correctly identified at the species level, although ten (4.2 %) were identified with a score lower than 2.0. Fourteen strains (5.9 %) from eight species were misidentified at the species level, including seven (3.0 %) with a significant score, suggesting an intraspecific variability of protein profiles within some species. MALDI-TOF-MS was reproducible but could not identify Legionella strains at the serogroup level. When compared with mip gene sequencing, MALDI-TOF-MS exhibited a sensitivity of 99.2 and 89.9 % for the identification of Legionella strains at the genus and species level, respectively. This study demonstrated that MALDI-TOF-MS is a reliable tool for the rapid identification of Legionella strains at the species level.

scholarly journals Efficacy of MALDI-TOF mass spectrometry as well as genotypic and phenotypic methods in identification of staphylococci other than Staphylococcus aureus isolated from intramammary infections in dairy cows in Poland

2019 ◽  
Vol 31 (4) ◽  
pp. 523-530 ◽  
Author(s):  
Anna Wanecka ◽  
Jarosław Król ◽  
Jan Twardoń ◽  
Jacek Mrowiec ◽  
Agnieszka Korzeniowska-Kowal ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
16S Rrna ◽  
Species Level ◽  
Confirmatory Test ◽  
Identification System ◽  
Maldi Tof Ms ◽  
Intramammary Infections ◽  
Maldi Tof ◽  
Staphylococcus Spp ◽  
Tof Ms

We compared the effectiveness of various methods for the identification of Staphylococcus spp. other than S. aureus isolated from intramammary infections of cows on 3 dairy farms in Lower Silesia, Poland. A total of 131 isolates belonging to 18 Staphylococcus species were identified by sequence analysis of the 16S rRNA and dnaJ genes, as well using a commercial identification system (ID 32 STAPH; bioMérieux) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS; Bruker Daltonics). Sequencing of the 16S rRNA gene was found to have low discriminatory value because only 43% of isolates were recognized unequivocally. Much better results were obtained with the dnaJ gene (all isolates were correctly identified at the species level). However, some of these isolates achieved a low similarity level (<97%) and required a confirmatory test (sequencing of the rpoB gene). The performance of ID 32 STAPH was poor. Regardless of the probability level used (80% or 90%), the commercial system obtained identification rates <40%. Using MALDI-TOF MS and the commercial Bruker database, 67% of isolates were identified correctly with scores ≥2.0 (acceptable species-level identification) but this number increased to 97% after the database was expanded. The definitive identification of Staphylococcus spp. other than S. aureus causing intramammary infections in cattle often requires a combination of different procedures, and the existing databases should be updated.

scholarly journals Evaluation of MALDI–TOF Mass Spectrometry in Diagnostic and Environmental Surveillance of Legionella Species: A Comparison With Culture and Mip-Gene Sequencing Technique

2020 ◽  
Vol 11 ◽  
Author(s):  
Maria Rosaria Pascale ◽  
Marta Mazzotta ◽  
Silvano Salaris ◽  
Luna Girolamini ◽  
Antonella Grottola ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Phylogenetic Analysis ◽  
Legionella Pneumophila ◽  
Gene Sequencing ◽  
Species Level ◽  
Environmental Surveillance ◽  
Routine Diagnostics ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

Legionella spp. are widespread bacteria in aquatic environments with a growing impact on human health. Between the 61 species, Legionella pneumophila is the most prevalent in human diseases; on the contrary, Legionella non-pneumophila species are less detected in clinical diagnosis or during environmental surveillance due to their slow growth in culture and the absence of specific and rapid diagnostic/analytical tools. Reliable and rapid isolate identification is essential to estimate the source of infection, to undertake containment measures, and to determine clinical treatment. Matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI–TOF MS), since its introduction into the routine diagnostics of laboratories, represents a widely accepted method for the identification of different bacteria species, described in a few studies on the Legionella clinical and environmental surveillance. The focus of this study was the improvement of MALDI–TOF MS on Legionella non-pneumophila species collected during Legionella nosocomial and community surveillance. Comparative analysis with cultural and mip-gene sequencing results was performed. Moreover, a phylogenetic analysis was carried out to estimate the correlations amongst isolates. MALDI–TOF MS achieved correct species-level identification for 45.0% of the isolates belonging to the Legionella anisa, Legionella rubrilucens, Legionella feeleii, and Legionella jordanis species, displaying a high concordance with the mip-gene sequencing results. In contrast, less reliable identification was found for the remaining 55.0% of the isolates, corresponding to the samples belonging to species not yet included in the database. The phylogenetic analysis showed relevant differences inside the species, regruped in three main clades; among the Legionella anisa clade, a subclade with a divergence of 3.3% from the main clade was observed. Moreover, one isolate, identified as Legionella quinlivanii, displayed a divergence of 3.8% from the corresponding reference strain. However, these findings require supplementary investigation. The results encourage the implementation of MALDI–TOF MS in routine diagnostics and environmental Legionella surveillance, as it displays a reliable and faster identification at the species level, as well as the potential to identify species that are not yet included in the database. Moreover, phylogenetic analysis is a relevant approach to correlate the isolates and to track their spread, especially in unconventional reservoirs, where Legionella prevention is still underestimated.

scholarly journals Identification of Photorhabdus symbionts by MALDI-TOF mass spectrometry

2020 ◽  
Author(s):  
Virginia Hill ◽  
Peter Kuhnert ◽  
Matthias Erb ◽  
Ricardo A. R. Machado
Keyword(s):  
Mass Spectrometry ◽  
Natural Products ◽  
Related Species ◽  
Entomopathogenic Nematodes ◽  
Species Level ◽  
Closely Related Species ◽  
Maldi Tof Ms ◽  
Bacterial Genus ◽  
Maldi Tof ◽  
Tof Ms

AbstractSpecies of the bacterial genus Photorhabus live in a symbiotic relationship with Heterorhabditis entomopathogenic nematodes. Besides their use as biological control agents against agricultural pests, some Photorhabdus species are also a source of natural products and are of medical interest due to their ability to cause tissue infections and subcutaneous lesions in humans. Given the diversity of Photorhabdus species, rapid and reliable methods to resolve this genus to the species level are needed. In this study, we evaluated the potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Photorhabdus species. To this end, we established a collection of 54 isolates consisting of type strains and multiple field strains that belong to each of the validly described species and subspecies of this genus. Reference spectra for the strains were generated and used to complement a currently available database. The extended reference database was then used for identification based on the direct transfer sample preparation method and protein fingerprint of single colonies. High discrimination of distantly related species was observed. However, lower discrimination was observed with some of the most closely related species and subspecies. Our results, therefore, suggest that MALDI-TOF MS can be used to correctly identify Photorhabdus strains at the genus and species level, but has limited resolution power for closely related species and subspecies. Our study demonstrates the suitability and limitations of MALDI-TOF-based identification methods for the assessment of the taxonomical position and identification of Photorhabdus isolates.Impact StatementSpecies of the bacterial genus Photorhabus live in close association with soil-born entomopathogenic nematodes. Under natural conditions, these bacteria are often observed infecting soil-associated arthropods, but under certain circumstances, can also infect humans. They produce a large variety of natural products including antibiotics, insecticides, and polyketide pigments that have substantial agricultural, biotechnological and medical potential. In this study, we implement MALDI-TOF MS-based identification method to resolve the taxonomic identity of this bacterial genus, providing thereby a rapid identification tool to understanding its taxonomic diversity to boost scientific progress in medical, agricultural, and biotechnological settings.

scholarly journals Performance of MALDI-TOF Mass Spectrometry for the Identification of the HACEK Group and Other Fastidious Gram-Negative Rods

2019 ◽  
Vol 13 (1) ◽  
pp. 216-221 ◽  
Author(s):  
Marisa Almuzara ◽  
Karen C. V. Cárdenas ◽  
Claudia Barberis ◽  
Maria S. Ramirez ◽  
Angela Famiglietti ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Formic Acid ◽  
Extraction Methods ◽  
Species Level ◽  
Acid Extraction ◽  
Gram Negative ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Routine Identification ◽  
Tof Ms

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.

scholarly journals Identification of fungal isolates by MALDI-TOF mass spectrometry in veterinary practice: validation of a web application

2019 ◽  
Vol 31 (3) ◽  
pp. 471-474 ◽  
Author(s):  
Pierre Becker ◽  
Anne-Cécile Normand ◽  
Gerty Vanantwerpen ◽  
Mia Vanrobaeys ◽  
Roel Haesendonck ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Web Application ◽  
Animal Health ◽  
Correct Identification ◽  
Human Pathogens ◽  
Online Application ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Fungal Isolates ◽  
Tof Ms

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a reliable method to identify fungal isolates. The success of this approach relies on the availability of exhaustive databases, but the latter were built with a focus on human pathogens. We assessed a large in-house database of reference spectra and a dedicated web application for their suitability for use in veterinary laboratories. A panel of 290 mold and yeast isolates representing 69 different fungal species was isolated from various animals (including pets, cattle, and zoo animals) and identified using both MALDI-TOF MS and conventional techniques. The performance of the 2 methods was compared, and identifications were confirmed by DNA sequencing. MALDI-TOF MS allowed distinction between some closely related species and achieved 89% correct identification at the species level. In comparison, only 60% of the isolates were correctly identified with conventional approaches. Using this online application, MALDI-TOF MS thus appears to be a relevant alternative for the identification of fungal isolates encountered by animal health professionals.

scholarly journals Rapid identification of bovine mastitis pathogens by MALDI-TOF Mass Spectrometry

2018 ◽  
Vol 38 (4) ◽  
pp. 586-594 ◽  
Author(s):  
Patrícia A.C. Braga ◽  
Juliano L. Gonçalves ◽  
Juliana R. Barreiro ◽  
Christina R. Ferreira ◽  
Tiago Tomazi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Bovine Mastitis ◽  
Species Level ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Alternative Method ◽  
Microbiological Methods ◽  
Identification Of Bacteria ◽  
Tof Ms

ABSTRACT: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been shown to be an alternative method for identification of bacteria via their protein profile spectra, being able to identify bacteria at the genus, species and even at subspecies level. With the aim of large-scale identification of pathogens causing mastitis by this platform, a total of 305 isolates of bacteria identified from cows with subclinical mastitis were analyzed by conventional microbiological culture (MC) as well as by MALDI-TOF MS coupled with Biotyper data processing. Approximately 89% of the identifications performed by MALDI-TOF MS were consistent with results obtained by MC. From the remaining isolates (11%), 6.3% of isolates were classified as misidentified (discordance for both genus and species level), and 4.7% showed identification agreement at the genus level but not at the species level, being classified as unidentified at species level. The disagreement results were mostly associated with identification of Streptococcus and Enterococcus species probably due to the narrow phenotypic similarity between these two genera. These disagreement results suggest that biochemical assays might be prone to identification errors and, MALDI-TOF MS therefore may be an alternative to overcome incorrect species-specific identification. Standard microbiological methods for bovine mastitis diagnosis are time consuming, laborious and prone to errors for some bacteria genera. In our study, we showed that MALDI-TOF MS coupled with Biotyper may be an alternative method for large-scale identification of bacteria isolated from milk samples compared to classical microbiological routine protocols.

scholarly journals Comparison of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and Molecular Biology Techniques for Identification of Culicoides (Diptera: Ceratopogonidae) Biting Midges in Senegal

2014 ◽  
Vol 53 (2) ◽  
pp. 410-418 ◽  
Author(s):  
Masse Sambou ◽  
Maxence Aubadie-Ladrix ◽  
Florence Fenollar ◽  
Becaye Fall ◽  
Hubert Bassene ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Species Level ◽  
Morphological Identification ◽  
Biting Midges ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Biting midges of the genusCulicoidesare implicated as vectors for a wide variety of pathogens. The morphological identification of these arthropods may be difficult because of a lack of detailed investigation of taxonomy for this species in Africa. However, matrix-assisted laser desorption ionization−time of flight mass spectrometry (MALDI-TOF MS) profiling is efficient for arthropod identification at the species level. This study established a spectrum database ofCulicoidesspp. from Senegal using MALDI-TOF. Identification ofCulicoidesinsects to the species level before mass spectrometry was performed on the basis of morphological characters. MALDI-TOF MS reference spectra were determined for 437 field-caughtCulicoidesof 10 species. The protein profiles of all testedCulicoidesrevealed several peaks with mass ranges of 2 to 20 kDa. In a validation study, 72Culicoidesspecimens in the target species were correctly identified at the species level with a similarity of 95 to 99.9%. FourCulicoidesprotein profiles were misidentified. Nevertheless, six SuperSpectra (C. imicola,C. enderleini,C. oxystoma,C. kingi,C. magnus, andC. fulvithorax) were created. Abdomens of midges were used to amplify and sequence a portion of the mitochondrial cytochrome oxidase I gene (COI). The results obtained using the MALDI-TOF MS method were consistent with the morphological identification and similar to the genetic identification. Protein profiling using MALDI-TOF is an efficient approach for the identification ofCulicoidesspp., and it is economically advantageous for approaches that require detailed and quantitative information of vector species that are collected in field. The database of AfricanCulicoidesMS spectra created is the first database in Africa. The COI sequences of fiveCulicoidesspecies that were previously noncharacterized using molecular methods were deposited in GenBank.

scholarly journals Speciation of the Mycobacterium tuberculosis complex using mass spectrometry: a proof-of-concept

2021 ◽  
Author(s):  
Simon Robinne ◽  
Jamal Saad ◽  
Madjid Morsli ◽  
Hamidou Zelika Harouna ◽  
Fatah Tazerart ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mycobacterium Tuberculosis ◽  
Dna Analysis ◽  
Species Level ◽  
Complex Species ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Source Tracing ◽  
Tof Ms

ABSTRACTMycobacteria that form the Mycobacterium tuberculosis complex are responsible for deadly tuberculosis in animals and patients. Identification of these pathogens at the species level is of primary importance for treatment and source tracing, and currently relies on DNA analysis, including whole genome sequencing (WGS), which takes a whole day. In this study, we report on the unprecedented identification of the M. tuberculosis complex species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), with WGS as the comparative gold standard. In a first step, an optimised peptide extraction applied to 24 isolates otherwise identified in three of the 11 M. tuberculosis complex species by WGS, yielded 94 MALDI-TOF spectra which clustered according to WGS identification. In a second step, 70/74 (95%) other isolates were correctly identified at the species level by this clustering method. This study is the first to report a MALDI-TOF-MS method of identification of M. tuberculosis complex mycobacteria at the species level and is easily implantable in clinical microbiology laboratories.

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

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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