scholarly journals Isolation and Identification of Optochin-Resistant Viridans Group Streptococci from the Sputum Samples of Adult Patients in Jakarta, Indonesia

2021 ◽  
Vol 2021 ◽  
pp. 1-5
Author(s):  
Wisiva Tofriska Paramaiswari ◽  
Nurma Sumar Sidik ◽  
Miftahuddin Majid Khoeri ◽  
Wisnu Tafroji ◽  
Wahyu Finasari Said ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Sputum Sample ◽  
Common Species ◽  
Species Level ◽  
Adult Patients ◽  
Isolation And Identification ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Viridans Group Streptococci ◽  
Tof Ms

Aim. To investigate optochin-resistant viridans group streptococci (VGS) strains isolated from the sputum sample of adult patients with different clinical symptoms. Materials and Methods. Optochin-resistant VGS isolates were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). recA sequencing was used to confirm identified isolates at the genus level by MALDI-TOF MS. Finding. We identified 79% of tested isolates (148/187) at the species-level identification using the MALDI-TOF MS tool. We identified that the most common species isolated from sputum specimens were S. oralis (44.9%) followed by S. mitis (25.7%), S. infantis (9.1%), S. parasanguinis (7.5%), S. peroris (3.7%), S. anginosus (2.7%), and S. sanguinis (2.1%). Discussion. The S. oralis strains were majority of optochin-resistant VGS isolates obtained from sputum of adult patients in Jakarta, Indonesia. MALDI-TOF MS showed potential for the rapid identification tool to identify optochin-resistant VGS isolates. Although there were discrepancies in identifying isolates at the genus/species level, the performance could be improved by expanding its database.

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.

scholarly journals Performance of Five Commercial Identification Platforms for Identification of Staphylococcus delphini

2019 ◽  
Vol 57 (11) ◽  
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.

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

2014 ◽  
Vol 63 (9) ◽  
pp. 1143-1147 ◽  
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.

scholarly journals 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

2016 ◽  
Vol 10 (1) ◽  
pp. 202-208 ◽  
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.

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

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.

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

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.

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

2018 ◽  
Vol 12 (10) ◽  
pp. e0006874 ◽  
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

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 MALDI-TOF MS Detection of Endophytic Bacteria Associated with Great Nettle (Urtica dioica L.), Grown in Algeria

2018 ◽  
Vol 67 (1) ◽  
pp. 67-72 ◽  
Author(s):  
Souheyla Toubal ◽  
Ouahiba Bouchenak ◽  
Djillali Elhaddad ◽  
Karima Yahiaoui ◽  
Sarah Boumaza ◽  
...  
Keyword(s):  
Endophytic Bacteria ◽  
Vascular System ◽  
Common Species ◽  
Urtica Dioica ◽  
Biochemical Tests ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Identification Of Bacteria ◽  
The Common ◽  
Tof Ms

Any plant with a vascular system has a specific endophytic microflora. The identification of bacteria is essential in plant pathology. Although identification methods are effective, they are costly and time consuming. The purpose of this work is to isolate and to identify the different bacteria from the internal tissues of Urtica dioica L. and to study their diversity. This last is based on the different parts of the plant (stems, leaves and roots) and the harvest regions (Dellys and Tlamcen). The identification of bacteria is done by biochemical tests and confirmed by MALDI-TOF MS. Seven genus and eleven species were isolated from the Great Nettle. They belong to the genera Bacillus, Escherichia, Pantoea, Enterobacter, Staphylococcus, Enterococcus and Paenibacillus. The majority of these bacteria were isolated from Tlemcen which makes this region the richest in endophytic bacteria compared to that harvested from Dellys. The results show also that the leaves are the most diversified in endophytic bacteria. Bacillus pumilus-ME is the common species of the three parts of the plant harvested in both regions. From this work, it emerges that the Great Nettle can be settled by various endophytic bacteria which are differently distributed within the same plant harvested in different regions.

scholarly journals Identification of Nocardia species using Autof MS 1000 and Bruker MALDI-TOF MS systems: A comparison

2021 ◽  
Author(s):  
Bing Ma ◽  
Yunqi Tian ◽  
Yungang Han ◽  
Lifang Ban ◽  
Junwen Yang ◽  
...  
Keyword(s):  
Species Identification ◽  
Protein Extraction ◽  
Reference Method ◽  
Invasive Disease ◽  
Species Level ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Significant Difference ◽  
Tof Ms

ABSTRACTNocardia is an important cause of clinically invasive disease, but for most clinical laboratories, identification of these isolates to the species level is challenging. Recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used for identification of most bacterial and fungal isolates. In this multicenter study, we evaluated the identification of Nocardia isolates using Autof MS1000 and Bruker Biotyper. A total of 86 non-duplicate Nocardia isolates from 7 hospital laboratories were evaluated. Further, we carried out sequence analysis of 16S rRNA, gyrB, secA1, hsp65, and rpoB genes as a reference method for Nocardia species identification. The 86 isolates were directly spotted on the target plate and plate protein extraction was performed. Data were analyzed by SPSS 19.0. In total, 72 (83.7%) strains (score ≥ 9.0) and 70 (81.4%) strains (score ≥ 2.0) were correctly identified by the Autof MS1000 and Bruker Biotyper systems, respectively, at the species level. There was no significant difference (P > 0.05) between the two systems using the same protein extraction method. In conclusion, the Autof MS 1000 and Bruker MALDI-TOF systems showed no difference in identification of Nocardia spp. to the species level and could meet the most important clinical requirement for species identification.

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