Laboratory identification and clinical characteristics of Streptococcus bovis/Streptococcus equinus complex bacteremia: a retrospective, multicenter study in Hiroshima, Japan

Abstract Background Bacteremia due to the Streptococcus bovis/Streptococcus equinus complex (SBSEC) is associated with specific diseases, such as colorectal cancer and infective endocarditis. This study aimed to evaluate the clinical characteristics of SBSEC bacteremia and the accuracy of identification of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and phenotypic identification systems for SBSEC isolates. Methods We analyzed patients with SBSEC bacteremia retrospectively between 2012 and 2019 at three hospitals in Japan. We re-identified each SBSEC isolate using sequencing superoxide dismutase (sodA) analysis, MALDI-TOF MS using the MALDI Biotyper, and phenotypic identification using the VITEK2. Results During the study period, 39 patients with SBSEC bacteremia were identified. S. gallolyticus subsp. pasteurianus (SGSP, n = 29), S. gallolyticus subsp. gallolyticus (SGSG, n = 5), S. lutetiensis (SL, n = 4), and S. infantarius subsp. infantarius (n = 1) were identified using sodA sequencing analysis. Primary bacteremia (36%) was the most common cause of bacteremia, followed by infective endocarditis (26%) and biliary tract infections (23%). Colorectal cancer was associated significantly with SGSG bacteremia, while the sources of bacteremia were similar in each SBSEC subspecies. The MALDI Biotyper was significantly more accurate in identifying the SBSEC isolates at the subspecies level compared to the VITEK2 (92% vs. 67%, P = 0.010). In contrast, there were no significant differences in the rates of correct identification of the SBSEC isolates at the species level between the MALDI Biotyper and the VITEK2 (100% vs. 87%, P = 0.055). Conclusions Bacteremia with SGSG was associated with colorectal cancer, and the sources of bacteremia were similar in each SBSEC subspecies. The MALDI-TOF MS was significantly more accurate in identifying SBSEC isolates at the subspecies level than the phenotypic identification systems. The accurate identification of SBSEC isolates using the MALDI-TOF MS and phenotypic identification systems was sufficient at the species level, but it was insufficient at the subspecies level. Therefore, it may be reasonable for clinicians to perform echocardiographies and colonoscopies in all patients with SBSEC bacteremia.

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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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Accuracy of conventional identification methods used for Enterobacteriaceae isolates in three Nigerian hospitals

PeerJ ◽

10.7717/peerj.2511 ◽

2016 ◽

Vol 4 ◽

pp. e2511 ◽

Cited By ~ 4

Author(s):

Christiana Jesumirhewe ◽

Peter Oladejo Ogunlowo ◽

Mitsan Olley ◽

Burkhard Springer ◽

Franz Allerberger ◽

...

Keyword(s):

Multidrug Resistant ◽

Species Level ◽

Accurate Identification ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Maldi Biotyper ◽

Identification Of Bacteria ◽

Identification Techniques ◽

Tof Ms

BackgroundEnterobacteriaceae are ubiquitously present in nature and can be found in the intestinal tract of humans and animals as commensal flora. Multidrug-resistant Enterobacteriaceae are increasingly reported and are a threat to public health implicating a need for accurate identification of the isolates to species level. In developing countries, identification of bacteria basically depends on conventional methods: culture and phenotypic methods that hamper the accurate identification of bacteria. In this study, matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) technique was compared to conventional identification techniques.Materials and MethodsIn total, 147 Enterobacteriaceae isolates were collected from March to May 2015 from three medical microbiology laboratories of hospitals in Edo state, Nigeria, after being tested according to the individual laboratories standard operating procedures. All isolates were stored at −20°C until tested centrally by MALDI-TOF MS.ResultsOne hundred and forty five (98.6%) isolates had a MALDI Biotyper best score > or =2.0, indicating a secure genus and probable species identification; and 2(1.36%) isolates had a best score <2.0 indicating probable genus identification. Isolates with best scores of > or =2.0 comprised nine genera and 10 species, respectively. A total of 57.2% and 33.1% of isolates identified had agreement between MALDI-TOF MS and conventional techniques for identification at genus and species level, respectively, when analyzing bacteria with MALDI Biotyper best scores > or =2.0.ConclusionThe results of our study show that the applied conventional identification techniques for Enterobacteriaceae in the investigated Nigerian hospitals are not very accurate. Use of state-of-the-art identification technologies for microorganisms is necessary to guarantee comparability of bacteriological results.

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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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Species identification of Streptococcus bovis group isolates causing bacteremia: a comparison of two MALDI-TOF MS systems

Diagnostic Microbiology and Infectious Disease ◽

10.1016/j.diagmicrobio.2017.02.007 ◽

2017 ◽

Vol 88 (1) ◽

pp. 23-25 ◽

Cited By ~ 2

Author(s):

Charlotte N. Agergaard ◽

Elisa Knudsen ◽

Rimtas Dargis ◽

Xiaohui C. Nielsen ◽

Jens J. Christensen ◽

...

Keyword(s):

Species Identification ◽

Streptococcus Bovis ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Tof Ms

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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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Discrimination of Streptococcus equi subsp. equi and Streptococcus equi subsp. zooepidemicus using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Journal of Veterinary Diagnostic Investigation ◽

10.1177/1040638717702687 ◽

2017 ◽

Vol 29 (5) ◽

pp. 622-627 ◽

Cited By ~ 7

Author(s):

Rinosh J. Mani ◽

Anil J. Thachil ◽

Akhilesh Ramachandran

Keyword(s):

Laser Desorption Ionization ◽

Biochemical System ◽

Ionization Time ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Subspecies Level ◽

Streptococcus Equi ◽

Level Identification ◽

Tof Ms

Accurate and timely identification of infectious etiologies is of great significance in veterinary microbiology, especially for critical diseases such as strangles, a highly contagious disease of horses caused by Streptococcus equi subsp. equi. We evaluated a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platform for use in species- and subspecies-level identification of S. equi isolates from horses and compared it with an automated biochemical system. We used 25 clinical isolates each of S. equi subsp. equi and S. equi subsp. zooepidemicus. Using the MALDI-TOF MS platform, it was possible to correctly identify all 50 isolates to the species level. Unique mass peaks were identified in the bacterial peptide mass spectra generated by MALDI-TOF MS, which can be used for accurate subspecies-level identification of S. equi. Mass peaks (mass/charge, m/ z) 6,751.9 ± 1.4 (mean ± standard deviation) and 5,958.1 ± 1.3 were found to be unique to S. equi subsp. equi and S. equi subsp. zooepidemicus, respectively. The automated biochemical system correctly identified 47 of 50 of the isolates to the species level as S. equi, whereas at the subspecies level, 24 of 25 S. equi subsp. equi isolates and 22 of 25 S. equi subsp. zooepidemicus isolates were correctly identified. Our results indicate that MALDI-TOF MS can be used for accurate species- and subspecies-level identification of S. equi.

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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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