Identification of Bacillus strains by MALDI TOF MS using geometric approach

Abstract

Microorganism identification by MALDI TOF mass-spectrometry is based on the comparison of the mass spectrum of the studied organism with those of reference strains. It is a rapid and reliable method. However, commercial databases and programs are mostly designed for identification of clinically important strains and can be used only for particular mass spectrometer models. The need for open platforms and reference databases is obvious. In this study we describe a geometric approach for microorganism identification by mass spectra and demonstrate its capabilities by analyzing 24 strains belonging to the Bacillus pumilus group. This method is based on representing mass spectra as points on a multidimensional space, which allows us to use geometric distances to compare the spectra. Delimitation of microorganisms performed by geometric approach correlates well with the results of molecular phylogenetic analysis and clustering using Biotyper 3.1. All three methods used allowed us to reliably divide the strains into two groups corresponding to closely related species, Bacillus pumilus and Bacillus altitudinis. The method developed by us will be implemented in a Web interface designed for using open reference databases for microorganism identification. The data is available at http://www.bionet.nsc.ru/mbl/database/database.html.

Identification and typing of Vagococcus salmoninarum using genomic and proteomic techniques

“…On the contrary, the combined use of cluster analysis and the identification of biomarkers by means of the Mass‐Up and SPSS programs (Fernández‐Álvarez et al, ; López‐Fernández et al, ) allowed us grouping strains according to their taxonomic position and the typing of bacterial strains according to the intra‐ and interspecific variability of their protein spectra. Numerous studies have demonstrated that cluster analysis of MALDI‐TOF data is robust and reliable methods for discrimination of bacteria (AlMasoud, Xu, Nicolaou, & Goodacre, ; Fernández‐Álvarez et al, ; Kim et al, ; Starostin et al, ). Similarity levels of the V. salmoninarum strains tested in this study range from 87% to 92%, and eight species‐specific mass biomarkers at m/z 4,521.41, 4,845.06, 5,291.74, 6,229.97, 6,965.50, 9,043.02, 9,686.66 and 10,579.43 were detected in 100% of strains of V. salmoninarum (20 to 20 strains tested) regardless of their source of isolation or geographical area.…”

Collection of microorganisms of ICG SB RAS as a genetic resource for biotechnology

“…Несмотря на то что в ряде работ про-демонстрирована более высокая точность идентификации с помощью МАЛДИ времяпролетной масс-спектрометрии по сравнению с секвенированием гена 16S рРНК (Rasko et al, 2005), надежная идентификация представителей Bacillus cereus group используемым методом требует нали-чия обширной и репрезентативной базы данных и про-двинутых математических методов анализа (Lasch et al, 2009). Таким образом, необходимо дальнейшее пополне-ние базы данных, созданной в ФИЦ ИЦиГ СО РАН (Starostin et al, 2015), как представителями обнаруженной группы микроорганизмов, так и другими таксонами, что позволит создать эффективный инструмент для быстрой и точной идентификации больших коллекций микроор-ганизмов, а также дифференциации микроорганизмов на внутригрупповом и внутривидовом уровне.…”

“…Кроме того, для штаммов коллекции ФИЦ ИЦиГ СО РАН проводится полногеномное секвенирование и проце-дура биотипирования на основании данных MALDI-TOF масс-спектрометрии (Bryanskaya et al, 2014;Starostin et al, 2015;Rozanov et al, 2017), а также скрининг штаммов для выявления возможности их трансформации. Выполняется поиск мобильных элементов и плазмид, пригодных для создания систем введения экзогенной ДНК в геном микро-организма; изучение системы рестрикции-модификации выбранных микроорганизмов; создание челночных векто-ров (Rozanov et al, 2014).…”

Industrial and artisanal fresh filled pasta: Quality evaluation

“…Suspected colonies of B. cereus were, also, confirmed by matrix assisted laser desorption/ionization‐time of flight mass spectrometry (MALDI‐TOF) technology. This technology generates characteristic mass spectral fingerprints, that are unique signatures for each microorganism (Charnot‐Katsikas, Tesic, Boonlayangoor, Bethel, & Frank, ; Starostin et al, ). All suspected colonies isolated in Tryptic soy agar medium (Biolife, Milano, Italy) with 5% sheep blood (Biolife, Milano, Italy) were mixed with 1 µl of α‐cyano‐4‐hydroxycinnamic acid (CHCA) matrix (bioMérieux, Firenze, Italy) on a conductive metal plate.…”