Strain level identification

Overall, the shotgun-proteomics findings were consistent with the minimal inhibitory concentration (MIC) determination results because all 20 A. baumannii clinical isolates were foimd resistant to carbapenem, monobactam, cephalosporin, and to a combination treatment of penicillin and P-lactamase inhibitors. The results obtained demonstrate that by augmenting the custom DB with strain-specific unique peptide sequences, it is possible to obtain simultaneously both strain-level identification of. baumannii clinical isolates and their antibiotic resistance mechanism information within 5-6 h. Therefore, the approach developed by Chang et al (2013) could be used for a rapid, sensitive, and specific detection of P-lactam-resistant strains of. baumannii. 

Bottom-up proteomics methods still need refinement of protocols, and improvements in the standardization and availability of bioinformatics tools for comprehensive data analysis on a routine basis. Although recent innovations in mass spec-trometric instramentation have aeeelerated the speed and sensitivity of proteome analysis (Hebert et al. 2014), further improvements can be obtained by emphasizing the optimization, simplification, and automation of sample preparation, for example, through single-tube proteomics approaches integrating all steps from cell lysis to peptide fractionation (Hughes et al. 2014 Fan et al. 2014), peptide separation techniques, and bioinformatics tools for fast, automated data interpretation for strain-level identification of cultivable bacteria and comprehensive characterization of each isolated microbial strain in the near future. 

Yadav JS, Khan lU, Eakhari E, et al. DNA-based methodologies for rapid detection, quantification, and species- or strain-level identification of respiratory pathogens (Mycobacteria and Pseudomonas) in metalworking fluids. Appl Occup Environ Hyg... 

The complete four-component system is necessary when the diagnostic requirement is rapid, low unit-cost analysis for both the strain-level characterization of pathogenic agents and identification of hoax bio-terror materials. Using the complete system, we are proposing to validate MS-based microbial taxonomy and to transfer the technology from an analytical research to a clinical or public health production-diagnosis environment. 

Due to the fact that Raman spectroscopy is a very sensitive technique, even identification on the strain level becomes possible. Various studies were performed distinguishing different strains of Acinetobacter baumannii [48], Staph, cohnii, and Staph, epidermidis strains [44], as well as various Bacillus strains [45]. Goeller et al. applied Raman spectroscopy not only to discriminate... 

By calculating an average Raman spectrum from a line scan over the long axis of yeast cells a differentiation of single yeast cells on a species and strain level can be performed [110, 111]. The application of Raman spectroscopy in combination with a supervised classification method allows for the identification of single yeast cells in a large data set [69]. 

Intact-cell MALDI-TOF analysis offers several attractive features for rapid screening of bacterial collections. Analysis is performed directly on the cells after minimal sample preparation, and data acquisition is complete in only a matter of minutes. Intact biomarkers are introduced into the MALDI-TOF instrument under these conditions. Whether the observed biomarker molecules are desorbed directly from the surface of the cell wall or are extracted from the cells and co-crystallized with the matrix is currently unresolved, but MALDI spectra of intact bacteria generally contain a large number of peaks in the mass range 1-20 kDa [31]. For bacterial cells, proteins are the most often observed biomarkers. While this approach samples only a small percentage of the total proteins produced in the cells, these profiles have been reported by many groups to be suitable for taxonomic identification, down to at least the strain level. The wide availability of the MALDI-TOF instrumentation and its relative ease of use, coupled with relatively simple sample preparation procedures, have been key features in the rapid advancement of this approach. 

Electronic nose technology is relatively new and holds great promise as a detection tool in food safety area because it is portable, rapid and has potential applicability in foodbome pathogen identification or detection. On the basis of the work described above, we have demonstrated that the E-nose integrated with chemometrics can be used to identify pathogen bacteria at genus, species and strains levels. 

Pramateftaki, P. V., Lanaridis, P, Typas, M. A. (2000). Molecular identification of wine yeasts at species or strain level a case study with strains from two vine-growing areas of Greece. 

Bottom-Up Proteomics Methods for Strain-Level Typing and Identification of Bacteria... 

Karlsson R, Davidson M, Svensson-Stadler L, et al. Strain-level typing and identification of bacteria using mass spectrometry-based proteomics. J Proteome Res. 2012 11 2710-20. doi 10.1021/pr2010633. 

Fig. 6.4 Objectives of strain-level applications of MALDl-TOF MS-enabled characterization of bacteria have included categorization (a), differentiation (b), and identification (c). The requisite level of taxonomie resolution tends to increase as one progresses from efforts to categorizing strains to identifying individual strains. (Adapted from Sandrin et al. 2013, copyright John Wiley...

Medium type has also aifected strain-level ddfeientiation and identification. The influence seems specific for particular species and strains. For example, Sedo et al. 

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