Carbohydrate profiling of bacteria by gas chromatography-mass spectrometry: chemical derivatization and analytical pyrolysis

Identification of Salmonella Taxon-Specific Peptide Markers to the Serovar Level by Mass Spectrometry

We present an LC-MS/MS pipeline to identify taxon-specific tryptic peptide markers for the identification of Salmonella at the genus, species, subspecies, and serovar levels of specificity. Salmonella enterica subsp. enterica serovars Typhimurium and its four closest relatives, Saintpaul, Heidelberg, Paratyphi B, and Muenchen, were evaluated. A decision-tree approach was used to identify peptides common to the five Salmonella proteomes for evaluation as genus-, species-, and subspecies-specific markers. Peptides identified for two or fewer Salmonella strains were evaluated as potential serovar markers. Currently, there are approximately 140 000 assembled bacterial genomes publicly available, more than 8500 of which are for Salmonella. Consequently, the specificity of each candidate peptide marker was confirmed across all publicly available protein sequences in the NCBI nonredundant (nr) database. The performance of a subset of candidate taxon-specific peptide markers was evaluated in a targeted mass-spectrometry method. The presented workflow offers a marked improvement in specificity over existing MALDI-TOF-based bacterial identification platforms for the identification of closely related Salmonella serovars.

Lipid phenotype of two distinct subpopulations of Mycobacterium bovis Bacillus Calmette-Guerin Tokyo 172 substrain

Bacillus Calmette-Guérin (BCG) Tokyo 172 is a predominant World Health Organization Reference Reagent for the BCG vaccine. Recently, the BCG Tokyo 172 substrain was reported to consist of two subpopulations with different colony morphologies, smooth and rough. Smooth colonies had a characteristic 22-bp deletion in Rv3405c of the region of difference (RD) 16 (type I), and rough colonies were complete in this region (type II). We hypothesized that the morphological difference is related to lipid phenotype and affects their antigenicity. We determined the lipid compositions and biosynthesis of types I and II. Scanning electron microscopy showed that type I was 1.5 times longer than type II. Phenolic glycolipid (PGL) and phthiocerol dimycocerosate (PDIM) were found only in type I. Although it has been reported that the RD16 is involved in the expression of PGL, type II did not possess PGL/PDIM. We examined the ppsA-E gene responsible for PGL/PDIM biosynthesis and found that the existence of PGL/PDIM in types I and II is caused by a ppsA gene mutation not regulated by the RD16. PGL suppressed the host recognition of total lipids via Toll-like receptor 2, and this suggests that PGL is antigenic and involved in host responses, acting as a cell wall component. This is the first report to show the difference between lipid phenotypes of types I and II. It is important to clarify the heterogeneity of BCG vaccine substrains to discuss and evaluate the quality, safety, and efficacy of the BCG vaccine.

Differentiation of Aeromonas Isolated from Drinking Water Distribution Systems Using Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry

The genus Aeromonas is one of several medically significant genera that have gained prominence due to their evolving taxonomy and controversial role in human diseases. In this study, matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) was used to analyze the whole cells of both reference strains and unknown Aeromonas isolates obtained from water distribution systems. A library of over 45 unique m/z signatures was created from 40 strains that are representative of the 17 recognized species of Aeromonas, as well as 3 reference strains from genus Vibrio and 2 reference strains from Plesiomonas shigelloides. The library was used to help speciate 52 isolates of Aeromonas. The environmental isolates were broken up into 2 blind studies. Group 1 contained isolates that had a recognizable phenotypic profile and group 2 contained isolates that had an atypical phenotypic profile. MALDI-MS analysis of the water isolates in group 1 matched the phenotypic identification in all cases. In group 2, the MALDI-MS-based determination confirmed the identity of 18 of the 27 isolates. These results demonstrate that MALDI-MS analysis can rapidly and accurately classify species of the genus Aeromonas, making it a powerful tool especially suited for environmental monitoring and detection of microbial hazards in drinking water.

Analysis of bacterial strains with pyrolysis-gas chromatography/differential mobility spectrometry

Eight vegetative bacterial strains and two spores were characterized by pyrolysis-gas chromatography with differential mobility spectrometry (py-GC/DMS) yielding topographic plots of ion intensity, retention time, and compensation voltage simultaneously for ions in positive and negative polarity. Biomarkers were found in the pyrolysate at characteristic retention times and compensation voltages and were confirmed by standard addition with GC/MS analyses providing discrimination between Gram negative and Gram positive bacterial types, but no recognition of individual strains within the Gram negative bacteria. Principal component analysis was applied using two dimensional data sets of ion intensity versus retention time at five compensation voltages including the reactant ion peaks all in positive and negative ion polarity. Clustering was observed with compensation voltage (CV) chromatograms associated with ion separation in the DMS detector and little or no clustering was observed with the reactant ion peaks or CV chromatograms where ion separation is poor. Consistent clustering of Gram positive B. odysseyi and Gram negative E. coli in both positive and negative polarities with the reactant ion peak chromatograms and key CV chromatograms suggests common but unknown common chemical compositions in the pyrolysate.

Microfabricated Differential Mobility Spectrometry with Pyrolysis Gas Chromatography for Chemical Characterization of Bacteria

A microfabricated drift tube for differential mobility spectrometry (DMS) was used with pyrolysis-gas chromatography (py-GC) to chemically characterize bacteria through three-dimensional plots of ion intensity, compensation voltage from differential mobility spectra, and chromatographic retention time. The DMS analyzer provided chemical information for positive and negative ions simultaneously from chemical reactions between pyrolysis products in the GC effluent and reactant ions of H+(H2O)n and O2-(H2O)n in air at ambient pressure. Authentic standards for chemicals formed in the pyrolysis of bacteria showed favorable matches with plots from py-GC/DMS analysis and were supported by py-GC/MS results. These and other yet-unidentified constituents provided a means to distinguish Escherichia coli from Micrococcus luteus. A Gram-positive spore former (Bacillus megaterium) was distinguished by an abundant peak for crotonic acid evident in positive and negative ions and not observed with M. luteus. In contrast, plots from py-GC/DMS of lipid A and lipoteichoic acid showed poor matches to plots for a Gram-negative (E. coli) bacterium and a Gram-positive (M. luteus) bacterium and the differences were attributed to differences in genus sources of the biopolymers. A significant percentage of the chemical information available in py-GC/DMS is unidentified, and the analytical utility must be established. Precision in the chemical measurement was determined as +/- 0.2 V, 10% relative standard deviation (RSD), and +/- 0.05 min for compensation voltage, peak intensity, and retention time, respectively. The minimum number of total bacteria (cell forming units) detected was 6000 though detection limits and resolution could be varied by the magnitude of the separation voltage in the differential mobility spectrometer.

Carbonaceous meteorites as a source of sugar-related organic compounds for the early Earth

The much-studied Murchison meteorite is generally used as the standard reference for organic compounds in extraterrestrial material. Amino acids and other organic compounds important in contemporary biochemistry are thought to have been delivered to the early Earth by asteroids and comets, where they may have played a role in the origin of life. Polyhydroxylated compounds (polyols) such as sugars, sugar alcohols and sugar acids are vital to all known lifeforms-they are components of nucleic acids (RNA, DNA), cell membranes and also act as energy sources. But there has hitherto been no conclusive evidence for the existence of polyols in meteorites, leaving a gap in our understanding of the origins of biologically important organic compounds on Earth. Here we report that a variety of polyols are present in, and indigenous to, the Murchison and Murray meteorites in amounts comparable to amino acids. Analyses of water extracts indicate that extraterrestrial processes including photolysis and formaldehyde chemistry could account for the observed compounds. We conclude from this that polyols were present on the early Earth and therefore at least available for incorporation into the first forms of life.

Muramic acid is not detectable in Chlamydia psittaci or Chlamydia trachomatis by gas chromatography-mass spectrometry

By using the powerful separation technique of capillary gas chromatography combined with the selectivity of mass spectrometric detection, muramic acid was not detectable in purified elementary bodies of Chlamydia psittaci Cal 10 (less than or equal to 0.006%) or C. trachomatis serovar E (less than or equal to 0.02%). This confirms previous reports which suggested the absence of a typical peptidoglycan in Chlamydia spp.

Chemotaxonomic differentiation of legionellae by detection and characterization of aminodideoxyhexoses and other unique sugars using gas chromatography-mass spectrometry

Legionellae have been differentiated previously by analyzing their carbohydrate contents by gas chromatography with flame ionization detection. In the present study, total ion mode gas chromatography-mass spectrometry (GC-MS) was used to detect a number of unusual sugars, including one that is structurally related to O-methyldideoxyheptoses. Increased sensitivity and selectivity for carbohydrate detection was achieved by selected ion-monitoring GC-MS. Two of the uncommon sugars previously discovered in the legionellae (X1 and X2) were identified as quinovosamine and fucosamine, respectively. Legionella pneumophila contained rhamnose and quinovosamine but not the quinovosamine isomer fucosamine. Tatlockia micdadei and Legionella maceachernii contained large amounts of rhamnose, fucose, and fucosamine but not quinovosamine. These two species were the only legionellae studied that contained another unusual sugar that is referred to as X3, pending determination of its structure. Fluoribacter dumoffi, Fluoribacter bozemanae, and Legionella anisa were varied in their carbohydrate contents, both within and between species, but could be distinguished from L. pneumophila and the T. micdadei and L. maceachernii group. Fluoribacter gormanii was unique among the legionellae in that it lacked both quinovosamine and fucosamine. Legionella jordanis contained other unusual carbohydrates in addition to quinovosamine. GC-MS may have wide application in the differentiation of bacterial species.

Rapid identification of Haemophilus influenzae serovar b by gas liquid chromatography using carbohydrate fingerprints

Carbohydrates from whole-cell hydrolysates of 18 strains of the species Haemophilus influenzae (5 strains belonging to serovar b) were analysed by gas-liquid chromatography. The identity of the carbohydrate components was confirmed by comparison with the retention times of reference sugars and by gas chromatography mass spectrometry. Evidence was obtained that Haemophilus influenzae serovar b can easily be identified by the presence of one large peak representing ribitol. The method described can be routinely applied in bacteriological laboratories equipped with a gas chromatograph. It gives results within approximately 4 h, it is reproducible and easy to perform. Even single colonies isolated directly from agar plates can be used for analysis without further subculturing.