Strain-level bacterial identification by CeO2-catalyzed MALDI-TOF MS fatty acid analysis and comparison to commercial protein-based methods.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid approach for clinical bacterial identification. However, current protein-based commercial bacterial ID methods fall short when differentiating closely related species/strains. To address this shortcoming, we employed CeO2-catalyzed fragmentation of lipids to produce fatty acids using the energy inherent to the MALDI laser as a novel alternative to protein profiling. Fatty acid profiles collected from Enterobacteriaceae, Acinetobacter, and Listeria using CeO2-catalyzed metal oxide laser ionization (MOLI MS), processed by principal component analysis, and validated by leave-one-out cross-validation (CV), showed 100% correct classification at the species level and 98% at the strain level. In comparison, protein profile data from the same bacteria yielded 32%, 54% and 67% mean species-level accuracy using two MALDI-TOF MS platforms, respectively. In addition, several pathogens were misidentified by protein profiling as non-pathogens and vice versa. These results suggest novel CeO2-catalyzed lipid fragmentation readily produced (i) taxonomically tractable fatty acid profiles by MOLI MS, (ii) highly accurate bacterial classification and (iii) consistent strain-level ID for bacteria that were routinely misidentified by protein-based methods.

Detection of bacteria from biological mixtures using immunomagnetic separation combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

A rapid method for identifying specific bacteria from complex biological mixtures using immunomagnetic separation coupled to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has been developed. The technique employs commercially available magnetic beads coated with polycolonal antibodies raised against specific bacteria and whole cell analysis by MALDI-MS. A suspension of a bacterial mixture is mixed with the immunomagnetic beads specific for the target microorganism. After a short incubation period (20 mins) the bacteria captured by the beads are washed, resuspended in deionized H(2)O and directly applied onto a MALDI probe. Liquid suspensions containing bacterial mixtures can be screened within 1 h total analysis time. Positive tests result in the production of a fingerprint mass spectrum primarily consisting of protein biomarkers characteristic of the targeted microorganism. Using this procedure, Salmonella choleraesuis was isolated and detected from standard bacterial mixtures and spiked samples of river water, human urine, and chicken blood.

On-probe sample pretreatment for the detection of proteins above 15 KDa from whole cell bacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

A rapid methodology is described for the enhancement of the signal-to-base-line (S/B) ratio of high molecular weight protein signals from whole cell bacteria analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The procedure involves depositing growing bacteria colonies from culture dishes directly onto the MALDI probe followed by treatment of the sample spot with a 2 microL aliquot of 40% ethanol prior to the addition of a ferulic acid matrix solution (12.5 mg dissolved in 17% formic acid/33% acetonitrile/50% H(2)O). Protein signals of more than 20 kDa were routinely produced from both Gram positive and Gram negative bacteria prepared in this manner. Moreover, a substantial number of intense protein signals were also produced in the more 'conventional' fingerprint region extending from 4 to 20 kDa. This approach is rapid, easy to implement into existing methodologies, and does not require any special hardware.

Electron monochromator mass spectrometry for the analysis of whole bacteria and bacterial spores.

Spores from a variety of Bacillus species were analyzed with direct probe mass spectrometry using an electron monochromator to select electrons of distinct energies for ionization. Electron energies were chosen to match the electron capture energies of taxonomically important compounds such as dipicolinic acid and fatty acids. Previous negative ion interferences were not observed when the monochromator was used, and the signal-to-noise ratio of targeted compounds was significantly enhanced using this approach. To demonstrate the selectivity of the technique, the monochromator was swept over a range of electron energies while monitoring the masses of compounds with known electron capture energies. Scanning the monochromator while the mass spectrometer was operated in single-ion mode enabled dipicolinic acid to be detected in 10(5) spores. The results presented here demonstrate the utility of the electron monochromator for selectively ionizing compounds directly in bacteria and bacterial spores.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric detection of bacterial biomarker proteins isolated from contaminated water, lettuce and cotton cloth.

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra of bacterial proteins were obtained from water, lettuce and cloth samples contaminated with Shigella flexneri, Escherichia coli, and Aeromonas hydrophila. Spectra were obtained using proteins directly isolated from water (or water used for rinsing samples) without culturing the bacteria. For S. flexneri and E. coli, two marker ions for specific proteins associated with a virulence-related property (acid resistance) were easily detected. For A. hydrophila, ions from two specifically selected marker proteins, as well as ions from the larger group of proteins isolated from pure cultures, all matched spectra from a contaminated water sample, providing strong evidence that A. hydrophila was the bacterial contaminant. Rinse water from contaminated lettuce and cloth samples showed the same marker ions as the contaminated water samples.

Direct mass spectrometric analysis of Bacillus spores.

Spores from the Bacillus species, B. cereus, B. anthracis, B. thuringensis, B. lichenformis, B. globigi, and B. subtilis, were examined by direct probe mass spectrometry using electron ionization (EI) and positive and negative chemical ionization (CI). Molecular ions from free fatty acids and nucleic acids were observed in the 70eV spectra as were fragments from glycerides. Spectra obtained with isobutane positive chemical ionization (CI(+)) were dominated by ions associated with pyranose compounds such as N-acetylglucosamine (NAG). Unlike the positive ion spectra, the negative ion spectra of the spores were very simple and contained few peaks. The M(-.) ion from dipicolinic acid (DPA) was the base peak in the negative ion spectra of all spore species except those from B. lichenformis. The negative ion of DPA produced such a strong signal that 10(8) colony forming units (CFUs) of B. cereus spores could be detected directly in 0.5 g of ground rice. Principal component analysis (PCA) of the spectra revealed that only CI(+) spectra contained differences that could be used to identify the spectra by species. Differentiation of the CI(+) spectra by PCA was attributed to variances in the peaks associated with the bacterial polymer poly(3-hydroxybutyrate) (PHB) and NAG. Similar differences in PHB and NAG peaks were detected in the CI(+) spectra of a suite of vegetative Bacillus stains grown with various media.

Identification of bacterial proteins observed in MALDI TOF mass spectra from whole cells.

Characteristic ions in the MALDI TOF mass spectra from bacterial cells have been associated with four known proteins. The proteins, observed both from cells and in filtered cellular suspensions, were isolated by HPLC and identified on the basis of their mass spectra and their partial amino acid sequence, determined using the Edman method (10-15 residues). The acid resistance proteins HdeA and HdeB give rise to ions near m/z 9735 and 9060 in MALDI TOF mass spectra from cells and from extracts of both Escherichia coli 1090 and Shigella flexneri PHS-1059. However, the proteins associated with proteolytic cleavage by the peptidase Lep, rather than the precursor proteins, were observed, both using cells and from cellular extracts. A cold-shock protein, CspA, was associated with the ion near m/z 7643 from Pseudomonas aeruginosa. Similarly, a cold-acclimation protein, CapB, was identified as the source of the ion near m/z 7684 in P. putida. This last protein was homologous with a known CapB from P. fragi. While these experiments involved the detection of known or homologous proteins from typical bacteria, this same approach could also be applied to the detection of unique proteins or biomarker proteins associated with other bacteria of public health significance.

The effects of electron and chemical ionization modes on the MS profiling of whole bacteria.

Free fatty acid profiling of whole bacteria [Francisella tularensis, Brucella melitensis, Yersinia pestis, Bacillus anthracis (vegetative and sporulated), and Bacillus cereus] was carried out with direct probe mass spectrometry under 70-eV electron ionization (EI) and isobutane chemical ionization in both the positive (CI+) and negative modes (CI-). Electron ionization produced spectra that contained molecular ions and fragment ions from various free fatty acids. Spectra acquired with isobutane chemical ionization in the positive mode yielded molecular ions of free fatty acids as well as ions from other bacterial compounds not observed under EI conditions. Spectra obtained with negative chemical ionization did not contain as much taxonomic information as EI or CI+; however, some taxonomically significant compounds such as dipicolinic acid and poly(3-hydroxybutyrate) did produce negative ions. All ionization modes yielded spectra that could separate the bacteria by Gram-type when observed with principle components analysis (PCA). Chemical ionization in the positive ion mode produced the greatest amount of differentiation between the four genera of bacteria when the spectra where examined by PCA.

Investigation of cell culture media infected with viruses by pyrolysis mass spectrometry: implications for bioaerosol detection.

Mass spectrometry coupled with a pyrolysis inlet system was used to investigate media from cell cultures infected with viruses. Cell culture media is an intricate mixture of numerous chemical constituents and cells that collectively produce complicated mass spectra. Cholesterol and free fatty acids were identified and attributed to lipid sources in the media (blood serum supplement and plasma membranes of host cells). These lipid moieties could be utilized as signature markers for rapidly detecting the cell culture media. Viruses are intracellular parasites and are dependent upon host cells in order to exist. Therefore, it is highly probable that significant quantities of media needed to grow and maintain viable host cells would be present if a viral agent were disseminated as an aerosol into the environment. Cholesterol was also detected from a purified virus sample, further substantiating its use as a target compound for detection. Implications of this research for detection of viral bioaerosols, using a field-portable pyrolysis mass spectrometer, is described.

Direct mass spectrometric analysis of in situ thermally hydrolyzed and methylated lipids from whole bacterial cells.

Fatty acid methyl esters (FAMEs) were generated in situ, during pyrolysis, from whole-cell bacterial samples and analyzed by mass spectrometry (MS). The FAME profiles obtained by an in situ thermal hydrolysis methylation (THM) step were compared with gas chromatography (GC) and MS analyses of the chemically extracted and methylated fatty acids. This correlation was based on the ability of each technique to differentiate a representative group of 15 bacteria at the species level as predicted by principal component analysis. All three analyses, GC/FAME, pyrolysis-MS/FAME, and in situ THM-MS/FAME differentiated the studied bacterial sample set into three discrete clusters. The bacteria comprising each cluster were the same for all three analyses, showing that taxonomic information of the lipid profiles was preserved in the Py-MS/FAME and in situ THM-MS/FAME analyses of whole cells. Contributions from saturated, unsaturated, cyclopropyl, and branched bacterial fatty acids to the differentiation of microorganisms were identified for all three analyses. The in situ THM-MS/FAME approach is simple, requires small samples (approximately 2 x 10(6) cells/profile), and is rapid, with a total analysis time under 5 min/sample.

Characterization of lipid fatty acids in whole-cell microorganisms using in situ supercritical fluid derivatization/extraction and gas chromatography/mass spectrometry.

In situ supercritical fluid derivatization and extraction was used as a sample preparation technique for the classification of bacteria using fatty acid profiling. Addition of a quaternary ammonium salt such as phenyltrimethylammonium hydroxide under static supercritical conditions directly to lyophilized, whole-cell bacteria in an extraction vessel resulted in the saponification of the bacterial lipids and derivatization of their fatty acids. The derivatized fatty acid methyl esters (FAMEs) were then extracted with supercritical CO2 and analyzed without additional treatment using GC/MS. Iso and anteiso C15:0 and C17:0 along with C18:0 were predominant in Gram-positive bacteria, while C16:1, C16:0, C18:1, and cyclopropyl cyC17:0 and cyC19:0 were significant in Gram-negative bacteria. Application of principal components analysis to the FAME GC/MS data resulted in the differentiation between Gram-positive and Gram-negative type bacteria. Differentiation between species among the same genera was also observed.

Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry.

Matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) was investigated as a method for the rapid identification of whole bacteria, either by comparison with archived reference spectra or by co-analysis with cultures of known bacteria. Bacteria were sampled from colonies on an agar plate, mixed with the matrix, air-dried, and introduced in batches into the mass spectrometer for analysis. In the first experiment, both bacterial strains that had been previously analyzed to obtain reference spectra and other strains that had not been analyzed were blind-numbered and their spectra were obtained. Those strains that matched reference spectra were found to be correctly identified. A second experiment involved co-analysis of reference strains and bind-numbered strains under identical conditions; species-specific identification was demonstrated by comparison of spectra of the blind-numbered strains with those of the standards. In all of the spectra obtained in these experiments, each bacterial strain showed a few characteristic high-mass ions which are thought to be derived from bacterial proteins. This work represents the first reported instance of successful bacterial chemotaxonomy by MALDI-TOFMS analysis of whole cells. For the strains tested, the method is rapid and simple.

In situ methylation of nucleic acids using pyrolysis/mass spectrometry.

Curie-point pyrolysis/triple quadrupole mass spectrometry (Py/MS/MS) has been used with tetramethylammonium hydroxide (TMAH) to conduct in situ methylation of nucleic acid bases. Nitrogen bases in free nucleotides, oligonucleotides, calf thymus DNA and whole bacterial cells reacted in situ during pyrolysis with TMAH to form the methylated bases. Derivatization increased the volatility of the nitrogen bases and the mass of the diagnostic base peaks, thereby removing them from the positions of lower-mass background peaks. The degree of methylation as a function of TMAH concentration for the oligonucleotide, calf thymus DNA, and the whole bacteria samples was determined and found to correlate with the nature of DNA. The methylated bases were identified by their positive-ion electron ionization fragmentation patterns and confirmed with tandem mass spectrometry. The detection of the methylated bases by Py/MS/MS facilitates the goal of identifying the nucleic acids in a complex mixture (i.e. whole bacterial cells) without extraction and prior derivatization.

A rapid approach for the detection of dipicolinic acid in bacterial spores using pyrolysis/mass spectrometry.

Curie-point pyrolysis/triple quadrupole mass spectrometry and micro-tube furnace pyrolysis/quadrupole ion trap mass spectrometry have been used to detect dipicolinic acid (DPA) in sporulated whole bacteria. DPA in whole cells of sporulated Bacillus anthracis reacted in situ during pyrolysis with tetramethylammonium hydroxide to form the dimethyl ester derivative of DPA, dimethyl-2,6-dipicolinate (mDPA). The mDPA was identified by its positive-ion electron ionization fragmentation pattern and confirmed with tandem mass spectrometry. In an oxidative pyrolysis/quadrupole ion trap instrument, the mDPA mass spectrum showed characteristic positive-ion electron ionization fragmentation along with a significant [M+1]+ ion due to self-chemical ionization. The characteristic collision-induced dissociation fragments of mDPA were used to establish the presence of sporulation in B. anthracis whole cells at a concentration of 2.2 x 10(7) CFU (colony-forming units)/mL using the triple quadrupole instrument. The total time for analysis, including sample preparation, was less than 10 minutes for both instruments.

Microorganism gram-type differentiation based on pyrolysis-mass spectrometry of bacterial Fatty Acid methyl ester extracts.

Curie-point pyrolysis (Py)-mass spectrometry has been used to differentiate 19 microorganisms by Gram type on the basis of the methyl esters of their fatty acid distribution. The mass spectra of gram-negative microorganisms were characterized by the presence of palmitoleic acid (C(inf16:1)) and oleic acid (C(inf18:1)), as well as a higher abundance of palmitic acid (C(inf16:0)) than pentadecanoic acid (C(inf15:0)). For gram-positive microorganisms, a signal of branched C(inf15:0) (isoC(inf15:0) and/or anteisoC(inf15:0)) more intense than that of palmitic acid was observed in the mass spectra. Principal components analysis of these mass spectral data segregated the microorganisms investigated in this study into three discrete clusters that correlated to their gram reactions and pathogenicities. Further tandem mass spectrometric analysis demonstrated that the nature of the C(inf15:0) fatty acid isomer (branched or normal) present in the mass spectrum of each microorganism was important for achieving the classification into three clusters.

An investigation of dipeptides containing polar and nonpolar side groups by curie-point pyrolysis tandem mass spectrometry.

Methionyl-leucine, leucyl-methionine, phenylalanyl-leucine, and leucyl-phenylalanine have been analyzed to determine dipeptide fragmentation mechanisms in Curie-point pyrolysis tandem mass spectrometry. Results show that fragmentations of dipeptides follow two general pathways, one involving direct cleavage of the dipeptide and the other involving cyclization of the dipeptide. Unique products and strong changes in relative mass spectral peak intensities arise, depending on constituent amino acid residues and their sequence. Also, the length and nature of the side groups strongly direct fragmentation. From these results, the major peaks in the spectra of eight other dipeptides could be readily explained; this suggests that a significant number of dipeptides follow the same general fragmentation mechanisms.

Direct analysis of bacterial fatty acids by Curie-point pyrolysis tandem mass spectrometry.

Although pyrolysis-mass spectrometry (Py-MS) has been used for bacterial taxonomy, many of the mass spectral peaks used for discrimination of organisms have not been correlated to known biomolecules. This work presents the discrimination of five bacterial species based on Py-MS patterns containing only peaks that can be correlated to fatty acids and fatty acid derivatives. These correlations were confirmed by pyrolysis-tandem mass spectrometry of authentic standards and the organisms. The pattern recognition procedures used gave better results when only the fatty acid peaks were used in the analysis than when full spectra were used.

The use of soot analysis as an investigative tool in aircraft fires.

Traditionally, carboxyhemoglobin analysis has been used to determine the extent of respiration during a postcrash fire. This is a useful and informative measurement, but advances in the chemical analysis of soot samples provide a new and useful forensic tool for the investigation of deaths by fire. One of the latest analytical techniques is a computer-interfaced pyrolysis mass spectrometry. Soot consists of a high percentage of carbon as well as fragments of the original polymer that are unique to that particular material. Consequently, analysis and identification of the fragment pattern makes it possible to identify the original material from which the soot was generated. In pyrolysis mass spectrometry the soot is pyrolyzed into the ion source and the resulting ion pattern is computer analyzed to identify the polymeric system or systems that generated the soot. Analysis of soot samples collected from the upper respiratory tract of aircraft accident victims and from the accident scene can provide information on the type of toxic insult (identifies specific toxic products), the material(s) that burned and generated the toxic atmosphere, and the relative time of survival following the crash. This technique has been applied to the investigation of fire deaths in a hotel fire and will be used to illustrate the identification of the materials that burned, the toxic products, and the potential for aircraft accident investigations.

Extreme toxicity from combustion products of a fire-retarded polyurethane foam.

The products from nonflaming combustion of wood and a trimethylol-propane-based rigid-urethane foam that was not fire-retarded produced elevated carboxyhemoglobin levels but no abnormal neurological effects. However, when this type of foam contained a reactive phosphate fire retardant, the combustion products caused grand mal seizures and death in rats. The toxic combustion product responsible for the seizures has been identified as 4-ethyl-1-phospha-2,6,7-trioxabicyclo(2.2.2.)octane-1-oxide.