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Appl Environ Microbiol. Nov 2009; 75(22): 7229–7242.
Published online Sep 18, 2009. doi:  10.1128/AEM.00857-09
PMCID: PMC2786504

Identification of Bacillus anthracis by Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Artificial Neural Networks [down-pointing small open triangle]

Abstract

This report demonstrates the applicability of a combination of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) and chemometrics for rapid and reliable identification of vegetative cells of the causative agent of anthrax, Bacillus anthracis. Bacillus cultures were prepared under standardized conditions and inactivated according to a recently developed MS-compatible inactivation protocol for highly pathogenic microorganisms. MALDI-TOF MS was then employed to collect spectra from the microbial samples and to build up a database of bacterial reference spectra. This database comprised mass peak profiles of 374 strains from Bacillus and related genera, among them 102 strains of B. anthracis and 121 strains of B. cereus. The information contained in the database was investigated by means of visual inspection of gel view representations, univariate t tests for biomarker identification, unsupervised hierarchical clustering, and artificial neural networks (ANNs). Analysis of gel views and independent t tests suggested B. anthracis- and B. cereus group-specific signals. For example, mass spectra of B. anthracis exhibited discriminating biomarkers at 4,606, 5,413, and 6,679 Da. A systematic search in proteomic databases allowed tentative assignment of some of the biomarkers to ribosomal protein or small acid-soluble proteins. Multivariate pattern analysis by unsupervised hierarchical cluster analysis further revealed a subproteome-based taxonomy of the genus Bacillus. Superior classification accuracy was achieved when supervised ANNs were employed. For the identification of B. anthracis, independent validation of optimized ANN models yielded a diagnostic sensitivity of 100% and a specificity of 100%.

Members of the genus Bacillus are rod-shaped bacteria that exhibit catalase activity and can be characterized as endospore-forming obligate or facultative aerobes. The genus Bacillus contains two important groups of bacteria named after B. subtilis and B. cereus. The best-characterized member of the former group is B. subtilis, a renowned model organism for genetic research. Other group members, like B. pumilis, B. licheniformis, B. atrophaeus, and B. amyloliquefaciens, exhibit a high degree of phenotypic similarity and are thus not easily distinguishable (15).

The B. cereus group comprises a number of closely related bacteria, some of which interfere with human health. Bacteria classified as B. cereus are occasionally associated with food poisoning (16, 28), while B. thuringiensis is primarily an insect pathogen because of its ability to produce toxins that have been widely used for the biocontrol of insect pests (28, 30). A third member of the B. cereus group, B. anthracis, is the causative agent of anthrax and is highly relevant to human and animal health. Other members of the B. cereus group are B. mycoides, B. pseudomycoides, and B. weihenstephanensis (4, 15).

B. anthracis is a possible agent in biological warfare and bioterrorism. Its applicability as a biological warfare agent was made apparent by an accidental release from a Soviet military facility in Sverdlovsk (1, 10). Also, the well-publicized mailing of B. anthracis spores in the United States, which caused 18 confirmed cases of cutaneous and inhalational anthrax and an additional 4 suspected cases of cutaneous anthrax (3, 22), demonstrated that B. anthracis may become a threat from terrorist groups (10).

Rapid detection of B. anthracis may be challenging because of its great genetic similarity to other species of the B. cereus group (10) and the difficulties of phenotypic differentiation of B. cereus group members (15). There is some controversy in the literature regarding the taxonomy of the B. cereus group. Indeed, some authors state that B. anthracis, B. cereus, and B. thuringiensis are one species with various virulence plasmids for the toxin pXO1 and the capsule pXO2 of B. anthracis and the insecticidal toxin of B. thuringiensis (10, 19). Other authors do not support this opinion and suggest the presence of even more species within the group (21).

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) intact-cell mass spectrometry (ICMS) has been suggested as a rapid, objective, and reliable technique for bacterial identification (8, 13, 23, 25, 38). As a proteomic technique, ICMS of whole bacterial cells, or cell lysates, relies on the reproducible detection of microbial protein patterns and thus delivers information complementary to genotypic or phenotypic test methods. With the pattern-matching approach, microbial identification is achieved by comparing experimental mass spectra with a collection of mass spectra of known organisms. This requires the compilation of large databases of bacterial reference spectra but has the advantage that an extensive knowledge of biomarker identities is not required. Another advantage of the pattern-matching approach is that genus- and species-specific procedures or consumables are not required, i.e., the same methodology can in principle be applied to all kinds of microorganisms (multiplex advantage).

It is thus believed that ICMS offers the possibility to systematically investigate the diversity of bacterial subproteomes, complementing existing methodologies of bacterial characterization. This potential and the need for a rapid, objective, and reliable microbial identification technique that does not rely on nucleic acid detection and the availability of an MS-compatible inactivation protocol for highly pathogenic biosafety level 3 microorganisms and bacterial endospores (26) prompted us to systematically study the MALDI-TOF MS profiles of Bacillus strains and to establish a database of bacterial mass spectra. In the present work, we describe strategies of spectral analysis that allow the identification and validation of group- and species-specific sets of biomarkers. Using unsupervised hierarchical cluster analysis (UHCA) and supervised artificial neural network (ANN) analysis, we also demonstrate how microbial spectra can be employed to establish an MS-based methodology for rapid, objective, and reliable identification of the target species, B. anthracis.

MATERIALS AND METHODS

Microbial strains and isolates.

Most of the bacterial strains originated from the strain collections of the Institute for Environmental and Animal Hygiene and Veterinary Medicine at the University of Hohenheim, Stuttgart, Germany, and the Robert Koch-Institut, Berlin, Germany. Isolates of B. anthracis from these culture collections were confirmed as target sequences of both virulence plasmids (where applicable) by culture diagnosis on blood agar, gamma phage susceptibility, and the presence of a chromosomal signature sequence by real-time PCR, as proposed previously (5, 40). Further Bacillus strains were obtained from the German Collection of Microorganisms and Cell Cultures GmbH (Braunschweig, Germany), from the strain collection of the Microbial Ecology Group at the Technical University Munich (M. Ehling-Schulz), and from the Bundeswehr Research Institute for Protective Technologies and NBC Protection (WIS) in Munster (B. Niederwöhrmeier). An overview of the Bacillus strains and isolates used throughout the study is provided in Table Table11.

TABLE 1.
Overview of the bacterial strains used in this study

Sample preparation.

Starting from a pure single colony on blood agar, Bacillus cultures were prepared by growing each strain for two passages under aerobic conditions on LB agar (Merck) for 24 h at 37°C. Cells were harvested by transferring the equivalent of three full blue plastic loops (equivalent to about 30 μl) from each agar plate into 20 μl of sterile water. The bacterial material was resuspended by vortexing it. Sample preparation and sample inactivation were carried out by using the modified trifluoroacetic acid (TFA) inactivation protocol for highly pathogenic microorganisms (26). Briefly, 80 μl of pure TFA (Uvasol; Merck) was added to 20 μl of the bacterial water suspensions. After being gently shaken for 30 min, the solutions were diluted 10-fold with high-performance liquid chromatography grade water (Mallinckrodt Baker B.V., Deventer, The Netherlands). No centrifugation or filtration was carried out. The sample dilutions were checked for sterility. For MALDI-TOF MS, 2 μl of the microbial dilution was then mixed with 2 μl of a 12-mg/ml α-cyano-4-hydroxycinnamic acid (HCCA) solution (Bruker Daltonics, Bremen, Germany). Preparation of the HCCA solution was achieved by dissolving HCCA in TA2, a 2:1 (vol/vol) mixture of 100% acetonitrile and 0.3% TFA. One microliter of the sample-HCCA mixture was spotted onto ground-steel sample targets from Bruker Daltonics.

MALDI-TOF MS.

Mass spectra of microbial extracts were collected using an Autoflex mass spectrometer from Bruker Daltonics. The instrument was equipped with a slightly defocused N2 laser operating at 337 nm at pulse rates up to 20 Hz. The pulse ion extraction time was 200 ns. Measurements were carried out in the linear mode using an acceleration voltage of 20.00 (ion source 1) or 18.45 (ion source 2) kV. The lens voltage was 6.70 kV. The mass spectra were stored in the low and intermediate mass range between 0.5 and 2 kDa and between 2 and 20 kDa, respectively. Insulin (5,734.52 Da), ubiquitin 1 (8,565.89 Da), cytochrome c (12,360.97 Da), and myoglobin (16,952.31 Da) were used as external calibrants, enabling a mass accuracy of about 300 ppm. At least 600 individual laser shots were coadded for each spectrum.

Data analysis.

Mass spectra were acquired by employing Bruker's Flex Control software package (v. 2.4; Bruker Daltonics). The analysis of mass spectral patterns was carried out using Matlab (Mathworks Inc., Natick, MA)-based software developed in house. The first steps of data analysis comprised spectral preprocessing procedures, such as smoothing, baseline correction, and intensity normalization. For advanced visualization of microbial biomarkers, the Matlab routines allowed the generation of simulated gel views from preprocessed mass spectra. These gel views displayed peak intensities gray-scaled with abscissa values as mass/charge ratios (m/z) and spectral numbers as the ordinates.

The Matlab routines allowed the preparation of peak lists from preprocessed mass spectra. These peak lists were automatically generated in predefined mass ranges using custom-designed concepts. For example, the procedure of peak list generation makes use of a sigmoidal weighting function that was introduced to correct for the decreased sensitivity of MALDI-TOF MS in the high mass range. Furthermore, the peak detection algorithm produces for each mass spectrum a peak-ranking table. Thus, peak lists contained not only m/z and intensity information, but also a parameter of the relative importance of individual mass signals. Peak ranks were found to be useful for multivariate spectral analyses, either as alternatives for peak intensities or for data reduction purposes. For the latter case, either the number of peaks included in subsequent analyses or thresholds of peak importance could be specifically defined. The peak lists were further converted to so-called bar code spectra. In bar code spectra, only information about peak presence, or absence, is employed, while the peak amplitude information (intensity) is omitted. The bar code spectra served as inputs for UHCA and analysis by ANNs.

Cluster analysis was carried out by means of distance or D values obtained from normalized Pearson's product-momentum correlation coefficients (20) with Ward's algorithm as the clustering method (36). D values are regarded as interspectral distance measures that vary between 0 and 2,000 (0 to 1,000 for positively correlated data). Within the context of the present work, UHCA of mass spectra from Bacillus isolates was carried out on the basis of the 30 most relevant mass signals taken from the mass range of 2 to 12 kDa (see above).

The in-house-developed Matlab routines also contained an interface with the NeuroDeveloper software package from Synthon (Synthon Analytics GmbH, Heidelberg, Germany). The NeuroDeveloper combines modules for feature selection, ANN model development (including modular ANN models), and ANN-based classification. A detailed description of these software functions can be found elsewhere (35). In the present study, the general strategy of ANN analysis included teaching and optimization of a neural network, followed by testing the classifier with independent (external) test spectra. Teaching and internal validation were done with mass spectra with known class assignments, which have been combined in so-called teaching and internal-validation subsets. The accuracy of the classification was subsequently determined by challenging the classifier with external test spectra that were kept totally separate during model development. The teaching subset of this study contained spectra from 296 bacterial samples. From this number, the NeuroDeveloper software allowed the automatic selection of 20% for internal validation. The number of randomly selected spectra of the external test set was 127. For network teaching, the bar code mass spectra of the microbial database were generated using peak tables with 75 mass signals per spectrum and a point spacing of 700 ppm. Subsequently, the spectra were imported into the NeuroDeveloper program, and 100 spectral features were chosen by the built-in UNIVAR feature selection method, which is based on univariate F statistics. The ANN consisted of a three-layer feed-forward multilayer perceptron (MLP) ANN with connected layers of 100 input, 7 hidden, and 3 output neurons with shortcut connections. Teaching of the ANNs was carried out by utilizing the resilient back-propagation (rprop) function (29).

Matlab-based software was also employed to calculate average mass spectra and for univariate statistical tests (two-sample t tests of independent samples).

RESULTS

Figure Figure11 displays representative MALDI-TOF mass spectra from four different Bacillus species: B. anthracis (A), B. cereus (B), B. thuringiensis (C), and B. licheniformis (D). The spectra were acquired from microbial samples prepared by using the modified TFA sample inactivation/protein extraction procedure, which included sample treatment with 80% TFA for 30 min (26). The mass spectra shown in Fig. Fig.11 were preprocessed as outlined in Materials and Methods. The spectra demonstrate a relatively high signal-to-noise ratio, which typically permits the detection of 50 to 100 mass peaks per spectrum. A closer inspection of these and other MALDI spectra showed a high degree of distinctness for most of the mass spectral patterns. The example in Fig. Fig.11 also shows the presence of species- or group-specific mass signals. For example, mass spectra from the B. cereus group members B. anthracis, B. cereus, and B. thuringiensis (Fig. 1A to C) display a number of group-specific peaks at 3,683, 4,334, 5,171, 5,886, and 7,368 Da. Depending on the degree of sporulation, individual mass patterns (particularly the intensities) may vary considerably. This important aspect is discussed below.

FIG. 1.
Representative MALDI-TOF mass spectra of four different Bacillus species in the mass range of 2 to 14 kDa. The spectra were acquired from microbial samples using a recently published sample preparation and inactivation protocol for highly pathogenic microorganisms ...

The spectra in Fig. Fig.22 were obtained by averaging preprocessed MALDI-TOF mass spectra from all available B. anthracis (105 spectra) and B. cereus (147 spectra) strains. At first glance, the two mean spectra appear to be quite different. A more detailed analysis, however, revealed a high number of common mass signals of these closely related species. In fact, there were very few mass peaks that could serve as potential candidates for species differentiation. For example, the spectrum of B. anthracis (Fig. (Fig.2A)2A) shows a peak at 5,413 Da that has no counterpart in the mean spectrum of B. cereus (Fig. 2A and B). For B. anthracis, other potential biomarkers can be found at 6,679 Da and for B. cereus at 6,695 and 6,711 Da. These markers were previously assigned to species-specific small acid-soluble proteins (SASPs) (6, 11, 17) and are discussed below. At this point, it should be noted that the analysis of mean spectra alone is certainly not sufficient for identifying species-, or group-specific biomarkers. For this purpose, a statistical analysis of the complete mass spectral database is required.

FIG. 2.
Mean MALDI-TOF mass spectra of (A) B. anthracis (105 spectra) and (B) B. cereus (147 spectra). The spectra were obtained by averaging the respective experimental mass spectra from all available strains (see Table Table11 and the text for details). ...

In order to give an overview of the database of microbial MALDI spectra, we prepared so-called gel views. These representations were obtained by converting spectral peak intensities to gray scales, which were then plotted as functions of the m/z values. It is important to note that the gel view representations were created on the basis of preprocessed spectra, i.e., spectra that had been smoothed, baseline corrected, and vector normalized. The spectra appear as rows, while vertical lines indicate reproducible mass peaks. In Fig. Fig.3A,3A, the gel view shows all 423 spectra obtained within the context of this study in the mass range of 2.5 to 8 kDa. The mass spectra of B. anthracis are shown in Fig. Fig.3A3A at lines 1 to 105 (105 spectra). The spectra of B. cereus strains form lines 106 to 252 (147 spectra). Lines 253 to 286 display spectra from the remaining B. cereus group members, B. thuringiensis, B. mycoides, B. pseudomycoides, and B. weihenstephanensis (34 spectra). Lines 287 to 423 (137 spectra) were generated from spectra of the non-B. cereus group members (18 species) (Table (Table1).1). The relative frequencies of the individual mass signals are shown in Fig. Fig.3B.3B. This peak frequency plot was obtained from mass peak tables with 30 entries per individual mass spectrum and illustrates the dominance of mass signals from B. cereus group members (see below).

FIG. 3.
(A) Gel view representation of mass spectra from Bacillus strains in the mass range of 2.5 to 8 kDa. In this gel view, the intensities of 423 MALDI-TOF mass spectra were gray scaled and plotted as functions of the m/z values. The spectra have been baseline ...

Analysis of the gel view in Fig. Fig.3A3A demonstrated a high degree of spectral reproducibility and indicated a relatively high degree of similarity between spectra from B. cereus group members and, conversely, large-scale heterogeneity for spectra from the remaining species. The analysis of the gel view also suggested the presence of species- and group-specific biomarkers. For example, MALDI-TOF mass spectra of B. cereus group members consistently exhibited signals at 3,683, 4,334, 5,171, 5,886, and 7,368 Da, among others. These signals were only rarely detected in mass spectra of the remaining species and therefore can be considered B. cereus group biomarker candidates. An example of a species-specific signal is the mass peak at 5,413 Da in spectra of B. anthracis. This signal was found to be present in most of the mass spectra (92%) of B. anthracis and was already mentioned when discussing the mean spectrum of B. anthracis (Fig. (Fig.2A).2A). As the gel view shows, the peak at 5,413 Da is, with a few exceptions, absent in the spectra of all other Bacillus species. The exceptions are the strains B. cereus DSM 4490, DSM 609, ATCC 12826, and B248; B. thuringiensis DSM 350, DSM 2046, and B8; and B. mycoides DSM 2048 and B335.

In order to illustrate selected aspects of species discrimination and identification by MALDI-TOF MS with particular emphasis on B. anthracis, the gel view in Fig. Fig.44 shows the spectra from the B. cereus group in the diagnostically important region between 5 and 7.5 kDa. This representation demonstrates again the existence of common B. cereus group mass peaks at 5,171, 5,886, and 7,368 Da (Fig. (Fig.3A).3A). More importantly, the illustration also suggests the existence of B. anthracis-specific peaks at 5,413 and 6,492 Da and a SASP signal at 6,679 Da. The last peak is of particular interest, because only two strains of B. cereus (B248 and B292) exhibit signals at this m/z value. Most of the strains of B. cereus exhibit strong mass peaks close to the 6,679-Da peak, either at 6,695 Da or at 6,711 Da. The latter signals also arise from SASPs and can be observed in some MALDI spectra of B. thuringiensis and B. mycoides.

FIG. 4.
Gel view of mass spectra from the B. cereus group in the diagnostically relevant mass range of 5 to 7.5 kDa. Mass spectra from B. cereus group members exhibit marker peaks at 5,171, 5,886, and 7,368 Da (arrows). Peaks at 6,679 Da (B. anthracis) or 6,695 ...

UHCA.

UHCA is a data-driven multivariate classification technique that was employed in this study to investigate the relatedness between the microbial mass patterns. As outlined above, UHCA was carried out on the basis of bar code spectra obtained from peak tables with 30 entries per mass spectrum. Figure Figure55 shows the dendrogram of a cluster analysis carried out with a mass spectral database of 423 spectra complemented by 14 additional spectra from B. cereus group members with unclear species assignments. The dendrogram clearly shows the existence of two main clusters, with a large cluster (I) formed by spectra of the B. cereus group and a second cluster (II) containing spectra from non-B. cereus group species. Cluster I consists of two main clusters, each subdivided into three subclusters (Ia to If). It is interesting that the MALDI spectra of B. anthracis form two of these clusters (Ib and Id), with the majority of the B. anthracis strains grouped in cluster Id. Spectra of B. cereus and the other species of the B. cereus group constitute the four remaining subclusters of cluster I. Cluster Ic contains exclusively spectra of B. cereus, while clusters Ia and Ie also comprise spectra of B. thuringiensis (Ia) or B. mycoides, B. pseudomycoides, B. thuringiensis, and B. weihenstephanensis (Ie). A special situation is observed for mass spectra of probiotic strains of B. cereus, which are all located in a separate cluster (If) clearly separated from the other B. cereus strains.

FIG. 5.
Hierarchical cluster analysis of microbial mass spectra. Peak tables containing 30 peaks from each mass spectrum were obtained from a total of 437 mass spectra of Bacillus species. The peak tables were converted into bar code spectra, which served as ...

Cluster II seems to be less structured, an observation that is backed by the heterogeneity of mass peaks in the gel view in Fig. Fig.3A.3A. It should be mentioned, however, that strains of the B. subtilis group members B. firmus/B. lentus (IIb), B. licheniformis (IIc), and B. subtilis/B. atrophaeus/B. amyloliquefaciens (IId) constitute separate clusters of closely related species with no or few outliers.

Classification analysis using ANNs.

MLP ANNs were employed in this study as pattern recognition tools for supervised classification analysis. The general strategy of ANN analysis included the procedures of teaching and optimization, in which nonlinear discriminant functions are established, which can be later used to model probabilities of class membership of independent validation data. For this purpose, the spectral database was split randomly into a combined teaching/internal-validation data set and an independent test set for external validation. The first spectral subset contained 296 MALDI-TOF spectra, with 20% of them randomly selected for internal validation. The independent test set consisted of 127 spectra. Furthermore, we defined three categories, or classes, of spectral input patterns, consisting of bar code MALDI spectra of B. anthracis (class i), spectra of B. cereus group members other than B. anthracis (class ii), and mass spectra of non-B. cereus group members (class iii).

The classification results achieved by an optimized ANN model for the teaching and the external test data are shown in Tables Tables22 and and3,3, respectively. The data suggest that B. anthracis is identified with 100% accuracy in the teaching data (see Table Table2)2) and, more importantly, also in the test data (see Table Table3),3), as no false-positive or false-negative classifications were observed. The accuracy values for the identification of members of the other two classes are smaller and vary between 99% in the teaching data and 96% in the test data for classes ii and iii. From the confusion matrix of Table Table3,3, it can also be concluded that the sensitivity of ANN classification of the independent test data was 94.5% for class ii (B. cereus group members other than B. anthracis) and 92.9% for class iii (non-B. cereus group members). The specificities were determined to be 97.2% and 97.6% for classes ii and iii, respectively.

TABLE 2.
Confusion matrix showing the classification results of the training data obtained by an optimized ANNa
TABLE 3.
Confusion matrix showing ANN classification results of independent test data

Discriminating spectral features.

ANN analysis of MALDI-TOF spectral fingerprints is a powerful classification technique, but it has the drawback that the decision rules are not easy to obtain. In order to identify the discriminating spectral information on which the ANN classification relies, we additionally employed univariate statistical methods, such as independent t tests. These t tests were carried out at any given m/z value for two-class classification problems, using bar code spectra obtained from peak tables with 30 peaks per spectrum as inputs. The tests were applied as a univariate measure of deviation and provided P values, which could be used to assess the discriminative power of the spectral feature under investigation (Fig. (Fig.6,6, curves A to C). Small P values cast doubt on the null hypothesis of equal class means.

FIG. 6.
Identification of discriminating spectral features by independent t tests. The t tests provided P values and were carried out on the basis of peak tables with 30 peaks per mass spectrum. Small P values cast doubt on the null hypothesis of equal class ...

In order to identify B. anthracis-specific biomarkers, univariate t tests were applied to a data set in which 105 spectra of B. anthracis strains were combined in class 1. Class 2 contained 318 spectra from the 23 remaining species. The m/z dependence of P values in Fig. Fig.6A6A indicated a number of biomarkers, among them peaks at 3,068, 3,214, 4,606, 5,413, and 6,679 Da. While the potential marker peaks at 5,413 and 6,679 Da could be visually identified from the gel views in Fig. Fig.33 and and4,4, the identification of the signal at 4,606 Da required a systematic statistical evaluation approach. The comparison of spectra from B. anthracis (105 spectra) and B. cereus (147 spectra) revealed exactly the same ranking of discriminative mass signals. The t tests showed that the peaks at 3,068, 3,214, 4,606, 5,413, and 6,679 Da were highly discriminative for these closely related species. When spectra from the B. cereus group (286 spectra; 6 species) were tested against spectra of the remaining species (137 spectra; 18 species, among them many B. subtilis group members), the P values of the t test indicated the presence of B. cereus group-specific peaks. The spectra of B. cereus group members exhibited mass signals at 3,683, 4,334, 5,171, 5,886, and 7,368 Da, which are typically absent in spectra of species not belonging to the B. cereus group of bacilli (Fig. (Fig.6C6C).

Molecular assignments of biomarkers.

MALDI-TOF MS of bacterial samples offers the possibility to reveal the molecular identities of bacterial protein biomarkers. For example, genome sequences of B. anthracis can be utilized to obtain protein sequences and to calculate protein masses. The molecular identities of biomarkers can be then determined by comparing experimental MS data with the molecular masses of proteins in databases such as UniProtKB. Although these types of assignments can only be of a tentative character (and should be carefully interpreted), the possibility of molecular identification of biomarkers constitutes one of the most valuable aspects of the MS-based identification technique.

Table Table44 gives an overview of the tentative assignments of 55 typical mass signals in MALDI spectra of B. anthracis. The assignments were made by considering posttranslational modifications (excision of N-terminal methionine) and the presence of double-charged protein species.

TABLE 4.
Tentative assignments of B. anthracis biomarker peaks

DISCUSSION

The importance of sample preparation.

The TFA sample preparation protocol for MALDI-TOF MS-compatible inactivation of highly pathogenic microorganisms permits the reproducible collection of mass spectra from bacterial samples with a large number of mass signals at a low noise level. The two factors—large numbers of mass signals and a high level of reproducibility—are considered equally important for the successful application of the MS technique in microbiological diagnostics. The relatively high number of signals in microbial mass spectra—we typically observe between 50 and 100 per individual spectrum—is in large part due to the ability of TFA to act as an organic solvent, i.e., to effectively solubilize bacterial proteins, preserving the structural integrity (primary structure) of the proteins under investigation (26). In this context, it should be emphasized that the combination of TFA inactivation and MALDI-TOF MS can be considered as effective as ICMS, a simple and widely used mass spectrometric technique in which microbial cells are analyzed directly with only minimal sample pretreatment (14).

A high level of spectral reproducibility, the other crucial aspect of the MS application, was achieved by establishing a rigorous sample preparation protocol that included standardization of cultivation conditions, such as the type of cultivation medium, the cultivation time and temperature, and also the definition of strict parameters for data acquisition.

Important aspects of spectral preprocessing.

In any spectrometry-based classification analysis, spectral preprocessing aims to improve the accuracy and robustness of subsequent pattern analysis. Also, in MALDI-TOF MS, an optimal preprocessing workflow is the key to reliable classification and included in our study routine tests for spectral quality, normalization, baseline correction, and peak detection. In particular, the strategy of peak detection was found to be highly relevant. Mainly for this reason, the in-house-developed Matlab routines (see Materials and Methods) included specifically designed preprocessing functions, among them a fast and robust peak detection routine. The key feature of the latter routine is a sigmoid function that models the lower analytical sensitivity of the MALDI-TOF MS technique in the high-mass range. Another vital element of our peak detection routine allows the definition of the number of peaks to be determined per mass spectrum. This turned out to be useful for subsequent pattern analysis by UHCA or ANNs. A detailed description of the methods, concepts, and principles of MS preprocessing and fingerprinting will be provided in a separate publication.

In the present work, the general strategy of analysis included statistical evaluation of a large number of microbial mass spectra. Based on a ranking of P values obtained in univariate and independent t tests, we have been able to determine species (B. anthracis)-specific and B. cereus group-specific biomarkers suitable for discrimination and identification of the microorganisms of interest (Fig. (Fig.6).6). Here, we discuss the molecular identities of some of these biomarkers.

Ribosomal biomarkers.

Ribosomal proteins and certain housekeeping proteins have been suggested to be responsible for many mass signals detected by ICMS (12, 27, 34). Since up to 21% of the cell's overall protein content is ribosomal (2) and because of the fact that ribosomal proteins, as part of the cellular translational machinery, are constitutively expressed in vegetative cells, these proteins constitute a stable ensemble of protein biomarkers suitable for use by fingerprinting techniques.

Within the scope of the present work, we found tentative evidence that the B. cereus group-specific biomarkers at 4,334, 5,171, and 5,886 Da (Table (Table4)4) are due to ribosomal proteins. For example, a search in the UniProtKB/Swiss-Prot database revealed that the 50S ribosomal proteins L36, L34, and L33-2 of B. anthracis have molecular weights (MW) of 4,334.3, 5,171.1, and 5,886.8, respectively. Thus, the agreement of sequence information contained in the proteomic database and accurate mass measurements of intact proteins by MALDI-TOF MS allowed us to tentatively assign at least some of the most discriminating B. cereus group-specific biomarkers. This preliminary assignment is additionally supported by the results of a BLAST search. For example, the program NCBI BLASTP 2.2.17 revealed for the 50S ribosomal protein L34 of B. anthracis (SwissProt entry Q81JG9), with a calculated MW of 5171.1, a total of 25 database entries with 100% amino acid sequence identity. It was interesting that all of these entries originated from strains of B. cereus group members, such as B. anthracis, B. cereus, B. thuringiensis, and B. weihenstephanensis. Conversely, none of the organisms with less than 100% coverage belonged to the B. cereus group. Interestingly, this BLAST search also revealed 86% sequence coverage with the 50S ribosomal protein L34 of B. licheniformis DSM 13 (entry Q65CM7). According to the proteomic database, in B. licheniformis, the MW of the L34 protein is 5,253, which again fits nicely with our experimental data (Fig. (Fig.1D,1D, peak at 5,254 Da).

Although final proof of the peak assignments is not available yet, we found ample evidence suggesting the ribosomal origin of many B. cereus group-specific biomarkers. A more detailed analysis could be carried out using tandem MS with some type of fragmentation and peptide analysis in a protein database. With such an approach, it is hoped that the molecular identities of other important biomarkers, such as the B. anthracis-specific marker at 5,413 Da (Fig. (Fig.22 to to44 and and6A),6A), can also be verified.

Spore biomarkers.

A closer inspection of the mass spectral profiles of B. anthracis and other members of the B. cereus group revealed further interesting details. For example, a large number of mass spectra from cultures of B. cereus group members exhibited prominent mass peaks at 6,679, 6,695, 6,711, and 6,835 Da. These signals are well known in the literature and have been described as spore biomarkers (6, 11, 17). These spore markers arise from SASPs, a group of proteins present in large amounts in the core regions of Bacillus endospores. SASPs play a key role in the protection of the spore's DNA from UV light (32, 33) and, upon germination, serve as a source for amino acids by their degradation (31). Because the amino acid sequences of selected SASPs are species specific, SASP peaks have been suggested as biomarkers for rapid differentiation and identification of spore preparations from B. anthracis and B. cereus using MS (6, 7, 11, 17, 18).

In agreement with the literature, we found in this work a B. anthracis-specific SASP spore marker at 6,679 Da (Fig. (Fig.11 to to4).4). This signal can be predicted from the sspB gene of B. anthracis, which codes for the α/β-type SASP with a nominal MW of 6,810. As suggested by Castanha et al. and Demirev et al. (6, 9), SASPs may undergo posttranslational modification in which a methionine with a mass of 131 is cleaved, giving the experimental mass of 6,679 Da. Furthermore, mass spectral profiles of B. cereus strains displayed two other spore marker peaks, either at 6,695 or at 6,711 Da (Fig. (Fig.4).4). In the present work, the latter peak was also found in B. mycoides and B. thuringiensis. According to the genome sequences of B. cereus (sasP-2 gene), these mass signals have been associated with α/β-type SASPs with masses of 6,826 and 6,842 Da (6, 7). Again, cleavage of the N-terminal Met could explain the discrepancy between predicted and experimental masses.

The presence of species-specific SASP peaks correlates well with a number of other mass signals. For example, a species-invariant mass peak at 6,835 Da is found in all spectra of Bacillus strains exhibiting one of the SASP peaks at 6,679, 6,695, and 6,711 Da (Fig. (Fig.33 and and4).4). This invariant signal is due to the presence of a second SASP encoded by the sasP-1 gene with a predicted MW of 6,835 (6,966, Met cleavage) (6). Experimental mass spectra with SASP peaks also show signals of double-charged ions. These signals can be found as species-specific SASP peaks at either 3,340, 3,348, or 3,356 Da and as an invariant SASP at 3,418 Da (Fig. (Fig.33).

From our experimental findings and the discussion above, it is quite clear that approximately 50% of the preparations of vegetative cells contained substantial amounts of SASPs. SASPs are known to be indicative of developing or dormant spores, so it was astonishing to us to detect high-intensity SASP peaks in mass spectra of growing cell cultures. On the other hand, the presence of strong SASP signals in mass spectra of Bacillus cultures may be the result of the specifically increased sensitivity of the TFA sample preparation technique for these markers. For example, it was reported earlier that acid treatment effectively extracts SASPs from spore preparations (31, 37). Second, SASPs are easy ionizable and are probably preferentially detected by MALDI-TOF MS. Finally, the concentration of SASPs in dormant endospores is substantial and varies between 8 and 20% of the total spore protein content (31). Consequently, it is likely that even small numbers of spores in a large surplus of vegetative cells give intense SASP signals. We have to admit, however, that no data are currently available that could prove these assumptions. Further systematic investigations will reveal at which sporulation stage one can detect SASPs by using MALDI-TOF MS.

Within the context of the present study, which aimed to establish an MS-based classification technique for bacilli, the presence or absence of SASP biomarkers must be considered a confounding factor that is not directly related to taxonomy. On the other hand, as some of the biomarkers have been proven to be species or group specific, SASP features may be beneficial and improve the accuracy of the MS-based detection method.

UHCA.

UHCA clearly demonstrated that mass spectra of bacilli contain taxonomic information. Although the classification observed with UHCA in the example of 437 individual microbial spectra is not perfect (Fig. (Fig.55 shows outliers), the dendrogram allows us to draw a number of important conclusions. First and foremost, UHCA demonstrates the existence of two main spectral groups: in the dendrogram in Fig. Fig.5,5, the first cluster is formed by B. cereus group members and the second contains the remaining species of the genus Bacillus plus a few species of related genera, such as Paenibacillus, Brevibacillus, Virgibacillus, and Sporosarcina. Second, spectra from B. anthracis clearly differed from the spectra of other B. cereus group species. For example, the large cluster Id of Fig. Fig.55 contains exclusively mass spectra of B. anthracis with no outliers. The second B. anthracis cluster, cluster Ib, is formed by mass spectral profiles of B. anthracis strains like vollum, A13, A23, and A65. More importantly, this cluster also contains one outlier from B. cereus (strain B292) and three replicate spectra of a B. cereus group member with unclear species assignment (strain BWB-B, an environmental isolate). Although we do not have an explanation that could account for the existence of two different B. anthracis clusters, it is evident that cluster Ib is composed of spectra with greater similarity to B. cereus and other B. cereus group members. The situation is further complicated by the presence or absence of spore marker bands (SASPs) that represent an additional source of variance not related to taxonomy in this context.

Analysis of the second cluster, cluster II, also demonstrated the similarity of spectra of B. subtilis group members. For example, with a few exceptions, clusters IIb to IId are formed only by species of the B. subtilis group. This demonstrates that MALDI-TOF MS, in combination with fingerprinting techniques, can be used to obtain taxonomic information that might be helpful to complement DNA sequencing methods. We are currently investigating the database of Bacillus spectra with adapted bioinformatics methods for its applicability to taxonomy. The details of these investigations are beyond the scope of this study and will be provided in a separate publication.

Supervised classification analysis by ANNs.

The term supervised, or concept-driven, classification analysis is used to describe a group of techniques in which a model is created that maps input objects (spectra) to desired outputs (class assignments) (39). Supervised classification analyses comprise a learning or teaching phase in which a classification function is obtained from class-labeled training data. The performance of the classifier can be subsequently evaluated on the basis of independent test data, which should kept totally separate from the training data. Different types of supervised classification techniques are known, among them the MLP ANNs employed in this study. Within the scope of the present work, we optimized ANN models by training and internal validation. The respective data sets comprised approximately 70% of the bacterial mass spectra. The remaining 30% of the spectra were utilized for objective testing of the ANN model. The results of ANN classification summarized in Tables Tables22 and and33 demonstrate that MALDI-TOF MS of Bacillus can be successfully applied to unambiguously identify strains of B. anthracis (class i) or to classify bacilli as members (class ii) or nonmembers (class iii) of the B. cereus group. Since the database of MS spectra contains a significant number of spectra with spore biomarkers (SASPs), the ANN classifier can be used to identify MS fingerprints of vegetative cells and mixtures of cells and spores. This is essential, because most of the studies in the field of B. anthracis detection by MALDI-TOF MS are limited to the detection of biomarkers from spores.

Conclusions.

With this comprehensive study carried out on 374 strains of the genus Bacillus and a few related genera, among them 102 strains of B. anthracis, we have extended previous work in the field of B. anthracis detection to vegetative cells. We have been able to detect and to tentatively assign B. anthracis-specific and B. cereus group-specific protein biomarkers that could be used for objective classification by cluster analysis and ANNs. Our study demonstrates the great potential of MALDI-TOF MS as a rapid, reliable, and objective identification technique for highly pathogenic microorganisms, not only for scientific research purposes, but also under routine conditions. The methodology used in this study can also be applied to identify microorganisms of other genera, such as Yersinia or Burkholderia (multiplex advantage). Preconditions for successful application of the MS-based technique are (i) rigorous standards for cultivation conditions, (ii) adequate sample preparation (TFA inactivation), (iii) the compilation of databases containing representative numbers of mass spectra, (iv) the application of effective data-preprocessing procedures, and (v) the use of supervised classification models for objective identification.

Acknowledgments

We thank R. Reissbrodt (Robert Koch-Institut, Berlin, Germany), B. Niederwöhrmeier (WIS, Munster), and M. Ehling-Schulz (Microbial Ecology Group at the Technical University Munich) for providing Bacillus strains. We are grateful to M. Erhard (AnagnosTec, Potsdam), T. Maier and M. Kostrzewa (Bruker Daltonics, Leipzig), and H. Russmann (WIS, Munster) for fruitful discussions and support. Furthermore, the excellent technical assistance of P. Lochau and R. Heinrich (Robert Koch-Institut, Berlin) is acknowledged.

This work was partly supported by the Federal Office of Civil Protection and Disaster Assistance, BBK (BBK F2-440-00-185/04) and WIS (E/E590/4Z015/N5129 and ZVZ-DRMZ-1368-652).

Footnotes

[down-pointing small open triangle]Published ahead of print on 18 September 2009.

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