Characterization of Bacillus cereus isolates associated with fatal pneumonias: strains are closely related to Bacillus anthracis and harbor B. anthracis virulence genes

A new minimal replicon of Bacillus anthracis plasmid pXO1

An 8,883-bp mini-pXO1 plasmid containing a replicon from Bacillus anthracis pXO1 (181.6 kb) was identified by making large deletions in the original plasmid using a newly developed Cre-loxP system. Portions of the truncated mini-pXO1 were cloned into an Escherichia coli vector unable to replicate in B. anthracis. A 5.95-kb region encompassing three putative genes was identified as the minimal pXO1 fragment required for replication of the resulting recombinant shuttle plasmid (named pMR) in B. anthracis. Deletion analysis showed that the only genes essential for replication were the pXO1-14 and pXO1-16 genes, which are transcribed in opposite directions and encode predicted proteins of 66.5 and 67.1 kDa, respectively. The ORF14 protein contains a helix-turn-helix motif, while the ORF16 upstream region contains attributes of a theta-replicating plasmid origin of replication (Ori), namely, an exclusively A+T-containing segment, five 9-bp direct repeats, an inverted repeat, and a sigma(A)-dependent promoter for the putative replication initiator Rep protein (ORF16). Spontaneous mutations generated in the ORF14, ORF16, and Ori regions of pMR during PCR amplification produced a temperature-sensitive plasmid that is unable to replicate in B. anthracis at 37 degrees C. The efficacy of transformation of plasmid-free B. anthracis Ames and Sterne strains by the original pMR was approximately 10(3) CFU/microg, while Bacillus cereus strains 569 and ATCC 10987 were transformed with efficiencies of 10(4) and 10(2) CFU/microg, respectively. Around 95% of B. anthracis cells retained pMR after one round of sporulation and germination.

Secondary cell wall polysaccharides of Bacillus anthracis are antigens that contain specific epitopes which cross-react with three pathogenic Bacillus cereus strains that caused severe disease, and other epitopes common to all the Bacillus cereus strains tested

The immunoreactivities of hydrogen fluoride (HF)-released cell wall polysaccharides (HF-PSs) from selected Bacillus anthracis and Bacillus cereus strains were compared using antisera against live and killed B. anthracis spores. These antisera bound to the HF-PSs from B. anthracis and from three clinical B. cereus isolates (G9241, 03BB87, and 03BB102) obtained from cases of severe or fatal human pneumonia but did not bind to the HF-PSs from the closely related B. cereus ATCC 10987 or from B. cereus type strain ATCC 14579. Antiserum against a keyhole limpet hemocyanin conjugate of the B. anthracis HF-PS (HF-PS-KLH) also bound to HF-PSs and cell walls from B. anthracis and the three clinical B. cereus isolates, and B. anthracis spores. These results indicate that the B. anthracis HF-PS is an antigen in both B. anthracis cell walls and spores, and that it shares cross-reactive, and possibly pathogenicity-related, epitopes with three clinical B. cereus isolates that caused severe disease. The anti-HF-PS-KLH antiserum cross-reacted with the bovine serum albumin (BSA)-conjugates of all B. anthracis and all B. cereus HF-PSs tested, including those from nonclinical B. cereus ATCC 10987 and ATCC 14579 strains. Finally, the serum of vaccinated (anthrax vaccine adsorbed (AVA)) Rhesus macaques that survived inhalation anthrax contained IgG antibodies that bound the B. anthracis HF-PS-KLH conjugate. These data indicate that HF-PSs from the cell walls of the bacilli tested here are (i) antigens that contain (ii) a potentially virulence-associated carbohydrate antigen motif, and (iii) another antigenic determinant that is common to B. cereus strains.

A simple and sensitive method for detection of Bacillus anthracis by loop-mediated isothermal amplification

AIMS

To develop a rapid and simple system for detection of Bacillus anthracis using a loop-mediated isothermal amplification (LAMP) method and determine the suitability of LAMP for rapid identification of B. anthracis infection.

METHODS AND RESULTS

A specific LAMP assay targeting unique gene sequences in the bacterial chromosome and two virulence plasmids, pXO1 and pXO2, was designed. With this assay, it was possible to detect more than 10 fg of bacterial DNA per reaction and obtain results within 30-40 min under isothermal conditions at 63 degrees C. No cross-reactivity was observed among Bacillus cereus group and other Bacillus species. Furthermore, in tests using blood specimens from mice inoculated intranasally with B. anthracis spores, the sensitivity of the LAMP assay following DNA extraction methods using a Qiagen DNeasy kit or boiling protocol was examined. Samples prepared by both methods showed almost equivalent sensitivities in LAMP assay. The detection limit was 3.6 CFU per test.

CONCLUSIONS

The LAMP assay is a simple, rapid and sensitive method for detecting B. anthracis.

SIGNIFICANCE AND IMPACT OF THE STUDY

The LAMP assay combined with boiling extraction could be used as a simple diagnostic method for identification of B. anthracis infection.

The microbiota of Lafun, an African traditional cassava food product

Lafun is a fermented cassava food product consumed in parts of West Africa. In the present work the microorganisms (aerobic bacteria (AB), lactic acid bacteria (LAB) and yeasts) associated with the fermentation of Lafun under traditional conditions have for the first time been studied using a combination of pheno- and genotypic methods. During Lafun fermentation the AB count ranged from 6-7 log(10) CFU/g at the beginning to 9 log(10) CFU/g at the end. Similarly, the number of LAB increased from 5 log(10) CFU/g to 9 log(10) CFU/g during the process while the yeast load increased from 3 log(10) CFU/g at the onset of the fermentation to 5-6 log(10) CFU/g at the end of the fermentation. A total of 168 isolates (31 AB, 88 LAB, and 49 yeasts) were isolated and identified by means of phenotypic tests, PCR-based methods and 16S rRNA gene sequencing. The aerobic bacteria were mostly identified as belonging to the Bacillus cereus group (71%). The B. cereus isolates lacked the genetic determinant specific for cereulide producers but harboured several genes encoding the heat-labile toxins hemolysin BL and nonhemolytic enterotoxin as detected by PCR. The other aerobic bacteria isolated were Gram negative and identified as Klebsiella pneumoniae and Pantoea agglomerans. The dominant LAB were identified as Lactobacillus fermentum (42% of LAB isolates) followed by Lactobacillus plantarum (30%) and Weissella confusa (18%). Seven isolates remained unidentified and constitute probably a novel LAB species. The predominant yeast species associated with Lafun fermentation were Saccharomyces cerevisiae (22% of yeast isolates), Pichia scutulata (20%), Kluyveromyces marxianus (18%), Hanseniaspora guilliermondii (12%), Pichia rhodanensis (8%) and Candida glabrata (8%) as well as Pichia kudriavzevii, Candida tropicalis and Trichosporon asahii at lower incidence (<5% each).

Short-term inhalation exposure to mild steel welding fume had no effect on lung inflammation and injury but did alter defense responses to bacteria in rats

Many workers worldwide are continually exposed to complex aerosols generated from welding processes. The objective was to assess the effect of inhalation exposure to mild steel (MS) welding fume on lung injury, inflammation, and defense responses. Male Sprague-Dawley rats were exposed to MS fume at a concentration of 40 mg/m(3) x 3 h/day x 3 or 10 days using a robotic welding fume generator. Controls were exposed to filtered air. To assess lung defense responses, a group of animals were intratracheally inoculated with 5 x 10(4) Listeria monocytogenes 1 day after the last daily exposure. Welding particles were collected during exposure, and chemical composition and particle size were determined. After exposure, lung injury, inflammation, and host defense (bacterial clearance) were measured. The particles were composed of iron (80.6 %) and manganese (14.7 %) with a mass median aerodynamic diameter of 0.31 microm. No significant difference was observed in lung injury or inflammation after MS fume inhalation at 1, 4, and 11 days after the last exposure. However, there were significantly more bacteria at 3 days after infection in the lungs of the animals exposed to MS fume compared to air controls. Acute exposure of rats to MS fume had no effect on injury and inflammation, but suppressed lung defense responses after infection. More chronic inhalation studies are needed to further examine the immune effects and to elucidate the possible mechanisms of the suppressed lung defense response to infection associated with the inhalation of MS welding fume.

Comparative transcriptional profiling of Bacillus cereus sensu lato strains during growth in CO2-bicarbonate and aerobic atmospheres

Background

Bacillus species are spore-forming bacteria that are ubiquitous in the environment and display a range of virulent and avirulent phenotypes. This range is particularly evident in the Bacillus cereus sensu lato group; where closely related strains cause anthrax, food-borne illnesses, and pneumonia, but can also be non-pathogenic. Although much of this phenotypic range can be attributed to the presence or absence of a few key virulence factors, there are other virulence-associated loci that are conserved throughout the B. cereus group, and we hypothesized that these genes may be regulated differently in pathogenic and non-pathogenic strains.

Methodology/Principal Findings

Here we report transcriptional profiles of three closely related but phenotypically unique members of the Bacillus cereus group—a pneumonia-causing B. cereus strain (G9241), an attenuated strain of B. anthracis (Sterne 34F₂), and an avirulent B. cereus strain (10987)—during exponential growth in two distinct atmospheric environments: 14% CO₂/bicarbonate and ambient air. We show that the disease-causing Bacillus strains undergo more distinctive transcriptional changes between the two environments, and that the expression of plasmid-encoded virulence genes was increased exclusively in the CO₂ environment. We observed a core of conserved metabolic genes that were differentially expressed in all three strains in both conditions. Additionally, the expression profiles of putative virulence genes in G9241 suggest that this strain, unlike Bacillus anthracis, may regulate gene expression with both PlcR and AtxA transcriptional regulators, each acting in a different environment.

Conclusions/Significance

We have shown that homologous and even identical genes within the genomes of three closely related members of the B. cereus sensu lato group are in some instances regulated very differently, and that these differences can have important implications for virulence. This study provides insights into the evolution of the B. cereus group, and highlights the importance of looking beyond differences in gene content in comparative genomics studies.

Evolution of pathogenicity in the Bacillus cereus group

The Bacillus cereus group of bacteria comprises soil-dwelling saprophytes but on occasion these bacteria can cause a wide range of diseases in humans, including food poisoning, systemic infections and highly lethal forms of anthrax. While anthrax is almost invariably caused by strains from a single evolutionary lineage, Bacillus anthracis, variation in the virulence properties of strains from other lineages has not been fully addressed. Using multi-locus sequence data from 667 strains, we reconstructed the evolutionary history of the B. cereus group in terms of both clonal inheritance and recombination. The strains included 155 clinical isolates representing B. anthracis, and isolates from emetic and diarrhoeal food poisoning, septicaemia and related infections, wound, and lung infections. We confirmed the existence of three major clades and found that clinical isolates of B. cereus (with the exception of emetic toxin-producing strains) are evenly distributed between and within clades 1 and 2. B. anthracis in particular and emetic toxin-producing B. cereus show more clonal structure and are restricted to clade 1. Our characterization of the patterns of genetic exchange showed that there exist partial barriers to gene flow between the three clades. The pathogenic strains do not exhibit atypically high or low rates of recombination, consistent with the opportunistic nature of most pathogenic infections. However, there have been a large number of recent imports in clade 1 of strains from external origins, which is indicative of an on-going shift in gene-flow boundaries for this clade.

Discrimination between biothreat agents and 'near neighbor' species using a resequencing array

Timely identification of biothreat organisms from large numbers of clinical or environmental samples in potential outbreak or attack scenario is critical for effective diagnosis and treatment. This study aims to evaluate the potential of resequencing arrays for this purpose. Albeit suboptimal, this report demonstrated that respiratory pathogen microarray version 1 can identify Bacillus anthracis, Francisella tularensis, Yersinia pestis and distinguish them from benign 'near neighbor' species in a single assay. Additionally, the sequence information can discriminate strains and possibly the sources of the strains. With further development, it is possible to use resequencing microarrays for biothreat surveillance.

Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing

Background

Bacillus cereus is most commonly associated with foodborne illness (diarrheal and emetic) but is also an opportunistic pathogen that can cause severe and fatal infections. Several multilocus sequence typing (MLST) schemes have recently been developed to genotype B. cereus and analysis has suggested a clonal or weakly clonal population structure for B. cereus and its close relatives B. anthracis and B. thuringiensis. In this study we used MLST to determine if B. cereus isolates associated with illnesses of varying severity (e.g., severe, systemic vs. gastrointestinal (GI) illness) were clonal or formed clonal complexes.

Results

A retrospective analysis of 55 clinical B. cereus isolates submitted to the Centers for Disease Control and Prevention between 1954 and 2004 was conducted. Clinical isolates from severe infections (n = 27), gastrointestinal (GI) illness (n = 18), and associated isolates from food (n = 10) were selected for analysis using MLST. The 55 isolates were diverse and comprised 38 sequence types (ST) in two distinct clades. Of the 27 isolates associated with serious illness, 13 clustered in clade 1 while 14 were in clade 2. Isolates associated with GI illness were also found throughout clades 1 and 2, while no isolates in this study belonged to clade 3. All the isolates from this study belonging to the clade 1/cereus III lineage were associated with severe disease while isolates belonging to clade1/cereus II contained isolates primarily associated with severe disease and emetic illness. Only three STs were observed more than once for epidemiologically distinct isolates.

Conclusion

STs of clinical B. cereus isolates were phylogenetically diverse and distributed among two of three previously described clades. Greater numbers of strains will need to be analyzed to confirm if specific lineages or clonal complexes are more likely to contain clinical isolates or be associated with specific illness, similar to B. anthracis and emetic B. cereus isolates.

Structural elucidation of the nonclassical secondary cell wall polysaccharide from Bacillus cereus ATCC 10987. Comparison with the polysaccharides from Bacillus anthracis and B. cereus type strain ATCC 14579 reveals both unique and common structural features

Nonclassical secondary cell wall polysaccharides constitute a major cell wall structure in the Bacillus cereus group of bacteria. The structure of the secondary cell wall polysaccharide from Bacillus cereus ATCC 10987, a strain that is closely related to Bacillus anthracis, was determined. This polysaccharide was released from the cell wall with aqueous hydrogen fluoride (HF) and purified by gel filtration chromatography. The purified polysaccharide, HF-PS, was characterized by glycosyl composition and linkage analyses, mass spectrometry, and one- and two-dimensional NMR analysis. The results showed that the B. cereus ATCC 10987 HF-PS has a repeating oligosaccharide consisting of a -->6)-alpha-GalNAc-(1-->4)-beta-ManNAc-(1-->4)-beta-GlcNAc-(1--> trisaccharide that is substituted with beta-Gal at O3 of the alpha-GalNAc residue and nonstoichiometrically acetylated at O3 of the N-acetylmannosamine (ManNAc) residue. Comparison of this structure with that of the B. anthracis HF-PS and with structural data obtained for the HF-PS from B. cereus type strain ATCC 14579 revealed that each HF-PS had the same general structural theme consisting of three HexNAc and one Hex residues. A common structural feature in the HF-PSs from B. cereus ATCC 10987 and B. anthracis was the presence of a repeating unit consisting of a HexNAc(3) trisaccharide backbone in which two of the three HexNAc residues are GlcNAc and ManNAc and the third can be either GlcNAc or GalNAc. The implications of these results with regard to the possible functions of the HF-PSs are discussed.

Transcriptional analysis of the conjugative plasmid pAW63 from Bacillus thuringiensis

The broad-host range plasmid pAW63 is a model for the study of molecular mechanisms associated with conjugation in the Gram-positive Bacillus cereus group. Its main features are a conjugative apparatus that includes Type IV Secretion System-like components and two Group II introns, B.th.I1 and B.th.I2, located within conjugation genes, as well as a putative regulatory control circuit. Furthermore, pAW63 shares a common backbone with pXO2, the second virulence plasmid of Bacillus anthracis, and with pBT9727 from the pathogenic Bacillus thuringiensis subsp. konkukian strain 97-27. In this study, the transcriptome of pAW63 was investigated using a custom DNA microarray, providing insight into the genetic clockwork of this conjugative plasmid. Gene expression profiles suggested that in the absence of mating partners, a partial 'standby mode' was in effect, with little production of many of the structural elements thought to be involved in mating pair formation and DNA transfer, while components of a proposed quorum sensing mechanism were actively expressed. Intron splicing was demonstrated for the B.th.I2 intron.

Bacillus cereus nosocomial infection from reused towels in Japan

It was noticed that there was an increase in Bacillus cereus nosocomial infections in the summer from 2000 to 2005. In 2005, five bloodstream infections occurred in five patients related to catheter use. The causative strains were distinct from each other and belonged to novel multilocus sequence types (ST): ST365, ST366, ST367 and ST368. Two ST365 strains from two patients were further distinguished by pulsed-field gel electrophoresis. B. cereus contamination was observed with reused (dried and steamed) towels (>10(6)cfu/towel) and washing machines in hospital linen rooms. B. cereus strains from towels belonged to ST167, ST365, ST380 and ST382, and a proportion of these were the same, or similar, to strains from patients. All the hospital strains of B. cereus were distinct from those from food-poisoning strains (ST26, ST142, ST381). Ciprofloxacin resistance was observed only in hospital strains. Neither emetic toxin nor cytotoxin K gene, usually present in food poisoning strains, were found in the hospital strains, except for one patient isolate. The data suggest that specific B. cereus strains are circulating within a hospital, with genotypes, antibiotic susceptibilities and virulence gene patterns generally distinct from those of food poisoning, and that in Japan, towels are an important source of contamination, especially in summer.

Survey of group I and group II introns in 29 sequenced genomes of the Bacillus cereus group: insights into their spread and evolution

Group I and group II introns are different catalytic self-splicing and mobile RNA elements that contribute to genome dynamics. In this study, we have analyzed their distribution and evolution in 29 sequenced genomes from the Bacillus cereus group of bacteria. Introns were of different structural classes and evolutionary origins, and a large number of nearly identical elements are shared between multiple strains of different sources, suggesting recent lateral transfers and/or that introns are under a strong selection pressure. Altogether, 73 group I introns were identified, inserted in essential genes from the chromosome or newly described prophages, including the first elements found within phages in bacterial plasmids. Notably, bacteriophages are an important source for spreading group I introns between strains. Furthermore, 77 group II introns were found within a diverse set of chromosomal and plasmidic genes. Unusual findings include elements located within conserved DNA metabolism and repair genes and one intron inserted within a novel retroelement. Group II introns are mainly disseminated via plasmids and can subsequently invade the host genome, in particular by coupling mobility with host cell replication. This study reveals a very high diversity and variability of mobile introns in B. cereus group strains.

A Bacillus thuringiensis strain producing a polyglutamate capsule resembling that of Bacillus anthracis

Bacillus thuringiensis serovar Monterrey strain BGSC 4AJ1 produced a microscopically visible capsule that reacted with a fluorescent antibody specific for the poly-gamma-d-glutamic acid (PGA) capsule of Bacillus anthracis. PGA capsule biosynthesis genes with 75%, 81%, 72%, 65% and 63% similarity, respectively, to those of the B. anthracis capBCADE cluster were present on a plasmid (pAJ1-1). Strain BGSC 4AJ1, together with five strains of Bacillus cereus that hybridized to a PGA cap gene probe, were analyzed phylogenetically using six housekeeping genes of a B. cereus multilocus sequence typing scheme. Bacillus thuringiensis BGSC 4AJ1 shared four identical alleles with B. anthracis and was the second most closely related to this bacterium of the 674 isolates in the multilocus sequence typing database. The other cap+ strains were distributed among various lineages of Clade 1 of the B. cereus group.

Real-time PCR system targeting a chromosomal marker specific for Bacillus anthracis

Specific identification of Bacillus anthracis and differentiation from closely related Bacillus cereus and Bacillus thuringiensis strains is still a major diagnostic problem. Commercially available diagnostic kits targeting plasmid-markers cannot differentiate between B. anthracis, non-anthracis Bacillus species harbouring anthrax-specific virulence plasmids, and plasmidless B. anthracis strains. A TaqMan PCR assay was designed targeting sequences of gene locus BA_5345 of the B. anthracis strain Ames. Specificity was determined by using a panel of 328 Bacillus strains; sensitivity was determined by probit analysis. All B. anthracis isolates (n=92) were specifically detected by using the genomic TaqMan PCR assay whereas 236 strains belonging to 19 Bacillus species other than B. anthracis were PCR negative. The detection limit was determined to be 12.7 copies per reaction (95% confidence interval 10.2-17.5 copies). Here we present an extensively evaluated and - to our current knowledge - specific TaqMan PCR assay for the detection of B. anthracis based on a chromosomal marker.

The Bacillus cereus containing sub-branch most closely related to Bacillus anthracis, have single amino acid substitutions in small acid-soluble proteins, while remaining sub-branches are more variable

Hoffmaster et al. [Hoffmaster AR, Ravel J, Rasko DA, Chapman GD, Chute MD, Marston CK, et al. Identification of anthrax toxin genes in Bacillus cereus associated with illness resembling inhalation anthrax. Proc Natl Acad Sci U S A 2004;101:8449-54; Hoffmaster AR, Hill KK, Gee JE, Marston CK, De BK, Popovic T, et al. Characterization of Bacillus cereus isolates associated with fatal pneumonias: strains are closely related to Bacillus anthracis and harbor B. anthracis virulence genes. J Clin Microbiol 2006;44:3352-60] phylogenetically divided Bacillus cereus strains into 10 branches by amplified fragment length polymorphism (AFLP) with Branch F including all Bacillus anthracis strains and pneumonia-causing strains of B. cereus. There are four sub-branches within Branch F, referred to here as F1-A, F1-B, F2-A and F2-B. The B. anthracis strains are found within sub-branch F1-B. Concerning, the currently available B. cereus pneumonia-causing isolates, one was found to categorize within sub-branch F1-B and two within F2-B. In the following work the sequence variation between B. cereus strains was determined by MALDI-TOF MS and MS-MS for each strain of B. cereus in Branch F. ESI-MS was performed on selected strains for confirmation. Small acid-soluble proteins (SASPs) of B. cereus strains found in F1-B showed a single amino acid substitution, while strains in the other three sub-branches were more variable generally showing one or two amino acid substitutions. The single substitutions always occurred in the C-terminus. Double substitutions occurred in both N and C termini. Of the pneumonia-causing strains, one exhibited a single amino acid substitution, while the other two exhibited a two amino acid substitution.

Serum IgG antibody response to the protective antigen (PA) of Bacillus anthracis induced by anthrax vaccine adsorbed (AVA) among U.S. military personnel

The seroconversion rates and geometric mean concentrations (GMC) of IgG anti-PA for stored sera from U.S. military personnel immunized 3, 4, and 6 times with the U.S. licensed anthrax vaccine adsorbed were studied. Anti-PA IgG concentrations were measured by ELISA. All 246 vaccinees had low but detectable pre-immunization anti-PA IgG (GMC 1.83 microg/mL). Three doses elicited a GMC of 59.92 microg/mL and a seroconversion rate of 85.3%, four doses elicited a GMC of 157.44 microg/mL and 67.9% and the sixth of 276.95 microg/mL and 45.5%, respectively. The forth dose elicited 100% seroconversion compared to the pre-immunization level. These results should facilitate comparison between different immunization schedules and new vaccines.

Self-transfer and mobilisation capabilities of the pXO2-like plasmid pBT9727 from Bacillus thuringiensis subsp. konkukian 97-27

Recent characterisations of plasmids related to the anthrax virulence plasmids pXO1 and pXO2 in clinical isolates of Bacillus cereus and Bacillus thuringiensis have contributed to the emerging picture of a virulence-associated plasmid pool in the B. cereus sensu lato group. The family of pXO2-like plasmids includes the conjugative plasmid pAW63 from the biopesticide strain B. thuringiensis subsp. kurstaki HD73 and the heretofore cryptic plasmid pBT9727 from the clinical strain B. thuringiensis subsp. konkukian 97-27. Comparative sequence analysis of these three plasmids suggested that they were derived from an ancestral conjugative plasmid, with pAW63 retaining its self-transfer capabilities, and pXO2 having lost them through genetic drift. Such properties had not been investigated in pBT9727, but sequence homologies led us to predict that it may possess self-transfer capabilities. Here, we report that pBT9727 is indeed conjugative, and is able to promote its own transfer as well as that of small mobilisable plasmids.

Cell wall carbohydrate compositions of strains from the Bacillus cereus group of species correlate with phylogenetic relatedness

Members of the Bacillus cereus group contain cell wall carbohydrates that vary in their glycosyl compositions. Recent multilocus sequence typing (MLST) refined the relatedness of B. cereus group members by separating them into clades and lineages. Based on MLST, we selected several B. anthracis, B. cereus, and B. thuringiensis strains and compared their cell wall carbohydrates. The cell walls of different B. anthracis strains (clade 1/Anthracis) were composed of glucose (Glc), galactose (Gal), N-acetyl mannosamine (ManNAc), and N-acetylglucosamine (GlcNAc). In contrast, the cell walls from clade 2 strains (B. cereus type strain ATCC 14579 and B. thuringiensis strains) lacked Gal and contained N-acetylgalactosamine (GalNAc). The B. cereus clade 1 strains had cell walls that were similar in composition to B. anthracis in that they all contained Gal. However, the cell walls from some clade 1 strains also contained GalNAc, which was not present in B. anthracis cell walls. Three recently identified clade 1 strains of B. cereus that caused severe pneumonia, i.e., strains 03BB102, 03BB87, and G9241, had cell wall compositions that closely resembled those of the B. anthracis strains. It was also observed that B. anthracis strains cell wall glycosyl compositions differed from one another in a plasmid-dependent manner. When plasmid pXO2 was absent, the ManNAc/Gal ratio decreased, while the Glc/Gal ratio increased. Also, deletion of atxA, a global regulatory gene, from a pXO2- strain resulted in cell walls with an even greater level of Glc.

Tentacle Probes: differentiation of difficult single-nucleotide polymorphisms and deletions by presence or absence of a signal in real-time PCR

BACKGROUND

False-positive results are a common problem in real-time PCR identification of DNA sequences that differ from near neighbors by a single-nucleotide polymorphism (SNP) or deletion. Because of a lack of sufficient probe specificity, post-PCR analysis, such as a melting curve, is often required for mutation differentiation.

METHODS

Tentacle Probes, cooperative reagents with both a capture and a detection probe based on specific cell-targeting principles, were developed as a replacement for 2 chromosomal TaqMan-minor groove binder (MGB) assays previously developed for Yersinia pestis and Bacillus anthracis detection. We compared TaqMan-MGB probes to Tentacle Probes for SNP and deletion detection based on the presence or absence of a growth curve.

RESULTS

With the TaqMan-MGB Y. pestis yp48 assays, false-positive results for Yersinia pseudotuberculosis occurred at every concentration tested, and with the TaqMan-MGB B. anthracis gyrA assays, false-positive results occurred in 21 of 29 boil preps of environmental samples of near neighbors. With Tentacle Probes no false-positive results occurred.

CONCLUSIONS

The high specificity exhibited by Tentacle Probes may eliminate melting curve analysis for SNP and deletion mutation detection, allowing the diagnostic use of previously difficult targets.

Genetic distribution of 295 Bacillus cereus group members based on adk-screening in combination with MLST (Multilocus Sequence Typing) used for validating a primer targeting a chromosomal locus in B. anthracis

The genetic distribution of 295 Bacillus cereus group members has been investigated by using a modified Multilocus Sequence Typing method (MLST). By comparing the nucleic acid sequence of the adk gene fragment, isolates of B. cereus group members most related to B. anthracis may be easily identified. The genetic distribution, with focus on the B. anthracis close neighbours, was used to evaluate a new primer set for specific identification of B. anthracis. This primer set, BA5510-1/2, targeted the putative B. anthracis specific gene BA5510. Real-time PCR using BA5510-1/2 amplified the target fragment from all B. anthracis strains tested and only two (of 289) non-B. anthracis strains analysed. This is one of the most thoroughly validated chromosomal B. anthracis markers for real-time PCR identification, in which the screened collection contained several very closely related B. anthracis strains.

Species-level identification of Bacillus strains isolates from marine sediments by conventional biochemical, 16S rRNA gene sequencing and inter-tRNA gene sequence lengths analysis

The aim of this study was to compare the ability of commonly used conventional biochemical tests, sequencing analysis of 16S rRNA genes and tDNA-intergenic spacer length polymorphism (tDNA-PCR) to identify species of the genus Bacillus recovered from marine sediments. While biochemical tests were not sufficiently sensitive to distinguish between the 23 marine strains analyzed, partial 16S rRNA gene sequences allowed a correct identification, clustering them into four species belonging to Bacillus licheniformis (n = 6), Bacillus cereus (n = 9), Bacillus subtilis (n = 7) and Bacillus pumilus (n = 1). The identification results obtained with 16S rRNA sequencing were validated by tDNA-PCR analysis of 23 marine isolates that were identified by the similarities of their fingerprints to those of reference strains. tDNA-PCR fingerprinting was as discriminatory as 16S rRNA sequencing analysis. Although it was not able to distinguish among the species of the B. cereus and B. subtilis groups, it should be considered a rapid and easy approach for the reliable identification of unknown Bacillus isolates or at least for the primary differentiation of Bacillus groups.

Bacillus cereus strains fall into two clusters (one closely and one more distantly related) to Bacillus anthracis according to amino acid substitutions in small acid-soluble proteins as determined by tandem mass spectrometry

Small acid-soluble proteins (SASPs) are located in the core region of Bacillus spores and have been previously demonstrated as reliable biomarkers for differentiating Bacillus anthracis and Bacillus cereus. Using MS and MS-MS analysis of SASPs further phylogenetic correlations among B. anthracis and B. cereus strains are described here. ESI was demonstrated to be a more comprehensive method, allowing for the analysis of intact proteins in both MS and MS-MS mode, thus providing molecular weight (MW) and sequence information in a single analysis, and requiring almost no sample preparation. MALDI MS was used for determination of MW of intact proteins; however, MS-MS analysis can only be achieved after enzymatic digestion of these proteins. It was demonstrated that the combination of the two different approaches provides confirmatory and complementary information, allowing for unambiguous protein characterization and sequencing. This study established that B. cereus strains fall into two clusters (one closely and one more distantly related) to B. anthracis as exhibited by amino acid substitutions. The closely related cluster was characterized by a beta-SASP with a single amino acid substitution, localized either close to the C terminus (phenylalanine-->tyrosine, 16 masses change) or close to the N terminus (serine-->alanine serine, also 16 masses change). The more distantly related cluster displayed both amino acid substitutions (32 masses change). One strain of B. cereus isolated from a patient with severe pneumonia (an anthrax-like disease) fell into the more distantly related cluster implying that pathogenicity and phylogenicity are not necessarily correlated features. Unlike PCR and DNA sequencing, protein sequence variation assessed by ESI MS-MS, essentially occurs in real-time, and involves simply extracting the protein and injecting into the instrument for analysis.

Genetic diversity in a Bacillus anthracis historical collection (1954 to 1988)

Bacillus anthracis, the etiologic agent of anthrax, has been widely described as a genetically monomorphic species. We used both multiple-locus variable-number tandem-repeat analysis (MLVA) and pagA gene sequencing to determine the genetic diversity of a historical collection of B. anthracis isolates collected from the 1950s to the 1980s from various geographic locations and sources. We sequenced the pagA gene of 124 diverse B. anthracis isolates and found all previously identified B. anthracis pagA types except type 4. Sixty-three of the 124 B. anthracis strains were identified as pagA type 6, while 44 were pagA type 5, 12 were pagA type 1, and individual isolates were identified for types 2 and 3, respectively. Two new pagA genotypes were discovered in three environmental isolates within the historical collection. Two isolates had the same new genotype, and an additional isolate produced a second new genotype. MLVA detected 22 previously described genotypes in the historical collection. In addition, 33 new MLVA genotypes were found. For 11 isolates, an MLVA genotype could not be assigned because one or more alleles did not amplify. While only two additional B. anthracis pagA types were identified, in two instances, the use of pagA sequencing discriminated isolates with the same MLVA genotype. MLVA revealed that 39 of the 124 isolates were previously undocumented genotypes and that 1 isolate was found to be in the C cluster when it was subtyped by MLVA.

The complete genome sequence of Bacillus thuringiensis Al Hakam

Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen, Appl. Environ. Microbiol. 69:2755-2764, 2003).

Fatal pneumonia among metalworkers due to inhalation exposure to Bacillus cereus Containing Bacillus anthracis toxin genes

Bacillus cereus pneumonia is unusual in nonimmunocompromised hosts. We describe fatal cases in 2 metalworkers and the associated investigation. Anthrax toxin genes were identified in B. cereus isolates from both patients using polymerase chain reaction. Finding anthrax toxin genes in non-Bacillus anthracis isolates has, to our knowledge, only been reported once previously.

Capsule production in Bacillus cereus strains associated with severe pneumonia

We identified three encapsulated Bacillus cereus strains, isolated from patients with severe pneumonia, in a collection of B. cereus isolates associated with human illness. We found that the extent of capsule expression was influenced by culturing conditions. Our findings highlight consequent clinical and laboratory diagnostic challenges posed by such isolates.