Eco-genetic structure of Bacillus cereus sensu lato populations from different environments in northeastern Poland

Insight into the phylogeny and antibiotic resistance of Pseudomonas spp. originating from soil of the Białowieża National Park in Northeastern Poland

The Pseudomonas genus includes species present in various environments and known for antibiotic resistance. However, only hospital-associated Pseudomonas aeruginosa have been extensively studied regarding antibiotic resistance. Thus, to fill the gap in knowledge on antibiotic resistance among other Pseudomonas spp., we investigated 41 isolates from soil samples taken in the Białowieża National Park in Northeastern Poland. This unique forest without notable anthropogenic influence, provides excellent conditions for research of antibiotic resistance from the perspective of natural environments. The phylogeny trees obtained based on the nucleotide sequence of the 16S rRNA gene and gyrB gene grouped the isolates into clusters belonging to the Pseudomonas fluorescens, Pseudomonas koreensis, and Pseudomonas putida groups, originating from the P. fluorescens lineage. All isolates under study demonstrated resistance to at least 12 out of the 24 antibiotics tested. Resistance to colistin, cefotaxime, and imipenem was detected in 73, 73, and 17% of the isolates, respectively. Most isolates showing resistance to imipenem and colistin clustered within the P. fluorescens group. Seven isolates were highly multi-resistant, to up to 18 of the 24 antibiotics tested. The presence of resistance genes related to intrinsic resistance of P. aeruginosa has been confirmed in environmental isolates.

Organic vs. Conventional Milk: Uncovering the Link to Antibiotic Resistance in Bacillus cereus sensu lato

Bacillus cereus sensu lato (B. cereus s.l.) comprises mesophilic and psychrotolerant bacteria commonly found in natural environments as well as in organic and conventional milk. Due to their potential toxigenicity and antibiotic resistance, these bacteria pose a significant threat to consumer health. Organic milk production, which prohibits the use of antibiotics and artificial additives, may influence the composition of microbiota between milk types. This study aimed to compare the antibiotic resistance profiles and enterotoxic potential of B. cereus s.l. isolates from organic and conventional milk. The results indicate that, although conventional milk contains on average 3 times fewer B. cereus s.l. isolates, it has 10-15% more resistant isolates to selected beta-lactams, macrolides, and aminoglycosides. Regarding drug resistance, 21% of B. cereus s.l. isolates were multidrug-resistant, and as many as 42% were non-susceptible to two classes of antibiotics. Even among the sensitive isolates, bacteria from conventional milk exhibited on average 2.05 times higher MICs (minimal inhibitory concentrations) for beta-lactams, 1.49 times higher for erythromycin, 1.38 times higher for vancomycin, and 1.38 times higher for azithromycin. Antibiotic resistance was mostly associated with the origin of the isolates. These findings underscore the need for ongoing monitoring of antibiotic resistance and enterotoxicity among opportunistic B. cereus s.l. strains, which may pose challenges for public health and veterinary medicine. The results highlight that selective pressure associated with antibiotic use can drive resistance development in bacteria that are not the primary targets of antimicrobial therapy.

Evaluating the Safety of Bacillus cereus GW-01 Obtained from Sheep Rumen Chyme

Bacillus cereus is responsible for 1.4-12% food poisoning outbreaks worldwide. The safety concerns associated with the applications of B. cereus in health and medicine have been controversial due to its dual role as a pathogen for foodborne diseases and a probiotic in humans and animals. In this study, the pathogenicity of B. cereus GW-01 was assessed by comparative genomic, and transcriptome analysis. Phylogenetic analysis based on a single-copy gene showed clustering of the strain GW-01, and 54 B. cereus strains from the NCBI were classified into six major groups (I-VI), which were then associated with the source region and sequence types (STs). Transcriptome results indicated that the expression of most genes related with toxins secretion in GW-01 was downregulated compared to that in the lag phase. Overall, these findings suggest that GW-01 is not directly associated with pathogenic Bacillus cereus and highlight an insightful strategy for assessing the safety of novel B. cereus strains.

Pan-Genome Portrait of Bacillus mycoides Provides Insights into the Species Ecology and Evolution

Bacillus mycoides is poorly known despite its frequent occurrence in a wide variety of environments. To provide direct insight into its ecology and evolutionary history, a comparative investigation of the species pan-genome and the functional gene categorization of 35 isolates obtained from soil samples from northeastern Poland was performed. The pan-genome of these isolates is composed of 20,175 genes and is characterized by a strong predominance of adaptive genes (∼83%), a significant amount of plasmid genes (∼37%), and a great contribution of prophages and insertion sequences. The pan-genome structure and phylodynamic studies had suggested a wide genomic diversity among the isolates, but no correlation between lineages and the bacillus origin was found. Nevertheless, the two B. mycoides populations, one from Białowieża National Park, the last European natural primeval forest with soil classified as organic, and the second from mineral soil samples taken in a farm in Jasienówka, a place with strong anthropogenic pressure, differ significantly in the frequency of genes encoding proteins enabling bacillus adaptation to specific stress conditions and production of a set of compounds, thus facilitating their colonization of various ecological niches. Furthermore, differences in the prevalence of essential stress sigma factors might be an important trail of this process. Due to these numerous adaptive genes, B. mycoides is able to quickly adapt to changing environmental conditions.

IMPORTANCE This research allows deeper understanding of the genetic organization of natural bacterial populations, specifically, Bacillus mycoides, a psychrotrophic member of the Bacillus cereus group that is widely distributed worldwide, especially in areas with continental cold climates. These thorough analyses made it possible to describe, for the first time, the B. mycoides pan-genome, phylogenetic relationship within this species, and the mechanisms behind the species ecology and evolutionary history. Our study indicates a set of functional properties and adaptive genes, in particular, those encoding sigma factors, associated with B. mycoides acclimatization to specific ecological niches and changing environmental conditions.

Divergence in environmental adaptation between terrestrial clades of the Bacillus cereus group

The Bacillus cereus group encompasses beneficial and harmful species in diverse niches and has a much debated taxonomy. Investigating whether selection has led to ecological divergence between phylogenetic clades can help understand the basis of speciation, and has implications for predicting biological safety across this group. Using three most terrestrial species in this group (B. cereus, Bacillus thuringiensis and Bacillus mycoides) we charactererized ecological specialization in terms of resource use, thermal adaptation and fitness in different environmental conditions and tested whether taxonomic species or phylogenetic clade best explained phenotypic variation. All isolates grew vigorously in protein rich media and insect cadavers, but exploitation of soil or plant derived nutrients was similarly weak for all. For B. thuringiensis and B. mycoides, clade and taxonomic species were important predictors of relative fitness in insect infections. Fully psychrotolerant isolates could outcompete B. thuringiensis in insects at low temperature, although psychrotolerance predicted growth in artificial media better than clade. In contrast to predictions, isolates in the Bacillus anthracis clade had sub-optimal growth at 37°C. The common ecological niche in these terrestrial B. cereus species is the ability to exploit protein rich resources such as cadavers. However, selection has led to different phylogenetic groups developing different strategies for accessing this resource. Thus, clades, as well as traditional taxonomic phenotypes, predict biologically important traits.

Identification and Characterization of 33 Bacillus cereus sensu lato Isolates from Agricultural Fields from Eleven Widely Distributed Countries by Whole Genome Sequencing

The phylogeny, identification, and characterization of 33 B. cereus sensu lato isolates originating from 17 agricultural soils from 11 countries were analyzed on the basis of whole genome sequencing. Phylogenetic analyses revealed all isolates are divided into six groups, which follows the generally accepted phylogenetic division of B. cereus sensu lato isolates. Four different identification methods resulted in a variation in the identity of the isolates, as none of the isolates were identified as the same species by all four methods—only the recent identification method proposed directly reflected the phylogeny of the isolates. This points to the importance of describing the basis and method used for the identification. The presence and percent identity of the protein product of 19 genes potentially involved in pathogenicity divided the 33 isolates into groups corresponding to phylogenetic division of the isolates. This suggests that different pathotypes exist and that it is possible to differentiate between them by comparing the percent identity of proteins potentially involved in pathogenicity. This also reveals that a basic link between phylogeny and pathogenicity is likely to exist. The geographical distribution of the isolates is not random: they are distributed in relation to their division into the six phylogenetic groups, which again relates to different ecotypes with different temperature growth ranges. This means that we find it easier to analyze and understand the results obtained from the 33 B. cereus sensu lato isolates in a phylogenetic, patho-type and ecotype-oriented context, than in a context based on uncertain identification at the species level.

Comparison of the antibiotic resistance between genetically diverse and toxigenic Bacillus cereus sensu lato from milk, pepper and natural habitats

AIMS

Bacillus cereus sensu lato is a complex group of closely related bacteria, which are commonly present in the natural environment and food products. These organisms may cause food poisoning and spoilage as well as opportunistic infections. Thus far, their resistance to selected antibiotics has been explored only in part, especially in the context of strain source. Therefore, our goal was to compare the resistance of B. cereus sl from milk (environment with the potential impact of antibiotics) with strains from soil and pepper (environment without contact with antibiotics) in relation to their origin, toxicity and phylogenetic relationships.

METHODS AND RESULTS

Antibiotic resistance of B. cereus sl was assessed by determining their minimal inhibitory concentrations (MICs) followed by statistical analyses. The phylogeny of the bacteria was investigated by multilocus sequence typing, and toxicity was determined with quantitative reverse-transcription real-time PCR. We found that the isolates from milk were more often multiresistant and exhibited a common resistance pattern to β-lactams but a varied sensitivity to the tested macrolides, clindamycin, tetracycline and vancomycin. Moreover they displayed often significantly higher average MICs; however, their resistance did not correlate with phylogeny, toxicity, or in most cases, with taxonomic affiliation.

CONCLUSION

We conclude that mainly food matrices may serve as an important reservoir of resistant isolates of B. cereus sl and that the use of antibiotics for the treatment of animal diseases must be carefully monitored as it strongly promotes natural selection for multiresistant strains, even among opportunist pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

The fact that compared to the isolates from natural habitats, nonpathogenic B. cereus sl isolated from food acquire antibiotic resistance faster, should increase producers and consumers awareness and result in protection of public health.

Potential Enterotoxicity of Phylogenetically Diverse Bacillus cereus Sensu Lato Soil Isolates from Different Geographical Locations

Bacillus cereus sensu lato comprises Gram-positive spore-forming bacteria producing toxins associated with foodborne diseases. Three pore-forming enterotoxins, nonhemolytic enterotoxin (Nhe), hemolysin BL (Hbl), and cytotoxin K (CytK), are considered the primary factors in B. cereus sensu lato diarrhea. The aim of this study was to determine the potential risk of enterotoxicity among soil B. cereus sensu lato isolates representing diverse phylogroups and originated from different geographic locations with various climates (Burkina Faso, Kenya, Argentina, Kazakhstan, and Poland). While nheA- and hblA-positive isolates were present among all B. cereus sensu lato populations and distributed across all phylogenetic groups, cytK-2-positive strains predominated in geographic regions with an arid hot climate (Africa) and clustered together on a phylogenetic tree mainly within mesophilic groups III and IV. The highest in vitro cytotoxicity to Caco-2 and HeLa cells was demonstrated by the strains clustered within phylogroups II and IV. Overall, our results suggest that B. cereus sensu lato pathogenicity is a comprehensive process conditioned by many intracellular factors and diverse environmental conditions.IMPORTANCE This research offers a new route for a wider understanding of the dependency between pathogenicity and phylogeny of a natural bacterial population, specifically within Bacillus cereus sensu lato, that is widely distributed around the world and easily transferred into food products. Our study indicates differences in the phylogenetic and geographical distributions of potential enterotoxigenic B. cereus sensu lato strains. Hence, these bacilli possess a risk for human health, and rapid testing methods for their identification are greatly needed. In particular, the detection of the CytK enterotoxin should be a supporting strategy for the identification of pathogenic B. cereus sensu lato.

A Study on Prevalence and Characterization of Bacillus cereus in Ready-to-Eat Foods in China

Bacillus cereus is widely distributed in different food products and can cause a variety of symptoms associated with food poisoning. Since ready-to-eat (RTE) foods are not commonly sterilized by heat treatment before consumption, B. cereus contamination may cause severe food safety problems. In this study, we investigated the prevalence of B. cereus in RTE food samples from different regions of China and evaluated the levels of bacterial contamination, antibiotic resistance, virulence gene distribution, and genetic polymorphisms of these isolates. Of the tested retail RTE foods, 35% were positive for B. cereus, with 39 and 83% of the isolated strains harboring the enterotoxin-encoding hblACD and nheABC gene clusters, respectively. The entFM gene was detected in all B. cereus strains. The cytK gene was present in 68% of isolates, but only 7% harbored the emetic toxin-encoding gene cesB. Antimicrobial susceptibility testing revealed that the majority of the isolates were resistant not only to most β-lactam antibiotics, but also to rifamycin. Multilocus sequence typing (MLST) revealed that the 368 isolates belonged to 192 different sequence types (STs) including 93 new STs, the most prevalent of which was ST26. Collectively, our study indicates the prevalence, bacterial contamination levels, and biological characteristics of B. cereus isolated from RTE foods in China and demonstrates the potential hazards of B. cereus in RTE foods.

Typing and evaluating heat resistance of Bacillus cereus sensu stricto isolated from the processing environment of powdered infant formula

Bacillus cereus sensu lato is one of the most harmful bacterial groups affecting the quality and safety of powdered infant formula (PIF). In this study, samples were collected from the raw materials and processing environments of PIF. A total of 84 isolates were identified as Bacillus cereus sensu stricto (B. cereus s. s.) by 16S rRNA analysis, molecular typing technology, and physiological and biochemical tests. The 84 B. cereus s. s. strains were assigned to panC group II, group III, and group IV. Then, the 7 housekeeping genes glpF, gmk, ilvD, pta, pur, pycA, and tpi were selected for multilocus sequence typing. Results showed that the 84 isolates were clustered into 24 sequence types (ST), and 14 novel ST were detected. Among the 24 ST, ST999 (19/84, 22.62%) and ST1343 (13/84, 15.48%) predominated. The correlation between processing areas and ST showed that the processing environments of the production and packing areas were the most susceptible to contamination by B. cereus s. s. Spores of these ST showed different heat resistance phenotypes evaluated by the analysis of D_T (time in minutes of spore decimal reduction at each temperature) and Z values (temperature increase required to reduce the D_T value to one-tenth of the original). Spores from group III according to panC gene analysis were the most heat resistant. These findings will help us to better understand B. cereus s. s. contamination and control in PIF processing environments.

Whole-genome comparative analysis of Campylobacter jejuni strains isolated from patients with diarrhea in northeastern Poland

BACKGROUND

Campylobacter jejuni is the leading cause of bacterial gastroenteritis (campylobacteriosis) in humans worldwide, and the most frequent pathogen associated with Guillain-Barré syndrome (GBS) and Miller-Fisher syndrome (MFS). The study was designed in order to assess similarities between genomes of Campylobacter jejuni strains, isolated from children suffering from acute diarrhea in northeastern Poland, in comparison to C. jejuni genomes stored in public databases. The analysis involved phylogeny, resistome and virulome. In addition, the Campylobacter PubMLST database was used to estimate the prevalence of the analyzed C. jejuni sequence type (STs) in other countries.

RESULTS

Campylobacter jejuni ST50, ST257 and ST51 represented 5.3%, 4.5% and 2.2% of the PubMLST records, respectively. Overall, strains representing the STs showed common resistance to tetracyclines (51.3%) and fluoroquinolones (31.8%), mediated through the tetO gene (98.2%) and point mutation (T86I) in the gyrA gene (100%). However, the latter was present in all our isolates. The major differences in virulence patterns concerned serotypes, lipooligosaccharide (LOS) classes and certain clinically relevant genes.

CONCLUSIONS

Campylobacter jejuni ST50, ST51 and ST257 are among the top ten of STs isolated in Europe. WGS revealed diversity of serotypes and LOS classes in ST50 strains, that deserves further clinical and epidemiological investigations as it might be related to a risk of post-infectious neurological sequels such as Guillain-Barré syndrome. Additionally, the results implicate lower pathogenic potential and distinct transmission chains or reservoirs for C. jejuni ST51 isolates responsible for campylobacteriosis in northeastern Poland.

Differentiation of Bacillus thuringiensis From Bacillus cereus Group Using a Unique Marker Based on Real-Time PCR

The efficiency of a novel biomarker (the transcriptional regulator, XRE) was tested and evaluated in differentiating Bacillus thuringiensis from Bacillus cereus group species in environmental and spiked samples based on PCR and real-time PCR. Totally 120 strains, representing two bacterial groups, B. cereus group and non-Bacillus sp., were used to evaluate the performance of XRE and crystal protein (cry2, an existing biomarker). Further, three diverse samples (kimbap, lettuce, and spinach) were inoculated with B. thuringiensis and prominent biomarkers XRE and cry2 were used as targets. Direct analysis of the detection results for the pure cultures of B. cereus group wild-types, references and type strains revealed an accuracy rate of 97.5% targeting XRE, and 83.3% targeting cry2. The real-time PCR was constructed with a R ²-value of 0.993. For the artificially contaminated samples, a concentration of 10³ CFU/g of B. thuringiensis in spiked food samples could be detected using real-time PCR targeting XRE. A good performance was obtained with XRE in discriminating B. thuringiensis from B. cereus groups, as well as detecting B. thuringiensis in spiked food samples with PCR or real-time PCR. Therefore, this real-time PCR targeting XRE can be used as a dependable and promising tool to identify B. thuringiensis in foods.

Systematic characterization of Bacillus Genetic Stock Center Bacillus thuringiensis strains using Multi-Locus Sequence Typing

The goal of this work was to perform a systematic characterization of Bacillus thuringiensis (Bt) strains from the Bacillus Genetic Stock Center (BGSC) collection using Multi-Locus Sequence Typing (MLST). Different genetic markers of 158 Bacillus thuringiensis (Bt) strains from 73 different serovars stored in the BGSC, that represented 92% of the different Bt serovars of the BGSC were analyzed, the 8% that were not analyzed were not available. In addition, we analyzed 72 Bt strains from 18 serovars available at the pubMLST bcereus database, and Bt strains G03, HBF18 and Bt185, with no H serovars provided by our laboratory. We performed a systematic MLST analysis using seven housekeeping genes (glpF, gmK, ilvD, pta, pur, pycA and tpi) and analyzed correlation of the results of this analysis with strain serovars. The 233 Bt strains analyzed were assigned to 119 STs from which 19 STs were new. Genetic relationships were established by phylogenetic analysis and showed that STs could be grouped in two major Clusters containing 21 sub-groups. We found that a significant number of STs (101 in total) correlated with specific serovars, such as ST13 that corresponded to nine Bt isolates from B. thuringiensis serovar kenyae. However, other serovars showed high genetic variability and correlated with multiple STs; for example, B. thuringiensis serovar morrisoni correlated with 11 different STs. In addition, we found that 16 different STs correlated with multiple serovars (2-4 different serovars); for example, ST12 correlated with B. thuringiensis serovar alesti, dakota, palmanyolensis and sotto/dendrolimus. These data indicated that only partial correspondence between MLST and serotyping can be established.

Spores and vegetative cells of phenotypically and genetically diverse Bacillus cereus sensu lato are common bacteria in fresh water of northeastern Poland

Gram-positive rods Bacillus cereus sensu lato (sl) are common in natural habitats and food products. It is believed that they are restricted to spores; however, their ecology in aquatic habitats is still poorly investigated. Thus, the aim of the study was to assess the rain-dependent fluctuations in the concentration of B. cereus sl vegetative cells and spores, with evaluation of their phylogenetic and population structure in relation to the toxicity and psychrotolerance. We proved that vegetative cells of B. cereus sl are widely distributed in fresh water of rivers and lakes, being as common as spores. Moreover, heavy rain has a huge impact on their concentration in undisturbed environments. The diversity of B. cereus sl reflects the multiple sources of bacteria and the differences between their distinct environments. Next, their diverse genetic structure and phenotypes better fit their ecological properties than their taxonomic affiliation.

Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data

The Bacillus cereus group comprises nine species, several of which are pathogenic. Differentiating between isolates that may cause disease and those that do not is a matter of public health and economic importance, but it can be particularly challenging due to the high genomic similarity within the group. To this end, we have developed BTyper, a computational tool that employs a combination of (i) virulence gene-based typing, (ii) multilocus sequence typing (MLST), (iii) panC clade typing, and (iv) rpoB allelic typing to rapidly classify B. cereus group isolates using nucleotide sequencing data. BTyper was applied to a set of 662 B. cereus group genome assemblies to (i) identify anthrax-associated genes in non-B. anthracis members of the B. cereus group, and (ii) identify assemblies from B. cereus group strains with emetic potential. With BTyper, the anthrax toxin genes cya, lef, and pagA were detected in 8 genomes classified by the NCBI as B. cereus that clustered into two distinct groups using k-medoids clustering, while either the B. anthracis poly-γ-d-glutamate capsule biosynthesis genes capABCDE or the hyaluronic acid capsule hasA gene was detected in an additional 16 assemblies classified as either B. cereus or Bacillus thuringiensis isolated from clinical, environmental, and food sources. The emetic toxin genes cesABCD were detected in 24 assemblies belonging to panC clades III and VI that had been isolated from food, clinical, and environmental settings. The command line version of BTyper is available at https://github.com/lmc297/BTyper. In addition, BMiner, a companion application for analyzing multiple BTyper output files in aggregate, can be found at https://github.com/lmc297/BMiner.

IMPORTANCEBacillus cereus is a foodborne pathogen that is estimated to cause tens of thousands of illnesses each year in the United States alone. Even with molecular methods, it can be difficult to distinguish nonpathogenic B. cereus group isolates from their pathogenic counterparts, including the human pathogen Bacillus anthracis, which is responsible for anthrax, as well as the insect pathogen B. thuringiensis. By using the variety of typing schemes employed by BTyper, users can rapidly classify, characterize, and assess the virulence potential of any isolate using its nucleotide sequencing data.

Pan-genome and phylogeny of Bacillus cereus sensu lato

BACKGROUND

Bacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes and novel bioinformatic workflows to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i.e., "pan-GWAS" analysis), and quantify the degree to which taxa sharing common attributes are phylogenetically clustered.

METHODS

A rapid k-mer based approach (Mash) was used to create reduced representations of selected Bacillus genomes, and a fast distance-based phylogenetic analysis of this data (FastME) was performed to determine which species should be included in B. cereus s. l. The complete genomes of eight B. cereus s. l. species were annotated de novo with Prokka, and these annotations were used by Roary to produce the B. cereus s. l. pan-genome. Scoary was used to associate gene presence and absence patterns with various phenotypes. The orthologous protein sequence clusters produced by Roary were filtered and used to build HaMStR databases of gene models that were used in turn to construct phylogenetic data matrices. Phylogenetic analyses used RAxML, DendroPy, ClonalFrameML, PAUP*, and SplitsTree. Bayesian model-based population genetic analysis assigned taxa to clusters using hierBAPS. The genealogical sorting index was used to quantify the phylogenetic clustering of taxa sharing common attributes.

RESULTS

The B. cereus s. l. pan-genome currently consists of ≈60,000 genes, ≈600 of which are "core" (common to at least 99% of taxa sampled). Pan-GWAS analysis revealed genes associated with phenotypes such as isolation source, oxygen requirement, and ability to cause diseases such as anthrax or food poisoning. Extensive phylogenetic analyses using an unprecedented amount of data produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering.

CONCLUSIONS

All phylogenetic analyses recapitulated two previously used classification systems, and taxa were consistently assigned to the same major clade and group. By including accessory genes from the pan-genome in the phylogenetic analyses, I produced an exceptionally well-supported phylogeny of 114 complete B. cereus s. l. genomes. The best-performing methods were used to produce a phylogeny of all 498 publicly available B. cereus s. l. genomes, which was in turn used to compare three different classification systems and to test the monophyly status of various B. cereus s. l. species. The majority of the methodology used in this study is generic and could be leveraged to produce pan-genome estimates and similarly robust phylogenetic hypotheses for other bacterial groups.

Ribosomal background of the Bacillus cereus group thermotypes

In this study we reconstructed the architecture of Bacillus cereus sensu lato population based on ribosomal proteins, and identified a link between the ribosomal proteins’ variants and thermal groups (thermotypes) of the bacilli. The in silico phyloproteomic analysis of 55 ribosomal proteins (34 large and 21 small subunit r-proteins) of 421 strains, representing 14 well-established or plausible B. cereus sensu lato species, revealed several ribosomal clusters (r-clusters), which in general were well correlated with the strains’ affiliation to phylogenetic/thermal groups I–VII. However, a conformity and possibly a thermal characteristic of certain phylogenetic groups, e.g. the group IV, were not supported by a distribution of the corresponding r-clusters, and consequently neither by the analysis of cold-shock proteins (CSPs) nor by a content of heat shock proteins (HSPs). Furthermore, a preference for isoleucine and serine over valine and alanine in r-proteins along with a lack of HSP16.4 were recognized in non-mesophilic thermotypes. In conclusion, we suggest that the observed divergence in ribosomal proteins may be connected with an adaptation of B. cereus sensu lato members to various thermal niches.

Production of hemolysin BL by Bacillus cereus group isolates of dairy origin is associated with whole-genome phylogenetic clade

BACKGROUND

Bacillus cereus group isolates that produce diarrheal or emetic toxins are frequently isolated from raw milk and, in spore form, can survive pasteurization. Several species within the B. cereus group are closely related and cannot be reliably differentiated by established taxonomical criteria. While B. cereus is traditionally recognized as the principal causative agent of foodborne disease in this group, there is a need to better understand the distribution and expression of different toxin and virulence genes among B. cereus group food isolates to facilitate reliable characterization that allows for assessment of the likelihood of a given isolate to cause a foodborne disease.

RESULTS

We performed whole genome sequencing of 22 B. cereus group dairy isolates, which represented considerable genetic diversity not covered by other isolates characterized to date. Maximum likelihood analysis of these genomes along with 47 reference genomes representing eight validly published species revealed nine phylogenetic clades. Three of these clades were represented by a single species (B. toyonensis -clade V, B. weihenstephanensis - clade VI, B. cytotoxicus - VII), one by two dairy-associated isolates (clade II; representing a putative new species), one by two species (B. mycoides, B. pseudomycoides - clade I) and four by three species (B. cereus, B. thuringiensis, B. anthracis - clades III-a, b, c and IV). Homologues of genes encoding a principal diarrheal enterotoxin (hemolysin BL) were distributed across all, except the B. cytotoxicus clade. Using a lateral flow immunoassay, hemolysin BL was detected in 13 out of 18 isolates that carried hblACD genes. Isolates from clade III-c (which included B. cereus and B. thuringiensis) consistently did not carry hblACD and did not produce hemolysin BL. Isolates from clade IV (B. cereus, B. thuringiensis) consistently carried hblACD and produced hemolysin BL. Compared to others, clade IV was significantly (p = 0.0001) more likely to produce this toxin. Isolates from clade VI (B. weihenstephanensis) carried hblACD homologues, but did not produce hemolysin BL, possibly due to amino acid substitutions in different toxin-encoding genes.

CONCLUSIONS

Our results demonstrate that production of diarrheal enterotoxin hemolysin BL is neither inclusive nor exclusive to B. cereus sensu stricto, and that phylogenetic classification of isolates may be better than taxonomic identification for assessment of B. cereus group isolates risk for causing a diarrheal foodborne disease.

MALDI-TOF MS portrait of emetic and non-emetic Bacillus cereus group members

The number of foodborne intoxications caused by emetic Bacillus cereus isolates has increased significantly. As such, rapid and reliable methods to identify emetic strains appear to be clinically relevant. In this study, intact cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to differentiate emetic and non-emetic bacilli. The phyloproteomic clustering of 34 B. cereus emetic and 88 non-emetic isolates classified as B. cereus, Bacillus thuringiensis, Bacillus weihenstephanensis, and Bacillus mycoides, showed (i) a clear separation of both groups at a similarity level of 43%, and (ii) a high relatedness among the emetic isolates (similarity of 78%). Specifically, 83 mass peak classes were recognized in the spectral window range between m/z 4000 and 12 000 that were tentatively assigned to 41 protein variants based on a bioinformatic approach. Mass variation between the emetic and the non-emetic subsets was recorded for 27 of them, including ten ribosomal subunit proteins, for which inter-strain polymorphism was confirmed by gene sequencing. Additional peaks were assigned to other proteins such as small acid soluble proteins, cold shock proteins and hypothetical proteins, e.g., carbohydrate kinase. Moreover, the results were supported by in silico analysis of the biomarkers in 259 members of B. cereus group, including Bacillus anthracis, based on their whole-genome sequences. In conclusion, the proteomic profiling by MALDI-TOF MS is a promising and rapid method for pre-screening B. cereus to identify medically relevant isolates and for epidemiologic purposes.

The worldwide distribution of genetically and phylogenetically diverse Bacillus cereus isolates harbouring Bacillus anthracis-like plasmids

Bacillus cereus is a close relative of B. anthracis, the causative agent of anthrax whose pathogenic determinants are located on pXO1 and pXO2 plasmids. Bacillus anthracis-like plasmids have been also noted among B. cereus, however, genetic features of B. cereus harbouring these elements remain largely undescribed, especially from the global perspective. Herein, we present the genetic polymorphism, population structure and phylogeny of B. cereus with pXO1-/pXO2-like plasmids originating from Argentina, Kazakhstan, Kenya and Poland. The plasmids were found in about 17% of the isolates, but their frequencies and expression of replicons differed within and between populations. In the multi-locus sequence typing, the bacteria exhibited high genetic polymorphism reflected by 116 sequencing types, including 84 singletons and 10 clonal complexes, which mainly consisted of isolates of the same origin. The phylogenetic analysis of pXO1-/pXO2-like positive B. cereus isolates revealed six independent clades; in certain clades individual populations predominated. Generally, B. cereus with pXO1-/pXO2-like plasmids did not indicate the genetic relationship with B. anthracis, and cannot be classified into an evolutionary independent anthrax line within the B. cereus group. Our report is of a crucial importance for discovering the genetic specificity and evolution of B. cereus bacilli.

Melanin-Like Pigment Synthesis by Soil Bacillus weihenstephanensis Isolates from Northeastern Poland

Although melanin is known for protecting living organisms from harmful physical and chemical factors, its synthesis is rarely observed among endospore-forming Bacillus cereus sensu lato. Here, for the first time, we reported that psychrotolerant Bacillus weihenstephanensis from Northeastern Poland can produce melanin-like pigment. We assessed physicochemical properties of the pigment and the mechanism of its synthesis in relation to B. weihenstephanensis genotypic and phenotypic characteristics. Electron paramagnetic resonance (EPR) spectroscopy displayed a stable free radical signal of the pigment from environmental isolates which are consistent with the commercial melanin. Fourier transform infrared spectroscopy (FT-IR) and physicochemical tests indicated the phenolic character of the pigment. Several biochemical tests showed that melanin-like pigment synthesis by B. weihenstephanensis was associated with laccase activity. The presence of the gene encoding laccase was confirmed by the next generation whole genome sequencing of one B. weihenstephanensis strain. Biochemical (API 20E and 50CHB tests) and genetic (Multi-locus Sequence Typing, 16S rRNA sequencing, and Pulsed-Field Gel Electrophoresis) characterization of the isolates revealed their close relation to the psychrotrophic B. weihenstephanensis DSMZ 11821 reference strain. The ability to synthesize melanin-like pigment by soil B. weihenstephanensis isolates and their psychrotrophic character seemed to be a local adaptation to a specific niche. Detailed genetic and biochemical analyses of melanin-positive environmental B. weihenstephanensis strains shed some light on the evolution and ecological adaptation of these bacteria. Moreover, our study raised new biotechnological possibilities for the use of water-soluble melanin-like pigment naturally produced by B. weihenstephanensis as an alternative to commercial non-soluble pigment.

Crystalliferous Bacillus cereus group bacteria from a Maryland hardwood forest are dominated by psychrotolerant strains

Crystal-forming bacteria of the Bacillus cereus group were isolated from soil samples collected at different elevations within a mixed hardwood forest in central Maryland, and their phylogenetic relationships determined by multilocus sequence analysis. The vast majority of isolates obtained were associated with two phylogenetic groups known to be psychrotolerant, with very few isolates representing phylogenetic groups more typically associated with Bacillus thuringiensis. Isolates from the psychrotolerant groups were found to grow on solid media at 7°C. Isolates of 11 highly related, novel sequence types (STs) from the psychrotolerant group that includes Bacillus weihenstephanensis were generally found at higher elevations, and were not associated with soils near streams. Isolates of two related STs from the second psychrotolerant group were nearly always found at the bottoms of ravines near streams, in areas abundant in earthworm castings.

Comparative analysis of quantitative reverse transcription real-time PCR and commercial enzyme imunoassays for detection of enterotoxigenic Bacillus thuringiensis isolates

Entomopathogenic Bacillus thuringiensis is closely related to Bacillus cereus, a human pathogen known to cause emesis and diarrhea. Standard detection methods do not distinguish these bacilli. Hemolysin BL (hbl) and non-hemolytic enterotoxin (nhe) genes that encode, respectively, HBL and NHE enterotoxins, are known to be harbored in both bacterial species, suggesting that differentiation of these bacilli is clinically and epidemiologically relevant. In this study the reliability of quantitative reverse transcription real-time PCR (qRT-PCR) and enzyme immunoassays (EIAs) in detecting hbl and nhe transcripts and corresponding toxins in environmental B. thuringiensis isolates was assessed. At least one enterotoxin gene was present in each isolate, and nhe or hbl genes were found in 85% and 55% of the strains, respectively. Based on statistical analyses, both BCET-RPLA and Duopath detected HBL at similar levels, and TECRA and Duopath can be used interchangeably for the detection of NHE, although TECRA has significantly lower sensitivity than Duopath. Thus, as potential enterotoxic B. thuringiensis strains occur in the natural environment, and EIA results may not correspond with the presence of enterotoxin genes and their expression, we suggest that reliable interpretation will be significantly enhanced by including qRT-PCR to support inferences based on EIAs.