From soil to gut:Bacillus cereusand its food poisoning toxins

Characterization of the Genome Feature and Toxic Capacity of a Bacillus wiedmannii Isolate From the Hydrothermal Field in Okinawa Trough

The Bacillus cereus group is frequently isolated from soil, plants, food, and other environments. In this study, we report the first isolation and characterization of a B. cereus group member, Bacillus wiedmannii SR52, from the hydrothermal field in the Iheya Ridge of Okinawa Trough. SR52 was isolated from the gills of shrimp Alvinocaris longirostris, an invertebrate species found abundantly in the ecosystems of the hydrothermal vents, and is most closely related to B. wiedmannii FSL W8-0169. SR52 is aerobic, motile, and able to form endospores. SR52 can grow in NaCl concentrations up to 9%. SR52 has a circular chromosome of 5,448,361 bp and a plasmid of 137,592 bp, encoding 5,709 and 189 genes, respectively. The chromosome contains 297 putative virulence genes, including those encoding enterotoxins and hemolysins. Fourteen rRNA operons, 107 tRNAs, and 5 sRNAs are present in the chromosome, and 7 tRNAs are present in the plasmid. SR52 possesses 13 genomic islands (GIs), all on the chromosome. Comparing to FSL W8-0169, SR52 exhibits several streaking features in its genome, notably an exceedingly large number of non-coding RNAs and GIs. In vivo studies showed that following intramuscular injection into fish, SR52 was able to disseminate in tissues and cause mortality; when inoculated into mice, SR52 induced acute mortality and disseminated transiently in tissues. In vitro studies showed that SR52 possessed hemolytic activity, and the extracellular product of SR52 exhibited a strong cytotoxic effect. These results provided the first insight into the cytotoxicity and genomic feature of B. wiedmannii from the deep-sea hydrothermal environment.

Advanced Proteomics as a Powerful Tool for Studying Toxins of Human Bacterial Pathogens

Exotoxins contribute to the infectious processes of many bacterial pathogens, mainly by causing host tissue damages. The production of exotoxins varies according to the bacterial species. Recent advances in proteomics revealed that pathogenic bacteria are capable of simultaneously producing more than a dozen exotoxins. Interestingly, these toxins may be subject to post-transcriptional modifications in response to environmental conditions. In this review, we give an outline of different bacterial exotoxins and their mechanism of action. We also report how proteomics contributed to immense progress in the study of toxinogenic potential of pathogenic bacteria over the last two decades.

Bacillus strains as human probiotics: characterization, safety, microbiome, and probiotic carrier

Both spore and vegetative forms of Bacillus species have been used as probiotics, and they have high stability to the surrounding atmospheric conditions such as heat, gastric conditions, and moisture. The commercial Bacillus probiotic strains in use are B. cereus, B. clausii, B. coagulans, B. licheniformis, B. polyfermenticus, B. pumilus, and B. subtilis. These strains have antimicrobial, anticancer, antioxidant, and vitamin production properties. However, Bacillus probiotics can also produce toxins and biogenic amines and transfer antibiotic resistance genes; therefore, their safety is a concern. Studies on the microbiome using probiotic Bacillus strains are limited in humans. Most microbiome research has been conducted in chicken, mouse, and pig. Some Bacillus probiotics are used as fermentation starters in plant and soybean and dietary supplement of baking foods as a probiotic carrier. This review summarizes the characterization of Bacillus species as probiotics for human use and their safety, microbiome, and probiotic carrier.

Characterization of LysBC17, a Lytic Endopeptidase from Bacillus cereus

Bacillus cereus, a Gram-positive bacterium, is an agent of food poisoning. B. cereus is closely related to Bacillus anthracis, a deadly pathogen for humans, and Bacillus thuringenesis, an insect pathogen. Due to the growing prevalence of antibiotic resistance in bacteria, alternative antimicrobials are needed. One such alternative is peptidoglycan hydrolase enzymes, which can lyse Gram-positive bacteria when exposed externally. A bioinformatic search for bacteriolytic enzymes led to the discovery of a gene encoding an endolysin-like endopeptidase, LysBC17, which was then cloned from the genome of B. cereus strain Bc17. This gene is also present in the B. cereus ATCC 14579 genome. The gene for LysBC17 encodes a protein of 281 amino acids. Recombinant LysBC17 was expressed and purified from E. coli. Optimal lytic activity against B. cereus occurred between pH 7.0 and 8.0, and in the absence of NaCl. The LysBC17 enzyme had lytic activity against strains of B. cereus, B. anthracis, and other Bacillus species.

An outbreak of Bacillus cereus toxin-mediated emetic and diarrhoeal syndromes at a restaurant in Canberra, Australia 2018

A cluster of gastrointestinal illness was detected following receipt of a complaint of becoming ill after a multi-course dinner at a restaurant in Canberra, Australian Capital Territory (ACT), Australia. The complaint led to an investigation by ACT Health. Food samples retained by the restaurant for microbiological analysis returned an unsatisfactory level of Bacillus cereus in beef (19,000 colony forming units/gram [cfu/g]) and a satisfactory level in arancini (50 cfu/g). These positive samples underwent whole genome sequencing and genes encoding diarrhoeal toxins were detected with no laboratory evidence of the emetic toxin. No stool specimens were collected. A cohort study was undertaken and 80% (33/41) of patrons took part in a structured interview. There was no significant difference in age or sex between those ill and not ill. Due to universal exposure most foods were unable to be statistically analysed and no significant results were found from the food history. The ill cohort diverged into two distinct groups based on incubation period and symptoms suggesting this outbreak involved B. cereus intoxication with both diarrhoeal and potentially emetic toxins. Some hygiene practices during food preparation were noted to be inadequate and heating and cooling procedures were unverified when questioned. A combination of the incubation periods and symptom profile, food laboratory evidence, and genomic sequencing of the B. cereus diarrhoeal gene suggest a probable aetiology of B. cereus intoxication. Public health action included the restaurant rectifying hygiene practices and documenting heating/cooling procedures.

Goat Colostrum—Source of Toxigenic Bacillus Cereus

The aim of this study was to evaluate the toxigenic potential of Bacillus cereus strains isolated from frozen goat colostrum. Of the 50 phenotypically suspected B. cereus isolates, 39 (78.0 %) were confirmed as B. cereus by the polymerase chain reaction (PCR) method based on the gyrB gene detection. In these isolates, genes encoding the production of haemolysin BL (Hbl), a complex of non-haemolytic enterotoxins (Nhe) and emetic toxin were detected by the PCR method. In 36 (92.3 %) confirmed B. cereus isolates, genes encoding at least one type of toxins of interest were detected. In all toxigenic isolates, we found the presence of genes for Nhe production, and in 16 (41.0 %) of the isolates, genes encoding both Nhe and haemolysin BL were shown. Eight (20.5 %) of the emetic strains of B. cereus were identified. The emetic toxin production gene was always detected simultaneously with genes encoding non-haemolytic enterotoxin production. The ability to produce BL haemolysin and non-haemolytic enterotoxins were confirmed by the immunochromatographic method. In summary, goat colostrum can be a significant source of toxigenic strains of B. cereus.

Toxigenic potential and antimicrobial susceptibility of Bacillus cereus group bacteria isolated from Tunisian foodstuffs

BACKGROUND

Despite the importance of the B. cereus group as major foodborne pathogens that may cause diarrheal and/or emetic syndrome(s), no study in Tunisia has been conducted in order to characterize the pathogenic potential of the B. cereus group. The aim of this study was to assess the sanitary potential risks of 174 B. cereus group strains isolated from different foodstuffs by detecting and profiling virulence genes (hblA, hblB, hblC, hblD, nheA, nheB, nheC, cytK, bceT and ces), testing the isolates cytotoxic activity on Caco-2 cells and antimicrobial susceptibility towards 11 antibiotics.

RESULTS

The entertoxin genes detected among B. cereus isolates were, in decreasing order, nheA (98.9%), nheC (97.7%) and nheB (86.8%) versus hblC (54.6%), hblD (54.6%), hblA (29.9%) and hblB (14.9%), respectively encoding for Non-hemolytic enterotoxin (NHE) and Hemolysin BL (HBL). The isolates are multi-toxigenic, harbouring at least one gene of each NHE and HBL complexes associated or not to bceT, cytK-2 and ces genes. Based on the incidence of virulence genes, the strains were separated into 12 toxigenic groups. Isolates positive for cytK (37,9%) harbored the cytK-2 variant. The detection rates of bceT and ces genes were 50.6 and 4%, respectively. When bacteria were incubated in BHI-YE at 30 °C for 18 h and for 5 d, 70.7 and 35% of the strains were shown to be cytotoxic to Caco-2 cells, respectively. The cytotoxicity of B. cereus strains depended on the food source of isolation. The presence of virulence factors is not always consistent with cytotoxicity. However, different combinations of enterotoxin genetic determinants are significantly associated to the cytotoxic potential of the bacteria. All strains were fully sensitive to rifampicin, chloramphenicol, ciprofloxacin, and gentamycin. The majority of the isolates were susceptible to streptomycin, kanamycin, erythromycin, vancomycin and tetracycline but showed resistance to ampicillin and novobiocin.

CONCLUSION

Our results contribute data that are primary to facilitate risk assessments in order to prevent food poisoning due to B. cereus group.

Comparative Genomic and Phylogenomic Analyses Clarify Relationships Within and Between Bacillus cereus and Bacillus thuringiensis: Proposal for the Recognition of Two Bacillus thuringiensis Genomovars

The present study was designed to clarify the taxonomic status of two species classified as Bacillus cereus sensu lato, namely B. cereus sensu stricto and Bacillus thuringiensis. To this end, nearly 900 whole genome sequences of strains assigned to these taxa were the subject of comparative genomic and phylogenomic analyses. A phylogenomic tree based on core gene sequences showed that the type strains of B. cereus and B. thuringiensis formed a well-supported monophyletic clade that was clearly separated from corresponding clades composed of the remaining validly published species classified as B. cereus sensu lato. However, since average nucleotide identity and digital DNA-DNA hybridization similarities between the two types of Bacillus were slightly higher than the thresholds used to distinguish between closely related species we conclude that B. cereus and B. thuringiensis should continue to be recognized as validly published species. The B. thuringiensis strains were assigned to two genomically distinct groups, we propose that these taxa be recognized as genomovars, that is, as B. thuringiensis gv. thuringiensis and B. thuringiensis gv. cytolyticus. The extensive comparative genomic data clearly show that the distribution of pesticidal genes is irregular as strains identified as B. thuringiensis were assigned to several polyphyletic groups/subclades within the B. cereus-B. thuringiensis clade. Consequently, we recommend that genomic or equivalent molecular systematic features should be used to identify B. thuringiensis strains as the presence of pesticidal genes cannot be used as a diagnostic marker for this species. Comparative taxonomic studies are needed to find phenotypic properties that can be used to distinguish between the B. thuringiensis genomovars and between them and B. cereus.

Why be serious about emetic Bacillus cereus: Cereulide production and industrial challenges

Cereulide, a potent toxin produced by Bacillus cereus, is a small, highly heat- and acid-resistant depsipeptide toxin, which confronts food industry with several challenges. Due to the ubiquitous presence of B. cereus in the environment, this opportunistic pathogen can enter food production and processing at almost any stage. Although the bacteria itself might be removed during food processing, the cereulide toxin will most likely not be destroyed or inactivated by these processes. Because of the high toxicity of cereulide and the high incidence rates often observed in connection with foodborne outbreaks, the understanding of the mechanisms of toxin production as well as accurate data on contamination sources and factors promoting toxin formation are urgently needed to prevent contamination and toxin production in food production processes. Over the last decade, considerable progress had been made on the understanding of cereulide toxin biosynthesis in emetic B. cereus, but an overview of current knowledge on this toxin with regards to food industry perspective is lacking. Thus, we aim in this work to summarize data available on extrinsic parameters acting on cereulide toxin synthesis in emetic B. cereus and to discuss the food industry specific challenges related to this toxin. Furthermore, we emphasize how identification of the cardinals in food production processes can lead to novel effective strategies for prevention of toxin formation in the food processing chain and could contribute to the improvement of existing HACCP studies.

Assessing the toxic potential of enteropathogenic Bacillus cereus

The diarrheal type of food poisoning caused by enteropathogenic Bacillus cereus has been linked to various exotoxins. Best described are the non-hemolytic enterotoxin (Nhe), hemolysin BL (Hbl), and cytotoxin K (CytK). Due to the ubiquitous prevalence of B. cereus in soil and crops and its ability to form highly resistant endospores, contaminations during food production and processing cannot be completely avoided. Although phylogenetically closely related, enteropathogenic B. cereus strains show a high versatility of their toxic potential. Thus, functional tools for evaluating the pathogenic potential are urgently needed in order to predict hazardous food contaminations. As the diarrheal syndrome is the result of a toxico-infection with enterotoxin production in the intestine, the entire passage of the bacteria within the host, from spore survival in the stomach, spore germination, host cell adherence, and motility, to enterotoxin production under simulated intestinal conditions was compared in a panel of 20 strains, including high pathogenic as well as apathogenic ones. This approach resulted in an overarching virulence analysis scheme. In parallel, we searched for potential toxico-specific secreted markers to discriminate low and high pathogenic strains. To this end, we targeted known exotoxins using an easy to implement immunoblotting approach as well as a caseinolytic exoprotease activity assay. Overall, Nhe component B, sphingomyelinase, and exoproteases showed good correlation with the complex virulence analysis scheme and can serve as a template for future fast and easy risk assessment tools to be implemented in routine diagnostic procedures and HACCP studies.

Prevalence and Diversity of the Thermotolerant Bacterium Bacillus cytotoxicus among Dried Food Products

HIGHLIGHTS

Bacillus cytotoxicus was found in all tested potato flakes but at loads lower than 10² CFU/g. B. cytotoxicus was observed in other potato-containing products and in millet flour. B. cytotoxicus isolates (n = 57) fell into six RAPD patterns and 11 plasmid profiles. A large proportion of B. cytotoxicus isolates contained small and/or large plasmids.

Bacillus cereus cshA Is Expressed during the Lag Phase of Growth and Serves as a Potential Marker of Early Adaptation to Low Temperature and pH

The spore-forming bacterium B. cereus is a major cause of foodborne outbreaks in Europe. Some B. cereus strains can grow at low temperatures and low pH in many processed foods. Modeling of the bacterial lag time is hampered by a lack of knowledge of the timing of events occurring during this phase. In this context, the identification of lag phase markers, not currently available, could be a real advance for the better prediction of lag time duration. Currently, no molecular markers of this phase are available. By determining that cshA was always expressed early during the lag phase, we provide a molecular marker of the early adaptation process of B. cereus cells when exposed to low temperature and pH.

Bacterial adaptation is characterized by a lag phase during which cells do not multiply or modify their physiology to cope with the constraints of their environment. Our aim was to determine a sequence of events during the lag phase of growth at low temperature and pH for three Bacillus cereus strains. The onsets of expression of two genes, one of which is essential for stress adaptation (cshA, coding for a RNA helicase) and one of which is involved in the transition between lag phase and exponential phase (abrB, coding for a transition regulator), were determined using fluorescent transcriptional reporter systems. Regardless of the stressing conditions and the tested strains, the cshA promoter was active very early, while the biomass increased and always did so before the first cell division. At 12°C and pH 7.0, the onset of cshA promoter activity occurred at between 3 h and 7 h, while the bacterial counts started to increase at between 12 h and 13 h. At pH 5.0 and at 20°C or 30°C, the onset of cshA promoter activity occurred before 1 h and earlier than at pH 7.0. In contrast, the onset of abrB promoter activity depended on the strain and the stressing conditions. In the ATCC 14579 strain, the onset of abrB promoter activity always started at between 30 min and 3 h, before biomass increased and cell division occurred. For the other strains, it took place along with the first cell division at 12°C but did so much later during growth under the other tested conditions.

IMPORTANCE The spore-forming bacterium B. cereus is a major cause of foodborne outbreaks in Europe. Some B. cereus strains can grow at low temperatures and low pH in many processed foods. Modeling of the bacterial lag time is hampered by a lack of knowledge of the timing of events occurring during this phase. In this context, the identification of lag phase markers, not currently available, could be a real advance for the better prediction of lag time duration. Currently, no molecular markers of this phase are available. By determining that cshA was always expressed early during the lag phase, we provide a molecular marker of the early adaptation process of B. cereus cells when exposed to low temperature and pH.

Elucidating the Hot Spot Residues of Quorum Sensing Peptidic Autoinducer PapR by Multiple Amino Acid Replacements

The quorum sensing (QS) system of Bacillus cereus, an opportunistic human pathogen, utilizes the autoinducing PapR peptide signal that mediates the activation of the pleiotropic virulence regulator PlcR. A set of synthetic 7-mer PapR-derived peptides (PapR₇; ADLPFEF) have been shown to inhibit efficiently the PlcR regulon activity and the production of virulence factors, reflected by a loss in hemolytic activity without affecting bacterial growth. Interestingly, these first potent synthetic inhibitors involved D-amino acid or alanine replacements of three amino acids; proline, glutamic acid, and phenylalanine of the heptapeptide PapR. To better understand the role of these three positions in PlcR activity, we report herein the second generation design, synthesis, and characterization of PapR₇-derived combinations, alternate double and triple alanine and D-amino acids replacement at these positions. Our findings generate a new set of non-native PapR₇-derived peptides that inhibit the PlcR regulon activity and the production of virulence factors. Using the amino acids substitution strategy, we revealed the role of proline and glutamic acid on PlcR regulon activation. Moreover, we demonstrated that the D-Glutamic acid substitution was crucial for the design of stronger PlcR antagonists. These peptides represent potent synthetic inhibitors of B. cereus QS and constitute new and readily accessible chemical tools for the study of the PlcR system. Our method might be applied to other quorum sensing systems to design new anti-virulence agents.

Polyphosphate recovery by a native Bacillus cereus strain as a direct effect of glyphosate uptake

Seven bacterial strains isolated from a glyphosate-exposed orange plantation site were exposed to 1 mM N-(phosphonomethyl)glycine supplied as a phosphorus source. While some exhibited good biodegradation profiles, the strain 6 P, identified as Bacillus cereus, was the only strain capable of releasing inorganic phosphate to the culture supernatant, while accumulating polyphosphate intracellularly along the experimentation time. The composition and purity of the intracellular polyphosphate accumulated by the strain 6 P were confirmed by FTIR analysis. To date, the biological conversion of glyphosate into polyphosphate has not been reported. However, given the importance of this biopolymer in the survival of microorganisms, it can be expected that this process could represent an important ecological advantage for the adaptation of this strain to an ecological niche exposed to this herbicide. The polyphosphate production yield was calculated as 4 mg l-1, while the glyphosate biodegradation kinetic constant was calculated on 0.003 h-1 using the modified Hockey-Stick first-order kinetic model, with a half-life of 279 h. Our results suggest that B. cereus 6 P is a potential candidate for the generation of an innovative biotechnological process to produce polyphosphate through the biodegradation of the herbicide glyphosate.

Multifaceted toxin profile, an approach toward a better understanding of probiotic Bacillus cereus

Strains of the Bacillus cereus group have been widely used as probiotics for human beings, food animals, plants, and environmental remediation. Paradoxically, B. cereus is responsible for both gastrointestinal and nongastrointestinal syndromes and represents an important opportunistic food-borne pathogen. Toxicity assessment is a fundamental issue to evaluate safety of probiotics. Here, we summarize the state of our current knowledge about the toxins of B. cereus sensu lato to be considered for safety assessment of probiotic candidates. Surfactin-like emetic toxin (cereulide) and various enterotoxins including nonhemolytic enterotoxin, hemolysin BL, and cytotoxin K are responsible for food poisoning outbreaks characterized by emesis and diarrhea. In addition, other factors, such as hemolysin II, Certhrax, immune inhibitor A1, and sphingomyelinase, contribute to toxicity and overall virulence of B. cereus.

Binding to The Target Cell Surface Is The Crucial Step in Pore Formation of Hemolysin BL from Bacillus cereus

A major virulence factor involved in Bacillus cereus food poisoning is the three-component enterotoxin hemolysin BL. It consists of the binding component B and the two lytic components L₁ and L₂. Studying its mode of action has been challenging, as natural culture supernatants additionally contain Nhe, the second three-component enterotoxin, and purification of recombinant (r) Hbl components has been difficult. In this study, we report on pore-forming, cytotoxic, cell binding and hemolytic activity of recently generated rHbl components expressed in E. coli. It is known that all three Hbl components are necessary for cytotoxicity and pore formation. Here we show that an excess of rHbl B enhances, while an excess of rHbl L₁ hinders, the velocity of pore formation. Most rapid pore formation was observed with ratios L₂:L₁:B = 1:1:10 and 10:1:10. It was further verified that Hbl activity is due to sequential binding of the components B - L₁ - L₂. Accordingly, all bioassays proved that binding of Hbl B to the cell surface is the crucial step for pore formation and cytotoxic activity. Binding of Hbl B took place within minutes, while apposition of the following L₁ and L₂ occurred immediately. Further on, applying toxin components simultaneously, it seemed that Hbl L₁ enhanced binding of B to the target cell surface. Overall, these data contribute significantly to the elucidation of the mode of action of Hbl, and suggest that its mechanism of pore formation differs substantially from that of Nhe, although both enterotoxin complexes are sequentially highly related.

Diversity of the Rap-Phr quorum-sensing systems in the Bacillus cereus group

Bacteria of the Bacillus cereus group colonize several ecological niches and infect different hosts. Bacillus cereus, a ubiquitous species causing food poisoning, Bacillus thuringiensis, an entomopathogen, and Bacillus anthracis, which is highly pathogenic to mammals, are the most important species of this group. These species are closely related genetically, and their specific toxins are encoded by plasmids. The infectious cycle of B. thuringiensis in its insect host is regulated by quorum-sensing systems from the RNPP family. Among them, the Rap-Phr systems, which are well-described in Bacillus subtilis, regulate essential processes, such as sporulation. Given the importance of these systems, we performed a global in silico analysis to investigate their prevalence, distribution, diversity and their role in sporulation in B. cereus group species. The rap-phr genes were identified in all selected strains with 30% located on plasmids, predominantly in B. thuringiensis. Despite a high variability in their sequences, there is a remarkable association between closely related strains and their Rap-Phr profile. Based on the key residues involved in RapH phosphatase activity, we predicted that 32% of the Rap proteins could regulate sporulation by preventing the phosphorylation of Spo0F. These Rap are preferentially located on plasmids and mostly related to B. thuringiensis. The predictions were partially validated by in vivo sporulation experiments suggesting that the residues linked to the phosphatase function are necessary but not sufficient to predict this activity. The wide distribution and diversity of Rap-Phr systems could strictly control the commitment to sporulation and then improve the adaptation capacities of the bacteria to environmental changes.

Bacillus cereus Isolated From Vegetables in China: Incidence, Genetic Diversity, Virulence Genes, and Antimicrobial Resistance

Bacillus cereus is a food-borne opportunistic pathogen that can induce diarrheal and emetic symptoms. It is widely distributed in different environments and can be found in various foods, including fresh vegetables. As their popularity grows worldwide, the risk of bacterial contamination in fresh vegetables should be fully evaluated, particularly in vegetables that are consumed raw or processed minimally, which are not commonly sterilized by enough heat treatment. Thereby, it is necessary to perform potential risk evaluation of B. cereus in vegetables. In this study, 294 B. cereus strains were isolated from vegetables in different cities in China to analyze incidence, genetic polymorphism, presence of virulence genes, and antimicrobial resistance. B. cereus was detected in 50% of all the samples, and 21/211 (9.95%) of all the samples had contamination levels of more than 1,100 MPN/g. Virulence gene detection revealed that 95 and 82% of the isolates harbored nheABC and hblACD gene clusters, respectively. Additionally, 87% of the isolates harbored cytK gene, and 3% of the isolates possessed cesB. Most strains were resistant to rifampicin and β-lactam antimicrobials but were sensitive to imipenem, gentamicin, ciprofloxacin, kanamycin, telithromycin, ciprofloxacin, and chloramphenicol. In addition, more than 95.6% of the isolates displayed resistance to three kinds of antibiotics. Based on multilocus sequence typing, all strains were classified into 210 different sequence types (STs), of which 145 isolates were assigned to 137 new STs. The most prevalent ST was ST770, but it included only eight isolates. Taken together, our research provides the first reference for the incidence and characteristics of B. cereus in vegetables collected throughout China, indicating a potential hazard of B. cereus when consuming vegetables without proper handling.

The Bacillus cereus Group: Bacillus Species with Pathogenic Potential

The Bacillus cereus group includes several Bacillus species with closely related phylogeny. The most well-studied members of the group, B. anthracis, B. cereus, and B. thuringiensis, are known for their pathogenic potential. Here, we present the historical rationale for speciation and discuss shared and unique features of these bacteria. Aspects of cell morphology and physiology, and genome sequence similarity and gene synteny support close evolutionary relationships for these three species. For many strains, distinct differences in virulence factor synthesis provide facile means for species assignment. B. anthracis is the causative agent of anthrax. Some B. cereus strains are commonly recognized as food poisoning agents, but strains can also cause localized wound and eye infections as well as systemic disease. Certain B. thuringiensis strains are entomopathogens and have been commercialized for use as biopesticides, while some strains have been reported to cause infection in immunocompromised individuals. In this article we compare and contrast B. anthracis, B. cereus, and B. thuringiensis, including ecology, cell structure and development, virulence attributes, gene regulation and genetic exchange systems, and experimental models of disease.

Assessing the Microbiota of Black Soldier Fly Larvae (Hermetia illucens) Reared on Organic Waste Streams on Four Different Locations at Laboratory and Large Scale

This study aimed to gain insight into the microbial quality, safety and bacterial community composition of black soldier fly larvae (Hermetia illucens) reared at different facilities on a variety of organic waste streams. For seven rearing cycles, both on laboratory-scale and in large-scale facilities at several locations, the microbiota of the larvae was studied. Also samples of the substrate used and the residue (= leftover substrate after rearing, existing of non-consumed substrate, exuviae and faeces) were investigated. Depending on the sample, it was subjected to plate counting, Illumina Miseq sequencing and/or detection of specific food pathogens. The results revealed that the substrates applied at the various locations differed substantially in microbial numbers as well as in the bacterial community composition. Furthermore, little similarity was observed between the microbiota of the substrate and that of the larvae reared on that substrate. Despite substantial differences between the microbiota of larvae reared at several locations, 48 species-level operational taxonomic units (OTUs) were shared by all larvae, among which most belonged to the phyla Firmicutes and Proteobacteria. Although the substrate is assumed to be an important source of bacteria, our results suggest that a variety of supposedly interacting factors-both abiotic and biotic-are likely to affect the microbiota in the larvae. In some larvae and/or residue samples, potential foodborne pathogens such as Salmonella and Bacillus cereus were detected, emphasising that decontamination technologies are required when the larvae are used in feed, just as for other feed ingredients, or eventually in food.

Detection and Identification of Bacillus cereus, Bacillus cytotoxicus, Bacillus thuringiensis, Bacillus mycoides and Bacillus weihenstephanensis via Machine Learning Based FTIR Spectroscopy

The Bacillus cereus group comprises genetical closely related species with variable toxigenic characteristics. However, detection and differentiation of the B. cereus group species in routine diagnostics can be difficult, expensive and laborious since current species designation is linked to specific phenotypic characteristic or the presence of species-specific genes. Especially the differentiation of Bacillus cereus and Bacillus thuringiensis, the identification of psychrotolerant Bacillus mycoides and Bacillus weihenstephanensis, as well as the identification of emetic B. cereus and Bacillus cytotoxicus, which are both producing highly potent toxins, is of high importance in food microbiology. Thus, we investigated the use of a machine learning approach, based on artificial neural network (ANN) assisted Fourier transform infrared (FTIR) spectroscopy, for discrimination of B. cereus group members. The deep learning tool box of Matlab was employed to construct a one-level ANN, allowing the discrimination of the aforementioned B. cereus group members. This model resulted in 100% correct identification for the training set and 99.5% correct identification overall. The established ANN was applied to investigate the composition of B. cereus group members in soil, as a natural habitat of B. cereus, and in food samples originating from foodborne outbreaks. These analyses revealed a high complexity of B. cereus group populations, not only in soil samples but also in the samples from the foodborne outbreaks, highlighting the importance of taking multiple isolates from samples implicated in food poisonings. Notable, in contrast to the soil samples, no bacteria belonging to the psychrotolerant B. cereus group members were detected in the food samples linked to foodborne outbreaks, while the overall abundancy of B. thuringiensis did not significantly differ between the sample categories. None of the isolates was classified as B. cytotoxicus, fostering the hypothesis that the latter species is linked to very specific ecological niches. Overall, our work shows that machine learning assisted (FTIR) spectroscopy is suitable for identification of B. cereus group members in routine diagnostics and outbreak investigations. In addition, it is a promising tool to explore the natural habitats of B. cereus group, such as soil.

Evaluation of enterotoxin gene expression and enterotoxin production capacity of the probiotic strain Bacillus toyonensis BCT-7112T

The aim of the present study was to evaluate the safety of the probiotic strain Bacillus toyonensis BCT-7112T (active ingredient of Toyocerin) in relation to the enterotoxins haemolysin BL (Hbl) and the non-haemolytic enterotoxin (Nhe) by performing a quantitative reverse transcription (RT) real-time polymerase chain reaction (PCR) and a Western blot assay. The expression levels of the enterotoxin genes hblA, hblD, nheA, nheB and nheC, determined by means of RT real-time PCR in B. toyonensis, were lower than those in B. cereus reference strains. No expression of hblC was detected. The Western blot assays of native and 25-fold concentrated supernatants from B. toyonensis, using monoclonal antibodies directed against the Hbl component L1 and the Nhe component NheB, showed weak bands. The NheC component was not detected in the native supernatant, but weakly in the 25-fold concentrated supernatant. According to the results of the present study, the enterotoxin expression and protein levels of B. toyonensis BCT-7112T were absent or clearly lower compared to the B. cereus reference strains. Thus, their ability to form functional enterotoxins can also be considered to be lower or unlikely compared to the B. cereus reference strains. This experimental approach can be implemented when studying the health and safety as well as harmlessness of probiotic microorganisms.

Removal of B. cereus cereulide toxin from monoclonal antibody bioprocess feed via two-step Protein A affinity and multimodal chromatography

A rapid and sensitive liquid chromatography-mass spectrometry assay was developed and used to quantify emetic cereulide peptide exotoxin, which can be related to possible Bacillus cereus contamination in monoclonal antibody (mAb) bioprocess feeds. The assay limit of detection was 0.05 ng/mL (~1 fmol injected) and limit of quantification 0.16 ng/mL (~3 fmol injected) over a standard curve with >3 orders of magnitude linear dynamic range. The assay allowed quantification of toxin removal in an established two-step mAb purification process consisting of Protein A affinity chromatography followed by multi-modal anion exchange chromatography. Toxin content was ascertained in process stream sample fractions as well as on the Protein A affinity column. An optimized analytical method allowed separation of cereulide toxin from other mAb cell culture components within 6 min. Spiking experiments showed that samples should be collected in high (80% v/v) content acetonitrile to reduce nonspecific losses of the cereulide. The majority of mAb purification process-associated cereulide was detected in the Protein A flow through fraction, whereas only residual amounts were found in wash, strip, and elution fractions. Column cleaning-in-place (CIP) procedures were evaluated to prevent carryover between affinity capture cycles. No carryover was detected between cycles, however trace amounts of cereulide were extracted from the Protein A resin. Increasing the CIP NaOH concentration from 0.1 M to 0.5 M, and contact time from 15 min to 1 h, improved removal of residual cereulide from the resin. Applicability of CIP clearance of cereulide during Protein A chromatography was confirmed with three different mAb feeds. Post Protein A polishing, via target flow through on a multi-modal anion exchange chromatography column, resulted in a product pool with no detectable cereulide. Approximately 5 logs of reduction in cereulide concentration was obtained over the two-step chromatography process. Cereulide contamination is well known and of concern in food processing, however this research may be the first LC-MS quantification of cereulide contamination, and its clearance, in biopharmaceutical mAb processing. The analytical method may also be used to rapidly screen for cereulide contamination in upstream cell culture process streams, prior to downstream product purification. This will allow appropriate measures to be taken to reduce toxin exposure to downstream bioprocess raw materials, consumables and equipment.

Functional and Genetic Diversity of Bacteria Associated with the Surfaces of Agronomic Plants

The main objective of this study was to evaluate the genetic diversity and agricultural significance of bacterial communities associated with the surfaces of selected agronomic plants (carrot, cabbage and turnip). The bacterial diversity of fresh agricultural produce was targeted to identify beneficial plant microflora or opportunistic human pathogens that may be associated with the surfaces of plants. Bacterial strains were screened in vitro for auxin production, biofilm formation and antibiotic resistance. 16S rRNA gene sequencing confirmed the presence of several bacterial genera including Citrobacter, Pseudomonas, Pantoea, Bacillus, Kluyvera, Lysinibacillus, Acinetobacter, Enterobacter, Serratia, Staphylococcus, Burkholderia, Exiguobacterium, Stenotrophomonas, Arthrobacter and Klebsiella. To address the biosafety issue, the antibiotic susceptibility pattern of strains was determined against different antibiotics. The majority of the strains were resistant to amoxicillin (25 µg) and nalidixic acid (30 µg). Strains were also screened for plant growth-promoting attributes to evaluate their positive interaction with colonized plants. Maximum auxin production was observed with Stenotrophomonas maltophilia MCt-1 (101 µg mL⁻¹) and Bacillus cereus PCt-1 (97 µg mL⁻¹). Arthrobacter nicotianae Lb-41 and Exiguobacterium mexicanum MCb-4 were strong biofilm producers. In conclusion, surfaces of raw vegetables were inhabited by different bacterial genera. Potential human pathogens such as Bacillus cereus, Bacillus anthracis, Enterobacter cloacae, Enterobacter amnigenus and Klebsiella pneumoniae were also isolated, which makes the biosafety of these vegetable a great concern for the local community. Nevertheless, these microbes also harbor beneficial plant growth-promoting traits that indicated their positive interaction with their host plants. In particular, bacterial auxin production may facilitate the growth of agronomic plants under natural conditions. Moreover, biofilm formation may help bacteria to colonize plant surfaces to show positive interactions with host plants.

Changes in the Soil Bacterial Community in a Chronosequence of Temperate Walnut-Based Intercropping Systems

Agroforestry (tree-based intercropping) is regarded as a promising practice in sustainable agricultural management. However, the impacts of converting cropland to an agroforestry system on microbial communities remain poorly understood. In this study, we assessed the soil bacterial communities in conventional wheat monoculture systems and a chronosequence (5–14 years) walnut-wheat agroforestry system through the high-throughput sequencing of 16S rRNA genes to investigate the effect of agroforestry age on soil bacterial communities and the correlation between soil properties and bacterial communities in the agroecosystem. Our results demonstrate that establishing and developing walnut tree-based agroforestry increased soil bacterial diversity and changed bacterial community structure. Firmicutes, Proteobacteria, Actinobacteria and Acidobacteria were the dominant soil bacterial phyla and Bacillus was the dominant genus. Crop monoculture systems were characterized by the Bacillus (Firmicutes)-dominated microbial community. The relative abundance of Bacillus decreased with agroforestry age; however, subgroups of Proteobacteria and Actinobacteria increased. Of the selected soil physicochemical properties, soil pH and bulk density were significantly correlated with bacterial alpha diversity, and soil pH and organic carbon were the principal drivers in shaping the soil microbial structure as revealed by redundancy analysis (RDA).

Porcine Gastric Mucin Triggers Toxin Production of Enteropathogenic Bacillus cereus

Enteropathogenic Bacillus cereus causes foodborne infections due to the production of pore-forming enterotoxins in the intestine. Before that, spores have to be ingested, survive the stomach passage, and germinate. Thus, before reaching epithelial cells, B. cereus comes in contact with the intestinal mucus layer. In the present study, different aspects of this interaction were analyzed. Total RNA sequencing revealed major transcriptional changes of B. cereus strain F837/76 upon incubation with porcine gastric mucin (PGM), comprising genes encoding enterotoxins and further putative virulence factors, as well as proteins involved in adhesion to and degradation of mucin. Indeed, PGM was partially degraded by B. cereus via secreted, EDTA-sensitive proteases. The amount of enterotoxins detectable in culture media supplemented with PGM was also clearly increased. Tests of further strains revealed that enhancement of enterotoxin production upon contact with PGM is broadly distributed among B. cereus strains. Interestingly, evidence was found that PGM can also strain-specifically trigger germination of B. cereus spores and that vegetative cells actively move toward mucin. Overall, our data suggest that B. cereus is well adapted to the host environment due to massive transcriptome changes upon contact with PGM, attributing mucin an important and, thus far, neglected role in pathogenesis.

Comparison of chemical composition and airborne bacterial community structure in PM2.5 during haze and non-haze days in the winter in Guilin, China

Haze is a typical type of air pollution and frequently has occurred in the winter in Guilin city recently, but information relating to chemical compositions and airborne bacterial community structure of atmospheric particulate matter (PM_2.5) during haze days remains very limited. In this study, the PM_2.5 concentration, chemical components including water-soluble ions and metal elements, and bacterial community compositions of PM_2.5 on both haze and non-haze days were characterized, and the relationships between them were studied. The results showed that levels of the secondary aerosol particles of SO₄^2-, NO₃^-, and NH₄⁺ in haze PM_2.5 associated with local fuel combustion and vehicle emissions were significantly higher than non-haze samples. Similar trends were observed for the detected trace metal elements. High-throughput sequencing results indicated that higher PM_2.5 concentration caused lower bacterial richness and diversity. However, the airborne bacterial community structure remained stable, and no significant difference was found between haze and non-haze PM_2.5. Firmicutes, Proteobacteria, and Bacteroidetes were the most abundant phyla accounting for a total of 97.2% on average. In contrast to non-haze PM_2.5, the bacterial community structure of haze PM_2.5 was mostly positively correlated with SO₄^2-, NO₃^-, NH₄⁺, K⁺, and Cl^-, suggesting these secondary aerosol particles were probably of great importance on haze pollution and variability of the bacterial compositions of PM_2.5.

Draft genome sequence of multidrug-resistant β-lactamase-producing Bacillus cereus S66 isolated from China

OBJECTIVES

Bacillus cereus is associated with a variety of human diseases such as haematological malignancies, tetanus, gas gangrene, food poisoning and pseudomembranous colitis. Our team found and isolated a strain, named B. cereus S66, from radiation-contaminated soil in Xinjiang Uygur Autonomous Region. In this study, the drug resistance and toxicity of B. cereus S66 was systematically studied and analysed.

METHODS

Genomic DNA of B. cereus S66 was sequenced using an Illumina HiSeq 2000 sequencing system. The generated reads were assembled using SOAPdenovo, and GapCloser was used to fill in the gaps. The draft genome was annotated, and virulence genes and drug resistance genes were identified by comparison with multiclass databases.

RESULTS

The genome of B. cereus strain S66 is 5 628 370 bp with a GC content of 34.95% and contains various genes related to toxicity and antimicrobial resistance. The number of toxicity genes identified was 496, some of which are associated with gastrointestinal infection, eye infection and neutrophil-activating protein NapA. Antimicrobial resistance-related genes comprised 3.23% of the total genes and conferred resistance to lincomycin, tetracycline, fosfomycin, aminoglycosides, linezolid, chloramphenicol, rifampicin, macrolides, daunorubicin and mupirocin. Three different β-lactamases were also found in isolate S66.

CONCLUSIONS

The genome sequence of B. cereus S66 provides a valuable reference to further research on multidrug resistance characteristics and pathogenic system analysis of Bacillus sp. in the clinic.

Evaluation of the microbial contamination of fresh produces and their cultivation environments from farms in Korea

In this study, a total of 195 samples including fresh produce and farming environments was used to perform the microbial risk assessment. Levels of total aerobic bacteria ranged from 2.77 to 5.99, 6.28 to 7.81, and 1.31 to 2.74 log₁₀ CFU/g, whereas levels of coliforms were ≤ 2.48, ≤ 3.35, and ≤ 0.85 log₁₀ CFU/g, levels of Escherichia coli were ≤ 1.04, ≤ 0.12, and ≤ 1.69 log₁₀ CFU/g in fresh produce, soil, and irrigation water, respectively. When the presence of pathogenic bacteria was detected, only Bacillus cereus and Staphylococcus aureus were isolated from 14 (7.2%) and 7 (3.6%) samples out of 195 samples, respectively. From the results, it was difficult to find a strong correlation between microbial contamination of fresh produce and their farming environments. However, continuous monitoring of agricultural products and related environments should be undertaken in order to ensure the microbial safety of fresh produce.

Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges

The Bacillus cereus group comprises multiple species capable of causing emetic or diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses each year in the U.S. alone, whole-genome sequencing (WGS) is not yet routinely employed to characterize B. cereus group isolates from foodborne outbreaks. Here, we describe the first WGS-based characterization of isolates linked to an outbreak caused by members of the B. cereus group. In conjunction with a 2016 outbreak traced to a supplier of refried beans served by a fast food restaurant chain in upstate New York, a total of 33 B. cereus group isolates were obtained from human cases (n = 7) and food samples (n = 26). Emetic (n = 30) and diarrheal (n = 3) isolates were most closely related to B. paranthracis (group III) and B. cereus sensu stricto (group IV), respectively. WGS indicated that the 30 emetic isolates (24 and 6 from food and humans, respectively) were closely related and formed a well-supported clade distinct from publicly available emetic group III genomes with an identical sequence type (ST 26). The 30 emetic group III isolates from this outbreak differed from each other by a mean of 8.3 to 11.9 core single nucleotide polymorphisms (SNPs), while differing from publicly available emetic group III ST 26 B. cereus group genomes by a mean of 301.7-528.0 core SNPs, depending on the SNP calling methodology used. Using a WST-1 cell proliferation assay, the strains isolated from this outbreak had only mild detrimental effects on HeLa cell metabolic activity compared to reference diarrheal strain B. cereus ATCC 14579. We hypothesize that the outbreak was a single source outbreak caused by emetic group III B. cereus belonging to the B. paranthracis species, although food samples were not tested for presence of the emetic toxin cereulide. In addition to showcasing how WGS can be used to characterize B. cereus group strains linked to a foodborne outbreak, we also discuss potential microbiological and epidemiological challenges presented by B. cereus group outbreaks, and we offer recommendations for analyzing WGS data from the isolates associated with them.

Bacillus cereus biofilm formation on central venous catheters of hospitalised cardiac patients

Formation of bacterial biofilms is a risk with many in situ medical devices. Biofilm-forming Bacillus species are associated with potentially life-threatening catheter-related blood stream infections in immunocompromised patients. Here, bacteria were isolated from biofilm-like structures within the lumen of central venous catheters (CVCs) from two patients admitted to cardiac hospital wards. Isolates belonged to the Bacillus cereus group, exhibited strong biofilm formation propensity, and mapped phylogenetically close to the B. cereus emetic cluster. Together, whole genome sequencing and quantitative PCR confirmed that the isolates constituted the same strain and possessed a range of genes important for and up-regulated during biofilm formation. Antimicrobial susceptibility testing demonstrated resistance to trimethoprim-sulphamethoxazole, clindamycin, penicillin and ampicillin. Inspection of the genome revealed several chromosomal β-lactamase genes and a sulphonamide resistant variant of folP. This study clearly shows that B. cereus persisting in hospital ward environments may constitute a risk factor from repeated contamination of CVCs.

Identification of cereulide producing Bacillus cereus by MALDI-TOF MS

The Bacillus (B.) cereus group consists of nine recognized species which are present worldwide. B. cereus play an important role in food-borne diseases by producing different toxins. Yet, only a small percentage of B. cereus strains are able to produce the heat stable cereulide, the causative agent of emetic food poisoning. To minimize the entry of emetic B. cereus into the food chain, food business operators are dependent on efficient and reliable methods enabling the differentiation between emetic and non-emetic strains. Currently, only time-consuming cell bioassays, molecular methods and tandem mass spectrometry are available for this purpose. Thus, the aim of the present study was to establish a fast and reliable method for the differentiation between emetic/non-emetic strains by MALDI-TOF MS. Selected strains/isolates of the B. cereus group as well as other Bacillus spp. (total n = 121) were cultured on sheep blood agar for 48 h before analysis. Subsequently, the cultures were directly analyzed by MALDI-TOF MS without prior extraction steps. The samples were measured in the mass range of m/z 800-1800 Da. Using ClinProTools 3.0 statistical software and Flex analysis software (Bruker Daltonics GmbH, Bremen, Germany), a differentiation between emetic/non-emetic isolates was possible with a rate of correct identification of 99.1% by means of the evaluation of two specific biomarkers (m/z 1171 and 1187 Da).

Effect of ultrasonication and thermal and pressure treatments, individually and combined, on inactivation of Bacillus cereus spores

Bacillus cereus spores are a concern to the food industry due to their high resistance to processing and their ability to germinate to vegetative cells under suitable conditions. This research aimed to elucidate the mechanisms of Bacillus cereus spore inactivation under ultrasonication (US) combined with thermal (thermosonication, TS) treatments, with pressure (manosonication, MS) treatments, and with thermal and pressure (manothermosonication, MTS) treatments. Electronic microscopy, dipicolinic acid (DPA) release, and flow cytometric assessments were used to investigate the inactivation effect and understand the inactivation mechanisms. The sporicidal effects of the US and thermal treatment were slight, and the MS and TS also showed little inactivation effect. However, ultrasonication promoted the detachment of the exosporium, thereby reducing the spore's ability to adhere to a surface, while the thermal treatment induced a decrease in the electron density in the nucleoid of bacterium, which retained a relatively intact exosporium and coat. MS caused 92.54% DPA release, which might be due to triggering of the germinant receptors or releasing of ions and Ca²⁺-DPA. In addition, the morphological changes such as core hydration and cortex degradation were significant after treatment with MS. The release of DPA and the morphological changes were responsible for the reduction in thermal resistance. The MTS showed a remarkable inactivation effect of 3.12 log CFU/mL reductions after 30 min of treatment. It was the most effective treatment and exhibited a large fraction of damage. In addition, the MTS had a significant impact on the intracellular structure of the spores, with the coat destroyed and the cortex damaged. These results indicated that ultrasonication combined with thermal and pressure treatments had a significant sporicidal effect on Bacillus cereus spores and could be a promising green sterilization technology.

Bacteria Co-colonizing with Clostridioides Difficile in Two Asymptomatic Patients

BACKGROUND

Clostridium difficile infection (CDI) is the leading cause of nosocomial diarrhea. Co-colonization of key bacterial taxa may prevent the transition from asymptomatic C. difficile colonization to CDI. However, little is known about the composition of key bacterial taxa in asymptomatic patients.

METHODS

In the present study, the culture method was used to examine the composition of stool microbiota in two asymptomatic patients from Guizhou, China.

RESULTS

A total of 111 strains were isolated and phylogenetic relationships were determined by 16S ribosomal gene sequencing and Molecular Evolutionary Genetics Analysis version 7. The results demonstrated that Escherichia (33.3%, 37/111), Clostridium (24.3%, 27/111) and Enterococcus (11.7%, 13/111) exhibited a high ratio in asymptomatic patients. These isolates derived from two phyla: Firmicutes (51.3%, 57/111) and Proteobacteria (44.1%, 49/111). In addition, co-colonization of human pathogens Fusobacterium nucleatum, Ralstonia pickettii, Klebsiella pneumoniae, Klebsiella quasipneumoniae and Clostridium tertium with C. difficile was identified. To the best of our knowledge, these pathogens have not been co-isolated with C. difficile previously.

CONCLUSIONS

In summary, the present study identified the composition of fecal microbiota in two asymptomatic patients in Guizhou, China. These results suggested that co-infection with human pathogens may be ubiquitous during CDI progression.