Genetic heterogeneity in Bacillus sporothermodurans as demonstrated by ribotyping and repetitive extragenic palindromic-PCR fingerprinting

Detection and quantification of Bacillus cereus and its spores in raw milk by qPCR, and distinguish Bacillus cereus from other bacteria of the genus Bacillus

Introduction

The raw milk is the basic raw material of dairy products, Bacillus cereus is a typical conditional pathogenic bacteria and cold-phagocytic spoilage bacteria in raw milk. This study established a qPCR method for detecting B. cereus in raw milk

Materials and Methods

In this study, a qPCR method for detecting B. cereus in raw milk was established. The specificity of the method was verified by using other Bacillus bacteria and pathogenic bacteria, the sensitivity of the method was evaluated by preparing recombinant plasmids and simulated contaminated samples, and the applicability of the method was verified by using pure spore DNA. The actual sample detection was completed by using the established qPCR method

Results

The qPCR established in this study can specifically detect B. cereus in raw milk. The LOD of the method was as low as 200 CFU/mL, and the LOQ ranged from 2 × 10 2 to 2 × 10 8 CFU/ml, the amplification efficiency of qPCR was 96.6%

Conclusins

The method established in this study can distinguish B. cereus from other Bacillus bacteria, and spore DNA can be used as the detection object. This method has the advantages of strong specificity, high sensitivity, wide application range and short detection time, which is expected to be applied in the dairy industry.

Incidence of Bacillus cereus, Bacillus sporothermodurans and Geobacillus stearothermophilus in ultra-high temperature milk and biofilm formation capacity of isolates

The presence of mesophilic and thermophilic spore-forming bacteria in UHT milk, as well as biofilm formation in dairy plants, are concerning. The current study explored the spore-forming bacilli diversity in 100 samples of UHT milk (skimmed and whole). Through this work, a total of 239 isolates from UHT milk samples were obtained. B. cereus s.s. was isolated from 7 samples, B. sporothermodurans from 19 and, G. stearothermophilus from 25 samples. Genes encoding hemolysin (HBL), and non-hemolytic (NHE) enterotoxins were detected in B. cereus s.s. isolates. All isolates of B. cereus s.s. (12) B. sporothermodurans (38), and G. stearothermophilus (47) were selected to verify the ability of biofilm formation in microtiter plates. The results showed all isolates could form biofilms. The OD₅₉₅ values of biofilm formation varied between 0.14 and 1.04 for B. cereus, 0.20 to 1.87 for B. sporothermodurans, and 0.49 to 2.77 for G. stearothermophilus. The data highlights that the dairy industry needs to reinforce control in the initial quality of the raw material and in CIP cleaning procedures; avoiding biofilm formation and consequently a persistent microbiota in processing plants, which can shelter pathogenic species such as B. cereus s.s.

Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences

The genetic heterogeneity of Heyndrickxia sporothermodurans (formerly Bacillussporothermodurans) was evaluated using whole genome sequencing. The genomes of 29 previously identified Heyndrickxiasporothermodurans and two Heyndrickxia vini strains isolated from ultra-high-temperature (UHT)-treated milk were sequenced by short-read (Illumina) sequencing. After sequence analysis, the two H. vini strains could be reclassified as H. sporothermodurans. In addition, the genomes of the H.sporothermodurans type strain (DSM 10599^T) and the closest phylogenetic neighbors Heyndrickxiaoleronia (DSM 9356^T) and Heyndrickxia vini (JCM 19841^T) were also sequenced using both long (MinION) and short-read (Illumina) sequencing. By hybrid sequence assembly, the genome of the H. sporothermodurans type strain was enlarged by 15% relative to the short-read assembly. This noticeable increase was probably due to numerous mobile elements in the genome that are presumptively related to spore heat tolerance. Phylogenetic studies based on 16S rDNA gene sequence, core genome, single-nucleotide polymorphisms and ANI/dDDH, showed that H. vini is highly related to H. sporothermodurans. When examining the genome sequences of all H.sporothermodurans strains from this study, together with 4 H. sporothermodurans genomes available in the GenBank database, the majority of the 36 strains examined occurred in a clonal lineage with less than 100 SNPs. These data substantiate previous reports on the existence and spread of a genetically highly homogenous and heat resistant spore clone, i.e., the HRS-clone.

Farm level survey of spore-forming bacteria on four dairy farms in the Waikato region of New Zealand

The aim of our study was to determine the occurrence and diversity of economically important spore-forming bacteria in New Zealand dairy farm systems. Farm dairy effluent (FDE) collected from Waikato dairy farms were tested for the presence of spore-forming bacteria, using a new culture-based methodology followed by genomic analysis. An enrichment step in which samples were inoculated in cooked meat glucose starch broth under anaerobic conditions, aided in the differential isolation of Bacillus and Clostridium species. Furthermore, the use of molecular methods such as ERIC genotyping, 16S rRNA gene sequence analysis identified different spore-forming bacteria present in FDE. C. sporogenes signature PCR gave further information on the phylogenetic relationship of the different Clostridium spp. isolated in this study. In total 19 Bacillus spp., 5 Paenibacillus spp. and 17 Clostridium spp. were isolated from farm dairy effluent. Sequence types similar to economically important food spoilage bacteria viz: C. butyricum, C. sporogenes and members of the Paenibacillus Genus were isolated from all four farms, whereas, sequence types similar to potential toxigenic, B. cereus, C. perfringens, C. butyricum, and C. botulinum were found on at least three of the farms. Sampling of farm dairy effluent provides a good indicator of farm level prevalence of bacterial load as it is used to irrigate dairy pasture in New Zealand. This study highlights the presence of various spore-forming bacteria in dairy waste water and indicates the implementation of good hygienic farm practices and dairy waste effluent management.

Advantages and limitations of potential methods for the analysis of bacteria in milk: a review

Contamination concerns in the dairy industry are motivated by outbreaks of disease in humans and the inability of thermal processes to eliminate bacteria completely in processed products. HACCP principles are an important tool used in the food industry to identify and control potential food safety hazards in order to meet customer demands and regulatory requirements. Milk testing is of importance to the milk industry regarding quality assurance and monitoring of processed products by researchers, manufacturers and regulatory agencies. Due to the availability of numerous methods used for analysing the microbial quality of milk in literature and differences in priorities of stakeholders, it is sometimes confusing to choose an appropriate method for a particular analysis. The objective of this paper is to review the advantages and disadvantages of selected techniques that can be used in the analysis of bacteria in milk. SSC, HRMA, REP, and RAPD are the top four techniques which are quick and cost-effective and possess adequate discriminatory power for the detection and profiling of bacteria. The following conclusions were arrived at during this review: HRMA, REP and RFLP are the techniques with the most reproducible results, and the techniques with the most discriminatory power are AFLP, PFGE and Raman Spectroscopy.

Inactivation of Bacillus sporothermodurans spores by nisin and temperature studied by design of experiments in water and milk

Spores of Bacillus sporothermodurans are known to be a contaminant of dairy products and to be extremely heat-resistant. A central composite experimental design with three factors using response surface methodology was used to evaluate the effect of nisin (50-150 UI/mL), temperature (80-100 °C), and temperature-holding time (10-20 min) on the inactivation of B. sporothermodurans LTIS27 spores in distilled water, in skim milk and in chocolate milk. The experimental values were shown to be significantly in good agreement with the values predicted by the quadratic equation since the adjusted determination coefficients (Radj(2)) were around 0.97. By analyzing the response surfaces plots, the inactivation was shown to be higher in distilled water than in skim milk under all the conditions tested. Five-log cycle reductions of B. sporothermodurans spores were obtained after a treatment at 95 °C for 12 min in presence of 125 UI of nisin/mL in distilled water or at 100 °C for 13 min in presence of 134 UI of nisin/mL in skim milk or at 100 °C for 15 min in presence of 135 UI of nisin/mL in chocolate milk. This study showed the efficiency of nisin (15-184 UI/mL) in combination with temperature (73-106 °C) to inactivate spores of B. sporothermodurans in milk.

The combined effect of nisin, moderate heating and high hydrostatic pressure on the inactivation of Bacillus sporothermodurans spores

AIMS

To investigate the combined effect of hydrostatic pressure (HP), moderate temperature and nisin on the inactivation of Bacillus sporothermodurans spores which are known to be contaminant of dairy products and to be extremely heat-resistant.

METHODS AND RESULTS

A central composite experimental design with three factors, using response surface methodology, was used. By analysing the response surfaces and their corresponding contour plots, an interesting interaction with the three factors was observed. The inactivation observed was shown to be well fitted with values predicted by the quadratic equation, since the adjusted determination coefficient (R(adj)(2)) was 0·979. The optimum process parameters for a 5-log spores ml(-1) reduction of B. sporothermodurans spores were obtained, 472 MPa/53°C for 5 min in presence of 121 UI ml(-1) of nisin.

CONCLUSION

Nisin and temperature treatments improve the effectiveness of pressure in the inactivation of highly heat-resistant spores of B. sporothermodurans.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows the potential of using high HP for a short time (5 min) in combination with moderate temperature and nisin to inactivate B. sporothermodurans spores in milk. Such treatments could be applied by the dairy industry to ensure the commercial sterility of UHT milk.

Decreasing Enterobacter sakazakii (Cronobacter spp.) food contamination level with bacteriophages: prospects and problems

Enterobacter sakazakii (Cronobacter spp.) is an opportunistic pathogen, which can cause rare, but life-threatening infections in neonates and infants through feeding of a contaminated milk formula. We isolated 67 phages from environmental samples and tested their lytic host range on a representative collection of 40 E. sakazakii strains. A cocktail of five phages prevented the outgrowth of 35 out of 40 test strains in artificially contaminated infant formula. Two E. sakazakii phages represented prolate head Myoviridae. Molecular tests identified them as close relatives of Escherichia coli phage T4. The remaining three phages represented isometric head Myoviridae with large genome size of 140 and 200 kb, respectively, which belonged to two different DNA hybridization groups. A high dose of 10(8) pfu ml(-1) of phage could effectively sterilize a broth contaminated with both high and low pathogen counts (10(6) and 10(2) cfu ml(-1)). In contrast, broth inoculated with 10(4) phage and 10(2) bacteria per ml first showed normal bacterial growth until reaching a cell titre of 10(5) cfu ml(-1). Only when crossing this threshold, phage replication started, but it could not reduce the contamination level below 100 cfu ml(-1). Phages could be produced with titres of 10(10) pfu ml(-1) in broth culture, but they were not stable upon freeze-drying. Addition of trehalose or milk formula stabilized the phage preparation, which then showed excellent storage stability even at elevated temperature.

Emended descriptions of Bacillus sporothermodurans and Bacillus oleronius with the inclusion of dairy farm isolates of both species

Bacillus sporothermodurans is an industrially important micro-organism because of its ability to produce endospores which resist ultra-high temperature (UHT) and industrial sterilization processes. It was described by Pettersson et al. (1996) [Pettersson, B., Lembke, F., Hammer, P., Stackebrandt, E. & Priest, F. G. (1996). Int J Syst Bacteriol 46, 759-764] based on seven genetically homogeneous isolates all from UHT milk. Bacillus oleronius, the closest phylogenetic neighbour of B. sporothermodurans, was described by Kuhnigk et al. (1995) [Kuhnigk, T., Borst, E.-M., Breunig, A., König, H., Collins, M. D., Hutson, R. A. & Kämpfer, P. (1995). Can J Microbiol 41, 699-706] based on a single strain, isolated from the hindgut of the termite Reticulitermes santonensis. A polyphasic study of a heterogeneous collection of B. sporothermodurans and B. oleronius strains isolated from various sources and geographical origins led to an emended description of both species. Additional data presented are the results of fatty acid, quinone and/or cell wall (polar lipid) analyses. DNA-DNA hybridization confirmed 3 subgroups of strains obtained after SDS-PAGE analysis of cellular proteins as B. sporothermodurans. One named B. sporothermodurans strain (R-7489) was reclassified as a Bacillus fordii strain. The phenotypic profiles of both species were rather heterogeneous, sometimes different from the original descriptions and did not differ in a large number of characteristics, although B. oleronius generally gave stronger reactions in its positive tests than did B. sporothermodurans; the variable and weak reactions for both organisms with some substrates blurred the distinction between the two. However, differences in polar lipid, SDS-PAGE and menaquinone profiles clearly allow distinction between the two species.

The taxonomy of Enterobacter sakazakii: proposal of a new genus Cronobacter gen. nov. and descriptions of Cronobacter sakazakii comb. nov. Cronobacter sakazakii subsp. sakazakii, comb. nov., Cronobacter sakazakii subsp. malonaticus subsp. nov., Cronobacter turicensis sp. nov., Cronobacter muytjensii sp. nov., Cronobacter dublinensis sp. nov. and Cronobacter genomospecies 1

Background

Enterobacter sakazakii is an opportunistic pathogen that can cause infections such as necrotizing enterocolitis, bacteraemia, meningitis and brain abscess/lesions. When the species was defined in 1980, 15 biogroups were described and it was suggested that these could represent multiple species. In this study the taxonomic relationship of strains described as E. sakazakii was further investigated.

Results

Strains identified as E. sakazakii were divided into separate groups on the basis of f-AFLP fingerprints, ribopatterns and full-length 16S rRNA gene sequences. DNA-DNA hybridizations revealed five genomospecies. The phenotypic profiles of the genomospecies were determined and biochemical markers identified.

Conclusion

This study clarifies the taxonomy of E. sakazakii and proposes a reclassification of these organisms.

Mesophilic and psychrotrophic aerobe sporulating microorganisms in raw cow’s milk

We studied the occurrence of mesophilic and psychrotrophic aerobic sporulating microorganisms (MPAS) in raw cow’s milk and their relations to microflora in milk. We took 294 samples of raw cow’s milk from 14 farms during one year. Briefly the method for MPAS assessment is to inactivate the milk sample by heating it to 80-82°C for 30 minutes. Mesophilic aerobic sporulates are incubated at 30°C for 3 days-, and psychrotrophic aerobic sporulates at 7°C for 10 days. Results of studied microbiological parameters characterize the sampled milk as complying with requirements of the EU regulation 92/46 and standard STN 57 0529. MPAS count was within the span 2.5–340 CFU/ml. The average value ofMPAS was 59.4 CFU/ml, with variation coefficient 93.1%. Counts up to 50 CFU/ml were in 55.4% samples, the value was not higher than 100 in 85%, and in 3.1% of the samples the MPAS count was higher than 200. MPAS do not show correlation with any of the studied microbiological parameters; marked influences of season were not observed either. On the basis of obtained results, it is possible to support the proposal of an initial limit of maximum 200 CFU/ml for the introduction of a MPAS parameter. MPAS count found in the same dishes at incubation for mesophilic and subsequently strictly psychrophilic microorganisms was 56.9 CFU/ml on average. This represents 95.8% of total CFU sums of individual dishes at two temperatures. The correlation coefficient of these two types of results, r = 0.99,gives evidence of close dependence expressed by the linear regression equation. Use of two incubation temperatures, one after another with an identical set of dishes, enables us to exclude overestimation of results due to sporulates able to grow at both incubation temperatures.

Bacillus sporothermodurans and other highly heat-resistant spore formers in milk

A recent example of a micro-organism causing undesired growth in consumer milk is Bacillus sporothermodurans producing highly heat-resistant spores (HRS) which may survive ultra-high temperature (UHT) treatment or industrial sterilization. Molecular typing showed a heterogeneous group of farm isolates (non-HRS strains), but a clonal group of UHT isolates from diverse European countries and other continents (HRS-clone) suggesting a common source. During a survey of Belgian dairy farms for the presence of potentially highly heat-resistant spore formers, high numbers of these spores were detected in filter cloth, green crop and fodder samples. The strain collection showed a high taxonomic diversity with 18 potentially new species and with Bacillus licheniformis and Geobacillus pallidus as predominating species overall. Seventeen B. sporothermodurans isolates were identified, mainly originating from feed concentrate. Heat resistance studies showed the UHT resistance of B. sporothermodurans spores present in industrially contaminated UHT milk, but a lower heat resistance of laboratory-grown strains (HRS and non-HRS). Hydrogen peroxide, used as sanitizer in the dairy industry, was found to induce higher heat resistance of laboratory-grown B. sporothermodurans strains to a certain level. This indicates that sublethal stress conditions may affect the heat resistance. By transmission electron microscopy, structural differences at the spore level were found between HRS and non-HRS strains. The data indicate that the attainment of extreme heat resistance is rather multifactorial.

Rapid Ped-2E9 cell-based cytotoxicity analysis and genotyping of Bacillus species

Bacillus species causing food-borne disease produce multiple toxins eliciting gastroenteritis. Toxin assays with mammalian cell cultures are reliable but may take 24 to 72 h to complete and also lack sensitivity. Here, a sensitive and rapid assay was developed using a murine hybridoma Ped-2E9 cell model. Bacillus culture supernatants containing toxins were added to a Ped-2E9 cell line and analyzed for cytotoxicity with an alkaline phosphatase release assay. Most Bacillus cereus strains produced positive cytotoxicity results within 1 h, and data were comparable to those obtained with the standard Chinese hamster ovary (CHO)-based cytotoxicity assay, which took about 72 h to complete. Moreover, the Ped-2E9 cell assay had 25- to 58-fold-higher sensitivity than the CHO assay. Enterotoxin-producing Bacillus thuringiensis also gave positive results with Ped-2E9 cells, while several other Bacillus species were negative. Eight isolates from food suspected of Bacillus contamination were also tested, and only one strain, which was later confirmed as B. cereus, gave a positive result. In comparison with two commercial diarrheal toxin assay kits (BDE-VIA and BCET-RPLA), the Ped-2E9 assay performed more reliably. Toxin fractions of >30 kDa showed the highest degree of cytotoxicity effects, and heat treatment significantly reduced the toxin activity, indicating the involvement of a heat-labile high-molecular-weight component in Ped-2E9 cytotoxicity. PCR results, in most cases, were in agreement with the cytotoxic potential of each strain. Ribotyping was used to identify cultures and indicated differences for several previously reported isolates. This Ped-2E9 cell assay could be used as a rapid (approximately 1-h) alternative to current methods for sensitive detection of enterotoxins from Bacillus species.

Incidence and diversity of potentially highly heat-resistant spores isolated at dairy farms

The presence of highly heat-resistant spores of Bacillus sporothermodurans in ultrahigh-temperature or sterilized consumer milk has emerged as an important item in the dairy industry. Their presence is considered undesirable since they hamper the achievement of commercial sterility requirements. By using a selective 30-min heat treatment at 100 degrees C, 17 Belgian dairy farms were screened to evaluate the presence, sources, and nature of potentially highly heat-resistant spores in raw milk. High numbers of these spores were detected in the filter cloth of the milking equipment and in green crop and fodder samples. About 700 strains were isolated after the selective heating, of which 635 could be screened by fatty acid methyl ester analysis. Representative strains were subjected to amplified ribosomal DNA restriction analysis, 16S rRNA gene sequencing, percent G+C content, and DNA-DNA reassociations for further identification. The strain collection showed a remarkable diversity, with representatives of seven aerobic spore-forming genera. Bacillus licheniformis and Bacillus pallidus were the most predominant species overall. Twenty-three percent of the 603 spore-forming isolates proved to belong to 18 separate novel species. These findings suggest that the selective heating revealed a pool of unknown organisms with a higher heat-resistant character. This study showed that high spore counts can occur at the dairy farm and that feed and milking equipment can act as reservoirs or entry points for potentially highly heat-resistant spores into raw milk. Lowering this spore load by good hygienic measures could probably further reduce the contamination level of raw milk, in this way minimizing the aerobic spore-forming bacteria that could lead to spoilage of milk and dairy products. Assessment and characterization of this particular flora are of great importance to allow the dairy or food industry to adequately deal with newly arising microbiological problems.

Morphological and phenotypical characterization of Bacillus sporothermodurans

AIMS

Enumeration of resistant bacteria in ultra-high temperature (UHT) treated milk; morphological characterization and phenotyping of resistant strains by traditional and nontraditional methods and their identification by molecular biology.

METHODS AND RESULTS

Modified standard plate count agar (PCA) and modified brain-heart infusion (BHI) agar were used for colony counts. Physiological culture traits were determined as suggested by Bergey's Manual of Systematic Bacteriology or in modified J-broth or in modified BHI agar. Scanning electron microscope (SEM) was used for microscopic examination. Strain identification was carried out by polymerase chain reaction (PCR). A total of 125 (62.81% of 199) samples were positive and the bacterial load was higher than 10(5) CFU ml(-1) in 46 samples (28.80% of 125). The 16S rRNA sequence of bacterial cultures obtained from UHT-treated milk was similar to that of Bacillus sporothermodurans M215 type strain((T)) and different biotypes were found by analysis of colony appearance, cell morphology and physiological traits.

CONCLUSIONS

Bacillus sporothermodurans was the predominant sporigenous micro-organisms in UHT milk.

SIGNIFICANCE AND IMPACT OF THE STUDY

BHI agar is more suitable than PCA for quality control of milk after UHT treatment. Modified J-broth medium is useful to determine selected physiological traits of B. sporothermodurans. The strains characterized and identified as B. sporothermodurans were significantly different compared with the type strain.

Characterization of Nocardia asteroides isolates from different ecological habitats on the basis of repetitive extragenic palindromic-PCR fingerprinting

Thirteen isolates of Nocardia asteroides from both soils and aquatic samples (lake and moat sediments, as well as scum from activated sludge), together with a type strain and two known clinical isolates of this species, were characterized by repetitive extragenic palindromic-PCR fingerprinting with the BOX-A1R primer. The resulting DNA fingerprint patterns proved to be strain specific, and cluster analysis distinguished the soil isolates, the aquatic isolates, and the known strains as being in separate groups.

Bacillus farraginis sp. nov., Bacillus fortis sp. nov. and Bacillus fordii sp. nov., isolated at dairy farms

Forty-eight bacterial strains were isolated at dairy farms from raw milk, the milking apparatus, green fodder or feed concentrate after a heat treatment of 30 min at 100 °C. In this way, spore-forming bacteria with a very high intrinsic heat resistance were selected for. The aerobic spore-forming isolates were subjected to a polyphasic taxonomical study, including repetitive element sequence-based PCR typing, whole-cell protein profiling, 16S rDNA sequence analysis, DNA–DNA hybridizations, DNA base composition, fatty acid analysis, and morphological and biochemical characteristics. A comparison of the REP- and (GTG)5-PCR and whole-cell protein SDS-PAGE profiles resulted in three clusters of similar strains. Analysis of the 16S rDNA sequences and DNA–DNA relatedness data showed that these clusters represented three novel species. The highest 16S rDNA similarity to a recognized species found for the three groups was around 94 % with Bacillus lentus and Bacillus sporothermodurans. Further phenotypic characterization supported the proposal of three novel species in the genus Bacillus, Bacillus farraginis, Bacillus fortis and Bacillus fordii. The respective type strains are R-6540T (=LMG 22081T=DSM 16013T), R-6514T (=LMG 22079T=DSM 16012T) and R-7190T (=LMG 22080T=DSM 16014T); their G+C DNA base contents are 43·7, 44·3 and 41·9 mol%, respectively. Although in variable amounts, a predominance of the branched fatty acids iso-C15 : 0 and anteiso-C15 : 0 was observed in all three novel species.