Randomly amplified polymorphic DNA (RAPD) assay for genomic fingerprinting of Bacillus cereus isolates

Bacillus "next generation" diagnostics: moving from detection toward subtyping and risk-related strain profiling

The highly heterogeneous genus Bacillus comprises the largest species group of endospore forming bacteria. Because of their ubiquitous nature, Bacillus spores can enter food production at several stages resulting in significant economic losses and posing a potential risk to consumers due the capacity of certain Bacillus strains for toxin production. In the past, food microbiological diagnostics was focused on the determination of species using conventional culture-based methods, which are still widely used. However, due to the extreme intra-species diversity found in the genus Bacillus, DNA-based identification and typing methods are gaining increasing importance in routine diagnostics. Several studies showed that certain characteristics are rather strain-dependent than species-specific. Therefore, the challenge for current and future Bacillus diagnostics is not only the efficient and accurate identification on species level but also the development of rapid methods to identify strains with specific characteristics (such as stress resistance or spoilage potential), trace contamination sources, and last but not least discriminate potential hazardous strains from non-toxic strains.

Sources of Bacillus cereus contamination in a pasteurized zucchini purée processing line, differentiated by two PCR-based methods

In previous work, raw materials used for processing pasteurized zucchini purée (zucchini, milk proteins and starch) and cultivation soil of zucchinis were found to be potential sources of stored product contamination with Bacillus cereus. 134 B. cereus strains originating from these sources and from the stored product were typed using coliphage M13 sequence-based polymerase chain reaction (M13-PCR) and DNA amplification fingerprinting. Combined patterns from the two methods were compared using Dice's coefficient and the unweighted pair group method with average cluster analysis. 16 combined profile groups and six unclustered strains were formed at 75% similarity level. Representative strains of each group were subsequently examined for growth at low temperature (4 degrees C, 7 degrees C and 10 degrees C). Based on strain relatedness, five major groups and two minor groups among the nine groups containing zucchini strains were common to both zucchini and soil origins, indicating that the soil was the main initial source of contamination for zucchinis. Strains from zucchinis and soil were heterogeneous compared with strains from dehydrated ingredients (milk proteins and starch), and were mainly composed of psychrotrophic strains. Convergent results from molecular typing and growth at low temperature showed that psychrotrophic contaminants of the stored product originated from zucchinis, whereas non-psychrotrophic contaminants originated from milk proteins. The number of genetic groups decreased during the purée processing, suggesting selection of strains during zucchini washing operations, heat treatment and storage.

Differentiation of Salmonella typhimurium from Salmonella enteritidis and other Salmonella serotypes using random amplified polymorphic DNA analysis

Salmonella enterica ssp. enterica serovar Typhimurium and Salmonella enterica ssp. enterica serovar Enteritidis are the major dominating serotypes of Salmonella in poultry and poultry products. Infection by Salmonella Typhimurium is an important cause of morbidity and mortality in poultry. Rapid differentiation of Salmonella Typhimurium from other Salmonella serotypes including Salmonella Enteritidis can be very crutial for public health and for epidemiologists and for the poultry industry. Ten arbitrarily designed short primers (8 to 10 bases) were used in the random amplified polymorphic DNA analysis of Salmonella Typhimurium. One of the primers, primer 3 (5'-CGT GCA CGC-3'), resulted in the amplification of a band pattern that was unique to Salmonella Typhimurium. In total, 24 strains of serotype Salmonella Typhimurium were used during the study. Eighteen of them are clinical isolates, 2 of them chicken isolates (A6, A20), 2 of them from the Pasteur Institute, 1 from Refik Saydam National Culture Collection, and 1 is a type culture strain from National Culture Type Collection. Serotype Salmonella Typhimurium strains, which were collected from several different hospitals, institutes, and culture collections, have all displayed the same amplification band by primer 3. Twenty-three strains of 16 different serotypes of salmoneallae including 11 Salmonella Enteritidis strains gave only a 300-bp amplification band or no bands, whereas an additional 700-bp amplification band was observed only in samples of Salmonella Typhimurium serotype. It is concluded that random amplified polymorphic DNA analysis with primer 3 is of potential use as a serotype-specific marker for Salmonella Typhimurium.

Prevalence and genetic diversity of Bacillus cereus in dried red pepper in Korea

Bacillus cereus is a foodborne spore-forming bacterial pathogen that is ubiquitous in the natural environment. Infections with this pathogen manifest as diarrheal or emetic types of food poisoning. In this study, 140 samples of dried red pepper purchased in Korea were assayed for the presence of B. cereus according to the U.S. Food and Drug Administration standard culture method. A multiplex PCR assay was developed for the rapid confirmation of B. cereus as an alternative to conventional biochemical confirmation tests. The genetic diversity of B. cereus isolates was investigated using a random amplified polymorphic DNA (RAPD) assay. B. cereus was found in 84.3% of the dried red pepper samples, with an average concentration of 1.9 x 10(4) CFU/g. B. cereus could be detected and distinguished from B. thuringiensis in the multiplex PCR assay by using the BCFW1 plus BCrevnew and the K3 plus K5 primer sets designed to detect the gyrB gene of B. cereus and B. thuringiensis and the cry gene of B. thuringiensis. A RAPD assay using the OPG 16 and MUP 3 primers was used to successfully distinguish among isolates, thus elucidating the genetic diversity of B. cereus isolates. The discriminating ability of the OPG 16 primer (142 types) was about threefold higher than that of MUP 3 (52 types) in the RAPD assay.

Development of PCR primers based on a fragment from randomly amplified polymorphic DNA for the detection of Escherichia coli O157:H7/NM

Serotype O157:H7 of EHEC is by far the most prevalent serotype associated with haemorrhagic colitis (HC) and haemolytic uremic syndrome (HUS). Although PCR methods aimed on the detection of genes associated with the pathogenicity of Escherichia coli O157:H7 have been reported, tests allowing the direct identification of this serotype are rare. In this study, we used RAPD-PCR tests to analyze strains of E. coli O157:H7 serotype, strains of non-pathogenic E. coli, and strains of other pathotypes, including enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enteroinvasive E. coli (EIEC), and enteroaggregation E. coli (EAggEC). One RAPD fragment co-shared by serotype O157:H7 strains was observed when 10-mer primer termed as OPQ3 was used. After sequencing this fragment, three primers were designed and combined to form two PCR primer pairs. These two primer pairs were highly specific to the strains belonging to E. coli O157:H7/NM (non-motile).

Diversity and functionality of Bacillus and related genera isolated from spontaneously fermented soybeans (Indian Kinema) and locust beans (African Soumbala)

A total of 126 isolates of Bacillus and related genera from indigenous, spontaneously fermented soybeans (Kinema) and locust beans (Soumbala) were characterized with the purpose of defining interspecific, as well as intraspecific relationships among the components of their microflora. B. subtilis was the dominant species, and species diversity was more pronounced in Soumbala than in Kinema. While from Kinema, six species were isolated (B. subtilis, B. licheniformis, B. cereus, B. circulans, B. thuringiensis and B. sphaericus), in Soumbala, the species found were B. subtilis, B. thuringiensis, B. licheniformis, B. cereu, B. badius, Paenibacillus alvei, B. firmus, P. larvae, Brevibacillus laterosporus, B. megaterium, B. mycoides and B. sphaericus. Genomic diversity in the isolates of B. subtilis was investigated by random amplified polymorphic DNA (RAPD) analysis using the polymerase chain reaction (PCR). The RAPD-PCR fingerprint analysis showed a high level of diversity. With more than 90% similarity, all 52 RAPD subdivisions were source and continent-wise homogeneous. Profiles of carbon source fermentation also showed a wide but corresponding phenotypic diversity, largely corresponding with RAPD subdivisions. The various strains were tested for several criteria for functionality in soybean fermentation, viz. protein degradation, pH increase, and development of desirable stickiness caused by viscous exopolymers. Profiles of functionality, based upon estimations of pH, free amino nitrogen and stickiness were associated with genotypic and phenotypic profiles. Notwithstanding the heterogenous fermentation results for some genotypic profiles, a ranking of RAPD groups is possible and can be useful in the further selection and study of B. subtilis strains.

Automated ribotyping and random amplified polymorphic DNA analysis for molecular typing of Salmonella enteritidis and Salmonella typhimurium strains isolated in Italy

AIMS

The ability of automated ribotyping and random amplified polymorphic DNA (RAPD) analysis to differentiate Salmonella enteritidis and Salmonella typhimurium isolates in relation to their origin was evaluated.

METHODS AND RESULTS

The restriction enzymes EcoRI, PvuII and PstI, and the random primers OPB17 and P1254, were tested for ribotyping and RAPD analysis, respectively. Seventeen subtypes were identified among the isolates of the two pathogenic Salmonella serovars using the RiboPrinter, and 25 subtypes using RAPD.

CONCLUSIONS

The greatest degree of genetic diversity was observed among Salm. typhimurium isolates using both automated ribotyping (Simpson's index of discrimination 0878) and RAPD (Simpson's index of discrimination 0886).

SIGNIFICANCE AND IMPACT OF THE STUDY

According to the results of this research, automated ribotyping and RAPD are two useful genotyping techniques for identifying unique and common subtypes associated with a specific source and location, and provide powerful tools for epidemiological investigations.

Homoduplex and heteroduplex polymorphisms of the amplified ribosomal 16S-23S internal transcribed spacers describe genetic relationships in the "Bacillus cereus group"

Bacillus anthracis, Bacillus cereus, Bacillus mycoides, Bacillus pseudomycoides, Bacillus thuringiensis, and Bacillus weihenstephanensis are closely related in phenotype and genotype, and their genetic relationship is still open to debate. The present work uses amplified 16S-23S internal transcribed spacers (ITS) to discriminate between the strains and species and to describe the genetic relationships within the "B. cereus group," advantage being taken of homoduplex-heteroduplex polymorphisms (HHP) resolved by polyacrylamide gel electrophoresis and silver staining. One hundred forty-one strains belonging to the six species were investigated, and 73 ITS-HHP pattern types were distinguished by MDE, a polyacrylamide matrix specifically designed to resolve heteroduplex and single-strand conformation polymorphisms. The discriminating bands were confirmed as ITS by Southern hybridization, and the homoduplex or heteroduplex nature was identified by single-stranded DNA mung bean nuclease digestion. Several of the ITS-HHP types corresponded to specific phenotypes such as B. anthracis or serotypes of B. thuringiensis. Unweighted pair group method arithmetic average cluster analysis revealed two main groups. One included B. mycoides, B. weihenstephanensis, and B. pseudomycoides. The second included B. cereus and B. thuringiensis, B. anthracis appeared as a lineage of B. cereus.

Comparison between automatic ribotyping and random amplified polymorphic DNA analysis of Bacillus cereus isolates from the dairy industry

Discrimination by automatic ribotyping and random amplified polymorphic DNA PCR, RAPD, was compared for 40 different B. cereus dairy isolates, 4 different B. mycoides isolates and 6 culture collection strains. RAPD-PCR has previously shown to be useful for tracing contamination routes of B. cereus to milk. Automatic ribotyping using EcoRI and PvuII separated the B. cereus and B. mycoides isolates/strains into 36 different ribotypes. RAPD-typing with primers generated 40 different RAPD-profiles. However, 17 isolates clustered into eight groups, irrespective of the primer and restriction enzyme used, and in all but one case, the isolates with the same pattern were isolated from the same dairy. Automatic ribotyping proved to be a useful, standardized and quick method to discriminate between B. cereus strains, only slightly less discriminatory than RAPD-typing.