BurkDiff: a real-time PCR allelic discrimination assay for Burkholderia pseudomallei and B. mallei

A real-time PCR assay, BurkDiff, was designed to target a unique conserved region in the B. pseudomallei and B. mallei genomes containing a SNP that differentiates the two species. Sensitivity and specificity were assessed by screening BurkDiff across 469 isolates of B. pseudomallei, 49 isolates of B. mallei, and 390 isolates of clinically relevant non-target species. Concordance of results with traditional speciation methods and no cross-reactivity to non-target species show BurkDiff is a robust, highly validated assay for the detection and differentiation of B. pseudomallei and B. mallei.     

Antigenic relatedness between Burkholderia pseudomallei and Burkholderia mallei

Burkholderia pseudomallei and Burkholderia mallei are causative agents of distinct diseases, namely, melioidosis and glanders, respectively. The two species are very closely related, based on DNA-DNA homology, base sequence of the 16S rRNA, and phenotypic characteristics. Based on the use of polyclonal antisera, B. pseudomallei and B. mallei are also found to be antigenically closely related to one another. We previously reported the production of monoclonal antibodies (MAbs) against B. pseudomallei antigens; one group was specific for the 200-kDa exopolysaccharide present on the surface of all B. pseudomallei isolates, and the other was specific for the lipopolysaccharide (LPS) structure present on more than 95% of the B. pseudomallei tested. In the present study, we showed that the MAbs against 200-kDa antigen of B. pseudomallei cross-reacted with a component present also in some B. mallei isolates (3/6), but the positive immunoblot reaction was noted below the 200-kDa position. On the other hand, none of the six B. mallei isolates reacted with the MAb specific for B. pseudomallei LPS. It was of interest to observe that only the 3 exopolysaccharide-positive B. mallei isolates reacted with a commercial MAb against B. mallei LPS. The data presented suggest that B. mallei can be classified antigenically into two types based on their reactivities with different MAbs, i.e., the presence or absence of exopolysaccharide and the types of lipopolysaccharide. The heterogeneity of the LPS from these two closely related organisms is most likely related to the differences in its O-polysaccharide side chain.     

Studies on enzyme variation in the murine malaria parasites Plasmodium berghei, P. yoelii, P. vinckei and P. chabaudi by starch gel electrophoresis.

Electrophoretic variation of the enzymes glucose phosphate isomerase, 6-phosphogluconate dehydrogenase, lactate dehydrogenase and glutamate dehydrogenase (NADP-dependent) has been studied in the African murine malaria parasites Plasmodium berghei, P. yoelii, P. vinckei and P. chabaudi and their subspecies. Horizontal starch gel electrophoresis was used throughout. The number of isolates examined in each subspecies varied from 1 (P. y. nigeriensis) to 24 (P. c. chabaudi). Extensive enzyme variation was found among isolates of most of the subspecies from which more than two such isolates were available for study. It is clear that the phenomenon of enzyme polymorphism is of common occurrence among malaria parasites. With the exception of P. berghei and P. yoelii, of which all isolates share an identical electrophoretic form of lactate dehydrogenase, no enzyme forms are shared between any of the 4 species of murine plasmodia. By contrast, within each species common enzyme forms are shared among each of the subspecies. The subspecies are nevertheless, distinguished from each other by the electrophoretic forms of at least one enzyme. The distribution and reassortment of enzyme variation among isolates of a single subspecies is in accordance with the concept of malaria parasites as sexually reproducing organisms. The study of variation among parasites present in individual wild-caught rodent hosts demonstrates that natural malarial infections usually comprise genetically heterogeneous populations of parasites. Nevertheless, the number of genetically distinct types of parasite of any one species present in a single infected host appears to be small. Generally not more than 2 or 3 clones of parasite of distinct genetic constitution are present in a single infected animal.     

A possible pitfall in the identification of Burkholderia mallei using molecular identification systems based on the sequence of the flagellin fliC gene

Amotile Burkholderia mallei and motile Burkholderia pseudomallei display a high similarity with regard to phenotype and clinical syndromes, glanders and melioidosis. The aim of this study was to establish a fast and reliable molecular method for identification and differentiation. Despite amotility, the gene of the filament forming flagellin (fliC) could be completely sequenced in two B. mallei strains. Only one mutation was identified discriminating between B. mallei and B. pseudomallei. A polymerase chain reaction-restriction fragment length polymorphism assay was designed making use of the absence of an AvaII recognition site in B. mallei. All seven B. mallei, 12 out of 15 B. pseudomallei and 36 closely related apathogenic Burkholderia thailandensis strains were identified correctly. However, in three B. pseudomallei strains a point mutation at gene position 798 (G to C) disrupted the AvaII site. Therefore, molecular systems based on the fliC sequence can be used for a reliable proof of strains of the three species but not for the differentiation of B. mallei and B. pseudomallei isolates.     

The use of multilocus sequence typing (MLST) and randomly amplified polymorphic DNA (RAPD) for the differentiation between strains of Burkholderia mallei

Burkholderia mallei is highly pathogenic microorganism for both humans and animals. In this work, the possibility of the use of the genotyping method for differentiation between strains of B. mallei was studied. A collection of 14 isolates of B. mallei was characterized using randomly amplified polymorphic DNA (RAPD) and multilocus sequence typing (MLST). RAPD was the best method used for detecting strain differences of B. mallei. It was suggested that this method would be an increasingly useful molecular epidemiological tool.     

Estimation of Jordanian isolated Pectobacterium cellulase,pectinase concentrations,RAPD polymorphism and their maceration activity

Forty-two Pectobacterium isolates were recovered from contaminated soil and rotted vegetables in Jordan. Twenty of them were belonged to; Pectobacterium carotovorum subsp. Carotovorum (Pbc) (= Erwinia carotovora subsp. carotovora), 11 isolates were belonged to Pectobacterium atrospeticum (= Erwinia carotovora subsp. atroseptica) (Pba) and 11 isolates were not classifiable (Pbs). Maceration activity of the 42 proved their ability to macerate potato, carrot and radish slices. Maceration activity of the isolates either of the same subspecies or in between the isolates of different subspecies isolated from the same host or from different hosts was varied. The measured concentration in μM?ml^?1 of both cellulase and pectinase enzymes was variable too. The Rapid amplified polymorphic DNA-PCR finger printing of total genomic DNA using a pair of 10-mer oligonucleotide primers amplification showed similar DNA bands with some polymorphic variations amongst the isolates.     

Differentiation of Lactobacillus delbrueckii subspecies by ribotyping and amplified ribosomal DNA restriction analysis (ARDRA)

AIMS: To differentiate the subspecies of Lactobacillus delbrueckii, subsp. delbrueckii, subsp. lactis and subsp. bulgaricus. METHODS AND RESULTS: Amplified ribosomal DNA restriction analysis (ARDRA) and ribotyping were applied to over 30 strains. Both methods analyse the ribosomal genes which carry useful information about the evolutionary and taxonomic relationship among bacteria. The methods proved to be reliable and highly reproducible. ARDRA was applied to 16S rDNA, 23S rDNA and the IGS region, thus covering the whole rrn operon with eight restriction enzymes. Only EcoRI differentiated Lact. delbrueckii subsp. bulgaricus from Lact. delbrueckii subsp. delbrueckii/Lact. delbrueckii subsp. lactis, which confirmed the finding of other authors. Ribotyping with different enzymes under precisely optimized conditions revealed a high level of strain polymorphism. Only ribotyping with EcoRI allowed differentiation of the three subspecies on the basis of typical hybridization patterns. CONCLUSION: The successful differentiation of the three subspecies of Lact. delbrueckii by EcoRI ribotyping offers a new possibility for precise identification and differentiation of strains and new isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: Both methods could be used for differentiation of Lact. delbrueckii subspecies.     

Ribotyping of Fusobacterium necrophorum strains isolated from bovine and ovine hepatic abscesses

A microbiological study was made of 100 strains of Fusobacterium necrophorum isolated from hepatic abscesses in bovine and ovine herds. Differences between the biological activity and ribotypes within the two F. necrophorum subspecies were studied. Conventional methods identified 89 isolates as F. necrophorum subsp. necrophorum and 11 as F. necrophorum subsp. funduliforme. For ribotyping, 50 strains (35 F.n. subsp. necrophorum, 11 F.n. subsp. funduliforme and 4 reference strains) were digested with restriction endonucleases (HindIII, EcoRI and BamHI) and examined after hybridization with digoxigenin-labelled cDNA probe transcribed from a 16 and 23S rRNAs from Escherichia coli. The most discriminating restriction endonuclease enzymes for ribotyping were EcoRI and BamHI. The presence or absence of two distinct band of 5 kb (EcoRI) and 10.5 kb (BamHI) differentiated the two subspecies. This technique also revealed genetic differences between isolates which could be used in the epidemiological study of clinical processes caused by F. necrophorum.     

A proposed core genome scheme for analyses of the Salmonella genus

The salmonellae are found in a wide range of animal hosts and many food products for human consumption. Most cases of human disease are caused by S. enterica subspecies I; however as opportunistic pathogens the other subspecies (II-VI) and S. bongori are capable of causing disease. Loci that were not consistently present in all of the species and subspecies were removed from a previously proposed core genome scheme (EBcgMLSTv2.0), the removal of these 252 loci resulted in a core genus scheme (SalmcgMLSTv1.0). SalmcgMLSTv1.0 clustered isolates from the same subspecies more rapidly and more accurately grouped isolates from different subspecies when compared with EBcgMLSTv2.0. All loci within the EBcgMLSTv2.0 scheme were present in over 98% of S. enterica subspecies I isolates and should, therefore, continue to be used for subspecies I analyses, while the SalmcgMLSTv1.0 scheme is more appropriate for cross genus investigations.     

Genome-wide expression analysis of iron regulation in Burkholderia pseudomallei and Burkholderia mallei using DNA microarrays

Burkholderia pseudomallei and B. mallei are the causative agents of melioidosis and glanders, respectively. As iron regulation of gene expression is common in bacteria, in the present studies, we have used microarray analysis to examine the effects of growth in different iron concentrations on the regulation of gene expression in B. pseudomallei and B. mallei. Gene expression profiles for these two bacterial species were similar under high and low iron growth conditions irrespective of growth phase. Growth in low iron led to reduced expression of genes encoding most respiratory metabolic systems and proteins of putative function, such as NADH-dehydrogenases, cytochrome oxidases, and ATP-synthases. In contrast, genes encoding siderophore-mediated iron transport, heme-hemin receptors, and a variety of metabolic enzymes for alternative metabolism were induced under low iron conditions. The overall gene expression profiles suggest that B. pseudomallei and B. mallei are able to adapt to the iron-restricted conditions in the host environment by up-regulating an iron-acquisition system and by using alternative metabolic pathways for energy production. The observations relative to the induction of specific metabolic enzymes during bacterial growth under low iron conditions warrants further experimentation.     

Efficacy of Bacillus thuringiensis against Lesser Grain Borer, Rhyzopertha dominica (Coleoptera: Bostrichidae)

Toxins from 36 isolates, representative of all available subspecies of Bacillus thuringiensis, were tested against larvae and adults of the lesser grain borer, Rhyzopertha dominica. beta -Exotoxin was effective against both larvae and adults. Spore-crystal complexes of subspecies darmstadiensis isolates from Germany were effective against larvae. Isolates of subspecies darmstadiensis from the US and Japan were not effective. The degree of control achieved by even the best isolate was not economically satisfactory.     

Ossicular density in golden moles (Chrysochloridae)

The densities of middle ear ossicles of golden moles (family Chrysochloridae, order Afrosoricida) were measured using the buoyancy method. The internal structure of the malleus was examined by high-resolution computed tomography, and solid-state NMR was used to determine relative phosphorus content. The malleus density of the desert golden mole Eremitalpa granti (2.44 g/cm³) was found to be higher than that reported in the literature for any other terrestrial mammal, whereas the ossicles of other golden mole species are not unusually dense. The increased density in Eremitalpa mallei is apparently related both to a relative paucity of internal vascularization and to a high level of mineralization. This high density is expected to augment inertial bone conduction, used for the detection of seismic vibrations, while limiting the skull modifications needed to accommodate the disproportionately large malleus. The mallei of the two subspecies of E. granti, E. g. granti and E. g. namibensis, were found to differ considerably from one another in both size and shape.     

Salmonella virulence plasmid. Modular acquisition of the spv virulence region by an F-plasmid in Salmonella enterica subspecies I and insertion into the chromosome of subspecies II,IIIa, IV and VII isolates.

The spv operon is common to all Salmonella virulence plasmids. DNA hybridization analysis indicates that the spv region is limited in distribution to serovars of Salmonella enterica subspecies I, II, IIIa, IV, and VII and is absent from Salmonella bongori isolates. Among strains of subspecies II, IIIa, and VII, all isolates examined contained sequences that hybridized with the spv region. However, among isolates of subspecies I, DNA sequences capable of hybridizing with the spv region were found in some isolates of certain serovars. Furthermore, in isolates of subspecies I, the virulence plasmid was found in the same set of isolates as an F-related plasmid, as determined by the presence of the spv region of the virulence plasmid and the finO, traD, and repA sequences of the F-plasmid. The concordance of the virulence plasmid and all three F-plasmid sequences in subspecies I serovar Choleraesuis, Paratyphi, and Typhimurium is most easily explained if the spv region is carried in an F-related plasmid in these isolates. In contrast, among S. enterica subspecies II, IIIa, IV, and VII, the isolates that contain spv sequences did not hybridize with an F-related plasmid or any other identifiable plasmid. With the use of pulse-field gel electrophoresis, the spv region in subspecies II, IIIa, and VII was found to be encoded on the chromosome. Analysis of the phylogenetic distribution of spv among Salmonella isolates and comparative nucleotide sequence analysis of spvA and spvC suggests that the spv region was acquired very recently, after speciation of the salmonellae.     

DNA:DNA reassociation analysis of Aeromonas salmonicida

DNA from 26 Aeromonas salmonicida strains, namely 11 'typical' and 15 so-called 'atypical' strains, was used to assess the taxonomic relatedness within the species. The genomes were characterized by determination of DNA base composition, DNA:DNA reassociation, calculation of sequence divergence following reassociation, and by genome size estimations. By comparison with DNA obtained from controls and the Aeromonas hydrophila group, A. salmonicida strains were determined to be correctly placed with respect to genus and species. A. salmonicida subspecies salmonicida (the 'typical' group) was an extremely homogeneous taxon. The 'atypical' strains were more diverse, but distinct biotypes were recognizable. The first biotype included several geographically diverse isolates from goldfish. The second recognizable biotype included strains isolated from European carp. Other 'atypical' isolates could not be grouped but showed enough internal homology to be retained within the species. The A. salmonicida subspecies achromogenes and masoucida were found to be closely related to the motile aeromonads. It is considered that the present classification of A. salmonicida is unsuitable and should be restructured to include A. salmonicida subspecies salmonicida, subspecies achromogenes (to include the present subspecies masoucida), and the reintroduced subspecies nova.     

Evaluation of a ribosomal RNA gene probe for the identification of species and subspecies within the genus Staphylococcus.

To evaluate a 16S rRNA gene probe for the identification of staphylococcal species and subspecies, we have augmented previous studies involving 12 staphylococcal species by analysing the remaining 16 species currently classified in the genus Staphylococcus. HindIII- and EcoRI-restricted DNA of isolates from validly described species of Staphylococcus was probed with radiolabelled plasmid pBA2 containing 16S rDNA from Bacillus subtilis. The Dice coefficient was used to assess similarity between the 74 HindIII- and the 81 EcoRI-hybridization patterns obtained from a total of 271 isolates belonging to 31 staphylococcal taxa (28 species, of which three include two subspecies). The use of HindIII yielded a better discrimination of the staphylococci than the use of EcoRI. All of the isolates belonging to the same species or subspecies, except S. hyicus isolates, were recovered as homogeneous clusters using their HindIII hybridization patterns. The phenotypically close taxa were clearly distinguished. Thus, the method presented in this study constitutes a powerful tool for the identification of taxa within the genus Staphylococcus.     

Characterization of Saccharomyces cerevisiae strains from spontaneously fermented maize dough by profiles of assimilation, chromosome polymorphism, PCR and MAL genotyping

Several isolates of Saccharomyces cerevisiae from indigenous spontaneously fermented maize dough have been characterized with the purpose of selecting appropriate starter cultures and methods for their subspecies typing. The techniques applied included assimilation of carbon compounds by the API ID 32 C kit, determination of chromosome profiles by PFGE, PCR and MAL genotyping. For the 48 isolates investigated, use of the API ID 32 C kit resulted in eight different assimilation profiles. The most common assimilation profile was the ability of 50% of the isolates to assimilate galactose, saccharose, DL-lactate, raffinose, maltose and glucose. Both chromosome and PCR profiles could be used for subspecies typing of the isolates and on this basis, the isolates were grouped into clusters. The discriminative power of the two techniques was equal; a few isolates not separated by their chromosome profiles could be separated by their PCR profiles and vice versa. Four different MAL genotypes were observed with MAL11 and MAL31 predominating. MAL11 was seen for all isolates whereas no evidence of MAL21 and MAL41 was observed. Based on the results obtained, a high number of Saccharomyces cerevisiae isolates were found to be involved throughout the spontaneous fermentation of maize dough. All methods included appeared to be suitable for subspecies typing. However, the discriminative power was highest for the PFGE and PCR techniques.     

A proposal to unify two subspecies of Staphylococcus equorum: Staphylococcus equorum subsp. equorum and Staphylococcus equorum subsp. linens

Twelve isolates from jeotgal, a Korean high-salt-fermented seafood, identified as Staphylococcus equorum were compared by phenotypic and genotypic methods to determine their precise taxonomic identities at the subspecies level. Four strains and three strains had complete 16S rRNA gene sequence matches with S. equorum subsp. equorum DSM 20674^T and S. equorum subsp. linens DSM 15097^T, respectively. Five strains showed 99.9 % identity with the sequences of both type strains. In our DNA–DNA hybridization analyses among two type strains and two isolates, the similarities were over 72 % and were higher than the similarities presented at the subspecies proposal. Physiological characteristics such as sugar utilization, β-galactosidase activity, novobiocin resistance and salt tolerance, which were adopted for subspecies separation, could not be applied to assign the isolates to a taxonomic unit. Antibiotic susceptibility, hemolytic activity, biofilm formation and protein profiles did not present markers to divide the isolates into either of the subspecies. Multilocus sequence typing of the sequences of the 16S rRNA gene and five housekeeping genes did not produce any coherent relationship among the isolates and type strains. Repetitive element-PCR fingerprinting using ERIC (enterobacterial repetitive intergenic consensus) primers classified 12 isolates to three genotypes, and the genotypes of both type strains coincided with two isolates expressing different characteristics. Based on these phenotypic and genotypic analyses results, we propose to unify the present two subspecies of S. equorum into one species, S. equorum.     

Salmonella diversity associated with wild reptiles and amphibians in Spain

During the spring and summer of 2001, faeces from 166 wild reptiles (94 individuals) and amphibians (72 individuals) from 21 different species found in central Spain were examined for the presence of Salmonella. Thirty-nine reptiles (41.5%) yielded 48 Salmonella isolates, whereas all the amphibians examined were negative. Subspecies Salmonella enterica enterica (I) accounted for up to 50% of isolates. Fourteen isolates (29.2%) belonged to subspecies diarizonae (IIIb), six isolates (12.5%) to subspecies salamae (II), and four isolates (8.3%) to subspecies arizonae (IIIa). Twenty-seven different serotypes were identified. Serotypes Anatum (12.5%), Herzliya (8.3%), Abony, 18:l,v:z, 9,12:z29:1,5 and 38:z10:z53 (6.2%/each) were the most frequently isolated. A high percentage (39.6%) of isolates belonged to serotypes previously associated with environmental sources. Also, 37.5% of isolates belonged to serotypes which had been related to human cases of salmonellosis. From these data, it is concluded that wild reptiles, but apparently not amphibians, may represent an important reservoir of Salmonella in nature and have potential implications for public health.     

Genetic variation and relationships between isolates and species of the entomopathogenic nematode genus Heterorhabditis deciphered through isozyme profiles

We studied variation in isozyme patterns of 8 metabolic enzymes in 5 species of Heterorhabditis (H. bacteriophora, H. indica, H. marelata, H. megidis, and H. zealandica) comprising 18 isolates. Isozyme banding patterns of all the 8 enzymes were species specific; however, 3 enzymes, i.e., arginine kinase, fumarate hydratase, and malate dehydrogenase, displayed distinct patterns among all the 18 isolates. Phylogenetic analysis of the isozyme patterns produced dendrograms depicting a high degree of genetic variation among Heterorhabditis species, with the average pairwise distance of 0.2000. Trees constructed using different phylogenetic methods showed a relatively close genetic relationship between H. megidis and H. zealandica and between H. bacteriophora and H. indica. Also, H. bacteriophora HP88 was the most distant species from H. megidis (UK isolate), H. marelatus (Oregon isolate), and H. zealandica (X1 isolate) with pairwise distance of 0.1957, 0.2228, and 0.2120, respectively. Phylogenetic analysis also revealed genetic variation among H. bacteriophora isolates with the average pairwise distance of 0.1507. GPS2 and GPS3 were the most closely related isolates with the average distance of only 0.0870, followed by GPS1 and GPS2 with average distance of 0.1087. In contrast, KMD19 and HP88, OH25, and HP88, and OH25 and Acows isolates were the most divergent populations with a pairwise distance of 0.2011 and 37 character differences. Pairwise distance analysis also revealed that genetic divergence among populations of H. bacteriophora is relatively independent of geographic distance. Overall, these results demonstrate strong subspecies structuring in H. bacteriophora.