A putative type III secretion gene cluster is widely distributed in the Burkholderia cepacia complex but absent from genomovar I.

Using probes constructed from Ralstonia solanacearum and Burkholderia pseudomallei, putative type III secretion (TTS) genes were identified in Burkholderia cepacia J2315 (genomovar III). A cosmid clone containing DNA with homology to five TTS genes was sub-cloned and regions were sequenced in order to design oligonucleotides for polymerase chain reaction assays. These indicated that two putative TTS genes (bcscQ and bcscV) were present in all members of the B. cepacia complex with the exception of strains from genomovar I. Southern blot assays confirmed this observation, suggesting that the lack of a TTS gene cluster may define a major difference between B. cepacia genomovar I and other members of the B. cepacia complex, including genomovar III. In contrast to TTS gene clusters in other bacteria, a putative gene homologous to the virB1 gene of Brucella suis was located directly downstream of bcscQR.

Detection of type III secretion system genes in animal isolates of Bordetella bronchiseptica.

A cosmid clone bank of Bordetella bronchiseptica genomic DNA was screened for the presence of type III secretion (TTS) genes using a probe derived from the TTS system genes of Ralstonia solanacearum. A 3.35kb PstI fragment, sub-cloned from a hybridising cosmid clone, was sequenced and found to contain a 97bp overlap with the previously reported B. bronchiseptica bscIJKLNO TTS gene cluster. DNA and predicted protein homology analysis suggests that a bscPQRST cluster lies immediately downstream of bscIJKLNO. A PCR amplification assay indicated that the bscT locus was present in 27 B. bronchiseptica animal isolates tested (100%). Dot-blot DNA hybridisation using probes for bscT and bscP confirmed the presence of these loci in six canine isolates associated with a variety of clinical signs. Although TTS has been implicated in the pathogenicity of B. bronchiseptica, it is likely that different clinical manifestations may be due to variations in gene expression or host factors, rather than the absence or presence of TTS genes.

Evidence for the presence in Burkholderia pseudomallei of a type III secretion system-associated gene cluster.

Burkholderia pseudomallei, the causative agent of melioidosis, contains a cluster of putative genes homologous to those encoding HpaP, HrcQ, HrcR, HrcS and HrpV in the plant pathogen Ralstonia solanacearum. In R. solanacearum, these genes form part of a type III secretion-associated pathogenicity island. The order of the genes in B. pseudomallei is directly equivalent to that found in R. solanacearum. The B. pseudomallei proteins share 49.5% (HpaP), 52.6% (HrcQ), 80.0% (HrcR), 72.1% (HrcS) and 46.7% (HrpV) similarity, respectively, with their equivalent R. solanacearum proteins. The presence of type III secretion-associated genes in B. pseudomallei pathogens suggests a possible role for type III secretion systems in the pathogenicity of this organism.

Variation in flagellin genes and proteins of Burkholderia cepacia.

The majority of isolates of Burkholderia cepacia, an important opportunistic pathogen associated with cystic fibrosis, can be classified into two types on the basis of flagellin protein size. Electron microscopic analysis indicates that the flagella of strains with the larger flagellin type (type I) are wider in diameter. Flagellin genes representative of both types were cloned and sequenced to design oligonucleotide primers for PCR amplification of the central variable domain of B. cepacia flagellin genes. PCR-restriction fragment length polymorphism analysis of amplified B. cepacia flagellin gene products from 16 strains enabled flagellin type classification on the basis of product size and revealed considerable differences in sequence, indicating that the flagellin gene is a useful biomarker for epidemiological and phylogenetic studies of this organism.

Flagellin gene variation between clinical and environmental isolates of Burkholderia pseudomallei contrasts with the invariance among clinical isolates.

The flagellin gene sequence from a clinical isolate of Burkholderia pseudomallei was used to design oligonucleotide primers for PCR/RFLP analysis of flagellin gene variation among clinical and environmental isolates of B. pseudomallei. Genes from four clinical and six environmental isolates were amplified and compared by RFLP. The clinical isolates were indistinguishable, but variation was detected among some of the environmental isolates. Sequence analysis of flagellin gene amplified products demonstrated high levels of conservation amongst the flagellin genes of clinical isolates (>99% similarity), compared to the variation observed between the clinical isolates and one of the environmental isolates (<90% similarity). Genomic comparisons with pulsed-field gel electrophoresis (PFGE) revealed differences between the relationships inferred by flagellin genotyping and PFGE, suggesting that a combination of molecular methods may be useful for the subtyping of B. pseudomallei strains.

Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis.

The presence of methanogenic bacteria was assessed in peat and soil cores taken from upland moors. The sampling area was largely covered by blanket bog peat together with small areas of red-brown limestone and peaty gley. A 30-cm-deep core of each soil type was taken, and DNA was extracted from 5-cm transverse sections. Purified DNA was subjected to PCR amplification with primers IAf and 1100Ar, which specifically amplify 1.1 kb of the archaeal 16S rRNA gene, and ME1 and ME2, which were designed to amplify a 0.75-kb region of the alpha-subunit gene for methyl coenzyme M reductase (MCR). Amplification with both primer pairs was obtained only with DNA extracted from the two deepest sections of the blanket bog peat core. This is consistent with the notion that anaerobiosis is required for activity and survival of the methanogen population. PCR products from both amplifications were cloned, and the resulting transformants were screened with specific oligonucleotide probes internal to the MCR or archaeal 16S rRNA PCR product. Plasmid DNA was extracted from probe-positive clones of both types and the insert was sequenced. The DNA sequences of 8 MCR clones were identical, as were those of 16 of the 17 16S rRNA clones. One clone showed marked variation from the remainder in specific regions of the sequence. From a comparison of these two different 16S rRNA sequences, an oligonucleotide was synthesized that was 100% homologous to a sequence region of the first 16 clones but had six mismatches with the variant. This probe was used to screen primary populations of PCR clones, and all of those that were probe negative were checked for the presence of inserts, which were then sequenced. By using this strategy, further novel methanogen 16S rRNA variants were identified and analyzed. The sequences recovered from the peat formed two clusters on the end of long branches within the methanogen radiation that are distinct from each other. These cannot be placed directly with sequences from any cultured taxa for which sequence information is available.

The large plasmids found in enterohemorrhagic and enteropathogenic Escherichia coli constitute a related series of transfer-defective Inc F-IIA replicons.

Forty-six of 52 (88.5%) enterohemorrhagic Escherichia coli (EHEC) strains screened carried a "common" plasmid of about 90 kb which encoded sequences homologous to the Inc F-IIA replicon. A similarly high incidence of Inc F-IIA plasmid-containing strains was observed in other groups of diarrheagenic E. coli, but not in random environmental coliform isolates. Enteropathogenic E. coli (EPEC) contain plasmids of similar properties and share a 23-kb DNA fragment with plasmids from EHEC. The common region encodes the F-IIA replication region and sequences homologous to the transfer operon of the Inc F-II plasmid R1. Sequence homology varied between plasmids isolated from different EHEC/EPEC strains with > 80% showing homology to the regions encoding the rep and par genes. Only 5% of plasmids from EHEC strains had intact sequences homologous to the DNA between these two regions, including the oriT site. Some plasmids with an apparently intact tra operon still failed to plaque F-pilus-specific phages. This is consistent with observations that the large plasmids of EHEC and EPEC are phenotypically nonconjugative. These results suggest that the large plasmids of EHEC/EPEC constitute a family of transfer-deficient Inc F-IIA plasmids with varying degrees of deletion in tra function. The evolutionary ramifications of this finding are considered.

Incidence of common DNA sequences in bovine and porcine Escherichia coli strains causing diarrhoea.

Seventeen bovine and 56 porcine Escherichia coli isolates from cases of diarrhoea and from healthy animals were examined for DNA sequences homologous to the genes for verocytotoxins (VT), enterotoxins and human enterohaemorrhagic E coli/enteropathogenic E coli (EHEC EPEC) sequences. VT-1 was the most common toxin among the bovine isolates and VT-2 the most common in the porcine isolates. No isolates had homologous sequences to enteropathogenic adherence factor, but 71.2 per cent hybridised to the DNA probe encoding specific EHEC sequences, and 95.9 per cent showed homology with a 23 kb DNA fragment common to EHEC and EPEC plasmids.

Molecular cloning and characterisation of the genes for a non-fimbrial adhesin from Escherichia coli.

A non-fimbrial adhesin (NFA-1) from the uropathogenic Escherichia coli strain 827 responsible for agglutination of human erythrocytes was cloned using the cos 4 cosmid vector. A clone was isolated which promoted haemagglutination and showed the same biological properties as the adhesin produced by the wild type strain. Both express adhesin at 37 degrees C, but not 18 degrees C nor in the presence of 1% glucose. Adhesin purified from the clone formed high molecular weight aggregates which were resolved to the 21 K dalton subunit protein seen in the wild type strain on denaturation. Binding to human kidney cells by the clone and the wild type E. coli, from which the genes were cloned, were compared in an ELISA assay and shown to be the same. The genes for the adhesin were isolated on a 15.5 kilobase BamHI-EcoRI fragment which was subjected to gamma delta mutagenesis. The NFA-1 operon was localised to a 6.5kb region of this fragment.

A block of urovirulence genes encoding multiple fimbriae and hemolysin in Escherichia coli O4:K12:H-.

Cosmid gene libraries were constructed from a uropathogenic isolate of Escherichia coli O4:K12:H- that secretes alpha-hemolysin and produces the F14, F12-rel, F1C, and F13 fimbrial antigens. A series of overlapping clones was generated, and individual cosmid clones were found to express various combinations of fimbriae and hemolysin, suggesting that the genes for these potential virulence factors are closely linked. By using Southern hybridization analysis and restriction endonuclease mapping, it was demonstrated that the cosmid clones carried a nested set of overlapping, cloned, genomic DNA fragments. A comparison of the phenotypic properties of individual cosmid clones and subclones allowed the order of the gene clusters encoding these factors to be deduced. The cloning also revealed the presence of a fifth fimbria that had P-adhesin specificity.

Acquisition of a gene encoding mannose-resistant haemagglutinating fimbriae by a resistance plasmid during long-term urinary infection.

Urine was collected twice weekly from one patient during a 25-month period. Escherichia coli harbouring a resistance plasmid, pUK28, which confers trimethoprim, ampicillin, sulphamethoxazole, spectinomycin and streptomycin resistance was identified in the urine. Carriage of strains containing plasmid pUK28 was observed during three separate periods which totalled 16 months, even though the patient did not receive antibacterial drug therapy for most of that time. The plasmid was able to acquire the genes responsible for mannose-resistant haemagglutination and these genes were increasingly associated with the plasmid towards the end of the study period.

The transfer of genes encoding production of mannose-resistant haemagglutinating fimbriae from uropathogenic enterobacteria.

Two hundred and thirty-seven bacterial strains, isolated from patients with urinary tract infections, were examined for the presence of plasmid-determined fimbrial adhesins. Ninety-nine strains were capable of producing mannose-resistant haemagglutination. Seventeen of these strains possessed transferable resistance plasmids and 11 of these were also able to transfer the mannose-resistant haemagglutination gene, suggesting that it was carried on the R plasmid or had been mobilized by it.

The effect of a range of antimicrobial drugs on the haemagglutination of two clinical isolates from urinary tract infections.

A range of nine common antimicrobial drugs were tested for their effect on adhesion of the mannose-resistant haemagglutination-positive Proteus vulgaris strain BH77 and Escherichia coli strain BH121, isolated from patients with urinary tract infections. Minimum inhibitory concentrations of the antimicrobials for these strains were determined in Mueller-Hinton broth and the effect of each antimicrobial, at the quarter MIC values, on the haemagglutination of the strains was then determined. Haemagglutination could only be prevented by inhibitors of protein synthesis. After the introduction of an R-plasmid into strain BH121 this effect was annihilated. When the new MICs were determined, the inhibition was still observed at the new quarter MIC values.