Genetic transfer systems in Bacteroides: cloning and mapping of the transferable tetracycline-resistance locus

Development of a noninvasive reporter system for gene expression in Porphyromonas gingivalis

Several reports have supported the association of Porphyromonas gingivalis with periodontal disease. Genetic studies are vital for understanding the relative importance of virulence factors in this organism. Thus, gene reporters may prove useful for the study of gene expression in this organism. We have investigated the use of the green fluorescent protein (GFP), bacterial luciferase, and bifunctional xylosidase/arabinosidase enzyme (XA) as reporters of gene expression in P. gingivalis. Fusion cassettes containing the promoterless tetracycline resistant gene [tetA(A)Q2] and the promoterless gfp, luxAB, or xa gene were placed under the control of the rgpA promoter in P. gingivalis W83 using recombinational allelic exchange. The rgpA gene encodes for an arginine-specific protease in P. gingivalis. No GFP activity was detected in P. gingivalis isogenic mutants carrying the rgpA::gfp-tetA(Q)2 fusion construct. Luciferase activity in P. gingivalis mutants carrying the rgpA::luxAB-tetA(Q)2 fusion was only detected in the presence of exogenous FMNH(2). xa gene expression in P. gingivalis with the rgpA::xa-tetA(Q)2 fusion construct was detected in crude extracts using rho-nitrophenol derivatives as substrate and on agar plates with methylumbelliferyl derivatives under long-wave ultraviolet light. This indicates that both luxAB and xa genes can be used as reporters of gene expression in P. gingivalis. However, only the xa gene can be used as a noninvasive reporter gene.

New tetracycline resistance determinants coding for ribosomal protection in streptococci and nucleotide sequence of tet(T) isolated from Streptococcus pyogenes A498

An approach based on PCR has been developed to identify new members of the tet gene family in streptococci resistant to tetracycline and minocycline. Degenerate primers, corresponding to portions of the conserved domains of the proteins Tet(M), Tet(O), TeTB(P), Tet(Q), and Tet(S), all specifying the tetracycline-minocycline resistance phenotype, were used to selectively amplify DNA fragments within the coding sequences. Nine streptococcal strains which do not carry the genes tet(M), tet(O), tetB(P), tet(Q), or tet(S) were investigated. Four of them gave no detectable PCR products. The five remaining strains each yielded a PCR product of 1.1 kbp. DNA hybridization experiments showed that these putative Tet determinants fell into four new hybridization classes, of which one, Tet T, was further analyzed. The gene tet(T) was isolated from Streptococcus pyogenes A498, and the nucleotide sequence that was necessary and sufficient for the expression of tetracycline resistance in Escherichia coli was determined. The deduced Tet(T) protein consists of 651 amino acids. The protein most closely related to Tet(T) was Tet(Q), which has 49% identical amino acid residues. A phylogenetic analysis revealed that Tet T represents a novel branching order among the Tet determinants so far described.

The hemagglutinin genes hagB and hagC of Porphyromonas gingivalis are transcribed in vivo as shown by use of a new expression vector

The hemagglutinin genes hagB and hagC of Porphyromonas gingivalis, a putative periodontopathic microorganism, have been cloned, sequenced, and characterized. However, the roles of these putative virulence genes have not yet been determined. In this study, an in vivo expression technology vector termed pPGIVET was constructed and used to determine if hagB and hagC were expressed during an infectious process. We constructed pPGIVET as a conjugative suicide plasmid containing a multiple-cloning site (MCS) upstream of two tandem promoterless reporter genes that encode tetracycline resistance [tetA(Q)2] and galactokinase (galK). The promoter and a portion of the open reading frame (ORF) of hagB were inserted into the MCS in both a positive and a negative orientation relative to the reporter genes. These constructs were conjugated into P. gingivalis 381. Southern blot analysis of different transconjugants indicated that Campbell insertions had occurred at the chromosomal hagB locus and also at the hagC locus, which has high (99%) homology to the ORF of hagB. pPGIVET-labeled clones in which the hag promoters were positively oriented relative to the reporter genes expressed tetracycline resistance and galactokinase activity in vitro and in vivo at significantly higher levels than did the wild-type strain or clones in which the hag promoters were negatively oriented. Expression of tetracycline resistance allowed substantial enrichment of heterodiploids over wild-type cells during a mixed infection in the mouse abscess model. These results indicate that hagB and hagC are transcriptionally active in vivo and suggested that pPGIVET may be used to isolate P. gingivalis genes expressed only during an infectious process.

Detection and prevalence of the tetracycline resistance determinant Tet Q in the microbiota associated with adult periodontitis

Subgingival plaque samples were collected from 68 patients with a history of moderate to severe adult periodontitis and enumerated on Trypticase-soy blood agar plates, with and without tetracycline at 4 micrograms/ml. Each different colony morphotype was enumerated, and a representative colony was subcultured for identification and examined for the tetracycline resistance gene tet(Q) by polymerase chain reaction (PCR) amplification and DNA hybridization, using a fragment of tetA(Q)2 from Bacteroides fragilis 1126. PCR primers (5'-GGCTTCTACGACATCTATTA-3' and 5'-CATCAACATTTATCTCTCTG-3') were chosen to amplify a 755 bp region of tet(Q). The subgingival plaque samples were also tested by PCR. Approximately 12% of the total cultivable flora was resistant to tetracycline, and the percentage of the tetracycline-resistant cultivable flora with the tet(Q) gene varied greatly from one patient to another with a range from 0.0 to 67%. Half of the 68 subgingival plaque samples were positive or weakly positive for tet(Q) by PCR. Approximately 15% of the 210 isolates subcultured with resistance to tetracycline, (> or = 4 micrograms/ml) contained tet(Q), and 60% contained tet(M). All of the tet(Q)-resistant isolates were gram-negative anaerobic bacilli and included all of the Prevotella and Bacteroides isolates.

The tet(Q) gene in bacteria isolated from patients with refractory periodontal disease

Twenty-two tetracycline-resistant (tetr) anaerobic and facultative anaerobic bacteria isolated from periodontal pockets of 12 patients with refractory periodontitis were examined for the presence of the Tet Q determinant by DNA-DNA hybridization. Dot blots of bacterial DNA were tested with an intragenic digoxigenin-labelled tet(Q) probe consisting of a 1.45 kb EcoRI/PvuII fragment from plasmid pNFD13-2. Southern blots of chromosomal DNA digested with the restriction enzyme EcoRI were also examined. The tet(Q) probe hybridized with DNA from 8 of the 22 tetr strains, including 2 Prevotella intermedia strains and one strain each of Prevotella nigrescens, Prevotella loescheii, Prevotella veroralis and Prevotella melaninogenica. The tetr strains of Mitsuokella dentalis and Capnocytophaga ochracea also hybridized with the probe. The lack of discernible plasmid DNA in all the probe-positive isolates suggests that these tetracycline-resistance genes were chromosomally encoded. The probe hybridized with a different size fragment in all the isolates. This study extends the number of species that carry the tet(Q) gene to include several outside the genera Prevotella and Bacteroides.

Sequencing of a tet(Q) gene isolated from Bacteroides fragilis 1126

Recently, Tet Q, a tetracycline resistance determinant that confers resistance by a ribosome protection mechanism, was described and added to the two previously described classes, Tet M and Tet O. The first representative of this class, tetA(Q)1, was isolated from Bacteroides thetaiotaomicron DOT. We report the sequencing of a gene isolated from B. fragilis 1126 which also confers tetracycline resistance. Because of its high degree of identity (97%) with the tetA(Q)1 gene, we defined it as tetA(Q)2. MIC studies revealed that tetA(Q)2 provides a low level of resistance to tetracycline when cloned into Escherichia coli. The extensive homology between tetA(Q)1 and tetA(Q)2 supports the idea of a recent horizontal transfer of tet(Q) genes among Bacteroides spp.

Identification of a circular intermediate in the transfer and transposition of Tn4555, a mobilizable transposon from Bacteroides spp

Transmissible cefoxitin (FX) resistance in Bacteroides vulgatus CLA341 was associated with the 12.5-kb, mobilizable transposon, Tn4555, which encoded the beta-lactamase gene cfxA. Transfer occurred by a conjugation-like mechanism, was stimulated by growth of donor cells with tetracycline (TC), and required the presence of a Bacteroides chromosomal Tcr element. Transconjugants resistant to either FX, TC, or both drugs were obtained, but only Fxr Tcr isolates could act as donors of Fxr in subsequent matings. Transfer of Fxr could be restored in Fxr Tcs strains by the introduction of a conjugal Tcr element from Bacteroides fragilis V479-1. A covalently closed circular DNA form of Tn4555 was observed in donor cells by Southern hybridization, and the levels of this circular transposon increased significantly in cells grown with TC. Both the cfxA gene and the Tn4555 mobilization region hybridized to the circular DNA, suggesting that this was a structurally intact transposon unit. Circular transposon DNA purified by CsCl-ethidium bromide density gradient centrifugation was used to transform Tcs B. fragilis 638, and Fxr transformants were obtained. Both the circular form and the integrated Tn4555 were observed in transformants, but the circular form was present at less than one copy per chromosomal equivalent. Examination of genomic DNA from Fxr transformants and transconjugants revealed that Tn4555 could insert at a wide variety of chromosomal sites. Multiple transposon insertions were present in many of the transconjugants, indicating that there was no specific barrier to the introduction of a second transposon copy.

Chromosomal gene transfer elements of the Bacteroides group

Many human colonic Bacteroides strains carry large ( > 60 kbp) chromosomal elements that can transfer themselves from the chromosome of the donor to the chromosome of the recipient. Most of these elements carry a tetracycline resistance gene (tetQ) and many also carry an erythromycin resistance gene (ermF), but at least one cryptic member of the family has been identified. Molecular analysis of excision and integration events has shown that the self-transmissible Bacteroides elements are not transposons but may represent a new class of integrating elements. The Bacteroides elements are most similar to the streptococcal conjugative transposons, such as Tn916. The Bacteroides Tcr/TcrEmr elements can mobilize DNA that is not contained within the elements themselves. They not only mobilize co-resident plasmids but also cause the excision, circularization and mobilization of discrete unlinked 10-11 kbp segments of chromosomal DNA. Self-transfer and other activities of the Tcr/TcrEmr elements are regulated by tetracycline. Thus, tetracycline not only selects for acquisition of an element but also stimulates element transfer in the first place.

Transfer of conjugal elements in oral black-pigmented Bacteroides (Prevotella) spp. involves DNA rearrangements

Conjugal genetic elements in isolates of oral black-pigmented Bacteroides denticola (Prevotella denticola) and B. intermedius (P. intermedia) transfer tetracycline and penicillin resistance in the absence of plasmids. Transverse alternating-field electrophoresis of restricted chromosomal DNAs from transconjugants revealed arrangements indicating that transfer and insertion can involve more than one 60-kb copy of the elements and occurs at strongly preferred sites in the recipient chromosome.

Heterologous gene expression in Bacteroides fragilis

Bacteroides fragilis and other gastrointestinal tract Bacteroides are unusual gram-negative eubacteria in that genes from other gram-negative eubacteria are not expressed when introduced into these organisms. To analyze gene expression in Bacteroides, expression vector and promoter probe (detection) vector systems were developed. The essential feature of the expression vector was the incorporation of a Bacteroides insertion sequence element, IS4351, which possesses promoter activity directed outward from its ends. Genes inserted into the multiple cloning site downstream from an IS4351 DNA fragment were readily expressed in B. fragilis. The chloramphenicol acetyltransferase (cat) structural gene from Tn9 was tested and conferred chloramphenicol resistance on B. fragilis. Both chloramphenicol resistance and CAT activity were shown to be dependent on the IS4351 promoters. Similar results were obtained with the Escherichia coli beta-glucuronidase gene (uidA) but activity was just 30% of the levels seen with cat. Two tetracycline resistance determinants, tetM from Streptococcus agalactiae and tetC from E. coli, also were examined. tetC did not result in detectable tetracycline resistance but the gram-positive tetM gene conferred high-level resistance to tetracycline and minocycline in Bacteroides hosts. Based on the cat results, promoter probe vectors containing the promoterless cat gene were constructed. These vectors were used to clone random B. fragilis promoters from partial genomic libraries and the recombinants displayed a range of CAT activities and chloramphenicol MICs in B. fragilis hosts. In addition, known E. coli promoters (Ptet, Ptac, Ptrc, Psyn, and P1P2rrnB) were tested for activity in B. fragilis. No chloramphenicol resistance or CAT activity was observed in B. fragilis with these promoters.

Molecular survey of clindamycin and tetracycline resistance determinants in Bacteroides species

We have examined 13 clinical isolates of the intestinal Bacteroides group using DNA probes representing Bacteroides macrolide-lincosamide-streptogramin B (MLS) (ermF) and tetracycline resistance (tetQ) determinants as well as an insertion sequence (IS4351) previously seen in association with erm genes. tetQ-hybridizing sequences were detected in 11 of 13 tetracycline-resistant clinical isolates. On the other hand, ermF-like sequences were detected in only three of eight clindamycin-resistant strains. One isolate displayed low-level, inducible resistance to clindamycin and was sensitive to erythromycin. This same isolate had IS4351-like sequences but was missing ermF-like sequences, in contrast to previous reports which demonstrated the common association of IS4351 and erm genes. Our results suggest the occurrence of unclassified MLS genes in the Bacteroides group and furthermore suggest that IS4351-like sequences are not always linked to Bacteroides ermF-like sequences. Finally, 4 of 13 isolates conjugally transferred tetracycline resistance or linked tetracycline-clindamycin (MLS) resistances, but this process did not involve plasmids.

A site-specific DNA inversion in Bacteroides plasmid pBF4 is influenced by the presence of the conjugal tetracycline resistance element

pBF4 is a 42-kb R plasmid from Bacteroides fragilis which transfers clindamycin resistance (Clr) independently of the chromosomal tetracycline resistance (Tcr) transfer element. We have found that this plasmid exists in two nonequimolar conformations, A and B. These forms differ by an inversion of approximately 11.5 kb which does not involve the repeated DNA sequences previously mapped on the plasmid. The presence of chromosomal tetracycline resistance conjugal elements influences the relative amounts of the two conformations: induction with tetracycline shifts the dominant form from B to A.

The RNA polymerases of Porphyromonas gingivalis and Fusobacterium nucleatum are unrelated to the RNA polymerase of Escherichia coli

Western blot analysis that used antisera to the E. coli core enzyme and sigma factors was used for examination of the RNA polymerase of Actinobacillus actinomycetemcomitans, Streptococcus mutans, Fusobacterium nucleatum, and Porphyromonas gingivalis. Both antisera reacted with proteins in A. actinomycetemcomitans and S. mutans whole-cell extracts. Reactions were seen with some F. nucleatum proteins when the anti-core RNA polymerase antisera were used, but the cross-reacting proteins were not of an expected molecular weight for beta or beta'. No reaction with F. nucleatum proteins was seen when extracts were reacted with antisera to E. coli sigma factor. There were no cross-reacting proteins detected in P. gingivalis extracts with either antisera. These results suggest that E. coli RNA polymerase may not be sufficiently similar to P. gingivalis and F. nucleatum RNA polymerase for E. coli RNA polymerase to recognize P. gingivalis or F. nucleatum promoters. Partially purified P. gingivalis and F. nucleatum RNA polymerase exhibited a specificity for a P. gingivalis DNA template, while having a decreased activity from an E. coli DNA template. The antibiotic sensitivity profile of P. gingivalis and F. nucleatum RNA polymerase activity was shown to differ from that of E. coli, with these activities not being affected by rifampicin, streptovaricin, or streptolydigin. We conclude that the efficient cloning and expression of P. gingivalis and F. nucleatum genes in E. coli will require the use of promoter-containing expression vectors.

Sequencing the gene for an imipenem-cefoxitin-hydrolyzing enzyme (CfiA) from Bacteroides fragilis TAL2480 reveals strong similarity between CfiA and Bacillus cereus beta-lactamase II

Using a newly constructed Bacteroides fragilis-Escherichia coli cloning shuttle vector, pJST61, we have cloned the cefoxitin (FOX)-imipenem (IMP) resistance determinant from B. fragilis TAL2480. FOX-IMP resistance in this strain results from the production of a periplasmic, Zn2(+)-containing beta-lactamase which hydrolyzes carbapenems and cephamycins and whose activity is resistant to clavulanic acid but sensitive to Zn2(+)-binding reagents, including EDTA. The pJST61 vector permits efficient library construction in E. coli and allows for the transfer of the library to B. fragilis recipients for the screening or selection of specific phenotypes. The library clone containing the FOX-IMP resistance gene was detected after transfer to B. fragilis TM4000 (Fox-Imps) selecting for Foxr. One of the isolates carrying plasmid pJST241 is resistant to FOX and IMP and synthesizes a periplasmic protein with substrate and inhibitor properties identical to those of strain TAL2480. On the basis of deletion analysis, Tn1000 insertion mutations, and DNA sequencing, we have defined the 747-base cfiA (FOX-IMP resistance) gene within the 3.6-kilobase cloned insert in pJST241. The cfiA gene contains an open reading frame that could code for a precursor protein of 249 amino acids and with a molecular mass of 27,260 daltons. A potential signal sequence has been identified at the N terminus of this protein; cleavage within this sequence would result in a protein of 231 amino acids with a molecular mass of 25,249 daltons. The CfiA protein shows remarkable similarities to the exported, Zn2(+)-requiring, type II beta-lactamase Blm proteins from Bacillus cereus 569/H and 5/B/6. Although overall amino acid identity is only 32%, the Zn ligand-binding His and Cys residues are precisely conserved and the amino acids in the vicinity of these sites show strong similarities (greater than 80%) when the CfiA and Blm proteins are compared.