Sequence homology of clindamycin resistance determinants in clinical isolates of 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.

Conjugal transfer of antibiotic resistance factors in Bacteroides fragilis: the btgA and btgB genes of plasmid pBFTM10 are required for its transfer from Bacteroides fragilis and for its mobilization by IncP beta plasmid R751 in Escherichia coli

Transferable plasmids play an important role in the dissemination of clindamycin-erythromycin resistance in Bacteroides fragilis. We previously described the isolation and properties of pBFTM10, a 14.9-kb ClnR transfer factor from B. fragilis TMP10. We also reported the isolation of a transfer-deficient deletion derivative of pBFTM10 contained in the B. fragilis-Escherichia coli shuttle vector pGAT400. In the present study we used pGAT400 and a similar shuttle vector, pGAT550, to characterize and sequence a region of pBFTM10 required for its transfer from B. fragilis to B. fragilis or E. coli recipients and for its mobilization by the broad-host-range plasmid R751 from E. coli donors to E. coli recipients. Deletion of certain BglII restriction fragments from pBFTM10 resulted in partial or complete loss of transfer ability. Tn1000 insertions into this same region also resulted in altered transfer properties. We used the sites of Tn1000 insertions to determine the DNA sequence of the transfer region. Two potential open reading frames encoding proteins of 23.2 and 33.8 kDa, corresponding to two genes, btgA or btgB, were identified in the sequence. Tn1000 insertions within btgA or btgB or deletion of all or portions of btgA or btgB resulted in either a transfer deficiency or greatly reduced transfer from B. fragilis donors and alterations in mobilization by R751 in E. coli. A potential oriT sequence showing similarity in organization to the oriT regions of the IncP plasmids was also detected. Thus, pBFTM10 encodes and requires at least two proteins necessary for efficient transfer from B. fragilis. These same functions are expressed in E. coli and are required for mobilization by R751.

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.

Susceptibility testing of anaerobic bacteria: myth, magic, or method?

The demand for susceptibility testing of anaerobes has increased, yet consensus as to procedure and interpretation in this area has not been achieved. While routine testing of anaerobic isolates is not needed, certain isolates in specific clinical settings should be tested. Also, laboratories may monitor their local antibiograms by doing periodic surveillance batch testing. The National Committee for Clinical Laboratory Standards has published a protocol of methods approved for susceptibility testing of anaerobic bacteria. Both agar and broth microdilution are included; however, the broth disk elution method is no longer approved by the National Committee for Clinical Laboratory Standards because of method-related interpretive errors. A number of newer methods are undergoing evaluation and seem promising. Clinicians and microbiologists reviewing susceptibility reports should be aware of sources of variability in the test results. Variables in susceptibility testing of anaerobes include the media and methods used, organisms chosen for testing, breakpoints chosen for interpretation, antibiotic, and determination of endpoint. Clustering of MICs around the breakpoint may lead to significant variability in test results. Adherence of testing laboratories to approved methods and careful descriptions of the method and the breakpoints used for interpretation would facilitate interlaboratory comparisons and allow problems of emerging resistance to be noted. A variety of resistance mechanisms occurs in anaerobic bacteria, including the production of beta-lactamase and other drug-inactivating enzymes, alteration of target proteins, and inability of the drug to penetrate the bacterial wall. Antimicrobial resistance patterns in the United States and abroad are described.

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.

Tn4399, a conjugal mobilizing transposon of Bacteroides fragilis

Conjugal transposons play an important role in the dissemination of antibiotic resistance determinants in the streptococci and have been postulated to exist in Bacteroides fragilis. To investigate the presence of conjugal transposons in B. fragilis, we employed a Tra- derivative of the transfer factor pBFTM10 contained in the chimeric plasmid pGAT400 delta BglII. We attempted to restore transferability to this plasmid from a series of transconjugants generated by crossing B. fragilis TMP230 containing the TET transfer factor with B. fragilis TM4000, a standard recipient. Transconjugant TM4.2321 transferred pGAT400 delta BglII to Escherichia coli HB101 at almost the same frequency as did the Tra+ parental plasmid, pGAT400. Analysis of the transferred plasmids revealed the presence of 9.6 kilobases of additional DNA in every case but at different positions in independent isolates. The presence of this DNA, designated Tn4399, allowed the pGAT400 delta BglII derivatives to retransfer from the TM4000 background to B. fragilis or E. coli recipients. DNA hybridization studies demonstrated the presence of one copy of Tn4399 in TMP230 and three copies at new sites in TM4.2321. Tn4399 is a new B. fragilis transposon with unique transfer properties that may play a role in the dissemination of drug resistance genes. It differs from previously described conjugal transposons by its ability to mobilize nonconjugal plasmids in cis.

Extrachromosomal systems and gene transmission in anaerobic bacteria

Obligately anaerobic bacteria are important in terms of their role as medical pathogens as well as their degradative capacities in a variety of natural ecosystems. Two major anaerobic genera, Bacteroides and Clostridium, are examined in this review. Plasmid elements in both genera are reviewed within the context of conjugal transfer and drug resistance. Genetic systems that facilitate the study of these anaerobic bacteria have emerged during the past several years. In large part, these developments have been linked to work centered on extrachromosomal genetic systems in these organisms. Conjugal transfer of antibiotic resistance has been a central focus in this regard. Transposable genetic elements in the Bacteroides are discussed and the evolution and spread of resistance to lincosamide antibiotics are considered at the molecular level. Recombinant DNA systems that employ shuttle vectors which are mobilized by conjugative plasmids have been developed for use in Bacteroides and Clostridium. The application of transmission and recombinant DNA genetic systems to study these anaerobes is under way and is likely to lead to an increased understanding of this important group of procaryotes.

Nucleic acid probes in clinical microbiology

The infectious disease applications of nucleic acid probe have been described. In addition, the basic procedures of nucleic acid probe technology have been discussed, as have the factors affecting implementation of probe technology in diagnostic laboratories. Despite the questions raised, nucleic acid probes will become part of the diagnostic laboratory in the near future. Commercial interests are developing and marketing new probes, reagents, and kits which will expedite the employment of this technology. High-volume reference laboratories will first use probes as part of a battery of tests which will include ELISA and monoclonal antibody methods. In all probability, probes will replace methods: that have proven to be ineffective, difficult, or costly such as culturing for some enteric pathogens and Legionella, that require long incubation periods, such as mycobacteria, or that have high costs and low yields, such as virology.

Recent advances in Bacteroides genetics

Bacteroides are Gram-negative, obligate anaerobes that are present in high concentrations within the intestinal tracts of humans and animals. Bacteroides are also important opportunistic pathogens of humans and animals. Methods for genetic manipulation of these important organisms have only recently begun to emerge. Shuttle vectors which can be transferred by conjugation between Escherichia coli to Bacteroides are now available. A method for transforming some strains of Bacteroides has been developed. Two Bacteroides transposons, Tn4351 and Tn4400, have been found and one of them, Tn4351, has been used for transposon mutagenesis of Bacteroides. Several different Bacteroides genes have now been cloned, including a gene that codes for resistance to clindamycin, genes that code for polysaccharidases (chondroitin lyase and pullulanase), and a gene that codes for a fimbrial subunit. These cloned genes have been used to study the organization and regulation of Bacteroides genes.

Beta-lactamase-mediated imipenem resistance in Bacteroides fragilis

Imipenem has excellent antimicrobial activity owing in part to beta-lactamase stability. We found that only 2 of over 350 Bacteroides fragilis group clinical isolates were resistant to imipenem, with an MIC of more than 16 micrograms/ml. These two isolates from the Tufts Anaerobe Laboratory (TAL) were resistant to all other beta-lactam agents tested. The organisms were able to inactivate imipenem in broth cultures and contained similar beta-lactamases that were able to hydrolyze carbapenems, cephamycins, cephalosporins, and penicillins. The molecular sizes of the beta-lactamases in TAL2480 and TAL3636 were estimated to be 44,000 daltons. The novel beta-lactamase contained Zn2+ as a cofactor. An additional factor contributing to resistance was determined. The outer membranes of these two organisms were found to limit free diffusion of the drugs into the periplasm. This novel beta-lactamase, associated with a barrier to drug permeation, resulted in high-grade beta-lactam drug resistance.

Tn4351 transposes in Bacteroides spp. and mediates the integration of plasmid R751 into the Bacteroides chromosome

The gene for resistance to erythromycin and clindamycin, which is carried on the conjugative Bacteroides plasmid, pBF4, has been shown previously to be part of an element (Tn4351) that transposes in Escherichia coli. We have now introduced Tn4351 into Bacteroides uniformis 0061 on the following two suicide vectors: (i) the broad-host-range IncP plasmid R751 (R751::Tn4351) and (ii) pSS-2, a chimeric plasmid which contains 33 kilobases of pBF4 (including Tn4351) cloned into the IncQ plasmid RSF1010 and which is mobilized by R751. When E. coli HB101, carrying either R751::Tn4351 or R751 and pSS-2, was mated with B. uniformis under aerobic conditions, Emr transconjugants were detected at a frequency of 10(-6) to 10(-5) (R751::Tn4351) or 10(-8) to 10(-6) (R751 and pSS-2). In matings involving pSS-2, all Emr transconjugants contained simple insertions of Tn4351 in the chromosome, whereas in matings involving R751::Tn4351, about half of the Emr transconjugants had R751 cointegrated with Tn4351 in the chromosome. Of the Emr transconjugants, 13% were auxotrophs. Bacteroides spp. which had R751 cointegrated with Tn4351 in the chromosome did not transfer R751 or Tn4351 to E. coli HB101 or to isogenic B. uniformis, nor did the intergrated R751 mobilize pE5-2, an E. coli-Bacteroides shuttle vector that contains a transfer origin that is recognized by R751.

Tn4400, a compound transposon isolated from Bacteroides fragilis, functions in Escherichia coli

Transfer factor pBFTM10, isolated from the obligate anaerobic bacterium Bacteroides fragilis, carries a clindamycin resistance determinant which we have suggested is part of a transposable element. DNA homologous to this determinant is found in many Clnr Bacteroides isolates, either in the chromosome or on plasmids. We have now established that Ccr resides on a transposon, Tn4400. In addition to the Ccr determinant that functions under anaerobic conditions in B. fragilis, Tn4400 also carries a determinant for tetracycline resistance (Tcr) which only functions in Escherichia coli under aerobic conditions. The presence of Tn4400 on pBFTM10 does not confer tetracycline resistance on B. fragilis cells containing it. DNA from pBFTM10 was cloned in E. coli, with pDG5 as the cloning vector, to form pGAT500. Using a mobilization assay involving pGAT500 and an F factor derivative, pOX38, we determined that a 5.6-kilobase region of pBFTM10 DNA was capable of mediating replicon fusion and transposition. Most of the mobilization products resulted from inverse transposition reactions, while some were the result of true cointegrate formation. Analysis of the cointegrate molecules showed that three were formed by the action of one of the ends of Tn4400 (IS4400), and one was formed by the action of the whole element (Tn4400). The cointegrate molecule carrying intact copies of Tn4400 at the junction of the two plasmids could resolve to yield an unaltered donor plasmid (pGAT500) and a conjugal plasmid containing a copy of Tn4400 or a copy of one insertion sequence element (pOX38::Tn4400 or pOX38::IS4400). Thus, Tn4400 is a compound transposon containing active insertion sequence elements as directly repeated sequences at its ends.

Evidence that the clindamycin-erythromycin resistance gene of Bacteroides plasmid pBF4 is on a transposable element

We constructed a shuttle vector, pE5-2, which can replicate in both Bacteroides spp. and Escherichia coli. pE5-2 contains a cryptic Bacteroides plasmid (pB8-51), a 3.8-kilobase (kb) EcoRI-D fragment from the 41-kb Bacteroides fragilis plasmid pBF4, and RSF1010, an IncQ E. coli plasmid. pE5-2 was mobilized by R751, an IncP E. coli plasmid, between E. coli strains with a frequency of 5 X 10(-2) to 3.8 X 10(-1) transconjugants per recipient. R751 also mobilized pE5-2 from E. coli donors to Bacteroides uniformis 0061RT and Bacteroides thetaiotaomicron 5482 with a frequency of 0.9 X 10(-6) to 2.5 X 10(-6). The Bacteroides transconjugants contained only pE5-2 and were resistant to clindamycin and erythromycin. Thus, the gene for clindamycin and erythromycin resistance must be located within the Eco RI-D fragment of BF4. A second recombinant plasmid, pSS-2, which contained 33 kb of pBF4 (including the EcoRI-D fragment and contiguous regions) could also be mobilized by R751 between E. coli strains. In some transconjugants, a 5.5-kb (+/- 0.3 kb) segment of the pBF4 portion of pSS2 was inserted into one of several sites on R751. In some other transconjugants this same 5.5-kb segment was integrated into the E. coli chromosome. This segment could transfer a second time onto R751. Transfer was RecA independent. The transferred segment included the entire EcoRI-D fragment, and thus the clindamycin-erythromycin resistance determinant, from pBF4.

Erythromycin: a microbial and clinical perspective after 30 years of clinical use (1)

Erythromycin is a macrolide that acts by inhibiting the translocation reaction during protein synthesis. Erythromycin is inactive against the Enterobacteriaceae and Pseudomonas aeruginosa except under alkaline conditions. Erythromycin is active against most gram-positive bacteria; some gram-negative bacteria, including Neisseria, Bordetella, Brucella, Campylobacter, and Legionella; and Treponema, Chlamydia, and Mycoplasma. The emergence of resistance to erythromycin is closely associated with its use and is often plasmid mediated. After its oral or parenteral administration, erythromycin diffuses readily into intracellular fluids and is actively concentrated intracellularly by polymorphonuclear leukocytes and alveolar macrophages.

Genetics of clindamycin resistance in Bacteroides

Results presented in this paper have shown that a widely distributed LM-resistance determinant is present on at least 3 distinct Bacteroides R-plasmids. In fact these plasmids bear no homology outside of the defined regions implicated in the LM resistance. This resistance determinant on pBF4, pBFTM10, and pBI136 is located within DNA segments bounded on each side by a directly repeated sequence of more than 500 bp. The intervening sequences of these 3 elements are variable, and range in size from about 3.7 kb to 7.2 kb (Fig. 7). Apart from the EcoRI/AvaI restriction sites which characterize the repeated sequence, there is a notable lack of common restriction sites within these elements. These results suggest that the elements do possess a certain degree of structural similarity but significant evolutionary divergence has occurred. The presence and location of the directly repeated sequences, their association with specific deletions, and their association with an antibiotic-resistance determinant, are features common to many antibiotic-resistance transposons described for other prokaryotes. In addition, these elements are highly mobile, being found on a number of R-plasmids. The unique relationship between pBF4, pBI106, and pBI136 described here is a clear indication of the potential for these DNA sequences to move from one molecule to another. Given the extensive dissemination and the genetic and structural characteristics described above, it seems likely that the LM-resistance determinant is carried on transposon-like elements present in pBF4, pBFTM10, and pBI136. However, further experimentation will be necessary to document the transposition event. Bacteroides strains such as B. fragilis V503, possess a transmissible LM-resistance determinant which does not appear to be associated with detectable extrachromosomal elements (5,9,10). Presently, a number of strains of this type have been found over a wide geographic area. The LM-resistance genes associated with these strains are apparently similar to the one carried on the Bacteroides R-plasmids because homology between the 2 has been observed. However, it is important to note that within the limits of Southern filter blot hybridization, neither V503 nor its transconjugants possess the directly repeated sequence found on the LM-resistance plasmids (Fig. 8). The elusive nature of the V503 LM-resistance elements presents an intriguing problem. One model that has been proposed is that these resistance determinants reside on a conjugative transposon similar to Tn916 of Streptococcus faecalis (3).(ABSTRACT TRUNCATED AT 400 WORDS)

Homology between clindamycin resistance plasmids in Bacteroides

Two different species of clindamycin-resistant Bacteroides were isolated from the same infection. One isolate contained a single 15-kb plasmid (pCP1) which encoded transferable clindamycin resistance. pCP1 appears similar to the Bacteroides clindamycin resistance plasmid pBFTM10 isolated independently by F.P. Tally, D.R. Snydman, M.J. Shimell, and M.H. Malamy (1982, J. Bacteriol. 151, 686-691). The second strain had a 10-kb plasmid (pCP2) but did not transfer resistance. DNA hybridization studies revealed that pCP1 shares a 5-kb region of homology with the B. fragilis R plasmid pBF4 studied by R.A. Welch and F.L. Macrina (1981, J. Bacteriol. 145, 867-872). This region in both plasmids was shown to be bounded by homologous direct repeats and contains the putative clindamycin resistance determinant. pCP1 and pCP2 were found to share extensive homology but sequences homologous to the clindamycin resistance region were missing from pCP2 and found instead in the whole cell DNA of the host strain. These results identify a transposon-like structure on Bacteroides clindamycin resistance plasmids.

Large transmissible clindamycin resistance plasmid in Bacteroides ovatus

Bacteroides ovatus IB106 contained two plasmids, pBI106 (46 kilobases) and pBI136 (82 kilobases). Transmissible clindamycin-erythromycin resistance (Ccr) was mediated by pBI136 , whose Ccr determinant was closely related to the determinant on the Bacteroides R plasmids pBF4 and pBFTM10 . Hybridization studies showed that pBI106 was not involved in Ccr transfer, but it shared extensive homology to pBF4 with the exception of the pBF4 region implicated in Ccr.