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Antimicrobial Agents and Chemotherapy, March 2003, p. 863-868, Vol. 47, No. 3
0066-4804/03/$08.00+0 DOI: 10.1128/AAC.47.3.863-868.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Institute for Infectious Diseases, University of Bern, University Hospital Bern, Bern, Switzerland
Received 29 July 2002/ Returned for modification 23 September 2002/ Accepted 21 November 2002
| ABSTRACT |
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4 mg/liter) has been mapped to point mutations in clusters I and III of rpoB of the pneumococcus. The molecular basis of low-level resistance (MICs,
0.5 and <4 mg/liter) was analyzed. Spontaneous mutants of clinical pneumococcal isolates were selected on Columbia sheep blood agar plates containing rifampin at 0.5, 4, 10, or 50 mg/liter. Low-level resistance could be assigned to mutations in cluster II (I545N, I545L). Sensitive (MIC, <0.048 mg/liter) wild-type strains acquired low-level resistance at a rate approximately 10 times higher than that at which they acquired high-level resistance (average mutation frequencies, 2.4 x 10-7 for low-level resistance versus 2.9 x 10-8 for high-level resistance [P < 0.0001]). In second-step experiments, the frequencies of mutations from low- to high-level resistance were over 10 times higher than the frequencies of mutations from susceptibility to high-level resistance (average mutation frequencies, 7.2 x 10-7 versus 5.0 x 10-8 [P < 0.001]). Mutants with low-level resistance were stable upon passage. Sequencing of a clinical isolate with low-level resistance (MIC, 0.5 mg/liter) revealed a Q150R mutation upstream of cluster I. The frequencies of mutations to high-level resistance for this strain were even higher than the rates observed for the in vitro mutants. Therefore, a resistance-mediating mutation located outside clusters I, II, and III has been described for the first time in the pneumococcus. In vitro low-level rifampin resistance in S. pneumoniae could be mapped to cluster II of rpoB. Mutants of pneumococcus with low-level resistance may be selected in vivo during therapy in tissue compartments with low antibiotic concentrations and play a role in the development of resistance. | INTRODUCTION |
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Rifampin resistance has been described in several bacterial species, such as Mycobacterium tuberculosis, Escherichia coli (12), S. aureus (2), and N. meningitidis (21). Resistance has also been reported in S. pneumoniae (8, 18, 23). Rifampin resistance is caused by an alteration of the ß subunit of RNA polymerase, the target of the antibiotic. Rifampin acts by binding to the ß subunit, which leads to the premature termination of DNA transcription. Resistance to rifampin has been linked to amino acid alterations found in three regions of rpoB, termed clusters I to III. These alterations arise mainly due to point mutations, but horizontal gene transfer may also play a role in the evolution of rifampin resistance in S. pneumoniae (8).
Rifampin resistance in clinical S. pneumoniae isolates seems to be rare at present. Reported rates of resistance vary between 0.4 and 1.5% (7, 15, 19). Resistance has been linked to point mutations within cluster I or III of S. pneumoniae rpoB (8, 18, 23). This study addresses the molecular basis of the low-level rifampin resistance (MICs,
0.5 to <4 mg/liter) and its role in the development of resistance in clinical isolates of S. pneumoniae. A large collection of nasopharyngeal S. pneumoniae isolates (17) was searched for isolates with low-level resistance. In addition, mutants with low-level resistance were selected in vitro, and the rpoB gene was analyzed for mutations. Stepwise increases in the rifampin MIC that resulted in resistance in S. pneumoniae were investigated.
(Part of the data presented here were presented orally at the 6th European Meeting on the Molecular Biology of the Pneumococcus, Siena, Italy, 20 to 23 March 2002.)
| MATERIALS AND METHODS |
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Susceptibility testing. Rifampin MICs were determined by using E-test strips (AB Biodisk, Solna, Sweden) on CSBA plates.
DNA methods. Chromosomal DNA was obtained from the S. pneumoniae isolates as follows. Bacteria from two CSBA plates were resuspended in TE buffer (10 mM Tris-HCl, 1 mM EDTA [pH 8.0]). The bacteria were lysed by the addition of the GES reagent (guanidium isothiocyanate, EDTA, sarcosyl). Ammonium acetate was added to the solution, followed by 10 min of incubation on ice. Chloroform-isoamyl alcohol was added to extract the proteins, and then the DNA was precipitated with isopropanol and washed with 70% ethanol. The DNA was resuspended in TE buffer.
PCR amplification and sequencing of rpoB. The rpoB gene was amplified from bp 405 to 2468 (S. pneumoniae strain R6 coordinates) by using primers slightly modified from those published previously (8, 16) (Table 1) and Taq DNA polymerase (Roche Molecular Biochemicals, Rotkreuz, Switzerland). PCR products were purified with the QIAquick PCR purification kit (Qiagen, Basel, Switzerland). The rpoB genes of different isolates were sequenced by using the sequencing primers described in Table 1. DNA sequences were aligned by using Lasergene (DNASTAR Inc., Madison, Wis.) software. rpoB sequences were translated, and the amino acids were aligned.
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Selection for mutants with high-level rifampin resistance (second-step mutation).
Two strains (strains 111.46 and 204.26) were chosen for the selection of mutants with high-level rifampin resistance. For each strain, single colonies each of a rifampin-sensitive (MIC <0.048 mg/liter) wild type and a mutant with low-level resistance (MICs,
0.5 and <4 mg/liter) were inoculated in BHI broth, and the bacteria were grown to an OD600 of 0.6 to 0.7. Aliquots from each culture were spread in duplicate on CSBA plates containing 4, 10, and 50 mg of rifampin per liter. The plates were incubated for 48 h prior to counting of the colonies. The total cell count was determined as described above. Colonies with high-level resistance (MICs,
4 mg/liter) derived from strains with low-level rifampin resistance were stored and further analyzed.
Transformation. Rifampin-susceptible (MIC, 0.023 mg/liter) pneumococcal isolate 106.44 was used as a recipient for transformation with rpoB from strains with low-level resistance. Competent cells were prepared by inoculating BHI broth with a single colony and growth overnight. A fresh culture was started in the morning by diluting the overnight culture 1:100 in fresh broth and was grown to an OD600 of 0.15. An aliquot of the culture was diluted 1:20 in BHI broth prewarmed at 30°C and incubated for 15 min. Competence-stimulating peptide (Neosystems, Strasbourg, France) was added to a final concentration of 200 ng/ml, and the culture was allowed to incubate for 30 min at 30°C. A total of 1 µg of DNA consisting of the rpoB gene (PCR fragment bp 372 to 2380) was added to the culture, which was allowed to incubate for 40 min at 30°C and then for 90 min at 37°C. Aliquots of the cultures were then spread onto CSBA plates containing rifampin at concentrations of 0.5, 1, 4, 10, and 50 mg/liter. The plates were incubated for 48 h prior to counting of the colonies. In parallel, serial dilutions of the same culture were spread onto CSBA plates to determine the total cell count. Single colonies from the plates with each rifampin concentration were stored at -80°C for further evaluation.
| RESULTS |
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0.5 and <4 mg/liter. The low-level resistance in isolate 205.09 was stable in vitro upon multiple passages. Analysis of isolate 205.09 with low-level resistance. The rpoB gene of strain 205.09 was amplified in two PCRs with primer pair 31f and 2380r and primer pair 399f and 3733r, respectively. Sequencing revealed no mutations within cluster I, II, or III. However, a Q150R (S. pneumoniae strain R6 numbering) amino acid change was identified upstream of cluster I. Transformation of strain 106.44 with this mutation led to low-level resistance (MIC, 0.5 mg/liter) and confirmed its resistance-mediating nature.
In vitro generation of S. pneumoniae strains with low-level rifampin resistance. Spontaneous mutants with low-level resistance were selected by plating S. pneumoniae cultures grown to the exponential phase on agar plates containing 0.5 mg of rifampin per liter. The cultures were also exposed to higher levels of rifampin to detect and compare high-level resistance to rifampin. The frequencies at which such spontaneous mutants arose are shown in Table 2. Sensitive (MICs, <0.048 mg/liter) wild-type strains acquired low-level resistance at a rate approximately 10 times higher, on average, than that at which they acquired high-level resistance (average mutation rates, 2.4 x 10-7 for low-level resistance versus 2.9 x 10-8 for high-level resistance [P < 0.0001]). However, there was some variability between different strains. Mutants with low-level resistance were stable upon multiple passages and storage at -80°C.
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Transformation for low-level rifampin resistance. To investigate whether the point mutations found in mutants with low-level resistance and mutations in cluster II mediated rifampin resistance, rpoB from two different strains, strains 777 and 111.46, were used for the transformation of rifampin-susceptible strain 106.44. The MICs for the transformants selected on agar plates containing rifampin at 0.5 mg/liter were the same as those for the donor strains. Transformation frequencies ranged between 0.3 and 0.5%. These experiments indicate that both mutations within cluster II do confer low-level rifampin resistance.
Selection for high-level rifampin resistance in mutants with low-level resistance (second-step mutation). The question of whether low-level resistance to rifampin can promote a further increase in resistance was addressed in two mutants with low-level resistance in vitro (strains 111.46-II and 204.26-II) and in the strain with natural low-level resistance (isolate 205.09). Spontaneous mutants were selected in the presence of rifampin at concentrations of 4, 10, and 50 mg/liter. The frequencies at which mutants with high-level resistance could be observed are summarized in Table 2.
In the second-step mutation experiments, the frequencies of mutations from low- to high-level resistance were over 10 times higher than the frequencies of mutations from susceptibility to high-level resistance (average mutation frequencies, 7.2 x 10-7 versus 5.0 x 10-8; P < 0.001 by the unpaired Student t test). The frequencies of mutations to high-level resistance for strain 205.09 (for rifampin at
4 mg/liter, 1.8 x 10-6; for rifampin at
10 mg/liter, 9.1 x 10-7; for rifampin at
50 mg/liter, 1.3 x 10-7) were even higher than the frequencies observed for the in vitro mutants.
Mapping of rifampin resistance in mutants obtained from second-step mutation experiments.
Clusters I to III were sequenced and analyzed for mutants with high-level resistance obtained from the four strains with which the second-step mutation experiments were performed. The amino acid alterations (S. pneumoniae strain R6 numbering) found in these mutants are shown in Table 3. In strains 777 and 111.46, cluster II was unaltered and second-step mutations were localized in cluster I. The H499Y amino acid change has been described in S. pneumoniae; but the Q483H, H499L, and R502C alterations have not been reported in S. pneumoniae. However, the R502C, D489Y, and R502H alterations have been described in E. coli (12). Different amino acid changes could be observed in strain 104.72. The amino acid change N545K (AAC/AAA) in cluster II could be detected in the second-step mutants of this strain selected on plates containing 4 and 10 mg of rifampin per liter. No additional point mutations occurred in cluster I in either mutant. Therefore, in these mutants the same DNA region which was already mutated during selection for low-level rifampin resistance was targeted again upon selection for high-level resistance. This was also the case in mutant 204.26-II4, in which amino acid 544, which is just adjacent to the cluster II mutation found in amino acid 545, was altered (L544V). The additional mutants of these two strains (mutants 104.72 and 204.26) kept the cluster II mutations and obtained additional amino acid changes in cluster I. The H499Y alteration has been described above, and the D489N and Q486K alterations have not yet been reported in S. pneumoniae but have been reported in E. coli (12). The resistance-mediating nature of the observed mutations and the not yet described mutations was confirmed by transformation experiments with PCR fragments containing the corresponding mutation (data not shown). No transformants could be obtained for the Q483H mutation (strain 777-II4). We do not believe that this indicates that the Q483H mutation has no influence on the rifampin MIC. Rather, transformation of cluster I with a PCR fragment obtained with primers 372f and 525dn (Table 1) is technically difficult, since the mutation to be transformed is close to one end of the DNA fragment. Transformation with second-step mutations yielded MICs
4 mg/liter.
| DISCUSSION |
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Only 1 of 100 clinical isolates screened was not susceptible to rifampin, according to the National Committee for Clinical Laboratory Standards breakpoints, but the MIC for the isolate was elevated (0.5 mg/liter). This is in accordance with the results of previous studies, in which the reported rifampin resistance rates were also low. One study performed in Spain (15) observed that 0.4% of isolates were rifampin resistant, another study conducted in the United States (7) observed that 0.5% of isolates were rifampin resistant, and a third one conducted in Brazil (19) observed that 1.5% of isolates were rifampin resistant. In the multicenter study performed in the United States, 7 of 1,527 S. pneumoniae isolates were resistant to rifampin. The MIC range detected was <0.015 to 32 mg/liter, the MIC50 was 0.03 mg/liter, and the MIC90 was 0.06 mg/liter.
Analysis of the wild-type isolate for which the rifampin MIC was increased (0.5 mg/liter) revealed a Q150R amino acid alteration upstream of cluster I that mediated low-level rifampin resistance; no mutations could be found within clusters I to III of this isolate. Interestingly, low- and high-level resistance-mediating mutations were described in the analogous region upstream of rpoB in E. coli (20). A mutation for rifampin resistance outside classical clusters I to III has not yet been described in S. pneumoniae. In fact, earlier studies concentrated on the classical clusters and did not investigate for (further) mutation sites outside clusters I to III. There is only one description in the literature of a clinical isolate of S. pneumoniae with low-level resistance (MIC, 2 mg/liter), and the isolate has been sequenced (18). Also, reports of studies with other bacterial species have proposed alternative mechanisms for rifampin resistance, including modification of the antibiotic (5, 22) and the presence of mutations in other subunits of the polymerase (11).
The in vitro-generated mutants with low-level resistance carried point mutations in cluster II of rpoB. These mutations have not been reported in S. pneumoniae. Exposure of S. pneumoniae to higher concentrations of rifampin therefore yielded mutations different from those obtained after exposure to low concentrations. This stands in contrast to a study performed with E. coli, in which no difference between the mutations that occurred after exposure to low or high concentrations of rifampin was found (12). As in this study, mutants with low-level resistance were selected about 10 times more frequently than mutants with high-level resistance. However, in contrast to the mutants of S. pneumoniae described here, mutants of E. coli with low-level resistance were not always stable upon multiple passages (12). Experiments with S. aureus showed that rifampin-resistant mutants were selected at similar frequencies on low and high concentrations of rifampin (2). On the basis of the results, it was suggested that resistance to high levels of rifampin arises in a single-step fashion and not by sequential independent events. We observed both mechanisms in our experiments. Mutants with high-level resistance could be selected directly upon exposure to high concentrations of rifampin but could also be selected by exposing mutants with low-level resistance to higher concentrations of the antibiotic. These mutants acquired new mutations within cluster I, which can explain the observed increase in the MIC, but more importantly, the mutants did preserve the mutations within cluster II. In addition, one of the mutants acquired a second point mutation in the same codon of cluster II.
In our experiments the frequency at which mutants with mutations for high-level resistance could be selected was significantly higher for bacteria with low-level resistance than for their rifampin-susceptible wild-type strain. This was also the case for the natural clinical isolate with low-level resistance. Therefore, low-level rifampin resistance may predispose S. pneumoniae and possibly other bacterial species to the acquisition of high-level resistance more rapidly. In a recent report, the emergence of a rifampin-resistant pneumococcus was described in three patients in The Netherlands receiving rifampin therapy (23). Interestingly, in two of the three patients, who were sampled repeatedly, isolates with low-level rifampin resistance (MICs, 1.5 and 3 mg/liter, respectively) were recovered by culture; this was followed over time by the recovery of isolates for which the MICs were higher (8 and 4 mg/liter, respectively). This observation provides further strength to our hypothesis that the stepwise development of rifampin resistance may be clinically important.
Rifampin is not one of the most routinely used antibiotics. However, it has an important role in the treatment of mycobacterial infections, osteomyelitis, and foreign-body infections, such as prosthetic valve endocarditis and infections of prosthetic joints due to staphylococci. Also, the drug is often used for prophylaxis for the contacts of patients with invasive meningococcal infection. More recently, rifampin has been recommended for the treatment of meningitis due to ß-lactam-resistant pneumococci in combination with an expanded-spectrum cephalosporin (10, 13, 14). Exposure of pneumococci to low concentrations of rifampin may especially occur in the nasopharynx during colonization (9), but it may also take place in the cerebrospinal fluid during the treatment of meningitis. The data presented here demonstrate the possibility for the stepwise selection of rifampin-resistant S. pneumoniae isolates.
In conclusion, this study shows that S. pneumoniae isolates with low-level resistance can easily be selected in vitro and that the point mutations responsible are concentrated in cluster II of rpoB. The results obtained in this study indicate the risk that S. pneumoniae isolates with low-level resistance may more rapidly gain high-level resistance. Furthermore, the study describes for the first time a (low-level) resistance-mediating mutation in rpoB outside clusters I, II, and III in S. pneumoniae.
| ACKNOWLEDGMENTS |
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The study was partly supported by a grant (grant 3100-052955.97/1) from the Swiss National Science Foundation to K. Mühlemann.
| FOOTNOTES |
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