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Antimicrob Agents Chemother. Apr 2008; 52(4): 1570–1572.
Published online Jan 22, 2008. doi:  10.1128/AAC.01098-07
PMCID: PMC2292563

Linezolid Resistance in Staphylococcus aureus: Gene Dosage Effect, Stability, Fitness Costs, and Cross-Resistances[down-pointing small open triangle]

Abstract

Linezolid resistance in Staphylococcus aureus is typically associated with mutations in the 23S rRNA gene. Here we show that the accumulation of a single point mutation, G2576T, in the different copies of this gene causes stepwise increases in resistance, impairment of the biological fitness, and cross-resistance to quinupristin-dalfopristin and chloramphenicol.

Linezolid, the first oxazolidinone in clinical use, is effective in the treatment of infections caused by various gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (2, 11). Linezolid binds to the 50S subunit of the bacterial ribosome via interaction with the 23S rRNA, thereby blocking protein synthesis (2, 9, 16). Linezolid resistance in S. aureus has been encountered in the clinical setting and has also been selected in vitro, but it is still a rare phenomenon (2, 6, 8, 19, 21). The resistance to this antibiotic has been associated with distinct nucleotide substitutions in domain V of the 23S rRNA gene, particularly G2447T, T2500A, and G2576T (3, 14, 18, 19, 21, 22). S. aureus possesses five to six rRNA (rrn) operons (14), which suggests that the presence of a resistance-mediating mutation in one, several, or all of the 23S rRNA gene copies might be associated with gradually increased levels of resistance.

This study was aimed at (i) correlating the level of linezolid resistance in S. aureus with the presence of mutations in the different copies of the 23S rRNA gene, (ii) analyzing the stability of linezolid resistance, (iii) determining the fitness costs associated with linezolid resistance, and (iv) assessing the issue of cross-resistance to other protein synthesis inhibitors.

Isolation of linezolid-resistant mutants of S. aureus T991.

S. aureus T991, a clinical linezolid-susceptible strain, was grown at 37°C in Mueller-Hinton broth and then serially passaged in medium containing successively increasing concentrations (1 to 128 mg/liter) of linezolid. In the course of these passages, five S. aureus T991 descendants, T1887, T1888, T1900, T1910, and T2019, were isolated which showed gradually increasing linezolid MICs between 4 and 128 mg/liter (Table (Table1).1). Clonal identity of the parental strain T991 and the most resistant derivative, T2019, was proven by pulsed-field gel electrophoresis (PFGE) as previously described (20) (data not shown).

TABLE 1.
Correlation of the presence of point mutation G2576T in the 23S rRNA genes with the level of linezolid resistance in S. aureus

Association of linezolid resistance with the presence of the G2576T mutation in the 23S rRNA genes.

Southern blot hybridization of EcoRI-digested genomic DNA from S. aureus T991 with a 883-bp DNA probe containing domain V of the S. aureus 23S rRNA gene revealed that T991 carries five copies of this gene (data not shown). To characterize the domain V regions of each of the five 23S rRNA gene copies from strain T991 and its descendants, these genes were individually amplified as previously described (15). DNA sequence analysis demonstrated that S. aureus T991 does not contain any mutations in domain V of its five 23S rRNA gene copies. The five T991 derivatives selected under linezolid selective pressure, however, showed a G2576T substitution in domain V within one or more of their 23S rRNA gene copies (Table (Table1).1). Other mutations were not found. The level of linezolid resistance observed for the different T991 derivatives directly correlated with the number of 23S rRNA gene copies carrying this nucleotide exchange; i.e., the higher the resistance the more gene copies showed the G2576T exchange (Table (Table1).1). Interestingly, the first G2576T mutation (observed in isolate T1887) required by far the longest time to occur. The faster acquisition of the same nucleotide exchange in the other 23S rRNA gene copies suggested that mechanisms other than independent mutations, such as homologous recombination, might have been involved in the spreading of this mutation.

Stability of the G2576T mutation.

To determine the stability of linezolid resistance associated with the G2576T mutation, a single colony of S. aureus T2019, the T991 descendant containing this mutation in all five 23S rRNA gene copies, was passaged 50 times in antibiotic-free medium, resulting in the isolation of S. aureus T2019/50. MIC testing demonstrated an approximately twofold decrease in the MIC for S. aureus T2019/50 compared to T2019 results. Furthermore, sequencing of the 23S rRNA genes of T2019/50 revealed a reversion of the G2576T mutation, i.e., T2576G, in one of the five 23S rRNA gene copies (Table (Table11).

Fitness costs of linezolid resistance associated with the G2576T mutation.

To investigate whether the G2576T mutation in the 23S rRNA genes influences the biological fitness of S. aureus, we analyzed the growth kinetics for S. aureus T991 and the different T991 descendants. For this purpose, S. aureus strains were grown in Mueller-Hinton broth to the logarithmic growth phase (optical density at 600 nm [OD600] = 1). A total of 100 μl of each culture with an OD of 1 was then inoculated into 10 ml of fresh medium and incubated with shaking (200 rpm) at 37°C. Bacterial growth was recorded for a total period of 12 h by measuring the OD600 of the cultures at intervals of 1 h. As shown in Fig. Fig.1,1, the growth rates decreased gradually with increasing numbers of mutant 23S rRNA gene copies. Several CFU determinations performed during the experiment also confirmed these observations (data not shown). The differences in the growth yields (OD600 values) observed in the midlogarithmic phase (after 7 h of growth) between T991, T1887, T1888, T1900, T1910, and T2019 were statistically significant (P < 0.05 as determined by analysis of variance). In three experiments, the ratios of the OD600 values (linezolid-resistant mutants versus linezolid-susceptible wild type) measured after 7 h of growth were 0.816 ± 0.007 (means ± standard deviations) for T1887 versus T991, 0.613 ± 0.003 for T1888 versus T991, 0.552 ± 0.004 for T1900 versus T991, 0.432 ± 0.004 for T1910 versus T991, and 0.302 ± 0.006 for T2019 versus T991. Although the possibility cannot totally be excluded that other mutations adversely affecting the fitness may have been selected during passaging of S. aureus T991, these data suggested that the accumulation of the G2576T mutation in the 23S rRNA gene copies causes a successive decline in the biological fitness of S. aureus. Interestingly, isolate T2019/50, showing a reversion of the G2576T mutation in one of the five 23S rRNA gene copies, exhibited a marked fitness gain compared to T2019; i.e., the ratio of OD600 values measured after 7 h of growth was 0.707 ± 0.007 for T2019/50 versus T991. Given that the fitness of T2019/50 is considerably higher than that of T1910 (both strains carry four G2576T mutations), it seems, however, unlikely that the fitness increase observed for T2019/50 is exclusively due to the reversion of one of the G2576T exchanges. In fact, previous studies indicated that the fitness loss caused in S. aureus by certain mutations conferring resistance to antibiotics such as fusidic acid can be compensated for by secondary mutations in the genome (1). It is hence tempting to speculate that a compensatory mutation(s) outside the domain V region of the 23S rRNA genes may be involved in the partial restoration of the biological fitness observed for S. aureus T2019/50.

FIG. 1.
Growth kinetics of S. aureus strain T991 and its descendants T1887, T1888, T1900, T1910, and T2019. Data are expressed as the means ± standard deviations of the results of three experiments.

Cross-resistances associated with the G2576T mutation.

Linezolid possesses a distinctive mechanism of action, suggesting that there is no cross-resistance with other antibiotics (5, 14). Nonetheless, while S. aureus T991 proved to be susceptible to chloramphenicol and quinupristin-dalfopristin, the linezolid-resistant mutant T2019 showed cross-resistances to these antibiotics (Table (Table2).2). Chloramphenicol acts on the 50S subunit by binding to the central loop of domain V of the 23S rRNA, thereby inhibiting the peptidyl transferase reaction (10). Footprint studies have indicated that chloramphenicol interacts strongly with the A2451 and G2505 sites in the peptidyl transferase region (10). Similarly, quinupristin-dalfopristin interacts closely with G2505 and C2586 (7). Thus, the close vicinity of G2505 and C2586 to G2576 might explain the observed phenomenon of cross-resistance, i.e., the G2576T mutation possibly decreases the binding affinity not only for linezolid but also for chloramphenicol and the streptogramins quinupristin-dalfopristin. In this regard, the recent identification of the cfr gene as part of a mobile genetic element from a human isolate of S. aureus that encodes a rRNA methyltransferase is of interest (17). This methyltransferase modifies adenosine at position 2503 in the 23S rRNA and has been shown to confer resistance to linezolid and chloramphenicol. Again, the close vicinity of A2503 to G2576 argues for overlapping binding sites of these antibiotics and the observed phenomenon of cross-resistance.

TABLE 2.
Cross-resistances associated with mutation G2576T in the 23S rRNA genes of S. aureus

Conclusions.

The data presented here show that the successive accumulation of a single point mutation, G2576T, in the 23S rRNA gene copies of S. aureus is associated with, and apparently causative of, a stepwise increase in the level of linezolid resistance. The current report thus ultimately verifies the similar gene dosage effects that have been described for clinical isolates as well as laboratory-derived linezolid-resistant mutants of S. aureus and enterococci (11-13, 15). Furthermore, we found that the increase in linezolid resistance mediated by the spreading of the G2576T mutation is paralleled by a decline in the biological fitness of the bacteria, which suggests a negative effect of the G2576T mutation on protein synthesis. In the S. aureus T991 descendant carrying the G2576T mutation in all five 23S rRNA gene copies, this mutation proved to be rather stable in the absence of linezolid-selective pressure, which is consistent with findings of Pillai et al. (15). Nevertheless, the reversion of this nucleotide exchange in one of these gene copies observed after multiple serial passages in antibiotic-free medium indicates that the fitness burden associated with the G2576T mutation is a driving force for the restoration of the wild-type sequence and hence for reversion to a more linezolid-susceptible phenotype.

Acknowledgments

We thank Denia Frank for excellent technical assistance.

Footnotes

[down-pointing small open triangle]Published ahead of print on 22 January 2008.

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