BackgroundThe World Health Organization recommends universal drug susceptibility testing for Mycobacterium tuberculosis complex to guide treatment decisions and improve outcomes. We assessed whether DNA sequencing can accurately predict antibiotic susceptibility profiles for first-line anti-tuberculosis drugs. MethodsWhole-genome sequences and associated phenotypes to isoniazid, rifampicin, ethambutol and pyrazinamide were obtained for isolates from 16 countries across six continents. For each isolate, mutations associated with drug-resistance and drug-susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These were predicted to be pan-susceptible if predicted susceptible to isoniazid and to other drugs, or contained mutations of unknown association in genes affecting these other drugs. We simulated how negative predictive value changed with drug-resistance prevalence.Results10,209 isolates were analysed. The greatest proportion of phenotypes were predicted for rifampicin (9,660/10,130; (95.4%)) and the lowest for ethambutol (8,794/9,794; (89.8%)). Isoniazid, rifampicin, ethambutol and pyrazinamide resistance was correctly predicted with 97.1%, 97.5% 94.6% and 91.3% sensitivity, and susceptibility with 99.0%, 98.8%, 93.6% and 96.8% specificity, respectively. 5,250 (89.5%) drug profiles were correctly predicted for 5,865/7,516 (78.0%) isolates with complete phenotypic profiles. Among these, 3,952/4,037 (97.9%) predictions of pan-susceptibility were correct. The negative predictive value for 97.5% of simulated drug profiles exceeded 95% where the prevalence of drug-resistance was below 47.0%. ConclusionsPhenotypic testing for first-line drugs can be phased down in favour of DNA sequencing to guide anti- tuberculosis drug therapy.

Twenty-six clinical isolates of Mycobacterium abscessus resistant to amikacin were identified. Most isolates were from patients with posttympanostomy tube placement otitis media or patients with cystic fibrosis who had received aminoglycoside therapy. Isolates were highly resistant (MICs ú1024 mg/mL) to amikacin, kanamycin, gentamicin, tobramycin, and neomycin (all 2-deoxystreptamine aminoglycosides) but not to streptomycin. Sequencing of their 16S ribosomal (r) RNA revealed that 16 (94%) of 17 had an AjG mutation at position 1408. In vitro -selected amikacinresistant mutants of M. abscessus and Mycobacterium chelonae had the same resistance phenotype, and 15 mutants all had the same AjG substitution at position 1408. Introducing an rRNA operon from Mycobacterium smegmatis with a mutated AjG at this position into a single functional allelic rRNA mutant of M. smegmatis produced the same aminoglycoside resistance phenotype. These studies demonstrate this 16S rRNA mutation is responsible for amikacin resistance in M. abscessus, which has only one copy of the rRNA operon. Aminoglycosides have been a major component of therapyKanamycin and the closely related amikacin are used for for mycobacterial diseases since the recognition of the remarktreatment of multidrug resistant tuberculosis [13]. [19]. The genetic basis of mycobacterial is complex, with high-level resistance associated with point resistance to amikacin, kanamycin, and tobramycin has, until mutations involving the ribosomal protein S12 (rpsL gene) and recently [20,21], been unknown. the 16S ribosomal RNA (rRNA) gene (rrs) [6 -11]. The 16S Phenotypic studies have shown that spontaneous mutants rRNA gene region that is mutated involves a pseudoknot strucselected in the laboratory for resistance to amikacin, kanamyture that is believed to be stabilized by the presence of the cin, and tobramycin (2-deoxystreptamine aminoglycosides) are S12 protein [9]. Low-level resistance to streptomycin in M.not cross-resistant to streptomycin for either M. tuberculosis tuberculosis is yet to be explained on the basis of genetic [22] or the rapidly growing mycobacteria [23]. In addition, alterations [12] but is believed to result from mutations involvrecent studies with Mycobacterium smegmatis have suggested ing cell wall transport [7].that the 16S rRNA position 1408 (Escherichia coli numbering system) may be important for resistance to amikacin, tobramycin, and gentamicin [20,21]. In the present study, we inves-

To study the cost of chromosomal drug resistance mutations to bacteria, we investigated the fitness cost of mutations that confer resistance to different classes of antibiotics affecting bacterial protein synthesis (aminocyclitols, 2-deoxystreptamines, macrolides). We used a model system based on an in vitro competition assay with defined Mycobacterium smegmatis laboratory mutants; selected mutations were introduced by genetic techniques to address the possibility that compensatory mutations ameliorate the resistance cost. We found that the chromosomal drug resistance mutations studied often had only a small fitness cost; compensatory mutations were not involved in low-cost or no-cost resistance mutations. When drug resistance mutations found in clinical isolates were considered, selection of those mutations that have little or no fitness cost in the in vitro competition assay seems to occur. These results argue against expectations that link decreased levels of antibiotic consumption with the decline in the level of resistance.The increasing rates of recovery of antimicrobial-resistant microorganisms in hospital and community settings are of growing concern (1, 42). Resistance may emerge from a mutation in an intrinsic chromosomal gene or by acquisition of exogenous genetic material bearing resistance determinants. Resistance to antibiotics frequently reduces the fitness of bacteria in the absence of antibiotics; this is referred to as the "cost" of resistance (38). In mathematical models, the fitness cost of resistance is the primary parameter that determines both the frequency of resistance at any given level of antibiotic use and the rate at which that frequency will change with changes in antibiotic use patterns (3,20,21).Restricted use of antibiotics is advocated not only to contain the dissemination of resistance but also to favor the nonexpansion and, finally, the disappearance of the resistant bacteria already present in human and environmental reservoirs (3, 38). As a consequence of decreased use of antibiotics, rates of drug resistance usually fall but do not vanish, and stable rates of resistance in the apparent absence of direct selection pressure has been observed (9, 12, 32). It is not clear whether this persistence of resistant bacteria is due to (i) low-level antibiotic contamination that maintains the selective pressure, (ii) selection by means other than antibiotics, or (iii) the stability of resistance genes.Analogous to the resistance mediated by exogenous genetic elements (13,14,19), chromosomal drug resistance-conferring mutations are commonly assumed to carry a fitness cost (38). This is supported by the observation that some drug resistance mutations selected in vitro involve a significant decrease in bacterial fitness (4,20,36); this fitness burden can subsequently be ameliorated by compensatory mutations (4, 5, 36). However, for streptomycin resistance-conferring rpsL mutations, a high level of selection for no-cost drug resistance mutations was suggested to exist in vivo (6). In order...

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Chromosomally acquired streptomycin resistance is frequently due to mutations in the gene encoding the ribosomal protein S12, rpsL. The presence of several rRNA operons (rrn) and a single rpsL gene in most bacterial genomes prohibits the isolation of streptomycin-resistant mutants in which resistance is mediated by mutations in the 16S rRNA gene (rrs). Three strains were constructed in this investigation: Mycobacterium smegmatis rrnB, M. smegmatis rpsL 3؉ , and M. smegmatis rrnB rpsL 3؉ . M. smegmatis rrnB carries a single functional rrn operon, i.e., rrnA (comprised of 16S, 23S, and 5S rRNA genes) and a single rpsL ؉ gene; M. smegmatis rpsL 3؉ is characterized by the presence of two rrn operons (rrnA and rrnB) and three rpsL ؉ genes; and M. smegmatis rrnB rpsL 3؉ carries a single functional rrn operon (rrnA) and three rpsL ؉ genes. By genetically altering the number of rpsL and rrs alleles in the bacterial genome, mutations in rrs conferring streptomycin resistance could be selected, as revealed by analysis of streptomycin-resistant derivatives of M. smegmatis rrnB rpsL 3؉ . Besides mutations well known to confer streptomycin resistance, novel streptomycin resistance conferring mutations were isolated. Most of the mutations were found to map to a functional pseudoknot structure within the 530 loop region of the 16S rRNA. One of the mutations observed, i.e., 524G3C, severely distorts the interaction between nucleotides 524G and 507C, a Watson-Crick interaction which has been thought to be essential for ribosome function. The use of the single rRNA allelic M. smegmatis strain should help to elucidate the principles of ribosome-drug interactions.