The competitive cost of antibiotic resistance in Mycobacterium tuberculosis

The population dynamics and control of tuberculosis

More than 36 million patients have been successfully treated via the World Health Organization's strategy for tuberculosis (TB) control since 1995. Despite predictions of a decline in global incidence, the number of new cases continues to grow, approaching 10 million in 2010. Here we review the changing relationship between the causative agent, Mycobacterium tuberculosis, and its human host and examine a range of factors that could explain the persistence of TB. Although there are ways to reduce susceptibility to infection and disease, and a high-efficacy vaccine would boost TB prevention, early diagnosis and drug treatment to interrupt transmission remain the top priorities for control. Whatever the technology used, success depends critically on the social, institutional, and epidemiological context in which it is applied.

The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts

Despite efforts from a range of disciplines, our ability to predict and combat the evolution of antibiotic resistance in pathogenic bacteria is limited. This is because resistance evolution involves a complex interplay between the specific drug, bacterial genetics and both natural and treatment ecology. Incorporating details of the molecular mechanisms of drug resistance and ecology into evolutionary models has proved useful in predicting the dynamics of resistance evolution. However, putting these models to practical use will require extensive collaboration between mathematicians, molecular biologists, evolutionary ecologists and clinicians.

Fitness of Mycobacterium tuberculosis strains of the W-Beijing and Non-W-Beijing genotype

BACKGROUND

Multidrug resistant tuberculosis (MDR-TB) is a major threat for global tuberculosis control. The W-Beijing Mycobacterium tuberculosis genotype has been associated with drug resistance. Elucidation of the mechanisms underlying this epidemiological finding may have an important role in the control of MDR-TB. The aim of this study was to evaluate the fitness of drug-susceptible and MDR M. tuberculosis strains of the W-Beijing genotype compared with that of Non-W-Beijing strains.

METHODOLOGY/PRINCIPAL FINDINGS

Fitness of M. tuberculosis strains was determined by evaluating the difference in the growth curves obtained in the MGIT960 automated system and assessing the competitive growth capacity between W-Beijing and non-W-Beijing strains. The W-Beijing MDR strains had a significant longer lag phase duration compared to the other strains but did not present a significant fitness cost. When grown in competition they had an advantage only in medium containing 0.1% Tween 80.

CONCLUSIONS/SIGNIFICANCE

It was not possible to confirm a selective advantage of W-Beijing strains to grow, except for differences in their resistance to Tween 80. Further studies are needed to elucidate the putative advantage of W-Beijing strains compared to other genotypes.

Mutations in extensively drug-resistant Mycobacterium tuberculosis that do not code for known drug-resistance mechanisms

BACKGROUND

Highly lethal outbreaks of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis are increasing. Whole-genome sequencing of KwaZulu-Natal MDR and XDR outbreak strains prevalent in human immunodeficiency virus (HIV)-infected patients by the Broad Institute identified 22 novel mutations which were unique to the XDR genome or shared only by the MDR and XDR genomes and not already known to be associated with drug resistance.

METHODS

We studied the 12 novel mutations which were not located in highly-repetitive genes to identify mutations that were truly associated with drug resistance or were likely to confer a specific fitness advantage.

RESULTS

None of these mutations could be found in a phylogenetically and geographically diverse set of drug-resistant and drug-susceptible Mycobacterium tuberculosis isolates, suggesting that these mutations are unique to the KZN clone. Examination of the 600-basepair region flanking each mutation revealed 26 new mutations. We searched for a convergent evolutionary signal in the new mutations for evidence that they emerged under selective pressure, consistent with increased fitness. However, all but 1 rare mutation were monophyletic, indicating that the mutations were markers of strain phylogeny rather than fitness or drug resistance.

CONCLUSIONS

Our results suggest that virulent XDR tuberculosis in immunocompromised HIV-infected patients can evolve without generalizable fitness changes or other XDR-specific mutations.

Drug-resistant tuberculosis: past, present, future

In a population of Mycobacterium tuberculosis, random chromosomal mutation that results in genetic resistance to anti-tuberculosis (TB) drugs occurs at a relatively low frequency. Anti-TB drugs impose selection pressure so that mycobacterial mutants gradually outnumber susceptible bacilli and emerge as the dominant strains. Resistance to two or more anti-TB drugs represents cumulative results of sequential mutation. The fourth report on global anti-TB drug resistance provides the latest data on the extent of such problem in the world. The median prevalence of multi-drug-resistant TB (MDR-TB) in new TB cases was 1.6%, and in previously treated TB cases 11.7%. Of the half a million MDR-TB cases estimated to have emerged in 2006, 50% were in China and India. The optimal duration of any given combination of anti-TB drugs for treatment of MDR- and extensively drug-resistant TB (XDR-TB) has not been defined in controlled clinical trials. Standardized treatment may be feasible for MDR-TB patients not previously treated with second-line drugs, but a different strategy needs to be applied in the treatment of MDR-TB patients who have received second-line drugs before. Unfortunately, the reliability of drug susceptibility testing of most second-line anti-TB drugs is still questionable. Drug-resistant TB is not necessarily less virulent. Findings from modelling exercise warned that if MDR-TB case detection and treatment rates increase to the World Health Organization target of 70%, without simultaneously increasing MDR-TB cure rates, XDR-TB prevalence could increase exponentially. Prevention of development of drug resistance must be accorded the top priority in the era of MDR-/XDR-TB.

Antibiotic resistance and its cost: is it possible to reverse resistance?

Most antibiotic resistance mechanisms are associated with a fitness cost that is typically observed as a reduced bacterial growth rate. The magnitude of this cost is the main biological parameter that influences the rate of development of resistance, the stability of the resistance and the rate at which the resistance might decrease if antibiotic use were reduced. These findings suggest that the fitness costs of resistance will allow susceptible bacteria to outcompete resistant bacteria if the selective pressure from antibiotics is reduced. Unfortunately, the available data suggest that the rate of reversibility will be slow at the community level. Here, we review the factors that influence the fitness costs of antibiotic resistance, the ways by which bacteria can reduce these costs and the possibility of exploiting them.

Does M. tuberculosis genomic diversity explain disease diversity?

The outcome of tuberculosis infection and disease is highly variable. This variation has been attributed primarily to host and environmental factors, but better understanding of the global genomic diversity in the M. tuberculosis complex (MTBC) suggests that bacterial factors could also be involved. Review of nearly 100 published reports shows that MTBC strains differ in their virulence and immunogenicity in experimental models, but whether this phenotypic variation plays a role in human disease remains unclear. Given the complex interactions between the host, the pathogen and the environment, linking MTBC genotypic diversity to experimental and clinical phenotypes requires an integrated systems epidemiology approach embedded in a robust evolutionary framework.

Resistance to rifampicin: at the crossroads between ecological, genomic and medical concerns

The first antibiotic of the ansamycin family, rifampicin (RIF), was isolated in 1959 and was introduced into therapy in 1962; it is still a first-line agent in the treatment of diseases such as tuberculosis, leprosy and various biofilm-related infections. The antimicrobial activity of RIF is due to its inhibition of bacterial RNA polymerase (RNAP). Most frequently, bacteria become resistant to RIF through mutation of the target; however, this mechanism is not unique. Other mechanisms of resistance have been reported, such as duplication of the target, action of RNAP-binding proteins, modification of RIF and modification of cell permeability. We suggest that several of these alternative resistance strategies could reflect the ecological function of RIF, such as autoregulation and/or signalling to surrounding microorganisms. Very often, resistance mechanisms found in the clinic have an environmental origin. One may ask whether the introduction of the RIF analogues rifaximin, rifalazil, rifapentine and rifabutin in the therapeutic arsenal, together with the diversification of the pathologies treated by these molecules, will diversify the resistance mechanisms of human pathogens against ansamycins.

23S rRNA mutation A2074C conferring high-level macrolide resistance and fitness cost in Campylobacter jejuni

To examine the development of macrolide resistance in Campylobacter jejuni and assess the fitness of the macrolide-resistant mutants, two macrolide-susceptible C. jejuni strains, American Type Culture Collection (ATCC) 33291 and H1, from different geographic areas were exposed to tylosin in vitro. Multiple mutant strains were obtained from the selection. Most of the high-level macrolide-resistant strains derived from the selection exhibited the A2074C transversion in all three copies of 23S rRNA and displayed strong stability in the absence of antibiotic selection pressure. The competition experiments demonstrated that the strains containing the A2074C transversion imposed a fitness cost in competition mixtures. In addition, the fitness cost of the mutation was not ameliorated after approximately 500 generations of evolution under laboratory conditions. These findings indicate that the A2074C transversion in C. jejuni is not only correlated with stable and high-level macrolide resistance but also associated with a fitness cost.

Impact of azithromycin resistance mutations on the virulence and fitness of Chlamydia caviae in guinea pigs

Azithromycin (AZM) is a major drug used in the treatment and prophylaxis of infections caused by Chlamydia, yet no significant clinical resistance has been reported for these obligate intracellular bacteria. Nevertheless, spontaneous AZM resistance (Azm(r)) arose in vitro at frequencies ranging from 3 x 10(-8) to 8 x 10(-10) for clonal isolates of Chlamydia caviae, which is a natural pathogen of guinea pigs. Sequencing of the unique 23S rRNA gene copy in 44 independent Azm(r) isolates identified single mutations at position A(2058) or A(2059) (Escherichia coli numbering system). While SP(6)AZ(1) (A(2058)C) and SP(6)AZ(2) (A(2059)C) Azm(r) mutants showed growth defects in cell culture and were less pathogenic in the guinea pig ocular infection model than in the parent SP(6), the three isogenic C. caviae isolates grew equally well in the animal. On the other hand, coinoculation of the C. caviae parent strain with one of the Azm(r) strains was detrimental for the mutant strain. This apparent lack of association between pathology and bacterial load in vivo showed that virulence of the two Azm(r) mutants of C. caviae was attenuated. While chlamydial growth in vitro reflects the ability of the bacteria to multiply in permissive cells, survival in the host is a balance between cellular multiplication and clearance by the host immune system. The obligate intracellular nature of Chlamydia may therefore limit emergence of resistance in vivo due to the strength of the immune response induced by the wild-type antibiotic-sensitive bacteria at the time of antibiotic treatment.

Rates and mechanisms of resistance development in Mycobacterium tuberculosis to a novel diarylquinoline ATP synthase inhibitor

R207910 (also known as TMC207) is an investigational drug currently in clinical studies for the treatment of multidrug-resistant (MDR) tuberculosis. It has a high degree of antimycobacterial activity and is equally effective against drug-susceptible and MDR Mycobacterium tuberculosis isolates. In the present study, we characterized the development of resistance to R207910 in vitro. Ninety-seven independent R207910-resistant mutants were selected from seven different clinical isolates of M. tuberculosis (three drug-susceptible and four MDR isolates) at 10x, 30x, and 100x the MIC. At a concentration of 0.3 mg/liter (10x the MIC), the mutation rates ranged from 4.7 x 10(-7) to 8.9 x 10(-9) mutations per cell per division, and at 1.0 mg/liter (30x the MIC) the mutation rate ranged from 3.9 x 10(-8) to 2.4 x 10(-9). No resistant mutants were obtained at 3 mg/liter (100x the MIC). The level of resistance ranged from 0.12 to 3.84 mg/liter for the mutants identified; these concentrations represent 4- to 128-fold increases in the MICs. For 53 of the resistant mutants, the atpE gene, which encodes a transmembrane and oligomeric C subunit of the ATP synthase and which was previously shown to be involved in resistance, was sequenced. For 15/53 mutants, five different point mutations resulting in five different amino acid substitutions were identified in the atpE gene. For 38/53 mutants, no atpE mutations were found and sequencing of the complete F0 ATP synthase operon (atpB, atpE, and atpF genes) and the F1 ATP synthase operon (atpH, atpA, atpG, atpD, and atpC genes) from three mutants revealed no mutations, indicating other, alternative resistance mechanisms. Competition assays showed no measurable reduction in the fitness of the mutants compared to that of the isogenic wild types.

Polymorphisms associated with resistance and cross-resistance to aminoglycosides and capreomycin in Mycobacterium tuberculosis isolates from South Korean Patients with drug-resistant tuberculosis

The aminoglycosides streptomycin, amikacin, and kanamycin and the cyclic polypeptide capreomycin are all widely used in second-line therapy for patients who develop multidrug-resistant tuberculosis. We have characterized a set of 106 clinical isolates of Mycobacterium tuberculosis using phenotypic drug susceptibility testing (DST) to determine the extent of resistance to each agent and cross-resistance between agents. These results were compared with polymorphisms in the DNA sequences of ribosome-associated genes previously implicated in resistance and with the clinical outcomes of subjects from whom these isolates were obtained. Thirty-six (34%) of these isolates displayed resistance to one or more of these agents, and the majority of these (20 of 36) showed cross-resistance to one or more agents. Most (33 of 36) of the resistant isolates showed polymorphisms in the 16S ribosome components RpsL and rrs. Three resistant strains (3 of 36) were identified that had no known polymorphisms in ribosomal constituents. For kanamycin and streptomycin, molecular DST significantly outperformed phenotypic DST using the absolute concentration method for predicting 4-month sputum conversion (likelihood ratios of 4.0 and 2.0, respectively) and was equivalent to phenotypic DST using the National Committee for Clinical Laboratory Standards (NCCLS)-approved agar proportion method for estimating MIC (likelihood ratio, 4.0). These results offer insight into mechanisms of resistance and cross-resistance among these agents and suggest that the development of rapid molecular tests to distinguish polymorphisms would significantly enhance clinical utility of this important class of second-line antituberculosis drugs.

Selection of mutations to detect multidrug-resistant Mycobacterium tuberculosis strains in Shanghai, China

Novel tools are urgently needed for the rapid, reliable detection of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of Mycobacterium tuberculosis. To develop such tools, we need information about the frequency and distribution of the mycobacterial mutations and genotypes that are associated with phenotypic drug resistance. In a population-based study, we sequenced specific genes of M. tuberculosis that were associated with resistance to rifampin and isoniazid in 242 phenotypically MDR isolates and 50 phenotypically pan-susceptible isolates from tuberculosis (TB) cases in Shanghai, China. We estimated the sensitivity and specificity of the mutations, using the results of conventional, culture-based phenotypic drug susceptibility testing as the standard. We detected mutations within the 81-bp core region of rpoB in 96.3% of phenotypically MDR isolates. Mutations in two structural genes (katG and inhA) and two regulatory regions (the promoter of mabA-inhA and the intergenic region of oxyR-ahpC) were found in 89.3% of the MDR isolates. In total, 88.0% (213/242 strains) of the phenotypic MDR strains were confirmed by mutations in the sequenced regions. Mutations in embB306 were also considered a marker for MDR and significantly increased the sensitivity of the approach. Based on our findings, an approach that prospectively screens for mutations in 11 sites of the M. tuberculosis genome (rpoB531, rpoB526, rpoB516, rpoB533, and rpoB513, katG315, inhA-15, ahpC-10, ahpC-6, and ahpC-12, and embB306) could detect 86.8% of MDR strains in Shanghai. This study lays the foundation for the development of a rapid, reliable molecular genetic test to detect MDR strains of M. tuberculosis in China.

The past and future of tuberculosis research

Renewed efforts in tuberculosis (TB) research have led to important new insights into the biology and epidemiology of this devastating disease. Yet, in the face of the modern epidemics of HIV/AIDS, diabetes, and multidrug resistance--all of which contribute to susceptibility to TB--global control of the disease will remain a formidable challenge for years to come. New high-throughput genomics technologies are already contributing to studies of TB's epidemiology, comparative genomics, evolution, and host-pathogen interaction. We argue here, however, that new multidisciplinary approaches--especially the integration of epidemiology with systems biology in what we call "systems epidemiology"--will be required to eliminate TB.

Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints

Background

Mycobacterium tuberculosis complex (MTBC), the causative agent of tuberculosis (TB), is characterized by low sequence diversity making this bacterium one of the classical examples of a genetically monomorphic pathogen. Because of this limited DNA sequence variation, routine genotyping of clinical MTBC isolates for epidemiological purposes relies on highly discriminatory DNA fingerprinting methods based on mobile and repetitive genetic elements. According to the standard view, isolates exhibiting the same fingerprinting pattern are considered direct progeny of the same bacterial clone, and most likely reflect ongoing transmission or disease relapse within individual patients.

Methodology/Principal Findings

Here we further investigated this assumption and used massively parallel whole-genome sequencing to compare one drug-susceptible (K-1) and one multidrug resistant (MDR) isolate (K-2) of a rapidly spreading M. tuberculosis Beijing genotype clone from a high incidence region (Karakalpakstan, Uzbekistan). Both isolates shared the same IS6110 RFLP pattern and the same allele at 23 out of 24 MIRU-VNTR loci.

We generated 23.9 million (K-1) and 33.0 million (K-2) paired 50 bp purity filtered reads corresponding to a mean coverage of 483.5 fold and 656.1 fold respectively. Compared with the laboratory strain H37Rv both Beijing isolates shared 1,209 SNPs. The two Beijing isolates differed by 130 SNPs and one large deletion. The susceptible isolate had 55 specific SNPs, while the MDR variant had 75 specific SNPs, including the five known resistance-conferring mutations.

Conclusions

Our results suggest that M. tuberculosis isolates exhibiting identical DNA fingerprinting patterns can harbour substantial genomic diversity. Because this heterogeneity is not captured by traditional genotyping of MTBC, some aspects of the transmission dynamics of tuberculosis could be missed or misinterpreted. Furthermore, a valid differentiation between disease relapse and exogenous reinfection might be impossible using standard genotyping tools if the overall diversity of circulating clones is limited. These findings have important implications for clinical trials of new anti-tuberculosis drugs.

Fitness study of the RDRio lineage and Latin American-Mediterranean family of Mycobacterium tuberculosis in the city of Rio Grande, Brazil

RD(Rio) is a novel Mycobacterium tuberculosis lineage of the Latin American-Mediterranean (LAM) family. LAM has been found worldwide but is more predominant in South America. The aim of this study was to assess the presence of the RD(Rio) lineage and LAM family in the city of Rio Grande, Brazil, and to investigate the fitness of these strains based on determination of their growth rate. Fifty clinical isolates of M. tuberculosis were genotyped and 43 different patterns were found by spoligotyping and mycobacterial interspersed repetitive units-variable number of tandem repeats. The predominant genotypes belonged to the LAM family (54% of the strains) followed by clade T (22%) and Haarlem (16%). The RD(Rio) lineage represented 38% of the total strains and 70.4% of the LAM strains found in this study. Strains belonging to the LAM family showed a fitness advantage when comparing their rate of growth with that of non-LAM strains, but a significant difference between RD(Rio) and non-RD(Rio) strains was not confirmed.

Mycobacterium tuberculosis strains with highly discordant rifampin susceptibility test results

The objectives of this study were to investigate the origin of highly discordant rifampin (rifampicin) (RMP) drug susceptibility test results obtained for Mycobacterium tuberculosis strains during proficiency testing. Nine Supra-National Tuberculosis Reference Laboratories tested the RMP susceptibilities of 19 selected M. tuberculosis strains, using standard culture-based methods. The strains were classified as definitely resistant (R) (n = 6) or susceptible (S) (n = 2) or probably resistant (PR) (n = 8) or susceptible (PS) (n = 3) based on rpoB mutations and treatment outcome. All methods yielded a susceptible result for the two S and three PS strains lacking an rpoB mutation and a resistant result for one R strain with a Ser531Leu mutation and one PR strain with a double mutation. Although the remaining 12 R and PR strains had rpoB mutations (four Asp516Tyr, three Leu511Pro, two Leu533Pro, one each His526Leu/Ser, and one Ile572Phe), they were all susceptible by the radiometric Bactec 460TB or Bactec 960 MGIT methods. In contrast, only one was susceptible by the proportion method on Löwenstein-Jensen medium and two on Middlebrook 7H10 agar. Low-level but probably clinically relevant RMP resistance linked to specific rpoB mutations is easily missed by standard growth-based methods, particularly the automated broth-based systems. Further studies are required to confirm these findings, to determine the frequency of these low-level-resistant isolates, and to identify technical improvements that may identify such strains.

The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis

The emergence of antibiotic resistance in Mycobacterium tuberculosis has raised the concern that pathogen strains that are virtually untreatable may become widespread. The acquisition of resistance to antibiotics results in a longer duration of infection in a host, but this resistance may come at a cost through a decreased transmission rate. This raises the question of whether the overall fitness of drug-resistant strains is higher than that of sensitive strains--essential information for predicting the spread of the disease. Here, we directly estimate the transmission cost of drug resistance, the rate at which resistance evolves, and the relative fitness of resistant strains. These estimates are made by using explicit models of the transmission and evolution of sensitive and resistant strains of M. tuberculosis, using approximate Bayesian computation, and molecular epidemiology data from Cuba, Estonia, and Venezuela. We find that the transmission cost of drug resistance relative to sensitivity can be as low as 10%, that resistance evolves at rates of approximately 0.0025-0.02 per case per year, and that the overall fitness of resistant strains is comparable with that of sensitive strains. Furthermore, the contribution of transmission to the spread of drug resistance is very high compared with acquired resistance due to treatment failure (up to 99%). Estimating such parameters directly from in vivo data will be critical to understanding and responding to antibiotic resistance. For instance, projections using our estimates suggest that the prevalence of tuberculosis may decline with successful treatment, but the proportion of cases associated with resistance is likely to increase.

Interplay in the selection of fluoroquinolone resistance and bacterial fitness

Fluoroquinolones are antibacterial drugs that inhibit DNA Gyrase and Topoisomerase IV. These essential enzymes facilitate chromosome replication and RNA transcription by regulating chromosome supercoiling. High-level resistance to fluoroquinolones in E. coli requires the accumulation of multiple mutations, including those that alter target genes and genes regulating drug efflux. Previous studies have shown some drug-resistance mutations reduce bacterial fitness, leading to the selection of fitness-compensatory mutations. The impact of fluoroquinolone-resistance on bacterial fitness was analyzed in constructed isogenic strains carrying up to 5 resistance mutations. Some mutations significantly decreased bacterial fitness both in vitro and in vivo. We identified low-fitness triple-mutants where the acquisition of a fourth resistance mutation significantly increased fitness in vitro and in vivo while at the same time dramatically decreasing drug susceptibility. The largest effect occurred with the addition of a parC mutation (Topoisomerase IV) to a low-fitness strain carrying resistance mutations in gyrA (DNA Gyrase) and marR (drug efflux regulation). Increased fitness was accompanied by a significant change in the level of gyrA promoter activity as measured in an assay of DNA supercoiling. In selection and competition experiments made in the absence of drug, parC mutants that improved fitness and reduced susceptibility were selected. These data suggest that natural selection for improved growth in bacteria with low-level resistance to fluoroquinolones could in some cases select for further reductions in drug susceptibility. Thus, increased resistance to fluoroquinolones could be selected even in the absence of further exposure to the drug.

The increasing frequency of human pathogens resistant to important classes of antibiotics poses a serious and growing challenge for medicine and society. We need improved strategies to reduce the rate of resistance development, for established and novel drugs, based on knowledge of the factors that drive the increase in resistance. Resistance to fluoroquinolones in most bacteria develops via a series of sequential genetic changes affecting several different genes. These are selected and enriched in bacterial populations by exposure to the drug. Relevant factors driving this increase include overuse, and inappropriate use, of these drugs. In this paper we show that mutant bacteria with low-level resistance (not itself a problem to treat with standard drug doses) can evolve by natural selection (for improved growth rate) to acquire mutations that dramatically increase their level of drug resistance. This means that we may need to consider how to reduce inappropriate drug use that can enrich for bacteria with low-levels of resistance, because at that stage some of the mutant bacteria in the population may continue to evolve higher level resistance even in the absence of any further drug exposure.

Positive epistasis drives the acquisition of multidrug resistance

The evolution of multiple antibiotic resistance is an increasing global problem. Resistance mutations are known to impair fitness, and the evolution of resistance to multiple drugs depends both on their costs individually and on how they interact—epistasis. Information on the level of epistasis between antibiotic resistance mutations is of key importance to understanding epistasis amongst deleterious alleles, a key theoretical question, and to improving public health measures. Here we show that in an antibiotic-free environment the cost of multiple resistance is smaller than expected, a signature of pervasive positive epistasis among alleles that confer resistance to antibiotics. Competition assays reveal that the cost of resistance to a given antibiotic is dependent on the presence of resistance alleles for other antibiotics. Surprisingly we find that a significant fraction of resistant mutations can be beneficial in certain resistant genetic backgrounds, that some double resistances entail no measurable cost, and that some allelic combinations are hotspots for rapid compensation. These results provide additional insight as to why multi-resistant bacteria are so prevalent and reveal an extra layer of complexity on epistatic patterns previously unrecognized, since it is hidden in genome-wide studies of genetic interactions using gene knockouts.

Understanding the nature of genetic interactions, known as epistasis, is crucial in biology. The strength and type of epistasis is relevant for the evolution of sex, buffering of genetic variation, speciation, and the topography of fitness landscapes. While epistasis between gene deletions has been the recent focus of research, interactions between randomly selected alleles, which are of the greatest evolutionary interest, have not. We have studied the strength and type of epistasis amongst alleles that confer antibiotic resistance and have found that: in an antibiotic-free environment, the cost of multiple resistance is smaller than expected—a signature of pervasive positive epistasis amongst alleles that confer resistance to antibiotics; epistatic interactions are allele specific; a significant fraction of resistant mutations can be beneficial in certain resistant genetic backgrounds; some double resistances entail no measurable cost; and some allelic combinations are hotspots for rapid compensation. Overall, our findings provide added reasoning as to why multi-resistance is so difficult to eradicate. Importantly, our results of allelic-specific epistasis reveal an extra layer of complexity on epistatic patterns previously unrecognized.

Factors affecting the reversal of antimicrobial-drug resistance

The persistence or loss of acquired antimicrobial-drug resistance in bacterial populations previously exposed to drug-selective pressure depends on several biological processes. We review mechanisms promoting or preventing the loss of resistance, including rates of reacquisition, effects of resistance traits on bacterial fitness, linked selection, and segregational stability of resistance determinants. As a case study, we discuss the persistence of glycopeptide-resistant enterococci in Norwegian and Danish poultry farms 12 years after the ban of the animal growth promoter avoparcin. We conclude that complete eradication of antimicrobial resistance in bacterial populations following relaxed drug-selective pressures is not straightforward. Resistance determinants may persist at low, but detectable, levels for many years in the absence of the corresponding drugs.

Rapid contemporary evolution and clonal food web dynamics

Character evolution that affects ecological community interactions often occurs contemporaneously with temporal changes in population size, potentially altering the very nature of those dynamics. Such eco-evolutionary processes may be most readily explored in systems with short generations and simple genetics. Asexual and cyclically parthenogenetic organisms such as microalgae, cladocerans and rotifers, which frequently dominate freshwater plankton communities, meet these requirements. Multiple clonal lines can coexist within each species over extended periods, until either fixation occurs or a sexual phase reshuffles the genetic material. When clones differ in traits affecting interspecific interactions, within-species clonal dynamics can have major effects on the population dynamics. We first consider a simple predator-prey system with two prey genotypes, parametrized with data from a well-studied experimental system, and explore how the extent of differences in defence against predation within the prey population determine dynamic stability versus instability of the system. We then explore how increased potential for evolution affects the community dynamics in a more general community model with multiple predator and multiple prey genotypes. These examples illustrate how microevolutionary 'details' that enhance or limit the potential for heritable phenotypic change can have significant effects on contemporaneous community-level dynamics and the persistence and coexistence of species.

Enhanced heterogeneity of rpoB in Mycobacterium tuberculosis found at low pH

OBJECTIVES

The aim of this study was to gain an insight into the molecular mechanisms of the evolution of rifampicin resistance in response to controlled changes in the environment.

METHODS

We determined the proportion of rpoB mutants in the chemostat culture and characterized the sequence of mutations found in the rifampicin resistance-determining region of rpoB in a steady-state chemostat at pH 7.0 and 6.2.

RESULTS

The overall proportion of rpoB mutants of strain H37Rv remained constant for 37 days at pH 7.0, ranging between 3.6 x 10(-8) and 8.9 x 10(-8); however, the spectrum of mutations varied. The most commonly detected mutation, serine to leucine mutation at codon 531 (S531L), increased from 40% to 89%, while other mutations (S531W, H526Y, H526D, H526R, S522L and D516V) decreased over the 37 day sampling period. Changing the pH from 7.0 to 6.2 did not significantly alter the overall proportion of mutants, but resulted in a decrease in the percentage of strains harbouring S531L (from 89% to 50%) accompanied by an increase in the range of different mutations from 4 to 12.

CONCLUSIONS

The data confirm that the fitness of strains with the S531L mutation is greater than that of strains containing other mutations. We also conclude that at low pH the environment is permissive for a wider spectrum of mutations, which may provide opportunities for a successful mutant to survive.

Averting epidemics of extensively drug-resistant tuberculosis

Extensively drug-resistant tuberculosis (XDR TB) has been detected in most provinces of South Africa, particularly in the KwaZulu-Natal province where several hundred cases have been reported since 2004. We analyzed the transmission dynamics of XDR TB in the region using mathematical models, and observed that nosocomial transmission clusters of XDR TB may emerge into community-based epidemics under the public health conditions of many South African communities. The effective reproductive number of XDR TB in KwaZulu-Natal may be around 2. Intensified community-based case finding and therapy appears critical to curtailing transmission. In the setting of delayed disease presentation and high system demand, improved diagnostic approaches may need to be employed in community-based programs rather than exclusively at tertiary hospitals. Using branching process mathematics, we observed that early, community-based drug-susceptibility testing and effective XDR therapy could help curtail ongoing transmission and reduce the probability of XDR TB epidemics in neighboring territories.

M. tuberculosis Central Asian Strain 1 MDR isolates have more mutations in rpoB and katG genes compared with other genotypes

Pakistan ranks eighth globally among TB burden countries, with a MDR rate of 2-5%. The most prevalent MTB genotype is Central Asian Strain1 (CAS1) followed by the Beijing genogroup. We investigated common mutations in multidrug resistance encoding genes rpoB, katG and inhA of CAS1 and Beijing strains using DNA sequencing and fluorescent resonance energy transfer (FRET) probe based real-time PCR methods. 30 CAS1, 12 Beijing and 20 unclustered spoligotypes, and 10 susceptible MTB strains were tested. The most common mutations in the rpoB gene were at codons 531 (60%), 526 (23%) and 516 (5%). CAS1 strains had a higher frequency of mutations at codon 526 (p<0.001), with more concurrent mutations (p<0.05) compared with Beijing and orphan types. Mutations at codon 315 of the katG gene were higher in CAS1 than Beijing strains (p=0.052). Only 1/62 MDR strain, which belonged to CAS1, had a mutation in the inhA gene. Sensitivity and specificity of probe based assay was 93% and 100% for rpoB, and 95% and 100% for katG, respectively. The FRET probes method detected 84% and 60% of rpoB and katG mutations and can therefore be used as a rapid method of screening MTB strains including CAS1.

Mycobacterium tuberculosis transmission is not related to household genotype in a setting of high endemicity

Among the different strains of Mycobacterium tuberculosis, Beijing has been identified as an emerging genotype. Enhanced transmissibility provides a potential mechanism for genotype selection. This study evaluated whether the Beijing genotype is more readily transmitted than other prevalent genotypes to children in contact with an adult tuberculosis (TB) index case in the child's household. We conducted a prospective, community-based study at two primary health care clinics in Cape Town, South Africa, from January 2003 through December 2004. Bacteriologically confirmed new adult pulmonary TB cases were genotyped by IS6110 DNA fingerprinting; household contacts less than 5 years were traced and screened for M. tuberculosis infection and/or disease. A total of 187 adult index cases were identified from 174 households with children aged less than 5 years. Of 261 child contacts aged 0 to 5 years, 219 (83.9%) were completely evaluated and the isolate from the index case was successfully genotyped. M. tuberculosis infection (induration of >or=10 mm by Mantoux tuberculin skin test) was documented in 118/219 (53.9%) children; 34 (15.5%) had radiographic signs suggestive of active TB. There was no significant difference in the ratio of infected children among those exposed to the Beijing genotype (51/89; 57.3%) and those exposed to non-Beijing genotypes (55/115; 47.8%) (odds ratio, 1.5; 95% confidence interval, 0.8 to 2.7). Genotyping was successful for six children diagnosed with active TB; the isolates from only two children had IS6110 fingerprints that were identical to the IS6110 fingerprint of the isolate from the presumed index case. We found no significant association between the M. tuberculosis genotype and transmissibility within the household. However, undocumented M. tuberculosis exposure may have been a major confounding factor in this setting with a high burden of TB.

Incongruent HIV and tuberculosis co-dynamics in Kenya: interacting epidemics monitor each other

OBJECTIVE

Kenya is heralded as an example of declining HIV in Africa, while its tuberculosis (TB) numbers continue rising. We conducted a comparative investigation of TB-HIV co-dynamics in Africa to determine the likelihood of reported trends.

METHODS AND RESULTS

Our mathematical modeling analysis exposes the notable incongruence of reported trends in Kenya because TB-HIV co-dynamics, tightly knit worldwide and most dramatically in sub-Saharan Africa, suggest that declining HIV trends should trigger reductions in TB trends. Moreover, a continental-scale analysis of TB-HIV trends places Kenya as an outlier in eastern and southern Africa, and shows TB outpacing HIV in western central Africa. We further investigate which TB processes across HIV stages have greater potential to reduce TB incidence via a sensitivity analysis.

CONCLUSIONS

There are two parsimonious explanations: an unaccounted improvement in TB case detection has occurred, or HIV is not declining as reported. The TB-HIV mismatch could be compounded by surveillance biases due to spatial heterogeneity in disease dynamics. Results highlight the need to re-evaluate trends of both diseases in Kenya, and identify the most critical epidemiological factors at play. Substantial demographic changes have occurred in Kenya, including rapid urbanization accompanied by poor living conditions, which could disproportionately increase TB incidence. Other possible contributors include immune reconstitution due to the recent delivery of antiretrovirals, and an increased presence of the virulent Beijing/W TB genotype. Results support the importance of integrating information from closely interacting epidemics, because this approach provides critical insights unobtainable when components of generalized epidemics are considered individually.

The cost of multiple drug resistance in Pseudomonas aeruginosa

The spread of bacterial antibiotic resistance mutations is thought to be constrained by their pleiotropic fitness costs. Here we investigate the fitness costs of resistance in the context of the evolution of multiple drug resistance (MDR), by measuring the cost of acquiring streptomycin resistance mutations (StrepR) in independent strains of the bacterium Pseudomonas aeruginosa carrying different rifampicin resistance (RifR) mutations. In the absence of antibiotics, StrepR mutations are associated with similar fitness costs in different RifR genetic backgrounds. The cost of StrepR mutations is greater in a rifampicin-sensitive (RifS) background, directly demonstrating antagonistic epistasis between resistance mutations. In the presence of rifampicin, StrepR mutations have contrasting effects in different RifR backgrounds: StrepR mutations have no detectable costs in some RifR backgrounds and massive fitness costs in others. Our results clearly demonstrate the importance of epistasis and genotype-by-environment interactions for the evolution of MDR.

Clinical characteristics and treatment outcomes of patients with isoniazid-monoresistant tuberculosis

BACKGROUND

Risk factors and treatment outcomes under program conditions for isoniazid (INH)-monoresistant tuberculosis have not been well described.

METHODS

Medical charts were retrospectively reviewed for all cases of culture-confirmed, INH-monoresistant tuberculosis ( n = 137) reported to the San Francisco Department of Public Health Tuberculosis Control Section from October 1992 through October 2005, and those cases were compared with a time-matched sample of drug-susceptible tuberculosis cases (n = 274)

RESULTS

In multivariate analysis, only a history of treatment for latent tuberculosis (odds ratio [OR], 3.1; 95% confidence interval [CI], 1.5-6.4; P = .003) or for active tuberculosis (OR, 2.7; 95% CI, 1.4-5.0; P = .002) were significantly associated with INH-monoresistant tuberculosis. Of the 119 patients who completed treatment, 49 (41%) completed a 6-month treatment regimen. Treatment was extended to 7-12 months for 53 (45%) of the patients and to >12 months for 17 (14%). Treatment was most commonly extended because pyrazinamide was not given for the recommended 6-month duration (35 patients [29%]). Despite variation in treatment regimens, the combined end point of treatment failure or relapse was uncommon among patients with INH-monoresistant tuberculosis and was not significantly different for patients with drug-susceptible tuberculosis (1.7% vs. 2.2%; P = .73).

CONCLUSIONS

A history of treatment for latent or active tuberculosis was associated with subsequent INH monoresistance. Treatment outcomes for patients with INH-monoresistant tuberculosis were excellent and were no different from those for patients with drug-susceptible tuberculosis. However, new, short-course regimens are needed because a small proportion of patients completed the 6-month treatment regimen recommended by the American Thoracic Society, Centers for Disease Control and Prevention, and Infectious Diseases Society of America, primarily because of pyrazinamide intolerance.

High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography

Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC). However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis.

Tuberculosis remains a worldwide public health emergency. The emergence of drug-resistant forms of tuberculosis in many parts of the world is threatening to make this important human disease incurable. Even though many resources are being invested into the development of new tuberculosis control tools, we still do not know the extent of genetic diversity in tuberculosis bacteria, nor do we understand the evolutionary forces that shape this diversity. To address these questions, we studied a large collection of human tuberculosis strains using DNA sequencing. We found that strains originating in different parts of the world are more genetically diverse than previously recognized. Our results also suggest that much of this diversity has functional consequences and could affect the efficacy of new tuberculosis diagnostics, drugs, and vaccines. Furthermore, we found that the global diversity in tuberculosis strains can be linked to the ancient human migrations out of Africa, as well as to more recent movements that followed the increases of human populations in Europe, India, and China during the past few hundred years. Taken together, our findings suggest that the evolutionary characteristics of tuberculosis bacteria could synergize with the effects of increasing globalization and human travel to enhance the global spread of drug-resistant tuberculosis.

DNA sequence analysis of a global collection ofM. tuberculosis strains reveals high functional diversity, severely reduced selective constraint, and global spread through both ancient and recent human migrations.

Gain of function mutations in CgPDR1 of Candida glabrata not only mediate antifungal resistance but also enhance virulence

CgPdr1p is a Candida glabrata Zn(2)-Cys(6) transcription factor involved in the regulation of the ABC-transporter genes CgCDR1, CgCDR2, and CgSNQ2, which are mediators of azole resistance. Single-point mutations in CgPDR1 are known to increase the expression of at least CgCDR1 and CgCDR2 and thus to contribute to azole resistance of clinical isolates. In this study, we investigated the incidence of CgPDR1 mutations in a large collection of clinical isolates and tested their relevance, not only to azole resistance in vitro and in vivo, but also to virulence. The comparison of CgPDR1 alleles from azole-susceptible and azole-resistant matched isolates enabled the identification of 57 amino acid substitutions, each positioned in distinct CgPDR1 alleles. These substitutions, which could be grouped into three different “hot spots,” were gain of function (GOF) mutations since they conferred hyperactivity to CgPdr1p revealed by constitutive high expression of ABC-transporter genes. Interestingly, the major transporters involved in azole resistance (CgCDR1, CgCDR2, and CgSNQ2) were not always coordinately expressed in presence of specific CgPDR1 GOF mutations, thus suggesting that these are rather trans-acting elements (GOF in CgPDR1) than cis-acting elements (promoters) that lead to azole resistance by upregulating specific combinations of ABC-transporter genes. Moreover, C. glabrata isolates complemented with CgPDR1 hyperactive alleles were not only more virulent in mice than those with wild type alleles, but they also gained fitness in the same animal model. The presence of CgPDR1 hyperactive alleles also contributed to fluconazole treatment failure in the mouse model. In conclusion, this study shows for the first time that CgPDR1 mutations are not only responsible for in vitro/in vivo azole resistance but that they can also confer a selective advantage under host conditions.

Candida glabrata is a yeast causing several diseases in humans and especially in immuno-compromised people. C. glabrata infections are treated with antifungal agents, however the use of some agents, for example azoles, is associated with the development of resistance. In this yeast species, azole resistance is mediated almost exclusively by ATP Binding Cassette (ABC) multidrug transporters. Their overexpression results in enhanced efflux of azoles and thus generates resistance. Regulation of ABC transporters is therefore of pivotal importance to understanding azole resistance. In C. glabrata, the expression of ABC transporters is mediated by a zinc finger transcription factor called CgPDR1. Gain of function (GOF) mutations in CgPDR1 result in high ABC transporter expression. In this study, we investigated the occurrence of GOF mutations in a large collection of azole-resistant isolates and found a high variety of mutations localized in three distinct domains of CgPDR1. We found that these mutations are not only associated with resistance but also enhanced virulence and fitness of C. glabrata in animal models. Our study provides for the first time evidence that mutations causing antifungal resistance can also provide a selective advantage under host conditions and thus highlights the need of carefully monitoring resistance in this pathogen.

Doomsday postponed? Preventing and reversing epidemics of drug-resistant tuberculosis

Extensively drug-resistant (XDR) strains of Mycobacterium tuberculosis, now known to be present in 50 countries, heighten the threat posed by untreatable and fatal human tuberculosis (TB). To combat epidemics of drug-resistant TB, it is vital to understand why some resistant strains have greater reproductive fitness--a greater propensity to spread--than drug-susceptible strains. If public health malpractice has been a more important determinant of reproductive success than genetic mechanisms, then improved diagnosis and treatment could keep the frequency of resistant strains among TB cases low in any population. Recent data suggest that national TB control programmes that use existing drugs efficiently can postpone and even reverse epidemics of multidrug-resistant TB, although the effect of such programmes on XDR strains remains largely unknown.

Rapid experimental evolution of pesticide resistance in C. elegans entails no costs and affects the mating system

Pesticide resistance is a major concern in natural populations and a model trait to study adaptation. Despite the importance of this trait, the dynamics of its evolution and of its ecological consequences remain largely unstudied. To fill this gap, we performed experimental evolution with replicated populations of Caenorhabditis elegans exposed to the pesticide Levamisole during 20 generations. Exposure to Levamisole resulted in decreased survival, fecundity and male frequency, which declined from 30% to zero. This was not due to differential susceptibility of males. Rather, the drug affected mobility, resulting in fewer encounters, probably leading to reduced outcrossing rates. Adaptation, i.e., increased survival and fecundity, occurred within 10 and 20 generations, respectively. Male frequency also increased by generation 20. Adaptation costs were undetected in the ancestral environment and in presence of Ivermectin, another widely-used pesticide with an opposite physiological effect. Our results demonstrate that pesticide resistance can evolve at an extremely rapid pace. Furthermore, we unravel the effects of behaviour on life-history traits and test the environmental dependence of adaptation costs. This study establishes experimental evolution as a powerful tool to tackle pesticide resistance, and paves the way to further investigations manipulating environmental and/or genetic factors underlying adaptation to pesticides.

Extensively drug-resistant tuberculosis in sub-Saharan Africa: an emerging public-health concern

The extensively drug-resistant tuberculosis (XDR-TB) categorisation has been developed as a phenotypic description of those TB strains that are resistant to most conventional anti-TB drugs. While widely accepted to have significant incidence in those areas, such as Eastern Europe, that have high levels of multidrug resistance, recent reports have described a cluster of XDR-TB cases in the KwaZulu-Natal province of South Africa. With very high case-fatality rates in this setting and a paucity of potential treatment options, concerns have grown about the possibility of an outbreak of highly lethal TB occurring in areas where TB prevalence, generally, is at its highest. In this article, we review previously documented case series of XDR-TB, and examine questions around the likelihood of rapid XDR-TB expansion in sub-Saharan Africa. We analyse how current TB control measures in the area might cope with such a challenge, and identify new areas for focus within the research and development community.

Rapid genotypic assays to identify drug-resistant Mycobacterium tuberculosis in South Africa

OBJECTIVES

Molecular assays to detect drug resistance in Mycobacterium tuberculosis are more rapid than standard drug susceptibility testing. To evaluate the efficacy of such assays in this setting, the GenoType MTBDRplus assay (HAIN Lifescience) and multiplex allele-specific PCR assays were carried out.

METHODS

The GenoType MTBDRplus assay was evaluated for the detection of rifampicin and isoniazid resistance in 223 M. tuberculosis isolates of known phenotypic drug sensitivity. The presence of KatG S315T and inhA C-15T mutations that confer isoniazid resistance was determined using multiplex allele-specific PCR assays. The relationship between isolate lineage and resistance determinant was investigated by spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat analysis.

RESULTS

The GenoType MTBDRplus assay detected multidrug-resistant, isoniazid-monoresistant and rifampicin-monoresistant isolates with sensitivities of 91.5%, 56.1% and 70%, respectively. Multiplex allele-specific PCR detected isoniazid resistance in 91.5% of the MDR isolates and 53.7% of the isoniazid-monoresistant isolates. The W-Beijing lineage was overrepresented in the MDR subgroup of strains (odds ratio, 3.29; 95% confidence interval, 1.76-6.16).

CONCLUSIONS

A proportion of isoniazid resistance, particularly in isoniazid-monoresistant isolates of lineage X3, is due to resistance determinants other than KatG S315T and inhA C-15T. The fact that these isolates will be indicated as drug susceptible highlights the need for determining local patterns of resistance mutations to provide users with information regarding the capabilities of rapid genotypic assays.

Origin, spread and demography of the Mycobacterium tuberculosis complex

The evolutionary timing and spread of the Mycobacterium tuberculosis complex (MTBC), one of the most successful groups of bacterial pathogens, remains largely unknown. Here, using mycobacterial tandem repeat sequences as genetic markers, we show that the MTBC consists of two independent clades, one composed exclusively of M. tuberculosis lineages from humans and the other composed of both animal and human isolates. The latter also likely derived from a human pathogenic lineage, supporting the hypothesis of an original human host. Using Bayesian statistics and experimental data on the variability of the mycobacterial markers in infected patients, we estimated the age of the MTBC at 40,000 years, coinciding with the expansion of "modern" human populations out of Africa. Furthermore, coalescence analysis revealed a strong and recent demographic expansion in almost all M. tuberculosis lineages, which coincides with the human population explosion over the last two centuries. These findings thus unveil the dynamic dimension of the association between human host and pathogen populations.

Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus

A small number of clonal lineages dominates the global population structure of methicillin-resistant Staphylococcus aureus (MRSA), resulting in the concept that MRSA has emerged on a few occasions after penicillinase-stable beta-lactam antibiotics were introduced to clinical practice, followed by intercontinental spread of individual clones. We investigated the evolutionary history of an MRSA clone (ST5) by mutation discovery at 108 loci (46 kb) within a global collection of 135 isolates. The SNPs that were ascertained define a radial phylogenetic structure within ST5 consisting of at least 5 chains of mutational steps that define geographically associated clades. These clades are not concordant with previously described groupings based on staphylococcal protein A gene (spa) typing. By mapping the number of independent imports of the staphylococcal cassette chromosome methicillin-resistance island, we also show that import has occurred on at least 23 occasions within this single sequence type and that the progeny of such recombinant strains usually are distributed locally rather than globally. These results provide strong evidence that geographical spread of MRSA over long distances and across cultural borders is a rare event compared with the frequency with which the staphylococcal cassette chromosome island has been imported.

The effects of the genetic background on herbicide resistance fitness cost and its associated dominance in Arabidopsis thaliana

The advantage of the resistance conferred by a mutation can sometimes be offset by a high fitness-cost penalty. This balance will affect possible fate of the resistance allele. Few studies have explored the impact of the genetic background on the expression of the resistance fitness cost and none has attempted to measure the variation in fitness-cost dominance. However, both the fitness penalty and its dominance may modify evolutionary trajectory and outcome. Here the impact of Arabidopsis thaliana intraspecific genetic diversity on fitness cost and its associated dominance was investigated by analysing 12 quantitative traits in crosses between a mutant conferring resistance to the herbicide 2,4-D and nine different natural genetic backgrounds. Fitness cost values were found to be more affected by intraspecific genetic diversity than fitness cost dominance, even though this effect depends on the quantitative trait measured. This observation has implications for the choice of the best strategy for preventing herbicide resistance development. In addition, our results pinpoint a potential compensatory improvement of the resistance fitness cost and its associated dominance by the genetic diversity locally present within a species.

Population structure analysis of the Mycobacterium tuberculosis Beijing family indicates an association between certain sublineages and multidrug resistance

Our population-based study of the Mycobacterium tuberculosis Beijing family examined the frequency of occurrence of each sublineage of this family, classified by using 10 synonymous single-nucleotide polymorphisms. The results revealed the overabundance of two evolutionary sublineages in a population of multidrug-resistant and extensively drug-resistant tuberculosis bacteria.

Impact of enhanced tuberculosis diagnosis in South Africa: a mathematical model of expanded culture and drug susceptibility testing

South Africa has high rates of tuberculosis (TB), including multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Expanding access to culture and drug susceptibility testing (DST) for TB diagnosis may help control this epidemic, but the potential impact of existing and novel TB diagnostics is uncertain. By fitting to World Health Organization epidemiological estimates, we developed a compartmental difference-equation model of the TB/HIV epidemic among South African adults. Performing culture and DST in 37% of new cases and 85% of previously treated cases was projected to save 47,955 lives (17.2% reduction in TB mortality, 95% simulation interval (S.I.) 8.9-24.4%), avert 7,721 MDR-TB cases (14.1% reduction, 95% S.I. 5.3-23.8%), and prevent 46.6% of MDR-TB deaths (95% S.I. 32.6-56.0%) in South Africa over 10 years. Used alone, expanded culture and DST did not reduce XDR-TB incidence, but they enhanced the impact of transmission-reduction strategies, such as respiratory isolation. In South Africa, expanding TB culture and DST could substantially reduce TB, and particularly MDR-TB, mortality. Control of XDR-TB will require additional interventions, the impact of which may be enhanced by improved TB diagnosis.

The evolution of drug resistance in Mycobacterium tuberculosis: from a mono-rifampin-resistant cluster into increasingly multidrug-resistant variants in an HIV-seropositive population

We describe the genotypic and phenotypic characteristics of a mono-rifampin-resistant (RIF(R)) Mycobacterium tuberculosis strain cluster (designated AU-RIF(R)) and the acquisition of additional drug resistance. Drug susceptibility, sequences of regions that determine drug resistance, and basic clinical data were examined. A rare codon duplication (514(TTC)) in rpoB conferring high levels of RIF(R) (minimum inhibitory concentration of >256 microg/mL) in 29 isolates was identified. AU-RIF(R) strains developed secondary resistance to isoniazid and 7 resistance combinations to 6 different antibiotics. Patients infected with AU-RIF(R) strains were primarily immunocompromised. These data suggest that host factors, such as HIV status, may allow dissemination of mono-RIF(R) strains and facilitate the accumulation of additional drug resistance.

Characterization of an inducible, antibiotic-resistant aminoacyl-tRNA synthetase gene in Streptomyces coelicolor

Streptomyces coelicolor has two genes encoding tryptophanyl-tRNA synthetases, one of which (trpRS1) is resistant to and transcriptionally activated by indolmycin. We found that this gene also confers resistance to chuangxinmycin (another antibiotic that inhibits bacterial tryptophanyl-tRNA synthetases) and that its transcription is not absolutely dependent on either antibiotic.

The transmission and control of XDR TB in South Africa: an operations research and mathematical modelling approach

Extensively drug-resistant tuberculosis (XDR TB) has emerged as a threat to TB control efforts in several high-burden areas, generating international concern. XDR TB is now found in every region of the world, but appears most worrisome in the context of HIV and in resource-limited settings with congregate hospital wards. Here, we examine the emergence and transmission dynamics of the disease, incorporating the mathematical modelling literature related to airborne infection and epidemiological studies related to the operations of TB control programmes in resource-limited settings. We find that while XDR TB may present many challenges in the setting of resource constraints, the central problems highlighted by the emergence of XDR TB are those that have plagued TB programmes for years. These include a slow rate of case detection that permits prolonged infectiousness, the threat of airborne infection in enclosed spaces, the problem of inadequate treatment delivery and treatment completion, and the need to develop health systems that can address the combination of TB and poverty. Mathematical models of TB transmission shed light on the idea that community-based therapy and rapid detection systems may be beneficial in resource-limited settings, while congregate hospital wards are sites for major structural reform.

Are survey-based estimates of the burden of drug resistant TB too low? Insight from a simulation study

Background

The emergence of tuberculosis resistant to multiple first- and second-line antibiotics poses challenges to a global control strategy that relies on standard drug treatment regimens. Highly drug-resistant strains of Mycobacterium tuberculosis have been implicated in outbreaks and have been found throughout the world; a comprehensive understanding the magnitude of this threat requires an accurate assessment of the worldwide burden of resistance. Unfortunately, in many settings where resistance is emerging, laboratory capacity is limited and estimates of the burden of resistance are obtained by performing drug sensitivity testing on a sample of incident cases rather than through the use of routine surveillance.

Methodology/Principal Findings

Using an individual-based dynamic tuberculosis model to simulate surveillance strategies for drug resistance, we found that current surveys may underestimate the total burden of resistant tuberculosis because cases of acquired resistance are undercounted and resistance among prevalent cases is not assessed. We explored how this bias is affected by the maturity of the epidemic and by the introduction of interventions that target the emergence and spread of resistant tuberculosis.

Conclusions

Estimates of drug resistant tuberculosis based on samples of incident cases should be viewed as a lower bound of the total burden of resistance.