The biological cost of antibiotic resistance

Adaptation to the cost of resistance: a model of compensation, recombination, and selection in a haploid organism

Populations of pathogenic organisms often evolve resistance in response to the use of pesticides or antibiotics. This rise of resistance may be followed by a fall when chemical control is suspended and resistance alleles carry a fitness cost. Another possibility is that mutations at secondary loci compensate for the cost, usually without loss of resistance. This enables resistant types to withstand invasion by the susceptible wild-type; resistance then persists in the population, which reduces the efficacy of future pesticide or antibiotic use. We examined a two-locus model of a haploid organism that adapts to the cost of resistance by a single compensatory mutation. We addressed the question how different combinations of cost and compensation and different levels of recombination affect the consequences of a single pesticide application. Resistance will become fixed in the population when the fraction of the population exposed to pesticide exceeds the cost of resistance. Compensatory mutations reduce the cost of resistance and therefore this threshold level of pesticide use. In the absence of pesticide, recombination promotes stability of equilibria. In the presence of pesticide, recombination accelerates the fixation of resistance and compensating alleles; recombination may also enable the persistence of compensated resistant types after pesticide use.

Heterogeneity of methicillin-resistant Staphylococcus aureus strains at a German university hospital during a 1-year period

Heterogeneous methicillin-resistant Staphylococcus aureus (MRSA) strains, including community-acquired MRSA strains, have been observed in Central Europe. The purpose of this study was to characterize by molecular methods MRSA isolated during the period 2002-2003 at the Otto-von-Guericke University Hospital in Magdeburg, Germany, and at a nearby chronic care facility. Strains were analyzed for their resistance phenotype. Selected isolates were typed by multilocus sequence typing (MLST), by a multiplex polymerase chain reaction (PCR) for the staphylococcal cassette chromosome mec (SCCmec), by an allele-specific PCR for the staphylococcal accessory gene regulator (agr), and by PCR for the presence of toxin genes (sea-sej, tsst-1, hlgA, C, and B, lukE/D, and luk-pvl). Of the 2,731 S. aureus isolates studied, 199 (7.3%) were MRSA, with a prevalence of 21.6%, 19.6%, and 12% in the department of dermatology, the chronic care facility, and the intensive care units. Six different sequence types (ST247, ST228, ST22, ST22a, ST225, and ST45) were observed. Of these, ST22, ST22a, and ST45 dominated (>50%) in the department of dermatology and the chronic care facility. Strains with these sequence types were usually not resistant to gentamicin and were associated with agr group I, the SCCmec type IV element, and the presence of the sec and sed toxin genes. ST228 strains were found mainly in the intensive care units and had a broader resistance phenotype and were associated with agr group II and the SCCmec type I element. All luk-pvl-positive MRSA isolates (n=8) belonged to agr group I and were typed as ST22 or ST45 and contained the SCCmec type I (n=1), type III (n=1), or type IV (n=6) element. The main observations of this study are in concordance with previously reported findings showing dissemination of MRSA in Central Europe. Through the multitude of applied methods, the data from this study contribute to a more precise knowledge about the heterogeneity of MRSA in a clinical setting. Rapid dissemination of MRSA clones at a university hospital was demonstrated, indicating that dissemination may depend on the environmental conditions within the individual departments.

Community-acquired meticillin-resistant Staphylococcus aureus: an emerging threat

Community-acquired meticillin-resistant Staphylococcus aureus (MRSA) is becoming an important public-health problem. New strains of S aureus displaying unique combinations of virulence factors and resistance traits have been associated with high morbidity and mortality in the community. Outbreaks of epidemic furunculosis and cases of severe invasive pulmonary infections in young, otherwise healthy people have been particularly noteworthy. We review the characteristics of these new strains of community-acquired MRSA that have contributed to their pathogenicity and discuss new approaches to the diagnosis and management of suspected and confirmed community-acquired MRSA infections.

[Antimicrobial resistance and bacterial virulence]

Hospitals are places with high selective pressure by antimicrobial agents. For this reason, bacteria producing nosocomial infections need to be not only virulent, but also resistant to antimicrobial agents. In the present review we analyse the effect of the acquisition of an antibiotic resistance phenotype in bacterial fitness and virulence. Besides that, we review as well the existence of common mechanisms for resistance to antimicrobial agents and bacterial virulence. In this line, we highlight the role of multidrug efflux pumps on bacterial virulence. Since opportunistic pathogens frequently have an environmental origin, we also discuss the role of natural ecosystems, as well as their potential contamination, on the selection of bacteria resistant to antimicrobial agents.

Compensatory adaptation to the loss of biological fitness associated with acquisition of fusidic acid resistance in Staphylococcus aureus

Recent studies have shown that individual amino acid exchanges within elongation factor G (EF-G) cause fusidic acid resistance in Staphylococcus aureus. The data from the present study illustrate that the fusidic acid resistance-mediating amino acid substitutions P406L and H457Y are associated with a marked impairment of the biological fitness of S. aureus. In particular, strains producing EF-G derivatives with these mutations showed reduced growth, decreased plasma coagulase activity, and an impaired capability to compete with the isogenic wild-type strain. Second-site mutations within EF-G, such as A67T and S416F, that have been encountered in clinical fusidic acid-resistant isolates containing the amino acid exchanges P406L and H457Y, respectively, were shown not to contribute to resistance. Furthermore, the substitution A67T had no impact on the biological fitness in vitro. The exchange S416F, however, was found to function as a fitness-compensating mutation in S. aureus carrying the substitution H457Y in EF-G. In conclusion, the data presented in this report provide evidence at the molecular level that the deleterious effects of fusidic acid resistance-mediating exchanges within EF-G of S. aureus can be reduced considerably by specific compensating mutations in this target protein. This compensatory adaptation most likely plays a significant role in the stabilization of resistant bacteria within a given population.

The coupon collector and the suppressor mutation: estimating the number of compensatory mutations by maximum likelihood

Compensatory mutation occurs when a loss of fitness caused by a deleterious mutation is restored by its epistatic interaction with a second mutation at a different site in the genome. How many different compensatory mutations can act on a given deleterious mutation? Although this quantity is fundamentally important to understanding the evolutionary consequence of mutation and the genetic complexity of adaptation, it remains poorly understood. To determine the shape of the statistical distribution for the number of compensatory mutations per deleterious mutation, we have performed a maximum-likelihood analysis of experimental data collected from the suppressor mutation literature. Suppressor mutations are used widely to assess protein interactions and are under certain conditions equivalent to compensatory mutations. By comparing the maximum likelihood of a variety of candidate distribution functions, we established that an L-shaped gamma distribution (alpha=0.564, theta=21.01) is the most successful at explaining the collected data. This distribution predicts an average of 11.8 compensatory mutations per deleterious mutation. Furthermore, the success of the L-shaped gamma distribution is robust to variation in mutation rates among sites. We have detected significant differences among viral, prokaryotic, and eukaryotic data subsets in the number of compensatory mutations and also in the proportion of compensatory mutations that are intragenic. This is the first attempt to characterize the overall diversity of compensatory mutations, identifying a consistent and accurate prior distribution of compensatory mutation diversity for theoretical evolutionary models.

Why has the dihydrofolate reductase 164 mutation not consistently been found in Africa yet?

Resistance to the antifolate sulfadoxine-pyrimethamine (SP), the current mass-treatment antimalarial drug, is associated with selection of point mutations in dihydrofolate reductase and dihydropteroate synthase. Among these mutations, the leucine 164 dihydrofolate reductase mutation (Leu-164) is associated with higher levels of SP resistance; this mutation is also associated with a decrease in the efficacy of chlorproguanil/dapsone, a newly developed antifolate antimalarial drug. Leu-164 has been detected in Southeast Asia and South America, regions where SP is no longer effective. Surprisingly, this mutation has not yet been detected in Africa, using the standard protocol based on PCR-RFLP, despite high SP resistance. In this paper, we discuss briefly the reasons why Leu-164 has not yet been selected in Africa and we propose a means that may slow down the selection of this mutation.

Isoniazid resistance and the future of drug-resistant tuberculosis

Bacterial chromosomal mutations that confer antibiotic resistance often have deleterious effects that impose costs on reproductive fitness. This observation has led to the generalization that in the absence of the selection pressure exerted through treatment, the frequency of resistance will decrease. This model implies that the prudent use of antibiotics will eventually result in a decline in the prevalence of drug resistance. Recent work, however, suggests that some resistance-conferring mutations may not significantly impair fitness and that others may be accompanied by compensatory mutations that restore the organisms' reproductive potential. Thus drug resistance, once introduced, may persist unless specific measures are implemented to target prevalent drug-resistant cases. Here we present ecological evidence to support the hypothesis that mutations at the 315 position of katG confer isoniazid resistance for Mycobacterium tuberculosis without diminishing virulence or transmissibility.

Overexpression of the multidrug efflux pumps MexCD-OprJ and MexEF-OprN is associated with a reduction of type III secretion in Pseudomonas aeruginosa

The Pseudomonas aeruginosa genome contains several different multidrug resistance (MDR) efflux pumps. Overproduction of these pumps reduces susceptibility to a variety of antibiotics. Some recently published works have analyzed the effect of the overproduction of MDR efflux pumps on bacterial virulence. Here we have studied the effect of overproduction of the efflux pumps MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY on type III secretion (T3S) in P. aeruginosa. The type III secretion system (T3SS) is used by P. aeruginosa to deliver toxins directly into the cytoplasm of the host cell. Our data indicate that overexpression of either MexCD-OprJ or MexEF-OprN is associated with the impairment of T3S in P. aeruginosa. No effect on overexpression of either MexAB-OprM or MexXY was detected. The observed defect in T3S was due to a lack of expression of genes belonging to the T3SS regulon. Transcription of this regulon is activated by ExsA in response to environmental signals. Overexpression of this transcriptional regulator complemented the defect in T3S observed in the MexCD-OprJ- and MexEF-OprN-overproducing strains. Taken together, these results suggest that overproduction of either MexCD-OprJ or MexEF-OprN is associated with a reduction in the transcription of the T3SS regulon due to the lack of expression of the exsA gene, encoding the master regulator of the system. The relevance of potential metabolic and quorum-sensing imbalances due to overexpression of MDR pumps associated with this phenotype is also discussed.

Pharmacodynamic modeling of ciprofloxacin resistance in Staphylococcus aureus

Three pharmacodynamic models of increasing complexity, designed for two subpopulations of bacteria with different susceptibilities, were developed to describe and predict the evolution of resistance to ciprofloxacin in Staphylococcus aureus by using pharmacokinetic, viable count, subpopulation, and resistance mechanism data obtained from in vitro system experiments. A two-population model with unique growth and killing rate constants for the ciprofloxacin-susceptible and -resistant subpopulations best described the initial killing and subsequent regrowth patterns observed. The model correctly described the enrichment of subpopulations with low-level resistance in the parent cultures but did not identify a relationship between the time ciprofloxacin concentrations were in the mutant selection window (the interval between the MIC and the mutant prevention concentration) and the enrichment of these subpopulations. The model confirmed the importance of resistant variants to the emergence of resistance by successfully predicting that resistant subpopulations would not emerge when a low-density culture, with a low probability of mutants, was exposed to a clinical dosing regimen or when a high-density culture, with a higher probability of mutants, was exposed to a transient high initial concentration designed to rapidly eradicate low-level resistant grlA mutants. The model, however, did not predict or explain the origin of variants with higher levels of resistance that appeared and became the predominant subpopulation during some experiments or the persistence of susceptible bacteria in other experiments where resistance did not emerge. Continued evaluation of the present two-population pharmacodynamic model and development of alternative models is warranted.

Impact of drug resistance on fitness of Mycobacterium tuberculosis strains of the W-Beijing genotype

Mycobacterium tuberculosis strains of the W-Beijing genotype became a common cause of tuberculosis during the past years and they are often associated with drug resistance. The biological factors facilitating the selection and wide dissemination of these strains are not known. To determine how acquisition of drug resistance affected growth of strains of the W-Beijing genotype, the growth of 55 M. tuberculosis isolates were studied using the BBL MGIT Mycobacteria Growth Indicator Tube and the BACTEC MGIT 960 System. Susceptible strains of non-Beijing genotypes were found to be the most fit strains. Drug-resistant strains of non-Beijing genotypes were more likely to grow slower than susceptible strains (P=0.001). Drug-resistant strains of the W-Beijing genotype had two tendencies of growth: some of them showed reduced growth compared to susceptible strains, while others did not show loss of fitness measured as growth.

Evolution of ciprofloxacin-resistant Staphylococcus aureus in in vitro pharmacokinetic environments

The development of novel antibacterial agents is decreasing despite increasing resistance to presently available agents among common pathogens. Insights into relationships between pharmacodynamics and resistance may provide ways to optimize the use of existing agents. The evolution of resistance was examined in two ciprofloxacin-susceptible Staphylococcus aureus strains exposed to in vitro-simulated clinical and experimental ciprofloxacin pharmacokinetic profiles for 96 h. As the average steady-state concentration (C(avg ss)) increased, the rate of killing approached a maximum, and the rate of regrowth decreased. The enrichment of subpopulations with mutations in grlA and low-level ciprofloxacin resistance also varied depending on the pharmacokinetic environment. A regimen producing values for C(avg ss) slightly above the MIC selected resistant variants with grlA mutations that did not evolve to higher levels of resistance. Clinical regimens which provided values for C(avg ss) intermediate to the MIC and mutant prevention concentration (MPC) resulted in the emergence of subpopulations with gyrA mutations and higher levels of resistance. A regimen producing values for C(avg ss) close to the MPC selected grlA mutants, but the appearance of subpopulations with higher levels of resistance was diminished. A regimen designed to maintain ciprofloxacin concentrations entirely above the MPC appeared to eradicate low-level resistant variants in the inoculum and prevent the emergence of higher levels of resistance. There was no relationship between the time that ciprofloxacin concentrations remained between the MIC and the MPC and the degree of resistance or the presence or type of ciprofloxacin-resistance mutations that appeared in grlA or gyrA. Regimens designed to eradicate low-level resistant variants in S. aureus populations may prevent the emergence of higher levels of fluoroquinolone resistance.

Enhanced in vivo fitness of fluoroquinolone-resistant Campylobacter jejuni in the absence of antibiotic selection pressure

Campylobacter jejuni, a major foodborne human pathogen, has become increasingly resistant to fluoroquinolone (FQ) antimicrobials. By using clonally related isolates and genetically defined mutants, we determined the fitness of FQ-resistant Campylobacter in chicken (a natural host and a major reservoir for C. jejuni) in the absence of antibiotic selection pressure. When monoinoculated into the host, FQ-resistant and FQ-susceptible Campylobacter displayed similar levels of colonization and persistence in the absence of FQ antimicrobials. The prolonged colonization in chickens did not result in loss of the FQ resistance and the resistance-conferring point mutation (C257 --> T) in the gyrA gene. Strikingly, when coinoculated into chickens, the FQ-resistant Campylobacter isolates outcompeted the majority of the FQ-susceptible strains, indicating that the resistant Campylobacter was biologically fit in the chicken host. The fitness advantage was not due to compensatory mutations in the genes targeted by FQ and was linked directly to the single point mutation in gyrA, which confers on Campylobacter a high-level resistance to FQ antimicrobials. In certain genetic backgrounds, the same point mutation entailed a biological cost on Campylobacter, as evidenced by its inability to compete with the FQ-susceptible Campylobacter. These findings provide a previously undescribed demonstration of the profound effect of a resistance-conferring point mutation in gyrA on the fitness of a major foodborne pathogen in its natural host and suggest that the rapid emergence of FQ-resistant Campylobacter on a worldwide scale may be attributable partly to the enhanced fitness of the FQ-resistant isolates.

Structure-activity relationship study of anoplin

Anoplin is a decapeptide amide, GLLKRIKTLL-NH2 derived from the venom sac of the solitary spider wasp, Anoplius samariensis. It is active against Gram-positive and Gram-negative bacteria and is not hemolytic towards human erythrocytes. The present paper reports a structure-activity study of anoplin based on 37 analogues including an Ala-scan, C- and N-truncations, and single and multiple residue substitutions with various amino acids. The analogues were tested for antibacterial activity against both S. aureus ATCC 25923 and E. coli ATCC 25922, and several potent antibacterial analogues were identified. The cytotoxicity of the analogues against human erythrocytes was assessed in a hemolytic activity assay. The antibacterial activity and selectivity of the analogues against S. aureus and E. coli varied considerably, depending on the hydrophobicity and position of the various substituted amino acids. In certain cases the selectivity for Gram-positive and Gram-negative bacteria was either reversed or altogether eliminated. In addition, it was generally found that antibacterial activity coincided with hemolytic activity.

Reduction of the fitness burden of quinolone resistance in Pseudomonas aeruginosa

OBJECTIVES

Quinolone resistance in the opportunistic pathogen Pseudomonas aeruginosa is commonly caused by mutations that alter the target molecules DNA gyrase/topoisomerase IV, or cause activation of various efflux systems. We have analysed the effect of quinolone resistance caused by DNA gyrase/topoisomerase IV mutations on bacterial fitness.

METHODS

Norfloxacin-resistant mutants were isolated and by DNA sequencing the mutations conferring resistance were identified. Mutant fitness was determined by measuring growth rates in vitro. Mutants with reduced growth rates were serially passaged to obtain growth-compensated mutants. The level of DNA supercoiling was determined by isolating plasmid DNA from the susceptible, resistant and compensated mutants and comparing the topoisomer distribution patterns by gel electrophoresis in the presence of chloroquine.

RESULTS

Low-level resistance (4-48 mg/L) was caused by single mutations in gyrA or gyrB. Among these strains, three out of eight mutants showed lower fitness, whereas high-level resistant (>256 mg/L) mutants with double mutations in gyrA and parC, parE, nfxB or unknown genes all showed a reduced fitness. Slow-growing resistant mutants with a gyrA mutation had decreased DNA supercoiling. After serial passage in laboratory medium, mutant fitness was increased by compensatory mutation(s) that restored supercoiling to normal levels. The compensatory mutation(s) was not located in any of the genes (gyrAB, topA, parCE, hupB, fis, hupN, himAD or PA5348) that were expected to affect supercoiling.

CONCLUSIONS

Our results show that 'no cost' and compensatory mutations are common in quinolone-resistant P. aeruginosa.

Analysis of mupirocin resistance and fitness in Staphylococcus aureus by molecular genetic and structural modeling techniques

Chromosomal resistance to mupirocin in clinical isolates of Staphylococcus aureus arises from V(588)F or V(631)F mutations in isoleucyl-tRNA synthetase (IRS). Whether these are the only IRS mutations that confer mupirocin resistance or simply those that survive in the clinic is unknown. Mupirocin-resistant mutants of S. aureus 8325-4 were therefore generated to examine their ileS genotypes and the in vitro and in vivo fitness costs associated with them before and after compensatory evolution. Most spontaneous first-step mupirocin-resistant mutants carried V(588)F or V(631)F mutations in IRS, but a new mutation (G(593)V) was also identified. Second-step mutants carried combinations of previously identified IRS mutations (e.g., V(588)F/V(631)F and G(593)V/V(631)F), but additional combinations also occurred involving novel mutations (R(816)C, H(67)Q, and F(563)L). First-step mupirocin-resistant mutants were not associated with substantial fitness costs, a finding that is consistent with the occurrence of V(588)F or V(631)F mutations in the IRS of clinical strains. Second-step mutants were unfit, but fitness could be restored by subculture in the absence of mupirocin. In most cases, this was the result of compensatory mutations that also suppressed mupirocin resistance (e.g., A(196)V, E(190)K, and E(195)K), despite retention of the original mutations conferring resistance. Structural explanations for mupirocin resistance and loss of fitness were obtained by molecular modeling of mutated IRS enzymes, which provided data on mupirocin binding and interaction with the isoleucyl-AMP reactive intermediate.

Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution

Antibiotic resistant bacteria are a constant threat in the battle against infectious diseases. One strategy for reducing their effect is to temporarily discontinue the use of certain antibiotics in the hope that in the absence of the antibiotic the resistant strains will be replaced by the sensitive strains. An experiment where this strategy is employed in vitro produces data which showed a slow accumulation of sensitive mutants. Here we propose a mathematical model and statistical analysis to explain this data. The stochastic model elucidates the trend and error structure of the data. It provides a guide for developing future sampling strategies, and provides a framework for long term predictions of the effects of discontinuing specific antibiotics on the dynamics of resistant bacterial populations.

Comparative analysis of Clostridium difficile clinical isolates belonging to different genetic lineages and time periods

Recent studies have shown that Clostridium difficile strains with variant toxins and those with resistance to macrolide-lincosamide-streptogramin B (MLSB) are increasingly causing severe disease and outbreaks in hospital settings. Here, the pathogenicity locus (PaLoc), the acquisition of binary toxin, and the genotypic and phenotypic characteristics of antibiotic resistance of 74 C. difficile clinical strains isolated from symptomatic patients in Italy during different time periods were studied. These strains were found to belong to two different lineages, and those isolated before 1991 were genetically unrelated to the more recent strains. The majority of recent C. difficile strains showed variations in toxin genes and in the toxin negative regulator (tcdC) and had the binary toxin. In 62 % of them, variations in tcdC and the presence of the binary toxin were associated. Five classes of susceptibility/resistance pattern (EC-a to -e) for erythromycin and clindamycin were identified in all strains studied. Most of the recent isolates belonged to EC-d and EC-e and, although erythromycin-resistant in vitro, did not harbour the commonly associated ermB determinant. Interestingly, two strains of the EC-d class were resistant to clindamycin only after induction with subinhibitory concentrations of the antibiotic. A decrease in tetracycline and chloramphenicol MIC values was also observed in the recently isolated strains, associated with less frequent detection of the catD and tetM genes. Two tetM-positive strains were resistant in vitro only after induction with subinhibitory concentrations of the antibiotic. The acquisition of the binary toxin, the possible increase in toxin production due to a mutated negative regulator and a decrease in the fitness cost as a result of lower levels of antibiotic resistance or other mechanisms may have led to the successful establishment of these new phenotypes, with potentially serious clinical implications.

Combinatorial Genetic Technology for the Development of New Anti-infectives

Context.—We previously developed a novel technology known as instant evolution for high-throughput analysis of mutations in Escherichia coli ribosomal RNA.

Objective.—To develop a genetic platform for the isolation of new classes of antiinfectives that are not susceptible to drug resistance based on the instant evolution system.

Design.—Mutation libraries were constructed in the 16S rRNA gene of E coli and analyzed. In addition, the rRNA genes from a number of pathogenic bacteria were cloned and expressed in E coli. The 16S rRNA genes were incorporated into the instant-evolution system in E coli.

Setting.—The Department of Biological Sciences, Wayne State University, Detroit, Mich.

Main Outcome Measures.—Ribosome function was assayed by measuring the amount of green fluorescent protein produced by ribosomes containing mutant or foreign RNA in vivo.

Results.—We have developed a new combinatorial genetic technology (CGT) platform that allows high-throughput in vivo isolation and analysis of rRNA mutations that might lead to drug resistance. This information is being used to develop anti-infectives that recognize the wild type and all viable mutants of the drug target. CGT also provides a novel mechanism for identifying new drug targets.

Conclusions.—Antimicrobials produced using CGT will provide new therapies for the treatment of infections caused by human pathogens that are resistant to current antibiotics. The new therapeutics will be less susceptible to de novo resistance because CGT identifies all mutations of the target that might lead to resistance during the earliest stages of the drug discovery process.

Residues of selected antibiotics in water and mud from shrimp ponds in mangrove areas in Viet Nam

In recent years, antibiotics have been used widely in intensive shrimp culture and this may lead to their contamination of the environment. Surveys on residues of trimethoprim (TMP), sulfamethoxazole (SMX), norfloxacin (NFXC) and oxolinic acid (OXLA) in water and mud in shrimp ponds in mangrove areas were conducted in the north as well as in south of Viet Nam in July and August, 2002. The results show that these antibiotics are found in all samples in both shrimp ponds and surrounding canals. The highest concentrations of TMP, SMX, NFXC and OXLA are 1.04, 2.39, 6.06, and 2.50 ppm in water samples; and 734.61, 820.49, 2615.96, 426.31 ppm (based on wet mud weight), respectively. The comparison of antibiotics residues between study sites and types of shrimp ponds will be discussed in this paper. The results also suggest that antibiotics residues may cause harmful effect on ecosystems in the study sites.

Combining mathematical models and statistical methods to understand and predict the dynamics of antibiotic-sensitive mutants in a population of resistant bacteria during experimental evolution

Temporarily discontinuing the use of antibiotics has been proposed as a means to eliminate resistant bacteria by allowing sensitive clones to sweep through the population. In this study, we monitored a tetracycline-sensitive subpopulation that emerged during experimental evolution of E. coli K12 MG1655 carrying the multiresistance plasmid pB10 in the absence of antibiotics. The fraction of tetracycline-sensitive mutants increased slowly over 500 generations from 0.1 to 7%, and loss of resistance could be attributed to a recombination event that caused deletion of the tet operon. To help understand the population dynamics of these mutants, three mathematical models were developed that took into consideration recurrent mutations, increased host fitness (selection), or a combination of both mechanisms (full model). The data were best explained by the full model, which estimated a high mutation frequency (lambda = 3.11 x 10(-5)) and a significant but small selection coefficient (sigma = 0.007). This study emphasized the combined use of experimental data, mathematical models, and statistical methods to better understand and predict the dynamics of evolving bacterial populations, more specifically the possible consequences of discontinuing the use of antibiotics.

Colony-forming analysis of bacterial community succession in deglaciated soils indicates pioneer stress-tolerant opportunists

We investigated the response of bacterial communities inhabiting two deglaciated soils (10 and 100 years post-deglaciation) to two stimuli: (i) physical disruption (mixing), and (ii) disruption plus nutrient addition. PCR/DGGE analysis of 16S rRNA genes extracted from soil during a 168-h incubation period following the stimuli revealed that more bacterial phylotypes were stimulated in the 10-y soil than in the 100-y soil. In addition to 10-y and 100-y soils, two additional soils (46 and 70 y) were further differentiated using colony-forming curve (CFC) analysis during a 168-h incubation period, which revealed that younger soils contained a higher proportion of rapidly colonizing bacteria than successively older soils. "Eco-collections" of CFC isolates that represented colonies that formed "fast" (during the first 24 h) and "slow" (final 36 h) were harvested from 10-y and 100-y soils and differentiated according to response to three stress parameters: (i) tolerance to nutrient limitation, (ii) tolerance to temperature change, and (iii) resistance to antibiotics. The tested parameters distinguished "fast" from "slow" bacteria regardless of the age of the soil from which they were isolated. Specifically, eco-collections of "fast" bacteria exhibited greater nutrient- and temperature-stress tolerance as well as more frequent antibiotic resistance than "slow" bacteria. Further DGGE analysis showed that several eco-collection phylotype bands matched (electrophoretically) those of soil phylotypes enriched by mixing and nutrient stimulus. Overall, the results of this study indicated that the succession of colony-forming bacteria was differentiated by bacterial opportunism and temporal response to stimuli. Furthermore, although stress tolerance strategies are associated with opportunistic bacteria regardless of successional age, it appears that the proportion of opportunistic bacteria distinguishes early vs late succession forefield bacterial populations.

Modeling epidemics of multidrug-resistant M. tuberculosis of heterogeneous fitness

Mathematical models have recently been used to predict the future burden of multidrug-resistant tuberculosis (MDRTB). These models suggest the threat of multidrug resistance to TB control will depend on the relative 'fitness' of MDR strains and imply that if the average fitness of MDR strains is considerably less than that of drug-sensitive strains, the emergence of resistance will not jeopardize the success of tuberculosis control efforts. Multidrug resistance in M. tuberculosis is conferred by the sequential acquisition of a number of different single-locus mutations that have been shown to have heterogeneous phenotypic effects. Here we model the impact of initial fitness estimates on the emergence of MDRTB assuming that the relative fitness of MDR strains is heterogeneous. We find that even when the average relative fitness of MDR strains is low and a well-functioning control program is in place, a small subpopulation of a relatively fit MDR strain may eventually outcompete both the drug-sensitive strains and the less fit MDR strains. These results imply that current epidemiological measures and short-term trends in the burden of MDRTB do not provide evidence that MDRTB strains can be contained in the absence of specific efforts to limit transmission from those with MDR disease.

Mechanisms of resistance among respiratory tract pathogens

Antimicrobial resistance among respiratory tract pathogens represents a significant health care threat. Identifying the antimicrobial agents that remain effective in the presence of resistance, and knowing why, requires a thorough understanding of the mechanisms of action of the various agents as well as the mechanisms of resistance demonstrated among respiratory tract pathogens. The primary goal of antimicrobial therapy is to eradicate the pathogen, via killing or inhibiting bacteria, from the site of infection; the defenses of the body are required for killing any remaining bacteria. Targeting a cellular process or function specific to bacteria and not to the host limits the toxicity to patients. Currently, there are four general cellular targets to which antimicrobials are targeted: cell wall formation and maintenance, protein synthesis, DNA replication, and folic acid metabolism. Resistance mechanisms among respiratory tract pathogens have been demonstrated for all four targets. In general, the mechanisms of resistance used by these pathogens fall into one of three categories: enzymatic inactivation of the antimicrobial, prevention of intracellular accumulation, and modification of the target site to which agents bind to exert an antimicrobial effect. Resistance to some agents can be overcome by modifying the dosage regimens (e.g., using high-dose therapy) or inhibiting the resistance mechanism (e.g., b-lactamase inhibitors), whereas other mechanisms of resistance can only be overcome by using an agent from a different class. Understanding the mechanisms of action of the various agents and the mechanisms of resistance used by respiratory tract pathogens can help clinicians identify the agents that will increase the likelihood of achieving optimal outcomes.

Fitness cost of SCCmec and methicillin resistance levels in Staphylococcus aureus

Transformation of a type I SCCmec element into Staphylococcus aureus yielded highly oxacillin-resistant transformants with a reduced growth rate. Faster-growing variants could again be selected at the cost of reduced resistance levels, demonstrating an inverse correlation between oxacillin resistance levels and growth rate.

Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution

Compensatory mutations, due to their ability to mask the deleterious effects of another mutation, are important for the adaptation and evolution of most organisms. Resistance to antibiotics, antivirals, antifungals, herbicides and insecticides is usually associated with a fitness cost. As a result of compensatory evolution, the initial fitness costs conferred by resistance mutations (or other deleterious mutations) can often be rapidly and efficiently reduced. Such compensatory evolution is potentially of importance for (i) the long-term persistence of drug resistance, (ii) reducing the rate of fitness loss associated with the accumulation of deleterious mutations in small asexual populations, and (iii) the evolution of complexity of cellular processes.

The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens

The evolution of ecological specialization is expected to carry a cost, due to either antagonistic pleiotropy or mutation accumulation. In general, it has been difficult to distinguish between these two possibilities. Here, we demonstrate that the experimental evolution of niche-specialist genotypes of the bacterium Pseudomonas fluorescens that colonize the air-broth interface of spatially structured microcosms is accompanied by pleiotropic fitness costs in terms of reduced carbon catabolism. Prolonged selection in spatially structured microcosms caused the cost of specialization to decline without loss of the benefits associated with specialization. The decline in the cost of specialization can be explained by either compensatory adaptation within specialist lineages or clonal competition among specialist lineages. These results provide a possible explanation of conflicting accounts for the cost of specialization.

Factors associated with antimicrobial resistance among clinical isolates of Klebsiella pneumoniae: 1-year survey in a French university hospital

Klebsiella pneumoniae is an opportunistic pathogen responsible for nosocomial infections. Both resistance to multiple antibiotics and the expression of virulence factors are likely to be involved in the physiopathological process. In this study, 227 isolates of K. pneumoniae collected over a 1-year period in a teaching hospital in Clermont-Ferrand, France, were investigated for their antibiotic resistance pattern and the presence of several potential virulence traits. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) indicated that most of the isolates were phylogenetically unrelated. When tested in an in vitro adhesion assay with Int-407 intestinal cells, the median adhesion index was 5.5x10(4) bacteria/cm(2) (range, 2.0x10(2)-3.4x10(5)). Isolates resistant to cefoxitin, chloramphenicol, and quinolones showed significantly lower adhesion indexes. The frequency of mutagenesis conferring resistance to rifampicin was low for most of the isolates. The median mutagenesis frequency was 1.0x10(-8) (range, 2.5x10(-9)-3.2x10(-6)) at 24 h and 1.1x10(-8) (range, 1.8x10(-9)-1.2x10(-5)) at 7 days. In contrast, isolates resistant to cefoxitin, chloramphenicol, and tetracycline showed a significantly greater ability to mutate. These results suggest a link between adhesion capabilities and resistance to certain antibiotics. They furthermore indicate that strains with a high mutagenesis capacity are more likely to acquire antibiotic resistance genes. The high pathogenicity island of Yersinia was detected in 16.3% of the strains and was more often associated with isolates resistant to nalidixic acid and augmentin.

Clinical manifestations and molecular epidemiology of necrotizing pneumonia and empyema caused by Streptococcus pneumoniae in children in Taiwan

Recently, there have been increasing numbers of pneumococcal pneumonia cases, with their associated complications. We conducted a retrospective review to increase the understanding of childhood pneumococcal pneumonia. Seventy-one patients with pneumococcal pneumonia were identified. Forty (56.3%) of them developed complicated pneumonia. Multivariate analysis showed that presence of immature polymorphonuclear leukocytes in peripheral blood (odds ratio [OR], 3.67; 95% confidence interval [CI], 1.08-12.63), high C-reactive protein levels (>12 mg/dL) (OR, 5.24; 95% CI, 1.10-24.93), and no underlying disease at presentation (OR, 5.48; 95% CI, 1.06-28.25) were independent predictors of the occurrence of necrosis or/and abscess. Fourteen isolates (35%), which were genotypically identical and had the same pulsed-field gel electrophoresis pattern (serogroup 14, with MICs of penicillin of 0.1-0.5 mu g/mL), were significantly associated with complicated pneumonia (P=.047). Whether the virulence of antibiotic-resistant pneumococci is evolving deserves further investigation.

Preliminary investigation on the environmental occurrence and effects of antibiotics used in aquaculture in Italy

A preliminary investigation has been carried out on the occurrence and effects of antibiotics used in Italian aquaculture with the objective of identifying priorities for monitoring programmes. According to the information available on the most pertinent and diffuse fish diseases and their related therapies, the presence of flumequine and oxytetracycline in sediments sampled from two trout farms and three sea-bass farms and in their surrounding environments was selected for an analytical investigation. The concentrations of oxytetracycline and flumequine varied up to a maximum of 246.3 and 578.8 microg/kg d.w., respectively. Flumequine was seen to have the highest toxicity in a bioluminescence assay with EC50 values varying within the range of 12-15 mg/l, while the EC50 values for oxytetracycline were within the range of 121-139 mg/l. The results of the present study indicate flumequine and oxytetracycline as priority chemicals to be monitored for possible environmental side effects of aquaculture in Italy. Apart from peak concentrations the chronic presence of flumequine and oxytetracycline in sediments both inside and outside farms should also be considered. In spite of the potential risks related to the use of antibiotics, the concentrations found in the sediments of the studied fish farms are significantly lower than those found in other areas.

Community-acquired Methicillin-resistant Staphylococcus aureus: Epidemiology and Potential Virulence Factors

Methicillin-resistant Staphylococcus aureus (MRSA) has been isolated from patients in the community. Some of these strains may have origins in the hospital, but others appear to be novel and unrelated to known hospital strains. Community MRSA strains have several distinguishing characteristics that may enable them to more readily colonize and infect otherwise healthy individuals. This article reviews recent publications addressing the epidemiology of MRSA in the community, risk factors associated with carriage, potentially associated virulence factors, and concepts of strain fitness as they pertain to MRSA. MRSA likely will be an increasingly important pathogen in the community.

Biological costs and mechanisms of fosfomycin resistance in Escherichia coli

Fosfomycin is a cell wall inhibitor used mainly for the treatment of uncomplicated lower urinary tract infections. As shown here, resistance to fosfomycin develops rapidly in Escherichia coli under experimental conditions, but in spite of the relatively high mutation rate in vitro, resistance in clinical isolates is rare. To examine this apparent contradiction, we mathematically modeled the probability of resistance development in the bladder during treatment. The modeling showed that during a typical episode of urinary tract infection, the probability of resistance development was high (>10(-2)). However, if resistance was associated with a reduction in growth rate, the probability of resistance development rapidly decreased. To examine if fosfomycin resistance causes a reduced growth rate, we isolated in vitro and in vivo a set of resistant strains. We determined their resistance mechanisms and examined the effect of the different resistance mutations on bacterial growth in the absence and presence of fosfomycin. The types of mutations found in vitro and in vivo were partly different. Resistance in the mutants isolated in vitro was caused by ptsI, cyaA, glpT, uhpA/T, and unknown mutations, whereas no cyaA or ptsI mutants could be found in vivo. All mutations caused a decreased growth rate both in laboratory medium and in urine, irrespective of the absence or presence of fosfomycin. According to the mathematical model, the reduced growth rate of the resistant strains will prevent them from establishing in the bladder, which could explain why fosfomycin resistance remains rare in clinical isolates.

Fitness cost of fluoroquinolone resistance in Salmonella enterica serovar Typhimurium

High-level fluoroquinolone (FQ) resistance is still infrequent in salmonellae, compared with other pathogenic enterobacteria. Data provided in this work support the hypothesis that the mechanisms that confer high-level FQ resistance on salmonellae have a prohibitive fitness cost and may thus limit the emergence of highly resistant clones. In vitro mutants that were highly resistant to ciprofloxacin (MIC = 8 and 16 micro g ml(-1)) showed generation times 1.4- and 2-fold longer than their parent strains and were unable to colonize the gut of chickens. Electron microscopy showed an altered morphology for one of these mutants grown to stationary phase. Mutants selected in vivo and exhibiting intermediate resistance to ciprofloxacin (MIC = 2 micro g ml(-1)) also showed growth defects on solid media but had normal generation times in liquid culture and colonized the gut of chickens. After in vitro or in vivo passage in the absence of antibiotic selective pressure, partial reversals of the fitness cost were observed, which were associated with slight decreases in resistance to quinolones and other unrelated antibiotics, but were not linked to the loss of gyrA mutations.

Arming the enemy: the evolution of resistance to self-proteins

A remarkable range of novel antibiotics is attracting increasing interest as a major new weapon in the campaign against bacterial infection. They are based on the toxic peptides that provide the innate immune system of animals, and it is claimed that bacteria will be unable to evolve resistance to them because they attack the 'Achilles' heel' of bacterial membrane structure. Both experimental evidence and theoretical arguments suggest that this claim is doubtful. If so, the introduction of these substances into general use may provoke the evolution of resistance to our own defence proteins and thus compromise our natural defences against infection.

Exploiting genomics, genetics and chemistry to combat antibiotic resistance

To address the worsening problem of antibiotic-resistant bacteria there is an urgent need to develop new antibiotics. Comparative genomics and molecular genetics are being applied to produce lists of essential new targets for compound screening programmes. Combinatorial chemistry and structural biology are being applied to rapidly explore and optimize the interactions between lead compounds and their biological targets. Several compounds that have been identified from target-based screens are now in development, but technical and economic constraints might result in a trickle, rather than a flood, of new antibiotics onto the market in the near future.

Impact of elements containing glycopeptide resistance genes on expression of virulence in Enterococcus faecalis peritonitis: a pilot study with rats

The relationship between virulence and chromosomal elements containing glycopeptide resistance genes was experimentally assessed for two transconjugant strains of Enterococcus faecalis (VanA and VanB phenotypes) and compared to that for a susceptible wild-type strain. Microbiologic and inflammatory effects were assessed in a polymicrobial rat model of peritonitis. Mean peritoneal enterococcus concentrations +/- standard deviations at day 1 were 2.1 +/- 1.9, 1.3 +/- 1.1, and 1.7 +/- 2.0 log(10) CFU/ml for susceptible, VanA, and VanB strains, respectively (P < 0.05). At day 3 also there were lower concentrations of glycopeptide-resistant enterococcal strains in peritoneal fluid (3.2 +/- 3.4, 1.8 +/- 1.8, and 2.1 +/- 2.4 log(10) CFU/ml for susceptible, VanA, and VanB strains, respectively [P < 0.05]). Transconjugant glycopeptide-resistant strains were associated with increased peritoneal cell counts at the different evaluation times of the experiment (P < 0.001). Plasma alpha1-acid glycoprotein concentrations were lower in the presence of the susceptible strain (667 +/- 189 mg/liter) than in the presence of the VanA or VanB strain (1,193 +/- 419 or 1,210 +/- 404 mg/liter, respectively [P < 0.05]), while concentrations of tumor necrosis factor alpha and interleukin-6 in peritoneal fluid remained similar for the strains. These results suggest a trend toward variation of virulence of transconjugant strains compared to the wild-type strain in this peritonitis model.

Mode of selection and experimental evolution of antifungal drug resistance in Saccharomyces cerevisiae

We show that mode of selection, degree of dominance of mutations, and ploidy are determining factors in the evolution of resistance to the antifungal drug fluconazole in yeast. In experiment 1, yeast populations were subjected to a stepwise increase in fluconazole concentration over 400 generations. Under this regimen, two mutations in the same two chromosomal regions rose to high frequency in parallel in three replicate populations. These mutations were semidominant and additive in their effect on resistance. The first of these mutations mapped to PDR1 and resulted in the overexpression of the ABC transporter genes PDR5 and SNQ2. These mutations had an unexpected pleiotropic effect of reducing the residual ability of the wild type to reproduce at the highest concentrations of fluconazole. In experiment 2, yeast populations were subjected to a single high concentration of fluconazole. Under this regimen, a single recessive mutation appeared in each of three replicate populations. In a genome-wide screen of approximately 4700 viable deletion strains, 13 were classified as resistant to fluconazole (ERG3, ERG6, YMR102C, YMR099C, YPL056C, ERG28, OSH1, SCS2, CKA2, SML1, YBR147W, YGR283C, and YLR407W). The mutations in experiment 2 all mapped to ERG3 and resulted in the overexpression of the gene encoding the drug target ERG11, but not PDR5 and SNQ2. Diploid hybrids from experiments 1 and 2 were less fit than the parents in the presence of fluconazole. In a variation of experiment 2, haploids showed a higher frequency of resistance than diploids, suggesting that degree of dominance and ploidy are important factors in the evolution of antifungal drug resistance.

Bacterial resistance to penicillin G by decreased affinity of penicillin-binding proteins: a mathematical model

Streptococcus pneumoniae and Neisseria meningitidis have very similar mechanisms of resistance to penicillin G. Although penicillin resistance is now common in S. pneumoniae, it is still rare in N. meningitidis. Using a mathematical model, we studied determinants of this difference and attempted to anticipate trends in meningococcal resistance to penicillin G. The model predicted that pneumococcal resistance in a population similar to that of France might emerge after 20 years of widespread use of beta-lactam antibiotics; this period may vary from 10 to 30 years. The distribution of resistance levels became bimodal with time, a pattern that has been observed worldwide. The model suggests that simple differences in the natural history of colonization, interhuman contact, and exposure to beta-lactam antibiotics explain major differences in the epidemiology of resistance of S. pneumoniae and N. meningitidis.

Geographic diversity and temporal trends of antimicrobial resistance in Streptococcus pneumoniae in the United States

Resistance of Streptococcus pneumoniae to antibiotics is increasing throughout the United States, with substantial variation among geographic regions. We show that patterns of geographic variation are best explained by the intensity of selection for resistance, which is reflected by differences between the proportions of resistance within individual serotypes, rather than by differences between the frequencies of particular serotypes. Using a mathematical transmission model, we analyzed temporal trends in the proportions of singly and dually resistant organisms and found that pneumococcal strains resistant to both penicillin and erythromycin are increasing faster than strains singly resistant to either. Using the model, we predict that by 1 July 2004, in the absence of a vaccine, 41% of pneumococci at the Centers for Disease Control and Prevention (CDC)'s Active Bacterial Core surveillance (ABCs) sites, taken together, will be dually resistant, with 5% resistant to penicillin only and 5% to erythromycin only.

Stability, persistence, and evolution of plasmid-encoded VanA glycopeptide resistance in enterococci in the absence of antibiotic selection in vitro and in gnotobiotic mice

Long-term persistence of VanA glycopeptide-resistant enterococci (GRE) has been observed in the absence of antibiotic selection. In the present study, we examined fitness parameters of a glycopeptide-susceptible Enterococcus faecium parent strain and its plasmid-mediated, VanA-resistant derivative before and after 1,000 generations in serial transfer broth cultures with or without antibiotic selection. With the exception of the vanA-containing plasmid, the strains were otherwise isogenic. The stability of the plasmid-encoded vanA resistance determinant was also investigated in vitro and in gnotobiotic mice. Competition experiments revealed that GRE with newly acquired VanA resistance had a 4% reduction in fitness relative to their susceptible parental counterpart. The relative difference in competitive fitness between resistant and susceptible strains was not significantly changed after 1,000 generations. Environmental adaptation was observed in all strains and exceeded the biological cost of resistance. Thus, the evolved VanA-resistant E. faecium populations out-numbered their unevolved ancestral susceptible E. faecium strain in mixed cultures, but remained less competitive than the evolved parent. The glycopeptide resistance determinant was similarly stably maintained during long-term colonization in gnotobiotic mice without antibiotic selection. In vivo vanA plasmid transfer was observed. The results suggest that environmental adaptation, in vivo gene transfer, and plasmid maintenance system(s) favor long-term VanA GRE persistence without antibiotic selection and compensate for the biological costs of possessing the resistance genes.

The growth and survivability of Streptococcus pneumoniae clinical isolates subjected to various environmental conditions

Historically, it has been hypothesized that environmental stress would favor the survival of antibiotic susceptible bacteria over resistant ones; however, there is little direct evidence to support this theory. Clinical isolates of S. pneumoniae were chosen and categorized as: penicillin susceptible, quinolone susceptible (PSQS, n = 3); penicillin resistant, quinolone susceptible (PRQS, n = 3); and penicillin resistant, quinolone resistant (PRQR, n = 5). Baseline growth of each isolate was measured by optical density for 24 h. The resulting optical density curves were compared to those obtained for the same isolates subjected to changes in environmental conditions, such as various temperature, pH, and diluted media. In addition, each isolate was inoculated onto cotton fiber disks, held at room temperature, and the recoverable CFU measured over 144 h. In comparison to controls grown under ideal conditions, the density of PSQS isolates was significantly lower than PRQR isolates after 24 h for the following conditions (p < 0.01): incubation at 40 degrees C (1.3 log10 lower); at pH 6.5 (1.6 log10 lower); and in limited nutrient conditions (1.36 log10 lower). When inoculated onto cotton fiber disks, the PRQR isolates decreased an average of 5.0 log10 after 72 h as compared to controls. In contrast, PSQS isolates decreased an average of 8.1 log10 (p < 0.01). Results of this study support the concept that antibiotic resistant isolates may not be at a competitive disadvantage in comparison to susceptible isolates when subjected to some adverse environmental conditions.

Molecular analysis of fusidic acid resistance in Staphylococcus aureus

Fusidic acid is a potent antibiotic against severe Gram-positive infections that interferes with the function of elongation factor G (EF-G), thereby leading to the inhibition of bacterial protein synthesis. In this study, we demonstrate that fusidic acid resistance in Staphylococcus aureus results from point mutations within the chromosomal fusA gene encoding EF-G. Sequence analysis of fusA revealed mutational changes that cause amino acid substitutions in 10 fusidic acid-resistant clinical S. aureus strains as well as in 10 fusidic acid-resistant S. aureus mutants isolated under fusidic acid selective pressure in vitro. Fourteen different amino acid exchanges were identified that were restricted to 13 amino acid residues within EF-G. To confirm the importance of observed amino acid exchanges in EF-G for the generation of fusidic acid resistance in S. aureus, three mutant fusA alleles encoding EF-G derivatives with the exchanges P406L, H457Y and L461K were constructed by site-directed mutagenesis. In each case, introduction of the mutant fusA alleles on plasmids into the fusidic acid-susceptible S. aureus strain RN4220 caused a fusidic acid-resistant phenotype. The elevated minimal inhibitory concentrations of fusidic acid determined for the recombinant bacteria were analogous to those observed for the fusidic acid-resistant clinical S. aureus isolates and the in vitro mutants containing the same chromosomal mutations. Thus, the data presented provide evidence for the crucial importance of individual amino acid exchanges within EF-G for the generation of fusidic acid resistance in S. aureus.