Modelling parasite drug resistance: lessons for management and control strategies

Plasmodium falciparum Genetic Diversity and Resistance Genotype Profile in Infected Placental Samples Collected After Delivery in Ouagadougou

Purpose

Intermittent preventive treatment with sulfadoxine-pyrimethamine is widely used for the prevention of malaria in pregnant women in Africa. Known resistance cases of sulfadoxine-pyrimethamine during pregnancy need to be follow up to support IPTp implementation in Burkina Faso. However, data on the development and spread of resistance to this molecule are lacking. This study aimed to investigating the genetic diversity of P. falciparum and the mutation prevalence in the dhfr and dhps genes infected from postpartum infected placentas.

Patients and Methods

This was a prospective and cross-sectional study conducted between April 2019 and March 2020 in four health districts of Ouagadougou capital city. From the placentas collected after delivery, P. falciparum detection and mps1 and msp2 polymorphism analysis were performed by nested PCR. The resistance profile was checked after analyzing the mutation point on dhfr and dhps genes.

Results

PCR-positive samples were estimated at 96% for msp1 and 98% for msp2. The polymorphism analysis showed that the RO33 and 3D7 allelic families were the most widespread with 62.5% and 91.83%, respectively. Multiple infections by msp1 and msp2 were frequent with 12.50% and 92.92%, respectively. The prevalence of individual dhfr mutation point, 51I, 108A, and 59R, was 1.96, 15.68, and 7.84, respectively, and the dhps mutation point, 437G, was 3.92. There is no detected mutation at the point 164L and 540E. The triple (51I+108A+59R) in dhfr and quadruple (51I+108A+59R+ 437G) mutation were not found.

Conclusion

The results showed that Plasmodium falciparum has a high genetic diversity of msp1 and msp2. This suggests that dhfr and dhps mutant genotypes are potential early warning factors in the increase in the sulfadoxine-pyrimethamine resistance.

Breaking the cycle of malaria treatment failure

Treatment of symptomatic malaria became a routine component of the clinical and public health response to malaria after the second world war. However, all antimalarial drugs deployed against malaria eventually generated enough drug resistance that they had to be removed from use. Chloroquine, sulfadoxine-pyrimethamine, and mefloquine are well known examples of antimalarial drugs to which resistance did and still does ready evolve. Artemisinin-based combination therapies (ACTs) are currently facing the same challenge as artemisinin resistance is widespread in Southeast Asia and emerging in Africa. Here, I review some aspects of drug-resistance management in malaria that influence the strength of selective pressure on drug-resistant malaria parasites, as well as an approach we can take in the future to avoid repeating the common mistake of deploying a new drug and waiting for drug resistance and treatment failure to arrive. A desirable goal of drug-resistance management is to reduce selection pressure without reducing the overall percentage of patients that are treated. This can be achieved by distributing multiple first-line therapies (MFT) simultaneously in the population for the treatment of uncomplicated falciparum malaria, thereby keeping treatment levels high but the overall selection pressure exerted by each individual therapy low. I review the primary reasons that make MFT a preferred resistance management option in many malaria-endemic settings, and I describe two exceptions where caution and additional analyses may be warranted before deploying MFT. MFT has shown to be feasible in practice in many endemic settings. The continual improvement and increased coverage of genomic surveillance in malaria may allow countries to implement custom MFT strategies based on their current drug-resistance profiles.

Population genetics, biofilm recalcitrance, and antibiotic resistance evolution

Biofilms are communities of bacteria forming high-density sessile colonies. Such a lifestyle comes associated with costs and benefits: while the growth rate of biofilms is often lower than that of their free-living counterparts, this cost is readily repaid once the colony is subjected to antibiotics. Biofilms can grow in antibiotic concentrations a thousand times higher than planktonic bacteria. While numerous mechanisms have been proposed to explain biofilm recalcitrance towards antibiotics, little is yet known about their effect on the evolution of resistance. We synthesize the current understanding of biofilm recalcitrance from a pharmacodynamic and a population genetics perspective. Using the pharmacodynamic framework, we discuss the effects of various mechanisms and show that biofilms can either promote or impede resistance evolution.

Subsidise the test, the treatment or both? Results of an individually randomised controlled trial of the management of suspected malaria fevers in the retail sector in western Kenya

INTRODUCTION

In many malaria-endemic countries, the private retail sector is a major source of antimalarial drugs. However, the rarity of malaria diagnostic testing in the retail sector leads to overuse of the first-line class of antimalarial drugs known as artemisinin-combination therapies (ACTs). The goal of this study was to identify the combination of malaria rapid diagnostic test (RDT) and ACT subsidies that maximises the proportion of clients seeking care in a retail outlet that choose to purchase an RDT (RDT uptake) and use ACTs appropriately.

METHODS

842 clients seeking care in 12 select retail outlets in western Kenya were recruited and randomised into 4 arms of different combinations of ACT and RDT subsidies, with ACT subsidies conditional on a positive RDT. The outcomes were RDT uptake (primary) and appropriate and targeted ACT use (secondary). Participants' familiarity with RDTs and their confidence in test results were also evaluated.

RESULTS

RDT uptake was high (over 96%) across the study arms. Testing uptake was 1.025 times higher (98% CI 1.002 to 1.049) in the RDT subsidised arms than in the unsubsidised groups. Over 98% of clients were aware of malaria testing, but only 35% had a previous experience with RDTs. Nonetheless, confidence in the accuracy of RDTs was high. We found high levels of appropriate use and targeting of ACTs, with 86% of RDT positives taking an ACT, and 93.4% of RDT negatives not taking an ACT. The conditional ACT subsidy did not affect the RDT test purchasing behaviour (risk ratio: 0.994; 98% CI 0.979 to 1.009).

CONCLUSION

Test dependent ACT subsidies may contribute to ACT targeting. However, in this context, high confidence in the accuracy of RDTs and reliable supplies of RDTs and ACTs likely played a greater role in testing uptake and adherence to test results.

Incorporating genetic selection into individual-based models of malaria and other infectious diseases

INTRODUCTION

Control strategies for human infections are often investigated using individual-based models (IBMs) to quantify their impact in terms of mortality, morbidity and impact on transmission. Genetic selection can be incorporated into the IBMs to track the spread of mutations whose origin and spread are driven by the intervention and which subsequently undermine the control strategy; typical examples are mutations which encode drug resistance or diagnosis- or vaccine-escape phenotypes.

METHODS AND RESULTS

We simulated the spread of malaria drug resistance using the IBM OpenMalaria to investigate how the finite sizes of IBMs require strategies to optimally incorporate genetic selection. We make four recommendations. Firstly, calculate and report the selection coefficients, s, of the advantageous allele as the key genetic parameter. Secondly, use these values of "s" to calculate the wait time until a mutation successfully establishes itself in the pathogen population. Thirdly, identify the inherent limits of the IBM to robustly estimate small selection coefficients. Fourthly, optimize computational efficacy: when "s" is small, fewer replicates of larger IBMs may be more efficient than a larger number of replicates of smaller size.

DISCUSSION

The OpenMalaria IBM of malaria was an exemplar and the same principles apply to IBMs of other diseases.

A model for the dynamics of the parasitic stages of equine cyathostomins

A model was developed to reproduce the dynamics of the parasitic stages of equine cyathostomins. Based on a detailed review of published literature, a deterministic simulation model was constructed using the escalator boxcar-train approach, which allows for fully-overlapping cohorts of worms and approximately normally distributed variations in age/size classes. Key biological features include a declining establishment of ingested infective stage larvae as horses age. Development rates are constant for all the parasitic stages except the encysted early third stage larvae, for which development rates are variable to reflect the sometimes extended arrestment of this stage. For these, development is slowed in the presence of adult worms in the intestinal lumen, and when ingestion of infective larvae on herbage is high or extended. In the absence of anthelmintic treatments, the life span of adult worms is approximately 12 months, and the presence of an established adult worm burden largely blocks the transition of luminal fourth stage larvae to the adult stage, resulting in mortality of the larvae. This inhibition is removed by effective anthelmintic treatment allowing the rapid replacement of adult worms from the pool of mucosal stages. Within the model, the rate and seasonality at which infective stage larvae are ingested strongly influences the dynamics of the pre-adult stages. While the adult worm burden remains relatively stable within a year, due to the negative feedback they have on developing stages, the numbers and proportions of larval stages relative to the total worm burden increase with the numbers of infective larvae ingested. Further, within the model, the seasonal rise and fall of encysted stages is largely driven by the seasonal pattern of infective larvae on pasture. Because of this, the model reproduces the contrasting seasonal patterns of mucosal larvae, typical of temperate and tropical environments, using only the appropriate seasonality of larvae on pasture. Thus, the model reproduces output typical of different climatic regions and suggests that observed patterns of arrested development may simply reflect the numbers and seasonality of free-living stages on pasture as determined by different management practices and weather patterns.

Improving rational use of ACTs through diagnosis-dependent subsidies: Evidence from a cluster-randomized controlled trial in western Kenya

BACKGROUND

More than half of artemisinin combination therapies (ACTs) consumed globally are dispensed in the retail sector, where diagnostic testing is uncommon, leading to overconsumption and poor targeting. In many malaria-endemic countries, ACTs sold over the counter are available at heavily subsidized prices, further contributing to their misuse. Inappropriate use of ACTs can have serious implications for the spread of drug resistance and leads to poor outcomes for nonmalaria patients treated with incorrect drugs. We evaluated the public health impact of an innovative strategy that targets ACT subsidies to confirmed malaria cases by coupling free diagnostic testing with a diagnosis-dependent ACT subsidy.

METHODS AND FINDINGS

We conducted a cluster-randomized controlled trial in 32 community clusters in western Kenya (population approximately 160,000). Eligible clusters had retail outlets selling ACTs and existing community health worker (CHW) programs and were randomly assigned 1:1 to control and intervention arms. In intervention areas, CHWs were available in their villages to perform malaria rapid diagnostic tests (RDTs) on demand for any individual >1 year of age experiencing a malaria-like illness. Malaria RDT-positive individuals received a voucher for a discount on a quality-assured ACT, redeemable at a participating retail medicine outlet. In control areas, CHWs offered a standard package of health education, prevention, and referral services. We conducted 4 population-based surveys-at baseline, 6 months, 12 months, and 18 months-of a random sample of households with fever in the last 4 weeks to evaluate predefined, individual-level outcomes. The primary outcome was uptake of malaria diagnostic testing at 12 months. The main secondary outcome was rational ACT use, defined as the proportion of ACTs used by test-positive individuals. Analyses followed the intention-to-treat principle using generalized estimating equations (GEEs) to account for clustering with prespecified adjustment for gender, age, education, and wealth. All descriptive statistics and regressions were weighted to account for sampling design. Between July 2015 and May 2017, 32,404 participants were tested for malaria, and 10,870 vouchers were issued. A total of 7,416 randomly selected participants with recent fever from all 32 clusters were surveyed. The majority of recent fevers were in children under 18 years (62.9%, n = 4,653). The gender of enrolled participants was balanced in children (49.8%, n = 2,318 boys versus 50.2%, n = 2,335 girls), but more adult women were enrolled than men (78.0%, n = 2,139 versus 22.0%, n = 604). At baseline, 67.6% (n = 1,362) of participants took an ACT for their illness, and 40.3% (n = 810) of all participants took an ACT purchased from a retail outlet. At 12 months, 50.5% (n = 454) in the intervention arm and 43.4% (n = 389) in the control arm had a malaria diagnostic test for their recent fever (adjusted risk difference [RD] = 9 percentage points [pp]; 95% CI 2-15 pp; p = 0.015; adjusted risk ratio [RR] = 1.20; 95% CI 1.05-1.38; p = 0.015). By 18 months, the ARR had increased to 1.25 (95% CI 1.09-1.44; p = 0.005). Rational use of ACTs in the intervention area increased from 41.7% (n = 279) at baseline to 59.6% (n = 403) and was 40% higher in the intervention arm at 18 months (ARR 1.40; 95% CI 1.19-1.64; p < 0.001). While intervention effects increased between 12 and 18 months, we were not able to estimate longer-term impact of the intervention and could not independently evaluate the effects of the free testing and the voucher on uptake of testing.

CONCLUSIONS

Diagnosis-dependent ACT subsidies and community-based interventions that include the private sector can have an important impact on diagnostic testing and population-wide rational use of ACTs. Targeting of the ACT subsidy itself to those with a positive malaria diagnostic test may also improve sustainability and reduce the cost of retail-sector ACT subsidies.

TRIAL REGISTRATION

ClinicalTrials.gov NCT02461628.

Using pay for performance incentives (P4P) to improve management of suspected malaria fevers in rural Kenya: a cluster randomized controlled trial

BACKGROUND

Inappropriate treatment of non-malaria fevers with artemisinin-based combination therapies (ACTs) is a growing concern, particularly in light of emerging artemisinin resistance, but it is a behavior that has proven difficult to change. Pay for performance (P4P) programs have generated interest as a mechanism to improve health service delivery and accountability in resource-constrained health systems. However, there has been little experimental evidence to establish the effectiveness of P4P in developing countries. We tested a P4P strategy that emphasized parasitological diagnosis and appropriate treatment of suspected malaria, in particular reduction of unnecessary consumption of ACTs.

METHODS

A random sample of 18 health centers was selected and received a refresher workshop on malaria case management. Pre-intervention baseline data was collected from August to September 2012. Facilities were subsequently randomized to either the comparison (n = 9) or intervention arm (n = 9). Between October 2012 and November 2013, facilities in the intervention arm received quarterly incentive payments based on seven performance indicators. Incentives were for use by facilities rather than as payments to individual providers. All non-pregnant patients older than 1 year of age who presented to a participating facility and received either a malaria test or artemether-lumefantrine (AL) were eligible to be included in the analysis. Our primary outcome was prescription of AL to patients with a negative malaria diagnostic test (n = 11,953). Our secondary outcomes were prescription of AL to patients with laboratory-confirmed malaria (n = 2,993) and prescription of AL to patients without a malaria diagnostic test (analyzed at the cluster level, n = 178 facility-months).

RESULTS

In the final quarter of the intervention period, the proportion of malaria-negative patients in the intervention arm who received AL was lower than in the comparison arm (7.3% versus 10.9%). The improvement from baseline to quarter 4 in the intervention arm was nearly three times that of the comparison arm (ratio of adjusted odds ratios for baseline to quarter 4 = 0.36, 95% CI: 0.24-0.57). The rate of prescription of AL to patients without a test was five times lower in the intervention arm (adjusted incidence rate ratio = 0.18, 95% CI: 0.07-0.48). Prescription of AL to patients with confirmed infection was not significantly different between the groups over the study period.

CONCLUSIONS

Facility-based incentives coupled with training may be more effective than training alone and could complement other quality improvement approaches.

TRIAL REGISTRATION

This study was registered with ClinicalTrials.gov (NCT01809873) on 11 March 2013.

Evolutionary biology and the avoidance of antimicrobial resistance

Evolutionary biologists have largely left the search for solutions to the drug resistance crisis to biomedical scientists, physicians, veterinarians and public health specialists. We believe this is because the vast majority of professional evolutionary biologists consider the evolutionary science of drug resistance to be conceptually uninteresting. Using malaria as case study, we argue that it is not. We review examples of evolutionary thinking that challenge various fallacies dominating antimalarial therapy, and discuss open problems that need evolutionary insight. These problems are unlikely to be resolved by biomedical scientists ungrounded in evolutionary biology. Involvement by evolutionary biologists in the science of drug resistance requires no intellectual compromises: the problems are as conceptually challenging as they are important.

High prevalence of pfcrt K76T and mdr1 N86Y mutations in Sonitpur district of Assam, India

Present study reports the prevalence and distribution of pfcrt K76T and mdr1 N86Y mutations in malaria endemic areas of Sonitpur district of Assam. Out of 163 individuals tested for malaria, 67 (SPR = 41.1 %) were detected positive for malaria infection using rapid detection kit in the field and PCR assay in the laboratory. Nested PCR-RFLP assay was used to amplify pfcrt K76T and mdr1 N86Y genes flanking the K76T and N86Y mutations. P. falciparum was most abundant (91.04 %) among the three Plasmodium species reported and its prevalence was significantly higher as compared to P. vivax and P. malariae (χ(2) = 150.76; p ≤ 0.0001; df = 2). Malaria was equally distributed among all the age groups and both the sexes. Hemoglobin contents in severe anaemic patients had a significant linear decreasing trend among patients with the increase in age (χ(2) = 4.33; p = 0.03), whereas non severe anaemic patients exhibited significant linear increasing trend among the patients with the increase in age (χ(2) = 18.38; p ≤ 0.0001). Pfcrt K76T mutation was recorded in 44 (72.13 %) isolates, whereas mdr1 N86Y mutation could be detected in 28 (41.79 %) isolates only. Only 32.7 % of the samples had both pfcrt K76T and mdr N86Y mutations. Number of pfcrt K76T mutant isolates was significantly higher than the wild type. However no significant difference was observed among the number of isolates with mdr1 N86Y mutant and wild isolates.

Detection of emamectin benzoate tolerance emergence in different life stages of sea lice, Lepeophtheirus salmonis, on farmed Atlantic salmon, Salmo salar L

Emamectin benzoate has been used to treat sea lice, Lepeophtheirus salmonis, infestations on farmed Atlantic salmon, Salmo salar. Recent evidence suggests a reduction in effectiveness in some locations. A major challenge in the detection of tolerance emergence can be the typically low proportion of resistant individuals in a population during the early phases. The objectives of this study were to develop a method for determining differences in temporal development of tolerance between sea lice life stages and to explore how these differences might be used to improve the monitoring of treatment effectiveness in a clinical setting. This study examined two data sets based on records of sea lice abundance following emamectin benzoate treatments from the west coast of Scotland (2002-2006) and from New Brunswick, Canada (2004-2008). Life stages were categorized into two groups (adult females and the remaining mobile stages) to examine the trends in mean abundance and treatment effectiveness. Differences in emamectin benzoate effectiveness were found between the two groups by year and location, suggesting that an important part of monitoring drug resistance development in aquatic ectoparasites may be the need to focus on key life stages.

High prevalence of drug resistance in animal trypanosomes without a history of drug exposure

Background

Trypanosomosis caused by Trypanosoma congolense is a major constraint to animal health in sub-Saharan Africa. Unfortunately, the treatment of the disease is impaired by the spread of drug resistance. Resistance to diminazene aceturate (DA) in T. congolense is linked to a mutation modifying the functioning of a P2-type purine-transporter responsible for the uptake of the drug. Our objective was to verify if the mutation was linked or not to drug pressure.

Methodology/Principal Findings

Thirty-four T. congolense isolates sampled from tsetse or wildlife were screened for the DA-resistance linked mutation using DpnII-PCR-RFLP. The results showed 1 sensitive, 12 resistant and 21 mixed DpnII-PCR-RFLP profiles. This suggests that the mutation is present on at least one allele of each of the 33 isolates. For twelve of the isolates, a standard screening method in mice was used by (i) microscopic examination, (ii) trypanosome-specific 18S-PCR after 2 months of observation and (iii) weekly trypanosome-specific 18S-PCR for 8 weeks. The results showed that all mice remained microscopically trypanosome-positive after treatment with 5 mg/kg DA. With 10 and 20 mg/kg, 8.3% (n = 72) and 0% (n = 72) of the mice became parasitologically positive after treatment. However, in these latter groups the trypanosome-specific 18S-PCR indicated a higher degree of trypanosome-positivity, i.e., with a unique test, 51.4% (n = 72) and 38.9% (n = 72) and with the weekly tests 79.2% (n = 24) and 66.7% (n = 24) for 10 and 20 mg/kg respectively.

Conclusion/Significance

The widespread presence of the DA-resistance linked mutation in T. congolense isolated from wildlife suggests that this mutation is favourable to parasite survival and/or its dissemination in the host population independent from the presence of drug. After treatment with DA, those T. congolense isolates cause persisting low parasitaemias even after complete elimination of the drug and with little impact on the host's health.

Trypanosomosis is responsible for the death of 3 million heads of cattle yearly, with 50 million animals at risk in sub-Saharan Africa. DA, a commonly used drug against the disease, was marketed decades ago. Drug resistance is reported in 21 African countries. A common argument about the origin of drug resistance is the selection by the drug of rare individuals that are naturally resistant and the propagation of those individuals in the population because of the competitive advantage they have when exposed to drug. When the drug pressure decreases, the wild-type individuals regain their supremacy. The principal objective of this study was thus to estimate the prevalence of trypanosomes resistant to DA in a population that was never exposed to the drug. Our results showing a high prevalence of drug resistance in environments free of any drug pressure is thought provoking and suggests that ceasing the use of DA will not allow for a return to a DA-sensitive population of trypanosomes. Drug resistance in animal trypanosomes thus present a pattern different from what is observed with Plasmodium sp. (causative agent of malaria) where a complete stoppage in the use of the chloroquine allows for a return to drug sensitivity.

Contribution of mathematical modeling to the fight against bacterial antibiotic resistance

PURPOSE OF REVIEW

Modeling of antibiotic resistance in pathogenic bacteria responsible for human disease has developed considerably over the last decade. Herein, we summarize the main published studies to illustrate the contribution of models for understanding both within-host and population-based phenomena. We then suggest possible topics for future studies.

RECENT FINDINGS

Model building of bacterial resistance has involved epidemiologists, biologists and modelers with two different objectives. First, modeling has helped largely in identifying and understanding the factors and biological phenomena responsible for the emergence and spread of resistant strains. Second, these models have become important decision support tools for medicine and public health.

SUMMARY

Major improvements of models in the coming years should take into account specific pathogen characteristics (resistance mechanisms, multiple colonization phenomena, cooperation and competition among species) and better description of the contacts associated with transmission risk within populations.

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.

The use of artemether-lumefantrine by febrile children following national implementation of a revised drug policy in Kenya

OBJECTIVES

To examine access to, timing and use of artemisinin-based combination therapy among rural Kenyan febrile children before and following the introduction of artemether-lumefantrine (AL) as first-line antimalarial drug policy.

METHODS

In August 2006, a cohort was established within 72 rural clusters in four sentinel districts to monitor the period prevalence of fever and treatment in children aged 0-4 years through four repeat cross-sectional surveys (one prior to introduction of AL and three post-AL introduction: January-June 2007). Mothers/guardians of children were asked about fever in the last 14 days and related treatment actions including the timing, drugs used, dosing and adherence supported by visual aids of commonly available drug products.

RESULTS

A total of 2526 child-observations were recorded during the four survey rounds. The period prevalence of fever was between 20% and 26% with little variation between survey rounds. The overall proportion of children with fever receiving antimalarial drugs for their fever was 31 % (95% CI, 26-36%) and the proportion of febrile children receiving antimalarial drugs within 48 h was 23.3% (95% CI, 18.6-28.0%). The proportion of febrile children who received first-line recommended AL within 48 h was 10.2% (95% CI, 7.0-13.4%), compared to only 4.6% (95% CI, 3.8-5.4%) of children receiving sulphadoxine-pyrimethamine first-line therapy in 2001.

CONCLUSIONS

Although Kenya was less than a year into the new policy implementation and AL is restricted to the public formal sector, access to antimalarial drugs among children within 48 h and to the first-line therapy has improved. But it remains well below national and international targets. The continued use of amodiaquine and artemisinin monotherapies constrains effective implementation of artemisinin-based combination therapy policy in Kenya.

Competitive release and facilitation of drug-resistant parasites after therapeutic chemotherapy in a rodent malaria model

Malaria infections frequently consist of mixtures of drug-resistant and drug-sensitive parasites. If crowding occurs, where clonal population densities are suppressed by the presence of coinfecting clones, removal of susceptible clones by drug treatment could allow resistant clones to expand into the newly vacated niche space within a host. Theoretical models show that, if such competitive release occurs, it can be a potent contributor to the strength of selection, greatly accelerating the rate at which resistance spreads in a population. A variety of correlational field data suggest that competitive release could occur in human malaria populations, but direct evidence cannot be ethically obtained from human infections. Here we show competitive release after pyrimethamine curative chemotherapy of acute infections of the rodent malaria Plasmodium chabaudi in laboratory mice. The expansion of resistant parasite numbers after treatment resulted in enhanced transmission-stage densities. After the elimination or near-elimination of sensitive parasites, the number of resistant parasites increased beyond that achieved when a competitor had never been present. Thus, a substantial competitive release occurred, markedly elevating the fitness advantages of drug resistance above those arising from survival alone. This finding may explain the rapid spread of drug resistance and the subsequently brief useful lifespans of some antimalarial drugs. In a second experiment, where subcurative chemotherapy was administered, the resistant clone was only partly released from competitive suppression and experienced a restriction in the size of its expansion after treatment. This finding raises the prospect of harnessing in-host ecology to slow the spread of drug resistance.

Structure of the scientific community modelling the evolution of resistance

Faced with the recurrent evolution of resistance to pesticides and drugs, the scientific community has developed theoretical models aimed at identifying the main factors of this evolution and predicting the efficiency of resistance management strategies. The evolutionary forces considered by these models are generally similar for viruses, bacteria, fungi, plants or arthropods facing drugs or pesticides, so interaction between scientists working on different biological organisms would be expected. We tested this by analysing co-authorship and co-citation networks using a database of 187 articles published from 1977 to 2006 concerning models of resistance evolution to all major classes of pesticides and drugs. These analyses identified two main groups. One group, led by ecologists or agronomists, is interested in agricultural crop or stock pests and diseases. It mainly uses a population genetics approach to model the evolution of resistance to insecticidal proteins, insecticides, herbicides, antihelminthic drugs and miticides. By contrast, the other group, led by medical scientists, is interested in human parasites and mostly uses epidemiological models to study the evolution of resistance to antibiotic and antiviral drugs. Our analyses suggested that there is also a small scientific group focusing on resistance to antimalaria drugs, and which is only poorly connected with the two larger groups. The analysis of cited references indicates that each of the two large communities publishes its research in a different set of literature and has its own keystone references: citations with a large impact in one group are almost never cited by the other. We fear the lack of exchange between the two communities might slow progress concerning resistance evolution which is currently a major issue for society.

Potential impact of intermittent preventive treatment (IPT) on spread of drug-resistant malaria

BACKGROUND

Treatment of asymptomatic individuals, regardless of their malaria infection status, with regularly spaced therapeutic doses of antimalarial drugs has been proposed as a method for reducing malaria morbidity and mortality. This strategy, called intermittent preventive treatment (IPT), is currently employed for pregnant women and is being studied for infants (IPTi) as well. As with any drug-based intervention strategy, it is important to understand how implementation may affect the spread of drug-resistant parasites. This is a difficult issue to address experimentally because of the limited size and duration of IPTi trials as well as the intractability of distinguishing the spread of resistance due to conventional treatment of malaria episodes versus that due to IPTi when the same drug is used in both contexts.

METHODS AND FINDINGS

Using a mathematical model, we evaluated the possible impact of treating individuals with antimalarial drugs at regular intervals regardless of their infection status. We translated individual treatment strategies and drug pharmacokinetics into parasite population dynamic effects and show that immunity, treatment rate, drug decay kinetics, and presumptive treatment rate are important factors in the spread of drug-resistant parasites. Our model predicts that partially resistant parasites are more likely to spread in low-transmission areas, but fully resistant parasites are more likely to spread under conditions of high transmission, which is consistent with some epidemiological observations. We were also able to distinguish between spread of resistance due to treatment of symptomatic infections and that due to IPTi. We showed that IPTi could accelerate the spread of resistant parasites, but this effect was only likely to be significant in areas of low or unstable transmission.

CONCLUSIONS

The results presented here demonstrate the importance of considering both the half-life of a drug and the existing level of resistance when choosing a drug for IPTi. Drugs to which little or no resistance exists are not advisable for IPT in high-transmission areas, but IPTi is not likely to significantly impact the spread of highly resistant parasites in areas where partial resistance is already established. IPTi is more likely to accelerate the spread of resistance in high-transmission areas than is IPT in adults (i.e., pregnant women).

Efficacy of chloroquine + sulfadoxine--pyrimethamine, mefloquine + artesunate and artemether + lumefantrine combination therapies to treat Plasmodium falciparum malaria in the Chittagong Hill Tracts, Bangladesh

Bangladesh faces growing levels of Plasmodium falciparum resistance to chloroquine (CQ) and sulfadoxine-pyrimethamine (SP). Alternative antimalarial therapies, particularly combination regimens, need to be considered. Therefore, the efficacy of three antimalarial combination therapies was assessed in Chittagong Hill Tracts. A total of 364 P. falciparum patients were recruited and randomly assigned to either CQ + SP, mefloquine + artesunate (MQ + AS) or lumefantrine + artemether (Coartem). Results showed that CQ + SP therapy was less effective than the two artemisinin-based combination therapies. The day 42 PCR-corrected efficacy rate was 62.4% for CQ + SP, 100% for MQ + AS and 97.1% for Coartem. Failures occurred at a shorter interval after CQ + SP treatment than after Coartem. The artemisinin-based therapies effectively prevented development of gametocytes, whereas CQ + SP did not. All three therapies were well tolerated, although reports of mild complaints during treatment appeared higher with MQ + AS. We conclude that CQ + SP is not a viable option for replacing CQ monotherapy as first-line P. falciparum treatment in this area of Bangladesh. A change to artemisinin-based combination therapy is recommended. Both Coartem and MQ + AS appear to be good options, effective in curing P. falciparum malaria and in preventing recrudescences following treatment.

A randomized trial comparing the efficacy of four treatment regimens for uncomplicated falciparum malaria in Assam state, India

A four-arm drug sensitivity study compared chloroquine, sulfadoxine-pyrimethamine (SP), mefloquine and mefloquine-artesunate in Sonitpur and Karbi Anglong districts in Assam state, India. Two criteria were used to ascertain outcome: success of clinical treatment and parasitologic cure. In Sonitpur, at 14 days, there were 36/56 early and late treatment failures plus late parasitologic failures to chloroquine and 16/56 for SP. In Karbi Anglong, combined treatment failure at 14 days was 16/56 to chloroquine and 8/60 to SP. Mefloquine and mefloquine-artesunate demonstrated 93.9% and 93.6% sustained responses respectively at 42 days. High failure rates to both chloroquine and SP preclude the use of these drugs as first-line treatment for uncomplicated falciparum malaria in this region. A mefloquine-artesunate combination presents an effective alternative utilizing the currently recommended higher dose of mefloquine.

Malaria transmission intensity and the rate of spread of chloroquine resistant Plasmodium falciparum: Why have theoretical models generated conflicting results?

The rate at which falciparum resistant malaria spreads in different transmission settings is still a controversial subject. We have assessed the spread of mutant Plasmodium falciparum parasites in six Ugandan populations with varying prevalence of chloroquine resistance (CQR), malaria transmission intensity, multiplicity of parasite clones and prevalence of CQ use. For each population, we have determined the wild and mutant allele frequency at codons 76 and 86 of the pfcrt and pfmdr1 genes, respectively. The highest frequency (median = 16.3%, range: 0.0-70.4%) of infections with two pure mutants (no wild genotype in either gene), adjusted for clone multiplicity, was observed at the extremes of malaria transmission intensity. The wild/mutant (W/M) allele ratio (an index for tracking the progression of CQR) was less than one in all sites (median = 0.51, range: 0.09-0.98) for the pfcrt-76 gene, while it was greater than one in two of six sites (median = 0.75, range: 0.4-1.6) for the pfmdr1-86 gene, suggesting that the pfcrt-76 mutants were the predominant parasites at all sites. Furthermore, the pfmdr1-86 W/M allele ratio was consistently higher than that of the pfcrt-76. The spread of mutations linked to CQR in P. falciparum commences with the pfcrt-76 gene mutations, followed later by the pfmdr1-86 gene mutations that modulate higher CQR. Such spread occurs faster at the extremes of the transmission spectrum and could explain why mathematical models have previously generated conflicting results with respect to malaria transmission intensity and spread of CQR.

The promise and potential challenges of intermittent preventive treatment for malaria in infants (IPTi)

Intermittent preventive treatment (IPT) administers a full therapeutic course of an anti-malarial drug at predetermined intervals, regardless of infection or disease status. It is recommended by the World Health Organization (WHO) for protecting pregnant women from the adverse effects of malaria (IPTp) and shows great potential as a strategy for reducing illness from malaria during infancy (IPTi). Administered concurrently with standard immunizations, IPTi is expected to reduce the frequency of clinical disease, but to allow blood-stage infections to occur between treatments, thus allowing parasite-specific immunity to develop. While wide deployment of IPTi is being considered, it is important to assess other potential effects. Transmission conditions, drug choice and administration schedule will likely affect the possibility of post-treatment rebound in child morbidity and mortality and the increased spread of parasite drug resistance and should be considered when implementing IPTi.

Intensity of malaria transmission and the evolution of drug resistance

The intensity of malaria transmission varies both naturally and as a consequence of human public health intervention. The relationship between transmission intensity and the rate at which antimalarial drug resistance evolves affects the design of surveillance programmes, and the likely impact of malaria control programmes. Several theoretical studies have investigated this relationship and their key results are summarised and interpreted. The most important result is that transmission intensity does not directly affect the evolution of resistance. It exerts its influence through three clinical/epidemiological "mediators" (clonal multiplicity, the threat of infection, level of human immunity) which ultimately determine the dynamics of resistance via five "effector" variables: sexual recombination, intrahost dynamics, community drug use, proportion of malaria infections treated, and the number of parasites per host. We argue that the evolution of resistance is likely to be a two-stage process: mutations encoding drug tolerance preceding those encoding resistance. The evolution of drug tolerance is determined solely by the level of drug use in the community which is likely to have an extremely weak relationship with transmission intensity. The evolution of resistance is more complex and affected by all five effectors. The most likely scenarios are that resistance evolves faster in areas of high transmission if encoded by a single gene but if encoded by two or more genes it evolves fastest in areas of high or low transmission, with a minimum at intermediate levels of transmission.

Public health impact of drug resistant Plasmodium falciparum malaria

The alarming increase in Plasmodium falciparum resistance to commonly used anti-malarial drugs represents a major public health threat. The impact is however difficult to quantify. In low transmission areas, an increase in acute manifestations ("epidemic") is often quickly apparent and resistance is rapidly propagated due to high drug pressure on existing parasite populations. In high transmission areas, the clinical effects are mainly prolonged/chronic infections with increasing risk of severe anemia. Mortality estimates from public health records in Africa generally suggest significant increases (from 2- to 11-fold) in malaria-associated mortality among children when resistance develops and spreads. Hospital attendances and admissions show similar trends. Change of policy to alternative efficacious treatment with radical cure is necessary at an earlier stage (from 10% treatment failure) than previously assumed in order to prevent deaths in millions of African children. Early switch to artemisinin based combination therapy (ACT) represents such a critical and urgent strategy.

Drug resistance models for malaria

The main factors affecting the evolution of drug resistance in malaria according to theoretical models are reviewed here. The overwhelming influence on the emergence and rate of spread of drug resistance is the proportion of infected hosts that are treated with drugs. A second important effect is drug efficacy in killing parasites. Factors such as average transmission rate, recombination, the biological cost of resistance, and the mode of gene action also influence the rate of spread but have relatively minor impacts. A simple population dynamics model that captures the epidemiological effects of drug treatment and resistance, as opposed to a population genetics model that does not, is presented in order to illustrate the main conclusions.

The interaction among evolutionary forces in the pathogenic fungus Mycosphaerella graminicola

The population genetic dynamic of a species is driven by interactions among mutation, migration, drift, mating system, and selection, but it is rare to have sufficient empirical data to estimate values for all of these forces and to allow comparison of the relative magnitudes of these evolutionary forces. We combined data from a mark-release-recapture experiment, extensive population surveys, and computer simulations to evaluate interactions among these evolutionary forces in the pathogenic fungus Mycosphaerella graminicola. The results from these studies showed that, on average, the immigration rate was 0.027, the fraction of outcrossing individuals was 0.035, and the selection coefficient associated with immigrants was 0.106 each generation. We also estimated that effective population sizes for this fungus were larger than 24,000 and the mutation rate for the RFLP markers used in surveys and field experiments was approximately 4 x 10(-5). Computer simulations based on these estimates indicate that, on average, the global population of M. graminicola has reached equilibrium. Population genetic parameters including number of alleles, gene diversity, and population subdivision estimated from the computer simulations were surprisingly close to empirical estimates. Simulations also revealed that random drift is the major evolutionary force decreasing genetic variation in this fungus, followed by natural selection. The major force adding to genetic variation was mutation, followed by gene flow and sexual recombination. Gene flow played the leading role in decreasing population subdivision while natural selection was the major factor increasing population subdivision.

Mathematical modelling and the control of lymphatic filariasis

The current global initiative to eliminate lymphatic filariasis represents one of the largest mass drug administration programmes ever conceived for the control of a parasitic disease. Yet, it is still not known whether the WHO-recommended primary strategy of applying annual single-dose mass chemotherapy with a combination of two drugs for 4-6 years will effectively break parasite transmission from all endemic communities. Here we review recent work on the development and application of a deterministic mathematical model of filariasis transmission, to show how models of parasite transmission will help resolve the key currently debated questions regarding the ultimate effectiveness of the global strategy to control filariasis. These critical questions include the required duration of mass treatment in different endemic areas, the optimal drug coverage required to meet control targets within prescribed timeframes, the impact and importance of adding vector control to mass chemotherapy regimens, and the likelihood of the development of drug resistance by treated worm populations. The results demonstrate the vital role that integrating these models into control programming can have in providing effective decision-support frameworks for undertaking the optimal design and monitoring of regional and global filariasis-control programmes. Operationally, the models show that the effectiveness of the strategy to achieve filariasis control will be determined by successfully addressing two key factors: the need to maintain high community treatment coverages, and the need to include vector control measures especially in areas of high endemicity.

History, dynamics, and public health importance of malaria parasite resistance

Despite considerable efforts, malaria is still one of the most devastating infectious diseases in the tropics. The rapid spread of antimalarial drug resistance currently compounds this grim picture. In this paper, we review the history of antimalarial drug resistance and the methods for monitoring it and assess the current magnitude and burden of parasite resistance to two commonly used drugs: chloroquine and sulfadoxine-pyrimethamine. Furthermore, we review the factors involved in the emergence and spread of drug resistance and highlight its public health importance. Finally, we discuss ways of dealing with such a problem by using combination therapy and suggest some of the research themes needing urgent answers.

Chloroquine, sulfadoxine-pyrimethamine and amodiaquine efficacy for the treatment of uncomplicated Plasmodium falciparum malaria in Upper Nile, south Sudan

The current first-line and second-line drugs for Plasmodium falciparum malaria in South Sudan, chloroquine and sulfadoxine-pyrimethamine (SP), were evaluated and compared with amodiaquine, in an MSF-Holland-run clinic in eastern Upper Nile, South Sudan from June to December 2001. Patients with uncomplicated malaria and fever were stratified by age group and randomly allocated to one of 3 treatment regimes. A total of 342 patients was admitted and followed for 14 d after treatment. The dropout rate was 10.2%. Of those who completed the study, 104 were treated with chloroquine (25 mg/kg, 3 d), 102 with SP (25 mg/kg sulfadoxine and 1.25 mg/kg pyrimethamine, single dose) and 101 with amodiaquine (25 mg/kg, 3 d). Adequate clinical response was observed in 88.5% of patients treated with chloroquine, 100% of patients treated with SP and 94.1% of patients treated with amodiaquine. In children aged < 5 years, the success rate was lower: 83.3% for chloroquine and 93.0% for amodiaquine. In adults no treatment failures were found, but children aged 5-15 years showed intermediate levels. In addition, we determined the initial genotypes of dhfr and dhps of 44 isolates from the SP-treated group and > 80% were found to be wild type for dhfr and 100% for dhps. Two percent of isolates had a single mutation and 16% had double mutations of dhfr. These data are in full agreement with the clinical effectiveness of SP. A change in malaria treatment protocols for South Sudan is recommended.