Surface micropattern reduces colonization and medical device-associated infections

PURPOSE

Surface microtopography offers a promising approach for infection control. The goal of this study was to provide evidence that micropatterned surfaces significantly reduce the potential risk of medical device-associated infections.

METHODOLOGY

Micropatterned and smooth surfaces were challenged in vitro against the colonization and transference of two representative bacterial pathogens - Staphylococcus aureus and Pseudomonas aeruginosa. A percutaneous rat model was used to assess the effectiveness of the micropattern against device-associated S. aureus infections. After the percutaneous insertion of silicone rods into (healthy or immunocompromised) rats, their backs were inoculated with S. aureus. The bacterial burdens were determined in tissues under the rods and in the spleens.

RESULTS

The micropatterns reduced adherence by S. aureus (92.3 and 90.5 % reduction for flat and cylindrical surfaces, respectively), while P. aeruginosa colonization was limited by 99.9 % (flat) and 95.5 % (cylindrical). The micropatterned surfaces restricted transference by 95.1 % for S. aureus and 94.9 % for P. aeruginosa, compared to smooth surfaces. Rats with micropatterned devices had substantially fewer S. aureus in subcutaneous tissues (91 %) and spleens (88 %) compared to those with smooth ones. In a follow-up study, immunocompromised rats with micropatterned devices had significantly lower bacterial burdens on devices (99.5 and 99.9 % reduction on external and internal segments, respectively), as well as in subcutaneous tissues (97.8 %) and spleens (90.7 %) compared to those with smooth devices.

CONCLUSION

Micropatterned surfaces exhibited significantly reduced colonization and transference in vitro, as well as lower bacterial burdens in animal models. These results indicate that introducing this micropattern onto surfaces has high potential to reduce medical device-associated infections.

Micropatterned Endotracheal Tubes Reduce Secretion-Related Lumen Occlusion

Tracheal intubation disrupts physiological homeostasis of secretion production and clearance, resulting in secretion accumulation within endotracheal tubes (ETTs). Novel in vitro and in vivo models were developed to specifically recapitulate the clinical manifestations of ETT occlusion. The novel Sharklet™ micropatterned ETT was evaluated, using these models, for the ability to reduce the accumulation of both bacterial biofilm and airway mucus compared to a standard care ETT. Novel ETTs with micropattern on the inner and outer surfaces were placed adjacent to standard care ETTs in in vitro biofilm and airway patency (AP) models. The primary outcome for the biofilm model was to compare commercially-available ETTs (standard care and silver-coated) to micropatterned for quantity of biofilm accumulation. The AP model's primary outcome was to evaluate accumulation of artificial airway mucus. A 24-h ovine mechanical ventilation model evaluated the primary outcome of relative quantity of airway secretion accumulation in the ETTs tested. The secondary outcome was measuring the effect of secretion accumulation in the ETTs on airway resistance. Micropatterned ETTs significantly reduced biofilm by 71% (p = 0.016) compared to smooth ETTs. Moreover, micropatterned ETTs reduced lumen occlusion, in the AP model, as measured by cross-sectional area, in distal (85%, p = 0.005), middle (84%, p = 0.001) and proximal (81%, p = 0.002) sections compared to standard care ETTs. Micropatterned ETTs reduced the volume of secretion accumulation in a sheep model of occlusion by 61% (p < 0.001) after 24 h of mechanical ventilation. Importantly, micropatterned ETTs reduced the rise in ventilation peak inspiratory pressures over time by as much as 49% (p = 0.005) compared to standard care ETTs. Micropatterned ETTs, demonstrated here to reduce bacterial contamination and mucus occlusion, will have the capacity to limit complications occurring during mechanical ventilation and ultimately improve patient care.

Micropatterned Protective Membranes Inhibit Lens Epithelial Cell Migration in Posterior Capsule Opacification Model

PURPOSE

To evaluate the ability of Sharklet (SK) micropatterns to inhibit lens epithelial cell (LEC) migration. Sharklet Technologies, Inc. (STI) and InSight Innovations, LLC have proposed to develop a Sharklet-patterned protective membrane (PM) to be implanted in combination with a posterior chamber intraocular lens (IOL) to inhibit cellular migration across the posterior capsule, and thereby reduce rates of posterior capsular opacification (PCO).

METHODS

A variety of STI micropatterns were evaluated versus smooth (SM) controls in a modified scratch wound assay for the ability to reduce or inhibit LEC migration. The best performing topography was selected, translated to a radial design, and applied to PM prototypes. The PM prototypes were tested in an in vitro PCO model for reduction of cell migration behind an IOL versus unpatterned prototypes and IOLs with no PM. In both assays, cell migration was analyzed with fluorescent microscopy.

RESULTS

All SK micropatterns significantly reduced LEC migration compared with SM controls. Micropatterns that protruded from the surface reduced migration more than recessed features. The best performing micropattern reduced LEC coverage by 80%, P = 0.0001 (ANOVA, Tukey Test). Micropatterned PMs reduced LEC migration in a PCO model by 50%, P = 0.0005 (ANOVA, Tukey Test) compared with both IOLs with no PM and IOLs with SM PMs.

CONCLUSIONS

Collectively, in vitro results indicate the implantation of micropatterned PMs in combination with posterior chamber IOLs could significantly reduce rates of clinically relevant PCO. This innovative technology is a globally accessible solution to high PCO rates.

TRANSLATIONAL RELEVANCE

A novel IOL incorporating the SK micropattern in a membrane design surrounding the optic may help increase the success of cataract surgery by reducing secondary cataract, or PCO.

An engineered micropattern to reduce bacterial colonization, platelet adhesion and fibrin sheath formation for improved biocompatibility of central venous catheters

Background

Catheter-related bloodstream infections (CRBSIs) and catheter-related thrombosis (CRT) are common complications of central venous catheters (CVC), which are used to monitor patient health and deliver medications. CVCs are subject to protein adsorption and platelet adhesion as well as colonization by the natural skin flora (i.e. Staphylococcus aureus and Staphylococcus epidermidis). Antimicrobial and antithrombotic drugs can prevent infections and thrombosis-related complications, but have associated resistance and safety risks. Surface topographies have shown promise in limiting platelet and bacterial adhesion, so it was hypothesized that an engineered Sharklet micropattern, inspired by shark-skin, may provide a combined approach as it has wide reaching anti-fouling capabilities. To assess the feasibility for this micropattern to improve CVC-related healthcare outcomes, bacterial colonization and platelet interactions were analyzed in vitro on a material common for vascular access devices.

Methods

To evaluate bacterial inhibition after simulated vascular exposure, micropatterned thermoplastic polyurethane surfaces were preconditioned with blood proteins in vitro then subjected to a bacterial challenge for 1 and 18 h. Platelet adhesion was assessed with fluorescent microscopy after incubation of the surfaces with platelet-rich plasma (PRP) supplemented with calcium. Platelet activation was further assessed by monitoring fibrin formation with fluorescent microscopy after exposure of the surfaces to platelet-rich plasma (PRP) supplemented with calcium in a flow-cell. Results are reported as percent reductions and significance is based on t-tests and ANOVA models of log reductions. All experiments were replicated at least three times.

Results

Blood and serum conditioned micropatterned surfaces reduced 18 h S. aureus and S. epidermidis colonization by 70% (p ≤ 0.05) and 71% (p < 0.01), respectively, when compared to preconditioned unpatterned controls. Additionally, platelet adhesion and fibrin sheath formation were reduced by 86% and 80% (p < 0.05), respectively, on the micropattern, when compared to controls.

Conclusions

The Sharklet micropattern, in a CVC-relevant thermoplastic polyurethane, significantly reduced bacterial colonization and relevant platelet interactions after simulated vascular exposure. These results suggest that the incorporation of the Sharklet micropattern on the surface of a CVC may inhibit the initial events that lead to CRBSI and CRT.

Surface micropattern limits bacterial contamination

BACKGROUND

Bacterial surface contamination contributes to transmission of nosocomial infections. Chemical cleansers used to control surface contamination are often toxic and incorrectly implemented. Additional non-toxic strategies should be combined with regular cleanings to mitigate risks of human error and further decrease rates of nosocomial infections. The Sharklet micropattern (MP), inspired by shark skin, is an effective tool for reducing bacterial load on surfaces without toxic additives. The studies presented here were carried out to investigate the MP surfaces capability to reduce colonization of methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) compared to smooth control surfaces.

METHODS

The MP and smooth surfaces produced in acrylic film were compared for remaining bacterial contamination and colonization following inoculation. Direct sampling of surfaces was carried out after inoculation by immersion, spray, and/or touch methods. Ultimately, a combination assay was developed to assess bacterial contamination after touch transfer inoculation combined with drying (persistence) to mimic common environmental contamination scenarios in the clinic or hospital environment. The combination transfer and persistence assay was then used to test antimicrobial copper beside the MP for the ability to reduce MSSA and MRSA challenge.

RESULTS

The MP reduced bacterial contamination with log reductions ranging from 87-99% (LR = 0.90-2.18; p < 0.05) compared to smooth control surfaces. The MP was more effective than the 99.9% pure copper alloy C11000 at reducing surface contamination of S. aureus (MSSA and MRSA) through transfer and persistence of bacteria. The MP reduced MSSA by as much as 97% (LR = 1.54; p < 0.01) and MRSA by as much as 94% (LR = 1.26; p < 0.005) compared to smooth controls. Antimicrobial copper had no significant effect on MSSA contamination, but reduced MRSA contamination by 80% (LR = 0.70; p < 0.005).

CONCLUSION

The assays developed in this study mimic hospital environmental contamination events to demonstrate the performance of a MP to limit contamination under multiple conditions. Antimicrobial copper has been implemented in hospital room studies to evaluate its impact on nosocomial infections and a decrease in HAI rate was shown. Similar implementation of the MP has potential to reduce the incidence of HAIs although future clinical studies will be necessary to validate the MP's true impact.

A surface with a biomimetic micropattern reduces colonization of Mycobacterium abscessus

Nontuberculous mycobacteria (NTM) are ubiquitous organisms found in soil, water, and biofilms. Engineered surface topography has been proposed as a method to reduce microbial biofilm formation. The Sharklet(®) micropattern silicone surface has been shown to reduce biofilm formation of pyogenic bacteria. We hypothesized that this micropattern surface will also reduce colonization by Mycobacterium abscessus, a human pathogen. Smooth and micropattern silicone samples were incubated with 1 × 10(6) M. abscessus mL(-1) for 2 and 4 days. After processing to optimize recovery of adhered mycobacteria, there was a 75% and 50% reduction in the number of viable M. abscessus recovered from the micropattern surfaces compared to the smooth surfaces at 2 and 4 days after inoculation, respectively. Ziehl-Neelsen staining after measures to remove the adherent microorganisms revealed fewer residual M. abscessus on the micropattern samples as compared to smooth samples, validating the quantitative culture results. Microscopic observation of 2, 4, and 8 day M. abscessus cultures on micropattern samples showed that the organisms preferentially colonized within the channels between the rectangular features. In summary, a micropattern surface reduces the colonization of a pathogenic NTM. It remains to be seen whether this micropattern can reduce infections in humans.

Micro-patterned surfaces reduce bacterial colonization and biofilm formation in vitro: Potential for enhancing endotracheal tube designs

Background

Ventilator-associated pneumonia (VAP) is a leading hospital acquired infection in intensive care units despite improved patient care practices and advancements in endotracheal tube (ETT) designs. The ETT provides a conduit for bacterial access to the lower respiratory tract and a substratum for biofilm formation, both of which lead to VAP. A novel microscopic ordered surface topography, the Sharklet micro-pattern, has been shown to decrease surface attachment of numerous microorganisms, and may provide an alternative strategy for VAP prevention if included on the surface of an ETT. To evaluate the feasibility of this micro-pattern for this application, the microbial range of performance was investigated in addition to biofilm studies with and without a mucin-rich medium to simulate the tracheal environment in vitro.

Methods

The top five pathogens associated with ETT-related pneumonia, Methicillin-Resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa, Klebsiella pneumonia, Acinetobacter baumannii, and Escherichia coli, were evaluated for attachment to micro-patterned and un-patterned silicone surfaces in a short-term colonization assay. Two key pathogens, MRSA and Pseudomonas aeruginosa, were evaluated for biofilm formation in a nutrient rich broth for four days and minimal media for 24 hours, respectively, on each surface type. P. aeruginosa was further evaluated for biofilm formation on each surface type in a mucin-modified medium mimicking tracheal mucosal secretions. Results are reported as percent reductions and significance is based on t-tests and ANOVA models of log reductions. All experiments were replicated at least three times.

Results

Micro-patterned surfaces demonstrated reductions in microbial colonization for a broad range of species, with up to 99.9% (p < 0.05) reduction compared to un-patterned controls. Biofilm formation was also reduced, with 67% (p = 0.12) and 52% (p = 0.05) reductions in MRSA and P. aeruginosa biofilm formation, respectively. Further, a 58% (p < 0.01) reduction was demonstrated on micro-patterned surfaces for P. aeruginosa biofilms under clinically-simulated conditions when compared to un-patterned controls.

Conclusions

This engineered micro-pattern reduces the colonization and biofilm formation of key VAP-associated pathogens in vitro. Future application of this micro-pattern on endotracheal tubes may prevent or prolong the onset of VAP without the need for antimicrobial agents.

Applications of fractals in ecology

Fractal models describe the geometry of a wide variety of natural objects such as coastlines, island chains, coral reefs, satellite ocean-color images and patches of vegetation. Cast in the form of modified diffusion models, they can mimic natural and artificial landscapes having different types of complexity of shape. This article provides a brief introduction to fractals and reports on how they can be used by ecologists to answer a variety of basic questions, about scale, measurement and hierarchy in, ecological systems.

Limit cycles in predator-prey communities

Essentially all models that have been proposed for predator-prey systems are shown to possess either a stable point equilibrium or a stable limit cycle. This stable limit cycle, an explicitly nonlinear feature, is commonly overlooked in conventional analyses of these models. Such a stable limit cycle provides a satisfying explanation for those animal communities in which populations are observed to oscillate in a rather reproducible periodic manner.

Species turnover rates on islands: dependence on census interval

Measurements of species turnover in island bird communities demonstrate two trends with increasing census interval t: (i) Apparent turnover rates T decrease greatly with t, and (ii) the coefficient of variation of T decreases asymptotically to a constant value. These effects are predicted by a statistical model whose parameters are the immigration and extinction probabilities of each species. Available bird censuses at intervals of decades underestimate turnover rates by about an order of magnitude.

How many species are there on Earth?

This article surveys current answers to the factual question posed in the title and reviews the kinds of information that are needed to make these answers more precise. Various factors affecting diversity are also reviewed. These include the structure of food webs, the relative abundance of species, the number of species and of individuals in different categories of body size, along with other determinants of the commonness and rarity of organisms.

Harvesting natural populations in a randomly fluctuating environment

As harvesting effort and yield are increased, animal populations that are being harvested for sustained yield will take longer to recover from environmentally imposed disturbances. One consequence is that the coefficient of variation (the relative variance) of the yield increases as the point of maximum sustained yield (MSY) is approached. When overexploitation has resulted in a population smaller than that for MSY, high effort produces a low average yield with high variance. These observations accord with observed trends in several fish and whaling industries. We expect these effects to be more pronounced for a harvesting strategy based on constant quotas than for one based on constant effort. Although developed in a MSY context, the conclusions also apply if the aim is to maximize the present value of (discounted) net economic revenue.

Introduction. Emerging infections: what have we learnt from SARS?

In the summer of 2003, as the first global severe acute respiratory syndrome (SARS) epidemic stuttered to a close, The Royal Society set about organizing a meeting that would take stock of the year's events and ask ‘what can we learn from SARS about emerging infections in general?’ Emerging infections are more than just a current biological fashion. The bitter ongoing experience of AIDS and the looming threat of an influenza pandemic teach us that the control of infectious disease is a problem we have not yet solved. It is a problem that needs to be addressed by a broad community. Scientists, policy makers and health care workers all need to be prepared, but prepared to do what? The purpose of the meeting was to use SARS as an example to enumerate the generic issues that must be considered when planning for the control of emerging infections.

Modelling vaccination strategies against foot-and-mouth disease

Vaccination has proved a powerful defence against a range of infectious diseases of humans and animals. However, its potential to control major epidemics of foot-and-mouth disease (FMD) in livestock is contentious. Using an individual farm-based model, we consider either national prophylactic vaccination campaigns in advance of an outbreak, or combinations of reactive vaccination and culling strategies during an epidemic. Consistent with standard epidemiological theory, mass prophylactic vaccination could reduce greatly the potential for a major epidemic, while the targeting of high-risk farms increases efficiency. Given sufficient resources and preparation, a combination of reactive vaccination and culling might control ongoing epidemics. We also explore a reactive strategy, 'predictive' vaccination, which targets key spatial transmission loci and can reduce markedly the long tail that characterizes many FMD epidemics. These analyses have broader implications for the control of human and livestock infectious diseases in heterogeneous spatial landscapes.

Infection dynamics on scale-free networks

We discuss properties of infection processes on scale-free networks, relating them to the node-connectivity distribution that characterizes the network. Considering the epidemiologically important case of a disease that confers permanent immunity upon recovery, we derive analytic expressions for the final size of an epidemic in an infinite closed population and for the dependence of infection probability on an individual's degree of connectivity within the population. As in an earlier study [R. Pastor-Satorras and A. Vesipignani, Phys. Rev. Lett. 86, 3200 (2001); Phys. Rev. E. 63, 006117 (2001)] for an infection that did not confer immunity upon recovery, the epidemic process--in contrast with many traditional epidemiological models--does not exhibit threshold behavior, and we demonstrate that this is a consequence of the extreme heterogeneity in the connectivity distribution of a scale-free network. Finally, we discuss effects that arise from finite population sizes, showing that networks of finite size do exhibit threshold effects: infections cannot spread for arbitrarily low transmission probabilities.

Infectious disease dynamics: What characterizes a successful invader?

Against the background of human immunodeficiency virus (HIV) and acquired immune deficiency syndrome (AIDS) and other potentially emerging (or re-emerging) infectious diseases, this review will focus on the properties which enable an infectious agent to establish and maintain itself within a specified host population. We shall emphasize that for a pathogen to cross a species barrier is one thing, but for it successfully to maintain itself in the new population is must have a 'basic reproductive number', R(0), which satisfies R(0) > 1. We shall further discuss how behavioural factors interweave with the basic biology of the production of transmission stages by the pathogen, all subject to possible secular changes, to determine the magnitude of R(0). Although primarily focusing on HIV and AIDS, we shall review wider aspects of these questions.

Ecology. Species-area relations in tropical forests

A power law called the species-area relationship describes the finding that the number of species is proportional to the size of the area in which they are found, raised to an exponent (usually, a number between 0.2 and 0.3). In their Perspective, May and Stumpf discuss new results from a survey of five tropical forest census areas containing a total of a million trees. They explain how this large data set can be used to fine-tune the existing power law so that it provides a better prediction of species diversity in small census samples.

The role of antigen-independent persistence of memory cytotoxic T lymphocytes

We use mathematical models to analyze the role of a memory cytotoxic T lymphocyte (CTL) response in viral infections. The model predicts that antigen-independent persistence of an elevated number of precursor CTL (CTLp) does not protect the host from clinical symptoms upon re-infection. Instead, we find that antigen-independent long-term persistence of CTLp is required to clear virus infections. This mechanism also applies to infection in hosts that have never experienced the pathogen before. Requirement of antigen for the long-term maintenance of CTLp results in failure to clear the infection, even in hosts characterized by a high CTL responsiveness. We compare the CTL model to a B cell model. In keeping with experimentally established findings, B cells are efficient in protecting against re-infection, but are unlikely to clear viral infections unless the virus is cytopathic. We conclude that the role of 'memory CTLp' is different from the role of memory B cells in viral infections: antigen-independent long-term persistence of CTLp is a pre-requisite to ensure clearance of infection.

Extinction and the loss of evolutionary history

Extinction episodes, such as the anthropogenic one currently under way, result in a pruned tree of life. But what fraction of the underlying evolutionary history survives when k of n species in a taxon are lost? This is relevant both to how species loss has translated into a loss of evolutionary history and to assigning conservation priorities. Here it is shown that approximately 80 percent of the underlying tree of life can survive even when approximately 95 percent of species are lost, and that algorithms that maximize the amount of evolutionary history preserved are not much better than choosing the survivors at random. Given the political, economic, and social realities constraining conservation biology, these findings may be helpful.

Virus dynamics and drug therapy

The recent development of potent antiviral drugs not only has raised hopes for effective treatment of infections with HIV or the hepatitis B virus, but also has led to important quantitative insights into viral dynamics in vivo. Interpretation of the experimental data depends upon mathematical models that describe the nonlinear interaction between virus and host cell populations. Here we discuss the emerging understanding of virus population dynamics, the role of the immune system in limiting virus abundance, the dynamics of viral drug resistance, and the question of whether virus infection can be eliminated from individual patients by drug treatment.

Anti-viral drug treatment: dynamics of resistance in free virus and infected cell populations

Anti-viral drug treatment of infections with the human immunodeficiency virus type I (HIV-1) usually leads to a rapid decline in the abundance of plasma virus. The effect of single drug therapy, however, is often only short-lived as the virus readily develops drug-resistant mutants. In this paper we provide analytic approximations for the rate of emergence of resistant virus. We study the decline of wildtype virus and the rise of resistant mutant virus in different compartments of the virus population such as free plasma virus, cells infected with actively replicating virus, long-lived infected cells and cells carrying defective provirus. The model results are compared with data on the rise of drug-resistant virus in three HIV-1 infected patients treated with neverapine (NVP). We find that the half-life of latently infected cells is between 10 and 20 days, whereas the half-life of cells with defective provirus is about 80 days. We also provide a crude estimate for the basic reproductive ratio of HIV-1 during NVP therapy.

Antigenic diversity thresholds and hazard functions

In this paper, we answer some points made in a recent paper by N.I. Stilianakis and coworkers on the antigenic diversity threshold model for acquired immune deficiency syndrome pathogenesis. An extended version of the model is then used to compute hazard functions for the human immunodeficiency virus incubation period that are in agreement with empirically observed hazard functions.

Cytotoxic T lymphocytes and viral turnover in HIV type 1 infection

To understand the role of the immune system in limiting HIV type 1 replication, it is critical to know to what extent the rapid turnover of productively infected cells is caused by viral cytopathicity or by immune-mediated lysis. We show that uncultured peripheral blood mononuclear cells of many patients contain cytotoxic T lymphocytes (CTL) that lyse target cells-at plausible peripheral blood mononuclear cell-to-target ratios-with half-lives of less than 1 day. In 23 patients with CD4 counts ranging from 10 to 900 per microliter, the average rate of CTL-mediated lysis corresponds to a target cell half-life of 0.7 day. We develop mathematical models to calculate the turnover rate of infected cells subjected to immune-mediated lysis and viral cytopathicity and to estimate the fraction of cells that are killed by CTL as opposed to virus. The models provide new interpretations of drug treatment dynamics and explain why the observed rate of virus decline is roughly constant for different patients. We conclude that in HIV type 1 infection, CTL-mediated lysis can reduce virus load by limiting virus production, with small effects on the half-life of infected cells.

The population biology of the interaction between HIV-1 and HIV-2: coexistence or competitive exclusion?

BACKGROUND

The emergence and rapid world-wide spread of HIV provides an unusual opportunity for the study of the evolution and maintenance of virulence in a major human pathogen.

OBJECTIVE

To analyse the available biological and epidemiological data on the pathogenicity, transmissibility and antigenic similarity of HIV-1 and HIV-2, and use simple mathematical models of competition between the two viral types within a defined host community.

RESULTS AND CONCLUSIONS

Analysis revealed a positive association between pathogenicity and reproductive success. A mathematical model of the concomitant transmission of the two viruses suggests that HIV-1 will competitively displace HIV-2 in the longer term in areas where both viruses are being transmitted within the same sexually active population.

Metapopulations and equilibrium stability: the effects of spatial structure

Recently, there has been a great deal of interest in the dynamics of metapopulations, where a number of local populations are coupled via dispersal. The importance of movement for the persistence of an ensemble of locally unstable patches has been established in many studies. In this paper, we present analytical and simulation results concerning the effects of spatial structure on the equilibrium stability of individual populations. We conclude that for general single-species and two-species competition models, the introduction of the spatial dimension in a biologically sensible way has no effect on the overall stability properties. In host-parasitoid models, however, strong host or parasitoid over-dispersal may be destabilizing.

Viral dynamics in vivo: limitations on estimates of intracellular delay and virus decay

Anti-viral drug treatment of human immunodeficiency virus type I (HIV-1) and hepatitis B virus (HBV) infections causes rapid reduction in plasma virus load. Viral decline occurs in several phases and provides information on important kinetic constants of virus replication in vivo and pharmacodynamical properties. We develop a mathematical model that takes into account the intracellular phase of the viral life-cycle, defined as the time between infection of a cell and production of new virus particles. We derive analytic solutions for the dynamics following treatment with reverse transcriptase inhibitors, protease inhibitors, or a combination of both. For HIV-1, our results show that the phase of rapid decay in plasma virus (days 2-7) allows precise estimates for the turnover rate of productively infected cells. The initial quasi-stationary phase (days 0-1) and the transition phase (days 1-2) are explained by the combined effects of pharmacological and intracellular delays, the clearance of free virus particles, and the decay of infected cells. Reliable estimates of the first three quantities are not possible from data on virus load only; such estimates require additional measurements. In contrast with HIV-1, for HBV our model predicts that frequent early sampling of plasma virus will lead to reliable estimates of the free virus half-life and the pharmacological properties of the administered drug. On the other hand, for HBV the half-life of infected cells cannot be estimated from plasma virus decay.

The maintenance of strain structure in populations of recombining infectious agents

Using mathematical models that combine population genetic and epidemiological processes, we resolve the paradox that many important pathogens appear to persist as discrete strains despite the constant exchange of genetic material. We show that dominant polymorphic determinants (that is, those that elicit the most effective immune responses) will be organized into nonoverlapping combinations as a result of selection by the host immune system, thereby defining a set of discrete independently transmitted strains. By analysing 222 isolates of Neisseria meningitidis, we show that two highly polymorphic epitopes of the outer membrane protein PorA exist in nonoverlapping combinations as predicted by this general framework. The model indicates that dominant polymorphic determinants will be in linkage disequilibrium, despite frequent genetic exchange, even though they may be encoded by several unlinked genes. This suggests that the detection of nonrandom associations between epitope regions can be employed as a novel strategem for identifying dominant polymorphic antigens.

Spatial heterogeneity in epidemic models

Spatial heterogeneity is believed to play an important role in the persistence and dynamics of epidemics of childhood diseases because asynchrony between populations within different regions allows global persistence, even if the disease dies out locally. A simple multi-patch (metapopulation) model for spatial heterogeneity in epidemics is analysed and we examine conditions under which patches become synchronized. We show that the patches in non-seasonal deterministic models often oscillate in phase for all but the weakest between patch coupling. Synchronization is also seen for stochastic models, although slightly stronger coupling is needed to overcome the random effects. We demonstrate that the inclusion of seasonal forcing in deterministic models can lead to the maintenance of phase differences between patches. Complex dynamic behaviour is observed in the seasonally forced spatial model, along with the coexistence of many different behaviours. Compared to the non-spatial model, chaotic solutions are observed for weaker seasonal forcing; these solutions have a more realistic minimum number of infectives.

Genetic heterogeneity in helminths - a reply

The previous paper in this issue Computer model of the maintenance and selection of genetic heterogeneity in polygamous helminths by Saul uses an individual-based computer simulation to explore aspects of the transmission and maintenance of genetic heterogeneity among polygamous intestinal helminths, both in the absence and in the presence of external selection pressures resulting from chemotherapy. Saul finds that, in the absence of any selective effects, genetic heterogeneity persists, contradicting the results presented by Anderson, May & Gupta (1989) that mating probability functions create density-dependent and frequency-dependent selective pressures against a rare allele, which eventually leads to its elimination.

Coinfection and the evolution of parasite virulence

Analyses of the selection pressures acting on parasite virulence are made more complicated when individual hosts can simultaneously harbour many different strains or genotypes of a parasite. Here we explore the evolutionary dynamics of host-parasite associations in which individual hosts can be coinfected with many different parasite strains. (We take coinfection to mean that each strain transmits at a rate unaffected by the presence of others in the same host.) This study thus represents the opposite extreme to our earlier work on superinfection in which there is a dominance hierarchy such that only the most virulent strain present in a host is transmitted. For highly diverse populations of parasite strains, we find that such coinfection leads to selection for strains whose virulence-levels lie in a relatively narrow band close to the maximum consistent with the parasite's basic preproductive ratio, R0, exceeding unity.

Immune responses against multiple epitopes

The current understanding of antigenic escape dynamics is based on models with single epitopes. The usual idea is that a mutation which enables a pathogen (virus, bacteria, etc) to escape from a given immune response confers a selective advantage. The "escape mutant" may then increase in abundance until it induces a new specific response against itself. In this paper a new picture is developed, based on mathematical models of immune responses against several epitopes; the simplest such models can have very complicated dynamics, with some surprising features. The emergence of an escape mutant can shift the immunodominant response to another epitope. Even in the absence of mutations, antigenic oscillation is found, with distinct peaks of different virus variants and fluctuations in the size and specificity of the immune responses. The model also provides a general theory for immunodominance in the presence of antigenic variation. Immunodominance is determined by the immunogenicity and by the antigenic diversity of the competing epitopes. Antigenic oscillations and fluctuations in the cytotoxic T-lymphocyte response have been observed in infections with the human immunodeficiency virus (HIV). Shifting the immune responses to weaker epitopes can represent a mechanism for disease progression based on evolutionary dynamics and antigenic diversity of the virus.

The population dynamics of vertically and horizontally transmitted parasites

We analyse a model of the transmission dynamics of a parasite transmitted both vertically and horizontally. The basic reproductive ratio (R0) of the parasite is shown to be a sum of horizontal and vertical components. We derive expressions for the equilibrium prevalence of infection for a mixture of horizontal and vertical transmission; prevalence can reach 100% if transmission is sufficiently high. At the endemic equilibrium, if prevalence is high, most transmission will in general be vertical, but horizontal transmission rates must be high to reach and stably maintain such an equilibrium. Surprisingly, for such parasites the highest equilibrium rates of vertical transmission are observed when horizontal transmission is very effective. We discuss the implications for assessing the importance of horizontal v. vertical transmission from field data, and we suggest some implications for the evolution of virulence.

Antigenic oscillations and shifting immunodominance in HIV-1 infections

A typical protein antigen contains several epitopes that can be recognized by cytotoxic T lymphocytes (CTL), but in a characteristic antiviral immune response in vivo, CTL recognize only a small number of these potential epitopes, sometimes only one, this phenomenon is known as immunodominance. Antigenic variation within CTL epitopes has been demonstrated for the human immunodeficiency virus HIV-1 (ref. 11) and other viruses and such 'antigenic escape' may be responsible for viral persistence. Here we develop a new mathematical model that deals with the interaction between CTL and multiple epitopes of a genetically variable pathogen, and show that the nonlinear competition among CTL responses against different epitopes can explain immunodominance. This model suggests that an antigenically homogeneous pathogen population tends to induce a dominant response against a single epitope, whereas a heterogeneous pathogen population can stimulate complicated fluctuating responses against multiple epitopes. Antigenic variation in the immunodominant epitope can shift responses to weaker epitopes and thereby reduce immunological control of the pathogen population. These ideas are consistent with detailed longitudinal studies of CTL responses in HIV-1 infected patients. For vaccine design, the model suggests that the major response should be directed against conserved epitopes even if they are subdominant.

The arithmetics of mutual help

Computer experiments show how cooperation rather than exploitation can dominate in the Darwinian struggle for survival.