Using computer simulations to compare pertussis vaccination strategies in Australia

Pertussis immunisation strategies to optimise infant pertussis control: A narrative systematic review

OBJECTIVE

Countries routinely offering acellular pertussis vaccine, where long-term protection is not sustained, have the challenge of selecting an optimal schedule to minimise disease among young infants. We conducted a narrative systematic review and synthesis of information to evaluate different pertussis immunisation strategies at controlling pertussis disease, hospitalisation, deaths, and vaccine effectiveness among young infants.

METHODS

We conducted a review of the literature on studies about the primary, booster, and/or maternal vaccination series and synthesised findings narratively. Countries offering the first three doses of vaccine within six-months of life and a booster on or before the second year or life were defined as accelerated primary and booster schedules, respectively. Countries offering primary and booster doses later were defined as extended primary and booster schedules. All search results were screened, and articles reviewed and reconciled, by two authors. The Risk of Bias in Non-randomised Studies of Intervention tool was used to evaluate the risk of bias.

FINDINGS

A total of 98 studies were included in the analyses and the following recurring themes were described: timing of vaccination, vaccine coverage, waning immunity/vaccine effectiveness, direct and indirect effectiveness, switching from an accelerated to extended schedule, impact of changes in testing. The risk of bias was generally low to moderate for most studies.

CONCLUSION

Comparing schedules is challenging and there was insufficient evidence to that one schedule was superior to another. Countries must select a schedule that maintains high vaccine coverage and reduced the risk of delaying the delivery vaccines to protect infants.

A computational framework for modeling and studying pertussis epidemiology and vaccination

BACKGROUND

Emerging and re-emerging infectious diseases such as Zika, SARS, ncovid19 and Pertussis, pose a compelling challenge for epidemiologists due to their significant impact on global public health. In this context, computational models and computer simulations are one of the available research tools that epidemiologists can exploit to better understand the spreading characteristics of these diseases and to decide on vaccination policies, human interaction controls, and other social measures to counter, mitigate or simply delay the spread of the infectious diseases. Nevertheless, the construction of mathematical models for these diseases and their solutions remain a challenging tasks due to the fact that little effort has been devoted to the definition of a general framework easily accessible even by researchers without advanced modelling and mathematical skills.

RESULTS

In this paper we describe a new general modeling framework to study epidemiological systems, whose novelties and strengths are: (1) the use of a graphical formalism to simplify the model creation phase; (2) the implementation of an R package providing a friendly interface to access the analysis techniques implemented in the framework; (3) a high level of portability and reproducibility granted by the containerization of all analysis techniques implemented in the framework; (4) a well-defined schema and related infrastructure to allow users to easily integrate their own analysis workflow in the framework. Then, the effectiveness of this framework is showed through a case of study in which we investigate the pertussis epidemiology in Italy.

CONCLUSIONS

We propose a new general modeling framework for the analysis of epidemiological systems, which exploits Petri Net graphical formalism, R environment, and Docker containerization to derive a tool easily accessible by any researcher even without advanced mathematical and computational skills. Moreover, the framework was implemented following the guidelines defined by Reproducible Bioinformatics Project so it guarantees reproducible analysis and makes simple the developed of new user-defined workflows.

Estimating seasonal variation in Australian pertussis notifications from 1991 to 2016: evidence of spring to summer peaks

Unlike for many other respiratory infections, the seasonality of pertussis is not well understood. While evidence of seasonal fluctuations in pertussis incidence has been noted in some countries, there have been conflicting findings including in the context of Australia. We investigated this issue by analysing the seasonality of pertussis notifications in Australia using monthly data from January 1991 to December 2016. Data were made available for all states and territories in Australia except for the Australian Capital Territory and were stratified into age groups. Using a time-series decomposition approach, we formulated a generalised additive model where seasonality is expressed using cosinor terms to estimate the amplitude and peak timing of pertussis notifications in Australia. We also compared these characteristics across different jurisdictions and age groups. We found evidence that pertussis notifications exhibit seasonality, with peaks observed during the spring and summer months (November–January) in Australia and across different states and territories. During peak months, notifications are expected to increase by about 15% compared with the yearly average. Peak notifications for children <5 years occurred 1–2 months later than the general population, which provides support to the theory that older household members remain an important source of pertussis infection for younger children. In addition, our results provide a more comprehensive spatial picture of seasonality in Australia, a feature lacking in previous studies. Finally, our findings suggest that seasonal forcing may be useful to consider in future population transmission models of pertussis.

Infection-acquired versus vaccine-acquired immunity in an SIRWS model

In some disease systems, the process of waning immunity can be subtle, involving a complex relationship between the duration of immunity-acquired either through natural infection or vaccination-and subsequent boosting of immunity through asymptomatic re-exposure. We present and analyse a model of infectious disease transmission where primary and secondary infections are distinguished to examine the interplay between infection and immunity. Additionally we allow the duration of infection-acquired immunity to differ from that of vaccine-acquired immunity to explore the impact on long-term disease patterns and prevalence of infection in the presence of immune boosting. Our model demonstrates that vaccination may induce cyclic behaviour, and the ability of vaccinations to reduce primary infections may not lead to decreased transmission. Where the boosting of vaccine-acquired immunity delays a primary infection, the driver of transmission largely remains primary infections. In contrast, if the immune boosting bypasses a primary infection, secondary infections become the main driver of transmission under a sufficiently long duration of immunity. Our results show that the epidemiological patterns of an infectious disease may change considerably when the duration of vaccine-acquired immunity differs from that of infection-acquired immunity. Our study highlights that for any particular disease and associated vaccine, a detailed understanding of the waning and boosting of immunity and how the duration of protection is influenced by infection prevalence are important as we seek to optimise vaccination strategies.

Evaluation of outbreak response immunization in the control of pertussis using agent-based modeling

Background

Pertussis control remains a challenge due to recently observed effects of waning immunity to acellular vaccine and suboptimal vaccine coverage. Multiple outbreaks have been reported in different ages worldwide. For certain outbreaks, public health authorities can launch an outbreak response immunization (ORI) campaign to control pertussis spread. We investigated effects of an outbreak response immunization targeting young adolescents in averting pertussis cases.

Methods

We developed an agent-based model for pertussis transmission representing disease mechanism, waning immunity, vaccination schedule and pathogen transmission in a spatially-explicit 500,000-person contact network representing a typical Canadian Public Health district. Parameters were derived from literature and calibration. We used published cumulative incidence and dose-specific vaccine coverage to calibrate the model’s epidemiological curves. We endogenized outbreak response by defining thresholds to trigger simulated immunization campaigns in the 10–14 age group offering 80% coverage. We ran paired simulations with and without outbreak response immunization and included those resulting in a single ORI within a 10-year span. We calculated the number of cases averted attributable to outbreak immunization campaign in all ages, in the 10–14 age group and in infants. The count of cases averted were tested using Mann–Whitney U test to determine statistical significance. Numbers needed to vaccinate during immunization campaign to prevent a single case in respective age groups were derived from the model. We varied adult vaccine coverage, waning immunity parameters, immunization campaign eligibility and tested stronger vaccination boosting effect in sensitivity analyses.

Results

189 qualified paired-runs were analyzed. On average, ORI was triggered every 26 years. On a per-run basis, there were an average of 124, 243 and 429 pertussis cases averted across all age groups within 1, 3 and 10 years of a campaign, respectively. During the same time periods, 53, 96, and 163 cases were averted in the 10–14 age group, and 6, 11, 20 in infants under 1 (p < 0.001, all groups). Numbers needed to vaccinate ranged from 49 to 221, from 130 to 519 and from 1,031 to 4,903 for all ages, the 10–14 age group and for infants, respectively. Most sensitivity analyses resulted in minimal impact on a number of cases averted.

Discussion

Our model generated 30 years of longitudinal data to evaluate effects of outbreak response immunization in a controlled study. Immunization campaign implemented as an outbreak response measure among adolescents may confer benefits across all ages accruing over a 10-year period. Our inference is dependent on having an outbreak of significant magnitude affecting predominantly the selected age and achieving a comprehensive vaccine coverage during the campaign. Economic evaluations and comparisons with other control measures can add to conclusions generated by our work.

Pertussis models to inform vaccine policy

Pertussis remains a challenging public health problem with many aspects of infection, disease and immunity poorly understood. Initially controlled by mass vaccination, pertussis resurgence has occurred in some countries with well-established vaccination programs, particularly among adolescents and young adults. Several studies have used mathematical models to investigate drivers of pertussis epidemiology and predict the likely impact of different vaccination strategies. We reviewed a number of these models to evaluate their suitability to answer questions of public health importance regarding optimal vaccine scheduling. We critically discuss the approaches adopted and the impact of chosen model structures and assumptions on study conclusions. Common limitations were a lack of contemporary, population relevant data for parameterization and a limited understanding of the relationship between infection and disease. We make recommendations for future model development and suggest epidemiologic data collections that would facilitate efforts to reduce uncertainty and improve the robustness of model-derived conclusions.

Defining long-term drivers of pertussis resurgence, and optimal vaccine control strategies

Pertussis resurgence has been reported from several developed countries with long-standing immunisation programs. Among these, Australia in 2003 discontinued an 18 months (fourth) booster dose in favour of an adolescent (fifth) dose. We developed a model to evaluate determinants of resurgence in Australia and alternative vaccine strategies for mitigation. Novel characteristics of our model included the use of seroepidemiologic data for calibration, and broad investigation of variables relevant to transmission of, and protection against, pertussis. We simulated multiple parameter combinations, retaining those consistent with observed data for subsequent use in predictive models comparing alternative vaccination schedules. Reproducing the early control of pertussis followed by late resurgence observed in Australia required natural immunity to last decades longer than vaccine-acquired immunity, with mean duration exceeding 50 years in almost 90% of simulations. Replacement of the dose at 18 months with an adolescent dose in 2003 resulted in a 40% increase in infections in the age group 18-47 months by 2013. A six dose strategy (2, 4, 6, 18 months, 4 and 15 years) yielded a reduction in infection incidence (pre-school 43%, infants 8%) greater than any alternative strategies considered for timing of five administered doses. Our finding that natural immunity drives long-term trends in pertussis cycles is relevant to a range of pertussis strategies and provides the necessary context in which to consider maternal vaccination. Comparatively short-lived vaccine-acquired immunity requires multiple boosters over the first two decades of life to maximise reduction in infections.

Modelling the impact of extended vaccination strategies on the epidemiology of pertussis

The aim of this study was to investigate the optimal pertussis booster vaccination strategy for The Netherlands. A realistic age-structured deterministic model was designed. Assuming a steady-state situation and correcting for underreporting, the model was calibrated using notification data from the period 1996–2000. Several sensitivity analyses were performed to explore the impact of different assumptions for parameters surrounded by uncertainty (e.g. duration of protection after natural infection, underreporting factors, and transmission probabilities). The optimal age of an additional booster dose is in the range of 10–15 years, and implementation of this booster dose will reduce both symptomatic and asymptomatic infections, although the incidence of symptomatic infections in older age groups will increase. The impact of the different assumptions used in the model was in general limited. We conclude that over a wide range of assumptions, an additional booster dose can reduce the incidence of pertussis in the population.

The impact of adolescent pertussis immunization, 2004-2009: lessons from Australia

OBJECTIVE

To compare the impact of three strategies for delivering a booster dose of adult-formulated tetanus-diphtheria-pertussis (Tdap) vaccine to adolescents in Australia. These comprise: (i) administering Tdap to: a one-year age cohort; (ii) administering Tdap to the entire high school and to subsequent entrant cohorts; and (iii) administering Tdap to the entire high school but without continuing to immunize entrant cohorts.

METHODS

A series of ecologic analyses of pertussis notifications during epidemic periods in relevant age cohorts were conducted. The primary outcome measure was the incidence rate ratio (IRR), calculated by dividing pertussis incidence after the introduction of Tdap delivery programmes by pertussis incidence during the most recent pre-programme epidemic.

FINDINGS

During the epidemic period of 2008-2009, the national-level IRR among age cohorts targeted for Tdap was 0.6 (95% confidence interval, CI: 0.6-0.7), but among other age cohorts it was 1.1 (95% CI: 1.1-1.2). Only the jurisdiction that implemented strategy 2 (Western Australia) experienced sustained decreases in pertussis notifications in both adolescents and infants under 6 months of age (IRR: 0.4; 95% CI: 0.3-0.6) until 2009.

CONCLUSION

If confirmed by longer experience in Australia and elsewhere, a broad school-based catch-up programme followed by immunization of school entrants may be the optimum strategy for the implementation of adolescent Tdap programmes.

Cost-effectiveness of adolescent pertussis vaccination for the Netherlands: using an individual-based dynamic model

BACKGROUND

Despite widespread immunization programs, a clear increase in pertussis incidence is apparent in many developed countries during the last decades. Consequently, additional immunization strategies are considered to reduce the burden of disease. The aim of this study is to design an individual-based stochastic dynamic framework to model pertussis transmission in the population in order to predict the epidemiologic and economic consequences of the implementation of universal booster vaccination programs. Using this framework, we estimate the cost-effectiveness of universal adolescent pertussis booster vaccination at the age of 12 years in the Netherlands.

METHODS/PRINCIPAL FINDINGS

We designed a discrete event simulation (DES) model to predict the epidemiological and economic consequences of implementing universal adolescent booster vaccination. We used national age-specific notification data over the period 1996-2000--corrected for underreporting--to calibrate the model assuming a steady state situation. Subsequently, booster vaccination was introduced. Input parameters of the model were derived from literature, national data sources (e.g. costing data, incidence and hospitalization data) and expert opinions. As there is no consensus on the duration of immunity acquired by natural infection, we considered two scenarios for this duration of protection (i.e. 8 and 15 years). In both scenarios, total pertussis incidence decreased as a result of adolescent vaccination. From a societal perspective, the cost-effectiveness was estimated at €4418/QALY (range: 3205-6364 € per QALY) and €6371/QALY (range: 4139-9549 € per QALY) for the 8- and 15-year protection scenarios, respectively. Sensitivity analyses revealed that the outcomes are most sensitive to the quality of life weights used for pertussis disease.

CONCLUSIONS/SIGNIFICANCE

To our knowledge we designed the first individual-based dynamic framework to model pertussis transmission in the population. This study indicates that adolescent pertussis vaccination is likely to be a cost-effective intervention for The Netherlands. The model is suited to investigate further pertussis booster vaccination strategies.

Pertussis in Portugal - time for a new strategy

The introduction of routine vaccination against Bordetella pertussis led to a drastic decline in the number of reported cases of pertussis. Nevertheless, a gradual increase in pertussis notifications has been observed in the last years, and political vaccination changes have been conducted in some countries. Pertussis epidemiology is reviewed, taking into account mathematical models studies concerning new vaccinal strategies for pertussis prevention and new international recommendations. Regarding Portugal, the need for a "booster" in adolescence is emphasized, and other recommendations for pertussis control are suggested.

Public vaccination policy using an age-structured model of pneumococcal infection dynamics

Public health professionals are charged with the task of designing prevention programs for the effective control of biologically intricate infectious diseases at a population level. The effective vaccination of a population for pneumococcal diseases (infections caused by Streptococcus pneumoniae) remains a relevant question in the scientific community. It is complicated by heterogeneity in individuals' responses to exposure to the bacterium and their responses to vaccination. Due to these complexities, most modelling efforts in this area have been on the cellular/bacteria level. Here, we introduce an age-structured SEIS-type model of pneumococcal diseases and their vaccination. We discuss the use of this framework in predicting the impact of vaccine strategies, with pneumococcal diseases as an example. Using parameter values reasonable for a developed country, we discuss the effects of targeting the colonization and/or infection stages on the age profiles of morbidity in a population.

Using Inverse Problem Methods with Surveillance Data in Pneumococcal Vaccination

The design and evaluation of epidemiological control strategies is central to public health policy. While inverse problem methods are routinely used in many applications, this remains an area in which their use is relatively rare, although their potential impact is great. We describe methods particularly relevant to epidemiological modeling at the population level. These methods are then applied to the study of pneumococcal vaccination strategies as a relevant example which poses many challenges common to other infectious diseases. We demonstrate that relevant yet typically unknown parameters may be estimated, and show that a calibrated model may used to assess implemented vaccine policies through the estimation of parameters if vaccine history is recorded along with infection and colonization information. Finally, we show how one might determine an appropriate level of refinement or aggregation in the age-structured model given age-stratified observations. These results illustrate ways in which the collection and analysis of surveillance data can be improved using inverse problem methods.

Adult vaccination strategies for the control of pertussis in the United States: an economic evaluation including the dynamic population effects

Background

Prior economic evaluations of adult and adolescent vaccination strategies against pertussis have reached disparate conclusions. Using static approaches only, previous studies failed to analytically include the indirect benefits derived from herd immunity as well as the impact of vaccination on the evolution of disease incidence over time.

Methods

We assessed the impact of different pertussis vaccination strategies using a dynamic compartmental model able to consider pertussis transmission. We then combined the results with economic data to estimate the relative cost-effectiveness of pertussis immunization strategies for adolescents and adults in the US. The analysis compares combinations of programs targeting adolescents, parents of newborns (i.e. cocoon strategy), or adults of various ages.

Results

In the absence of adolescent or adult vaccination, pertussis incidence among adults is predicted to more than double in 20 years. Implementing an adult program in addition to childhood and adolescent vaccination either based on 1) a cocoon strategy and a single booster dose or 2) a decennial routine vaccination would maintain a low level of pertussis incidence in the long run for all age groups (respectively 30 and 20 cases per 100,000 person years). These strategies would also result in significant reductions of pertussis costs (between −77% and −80% including additional vaccination costs). The cocoon strategy complemented by a single booster dose is the most cost-effective one, whereas the decennial adult vaccination is slightly more effective in the long run.

Conclusions

By providing a high level of disease control, the implementation of an adult vaccination program against pertussis appears to be highly cost-effective and often cost-saving.

EPIREVIEW. Pertussis in New South Wales, 1993-2005: the impact of vaccination policy on pertussis epidemiology

OBJECTIVE

To assess whether changes in vaccination policy have affected the epidemiology of pertussis in NSW between 1993 and 2005.

METHODS

Surveillance data from the NSW Notifiable Diseases Database was reviewed for the period.

RESULTS

35,695 cases of pertussis were notified; annual incidence rates varied from 18.4 to 84.2 per 100,000 people. The highest rates of pertussis were consistently found in infants aged 0-6 months. Rates of disease in other age groups changed markedly over the study period, with high rates currently observed in adult age groups.

CONCLUSIONS

New strategies may be needed to control pertussis in infants and in adults who now comprise the largest proportion of cases.

An evaluation of public health interventions during a pertussis outbreak in the ACT, 2003

OBJECTIVE

To assess whether issuing information alerts increased the proportion of pertussis cases notified within the 21-day infectious period during a pertussis outbreak in the Australian Capital Territory (ACT) in 2003.

METHOD

The study included all persons resident in the ACT for whom a notification of pertussis was received with onset of disease between 1 March and 31 December 2003. Cases notified within 21 days of onset were called 'early notifications'. The effectiveness of information alerts was assessed by comparing the proportion of early notifications before and after each alert and over the course of the outbreak.

MAIN OUTCOME MEASURE

The proportion of early notifications.

RESULTS

The proportion of early notifications ranged from 1/36 (2.7%) prior to the first intervention to 29/52 (55.7%) after the final intervention (p < 0.001).

CONCLUSIONS

This study supports the hypothesis that information alerts by ACT Health increase the proportion of cases notified within the infectious period of 21 days.

IMPLICATIONS FOR PUBLIC HEALTH PRACTICE

Early diagnosis of pertussis cases (within the infectious period) has the potential to limit transmission and protect susceptible infants.

Shift in the Epidemiology of Pertussis Infection

Pertussis vaccination of young children has been effective in reducing the overall disease burden due to Bordetella pertussis in many countries. However, the disease has not been eliminated, although humans are the only known host of this pathogen. In fact, in some countries, the number of reported cases has increased dramatically from their nadir and epidemics routinely occur. In areas where >80% of children <2 years of age have been vaccinated, the burden of disease has shifted from elementary school-aged children (who are presumably protected by vaccination) to young infants (<6 months of age) and individuals >11 years of age. With the recent availability of acellular pertussis vaccines for older children to adults, consideration of a change in current vaccination policy is necessary in order to provide better disease control.

A modelling analysis of pertussis transmission and vaccination in Rio de Janeiro, Brazil

Pertussis is an infectious respiratory disease for which mass vaccination is an effective preventive strategy. In many developed countries, where high vaccination coverage has been maintained for approximately 50 years, re-emergence of the disease has been observed in all age groups. In the municipality of Rio de Janeiro (RJ), where vaccination started in the 1980s, surveillance data show no sign of disease re-emergence. We developed a mathematical model that incorporates the major demographic aspects of a large urban centre in a developing nation, in addition to the most important epidemiological aspects of disease transmission. Parameter values were estimated based on RJ demographic and vaccine coverage data. Overall, all vaccination strategies determined a major decrease (over 95% decrease when compared to the pre-vaccine era) in the incidence of primary infections (occurring in individuals who have never been immunized through infection or vaccine). On the other hand, the strategies (a) three doses at age 2-11 months, (b) three doses plus booster at age 12-23 months, (c) three doses plus booster at age 4-5 years, and (d) three doses plus both boosters, differently affected the incidence of secondary infections (occurring in previously infected/vaccinated individuals). Given that the immunity against pertussis wanes with time and that the infectious agent has not been eliminated from the population, it is expected that pertussis will continue to be a problem in RJ. Actually, since immunity acquired from vaccine wanes faster than disease-acquired immunity and the possibility of natural boosters has decreased with mass vaccination, an increase in the incidence of secondary infections among older age groups is expected (and predicted by the model). Possible explanations as to why this dynamics is not captured by the RJ surveillance system are discussed. A poorly effective surveillance system and a lack of awareness regarding loss of immunity and the possibility of pertussis infection in older age groups are among them. Finally, we bring attention to the need of (i) field studies for the measurement of pertussis incidence in adolescents and adults; (ii) better understanding of the transmission dynamics currently occurring in RJ, and (iii) re-evaluation of vaccination strategies with the possible introduction of acellular vaccines for the vaccination of older individuals.

Pertussis vaccination for adolescents and adults

Following the introduction of vaccines, the incidence of pertussis declined; however, since 1990, a progressive increase was noted, even in highly immunised populations. Periodic pertussis outbreaks are due to suboptimal efficacy of the vaccine and waning immunity with increasing age. A significant proportion of adolescents and adults with a prolonged cough present Bordetella pertussis, and infection is often transmitted to infants too young to be vaccinated. A high vaccination coverage in the whole population would be necessary to interrupt the circulation of B. pertussis, but immunisation programmes for adolescents and adults have been introduced recently and are accepted with difficulty. The lack of cost-benefit analysis and consistent epidemiological data makes it difficult to assess the role of pertussis elimination among public health priorities. At present, programmes targeted at risk groups for close contacts with infants are the most convenient for adult population, as more epidemiological and economic evidence is needed before a universal strategy can be discussed.