Current crisis or artifact of surveillance: insights into rebound chlamydia rates from dynamic modelling

Real-Time Epidemiology and Acute Care Need Monitoring and Forecasting for COVID-19 via Bayesian Sequential Monte Carlo-Leveraged Transmission Models

COVID-19 transmission models have conferred great value in informing public health understanding, planning, and response. However, the pandemic also demonstrated the infeasibility of basing public health decision-making on transmission models with pre-set assumptions. No matter how favourably evidenced when built, a model with fixed assumptions is challenged by numerous factors that are difficult to predict. Ongoing planning associated with rolling back and re-instituting measures, initiating surge planning, and issuing public health advisories can benefit from approaches that allow state estimates for transmission models to be continuously updated in light of unfolding time series. A model being continuously regrounded by empirical data in this way can provide a consistent, integrated depiction of the evolving underlying epidemiology and acute care demand, offer the ability to project forward such a depiction in a fashion suitable for triggering the deployment of acute care surge capacity or public health measures, and support quantitative evaluation of tradeoffs associated with prospective interventions in light of the latest estimates of the underlying epidemiology. We describe here the design, implementation, and multi-year daily use for public health and clinical support decision-making of a particle-filtered COVID-19 compartmental model, which served Canadian federal and provincial governments via regular reporting starting in June 2020. The use of the Bayesian sequential Monte Carlo algorithm of particle filtering allows the model to be regrounded daily and adapt to new trends within daily incoming data-including test volumes and positivity rates, endogenous and travel-related cases, hospital census and admissions flows, daily counts of dose-specific vaccinations administered, measured concentration of SARS-CoV-2 in wastewater, and mortality. Important model outputs include estimates (via sampling) of the count of undiagnosed infectives, the count of individuals at different stages of the natural history of frankly and pauci-symptomatic infection, the current force of infection, effective reproductive number, and current and cumulative infection prevalence. Following a brief description of the model design, we describe how the machine learning algorithm of particle filtering is used to continually reground estimates of the dynamic model state, support a probabilistic model projection of epidemiology and health system capacity utilization and service demand, and probabilistically evaluate tradeoffs between potential intervention scenarios. We further note aspects of model use in practice as an effective reporting tool in a manner that is parameterized by jurisdiction, including the support of a scripting pipeline that permits a fully automated reporting pipeline other than security-restricted new data retrieval, including automated model deployment, data validity checks, and automatic post-scenario scripting and reporting. As demonstrated by this multi-year deployment of the Bayesian machine learning algorithm of particle filtering to provide industrial-strength reporting to inform public health decision-making across Canada, such methods offer strong support for evidence-based public health decision-making informed by ever-current articulated transmission models whose probabilistic state and parameter estimates are continually regrounded by diverse data streams.

Rapid-cycle systems modeling to support evidence-informed decision-making during system-wide implementation

Background

To “model and simulate change” is an accepted strategy to support implementation at scale. Much like a power analysis can inform decisions about study design, simulation models offer an analytic strategy to synthesize evidence that informs decisions regarding implementation of evidence-based interventions. However, simulation modeling is under-utilized in implementation science. To realize the potential of simulation modeling as an implementation strategy, additional methods are required to assist stakeholders to use models to examine underlying assumptions, consider alternative strategies, and anticipate downstream consequences of implementation. To this end, we propose Rapid-cycle Systems Modeling (RCSM)—a form of group modeling designed to promote engagement with evidence to support implementation. To demonstrate its utility, we provide an illustrative case study with mid-level administrators developing system-wide interventions that aim to identify and treat trauma among children entering foster care.

Methods

RCSM is an iterative method that includes three steps per cycle: (1) identify and prioritize stakeholder questions, (2) develop or refine a simulation model, and (3) engage in dialogue regarding model relevance, insights, and utility for implementation. For the case study, 31 key informants were engaged in step 1, a prior simulation model was adapted for step 2, and six member-checking group interviews (n = 16) were conducted for step 3.

Results

Step 1 engaged qualitative methods to identify and prioritize stakeholder questions, specifically identifying a set of inter-related decisions to promote implementing trauma-informed screening. In step 2, the research team created a presentation to communicate key findings from the simulation model that addressed decisions about programmatic reach, optimal screening thresholds to balance demand for treatment with supply, capacity to start-up and sustain screening, and availability of downstream capacity to provide treatment for those with indicated need. In step 3, member-checking group interviews with stakeholders documented the relevance of the model results to implementation decisions, insight regarding opportunities to improve system performance, and potential to inform conversations regarding anticipated implications of implementation choices.

Conclusions

By embedding simulation modeling in a process of stakeholder engagement, RCSM offers guidance to realize the potential of modeling not only as an analytic strategy, but also as an implementation strategy.

The Use of Mathematical Models of Chlamydia Transmission to Address Public Health Policy Questions: A Systematic Review

BACKGROUND

Mathematical models of chlamydia transmission can help inform disease control policy decisions when direct empirical evaluation of alternatives is impractical. We reviewed published chlamydia models to understand the range of approaches used for policy analyses and how the studies have responded to developments in the field.

METHODS

We performed a literature review by searching Medline and Google Scholar (up to October 2015) to identify publications describing dynamic chlamydia transmission models used to address public health policy questions. We extracted information on modeling methodology, interventions, and key findings.

RESULTS

We identified 47 publications (including two model comparison studies), which reported collectively on 29 distinct mathematical models. Nine models were individual-based, and 20 were deterministic compartmental models. The earliest studies evaluated the benefits of national-level screening programs and predicted potentially large benefits from increased screening. Subsequent trials and further modeling analyses suggested the impact might have been overestimated. Partner notification has been increasingly evaluated in mathematical modeling, whereas behavioral interventions have received relatively limited attention.

CONCLUSIONS

Our review provides an overview of chlamydia transmission models and gives a perspective on how mathematical modeling has responded to increasing empirical evidence and addressed policy questions related to prevention of chlamydia infection and sequelae.

Possible changes in the transmissibility of trachoma following MDA and transmission reduction: implications for the GET2020 goals

BACKGROUND

The role of mass drug administration (MDA) and the implementation of transmission reduction measures are essential to successfully control and eliminate a wide range of NTDs, including the ocular disease trachoma. Immunity to trachoma infection acts by reducing the duration of an individual's infectious period and by reducing their infectivity with each successive infection.

METHODS

In this study, we use a model of trachoma infection, which includes population immunity, to explore the impact of treatment and transmission reduction measures on trachoma prevalence. Specifically, we investigate the possibility of increasing transmissibility of trachoma arising as MDA and transmission reduction measures are scaled up in endemic settings.

RESULTS

We demonstrate this increase in transmissibility by calculating the effective reproduction number during several simulated control programmes and show that it is related to a decrease in the level of immunity in the population.

CONCLUSIONS

This effect should be studied in the field by measuring the rate of return of infection and disease in at least two separate age groups. If the decline of population immunity is operating, it should be accounted for when planning for the GET2020 goal of eliminating blinding trachoma by 2020.

Pelvic inflammatory disease: identifying research gaps--proceedings of a workshop sponsored by Department of Health and Human Services/National Institutes of Health/National Institute of Allergy and Infectious Diseases, November 3-4, 2011

In November 2011, the National Institutes of Health convened a workshop of basic researchers, epidemiologists, and clinical experts in pelvic inflammatory disease to identify research gaps hindering advances in diagnosis, treatment, and prevention. This article summarizes the presentations, discussions, and conclusions of this group and highlights significant controversies that reveal aspects of pelvic inflammatory disease research that would most greatly benefit from the application of newer molecular, immunologic, and radiologic techniques. Multiple limitations to performing new clinical trials exist; however, emerging data from ongoing clinical trials will add to the current body of knowledge regarding prevention and treatment strategies. In addition, use of established health care databases could serve as a valuable tool for performance of unbiased epidemiologic outcome studies.

Advances in sampling and screening for chlamydia

Chlamydia is the most commonly diagnosed bacterial sexually transmitted infection in the developed world, with diagnosis rates continuing to increase each year. As chlamydia is largely asymptomatic, screening and treatment is the main way to detect cases and reduce transmission. Recent advances in self-collected specimens and laboratory tests has made chlamydia screening easier to implement as well as possible in nonclinical settings. This review will discuss new approaches to specimen collection and how these have expanded opportunities for reaching target populations for chlamydia screening. Furthermore, it will discuss how advanced molecular microbiological methods can be used with self-collected specimens to further our knowledge of the epidemiology of chlamydia and the dynamics of transmission.

Chlamydia screening practices among physicians and community nurses in Yukon, Canada

BACKGROUND

Yukon, a territory in northern Canada, has one of the highest reported sexually transmitted chlamydia infection rates in the country.

OBJECTIVE

We examined screening practices among physicians and community nurses to elucidate factors that may be contributing to the high rates.

DESIGN

Cross-sectional survey.

METHODS

A questionnaire was distributed to all physicians in Yukon and all community nurses in Yukon's communities. We surveyed sexual health assessment frequency, chlamydia testing frequency and barriers to screening. Comparison of physician testing practices was performed to another Canadian jurisdiction, which previously undertook a similar survey. Survey results were compared to the available laboratory data in Yukon.

RESULTS

Eligible physicians and nurses, 79% and 77%, respectively, participated in the survey. Physicians tested 15 to 24-year-old females more frequently than 15 to 24-year-old males for chlamydia (p = 0.007). Physicians who asked sexual health assessment questions were more likely to test for chlamydia in both females (p < 0.001) and males (p = 0.032). More physicians screened females based on risk factors compared to males. General practice physicians in Yukon were more likely to test females for chlamydia than general practice physicians in Toronto, Canada (p < 0.001). Community nurses had different testing patterns than physicians, with a lower overall frequency of testing, equal frequency of testing males and females, and in applying risk factor-based screening to both males and females. Barriers to screening included testing causing patient discomfort, patients reluctant to discuss screening, health provider uncomfortable conducting sexually transmitted infection tests and sexual health assessments, among others. Laboratory data in Yukon appear to confirm provider screening patterns.

CONCLUSIONS

This survey provides valuable information on health provider screening patterns. We have some evidence which suggests that chlamydia testing rates may be higher among patients seen by physicians in Yukon in comparison to another Canadian jurisdiction. However, more consistent application of optimal screening methods with support to "start the conversation" around sexual health may assist in overcoming barriers to screening and in addressing Yukon's high rate of chlamydia.

Dynamic transmission modeling: a report of the ISPOR-SMDM Modeling Good Research Practices Task Force Working Group-5

The transmissible nature of communicable diseases is what sets them apart from other diseases modeled by health economists. The probability of a susceptible individual becoming infected at any one point in time (the force of infection) is related to the number of infectious individuals in the population, will change over time, and will feed back into the future force of infection. These nonlinear interactions produce transmission dynamics that require specific consideration when modeling an intervention that has an impact on the transmission of a pathogen. Best practices for designing and building these models are set out in this paper.

Dynamic transmission modeling: a report of the ISPOR-SMDM Modeling Good Research Practices Task Force--5

The transmissible nature of communicable diseases is what sets them apart from other diseases modeled by health economists. The probability of a susceptible individual becoming infected at any one point in time (the force of infection) is related to the number of infectious individuals in the population, will change over time, and will feed back into the future force of infection. These nonlinear interactions produce transmission dynamics that require specific consideration when modeling an intervention that has an impact on the transmission of a pathogen. Best practices for designing and building these models are set out in this article.

The recall response induced by genital challenge with Chlamydia muridarum protects the oviduct from pathology but not from reinfection

The significant morbidities of ectopic pregnancy and infertility observed in women after Chlamydia trachomatis genital infection result from ascension of the bacteria from the endocervix to the oviduct, where an overly aggressive inflammatory response leads to chronic scarring and Fallopian tube obstruction. A vaccine to prevent chlamydia-induced disease is urgently needed. An important question for vaccine development is whether sterilizing immunity at the level of the oviduct is essential for protection because of the possibility that a chlamydial component drives a deleterious anamnestic T cell response upon oviduct reinfection. We show that mice inoculated with attenuated plasmid-cured strains of Chlamydia muridarum are protected from oviduct pathology upon challenge with wild-type C. muridarum Nigg despite induction of a response that did not prevent reinfection of the oviduct. Interestingly, repeated abbreviated infections with Nigg also elicited recall responses that protected the oviduct from pathology despite low-level reinfection of this vulnerable tissue site. Challenged mice displayed significant decreases in tissue infiltration of inflammatory leukocytes with marked reductions in frequencies of neutrophils but significant increases in frequencies of CD4 Th1 and CD8 T cells. An anamnestic antibody response was also detected. These data indicate that exposure to a live attenuated chlamydial vaccine or repeated abbreviated genital infection with virulent chlamydiae promotes anamnestic antibody and T cell responses that protect the oviduct from pathology despite a lack of sterilizing immunity at the site.

Systems science methods in public health: dynamics, networks, and agents

Complex systems abound in public health. Complex systems are made up of heterogeneous elements that interact with one another, have emergent properties that are not explained by understanding the individual elements of the system, persist over time, and adapt to changing circumstances. Public health is starting to use results from systems science studies to shape practice and policy, for example in preparing for global pandemics. However, systems science study designs and analytic methods remain underutilized and are not widely featured in public health curricula or training. In this review we present an argument for the utility of systems science methods in public health, introduce three important systems science methods (system dynamics, network analysis, and agent-based modeling), and provide three case studies in which these methods have been used to answer important public health science questions in the areas of infectious disease, tobacco control, and obesity.

Pertussis resurgence in Toronto, Canada: a population-based study including test-incidence feedback modeling

BACKGROUND

Pertussis continues to challenge medical professionals; recently described increases in incidence may be due to age-cohort effects, vaccine effectiveness, or changes in testing patterns. Toronto, Canada has recently experienced increases in pertussis incidence, and provides an ideal jurisdiction for evaluating pertussis epidemiology due to centralized testing. We evaluated pertussis trends in Toronto using all available specimen data, which allowed us to control for changing testing patterns and practices.

METHODS

Data included all pertussis culture and PCR test records for Greater Toronto from 1993 to 2007. We estimated incidence trends using Poisson regression models; complex relationships between disease incidence and test submission were explored with vector autoregressive models.

RESULTS

From 1993 to 2007, 26988 specimens were submitted for testing; 2545 (9.4%) were positive. Pertussis incidence was 2 per 100,000 from 1993 to 2004 and increased to 10 per 100,000 from 2005-2007, with a concomitant 6-fold surge in test specimen submissions after the introduction of a new, more sensitive PCR assay. The relative change in incidence was less marked after adjustment for testing volumes. Bidirectional feedbacks between test positivity and test submissions were identified.

CONCLUSIONS

Toronto's recent surge in pertussis reflects a true increase in local disease activity; the apparent size of the outbreak has likely been magnified by increasing use of pertussis testing by clinicians, and by improved test sensitivity since 2005. These findings may be applicable to changes in pertussis epidemiology that have been noted elsewhere in North America.

Surveillance of community genital Chlamydia trachomatis testing in the East of England, 2008-2010

BACKGROUND

Widespread testing for chlamydia is expected to result in a reduction in prevalence. In 2008, coverage indicators introduced by the Department of Health (DH) required collection and submission of all tests performed outside of genitourinary medicine clinics. No mechanism existed to collect community-based tests conducted outside of the National Chlamydia Screening Programme. The Health Protection Agency Regional Epidemiology Unit in the East of England (EoE) set up a new system to routinely collect and submit these tests on behalf of the regional Primary Care Organizations (PCOs).

METHODS

Testing data were requested from all laboratories commissioned to undertake chlamydia testing by EoE PCOs. Data were imported into a bespoke Structured Query Language server database and automated data processing routines were run. Data fulfilling national criteria were submitted for inclusion in the DH indicators.

RESULTS

High-quality data were submitted to set deadlines with minimum impact on laboratories. Completeness of data variables varied by laboratory and by variable type. After complex data processing, 96% of laboratory reported tests in the 15-24 year age range were eligible for submission.

CONCLUSIONS

This centralized method of data collection provides high-quality data, allowing for further analysis, which can be used to inform improvements in health care. These methods could be transferred to any of the hundreds of organisms for which similar laboratory data exist.

Management of Chlamydia trachomatis genital tract infection: screening and treatment challenges

Chlamydia trachomatis is a prevalent sexually transmitted infection that can lead to serious reproductive morbidity. Management and control of C. trachomatis is a challenge, largely due to its asymptomatic nature and our incomplete understanding of its natural history. Although chlamydia screening programs have been implemented worldwide, several countries have observed increasing rates of reported chlamydia cases. We reviewed the literature relating to the long-term complications of C. trachomatis, as well as screening strategies, treatment, and prevention strategies for reducing chlamydia in the population. Articles from 1950-2010 were identified through a Medline search using the keyword "Chlamydia trachomatis" combined with "screening", "pelvic inflammatory disease", "endometritis", "salpingitis", "infertility", "ectopic pregnancy", "urethritis", "epididymitis", "proctitis", "prostatitis", "reinfection", "cost-effectiveness", "treatment", "vaccines", or "prevention". Progression of C. trachomatis varies, and recurrent infections are common. Currently, there is limited evidence on the effectiveness of chlamydia screening. Higher quality studies are needed to determine the efficacy of more frequent screening, on a broader range of sequelae, including infertility and ectopic pregnancy, in addition to pelvic inflammatory disease. Studies should focus on delineating the natural history of recurrent infections, paying particular attention to treatment failures. Furthermore, alternatives to screening, such as vaccines, should continue to be explored.