Modeling Biphasic Environmental Decay of Pathogens and Implications for Risk Analysis

As the appreciation for the importance of the environment in infectious disease transmission has grown, so too has interest in pathogen fate and transport. Fate has been traditionally described by simple exponential decay, but there is increasing recognition that some pathogens demonstrate a biphasic pattern of decay-fast followed by slow. While many have attributed this behavior to population heterogeneity, we demonstrate that biphasic dynamics can arise through a number of plausible mechanisms. We examine the identifiability of a general model encompassing three such mechanisms: population heterogeneity, hardening off, and the existence of viable-but-not-culturable states. Although the models are not fully identifiable from longitudinal sampling studies of pathogen concentrations, we use a differential algebra approach to determine identifiable parameter combinations. Through case studies using Cryptosporidium and Escherichia coli, we show that failure to consider biphasic pathogen dynamics can lead to substantial under- or overestimation of disease risks and pathogen concentrations, depending on the context. More reliable models for environmental hazards and human health risks are possible with an improved understanding of the conditions in which biphasic die-off is expected. Understanding the mechanisms of pathogen decay will ultimately enhance our control efforts to mitigate exposure to environmental contamination.

Age Effects and Temporal Trends in HPV-Related and HPV-Unrelated Oral Cancer in the United States: A Multistage Carcinogenesis Modeling Analysis

Differences in prognosis in HPV-positive and HPV-negative oral (oropharyngeal and oral cavity) squamous cell carcinomas (OSCCs) and increasing incidence of HPV-related cancers have spurred interest in demographic and temporal trends in OSCC incidence. We leverage multistage clonal expansion (MSCE) models coupled with age-period-cohort (APC) epidemiological models to analyze OSCC data in the SEER cancer registry (1973-2012). MSCE models are based on the initiation-promotion-malignant conversion paradigm in carcinogenesis and allow for interpretation of trends in terms of biological mechanisms. APC models seek to differentiate between the temporal effects of age, period, and birth cohort on cancer risk. Previous studies have looked at the effect of period and cohort on tumor initiation, and we extend this to compare model fits of period and cohort effects on each of tumor initiation, promotion, and malignant conversion rates. HPV-related, HPV-unrelated except oral tongue, and HPV-unrelated oral tongue sites are best described by placing period and cohort effects on the initiation rate. HPV-related and non-oral-tongue HPV-unrelated cancers have similar promotion rates, suggesting similar tumorigenesis dynamics once initiated. Estimates of promotion rates at oral tongue sites are lower, corresponding to a longer sojourn time; this finding is consistent with the hypothesis of an etiology distinct from HPV or alcohol and tobacco use. Finally, for the three subsite groups, men have higher initiation rates than women of the same race, and black people have higher promotion than white people of the same sex. These differences explain part of the racial and sex differences in OSCC incidence.

Trends in HPV cervical and seroprevalence and associations between oral and genital infection and serum antibodies in NHANES 2003-2012

BACKGROUND

HPV infects multiple sites in the epithelium, including the genitals and oral cavity. The relation between genital and oral infections and serum antibodies can help explain the natural history and epidemiology of HPV.

METHODS

We analyzed HPV data from NHANES derived from self-collected vaginal swabs (women ages 14-59, 2003-12), oral rinses (men and women 14-69, 2009-12), and serum (men and women 14-59, 2003-10).

RESULTS

Type-concordance of cervicogenital and oral infections in women was found to vary widely by age. Prevalence of oral infections with type-concordant antibodies was low but varied by sex: 0.2 % (95 % CI 0.0-0.8) for women vs 0.8 % (95 % CI 0.4-1.3) for men. Vaccination was associated with a reduced risk of cervicogenital infection for vaccine genotypes among ages 14-17 (0.2 (95 % CI 0.1-0.8)) and 18-24 (0.2 (95 % CI 0.1-0.3). Seroprevalence trends in women showed a dramatic increase for recent birth cohorts, likely due to vaccination. By contrast, trends for men remained relatively constant. Age-specific cervicogenital prevalence showed a consistent peak in the late teens and twenties. Relative cervicogenital prevalence has largely been decreasing since the 1940-50 birth cohort.

CONCLUSIONS

There are complex patterns in HPV prevalence trends and type-concordance across infection sites and serum antibodies. A multisite sampling scheme is needed to better understand the epidemiology and natural history of HPV.

Transmission heterogeneity and autoinoculation in a multisite infection model of HPV

The human papillomavirus (HPV) is sexually transmitted and can infect oral, genital, and anal sites in the human epithelium. Here, we develop a multisite transmission model that includes autoinoculation to study HPV and other multisite diseases. Under a homogeneous-contacts assumption, we analyze the basic reproduction number R0, as well as type and target reproduction numbers, for a two-site model. In particular, we find that R0 occupies a space between taking the maximum of next generation matrix terms for same site transmission and taking the geometric average of cross-site transmission terms in such a way that heterogeneity in the same-site transmission rates increases R0 while heterogeneity in the cross-site transmission decreases it. Additionally, autoinoculation adds considerable complexity to the form of R0. We extend this analysis to a heterosexual population, which additionally yields dynamics analogous to those of vector-host models. We also examine how these issues of heterogeneity may affect disease control, using type and target reproduction numbers.

The Dynamic Anaerobic Reactor & Integrated Energy System (DARIES) model: model development, validation, and sensitivity analysis

The Dynamic Anaerobic Reactor & Integrated Energy System (DARIES) model has been developed as a biogas and electricity production model of a dairy farm anaerobic digester system. DARIES, which incorporates the Anaerobic Digester Model No. 1 (ADM1) and simulations of both combined heat and power (CHP) and digester heating systems, may be run in either completely mixed or plug flow reactor configurations. DARIES biogas predictions were shown to be statistically coincident with measured data from eighteen full-scale dairy operations in the northeastern United States. DARIES biogas predictions were more accurate than predictions made by the U.S. AgSTAR model FarmWare 3.4. DARIES electricity production predictions were verified against data collected by the NYSERDA DG/CHP Integrated Data System. Preliminary sensitivity analysis demonstrated that DARIES output was most sensitive to influent flow rate, chemical oxygen demand (COD), and biodegradability, and somewhat sensitive to hydraulic retention time and digester temperature.

[Treatment of asthma in children: more than merely 'puffing']

Five children, four boys aged 6, 9, 12 and 13 years and one girl aged 6 years, had persistent asthmatic symptoms despite maintenance treatment with inhaled corticosteroids and short-acting bronchodilators on demand. One of them required the addition of a long-acting beta 2-agonist to become symptom-free. The other four patients did not need to step up their asthma medication after correction of poor inhaler technique, treatment of dysfunctional breathing, treatment of allergic rhinitis, and elimination of passive cigarette-smoke exposure, respectively. All current guidelines on the treatment of asthma in children advise, in case of persistent asthmatic symptoms despite inhaled corticosteroids and short-acting bronchodilators, the addition of long-acting beta 2-agonists. However, various factors may play a role in the persistence of asthma despite adequate therapy and these factors should be evaluated before stepping up the medication.

[Perinatal pertussis: from mother to child]

Two infants, a girl, aged four weeks, and a boy, aged three weeks, came to our attention with poor feeding and weight loss. Later the typical cough of pertussis appeared. Serological testing confirmed that both patients' mothers had recently had pertussis. One mother suffered from severe and typical coughing periods even throughout labour. Despite the vaccination program in the Netherlands, each year new-born infants with pertussis require hospitalisation. Pertussis during the neonatal period is seldom described. Adults can suffer from pertussis, even when they have been vaccinated in childhood. They then become contagious for unvaccinated infants. Pertussis during the neonatal period is an insidious disease with sometimes severe complications. If pertussis is suspected in mothers with new-born infants or pregnant women towards the end of the pregnancy, they should be treated with antibiotics to prevent pertussis in the new-born infant.