Approximate likelihood-based estimation method of multiple-type pathogen interactions: An application to longitudinal pneumococcal carriage data

While the serotypes of Streptococcus pneumoniae are known to compete during colonization in human hosts, our knowledge of how competition occurs is still incomplete. New insights of pneumococcal between‐type competition could be generated from carriage data obtained by molecular‐based detection methods, which record more complete sets of serotypes involved in co‐carriage than when detection is done by culture. Here, we develop a Bayesian estimation method for inferring between‐type interactions from longitudinal data recording the presence/absence of the types at discrete observation times. It allows inference from data containing co‐carriage of two or more serotypes, which is often the case when pneumococcal presence is determined by molecular‐based methods. The computational burden posed by the increased number of types detected in co‐carriage is addressed by approximating the likelihood under a multi‐state model with the likelihood of only those trajectories with minimum number of acquisition and clearance events between observation times. The proposed method's performance was validated on simulated data. The estimates of the interaction parameters of acquisition and clearance were unbiased in settings with short sampling intervals between observation times. With less frequent sampling, the estimates of the interaction parameters became more biased, but their ratio, which summarizes the total interaction, remained unbiased. Confounding due to unobserved heterogeneity in exposure could be corrected by including individual‐level random effects. In an application to empirical data about pneumococcal carriage in infants, we found new evidence for between‐serotype competition in clearance, although the effect size was small.

Pneumococcal Acquisition Among Infants Exposed to HIV in Rural Malawi: A Longitudinal Household Study

The prevalence of Streptococcus pneumoniae (pneumococcus) carriage is higher in adults who are infected with human immunodeficiency virus (HIV) than in adults who are not. We hypothesized that infants exposed to HIV become carriers of nasopharyngeal pneumococcus earlier and more frequently than infants who are not exposed to HIV. We compared infant pneumococcal acquisition by maternal HIV status and household exposure in Karonga District, Malawi, in 2009–2011, before the introduction of pneumococcal conjugate vaccine. Nasopharyngeal swabs were collected every 4–6 weeks in the first year of life from infants with known HIV-exposure status, their mothers, and other household members. We studied infant pneumococcal acquisition by maternal HIV status, serotype-specific household exposure, and other risk factors, including seasonality. We recruited 54 infants who were exposed to HIV and 131 infants who were not. There was no significant difference in pneumococcal acquisition by maternal HIV status (adjusted rate ratio (aRR) = 1.00, 95% confidence interval (CI): 0.87, 1.15). Carriage by the mother was associated with greater acquisition of the same serotype (aRR = 3.09, 95% CI: 1.47, 6.50), but the adjusted population attributable fraction was negligible (1.9%, 95% CI: 0.0, 4.3). Serotype-specific exposure to children under 5 years of age was associated with higher acquisition (aRR = 4.30, 95% CI: 2.80, 6.60; adjusted population attributable fraction = 8.8%, 95% CI: 4.0, 13.4). We found no evidence to suggest that maternal HIV infection would affect the impact of pneumococcal vaccination on colonization in this population.

Choosing between 7-, 10- and 13-valent pneumococcal conjugate vaccines in childhood: a review of economic evaluations (2006-2014)

BACKGROUND

Seven-valent pneumococcal conjugate vaccines (PCV7) have been used in children for more than a decade. Given the observed increase in disease caused by pneumococcal serotypes not covered by PCV7, an increasing number of countries are switching from 7-valent to 10- and 13-valent PCVs ("PCV10" and "PCV13"). Economic evaluations are important tools to inform decisions and price negotiations to make such a switch.

OBJECTIVE

This review aims to provide a critical assessment of economic evaluations involving PCV10 or PCV13, published since 2006.

METHODS

We searched Scopus, ISI Web of Science (SCI and SSCI) and Pubmed to retrieve, select and review relevant studies, which were archived between 1st January 2006 and 31st January 2014. The review protocol involved standard extraction of assumptions, methods, results and sponsorships from the original studies.

RESULTS

Sixty-three economic evaluations on PCVs published since January 2006 were identified. About half of these evaluated PCV10 and/or PCV13, the subject of this review. At current prices, both PCV13 and PCV10 were likely judged preferable to PCV7. However, the combined uncertainty related to price differences, burden of disease, vaccine effectiveness, herd and serotype replacement effects determine the preference base for either PCV10 or PCV13. The pivotal assumptions and results of these analyses also depended on which manufacturer sponsored the study.

CONCLUSION

A more thorough exploration of uncertainty should be made in future analyses on this subject, as we lack understanding to adequately model herd and serotype replacement effects to reliably predict the population impact of PCVs. The introduction of further improved PCVs in an environment of evolving antibiotic resistance and under the continuing influence of previous PCVs implies that the complexity and data requirements for relevant analyses will further increase. Decision makers using these analyses should not just rely on an analysis from a single manufacturer.

Dynamics of pneumococcal transmission in vaccine-naive children and their HIV-infected or HIV-uninfected mothers during the first 2 years of life

Pneumococcal vaccine-naïve mother-child dyads in South Africa had nasopharyngeal swabs taken 9 times within the first 2 years of the children's lives between January 2007 and May 2009. To quantify the strength of the association of serotype-specific carriage in mother-child dyads, a stochastic transmission model was fitted to the data. Children were more susceptible to individual serotypes included in the 7-valent pneumococcal conjugate vaccine (PCV7) transmitted by their mothers than vice versa; however, children infected their mothers with these serotypes more frequently than mothers infected children. The child-to-mother steady-state forces of pneumococcal acquisition were between 0.36 and 3.29 (per 1,000 days) compared with 0.06-0.51 for mother-to-child transmission. Although children of mothers infected with human immunodeficiency virus were more often exposed to PCV7 serotypes by their mothers, their risk of acquisition remained low compared with the risk of child-to-mother transmission. Mothers acquired pneumococci at lower rates (per 1,000 days) from unmeasured exposure within families and in the wider community (range, 0.12-1.69 per 1,000 days) than did children (range, 1.10-5.21 per 1,000 days). Pneumococcal immunization of young children is expected to have an indirect effect of reducing PCV7 serotype maternal colonization and possibly disease even in settings such as ours, in which there is a high prevalence of human immunodeficiency virus-infected mothers.

Comparative analysis of Streptococcus pneumoniae transmission in Portuguese and Finnish day-care centres

Background

Day-care centre (DCC) attendees play a central role in maintaining the circulation of Streptococcus pneumoniae (pneumococcus) in the population. The prevalence of pneumococcal carriage is highest in DCC attendees but varies across countries and is found to be consistently lower in Finland than in Portugal. We compared key parameters underlying pneumococcal transmission in DCCs to understand which of these contributed to the observed differences in carriage prevalence.

Methods

Longitudinal data about serotype-specific carriage in DCC attendees in Portugal (47 children in three rooms; mean age 2 years; range 1–3 years) and Finland (91 children in seven rooms; mean age 4 years; range 1–7 years) were analysed with a continuous-time event history model in a Bayesian framework. The monthly rates of within-room transmission, community acquisition and clearing carriage were estimated.

Results

The posterior mean of within-room transmission rate was 1.05 per month (Portugal) vs. 0.63 per month (Finland). The smaller rate of clearance in Portugal (0.57 vs. 0.73 per month) is in accordance with the children being younger. The overall community rate of acquisition was larger in the Portuguese setting (0.25 vs. 0.11 per month), in agreement with that the groups belonged to a larger DCC. The model adequately predicted the observed levels of carriage prevalence and longitudinal patterns in carriage acquisition and clearance.

Conclusions

The difference in prevalence of carriage (61% in Portuguese vs. 26% among Finnish DCC attendees) was assigned to the longer duration of carriage in younger attendees and a significantly higher rate of within-room transmission and community acquisition in the Portuguese setting.

Influenza infection rates, measurement errors and the interpretation of paired serology

Serological studies are the gold standard method to estimate influenza infection attack rates (ARs) in human populations. In a common protocol, blood samples are collected before and after the epidemic in a cohort of individuals; and a rise in haemagglutination-inhibition (HI) antibody titers during the epidemic is considered as a marker of infection. Because of inherent measurement errors, a 2-fold rise is usually considered as insufficient evidence for infection and seroconversion is therefore typically defined as a 4-fold rise or more. Here, we revisit this widely accepted 70-year old criterion. We develop a Markov chain Monte Carlo data augmentation model to quantify measurement errors and reconstruct the distribution of latent true serological status in a Vietnamese 3-year serological cohort, in which replicate measurements were available. We estimate that the 1-sided probability of a 2-fold error is 9.3% (95% Credible Interval, CI: 3.3%, 17.6%) when antibody titer is below 10 but is 20.2% (95% CI: 15.9%, 24.0%) otherwise. After correction for measurement errors, we find that the proportion of individuals with 2-fold rises in antibody titers was too large to be explained by measurement errors alone. Estimates of ARs vary greatly depending on whether those individuals are included in the definition of the infected population. A simulation study shows that our method is unbiased. The 4-fold rise case definition is relevant when aiming at a specific diagnostic for individual cases, but the justification is less obvious when the objective is to estimate ARs. In particular, it may lead to large underestimates of ARs. Determining which biological phenomenon contributes most to 2-fold rises in antibody titers is essential to assess bias with the traditional case definition and offer improved estimates of influenza ARs.

Each year, seasonal influenza is responsible for about three to five million severe illnesses and about 250,000 to 500,000 deaths worldwide. In order to assess the burden of disease and guide control policies, it is important to quantify the proportion of people infected by an influenza virus each year. Since infection usually leaves a “signature” in the blood of infected individuals (namely a rise in antibodies), a standard protocol consists in collecting blood samples in a cohort of subjects and determining the proportion of those who experienced such rise. However, because of inherent measurement errors, only large rises are accounted for in the standard 4-fold rise case definition. Here, we revisit this 70 year old and widely accepted and applied criterion. We present innovative statistical techniques to better capture the impact of measurement errors and improve our interpretation of the data. Our analysis suggests that the number of people infected by an influenza virus each year might be substantially larger than previously thought, with important implications for our understanding of the transmission and evolution of influenza – and the nature of infection.