Study population and design
The study population was pregnant women attending antenatal clinics (ANCs) at the Shoklo Malaria Research Unit (SMRU) (20, 21), where malaria transmission is low and peaks between May and September. The ANCs were located in the Maela refugee camps (22).
Details of the nested case-control study design and procedures have been published previously (18). In brief, participants were identified from 1000 Karen women who were enrolled in a
placebo randomized controlled trial of chloroquine prophylaxis against P. vivax infection during pregnancy from November 1998 through January 2000 (23). Samples were obtained weekly from the women for Plasmodium species infection detection by microscopic examination of blood smears and fortnightly for serum sample collection. Case subjects were women with Plasmodium infection detected by light microscopy at any time during pregnancy during the trial (n = 136). Of the 864 women with no detectable parasitemia at any time while pregnant during the trial, 331 were randomly selected to be control subjects (3:1 ratio).
Antibody determination
All available serum samples from the 136 case subjects were selected. A subset of 115 control subjects was selected for longitudinal antibody determination based on IgG responses to schizont extract at enrollment. The 115 controls were selected as follows. All available control enrollment samples (320 of the 331 randomly selected controls had serum samples measured at enrollment) were tested for total IgG in response to schizont extract. A cut-off threshold for seropositivity to schizont extract was set to the mean + 3 standard deviations of the IgG responses to schizont extract for 8 negative controls (non-exposed Melbourne donors). The subset of 115 controls consisted of 78 individuals seropositive to schizont extract at enrollment together with 37 randomly selected individuals that were seronegative to schizont extract at enrollment (Fig. 1). See Supplementary material, Fowkes et al. 2012 (18) for further details. High throughput enzyme-linked immunosorbent assay (ELISA) was used to determine the total IgG titer (measured as optical density (OD) values) of P. falciparum merozoite antigens (apical membrane antigen, PfAMA1), erythrocyte binding antigen 175 (PfEBA175; region 3–5, merozoite surface protein, PfMSP2, PfMSP3), schizont extract, PfVAR2CSA (DBL5ɛ domain), and P. vivax merozoite antigen (PvAMA1) (Supplementary material, Fowkes et al. 2012 (18)).
Statistical Analysis
Patient characteristics at baseline were summarised using median (25th – 75th percentiles) for continuous variables or frequency (%) for categorical variables.
A multivariate mixture linear mixed model was used to identify clusters (i.e., latent classes) of pregnant women that have similar antibody responses to all six antigens over gestational age (24). To construct a multivariate mixture linear mixed effects model, first a linear mixed effects model was specified for each of the six antibody responses. The following covariates were included as fixed effects for each antibody response: age (years), primigravidae (1 if primigravidae and 0 if multigravida), treatment arm (1 if given chloroquine (CQ) as prophylaxis at enrolment and 0 if given a placebo) and having a history of malaria prior to enrolment (1 if exposed to malaria at least once prior to enrolment and 0 otherwise). To capture the between subject variability in the six antibody responses over gestational age, a random intercept and random slope for gestational age were included in the linear mixed effects model for each antibody response. The random intercepts and slopes for each response and woman (i.e., 12 random effects per woman) are assumed to follow a mixture of multivariate normal distributions.
The mixAK package in R (25) was used to fit the multivariate mixture linear mixed effects model to the six antibody response profiles available from each of the 250 women (135 cases and 115 controls) in this study. The mixAK package adopts a Bayesian approach to inference and implements a block Gibbs sampler with Metropolis-Hastings steps to sample parameter values from the posterior distribution (Supplementary material, Komárek and Komárková (2013, Appendix B) (24)). Weakly informative prior hyperparameters in the mixAK package were used (Supplementary material, Komárek and Komárková (2013, Appendix A) (24)). Two chains were initialised. The first 500 parameter values sampled for each chain were discarded as burn-in and an additional 5,000,000 parameter values (in total for both chains) were sampled after burn-in. Every 50th iteration after burin-in was kept, resulting in 100,000 (50,000 per chain) samples per parameter for calculation of posterior summaries. Results are presented as the posterior median (50th percentile) and 95% credible interval, calculated as the 2.5th and 97.5th percentiles of the 100,000 samples for each parameter. Traceplots were examined to assess whether the 50,000 parameter draws from each chain had appropriately converged.
The number of clusters was selected by fitting a mixture model assuming each of 1–4 clusters. The number of clusters was selected according to the model that produced the lowest penalized expected deviance and/or greatest shift of the posterior distribution of deviances to lower values (24).
The posterior probability of a woman belonging to a cluster (posterior class probability) was calculated at each iteration of the fitting algorithm and these probabilities were used to assign a woman to a cluster as follows. First, a woman was assigned to the cluster which had the highest median posterior class probability. Second, the woman remained in the cluster if the lower limit of the 95% credible interval for the posterior class probability exceeded 0.5; otherwise, the woman was considered unclassified (Supplementary methods, Sect. 4).
The variable-specific entropy was calculated to identify the antibody responses that have the highest influence on the classification of the women into clusters. The variable-specific entropy indicates how well the antibody response to a single antigen predicts the classification based on antibody responses to all six antigens, and ranges from 0–1 (26). Antibody responses with
variable-specific entropy values close to 1 drive the classification of women into clusters (Supplementary methods, Sect. 6).
To compare and identify the best antibodies for classifying women as being a case (exposed to malaria during pregnancy) or control, additional univariate and pairwise multivariate mixture linear mixed-effects modelling were performed with the number of clusters set at two groups, and the proportion of cases and controls classified in the high and low antibody response groupings calculated.