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Background: WHO initiated lymphatic filariasis (LF) elimination globally. Pekalongan District, as LF endemic area, started a program of mass drug administration (MDA) to combat LF in 2015. This study aimed to determine prevalence of Wuchereria bancrofti infection prior to the MDA. Methods: LF infection was detected by the existence of circulating filarial antigen (CFA) W. bancrofti using immunochromatographic card test (ICT). The study population consisted of 1404 elementary school (ES) students living in Pekalongan District. Overall, 1033 were selected as study subjects. Prevalence survey was also conducted on 436 general population in areas where infected students were found. Results: The subjects ranged from 7-17 yr old (mean 9.85±1.296) and equally distributed between both sexes. Prevalence of W. bancrofti infection was 1.98% in children. Infection was mostly found in older students (12 yr old), male, in 6th grade, but did not differ significantly (P=0.129, 0.376, and 0.212 respectively). On the other hand, distribution of infection was significantly different by school (P=0.009) and sub-district (P=0000). Most of children with LF infection were found in Tirto Sub District. In general population, the prevalence of W. bancrofti infection in Tirto was 4.4%. Proportion of infection in males (12.2%) was greater than females (3.8%), with 78.9% of positive cases were in adult over 20 yr old. Conclusion: Cases of W. bancrofti infection exist in Pekalongan District, both in children and adults. Implementation of MDA must be carefully monitored in order to achieve elimination target.

Background: Soil-transmitted helminths have been shown to have the immune regulatory capacity, which they use to enhance their long term survival within their host. As these parasites reside in the gastrointestinal tract, they might modulate the immune system through altering the gut bacterial composition. Although the relationships between helminth infections or the microbiome with the immune system have been studied separately, their combined interactions are largely unknown. In this study we aim to analyze the relationship between bacterial communities with cytokine response in the presence or absence of helminth infections. Results: For 66 subjects from a randomized placebo-controlled trial, stool and blood samples were available at both baseline and 21 months after starting three-monthly albendazole treatment. The stool samples were used to identify the helminth infection status and fecal microbiota composition, while whole blood samples were cultured to obtain cytokine responses to innate and adaptive stimuli. When subjects were free of helminth infection (helminth-negative), increasing proportions of Bacteroidetes was associated with lower levels of IL-10 response to LPS {estimate [95% confidence interval (CI)] −1.96 (−3.05, −0.87)}. This association was significantly diminished when subjects were helminth-infected (helminth positive) (p-value for the difference between helminth-negative versus helminth-positive was 0.002). Higher diversity was associated with greater IFN-γ responses to PHA in helminth-negative (0.95 (0.15, 1.75); versus helminth-positive [−0.07 (−0.88, 0.73), p-value = 0.056] subjects. Albendazole treatment showed no direct effect in the association between bacterial proportion and cytokine responses, although the Bacteroidetes’ effect on IL-10 responses to LPS tended downward in the albendazole-treated group [−1.74 (−4.08, 0.59)] versus placebo [−0.11 (−0.84, 0.62); p-value = 0.193]. Conclusion: We observed differences in the relationship between gut microbiome composition and immune responses, when comparing individuals infected or uninfected with geohelminths. Although these findings are part of a preliminary exploration, the data support the hypothesis that intestinal helminths may modulate immune responses, in unison with the gut microbiota. Trial Registration: ISRCTN, ISRCTN83830814. Registered 27 February 2008 — Retrospectively registered, http://www.isrctn.com/ISRCTN83830814.

Clustered overdispersed multivariate count data are challenging to model due to the presence of correlation within and between samples. Typically, the first source of correlation needs to be addressed but its quantification is of less interest. Here, we focus on the correlation between time points. In addition, the effects of covariates on the multivariate counts distribution need to be assessed. To fulfill these requirements, a regression model based on the Dirichlet-multinomial distribution for association between covariates and the categorical counts is extended by using random effects to deal with the additional clustering. This model is the Dirichlet-multinomial mixed regression model. Alternatively, a negative binomial regression mixed model can be deployed where the corresponding likelihood is conditioned on the total count. It appears that these two approaches are equivalent when the total count is fixed and independent of the random effects. We consider both subject-specific and categorical-specific random effects. However, the latter has a larger computational burden when the number of categories increases. Our work is motivated by microbiome data sets obtained by sequencing of the amplicon of the bacterial 16S rRNA gene. These data have a compositional structure and are typically overdispersed. The microbiome data set is from an epidemiological study carried out in a helminth-endemic area in Indonesia. The conclusions are as follows: time has no statistically significant effect on microbiome composition, the correlation between subjects is statistically significant, and treatment has a significant effect on the microbiome composition only in infected subjects who remained infected.

The main objective of this thesis is to improve the understanding of the role of helminth infections in the development of insulin resistance, hence type 2 diabetes, and to gain insight into the immunological mechanisms underlying this possible interaction. To this end, we initiated a large scale cluster randomized controlled trial, assessing the effect of anthelmintic treatment on insulin resistance and other metabolic, as well as immunological parameters, in a rural area of Indonesia. Deworming significantly reduced the prevalence of helminths, as well as infection intensity. Although treatment did not lead to an increase of whole-body insulin resistance at the community level, a significant increase in insulin resistance was observed among helminth-infected subjects. Furthermore, by comparing immune cells of helminth-infected Indonesians before and after treatment, we gained insight into the specific cell populations that participate in the type 2 and regulatory networks, and show that treatment affects specific cell subsets in these networks. Altogether, the studies described in this thesis show that helminth infections in humans, as well as the administration of helminth molecules in obese mice, have a beneficial effect on the insulin sensitivity, and have shed light on the immunomodulatory effects of helminths.

Background Microbiome studies suggest the presence of an interaction between the human gut microbiome and soil-transmitted helminth. Upon deworming, a complex interaction between the anthelminthic drug, helminths and microbiome composition might occur. To dissect this, we analyse the changes that take place in the gut bacteria profiles in samples from a double blind placebo controlled trial conducted in an area endemic for soil transmitted helminths in Indonesia. Methods Either placebo or albendazole were given every three months for a period of one and a half years. Helminth infection was assessed before and at 3 months after the last treatment round. In 150 subjects, the bacteria were profiled using the 454 pyrosequencing. Statistical analysis was performed cross-sectionally at pre-treatment to assess the effect of infection, and at post-treatment to determine the effect of infection and treatment on microbiome composition using the Dirichlet-multinomial regression model. Results At a phylum level, at pre-treatment, no difference was seen in microbiome composition in terms of relative abundance between helminth-infected and uninfected subjects and at post-treatment, no differences were found in microbiome composition between albendazole and placebo group. However, in subjects who remained infected, there was a significant difference in the microbiome composition of those who had received albendazole and placebo. This difference was largely attributed to alteration of Bacteroidetes. Albendazole was more effective against Ascaris lumbricoides and hookworms but not against Trichuris trichiura, thus in those who remained infected after receiving albendazole, the helminth composition was dominated by T. trichiura. Discussion We found that overall, albendazole does not affect the microbiome composition. However, there is an interaction between treatment and helminths as in subjects who received albendazole and remained infected there was a significant alteration in Bacteroidetes. This helminth-albendazole interaction needs to be studied further to fully grasp the complexity of the effect of deworming on the microbiome. Trial registration ISRCTN Registy, ISRCTN83830814., Author summary Studying the relationship between soil-transmitted helminthiasis and gut microbiota is becoming more important as both have been implicated in modulating immune system in various inflammatory diseases. However, findings of previous studies of the effect of helminth on the microbiome are inconsistent. In this study, an optimal design, a placebo-controlled anthelminthic trial was conducted to dissect the effect of helminths and anthelminthic treatment on gut microbial profile. In addition, a novel statistical model was used to analyse the association by taking into account the correlation structures between bacterial categories by applying multivariate analysis whereby the multiple testing correction is not needed.

Parasitic helminths are important organisms to study because their infections have both adverse and beneficial effects on the human host. Helminth infections are considered a burden, as these infections cause significant morbidity in a large proportion worldwide. However, helminth infections, by means of their ability to modify host immune responses can also provide protection against inflammatory diseases (inflammatory bowel disease, diabetes, and asthma). It is important to better understand the underlying mechanisms of these Yin (positive) and Yang (negative) consequences of helminth infections. The general objective of this thesis is to track helminths at different levels. On the one hand to improve the detection of helminth infections, essential for the studying helminths and the interaction with their human host. Moreover, a more sensitive diagnostics is instrumental for monitoring the distribution of helminth infections and to evaluate the helminth infections elimination program. On the other hand, to understand the mechanistic insights of the interplay between helminths and the host immune system results in priming of Th2 and regulatory T cell responses. This could contribute to the identification of targeted pathways to manipulate immune responses, as part of developing therapeutics to treat inflammatory disorders characterized by deregulated Th2 and/or Treg responses.

The main objective of this thesis is to improve understanding of the role of helminth infections in the development of insulin resistance (IR), hence Type 2 Diabetes (T2D), in the light of increasing urbanization in Indonesia. Our large-scale cluster-randomized controlled trial was performed in a rural area of Indonesia, which is endemic for soil-transmitted helminth (STH), and has been previously reported to have a low prevalence of IR and T2D. In STH-infected subjects, as assessed by microscopy, 12-month anthelmintic treatment increased IR, which was mediated by an increase in BMI and leptin to adiponectin ratio, as well as reduction in eosinophil count. Next, we also aimed to assess the different metabolic profile between populations living in rural and urban area, and to study the relative protective effect of rural environment to high-fat diet (HFD). In comparison to those living in rural area, individuals living in urban area had higher whole body IR, which was mainly mediated by the higher adiposity and leptin level, which were progressively increased with increased duration of time spent in urban area. Different environmental factors (including past or current exposure to STH) did not seem to affect the metabolic response to HFD intervention, independent from adiposity.

In this thesis we reported our investigations of the relationship between soil-transmitted helminths (STH) and a number of outcomes, in particular malaria, insulin resistance (a marker for type-2 diabetes (T2D)) and atherosclerosis (a marker for cardiovascular diseases (CVD)) on Flores island, Indonesia. In the study on Flores Island, the use of albendazole as a single dose at three monthly intervals decreased helminth infections significantly. However, this intensive deworming could not eliminate helminth infections. Despite no effect on malaria parasitemia and clinical symptoms was found, we noted that in vitro immune responses were improved after albendazole treatment and significant increases in malaria-specific and mitogen-induced tumor necrosis factor and interferon _ cytokine production were observed. We also reported that helminth infections are associated with improved insulin sensitivity and lower risk factors for CVD. A possible approach to confirm our results will be a long-term, well-powered, placebo controlled (adequate) anthelminthic trials to investigate asymptomatic malaria (in area where clinical malaria is highly prevalent); as well as to study whether alleviation of helminthic pressure is inversely correlated with anti-inflammation, lipid levels and insulin sensitivity, and therefore leads to an accelerated development of T2D and CVD.

Early childhood is a critical period where the maturation of the immune system occurs while it receives various challenges from the environment shared with the mother. Children growing in an environment rich in micro-organisms and parasites are thought to have a different pattern of immune response compared to those children growing in a more hygienic environment. This difference might contribute to the lower prevalence of allergic and autoimmune disorders in developing countries compared to affluent countries. Within this context, a number of cohort studies mostly performed in developed countries have focused on finding the link between the pattern of immune responses in early life and health outcomes in later life. In this thesis, we studied child__s innate and adaptive responses during the first 4 years of life in a helminth-endemic area in Indonesia

Helminth parasites are able to induce immune regulation in their host. Suppression of the host immune system is beneficial for both the parasite, by inhibiting anti-parasite immunity, and for the host, by preventing tissue damage due to excessive inflammation. There are indications that in countries where parasites have been eliminated the immune regulatory network is impaired, leading to inflammatory diseases such as allergies and asthma. An important player in immune regulation is the regulatory T cell (Treg). We have shown that the number and/or function of Tregs were indeed enhanced in several helminth and also malaria infections in humans. Tregs were not only involved in suppression of anti-parasite responses, but also of responses to other infections or vaccines. We further investigated the effect of helminth elimination in a randomized placebo-controlled trial. Treatment of helminths led to a strong increase in __mainly pro-inflammatory__ immune responses, which confirms the importance of immune regulation during infection. Furthermore, the prevalence of malaria was transiently increased and allergy was slightly on the rise in treated school children. These results further endorse the possible beneficial effects of helminthic therapy, which is currently being tested in a number of clinical trials.