The potential importance of the built-environment microbiome and its impact on human health.

There is increasing evidence that interactions between microbes and their hosts not only play a role in determining health and disease but also in emotions, thought, and behavior. Built environments greatly influence microbiome exposures because of their built-in highly specific microbiomes coproduced with myriad metaorganisms including humans, pets, plants, rodents, and insects. Seemingly static built structures host complex ecologies of microorganisms that are only starting to be mapped. These microbial ecologies of built environments are directly and interdependently affected by social, spatial, and technological norms. Advances in technology have made these organisms visible and forced the scientific community and architects to rethink gene-environment and microbe interactions respectively. Thus, built environment design must consider the microbiome, and research involving host-microbiome interaction must consider the built-environment. This paradigm shift becomes increasingly important as evidence grows that contemporary built environments are steadily reducing the microbial diversity essential for human health, well-being, and resilience while accelerating the symptoms of human chronic diseases including environmental allergies, and other more life-altering diseases. New models of design are required to balance maximizing exposure to microbial diversity while minimizing exposure to human-associated diseases. Sustained trans-disciplinary research across time (evolutionary, historical, and generational) and space (cultural and geographical) is needed to develop experimental design protocols that address multigenerational multispecies health and health equity in built environments.

The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome.

The COVID-19 pandemic has the potential to affect the human microbiome in infected and uninfected individuals, having a substantial impact on human health over the long term. This pandemic intersects with a decades-long decline in microbial diversity and ancestral microbes due to hygiene, antibiotics, and urban living (the hygiene hypothesis). High-risk groups succumbing to COVID-19 include those with preexisting conditions, such as diabetes and obesity, which are also associated with microbiome abnormalities. Current pandemic control measures and practices will have broad, uneven, and potentially long-term effects for the human microbiome across the planet, given the implementation of physical separation, extensive hygiene, travel barriers, and other measures that influence overall microbial loss and inability for reinoculation. Although much remains uncertain or unknown about the virus and its consequences, implementing pandemic control practices could significantly affect the microbiome. In this Perspective, we explore many facets of COVID-19-induced societal changes and their possible effects on the microbiome, and discuss current and future challenges regarding the interplay between this pandemic and the microbiome. Recent recognition of the microbiome's influence on human health makes it critical to consider both how the microbiome, shaped by biosocial processes, affects susceptibility to the coronavirus and, conversely, how COVID-19 disease and prevention measures may affect the microbiome. This knowledge may prove key in prevention and treatment, and long-term biological and social outcomes of this pandemic.

Multidisciplinarity in Microbiome Research: A Challenge and Opportunity to Rethink Causation, Variability, and Scale.

This essay, written by a biologist, a microbial ecologist, a biological anthropologist, and an anthropologist-historian, examines tensions and translations in microbiome research on animals in the laboratory and field. The authors trace how research questions and findings in the laboratory are extrapolated into the field and vice versa, and the shifting evidentiary standards that these research settings require. Showing how complexities of microbiomes challenge traditional standards of causation, the authors contend that these challenges require new approaches to inferences used in ecology, anthropology, and history. As social scientists incorporate investigations of microbial life into their human studies, microbiome researchers venture into field settings to develop mechanistic understandings about the functions of complex microbial communities. These efforts generate new possibilities for cross-fertilizations and inference frameworks to interpret microbiome findings. Microbiome research should integrate multiple scales, levels of variability, and other disciplinary approaches to tackle questions spanning conditions from the laboratory to the field.

Factors Associated with Stunted Growth in Children Under Five Years in Antananarivo, Madagascar and Bangui, Central African Republic.

OBJECTIVES: With a fourth of all under-five children affected, stunting remains one of the biggest health challenges worldwide. Even though the main underlying factors are known, the exact pathways to stunting varying in affected regions, and interventions thus need to be tailored to the local contexts. This study aimed assessing and comparing factors associated with stunting in two understudied sub-Saharan urban contexts with some of the highest stunting prevalence globally: Bangui, Central African Republic (~ 36%) and Antananarivo, Madagascar (42%). METHODS: We performed a case-control study on 175 + 194 stunted and 237 + 230 non-stunted control children aged 2-5 years and matched for age, gender and district of residency. Factors associated with stunting were identified using a standardized, paper questionnaire delivered by trained interviewers. Statistical analysis was done using logistic regression modelling. RESULTS: In both sites, formal maternal education lowered the risk of being stunted and restricted access to soap, suffering of anaemia and low birth weight were associated with higher risk of stunting. Short maternal stature, household head different from parents, diarrhoea and coughing were associated with an increased risk and continuing breastfeeding was associated with a lower risk of stunting in Antananarivo. Previous severe undernutrition and dermatitis/ fungal skin infections were associated with higher and changes in diet during pregnancy with lower risk of stunting in Bangui. CONCLUSIONS: Our results suggest maternal education, antenatal care, iron supplementation and simple WASH interventions such as using soap and infection control as general and breastfeeding (Antananarivo) or better nutrition (Bangui) as area-specified interventions.

Prevention and care of hepatitis B in the rural region of Fatick in Senegal: a healthcare workers' perspective using a mixed methods approach.

BACKGROUND: In countries where hepatitis B virus (HBV) is endemic, including Senegal, the World Health Organization recommends systematic HBV screening of pregnant women and vaccination at birth to prevent mother-to-child transmission (MTCT). This study investigated healthcare workers' (HCW) knowledge and practices regarding HBV prevention and care in the rural region of Fatick in Senegal, as well as challenges they faced in implementing prevention activities related to HBV MTCT. METHODS: A mixed-methods survey was conducted between May-July 2017 among 112 HCW working in 15 healthcare facilities in two districts of the Fatick region using face-to-face questionnaires and semi-structured interviews. Descriptive statistics and chi-square/Mann-Whitney tests were used to analyze quantitative data, while qualitative data were analyzed thematically. RESULTS: The study population included 87 HCW in the quantitative component (83% women, median age [interquartile range, IQR] = 35 [31-40] years) and 11 in the qualitative component. A knowledge gap was observed in key areas of HBV infection: only 24, 51 and 38%, respectively, correctly reported that early HBV acquisition is associated with a high risk of developing chronic infection, that perinatal transmission is one of the main modes of HBV transmission in Senegal, and that three to four doses of HBV vaccine are required to ensure immunization in children. Despite good acceptability of systematic screening of pregnant women and vaccination at birth, only 48% of HCW mainly involved in prenatal care and 71% of those involved exclusively in vaccination routinely performed these two key interventions. HCW reported several structural barriers that may hinder their implementation: a lack of training in HBV and in counseling, poor availability of rapid diagnostic tests (RDT), high costs of both screening and treatment, a lack of adequate information on treatment options and missed opportunities for vaccination at birth. CONCLUSIONS: HCW working in the Fatick region may be insufficiently trained and supported to effectively implement HBV prevention strategies. Our findings suggest an urgent need to strengthen MTCT prevention in this region, by improving HCW knowledge in key areas of HBV infection, providing RDT and antiviral treatment at low cost, and enhancing community-based interventions for the timely vaccination of newborns.

Identifying the etiology and pathophysiology underlying stunting and environmental enteropathy: study protocol of the AFRIBIOTA project.

BACKGROUND: Globally one out of four children under 5 years is affected by linear growth delay (stunting). This syndrome has severe long-term sequelae including increased risk of illness and mortality and delayed psychomotor development. Stunting is a syndrome that is linked to poor nutrition and repeated infections. To date, the treatment of stunted children is challenging as the underlying etiology and pathophysiological mechanisms remain elusive. We hypothesize that pediatric environmental enteropathy (PEE), a chronic inflammation of the small intestine, plays a major role in the pathophysiology of stunting, failure of nutritional interventions and diminished response to oral vaccines, potentially via changes in the composition of the pro- and eukaryotic intestinal communities. The main objective of AFRIBIOTA is to describe the intestinal dysbiosis observed in the context of stunting and to link it to PEE. Secondary objectives include the identification of the broader socio-economic environment and biological and environmental risk factors for stunting and PEE as well as the testing of a set of easy-to-use candidate biomarkers for PEE. We also assess host outcomes including mucosal and systemic immunity and psychomotor development. This article describes the rationale and study protocol of the AFRIBIOTA project. METHODS: AFRIBIOTA is a case-control study for stunting recruiting children in Bangui, Central African Republic and in Antananarivo, Madagascar. In each country, 460 children aged 2-5 years with no overt signs of gastrointestinal disease are recruited (260 with no growth delay, 100 moderately stunted and 100 severely stunted). We compare the intestinal microbiota composition (gastric and small intestinal aspirates; feces), the mucosal and systemic immune status and the psychomotor development of children with stunting and/or PEE compared to non-stunted controls. We also perform anthropological and epidemiological investigations of the children's broader living conditions and assess risk factors using a standardized questionnaire. DISCUSSION: To date, the pathophysiology and risk factors of stunting and PEE have been insufficiently investigated. AFRIBIOTA will add new insights into the pathophysiology underlying stunting and PEE and in doing so will enable implementation of new biomarkers and design of evidence-based treatment strategies for these two syndromes.

Home Care of Children With Diarrhea in Bangui's Therapeutic Landscape (Central African Republic).

We explore how the therapeutic landscape of Bangui, capital of the Central African Republic, shaped and reflected caregivers' home care of childhood diarrhea. Using interviews, group discussions, and participant observation, we found that caregivers described several categories of diarrhea, but in practice, adopted an experimental approach to home diarrheal care. Many managed incertitude by initially dosing children with street medicines and herbal infusions; they delayed seeking professional medical care to avoid expenses, observed their children's symptoms, consulted social networks, and used therapeutic foods. The logics underpinning these practices emerged from caregivers' conviction that diarrhea necessitated medical therapy and restricted choices within Bangui's therapeutic landscape, a consequence of lengthy political economic crisis. This crisis impoverished Bangui populations, eroded formal health care, and sharpened religious differences, discouraging care seeking from traditional healers. Analyses of therapeutic landscapes illuminate why caregivers embraced specific practices and logics and should guide the elaboration of more effective public health interventions.

Incertitude, Hepatitis B, and Infant Vaccination in West and Central Africa.

This comparative study explores incertitude about hepatitis B (HBV) and its implications for childhood vaccination in Bangui, Central African Republic, and the Cascades region, Burkina Faso. Anthropological approaches to vaccination, which counter stereotypes of "ignorant" publics needing education to accept vaccination, excavate alternative ways of knowing about illness and vaccination. We build on these approaches, evaluating different kinds of incertitude (ambiguity, uncertainty, ignorance) about infancy, HBV, health protection, and vaccination. Using interviews and participant observation, we find that Bangui and Cascades publics framed their incertitude differently through stories of infancy, illness, and protection. We locate different forms of incertitude within their historical contexts to illuminate why vaccination practices differ in the Cascades region and Bangui. A more nuanced approach to incomplete knowledge, situated in political, economic, and social histories of the state and vaccination, can contribute to more appropriate global health strategies to improve HBV prevention.

Seasonal Patterns of Buruli Ulcer Incidence, Central Africa, 2002-2012.

To determine when risk for Buruli ulcer is highest, we examined seasonal patterns in a highly disease-endemic area of Cameroon during 2002-2012. Cases peaked in March, suggesting that risk is highest during the high rainy season. During and after this season, populations should increase protective behaviors, and case detection efforts should be intensified.

HBV immunization and vaccine coverage among hospitalized children in Cameroon, Central African Republic and Senegal: a cross-sectional study.

BACKGROUND: Hepatitis B is a major health concern in Africa. The vaccine against hepatitis B virus (HBV) was introduced into the Expanded Programme on Immunization (EPI) of Cameroon and Senegal in 2005, and of CAR (Central African Republic) in 2008. A cross-sectional study was conducted to assess HBV immunization coverage following the vaccine's introduction into the EPI and factors associated with having been vaccinated. METHODS: All hospitalized children, regardless of the reasons for their hospitalization, between 3 months and 6 years of age, for whom a blood test was scheduled during their stay and whose condition allowed for an additional 2 mL blood sample to be taken, and who provided the parent's written consent were included. All children anti-HBs- and anti-HBc + were tested for HBsAg. Vaccination coverage was assessed in three different ways: immunization card, maternal recall and serologic anti-HBs profile. RESULTS: 1783 children were enrolled between April 2009 and May 2010. An immunization card was only available for 24 % of the children. The median age was 21 months. Overall HBV immunization coverage based on immunization cards was 99 %, 49 % and 100 % in Cameroon, CAR and Senegal, respectively (p < 0,001). The immunization rate based on maternal recall was 91 %, 17 % and 88 % in Cameroon, CAR and Senegal, respectively (p < 0,001). According to serology (anti-HBs titer ≥ 10 mUI/mL and anti-HBc-), the coverage rate was 68 %, 13 % and 46 % in Cameroon, CAR and Senegal, respectively (p < 0,001). In Senegal and Cameroon, factors associated with having been vaccinated were: mother's higher education (OR = 2.2; 95 % CI [1.5-3.2]), no malnutrition (OR = 1.6; 95 % CI [1.1-2.2]), access to flushing toilets (OR = 1.6; 95 % CI [1.1-2.3]), and < 24 months old (OR = 2.1; 95 % CI [1.3-3.4] between 12 and 23 months and OR = 2.7; 95 % CI [1.6-4.4] < 12 months). The prevalence of HBV-infected children (HBsAg+) were 0.7 %, 5.1 %, and 0.2 % in Cameroon, CAR and Senegal, respectively (p < 0.001). CONCLUSIONS: Assessing immunization coverage based on immunization cards, maternal recall or administrative data could be usefully reinforced by epidemiological data combined with immunological profiles. Serology-based studies should be implemented regularly in African countries, as recommended by the WHO. Malnutrition, lack of maternal education and poverty are factors associated with vaccine non-compliance. The countries' vaccination programs should actively address these problems.

A time of decline: An eco-anthropological and ethnohistorical investigation of mpox in the Central African Republic.

The Central African Republic (CAR) has experienced repeated mpox outbreaks since 2001. Although several mpox epidemiological risk factors for zoonotic and interhuman transmission have been documented, the reasons for more frequent epidemic outbreaks are less well understood, relying on vague explanatory categories, including deforestation, hunting, and civil unrest. To gain insight into increasingly frequent outbreaks, we undertook an ethnohistorical, eco-anthropological analysis in two CAR regions: the Lobaye prefecture, experiencing one or more annual outbreaks in the past decade, and the Sangha-Mbaere prefecture, with a longer history of mpox but less frequent outbreaks. We comparatively examined changing political economies, forest use practices, and understandings of mpox. In 2022, we conducted 40 qualitative ethnohistorical, anthropological interviews and participant-observation of forest activities in two languages (Sango and French). We compared contemporary practices with hunting, trapping, and meet consumption practices, documented through quantitative and qualitative observation in one research site, over 6 months in 1993. We find increased rodent capture and consumption in both sites in the past 30 years and expanded practices of other potentially risky activities. Simultaneously, we also identify important differences in risky practices between our Lobaye and Sangha-Mbaere participants. In addition, Lobaye and Sangha participants underscored historical processes of decline producing mpox among other emergences, but they framed these declension processes diversely as economic, political, nutritional, and moral. Our findings are important because they mobilize new types of evidence to shed light on the processual dynamics of mpox outbreaks in the CAR. This study also reveals variability across two sites within the same country, highlighting the importance of comparative, fine-grained anthropological and historical research to identify underlying dynamics of mpox outbreaks. Finally, our study points to the need for mpox interventions and risk communication accounting for these regional differences, even within a single country.

Future coexistence with great apes will require major changes to policy and practice.

The great apes-bonobos, chimpanzees, gorillas and orangutans-are critically threatened by human activities. We have destroyed their habitats, hunted them and transmitted fatal diseases to them. Yet we also conduct research on them, try to protect them and live alongside them. They are endangered, and time is running out. Here we outline what must be done to ensure that future generations continue to share this planet with great apes. We urge dialogue with those who live with great apes and interact with them often. We advocate conservation plans that acknowledge the realities of climate change, economic drivers and population growth. We encourage researchers to use technology to minimize risks to great apes. Our proposals will require substantial investment, and we identify ways to generate these funds. We conclude with a discussion of how field researchers might alter their work to protect our closest living relatives more effectively.

Seroprevalence and molecular characterization of viral hepatitis and HIV co-infection in the Central African Republic.

BACKGROUND: The Central African Republic (CAR) is one of the countries with the highest prevalence of viral hepatitis infection in the world. Coinfection with HIV increases the morbidity and mortality beyond that of mono-infection with either hepatitis or HIV. The present study describes the geographic distribution of viral hepatitis infections and molecular characterization of these viruses in the CAR. METHODOLOGY: Out of 12,599 persons enrolled during the fourth Multiple Indicator Cluster Survey of 2010 in the CAR, 10,621 Dried Blood Spot (DBS) samples were obtained and stored at -20°C. Of these DBS, 4,317 samples were randomly selected to represent all regions of the CAR. Serological tests for hepatitis B, D, and C viruses were performed using the ELISA technique. Molecular characterization was performed to identify strains. RESULTS: Of the 4,317 samples included, 53.2% were from men and 46.8% from women. The HBsAg prevalence among participants was 12.9% and that HBc-Ab was 19.7%. The overall prevalence of HCV was 0.6%. Co-infection of HIV/HBV was 1.1% and that of HBV/HDV was 16.6%. A total of 77 HBV, 6 HIV, and 6 HDV strains were successfully sequenced, with 72 HBV (93.5%) strains belonging to genotype E and 5 (6.5%) strains belonging to genotype D. The 6 HDV strains all belonged to clade 1, while 4 recombinants subtype were identified among the 6 strains of HIV. CONCLUSION: Our study found a high prevalence of HBV, HBV/HDV and HBV/HIV co-infection, but a low prevalence of HCV. CAR remains an area of high HBV endemicity. This study's data and analyses would be useful for establishing an integrated viral hepatitis and HIV surveillance program in the CAR.

Influence of COVID-19 on trust in routine immunization, health information sources and pandemic preparedness in 23 countries in 2023.

It is unclear how great a challenge pandemic and vaccine fatigue present to public health. We assessed perspectives on coronavirus disease 2019 (COVID-19) and routine immunization as well as trust in pandemic information sources and future pandemic preparedness in a survey of 23,000 adults in 23 countries in October 2023. The participants reported a lower intent to get a COVID-19 booster vaccine in 2023 (71.6%), compared with 2022 (87.9%). A total of 60.8% expressed being more willing to get vaccinated for diseases other than COVID-19 as a result of their experience during the pandemic, while 23.1% reported being less willing. Trust in 11 selected sources of vaccine information each averaged less than 7 on a 10-point scale with one's own doctor or nurse and the World Health Organization, averaging a 6.9 and 6.5, respectively. Our findings emphasize that vaccine hesitancy and trust challenges remain for public health practitioners, underscoring the need for targeted, culturally sensitive health communication strategies.

Drawing a pandemic vulnerabilities' map: The SoNAR-global Vulnerabilities Assessment digital and its output.

This paper describes the process, advantages and limitations of a qualitative methodology for defining and analyzing vulnerabilities during the COVID-19 pandemic. Implemented in Italy in two sites (Rome and outside Rome, in some small-medium sized municipalities in Latium) in 2021, this investigation employed a mixed digital research tool that was also used simultaneously in four other European countries. Its digital nature encompasses both processes of data collection. Among the most salient is that the pandemic catalyzed new vulnerabilities in addition to exacerbating old ones, particularly economic. Many of the vulnerabilities detected, in fact, are linked to previous situations, such as the uncertainties of labor markets, having in COVID-19 to the greatest negative effects on the most precarious workers (non-regular, part-time, and seasonal). The consequences of the pandemic are also reflected in other forms of vulnerability that appear less obvious, having exacerbated social isolation, not only out of fear of contagion, but because of the psychological challenges posed by containment measures themselves. These measures created not mere discomfort, but behavioral changes characterized by anxiety, fearfulness, and disorientation. More generally, this investigation reveals the strong influence of social determinants throughout the COVID-19 pandemic, creating new forms of vulnerability, as the effects of social, economic, and biological risk factors were compounded, in particular, among already marginalized populations.

A rapid qualitative methods assessment and reporting tool for epidemic response as the outcome of a rapid review and expert consultation.

During the first year of the COVID-19 pandemic, the Methods Sub-Group of the WHO COVID-19 Social Science Research Roadmap Working Group conducted a rapid evidence review of rapid qualitative methods (RQMs) used during epidemics. The rapid review objectives were to (1) synthesize the development, implementation, and uses of RQMs, including the data collection tools, research questions, research capacities, analytical approaches, and strategies used to speed up data collection and analysis in their specific epidemic and institutional contexts; and (2) propose a tool for assessing and reporting RQMs in epidemics emergencies. The rapid review covered published RQMs used in articles and unpublished reports produced between 2015 and 2021 in five languages (English, Mandarin, French, Portuguese, and Spanish). We searched multiple databases in these five languages between December 2020 and January 31, 2021. Sources employing "rapid" (under 6 months from conception to reporting of results) qualitative methods for research related to epidemic emergencies were included. We included 126 published and unpublished sources, which were reviewed, coded, and classified by the research team. Intercoder reliability was found to be acceptable (Krippendorff's α = 0.709). We employed thematic analysis to identify categories characterizing RQMs in epidemic emergencies. The review protocol was registered at PROSPERO (no. CRD42020223283) and Research Registry (no. reviewregistry1044). We developed an assessment and reporting tool of 13 criteria in three domains, to document RQMs used in response to epidemic emergencies. These include I. Design and Development (i. time frame, ii. Training, iii. Applicability to other populations, iv. Applicability to low resource settings, v. community engagement, vi. Available resources, vii. Ethical approvals, viii. Vulnerability, ix. Tool selection); II. Data Collection and Analysis (x. concurrent data collection and analysis, xi. Targeted populations and recruitment procedures); III. Restitution and Dissemination (xii. Restitution and dissemination of findings, xiii. Impact). Our rapid review and evaluation found a wide range of feasible and highly effective tools, analytical approaches and timely operational insights and recommendations during epidemic emergencies.

Embracing context: Lessons from designing a dialogue-based intervention to address vaccine hesitancy.

Dialogue with people who are vaccine hesitant has been recommended as a method to increase vaccination uptake. The process of cultivating dialogue is shaped by the context in which it occurs, yet the development of interventions addressing vaccine hesitancy with dialogue often overlooks the role of context and favors relatively fixed solutions. This reflexive paper shares three key lessons related to context for dialogue-based interventions. These lessons emerged during a participatory research project to develop a pilot intervention to create open dialogue among healthcare workers in Belgium about COVID-19 vaccination concerns. Through a mixed methods study consisting of in-depth interviews, focus group discussions, and surveys, we engaged healthcare workers in the design, testing, and evaluation of a digital platform featuring text-based and video-based (face-to-face) interactions. The lessons are: (1) what dialogue means, entails, and requires can vary for a population and context, (2) inherent tension exists between helping participants voice (and overcome) their concerns and exposing them to others' ideas that may exacerbate those concerns, and (3) interactional exchanges (e.g., with peers or experts) that matter to participants may shape the dialogue in terms of its content and form. We suggest that having a discovery-orientation-meaning to work not only inductively and iteratively but also reflexively-is a necessary part of the development of dialogue-based interventions. Our case also sheds light on the influences between: dialogue topic/content, socio-political landscape, population, intervention aim, dialogue form, ethics, researcher position, and types of interactional exchanges.

Higher convergence of human-great ape enteric eukaryotic viromes in central African forest than in a European zoo: a One Health analysis.

Human-animal pathogenic transmissions threaten both human and animal health, and the processes catalyzing zoonotic spillover and spillback are complex. Prior field studies offer partial insight into these processes but overlook animal ecologies and human perceptions and practices facilitating human-animal contact. Conducted in Cameroon and a European zoo, this integrative study elucidates these processes, incorporating metagenomic, historical, anthropological and great ape ecological analyses, and real-time evaluation of human-great ape contact types and frequencies. We find more enteric eukaryotic virome sharing between Cameroonian humans and great apes than in the zoo, virome convergence between Cameroonian humans and gorillas, and adenovirus and enterovirus taxa as most frequently shared between Cameroonian humans and great apes. Together with physical contact from hunting, meat handling and fecal exposure, overlapping human cultivation and gorilla pillaging in forest gardens help explain these findings. Our multidisciplinary study identifies environmental co-use as a complementary mechanism for viral sharing.