Biology subjects

Muyembe-Tamfum, J.-J.

Publications and source records attributed to Muyembe-Tamfum, J.-J..

7 recordsLinked to original sources

bioRxiv2026

Continental-scale survey of Treponema pallidum in African nonhuman primates: expanding the range to the Mediterranean basin

Background: Treponema pallidum, the causative agent of yaws, bejel, and syphilis, is a significant pathogen affecting both humans and nonhuman primates (NHPs). While its presence is documented in several African NHP species, the continental-scale distribution, ecological drivers, and status in North African populations remain poorly understood. We conducted a large-scale, non-invasive survey to investigate the circulation of T. pallidum across African NHP populations and evaluate geographical and ecological patterns of exposure. Results: A total of 1,696 fecal samples from 11 wild NHP species collected across five African countries were screened for anti-T. pallidum antibodies using an automated chemiluminescent Simple Western assay, and fecal and dipteran samples were analyzed by molecular methods. Widespread seropositivity was observed across all African sites and multiple primate taxa, including great apes and cercopithecids. We provide the first evidence of T. pallidum antibodies in Barbary macaques (Macaca sylvanus) from North Africa, extending the known distribution of the pathogen to the Mediterranean basin. In West Africa, chimpanzees (Pan troglodytes verus) from Senegal and Guinea exhibited particularly high seroprevalence, confirming this region as a major endemic hotspot. In Central Africa, substantial circulation was documented in Cercopithecus wolfi, Cercopithecus ascanius, and western lowland gorillas (Gorilla gorilla gorilla). Arid/savanna biomes showed significantly higher exposure than Mediterranean and tropical rainforest biomes. No T. pallidum DNA was detected in fecal or dipteran samples. Conclusion: Our findings demonstrate widespread circulation of T. pallidum among African NHPs, reveal its presence in North African primate populations for the first time. The observed high seroprevalence, coupled with significant variations across species and geographical regions, suggests the existence of multiple transmission pathways adapted to specific host behaviors and environmental constraints. These results support the existence of a broad multihost sylvatic reservoir and provide new insights into the ecology of T. pallidum, with important implications for wildlife health, One Health surveillance, and yaws eradication efforts.

microbiology↗

bioRxiv2026

Silent Footprints of Ebolavirus in the Forest: Serological Clues from Wild Non-Human Primates in the Democratic Republic of Congo

Filoviruses, particularly Ebola virus (EBOV), remain a major public health concern in Central Africa. However, their circulation in wildlife during inter-epidemic periods remains poorly documented. Non-human primates (NHPs) may serve as ecological sentinels of viral dynamics at human-forest interfaces, yet surveillance is constrained by the limitations of invasive sampling. We conducted a non-invasive investigation of EBOV exposure in free-ranging NHPs from the Mabali Forest Reserve (Equateur Province, Democratic Republic of Congo) for Ebola virus disease. A total of 630 fecal samples were collected and screened for active infection by PCR targeting the EBOV nucleoprotein gene; all samples tested negative. Molecular identification of host species was achieved in 569 samples (90.3%). Fecal serology using an automated capillary western blot platform (JESS), targeting EBOV nucleoprotein, glycoprotein and viral protein 40 antigens, identified four seropositive individuals (0.70%), including two Cercopithecus ascanius and two C. wolfi. The detection of discrete immunoreactive bands consistent with EBOV-specific antibodies suggests prior exposure despite the absence of active outbreaks. These findings provide the first serological evidence compatible with EBOV exposure in these two Cercopithecus species and support the hypothesis of low-level or cryptic viral circulation in forest ecosystems. The study highlights the feasibility and value of fecal serology as a non-invasive One Health surveillance tool for monitoring zoonotic pathogens at wildlife-human interfaces.

microbiology↗

bioRxiv2025

Gut microbiome associations with poliovirus vaccine seroconversion in children in the Democratic Republic of the Congo

BackgroundDespite efforts to increase global immunization, vaccination seroconversion in low and middle income countries (LMICs) is often lower than in high income countries (HICs). The reasons for this disparity are not fully understood. Given the role of the gut microbiome in immune development, we investigated the relationship between the gut microbiome and polio vaccine seroconversion in children in the Democratic Republic of the Congo (DRC). MethodsThis cross-sectional analysis included children ages 6-24 months old (n=90) enrolled in the DRC. Vaccine history was obtained from health records and/or self-report and poliovirus serostatus surveyed using dried blood spots. Nutritional status was evaluated using anthropomorphic measures. Microbiome profiling (16S rRNA gene) was performed and associations with poliovirus serostatus and malnutrition were examined. ResultsThe average age of the study population was 13.6 months (SD=5.6) with 58% female. Poliovirus seropositivity was 65.5% and 22% of the children were malnourished. We found that presence of Campylobacter and Veillonella, especially at an early age, was associated with low poliovirus vaccination seroconversion. These bacterial taxa differed from those associated with malnutrition. ConclusionsThe presence of enteropathogens such as Campylobacter at a young age could be an important factor contributing to low vaccination seroconversion in children in LMICs.

microbiology↗

bioRxiv2023

Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids

Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we performed high-resolution metagenomic-based analyses of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in humans populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer new and exciting insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids, demonstrating that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.

evolutionary biology↗

bioRxiv2020

Primate phageomes are structured by superhost phylogeny and environment

The evolutionary origins of human-associated bacteriophage communities are poorly understood. To address this question, we examined fecal phageomes of 23 wild non-human primate taxa, including multiple representatives of all the major primate radiations, and find relatives of the majority of human-associated phages. Primate taxa have distinct phageome compositions that exhibit a clear phylosymbiotic signal, and phage-superhost co-divergence is detected for 44 individual phages. Within species, neighboring social groups harbor evolutionarily and compositionally distinct phageomes, structured by superhost social behavior. However, captive non-human primate phageomes are more similar to humans than their wild counterparts, revealing replacement of wild-associated phages with human-associated ones. Together, our results suggest that potentially labile primate-phage associations persisted across millions of years of evolution, potentially facilitated by transmission between groupmates. One Sentence SummaryRelatives of human-associated phages in wild primates reveal ancient but dynamic superhost-phage associations shaped by social transmission.

microbiology↗

bioRxiv2019

A near-full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue

Although estimated to have emerged in humans in Central Africa in the early 1900s, HIV-1, the main causative agent of AIDS, was only discovered in 1983. With very little direct biological data of HIV-1 from before the 1980s, far-reaching evolutionary and epidemiological inferences regarding the long pre-discovery phase of this pandemic are based on extrapolations by phylodynamic models of HIV-1 genomic sequences gathered mostly over recent decades. Here, using a very sensitive multiplex RT-PCR assay, we screened 1,652 formalin-fixed paraffin-embedded tissue specimens collected for pathology diagnostics in Kinshasa, Democratic Republic of Congo (DRC), between 1959 and 1967. We report the near-complete genome of one positive from 1966 (\"DRC66\")--a non-recombinant sister lineage to subtype C that constitutes the oldest HIV-1 near-full-length genome recovered to date. Root-to-tip plots showed the DRC66 sequence is not an outlier as would be expected if dating estimates from more recent genomes were systematically biased; and inclusion of DRC66 sequence in tip-dated BEAST analyses did not significantly alter root and internal node age estimates based on post-1978 HIV-1 sequences. There was larger variation in divergence time estimates among datasets that were subsamples of the available HIV-1 genomes from 1978-2015, showing the inherent phylogenetic stochasticity across subsets of the real HIV-1 diversity. In conclusion, this unique archival HIV-1 sequence provides direct genomic insight into HIV-1 in 1960s DRC, and, as an ancient-DNA calibrator, it validates our understanding of HIV-1 evolutionary history.\n\nSignificanceInferring the precise timing of the origin of the HIV/AIDS pandemic is of great importance because it offers insights into which factors did--or did not--facilitate the emergence of the causal virus. Previous estimates have implicated rapid development during the early 20th century in Central Africa, which wove once-isolated populations into a more continuous fabric. We recovered the first HIV-1 genome from the 1960s, and it provides direct evidence that HIV-1 molecular clock estimates spanning the last half-century are remarkably reliable. And, because this genome itself was sampled only about a half-century after the estimated origin of the pandemic, it empirically anchors this crucial inference with high confidence.

evolutionary biology↗

bioRxiv2019

Quantifying transmission of emerging zoonoses: Using mathematical models to maximize the value of surveillance data

Understanding and quantifying the transmission of zoonotic pathogens is essential for directing public health responses, especially for pathogens capable of transmission between humans. However, determining a pathogens transmission dynamics is complicated by challenges often encountered in zoonotic disease surveillance, including unobserved sources of transmission (both human and zoonotic), limited spatial information, and unknown scope of surveillance. In this work, we present a model-based inference method that addresses these challenges for subcritical zoonotic pathogens using a spatial model with two levels of mixing. After demonstrating the robustness of the method using simulation studies, we apply the new method to a dataset of human monkeypox cases detected during an active surveillance program from 1982-1986 in the Democratic Republic of the Congo (DRC). Our results provide estimates of the reproductive number and spillover rate of monkeypox during this surveillance period and suggest that most human-to-human transmission events occur over distances of 30km or less. Taking advantage of contact-tracing data available for a subset of monkeypox cases, we find that around 80% of contact-traced links could be correctly recovered from transmission trees inferred using only date and location. Our results highlight the importance of identifying the appropriate spatial scale of transmission, and show how even imperfect spatiotemporal data can be incorporated into models to obtain reliable estimates of human-to-human transmission patterns.\n\nAuthor SummarySurveillance datasets are often the only sources of information about the ecology and epidemiology of zoonotic infectious diseases. Methods that can extract as much information as possible from these datasets therefore provide a key advantage for informing our understanding of the disease dynamics and improving our ability to choose the optimal intervention strategy. We developed and tested a likelihood-based inference method based on a mechanistic model of the spillover and human-to-human transmission processes. We first used simulated datasets to explore which information about the disease dynamics of a subcritical zoonotic pathogen could be successfully extracted from a line-list surveillance dataset with non-localized spatial information and unknown geographic coverage. We then applied the method to a dataset of human monkeypox cases detected during an active surveillance program in the Democratic Republic of the Congo between 1982 and 1986 to obtain estimates of the reproductive number, spillover rate, and spatial dispersal of monkeypox in humans.

epidemiology↗