Human and animal infections with bacteria of the genusSarcina(familyClostridiaceae) are associated with gastric dilation and emphysematous gastritis. However, the potential roles of sarcinae as commensals or pathogens remain unclear. Here, we investigate a lethal disease of unknown etiology that affects sanctuary chimpanzees (Pan troglodytes verus) in Sierra Leone. The disease, which we have named “epizootic neurologic and gastroenteric syndrome” (ENGS), is characterized by neurologic and gastrointestinal signs and results in death of the animals, even after medical treatment. Using a case-control study design, we show that ENGS is strongly associated withSarcinainfection. The microorganism is distinct fromSarcina ventriculiand other known members of its genus, based on bacterial morphology and growth characteristics. Whole-genome sequencing confirms this distinction and reveals the presence of genetic features that may account for the unusual virulence of the bacterium. Therefore, we propose that this organism be considered the representative of a new species, named “CandidatusSarcina troglodytae”. Our results suggest that a heretofore unrecognized complex of related sarcinae likely exists, some of which may be highly virulent. However, the potential role of “Ca. S. troglodytae” in the etiology of ENGS, alone or in combination with other factors, remains a topic for future research.

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-22494-5

Introduction. Since 2005, the leading cause of death for western chimpanzees (Pan troglodytes verus) at Tacugama Chimpanzee Sanctuary (TCS) in Sierra Leone has been epizootic neurologic and gastroenteric syndrome (ENGS), associated with the bacterium Sarcina troglodytae (family Clostridiaceae). Gap Statement. The prevalence of S. troglodytae at TCS in clinically normal chimpanzees and the environment remains unknown, as does its distribution in other captive and wild chimpanzee populations and their environments across Africa. Aim. The aim of this study was to determine the distribution and prevalence of Sarcina bacteria in sanctuary and wild chimpanzee populations across Africa and to identify demographic and ecological risk factors for S. troglodytae in chimpanzees and the environment. Methodology. We conducted a prospective, multi-season epidemiological investigation of S. troglodytae in chimpanzees and the environment at TCS and a parallel study at a sanctuary in the Republic of Congo. We also describe the results of surveys of chimpanzees at a sanctuary in Uganda and wild chimpanzee populations in Sierra Leone and Uganda for S. troglodytae. In total, we tested 637 chimpanzee and environmental samples using a species-specific PCR for S. troglodytae and a pan-Sarcina PCR. Results. S. troglodytae was more prevalent in chimpanzees at TCS (n=60) during the dry season (96.7%) than during the rainy season (55.2%). Soil was the most common environmental source of the bacterium (54% dry season vs. 4.8% rainy season). Notably, we did not detect S. troglodytae in faecal samples from sanctuary chimpanzees in the Republic of Congo (n=79) or in wild chimpanzees in Sierra Leone (n=18). We did detect the bacterium in East African chimpanzees (n=84) but at low prevalence (2.6%–10.9%). In contrast, we found the genus Sarcina to be ubiquitous in all chimpanzee populations with a higher prevalence in sanctuary chimpanzees (93.1%–100%) than in wild chimpanzees (66.7%–68.4%). Conclusion. S. troglodytae is markedly more prevalent at TCS, the only location affected by ENGS, than at any other location tested, and soil is a likely reservoir of S. troglodytae. These findings strengthen the association between S. troglodytae and ENGS and have implications for sanctuary management and conservation of western chimpanzees.

Cholesterol, triglycerides, high-density lipoproteins (HDLs), low-density lipoproteins (LDLs), and very-low-density lipoproteins (VLDLs) were evaluated in chimpanzees at Tacugama Chimpanzee Sanctuary, Sierra Leone. Blood from 75 visually healthy chimpanzees was collected, centrifuged within one hour of collection, and analyzed at Choithram Hospital within 24 h. Statistical analyses assessed differences and interactions based on age, body condition score (BCS), housing group, and sex. HDLs varied widely by housing group; HDLs and LDLs were higher in males than in females. Cholesterol and LDLs were higher in prepubertal individuals while VLDLs and triglycerides were higher in postpubertal individuals. Lipid biomarker differences by age and age ∗ sex statistical interactions were not observed. These data represent a novel compilation of serum lipid biomarkers from a large population of sanctuary-housed Western chimpanzees (Pan troglodytes verus) within a range country, a population not previously studied with regard to serum lipid biomarkers. This study has documented significant differences compared to known values from managed chimpanzees and human reference ranges. The relationship of serum lipid biomarkers with health and disease in great apes remains understudied, but the present data set provides a basis for future studies to ascertain whether these differences are healthy biomarker variations or represent an elevated risk factor for disease.

“Candidatus Sarcina troglodytae” (“Ca. S. troglodytae”), a proposed bacterial species in the family Clostridiaceae, has been epidemiologically associated with a lethal disease in sanctuary chimpanzees in Sierra Leone, epizootic neurologic and gastroenteric syndrome (ENGS). As sarcinae are known to be difficult to culture, a lack of viable in vitro growth conditions has limited further characterization of this bacterium. Such studies are critical to elucidating the relationship between “Ca. S. troglodytae” and ENGS. Here, we isolate a Gram-stain-positive, endospore-forming, coccus and anaerobic bacterial strain, designated JB3T, from brain tissue of a western chimpanzee (Pan troglodytes verus) using a reinforced clostridial medium. We describe the growth of strain JB3T at a pH range of 6 to 9 (optimum 6) at 37°C in an atmosphere composed of 5% H2, 5% CO2, and 90% N2 and demonstrate endospore production under alkaline conditions, suggesting the possibility of an environmental reservoir. We identify ethanol as the primary non-gaseous fermentation byproduct which we hypothesize to have relevance for ENGS. Antibiotic susceptibility testing shows susceptibility to common antimicrobial agents with notable resistance to ceftriaxone. By establishing in vitro conditions for the viable culture, propagation, and storage of “Ca. S. troglodytae”, this study lays the groundwork for future infection studies to test hypotheses about pathogenic mechanisms and prevention/treatment measures for ENGS.

‘ Candidatus Sarcina troglodytae’ (‘ Ca . S. troglodytae’), a proposed bacterial species in the family Clostridiaceae , has been epidemiologically associated with a lethal disease in sanctuary chimpanzees in Sierra Leone, epizootic neurologic and gastroenteric syndrome (ENGS). As sarcinae are known to be difficult to culture, a lack of viable in vitro growth conditions has limited further characterization of this bacterium. Such studies are critical to elucidating the relationship between ‘ Ca . S. troglodytae’ and ENGS. Here, we isolate a Gram-stain-positive, endospore-forming coccus and anaerobic bacterial strain, designated JB3 ^T , from brain tissue of a western chimpanzee ( Pan troglodytes verus ) using a reinforced clostridial medium. We describe the growth of strain JB3 ^T at a pH range of 6 to 9 (optimum 6) at 37 °C in an atmosphere composed of 5% H ₂ , 5% CO ₂ and 90% N ₂ and demonstrate endospore production under alkaline conditions, suggesting the possibility of an environmental reservoir. We identify ethanol as the primary non-gaseous fermentation byproduct which we hypothesize to have relevance for ENGS. Antibiotic susceptibility testing shows susceptibility to common antimicrobial agents with notable resistance to ceftriaxone. By establishing in vitro conditions for the viable culture, propagation and storage of ‘ Ca . S. troglodytae’, this study lays the groundwork for future infection studies to test hypotheses about pathogenic mechanisms and prevention/treatment measures for ENGS.