High level of intrinsic phenotypic antimicrobial resistance in enterobacteria from terrestrial wildlife in Gabonese national parks

Data on the prevalence of antibiotic resistance in Enterobacteriaceae in African wildlife are still relatively limited. The aim of this study was to estimate the prevalence of phenotypic intrinsic and acquired antimicrobial resistance of enterobacteria from several species of terrestrial wild mammals in national parks of Gabon. Colony culture and isolation were done using MacConkey agar. Isolates were identified using the VITEK 2 and MALDI-TOF methods. Antibiotic susceptibility was analysed and interpreted according to the European Committee on Antimicrobial Susceptibility Testing guidelines. The preliminary test for ESBL-producing Enterobacteriaceae was performed by replicating enterobacterial colonies on MacConkey agar supplemented with 2 mg/L cefotaxime (MCA+CTX). Extended-spectrum beta-lactamase (ESBL) production was confirmed with the double-disc synergy test (DDST). The inhibition zone diameters were read with SirScan. Among the 130 bacterial colonies isolated from 125 fecal samples, 90 enterobacterial isolates were identified. Escherichia coli (61%) was the most prevalent, followed by Enterobacter cloacae (8%), Proteus mirabilis (8%), Klebsiella variicola (7%), Klebsiella aerogenes (7%), Klebsiella oxytoca (4%), Citrobacter freundii (3%), Klebsiella pneumoniae (1%) and Serratia marcescens (1%). Acquired resistance was carried by E. coli (11% of all E. coli isolates) and E. cloacae (3% of all E. cloacae) isolates, while intrinsic resistance was detected in all the other resistant isolates (n = 31); K. variicola, K. oxytoca, K. pneumoniae, E. cloacae, K. aerogenes, S. marcescens and P. mirabilis). Our data show that most strains isolated in protected areas in Gabon are wild type isolates and carry intrinsic resistance rather than acquired resistance.

A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo

Comparisons of mammalian gut microbiota across different environmental conditions shed light on the diversity and composition of gut bacteriome and suggest consequences for human and animal health. Gut bacteriome comparisons across different environments diverge in their results, showing no generalizable patterns linking habitat and dietary degradation with bacterial diversity. The challenge in drawing general conclusions from such studies lies in the broad terms describing diverse habitats ("wild", "captive", "pristine"). We conducted 16S ribosomal RNA gene sequencing to characterize intestinal microbiota of free-ranging sympatric chimpanzees and gorillas in southeastern Cameroon and sympatric chimpanzees and gorillas in a European zoo. We conducted participant-observation and semi-structured interviews among people living near these great apes to understand better their feeding habits and habitats. Unexpectedly, bacterial diversity (ASV, Faith PD and Shannon) was higher among zoo gorillas than among those in the Cameroonian forest, but zoo and Cameroonian chimpanzees showed no difference. Phylogeny was a strong driver of species-specific microbial composition. Surprisingly, zoo gorilla microbiota more closely resembled that of zoo chimpanzees than of Cameroonian gorillas. Zoo living conditions and dietary similarities may explain these results. We encourage multidisciplinary approach integrating environmental sampling and anthropological evaluation to characterize better diverse environmental conditions of such investigations.

Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla)

The mammalian gastrointestinal (GI) microbiome, which plays indispensable roles in host nutrition and health, is affected by numerous intrinsic and extrinsic factors. Among them, antibiotic (ATB) treatment is reported to have a significant effect on GI microbiome composition in humans and other animals. However, the impact of ATBs on the GI microbiome of free-ranging or even captive great apes remains poorly characterized. Here, we investigated the effect of cephalosporin treatment (delivered by intramuscular dart injection during a serious respiratory outbreak) on the GI microbiome of a wild habituated group of western lowland gorillas (Gorilla gorilla gorilla) in the Dzanga Sangha Protected Areas, Central African Republic. We examined 36 fecal samples from eight individuals, including samples before and after ATB treatment, and characterized the GI microbiome composition using Illumina-MiSeq sequencing of the bacterial 16S rRNA gene. The GI microbial profiles of samples from the same individuals before and after ATB administration indicate that the ATB treatment impacts GI microbiome stability and the relative abundance of particular bacterial taxa within the colonic ecosystem of wild gorillas. We observed a statistically significant increase in Firmicutes and a decrease in Bacteroidetes levels after ATB treatment. We found disruption of the fibrolytic community linked with a decrease of Ruminoccocus levels as a result of ATB treatment. Nevertheless, the nature of the changes observed after ATB treatment differs among gorillas and thus is dependent on the individual host. This study has important implications for ecology, management, and conservation of wild primates.

Non-contiguous-Finished Genome Sequence and Description of Paenibacillus camerounensis sp. nov

Strain G4(T) was isolated from the stool sample of a wild gorilla (Gorilla gorilla gorilla) from Cameroon. It is a facultative anaerobic, Gram-negative, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.48% with Paenibacillus typhae, the phylogenetically closest species with standing nomenclature. Moreover, the strain G4(T) presents some phenotypic differences when compared to other Paenibacillus species and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here, we describe the characteristics of this organism, complete genome sequence, and annotation. The 6,933,847 bp size genome (1 chromosome but no plasmid) contains 5972 protein-coding genes and 54 RNAs genes, including 44 tRNA genes. In addition, digital DNA-DNA hybridization values for the genome of the strain G4(T) against the closest Paenibacillus genomes range between 19.7 and 22.1, once again confirming its new status as a new species. On the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we propose the creation of Paenibacillus camerounensis sp. nov. that contains the strain G4(T).

Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp

Although the critical role that our gastrointestinal microbes play in host physiology is now well established, we know little about the factors that influenced the evolution of primate gut microbiomes. To further understand current gut microbiome configurations and diet-microbe co-metabolic fingerprints in primates, from an evolutionary perspective, we characterized fecal bacterial communities and metabolomic profiles in 228 fecal samples of lowland and mountain gorillas (G. g. gorilla and G. b. beringei, respectively), our closest evolutionary relatives after chimpanzees. Our results demonstrate that the gut microbiomes and metabolomes of these two species exhibit significantly different patterns. This is supported by increased abundance of metabolites and bacterial taxa associated with fiber metabolism in mountain gorillas, and enrichment of markers associated with simple sugar, lipid and sterol turnover in the lowland species. However, longitudinal sampling shows that both species' microbiomes and metabolomes converge when hosts face similar dietary constraints, associated with low fruit availability in their habitats. By showing differences and convergence of diet-microbe co-metabolic fingerprints in two geographically isolated primate species, under specific dietary stimuli, we suggest that dietary constraints triggered during their adaptive radiation were potential factors behind the species-specific microbiome patterns observed in primates today.

Sympatric chimpanzees and gorillas harbor convergent gut microbial communities

The gut microbial communities within great apes have been shown to reflect the phylogenetic history of their hosts, indicating codiversification between great apes and their gut microbiota over evolutionary timescales. But because the great apes examined to date represent geographically isolated populations whose diets derive from different sources, it is unclear whether this pattern of codiversification has resulted from a long history of coadaptation between microbes and hosts (heritable factors) or from the ecological and geographic separation among host species (environmental factors). To evaluate the relative influences of heritable and environmental factors on the evolution of the great ape gut microbiota, we assayed the gut communities of sympatric and allopatric populations of chimpanzees, bonobos, and gorillas residing throughout equatorial Africa. Comparisons of these populations revealed that the gut communities of different host species can always be distinguished from one another but that the gut communities of sympatric chimpanzees and gorillas have converged in terms of community composition, sharing on average 53% more bacterial phylotypes than the gut communities of allopatric hosts. Host environment, independent of host genetics and evolutionary history, shaped the distribution of bacterial phylotypes across the Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria, the four most common phyla of gut bacteria. Moreover, the specific patterns of phylotype sharing among hosts suggest that chimpanzees living in sympatry with gorillas have acquired bacteria from gorillas. These results indicate that geographic isolation between host species has promoted the evolutionary differentiation of great ape gut bacterial communities.

No evidence for transmission of antibiotic-resistant Escherichia coli strains from humans to wild western lowland gorillas in Lopé National Park, Gabon

The intensification of human activities within the habitats of wild animals is increasing the risk of interspecies disease transmission. This risk is particularly important for great apes, given their close phylogenetic relationship with humans. Areas of high human density or intense research and ecotourism activities expose apes to a high risk of disease spillover from humans. Is this risk lower in areas of low human density? We determined the prevalence of Escherichia coli antibiotic-resistant isolates in a population of the critically endangered western lowland gorilla (Gorilla gorilla gorilla) and other wild mammals in Lopé National Park (LNP), Gabon, and we tested whether the observed pattern could be explained by bacterial transmission from humans and domestic animals into wildlife populations. Our results show a high prevalence of antibiotic-resistant bacterial isolates in humans and low levels in gorillas and other wildlife. The significant differences in the genetic background of the resistant bacteria isolated from humans and gorillas suggest that transmission is low or does not occur between these two species. These findings indicate that the presence of antibiotic-resistant strains in wildlife do not imply direct bacteria transmission from humans. Thus, in areas of low human density, human-wildlife E. coli transmission seems to be low. The presence of antibiotic-resistant isolates in gorillas may be better explained by other mechanisms for resistance acquisition, such as horizontal gene exchange among bacteria or naturally acquired resistance.

Characterization of Bacillus anthracis-like bacteria isolated from wild great apes from Cote d'Ivoire and Cameroon

We present the microbiological and molecular characterization of bacteria isolated from four chimpanzees and one gorilla thought to have died of an anthrax-like disease in Côte d'Ivoire and Cameroon. These isolates differed significantly from classic Bacillus anthracis by the following criteria: motility, resistance to the gamma phage, and, for isolates from Cameroon, resistance to penicillin G. A capsule was expressed not only after induction by CO(2) and bicarbonate but also under normal growth conditions. Subcultivation resulted in beta-hemolytic activity and gamma phage susceptibility in some subclones, suggesting differences in gene regulation compared to classic B. anthracis. The isolates from Côte d'Ivoire and Cameroon showed slight differences in their biochemical characteristics and MICs of different antibiotics but were identical in all molecular features and sequences analyzed. PCR and Southern blot analyses confirmed the presence of both the toxin and the capsule plasmid, with sizes corresponding to the B. anthracis virulence plasmids pXO1 and pXO2. Protective antigen was expressed and secreted into the culture supernatant. The isolates possessed variants of the Ba813 marker and the SG-749 fragment differing from that of classic B. anthracis strains. Multilocus sequence typing revealed a close relationship of our atypical isolates with both classic B. anthracis strains and two uncommonly virulent Bacillus cereus and Bacillus thuringiensis isolates. We propose that the newly discovered atypical B. anthracis strains share a common ancestor with classic B. anthracis or that they emerged recently by transfer of the B. anthracis plasmids to a strain of the B. cereus group.

Fecal bacterial diversity in a wild gorilla

We describe the bacterial diversity in fecal samples of a wild gorilla by use of a 16S rRNA gene clone library and terminal-restriction fragment length polymorphism (T-RFLP). Clones were classified as Firmicutes, Verrucomicrobia, Actinobacteria, Lentisphaerae, Bacteroidetes, Spirochetes, and Planctomycetes. Our data suggest that fecal populations did not change temporally, as determined by T-RFLP.

Intestinal parasites and bacteria of mountain gorillas (Gorilla beringei beringei) in Bwindi Impenetrable National Park, Uganda

A survey in 1994 examined intestinal helminths and bacterial flora of mountain gorillas (Gorilla beringei beringei) in Bwindi Impenetrable National Park, Uganda. Parasites and bacteria were identified to genus in the feces of two groups of tourist-habituated and one group of non-tourist-habituated mountain gorillas. Eggs were identified as those of an anoplocephalid cestode, and nematode eggs representative of the genera: Trichuris, Ascaris, Oesophagostomum, Strongyloides, and Trichostrongylus. This is the first report of Ascaris lumbricoides-like eggs in mountain gorillas. Fecal samples (n=76) from all groups contained helminth eggs, with strongyle eggs and anoplocephalid eggs being the most common. Salmonella and Campylobacter were found in both gorilla groups. Regular long-term non-invasive fecal monitoring of the populations of mountain gorillas is essential for the prevention and identification of potential health threats by intestinal parasites and bacteria in this highly endangered subspecies.

Evidence for an alpha-herpesvirus indigenous to mountain gorillas

Sera from wild mountain gorillas were screened for antibodies reactive with primate alpha-herpesviruses. Four of seven individuals tested (58%) were positive. In all four sera the highest titers were to HSV-2 followed by HSV-1 and SA8. Immunoblot analysis confirmed a preferential reactivity with HSV-2 antigen. Further analysis by competition ELISA indicated that these gorillas had experienced infection with a virus antigenically similar but not identical to HSV-2. These results represent the first evidence for an alpha-herpesvirus indigenous in a free ranging, nonhuman anthropoid species.

Varicella in a gorilla

Naturally occurring varicella was observed in a young gorilla in captivity. The isolate was demonstrated to be varicella-zoster virus by restriction enzyme analysis.

Chronic fatal disease in gorillas seropositive for simian T-lymphotropic virus I antibodies

Sera from 10 gorillas were tested by indirect immunofluorescent antibody assay, Western blotting and ELISA to Human T-lymphotropic viruses for cross-reacting with antibodies to Simian T-lymphotropic virus I (STLV-I). Four were antibody positive. Of the 4 seropositive gorillas, one has remained healthy, while 3 have died with similar disease problems as reconstructed from clinical records. It is not known whether a causal relationship exists between these diseases and STLV-I retrovirus infection.

Human T-cell leukemia virus I provirus and antibodies in a captive gorilla with non-Hodgkin's lymphoma

Antibodies reactive against human T-cell leukemia virus I (HTLV-I) were detected by indirect immunofluorescence assay using MT-2 as target cells, enzyme linked immunosorbent assay screen and competition assay, and Western blot analysis in three sera (one collected in 1979) from a captive gorilla which developed diffuse histiocytic lymphoma in 1983. The sera from four other healthy gorillas housed separately were HTLV-I antibody negative. All sera were negative for HTLV-III antibodies by enzyme linked immunosorbent assay. Southern blot analysis of DNA from lymphoma tissue after digestion with BamHI and using complete HTLV-I genome probe gave one 10-kilobase fragment and a characteristic 1.05-kilobase internal fragment detected in all known HTLV-I isolates. These results indicate that the gorilla was infected with HTLV-I or a closely related simian virus several years before the development of lymphoma.

Calicivirus isolation from three species of primates: an incidental finding

Calicivirus isolations were made from 3 species of subhuman primates. Viruses were recovered from gingival lesions associated with periodontal disease in a spider monkey, from the oropharynx of a healthy silver leaf langur, and from the spleen of a lowland gorilla that had died of systemic coccidioidomycosis. Based on the results of cross-neutralization tests, all 3 isolates were serologically indistinguishable from a primate calicivirus Pan paniscus type 1. These isolations appeared to be incidental in nature and could not be associated causally with any specific disease entity.

Establishment of a lymphoblastoid cell line and isolation of an Epstein-Barr-related virus of gorilla origin

A B-lymphoid cell line was established from a normal gorilla. The cells contained Epstein-Barr virus-related antigens, and herpesvirus particles were demonstrated by electron microscopy. DNA-DNA reassociation kinétics revealed 30 to 40% hybridization to Epstein-Barr virus with 50 genomes per cell. Examination of the viral nuclear antigen with gorilla sera showed this to be a unique isolate termed Herpesvirus gorilla. H. gorilla transformed gibbon B-lymphocytes in vitro.

Normal human tissues contain RNA and antigens related to infectious adenovirus type 2

Normal human tissues have been found to contain RNA which hybridises with four regions of the adenovirus type 2 genome, including one which contains the transforming gene(s) of this virus. The RNAs have also been extracted from gorilla organs, but not from those of chickens, suggesting that they are a feature of all normal higher primate tissues. Serological test suggest that these homologous RNAs are translated into proteins connected with essentially normal and virus-infected cell functions.