AMR in the studied hosts
Our findings indicated that isolates from HS has the highest levels of resistance amongst the three hosts. Frequent antibiotic exposure in humans is the most probable cause of antibiotic resistance [
13]. We initially postulated that the wild NHPs would exhibit lower levels of antibiotic resistance compared to HS due to limited interaction with humans, as well as absence of antibiotic exposure. Evidence from a previous study showed that NHPs at ecotourism sites might have a higher AMR carriage rate due to constant human presence compared to entirely wild counterparts [
14]. The acquisition of antibiotic resistance in wild animals may have a serious consequence on the transmission of antibiotic resistance strains. For instance, the wild animal may act as the carrier of the antibiotic resistance strains. The resistant strains may be further transferred to other members of ecosystems through contact and medium such as soil and water [
15].
Macaca facsicularis, an endemic species in Asia was found to harbour bacterial species with higher levels of antibiotic resistance than TC. MF is ubiquitous in Peninsular Malaysia, Sabah and Sarawak. Although the species is generally considered to be wild, MF resides at the fringe of the jungle and are well adapted to interact with humans (e.g. scavenging food waste). In addition, tourists commonly feed the macaques and this interaction alters the behaviour of animals [
16,
17]. Human-animal interactions may also increase the transmission of zoonotic disease to human especially if the subject had been bitten or scratched by the primates [
2,
9,
16]. In comparison, TC which are shy and rarely interact with humans [
18] showed the lowest carriage rate of antibiotic resistance strains amongst the three hosts studied. Historically, MF’s have been reported to be in closer contact with people and only in recent years have the TC’s been monitored to be interacting with people in an urban setting [
19].
From our study,
Enterococcus species had the highest level of resistance in all hosts, especially for HS. The high levels of resistance to vancomycin for the isolates from the two NHPs is unexplained and require further investigation. A parallel study on black capuchin monkey in Brazil detected no resistance in the isolated
Enterococcus spp. while resistance to other antibiotics including rifampicin, tetracycline, erythromycin, nitrofurantoin, chloramphenicol, and ampicillin were associated with the anthropogenic impact [
14]. On the other hand, the Enterobacteriaceae showed highest susceptibility to all antibiotics tested. However, this particular finding contract that of Bachiri et al. [
20] which showed high prevalence of CTX-M-15 gene in
E.coli isolated from Barbary macaque, suggesting wide spread resistance to beta-lactam antibiotic among the wild life in Algeria.
Staphylococcus aureus is 100% resistant to oxacillin but susceptible to most tested antibiotics. It is interesting to note that resistance to oxacillin is a characteristic of community acquired (CA)-MRSA infection [
21]. This might suggest that there is a higher risk of human to primate transfer of resistance
S. aureus than a zoonotic transfer. In line with this, anthropozoonosis transmission of
S. aureus was reported from Gambia [
22]. Nonetheless, the isolation of unique
S. aureus ST type in primate suggested that the animal can also be an unappreciated source of MRSA transmission [
23].
Host, gut microbiota and AMR carriage rate
The differences in gut microbiota across the studied hosts coincided with the hosts’ diet. Firmicutes and Bacteroidetes are the main dominant phyla in both NHPs and HS. The NHPs in this study both share some similarly to their diet which mainly consists of plants although MFs are omnivorous. Higher abundance of Firmicutes such as
Ruminococceae in MF and TC may be associated with higher fiber diet [
24]. For instance, genus
Oscillospira which is able to degrade a wide range of glycans is affiliated with the plant-based diets in humans [
25]. Conversely, HS was found to harbour higher proportion of Bacteroidetes (Fig.
6a). Members of Bacteroides was previously found to be prevalent in animal-based diet due to its’ bile-resistant characteristics and the ability to degrade fatty acid into short chain fatty acids (SCFAs) [
26]. Interestingly,
Bacteroides caccae which has the capacity to digest dietary plant polysaccharides was enriched in HS [
27].
Overall, the predicted functional metagenome of HS showed greater representation of KEGG orthologs related to functions such as amino acid and fatty acid degradation, as well as bile acid catalysis. In contrast, the gut microbial community of NHPs exhibited more functions related to bacterial colonization and replication, potentially reflecting the ecological process of functionally diverse environmental bacteria establishing within the animal host [
28].
It is noteworthy that the lower bacterial diversity in HS (Additional file
1: Fig. S1) correlated with the higher abundance of antibiotic resistant strains (Fig.
1). In addition, the distribution of antibiotic resistance profile (Fig.
3) is consistent with the composition of gut microbial community and functions (Fig.
4) where higher similarity in MF and TC as opposed to HS was observed. It is recognized that the gut bacterial assemblage may control for the colonization of pathogenic bacteria, including those that are antibiotic resistance [
29,
30]. As such, while the lower presentation of antibiotic resistant isolates in the primate may be explained by lower exposure to antibiotic, the native bacterial composition may also play a role in preventing the establishment of the viable colony of the resistant strains in the gut. Furthermore, the gut microbiota may be the reservoir for transfer of antibiotic resistance gene via horizontal gene transfer [
31]. As NHPs harbour different gut microbiota in comparison to humans, the transmission of antibiotic resistant pathogens may facilitate transfer of resistance to conventionally susceptible bacterial taxa.