Accumulation of antimicrobial resistance genes in wild chimpanzees

Emergence of antimicrobial resistance (AMR) is a critical public health issue. The unregulated use of antibiotics in some regions of Sub-Saharan Africa make AMR emergence a prominent problem. Complex human-animal interfaces in these regions are hypothesized to create opportunities to transmit AMR, both in the form of resistant bacteria and mobile genetic elements carrying antibiotic resistance genes (ARGs). However, assessing the spread of ARGs into wildlife populations is complicated by naturally occurring resistance. Here, we use a longitudinal approach to explore whether the widespread use of antimicrobial compounds in West Africa was accompanied by an increase of ARGs in wild chimpanzees (Pan troglodytes verus) in Taï National Park (TNP), Côte d’Ivoire, the largest remaining piece of primary rainforest in West Africa. We analyzed 410 fecal samples from three groups collected over 17 years using hybridization capture and high-throughput sequencing to screen for over 2,000 ARGs. Both ARG abundance and the diversity of AMR classes increased. Results provide clear evidence of an increase of ARGs in this remote wild chimpanzee population during a period when ARGs increased regionally and across the globe. To detect ARGs in our reads, we used the Comprehensive Antibiotic Resistance Database version 1.0.1 (CARD) that was used to design the capture probes to characterize the ARGs present. CARD provides comprehensive information on resistance genes, mechanisms and antibiotic classes and allows for accurate identification of these genes in complex microbial samples. To reduce sequence redundancy in the CARD database, we employed CD-HIT to cluster similar nucleotide sequences (using a 95% sequence identity threshold), and retained a representative sequence from each cluster. This clustered dataset is provided in the zip dataset, along with a script highlighting the processing of reads using AMR++ v3.0 v3.