One Health assessment of antimicrobial-resistant Enterobacterales and ESKAPE pathogens in little stints (Calidris minuta) and aquatic ecosystems of the Kenyan Rift Valley

Palearctic migratory little stints (Calidris minuta) can acquire resistant bacteria from anthropized environments and spread them across different hosts and borders. This two-year cross-sectional study assessed the prevalence of multidrug-resistant (MDR) and extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales and ESKAPE pathogens isolated from C. minuta and their aquatic foraging ecosystems at two Kenyan Rift Valley lakes, Bogoria (low anthropogenic activities) and Magadi (high impact). A total of 184 fecal samples from C. minuta and 48 water samples were collected during the birds arrivals (cohort 1) and departures (cohort 2). Samples were cultured, bacterial isolates were identified using MALDI-TOF MS platform and tested against 12 antimicrobials using the Kirby-Bauer disk method. Of the 294 isolates (16 genera and 33 species), Enterobacter species (31%) and Escherichia coli (17.3%) were predominant. Resistance was highest for ampicillin (50%), amoxicillin-clavulanic acid (36.4%), and tetracycline (32.7%), and lowest for meropenem (1.0%) and cefepime (3.4%). The predominant MDR phenotype was a combination of resistances to ampicillin, tetracycline, and trimethoprim-sulfamethoxazole. Enterobacter species showed the highest frequencies of MDR (8.5%) and ESBL-MDR (4.4%) phenotypes, while Acinetobacter species were the most frequent ESBL producers. Despite observing higher median resistances in isolates from Lake Magadi (7.1), C. minuta (8.0) and cohort 2 (7.1) than those from Lake Bogoria (6.7), water samples (5.9) and cohort 1 (6.5), these differences were statistically insignificant (p-values= 0.833, 0.147, 0.210). This suggests that while human activities drive AMR spread, resistant strains are pervasive even in minimal human-influenced environments. This is the first study to link C. minuta to the AMR epidemiological circuit. Our findings underscore the need to include migratory wild birds in AMR surveillance in the Kenyan Rift Valley, to implement stringent environmental stewardship measures to curb anthroponotic AMR transmissions and utilizing whole-genome sequencing to accurately trace the origin and dissemination pathways of AMR strains.