Rectal Bacteria and Antibiotic Resistance in Zoo Animals in Algeria

Background/Objectives: Healthy animals can harbor complex and diverse bacterial communities, including pathogenic taxa capable of causing disease and mortality, and individuals that are kept in zoos may act as asymptomatic carriers of a broad range of pathogens. Therefore, this study aimed to investigate the rectal bacterial microbiota of multiple animal classes (reptiles, birds, and mammals), maintained in enclosures, identify known or emerging bacterial pathogens, and characterize the antibiotic resistance profiles of the isolated strains. Methods: A total of 40 samples were collected by rectal swabbing for bacteriological analysis from 31 different animal species living in enclosures in four Algerian zoos. The isolated and identified bacterial strains were tested against certain antibiotics used in human and veterinary medicine. Statistical analyses were performed to assess differences in bacterial isolation among animal classes, sex, age categories, and zoological facilities, as well as the degree of similarity between isolated strains based on their antibiotic resistance profiles. Results: A total of 94 bacterial isolates were recovered from 40 fecal samples. Overall, the bacterial isolates belonged to seven families, 13 genera, and 16 taxa. The families identified were Enterobacteriaceae (50/94; 53.19%), Staphylococcaceae (28/94; 29.78%), Pseudomonadaceae (6/94; 6.38%), Brucellaceae (2/94; 2.12%), Morganellaceae (4/94; 4.25%), Yersiniaceae (3/94; 3.19%), and Erwiniaceae (1/94; 1.06%). Reptiles accounted for the highest number of isolates (37/94; 39.36%), followed by 31/94 isolates (32.97%) for birds and 26/94 isolates (27.65%) for mammals. The highest resistance rates were observed for ampicillin (AMP; 95.73%), followed by amoxicillin/clavulanic acid (AMC; 75.54%) and cephalothin (CEP; 44.90%). Lower resistance rates were detected for trimethoprim–sulfamethoxazole (SXT; 18.87%), cefotaxime (CTX; 17.41%), ceftazidime (CX; 13.67%), ciprofloxacin (CIP; 6.38%), and gentamicin (GEN; 1.05%). Conclusion: This study shows the first report that vertebrates in Algerian zoos can harbor a diverse range of cultivable bacteria, often with polymicrobial carriage. Antimicrobial resistance patterns were generally consistent with commonly used veterinary drugs. Overall, these findings contribute to a better understanding of the composition of rectal bacterial carriage in zoos.