Enteritis remains a significant cause of mortality in farmed Nile crocodile (Crocodylus niloticus) hatchlings, with Escherichia coli frequently implicated in disease outbreaks. This study aimed to assess the antimicrobial susceptibility profiles of E. coli isolates from affected hatchlings and characterize the gut microbiome dynamics during enteritis episodes in intensive farming systems. A longitudinal investigation (2018–2024) was conducted across four Zambian crocodile farms, involving bacterial isolation and antibiotic susceptibility testing of E. coli from 62 confirmed outbreaks. In 2024, 16S rRNA gene sequencing was performed on gastrointestinal tract samples to analyze microbial community composition along the stomach, anterior, mid, and posterior intestines.
Results revealed a marked increase in antimicrobial resistance among E. coli isolates over time, with complete resistance to amoxicillin–clavulanic acid, tetracyclines, and trimethoprim–sulfamethoxazole observed by 2024. Enrofloxacin remained the most effective antibiotic, with approximately 70% susceptibility retained. Gut microbiome profiling showed dominance of Proteobacteria, particularly Enterobacteriaceae, across all intestinal segments, indicative of microbial dysbiosis. Diversity increased distally along the gut, with Fusobacteriota, Clostridiota, and Bacteroidota becoming more prominent in the posterior intestine, though Enterobacteriaceae persisted at high levels.
The study highlights a concerning trend of multidrug-resistant E. coli in crocodile hatchlings, likely driven by antibiotic misuse, and underscores the role of gut dysbiosis in enteric disease pathogenesis. These findings emphasize the need for integrated health management strategies that promote prudent antibiotic use and explore microbiome-restoring interventions such as probiotics. Improved biosecurity, targeted treatment guided by antibiograms, and support for healthy gut flora may enhance hatchling resilience and reduce outbreak frequency in commercial crocodile farming.