Genomic Investigation of Bacterial Co-Infection in Southern Pudu (Pudu puda) with Fatal Outcome: Application of Forensic Microbiology in Wildlife Impacted by Anthropogenic Disasters

The southern pudu (Pudu puda) faces significant threats from anthropogenic activities and infectious diseases. Using whole-genome sequencing (WGS) and forensic microbiology research, we describe a triple bacterial co-infection in a southern pudu impacted by wildfire disasters. The deer presented infected burn wounds on the extremities and dog bite wounds in the lumbosacral region, from which a multidrug-resistant CTX-M-1-producing Escherichia coli sequence type (ST) ST224 and a Klebsiella oxytoca ST145 were isolated, respectively. The patient died 13 days after admission in a wildlife rehabilitation center. During the necropsy, a sample from intracardiac blood was collected, and WGS analyses confirmed systemic dissemination of an E. coli ST224 clone. The broad virulome (adhesins, invasins, toxins, and immune evasion genes) and resistome against beta-lactams (blaCTX-M-1), aminoglycosides [aac(3)-IId, aph(3′)-Ia, aph(3″)-Ib, aph(6)-Id], macrolides [mph(A)], sulfonamides (sul2), trimethoprim (dfrA17), and fluoroquinolones (gyrA and parC mutations) of E. coli ST224 contributed to the treatment failure and death of the wild animal. Additionally, an oval nodule was identified in the abdominal cavity caused by Acinetobacter baumannii ST1365, the first WGS-confirmed report in wildlife. This study highlights the value of applying forensic microbiology and WGS to investigate and understand One Health pathogens threatening wildlife impacted by natural and anthropogenic disasters.