Genomic Investigation of Bacterial Co-Infection in Southern Pudu (<i>Pudu puda</i>) with Fatal Outcome: Application of Forensic Microbiology in Wildlife Impacted by Anthropogenic Disasters
2025
Valentina Aravena-Ramírez | Edhnita Inostroza-Muñoz | Fredy Riquelme | César Mellado | Nilton Lincopan | Paula Aravena | Danny Fuentes-Castillo
The southern pudu (<i>Pudu puda</i>) 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 <i>Escherichia coli</i> sequence type (ST) ST224 and a <i>Klebsiella oxytoca</i> 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 <i>E. coli</i> ST224 clone. The broad virulome (adhesins, invasins, toxins, and immune evasion genes) and resistome against beta-lactams (<i>bla</i><sub>CTX-M-1</sub>), aminoglycosides [<i>aac(3)-IId</i>, <i>aph(3′)-Ia</i>, <i>aph(3″)-Ib</i>, <i>aph(6)-Id</i>], macrolides [<i>mph(A)</i>], sulfonamides (<i>sul2</i>), trimethoprim (<i>dfrA17</i>), and fluoroquinolones (<i>gyrA</i> and <i>parC</i> mutations) of <i>E. coli</i> ST224 contributed to the treatment failure and death of the wild animal. Additionally, an oval nodule was identified in the abdominal cavity caused by <i>Acinetobacter baumannii</i> 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.
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