The emergence of mobile mcr genes mediating resistance to colistin is a critical public health issue that has hindered the treatment of serious infections caused by multidrug-resistant pathogens in humans and other animals. We report the emergence of the mcr-9.1 gene in a polymyxin-resistant extended-spectrum β-lactamase (ESBL)-producing Enterobacter kobei infecting a free-living Franciscana dolphin (Pontoporia blainvillei), threatened with extinction in South America. Genomic analysis confirmed a wide resistome with additional presence of genes conferring resistance to clinically relevant β-lactam [blaCTX-M-15, blaACT-9, blaOXA-1 and blaTEM-1B], aminoglycoside [aac(3)-IIa, aadA1, aph(3’‘)-Ib and aph(6)-Id], trimethoprim [dfrA14], tetracycline [tetA], quinolone [aac(6’)-Ib-cr and qnrB1], fosfomycin [fosA], sulphonamide [sul2], and phenicol [catA1 and catB3] antibiotics. The identification of mcr-9.1 in a CTX-M-15-producing pathogen infecting a critically endangered animal is worryingly, due to the restricted therapeutic options, and should be interpreted as a sign of further spread of critical-priority pathogens and their resistance genes in threatened ecosystems.
Even though antimicrobial-resistant bacteria have begun to be detected in wildlife, raising important issues related to their transmission and persistence of clinically important pathogens in the environment, little is known about the role of these bacteria on wildlife health, especially on endangered species. The Brazilian merganser (Mergus octosetaceus) is one of the most threatened waterfowl in the world, classified as Critically Endangered by the International Union for Conservation of Nature. In 2019, a fatal case of sepsis was diagnosed in an 8-day-old Brazilian merganser inhabiting a zoological park. At necropsy, major gross lesions were pulmonary and hepatic congestion. Using microbiologic and genomic methods, we identified a multidrug-resistant (MDR) extended-spectrum β-lactamase (ESBL) CTX-M-8-producing Escherichia coli (designed as PMPU strain) belonging to the international clone ST58, in celomic cavity, esophagus, lungs, small intestine and cloaca samples. PMPU strain harbored a broad resistome against antibiotics (cephalosporins, tetracyclines, aminoglycosides, sulfonamides, trimethoprim, and quinolones), domestic/hospital disinfectants, and heavy metals (arsenic, mercury, lead, copper, and silver). Additionally, the virulence of E. coli PMPU strain was confirmed using a wax moth (Galleria mellonella) infection model, and it was supported by the presence of virulence genes encoding toxins, adherence factors, invasins and iron acquisition systems. Broad resistome and virulome of PMPU contributed to therapeutic failure and death of the animal. In brief, we report for the first time a fatal colibacillosis by MDR-ESBL-producing E. coli in critically endangered Brazilian merganser, highlighting that besides colonization, critical priority pathogens are threatening wildlife. E. coli ST58 clone has been previously reported in humans, food-producing animals, wildlife, and environment, supporting broad adaptation and persistence at human-animal-environment interface.