Salmonella in Coastal Birds in Chile: Detection of a Multidrug-Resistant S. Infantis Bearing the blaCTX-M−65 Gene in a pESI-Like Megaplasmid in Humboldt Penguins

Abstract

Salmonella enterica is one of the most important foodborne pathogens worldwide, and the emergence of multidrug resistance (MDR) clones can aggravate its public health importance. Wildlife species may act as reservoirs of these clones, but their role is not well understood. In this study, faecal samples from shorebirds, with a focus on the endangered Humboldt penguin (Spheniscus humboldti), collected from five sites in central Chile with different levels of anthropogenic pressure were analysed to characterize antimicrobial resistant S. enterica serovars. Overall, Salmonella was isolated from 22 of the 595 samples (3.7%), with positivity ranging between 1.6% and 9.5%, depending on the sampling site. Four of the Salmonella isolates were retrieved from Humboldt penguin samples (1.4% positive samples in this species). Serovars Infantis (nine isolates), Typhimurium (six), Goldcoast (four), and Enteritidis, Agona, and Give (one isolate each) were identified. Resistance levels were the highest for sulphamethoxazole (13/21 isolates with a non-wild-type phenotype), ciprofloxacin, tetracycline, and trimethoprim (11/21 each). Whole-genome sequencing performed on eight S. Infantis strains revealed that seven carried the plasmid replicon IncFIB (pN55391), indicating the presence of the pESI-like megaplasmid, harbouring resistance determinants to multiple antimicrobial classes as well as heavy metal, biocides, and virulence-related genes. Furthermore, five S. Infantis isolates that showed an ESBL phenotype carried the bla_CTX-M−65 gene, three of which were detected in Humboldt penguin faeces. The finding of an international emerging S. Infantis clone in protected wildlife is of concern to environmental, animal, and public health specialists, supporting initiatives for an active surveillance of resistance and virulence traits in wildlife exposed to anthropogenic areas.