Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands

Abstract

<i>Salmonella</i> Infantis, a common contaminant of poultry products, is known to harbor mobile genetic elements that confer multi-drug resistance (MDR) and have been detected in many continents. Here, we report four MDR <i>S</i>. <i>Infantis</i> strains recovered from poultry house environments in Santa Cruz Island of the Galapagos showing extended-spectrum β-lactamase (ESBL) resistance and reduced fluoroquinolone susceptibility. Whole-genome sequencing (WGS) revealed the presence of the ESBL-conferring <i>bla</i>_CTX-M-65 gene in an IncFIB-like plasmid in three <i>S</i>. Infantis isolates. Multi-locus sequence typing (MLST) and single nucleotide variant/polymorphism (SNP) SNVPhyl analysis showed that the <i>S</i>. Infantis isolates belong to sequence type ST32, likely share a common ancestor, and are closely related (1-3 SNP difference) to <i>bla</i>_CTX-M-65-containing clinical and veterinary <i>S</i>. Infantis isolates from the United States and Latin America. Furthermore, phylogenetic analysis of SNPs following core-genome alignment (i.e., ParSNP) inferred close relatedness between the <i>S</i>. Infantis isolates from Galapagos and the United States. Prophage typing confirmed the close relationship among the Galapagos <i>S</i>. Infantis and was useful in distinguishing them from the United States isolates. This is the first report of MDR <i>bla</i>_CTX-M-65-containing <i>S</i>. Infantis in the Galapagos Islands and highlights the need for increased monitoring and surveillance programs to determine prevalence, sources, and reservoirs of MDR pathogens.