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

Elton Burnett; Maria Ishida; Sofia de Janon; Sohail Naushad; Marc-Olivier Duceppe; Ruimin Gao; Armando Jardim; Jessica C Chen; Kaitlin A Tagg; Dele Ogunremi; Christian Vinueza-Burgos

doi:10.3390/antibiotics10030267

Whole-Genome Sequencing Reveals the Presence of the bla_CTX-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

Antibiotics (Basel). 2021 Mar 5;10(3):267. doi: 10.3390/antibiotics10030267.

Authors

Affiliations

¹ Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada.
² Division of Food Laboratory, New York State Department of Agriculture and Markets, Albany, NY 12206, USA.
³ Unidad de investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito 170103, Ecuador.
⁴ Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON K2J 4S1, Canada.
⁵ Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
⁶ Weems Design Studio Inc., Decatur, GA 30032, USA.

Abstract

Salmonella 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 S. Infantis 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 bla_CTX-M-65 gene in an IncFIB-like plasmid in three S. Infantis isolates. Multi-locus sequence typing (MLST) and single nucleotide variant/polymorphism (SNP) SNVPhyl analysis showed that the S. Infantis isolates belong to sequence type ST32, likely share a common ancestor, and are closely related (1-3 SNP difference) to bla_CTX-M-65-containing clinical and veterinary S. 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 S. Infantis isolates from Galapagos and the United States. Prophage typing confirmed the close relationship among the Galapagos S. Infantis and was useful in distinguishing them from the United States isolates. This is the first report of MDR bla_CTX-M-65-containing S. Infantis in the Galapagos Islands and highlights the need for increased monitoring and surveillance programs to determine prevalence, sources, and reservoirs of MDR pathogens.

Keywords: Galapagos; Salmonella Infantis; extended-spectrum β-lactamase; multi-drug resistance.