Comparative Genomic Analysis Discloses Differential Distribution of Antibiotic Resistance Determinants between Worldwide Strains of the Emergent ST213 Genotype of Salmonella Typhimurium

Abstract

Salmonella enterica constitutes a global public health concern as one of the main etiological agents of human gastroenteritis. The Typhimurium serotype is frequently isolated from human, animal, food, and environmental samples, with its sequence type 19 (ST19) being the most widely distributed around the world as well as the founder genotype. The replacement of the ST19 genotype with the ST213 genotype that has multiple antibiotic resistance (MAR) in human and food samples was first observed in Mexico. The number of available genomes of ST213 strains in public databases indicates its fast worldwide dispersion, but its public health relevance is unknown. A comparative genomic analysis conducted as part of this research identified the presence of 44 genes, 34 plasmids, and five point mutations associated with antibiotic resistance, distributed across 220 genomes of ST213 strains, indicating the MAR phenotype. In general, the grouping pattern in correspondence to the presence/absence of genes/plasmids that confer antibiotic resistance cluster the genomes according to the geographical origin where the strain was isolated. Genetic determinants of antibiotic resistance group the genomes of North America (Canada, Mexico, USA) strains, and suggest a dispersion route to reach the United Kingdom and, from there, the rest of Europe, then Asia and Oceania. The results obtained here highlight the worldwide public health relevance of the ST213 genotype, which contains a great diversity of genetic elements associated with MAR.

BacSeq: A User-Friendly Automated Pipeline for Whole-Genome Sequence Analysis of Bacterial Genomes

“…and Klebsiella spp. [ 39 , 40 , 41 , 42 ], implying that the ST028 isolate may be contaminated with Salmonella spp. and/or Klebsiella spp.…”

Genomic Analysis of Antibiotics Resistance in Pathogens

“…This collection also gathers papers on antibiotic resistance of some of the major emerging infections pathogens such as Mycobacteroides abscessus [ 3 ], Klebsiella pneumoniae [ 4 , 5 ], Salmonella sp. [ 6 , 7 ], Francisella tularensis [ 8 ], Acinetobacter baumannii [ 9 , 10 ], or Pseudomonas aeruginosa [ 11 ] and other human pathogens such as Neisseria gonorrhoea [ 12 ], Staphylococcus aureus [ 13 ], or Escherichia coli [ 14 ]. Most of them are high-priority pathogens [ 15 ], according to the National Institute of Allergy and Infectious Diseases, and are globally and medically important pathogens.…”

“…and Escherichia coli . Hernández-Díaz and colleagues performed a comparative genomic analysis of Typhimurium serotypes of S. enterica that led to the identification of 44 genes, 34 plasmids, and 5 point mutations associated with antibiotic resistance, distributed across 220 genomes of ST213 strains [ 6 ]. Vázquez et al, on the other hand, performed a genomic analysis of S. enterica serotype Infantis to identify pESI -like plasmids encoding blaCTX-M-65 [ 7 ].…”