ena-STUDY-UTRECHT UNIVERSITY-13-11-2018-13:58:43:083-108
Dissemination of IncI1-I? plasmids harboring blaCMY-2 and blaSHV-12 in Salmonella enterica and Escherichia coli in multiple countries: A phylogenomic investigation
blaCMY-2 and blaSHV-12 are prevalent genes conferring resistance to Extended-Spectrum-Cephalosporins (ESC) in Salmonella enterica and Escherichia coli from Colombian poultry. The objective of this study was to investigate the genetic relatedness of blaCMY-2 and blaSHV-12-carrying IncI1-I? plasmids from animal and human sources.Sequences of blaCMY-2- and blaSHV-12-carrying IncI1 plasmids from S. enterica and E. coli were extracted from whole genome sequence data and characterized by pMLST. Publicly available plasmid sequences with relevant pMLST types and/or resistance genes were collected from GenBank and the European Nucleotide Archive (ENA). Genes were identified and phylogenomic analysis based on core genome alignments and gene presence absence was performed. Most IncI1/ST12 plasmids originated from poultry. IncI1/ST12 and its Single-Locus Variants (SLVs) in Salmonella and E. coli from American and European countries had near-identical plasmid core genomes. A sublineage of IncI1/ST231 plasmids was observed and grouped plasmids from Salmonella and E. coli from Colombian poultry and E. coli from the USA, originating from human samples. Plasmids belonging to SLVs of IncI1/ST231 were distributed in different clusters. In most blaCMY-2-carrying IncI1/ST12 plasmids from Salmonella and E. coli, the genetic environment of blaCMY-2 was identical, while it differed for blaSHV-12-carrying IncI1/ST231 plasmids. The high genomic relatedness and similarity of the genetic environment of blaCMY-2 across IncI1/ST12 plasmids suggests that blaCMY-2-carrying IncI1/ST12 plasmids originated from a common ancestor and share a common source of origin. In contrast, the differences in the genetic environment of blaSHV-12 suggests the insertion of blaSHV-12 has occurred multiple times independently.
blaCMY-2 and blaSHV-12 are prevalent genes conferring resistance to Extended-Spectrum-Cephalosporins (ESC) in Salmonella enterica and Escherichia coli from Colombian poultry. The objective of this study was to investigate the genetic relatedness of blaCMY-2 and blaSHV-12-carrying IncI1-I? plasmids from animal and human sources.Sequences of blaCMY-2- and blaSHV-12-carrying IncI1 plasmids from S. enterica and E. coli were extracted from whole genome sequence data and characterized by pMLST. Publicly available plasmid sequences with relevant pMLST types and/or resistance genes were collected from GenBank and the European Nucleotide Archive (ENA). Genes were identified and phylogenomic analysis based on core genome alignments and gene presence absence was performed. Most IncI1/ST12 plasmids originated from poultry. IncI1/ST12 and its Single-Locus Variants (SLVs) in Salmonella and E. coli from American and European countries had near-identical plasmid core genomes. A sublineage of IncI1/ST231 plasmids was observed and grouped plasmids from Salmonella and E. coli from Colombian poultry and E. coli from the USA, originating from human samples. Plasmids belonging to SLVs of IncI1/ST231 were distributed in different clusters. In most blaCMY-2-carrying IncI1/ST12 plasmids from Salmonella and E. coli, the genetic environment of blaCMY-2 was identical, while it differed for blaSHV-12-carrying IncI1/ST231 plasmids. The high genomic relatedness and similarity of the genetic environment of blaCMY-2 across IncI1/ST12 plasmids suggests that blaCMY-2-carrying IncI1/ST12 plasmids originated from a common ancestor and share a common source of origin. In contrast, the differences in the genetic environment of blaSHV-12 suggests the insertion of blaSHV-12 has occurred multiple times independently.