Whole-Genome Sequencing of a Salmonella enterica subsp. enterica Serovar Infantis Strain Isolated from Broiler Chicken in Peru

Abstract

This report shows the whole-genome sequence of the multidrug-resistant Salmonella enterica subsp. enterica serovar Infantis strain FARPER-219. Antibiotic resistance genes are found mainly in the plasmid. Our findings show important genetic information that provides an understanding of the recent spread of this serotype in poultry.

Genomic Epidemiology of Salmonella Infantis in Ecuador: From Poultry Farms to Human Infections

“…Infantis isolate (U2449s) presented one plasmid determinant (IncX1 and IncX1_1) despite the multidrug resistance patterns found in our isolates ( Figure 1 and Supplementary File 2 ). To further analyze the low incidence of plasmids, we mapped the raw reads from our samples against the megaplasmid p-F219 described by Vallejos-Sánchez et al ( 35 ). We found two p-F219-like plasmids.…”

“…Phenotype resistance was compared with the presence of resistance genes found by WGS. Additionally, we performed a mapping against the megaplasmid p-F219 described by Vallejos-Sánchez et al ( 35 ) using Burrows-Wheeler Aligner with BWA-MEM algorithm ( 36 ). BCFtools and vcfutils from SAMtools ( 37 ) were used to obtain the fastq files from SAM files, and the fasta sequences were transformed from fastq with Seqtk ( 38 ).…”

“…A Peruvian S . Infantis strain, FARPER-219 ( 35 ), and two Ecuadorian isolates (SRR4019589 and SRR4019602) analyzed by the US Centers for Disease Control and Prevention from two patients that developed salmonellosis after traveling to Ecuador ( 10 ) were added as references in the phylogenetic analysis of all S . Infantis isolates.…”

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

“…This feature has been reported in other studies in Ecuador, where most S. Infantis isolates presented multi-resistant phenotypes [ 16 , 17 ]. Moreover, resistance to third-generation cephalosporines mediated by the bla CTX-M-65 gene has been reported in Latin American countries, the United States and Europe [ 22 , 53 , 54 ]. Recently, this phenotype was reportedly associated with travel to South America [ 24 ], but more research is needed to ascertain whether S. Infantis strains carrying the bla CTX-M-65 gene are now endemic in countries where they are being increasingly detected.…”

“…Extended-spectrum β-lactamase-producing (ESBL) strains of NTS are resistant to extended-spectrum cephalosporins and are frequently isolated from poultry sources in Latin America [ 16 , 18 , 19 ]. The bla CTX-M gene family codes for a number of β-lactamase type enzymes that confer ESBL-producing properties to NTS and are commonly found in poultry-associated isolates from developing regions such as Latin America [ 18 , 20 , 21 , 22 ]. In Ecuador, S. Infantis is the most prevalent NTS associated with poultry, and bla CTX-M-65 is frequently detected in ESBL-producing isolates from this country [ 17 , 23 ].…”