Mega-plasmid found worldwide confers multiple antimicrobial resistance in Salmonella Infantis of broiler origin in Russia

• Published in: International journal of food microbiology Vol. 319; p. 108497
• Main Authors: Bogomazova, Alexandra N., Gordeeva, Veronika D., Krylova, Ekaterina V., Soltynskaya, Irina V., Davydova, Ekaterina E., Ivanova, Olga E., Komarov, Alexander A.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 16.04.2020; Elsevier BV
• Subjects: Antimicrobial agents; Antimicrobial resistance; Antitoxins; Bioinformatics; Chicken food products; Clusters; Drug resistance; Fluoroquinolones; Food production; Gene sequencing; Genes; Genomes; Modules; Multidrug resistance; Mutation; Operons; pESI-like plasmid; Plasmids; pMLST; Poultry; Salmonella; Salmonella enterica; Salmonella Infantis; Toxins; Virulence; Whole genome sequencing; United States > US; Japan; Russia; ST; MLST; AMR; Multidrug resistance; pESI-like plasmid; IS; Salmonella enterica; Chicken food products; BMD; ESBL; pESI; MDR; pMLST
• ISSN: 0168-1605; 1879-3460
• DOI: 10.1016/j.ijfoodmicro.2019.108497

Plasmids which are the mobile part of the bacterial genome can acquire and carry over genes conferring antimicrobial resistance, thus contributing to rapid adaptation of bacterial community to human-defined environment. In 2014, Israeli scientists have reported a large conjugative mega-plasmid pESI (plasmid for emerging S. Infantis) that provides multiple drug resistance (MDR) of Salmonella Infantis isolated from broilers. Later, very similar pESI-like plasmids have been found in Salmonella isolated from poultry in the United States, Italy, Switzerland, Hungary, and Japan. Here we report detection of pESI-like plasmids in Salmonella Infantis isolated from chicken food products in Russia. Whole genome sequencing of three MDR isolates revealed pESI-like plasmids in all three cases. These plasmids have such typical pESI features as a locus for siderophore yersiniabactin, a cluster of IncI1 conjugative genes, a cluster of type IV pilus genes, and three toxin-antitoxin modules. The pESI-like plasmids carry from two to five resistance genes in each isolate. In total, we observed six antimicrobial resistance genes associated with pESI-like plasmids (aadA1, blaCTX-M-14, dfrA14, sul1, tetA/tetR, tetM). Besides plasmid genes of antimicrobial resistance, all three MDR isolates of S. Infantis harbor a mutation in chromosomal gene gyrA (p.S83Y or p.D87Y) that is associated with resistance to fluoroquinolones. In addition, we performed a comparative bioinformatics meta-analysis of 25 pESI-like plasmids hosted by S. Infantis from the USA, Europe, Latin America, Israel, and Japan. This analysis identified a 173 kB sequence that is common for all pESI-like plasmids and carries virulence operons and toxin-antitoxin modules. •The pESI-like plasmids largely defined MDR phenotype of three strains S. Infantis isolated from broilers in Russia.•The pESI-like plasmids occurred globally in S. Infantis associated with poultry.•The pESI-like plasmids shared 173 kB sequence that carried two virulence operons and three toxin-antitoxin modules.•Some pESI-like plasmids acquired the bulk of AMR genes via integration into preexisting IncI11 plasmid that carried AMR genes.