Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the blaCTX-M-65 Gene with or without fosA3 in pESI-like Plasmids

Abstract

Salmonella enterica serovar Infantis (S. Infantis) is a broiler-associated pathogen which ranks in the fourth position as a cause of human salmonellosis in the European Union. Here, we report a comparative genomic analysis of two clinical S. Infantis isolates recovered in Spain from children who just returned from Peru. The isolates were selected on the basis of resistance to cefotaxime, one of the antibiotics of choice for treatment of S. enterica infections. Antimicrobial susceptibility testing demonstrated that they were resistant to eight classes of antimicrobial agents: penicillins, cephalosporins, phenicols, aminoglycosides, tetracyclines, inhibitors of folate synthesis, (fluoro)quinolones and nitrofurans, and one of them was also resistant to fosfomycin. As shown by whole-genome sequence analysis, each isolate carried a pESI-like megaplasmid of ca. 300 kb harboring multiple resistance genes [blaCTX-M-65, aph(4)-Ia, aac(3)-IVa, aph(3′)-Ia, floR, dfrA14, sul1, tet(A), aadA1 ± fosA3], as well as genes for resistance to heavy metals and disinfectants (mer, ars and qacEΔ1). These genes were distributed in two complex regions, separated by DNA belonging to the plasmid backbone, and associated with a wealth of transposable elements. The two isolates had a D87Y amino acid substitution in the GyrA protein, and truncated variants of the nitroreductase genes nfsA and nsfB, accounting for chromosomally encoded resistances to nalidixic acid and nitrofurantoin, respectively. The two S. Infantis isolates were assigned to sequence type ST32 by in silico multilocus sequence typing (MLST). Phylogenetic analysis revealed that they were closely related, differing only by 12 SNPs, although they were recovered from different children two years apart. They were also genetically similar to blaCTX-M-65-positive ± fosA3 isolates obtained from humans and along the poultry production chain in the USA, South America, as well as from humans in several European countries, usually associated with a travel history to America. However, this is the first time that the S. Infantis blaCTX-M-65 ± fosA3 MDR clone has been reported in Spain.

Plasmid Composition, Antimicrobial Resistance and Virulence Genes Profiles of Ciprofloxacin- and Third-Generation Cephalosporin-Resistant Foodborne Salmonella enterica Isolates from Russia

“…Furthermore, recently pESI-like megaplasmids were revealed in Russia [ 18 , 19 ]. These plasmids are conjugative with up to 300 kb length and harbor AMR genes including ESBL genes, as well as genes conferring resistance to tetracyclines, sulphonamides, and aminoglycosides [ 20 ].…”

Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing

“…Infantis isolated from broilers and humans in Italy ( Franco et al, 2015 ), in E. coli from cattle in the Netherlands ( Dantas Palmeira and Ferreira, 2020 ) and more recently from beef and pork samples collected at retail in Portugal ( Leão et al, 2021 ) and in S . Infantis from human cases in Spain ( Vázquez et al, 2022 ). To the best of the authors’ knowledge, this is the first reported case of a bla CTX-M-65 isolated from the environment in Ireland.…”

Antimicrobial Resistance and Genomic Characterization of Salmonella Infantis from Different Sources

“…Antibiotic resistance (AR) plays an important role in the increased incidence of different bacterial infections. Indeed, the high level of resistance and multi-drug resistance (MDR) recorded in S. Infantis in multiple countries (i.e., Italy, Hungary, Germany, Russia, United States) can be considered another reason for the epidemiological success of this serovar [ 13 , 14 ]. The extended AR exhibited by Salmonella species and other pathogenic bacteria is due to the use and misuse of antibiotics in humans and animals (both in livestock and aquaculture species); these latter, moreover, may spread antibiotic-resistant bacteria (ARB) via their faces and contaminate the terrestrial and marine environment [ 12 ].…”