Incidence and Genomic Background of Antibiotic Resistance in Food-Borne and Clinical Isolates of Salmonella enterica Serovar Derby from Spain

Abstract

Salmonella enterica serovar Derby (S. Derby) ranks fifth among nontyphoidal Salmonella serovars causing human infections in the European Union. S. Derby isolates (36) collected between 2006 and 2018 in a Spanish region (Asturias) from human clinical samples (20) as well as from pig carcasses, pork- or pork and beef-derived products, or wild boar (16) were phenotypically characterized with regard to resistance, and 22 (12 derived from humans and 10 from food-related samples) were also subjected to whole genome sequence analysis. The sequenced isolates belonged to ST40, a common S. Derby sequence type, and were positive for SPI-23, a Salmonella pathogenicity island involved in adherence and invasion of the porcine jejune enterocytes. Isolates were either susceptible (30.6%), or resistant to one or more of the 19 antibiotics tested for (69.4%). Resistances to tetracycline [tet(A), tet(B) and tet(C)], streptomycin (aadA2), sulfonamides (sul1), nalidixic acid [gyrA (Asp87 to Asn)] and ampicillin (blaTEM-1-like) were detected, with frequencies ranging from 8.3% to 66.7%, and were higher in clinical than in food-borne isolates. The fosA7.3 gene was present in all sequenced isolates. The most common phenotype was that conferred by the tet(A), aadA2 and sul1 genes, located within identical or closely related variants of Salmonella Genomic Island 1 (SGI1), where mercury resistance genes were also present. Diverse IncI1-I(α) plasmids belonging to distinct STs provided antibiotic [blaTEM-1, tet(A) and/or tet(B)] and heavy metal resistance genes (copper and silver), while small pSC101-like plasmids carried tet(C). Regardless of their location, most resistance genes were associated with genetic elements involved in DNA mobility, including a class one integron, multiple insertion sequences and several intact or truncated transposons. By phylogenetic analysis, the isolates were distributed into two distinct clades, both including food-borne and clinical isolates. One of these clades included all SGI1-like positive isolates, which were found in both kinds of samples throughout the entire period of study. Although the frequency of S. Derby in Asturias was very low (0.5% and 3.1% of the total clinical and food isolates of S. enterica recovered along the period of study), it still represents a burden to human health linked to transmission across the food chain. The information generated in the present study can support further epidemiological surveillance aimed to control this zoonotic pathogen.

Antimicrobial resistance, virulence potential and genomic epidemiology of global genomes of the rare Salmonella enterica serovar Orion

“…Col(MGD2), IncI1‐I(Alpha) and Col(pHAD28) were the only ones detected in more than 10% of the genomes analysed (Table 2). IncI1‐I(Alpha), identified as R64, was initially reported as a streptomycin and tetracycline resistance Salmonella plasmid (Sampei et al., 2010) and has been found in several NTS serovars worldwide (Chiou et al., 2023; Hurtado et al., 2022; Vázquez et al., 2023; Vilela et al., 2022; Vilela, Dos Prazeres, et al., 2023). Col(MGD2), identified as pMGD2, was described as a small cryptic Klebsiella pneumoniae plasmid with unknown functions.…”

Insights into the Evolution of IncR Plasmids Found in the Southern European Clone of the Monophasic Variant of Salmonella enterica Serovar Typhimurium

“…Results were interpreted according to EUCAST (The European Committee on Antimicrobial Susceptibility Testing; https://eucast.org/clinical_breakpoints/; last accessed on 12 December 2023) or to CLSI (Clinical and Laboratory Standards Institute) guidelines [33]). Genes responsible for resistance to ampicillin [bla TEM-1B , bla OXA-1 , bla PSE-1 ], chloramphenicol [cmlA1, catA1, floR], aminoglycosides [aac(3)-IV, aadA1-like, aadA2, strA, strB], sulfonamides [sul1, sul2, sul3], tetracycline [tet(B), tet(A)] and trimethoprim (dfrA1-like, dfrA12) were detected by simplex or multiplex PCR-amplifications [34]. The MIC (Minimum Inhibitory Concentration) of silver was determined by microdilution tests using AgNO 3 at concentrations ranging between 0 and 125 µM.…”

“…However, it soon became clear that S. 4, [5],12:i:-is a heterogeneous serovar, comprising multiple clonal lines which emerged at different geographical locations through independent deletion events affecting the hin-fljBA chromosomal region of diverse S. Typhimurium ancestors [16]. The predominant clone, known as the European clone, displays multidrug resistance (MDR) encoded by chromosomal genes, and belongs to sequence type (ST) 34. First reported in Europe, this clone has spread all over the world, with its proportion increasing constantly since around 2005 [5,7,15,17].…”