Transduction as a Potential Dissemination Mechanism of a Clonal qnrB19-Carrying Plasmid Isolated From Salmonella of Multiple Serotypes and Isolation Sources

Abstract

Antimicrobial resistance is an increasing problem worldwide, and Salmonella spp. resistance to quinolone was classified by WHO in the high priority list. Recent studies in Europe and in the US reported the presence of small plasmids carrying quinolone resistance in Enterobacteriaceae isolated from poultry and poultry products. The aims of this study were to identify and characterize plasmid-mediated quinolone resistance in Salmonella spp. and to investigate transduction as a possible mechanism associated to its dissemination. First, we assessed resistance to nalidixic acid and/or ciprofloxacin in 64 Salmonella spp. and detected resistance in eight of them. Genomic analyses determined that six isolates of different serotypes and sources carried an identical 2.7-kb plasmid containing the gene qnrB19 which confers quinolone resistance. The plasmid detected also has high identity with plasmids reported in the US, Europe, and South America. The presence of similar plasmids was later surveyed by PCR in a local Salmonella collection (n = 113) obtained from diverse sources: food (eggs), wild and domestic animals (pigs, horse, chicken), and human clinical cases. qnrB19-carrying plasmids were found in 8/113 Salmonella tested strains. A bioinformatics analysis including Chilean and previously described plasmids revealed over 95.0% of nucleotide identity among all the sequences obtained in this study. Furthermore, we found that a qnrB19-carrying plasmid can be transferred between Salmonella of different serotypes through a P22-mediated transduction. Altogether our results demonstrate that plasmid-mediated quinolone resistance (PMQR) is widespread in Salmonella enterica of different serotypes isolated from human clinical samples, wild and domestic animals, and food in Chile and suggest that transduction could be a plausible mechanism for its dissemination. The occurrence of these antimicrobial resistance elements in Salmonella in a widespread area is of public health and food safety concern, and it indicates the need for increased surveillance for the presence of these plasmids in Salmonella strains and to assess their actual impact in the rise and spread of quinolone resistance.

Keywords: Chile; Salmonella spp.; antimicrobial resistance; foodborne diseases; plasmid; plasmid-mediated quinolone resistance; qnrB19; quinolones.

Figure 1

Linear representation of plasmids carrying the qnrB19 gene. Plasmids pPAB19-4, pHAD28, and pN44358F were selected to represent different clusters resulting from the phylogenetic analysis (Supplementary Figure S1). Alignment was crafted with the ClustalW plug-in in Geneious Prime 2019 using default parameters. Consensus identity bar: green represents 100% identity among all sequences, green-brown indicates 30 to <100% identity, and red shows <30% identity. Genomic features are represented by different colors; brown: plasmid origin of replication (rep_origin; nt 1-564); orange: Origen of transfer (oriT; nt 677-851); red: genes qnrB-19 (nt 2,402-1,758) and gene pspF (nt2,647-2,496); yellow: ISEcp1C-like insertion sequence (nt 2,512-2,409). Primer alignment sites are represented in blue: INT-F and INT-R represent primers for the intergenic region. QNR-F and QNR-R represent primers for the qnrB-19 gene region.

Figure 2

Phylogenetic tree of 16 pPAB-19-like plasmids inferred by maximum-likelihood analysis The analysis included 16 plasmids including six previously described plasmids and 10 plasmids described in the present study. Phylogeny was inferred with RAxML in Geneious Prime (Biomatters, New Zealand) with 1,000 replicates. Colored names represent plasmid sequence source. Red: data from NCBI; blue: genomes reported in Toro et al. (2015) and Toro et al. (2016); green: this study.

Figure 3

Whole plasmid sequence comparison of 16 qnrB-19-like plasmids. The analysis included 16 plasmids including six previously described plasmids and 10 plasmids described in the present study. Whole plasmid sequence comparison was performed with the Mauve plug-in in Geneious Prime with default settings. White box represents location of the qnrB-19 gene in each plasmid sequence. Red filled bars represent identity among tested sequences.