First Known Report of mcr-Harboring Enterobacteriaceae in the Dominican Republic

Abstract

Colistin is a last-resort antibiotic used to treat infections caused by multidrug-resistant Gram-negative bacteria. People with a history of travel to the Dominican Republic have become sick with pathogenic bacteria carrying the mobile colistin resistance gene, mcr-1, during and after traveling. This investigation aimed to identify mcr genes in Enterobacteriaceae isolated from food animal sources in the Dominican Republic. Three hundred and eleven samples were tested, from which 1354 bacterial isolates were obtained. Real-time PCR tests showed that 70.7% (220 out of 311) of the samples and 3.2% (44 out of 1354) of the isolates tested positive for the mcr gene. All RT-PCR presumptive mcr-positive isolates (n = 44) and a subset (n = 133) of RT-PCR presumptive mcr-negative isolates were subjected to whole-genome sequencing. WGS analysis showed that 39 isolates carried the mcr gene, with 37 confirmed as positive through RT-PCR and two as negative. Further, all of the mcr-positive genomes were identified as Escherichia coli and all contained a IncX4 plasmid replicon. Resistant determinants for other antibiotics important for human health were found in almost all isolates carrying mcr genes.

Keywords: Enterobacteriaceae; Escherichia coli; IncX4; antimicrobial resistance; colistin resistance; mcr genes.

Figure 1

Sample collection sites in the Dominican Republic. Sampling locations throughout the country are marked with a red symbol.

Figure 2

Distribution of AMR determinants on mcr-positive isolates for aminoglycosides, quinolones, beta-lactams, macrolides, tetracyclines, phenicol, trimethoprim, and sulfonamides. Black cells and white cells indicate the presence and absence of genes in the bacterial genome, respectively. For origin ¹, the colors navy blue, yellow, and green, represent beef cattle, chicken, and swine, respectively. For sample ², the colors brown and red represent feces and meat, respectively. For isolation media ³, the colors pink and light blue represent VRBG0 and XLT4/BGS, respectively.

Figure 3

Black cells and white cells, indicate the presence or absence of plasmid replicon in the bacterial genome, respectively. For origin, the colors navy blue, yellow, and green, represent beef cattle, chicken, and swine, respectively. For origin ¹, the colors navy blue, yellow, and green, represent beef cattle, chicken, and swine, respectively. For sample ², the colors brown and red represent feces and meat, respectively. For isolation media ³, the colors pink and light blue represent VRBG0 and XLT4/BGS, respectively.

Figure 4

Diagrams of the genetic variation of the mcr-1 and IncX4 harboring contigs. An IncX4 plasmid replicon, mcr-1, and two partial IS26 with direct repeats (TCACACAG) were identified in variation (A–G). The IncX4 and mcr-1 were on the same contig in variations (A–F), which differed in length due to the presence of partial insertion sequences either at one end of the contig resulting in shorter contigs ((B–F); IS1294, IS903C, or IS10) or by the presence of a single ISApl1 ~2.4 kb upstream of the mcr-1 (A). In variation G, mcr-1 and IncX4 were on different contigs and portions of IS3 with direct repeats (AGT) were found on one end of each contig.