International Spread of Multidrug-Resistant Rhodococcus equi

Abstract

A multidrug-resistant clone of the animal and human pathogen Rhodococcus equi, MDR-RE 2287, has been circulating among equine farms in the United States since the 2000s. We report the detection of MDR-RE 2287 outside the United States. Our finding highlights the risk for MDR-RE spreading internationally with horse movements.

Keywords: MDR R. equi; MDR-RE; R. equi MDR 2287 clone; Rhodococcus equi; TnRErm46; United States; antimicrobial resistance; bacteria; erm(46); macrolide resistance; multidrug-resistant Rhodococcus equi; pRErm46; rifampin resistance; zoonoses.

Figure 1

Whole-genome phylogenetic analysis of Rhodococcus equi and its multidrug-resistant 2287 clone. Asterisk indicates strain 103S used as reference genome (GenBank accession no. FN563149). For analysis we used 92 R. equi genome sequences including 68 macrolide-resistant and -susceptible equine isolates from the United States and 22 global strains from a previously reported R. equi diversity set (14) (italics). Macrolide-resistant isolates include 36 members of the MDR-RE 2287 clonal complex (red text) as well as isolates representing spillages of the pRErm46 plasmid to other R. equi genotypes (8,10). Arrows indicate the 2 MDR-RE 2287 isolates from Ireland. Labels indicate geographic origin, year of isolation, and resistance phenotype when applicable (MR^R, macrolide and rifampin resistance; M^R, macrolide resistance; R^R, rifampin resistance). Symbols indicate pRErm46 carriage in macrolide-resistant isolates, described in the key; open circles indicate MDR-RE isolates where pRErm46 has been lost after transposition of the TnRErm46 element to the host genome (8). Numbers at nodes indicate bootstrap values for 1,000 replicates. Tree was drawn with FigTree (http://tree.bio.ed.ac.uk/software/figtree).

Figure 2

Unrooted maximum-likelihood tree of multidrug-resistant Rhodococcus equi 2287 clonal complex showing the relationships of the isolates from Ireland (arrows). Whole-genome phylogeny inferred from 45 parsimony informative sites using SNIPPY (https://github.com/tseemann/snippy) and IQ-tree (http://www.iqtree.org) for tree reconstruction. Best-fit model was selected by IQ-tree’s ModelFinder module. Bootstrap values >50 are shown. The genome of the prototype MDR-RE 2287 isolate PAM2287 (National Center for Biotechnology Information assembly accession no. GCA_002094405.1) was used as a reference for SNP calling. Labels indicate isolate name, geographic origin (FL, Florida; IRL, Ireland, KY, Kentucky; NY, New York; TX, Texas), and year of isolation. Symbols indicate pRErm46 plasmid type. Tree was drawn with FigTree (http://tree.bio.ed.ac.uk/software/figtree).