International Spread of Multidrug-Resistant Rhodococcus equi

Abstract

R hodococcus equi is a soilborne aerobic actinomycete bacterium that infects animals and humans. Human infections are opportunistic, zoonotic in origin, and considered to be linked to exposure to farm environments (1-3). Although clinical R. equi infections are relatively rare in most animal species, foals are commonly affected, and incidence is often high in horse farms in equine breeding countries (4). Long courses of rifampin and a macrolide is the mainstay therapy for foal rhodococcosis. This treatment has been systematically used since the 1980s and no significant resistance was detected until the early 2000s, after mass prophylactic application at R. equiendemic farms in the United States (5,6).The emerging dual macrolide-rifampin resistance is attributable to a multidrug-resistant R. equi (MDR-RE) clone, named 2287, which has spread among horse farms across the United States. MDR-RE 2287 arose by co-acquisition of the conjugative plasmid pRErm46 and a specific rpoB S531F (TCG to TTC) mutation conferring high-level rifampin resistance (7,8). pRErm46 specifies resistance to macrolides, lincosamides, and streptogramins via the erm(46) gene carried on TnRErm46, a highly mobile transposon, and to sulfonamides, streptomycin, spectinomycin, tetracycline, and doxycycline via a class 1 integron (C1I) and associated tetRA(33) determinant (9). Although it has so far been found only in the United States, we predicted MDR-RE could spread to other countries with the movement of equids (10). The StudyAfter MDR-RE was characterized in 2019 (8), we established an informal surveillance network with colleagues in North and South America, Europe, the United Kingdom, Africa, Asia, and Australia. We asked collaborating laboratories to review their retrospective R. equi collections and prospectively identify isolates with erythromycin MIC >4 μg/mL, potentially denoting erm(46)-mediated macrolide resistance. Two equine clinical strains from necropsied foals in Ireland met the criterion: PAM2528, recovered in 2016, and PAM2578, recovered in 2021 (henceforth designated as 2528 and 2578). Both strains originated from the same farm and had MICs >32 μg/mL for erythromycin and >256 μg/mL for rifampin, consistent with MDR-RE's resistance phenotype (7-10).We confirmed that both isolates were erm(46) positive by PCR and carried the rpoB S531F mutation unique to the MDR-RE 2287 clone using previously described methods (9). A PCR using primers 5′-CCGAGATGTGTCGGACTTC-3′ (forward) and 5′-CGCCGAAGAACAACCCGAGGATG-3′ (reverse) showed the pRErm46 resistance plasmid carried the ΔC1I-tetRA deletion, observed in some recent MDR-RE isolates (9,10). Accordingly, 2528 and 2578 were susceptible to trimethoprim/sulfamethoxazole, streptomycin, spectinomycin, and tetracycline, to which the C1I-tetRA(33) determinant confers resistance (9). We used paired-end Illumina sequencing (Illumina, https://www.illumina.com) to obtain genomic libraries of the isolates. Reads were quality-checked using FastQC version 0.11.9 (https://www.bioinformatics.babraham.ac.uk/pr...

Update on emerging multidrug‐resistant Rhodococcus equi

“…We have now detected pRErm46 in other R equi genomotypes (either associated with different rpoB mutations – eg, S531L, S531Y – or without them), indicating that the pRErm46 plasmid has begun to spill across the equine‐associated R equi population 15,21 . pRErm46 plasmid loss with macrolide resistance linked to transposition of Tn RErm46 onto the host genome has also been detected in some MDR‐RE 2287 sublineages 15,20 …”

“…Interestingly, despite the high horizontal transferability of pRErm46, the vast majority of the macrolide‐resistant R equi isolates belong to the same strain, a specific clonal subpopulation named MDR‐RE ‘2287‘ (after the designation of the prototype isolate kept in our laboratory in Edinburgh, PAM2287) 15,17,19,20 …”

“…However, about 30 per cent of the MDR‐RE isolates (mostly more recent ones) harbour pRErm46 variants with spontaneous deletions in the C1I and/or adjacent tetRA (33) locus, with loss of the corresponding resistances (sulfonamides/streptomycin/spectinomycin and/or tetracycline/doxycycline) 15,20,21 …”

“…Arrows point to two of the three MDR‐RE 2287 isolates recently identified from Ireland. Reproduced from Val‐Calvo et al 2022 20 …”

Antimicrobial Residue Accumulation Contributes to Higher Levels of Rhodococcus equi Carrying Resistance Genes in the Environment of Horse-Breeding Farms

“…Apart from the potential long-term selection of MDR R. equi and its detrimental effect on equine health, the accumulation of antimicrobial residues establishes constant antimicrobial pressure for the enhancement and spread of MDR pathogens with the potential to threaten humans and other animals through contact or the consumption of contaminated food and water [ 36 ]. Previous studies have shown that antimicrobial-resistant R. equi have spread internationally [ 37 ], demonstrating the potential global impact of even a single event of AMRGs acquisition [ 38 ]. Moreover, the accumulation of residues can have ecotoxicological effects, interfering with the normal microbiome of soils and plants and affecting agricultural yield [ 39 ].…”