Antimicrobial Resistance Spectrum Conferred by pRErm46 of Emerging Macrolide (Multidrug)-Resistant Rhodococcus equi.

Clonal multidrug resistance recently emerged in Rhodococcus equi, complicating the therapeutic management of this difficult-to-treat animal- and human-pathogenic actinomycete. The currently spreading multidrug-resistant (MDR) "2287" clone arose in equine farms upon acquisition, and coselection by mass macrolide-rifampin therapy, of the pRErm46 plasmid carrying the erm(46) macrolide-lincosamide-streptogramin resistance determinant, and of an rpoBS531F mutation. Here, we screened a collection of susceptible and macrolide-resistant R. equi strains from equine clinical cases using a panel of 15 antimicrobials against rapidly growing mycobacteria (RGM) and nocardiae and other aerobic actinomycetes (NAA). R. equi isolates-including MDR ones-were generally susceptible to linezolid, minocycline, tigecycline, amikacin, and tobramycin according to Staphylococcus aureus interpretive criteria, plus imipenem, cefoxitin, and ceftriaxone based on Clinical and Laboratory Standards Institute (CLSI) guidelines for RGM/NAA. Susceptibility to ciprofloxacin and moxifloxacin was borderline according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Molecular analyses linked pRErm46 to significantly increased MICs for trimethoprim-sulfamethoxazole and doxycycline, in addition to clarithromycin, within the RGM/NAA panel, and to streptomycin, spectinomycin, and tetracycline resistance. pRErm46 variants with spontaneous deletions in the class 1 integron (C1I) region, observed in ≈30% of erm(46)-positive isolates, indicated that the newly identified resistances were attributable to the C1I's sulfonamide (sul1) and aminoglycoside (aaA9) resistance cassettes and adjacent tetRA(33) determinant. Most MDR isolates carried the rpoBS531F mutation of the 2287 clone, while different rpoB mutations (S531L, S531Y) detected in two cases suggest the emergence of novel MDR R. equi strains.

Genomics accurately predicts antimicrobial resistance in Staphylococcus pseudintermedius collected as part of Vet-LIRN resistance monitoring.

Whole-genome sequencing (WGS) has changed our understanding of bacterial pathogens, aiding outbreak investigations and advancing our knowledge of their genetic features. However, there has been limited use of genomics to understand antimicrobial resistance of veterinary pathogens, which would help identify emerging resistance mechanisms and track their spread. The objectives of this study were to evaluate the correlation between resistance genotypes and phenotypes for Staphylococcus pseudintermedius, a major pathogen of companion animals, by comparing broth microdilution antimicrobial susceptibility testing and WGS. From 2017-2019, we conducted antimicrobial susceptibility testing and WGS on S. pseudintermedius isolates collected from dogs in the United States as a part of the Veterinary Laboratory Investigation and Response Network (Vet-LIRN) antimicrobial resistance monitoring program. Across thirteen antimicrobials in nine classes, resistance genotypes correlated with clinical resistance phenotypes 98.4 % of the time among a collection of 592 isolates. Our findings represent isolates from diverse lineages based on phylogenetic analyses, and these strong correlations are comparable to those from studies of several human pathogens such as Staphylococcus aureus and Salmonella enterica. We uncovered some important findings, including that 32.3 % of isolates had the mecA gene, which correlated with oxacillin resistance 97.0 % of the time. We also identified a novel rpoB mutation likely encoding rifampin resistance. These results show the value in using WGS to assess antimicrobial resistance in veterinary pathogens and to reveal putative new mechanisms of resistance.

Antimicrobial susceptibility patterns of Rhodococcus equi from necropsied foals with rhodococcosis.

Mainstay therapy for rhodococcosis in foals is the combination of rifampicin and a macrolide. While emergence of resistance to rifampicin and macrolides has been reported, studies demonstrating the development of resistance to such drugs is limited in necropsied foals with rhodococcosis. In this study, the foal necropsy records between 01/01/2011 and 08/30/2019 were reviewed for culture-positive R. equi with MICs and, whether or not the affected foals received any mainstay dual therapy before their deaths. Resistance to antimicrobials in the R. equi isolates from necropsied foals were then compared between treated foals with dual therapy and untreated foals to determine the association between the administration of antimicrobials and development of the drug resistance. In a total of 256 R. equi isolates from each of the 256 necropsied foals with rhodococcosis, rifampicin, azithromycin, clarithromycin and erythromycin showed high rates of resistance, 22.65 %, 16.01 %, 14.84 % and 15.23 %, respectively. The most active antimicrobials exhibiting MIC50/90 values were imipenem, doxycycline, amikacin and gentamicin including in the rifampicin- and macrolides-resistant R. equi isolates. Based on the treatment histories available for the 114 necropsied foals with rhodococcosis, R. equi isolates resistant to rifampicin, and macrolides were significantly more isolated from treated foals with mainstay dual therapy compared to untreated foals. Despite dual therapy, development of resistance against rifampicin and macrolides warrants evaluation of new treatment protocols in foals.