Prevalence and Genetic Basis of Antimicrobial Resistance in Non- aureus Staphylococci Isolated from Canadian Dairy Herds

Abstract

Emergence and spread of antimicrobial resistance is a major concern for the dairy industry worldwide. Objectives were to determine: (1) phenotypic and genotypic prevalence of drug-specific resistance for 25 species of non-aureus staphylococci, and (2) associations between presence of resistance determinants and antimicrobial resistance. Broth micro-dilution was used to determine resistance profiles for 1,702 isolates from 89 dairy herds. Additionally, 405 isolates were sequenced to screen for resistance determinants. Antimicrobial resistance was clearly species-dependent. Resistance to quinupristin/dalfopristin was common in Staphylococcus gallinarum (prevalence of 98%), whereas S. cohnii and S. arlettae were frequently resistant to erythromycin (prevalence of 63 and 100%, respectively). Prevalence of resistance was 10% against β-lactams and tetracyclines. In contrast, resistance to antimicrobials critically important for human medicine, namely vancomycin, fluoroquinolones, linezolid and daptomycin, was uncommon (< 1%). Genes encoding multidrug-resistance efflux pumps and resistance-associated residues in deducted amino acid sequences of the folP gene were the most frequent mechanisms of resistance, regardless of species. The estimated prevalence of the mecA gene was 17% for S. epidermidis. Several genes, including blaZ, mecA, fexA, erm, mphC, msrA, and tet were associated with drug-specific resistance, whereas other elements were not. There were specific residues in gyrB for all isolates of species intrinsically resistant to novobiocin. This study provided consensus protein sequences of key elements previously associated with resistance for 25 species of non-aureus staphylococci from dairy cattle. These results will be important for evaluating effects of interventions in antimicrobial use in Canadian dairy herds.

Keywords: antimicrobial resistance; antimicrobial resistance genes; coagulase-negative staphylococci; dairy; mastitis; non-aureus staphylococci; prevalence.

Figure 1

Flow diagram for determining genetic elements associated with antimicrobial resistance (AMR) in 405 bovine non-aureus staphylococci (NAS).

Figure 2

Common gene patterns in susceptible non-aureus staphylococci isolates (A), isolates resistant to β-lactams (B), erythromycin (C), tetracycline (D), and in multidrug resistant (MDR) isolates (E) when excluding any MDR efflux pumps and antimicrobial resistance-associated residues in the deduced amino acid sequence of any gene evaluated.

Figure 3

Consensus of residue composition of genes associated with drug-specific antimicrobial resistance for various non-aureus staphylococci species (NAS). Positions screened per gene deduced amino acid sequences, in addition to S. aureus wild and resistance-associated residues, are also presented. Presence of a red residue for a particular species indicates residues associated with antimicrobial resistance in Staphylococcus spp., according to the literature. ¹SAG, S. agnetis; SAR, S. arlettae; SAU, S. auricularis; SCA, S. capitis; SCP, S. caprae; SCH, S. chromogenes; SCO, S. cohnii; SDE, S. devriesei; SEP, S. epidermidis; SEQ, S. equorum; SFL, S. fleuretti; SGA, S. gallinarum; SHA, S. haemolyticus; SHO, S. hominis; SHY, S. hyicus; SKL, S. kloosii; SNE, S. nepalensis; SPA, S. pasteuri; SSA, S. saprophyticus; SSC, S. sciuri; SSI, S. simulans; SSU, S. succinus; SVI, S. vitulinus; SWA, S. warneri; SXY, S. xylosus; ²Two-residues insertion at position 256; ³A, F, I, L, V, or Y; ⁴F, I, L, V, or Y; ⁵A, G, K, N, V, or Y; ⁶Position 140 for NAS; 142 for S. aureus; ⁷K, I or S.