Emergence of Daptomycin (DAP) Resistance in Community-Associated MRSA USA300 Latin American Variant (USA300-LV)

The conventional detection of antibiotic resistance in clinical laboratories by automated systems might overlook resistance, including that to last resort antibiotics that could be helpful for salvage therapy of complicated infections. DAP is a lipopetide antibiotic approved for the treatment of complicated skin and soft-tissue infections (cSSTI) and bacteremia and remains one of the last-line anti-staphylococcal agents. DAP resistance has not been observed in MRSA isolates in Colombia, however a DAP MIC creep has been noted since 2016 in MRSA USA300-LV isolates causing cSSTI in one hospital. We aimed to study the possible vancomycin (VAN) and DAP resistance mechanisms in a representative MRSA isolate from this hospital. We identified an MRSA isolate recovered from a patient with cSSTI who was failing VAN and DAP therapies. The organism was reported to be susceptible to both antibiotics. We confirmed DAP and VAN MICs by E-test and broth micro dilution respectively. We performed whole-genome sequencing on an Illumina platform to characterize the resistome and genetic changes potentially associated with DAP resistance, including 22 proteins associated with development of the VISA phenotype. The MRSA isolate belonged to ST2802 (single locus variant of ST8, Clonal complex 8) and exhibited the common characteristics of the USA300-LV (SCCmecIVc-E, absence of ACME and presence of PVL and COMER elements). VAN and DAP MICs were 2 and 4 μg/ml, respectively. The isolate tested negative for VISA using CLSI recommended screening method. The resistome only detected genes associated with β-lactam resistance genes (mecA and blaZ). We found relevant changes in four proteins associated with VISA and DAP-NS phenotypes: MprF, VraS, TcaA and in GraS. We were able to confirm the emergence of DAP resistance in a representative isolate of the prevalent community-associated USA300-LV lineage in Colombia. Detection of unusual resistance by conventional methods in clinical laboratories is challenging, where a continuous surveillance and confirmatory tests are recommended. WGS is a powerful method to detect a resistance phenotypes influenced by multiple genes. E. Martinez, Merck Sharp & Dohme: Consultant, Consulting fee. Pfizer: Consultant, Consulting fee. C. Hernández-Gómez, Merck Sharp & Dohme: Consultant, Consulting fee. Pfizer: Consultant, Consulting fee. M. V. Villegas, Merck Sharp & Dohme: Consultant, Consulting fee and Research support. Pfizer: Consultant, Consulting fee and Research support. C. Arias, Merck: Consultant and Speaker’s Bureau, Consulting fee and Research support. Theravance: Consultant, Consulting fee and Research support. Allergan: Consultant and Speaker’s Bureau, Consulting fee and Research support. The Medicines Company: Consultant and Speaker’s Bureau, Consulting fee and Research support. Bayer Global: Consultant, Consulting fee.