Dissecting vancomycin-intermediate resistance in staphylococcus aureus using genome-wide association.
Vancomycin-intermediate Staphylococcus aureus (VISA) is currently defined as having minimal inhibitory concentration (MIC) of 4-8 µg/ml. VISA evolves through changes in multiple genetic loci with at least 16 candidate genes identified in clinical and in vitro-selected VISA strains. We report a whole-genome comparative analysis of 49 vancomycin-sensitive S. aureus and 26 VISA strains. Resistance to vancomycin was determined by broth microdilution, Etest, and population analysis profile-area under the curve (PAP-AUC). Genome-wide association studies (GWAS) of 55,977 single-nucleotide polymorphisms identified in one or more strains found one highly significant association (P = 8.78 E-08) between a nonsynonymous mutation at codon 481 (H481) of the rpoB gene and increased vancomycin MIC. Additionally, we used a database of public S. aureus genome sequences to identify rare mutations in candidate genes associated with VISA. On the basis of these data, we proposed a preliminary model called ECM+RMCG for the VISA phenotype as a benchmark for future efforts. The model predicted VISA based on the presence of a rare mutation in a set of candidate genes (walKR, vraSR, graSR, and agrA) and/or three previously experimentally verified mutations (including the rpoB H481 locus) with an accuracy of 81% and a sensitivity of 73%. Further, the level of resistance measured by both Etest and PAP-AUC regressed positively with the number of mutations present in a strain. This study demonstrated 1) the power of GWAS for identifying common genetic variants associated with antibiotic resistance in bacteria and 2) that rare mutations in candidate gene, identified using large genomic data sets, can also be associated with resistance phenotypes.
Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine.
Md Tauqeer
MT
Alam
Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine.
Robert A
RA
Petit
Division of Infectious Diseases, Department of Medicine, Emory University School of MedicineAtlanta Veterans Affairs Medical Center.
Emily K
EK
Crispell
Department of Biostatistics, University of Washington.
Timothy A
TA
Thornton
Department of Human Genetics, Emory University School of Medicine.
Karen N
KN
Conneely
Department of Human Genetics, Emory University School of MedicineDepartment of Biostatistics and Bioinformatics, Emory University School of Public Health.
Yunxuan
Y
Jiang
Division of Infectious Diseases, Department of Medicine, Emory University School of MedicineAtlanta Veterans Affairs Medical Center.
Sarah W
SW
Satola
Division of Infectious Diseases, Department of Medicine, Emory University School of MedicineDepartment of Human Genetics, Emory University School of Medicine tread@emory.edu.
Timothy D
TD
Read
D001426:Bacterial Proteins / Q000235:genetics; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D008826:Microbial Sensitivity Tests; D008957:Models, Genetic; D009154:Mutation; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013211:Staphylococcus aureus / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D014640:Vancomycin / Q000494:pharmacology; D020713:Vancomycin Resistance / Q000235:genetics*
D001426:Bacterial Proteins; D014640:Vancomycin
bacteria; genomics; phylogeny; whole-genome sequencing