Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus

Abstract

BackgroundAs next generation sequencing (NGS) technologies have experienced a rapid development over the last decade, the investigation of the bacterial genetic architecture reveals a high potential to dissect causal loci of antibiotic resistance phenotypes. Although genome-wide association studies (GWAS) have been successfully applied for investigating the basis of resistance traits, complex resistance phenotypes have been omitted so far. For S. aureus this especially refers to antibiotics of last resort like daptomycin and ceftaroline. Therefore, we aimed to perform GWAS for the identification of genetic variants associated with DAP and CPT resistance in clinical S. aureus isolates.Materials/methodsTo conduct microbial GWAS, we selected cases and controls according to their clonal background, date of isolation, and geographical origin. Association testing was performed with PLINK and SEER analysis. By using in silico analysis, we also searched for rare genetic variants in candidate loci that have previously been described to be involved in the development of corresponding resistance phenotypes.ResultsGWAS revealed MprF P314L and L826F to be significantly associated with DAP resistance. These mutations were found to be homogenously distributed among clonal lineages suggesting convergent evolution. Additionally, rare and yet undescribed single nucleotide polymorphisms could be identified within mprF and putative candidate genes. Finally, we could show that each DAP resistant isolate exhibited at least one amino acid substitution within the open reading frame of mprF. Due to the presence of strong population stratification, no genetic variants could be associated with CPT resistance. However, the investigation of the staphylococcal cassette chromosome mec (SCCmec) revealed various mecA SNPs to be putatively linked with CPT resistance. Additionally, some CPT resistant isolates revealed no mecA mutations, supporting the hypothesis that further and still unknown resistance determinants are crucial for the development of CPT resistance in S. aureus.ConclusionWe hereby confirmed the potential of GWAS to identify genetic variants that are associated with antibiotic resistance traits in S. aureus. However, precautions need to be taken to prevent the detection of spurious associations. In addition, the implementation of different approaches is still essential to detect multiple forms of variations and mutations that occur with a low frequency.

Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants

“…However, in a previous study applying GWAS to a collection of DAP-resistant S. aureus , no association to mutational changes in gdp P was observed [57]. Furthermore, in the strain collection described here, none of the MRLM isolates examined were DAP resistant.…”

“…In addition to β-lactam resistance in S. aureus , gdp P mutations have also been implicated in DAP non-susceptibility in enterococci. However, in a previous study applying GWAS to a collection of DAP-resistant S. aureus , no association to mutational changes in gdp P was observed [ 57 ]. Furthermore, in the strain collection described here, none of the MRLM isolates examined were DAP resistant.…”

Loss of RNase J leads to multi-drug tolerance and accumulation of highly structured mRNA fragments in Mycobacterium tuberculosis

“…We and others have reported genome-wide association studies (GWAS) in cohorts of Mtb clinical isolates [16][17][18][19] and other bacterial pathogens [20][21][22] from around the globe. Many of the Mtb studies have identified drug resistance associated mutations in Rv2752c, here called rnj, encoding the ribonuclease RNase J.…”

Molecular mechanisms of antibiotic resistance revisited

“…Studying large isolate panels has been used to predict novel mechanisms of resistance. An analysis of 95 Staphylococcus aureus isolates was used to identify genes involved in daptomycin resistance, which was previously not well understood 185 , and a genome-wide association study suggested that convergent evolution has selected for daptomycin-resistant mprF mutants on multiple occasions 231 .…”