Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

Abstract

Traditional genetic association studies are very difficult in bacteria, as the generally limited recombination leads to large linked haplotype blocks, confounding the identification of causative variants. Beta-lactam antibiotic resistance in Streptococcus pneumoniae arises readily as the bacteria can quickly incorporate DNA fragments encompassing variants that make the transformed strains resistant. However, the causative mutations themselves are embedded within larger recombined blocks, and previous studies have only analysed a limited number of isolates, leading to the description of “mosaic genes” as being responsible for resistance. By comparing a large number of genomes of beta-lactam susceptible and non-susceptible strains, the high frequency of recombination should break up these haplotype blocks and allow the use of genetic association approaches to identify individual causative variants. Here, we performed a genome-wide association study to identify single nucleotide polymorphisms (SNPs) and indels that could confer beta-lactam non-susceptibility using 3,085 Thai and 616 USA pneumococcal isolates as independent datasets for the variant discovery. The large sample sizes allowed us to narrow the source of beta-lactam non-susceptibility from long recombinant fragments down to much smaller loci comprised of discrete or linked SNPs. While some loci appear to be universal resistance determinants, contributing equally to non-susceptibility for at least two classes of beta-lactam antibiotics, some play a larger role in resistance to particular antibiotics. All of the identified loci have a highly non-uniform distribution in the populations. They are enriched not only in vaccine-targeted, but also non-vaccine-targeted lineages, which may raise clinical concerns. Identification of single nucleotide polymorphisms underlying resistance will be essential for future use of genome sequencing to predict antibiotic sensitivity in clinical microbiology.

Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage

“…In S. pneumoniae, beta-lactam resistance has been shown to associate with a number of variants outside the direct target of beta-lactams (the peptidoglycan biosynthesis pathway) (20). It seems plausible that some of these variants may play a role in determining duration of carriage.…”

Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective

“…The majority of these assays are solely PCR based (40)(41)(42)(43), although sequencing approaches and microarrays have also been used (45,46). Several recent studies have also compared phenotypic drug susceptibility testing results with predictions based on whole-genome sequencing (WGS) data for a variety of bacterial pathogens (47), including S. pneumoniae (48,49). Our CDC-based laboratory has developed a promising WGS-based "typing pipeline" for rapid and automated predictions of pneumococcal serotypes, MICs, genotypes, and additional features (50).…”

Molecular mechanisms and epidemiology of resistance in Streptococcus pneumoniae in the Middle East region

“…Another recent genomewide association study identified a set of 301 single nucleotide polymorphisms, from which 73 caused amino acid alterations in cell-wall synthesis genes [20].…”