[R21] Uncovering genetic determinants of carbapenem resistance in Klebsiella pneumoniae
Ente: National Institute of Allergy and Infectious Diseases
Scadenza: 2028-05-31
Importo max: 480.650 EUR
Paese: US
Descrizione
Carbapenem-resistant Klebsiella pneumoniae represents an urgent global health threat due to its
increasing prevalence and high mortality rates, necessitating a comprehensive understanding of its resistance
mechanisms. While key resistance mechanisms and their genetic determinants are known, such as beta-
lactamases and porin mutations, the cause of resistance in many strains remains elusive. Moreover, other strains
that carry known genetic carbapenem-resistance factors have been found to still be susceptible to carbapenems
for unclear reasons. Further, strains can carry genetic elements which, while not conferring resistance directly,
can promote resistance indirectly by accelerating its acquisition, such as through mutations in DNA repair
systems or mobile genetic elements.
To address these knowledge gaps, we propose a genome-wide association study (GWAS), with the
aim of maximizing the discovery of gene variants associated with meropenem resistance, with
experimental validation of candidates to identify true causal variants. We will overcome limitations of prior
studies in the following ways: 1) We have compiled an expanded data set of publicly available K. pneumoniae
genomes from strains isolated across a wide distribution of countries, with in hand access to >100 isolates upon
which experimental validation studies will be performed. 2) We will perform comprehensive capture of genetic
variants by employing a reference-free GWAS, utilizing unitigs, stretches of DNA sequence that represent the
entire spectrum of genetic variation. 3) We will enhance statistical power to detect genetic variants with even
subtle effects on resistance by using a quantitative, continuous minimum inhibitory concentration (MIC)
phenotype to meropenem rather than a binary designation of resistant or susceptible. 4) We will reduce the
number of false positives arising from correlation, or linkage disequilibrium (LD), with known carbapenemase
and other known resistance factors by performing a conditional GWAS, where known factors are included as
covariates. 5) We will further mitigate confounding effects due to population structure and LD, which cause
non-random relationships between variants, by utilizing a pangenome-wide regression with an elastic net penalty.
6) Crucially, we will functionally validate our findings, which will include genetic variants associated with
increased resistance, whether through direct or indirect mechanisms, as well as those that may restore
susceptibility in strains already possessing known resistance factors. We will bridge the gap between GWAS
findings and functional validation by leveraging our high-throughput experimental capabilities. This integrated
approach promises to uncover novel mechanisms of carbapenem resistance, its acquisition, and susceptibility
in K. pneumoniae, with the potential to inform the development of future diagnostics or therapeutic strategies.
Istituzione: BROAD INSTITUTE, INC.
PI: Josephine W Bagnall
Progetto: 1R21AI199686-01
Settori: National Institute of Allergy and Infectious Diseases
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