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Nelson, P.

Publications and source records attributed to Nelson, P..

2 recordsLinked to original sources

Modeling the emergence of antibiotic resistance in the environment: an analytical solution for the minimum selection concentration

Environmental antibiotic risk management requires an understanding of how subinhibitory antibiotic concentrations contribute to the spread of resistance. We develop a simple model of competition between sensitive and resistant bacterial strains to predict the minimum selection concentration (MSC), the lowest level of antibiotic at which resistant bacteria are selected. We present an analytical solution for the MSC based on the routinely measured minimum inhibitory concentration (MIC) and the selection coefficient (sc) that expresses fitness differences between strains. We calibrated the model by optimizing the shape of the bacterial growth dose-response curve to antibiotic or metal exposure (the Hill coefficient, {kappa}) to fit previously published experimental growth rate difference data. The model fit varied among nine compound-taxa combinations examined, but predicted the experimentally observed MSC/MIC ratio well (R2 [≥] 0.95). The shape of the antibiotic response curve varied among compounds (0.7 [≤] {kappa} [≤] 10.5), with the steepest curve for the aminoglycosides streptomycin and kanamycin. The model was sensitive to this antibiotic response curve shape and to the sc, indicating the importance of fitness differences between strains for determining the MSC. The MSC can be more than one order of magnitude lower than the MIC, typically by a factor sc{kappa}. This study provides an initial quantitative depiction and a framework for a research agenda to examine the growing evidence of selection for resistant bacteria communities at low environmental antibiotic concentrations.

microbiology

Discovery and reporting of clinically-relevant germline variants in advanced cancer patients assessed using whole-exome sequencing

PurposeIn precision cancer care, WES-based analysis of tumor-normal samples helps reveal somatic alterations but can also identify cancer-associated germline variants important for disease surveillance, treatment choice and cancer prevention. WES can also identify germline secondary findings impacting risk of cardiac, neurodegenerative or metabolic diseases. In patients with advanced cancer, the frequency of reportable secondary findings encountered with WES is not well defined.\n\nMethodsTo address this question, we analyzed a cohort of 343 patients with advanced, metastatic cancer for whom we have performed tumor and germline WES interrogating more than 21,000 genes using a CLIA/CLEP approved assay.\n\nResults17% of patients in our cohort have one or more reportable germline variants, including patients with pathogenic variants in the BRCA1 and BRCA2 genes. The frequency of non-cancer clinically relevant germline variants (8.8%) was within the range of two control non-cancer cohorts (11.0% and 6.5%). The frequency of variants in cancer-associated genes was significantly higher (p<0.0005) in our advanced cancer cohort (8.2%) compared to control cohorts (2.7% and 3.8%). More than 50% of patients with reportable germline cancer variants had a family history of cancer.\n\nConclusionthese results stress the importance of returning germline results found during somatic genomic tumor testing.

genomics