Predicting Pseudomonas aeruginosa susceptibility phenotypes from whole genome sequence resistome analysis

Abstract

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Antibiotic resistance in chronic respiratory diseases: from susceptibility testing to the resistome

“…The genotypic prediction of phenotypic bacterial resistance is an expected benefit from resistome analysis (figure 2). Recently, a scoring system based on mutation-driven and horizontally acquired resistance analysis by whole-genome sequencing has been established for several antibiotics in P. aeruginosa [81].…”

“…No gold-standard sample has been defined for lung microbiome and resistome studies [83]. Differences in bacterial communities have been demonstrated between the types of respiratory specimens in CF patients, with distinct communities in the upper and lower airways [81]. Oral contamination of respiratory samples could, therefore, also have an impact on lung resistome results.…”

“…Threedimensional structure-based method [64] Scoring system based on analysis of mutations and horizontally acquired ARGs [81] Functional metagenomics [60] Targeted analysis [52] Machine learning [82] Objectives Underlying issues…”

“…Resistome data interpretation for the implementation of antibiotic resistance prediction relies on different strategies. A scoring system, based on analysis of mutations and horizontally acquired antibiotic-resistance genes (ARGs), has been developed [81]. Another method uses machine-learning strategies to predict phenotypic resistance by combining sequencing and transcriptome analysis [82].…”

Genomic-based transmission analysis of carbapenem-resistant Pseudomonas aeruginosa at a tertiary care centre in Cologne (Germany) from 2015 to 2020

“…This is more complex and not completely validated yet and out of the scope of our investigation, which is basically epidemiological. 46 Fourthly, we did not conduct environmental sampling in this study to detect an inanimate reservoir; however we want to point out that on two out of four of the ICUs, sinks in most of the patient rooms were removed during the study period.…”