Pathogen-Directed Antimicrobial Stewardship Audit Rounds: Evaluation of an Objectively Planned, Clinical Microbiology-Driven Antimicrobial Stewardship Approach to Influence Antimicrobial Prescriptions of Prescribers.

Introduction: Correct and prompt antimicrobial prescription modifications by the treating team based on the culture and antimicrobial susceptibility test (AST) reports are crucial. Pathogen-directed antimicrobial stewardship (PD-AMS) audit rounds are a clinical microbiology-driven approach to combine prompt appropriate patient management goals with goals of preventing irrational and improper use of antimicrobials.

Methods: The study was a prospective before-after interventional study to evaluate the effectiveness of PD-AMS audit rounds in modifying antimicrobial usage by prescribers on an individual patient basis.

Accuracy of various matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based rapid identification methods-As a tool to augment diagnostic stewardship in blood culture laboratory, South India.

Background: Blood stream infection is a medical emergency associated with high morbidity and mortality. Prompt identification of bloodstream infection-causing microorganisms directly from positive blood culture will significantly enhance patient care by reducing the turnaround time of pathogen recognition.

Methods: A total of 256 freshly flagged positive blood culture bottles were subjected to Gram staining.

iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.

Public gene expression databases are a rapidly expanding resource of organism responses to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics workflows to extract actionable knowledge of transcription regulatory network function. Here, we introduce a five-step computational pipeline, called iModulonMiner, to compile, process, curate, analyze, and characterize the totality of RNA-seq data for a given organism or cell type. This workflow is centered around the data-driven computation of co-regulated gene sets using Independent Component Analysis, called iModulons, which have been shown to have broad applications.

Machine learning reveals the transcriptional regulatory network and circadian dynamics of PCC 7942.

is an important cyanobacterium that serves as a versatile and robust model for studying circadian biology and photosynthetic metabolism. Its transcriptional regulatory network (TRN) is of fundamental interest, as it orchestrates the cell's adaptation to the environment, including its response to sunlight. Despite the previous characterization of constituent parts of the TRN, a comprehensive layout of its topology remains to be established.

Diagnosis and mitigation of the systemic impact of genome reduction in DGF-298.

Unlabelled: Microorganisms with simplified genomes represent interesting cell chassis for systems and synthetic biology. However, genome reduction can lead to undesired traits, such as decreased growth rate and metabolic imbalances. To investigate the impact of genome reduction on strain DGF-298, a strain in which ~ 36% of the genome has been removed, we reconstructed a strain-specific metabolic model (AC1061), investigated the regulation of gene expression using iModulon-based transcriptome analysis, and performed adaptive laboratory evolution to let the strain correct potential imbalances that arose during its simplification.