Critical Steps in Shotgun Metagenomics-Based Diagnosis of Bloodstream Infections Using Nanopore Sequencing.

Shotgun metagenomics offers a broad detection of pathogens for rapid blood stream infection of pathogens but struggles with often low numbers of pathogens combined with high levels of human background DNA in clinical samples. This study aimed to develop a shotgun metagenomics protocol using blood spiked with various bacteria and to assess bacterial DNA extraction efficiency with human DNA depletion. The Blood Pathogen Kit (Molzym) was used to extract DNA from EDTA-whole blood (WB) and plasma samples, using contrived blood specimens spiked with bacteria for shotgun metagenomics diagnostics via Oxford Nanopore sequencing and PCR-based library preparation.

Early prediction of blood stream infection in a prospectively collected cohort.

Background: Blood stream infection (BSI) and sepsis are serious clinical conditions and identification of the disease-causing pathogen is important for patient management. The RISE (Rapid Identification of SEpsis) study was carried out to collect a cohort allowing high-quality studies on different aspects of BSI and sepsis. The aim of this study was to identify patients at high risk for BSI who might benefit most from new, faster, etiological testing using neutrophil to lymphocyte count ratio (NLCR) and Shapiro score.

Evaluation of the FilmArray™ Meningitis/Encephalitis panel with focus on bacteria and Cryptococcus spp.

Purpose: Molecular methods provide fast and accurate detection of both bacteria and viruses in the cerebrospinal fluid (CSF) causing infection in the central nervous system (CNS). In the present study we evaluated the bacterial detection performance of the fully automated FilmArray™ Meningitis/Encephalitis (ME) panel (bioMérieux) by comparing it with culture and multiplexed in-house PCR.

Methods: Three sample types were analysed; Contrived samples with known bacterial/fungal concentration (n = 29), clinical samples from patients with verified cause of CNS infection (n = 17) and external quality assessment (EQA) samples (n = 11).

Bacterial Endocarditis of the Pulmonic Valve in a Dog.

An 11 yr old female spayed golden retriever weighing 30.3 kg presented for evaluation of progressive lethargy, anorexia, tachypnea, stiff gait, and nonlocalized pain. On physical exam, the patient was febrile and tachycardic, and an arrhythmia with pulse deficits was noted.