scholarly journals Shotgun-Metagenomics on Positive Blood Culture Bottles Inoculated With Prosthetic Joint Tissue: A Proof of Concept Study

2020 ◽  
Vol 11 ◽  
Author(s):  
Adriana Sanabria ◽  
Erik Hjerde ◽  
Mona Johannessen ◽  
Johanna Ericson Sollid ◽  
Gunnar Skov Simonsen ◽  
...  
Keyword(s):  
Blood Culture ◽  
Positive Blood Culture ◽  
Proof Of Concept ◽  
Shotgun Metagenomics ◽  
Joint Tissue ◽  
Concept Study ◽  
Prosthetic Joint

scholarly journals Shotgun-Metagenomics Based Prediction Of Antibiotic Resistance And Virulence Determinants In Staphylococcus Aureus From Prosthetic Joint Tissue On Blood Culture Bottles

2021 ◽  
Author(s):  
Adriana Maria Sanabria ◽  
Jessin Janice ◽  
Erik Hjerde ◽  
Gunnar Skov Simonsen ◽  
Anne-Merethe Hanssen
Keyword(s):  
Staphylococcus Aureus ◽  
Blood Culture ◽  
Virulence Genes ◽  
Sequence Data ◽  
Joint Infection ◽  
Clinical Samples ◽  
Shotgun Metagenomics ◽  
Joint Tissue ◽  
Genome Coverage ◽  
Prosthetic Joint

Abstract Shotgun-metagenomics may give valuable clinical information beyond the detection of potential pathogen(s). Identification of antimicrobial resistance (AMR), virulence genes and typing directly from clinical samples has been limited due to challenges arising from incomplete genome coverage. We assessed the performance of shotgun-metagenomics on positive blood culture bottles (n = 19) with prosthetic joint tissue for typing and prediction of AMR and virulence profiles in Staphylococcus aureus. We used different approaches to determine if sequence data from reads provides more information than from assembled contigs. Only 0.18% of total reads was derived from human DNA. Shotgun-metagenomics results and conventional method results were consistent in detecting S. aureus in all samples. AMR and known prosthetic joint infection virulence genes were predicted from S. aureus. Mean coverage depth, when predicting AMR genes was 209x. Resistance phenotypes could be explained by genes predicted in the sample in most of the cases. The choice of bioinformatic data analysis had a significant impact on the results. Read-based analysis was more accurate for pathogen identification, while contigs seemed better for AMR profiling. Our study demonstrates high genome coverage and potential for typing and prediction of AMR and virulence profiles in S. aureus from shotgun-metagenomics data.

scholarly journals A molecular based diagnosis of positive blood culture in the context of viral haemorrhagic fever: proof of concept

2019 ◽  
Vol 25 (10) ◽  
pp. 1289.e1-1289.e4 ◽  
Author(s):  
A. Cherkaoui ◽  
P. Cherpillod ◽  
G. Renzi ◽  
J. Schrenzel ◽  
L. Kaiser ◽  
...  
Keyword(s):  
Blood Culture ◽  
Positive Blood Culture ◽  
Haemorrhagic Fever ◽  
Proof Of Concept ◽  
Viral Haemorrhagic Fever

scholarly journals Waltzing around Sacred Cows on the Way to the Future

2017 ◽  
Vol 56 (3) ◽  
Author(s):  
Stephen M. Brecher
Keyword(s):  
Blood Culture ◽  
Positive Blood Culture ◽  
Clinical Microbiology ◽  
Clinical Microbiology Laboratory ◽  
Proof Of Concept ◽  
Microbiology Laboratory ◽  
Trained Personnel ◽  
The Future ◽  
Medical Technologists ◽  
The Way

ABSTRACT Our mostly manual, agar-based clinical microbiology laboratory is slowly but steadily being redefined by automation and innovation. Ironically, the oldest test, the Gram stain test, is still manually read and interpreted by trained personnel. In a proof-of-concept study, Smith et al. (J. Clin. Microbiol. 56:e01521-17, 2018, https://doi.org/10.1128/JCM.01521-17 ) used computer imaging with a deep convolutional neural network to examine and interpret Gram-stained slides from positive blood culture bottles. In light of the shortage of medical technologists/microbiologists and the need for results from positive blood culture bottles 24/7, this paper paves the way for the next innovations for the clinical microbiology laboratory of the future.

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