Bacterial DNA enrichment for low-inoculum fracture-related infection diagnostic using high-throughput sequencing.

Autor: Delarbre D; Division of Internal Medicine and Infectious Diseases, Military Teaching Hospital Sainte-Anne, 2, boulevard Sainte-Anne, BP 600, Cedex 9, 83800, Toulon, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR (VITROME), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France. Electronic address: david.delarbre@yahoo.fr., Lavrard P; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR (VITROME), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France., Elias A; Centre Hospitalier Intercommunal Toulon - La Seyne sur Mer (C.H.I.T.S.), Toulon, France., Bossi V; Institut Méditerranée-Infection, Marseille, France., Kacel I; Institut Méditerranée-Infection, Marseille, France., Janvier F; Division of microbiology, Military Teaching Hospital Sainte-Anne, 2, boulevard Sainte-Anne, BP 600, Cedex 9, 83800, Toulon, France., Fournier PE; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR (VITROME), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France.
Jazyk: angličtina
Zdroj: Diagnostic microbiology and infectious disease [Diagn Microbiol Infect Dis] 2024 Sep; Vol. 110 (1), pp. 116411. Date of Electronic Publication: 2024 Jun 22.
DOI: 10.1016/j.diagmicrobio.2024.116411
Abstrakt: One of the main barriers for the implementation of metagenomic sequencing in routine diagnosis of infectious diseases is the presence of host DNA. While several enrichment methods are likely to overcome this issue, their effectiveness for specimens such as bone in the case of chronic infections remains to be determined. We compared the relevance of two methods for bacterial DNA enrichment when compared to a reference protocol during pretreatment of bone samples from fracture-related infections before HTS by both Illumina Miseq and Oxford Nanopore Technology (ONT). The bacterial/human DNA ratio was higher for either protocols than the reference technique (p = 0.00012), without any significant difference between them. HTS sensitivity over culture ranged from 21.7 % to 85 %. The ability of the studied protocols to improve the bacterial/human DNA ratio depends on the sequencing technique employed. In this context, there is room for improvement in enhancing the sensitivity of HTS for diagnostic purpose.
Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: David DELARBRE reports administrative support was provided by Hôpital Sainte Musse. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2024 Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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