Molecular sequencing technologies in the diagnosis and management of prosthetic joint infections

Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections

“…The high performance (sensitivity and specificity) of SMg has been recently highlighted for the etiological diagnosis of a number of infectious diseases ( Miao et al, 2018 ; Filkins et al, 2020 ; Gu et al, 2021 ; Miller and Chiu, 2021 ), including bone and joint infections ( Street et al, 2017 ; Thoendel et al, 2018 ; Gamie et al, 2021 ; Goswami et al, 2021 ), meningitis and encephalitis ( Wilson et al, 2019 ; Rodino et al, 2020 ), or necrotizing fasciitis ( Rodriguez et al, 2020c ). Indeed, by allowing the detection and quantification of an unlimited panel of microorganisms, including bacteria, viruses, fungi, or parasites without a priori orientation, SMg is capable to identify the etiology of any infectious disease, including those due to microorganisms that have never been previously described in human infections ( Rodriguez et al, 2020b ).…”

“…Among them, NGS-based approaches, as shotgun metagenomics (SMg) or amplification of the universal bacterial 16S rRNA gene and NGS sequencing of the PCR products (NGS 16S), appear to be particularly promising. Focusing on SMg, recent studies have demonstrated its utility for the etiological diagnosis of infections ( Miao et al, 2018 ; Filkins et al, 2020 ; Gu et al, 2021 ; Miller and Chiu, 2021 ), including meningitidis/encephalitis ( Wilson et al, 2019 ; Rodino et al, 2020 ), necrotizing soft-tissue infections ( Rodriguez et al, 2020c ), pneumonia ( Hilton et al, 2016 ; Zhou et al, 2021 ), bloodstream infections ( Grumaz et al, 2016 ), bone and joint infections ( Street et al, 2017 ; Thoendel et al, 2018 ; Gamie et al, 2021 ; Goswami et al, 2021 ) or fever with unknown origin ( Fu et al, 2022 ). Moreover, because SMg has the capacity to generate the full-length sequence of bacterial genomes (unlike 16S approaches), this method could be used for the study of antimicrobial susceptibility and molecular typing.…”

Highlighting New Perspectives on Musculoskeletal Infections

“…Beyond the strictly clinical aspects, demonstrated in the papers addressing the need for an “orthoplastic” approach on the most demanding cases [ 2 ], we were impressed by the evident interest in the laboratory and instrumental aspects. This was evident in the attention paid to establishing novel imaging methods, as well as in the focus on biological and molecular considerations [ 3 ]. Genetics, molecular biology, and microbiology are fast-evolving fields in the context of musculoskeletal infections.…”