Pathogen identification by shotgun metagenomics of patients with necrotizing soft‐tissue infections

Rodriguez, Christophe; Jary, Aude; Hua, Camille; Woerther, Paul‐Louis; Bosc, Romain; Desroches, Marine; Sitterlé, Emilie; Gricourt, Guillaume; Prost, Nicolas de; Pawlotsky, Jean‐Michel; Chosidow, Olivier; Sbidian, É.; Decousser, J.-W.

doi:10.1111/bjd.18611

Cited by 42 publications

(40 citation statements)

References 36 publications

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“…We pair-end sequenced libraries, 2 × 150 bp, with High Output Kit version 2 on a Next-Seq500 device (Illumina). We analyzed the sequences with MetaMIC software (6).…”

Section: The Studymentioning

confidence: 99%

“…Broad-spectrum diagnostic tests, such as metagenomics methods, are useful to discover new viruses, especially in patients with encephalitis of unknown etiology (2,5). We have developed an original method based on shotgun metagenomics (MetaMIC) for the diagnosis of bacterial, viral, fungal, and parasitic infections from any human fluid or tissue (6). We used it to discover a previously unknown member of the Orthobunyavirus genus of the Peribunyaviridae family, Cristoli virus, in a patient with fatal encephalitis.…”

mentioning

confidence: 99%

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Fatal Encephalitis Caused by Cristoli Virus, an Emerging Orthobunyavirus, France

Rodriguez¹,

Gricourt²,

N’Debi³

et al. 2020

Emerg. Infect. Dis.

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“…We pair-end sequenced libraries, 2 × 150 bp, with High Output Kit version 2 on a Next-Seq500 device (Illumina). We analyzed the sequences with MetaMIC software (6).…”

Section: The Studymentioning

confidence: 99%

mentioning

confidence: 99%

Fatal Encephalitis Caused by Cristoli Virus, an Emerging Orthobunyavirus, France

Rodriguez¹,

Gricourt²,

N’Debi³

et al. 2020

Emerg. Infect. Dis.

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“…In the study by Rodriguez et al ., SM had higher sensitivity than 16S rRNA gene‐target sequencing for the detection of bacterial DNA. SM had higher sensitivity than standard cultures for the detection of anaerobic bacteria.…”

mentioning

confidence: 96%

“…In this edition of the BJD , Rodriguez et al . assess the potential of shotgun metagenomics (SM) in pathogen identification in patients with NSTIs . SM is the high‐throughput untargeted sequencing of all genomes of a sample .…”

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confidence: 99%

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New perspectives for necrotizing soft‐tissue infections pathogen detection

2020

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Omicron induced distinct immune respiratory transcriptomics signatures compared to pre‐existing variants in critically ill COVID‐19 patients

Bay,

Rodriguez,

Caruso

et al. 2023

Journal of Medical Virology

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Severe coronavirus disease 2019 (COVID‐19) is related to dysregulated immune responses. We aimed to explore the effect of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants on the immune response by nasopharyngeal transcriptomic in critically‐ill patients. This prospective monocentric study included COVID‐19 patients requiring intensive care unit (ICU) admission between March 2020 and 2022. Patients were classified according to VOC (ancestral, Alpha, Delta, and Omicron). Eighty‐eight patients with severe COVID‐19 were included after matching (on prespecified clinical criteria). Profiling of gene expression markers of innate and adaptive immune responses were investigated by respiratory transcriptomics at ICU admission. Eighty‐eight patients were included in the study after matching (ancestral [n = 24], Alpha [n = 24], Delta [n = 22], and Omicron [n = 18] variants). Respiratory transcriptomic analysis revealed distinct innate and adaptive immune profiling between variants. In comparison with the ancestral variant, there was a reduced expression of neutrophil degranulation, T cell activation, cytokines signalling pathways in patients infected with Alpha and Delta variants. In contrast, there was a higher expression of neutrophil degranulation, T and B cells activation, and inflammatory interleukins pathways in patients infected with Omicron. To conclude, Omicron induced distinct immune respiratory transcriptomics signatures compared to pre‐existing variants in patients with severe COVID‐19, pointing to an evolving pathophysiology of severe COVID‐19 in the Omicron era.

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Pathogen identification by shotgun metagenomics of patients with necrotizing soft‐tissue infections

Abstract: The members of the Multidisciplinary Necrotizing Fasciitis Study Group are listed in the Appendix.

Cited by 42 publications

References 36 publications

Fatal Encephalitis Caused by Cristoli Virus, an Emerging Orthobunyavirus, France

Fatal Encephalitis Caused by Cristoli Virus, an Emerging Orthobunyavirus, France

New perspectives for necrotizing soft‐tissue infections pathogen detection

Omicron induced distinct immune respiratory transcriptomics signatures compared to pre‐existing variants in critically ill COVID‐19 patients

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