Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai.

Journal of Microbiology, Immunology, and Infection = Wei Mian Yu Gan Ran Za Zhi
Qing MiaoBijie Hu

Abstract

In COVID-19 patients, information regarding superinfection, antimicrobial assessment, and the value of metagenomic sequencing (MS) could help develop antimicrobial stewardship. This retrospective study analyzed 323 laboratory-confirmed COVID-19 patients for co-infection rate and antimicrobial usage in the Shanghai Public Health Clinical Center (SPHCC) from January 23rd to March 14th 2020. The microbiota composition was also investigated in patients with critically severe COVID-19. The total population co-infection rate was 17/323 (5.3%) and 0/229 (0), 4/78 (5.1%), and 13/16 (81.3%) for the mild, severe, and critically severe subgroups, respectively. Proven fungal infection was significantly associated with a higher mortality rate (p = 0.029). In critically severe patients, the rate of antimicrobials and carbapenem usage were 16/16 (100%) and 13/16 (81.3%), respectively, in which the preemptive and empiric antimicrobial days accounted for 51.6% and 30.1%, respectively. Targeted therapy only accounted for 18.3%. MS was implemented to detect non-COVID-19 virus co-existence and the semi-quantitative surveillance of bacteremia, with clear clinical benefit seen in cases with MS-based precision antimicrobial management. Airway microbi...Continue Reading

References

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Apr 7, 2018·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·I Rodriguez-GoncerT W Felton
Nov 14, 2018·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Qing MiaoBijie Hu
Jan 25, 2020·American Journal of Respiratory and Critical Care Medicine·Robert P DicksonUNKNOWN Biomarker Analysis in Septic ICU Patients (BASIC) Consortium
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Apr 28, 2020·Mycoses·Philipp KoehlerAlexander Shimabukuro-Vornhagen
May 31, 2020·The Journal of Infection·Louise LansburyWei Shen Lim

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Citations

Aug 28, 2021·Microorganisms·Yuan-Pin HungWen-Chien Ko

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PERMANOVA

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