1. Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai
- Author
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Yi Su, Yao Zhang, Jianying Yuan, Honglong Wu, Qingqing Wang, Qing Miao, Yun Ling, Bijie Hu, Yuyan Ma, Wenting Jin, Jue Pan, and Hongyou Chen
- Subjects
Male ,0301 basic medicine ,Respiratory System ,medicine.disease_cause ,Cohort Studies ,Escalation ,Antimicrobial Stewardship ,0302 clinical medicine ,Immunology and Allergy ,Antimicrobial stewardship ,030212 general & internal medicine ,Aged, 80 and over ,Coinfection ,Antimicrobials ,Microbiota ,Mortality rate ,High-Throughput Nucleotide Sequencing ,General Medicine ,Middle Aged ,Antimicrobial ,QR1-502 ,Anti-Bacterial Agents ,Infectious Diseases ,Superinfection ,Cohort ,Female ,Original Article ,Cohort study ,Adult ,Microbiology (medical) ,China ,medicine.medical_specialty ,Critical Illness ,030106 microbiology ,Microbiology ,03 medical and health sciences ,Internal medicine ,medicine ,Humans ,Aged ,Retrospective Studies ,General Immunology and Microbiology ,SARS-CoV-2 ,business.industry ,COVID-19 ,Retrospective cohort study ,medicine.disease ,Mycoses ,Bacteremia ,Metagenomics ,business ,Metagenomic sequencing - Abstract
Background In COVID-19 patients, information regarding superinfection, antimicrobial assessment, and the value of metagenomic sequencing (MS) could help develop antimicrobial stewardship. Method 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. Results 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 microbiome analysis suggested that the microbiota compositions in critically severe COVID-19 patients were likely due to intubation and mechanical ventilation. Conclusions In the SPHCC cohort, we observed a non-negligible rate of super-infection, especially for the critically ill COVID-19 patients. Fungal co-infection requires intensive attention due to the high risk of mortality, and the clinical benefit of MS in guiding antimicrobial management warrants further investigation.
- Published
- 2021