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.

中文翻译：

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通过宏基因组测序评估 COVID-19 患者的重复感染、抗生素使用和气道微生物组：一项在上海的队列研究

背景

在 COVID-19 患者中，有关重复感染、抗菌评估和宏基因组测序 (MS) 价值的信息可以帮助制定抗菌药物管理。

方法

这项回顾性研究分析了 2020 年 1 月 23 日至 3 月 14 日在上海公共卫生临床中心 (SPHCC) 的 323 名实验室确诊的 COVID-19 患者的合并感染率和抗生素使用情况。还调查了重症 COVID-19 患者的微生物群组成-19.

结果

轻度、重度和危重亚组的总人群合并感染率为 17/323 (5.3%) 和 0/229 (0)、4/78 (5.1%) 和 13/16 (81.3%)，分别。经证实的真菌感染与较高的死亡率显着相关（p = 0.029）。在重症患者中，抗菌药物和碳青霉烯类药物的使用率分别为16/16（100%）和13/16（81.3%），其中优先使用和经验性抗菌天数分别占51.6%和30.1%。靶向治疗仅占18.3%。实施 MS 以检测非 COVID-19 病毒共存和菌血症的半定量监测，在基于 MS 的精确抗菌管理的病例中看到了明显的临床益处。

结论

在 SPHCC 队列中，我们观察到不可忽视的重复感染率，尤其是对于重症 COVID-19 患者。由于死亡风险高，真菌合并感染需要密切关注，并且 MS 在指导抗菌药物管理方面的临床益处值得进一步研究。