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Antibiotics and probiotics impact gut antimicrobial resistance gene reservoir in COVID-19 patients

Su et al., Gut Microbes, doi:10.1080/19490976.2022.2128603, NCT04581018

Oct 2022

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Analysis of 142 hospitalized COVID-19 patients showing antibiotics further expanded the gut antimicrobial resistance gene (AMR) reservoir while probiotics (synbiotic formula SIM01) reduced AMR genes. At admission, antibiotic-naive COVID-19 patients had higher AMR gene diversity and abundance compared to controls. AMR genes further increased during infection and persisted 6 months after viral clearance. Antibiotic treatment led to additional AMR gene expansion while SIM01 probiotics significantly reduced AMR genes during and after infection without rebound in 12 weeks. Expanded AMR genes were associated with increased Klebsiella prevalence and post-acute COVID-19 syndrome risk.

The immune effects of probiotics are strain-specific.

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Su et al., 6 Oct 2022, China, peer-reviewed, 16 authors, trial NCT04581018 (history). Contact: siewchienng@cuhk.edu.hk.

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Antibiotics and probiotics impact gut antimicrobial resistance gene reservoir in COVID-19 patients

Qi Su, Qin Liu, Lin Zhang, Zhilu Xu, Chenyu Liu, Wenqi Lu, Jessica Yl Ching, Amy Li, Joyce Wing Yan Mak, Grace Chung Yan Lui, Susanna So Shan Ng, Kai Ming Chow, David Sc Hui, Paul Ks Chan, Francis Ka Leung Chan, Siew C Ng

Gut Microbes, doi:10.1080/19490976.2022.2128603

Dysbiosis of gut microbiota is well-described in patients with coronavirus 2019 (COVID-19), but the dynamics of antimicrobial resistance genes (ARGs) reservoir, known as resistome, is less known. Here, we performed longitudinal fecal metagenomic profiling of 142 patients with COVID-19, characterized the dynamics of resistome from diagnosis to 6 months after viral clearance, and reported the impact of antibiotics or probiotics on the ARGs reservoir. Antibiotic-naive patients with COVID-19 showed increased abundance and types, and higher prevalence of ARGs compared with non-COVID-19 controls at baseline. Expansion in resistome was mainly driven by tetracycline, vancomycin, and multidrug-resistant genes and persisted for at least 6 months after clearance of SARS-CoV-2. Patients with expanded resistome exhibited increased prevalence of Klebsiella sp. and post-acute COVID-19 syndrome. Antibiotic treatment resulted in further increased abundance of ARGs whilst oral probiotics (synbiotic formula, SIM01) significantly reduced the ARGs reservoir in the gut microbiota of COVID-19 patients during the acute infection and recovery phase. Collectively, these findings shed new insights on the dynamic of ARGs reservoir in COVID-19 patients and the potential role of microbiota-directed therapies in reducing the burden of accumulated ARGs.

Disclosure statement FKLC and SCN are the scientific co-founders and sit on the board of Directors of GenieBiome Ltd. SCN, FKLC and ZX are inventors of patent applications related to SIM01. SCN has

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