As the
COVID-19 pandemic spread globally, the consumption of
antibiotics increased. However, no studies exist evaluating the effect of
antibiotics use on the antibiotic resistance of intestinal flora in
COVID-19 patients during the pandemic. To explore this issue, we collected 15 metagenomic data of fecal samples from healthy controls (HCs) with no use history of
antibiotics, 23 metagenomic data of fecal samples from
COVID-19 patients who received empirical
antibiotics [
COVID-19 (abx+)], 18 metagenomic data of fecal samples from
antibiotics-naïve
COVID-19 patients [
COVID-19 (abx-)], and six metagenomic data of fecal samples from patients with community-acquired
pneumonia [PC (abx+)] from the Sequence Read Archive database. A total of 513
antibiotic-resistant gene (ARG) subtypes of 18 ARG types were found.
Antibiotic treatment resulted in a significant increase in the abundance of ARGs in intestinal flora of
COVID-19 patients and markedly altered the composition of ARG profiles. Grouped comparisons of pairs of Bray-Curtis dissimilarity values demonstrated that the dissimilarity of the HC versus the
COVID-19 (abx+) group was significantly higher than the dissimilarity of the HC versus the
COVID-19 (abx-) group. The mexF, mexD, OXA_209, major facilitator superfamily transporter, and EmrB_QacA family major facilitator transporter genes were the discriminative ARG subtypes for the
COVID-19 (abx+) group. IS621, qacEdelta,
transposase, and ISCR were significantly increased in
COVID-19 (abx+) group; they greatly contributed toward explaining variation in the relative abundance of ARG types. Overall, our data provide important insights into the effect of
antibiotics use on the antibiotic resistance of
COVID-19 patients during the
COVID-19 epidemic.