Metatranscriptomics Reveals Antibiotic-Induced Resistance Gene Expression in the Murine Gut Microbiota

Abstract

Antibiotic resistance is a current and expanding threat to the practice of modern medicine. Antibiotic therapy has been shown to perturb the composition of the host microbiome with significant health consequences. In addition, the gut microbiome is known to be a reservoir of antibiotic resistance genes. Work has demonstrated that antibiotics can alter the collection of antibiotic resistance genes within the microbiome through selection and horizontal gene transfer. While antibiotics also have the potential to impact the expression of resistance genes, metagenomic-based pipelines currently lack the ability to detect these shifts. Here, we utilized a dual sequencing approach combining shotgun metagenomics and metatranscriptomics to profile how three antibiotics, amoxicillin, doxycycline, and ciprofloxacin, impact the murine gut resistome at the DNA and RNA level. We found that each antibiotic induced broad, but untargeted impacts on the gene content of the resistome. In contrast, changes in ARG transcript abundance were more targeted to the antibiotic treatment. Doxycycline and amoxicillin induced the expression of tetracycline and beta-lactamase resistance genes, respectively. Furthermore, the increased beta-lactamase resistance gene transcripts could contribute to an observed bloom of Bacteroides thetaiotaomicron during amoxicillin treatment. Based on these findings, we propose that the utilization of a dual sequencing methodology provides a unique capacity to fully understand the response of the resistome to antibiotic perturbation. In particular, the analysis of transcripts reveals that the expression and utilization of resistance genes is far narrower than their abundance at the genomic level would suggest.

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease

“…In addition, metatranscriptomic studies focused on RNA sequencing (RNA seq) also allow functional changes to be discovered to decipher what can affect antibiotic resistance gene expression after exposure to antibiotics. They can also study changes in the virulence factors of specific pathogens and epigenomic studies of some neoplastic conditions ( Sharma et al, 2010 ; Korry et al, 2020 ; Auld et al, 2022 ).…”

The Spread of Antibiotic Resistance Genes In Vivo Model

“…Wu et al [ 101 ] found that levofloxacin could induce transformation and promote the spread of drug-resistant E. coli . Misuse of antibiotics alters gut microbiota homeostasis and promotes horizontal transfer of resistance genes in vivo [ 98 ]. The antimicrobial treatment enhances the selection of resistant strains and results in an increase in the resistance gene pool, which ultimately raises the risk of spreading resistance genes [ 102 ].…”

“…Antibiotics. As a huge reservoir of antibiotic resistance genes, the human gut microbiome may be involved in the spread of resistance genes to pathogens [98]. External intake of antibiotics or resistance genes may affect the resistance changes of intestinal flora.…”

Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance

“…Furthermore, the traditional best hit approach would fail to predict the novel metallo beta lactamase genes, indicating the sensitivity and robustness of machine learning approaches in ARG surveillance (Arango-Argoty et al, 2018). DeepArg has been widely used in several studies that have revealed correlations of total ARGs with anthropogenic impacts in natural environments (Collins-Fairclough et al, 2018;Chen et al, 2019b;Zeng et al, 2019), increased ARGs in murin gut under antibiotic treatments (Korry et al, 2020), and reduction of ARGs in bioreactors upon ozone pre-treatment (Xia et al, 2020).…”