ARGs Prevalence Among Hospitalized COVID‐19 Patients with Bacterial Infections and Resistome abundance

Abstract

BackgroundThe burden of antimicrobial resistance AMR worldwide is substantial and is growing. Many factors play a role in the emergence of resistance. Our microbiome is a significant reservoir for antimicrobial resistance genes (ARGs). The use and misuse of antimicrobials can select multi‐resistant bacteria and modify the repertoire of ARGs in the gut microbiota. There is clear evidence that hospitalized COVID patients have altered gut microbiota that might affect the prevalence and abundance of AMR. The World Health Organization (WHO) has reported 364 million cases worldwide. Moreover, the CDC announced 72 million positives with more than 4.2 million hospitalized cases in the US alone.ObjectiveThe purpose of the current study is to review AMGs prevalence among hospitalized COVID‐19 patients with bacterial infections and explore the alteration of resistome abundance.MethodologyWe searched the pathogen detection of the National Center for Biotechnology database for hospitalized positive COVID‐19 cases with microbiome sequencing submission using the following keywords: antimicrobial resistance, antibiotic stewardship, prevalence, epidemiology, mechanism of resistance, and COVID‐19, SARS‐CoV‐2, bacterial infection, hospitalization, healthcare‐associated infection, antibiotic resistance, antimicrobial resistance, multi‐drug resistance, Acinetobacter, Klebsiella, Streptococcus, Staphylococcus, Pseudomonas, Escherichia, Enterococcus, Methicillin‐resistant Staphylococcus aureus, New Delhi Metallo‐β‐lactamase‐producing carbapenem‐resistant enterobacterales, Severe acute respiratory syndrome coronavirus 2, Vancomycin‐resistant enterococcus. Web‐based pipelines ResistoXplorer and Qiime2 and different databases, including RESfinder, Card, and ARGminer, are used for the metagenomics analysis. They are mainly based on programming languages ‐ JavaScript (version: 1.2.0) and R (version: 4.1.0).ResultsOur preliminary results showed that, to date, 11,129 isolates were detected worldwide between the declaration of the covid as a pandemic and January 2022. Moreover, the isolates prevalence was Acinetobacter baumannii at 39.7%, followed by Klebsiella pneumonia at 32.2%, then E.coli and Shigella at 11.7%, Enterobacter at 5.4%, and Pseudomonas aeruginosa 2.5%. Finally, infections such as Klebsiella oxytoca, Citrobacter freundii, and Providencia alcalifaciens were around 10%. We explored the genetic diversity of MRGs, including: aac(6′)‐Ib′, aadA1, and(3′′)‐IIa, aph(3′′)‐Ib, aph(3′)‐Ia, aph(6)‐Id, armA, arr‐2, blaADC‐30, blaOXA‐23, blaOXA‐66, blaOXA. Currently, we are working on WGS and 16s sequencing analysis, and our future work includes data analysis on abundance profiles and exploring the resistome signatures generated from AMR metagenomics of the microbiota of positive COVID‐ hospitalized patients.ConclusionWe are anticipating that there will be a significant change take place in the gut microbiome, hence the ARGs and resistome abundance in patients with COVID‐19.