Shotgun metagenomics unravels higher antibiotic resistome profile in Bangladeshi gut microbiome

Abstract

Antibiotic resistance management is a challenging task in Low and Middle-Income Countries (LMICs) such as Bangladesh. Improper regulation and uncontrolled spreading of Antibiotic Resistant Genes (ARGs) from LIMCs pose a great threat to global public health. The human gut microbiome is a massive reservoir of Antibiotic Resistant Genes (ARGs). In this study, we unraveled the ARGs in the gut microbiome of the Bangladeshi population and compared them with several other countries around the world. Here, 31 fecal samples from different ethnic groups living in Bangladesh namely Bengali (n=9), Chakma (n=6), Khyang (n=5), Marma (n=6), and Tripura (n=5) were collected. Shotgun metagenomic sequencing method was implemented for revealing the ARGs. The resistome profiling was executed on three levels-the total microbiome, the plasmidome, and the virome. In all three levels, samples from Bangladeshi cohorts showed higher ARG profiles compared to foreign samples. On average, the number of ARGs in the Bangladeshi samples ranged between 75.11 and 88. Among them, class C beta-lactamases, quinolone resistance genes, and tetracycline efflux pumps were relatively more abundant. Additionally, the MexPQ-OpmE drug resistance pathway was found to be more prevalent. Findings from our study suggest that the spread of antibiotic resistance within the Bangladeshi population is being facilitated by the gut microbiome especially via the mobilome. Therefore, strict regulation on antibiotic usage is necessary to halt the spread of ARGs.