The Gut Microbiome of Healthy Vietnamese Adults and Children Is a Major Reservoir for Resistance Genes Against Critical Antimicrobials.

Hao Chung The,Tuyen Ha Thanh,To Nguyen Thi Nguyen,Ellen E Higginson,Joana Pereira-Dias,Stephen Baker,Chau Tran Thi Hong,Lindsay Pike,Chau Nguyen Ngoc Minh,Caroline Zellmer

doi:10.1093/infdis/jiab398

Abstract

Antimicrobials are a key group of therapeutic agents. Given the animal/human population density and high antimicrobial consumption rate in Southeast Asia, the region is a focal area for monitoring antimicrobial resistance (AMR). Hypothesizing that the gastrointestinal tract of healthy individuals in Vietnam is a major source of AMR genes that may be transferred to pathogens, we performed shotgun metagenomic sequencing on fecal samples from 42 healthy Vietnamese people (21 children and 21 adults). We compared their microbiome profiles by age group and determined the composition of AMR genes. An analysis of the taxonomic profiles in the gut microbiome showed a clear differentiation by age, with young children (age <2 years) exhibiting a unique structure in comparison to adults and older children. We identified a total of 132 unique AMR genes, with macrolide, lincosamide, and streptogramin class resistance genes (ermB and lnuC) and tetracycline resistance genes being almost ubiquitous across the study population. Notably, samples from younger children were significantly associated with a greater number of AMR genes than other age groups, including key signature genes associated with AMR pathogens (eg, blaCTX-M, mphA). Our data suggest that the gut microbiome of those living in Vietnam, particularly young children, is a substantial reservoir of AMR genes, which can be transferred to circulating enteric pathogens. Our data support the generation of longitudinal cohort studies of those living in urban and rural areas of developing countries to understand the behavior of these AMR reservoirs and their role in generating multidrug-resistant and extensively drug-resistant pathogens.

Highlights

Vietnam is an LMIC in Southeast Asia with high rates of AMR pathogens
Following our previous work and hypothesizing that the gut microbiome is a major reservoir of AMR genes in this location, we recruited a cohort of Vietnamese adults and children to generate a detailed overview of the gut microbiome and antimicrobial resistome in these individuals
AMR surveillance and microbiome characterization are practical approaches for establishing a baseline measure of AMR genes circulating within a given population in LMICs, which can be used to inform strategies to reduce AMR [21]

Summary

Introduction

Vietnam is an LMIC in Southeast Asia with high rates of AMR pathogens. Unregulated antimicrobial consumption has a major impact on AMR [6], and 81.5% of antimicrobials in Vietnam are provided without prescription, an issue arising in both in Presented in part: 15th Asian Conference on Diarrhoeal Disease and Nutrition, Dhaka, Bangladesh, January 2020. S840 jid 2021:224 (Suppl 7) Pereira-Dias et al constitute a vast reservoir of AMR genes, which may be transferred to infecting pathogens via their associated vehicles and compound the mounting AMR crisis This observation is worrisome given the potential rollout of mass drug administration in LMICs using various antimicrobial classes (including ciprofloxacin and azithromycin) that are likely to favor the sustainment of multiple AMR genes and organisms and cause disruption to the microbiome [13]. Given this potential scenario, the paucity of microbiome and AMR gene burden data from LMICs is stark. Following our previous work and hypothesizing that the gut microbiome is a major reservoir of AMR genes in this location, we recruited a cohort of Vietnamese adults and children to generate a detailed overview of the gut microbiome and antimicrobial resistome in these individuals

Methods

Results

Conclusion