Systematic review of human gut resistome studies revealed variable definitions and approaches

Abstract

In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.

The ‘thanato-resistome’ - The funeral industry as a potential reservoir of antibiotic resistance: Early insights and perspectives

“…‘ Thanato-resistome ’ is derived from ‘ thanatos ’, the Greek term for death, and ‘resistome’. The term antibiotic resistome or simply resistome, which is widely used in literature on antibiotic resistance, refers to the complete collective assemblage of antibiotic resistant bacteria and their resistance genes in a microbial ecosystem ( Ho et al, 2020 ). An antibiotic resistome acts as a reservoir that receives, harbours, and subsequently transfers antibiotic resistance.…”

“…Human cadavers are putative hotspot reservoirs of intrinsic or induced antibiotic resistance derived from the human resistome. The human resistome consists of various sub-compartments, including the gut, oral, urogenital and skin resistomes ( Pal et al, 2016 ; Ho et al, 2020 ). Evidence shows that the human resistome is a hotspot reservoirs of a broad spectrum of antibiotic resistant bacteria and their resistance genes ( Pal et al, 2016 ; Ho et al, 2020 ; McInnes et al, 2020 ).…”

“…The human resistome consists of various sub-compartments, including the gut, oral, urogenital and skin resistomes ( Pal et al, 2016 ; Ho et al, 2020 ). Evidence shows that the human resistome is a hotspot reservoirs of a broad spectrum of antibiotic resistant bacteria and their resistance genes ( Pal et al, 2016 ; Ho et al, 2020 ; McInnes et al, 2020 ). For example, studies show that the urogenital and oral antibiotic resistomes harbour resistance genes to macrolides and tetracyclines ( Pal et al, 2016 ).…”

“…Several studies, including reviews, have reported antibiotic resistant bacteria and their resistance genes in both healthy and unhealthy populations ( Forslund et al, 2014 ; Ho et al, 2020 ; Yokoyama et al, 2020 ). To date, several resistance genes have been detected, including those encoding resistance to the following antibiotics, among others: (1) macrolides ( ermB , ereA ), (2) aminoglycosides ( strA , strB ), (3) β-lactamases ( bla TEM ), (4) sulfonamides ( sul2 ), (5) trimethoprim ( dfrA14 ), (6) bacitracin, and (7) tetracyclines ( tetM , tetQ , tetW ) ( Ho et al, 2020 ). Antibiotic resistant bacteria detected in the human gut include the ESKAPE pathogens such as Escherichia coli , and Clostridium difficile ( De Oliveira et al, 2020 ).…”

Influence of Human Eating Habits on Antimicrobial Resistance Phenomenon: Aspects of Clinical Resistome of Gut Microbiota in Omnivores, Ovolactovegetarians, and Strict Vegetarians

“…The clinical resistome is defined as the set of genes related to antimicrobial resistance to drugs commonly used to treat infectious diseases in a particular environment [ 1 , 2 ]. The human gut microbiota is assumed to be an important reservoir of antimicrobial resistance genes (ARG), since it is always in contact with environmental microorganisms, which are introduced by oral contamination through food and water ingestion, and by contact with animals and other people.…”