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

Jeffery Ho; Yun Kit Yeoh; Nilakshi Barua; Zigui Chen; Grace Lui; Sunny H Wong; Xiao Yang; Martin CW Chan; Paul KS Chan; Peter M Hawkey; Margaret Ip

doi:10.1080/19490976.2019.1700755

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

Jeffery Ho, Yun Kit Yeoh, Nilakshi Barua, Zigui Chen, Grace Lui, Sunny H Wong, Xiao Yang, Martin CW Chan, Paul KS Chan, Peter M Hawkey, Margaret Ip^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

23 Citations (Scopus)

68 Downloads (CityUHK Scholars)

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.

Original language	English
Article number	1700755
Number of pages	12
Journal	Gut Microbes
Volume	12
Issue number	1
Online published	16 Jan 2020
DOIs	https://doi.org/10.1080/19490976.2019.1700755
Publication status	Published - 2020
Externally published	Yes

Funding

We thank the support of funding from Health and Medical Research Fund (Project number 18170082, PI: MI), Food and Health Bureau of the Hong Kong Special Administrative Region, People's Republic of China. The study was partially supported by a seed fund for gut microbiota research provided by the Faculty of Medicine, The Chinese University of Hong Kong. The funding bodies did not involve in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

Research Keywords

Resistome
antibiotic resistance
gut microbiota
meta-genomics
fecal microbiota transplantation
ANTIBIOTIC-RESISTANCE GENES
DETERMINANTS
DATABASE

Publisher's Copyright Statement

This full text is made available under CC-BY-NC-ND 4.0. https://creativecommons.org/licenses/by-nc-nd/4.0/

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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.",

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AU - Yeoh, Yun Kit

AU - Barua, Nilakshi

AU - Chen, Zigui

AU - Lui, Grace

AU - Wong, Sunny H

AU - Yang, Xiao

AU - Chan, Martin CW

AU - Chan, Paul KS

AU - Hawkey, Peter M

AU - Ip, Margaret

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

Abstract

Funding

Research Keywords

Publisher's Copyright Statement

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