Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective : advances and applications

dc.contributor.authorAsante, Jonathan
dc.contributor.authorOsei Sekyere, John
dc.date.accessioned2019-02-05T12:18:04Z
dc.date.issued2019-04
dc.description.abstractOur inability to cultivate most micro‐organisms, specifically bacteria, in the laboratory has for many years restricted our view and understanding of the bacterial meta‐resistome in all living and non‐living environments. As a result, reservoirs, sources, and distribution of antibiotic resistance genes (ARGS) and antibiotic‐producers, as well as the effects of human activity and antibiotics on the selection and dissemination of ARGs were not well comprehended. With the advances made in the fields of metagenomics and metatranscriptomics, many of the hitherto little‐understood concepts are becoming clearer. Further, the discovery of antibiotics such as lugdinin and lactocillin from the human microbiota, buttressed the importance of these new fields. Metagenomics and metatranscriptomics are becoming important clinical diagnostic tools for screening and detecting pathogens and ARGs, assessing the effects of antibiotics, other xenobiotics, and human activity on the environment, characterizing the microbiome and the environmental resistome with lesser turnaround time and decreasing cost, as well as discovering antibiotic‐producers. However, challenges with accurate binning, skewed ARGs databases, detection of less abundant and allelic variants of ARGs, and efficient mobilome characterization remain. Ongoing efforts in long‐read, phased‐ and single‐cell sequencing, strain‐resolved binning, chromosomal‐conformation capture, DNA‐methylation binning, and deep‐learning bioinformatic approaches offer promising prospects in reconstructing complete strain‐level genomes and mobilomes from metagenomes.en_ZA
dc.description.departmentMedical Microbiologyen_ZA
dc.description.embargo2020-04-01
dc.description.librarianhj2019en_ZA
dc.description.urihttps://onlinelibrary.wiley.com/journal/17582229en_ZA
dc.identifier.citationAsante, J. & Osei Sekyere, J. 2019, 'Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: Advances and applications', Environmental Microbiology Reports, vol. 11, no. 2, pp. 62-86.en_ZA
dc.identifier.issn1758-2229
dc.identifier.other10.1111/1758-2229.12735
dc.identifier.urihttp://hdl.handle.net/2263/68410
dc.language.isoenen_ZA
dc.publisherWileyen_ZA
dc.rights© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd. All rights reserved. This is the pre-peer reviewed version of the following article :'Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: Advances and applications', Environmental Microbiology Reports, vol. 11, no. 2, pp. 62-86, 2019, doi : 10.1111/1758-2229.12735. The definite version is available at :https://onlinelibrary.wiley.com/journal/17582229.en_ZA
dc.subjectAntibiotic resistance genes (ARGs)en_ZA
dc.subjectMicrobiomeen_ZA
dc.subjectSingle-cell sequencingen_ZA
dc.subjectResistance genesen_ZA
dc.subjectMobilomeen_ZA
dc.subjectMeta-resistomeen_ZA
dc.subjectMethylomeen_ZA
dc.subjectPhased-sequencingen_ZA
dc.titleUnderstanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective : advances and applicationsen_ZA
dc.typePostprint Articleen_ZA

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