Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview

被引:46
作者
de Abreu, Vinicius A. C. [1 ]
Perdigao, Jose [1 ]
Almeida, Sintia [2 ]
机构
[1] Univ Fed Para, Fac Comp FACOMP, Lab Bioinformat & Comp Alto Desempenho LaBioCad, Belem, Para, Brazil
[2] Univ Fed Fortaleza, Dept Fisiol & Farmacol, Nucleo Pesquisa & Desenvolvimento Medicamentos NP, Cent Genom & Bioinformat CeGenBio, Fortaleza, Ceara, Brazil
关键词
antimicrobial resistance genes; horizontal gene transfer; metagenomic analysis; resistome; Shotgun metagenome sequencing; database; ANTIBIOTIC-RESISTANCE; ENTEROCOCCUS-FAECALIS; GENE; MECHANISMS; SEARCH; SOIL; CHLORAMPHENICOL; ENVIRONMENT; EXPLORATION; GENERATION;
D O I
10.3389/fgene.2020.575592
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Antimicrobial resistance is a major global public health problem, which develops when pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic recombination between commensal and pathogenic microbes. The resistome is a collection of all ARGs. In microorganisms, the primary method of ARG acquisition is horizontal gene transfer (HGT). Thus, understanding and identifying HGTs, can provide insight into the mechanisms of antimicrobial resistance transmission and dissemination. The use of high-throughput sequencing technologies has made the analysis of ARG sequences feasible and accessible. In particular, the metagenomic approach has facilitated the identification of community-based antimicrobial resistance. This approach is useful, as it allows access to the genomic data in an environmental sample without the need to isolate and culture microorganisms prior to analysis. Here, we aimed to reflect on the challenges of analyzing metagenomic data in the three main approaches for studying antimicrobial resistance: (i) analysis of microbial diversity, (ii) functional gene analysis, and (iii) searching the most complete and pertinent resistome databases.
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页数:9
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