从巴西受污染土壤中分离出的肠炎沙门氏菌SE3的混合基因组分析

Hybrid Genomic Analysis of Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil.

作者信息

Romero-Calle Danitza Xiomara, Pedrosa-Silva Francisnei, Tomé Luiz Marcelo Ribeiro, Sousa Thiago J, de Oliveira Santos Leila Thaise Santana, de Carvalho Azevedo Vasco Ariston, Brenig Bertram, Benevides Raquel Guimarães, Venancio Thiago M, Billington Craig, Góes-Neto Aristóteles

机构信息

Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana 44036-900, BA, Brazil.

Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil.

出版信息

Microorganisms. 2022 Dec 31;11(1):111. doi: 10.3390/microorganisms11010111.

DOI:10.3390/microorganisms11010111

PMID:36677403

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9861973/

Abstract

In Brazil, Salmonella enterica serovar Enteritidis is a significant health threat. Salmonella enterica serovar Enteritidis SE3 was isolated from soil at the Subaé River in Santo Amaro, Brazil, a region contaminated with heavy metals and organic waste. Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing were used for de novo hybrid assembly of the Salmonella SE3 genome. This approach yielded 10 contigs with 99.98% identity with S. enterica serovar Enteritidis OLF-SE2-98984-6. Twelve Salmonella pathogenic islands, multiple virulence genes, multiple antimicrobial gene resistance genes, seven phage defense systems, seven prophages and a heavy metal resistance gene were encoded in the genome. Pangenome analysis of the S. enterica clade, including Salmonella SE3, revealed an open pangenome, with a core genome of 2137 genes. Our study showed the effectiveness of a hybrid sequence assembly approach for environmental Salmonella genome analysis using HiSeq and MinION data. This approach enabled the identification of key resistance and virulence genes, and these data are important to inform the control of Salmonella and heavy metal pollution in the Santo Amaro region of Brazil.

摘要

在巴西，肠炎沙门氏菌血清型肠炎亚种是一个重大的健康威胁。肠炎沙门氏菌血清型肠炎亚种SE3是从巴西圣阿马罗苏巴埃河的土壤中分离出来的，该地区受到重金属和有机废物的污染。使用Illumina HiSeq和牛津纳米孔技术MinION测序对沙门氏菌SE3基因组进行从头混合组装。这种方法产生了10个重叠群，与肠炎沙门氏菌血清型肠炎亚种OLF-SE2-98984-6的同一性为99.98%。该基因组编码了12个沙门氏菌致病岛、多个毒力基因、多个抗菌基因抗性基因、7个噬菌体防御系统、7个原噬菌体和一个重金属抗性基因。对包括沙门氏菌SE3在内的肠炎沙门氏菌进化枝进行的泛基因组分析显示，其泛基因组是开放的，核心基因组有2137个基因。我们的研究表明了一种使用HiSeq和MinION数据进行环境沙门氏菌基因组分析的混合序列组装方法的有效性。这种方法能够识别关键的抗性和毒力基因，这些数据对于指导巴西圣阿马罗地区沙门氏菌和重金属污染的控制非常重要。