Antimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock.
Antimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock.
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DOI：
10.1038/s41598-023-42838-z
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发表时间：
2023-10-30
影响因子：
4.6
通讯作者：
Hemly, Yosra A.
中科院分区：
文献类型：
--
作者：
El Zowalaty, Mohamed E.;Lamichhane, Bibek;Falgenhauer, Linda;Mowlaboccus, Shakeel;Zishiri, Oliver T.;Forsythe, Stephen;Hemly, Yosra A.
出现抗生素耐药性的牲畜相关粪肠球菌是一个公共卫生问题。本文报道了20种肠球菌的分离、毒力和耐药决定簇的分子检测，以及15株粪肠球菌（包括3种新序列型的6株、3株屎肠球菌和2株硬肠球菌）的全基因组测序分析。所有菌株均分离自南非的食物链动物。在胆汁七叶皂苷叠氮琼脂上分离肠球菌菌株，然后使用MALDI-TOF MS分析进行鉴定。采用Kirby-Bauer纸片扩散法进行药敏试验。提取分离株的基因组DNA，并使用Illumina MiSeq平台进行测序。修剪序列读数并从头组装。分析组装的重叠群的抗菌素耐药基因和染色体突变、染色体外质粒和多位点序列类型（MLST）。鉴定了赋予对氨基糖苷类（ant（6）-Ia、aph（3′）-IIIa、sat 4和spw）、林可酰胺类（lnu（B）、lsa（A）和lsa（E））、大环内酯类（nu（B））、甲氧苄啶（dfrG）和四环素类（泰特（L）和泰特（M））耐药的多药抗菌药物耐药基因。在7株大肠杆菌中检测到质粒复制子。faecalis和3株E.粪菌分离物。使用Enterococcus PubMLST数据库确定每个分离株的序列类型（ST）。在收集中确定了10种ST，其中3种（ST 1240、ST 1241和ST 1242）以前未报告，在本研究中首次描述。将测序的菌株与其他已测序的E. faecalis菌株、E.从PubMLST数据库下载来自家畜的粪便。使用ParSNP进行基于核心基因组的系统发育分析。包括大肠埃希菌在内的肠球菌属多重耐药检测。粪肠球菌E. faecium强调了基因组监测对监测食物链动物中抗菌素耐药性传播的重要性。此外，本研究中报道的肠球菌菌株的基因组序列将作为未来家畜相关和耐药肠球菌的分子流行病学研究的参考点。非洲的粪菌此外，本研究还为深入分析E.粪肠球菌基因组结构，以及提供了有价值的信息表型和基因型的抗菌药物耐药性，和发病机制的牲畜相关的E。粪肠球菌E.屎室
The emergence of antimicrobial-resistant, livestock-associated Enterococcus faecalis represents a public health concern. Here, we report the isolation, molecular detection of virulence and antimicrobial resistance determinants, in addition to the phylogenetic analyses of 20 Enterococcus species using whole genome sequencing analysis of 15 Enterococcus faecalis strains including six strains of three novel sequence types, three Enterococcus faecium and two Enterococcus durans. All strains were isolated from food chain animals in South Africa. Enterococcus strains were isolated on bile aesculin azide agar, followed by identification using MALDI-TOF MS analysis. Antibiotic susceptibility testing was performed using the Kirby–Bauer disk diffusion method. The genomic DNA of the isolates was extracted and sequencing was performed using the Illumina MiSeq platform. Sequence reads were trimmed and de novo assembled. The assembled contigs were analyzed for antimicrobial resistance genes and chromosomal mutations, extra-chromosomal plasmids, and multi-locus sequence type (MLST). Multidrug antimicrobial resistance genes conferring resistance to aminoglycosides (ant(6)-Ia, aph(3′)-IIIa, sat4, and spw), lincosamides (lnu(B), lsa(A), and lsa(E)), macrolides (erm(B)), trimethoprim (dfrG) and tetracyclines (tet(L) and tet(M)) were identified. Plasmid replicons were detected in seven E. faecalis and three E. faecium isolates. The sequence type (ST) of each isolate was determined using the Enterococcus PubMLST database. Ten STs were identified in the collection, three of which (ST1240, ST1241, and ST1242) have not been previously reported and are described in the present study for the first time. To compare the sequenced strains to other previously sequenced E. faecalis strains, assembled sequences of E. faecalis from livestock were downloaded from the PubMLST database. Core genome-based phylogenetic analysis was performed using ParSNP. The detection of multiple drug-resistance in Enterococcus including E. faecalis and E. faecium highlights the significance of genomic surveillance to monitor the spread of antimicrobial resistance in food chain animals. In addition, the genome sequences of Enterococcus strains reported in the present study will serve as a reference point for future molecular epidemiological studies of livestock-associated and antibiotic-resistant E. faecalis in Africa. In addition, this study enables the in-depth analysis of E. faecalis genomic structure, as well as provides valuable information on the phenotypic and genotypic antimicrobial resistance, and the pathogenesis of livestock-associated E. faecalis and E. faecium.
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影响因子：
4.6
作者：
Alemayehu T;Hailemariam M
通讯作者：
Hailemariam M
自上而下的基因组监测方法，用于调查阿肯色州癌症患者中检测到的屎肠球菌的基因组流行病学和抗生素耐药性模式。
影响因子：
3.7
作者：
通讯作者：
--
影响因子：
5.2
作者：
Hanchi H;Mottawea W;Sebei K;Hammami R
通讯作者：
Hammami R
影响因子：
28.3
作者：
Gouliouris T;Coll F;Ludden C;Blane B;Raven KE;Naydenova P;Crawley C;Török ME;Enoch DA;Brown NM;Harrison EM;Parkhill J;Peacock SJ
通讯作者：
Peacock SJ
影响因子：
14.9
作者：
Letunic I;Bork P
通讯作者：
Bork P