Identification of a novel genomic resistance island PmGRI1-STP3 and an SXT/R391 integrative conjugative element in Proteus mirabilis of swine origin in China
Identification of a novel genomic resistance island PmGRI1-STP3 and an SXT/R391 integrative conjugative element in Proteus mirabilis of swine origin in China
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DOI：
10.1016/j.jgar.2021.02.018
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发表时间：
2021-03-26
影响因子：
4.6
通讯作者：
Wang, Hongning
中科院分区：
文献类型：
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作者：
He, Juan;Lei, Changwei;Wang, Hongning
目的：本研究旨在确定从四川省某猪场分离的奇异变形杆菌菌株STP 3的耐药基因遗传环境。使用Illumina MiSeq（200 x覆盖度）和Nanopore PromethiON（100 x覆盖度）平台进行基因组测序。结果：构建的奇异变形杆菌STP 3环状基因组全长4115975 bp，GC含量为39.58%，未检测到质粒序列。在奇异变形杆菌STP 3中表征了一种新的基因组抗性岛（PmGRI 1-STP 3）和一种SXT/R391整合接合元件（ICE）变体（ICEPmiChnSTP 3）。PmGRI 1-STP 3位于tRNA-Sec的3'端，大小为52.7kb，与PmGRI 1-C55同源性最高（覆盖率为54%，同源性为99.99%）。PmGRI 1-STP 3携带16个耐药基因，包括临床上重要的超广谱β-内酰胺酶（ESBL）基因bla（CTX-M-3）。将ICEPmiChnSTP 3插入prfC基因中。它携带18个耐药基因，包括rRNA甲基转移酶基因cfr和氟喹诺酮耐药基因aac（6 '）-Ib-cr。在转座子Tn 7上还鉴定了2类整合子（dfrA 1-sat 2-aadA 1）。动员实验表明，ICEPmiChnSTP 3是共轭动员大肠杆菌。结论：两个基因组岛（GI）的鉴定表明，遗传元件可能是奇异变形杆菌获得抗性基因的关键介质，IS 26介导的重排促进了GI的多样性。(C)2021由Elsevier Ltd代表国际抗菌药物化学治疗学会发表。
Objectives: This study aimed to determine the genetic environment of antimicrobial resistance genes in Proteus mirabilis strain STP3 isolated from a diarrhoeic pig on a swine farm in Sichuan Province, China.Methods: Strain STP3 was subjected to antimicrobial susceptibility testing. Illumina MiSeq (200x coverage) and Nanopore PromethiON (100x coverage) platforms were used for genome sequencing. A conjugation experiment was performed to determine the transferability and stability of antimicrobial resistance genes in this strain.Results: The assembled circular genome of P. mirabilis STP3 was 4 115 975 bp with a GC content of 39.58%; no plasmid sequence was detected. A novel genomic resistance island (PmGRI1-STP3) and an SXT/R391 integrative conjugative element (ICE) variant (ICEPmiChnSTP3) were characterised in P. mirabilis STP3. PmGRI1-STP3 of 52.7 kb was located at the 3' end of tRNA-Sec and shared the greatest identity with PmGRI1-C55 (54% coverage, 99.99% identity). PmGRI1-STP3 carried 16 resistance genes, including the clinically important extended-spectrum beta-lactamase (ESBL) gene bla(CTX-M-3). ICEPmiChnSTP3 was inserted into the prfC gene. It carried 18 resistance genes, including the rRNA methyltransferase gene cfr and the fluoroquinolone resistance gene aac(6')-Ib-cr. A class 2 integron (dfrA1-sat2-aadA1) was also identified on transposon Tn7. Mobilisation experiments indicated that ICEPmiChnSTP3 was conjugally mobilised to Escherichia coli. However, PmGRI1-STP3 appeared to lose its mobilisation ability.Conclusion: The identification of two genomic islands (GIs) in this study suggested that genetic elements might be key mediators for resistance gene acquisition in P. mirabilis and that IS26-mediated rearrangements promote the diversity of GIs. (C) 2021 Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.