人源单核细胞增生李斯特菌的基因组进化及耐药性分析

doi:10.13481/j.1671-587x.20210125

摘要/Abstract

摘要： 目的

利用新一代测序技术鉴定1例脑膜炎患者脑脊液中分离培养的单核细胞增生李斯特菌（LM），并进行基因组进化和耐药性分析，探讨患者病情迅速进展和治疗失败的原因。

方法

从该例脑膜炎患者脑脊液中培养、分离并鉴定出LM，采用Illumina HiSeq 3000 系统进行细菌De novo测序，利用基因组装、基因预测、基因注释、单核苷酸多态性（SNP）分析和系统进化分析等生物信息学方法，构建LM属的进化树，并进行耐药基因分析。

结果

患者脑脊液细菌分离培养，经质谱法鉴定为LM；经过测序，数据组装细菌基因组大小为3 008 507 bp。与数据库比较，获得的LM基因组-致率为88%，确定培养细菌为LM属；对比美国国家生物技术信息中心（NCBI）数据库中38个代表性LM基因组构建系统发生树，检测LM株与数据库中FSL N1-017和SLCC2540距离较近，并且共线性良好，与已报道的国内外人源感染的LM均无进化关系，为中国新发现的临床感染型致病LM。耐药性分析，检测到的LM基因组包含与主要协同转运蛋白超家族（MFS）转运体相关的耐药基因，其中4个基因与数据库EDG-e株转运体注释中的耐药基因相匹配，提示该菌株临床耐药性较强。

结论

鉴定出来源于临床脑膜炎患者脑脊液培养菌为新型临床感染型致病LM菌株，且临床耐药性较强。

关键词: 单核细胞增生李斯特菌, 脑膜炎, 全基因组测序, 主要协同转运蛋白超家族转运体, 耐药性

Abstract: Objective

To identify the Listeria monocytogenes（LM） obtained from the cerebrospinal fluid of one patient with meningitis with new generation sequencing technology and analyze genomic evolution and drug resistance， and to explore the possible causes of rapid progression of disease and treatment failure.

Methods

The LM were cultivated， isolated and identified from the patient’s cerebrospinal fluid， and bacterial De novo sequencing was conducted by the Illumina HiSeq 3000 system to obtain the whole genome data of the strain.Furthermore， the evolutionary tree of the LM was constructed and the drug-resistant related genes were identified by gene assembly， gene prediction， gene annotation， single nucleotide polymorphism（SNP） analysis， and phylogenetic analysis and other bioinformatics methods.

Results

The bacteria in the cerebrospinal fluid were isolated and cultured， and identified as LM by mass spectrometry.The size of the assembled bacterial genome after sequencing was 3 008 507 bp.By aligned with database， its genome was accordance with 88% of LM genome， confirming that the bacteria was LM.The obtained listeria strains were close to FSL N1-017 and SLCC2540 by aligning 38 representative listeria genome construction phylogenetic trees in the NCBI database，and they had no evolutionary relationships with human-derived LM that were reported worldwide. It was considered to be a newly discovered clinically infectious LM in China.The drug resistance analysis revealed that the obtained LM genome contained some drug-resistant genes associated with the major facilitator superfamily（MFS）transporters，and four of them were matched the drug resistance genes in the database EDG-e strain transporter annotation， suggesting that the strain had strong clinical resistance.

Conclusion

The cultured bacteria from cerebrospinal fluid of clinical meningitis patient is identified as a new type of clinically infectious pathogenic LM strain with strong clinical drug resistance.

Key words: Listeria monocytogenes, meningitis, whole genome sequencing, major facilitator superfamily transporter, drug resistance

中图分类号:

R446.5

姚广,陆玉颖,张庆华,朱海霞,陈益伟,孙东,庄振,张峰,刘鼎,宋治. 人源单核细胞增生李斯特菌的基因组进化及耐药性分析[J]. 吉林大学学报(医学版), 2021, 47(1): 180-186.

Guang YAO,Yuying LU,Qinghua ZHANG,Haixia ZHU,Yiwei CHEN,Dong SUN,Zhen ZHUANG,Feng ZHANG,Ding LIU,Zhi SONG. Genomic evolution and drug resistance analysis of human-derived Listeria monocytogenes[J]. Journal of Jilin University(Medicine Edition), 2021, 47(1): 180-186.

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XY1803	Combined gene	Definition
LMXY_51	lmrB	MFS transporter, DHA2 family, lincomycin resistance protein
LMXY_363	tetA	MFS transporter, DHA1 family, tetracycline resistance protein
LMXY_377	sugE	quaternary ammonium compound-resistance protein SugE
LMXY_378	sugE	quaternary ammonium compound-resistance protein SugE
LMXY_1367	mdtG	MFS transporter, DHA1 family, multidrug resistance protein
LMXY_1443	norB, norC	MFS transporter, DHA2 family, multidrug resistance protein
LMXY_1747	lmrP	MFS transporter, DHA1 family, multidrug resistance protein B
LMXY_2435	TC.MATE, SLC47A, norM, mdtK, dinF	multidrug resistance protein, MATE family
LMXY_2511	lmrB	MFS transporter, DHA2 family, lincomycin resistance protein
LMXY_2724	mdtG	MFS transporter, DHA1 family, multidrug resistance protein

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