基于NCBI数据库的皮氏不动杆菌分子分型及bla0XA基因分析
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国家重点研发计划项目( EKA -04201901)


Molecular typing and blaoxA gene analysis of Acinetobacter pittii based on NCBI database
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    摘要:

    摘要:目的分析全球皮氏不动杆菌 的分布特点、序列分型(ST)及blaox基因分布,为感染防控及临床用药提供参考。方法采用Aspera软件从NCBI批量下载所有皮氏不动杆菌基因组序列(截止日期为2023年11月30日),并使用perl脚本从下载的gbk文件中批量提取菌株元信息。使用自制的Perl程序从每个皮氏不动杆菌基因组序列文件中提取该基因的核苷酸编码序列作为分析数据库。从网站下载不动杆菌属7个管家基因的等位基因序列作为查询数据库进行BLASTN比较分析,确定每个基因组的ST。从NCBI病原细菌耐药基因数据库下载耐药基因blaoxa 的核苷酸序列,采用自我编写的AMRG软件进行blaoxa基因的分布分析。结果共获取 305株皮氏不动杆菌的基因组,主要分离自1990年至2020年,分离率呈逐年增长趋势,其中2015年分离率最高。美国、中国、德国的分离率位居前三位,分别为29.5%(90株)、15.7%(48株)、13.4%(41株)。180株(59.0%)标本来源为人类,其中,痰液[42株(23.3%)]、血液[27株(15.0%)]和皮肤软组织[ 15株(8.3%)]位居前三位。305 株皮氏不动杆菌共鉴定出79种ST,其中,ST93( 14.4%)、ST64(12.1%)和ST63( 11.8%)占比较高。美国、中国、德国分别以ST64、ST63、ST93流行分布为主。305 株皮氏不动杆菌中除6株不携带blaoxA 基因外,其余299株菌共携带31种blaoxA .变异体,其中252个blaox基因具有碳青霉烯酶水解活性,另有146株携带bax.00基因。结论皮氏不动杆菌 全球流行分布存在地域差异,D型碳青霉烯酶基因blaoxx的高度流行提示其潜在多药耐药趋势,值得临床监测。

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    Abstract: Objective To analyze the prevalent characteristics, sequence type (ST),and blaoxa gene distribution of global Acinetobacter pitii, and provide reference for prevention and clinical medication against this infection. Methods All the sequences of A. pittii genomes were downloaded in batch from NCBI by using Aspera software with deadline of November 30, 2023, and perl script was used to extract the meta information of strains in batch from the downloaded GBK file. A self. -made Perl program was utilized to extract the nucleotide coding sequence of the gene from each genome sequence file of A. pittii as the analysis database. BLASTN comparative analysis was implemented by using the allelic sequences of 7 housekeeping genes of the genus Acinetobacter Sp downloaded from the website as a query database to determine the ST of each genome. The nucleotide sequences of the blaoxA genes were downloaded from the NCBI pathogen resistance gene database and the self-witten AMRG software was utilized to analyze the distribution of blaoxA gene among A. pitii. Results A total of 305 A. pittii genomes were obtained, which were mainly isolated from 1990 to 2020. The isolation rates showed an increasing trend of year by year with the highest isolation rate in 2015. The separation rates of the United States, China and Germany ranked in the top three positions, with the separation rates of 29.5% (90 strains), 15.7% (48 strains), and 13.4% (41 strains),respectively. A total of 180 ( 59.0%) specimens were sourced from humans, of which 42 ( 23.3%) were from sputum, 27(15.0%) from blood, and 15 (8.3%) from skin and soft tissues. The 305 strains of A. pittii were assigned into 79 STs,among which ST93 (14.4%), ST64 ( 12.1%) and ST63 (11.8% ) accounted for the highest proportion. In the United States, China and Germany, the infections were mainly affected by ST64, ST63 and ST93, respectively. The 305 A. pitti cried the blaoxA gene except 6 strains,while the remained 299 strains carried 31 blaoxA variants, of which,252 blaoxA genes were found to own the carbapenemase hydrolysis activity and 146 strains carried bax-5o gene. Conclusion There should be regional diferences in the global distribution of A. piti,and the high prevalence of the carbapenemase gene blaoxa suggested a potential trend of multi-drug resistance, which is worthy to be monitored.

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纪静茹,曹小利,吴超.基于NCBI数据库的皮氏不动杆菌分子分型及bla0XA基因分析[J].临床检验杂志,2024,42(4):298-303

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  • 收稿日期:2023-12-28
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  • 在线发布日期: 2024-06-14
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