Relationship between homology and genomics of Klebsiella pneumoniae in patients with neurocritical infection
10.3760/cma.j.cn101721-20210512-00020
- VernacularTitle:神经危重症感染患者肺炎克雷伯菌同源性与基因组学关系
- Author:
Pingshu ZHANG
1
;
Qing LIU
;
Yan LI
;
Yan LIU
;
Hemei GENG
;
Heyong WANG
;
Shuqing ZHANG
;
Xiaodong YUAN
Author Information
1. 开滦总医院神经内科，河北省唐山市 063000
- Keywords:
Neurocritical;
Klebert pneumoniae;
Homology;
Genomics;
Single nucleotide polymorphism;
Specific gene family
- From:
Clinical Medicine of China
2021;37(6):508-514
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To analyze the relationship between homology of Kleber pathogen pneumoniae (KP) in patients with neurocritical infections and the Genomics.Method:Five non-multidrug resistant pathogen KP were identified in 2015 to 2018, including the same cloning strain of P90 and P91, the same popular cloning system of P66,P90 and P91, and there is no homology between P20,P39 and other strains, which makes a second generation full genome sequencing. A variety of bioinformatics software were used for genomic analysis to understand the basic genomic information, chromosomal and plasmid distribution, single nucleotide polymorphism (SNP) differences and gene family clustering characteristics, meanwhile with the National Center for Biotechnology Information (NCBI) website registered 18 KP strains (2013--2016) to analyze the evolutionary affinity between strains.Results:The total genome sizes of P20, P39, P66, P90 and P91 were 5 469 543 bp, 5 480 332 bp, 5 768 352 bp, 5 745 666 bp, 5 722 999 bp. The GC contents were 57.07% (1 559 929+1 561 432)/5 469 543, 57.27% (1 566 970+1 571 424)/5 480 322, 56.96% (1 640 438+1 645 432)/5 768 352, 56.88% (1 634 285+1 634 038)/5 745 666, and 56.95% (1 627 360+1 631 781)/5 722 999, respectively. Compared with P20 reference strains, the total number of SNP in P39, P66, P90 and P91 were 32 682, 34 226, 34 292, 34 375, and the total mutation rates of gene coding region sequences were87.18% (28 491/32 682), 86.71% (29 679/34 226), 85.26% (29 238/34 292), 86.22% (29 638/34 375), respectively. Nonsynonymous mutations accounted for some advantages, and the rates were 44.57% (14 566/32 682), 44.01% (15 063/34 226), 48.01% (16 465/34 292), 48.75% (16 758/34 375), and synonymous mutations were 42.61% (13 925/32 682), 42.70% (14 616/34 226), 37.25% (12 773/34 292), 37.47% (12 880/34 375), respectively. P90 and P91 have 6 specific gene families, and P66 has 4 specific gene families. The same popular clone lines P66, P90 and P99 are on the same evolutionary branch of the phylogenetic tree. The same clone P90 and P99 are on the same subbranch. P20 and P39 without homology are on different evolutionary branches respectively. P20, P39, P66, P90 and P91 on the evolutionary branches of phylogenetic tree are closely related to the evolutionary grade of strain KP52-145 from France and strain ED23 from Taiwan, China submitted on NCBI website.Conclusion:Klebsiella pneumoniae in patients with neurocritical infection has the same clone, and the number of unique gene families among strains is the same. There are small differences in the number of unique gene families and the total number of SNPs among the same epidemic clone lines, and they are characteristic of the same evolutionary branch of the phylogenetic tree. The number of unique gene families and the total number of SNPs of non homologous strains are quite different, and they are in different evolutionary branches of the phylogenetic tree.
