多重耐药胸膜肺炎放线杆菌GD2107株全基因组测序及生物信息学分析

doi:10.16431/j.cnki.1671-7236.2022.10.035

Abstract

Abstract: 【Objective】 Through genome sequencing and bioinformatics analysis of GD2107 strain of multi-drug resistant Actinobacillus pleuropneumoniae (APP),the genome database information of APP was enriched,the phylogenetic tree based on ApxⅣ gene was constructed,and the evolutionary relationship of the strain was analyzed,so as to provide reference for exploring the pathogenic mechanism of APP and clinical prevention and control of porcine infectious porcine contagious pleuropneumia (PCP).【Method】 The drug resistance spectrum of the isolated strains was determined by drug sensitivity test. The whole genome of bacterial DNA was sequenced by whole genome sequencing (WGS) method.Based on Illumina NovaSeq and PacBio SequeI sequencing platforms,the whole genome sequencing results were analyzed by gene function annotation and bioinformatics analysis (including basic genome information,functional element analysis and subsystem analysis,etc.). Phylogenetic tree was constructed based on ApxⅣ gene.【Result】 The results of drug sensitivity test of GD2107 strain showed that it was resistant to 14 kinds of antimicrobials including penicillin,cefradine (pioneer Ⅵ),kanamycin and so on.The whole genome of GD2107 strain was sequenced to obtain a circular chromosome of 2 271 987 bp (GC content was 41.21%) and two circular plasmids of 5 027 and 3 497 bp,respectively.A total of 2 290 coding genes were predicted,including 19 rRNA (7 5S rRNA,6 16S rRNA,6 23S rRNA),21 tRNA genes,20 ncRNA;23 gene islands,4 prophages and 2 groups of CRISPR related sequences.2 112,1 549 and 1 866 genes were annotated in the databases of COG,KEGG and GO,respectively,and the related proteins were mainly distributed in the metabolic process of APP.In addition,48 virulence genes and 22 drug resistance genes were annotated in VFDB and CARD databases (only floR gene was located on the plasmid).The whole genome circle map of the strain was drawn and the genome information was submitted to NCBI.The chromosome GenBank accession No. was CP097377 and the plasmids accession No. were CP097378 and CP097379, respectively. Phylogenetic tree analysis showed that the evolutionary relationship between this strain and APP strain from China (CP063424.1) was the closest.【Conclusion】 In this study, we completed the whole genome sequencing and bioinformatics analysis of the multi-drug resistant strain GD2107, fully understood the structure and function of the genome of the strain, and explored the related genes in drug resistance and pathogenic mechanism. The evolutionary relationship showed that the strain had a certain regional epidemic, which provided a reference for preventing the epidemic of PCP and exploring the pathogenic mechanism of APP.

Key words: Actinobacillus pleuropneumoniae (APP); whole genome sequencing; bioinformatics analysis; resistance genes; phylogenetic analysis

CLC Number:

S852.61^＋9

XU Minsheng, KE Haiyi, YANG Dongxia, SHI Keda, SUN Zeyi, NIU Jiawei, CHANG Xin, ZHAI Shaolun, ZANG Yingan, LI Chunling. Whole Genome Sequencing and Biological Characteristics Analysis of Multidrug-resistant Actinobacillus pleuropneumoniae GD2107 Strain[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(10): 4019-4031.

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Whole Genome Sequencing and Biological Characteristics Analysis of Multidrug-resistant Actinobacillus pleuropneumoniae GD2107 Strain

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