一株林麝源丙二酸盐克罗诺杆菌的分离鉴定及其全基因组序列分析

Isolation, identification, and whole genome sequencing of Cronobacter malonaticus from forest musk deer

摘要:

【背景】 克罗诺杆菌(Cronobacter spp.)作为食源性致病菌，常出现在新生儿患病的报道中，目前尚无在林麝中检出克罗诺杆菌的报道。【目的】 对分离自林麝肾脏的一株丙二酸盐克罗诺杆菌(C. malonaticus)进行鉴定和全基因组测序，为林麝相关疾病的预防治疗奠定基础。【方法】 将病原菌分离纯化后，依次进行生化试验、药敏试验、小鼠致病性试验及全基因组测序，以测序结果为基础，进一步分析群体进化、物种分型及基因功能注释。【结果】 该病原菌经过平均核苷酸一致性(average nucleotide identity, ANI)分类和系统发育树分析可知属于丙二酸盐克罗诺杆菌，生化结果符合克罗诺杆菌的一般特性。该菌株被命名为Dcc0527，对部分喹诺酮类药物、酰胺醇类药物、氨基糖苷类药物和β-内酰胺类药物敏感，对部分磺胺类药物和大环内酯类药物耐药；全基因组测序结果表明该菌株包含1个环状染色体和4个环形质粒，全基因组大小为1 257 547 026 bp，G+C含量为57.08%，多位点序列分型显示该菌株属于ST211序列类型。在菌株Dcc0527基因组内存在阿尔法霉素、氟喹诺酮、四环素等多种耐药基因，同时该菌株还存在Type IV pili、kpsD、iroN等多种毒力基因。菌株Dcc0527基因组的染色体和质粒中还存在3个比较完整的噬菌体区域。【结论】 从林麝肾脏分离得到一株丙二酸盐克罗诺杆菌，并获得了该ST211型菌株的全基因组序列，为林麝细菌性疾病的防治提供参考。

Abstract:

[Background] As foodborne pathogens, Cronobacter spp. often appear in the reports of neonatal illness. So far, there has been no report of Cronobacter spp. in forest musk deer. [Objective] We identified and sequenced a strain of Cronobacter malonaticus isolated from the kidney of forest musk deer, aiming to lay a foundation for the prevention and treatment of related diseases in forest musk deer. [Methods] After the pathogen was isolated, biochemical tests, drug susceptibility tests, pathogenicity test in mice, and whole genome sequencing were conducted. Based on the sequencing results, the population evolution analysis, species typing, and gene function annotation were performed. [Results] The pathogen was identified as C. malonaticus based on the average nucleotide identity (ANI) and phylogenetic tree, with the biochemical test results consistent with the general characteristics of C. malonaticus. The strain, named Dcc0527, was sensitive to some quinolones, amphenicols, aminoglycosides, and β-lactams and resistant to some sulfonamides and macrolides. The results of whole genome sequencing showed that the strain contained one ring chromosome and four ring plasmids, with the whole genome size of 1 257 547 026 bp and the G+C content of 57.08%. The multilocus sequence typing showed that the strain presented the sequence type ST211. The genome of strain Dcc0527 carried the genes conferring resistance to several antibiotics, such as elfamycin, fluoroquinolone, and tetracycline and several virulence genes, such as Type IV pili, kpsD, and iroN. In addition, there were three complete phage regions in the chromosome and plasmids of strain Dcc0527. [Conclusion] We isolated a strain of C. malonaticus from the kidney of forest musk deer and obtained the whole genome sequence of this strain (ST211). The findings provide reference for the prevention and control of bacterial diseases in forest musk deer.