基于基因组学的肺炎克雷伯菌噬菌体安全性评估

Safety Assessment of Klebsiella pneumoniae Phages Based on Genomics

泛耐药肺炎克雷伯菌的流行,使得临床面临无药可用,越来越多的肺炎克雷伯菌噬菌体近年来被报道,并在动物模型中证明了它们用于防控细菌感染的有效性。然而,噬菌体作为病毒的一类,不同于传统的抗菌药物,在临床应用之前需要进行更为全面的评估,本研究将基于基因组学对已报道的肺炎克雷伯菌噬菌体安全性进行评估。通过生物信息学分析噬菌体基因组上是否含有肺炎克雷伯菌限制性内切酶识别位点来评估其基因组稳定性,并就其是否携带有害基因和是否属于溶原性噬菌体等方面进行分析研究。目前已报道22株肺炎克雷伯菌噬菌体的全基因组,7株属于肌尾科,12株属于短尾科,3株属于长尾科;而本研究基于噬菌体全基因组同源性分析结果将短尾科、长尾科和肌尾科中的JD001归为一类,定义为Kp_PhageⅠ;肌尾科分为Kp_phageⅡa和Kp_PhageⅡb两类。噬菌体基因组上含有数目不等的肺炎克雷伯菌限制性内切酶识别位点,不携带有毒力基因和耐药基因。5株属于温和噬菌体,17株属于烈性噬菌体。研究显示肺炎克雷伯菌噬菌体在基因组水平具有良好的安全性,但是基因组上较多的肺炎克雷伯菌限制性内切酶识别位点,使其抗菌谱可能较窄。在使用噬菌体用于防控细菌感染时部分温和噬菌体需要谨慎排除。

The dissemination of pan-drug resistant Klebsiella pneumoniae leads to the situation of no drugs available for the treatment of infections, while increasing numbers of K. pneumonia phages have been reported in recent years, and some of them have been demonstrated to be effective for the prevention and control of infections in animal models. However, unlike traditional antibiotics, bacteriophages are seen as live viruses, which should be comprehensively evaluated before clinical applications. The purpose of this study was to analyze the safety of the reported K. pneumoniae phages based on their complete genome. The bioinformatics method was used to analyze whether there were restriction endonuclease recognition sites in the phages＇ genome to assess the stability of its genome, and whether they carried detrimental and belonged to lysogenic phage were also studied. 22 K. pneumoniae phages with complete genomes have been reported, among which 7 strains belong to Myoviridae, 12 strains belong to Podoviridae, and 3 strains belong to Siphoviridae; Based on the results of phage genome homology analysis, our study divided JD001 in Podoviridae, Siphoviridae and Myoviridae into one group, defining it as Kp_PhageI; Myoviridae was divided into Kp_phage Ⅱ a and Kp Phage Ⅱb two groups. The phage genome contained a number of restriction enzyme recognition sites of K. p neumoniae, but there were no virulent genes and resistant genes. 5 strains belonged to moderate phages and 17 strains belonged to virulent phages. The study showed that K. pneumoniae phages had good safety at the genomic level, while the large number of KpnI and Kpn2I recognition sites on their genome might result in their narrow antimicrobial spectrum. Some moderate phages should be carefully excluded when the phages were used for the prevention and control of bacterial infection.