中文摘要：肺炎克雷伯菌对公共卫生的威胁越来越大，是危及生命的病原体之一。其耐药和毒力决定因子由可移动的基因元件编码，这些基因元件很容易在细菌群体之间传播，并与其基因组宿主共同进化。本研究展示了从葡萄牙一家医院爆发的40株肺炎克雷伯菌临床分离株中发现的150个原噬菌体的全基因组序列、插入位点和系统发育分析。研究发现所有菌株至少含有一种原噬菌体，共鉴定出104种完整的原噬菌体（69.3%）；原噬菌体大小在29.7-50.6kbp之间，编码32-78个假定基因；原噬菌体的GC含量为51.2%，低于肺炎克雷伯菌的平均GC含量57.1%；完整的原噬菌体按尾状病毒目的顺序分为三个科：肌病毒科（59.6%）、长尾病毒科（38.5%）和短尾病毒科（1.9%）。此外，比对和系统发育分析显示了九个不同聚类；在一些原噬菌体的基因组内检测到重组，但在大多数情况下，参与病毒结构、转录、复制和调控（溶原/裂解）的蛋白质仍被保留。本研究支持了原噬菌体在肺炎克雷伯菌基因组中具有多样性和广泛分布的认知，促进该物种的进化并赋予额外的表型。此外，还在一组内溶素基因中鉴定了肺炎克雷伯菌原噬菌体，发现内溶素基因编码具有溶菌酶活性的蛋白质，切割肽聚糖网络中N-乙酰壁酸和N-乙酰-D-葡萄糖胺残基之间的β-1,4键，从而代表具有细胞裂解酶噬菌体治疗潜力的基因。
外文摘要：Klebsiella pneumoniae is an increasing threat to public health and represents one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic elements which can easily spread between bacteria populations and co-evolve with its genomic host. In this study, we present the full genomic sequences, insertion sites and phylogenetic analysis of 150 prophages found in 40 K. pneumoniae clinical isolates obtained from an outbreak in a Portuguese hospital. All strains harbored at least one prophage and we identified 104 intact prophages (69.3%). The prophage size ranges from 29.7 to 50.6 kbp, coding between 32 and 78 putative genes. The prophage GC content is 51.2%, lower than the average GC content of 57.1% in K. pneumoniae. Complete prophages were classified into three families in the order Caudolovirales: Myoviridae (59.6%), Siphoviridae (38.5%) and Podoviridae (1.9%). In addition, an alignment and phylogenetic analysis revealed nine distinct clusters. Evidence of recombination was detected within the genome of some prophages but, in most cases, proteins involved in viral structure, transcription, replication and regulation (lysogenic/lysis) were maintained. These results support the knowledge that prophages are diverse and widely disseminated in K. pneumoniae genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified K. pneumoniae prophages in a set of endolysin genes, which were found to code for proteins with lysozyme activity, cleaving the beta-1,4 linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in the peptidoglycan network and thus representing genes with the potential for lysin phage therapy.
外文关键词：K. pneumoniae genomes；prophages；bacteriophage；bioinformatics；genomic analysis；comparative genomics；phylogeny；sequence annotation and comparison；phage endolysins
作者：Marques, AT；Tanoeiro, L；Duarte, A；Goncalves, L；Vitor, JMB；Vale, FF
作者单位：Univ Lisbon；Inst Univ Egas Moniz；Hosp SAMS
期刊名称：MICROORGANISMS
期刊影响因子：4.152
出版年份：2021
出版刊次：11
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