在整个人类历史中,细菌病原体发挥了重要作用,甚至塑造了文明的命运。在过去的27年中,基因组学的应用彻底改变了我们理解这些病原体的生物学和进化的方式。在这次审查中,我们讨论了短期(Illumina)和长期(PacBio,牛津纳米孔)测序技术塑造了细菌病原体基因组学的学科,在基础研究方面(即,致病性进化),取证,食品安全,和常规临床微生物学。我们已经挖掘并讨论了一些最突出的数据/生物信息学资源,如NCBI病原体,PATRIC,和Pathogenwatch.基于这种挖掘,我们介绍了一些最流行的测序技术,混合方法,装配工,和注释管道。少数细菌病原体非常重要,我们还提供了这些物种的丰富基因组数据(即,他们是哪个,每个基因组的抗菌素抗性基因的数量,毒力因子的数量)。最后,我们讨论这个学科在不久的将来可能会如何转变,特别是通过过渡到宏基因组组装的基因组(MAG),感谢长期阅读测序。
Throughout the entirety of human history, bacterial pathogens have played an important role and even shaped the fate of civilizations. The application of genomics within the last 27 years has radically changed the way we understand the biology and evolution of these pathogens. In this review, we discuss how the short- (Illumina) and long-read (PacBio, Oxford Nanopore) sequencing technologies have shaped the discipline of bacterial pathogen genomics, in terms of fundamental research (i.e., evolution of pathogenicity), forensics, food safety, and routine clinical microbiology. We have mined and discuss some of the most prominent data/bioinformatics resources such as NCBI pathogens, PATRIC, and Pathogenwatch. Based on this mining, we present some of the most popular sequencing technologies, hybrid approaches, assemblers, and annotation pipelines. A small number of bacterial pathogens are of very high importance, and we also present the wealth of the genomic data for these species (i.e., which ones they are, the number of antimicrobial resistance genes per genome, the number of virulence factors). Finally, we discuss how this discipline will probably be transformed in the near future, especially by transitioning into metagenome-assembled genomes (MAGs), thanks to long-read sequencing.