Amoutzias Grigorios D, Nikolaidis Marios, Hesketh Andrew
Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece.
School of Applied Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK.
Microorganisms. 2022 May 17;10(5):1040. doi: 10.3390/microorganisms10051040.
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.
在整个人类历史中，细菌病原体一直发挥着重要作用，甚至塑造了文明的命运。在过去27年里，基因组学的应用彻底改变了我们理解这些病原体生物学和进化的方式。在这篇综述中，我们讨论了短读长（Illumina）和长读长（PacBio、牛津纳米孔）测序技术如何在基础研究（即致病性进化）、法医学、食品安全和常规临床微生物学等方面塑造了细菌病原体基因组学这一学科。我们挖掘并讨论了一些最著名的数据/生物信息学资源，如NCBI病原体数据库、PATRIC和Pathogenwatch。基于此挖掘，我们介绍了一些最流行的测序技术、混合方法、组装工具和注释流程。少数细菌病原体非常重要，我们还展示了这些物种丰富的基因组数据（即它们是哪些物种、每个基因组中抗菌抗性基因的数量、毒力因子的数量）。最后，我们讨论了这一学科在不久的将来可能会如何转变，特别是由于长读长测序技术，向宏基因组组装基因组（MAGs）转变。
