The Notable Achievements and the Prospects of Bacterial Pathogen Genomics - PubMed (original) (raw)

The Notable Achievements and the Prospects of Bacterial Pathogen Genomics

Grigorios D Amoutzias et al. Microorganisms. 2022.

Abstract

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.

Keywords: Illumina; Oxford Nanopore; Pacific Biosciences; bacterial pathogen; clinical microbiology; evolution; food-borne pathogens; forensics; genomics; metagenome-assembled genomes.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1

Most frequently used sequencing platforms according to PATRIC, for bacterial pathogens, (A) used as single technology and (B) used in combinations (hybrid approaches).

Figure 2

The number of genomes in each bacterial taxonomic group of the NCBI pathogens. (A) The total number of genomes reported in each taxonomic group. (B) The number of complete genomes in each taxonomic group.

Figure 3

Most of the commonly used assemblers reported in the NCBI bacterial pathogens database as of March 2022.

Figure 4

Pathogen annotation data for the virulence, resistance, and drug susceptibility. (A) The number of genomes with a certain number of virulence genes. (B) The number of genomes with a certain number of AMR (antimicrobial resistance) genes. (C) The number of genomes with a certain number of drugs to which they are susceptible (based on experiments). (D) The number of genomes with a certain number of drugs to which they are resistant (based on experiments). Source: The NCBI pathogens (March 2022).

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Grants and funding

M.N. thanks the University of Thessaly (PhD studentship: DEKA-UTH-259) for their financial support.

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