The Notable Achievements and the Prospects of Bacterial Pathogen Genomics

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.

Advantages of long- and short-reads sequencing for the hybrid investigation of the Mycobacterium tuberculosis genome

“…Comparing the results between SRS and LRS, different studies highlight genome regions where the SRS lacks accuracy due to limit of the technology ( Modlin et al, 2021 ; Peker et al, 2021 ; Gómez-González et al, 2022 ; Marin et al, 2022 ). Although LRS approaches still present a high-error rate (~5–15%), their random nature allows to improve accuracy with higher coverage ( Rhoads and Au, 2015 ; Athanasopoulou et al, 2021 ; Amoutzias et al, 2022 ).…”

Impact of NG-Test CTX-M MULTI Immunochromatographic Assay on Antimicrobial Management of Escherichia coli Bloodstream Infections

“…Rapid tests for the detection of the main resistance enzymes in Gram-negative bacteria have been developed with the final objectives of implementing efficient infection control measures and identifying resistance mechanisms so that the most appropriate antibiotic treatment can be started. E. coli belongs to the small number of Gram-negative bacteria with significant clinical impact and is, therefore, one of the most studied [ 24 ]. This study reported a real-life experience assessing the impact on clinicians’ confidence and antimicrobial prescription of a newly introduced diagnosis of direct detection of CTX-M ESBL-producers in E. coli -positive BCs in a hospital in which carbapenem-sparing strategies were implemented during the last years, mainly as educational interventions.…”

Mining the nanotube-forming Bacillus amyloliquefaciens MR14M3 genome for determining anti-Candida auris and anti-Candida albicans potential by pathogenicity and comparative genomics analysis

“…Whole-genome sequencing was carried out utilizing long-read Nanopore sequencing, a relatively portable instrument that generates reads with a maximum length and is capable of presenting sequences in real time, to confirm the isolate's correct identification [75] , [76] , [77] , [78] . Long-read Nanopore sequencing was chosen over other short-read high-throughput sequencing methods because they offer insufficient phylogenetic resolution and have a low level of integrity for the majority of the assembled area [79] .…”