ArticleMicroorganisms2022
The Notable Achievements and the Prospects of Bacterial Pathogen Genomics.
Article in Microorganisms, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 24 citations in OpenAlex.
- Article
- Antibiotic Resistance Crisis: From Bacterial Bioprospecting to Artificial Intelligence.Environmental microbiology reports · 2025Review
- Fighting Antimicrobial Resistance: Innovative Drugs in Antibacterial Research.Angewandte Chemie (International ed. in English) · 2025Review
- Enhancing public health infectious disease response through the Australian Pathogen Genomics program (AusPathoGen): evaluation protocol.Frontiers in public health · 2025Article
- Unravelling Antimicrobial Resistance inVeterinary sciences · 2024Review
- Genome-Guided Identification of Surfactin-ProducingInternational journal of molecular sciences · 2024Article
- pyPGCF: A Python Software for Phylogenomic Analysis, Species Demarcation, Identification of Core, and Fingerprint Proteins of Bacterial Genomes That Are Important for Plants.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Genomic classification and antimicrobial resistance profiling of Streptococcus pneumoniae and Haemophilus influenza isolates associated with paediatric otitis media and upper respiratory infection.BMC infectious diseases · 2023Article
- Economic and health impact modelling of a whole genome sequencing-led intervention strategy for bacterial healthcare-associated infections for England and for the USA.Microbial genomics · 2023Article
- Impact of NG-Test CTX-M MULTI Immunochromatographic Assay on Antimicrobial Management ofAntibiotics (Basel, Switzerland) · 2023Article
- Mining the nanotube-formingComputational and structural biotechnology journal · 2023Article
- Advantages of long- and short-reads sequencing for the hybrid investigation of theFrontiers in microbiology · 2023Article
- Antimicrobial Susceptibility and Genetic Prevalence of Extended-Spectrum β-Lactamases in Gram-Negative Rods Isolated from Clinical Specimens in Pakistan.Antibiotics (Basel, Switzerland) · 2022Article
- A Comparative Analysis of the Core Proteomes within and among theMicroorganisms · 2022Article
- Flagellotropic Bacteriophages: Opportunities and Challenges for Antimicrobial Applications.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.