pathogenomes

Pathogenomes are the complete set of genetic material encoded by disease-causing organisms, including bacteria, viruses, fungi, and parasites. Studied within the field of pathogenomics, these genomes provide the blueprint for virulence, replication, host interaction, and resistance traits. Pathogenomes are distinct from host and commensal genomes and can be composed of DNA or RNA, single- or multi-segmented, and linear or circular, depending on the lineage.

Sequencing pathogen genomes involves laboratory methods and computational analysis. High-throughput short-read sequencing and long-read technologies enable reconstruction of reference genomes, while metagenomic sequencing can recover genomes directly from clinical or environmental samples. Genome annotation identifies genes, regulatory elements, and structural features; analyses may annotate virulence factors, antimicrobial resistance genes, plasmids, prophages, and mobile elements.

Pathogen genomes vary widely in size and content. Bacterial genomes typically range from hundreds of thousands to several million base pairs, viruses from a few thousand to hundreds of thousands, and eukaryotic parasites and fungi can be even larger. Genome features such as GC content, gene density, and recombination rate influence evolution and epidemiology.

Public databases house pathogen genomes and associated metadata, enabling comparative genomics and phylogenetics. Applications include outbreak surveillance, transmission tracking, diagnostics development, vaccine target discovery, and antimicrobial resistance monitoring. Pathogenomic analyses support understanding of evolution, host adaptation, and disease mechanisms.

Challenges include genetic diversity, recombination, incomplete assemblies, sample contamination, and ethical considerations around sequencing pathogens from clinical samples.