• Frontiers in Microbiology
  • Evolutionary and Genomic Microbiology
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  • What can long-read technology and comparative microbial genomics reveal about evolution and spreading of pathogens under the ONE Health perspective?

What can long-read technology and comparative microbial genomics reveal about evolution and spreading of pathogens under the ONE Health perspective?

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About this Research Topic

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Background

ONE Health initiative now recognizes that the health of people is interconnected with the health of animals and the environment. It has come to the attention of many scientists that most human diseases have a strong relationship with environmental factors. Having that in mind, this initiative tries to integrate a multisectoral, multidisciplinary, and collaborative effort – working at all levels (local, national, and international) - to reach a better health outcome recognizing the interconnection between humans, animals, plants and their environment. Examples of zoonotic diseases are: Salmonella, rabies, Escherichia coli (either EPEC or EHEC), H1N1 virus, among many others. The presence of known or unknown pathogens affecting only animals can serve as an early warning of potential transmission to humans.

One of the most frequent challengers in modern genomic analyses has been the successful completion of assemblies of viruses, bacterial genomes, and plasmids using short reads due to ambiguities in the sequences, such as repetitive regions. The recent advent of the long-read sequencing technology has revolutionized the world of microbial genomics with the introduction of a new level of resolution in genomic studies to cope with these limitations. We are now able to obtain completely closed viruses and microbial genomes using the third-generation, single molecule, real-time DNA sequencing technologies and correctly assemble complex mobile elements such as phages, plasmids, insertion sequences, and pathogenicity islands. These enhanced sequencing capabilities provide a comprehensive view of genomic composition that allows, among others, to generate: 1) high-quality reference genomes for source tracking during outbreak investigations and disease transmission, 2) understanding long-term evolution of pathogens, 3) new insights in drug resistance and transmission of mobile elements carrying antimicrobial resistance markers, and 4) information about the contribution of DNA modification on the evolution of pathogenesis.

The benefits of the use of closed genomes in routine surveillance, viruses diversity and evolution, bacterial evolution, traceback investigations and disease transmission, will be covered in this special issue discussing key topics in this area with examples where the use of long reads and closed genomes has played a fundamental contribution to answer crucial questions in the field that could not have been achieved using draft genomes generated by short-read sequencing technology. Further, the contributions of the availability of fully closed reference genomes in epidemiological investigations increase the accuracy of clustering, which is needed to facilitate outbreak cluster detection and source tracking and provide deeper insights into structural variations, a critically important aspect for public health.

Manuscripts we would like to be submitted include:

1. Methodological developments for improving DNA extraction, resulting in less sheared DNA.
2. Application of long read technologies in de novo characterization of viruses.
3. Application of long read technologies in de novo characterization of AMR plasmids.
4. Application of single molecule, long read sequencing in de novo characterization of different bacterial isolates (ranging from Gram (+/-) to large (> 6 Mb) or complex genomes (2 or more chromosomes).
5. Methodological developments for improving plasmid sequencing from complex bacteria isolates (low copy number).
6. Data analysis approaches for improving de novo assembly using long reads.
7. Methodological developments for improving RNA extraction for use in transcript profiling studies using single molecule sequencing.
8. Data analysis approaches for fast characterization of metagenomes.
9. Development of visualization tools for various applications of long read sequencing such as variant calling, metagenomic analyses, source tracking and phylo-geography.

Keywords: nanopore, pacbio, long-reads, antimicrobial resistance, plasmids, genomes, phyla-geography, phylogenetic, evolution, spreading, RNA, DNA, viruses, One Health

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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