Bacterial phylodynamics

Bacterial phylodynamics is the study of immunology, epidemiology, and phylogenetics of bacterial pathogens to better understand the evolutionary role of these pathogens.[1][2][3] Phylodynamic analysis includes analyzing genetic diversity, natural selection, and population dynamics of infectious disease pathogen phylogenies during pandemics and studying intra-host evolution of viruses.[4] Phylodynamics combines the study of phylogenetic analysis, ecological, and evolutionary processes to better understand of the mechanisms that drive spatiotemporal incidence and phylogenetic patterns of bacterial pathogens.[2][4] Bacterial phylodynamics uses genome-wide single-nucleotide polymorphisms (SNP) in order to better understand the evolutionary mechanism of bacterial pathogens.[5] Many phylodynamic studies have been performed on viruses, specifically RNA viruses (see Viral phylodynamics) which have high mutation rates. The field of bacterial phylodynamics has increased substantially due to the advancement of next-generation sequencing and the amount of data available.

  1. ^ Volz, Erik M.; Koelle, Katia; Bedford, Trevor (2013-03-21). "Viral Phylodynamics". PLOS Computational Biology. 9 (3): e1002947. Bibcode:2013PLSCB...9E2947V. doi:10.1371/journal.pcbi.1002947. ISSN 1553-7358. PMC 3605911. PMID 23555203.
  2. ^ a b Grenfell, Bryan T.; Pybus, Oliver G.; Gog, Julia R.; Wood, James L. N.; Daly, Janet M.; Mumford, Jenny A.; Holmes, Edward C. (2004-01-16). "Unifying the epidemiological and evolutionary dynamics of pathogens". Science. 303 (5656): 327–332. Bibcode:2004Sci...303..327G. doi:10.1126/science.1090727. ISSN 1095-9203. PMID 14726583. S2CID 4017704.
  3. ^ Frost, Simon D.W.; Pybus, Oliver G.; Gog, Julia R.; Viboud, Cecile; Bonhoeffer, Sebastian; Bedford, Trevor (2015). "Eight challenges in phylodynamic inference". Epidemics. 10: 88–92. doi:10.1016/j.epidem.2014.09.001. PMC 4383806. PMID 25843391.
  4. ^ a b Norström, Melissa M.; Karlsson, Annika C.; Salemi, Marco (2012-04-01). "Towards a new paradigm linking virus molecular evolution and pathogenesis: experimental design and phylodynamic inference". The New Microbiologica. 35 (2): 101–111. ISSN 1121-7138. PMID 22707126.
  5. ^ Azarian, Taj; Ali, Afsar; Johnson, Judith A.; Mohr, David; Prosperi, Mattia; Veras, Nazle M.; Jubair, Mohammed; Strickland, Samantha L.; Rashid, Mohammad H. (2014-12-31). "Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection". mBio. 5 (6): e01824–14. doi:10.1128/mBio.01824-14. ISSN 2150-7511. PMC 4278535. PMID 25538191.