Novel Insights Into the Spread of Enteric Pathogens Using Genomics

Domman, Daryl; Ruis, Christopher; Dorman, Matthew J.; Shakya, Migun; Chain, Patrick Sam Guy

doi:10.1093/infdis/jiz220

Title: Novel Insights Into the Spread of Enteric Pathogens Using Genomics

Journal Article · 19 September 2019 · Journal of Infectious Diseases

DOI: https://doi.org/10.1093/infdis/jiz220 · OSTI ID:1570626

^[1]; Ruis, Christopher ^[2]; Dorman, Matthew J. ^[3];

^[1];

^[1]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Wellcome Sanger Institute, Hinxton (United Kingdom); Univ. of Cambridge, Cambridge (United Kingdom)
Wellcome Sanger Institute, Hinxton (United Kingdom)

Diarrheal diseases continue to be a leading cause of mortality and morbidity across the globe. The use of next-generation sequencing data has provided major insights into understanding epidemiological spread, antimicrobial resistance, vaccine effects, and basic mechanisms of bacterial and viral evolution. Furthermore, we discuss how genomic data have informed investigations across enteric pathogens, such as Shigella, Vibrio cholerae, Salmonella Typhi, rotavirus, and norovirus.

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Research Organization:: Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Laboratory Directed Research and Development (LDRD) Program

Grant/Contract Number:: 89233218CNA000001

OSTI ID:: 1570626

Report Number(s):: LA-UR--19-23908

Journal Information:: Journal of Infectious Diseases, Journal Name: Journal of Infectious Diseases Journal Issue: Supplement_3 Vol. 221; ISSN 0022-1899

Publisher:: Infectious Diseases Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

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Evolutionary Dynamics of Human Rotaviruses: Balancing Reassortment with Preferred Genome Constellations McDonald, Sarah M.; Matthijnssens, Jelle; McAllen, John K. PLoS Pathogens, Vol. 5, Issue 10 https://doi.org/10.1371/journal.ppat.1000634	journal	October 2009
Rapid Evolution of Pandemic Noroviruses of the GII.4 Lineage Bull, Rowena A.; Eden, John-Sebastian; Rawlinson, William D. PLoS Pathogens, Vol. 6, Issue 3 https://doi.org/10.1371/journal.ppat.1000831	journal	March 2010
Immunogenetic Mechanisms Driving Norovirus GII.4 Antigenic Variation Lindesmith, Lisa C.; Beltramello, Martina; Donaldson, Eric F. PLoS Pathogens, Vol. 8, Issue 5 https://doi.org/10.1371/journal.ppat.1002705	journal	May 2012
Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity Parra, Gabriel I.; Squires, R. Burke; Karangwa, Consolee K. PLOS Pathogens, Vol. 13, Issue 1 https://doi.org/10.1371/journal.ppat.1006136	journal	January 2017
Emergence of New Pandemic GII.4 Sydney Norovirus Strain Correlates With Escape From Herd Immunity S., Baric, Ralph; Kari, Debbink,; C., Lindesmith, Lisa The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/akg3-8f60	text	January 2013
Emergence of novel human norovirus GII.17 strains correlates with changes in blockade antibody epitopes F., Donaldson, Eric; S., Baric, Ralph; Kari, Debbink, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/t66g-cb88	text	January 2017
Norovirus GII.4 Strain Antigenic Variation C., Lindesmith, L.; S., Baric, R.; F., Donaldson, E. The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/wh1x-1e28	text	January 2011
Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins. Klemm, Elizabeth J.; Shakoor, Sadia; Page, Andrew J. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.24802	text	January 2018
The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. Park, Se Eun; Pham, Duy Thanh; Boinett, Christine Springer Science and Business Media LLC https://doi.org/10.17863/cam.36238	journalarticle	January 2018
Genomic history of the seventh pandemic of cholera in Africa. Weill, François-Xavier; Domman, Daryl; Njamkepo, Elisabeth Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.36741	text	January 2017
An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Wong, Vanessa; Baker, Stephen; Connor, Thomas R. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.36936	text	January 2016
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter-and intracontinental transmission events Wong, Vanessa; Baker, Stephen; Pickard, Derek Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.36989	text	January 2015
A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection. Dung, Tran Thi Ngoc; Duy, Pham Thanh; Sessions, October M. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.38615	text	January 2017
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Wong, Vanessa; Baker, Stephen; Pickard, Derek Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.47674	text	January 2015
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Shigella Diversity and Changing Landscape: Insights for the Twenty-First Century Anderson, Mark; Sansonetti, Philippe J.; Marteyn, Benoit S. Frontiers in Cellular and Infection Microbiology, Vol. 6 https://doi.org/10.3389/fcimb.2016.00045	journal	April 2016
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World Health Organization estimates of the global and regional disease burden of 22 foodborne bacterial, protozoal, and viral diseases, 2010: a data synthesis Kirk, Martyn D.; Pires, Sara M.; Black, Robert E. Public Library of Science (PLoS) https://doi.org/10.5167/uzh-116086	text	January 2015
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