Pathogen Genomics in Public Health

  • 1. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 2016;17:333351.

  • 2. MacCannell D. Platforms and analytical tools used in nucleic acid sequence-based microbial genotyping procedures. Microbiol Spectr 2019;7(1):AME-0005-2018AME-0005-2018.

  • 3. DNA sequencing costs: data. Bethesda, MD: National Human Genomics Research Institute, 2019 (

  • 4. Köser CU, Ellington MJ, Cartwright EJ, et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 2012;8(8):e1002824e1002824.

  • 5. Walker TM, Ip CL, Harrell RH, et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 2013;13:137146.

  • 6. Satta G, Lipman M, Smith GP, Arnold C, Kon OM, McHugh TD. Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential? Clin Microbiol Infect 2018;24:604609.

  • 7. Mook P, Gardiner D, Verlander NQ, et al. Operational burden of implementing Salmonella Enteritidis and Typhimurium cluster detection using whole genome sequencing surveillance data in England: a retrospective assessment. Epidemiol Infect 2018;146:14521460.

  • 8. Jenkins C, Dallman TJ, Grant KA. Impact of whole genome sequencing on the investigation of food-borne outbreaks of Shiga toxin-producing Escherichia coli serogroup O157:H7, England, 2013 to 2017. Euro Surveill 2019;24:2424.

  • 9. Blue Ribbon Panel: future strategies for bioinformatics in CDC’s Infectious Diseases laboratories. Atlanta: Centers for Disease Control and Prevention, 2011 (

  • 10. Gwinn M, MacCannell D, Armstrong GL. Next-generation sequencing of infectious pathogens. JAMA 2019;321:893894.

  • 11. Chattaway MA, Dallman TJ, Gentle A, et al. Whole genome sequencing for public health surveillance of Shiga toxin-producing Escherichia coli other than serogroup O157. Front Microbiol 2016;7:258258.

  • 12. Lindsey RL, Pouseele H, Chen JC, Strockbine NA, Carleton HA. Implementation of whole genome sequencing (WGS) for identification and characterization of Shiga toxin-producing Escherichia coli (STEC) in the United States. Front Microbiol 2016;7:766766.

  • 13. Joensen KG, Tetzschner AM, Iguchi A, Aarestrup FM, Scheutz F. Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data. J Clin Microbiol 2015;53:24102426.

  • 14. Bale J, Meunier D, Weill FX, dePinna E, Peters T, Nair S. Characterization of new Salmonella serovars by whole-genome sequencing and traditional typing techniques. J Med Microbiol 2016;65:10741078.

  • 15. Ashton PM, Nair S, Peters TM, et al. Identification of Salmonella for public health surveillance using whole genome sequencing. PeerJ 2016;4:e1752e1752.

  • 16. Metcalf BJ, Chochua S, Gertz RE Jr, et al. Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcus agalactiae recovered in the USA. Clin Microbiol Infect 2017;23(8):574.e7574.e14.

  • 17. McDermott PF, Tyson GH, Kabera C, et al. Whole-genome sequencing for detecting antimicrobial resistance in nontyphoidal Salmonella. Antimicrob Agents Chemother 2016;60:55155520.

  • 18. Tyson GH, Zhao S, Li C, et al. Establishing genotypic cutoff values to measure antimicrobial resistance in Salmonella. Antimicrob Agents Chemother 2017;61(3):e0214016.

  • 19. Tyson GH, McDermott PF, Li C, et al. WGS accurately predicts antimicrobial resistance in Escherichia coli. J Antimicrob Chemother 2015;70:27632769.

  • 20. Metcalf BJ, Chochua S, Gertz RE Jr, et al. Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States. Clin Microbiol Infect 2016;22(12):1002.e11002.e8.

  • 21. Grad YH, Harris SR, Kirkcaldy RD, et al. Genomic epidemiology of gonococcal resistance to extended-spectrum cephalosporins, macrolides, and fluoroquinolones in the United States, 2000-2013. J Infect Dis 2016;214:15791587.

  • 22. Glebova O, Knyazev S, Melnyk A, et al. Inference of genetic relatedness between viral quasispecies from sequencing data. BMC Genomics 2017;18:Suppl 10:918918.

  • 23. Longmire AG, Sims S, Rytsareva I, et al. GHOST: Global Hepatitis Outbreak and Surveillance Technology. BMC Genomics 2017;18:Suppl 10:916916.

  • 24. Ribot EM, Hise KB. Future challenges for tracking foodborne diseases: PulseNet, a 20-year-old US surveillance system for foodborne diseases, is expanding both globally and technologically. EMBO Rep 2016;17:14991505.

  • 25. Cartwright EJ, Jackson KA, Johnson SD, Graves LM, Silk BJ, Mahon BE. Listeriosis outbreaks and associated food vehicles, United States, 1998-2008. Emerg Infect Dis 2013;19:19.

  • 26. Crowe SJ, Green A, Hernandez K, et al. Utility of combining whole genome sequencing with traditional investigational methods to solve foodborne outbreaks of Salmonella infections associated with chicken: a new tool for tackling this challenging food vehicle. J Food Prot 2017;80:654660.

  • 27. Berenger BM, Berry C, Peterson T, et al. The utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157:H7 outbreaks. Euro Surveill 2015;20:30073.

  • 28. Joensen KG, Scheutz F, Lund O, et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol 2014;52:15011510.

  • 29. Carleton HA. Whole-genome sequencing is taking over foodborne disease surveillance. Microbe 2016;11:311317.

  • 30. Allard MW, Strain E, Melka D, et al. Practical value of food pathogen traceability through building a whole-genome sequencing network and database. J Clin Microbiol 2016;54:19751983.

  • 31. Allard MW, Bell R, Ferreira CM, et al. Genomics of foodborne pathogens for microbial food safety. Curr Opin Biotechnol 2018;49:224229.

  • 32. Besser J, Carleton HA, Gerner-Smidt P, Lindsey RL, Trees E. Next-generation sequencing technologies and their application to the study and control of bacterial infections. Clin Microbiol Infect 2018;24:335341.

  • 33. Dallman TJ, Byrne L, Ashton PM, et al. Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157. Clin Infect Dis 2015;61:305312.

  • 34. Guthrie JL, Gardy JL. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Ann N Y Acad Sci 2017;1388:5977.

  • 35. Althomsons SP, Hill AN, Harrist AV, et al. Statistical method to detect tuberculosis outbreaks among endemic clusters in a low-incidence setting. Emerg Infect Dis 2018;24:573575.

  • 36. Gardy JL, Johnston JC, Ho Sui SJ, et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 2011;364:730739.

  • 37. Guthrie JL, Delli Pizzi A, Roth D, et al. Genotyping and whole-genome sequencing to identify tuberculosis transmission to pediatric patients in British Columbia, Canada, 2005-2014. J Infect Dis 2018;218:11551163.

  • 38. Jajou R, de Neeling A, van Hunen R, et al. Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: a population-based study. PLoS One 2018;13(4):e0195413e0195413.

  • 39. Guthrie JL, Strudwick L, Roberts B, et al. Whole genome sequencing for improved understanding of Mycobacterium tuberculosis transmission in a remote circumpolar region. Epidemiol Infect 2019;147:e188e188.

  • 40. Parvaresh L, Crighton T, Martinez E, Bustamante A, Chen S, Sintchenko V. Recurrence of tuberculosis in a low-incidence setting: a retrospective cross-sectional study augmented by whole genome sequencing. BMC Infect Dis 2018;18:265265.

  • 41. Luo T, Yang C, Peng Y, et al. Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis. Tuberculosis (Edinb) 2014;94:434440.

  • 42. The CRyPTIC Consortium and the 100,000 Genomes Project. Prediction of susceptibility to first-line tuberculosis drugs by DNA sequencing. N Engl J Med 2018;379:14031415.

  • 43. Doyle RM, Burgess C, Williams R, et al. Direct whole-genome sequencing of sputum accurately identifies drug-resistant Mycobacterium tuberculosis faster than MGIT culture sequencing. J Clin Microbiol 2018;56(8):e00666-18e00666-18.

  • 44. Votintseva AA, Bradley P, Pankhurst L, et al. Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples. J Clin Microbiol 2017;55:12851298.

  • 45. Shea J, Halse TA, Lapierre P, et al. Comprehensive whole-genome sequencing and reporting of drug resistance profiles on clinical cases of Mycobacterium tuberculosis in New York State. J Clin Microbiol 2017;55:18711882.

  • 46. Papaventsis D, Casali N, Kontsevaya I, Drobniewski F, Cirillo DM, Nikolayevskyy V. Whole genome sequencing of Mycobacterium tuberculosis for detection of drug resistance: a systematic review. Clin Microbiol Infect 2017;23:6168.

  • 47. Dolinger DL, Colman RE, Engelthaler DM, Rodwell TC. Next-generation sequencing-based user-friendly platforms for drug-resistant tuberculosis diagnosis: a promise for the near future. Int J Mycobacteriol 2016;5:Suppl 1:S27S28.

  • 48. Ziegler T, Mamahit A, Cox NJ. 65 Years of influenza surveillance by a World Health Organization-coordinated global network. Influenza Other Respir Viruses 2018;12:558565.

  • 49. Blanton L, Dugan VG, Abd Elal AI, et al. Update: influenza activity — United States, September 30, 2018 February 2, 2019. MMWR Morb Mortal Wkly Rep 2019;68:125134.

  • 50. Hampson A, Barr I, Cox N, et al. Improving the selection and development of influenza vaccine viruses — report of a WHO informal consultation on improving influenza vaccine virus selection, Hong Kong SAR, China, 18-20 November 2015. Vaccine 2017;35:11041109.

  • 51. Zhou B, Donnelly ME, Scholes DT, et al. Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and swine origin human influenza A viruses. J Virol 2009;83:1030910313.

  • 52. Zhou B, Lin X, Wang W, et al. Universal influenza B virus genomic amplification facilitates sequencing, diagnostics, and reverse genetics. J Clin Microbiol 2014;52:13301337.

  • 53. Recommended composition of influenza virus vaccines for use in the 2019 2020 northern hemisphere influenza season. Geneva: World Health Organization, February 2019 (

  • 54. Addendum to the recommended composition of influenza virus vaccines for use in the 2019 2020 northern hemisphere influenza season. Geneva: World Health Organization, March 21, 2019 (

  • 55. Burke SA, Trock SC. Use of influenza risk assessment tool for prepandemic preparedness. Emerg Infect Dis 2018;24:471477.

  • 56. Cox NJ, Trock SC, Burke SA. Pandemic preparedness and the Influenza Risk Assessment Tool (IRAT). Curr Top Microbiol Immunol 2014;385:119136.

  • 57. Russell CA, Kasson PM, Donis RO, et al. Improving pandemic influenza risk assessment. Elife 2014;3:e03883e03883.

  • 58. Flannery B, Zimmerman RK, Gubareva LV, et al. Enhanced genetic characterization of influenza A(H3N2) viruses and vaccine effectiveness by genetic group, 2014-2015. J Infect Dis 2016;214:10101019.

  • 59. Uyeki TM, Katz JM, Jernigan DB. Novel influenza A viruses and pandemic threats. Lancet 2017;389:21722174.

  • 60. Wilson JR, Belser JA, DaSilva J, et al. An influenza A virus (H7N9) anti-neuraminidase monoclonal antibody protects mice from morbidity without interfering with the development of protective immunity to subsequent homologous challenge. Virology 2017;511:214221.

  • 61. Flaherty BR, Talundzic E, Barratt J, et al. Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing. Microbiome 2018;6:164164.

  • 62. Talundzic E, Ravishankar S, Kelley J, et al. Next-generation sequencing and bioinformatics protocol for malaria drug resistance marker surveillance. Antimicrob Agents Chemother 2018;62(4):e02474-17e02474-17.

  • 63. Zhong D, Lo E, Wang X, et al. Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa. Malar J 2018;17:185185.

  • 64. Qvarnstrom Y, Wei-Pridgeon Y, Van Roey E, et al. Purification of Cyclospora cayetanensis oocysts obtained from human stool specimens for whole genome sequencing. Gut Pathog 2018;10:4545.

  • 65. Barratt JLN, Park S, Nascimento FS, et al. Genotyping genetically heterogeneous Cyclospora cayetanensis infections to complement epidemiological case linkage. Parasitology 2019;146:12751283.

  • 66. Lapierre P, Nazarian E, Zhu Y, et al. Legionnaires’ disease outbreak caused by endemic strain of Legionella pneumophila, New York, New York, USA, 2015. Emerg Infect Dis 2017;23:17841791.

  • 67. Lévesque S, Plante PL, Mendis N, et al. Genomic characterization of a large outbreak of Legionella pneumophila serogroup 1 strains in Quebec City, 2012. PLoS One 2014;9(8):e103852e103852.

  • 68. David S, Mentasti M, Lai S, et al. Spatial structuring of a Legionella pneumophila population within the water system of a large occupational building. Microb Genom 2018;4(10):e000226e000226.

  • 69. Popovich KJ, Snitkin ES. Whole genome sequencing — implications for infection prevention and outbreak investigations. Curr Infect Dis Rep 2017;19:1515.

  • 70. Snitkin ES, Zelazny AM, Thomas PJ, et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 2012;4:148ra116148ra116.

  • 71. Chow NA, Gade L, Tsay SV, et al. Multiple introductions and subsequent transmission of multidrug-resistant Candida auris in the USA: a molecular epidemiological survey. Lancet Infect Dis 2018;18:13771384.

  • 72. Oster AM, France AM, Mermin J. Molecular epidemiology and the transformation of HIV prevention. JAMA 2018;319:16571658.

  • 73. Oster AM, France AM, Panneer N, et al. Identifying clusters of recent and rapid HIV transmission through analysis of molecular surveillance data. J Acquir Immune Defic Syndr 2018;79:543550.

  • 74. Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. HIV-TRACE (TRAnsmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens. Mol Biol Evol 2018;35:18121819.

  • 75. Olmstead AD, Joy JB, Montoya V, et al. A molecular phylogenetics-based approach for identifying recent hepatitis C virus transmission events. Infect Genet Evol 2015;33:101109.

  • 76. Lockhart SR, Etienne KA, Vallabhaneni S, et al. Simultaneous emergence of multidrug-resistant Candida auris on 3 continents confirmed by whole-genome sequencing and epidemiological analyses. Clin Infect Dis 2017;64:134140.

  • 77. Riveron JM, Ibrahim SS, Mulamba C, et al. Genome-wide transcription and functional analyses reveal heterogeneous molecular mechanisms driving pyrethroids resistance in the major malaria vector Anopheles funestus across Africa. G3 (Bethesda) 2017;7:18191832.

  • 78. Weetman D, Wilding CS, Neafsey DE, et al. Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae. Sci Rep 2018;8:29202920.

  • 79. Chochua S, Metcalf BJ, Li Z, et al. Population and whole genome sequence based characterization of invasive group A streptococci recovered in the United States during 2015. MBio 2017;8(5):e01422-17e01422-17.

  • 80. Topaz N, Boxrud D, Retchless AC, et al. BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species. BMC Infect Dis 2018;18:405405.

  • 81. Gardy JL, Loman NJ. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat Rev Genet 2018;19:920.

  • 82. Quick J, Loman NJ, Duraffour S, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 2016;530:228232.

  • 83. Faria NR, Quick J, Claro IM, et al. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 2017;546:406410.

  • 84. Grubaugh ND, Saraf S, Gangavarapu K, et al. Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic. Cell 2019;178(5):10571071.e11.

  • 85. Dudas G, Carvalho LM, Bedford T, et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 2017;544:309315.

  • 86. Iwamoto M, Huang JY, Cronquist AB, et al. Bacterial enteric infections detected by culture-independent diagnostic tests — FoodNet, United States, 2012 2014. MMWR Morb Mortal Wkly Rep 2015;64:252257.

  • 87. Marder EP, Cieslak PR, Cronquist AB, et al. Incidence and trends of infections with pathogens transmitted commonly through food and the effect of increasing use of culture-independent diagnostic tests on surveillance — Foodborne Diseases Active Surveillance Network, 10 U.S. sites, 2013 2016. MMWR Morb Mortal Wkly Rep 2017;66:397403.

  • 88. Huang JY, Henao OL, Griffin PM, et al. Infection with pathogens transmitted commonly through food and the effect of increasing use of culture-independent diagnostic tests on surveillance — Foodborne Diseases Active Surveillance Network, 10 U.S. sites, 2012 2015. MMWR Morb Mortal Wkly Rep 2016;65:368371.

  • 89. Clark SA, Doyle R, Lucidarme J, Borrow R, Breuer J. Targeted DNA enrichment and whole genome sequencing of Neisseria meningitidis directly from clinical specimens. Int J Med Microbiol 2018;308:256262.

  • 90. Sintchenko V, Holmes EC. The role of pathogen genomics in assessing disease transmission. BMJ 2015;350:h1314h1314.

  • 91. Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol 2014;15:538538.

  • 92. Crisan A, Gardy JL, Munzner T. A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT. Bioinformatics 2019;35:16681676.

  • 93. Argimón S, Abudahab K, Goater RJE, et al. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom 2016;2(11):e000093e000093.

  • 94. Hadfield J, Megill C, Bell SM, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:41214123.

  • 95. Letunic I, Bork P. Interactive Tree of Life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016;44(W1:W242-5W242-5.

  • 96. Aldridge RW. Research and training recommendations for public health data science. Lancet Public Health 2019;4(8):e373e373.

  • 97. Greninger AL. Societal implications of the internet of pathogens. J Clin Microbiol 2019;57(6):e01914-18e01914-18.

  • 98. Kostkova P. Disease surveillance data sharing for public health: the next ethical frontiers. Life Sci Soc Policy 2018;14:1616.

  • Source Link


    This blog is for information purposes only. The content is not intended as medical advice, diagnosis, or treatment. Should you have a medical or dermatological problem, please consult with your physician. None of the information or recommendations on this website should be interpreted as medical advice.

    All product reviews, recommendations, and references are based on the author’s personal experience and impressions using the products. All views and opinions are the author’s own.

    This blog post may contain affiliate links. An affiliate link means we may earn a commission if you click on a link and make a purchase, without any extra cost to you.

    Please see our Disclaimer for more information.

    diseases, diagnosis and treatment methods, drugs and their side effects on this site. online diseases, diagnosis and treatment methods

    Related Articles

    Back to top button
    %d bloggers like this: