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Advances in Molecular Epidemiology of Infectious Diseases: Definitions, Approaches, and Scope of the Field *

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  • Authors: Lee W. Riley1, Ronald E. Blanton2
  • Editor: Michael Sadowsky3
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720; 2: Center for Global Health & Diseases, Case Western Reserve University, Cleveland, OH 44106; 3: BioTechnology Institute, University of Minnesota, St. Paul, MN
  • Source: microbiolspec November 2018 vol. 6 no. 6 doi:10.1128/microbiolspec.AME-0001-2018
  • Received 05 March 2018 Accepted 18 June 2018 Published 02 November 2018
  • Lee W. Riley, [email protected]
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  • Abstract:

    Molecular epidemiology is a discipline that uses molecular microbiology tools to study the distribution and determinants of diseases in human populations and veterinary animals. Our understanding of epidemiology of infectious diseases has evolved with technological advancements made in molecular biology that refine our perception of the identity and dynamics of microorganisms. This review is an introduction to the Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases that will discuss how these advancements have contributed to investigations of infectious disease outbreaks/epidemics, surveillance, transmission dynamics, risk factor identification, pathogenesis, and etiologic attribution of bacterial, viral, protozoan, and helminthic pathogens to a disease. Here we define “molecular epidemiology” and distinguish it from other disciplines that use many of the same molecular biology tools—taxonomy, phylogenetics, and molecular evolution of microorganisms. The Curated Collection will be spread throughout multiple issues of and will be divided into four general sections: (i) laboratory methods used to strain type microbial pathogens, (ii) methods used to analyze genotyping data, (iii) examples of molecular epidemiologic investigations of bacterial, viral, and parasitic diseases, and (iv) applications of molecular epidemiology to address new research questions in communicable and noncommunicable diseases. The major theme of this Curated Collection is to address the following question frequently asked by clinicians, clinical microbiologists, and public health professionals: what is the advantage or unique contribution of molecular epidemiology in solving infectious disease problems in the clinical and public health arenas?

    *This article is part of a curated collection.

  • Citation: Riley L, Blanton R. 2018. Advances in Molecular Epidemiology of Infectious Diseases: Definitions, Approaches, and Scope of the Field * . Microbiol Spectrum 6(6):AME-0001-2018. doi:10.1128/microbiolspec.AME-0001-2018.

References

1. Huang ES, Alford CA, Reynolds DW, Stagno S, Pass RF. 1980. Molecular epidemiology of cytomegalovirus infections in women and their infants. N Engl J Med 303:958–962. http://dx.doi.org/10.1056/NEJM198010233031702. [PubMed]
2. Riley LW. 2004. Molecular Epidemiology of Infectious Diseases: Principles and Practices. ASM Press, Washington, DC. http://dx.doi.org/10.1128/9781555817688.
3. Hitchens AP, Leikind MC. 1939. The introduction of agar-agar into bacteriology. J Bacteriol 37:485–493. [PubMed]
4. Brock TD. 1988. Robert Koch. A Life in Medicine and Bacteriology. Science Tech Publishers, Madison, WI.
5. Mausner JS, Bahn AK. 1974. Epidemiology. An Introductory Text. WB Saunders Co, Philadelphia, PA. [PubMed]
6. Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York, NY.
7. Lopes JS, Marques I, Soares P, Nebenzahl-Guimaraes H, Costa J, Miranda A, Duarte R, Alves A, Macedo R, Duarte TA, Barbosa T, Oliveira M, Nery JS, Boechat N, Pereira SM, Barreto ML, Pereira-Leal J, Gomes MG, Penha-Goncalves C. 2013. SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil. Infect Genet Evol 18:238–246. http://dx.doi.org/10.1016/j.meegid.2013.04.028. [PubMed]
8. Ritacco V, Iglesias MJ, Ferrazoli L, Monteserin J, Dalla Costa ER, Cebollada A, Morcillo N, Robledo J, de Waard JH, Araya P, Aristimuño L, Díaz R, Gavin P, Imperiale B, Simonsen V, Zapata EM, Jiménez MS, Rossetti ML, Martin C, Barrera L, Samper S. 2012. Conspicuous multidrug-resistant Mycobacterium tuberculosis cluster strains do not trespass country borders in Latin America and Spain. Infect Genet Evol 12:711–717. http://dx.doi.org/10.1016/j.meegid.2011.06.006. [PubMed]
9. Cardoso Oelemann M, Gomes HM, Willery E, Possuelo L, Batista Lima KV, Allix-Béguec C, Locht C, Goguet de la Salmonière YO, Gutierrez MC, Suffys P, Supply P. 2011. The forest behind the tree: phylogenetic exploration of a dominant Mycobacterium tuberculosis strain lineage from a high tuberculosis burden country. PLoS One 6:e18256. http://dx.doi.org/10.1371/journal.pone.0018256. [PubMed]
10. Wan K, Liu J, Hauck Y, Zhang Y, Liu J, Zhao X, Liu Z, Lu B, Dong H, Jiang Y, Kremer K, Vergnaud G, van Soolingen D, Pourcel C. 2011. Investigation on Mycobacterium tuberculosis diversity in China and the origin of the Beijing clade. PLoS One 6:e29190. http://dx.doi.org/10.1371/journal.pone.0029190. [PubMed]
11. Filliol I, Driscoll JR, van Soolingen D, Kreiswirth BN, Kremer K, Valétudie G, Dang DA, Barlow R, Banerjee D, Bifani PJ, Brudey K, Cataldi A, Cooksey RC, Cousins DV, Dale JW, Dellagostin OA, Drobniewski F, Engelmann G, Ferdinand S, Gascoyne-Binzi D, Gordon M, Gutierrez MC, Haas WH, Heersma H, Kassa-Kelembho E, Ho ML, Makristathis A, Mammina C, Martin G, Moström P, Mokrousov I, Narbonne V, Narvskaya O, Nastasi A, Niobe-Eyangoh SN, Pape JW, Rasolofo-Razanamparany V, Ridell M, Rossetti ML, Stauffer F, Suffys PN, Takiff H, Texier-Maugein J, Vincent V, de Waard JH, Sola C, Rastogi N. 2003. Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. J Clin Microbiol 41:1963–1970. http://dx.doi.org/10.1128/JCM.41.5.1963-1970.2003 [PubMed]
12. Mokrousov I, Ly HM, Otten T, Lan NN, Vyshnevskyi B, Hoffner S, Narvskaya O. 2005. Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: clues from human phylogeography. Genome Res 15:1357–1364. http://dx.doi.org/10.1101/gr.3840605. [PubMed]
13. Blake PA, Allegra DT, Snyder JD, Barrett TJ, McFarland L, Caraway CT, Feeley JC, Craig JP, Lee JV, Puhr ND, Feldman RA. 1980. Cholera—a possible endemic focus in the United States. N Engl J Med 302:305–309. http://dx.doi.org/10.1056/NEJM198002073020601. [PubMed]
14. Centers for Disease Control and Prevention. 2000. Surveillance for foodborne-disease outbreaks—United States, 1993–1997. MMWR Surveill Summ 49:1–62.
15. Mead PS, Slutsker L, Dietz V, McCaig LF, Bresee JS, Shapiro C, Griffin PM, Tauxe RV. 1999. Food-related illness and death in the United States. Emerg Infect Dis 5:607–625. http://dx.doi.org/10.3201/eid0505.990502. [PubMed]
16. Musso D, Roche C, Robin E, Nhan T, Teissier A, Cao-Lormeau VM. 2015. Potential sexual transmission of Zika virus. Emerg Infect Dis 21:359–361. http://dx.doi.org/10.3201/eid2102.141363. [PubMed]
17. Turmel JM, Abgueguen P, Hubert B, Vandamme YM, Maquart M, Le Guillou-Guillemette H, Leparc-Goffart I. 2016. Late sexual transmission of Zika virus related to persistence in the semen. Lancet 387:2501. http://dx.doi.org/10.1016/S0140-6736(16)30775-9.
18. Foy BD, Kobylinski KC, Chilson Foy JL, Blitvich BJ, Travassos da Rosa A, Haddow AD, Lanciotti RS, Tesh RB. 2011. Probable non-vector-borne transmission of Zika virus, Colorado, USA. Emerg Infect Dis 17:880–882. http://dx.doi.org/10.3201/eid1705.101939. [PubMed]
19. Davidson A, Slavinski S, Komoto K, Rakeman J, Weiss D, Centers for Disease Control and Prevention. 2016. Suspected female-to-male sexual transmission of Zika virus—New York City, 2016. MMWR Morb Mortal Wkly Rep 65:716–717. http://dx.doi.org/10.15585/mmwr.mm6528e2. [PubMed]
20. Hills SL, Russell K, Hennessey M, Williams C, Oster AM, Fischer M, Mead P, Centers for Disease Control and Prevention. 2016. Transmission of Zika virus through sexual contact with travelers to areas of ongoing transmission—continental United States, 2016. MMWR Morb Mortal Wkly Rep 65:215–216. http://dx.doi.org/10.15585/mmwr.mm6508e2. [PubMed]
21. Christie A, Davies-Wayne GJ, Cordier-Lassalle T, Blackley DJ, Laney AS, Williams DE, Shinde SA, Badio M, Lo T, Mate SE, Ladner JT, Wiley MR, Kugelman JR, Palacios G, Holbrook MR, Janosko KB, de Wit E, van Doremalen N, Munster VJ, Pettitt J, Schoepp RJ, Verhenne L, Evlampidou I, Kollie KK, Sieh SB, Gasasira A, Bolay F, Kateh FN, Nyenswah TG, De Cock KM, Centers for Disease Control and Prevention. 2015. Possible sexual transmission of Ebola virus—Liberia, 2015. MMWR Morb Mortal Wkly Rep 64:479–481. [PubMed]
22. Mate SE, Kugelman JR, Nyenswah TG, Ladner JT, Wiley MR, Cordier-Lassalle T, Christie A, Schroth GP, Gross SM, Davies-Wayne GJ, Shinde SA, Murugan R, Sieh SB, Badio M, Fakoli L, Taweh F, de Wit E, van Doremalen N, Munster VJ, Pettitt J, Prieto K, Humrighouse BW, Ströher U, DiClaro JW, Hensley LE, Schoepp RJ, Safronetz D, Fair J, Kuhn JH, Blackley DJ, Laney AS, Williams DE, Lo T, Gasasira A, Nichol ST, Formenty P, Kateh FN, De Cock KM, Bolay F, Sanchez-Lockhart M, Palacios G. 2015. Molecular evidence of sexual transmission of Ebola virus. N Engl J Med 373:2448–2454. http://dx.doi.org/10.1056/NEJMoa1509773. [PubMed]
23. Magill SS, Edwards JR, Bamberg W, Beldavs ZG, Dumyati G, Kainer MA, Lynfield R, Maloney M, McAllister-Hollod L, Nadle J, Ray SM, Thompson DL, Wilson LE, Fridkin SK, Emerging Infections Program Healthcare-Associated Infections and Antimicrobial Use Prevalence Survey Team. 2014. Multistate point-prevalence survey of health care-associated infections. N Engl J Med 370:1198–1208. http://dx.doi.org/10.1056/NEJMoa1306801. [PubMed]
24. Zimlichman E, Henderson D, Tamir O, Franz C, Song P, Yamin CK, Keohane C, Denham CR, Bates DW. 2013. Health care-associated infections: a meta-analysis of costs and financial impact on the US health care system. JAMA Intern Med 173:2039–2046. http://dx.doi.org/10.1001/jamainternmed.2013.9763. [PubMed]
25. Elwell LP, Inamine JM, Minshew BH. 1978. Common plasmid specifying tobramycin resistance found in two enteric bacteria isolated from burn patients. Antimicrob Agents Chemother 13:312–317. http://dx.doi.org/10.1128/AAC.13.2.312. [PubMed]
26. Sadowski PL, Peterson BC, Gerding DN, Cleary PP. 1979. Physical characterization of ten R plasmids obtained from an outbreak of nosocomial Klebsiella pneumoniae infections. Antimicrob Agents Chemother 15:616–624. http://dx.doi.org/10.1128/AAC.15.4.616. [PubMed]
27. Schaberg DR, Tompkins LS, Falkow S. 1981. Use of agarose gel electrophoresis of plasmid deoxyribonucleic acid to fingerprint gram-negative bacilli. J Clin Microbiol 13:1105–1108. [PubMed]
28. Tompkins LS, Plorde JJ, Falkow S. 1980. Molecular analysis of R-factors from multiresistant nosocomial isolates. J Infect Dis 141:625–636. http://dx.doi.org/10.1093/infdis/141.5.625. [PubMed]
29. Snitkin ES, Zelazny AM, Thomas PJ, Stock F, Henderson DK, Palmore TN, Segre JA, NISC Comparative Sequencing Program Group. 2012. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 4:148ra116. http://dx.doi.org/10.1126/scitranslmed.3004129. [PubMed]
30. Singh A, Goering RV, Simjee S, Foley SL, Zervos MJ. 2006. Application of molecular techniques to the study of hospital infection. Clin Microbiol Rev 19:512–530. http://dx.doi.org/10.1128/CMR.00025-05. [PubMed]
31. Carle GF, Frank M, Olson MV. 1986. Electrophoretic separations of large DNA molecules by periodic inversion of the electric field. Science 232:65–68. http://dx.doi.org/10.1126/science.3952500. [PubMed]
32. Salipante SJ, SenGupta DJ, Cummings LA, Land TA, Hoogestraat DR, Cookson BT. 2015. Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology. J Clin Microbiol 53:1072–1079. http://dx.doi.org/10.1128/JCM.03385-14. [PubMed]
33. Rothman KJGS, Lash TL. 2008. Modern Epidemiology, 3rd ed. Wolters Kluwer/Lippincott Williams and Wilkins, Philadelphia, PA.
34. Savage DC. 1977. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 31:107–133. http://dx.doi.org/10.1146/annurev.mi.31.100177.000543. [PubMed]
35. Luckey TD. 1972. Introduction to intestinal microecology. Am J Clin Nutr 25:1292–1294. http://dx.doi.org/10.1093/ajcn/25.12.1292.
36. Sender R, Fuchs S, Milo R. 2016. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol 14:e1002533. http://dx.doi.org/10.1371/journal.pbio.1002533. [PubMed]
37. Sender R, Fuchs S, Milo R. 2016. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell 164:337–340. http://dx.doi.org/10.1016/j.cell.2016.01.013. [PubMed]
38. Harris K, Kassis A, Major G, Chou CJ. 2012. Is the gut microbiota a new factor contributing to obesity and its metabolic disorders? J Obes 2012:879151. [PubMed]
39. Blaser M. 2014. Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. Henry Holt & Company, Inc, New York, NY.
40. Riley LW, Raphael E, Faerstein E. 2013. Obesity in the United States—dysbiosis from exposure to low-dose antibiotics? Front Public Health 1:69. http://dx.doi.org/10.3389/fpubh.2013.00069. [PubMed]
41. Brandt LJ. 2012. Fecal transplantation for the treatment of Clostridium difficile infection. Gastroenterol Hepatol (N Y) 8:191–194.
42. Alang N, Kelly CR. 2015. Weight gain after fecal microbiota transplantation.Open Forum Infect Dis 2:ofv004. http://dx.doi.org/10.1093/ofid/ofv004. [PubMed]
43. Caldwell GG. 1990. Twenty-two years of cancer cluster investigations at the Centers for Disease Control. Am J Epidemiol 132(Suppl):S43–S47. http://dx.doi.org/10.1093/oxfordjournals.aje.a115787. [PubMed]
44. Thun MJ, Sinks T. 2004. Understanding cancer clusters. CA Cancer J Clin 54:273–280. http://dx.doi.org/10.3322/canjclin.54.5.273.
45. Francis SS, Plucinski MM, Wallace AD, Riley LW. 2016. Genotyping oral commensal bacteria to predict social contact and structure. PLoS One 11:e0160201. http://dx.doi.org/10.1371/journal.pone.0160201. [PubMed]
46. Harrison L, Griffin DE. 1993. Infectious Diseases. Academic Press,Inc, San Diego, CA. http://dx.doi.org/10.1016/B978-0-08-092566-0.50016-1.
47. Khoury MJBT, Cohen BH. 1993. Fundamentals of Genetic Epidemiology. Oxford University Press, New York, NY.
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2018-11-02
2018-11-15

Abstract:

Molecular epidemiology is a discipline that uses molecular microbiology tools to study the distribution and determinants of diseases in human populations and veterinary animals. Our understanding of epidemiology of infectious diseases has evolved with technological advancements made in molecular biology that refine our perception of the identity and dynamics of microorganisms. This review is an introduction to the Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases that will discuss how these advancements have contributed to investigations of infectious disease outbreaks/epidemics, surveillance, transmission dynamics, risk factor identification, pathogenesis, and etiologic attribution of bacterial, viral, protozoan, and helminthic pathogens to a disease. Here we define “molecular epidemiology” and distinguish it from other disciplines that use many of the same molecular biology tools—taxonomy, phylogenetics, and molecular evolution of microorganisms. The Curated Collection will be spread throughout multiple issues of and will be divided into four general sections: (i) laboratory methods used to strain type microbial pathogens, (ii) methods used to analyze genotyping data, (iii) examples of molecular epidemiologic investigations of bacterial, viral, and parasitic diseases, and (iv) applications of molecular epidemiology to address new research questions in communicable and noncommunicable diseases. The major theme of this Curated Collection is to address the following question frequently asked by clinicians, clinical microbiologists, and public health professionals: what is the advantage or unique contribution of molecular epidemiology in solving infectious disease problems in the clinical and public health arenas?

*This article is part of a curated collection.

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FIGURE 1

Differentiating molecular epidemiology from taxonomy, phylogenetics, and molecular evolution. In taxonomy, phylogenetics, and molecular evolution, microbes’ genetic profiles and relatedness are compared to each other. The main goal of these disciplines is to identify biologic relationships among collections of microbes based on their genetic or phenotypic characteristics. In infectious disease molecular epidemiology, the genotyped microbes are also compared to each other, but the microbial relationship data are linked to a population of hosts from which these microbes are isolated in a particular environment or transmission pathways of these microbes. Recent observations highlight the important contribution of microbiomes in the host-microbe-environment relationship. (Illustrated by Paolo Harris Paz.)

Source: microbiolspec November 2018 vol. 6 no. 6 doi:10.1128/microbiolspec.AME-0001-2018
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