Molecular epidemiology of infectious diseases
Keywords:
Epidemiology, Molecular; Infectious diseaseAbstract
Molecular epidemiology (ME) is a branch of epidemiology developed by merging molecular biology into epidemiological studies. In this paper, the authors try to discuss the ways that molecular epidemiology studies identify infectious diseases’ causation and pathogenesis, and unravel infectious agents’ sources, reservoirs, circulation pattern, transmission pattern, transmission probability, and transmission order. They bring real-world examples of research works in each area to make each study design more understandable. They also address some research areas and study design aspects that need further attention in future. They close with some thoughts about future directions in this field and emphasize on the need for training competent molecular epidemiology specialists that are capable of dealing with rapid advances in the field.
References
Arnold FA Jr, Dean HT, Jay P, Knutson JW. Effects of fluoridated water supplies on dental caries
incidence: Results of the seventh year of study at Grand Rapids and Muskegon, Mich. Public Health Rep.
; 68: 141-8.
Oppenheimer GM. Becoming the Framingham Study 1947-1950. Am J Public Health. 2005; 95(4): 602-10.
doi: 10.2105/AJPH.2003.026419. PMID: 15798116, PMCID: PMC1449227.
Francis T, Korns R, Voight R, Boisen M, Hemphill F, Napier J. An evaluation of the 1954 poliomyelitis
vaccine trials. Am J Public Health Nations Health. 1955; 45(5 Pt 2): 1-63. PMID: 14361811, PMCID:
PMC1622939.
Susser M. Does risk factor epidemiology put epidemiology at risk? Peering into the future. J Epidemiol
Community Health. 1998; 52: 608-11. PMID: 10023453, PMCID: PMC1756623.
Haghdoost AA. Molecular Epidemiology, Concepts and Domains. J Kerman University of Medical
Sciences. 2008; 15(1): 97-104.
Vineis P. Commentary: First steps in molecular epidemiology: Lower et al. 1979. Int J Epidemiol. 2007;
(1): 20-2. doi: 10.1093/ije/dyl291.
Kilbourne ED. The molecular epidemiology of influenza. J Infect Dis. 1973; 127(4): 478-87. PMID:
Giesecke I. Modern Infectious Disease Epidemiology, Second Edition. Boca Raton: CRC Press; 2001.
Hugenholtz P, Goebel BM, Pace NR. Impact of culture-independent studies on the emerging phylogenetic
view of bacterial diversity. J Bacteriol. 1998; 180(18): 4765-74. PMID: 9733676, PMCID: PMC107498.
Foxman B. Molecular Tools and Infectious Disease Epidemiology. Burlington, MA: Elsevier; 2012.
Chang Y, Cesarman E, Pessin MS, Lee F, Culpepper J, Knowles DM, et al. Identification of herpesviruslike DNA sequences in AIDS-associated Kaposi's sarcoma. Science. 1994; 266(5192): 1865-9. PMID:
Hill AB. The Environment and Disease: Association or Causation? Proc R Soc Med. 1965; 58(5): 295-300. PMID: 14283879, PMCID: PMC1898525.
Moore PS, Kingsley LA, Holmberg SD, Spira T, Gupta P, Hoover DR, et al. Kaposi's sarcoma-associated
herpesvirus infection prior to onset of Kaposi's sarcoma. AIDS. 1996: 10(2): 175-80. PMID: 8838705.
Baba T, Takeuchi F, Kuroda M, Yuzawa H, Aoki K, Oguchi A, et al. Genome and virulence determinants
of high virulence community-acquired MRSA. Lancet. 2002; 359(9320): 1819-27. PMID: 12044378.
McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, Carrington M, et al. Association study
of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls. PLoS
Pathog. 2013; 9(7): e1003515. doi: 10.1371/journal.ppat.1003515. PMID: 23935489, PMCID:
PMC3723635.
Lingappa JR, Petrovski S, Kahle E, Fellay J, Shianna K, McElrath MJ, et al. Genomewide association study
for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified
virus exposure. PLoS One. 2011; 6(12): e28632. doi: 10.1371/journal.pone.0028632. PMID: 22174851,
PMCID: PMC3236203.
Petrovski S, Fellay J, Shianna KV, Carpenetti N, Kumwenda J, Kamanga G, et al. Common human genetic
variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population. AIDS.
; 25(4): 513-8. doi: 10.1097/QAD.0b013e328343817b. PMID: 21160409, PMCID: PMC3150594.
Herbeck JT, Gottlieb GS, Winkler CA, Nelson GW, An P, Maust BS, et al. Multistage genomewide
association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical
AIDS. J Infect Dis. 2010; 201(4): 618-26. doi: 10.1086/649842. PMID: 20064070, PMCID: PMC2928718.
Chimusa ER, Zaitlen N, Daya M, Möller M, van Helden PD, Mulder NJ, et al. Genome-wide association
study of ancestry-specific TB risk in the South African Coloured population. Hum Mol Genet. 2014; 23(3):
-809. doi: 10.1093/hmg/ddt462. PMID: 24057671, PMCID: PMC3888262.
Mahasirimongkol S, Yanai H, Mushiroda T, Promphittayarat W, Wattanapokayakit S, Phromjai J,
Yuliwulandari R, et al. Genome-wide association studies of tuberculosis in Asians identify distinct at-risk
locus for young tuberculosis. J Hum Genet. 2012; 57(6): 363-7. doi: 10.1038/jhg.2012.35. PMID:
Timmann C, Thye T, Vens M, Evans J, May J, Ehmen C, et al. Genome-wide association study indicates
two novel resistance loci for severe malaria. Nature. 2012; 489(7416): 443-6. doi: 10.1038/nature11334.
PMID: 22895189.
Jallow M, Teo YY, Small KS, Rockett KA, Deloukas P, Clark TG, et al. Genome-wide and fine-resolution
association analysis of malaria in West Africa. Nat Genet. 2009; 41(6): 657-65. doi: 10.1038/ng.388.
PMID: 19465909, PMCID: PMC2889040.
Singer M. Pathogen-pathogen interaction: a syndemic model of complex biosocial processes in disease.
Virulence. 2010; 1(1): 10-8. doi: 10.4161/viru.1.1.9933. PMID: 21178409, PMCID: PMC3080196.
Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett C, Knight R, Gordon JI. The human microbiome
project. Nature. 2007; 449(7164): 804–10. doi: 10.1038/nature06244. PMID: 17943116, PMCID:
PMC3709439.
Samb-Ba B, Mazenot C, Gassama-Sow A, Dubourg G, Richet H, Hugon P, et al. MALDI-TOF
Identification of the Human Gut Microbiome in People with and without Diarrhea in Senegal. PLoS One.
; 9(5): e87419. doi: 10.1371/journal.pone.0087419. PMID: 24784934, PMCID: PMC4006720.
George DB, Manges AR. A systematic review of outbreak and non-outbreak studies of extraintestinal
pathogenic Escherichia coli causing community-acquired infections. Epidemiol Infect. 2010; 138: 1679-90.
doi: 10.1017/S0950268810001639. PMID: 20642873.
Cortés P, Blanc V, Mora A, Dahbi G, Blanco JE, Blanco M, et al. Isolation and characterization of
potentially pathogenic antimicrobial-resistant Escherichia coli strains from chicken and pig farms in Spain.
Appl Environ Microbiol. 2010; 76(9): 2799-805. doi: 10.1128/AEM.02421-09. PMID: 20228098, PMCID:
PMC2863447.
Bergeron CR, Prussing C, Boerlin P, Daignault D, Dutil L, Reid-Smith RJ, et al. Chicken as reservoir for
extraintestinal pathogenic Escherichia coli in humans, Canada. Emerg Infect Dis. 2012; 18(3): 415-21. doi:
3201/eid1803.111099. PMID: 22377351, PMCID: PMC3309577.
Shafer RW, Rhee SY, Bennett DE. Consensus drug resistance mutations for epidemiological surveillance:
basic principles and potential controversies. Antivir Ther. 2008; 13(Suppl 2): 59-68. PMID: 18575192,
PMCID: PMC4388302.
Wang R, Taubenberger JK. Methods for molecular surveillance of influenza. Expert Rev Anti Infect Ther.
; 8(5): 517-27. doi: 10.1586/eri.10.24. PMID: 20455681, PMCID: PMC2882197.
Haghdoost A, Baneshi MR, Zolala F, Farvahari S, Safizadeh H. Estimation of Basic Reproductive Number
of Flu-like Syndrome in a Primary School in Iran. Int J Prev Med. 2012; 3(6): 408-13. PMID: 22783467,
PMCID: PMC3389438.
Hooper RR, Reynolds GH, Jones OG, Zaidi A, Wiesner PJ, Latimer KP, et al. Cohort study of venereal
disease. I: the risk of gonorrhea transmission from infected women to men. Am J Epidemiol. 1978; 108(2):
-44. PMID: 707474.
Lemey P, Salemi M, Vandamme A. The phylogenetic handbook: a practical approach to phylogenetic
analysis and hypothesis testing. 2nd edition. Cambridge: Cambridge University Press; 2009.
Jahanbakhsh F, Eybpoosh S, Mostafavi E, Haghdoost AA, Azadmanesh K. Molecular Epidemiology of
HIV-1 in Afghanistan, Iran, and Pakistan. J Med Microbiol Infec Dis, 2015, 3 (3-4): 44-47
Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian phylogeography finds its roots. PLoS
Comput Biol. 2009; 5: e1000520. doi: 10.1371/journal.pcbi.1000520. PMID: 19779555, PMCID:
PMC2740835.
Holmes E. The phylogeography of human viruses. Mol Ecol. 2004; 13: 745-56. doi: 10.1046/j.1365- 294X.2003.02051.x. PMID: 15012753.
Slatkin M, Maddison WP. A cladistic measure of gene flow inferred from the phylogenies of alleles.
Genetics. 1989; 123: 603-13. PMID: 2599370, PMCID: PMC1203833.
Templeton A. Statistical phylogeography: methods for evaluating and minimizing inference errors. Mol
Ecol. 2004; 13: 789-809. doi: 10.1046/j.1365-294X.2003.02041.x. PMID: 15012756.
Lanciotti R, Gubler D, Trent D. Molecular evolution and phylogeny of dengue-4 viruses. J Gen Virol.
; 78: 2279-86. doi: 10.1099/0022-1317-78-9-2279. PMID: 9292015.
Swofford WM. Systematics, Historical Ecology, and North American Freshwater Fishes. Parsimony,
character-state reconstructions and evolutionary inferences. Stanford University Press; 1992.
Eybpoosh S, Bahrampour A, Karamouzian M, Azadmanesh K, Jahanbakhsh F, Mostafavi E, et al. Spatio- Temporal History of HIV-1 CRF35_AD in Afghanistan and Iran. PLoS One. 2016; 11(6): e0156499. doi:
1371/journal.pone.0156499. PMID: 27280293, PMCID: PMC4900578.
Sarrami-Forooshani R, Das SR, Sabahi F, Adeli A, Esmaeili R, Wahren B, et al. Molecular analysis and
phylogenetic characterization of HIV in Iran. J Med Virol. 2006; 78: 853-63. doi: 10.1002/jmv.20634.
PMID: 16721846.
Soheilli ZS, Ataiee Z, Tootian S, Zadsar M, Amini S, Abadi K, et al. Presence of HIV-1 CRF35_AD in
Iran. AIDS Res Hum Retroviruses. 2009; 25: 123-4. doi: 10.1089/aid.2008.0199. PMID: 19182925.
Eybpoosh S, Bahrampour A, Azadmanesh K, Mostafavi E, Haghdoost AA, Zolala F. Spatio-temporal
dynamics of HIV-I subtype B and Circulating Recombinant Form 01_AE clades in Iran: a phylogeographic
approach. Iran Red Crescent Med J. 2017; 19(2): e34609
Khoury MJ, Feero WG, Reyes M, Citrin T, Freedman A, Leonard D, et al. The genomic applications in
practice and prevention network. Genet Med. 2009; 11(7): 488-94. doi: 10.1097/GIM.0b013e3181a551cc.
PMID: 19471162, PMCID: PMC2743616.
Samzadeh M, Hasanzad M, Jamaldini SH, Haghdoost AA, Afshari M, Ziaee SA. Association of G/A
polymorphism, rs266882, in AREI region of the prostate-specific antigen gene with prostate cancer risk
and clinicopathological features. Urol J. 2012; 9(4): 691-9. PMID: 23235975.
Ziaei SA, Samzadeh M, Jamaldini SH, Afshari M, Haghdoost AA, Hasanzad M. Endothelial nitric oxide
synthase Glu298Asp polymorphism as a risk factor for prostate cancer. Int J Biol Markers. 2013; 28(1): 43- 8. doi: 10.5301/JBM.2012.9585. PMID: 23015399.
Paynter NP, Chasman DI, Paré G, Buring JE, Cook NR, Miletich JP, et al. Association between a
Literature-Based Genetic Risk Score and Cardiovascular Events in 19,313 Women. JAMA. 2010; 303 (7):
-7. doi: 10.1001/jama.2010.119PMID: 20159871, PMCID: PMC2845522.
Muehlschlegel JD, Liu KY, Perry TE, Fox AA, Collard CD, Shernan SK, et al. Chromosome 9p21 Variant
Predicts Mortality after CABG Surgery. Circulation. 2010; 122 (11 Suppl): S60-5. doi:
1161/CIRCULATIONAHA.109.924233. PMID: 20837927, PMCID: PMC2943860.
Published
Issue
Section
License
Copyright (c) 2020 KNOWLEDGE KINGDOM PUBLISHING
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.