When are pathogen genome sequences informative of transmission events?

PLoS Pathogens

Volumn 14, Issue 2, 2018, Pages

  Campbell, Finlay ^a   Strang, Camilla ^b   Ferguson, Neil ^a   Cori, Anne ^a   Jombart, Thibaut ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b ANIMAL HEALTH TRUST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BASIC REPRODUCTION NUMBER; DISEASE TRANSMISSION; EPIDEMIC; EPIDEMIOLOGICAL MONITORING; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; INFECTION; MICROBIAL GENOME; MUTATION RATE; NONHUMAN; PEPTOCLOSTRIDIUM DIFFICILE; RNA VIRUS; SHIGELLA SONNEI; SIMULATION; STREPTOCOCCUS PNEUMONIAE; WHOLE GENOME SEQUENCING; BACTERIAL GENOME; BACTERIUM; CHROMOSOMAL MAPPING; COMMUNICABLE DISEASE; DNA SEQUENCE; GENETIC PREDISPOSITION; GENETIC VARIATION; GENETICS; HUMAN; NUCLEOTIDE SEQUENCE; PATHOGENICITY; PHYLOGENY; STATISTICS AND NUMERICAL DATA; TRANSMISSION; VIRUS; VIRUS GENOME;

BACTERIA; BASE SEQUENCE; CHROMOSOME MAPPING; COMMUNICABLE DISEASES; DISEASE OUTBREAKS; DISEASE TRANSMISSION, INFECTIOUS; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME, BACTERIAL; GENOME, VIRAL; HUMANS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; VIRUSES; WHOLE GENOME SEQUENCING;

EID: 85042693214     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.1006885     Document Type: Article

References (115)

1. Ferguson NM, Donnelly CA, Anderson RM, Transmission intensity and impact of control policies on the foot and mouth epidemic in Great Britain. Nature. 2001;413: 542–548. doi: 10.1038/35097116 11586365
2. Wallinga J, Teunis P, Different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures. Am J Epidemiol. 2004;160: 509–516. doi: 10.1093/aje/kwh255 15353409
3. Spada E, Sagliocca L, Sourdis J, Garbuglia AR, Poggi V, De Fusco C, et al. Use of the minimum spanning tree model for molecular epidemiological investigation of a nosocomial outbreak of hepatitis C virus infection. J Clin Microbiol. 2004;42: 4230–4236. doi: 10.1128/JCM.42.9.4230-4236.2004 15365016
4. Lloyd-Smith JO, Schreiber SJ, Kopp PE, Getz WM, Superspreading and the effect of individual variation on disease emergence. Nature. 2005;438: 355–359. doi: 10.1038/nature04153 16292310
5. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N, Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. PLoS Comput Biol. 2014;10. doi: 10.1371/journal.pcbi.1003457 24465202
6. Morelli MJ, Thébaud G, Chadœuf J, King DP, Haydon DT, Soubeyrand S, A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data. PLoS Comput Biol. 2012;8. doi: 10.1371/journal.pcbi.1002768 23166481
7. Mollentze N, Nel LH, Townsend S, le Roux K, Hampson K, Haydon DT, et al. A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data. Proc Biol Sci. 2014;281: 20133251. doi: 10.1098/rspb.2013.3251 24619442
8. Worby CJ, O’Neill PD, Kypraios T, Robotham JV, De Angelis D, Cartwright EJP, et al. Reconstructing transmission trees for communicable diseases using densely sampled genetic data. Ann Appl Stat. 2016;10: 395–417. 27042253
9. Lau MSY, Marion G, Streftaris G, Gibson G, A Systematic Bayesian Integration of Epidemiological and Genetic Data. PLoS Comput Biol. 2015;11: e1004633. doi: 10.1371/journal.pcbi.1004633 26599399
10. Cottam EM, Thébaud G, Wadsworth J, Gloster J, Mansley L, Paton DJ, et al. Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus. Proc Biol Sci. 2008;275: 887–895. doi: 10.1098/rspb.2007.1442 18230598
11. Didelot X, Gardy J, Colijn C, Bayesian inference of infectious disease transmission from whole-genome sequence data. Mol Biol Evol. 2014;31: 1869–1879. doi: 10.1093/molbev/msu121 24714079
12. Didelot X, Fraser C, Gardy J, Colijn C, Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks. Mol Biol Evol. 2017; doi: 10.1093/molbev/msw275 28100788
13. Ypma RJF, van Ballegooijen WM, Wallinga J, Relating phylogenetic trees to transmission trees of infectious disease outbreaks. Genetics. 2013;195: 1055–1062. doi: 10.1534/genetics.113.154856 24037268
14. De Maio N, Wu C-H, Wilson DJ, SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent. PLoS Comput Biol. 2016;12: e1005130. doi: 10.1371/journal.pcbi.1005130 27681228
15. Hall M, Woolhouse M, Rambaut A, Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set. PLoS Comput Biol. 2015;11: e1004613. doi: 10.1371/journal.pcbi.1004613 26717515
16. Sabat AJ, Budimir A, Nashev D, Sá-Leão R, van Dijl J m., Laurent F, et al. Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill. 2013;18: 20380. 23369389
17. Eyre DW, Cule ML, Wilson DJ, Griffiths D, Vaughan A, O’Connor L, et al. Diverse sources of C. difficile infection identified on whole-genome sequencing. N Engl J Med. 2013;369: 1195–1205. doi: 10.1056/NEJMoa1216064 24066741
18. Walker TM, Ip CLC, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis. 2013;13: 137–146. doi: 10.1016/S1473-3099(12)70277-3 23158499
19. Walker TM, Lalor MK, Broda A, Ortega LS, Morgan M, Parker L, et al. Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study. The Lancet Respiratory Medicine. 2014/4;2: 285–292. doi: 10.1016/S2213-2600(14)70027-X 24717625
20. Ypma RJF, Bataille AMA, Stegeman A, Koch G, Wallinga J, van Ballegooijen WM, Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data [Internet]. Proceedings of the Royal Society B: Biological Sciences. 2012. pp. 444–450. doi: 10.1098/rspb.2011.0913 21733899
21. Hatherell H-A, Didelot X, Pollock SL, Tang P, Crisan A, Johnston JC, et al. Declaring a tuberculosis outbreak over with genomic epidemiology. Microbial Genomics. Microbiology Society; 2016;2. doi: 10.1099/mgen.0.000060 28348853
22. Chung The H, Karkey A, Pham Thanh D, Boinett CJ, Cain AK, Ellington M, et al. A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae. EMBO Mol Med. 2015;7: 227–239. doi: 10.15252/emmm.201404767 25712531
23. Didelot X, Eyre DW, Cule M, Ip CLC, Ansari MA, Griffiths D, et al. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol. 2012;13: R118. doi: 10.1186/gb-2012-13-12-r118 23259504
24. Fine PEM, The interval between successive cases of an infectious disease. Am J Epidemiol. 2003;158: 1039–1047. 14630599
25. Kermack WO, McKendrick AG. A contribution to the mathematical theory of epidemics. A: mathematical, …. rspa.royalsocietypublishing.org; 1927; Available: http://rspa.royalsocietypublishing.org/content/royprsa/115/772/700.full.pdf
26. Klinkenberg D, Backer JA, Didelot X, Colijn C, Wallinga J, Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput Biol. 2017;13: e1005495. doi: 10.1371/journal.pcbi.1005495 28545083
27. R Core TeamR: A Language and Environment for Statistical Computing [Internet]. Vienna, Austria: R Foundation for Statistical Computing; 2017. Available: https://www.R-project.org/
28. WHO Ebola Response TeamEbola Virus Disease in West Africa—The First 9 Months of the Epidemic and Forward Projections. The England New Journal of Medecine. 2014;371: 1481–1495.
29. WHO Ebola Response TeamWest African Ebola Epidemic after One Year—Slowing but Not Yet under Control. N Engl J Med. 2015;372: 584–587. doi: 10.1056/NEJMc1414992 25539446
30. Faye O, Boëlle P-Y, Heleze E, Faye O, Loucoubar C, Magassouba N ‘faly, et al. Chains of transmission and control of Ebola virus disease in Conakry, Guinea, in 2014: an observational study. Lancet Infect Dis. 2015;15: 320–326. doi: 10.1016/S1473-3099(14)71075-8 25619149
31. Hoenen T, Groseth A, Feldmann F, Marzi A, Ebihara H, Kobinger G, et al. Complete Genome Sequences of Three Ebola Virus Isolates from the 2014 Outbreak in West Africa. Genome Announc. 2014;2: 647–648.
32. Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, Kanneh L, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014;345: 1369–1372. doi: 10.1126/science.1259657 25214632
33. Tong Y-G, Shi W-F, Di Liu, Qian J, Liang L, Bo X-C, et al. Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone. Nature. 2015; doi: 10.1038/nature14490 25970247
34. Baize S, Pannetier D, Oestereich L, Rieger T, Koivogui L, Magassouba N ‘faly, et al. Emergence of Zaire Ebola Virus Disease in Guinea—Preliminary Report. N Engl J Med. 2014; 1–8.
35. Cauchemez S, Fraser C, Van Kerkhove MD, Donnelly CA, Riley S, Rambaut A, et al. Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility. Lancet Infect Dis. Elsevier; 2014;14: 50–56. doi: 10.1016/S1473-3099(13)70304-9 24239323
36. Assiri A, McGeer A, Perl TM, Price CS, Al Rabeeah AA, Cummings DAT, et al. Hospital outbreak of Middle East respiratory syndrome coronavirus. N Engl J Med. 2013;369: 407–416. doi: 10.1056/NEJMoa1306742 23782161
37. Memish ZA, Zumla AI, Al-Hakeem RF, Al-Rabeeah AA, Stephens GM, Family cluster of Middle East respiratory syndrome coronavirus infections. N Engl J Med. 2013;368: 2487–2494. doi: 10.1056/NEJMoa1303729 23718156
38. Cotten M, Watson SJ, Kellam P, Al-Rabeeah AA, Makhdoom HQ, Assiri A, et al. Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. Lancet. 2013;382: 1993–2002. doi: 10.1016/S0140-6736(13)61887-5 24055451
39. Cotten M, Watson SJ, Zumla AI, Makhdoom HQ, Palser AL, Ong SH, et al. Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus. MBio. 2014;5. doi: 10.1128/mBio.01062-13 24549846
40. de Groot RJ, Baker SC, Baric RS, Brown CS, Drosten C, Enjuanes L, et al. Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus Study Group. J Virol. 2013;87: 7790–7792. doi: 10.1128/JVI.01244-13 23678167
41. Lipsitch M, Transmission Dynamics and Control of Severe Acute Respiratory Syndrome. Science. 2003;300: 1966–1970. doi: 10.1126/science.1086616 12766207
42. Reynolds MG, Anh BH, Thu VH, Montgomery JM, Bausch DG, Shah JJ, et al. Factors associated with nosocomial SARS-CoV transmission among healthcare workers in Hanoi, Vietnam, 2003. BMC Public Health. 2006;6: 207. doi: 10.1186/1471-2458-6-207 16907978
43. Varia M, Wilson S, Sarwal S, McGeer A, Gournis E, Galanis E, et al. Investigation of a nosocomial outbreak of severe acute respiratory syndrome (SARS) in Toronto, Canada. CMAJ. 2003;169: 285–292. 12925421
44. Vega VB, Ruan Y, Liu J, Lee WH, Wei CL, Se-Thoe SY, et al. Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003. BMC Infect Dis. 2004;4: 32. doi: 10.1186/1471-2334-4-32 15347429
45. Zhao Z, Li H, Wu X, Zhong Y, Zhang K, Zhang Y-P, et al. Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol Biol. 2004;4: 21. doi: 10.1186/1471-2148-4-21 15222897
46. Wu S-F, Du C-J, Wan P, Chen T-G, Li J-Q, Li D, et al. The genome comparison of SARS-CoV and other coronaviruses. Yi chuan = Hereditas/Zhongguo yi chuan xue hui bian ji. 2003;25: 373–382.
47. Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, et al. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science. 2003;300: 1394–1399. doi: 10.1126/science.1085952 12730500
48. Ruan YJ, Wei CL, Ee AL, Vega VB, Thoreau H, Su STY, et al. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection. Lancet. 2003;361: 1779–1785. 12781537
49. Riley S, Fraser C, Donnelly CA, Ghani AC, Abu-Raddad LJ, Hedley AJ, et al. Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions. Science. 2003;300: 1961–1966. doi: 10.1126/science.1086478 12766206
50. Levy JW, Cowling BJ, Simmerman JM, Olsen SJ, Fang VJ, Suntarattiwong P, et al. The serial intervals of seasonal and pandemic influenza viruses in households in Bangkok, Thailand. Am J Epidemiol. 2013;177: 1443–1451. doi: 10.1093/aje/kws402 23629874
51. Hahné S, Donker T, Meijer A, Timen A, Van Steenbergen J, Osterhaus A, et al. Epidemiology and control of influenza A (H1N1) v in the Netherlands: the first 115 cases. Euro surveillance: bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin. 2009;14: 2335–2346.
52. Cauchemez S, Donnelly CA, Reed C, Ghani AC, Fraser C, Kent CK, et al. Household transmission of 2009 pandemic influenza A (H1N1) virus in the United States. N Engl J Med. 2009;361: 2619–2627. doi: 10.1056/NEJMoa0905498 20042753
53. Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature. 2009;459: 1122–1125. doi: 10.1038/nature08182 19516283
54. Rambaut A, Holmes E, The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic. PLoS Curr. 2009;1: RRN1003.
55. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, et al. The influenza virus resource at the National Center for Biotechnology Information. J Virol. 2008;82: 596–601. doi: 10.1128/JVI.02005-07 17942553
56. Boëlle P-Y, Ansart S, Cori A, Valleron A-J, Transmission parameters of the A/H1N1 (2009) influenza virus pandemic: a review. Influenza Other Respi Viruses. 2011;5: 306–316.
57. Patel M, Thomas HC, Room J, Wilson Y, Kearns A, Gray J, Successful control of nosocomial transmission of the USA300 clone of community-acquired meticillin-resistant Staphylococcus aureus in a UK paediatric burns centre. J Hosp Infect. 2013/8;84: 319–322. doi: 10.1016/j.jhin.2013.04.013 23711818
58. Köser CU, Holden MTG, Ellington MJ, Cartwright EJP, Brown NM, Ogilvy-Stuart AL, et al. Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak [Internet]. New England Journal of Medicine. 2012. pp. 2267–2275. doi: 10.1056/NEJMoa1109910 22693998
59. Lee H, Kim ES, Choi C, Seo H, Shin M, Bok JH, et al. Outbreak among healthy newborns due to a new variant of USA300-related meticillin-resistant Staphylococcus aureus. J Hosp Infect. 2014;87: 145–151. doi: 10.1016/j.jhin.2014.04.003 24856113
60. Uhlemann A- C, Dordel J, Knox JR, Raven KE, Parkhill J, Holden MTG, et al. Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community. Proc Natl Acad Sci U S A. 2014;111: 6738–6743. doi: 10.1073/pnas.1401006111 24753569
61. Holden MTG, Hsu L-Y, Kurt K, Weinert LA, Mather AE, Harris SR, et al. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res. 2013;23: 653–664. doi: 10.1101/gr.147710.112 23299977
62. McAdam PR, Templeton KE, Edwards GF, Holden MTG, Feil EJ, Aanensen DM, et al. Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci U S A. 2012;109: 9107–9112. doi: 10.1073/pnas.1202869109 22586109
63. Harris SR, Feil EJ, Holden MTG, Quail MA, Nickerson EK, Chantratita N, et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science. 2010;327: 469–474. doi: 10.1126/science.1182395 20093474
64. Harris SR, Cartwright EJP, Török ME, Holden MTG, Brown NM, Ogilvy-Stuart AL, et al. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis. 2013;13: 130–136. doi: 10.1016/S1473-3099(12)70268-2 23158674
65. Holden MTG, Feil EJ, Lindsay JA, Peacock SJ, Day NPJ, Enright MC, et al. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A. 2004;101: 9786–9791. doi: 10.1073/pnas.0402521101 15213324
66. Holt DC, Holden MTG, Tong SYC, Castillo-Ramirez S, Clarke L, Quail MA, et al. A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin. Genome Biol Evol. 2011;3: 881–895. doi: 10.1093/gbe/evr078 21813488
67. Diep BA, Gill SR, Chang RF, Phan TH, Chen JH, Davidson MG, et al. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet. 2006;367: 731–739. doi: 10.1016/S0140-6736(06)68231-7 16517273
68. Wang X, Panchanathan S, Chowell G, A data-driven mathematical model of CA-MRSA transmission among age groups: evaluating the effect of control interventions. PLoS Comput Biol. 2013;9: e1003328. doi: 10.1371/journal.pcbi.1003328 24277998
69. Van’t Veen A, Van Der Zee A, Nelson J, Speelberg B, Kluytmans JAJW, Buiting AGM, Outbreak of infection with a multiresistant Klebsiella pneumoniae strain associated with contaminated roll boards in operating rooms. J Clin Microbiol. 2005;43: 4961–4967. doi: 10.1128/JCM.43.10.4961-4967.2005 16207948
70. Kassis-Chikhani N, Decré D, Gautier V, Burghoffer B, Saliba F, Mathieu D, et al. First outbreak of multidrug-resistant Klebsiella pneumoniae carrying blaVIM-1 and blaSHV-5 in a French university hospital. J Antimicrob Chemother. 2006;57: 142–145. doi: 10.1093/jac/dki389 16284103
71. Macrae MB, Shannon KP, Rayner DM, Kaiser AM, Hoffman PN, French GL, simultaneous outbreak on a neonatal unit of two strains of multiply antibiotic resistant Klebsiella pneumoniae controllable only by ward closure. J Hosp Infect. 2001;49: 183–192. doi: 10.1053/jhin.2001.1066 11716635
72. Mathers AJ, Stoesser N, Sheppard AE, Pankhurst L, Giess A, Yeh AJ, et al. Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing. Antimicrob Agents Chemother. 2015;59: 1656–1663. doi: 10.1128/AAC.04292-14 25561339
73. Karkey A, Thanh DP, Boinett CJ, Cain AK, Ellington M, Baker KS, et al. A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae. EMBO Mol Med. EMBO Press; 2015;7: 227–239. doi: 10.15252/emmm.201404767 25712531
74. De Champs C, Rich C, Chandezon P, Chanal C, Sirot D, Forestier C, Factors associated with antimicrobial resistance among clinical isolates of Klebsiella pneumoniae: 1-year survey in a French university hospital. Eur J Clin Microbiol Infect Dis. 2004;23: 456–462. doi: 10.1007/s10096-004-1144-2 15148654
75. Liu P, Li P, Jiang X, Bi D, Xie Y, Tai C, et al. Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. J Bacteriol. 2012;194: 1841–1842. doi: 10.1128/JB.00043-12 22408243
76. Fookes M, Yu J, De Majumdar S, Thomson N, Schneiders T, Genome Sequence of Klebsiella pneumoniae Ecl8, a Reference Strain for Targeted Genetic Manipulation. Genome Announc. 2013;1. doi: 10.1128/genomeA.00027-12 23405357
77. Shin SH, Kim S, Kim JY, Lee S, Um Y, Oh M-K, et al. Complete genome sequence of the 2, 3-butanediol-producing Klebsiella pneumoniae strain KCTC 2242. J Bacteriol. Am Soc Microbiol; 2012;194: 2736–2737.
78. Sypsa V, Psichogiou M, Bouzala G-A, Hadjihannas L, Hatzakis A, Daikos GL, Transmission dynamics of carbapenemase-producing Klebsiella pneumoniae and anticipated impact of infection control strategies in a surgical unit. PLoS One. 2012;7: e41068. doi: 10.1371/journal.pone.0041068 22859965
79. Crum NF, Wallace MR, Lamb CR, Conlin AMS, Amundson DE, Olson PE, et al. Halting a pneumococcal pneumonia outbreak among United States Marine Corps trainees. Am J Prev Med. 2003;25: 107–111.
80. Thomas HL, Gajraj R, Slack MPE, Sheppard C, Hawkey P, Gossain S, et al. An explosive outbreak of Streptococcus pneumoniae serotype-8 infection in a highly vaccinated residential care home, England, summer 2012. Epidemiol Infect. 2015;143: 1957–1963. doi: 10.1017/S0950268814002490 25298247
81. Kuroki T, Ishida M, Suzuki M, Furukawa I, Ohya H, Watanabe Y, et al. Outbreak of Streptococcus pneumoniae serotype 3 pneumonia in extremely elderly people in a nursing home unit in Kanagawa, Japan, 2013. J Am Geriatr Soc. 2014;62: 1197–1198. doi: 10.1111/jgs.12863 24925560
82. Stevens KE, Sebert ME, Frequent beneficial mutations during single-colony serial transfer of Streptococcus pneumoniae. PLoS Genet. 2011;7: e1002232. doi: 10.1371/journal.pgen.1002232 21876679
83. Henderson-Begg SK, Livermore DM, Hall LMC, Effect of subinhibitory concentrations of antibiotics on mutation frequency in Streptococcus pneumoniae. J Antimicrob Chemother. 2006;57: 849–854. doi: 10.1093/jac/dkl064 16531433
84. Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, et al. Rapid pneumococcal evolution in response to clinical interventions. Science. 2011;331: 430–434. doi: 10.1126/science.1198545 21273480
85. Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, et al. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science. 2001;293: 498–506. doi: 10.1126/science.1061217 11463916
86. Camilli R, Bonnal RJP, Del Grosso M, Iacono M, Corti G, Rizzi E, et al. Complete genome sequence of a serotype 11A, ST62 Streptococcus pneumoniae invasive isolate. BMC Microbiol. 2011;11: 25. doi: 10.1186/1471-2180-11-25 21284853
87. Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, et al. Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol. 2010;11: R107. doi: 10.1186/gb-2010-11-10-r107 21034474
88. Hoti F, Erästö P, Leino T, Auranen K, Outbreaks of Streptococcus pneumoniae carriage in day care cohorts in Finland—implications for elimination of transmission. BMC Infect Dis. BioMed Central; 2009;9: 102. doi: 10.1186/1471-2334-9-102 19558701
89. ten Asbroek AH, Borgdorff MW, Nagelkerke NJ, Sebek MM, Devillé W, van Embden JD, et al. Estimation of serial interval and incubation period of tuberculosis using DNA fingerprinting. Int J Tuberc Lung Dis. 1999;3: 414–420. 10331731
90. Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, et al. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med. 2013;10: e1001387. doi: 10.1371/journal.pmed.1001387 23424287
91. Guerra-Assunção JA, Crampin AC, Houben RMGJ, Mzembe T, Mallard K, Coll F, et al. Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. Elife. 2015;4. doi: 10.7554/eLife.05166 25732036
92. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393: 537–544. doi: 10.1038/31159 9634230
93. Camus J-C, Pryor MJ, Médigue C, Cole ST, Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology. 2002;148: 2967–2973. doi: 10.1099/00221287-148-10-2967 12368430
94. Dye C, Williams BG, Criteria for the control of drug-resistant tuberculosis. Proc Natl Acad Sci U S A. 2000;97: 8180–8185. doi: 10.1073/pnas.140102797 10859359
95. Makintubee S, Mallonee J, Istre GR, Shigellosis outbreak associated with swimming. Am J Public Health. 1987;77: 166–168. 3541651
96. World Health OrganizationGuidelines for the control of shigellosis, including epidemics due to Shigella dysenteriae type 1. Geneva: World Health Organization; 2005; Available: http://apps.who.int/iris/handle/10665/43252
97. European Centre for Disease Prevention and Control. Systematic review on the incubation and infectiousness/shedding period of communicable diseases in children. 2016;Stockholm.
98. Holt KE, Baker S, Weill F-X, Holmes EC, Kitchen A, Yu J, et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet. 2012;44: 1056–1059. doi: 10.1038/ng.2369 22863732
99. Yang F, Yang J, Zhang X, Chen L, Jiang Y, Yan Y, et al. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 2005;33: 6445–6458. doi: 10.1093/nar/gki954 16275786
100. Joh RI, Hoekstra RM, Barzilay EJ, Bowen A, Mintz ED, Weiss H, et al. Dynamics of shigellosis epidemics: estimating individual-level transmission and reporting rates from national epidemiologic data sets. Am J Epidemiol. 2013;178: 1319–1326. doi: 10.1093/aje/kwt122 24008913
101. Pépin J, Gonzales M, Valiquette L, Risk of secondary cases of Clostridium difficile infection among household contacts of index cases. J Infect. 2012;64: 387–390. doi: 10.1016/j.jinf.2011.12.011 22227466
102. Sarah Walker A, Eyre DW, Wyllie DH, Dingle KE, Harding RM, O’Connor L, et al. Characterisation of Clostridium difficile Hospital Ward–Based Transmission Using Extensive Epidemiological Data and Molecular Typing. PLoS Med. Public Library of Science; 2012;9: e1001172.
103. Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N, Stabler R, et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet. 2006;38: 779–786. doi: 10.1038/ng1830 16804543
104. Lanzas C, Dubberke ER, Lu Z, Reske KA, Gröhn YT, Epidemiological model for Clostridium difficile transmission in healthcare settings. Infect Control Hosp Epidemiol. 2011;32: 553–561. doi: 10.1086/660013 21558767
105. Norén T, Akerlund T, Bäck E, Sjöberg L, Persson I, Alriksson I, et al. Molecular epidemiology of hospital-associated and community-acquired Clostridium difficile infection in a Swedish county. J Clin Microbiol. 2004;42: 3635–3643. doi: 10.1128/JCM.42.8.3635-3643.2004 15297509
106. Snitkin ES, Zelazny AM, Thomas PJ, Stock F, Henderson DK, Palmore TN, et al. Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing [Internet]. Science Translational Medicine. 2012. pp. 148ra116–148ra116. doi: 10.1126/scitranslmed.3004129 22914622
107. Worby CJ, Lipsitch M, Hanage WP, Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data. PLoS Comput Biol. 2014;10: e1003549. doi: 10.1371/journal.pcbi.1003549 24675511
108. Didelot X, Walker AS, Peto TE, Crook DW, Wilson DJ, Within-host evolution of bacterial pathogens. Nat Rev Microbiol. 2016;14: 150–162. doi: 10.1038/nrmicro.2015.13 26806595
109. Pybus OG, Rambaut A, Evolutionary analysis of the dynamics of viral infectious disease. Nat Rev Genet. 2009;10: 540–550. doi: 10.1038/nrg2583 19564871
110. Baele G, Suchard MA, Rambaut A, Lemey P, Emerging Concepts of Data Integration in Pathogen Phylodynamics. Syst Biol. 2017;66: e47–e65. doi: 10.1093/sysbio/syw054 28173504
111. Cori A, Ferguson NM, Fraser C, Cauchemez S, A new framework and software to estimate time-varying reproduction numbers during epidemics. Am J Epidemiol. 2013;178: 1505–1512. doi: 10.1093/aje/kwt133 24043437
112. He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, Martin MJ, et al. Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A. 2010;107: 7527–7532. doi: 10.1073/pnas.0914322107 20368420
113. Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW, GenBank. Nucleic Acids Res. 2016;44: D67–72. doi: 10.1093/nar/gkv1276 26590407
114. Gibbons A, Algorithmic Graph Theory. Cambridge University Press; 1985.
115. Shannon C, A mathematical theory of communication, Bell System Technical Journal27: 379–423 and 623–656. Mathematical Reviews (MathSciNet): MR10, 133e. 1948;