Frontiers of Medicine

, Volume 12, Issue 1, pp 23–33 | Cite as

Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the trace



Two decades have passed since the first bacterial whole-genome sequencing, which provides new opportunity for microbial genome. Consequently, considerable genetic diversity encoded by bacterial genomes and among the strains in the same species has been revealed. In recent years, genome sequencing techniques and bioinformatics have developed rapidly, which has resulted in transformation and expedited the application of strategy and methodology for bacterial genome comparison used in dissection of infectious disease epidemics. Bacterial whole-genome sequencing and bioinformatic computing allow genotyping to satisfy the requirements of epidemiological study in disease control. In this review, we outline the significance and summarize the roles of bacterial genome sequencing in the context of bacterial disease control and prevention.We discuss the applications of bacterial genome sequencing in outbreak detection, source tracing, transmission mode discovery, and new epidemic clone identification. Wide applications of genome sequencing and data sharing in infectious disease surveillance networks will considerably promote outbreak detection and early warning to prevent the dissemination of bacterial diseases.


genome sequencing genomic epidemiology bacteria surveillance infectious diseases 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.



This work was supported by the National Key Basic Research Program (No. 2015CB554201) and the National Key Research and Development Program (No. 2016YFC1200103) of the Ministry of Health of China.


  1. 1.
    Ranjbar R, Karami A, Farshad S, Giammanco GM, Mammina C. Typing methods used in the molecular epidemiology of microbial pathogens: a how-to guide. New Microbiol 2014; 37(1): 1–15Google Scholar
  2. 2.
    Tang P, Croxen MA, Hasan MR, Hsiao WW, Hoang LM. Infection control in the new age of genomic epidemiology. Am J Infect Control 2017; 45(2): 170–179CrossRefPubMedGoogle Scholar
  3. 3.
    Baker S, Hanage WP, Holt KE. Navigating the future of bacterial molecular epidemiology. Curr Opin Microbiol 2010; 13(5): 640–645CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Chin CS, Sorenson J, Harris JB, Robins WP, Charles RC, Jean- Charles RR, Bullard J, Webster DR, Kasarskis A, Peluso P, Paxinos EE, Yamaichi Y, Calderwood SB, Mekalanos JJ, Schadt EE, Waldor MK. The origin of the Haitian cholera outbreak strain.N Engl J Med 2011; 364(1): 33–42CrossRefPubMedGoogle Scholar
  5. 5.
    Hendriken RS, Price LB, Schupp JM, Gillece JD, Kaas RS, Engelthaler DM, Bortolaia V, Pearson T,Waters AE, Upadhyay BP, Shrestha SD, Adhikari S, Shakya G, Keim PS, Aarestrup FM. Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak. MBio2011; 2(4): e00157–e11Google Scholar
  6. 6.
    Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, Rico A, Prior K, Szczepanowski R, Ji Y, Zhang W, McLaughlin SF, Henkhaus JK, Leopold B, Bielaszewska M, Prager R, Brzoska PM, Moore RL, Guenther S, Rothberg JM, Karch H. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 2011; 6(7): e22751CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, Fitzgerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, Desmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Mller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci USA 2012; 109(8): 3065–3070CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen MJ, Wang J, Aepfelbacher M, Yang R; E. coliO104:H4 Genome Analysis Crowd-Sourcing Consortium. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 2011; 365(8): 718–724CrossRefPubMedGoogle Scholar
  9. 9.
    Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics 2015; 15(2): 141–161CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature 2000; 405(6784): 299–304CrossRefPubMedGoogle Scholar
  11. 11.
    Jackson BR, Tarr C, Strain E, Jackson KA, Conrad A, Carleton H, Katz LS, Stroika S, Gould LH, Mody RK, Silk BJ, Beal J, Chen Y, Timme R, Doyle M, Fields A, Wise M, Tillman G, Defibaugh- Chavez S, Kucerova Z, Sabol A, Roache K, Trees E, Simmons M, Wasilenko J, Kubota K, Pouseele H, Klimke W, Besser J, Brown E, Allard M, Gerner-Smidt P. Implementation of nationwide real-time whole-genome sequencing to enhance listeriosis outbreak detection and investigation. Clin Infect Dis 2016; 63(3): 380–386CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 2016; 17(6): 333–351CrossRefPubMedGoogle Scholar
  13. 13.
    Loman NJ, Pallen MJ. Twenty years of bacterial genome sequencing. Nat Rev Microbiol 2015; 13(12): 787–794CrossRefPubMedGoogle Scholar
  14. 14.
    Hedge J, Wilson DJ. Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not. MBio 2014; 5(6): e02158–14CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Sabat AJ, Budimir A, Nashev D, Sá-Leão R, van Dijl J, Laurent F, Grundmann H, Friedrich AW; ESCMID Study Group of Epidemiological Markers (ESGEM). Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill 2013; 18(4): 20380PubMedGoogle Scholar
  16. 16.
    Croucher NJ, Didelot X. The application of genomics to tracing bacterial pathogen transmission. Curr Opin Microbiol 2015; 23: 62–67CrossRefPubMedGoogle Scholar
  17. 17.
    Deng X, den Bakker HC, Hendriksen RS. Genomic epidemiology: whole-genome-sequencing-powered surveillance and outbreak investigation of foodborne bacterial pathogens. Annu Rev Food Sci Technol 2016; 7(1): 353–374CrossRefPubMedGoogle Scholar
  18. 18.
    Franz E, Gras LM, Dallman T. Significance of whole genome sequencing for surveillance, source attribution and microbial risk assessment of foodborne pathogens. Curr Opin Food Sci 2016; 8: 74–79CrossRefGoogle Scholar
  19. 19.
    Gilchrist CA, Turner SD, Riley MF, Petri WA Jr, Hewlett EL. Whole-genome sequencing in outbreak analysis. Clin Microbiol Rev 2015; 28(3): 541–563CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Jolley KA, Maiden MC. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010; 11(1): 595CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Sheppard SK, Jolley KA, Maiden MC. A gene-by-gene approach to bacterial population genomics: whole genome MLST of campylobacter. Genes (Basel) 2012; 3(2): 261–277CrossRefGoogle Scholar
  22. 22.
    Maiden MC, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol 2013; 11(10): 728–736CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Bratcher HB, Corton C, Jolley KA, Parkhill J, Maiden MC. A geneby-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics 2014; 15(1): 1138CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Ruppitsch W, Pietzka A, Prior K, Bletz S, Fernandez HL, Allerberger F, Harmsen D, Mellmann A. Defining and evaluating a core genome multilocus sequence typing scheme for wholegenome sequence-based typing of Listeria monocytogenes. J Clin Microbiol 2015; 53(9): 2869–2876CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Kohl TA, Diel R, Harmsen D, Rothgänger J, Walter KM, Merker M, Weniger T, Niemann S. Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach. J Clin Microbiol 2014; 52(7): 2479–2486CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Leopold SR, Goering RV, Witten A, Harmsen D, Mellmann A. Bacterial whole-genome sequencing revisited: portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes. J Clin Microbiol 2014; 52(7): 2365–2370CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Moran-Gilad J, Prior K, Yakunin E, Harrison TG, Underwood A, Lazarovitch T, Valinsky L, Luck C, Krux F, Agmon V, Grotto I, Harmsen D. Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires’ disease incidents. Euro Surveill 2015; 20(28): 21186CrossRefPubMedGoogle Scholar
  28. 28.
    de Been M, Pinholt M, Top J, Bletz S, Mellmann A, van Schaik W, Brouwer E, Rogers M, Kraat Y, Bonten M, Corander J, Westh H, Harmsen D, Willems RJ. Core genome multilocus sequence typing scheme for high-resolution typing of Enterococcus faecium. J Clin Microbiol 2015; 53(12): 3788–3797CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas- Chanoine MH, Decré D, Brisse S. Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. Emerg Infect Dis 2014; 20(11): 1812–1820CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Zhou H, Liu W, Qin T, Liu C, Ren H. Defining and evaluating a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of Klebsiella pneumoniae. Front Microbiol 2017; 8: 371PubMedPubMedCentralGoogle Scholar
  31. 31.
    Davis S, Pettengill JB, Luo Y, Payne J, Shpuntoff A, Rand H, Strain E. CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data. PeerJ Comput Sci 2015; 1: e20CrossRefGoogle Scholar
  32. 32.
    Chan CHS, Octavia S, Sintchenko V, Lan R. SnpFilt: a pipeline for reference-free assembly-based identification of SNPs in bacterial genomes. Comput Biol Chem 2016; 65: 178–184CrossRefPubMedGoogle Scholar
  33. 33.
    Katz LS, Griswold T, Williams-Newkirk AJ, Wagner D, Petkau A, Sieffert C, Van Domselaar G, Deng X, Carleton HA. A comparative analysis of the Lyve-SET phylogenomics pipeline for genomic epidemiology of foodborne pathogens. Front Microbiol 2017; 8: 375CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Moura A, Criscuolo A, Pouseele H, Maury MM, Leclercq A, Tarr C, Björkman JT, Dallman T, Reimer A, Enouf V, Larsonneur E, Carleton H, Bracq-Dieye H, Katz LS, Jones L, Touchon M, Tourdjman M, Walker M, Stroika S, Cantinelli T, Chenal- Francisque V, Kucerova Z, Rocha EP, Nadon C, Grant K, Nielsen EM, Pot B, Gerner-Smidt P, Lecuit M, Brisse S. Whole genomebased population biology and epidemiological surveillance of Listeria monocytogenes. Nat Microbiol 2016; 2: 16185CrossRefPubMedGoogle Scholar
  35. 35.
    Angelo KM, Chu A, Anand M, Nguyen TA, Bottichio L, Wise M, Williams I, Seelman S, Bell R, Fatica M, Lance S, Baldwin D, Shannon K, Lee H, Trees E, Strain E, Gieraltowski L; Centers for Disease Control and Prevention (CDC). Outbreak of Salmonella newport infections linked to cucumbers—United States, 2014. MMWR Morb Mortal Wkly Rep 2015; 64(6): 144–147PubMedPubMedCentralGoogle Scholar
  36. 36.
    Bottichio L, Medus C, Sorenson A, Donovan D, Sharma R, Dowell N, Williams I, Wellman A, Jackson A, Tolar B, Griswold T, Basler C. Outbreak of Salmonella oslo infections linked to Persian cucumbers — United States, 2016. MMWR Morb Mortal Wkly Rep 2016; 65(5051): 1430–1433CrossRefPubMedGoogle Scholar
  37. 37.
    Hassan R, Rounds J, Sorenson A, Leos G, Concepción-Acevedo J, Griswold T, Tesfai A, Blessington T, Hardy C, Basler C. Multistate outbreak of Salmonella anatum infections linked to imported hot peppers — United States, May–July 2016. MMWR Morb Mortal Wkly Rep 2017; 66(25): 663–667CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Self JL, Conrad A, Stroika S, Jackson A, Burnworth L, Beal J, Wellman A, Jackson KA, Bidol S, Gerhardt T, Hamel M, Franklin K, Kopko C, Kirsch P, Wise ME, Basler C. Notes from the field: outbreak of listeriosis associated with consumption of packaged salad — United States and Canada, 2015–2016.MMWR Morb Mortal Wkly Rep 2016; 65(33): 879–881CrossRefPubMedGoogle Scholar
  39. 39.
    Dahl V, Sundqvist L, Hedenström I, Löfdahl M, Alm E, Ringberg H, Lindblad M, Wallensten A, Thisted Lambertz S, Jernberg C. A nationwide outbreak of listeriosis associated with cold-cuts, Sweden 2013–2014. Infect Ecol Epidemiol 2017; 7(1): 1324232CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Eyre DW, Golubchik T, Gordon NC, Bowden R, Piazza P, Batty EM, Ip CL, Wilson DJ, Didelot X, O’Connor L, Lay R, Buck D, Kearns AM, Shaw A, Paul J, Wilcox MH, Donnelly PJ, Peto TE, Walker AS, Crook DW. A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open 2012; 2(3): e001124CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Bergholz TM, den Bakker HC, Katz LS, Silk BJ, Jackson KA, Kucerova Z, Joseph LA, Turnsek M, Gladney LM, Halpin JL, Xavier K, Gossack J, Ward TJ, Frace M, Tarr CL. Determination of evolutionary relationships of outbreak-associated Listeria monocytogenes strains of serotypes 1/2a and 1/2b by whole-genome sequencing. Appl Environ Microbiol 2016; 82(3): 928–938CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Ågren EC, Wahlström H, Vesterlund-Carlson C, Lahti E, Melin L, Söderlund R. Comparison of whole genome sequencing typing results and epidemiological contact information from outbreaks of Salmonella dublin in Swedish cattle herds. Infect Ecol Epidemiol 2016; 6(1): 31782CrossRefPubMedGoogle Scholar
  43. 43.
    Bloomfield SJ, Benschop J, Biggs PJ, Marshall JC, Hayman DTS, Carter PE, Midwinter AC, Mather AE, French NP. Genomic analysis of Salmonella enterica serovar Typhimurium DT160 associated with a 14-year outbreak, New Zealand, 1998–2012. Emerg Infect Dis 2017; 23(6): 906–913CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Kuijpers LMF, Le Hello S, Fawal N, Fabre L, Tourdjman M, Dufour M, Sar D, Kham C, Phe T, Vlieghe E, Bouchier C, Jacobs J, Weill FX. Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia, 2013–2015. Microb Genom 2016; 2(11): e000092PubMedPubMedCentralGoogle Scholar
  45. 45.
    Dallman T, Inns T, Jombart T, Ashton P, Loman N, Chatt C, Messelhaeusser U, Rabsch W, Simon S, Nikisins S, Bernard H, le Hello S, Jourdan da-Silva N, Kornschober C, Mossong J, Hawkey P, de Pinna E, Grant K, Cleary P. Phylogenetic structure of European Salmonella enteritidis outbreak correlates with national and international egg distribution network. Microb Genom 2016; 2(8): e000070PubMedPubMedCentralGoogle Scholar
  46. 46.
    Wilson MR, Brown E, Keys C, Strain E, Luo Y, Muruvanda T, Grim C, Jean-Gilles Beaubrun J, Jarvis K, Ewing L, Gopinath G, Hanes D, Allard MW, Musser S. Whole genome DNA sequence analysis of Salmonella subspecies enterica serotype Tennessee obtained from related peanut butter foodborne outbreaks. PLoS One 2016; 11 (6): e0146929CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Chen Y, Luo Y, Carleton H, Timme R, Melka D, Muruvanda T, Wang C, Kastanis G, Katz LS, Turner L, Fritzinger A, Moore T, Stones R, Blankenship J, Salter M, Parish M, Hammack TS, Evans PS, Tarr CL, Allard MW, Strain EA, Brown EW. Whole genome and core genome multilocus sequence typing and single nucleotide polymorphism analyses of Listeria monocytogenes associated with an outbreak linked to cheese, United States, 2013. Appl Environ Microbiol 2017; 83(15): AEM.00633–17Google Scholar
  48. 48.
    van Ingen J, Kohl TA, Kranzer K, Hasse B, Keller PM, Katarzyna Szafranska A, Hillemann D, Chand M, Schreiber PW, Sommerstein R, Berger C, Genoni M, Rüegg C, Troillet N, Widmer AF, Becker SL, Herrmann M, Eckmanns T, Haller S, Höller C, Debast SB, Wolfhagen MJ, Hopman J, Kluytmans J, Langelaar M, Notermans DW, Ten Oever J, van den Barselaar P, Vonk ABA, Vos MC, Ahmed N, Brown T, Crook D, Lamagni T, Phin N, Smith EG, Zambon M, Serr A, Götting T, Ebner W, Thürmer A, Utpatel C, Spröer C, Bunk B, Nübel U, Bloemberg GV, Böttger EC, Niemann S, Wagner D, Sax H. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study. Lancet Infect Dis 2017; 17(10): 1033–1041CrossRefPubMedGoogle Scholar
  49. 49.
    Jackson KA, Stroika S, Katz LS, Beal J, Brandt E, Nadon C, Reimer A, Major B, Conrad A, Tarr C, Jackson BR, Mody RK. Use of whole genome sequencing and patient interviews to link a case of sporadic listeriosis to consumption of prepackaged lettuces. J Food Prot 2016; 79(5): 806–809CrossRefPubMedPubMedCentralGoogle Scholar
  50. 50.
    Jackson BR, Salter M, Tarr C, Conrad A, Harvey E, Steinbock L, Saupe A, Sorenson A, Katz L, Stroika S, Jackson KA, Carleton H, Kucerova Z, Melka D, Strain E, Parish M, Mody RK; Centers for Disease Control and Prevention (CDC). Notes from the field: listeriosis associated with stone fruit—United States, 2014. MMWR Morb Mortal Wkly Rep 2015; 64(10): 282–283PubMedPubMedCentralGoogle Scholar
  51. 51.
    Thompson CK,Wang Q, Bag SK, Franklin N, Shadbolt CT, Howard P, Fearnley EJ, Quinn HE, Sintchenko V, Hope KG. Epidemiology and whole genome sequencing of an ongoing point-source Salmonella agona outbreak associated with sushi consumption in western Sydney, Australia 2015. Epidemiol Infect 2017; 145(10): 2062–2071CrossRefPubMedGoogle Scholar
  52. 52.
    Mellmann A, Bletz S, Böking T, Kipp F, Becker K, Schultes A, Prior K, Harmsen D. Real-time genome sequencing of resistant bacteria provides precision infection control in an institutional setting. J Clin Microbiol 2016; 54(12): 2874–2881CrossRefPubMedPubMedCentralGoogle Scholar
  53. 53.
    Cui Y, Yu C, Yan Y, Li D, Li Y, Jombart T, Weinert LA, Wang Z, Guo Z, Xu L, Zhang Y, Zheng H, Qin N, Xiao X, Wu M, Wang X, Zhou D, Qi Z, Du Z, Wu H, Yang X, Cao H, Wang H, Wang J, Yao S, Rakin A, Li Y, Falush D, Balloux F, Achtman M, Song Y, Wang J, Yang R. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci USA 2013; 110(2): 577–582CrossRefPubMedGoogle Scholar
  54. 54.
    Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E, Achtman M. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet 2010; 42(12): 1140–1143CrossRefPubMedPubMedCentralGoogle Scholar
  55. 55.
    Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, Brunham RC, Tang P. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 2011; 364(8): 730–739CrossRefPubMedGoogle Scholar
  56. 56.
    Yan M, Yang B, Wang Z, Wang S, Zhang X, Zhou Y, Pang B, Diao B, Yang R, Wu S, Klena JD, Kan B. A Large-scale community- based outbreak of paratyphoid fever caused by hospital-derived transmission in Southern China. PLoS Negl Trop Dis 2015; 9(7): e0003859CrossRefPubMedPubMedCentralGoogle Scholar
  57. 57.
    Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA, Edgeworth JD, de Lencastre H, Parkhill J, Peacock SJ, Bentley SD. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010; 327(5964): 469–474CrossRefPubMedPubMedCentralGoogle Scholar
  58. 58.
    Jia H, Du P, Yang H, Zhang Y, Wang J, Zhang W, Han G, Han N, Yao Z, Wang H, Zhang J, Wang Z, Ding Q, Qiang Y, Barbut F, Gao GF, Cao Y, Cheng Y, Chen C. Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012–2014, traced by whole genome sequencing. BMC Genomics 2016; 17(1): 405PubMedGoogle Scholar
  59. 59.
    Snitkin ES, Zelazny AM, Thomas PJ, Stock F; NISC Comparative Sequencing Program Group, Henderson DK, Palmore TN, Segre JA. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 2012; 4(148): 148ra116CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Yu H, Jing H, Chen Z, Zheng H, Zhu X, Wang H, Wang S, Liu L, Zu R, Luo L, Xiang N, Liu H, Liu X, Shu Y, Lee SS, Chuang SK,Wang Y, Xu J, Yang W; Streptococcus suis study groups. Human Streptococcus suis outbreak, Sichuan, China. Emerg Infect Dis 2006; 12(6): 914–920CrossRefPubMedPubMedCentralGoogle Scholar
  61. 61.
    Ye C, Zhu X, Jing H, Du H, Segura M, Zheng H, Kan B, Wang L, Bai X, Zhou Y, Cui Z, Zhang S, Jin D, Sun N, Luo X, Zhang J, Gong Z, Wang X, Wang L, Sun H, Li Z, Sun Q, Liu H, Dong B, Ke C, Yuan H, Wang H, Tian K, Wang Y, Gottschalk M, Xu J. Streptococcus suis sequence type 7 outbreak, Sichuan, China. Emerg Infect Dis 2006; 12(8): 1203–1208CrossRefPubMedPubMedCentralGoogle Scholar
  62. 62.
    Du P, Zheng H, Zhou J, Lan R, Ye C, Jing H, Jin D, Cui Z, Bai X, Liang J, Liu J, Xu L, Zhang W, Chen C, Xu J. Detection of multiple parallel transmission outbreak of Streptococcus suis human infection by use of genome epidemiology, China, 2005. Emerg Infect Dis 2017; 23(2): 204–211CrossRefPubMedPubMedCentralGoogle Scholar
  63. 63.
    Lu X, Li Z, Yan M, Pang B, Xu J, Kan B. Regional transmission of Salmonella paratyphi A, China, 1998–2012. Emerg Infect Dis 2017; 23(5): 833–836CrossRefPubMedPubMedCentralGoogle Scholar
  64. 64.
    Dasgupta A, Banerjee R, Das S, Basak S. Evolutionary perspective on the origin of Haitian cholera outbreak strain. J Biomol Struct Dyn 2012; 30(3): 338–346CrossRefPubMedGoogle Scholar
  65. 65.
    Eppinger M, Pearson T, Koenig SS, Pearson O, Hicks N, Agrawal S, Sanjar F, Galens K, Daugherty S, Crabtree J, Hendriksen RS, Price LB, Upadhyay BP, Shakya G, Fraser CM, Ravel J, Keim PS. Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic. MBio 2014; 5(6): e01721–14CrossRefPubMedPubMedCentralGoogle Scholar
  66. 66.
    Köser CU, Holden MT, Ellington MJ, Cartwright EJ, Brown NM, Ogilvy-Stuart AL, Hsu LY, Chewapreecha C, Croucher NJ, Harris SR, Sanders M, Enright MC, Dougan G, Bentley SD, Parkhill J, Fraser LJ, Betley JR, Schulz-Trieglaff OB, Smith GP, Peacock SJ. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med 2012; 366(24): 2267–2275CrossRefPubMedPubMedCentralGoogle Scholar
  67. 67.
    Chen C, Zhang W, Zheng H, Lan R, Wang H, Du P, Bai X, Ji S, Meng Q, Jin D, Liu K, Jing H, Ye C, Gao GF, Wang L, Gottschalk M, Xu J. Minimum core genome sequence typing of bacterial pathogens: a unified approach for clinical and public health microbiology. J Clin Microbiol 2013; 51(8): 2582–2591CrossRefPubMedPubMedCentralGoogle Scholar
  68. 68.
    Qin T, Zhang W, Liu W, Zhou H, Ren H, Shao Z, Lan R, Xu J. Population structure and minimum core genome typing of Legionella pneumophila. Sci Rep 2016; 6(1): 21356CrossRefPubMedPubMedCentralGoogle Scholar
  69. 69.
    Ashton PM, Nair S, Peters TM, Bale JA, Powell DG, Painset A, Tewolde R, Schaefer U, Jenkins C, Dallman TJ, de Pinna EM, Grant KA; Salmonella Whole Genome Sequencing Implementation Group. Identification of Salmonella for public health surveillance using whole genome sequencing. PeerJ 2016; 4: e1752PubMedGoogle Scholar
  70. 70.
    Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I, Concepcion-Acevedo J, Gilpin B, Smith AM, Man Kam K, Perez E, Trees E, Kubota K, Takkinen J, Nielsen EM, Carleton H; FWDNEXT Expert Panel. PulseNet International: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. Euro Surveill 2017; 22(23): 30544CrossRefPubMedPubMedCentralGoogle Scholar
  71. 71.
    Moran-Gilad J, Sintchenko V, Pedersen SK, Wolfgang WJ, Pettengill J, Strain E, Hendriksen RS; Global Microbial Identifier initiative’s Working Group 4 (GMI-WG4). Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities. BMC Infect Dis 2015; 15 (1): 174CrossRefPubMedPubMedCentralGoogle Scholar
  72. 72.
    Gilmour MW, Graham M, Reimer A, Van Domselaar G. Public health genomics and the new molecular epidemiology of bacterial pathogens. Public Health Genomics 2013; 16(1-2): 25–30CrossRefPubMedGoogle Scholar
  73. 73.
    Aarestrup FM, Brown EW, Detter C, Gerner-Smidt P, Gilmour MW, Harmsen D, Hendriksen RS, Hewson R, Heymann DL, Johansson K, Ijaz K, Keim PS, Koopmans M, Kroneman A, Lo Fo Wong D, Lund O, Palm D, Sawanpanyalert P, Sobel J, Schlundt J. Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response. Emerg Infect Dis 2012; 18(11): e1CrossRefPubMedPubMedCentralGoogle Scholar
  74. 74.
    Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, Persing DH, Swaminathan B. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol 1995; 33(9): 2233–2239PubMedPubMedCentralGoogle Scholar

Copyright information

© Higher Education Press and Springer-Verlag GmbH Germany 2018

Authors and Affiliations

  1. 1.State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
  2. 2.Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesHangzhouChina
  3. 3.Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina

Personalised recommendations