Top

Published in:

Open Access 01-12-2019 | Public Health | Systematic review

Status and potential of bacterial genomics for public health practice: a scoping review

Authors: Nina Van Goethem, Tine Descamps, Brecht Devleesschauwer, Nancy H. C. Roosens, Nele A. M. Boon, Herman Van Oyen, Annie Robert

Published in: Implementation Science | Issue 1/2019

Abstract

Background

Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist’s perspective.

Methods

In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed.

Results

Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data.

Conclusions

For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist’s perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.

Available only for authorised users

Kan B, Zhou H, Du P, Zhang W, Lu X, Qin T, et al. Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the trace. Front Med. 2018;12(1):23–33.PubMedCrossRef

Tang P, Croxen MA, Hasan MR, Hsiao WWL, Hoang LM. Infection control in the new age of genomic epidemiology. Am J Infect Control. 2017;45:170–9.PubMedCrossRef

Struelens MJ, Brisse S. From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases. Eurosurveillance. 2013;18(4):pii = 20386. Available from: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId = 20386

Gwinn M, MacCannell RD, Khabbaz FR. Integrating advanced molecular technologies into public health. J Clin Microbiol. 2017;55(3):703–14.PubMedPubMedCentralCrossRef

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(4):335–41.PubMedCrossRef

Baker MG, Easther S, Wilson N. A surveillance sector review applied to infectious diseases at a country level. BMC Public Health. 2010. https://doi.org/10.1186/1471-2458-10-332.

Palmer SR. Review article: Epidemiology in search of infectious diseases: methods in outbreak investigation. J Epidemiol Community Health. 1989;43(4):311–4.PubMedPubMedCentralCrossRef

Thacker SB, Berkelman RL. Public health surveillance in the United States. Epidemiol Rev. 1988;10:164–90.PubMedCrossRef

Muellner P, Pleydell E, Pirie R, Baker MG, Campbell D, Carter PE, et al. Molecular-based surveillance of campylobacteriosis in New Zealand - from source attribution to genomic epidemiology. Eurosurveillance. 2013;18(3):pii = 20365. Available from: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId = 20365

10.

European Centre for Disease Prevention and Control. ECDC roadmap for integration of molecular and genomic typing into European-level surveillance and epidemic preparedness – Version 2.1, 2016-19. 2016. Available from: https://ecdc.europa.eu/sites/portal/files/media/en/publications/Publications/molecular-typing-EU-surveillance-epidemic-preparedness-2016-19-roadmap.pdf

11.

Kwong JC, Mccallum N, Sintchenko V, Howden BP. Whole genome sequencing in clinical and public health microbiology. Pathology. 2015;47(3):199–210.PubMedCrossRef

12.

Goldberg B, Sichtig H, Geyer C, Ledeboer N, Weinstock GM. Making the leap from research laboratory to clinic: challenges and opportunities for Next-Generation Sequencing in infectious disease diagnostics. MBio. 2015;6(6). https://doi.org/10.1128/mBio.01888-15.

13.

MacCannell D. Next generation sequencing in clinical and public health microbiology. Clin Microbiol Newsl. 2016;38(21):169–76.CrossRef

14.

Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, García-Cobos S, et al. Application of next generation sequencing in clinical microbiology and infection prevention. J Biotechnol. 2017;243:16–24.PubMedCrossRef

15.

Loman NJ, Pallen MJ. Twenty years of bacterial genome sequencing. Nat Rev Microbiol. 2015;13(12):787–94.PubMedCrossRef

16.

Fournier P-E, Dubourg G, Raoult D. Clinical detection and characterization of bacterial pathogens in the genomics era. Genome Med. 2014. https://doi.org/10.1186/s13073-014-0114-2.

17.

Grant MJ, Booth A. A typology of reviews: an analysis of 14 review types and associated methodologies. Health Info Libr J. 2009;26(2):91–108.PubMedCrossRef

18.

Moher D, Liberati A, Tetzlaff J, Altman DG, Antes G, Atkins D, et al. Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. PLoS Med. 2009;6(7):e1000097.PubMedPubMedCentralCrossRef

19.

Peters MDJ, Godfrey C, McInerney P, Baldini Soares C, Khalil H, Parker D. Chapter 11: Scoping Reviews. Aromataris E, Munn Z (Editors). Joanna Briggs Institute Reviewer's Manual. The Joanna Briggs Institute. 2017. Available from https://reviewersmanual.joannabriggs.org/.

20.

Arksey H, O’Malley L. Scoping studies: towards a methodological framework. Int J Soc Res Methodol Theory Pract. 2005;8(1):19–32.CrossRef

21.

Bekal S, Berry C, Reimer AR, Van Domselaar G, Beaudry G, Fournier E, et al. Usefulness of high-quality core genome single-nucleotide variant analysis for subtyping the highly clonal and the most prevalent Salmonella enterica Serovar heidelberg clone in the context of outbreak investigations. J Clin Microbiol. 2016;54(2):289–95.PubMedPubMedCentralCrossRef

22.

Vincent C, Usongo V, Berry C, Tremblay DM, Moineau S, Yousfi K, et al. Comparison of advanced whole genome sequence-based methods to distinguish strains of Salmonella enterica serovar Heidelberg involved in foodborne outbreaks in Québec. Food Microbiol. 2018;73:99–110.PubMedCrossRef

23.

Chen Y, Luo Y, Pettengill J, Timme R, Melka D, Doyle M, et al. Singleton sequence type 382, an emerging clonal group of Listeria monocytogenes associated with three multistate outbreaks linked to contaminated stone fruit, caramel apples, and leafy green salad. J Clin Microbiol. 2017;55(3):931–41.PubMedPubMedCentralCrossRef

24.

Taylor AJ, Lappi V, Wolfgang WJ, Lapierre P, Palumbo MJ, Medus C, et al. Characterization of foodborne outbreaks of Salmonella enterica serovar enteritidis with whole-genome sequencing single nucleotide polymorphism-based analysis for surveillance and outbreak detection. J Clin Microbiol. 2015;53(10):3334–40.PubMedPubMedCentralCrossRef

25.

Wuyts V, Denayer S, Roosens NHC, Mattheus W, Bertrand S, Marchal K, et al. Whole genome sequence analysis of salmonella enteritidis PT4 outbreaks from a national reference laboratory’s viewpoint. PLoS Curr. 2015. https://doi.org/10.1371/currents.outbreaks.aa5372d90826e6cb01.

26.

Wilson MR, Brown E, Keys C, Strain E, Luo Y, Muruvanda T, et al. Whole genome DNA sequence analysis of Salmonella subspecies enterica serotype Tennessee obtained from related peanut butter foodborne outbreaks. PLoS One. 2016;11(6):e0146929.PubMedPubMedCentralCrossRef

27.

Chen Y, Luo Y, Curry P, Timme R, Melka D, Doyle M, et al. Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States. PLoS One. 2017;12(2):e0171389.PubMedPubMedCentralCrossRef

28.

Dahl V, Sundqvist L, Hedenström I, Löfdahl M, Alm E, Ringberg H, et al. A nationwide outbreak of listeriosis associated with cold-cuts, Sweden 2013-2014. Infect Ecol Epidemiol. 2017;7(1). https://doi.org/10.1080/20008686.2017.1324232.CrossRef

29.

Raphael BH, Baker DJ, Nazarian E, Lapierre P, Bopp D, Kozak-muiznieks NA, et al. Genomic resolution of outbreak-associated Legionella pneumophila Serogroup 1 Isolates from New York State. Appl Environ Microbiol. 2016;82(12):3582–90.PubMedPubMedCentralCrossRef

30.

Yacisin K, Hsieh JL, Weiss D, Ackelsberg J, Lee E, Jones L, et al. Outbreak of non-tuberculous mycobacteria skin or soft tissue infections associated with handling fish - New York City, 2013-2014. Epidemiol Infect. 2017;145(11):2269–79.PubMedCrossRef

31.

Crowe SJ, Green A, Hernandez K, Peralta V, Bottichio L, Defibaugh-Chavez S, 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(4):654–60.PubMedPubMedCentralCrossRef

32.

Simon S, Trost E, Bender J, Fuchs S, Malorny B, Rabsch W, et al. Evaluation of WGS based approaches for investigating a food-borne outbreak caused by Salmonella enterica serovar Derby in Germany. Food Microbiol. 2018;71:46–54.PubMedCrossRef

33.

Hassan R, Tecle S, Adcock B, Kellis M, Weiss J, Saupe A, et al. Multistate outbreak of Salmonella Paratyphi B variant L(+) tartrate(+) and Salmonella Weltevreden infections linked to imported frozen raw tuna: USA, March-July 2015. Epidemiol Infect. 2018;146(11):1461–7.PubMedCrossRef

34.

Inns T, Ashton PM, Herrera-Leon S, Lighthill J, Foulkes S, Jombart T, et al. Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis. Epidemiol Infect. 2017;145(2):289–98.PubMedCrossRef

35.

Kuijpers F, Le Hello S, Fawal N, Fabre L, Tourdjman M, Dufour M, et al. Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia , 2013 – 2015. Microb Genomics. 2016;2(11):e000092.

36.

Hassan R, Rounds J, Sorenson A, Leos G, Concepción-Acevedo J, Griswold T, et al. Multistate outbreak of Salmonella anatum infections linked to imported hot peppers — United States, May–July 2016. Morb Mortal Wkly Rep. 2017;66(25):663–7.CrossRef

37.

Mair-Jenkins J, Borges-Stewart R, Harbour C, Cox-Rogers J, Dallman T, Ashton P, et al. Investigation using whole genome sequencing of a prolonged restaurant outbreak of Salmonella Typhimurium linked to the building drainage system, England, February 2015 to March 2016. Euro Surveill. 2015;22(49):pii = 17-00037. Available from: https://doi.org/10.2807/1560-7917.ES.2017.22.49.17-00037

38.

Angelo KM, Chu A, Anand M, Nguyen T-A, Bottichio L, Wise M, et al. Outbreak of Salmonella newport infections linked to cucumbers - United States, 2014. Morb Mortal Wkly Rep. 2015;64(6):144–7.

39.

Davis RJ, Jensen SO, Van Hal S, Espedido B, Gordon A, Farhat R, et al. Whole genome sequencing in real-time investigation and management of a Pseudomonas aeruginosa outbreak on a neonatal intensive care unit. Infect Control Hosp Epidemiol. 2015;36(9):1058–64.PubMedCrossRef

40.

Lapierre P, Nazarian E, Zhu Y, Wroblewski D, Saylors A, Passaretti T, et al. Legionnaires’ disease outbreak caused by endemic strain of Legionella pneumophila, New York, New York, USA, 2015. Emerg Infect Dis. 2017;23(11):1784–91.PubMedPubMedCentralCrossRef

41.

Quick J, Ashton P, Calus S, Chatt C, Gossain S, Hawker J, et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 2015;16(114):doi:https://doi.org/10.1186/s13059-015-0677-2. Available from: https://doi.org/10.1186/s13059-015-0677-2

42.

Weiss D, Boyd C, Rakeman JL, Greene SK, Fitzhenry R, McProud T, et al. A large community outbreak of Legionnaires’ disease associated with a cooling tower in New York City, 2015. Public Health Rep. 2017;132(2):241–50.PubMedPubMedCentralCrossRef

43.

Gillesberg Lassen S, Ethelberg S, Björkman JT, Jensen T, Sørensen G, Kvistholm Jensen A, et al. Two listeria outbreaks caused by smoked fish consumption—using whole-genome sequencing for outbreak investigations. Clin Microbiol Infect. 2016;22:620–4.PubMedCrossRef

44.

Schjørring S, Gillesberg Lassen S, Jensen T, Moura A, Kjeldgaard JS, Müller L, et al. Cross-border outbreak of listeriosis caused by cold-smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017. Eurosurveillance. 2017;22(50):pii = 17-00762. Available from: https://doi.org/10.2807/1560-7917.ES.2017.22.50.17-00762.

45.

Self JL, Conrad A, Stroika S, Jackson A, Burnworth L, Beal J, et al. Notes from the field: outbreak of listeriosis associated with consumption of packaged salad - United States and Canada, 2015-2016. Morb Mortal Wkly Rep. 2016;65(33):879–81.CrossRef

46.

Dallman T, Inns T, Jombart T, Ashton P, Loman N, Chatt C, et al. Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network. Microb Genomics. 2016;2(8):e000070.CrossRef

47.

Fonteneau L, Jourdan Da Silva N, Fabre L, Ashton P, Torpdahl M, Müller L, et al. Multinational outbreak of travel-related Salmonella chester infections in europe, summers 2014 and 2015. Eurosurveillance. 2017;22(7):pii = 30463. Available from: https://doi.org/10.2807/1560-7917.ES.2017.22.7.3046

48.

Inns T, Lane C, Peters T, Dallman T, Chatt C, McFarland N, et al. A multi-country Salmonella Enteritidis phage type 14b outbreak associated with eggs from a German producer: “near real-time” application of whole genome sequencing and food chain investigations, United Kingdom, may to september 2014. Eurosurveillance. 2015;20(16):pii = 21098. Available from: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId = 21098

49.

Pärn T, Dahl V, Lienemann T, Perevosčikovs J, De Jong B. Multi-country outbreak of Salmonella enteritidis infection linked to the international ice hockey tournament. Epidemiol Infect. 2017;145:2221–30.PubMedCrossRef

50.

Butcher H, Elson R, Chattaway MA, Featherstone CA, Willis C, Jorgensen F, et al. Whole genome sequencing improved case ascertainment in an outbreak of Shiga toxin-producing Escherichia coli O157 associated with raw drinking milk. Epidemiol Infect. 2016;144(13):2812–23.PubMedCrossRef

51.

Moran-Gilad J, Rokney A, Danino D, Ferdous M, Alsana F, Baum M, et al. Real-time genomic investigation underlying the public health response to a Shiga toxin-producing Escherichia coli O26:H11 outbreak in a nursery. Epidemiol Infect. 2017;145(14):2998–3006.PubMedCrossRef

52.

Usein CR, Ciontea AS, Militaru CM, Condei M, Dinu S, Oprea M, et al. Molecular characterisation of human Shiga toxin-producing Escherichia coli O26 strains: results of an outbreak investigation, Romania, february to august 2016. Eurosurveillance. 2017;22(47):pii = 17-00148.

53.

Oakeson KF, Wagner JM, Rohrwasser A, Atkinson-Dunn R. Whole genome sequencing and bioinformatic analysis of two foodborne illness outbreaks: Campylobacter jejuni and Salmonella enterica. J Clin Microbiol. 2018. https://doi.org/10.1128/JCM.00161-18.

54.

Azarian T, Cook RL, Johnson JA, Guzman N, McCarter YS, Gomez N, et al. Whole-genome sequencing for outbreak investigations of Methicillin-Resistant Staphylococcus aureus in the neonatal intensive care unit: time for routine practice? Infect Control Hosp Epidemiol. 2015;36(7):777–85.PubMedPubMedCentralCrossRef

55.

Roe CC, Horn KS, Driebe EM, Bowers J, Terriquez JA, Keim P, et al. Whole genome SNP typing to investigate methicillin-resistant Staphylococcus aureus carriage in a health-care provider as the source of multiple surgical site infections. Hereditas. 2016. https://doi.org/10.1186/s41065-016-0017-x.

56.

Hughes HY, Conlan SP, Lau AF, Dekker JP, Michelin AV, Youn JH, et al. Detection and whole-genome sequencing of carbapenemase-producing Aeromonas hydrophila isolates from routine perirectal surveillance culture. J Clin Microbiol. 2016;54(4):1167–70.PubMedPubMedCentralCrossRef

57.

Durand G, Javerliat F, Bes M, Veyrieras JB, Guigon G, Mugnier N, et al. Routine whole-genome sequencing for outbreak investigations of Staphylococcus aureus in a national reference center. Front Microbiol. 2018. https://doi.org/10.3389/fmicb.2018.00511.

58.

Ashton PM, Peters T, Ameh L, McAleer R, Petrie S, Nair S, et al. Whole genome sequencing for the retrospective investigation of an outbreak of Salmonella Typhimurium DT 8. PLoS Curr. 2015. https://doi.org/10.1371/currents.outbreaks.2c05a47d292f376afc.

59.

Thompson CK, Wang Q, Bag SK, Franklin N, Shadbolt CT, Howard P, et al. 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):2062–71.PubMedCrossRef

60.

Hoffmann M, Luo Y, Monday SR, Gonzalez-Escalona N, Ottesen AR, Muruvanda T, et al. Tracing origins of the Salmonella Bareilly strain causing a food-borne outbreak in the United States. J Infect Dis. 2016;213(4):502–8.PubMedCrossRef

61.

Barkley JS, Gosciminski M, Miller A. Whole-genome sequencing detection of ongoing Listeria contamination at a restaurant, Rhode Island, USA, 2014. Emerg Infect Dis. 2016;22(8):1474–6.PubMedPubMedCentralCrossRef

62.

Chen Y, Luo Y, Carleton H, Timme R, Melka D, Muruvanda T, et al. Whole genome and core genome multilocus sequence typing and single nucleotide polymorphism analyses of Listeria monocytogenes isolates associated with an outbreak linked to cheese, United States, 2013. Appl Environ Microbiol. 2017;83(15):e00633–17.PubMedPubMedCentral

63.

Fernandes AM, Balasegaram S, Willis C, Wimalarathna HML, Maiden MC, McCarthy ND. Partial failure of milk pasteurization as a risk for the transmission of Campylobacter from cattle to humans. Clin Infect Dis. 2015;61(6):903–9.PubMedPubMedCentralCrossRef

64.

Norheim G, Seterelv S, Arnesen T, Mengshoel A, Tonjum T, Ronning JO, et al. Tuberculosis outbreak in an educational institution in Norway. J Clin Microbiol. 2017;55(5):183–98.CrossRef

65.

David S, Afshar B, Mentasti M, Ginevra C, Podglajen I, Harris SR, et al. Seeding and establishment of Legionella pneumophila in hospitals: Implications for genomic investigations of nosocomial legionnaires’ disease. Clin Infect Dis. 2017;64(9):1251–9.PubMedPubMedCentralCrossRef

66.

Rosendahl Madsen AM, Holm A, Jensen TG, Knudsen E, Lundgaard H, Skov MN, et al. Whole-genome sequencing for identification of the source in hospital-acquired Legionnaires’ disease. J Hosp Infect. 2017;96(4):392–5.PubMedCrossRef

67.

Casali N, Broda A, Harris SR, Parkhill J, Brown T, Drobniewski F. Whole genome sequence analysis of a large isoniazid-resistant tuberculosis outbreak in London: a retrospective observational study. PLoS Med. 2016;13(10). https://doi.org/10.1371/journal.pmed.1002137.PubMedPubMedCentralCrossRef

68.

Yang S, Hemarajata P, Hindler J, Li F, Adisetiyo H, Aldrovandi G, et al. Evolution and transmission of carbapenem-resistant Klebsiella pneumoniae expressing the blaOXA-232 gene during an institutional outbreak associated with endoscopic retrograde cholangiopancreatography. Clin Infect Dis. 2017;64(7):894–901.PubMedCrossRef

69.

Ruppé E, Olearo F, Pires D, Baud D, Renzi G, Cherkaoui A, et al. Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing. Clin Microbiol Infect. 2017;23(7):470–5.PubMedCrossRef

70.

McRobb E, Sarovich DS, Price EP, Kaestli M, Mayo M, Keim P, et al. Tracing melioidosis back to the source: using whole-genome sequencing to investigate an outbreak originating from a contaminated domestic water supply. J Clin Microbiol. 2015;53(4):1144–8.PubMedPubMedCentralCrossRef

71.

Haller S, Eller C, Hermes J, Kaase M, Steglich M, Radonic A, et al. What caused the outbreak of ESBL-producing Klebsiella pneumoniae in a neonatal intensive care unit, Germany 2009 to 2012? Reconstructing transmission with epidemiological analysis and whole-genome sequencing. BMJ Open. 2015;5(5):1–9.CrossRef

72.

Parcell BJ, Oravcova K, Pinheiro M, Holden MTG, Phillips G, Turton JF, et al. Pseudomonas aeruginosa intensive care unit outbreak: winnowing of transmissions with molecular and genomic typing. J Hosp Infect. 2018;98(3):282–8.PubMedPubMedCentralCrossRef

73.

Stucki D, Ballif M, Bodmer T, Coscolla M, Maurer AM, Droz S, et al. Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing. J Infect Dis. 2015;211(8):1306–16.PubMedCrossRef

74.

Gordon NC, Pichon B, Golubchik T, Wilson DJ, Paul J, Blanc DS, et al. Whole-genome sequencing reveals the contribution of long-term carriers in Staphylococcus aureus outbreak investigation. J Clin Microbiol. 2017;55(7):2188–97.PubMedPubMedCentralCrossRef

75.

Kwong JC, Mercoulia K, Tomita T, Easton M, Li HY, Bulach DM, et al. Prospective whole-genome sequencing enhances national surveillance of Listeria monocytogenes. J Clin Microbiol. 2016;54(2):333–42.PubMedPubMedCentralCrossRef

76.

Moura A, Tourdjman M, Leclercq A, Hamelin E, Laurent E, Fredriksen N, et al. Real-time whole-genome sequencing for surveillance of Listeria monocytogenes. France. Emerg Infect Dis. 2017;23(9):1462–70.PubMedCrossRef

77.

Jackson BR, Tarr C, Strain E, Jackson KA, Conrad A, Carleton H, et al. Implementation of nationwide real-time whole-genome sequencing to enhance listeriosis outbreak detection and investigation. Clin Infect Dis. 2016;63(3):380–6.PubMedPubMedCentralCrossRef

78.

Dallman TJ, Byrne L, Ashton PM, Cowley LA, Perry NT, Adak G, et al. Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157. Clin Infect Dis. 2015;61(3):305–12.PubMedPubMedCentralCrossRef

79.

Holmes A, Allison L, Ward M, Dallman TJ, Clark R, Fawkes A, et al. Utility of whole-genome sequencing of Escherichia coli O157 for outbreak detection and epidemiological surveillance. J Clin Microbiol. 2015;53(11):3565–73.PubMedPubMedCentralCrossRef

80.

Chattaway MA, Dallman TJ, Gentle A, Wright MJ, Long SE, Ashton PM, et al. Whole genome sequencing for public health surveillance of Shiga Toxin-producing Escherichia coli other than serogroup o157. Front Microbiol. 2016. https://doi.org/10.3389/fmicb.2016.00258.

81.

Ford L, Carter GP, Wang Q, Seemann T, Sintchenko V, Glass K, et al. Incorporating whole-genome sequencing into public health surveillance: lessons from prospective sequencing of Salmonella Typhimurium in Australia. Foodborne Pathog Dis. 2018;15(3). https://doi.org/10.1089/fpd.2017.2352.PubMedCrossRef

82.

Chattaway MA, Greig DR, Gentle A, Hartman HB, Dallman TJ, Jenkins C. Whole-genome sequencing for national surveillance of Shigella flexneri. Front Microbiol. 2017;8(1700). https://doi.org/10.3389/fmicb.2017.01700.

83.

Gymoese P, Sørensen G, Litrup E, Olsen JE, Nielsen EM, Torpdahl M. Investigation of outbreaks of Salmonella enterica serovar typhimurium and its monophasic variants using whole-genome sequencing Denmark. Emerg Infect Dis. 2017;23(10):1631–9.PubMedPubMedCentralCrossRef

84.

Dallman TJ, Chattaway MA, Mook P, Godbole G, Crook PD, Jenkins C. Use of whole genome sequencing for the public health surveillance of Shigella sonnei in England and Wales, 2015. J Med Microbiol. 2016;65(8):882–4.PubMedCrossRef

85.

Aanensen DM, Feil EJ, Holden MTG, Dordel J, Yeats CA, Fedosejev A, et al. Whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive Staphylococcus aureus in Europe. MBio. 2016;7(3):e00444–16.PubMedPubMedCentralCrossRef

86.

Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Lund O, et al. Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania. Eur J Clin Microbiol Infect Dis. 2018;37(10):1901–14.PubMedCrossRef

87.

Jajou R, De Neeling A, Van Hunen R, De Vries G, Schimmel H, Mulder A, 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(5):e0197556.PubMedPubMedCentralCrossRef

88.

Brown TS, Narechania A, Walker JR, Planet PJ, Bifani PJ, Kolokotronis SO, et al. Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999–2009. BMC Genomics. 2016. https://doi.org/10.1186/s12864-016-3298-6.

89.

Stucki D, Ballif M, Egger M, Furrer H, Altpeter E, Battegay M, et al. Standard genotyping overestimates transmission of Mycobacterium tuberculosis among immigrants in a low incidence country. J Clin Microbiol. 2016;54(7):1862–70.PubMedPubMedCentralCrossRef

90.

Gurjav U, Outhred AC, Jelfs P, McCallum N, Wang Q, Hill-Cawthorne GA, et al. Whole genome sequencing demonstrates limited transmission within identified Mycobacterium tuberculosis clusters in New South Wales. Australia. PLoS One. 2016;11(10):e0163612.PubMedCrossRef

91.

Dyson ZA, Thanh DP, Bodhidatta L, Mason CJ, Srijan A, Rabaa MA, et al. Whole genome sequence analysis of Salmonella Typhi isolated in Thailand before and after the introduction of a national immunization program. PLoS Negl Trop Dis. 2017;11(1):e0005274.PubMedPubMedCentralCrossRef

92.

Hill DMC, Lucidarme J, Gray SJ, Newbold LS, Ure R, Brehony C, et al. Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study. Lancet Infect Dis. 2015;15(12):1420–8.PubMedPubMedCentralCrossRef

93.

Moore CE, Giess A, Soeng S, Sar P, Kumar V, Nhoung P, et al. Characterisation of invasive Streptococcus pneumoniae isolated from Cambodian children between 2007-2012. PLoS One. 2016;11(7):e0159358.PubMedPubMedCentralCrossRef

94.

Duvvuri VR, Deng X, Teatero S, Memari N, Athey T, Fittipaldi N, et al. Population structure and drug resistance patterns of emerging non-PCV-13 Streptococcus pneumoniae serotypes 22F, 15A, and 8 isolated from adults in Ontario. Canada. Infect Genet Evol. 2016;42:1–8.PubMedCrossRef

95.

Sealey KL, Harris SR, Fry NK, Hurst LD, Gorringe AR, Parkhill J, et al. Genomic analysis of isolates from the United Kingdom 2012 pertussis outbreak reveals that vaccine antigen genes are unusually fast evolving. J Infect Dis. 2015;212(2):294–301.PubMedCrossRef

96.

Xu Y, Liu B, Gröndahl-Yli-Hannuksila K, Tan Y, Feng L, Kallonen T, et al. Whole-genome sequencing reveals the effect of vaccination on the evolution of Bordetella pertussis. Sci Rep. 2015;5(12888). Available from: https://doi.org/10.1038/srep12888.

97.

Mowlaboccus S, Perkins TT, Smith H, Sloots T, Tozer S, Prempeh LJ, et al. Temporal changes in BEXSERO® antigen sequence type associated with genetic lineages of Neisseria meningitidis over a 15-year period in Western Australia. PLoS One. 2016;11(6):e0158315.PubMedPubMedCentralCrossRef

98.

Rodrigues CMC, Lucidarme J, Borrow R, Smith A, Cameron JC, Moxon ER, et al. Genomic surveillance of 4CMenB vaccine antigenic variants among disease-causing Neisseria meningitidis isolates, United Kingdom, 2010-2016. Emerg Infect Dis. 2018;24(4):673–82.PubMedPubMedCentralCrossRef

99.

Sidikou F, Zaneidou M, Alkassoum I, Schwartz S, Issaka B, Obama R, et al. Emergence of epidemic Neisseria meningitidis serogroup C in Niger, 2015: an analysis of national surveillance data. Lancet Infect Dis. 2016;16(11):1288–94.PubMedPubMedCentralCrossRef

100.

Chochua S, Metcalf BJ, Li Z, Walker H, Tran T, McGee L, et al. Invasive serotype 35B pneumococci including an expanding serotype switch lineage, United States, 2015–2016. Emerg Infect Dis. 2017;23(6):922–30.PubMedPubMedCentralCrossRef

101.

Mowlaboccus S, Mullally CA, Richmond PC, Howden BP, Stevens K, Speers DJ, et al. Differences in the population structure of Neisseria meningitidis in two Australian states: Victoria and Western Australia. PLoS One. 2017;12(10):e0186839.PubMedPubMedCentralCrossRef

102.

Ellington MJ, Reuter S, Harris SR, Holden MTG, Cartwright EJ, Greaves D, et al. Emergent and evolving antimicrobial resistance cassettes in community-associated fusidic acid and meticillin-resistant Staphylococcus aureus. Int J Antimicrob Agents. 2015;45(5):477–84.PubMedPubMedCentralCrossRef

103.

Hughes J, Stabler R, Gaunt M, Karadag T, Desai N, Betley J, et al. Clonal variation in high- and low-level phenotypic and genotypic mupirocin resistance of MRSA isolates in south-east London. J Antimicrob Chemother. 2015. https://doi.org/10.1093/jac/dkv248.

104.

Alam MT, Read TD, Petit RA, Boyle-Vavra S, Miller LG, Eells SJ, et al. Transmission and microevolution of USA300 MRSA in U.S. households: evidence from whole-genome sequencing. MBio. 2015;6(2):e00054–15.PubMedPubMedCentralCrossRef

105.

Chow A, Lim VW, Khan A, Pettigrew K, Lye DCB, Kanagasabai K, et al. MRSA transmission dynamics among interconnected acute, intermediate-term, and long-term healthcare facilities in Singapore. Clin Infect Dis. 2017;64(Suppl 1):76–81.CrossRef

106.

Harrison EM, Ludden C, Brodrick HJ, Blane B, Brennan G, Morris D, et al. Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks. Genome Med. 2016. https://doi.org/10.1186/s13073-016-0353-5.

107.

Bowen AC, Harris T, Holt DC, Giffard PM, Carapetis JR, Campbell PT, et al. Whole genome sequencing reveals extensive community-level transmission of group A Streptococcus in remote communities. Epidemiol Infect. 2016;144(9):1991–8.PubMedCrossRef

108.

Widmer AF, Frei R, Erb S, Stranden A, Kuijper EJ, Knetsch CW, et al. Transmissibility of Clostridium difficile without contact isolation: results from a prospective observational study with 451 patients. Clin Infect Dis. 2017. https://doi.org/10.1093/cid/ciw758..

109.

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:e05166.PubMedCentralCrossRef

110.

Bosch T, Witteveen S, Haenen A, Landman F, Schouls LM. Next generation sequencing confirms presumed nosocomial transmission of LA-MRSA in the Netherlands. Appl Environ Microbiol. 2016;82(14):4081–9.PubMedPubMedCentralCrossRef

111.

Earls MR, Kinnevey PM, Brennan GI, Lazaris A, Skally M, O’Connell B, et al. The recent emergence in hospitals of multidrug-resistant community-associated sequence type 1 and spa type t127 methicillin-resistant Staphylococcus aureus investigated by whole-genome sequencing: Implications for screening. PLoS One. 2017;12(4):e0175542.PubMedPubMedCentralCrossRef

112.

Price JR, Cole K, Bexley A, Kostiou V, Eyre DW, Golubchik T, et al. Transmission of Staphylococcus aureus between health-care workers, the environment, and patients in an intensive care unit: a longitudinal cohort study based on whole-genome sequencing. Lancet Infect Dis. 2017;17(2):207–14.PubMedPubMedCentralCrossRef

113.

Arnott A, Wang Q, Bachmann N, Sadsad R, Biswas C, Sotomayor C, et al. Multidrug-resistant Salmonella enterica 4,[5],12:i:- Sequence Type 34, New South Wales, Australia, 2016–2017. Emerg Infect Dis. 2018;24(4):751–3.PubMedPubMedCentralCrossRef

114.

Moradigaravand D, Martin V, Peacock SJ, Parkhill J. Evolution and epidemiology of multidrug-resistant Klebsiella pneumoniae in the United Kingdom and Ireland. MBio. 2017;8(1):e01976–16.PubMedPubMedCentralCrossRef

115.

Hargreaves ML, Shaw KM, Dobbins G, Snippes Vagnone PM, Harper JE, Boxrud D, et al. Clonal Dissemination of Enterobacter cloacae Harboring blaKPC-3 in the Upper Midwestern United States. Antimicrob Agents Chemother. 2015;59(12):7723–34.PubMedPubMedCentralCrossRef

116.

Steglich M, Nitsche A, Von Müller L, Herrmann M, Kohl TA, Niemann S, et al. Tracing the spread of clostridium difficile ribotype 027 in Germany based on bacterial genome sequences. PLoS One. 2015;10(10):e0139811.PubMedPubMedCentralCrossRef

117.

Pecora ND, Li N, Allard M, Li C, Albano E, Delaney M, et al. Genomically informed surveillance for carbapenem-resistant Enterobacteriaceae in a health care system. MBio. 2015;6(4):e01030–15.PubMedPubMedCentralCrossRef

118.

Peirano G, Matsumura Y, Adams MD, Bradford P, Motyl M, Chen L, et al. Genomic epidemiology of global carbapenemase-producing Enterobacter spp., 2008–2014. Emerg Infect Dis 2018;24(6):1010–1019.PubMedPubMedCentralCrossRef

119.

Schaufler K, Semmler T, Wieler LH, Wöhrmann M, Baddam R, Ahmed N, et al. Clonal spread and interspecies transmission of clinically relevant ESBL-producing Escherichia coli of ST410 - another successful pandemic clone? FEMS. Microbiol Ecol. 2016;92(1). https://doi.org/10.1093/femsec/fiv155.PubMedCrossRef

120.

Sandoval-Azuara SE, Muñiz-Salazar R, Perea-Jacobo R, Robbe-Austerman S, Perera-Ortiz A, López-Valencia G, et al. Whole genome sequencing of Mycobacterium bovis to obtain molecular fingerprints in human and cattle isolates from Baja California. Mexico. Int J Infect Dis. 2017;63:48–56.PubMedCrossRef

121.

Edirmanasinghe R, Finley R, Parmley EJ, Avery BP, Carson C, Bekal S, et al. A whole-genome sequencing approach to study cefoxitin-resistant Salmonella enterica serovar Heidelberg isolates from various sources. Antimicrob Agents Chemother. 2017;61(4):e01919–6.PubMedPubMedCentralCrossRef

122.

Falgenhauer L, Imirzalioglu C, Ghosh H, Gwozdzinski K, Schmiedel J, Gentil K, et al. Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany. Int J Antimicrob Agents. 2016;47(6):457–65.PubMedCrossRef

123.

Fischer J, Hille K, Ruddat I, Mellmann A, Köck R, Kreienbrock L. Simultaneous occurrence of MRSA and ESBL-producing Enterobacteriaceae on pig farms and in nasal and stool samples from farmers. Vet Microbiol. 2017;200:107–13.PubMedCrossRef

124.

Grøntvedt CA, Elstrøm P, Stegger M, Skov RL, Andersen PS, Larssen KW, et al. Methicillin-resistant Staphylococcus aureus CC398 in humans and pigs in Norway: a “One Health” perspective on introduction and transmission. Clin Infect Dis. 2016;63(11):1431–8.PubMedPubMedCentralCrossRef

125.

Sparham SJ, Kwong JC, Valcanis M, Easton M, Trott DJ, Seemann T, et al. Emergence of multidrug resistance in locally-acquired human infections with Salmonella Typhimurium in Australia owing to a new clade harbouring blaCTX-M-9. Int J Antimicrob Agents. 2017;50(1):101–5.PubMedCrossRef

126.

Tate H, Folster JP, Hsu C-H, Chen J, Hoffmann M, Li C, et al. Comparative analysis of extended-spectrum-B-lactamase CTX-M-65-producing Salmonella enterica serovar Infantis isolates from humans, food animals, and retail chickens in the United States. Antimicrob Agents Chemother. 2017;61(7). https://doi.org/10.1128/AAC.00488-17.

127.

Chand M, Lamagni T, Kranzer K, Hedge J, Moore G, Parks S, et al. Insidious risk of severe Mycobacterium chimaera infection in cardiac surgery patients. Clin Infect Dis. 2017;64(3):335–42.PubMedCrossRef

128.

Afset JE, Larssen KW, Bergh K, Lärkeryd A, Sjödin A, Johansson A, et al. Phylogeographical pattern of Francisella tularensis in a nationwide outbreak of tularaemia in Norway, 2011. Eurosurveillance. 2015;20(19):pii = 21125. Available from: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId = 21125PubMedCrossRef

129.

Burall LS, Grim CJ, Datta AR. A clade of Listeria monocytogenes serotype 4b variant strains linked to recent listeriosis outbreaks associated with produce from a defined geographic region in the US. PLoS One. 2017;12(5):e0176912.PubMedPubMedCentralCrossRef

130.

Dangel A, Berger A, Konrad R, Bischoff H, Sing A. Geographically diverse clusters of nontoxigenic Corynebacterium diphtheriae infection, Germany, 2016–2017. Emerg Infect Dis. 2018;24(7):1239–45.PubMedPubMedCentralCrossRef

131.

Deng X, Peirano G, Schillberg E, Mazzulli T, Gray-Owen SD, Wylie JL, et al. Whole-genome sequencing reveals the origin and rapid evolution of an emerging outbreak strain of Streptococcus pneumoniae 12F. Clin Infect Dis. 2016;62(9):1126–32.PubMedCrossRef

132.

Layer F, Sanchini A, Strommenger B, Cuny C, Breier AC, Proquitté H, et al. Molecular typing of toxic shock syndrome toxin-1- and Enterotoxin A-producing methicillin-sensitive Staphylococcus aureus isolates from an outbreak in a neonatal intensive care unit. Int J Med Microbiol. 2015;305(7):790–8.PubMedCrossRef

133.

Rimoldi SG, Gentile B, Pagani C, Di Gregorio A, Anselmo A, Palozzi AM, et al. Whole genome sequencing for the molecular characterization of carbapenem-resistant Klebsiella pneumoniae strains isolated at the Italian ASST Fatebenefratelli Sacco Hospital, 2012-2014. BMC Infect Dis. 2017. https://doi.org/10.1186/s12879-017-2760-7.

134.

Ferdous M, Friedrich AW, Grundmann H, de Boer RF, Croughs PD, Islam MA, et al. Molecular characterization and phylogeny of Shiga toxin–producing Escherichia coli isolates obtained from two Dutch regions using whole genome sequencing. Clin Microbiol Infect. 2016;22(7):642.e1–9.CrossRef

135.

Toleman MS, Reuter S, Coll F, Harrison EM, Blane B, Brown NM, et al. Systematic surveillance detects multiple silent introductions and household transmission of methicillin-resistant Staphylococcus aureus USA300 in the East of England. J Infect Dis. 2016;214(3):447–53.PubMedPubMedCentralCrossRef

136.

Waldram A, Dolan G, Ashton PM, Jenkins C, Dallman TJ. Epidemiological analysis of Salmonella clusters identified by whole genome sequencing, England and Wales 2014. Food Microbiol. 2018;71:39–45.PubMedCrossRef

137.

Demczuk W, Lynch T, Martin I, Van Domselaar G, Graham M, Bharat A, et al. Whole-genome phylogenomic heterogeneity of Neisseria gonorrhoeae isolates with decreased cephalosporin susceptibility collected in Canada between 1989 and 2013. J Clin Microbiol. 2015;53(1):191–200.PubMedCrossRef

138.

Gray MD, Lacher DW, Leonard SR, Abbott J, Zhao S, Lampel KA, et al. Prevalence of Stx-producing Shigella species isolated from French travelers returning from the Caribbean: an emerging pathogen with international implications. Clin Microbiol Infect. 2015;21(8):765–9.PubMedPubMedCentralCrossRef

139.

Pham Thanh D, Thompson CN, Rabaa MA, Sona S, Sopheary S, Kumar V, et al. The molecular and spatial epidemiology of typhoid fever in rural Cambodia. PLoS Negl Trop Dis. 2016;10(6):e0004785.PubMedPubMedCentralCrossRef

140.

Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Lund O, et al. Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in Kilimanjaro, Tanzania. Eur J Clin Microbiol Infect Dis. 2018;37(5):897–906.PubMedPubMedCentralCrossRef

141.

Chalker V, Jironkin A, Coelho J, Al-Shahib A, Platt S, Kapatai G, et al. Genome analysis following a national increase in Scarlet Fever in England 2014. BMC Genomics. 2017. https://doi.org/10.1186/s12864-017-3603-z.

142.

Brodrick HJ, Raven KE, Harrison EM, Blane B, Reuter S, Török ME, et al. Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network. Genome Med. 2016. https://doi.org/10.1186/s13073-015-0259-7.

143.

Stoesser N, Xayaheuang S, Vongsouvath M, Phommasone K, Elliott I, Del Ojo EC, et al. Colonization with Enterobacteriaceae producing ESBLs in children attending pre-school childcare facilities in the Lao People’s Democratic Republic. J Antimicrob Chemother. 2015. https://doi.org/10.1093/jac/dkv021.

144.

Coscolla M, Barry PM, Oeltmann JE, Koshinsky H, Shaw T, Cilnis M, et al. Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread. J Infect Dis. 2015;212(2):302–10.PubMedPubMedCentralCrossRef

145.

Lee RS, Radomski N, Proulx J, Manry J, McIntosh F, Desjardins F, et al. Re-emergence and amplification of tuberculosis in the Canadian Arctic. J Infect Dis. 2015;211(12):1905–14.PubMedCrossRef

146.

Halbedel S, Prager R, Fuchs S, Trost E, Werner G, Flieger A. Whole-genome sequencing of recent Listeria monocytogenes isolates from Germany reveals population structure and disease clusters. J Clin Microbiol. 2018, 56;(6). https://doi.org/10.1128/JCM.00119-18.

147.

Kvistholm Jensen A, Møller Nielsen E, Torgny Björkman J, Jensen T, Müller L, Persson S, et al. Whole-genome sequencing used to investigate a nationwide outbreak of listeriosis caused by ready-to-eat delicatessen meat, Denmark, 2014. Clin Infect Dis. 2016;63(1):64–70.PubMedCrossRef

148.

Grant K, Jenkins C, Arnold C, Green J, Zambon M. Implementing pathogen genomics: a case study. 2018. Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/731057/implementing_pathogen_genomics_a_case_study.pdf

149.

Bartels MD, Larner-Svensson H, Meiniche H, Kristoffersen K, Schønning K, Nielsen JB, et al. Monitoring meticillin resistant Staphylococcus aureus and its spread in Copenhagen, Denmark, 2013, through routine whole genome sequencing. Eurosurveillance. 2015;20(17):pii = 21112. Available from: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId = 21112PubMedCrossRef

150.

Pinholt M, Larner-Svensson H, Littauer P, Moser CE, Pedersen M, Lemming LE, et al. Multiple hospital outbreaks of vanA Enterococcus faecium in Denmark, 2012-13, investigated by WGS. MLST and PFGE. J Antimicrob Chemother. 2015;70(9):2474–82.PubMedCrossRef

151.

European Centre for Disease Prevention and Control. Monitoring the use of whole-genome sequencing in infectious disease surveillance in Europe 2015–2017. 2017. Available from: https://ecdc.europa.eu/sites/portal/files/documents/monitoring-WGS-infectious-disease-surveillance-in-Europe-2015-2017-updated-Dec-2018.pdf.

152.

Mellmann A, Bletz S, Böking T, Kipp F, Becker K, Schultes A, et al. Real-time genome sequencing of resistant bacteria provides precision infection control in an institutional setting. J Clin Microbiol. 2016;54(12):2874–81.PubMedPubMedCentralCrossRef

153.

Mulhall RM, Brehony C, O’Connor L, Meyler K, Jolley KA, Bray J, et al. Resolution of a protracted Serogroup B meningococcal outbreak with whole-genome sequencing shows interspecies genetic transfer. J Clin Microbiol. 2016;54(12):2891–9.PubMedPubMedCentralCrossRef

154.

Schlebusch S, Price GR, Gallagher RL, Horton-Szar V, Elbourne LDH, Griffin P, et al. MALDI-TOF MS meets WGS in a VRE outbreak investigation. Eur J Clin Microbiol Infect Dis. 2017;36(3):495–9.PubMedCrossRef

155.

Mossong J, Decruyenaere F, Moris G, Ragimbeau C, Olinger CM, Johler S, et al. Investigation of a staphylococcal food poisoning outbreak combining case-control, traditional typing and whole genome sequencing methods, Luxembourg, June 2014. Eurosurveillance. 2015;20(45):pii = 30059. Available from: https://doi.org/10.2807/1560-7917.ES.2015.20.45.30059

156.

Weterings V, Zhou K, Rossen JW, van Stenis D, Thewessen E, Kluytmans J, et al. An outbreak of colistin-resistant Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae in the Netherlands (July to December 2013), with inter-institutional spread. Eur J Clin Microbiol Infect Dis. 2015;34(8):1647–55.PubMedCrossRef

157.

Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet. 2012;13(9):601–12.PubMedPubMedCentralCrossRef

158.

Rowell S, King C, Jenkins C, Dallman TJ, Decraene V, Lamden K, et al. An outbreak of Shiga toxin-producing Escherichia coli serogroup O157 linked to a lamb-feeding event. Epidemiol Infect. 2016;144(12):2494–500.PubMedCrossRef

159.

Pightling AW, Pettengill JB, Luo Y, Baugher JD, Rand H, Strain E. Interpreting whole-genome sequence analyses of foodborne bacteria for regulatory applications and outbreak investigations. Front Microbiol. 2018. https://doi.org/10.3389/fmicb.2018.01482.

160.

Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol. 2014. https://doi.org/10.1186/s13059-014-0538-4.

161.

Fitzpatrick MA, Ozer EA, Hauser AR. Utility of whole-genome sequencing in characterizing Acinetobacter epidemiology and analyzing hospital outbreaks. J Clin Microbiol. 2016;54(3):593–612.PubMedPubMedCentralCrossRef

162.

Tyler AD, Randell E, Baikie M, Antonation K, Janella D, Christianson S, et al. Application of whole genome sequence analysis to the study of Mycobacterium tuberculosis in Nunavut Canada. PLoS One. 2017;12(10):e0185656.PubMedPubMedCentralCrossRef

163.

Muellner P, Stark KDC, Dufour S, Zadoks RN. ‘Next- Generation’ surveillance: an epidemiologists’ perspective on the use of molecular information in food safety and animal health decision-making. Zoonoses Public Health. 2016;63(5):351–7.PubMedCrossRef

164.

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;8:74–9.CrossRef

165.

Hill AA, Crotta M, Wall B, Good L, O’Brien SJ, Guitian J. Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata. R Soc Open Sci. 2017;4(3):160721.PubMedPubMedCentralCrossRef

166.

Tagini F, Aubert B, Troillet N, Pillonel T, Praz G, Crisinel PA, et al. Importance of whole genome sequencing for the assessment of outbreaks in diagnostic laboratories: analysis of a case series of invasive Streptococcus pyogenes infections. Eur J Clin Microbiol Infect Dis. 2017;36(7):1173–80.PubMedPubMedCentralCrossRef

167.

Neuert S, Nair S, Day MR, Doumith M, Ashton PM, Mellor KC, et al. Prediction of phenotypic antimicrobial resistance profiles from whole genome sequences of non-typhoidal Salmonella enterica. Front Microbiol. 2018. https://doi.org/10.3389/fmicb.2018.00592.

168.

Salathé M. Digital epidemiology: what is it, and where is it going? Life Sci Soc Policy. 2018;14(1). https://doi.org/10.1186/s40504-017-0065-7.

169.

Johnson I, Hansen A, Bi P. The challenges of implementing an integrated One Health surveillance system in Australia. Zoonoses Public Health. 2018;65:e229–36.PubMedCrossRef

170.

Rantsiou K, Kathariou S, Winkler A, Skandamis P, Saint-Cyr MJ, Rouzeau-Szynalski K, et al. Next generation microbiological risk assessment: opportunities of whole genome sequencing (WGS) for foodborne pathogen surveillance, source tracking and risk assessment. Int J Food Microbiol. 2017; Available from:. https://doi.org/10.1016/j.ijfoodmicro.2017.11.007.PubMedCrossRef

171.

Kao RR, Haydon DT, Lycett SJ, Murcia PR. Supersize me: how whole-genome sequencing and big data are transforming epidemiology. Trends Microbiol. 2014;22(5):282–91.PubMedCrossRefPubMedCentral

172.

Luheshi L, Raza S, Moorthie S, Hall A, Blackburn L, Rands C, et al. Pathogen genomics into practice. 2015. Available from: http://www.phgfoundation.org/documents/report_pathogen_genomics_practice.pdf.

Title: Status and potential of bacterial genomics for public health practice: a scoping review
Authors: Nina Van Goethem
Tine Descamps
Brecht Devleesschauwer
Nancy H. C. Roosens
Nele A. M. Boon
Herman Van Oyen
Annie Robert
Publication date: 01-12-2019
Publisher: BioMed Central
Keyword: Public Health
Published in: Implementation Science / Issue 1/2019
Electronic ISSN: 1748-5908
DOI: https://doi.org/10.1186/s13012-019-0930-2

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Status and potential of bacterial genomics for public health practice: a scoping review

Abstract

Background

Methods

Results

Conclusions

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Abstract

Background

Methods

Results

Conclusions

Please log in to get access to this content

Other articles of this Issue 1/2019

Spread tools: a systematic review of components, uptake, and effectiveness of quality improvement toolkits

Stroke Ready: a multi-level program that combines implementation science and community-based participatory research approaches to increase acute stroke treatment: protocol for a stepped wedge trial

Sustainment, Sustainability, and Spread Study (SSaSSy): protocol for a study of factors that contribute to the sustainment, sustainability, and spread of practice changes introduced through an evidence-based quality-improvement intervention in Canadian nursing homes

Training in Implementation Practice Leadership (TRIPLE): evaluation of a novel practice change strategy in behavioral health organizations

Implementation of change in health care in Sweden: a qualitative study of professionals’ change responses

Evaluation of a targeted, theory-informed implementation intervention designed to increase uptake of emergency management recommendations regarding adult patients with mild traumatic brain injury: results of the NET cluster randomised trial