Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014

BMC Microbiology

Volumn 16, Issue 1, 2016, Pages

  Phillips, Anastasia ^a   Sotomayor, Cristina ^a,b   Wang, Qinning ^a,b,c   Holmes, Nadine ^a,b   Furlong, Catriona ^d   Ward, Kate ^d   Howard, Peter ^c   Octavia, Sophie ^e   Lan, Ruiting ^e   Sintchenko, Vitali ^a,b,c  

^a WESTMEAD HOSPITAL   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

^c Centre for Infectious Diseases   (Australia)

^d Health Protection   (Australia)

^e UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

Foodborne outbreaks; Molecular epidemiology; Public health surveillance; Salmonella Typhimurium; Whole genome sequencing

Indexed keywords

ARTICLE; AUSTRALIA; BACTERIAL GENOME; BACTERIUM ISOLATE; CONTROLLED STUDY; GENE SEQUENCE; GENETIC DISTANCE; NONHUMAN; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VARIABLE NUMBER OF TANDEM REPEAT; WHOLE GENOME SEQUENCING; CLUSTER ANALYSIS; DNA SEQUENCE; ENDEMIC DISEASE; ENVIRONMENTAL MICROBIOLOGY; EPIDEMIC; FOODBORNE DISEASES; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR EPIDEMIOLOGY; MOLECULAR TYPING; NEW SOUTH WALES; NUCLEOTIDE SEQUENCE; PATHOGENICITY; PROCEDURES; PUBLIC HEALTH; SALMONELLA FOOD POISONING; SALMONELLA INFECTIONS;

BACTERIAL DNA;

BASE SEQUENCE; CLUSTER ANALYSIS; DISEASE OUTBREAKS; DNA, BACTERIAL; ENDEMIC DISEASES; ENVIRONMENTAL MICROBIOLOGY; FOODBORNE DISEASES; GENOME, BACTERIAL; HUMANS; MINISATELLITE REPEATS; MOLECULAR EPIDEMIOLOGY; MOLECULAR TYPING; NEW SOUTH WALES; POLYMORPHISM, SINGLE NUCLEOTIDE; PUBLIC HEALTH; SALMONELLA FOOD POISONING; SALMONELLA INFECTIONS; SALMONELLA TYPHIMURIUM; SEQUENCE ANALYSIS, DNA;

EID: 84987851234     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/s12866-016-0831-3     Document Type: Article

References (39)

1. Majowicz S, Musto J, Scallan E, Angulo F, Kirk M, O'Brien S, et al. The Global Burden of Nontyphoidal Salmonella Gastroenteritis. Clin Infect Dis. 2010;50(6):882-9.
2. Australian Institute of Health and Welfare. Australia's health 2012. Canberra (AUST): AIHW2012 Contract No.: Cat. no. AUS 156.
3. Greig J, Ravel A. Analysis of foodborne outbreak data reported internationally for source attribution. Int J Food Microbiol. 2009;130:77-87.
4. King N, Lake R, Campbell D. Source Attribution of Nontyphoid Salmonellosis in New Zealand Using Outbreak Surveillance Data. J Food Prot. 2011;74(3):438-45.
5. The OzFoodNet Working Group. OzFoodNet enhanced foodborne disease surveillance, 1 January to 31 March 2013. CDI. 2014;38(1):E70-77.
6. Hedberg C, Greenblatt J, Matyas B, Lemmings J, Sharp D, Skibicki R, et al. Timeliness of Enteric Disease Surveillance in 6 US States. Emerg Infect Dis. 2008;14(2):311-3.
7. Wang Q, Chiew R, Howard P, Gilbert G. Salmonella typing in New South Wales: current methods and application of improved epidemiological tools. NSW Public Health Bull. 2008;19(1-2):24-8.
8. Gilbert G. Using MLVA to type strains of Salmonella Typhimurium in New South Wales. NSW Public Health Bull. 2008;19(1-2):29-31.
9. Sintchenko V, Wang Q, Howard P, Ha C, Kardamanidis K, Musto J et al. Improving resolution of public health surveillance for human Salmonella enterica serovar Typhimurium infection: 3 years of prospective multiple-locus variable-number tandem-repeat analysis (MLVA). BMC Infect Dis. 2012;12(78). doi: 10.1186/1471-2334-12-78.
10. Köser C, Holden M, Ellington M, Cartwright E, Brown N, Ogilvy-Stuart A, et al. Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak. NEJM. 2012;366:2267-75.
11. Le V, Diep B. Selected insights from application of whole-genome sequencing for outbreak investigations. Curr Opin Crit Care. 2013;19(5):432-9.
12. Didelot X, Bowden R, Wilson D, Peto T, Crook D. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet. 2012;13(9):601-12.
13. Gilbert G, Sintchenko V. The use of mycobacterial interspersed repetitive unit typing and whole genome sequencing to inform tuberculosis prevention and control activities. NSW Public Health Bull. 2013;24(1):10-4.
14. Joensen K, Scheutz F, Lund O, Hasman H, Kaas R, Nielsen E, et al. Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli. J Clin Microbiol. 2014;52(5):1501-10.
15. Leekitcharoenphon P, Nielsen E, Kaas R, Lund O, Aarestrup F. Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica. PLoS ONE. 2014;9(2):e87991.
16. Grad Y, Lipsitch M, Feldgarden M, Arachchi H, Cerqueira G, Fitzgerald M, et al. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci U S A. 2011;109(8):3065-70.
17. McDonnell J, Dallman T, Atkin S, Turbitt D, Connor T, Grant K, et al. Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK. Epidemiol Infect. 2013;141:2568-75.
18. Underwood A, Dallman T, Thomson N, Williams M, Harker K, Perry N, et al. Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak. J Clin Microbiol. 2013;51(1):232-7.
19. Lavezzo E, Toppo S, Franchin E, Di Camillo B, Finotello F, Falda M et al. Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak. BMC Infect Dis. 2013;13(554). doi: 10.1186/1471-2334-13-554.
20. Miller R, Price J, Batty E, Didelot X, Wyllie D, Golubchik T, et al. Healthcare-associated outbreak of methicillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone. J Hosp Infect. 2014;86(2):83-9.
21. Hawkey J, Edwards D, Dimovski K, Hiley L, Billman-Jacobe H, Hogg G et al. Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm. BMC Genomics. 2013;14(800). doi: 10.1186/1471-2164-14-800.
22. Larsson J, Torpdahl M, Petersen R, Sørensen G, Lindsted B, Nielsen E. Development of a new nomenclature for Salmonella Typhimurium multilocus variable number of tandem repeats analysis (MLVA). Euro Surveill. 2009;14(15).
23. Wang Q, Kong F, Jelfs P, Gilbert G. Extended phage locus typing of Salmonella enterica serovar Typhimurium, using multiplex PCR-based reverse line blot hybridization. J Med Microbiol. 2008;57:827-38.
24. Lindstedt B, Vardund T, Aas L, Kapperud G. Multiple-locus variable-number tandem-repeats analysis of Salmonella enterica subsp. enterica serovar Typhimurium using PCR multiplexing and multicolor capillary electrophoresis. J Microbiol Methods. 2004;59:163-72.
25. Octavia S, Wang Q, Tanaka M, Kaur S, Sintchenko V, Lan R. Delineating Community Outbreaks of Salmonella enterica Serovar Typhimurium by Use of Whole-Genome Sequencing: Insights into Genomic Variability within an Outbreak. J Clin Microbiol. 2015;53(4):1063-71.
26. Dimovski K, Cao H, Wijburg O, Strugnell R, Mantena R, Whipp M, et al. Analysis of Salmonella enterica Serovar Typhimurium variable-number tandem-repeat data for public health investigation based on measured mutation rates and whole-genome sequence comparisons. J Bacteriol. 2014;196(16):3036-44.
27. WHO Collaborating Centre for Reference and Research on Salmonella. Antigenic Formulae of the Salmonella Serovars 9th ed. Paris: World Health Organisation; 2007.
28. Fu S, Octavia S, Tanaka M, Sintchenko V, Lan R. Defining the core genome of Salmonella enterica serovar Typhimurium for genomic surveillance and epidemiological typing. J Clin Microbiol. 2015;53(8):2530-8.
29. Pang S, Octavia S, Feng L, Liu B, Reeves PR, Lan R, et al. Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types. BMC Genomics. 2013;14:718.
30. Kingsley R, Msefula C, Thomson N, Kariuki S, Holt K, Gordon M, et al. Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res. 2009;19(12):2279-87.
31. Mather A, Reid S, Maskell D, Parkhill J, Fookes M, Harris S, et al. Distinguishable epidemics within different hosts of the multidrug resistant Zoonotic pathogen Salmonella Typhimurium DT104. Science. 2013;341(6153):1514-7.
32. Okoro C, Kingsley A, Connor T, Harris R, Parry C, Al-Mashhadani M, et al. Intra-continental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet. 2012;44(11):1215-21.
33. Inns T, Lane C, Peters T, Dallman T, Chatt C, McFarland N, et al. A multicountry 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 Kingdon, May to September 2014. Euro Surveill. 2015;20(16):21098.
34. Byrne L, Fisher I, Peters T, Mather A, Thomson N, Rosner B, et al. A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012. Euro Surveill. 2014;19(31):6-13.
35. den Bakker H, Allard M, Bopp D, Brown E, Fontana J, Iqbal Z, et al. Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar Enteritidis. Emerg Infect Dis. 2014;20(8):1306-14.
36. Food US, Administration D. Whole Genome Sequencing (WGS) Program. Silver Spring: US Department of Health and Human Services; 2015. http://www.fda.gov/Food/FoodScienceResearch/WholeGenomeSequencingProgramWGS/. Accessed 3 May 2015.
37. Price J, Gordon N, Crook D, Llewelyn M, Paul J. The usefulness of whole genome sequencing in the management of Staphylococcus aureus infections. Clin Microbiol Infect. 2013;19(9):784-9.
38. Sabat A, Budimir A, Nashev D, Sa-Leao R, van Dijl J, Laurent F, et al. Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill. 2013;18(4):20380.
39. Cheung M, Kwan H. Fighting outbreaks with bacterial genomics: case review and workflow proposal. Public Health Genomics. 2012;15(6):341-51.