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Volume 23, Number 6—June 2017
Research

Genomic Analysis of Salmonella enterica Serovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998–2012

Samuel J. BloomfieldComments to Author , Jackie Benschop, Patrick J. Biggs1, Jonathan C. Marshall1, David T.S. Hayman1, Philip E. Carter1, Anne C. Midwinter, Alison E. Mather, and Nigel P. French
Author affiliations: Athor affiliations: Massey University, Palmerston North, New Zealand (S.J. Bloomfield, J. Benschop, P.J. Biggs, J.C. Marshall, D.T.S. Hayman, A.C. Midwinter, N.P. French); Institute of Environmental Science and Research, Wellington, New Zealand (P.E. Carter); University of Cambridge, Cambridge, UK (A.E. Mather)

Main Article

Figure 1

Number of Salmonella enterica serovar Typhimurium DT160 cases and isolates reported during an outbreak in New Zealand, 1998–2012. A) Cases in humans (8,9). B) Isolates from nonhuman sources (8,10).

Figure 1. Number of Salmonella enterica serovar Typhimurium DT160 cases and isolates reported during an outbreak in New Zealand, 1998–2012. A) Cases in humans (8,9). B) Isolates from nonhuman sources (8,10).

Main Article

References
  1. Majowicz  SE, Musto  J, Scallan  E, Angulo  FJ, Kirk  M, O’Brien  SJ, et al.; International Collaboration on Enteric Disease ‘Burden of Illness’ Studies. The global burden of nontyphoidal Salmonella gastroenteritis. Clin Infect Dis. 2010;50:8829. DOIPubMed
  2. Institute of Environmental Science and Research Ltd. (ESR). Notifiable diseases. New Zealand public health observatory. 2014 [cited 2016 Feb 2]. http://www.nzpho.org.nz/NotifiableDisease.aspx
  3. King  N, Lake  R, Campbell  D. Source attribution of nontyphoid salmonellosis in new zealand using outbreak surveillance data. J Food Prot. 2011;74:43845. DOIPubMed
  4. Eswarappa  SM, Janice  J, Nagarajan  AG, Balasundaram  SV, Karnam  G, Dixit  NM, et al. Differentially evolved genes of Salmonella pathogenicity islands: insights into the mechanism of host specificity in Salmonella. PLoS One. 2008;3:e3829. DOIPubMed
  5. Lal  A, Baker  MG, French  NP, Dufour  M, Hales  S. The epidemiology of human salmonellosis in New Zealand, 1997-2008. Epidemiol Infect. 2012;140:168594. DOIPubMed
  6. Lal  A, Ikeda  T, French  N, Baker  MG, Hales  S. Climate variability, weather and enteric disease incidence in New Zealand: time series analysis. PLoS One. 2013;8:e83484. DOIPubMed
  7. Alley  MR, Connolly  JH, Fenwick  SG, Mackereth  GF, Leyland  MJ, Rogers  LE, et al. An epidemic of salmonellosis caused by Salmonella Typhimurium DT160 in wild birds and humans in New Zealand. N Z Vet J. 2002;50:1706. DOIPubMed
  8. Institute of Environmental Science and Research Ltd (ESR). ESR LabLink. Quarterly surveillance summaries for New Zealand, March 2000–March 2003 [cited 2016 Nov 25]. https://surv.esr.cri.nz/PDF_surveillance/Lablink/
  9. Institute of Environmental Science and Research Ltd (ESR). Public Health Surveillance; Information for New Zealand public health action. 2003–2012 human Salmonella isolates [cited 2016 Nov 25]. https://surv.esr.cri.nz/enteric_reference/human_salmonella.php
  10. Institute of Environmental Science and Research Ltd (ESR). Public Health Surveillance; Information for New Zealand public health action. Non-human Salmonella isolates, 2003–2012 [cited 2016 Nov 25]. https://surv.esr.cri.nz/enteric_reference/nonhuman_salmonella.php
  11. Penfold  JB, Amery  HC, Peet  PJ. Gastroenteritis associated with wild birds in a hospital kitchen. Br Med J. 1979;2:802.PubMed
  12. Tizard  IR, Fish  NA, Harmeson  J. Free flying sparrows as carriers of salmonellosis. Can Vet J. 1979;20:1434.PubMed
  13. Lawson  B, Howard  T, Kirkwood  JK, Macgregor  SK, Perkins  M, Robinson  RA, et al. Epidemiology of salmonellosis in garden birds in England and Wales, 1993 to 2003. EcoHealth. 2010;7:294306. DOIPubMed
  14. Piccirillo  A, Mazzariol  S, Caliari  D, Menandro  ML. Salmonella Typhimurium phage type DT160 infection in two Moluccan cockatoos (Cacatua moluccensis): clinical presentation and pathology. Avian Dis. 2010;54:1315. DOIPubMed
  15. Grillo  T, Post  L. Salmonella Typhimurium DT160 outbreak in Tasmania. Animal Health Surveillance Quarterly Reports. 2010;14:8–8. http://www.sciquest.org.nz/node/72986
  16. QIAGEN. QIAamp DNA mini and blood mini handbook. Third edition. 2012 [cited 2015 Feb 12]. https://moodle.ufsc.br/pluginfile.php/1379318/mod_resource/content/0/QIAamp_DNA_Mini_Blood.pdf
  17. Aronesty  E. Comparison of sequencing utility programs. Open Bioinform J. 2013;7:18. DOI
  18. Zerbino  DR, Birney  E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:8219. DOIPubMed
  19. Gurevich  A, Saveliev  V, Vyahhi  N, Tesler  G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:10725. DOIPubMed
  20. Gardner  SN, Slezak  T, Hall  BG. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics. 2015;31:28778. DOIPubMed
  21. Li  H, Durbin  R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:175460. DOIPubMed
  22. Li  H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27:298793. DOIPubMed
  23. Garrison  E, Marth  G. Haplotype-based variant detection from short-read sequencing. 2012 [cited 2017 Feb 2]. https://arxiv.org/abs/1207.3907
  24. Petrovska  L, Mather  AE, AbuOun  M, Branchu  P, Harris  SR, Connor  T, et al. Microevolution of monophasic Salmonella Typhimurium during epidemic, United Kingdom, 2005–2010. Emerg Infect Dis. 2016;22:61724. DOIPubMed
  25. Stamatakis  A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:13123. DOIPubMed
  26. He  Z, Zhang  H, Gao  S, Lercher  MJ, Chen  WH, Hu  S. Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Res. 2016;44(W1):W236-41. DOIPubMed
  27. Huson  DH, Bryant  D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23:25467. DOIPubMed
  28. Tamura  K, Stecher  G, Peterson  D, Filipski  A, Kumar  S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013;30:27259. DOIPubMed
  29. Tamura  K, Nei  M, Kumar  S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A. 2004;101:110305. DOIPubMed
  30. Drummond  AJ, Suchard  MA, Xie  D, Rambaut  A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:196973. DOIPubMed
  31. Hasegawa  M, Kishino  H, Yano  T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985;22:16074. DOIPubMed
  32. Minin  VN, Bloomquist  EW, Suchard  MA. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol. 2008;25:145971. DOIPubMed
  33. Drummond  AJ, Ho  SYW, Phillips  MJ, Rambaut  A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006;4:e88. DOIPubMed
  34. Rambaut  A, Suchard  MA, Xie  D, Drummond  AJ. Beast. Tracer 1.6 2014 [cited 2016 Sep 27]. http://beast.bio.ed.ac.uk/Tracer
  35. Lemey  P, Rambaut  A, Drummond  AJ, Suchard  MA. Bayesian phylogeography finds its roots. PLOS Comput Biol. 2009;5:e1000520. DOIPubMed
  36. Seemann  T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:20689. DOIPubMed
  37. Page  AJ, Cummins  CA, Hunt  M, Wong  VK, Reuter  S, Holden  MTG, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31:36913. DOIPubMed
  38. Thompson  JD, Higgins  DG, Gibson  TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:467380. DOIPubMed
  39. Inouye  M, Dashnow  H, Raven  LA, Schultz  MB, Pope  BJ, Tomita  T, et al. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 2014;6:90. DOIPubMed
  40. Tatusov  RL, Galperin  MY, Natale  DA, Koonin  EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28:336. DOIPubMed
  41. Clark  KR, Gorle  RN. PRIMER v6: user manual/tutorial. Plymouth (UK): PRIMER-E; 2006. p. 296.
  42. Anderson  MJ. Distance-based tests for homogeneity of multivariate dispersions. Biometrics. 2006;62:24553. DOIPubMed
  43. Popoff  MY, Le Minor  LE. Genus XXXIII. Salmonella. In: Brenner DJ, Staley JT, editors. Bergey’s manual of systematic bacteriology. New York: Springer; 2005. p. 764–99.
  44. Thornley  CN, Simmons  GC, Callaghan  ML, Nicol  CM, Baker  MG, Gilmore  KS, et al. First incursion of Salmonella enterica serotype typhimurium DT160 into New Zealand. Emerg Infect Dis. 2003;9:4935. DOIPubMed
  45. Mather  AE, Reid  SWJ, Maskell  DJ, Parkhill  J, Fookes  MC, Harris  SR, et al. Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science. 2013;341:15147. DOIPubMed
  46. Okoro  CK, Kingsley  RA, Connor  TR, Harris  SR, Parry  CM, Al-Mashhadani  MN, et al. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet. 2012;44:121521. DOIPubMed
  47. Gieraltowski  L, Julian  E, Pringle  J, Macdonald  K, Quilliam  D, Marsden-Haug  N, et al. Nationwide outbreak of Salmonella Montevideo infections associated with contaminated imported black and red pepper: warehouse membership cards provide critical clues to identify the source. Epidemiol Infect. 2013;141:124452. DOIPubMed
  48. Byrne  L, Fisher  I, Peters  T, Mather  A, Thomson  N, Rosner  B, et al.; International Outbreak Control Team. 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;19:613. DOIPubMed
  49. Hottes  AK, Freddolino  PL, Khare  A, Donnell  ZN, Liu  JC, Tavazoie  S. Bacterial adaptation through loss of function. PLoS Genet. 2013;9:e1003617. DOIPubMed
  50. Koskiniemi  S, Sun  S, Berg  OG, Andersson  DI. Selection-driven gene loss in bacteria. PLoS Genet. 2012;8:e1002787. DOIPubMed

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1These authors contributed equally to this article.

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