High resolution assembly and characterization of genomes of Canadian isolates of Salmonella Enteritidis

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Ogunremi, Dele ^a   Devenish, John ^a   Amoako, Kingsley ^a   Kelly, Hilary ^a   Dupras, Andrée A ^a   Belanger, Sebastien ^a   Wang, Lin R ^a  

^a CANADIAN FOOD INSPECTION AGENCY   (Canada)

Author keywords

Accessory; Core; Genomes; Salmonella enteritidis; Single nucleotide polymorphism; Subtyping; Tracking

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATE; CANADA; CHICKEN; CLAM; CONTROLLED STUDY; GENETIC DISTANCE; GENETIC LINE; GENETIC VARIABILITY; GENOME SIZE; LABORATORY TEST; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; POULTRY FARMING; PROPHAGE; SALMONELLA ENTERITIDIS; SINGLE NUCLEOTIDE POLYMORPHISM; STRAIN DIFFERENCE; BIOLOGY; CHROMOSOME MAP; DNA BASE COMPOSITION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PROCEDURES; SALMONELLA ENTERICA SEROVAR ENTERITIDIS;

SALMONELLA ENTERITIDIS;

BASE COMPOSITION; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENOME SIZE; GENOME, BACTERIAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SALMONELLA ENTERITIDIS;

EID: 84907015001     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-713     Document Type: Article

References (54)

1. Vieira AR. WHO global foodborne infections network country databank - a resource to link human and non-human sources of salmonella Durban, South Africa: ISVEE Conference, http://www.who.int/gfn/activities/CDB_poster_Sept09.pdf Accessed 23 October 2013.
2. Nesbitt A, Ravel A, Murray R, McCormick R, Savelli C, Finley R, Parmley J, Agunos A, Majowicz SE, Gilmour M. Integrated surveillance and potential sources of Salmonella Enteritidis in human cases in Canada from 2003 to 2009. Epidemiol Infect 2012, 140:1757-1772. 10.1017/S0950268811002548, 3443964, 22166269.
3. Rodrigue DC, Tauxe RV, Rowe B. International increase in Salmonella enteritidis: a new pandemic?. Epidemiol Infect 1990, 105:21-27. 10.1017/S0950268800047609, 2271793, 2200698.
4. Batz MB, Hoffmann S, Morris JG. Ranking the risks: the 10 pathogen-food combinations with the greatest burden on public health 2011, Emerging Pathogen Institute: University of Florida, Gainesville.
5. Timme RE, Allard MW, Luo Y, Strain E, Pettengill J, Wang C, Li C, Keys CE, Zheng J, Stones R, Wilson MR, Musser SM, Brown EW. Draft genome sequences of 21 Salmonella enterica serovar Enteritidis strains. J Bacteriol 2012, 194:5994-5995. 10.1128/JB.01289-12, 3486122, 23045502.
6. Landry L, Dutil L. Overview of salmonella enteritidis in Canada. Proceedings of the Canadian salmonella enteritidis symposium and workshop. 1 Dec 2010 2010, 3-4. Vancuover, Canada: British Columbia Centre for Disease Control, http://www.bccdc.ca/dis-cond/a-z/_s/SalmonellaInfection/SalmonellaSymposium.htm.
7. Kuehn BM. Salmonella cases traced to egg producers: findings trigger recall of more than 500 million eggs. JAMA 2010, 304:1316. 10.1001/jama.2010.1330, 20858872.
8. Crosa JH, Brenner DJ, Ewing WH, Falkow S. Molecular relationships among the salmonellae. J Bacteriol 1973, 115:307-315. 246244, 4717519.
9. Vandamme PAR. Taxonomy and classification of bacteria. Manual of clinical microbiology 2003, 271-285. Washington DC: United States: ASM Press, Murray PR, Baron EJ, Jorgensen JH, Pfaller MA, Yolken RH.
10. Brenner FW, Villar RG, Angulo FJ, Tauxe R, Swaminathan B. Salmonella nomenclature. J Clin Microbiol 2000, 38:2465-2467. 86943, 10878026.
11. Guibourdenche M, Roggentin P, Mikoleit M, Fields PI, Bockemu¨hl J, Grimont PAD, Weil F-X. Supplement 2003-2007 (No 47) to the white-Kauffmann-Le minor scheme. Res Microbiol 2010, 161:26-29. 10.1016/j.resmic.2009.10.002, 19840847.
12. Tindall BJ, Grimont PAD, Garrity GM, Euzeby JP. Nomenclature and taxonomy of the genus Salmonella. Int J Syst Evol Microbiol 2005, 55:521-524. 10.1099/ijs.0.63580-0, 15653930.
13. Marlony B, Hauser E, Dieckmann R. New approaches in subspecies-level Salmonella classification. Salmonella - from genome to function 2011, 1-24. United Kingdom: Caister Academic Press, Porwollik S.
14. Hudson CR, Garcia M, Gast RK, Maurer JJ. Determination of close genetic relatedness of the major Salmonella Enteritidis phage types by pulsed-field gel electrophoresis and DNA sequences analysis of several Salmonella virulence genes. Avian Dis 2001, 45:875-886. 10.2307/1592867, 11785892.
15. Olson AB, Andrysiak AK, Tracz DM, Guard-Bouldin J, Demczuk W, Ng LK, Maki A, Jamieson F, Gilmour MW. Limited genetic diversity in Salmonella enterica serovar Enteritidis PT13. BMC Microbiol 2007, 7:87. 10.1186/1471-2180-7-87, 2137926, 17908316.
16. Marlony B, Junker E, Helmuth R. Multi-locus variable-number tandem repeat analysis for outbreak studies of Salmonella enterica serotype Enteritidis. BMC Microbiol 2008, 8:84. 10.1186/1471-2180-8-84, 2430564, 18513386.
17. Guard J, Morales CA, Fedorka-Cray P, Gast RK. Single nucleotide polymorphisms that differentiate two populations of Salmonella enteritidis within phage type. BMC Res Notes 2011, 4:369. 10.1186/1756-0500-4-369, 3220660, 21942987.
18. Guard-Petter J. Variants of smooth Salmonella enterica serovar Enteritidis that grow to higher cell density than the wild type are more virulent. Appl Environ Microbiol 1998, 64:2166-2172. 106294, 9603830.
19. Humphrey TJ, Williams A, McAlpine K, Lever MS, Guard-Petter J, Cox JM. Isolates of Salmonella enterica Enteritidis PT4 with enhanced heat and acid tolerance are more virulent in mice and more invasive in chickens. Epidemiol Infect 1996, 117:79-88. 10.1017/S0950268800001151, 2271678, 8760953.
20. Kircher M, Kelso J. High-throughput DNA sequencing-concepts and limitations. BioEssays 2010, 32:524-536. 10.1002/bies.200900181, 20486139.
21. Loman NJ, Constantinidou C, Chan JZM, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ. High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev 2012, 10:599-606.
22. Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM. Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. PLoS ONE 2014, 9:e87991. 10.1371/journal.pone.0087991, 3913712, 24505344.
23. Thompson NR, Clayton DJ, Windhort D, Vernikos G, Davidson S, Churcher C, Quail MA, Stevens M, Jones MA, Watson M, Barron A, Layton A, Pickard D, Kingsley RA, Bignell A, Clark L, Harris B, Ormond D, Abdellah Z, Brooks K, Cherevach I, Chillingworth T, Woodward J, Norberczak H, Lord A, Arrowsmith C, Jagels K, Moule S, Mungall K, Sanders M, et al. Comparative genome analysis of Salmonella Enteritidis PT 4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res 2008, 18:1624-1637. 10.1101/gr.077404.108, 2556274, 18583645.
24. Allard MW, Luo Y, Strain E, Pettengill J, Timme R, Wang C, Li C, Keys CE, Zheng J, Stones R, Wilson MR, Musser SM, Brown EW. On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX011.0004. PLoS ONE 2013, 8:e55254. 1-21, 10.1371/journal.pone.0055254, 3559427, 23383127.
25. Guard J, Shah D, Morales CA, Call D. Evolutionary trend associated with niche specialization as modelled by whole genome analysis of egg-contaminating Salmonella enterica serovar Enteritidis. Salmonella - From genome to function 2011, 91-106. United Kingdom: Caister Academic Press, Porwollik S.
26. Lescat M, Calteau A, Hoede C, Barbe V, Touchon M, Rocha E, Tenaillon O, Me´digue C, Johnson JR, Denamur E. A module located at a chromosomal integration hot spot is responsible for the multidrug resistance of a reference strain from Escherichia coli clonal group A. Antimicrob Agents Ch 2009, 53:2283-2288.
27. Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Resour 2011, 11:759-769. 10.1111/j.1755-0998.2011.03024.x, 21592312.
28. Liu SL, Hessel A, Sanderson KE. Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci U S A 1993, 90:6874-6878. 10.1073/pnas.90.14.6874, 47035, 8341713.
29. Onmus-Leone F, Hang J, Clifford RJ, Yang Y, Riley MC, Kuschner RA, Waterman PE, Lesho EP. Enhanced de novo assembly of high throughput pyrosequencing data using whole genome mapping. PLoS ONE 2013, 8:E61762. 10.1371/journal.pone.0061762, 3629165, 23613926.
30. Liang W, Zhao Y, Chen C, Cui X, Yu J, Xiao J, Kan B. Pan-Genomic Analysis Provides Insights into the Genomic Variation and Evolution of Salmonella Paratyphi A. PLoS ONE 2012, 7:e45346. 10.1371/journal.pone.0045346, 3446902, 23028950.
31. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, DeBoy RT, Davidsen TM, Mora M, Scarselli M, Margarit Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial " pan-genome. Proc Natl Acad Sci U S A 2005, 102:13950-13955. 10.1073/pnas.0506758102, 1216834, 16172379.
32. Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W. Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification. BMC Genomics 2010, 11:500-520. 10.1186/1471-2164-11-500, 2996996, 20846431.
33. Kruczkiewicz P. A comparative genomic framework for the in silico design and assessment of molecular typing methods using whole-genome sequence data with application to Listeria monocytogenes. MSc thesis 2013, University of Lethbridge, Canada: Department of Biology.
34. Hanna LF, Matthews TD, Dinsdale EA, Hasty D, Edwards R. High-thoroughput identification of horizontal gene transfer: detection of viable phage in Salmonella enterica serovar Enteritidis strain LK5. Appl Environ Microbiol 2012, 78:1785-1793. 10.1128/AEM.07241-11, 3298174, 22247173.
35. Ravel J, Fricke WF, White D, McDermott P, Mammel M, Rosovitz M, Leclerc J, Cebula T, Sebastian Y. Complete genome of Salmonella newport strain SL254. http://www.ncbi.nlm.nih.gov/nuccore/CP006631.1.
36. Liu WQ, Feng Y, Wang Y, Zou QH, Chen F, Guo JT, Peng YH, Jin Y, Li YG, Hu SN, Johnston RN, Liu GR, Liu SL. Salmonella Paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi. PLoS ONE 2009, 4:e4510. 10.1371/journal.pone.0004510, 2640428, 19229335.
37. McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P, McLellan M, Harkins CR, Wang C, Nguyen C, Berghoff A, Elliot G, Kohlberg S, Strong C, Du F, Carter J, Kremizki C, Layman D, Leonard S, Sun H, Fulton L, Nash W, Miner T, Minx P, Delehaunty K, Fronick C, Magrini V, et al. Comparison of genome degradation in Paratyphi A and Typhi, human-restriced serovars of Salmonella enterica that cause typhoid. Nat Genet 2004, 36:1268-1274. 10.1038/ng1470, 15531882.
38. Fricke WF, Mammel MK, McDermott FF, Tartera C, While DG, Leclerc JE, Ravel J, Cebula TA. Salmonella enterica subsp. enterica serovar Heidelberg str. SL 476. Comparative genomes of 28 Salmonella enterica isolates; evidence for CRISPR-mediated adaptive sublineage evolution. J Bacteriol 2011, 193:3556-3568. 10.1128/JB.00297-11, 3133335, 21602358.
39. Marti R, Hagens S, Loessner MJ, Klumpp J. Genome sequence of Salmonella bongori N268-08 - a rare clinical isolate. 2013, http://www.ncbi.nlm.nih.gov/nuccore/CP006608.
40. Ren Y, Ren Y, Zhou Z, Guo X, Li Y, Feng L, Wang L. Complete genome sequence of Enterobacter cloacae subsp. cloacae type strain ATCC 134047. J Bacteriol 2010, 192:2463-2464. 10.1128/JB.00067-10, 2863489, 20207761.
41. Power KA, Yan Q, Fox EM, Cooney S, Fanning S. Genome sequence of Cronobacter sakazakii SP291, a persistent thermotolerant isolate derived from a factory producing powdered infant formula. Genome Announc 2013, 1:e0008213. 3622955, 23516209.
42. Izumiya H, Sekizuka T, Nakaya H, Taguchi M, Oguchi A, Ichikawa N, Nishiko R, Yamazaki S, Fujita N, Watanabe H, Ohnishi M, Kuroda M. Whole-genome analysis of Salmonella enterica serovar Typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome. Antimicrob Agents Ch 2010, 55:623-630.
43. Windhorst D. Analysis and characterization of the prophage content in Salmonella Enteritidis. PhD dissertation 2010, Leibnitz University of Hannover, Germany: Faculty of Natural Science.
44. Rabsch W, Truepschuch S, Windhorst D, Gerlach RG. Typing phages and prophages of Salmonella. Salmonella - From genome to function 2011, 25-48. United Kingdom: Caister Academic Press, Porwollik S.
45. Ward LR, de Sa JDH, Rowe B. A phage-typing scheme for Salmonella enteritidis. Epidemiol Infect 1987, 99:291-294. 10.1017/S0950268800067765, 2249269, 3315705.
46. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23:673-679. 10.1093/bioinformatics/btm009, 2387122, 17237039.
47. Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 2005, 33:W686-W689. 10.1093/nar/gki366, 1160127, 15980563.
48. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007, 35:3100-3108. 10.1093/nar/gkm160, 1888812, 17452365.
49. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
50. Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS. BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res 2005, 33(Web Server issue):W455-W459. 1160269, 15980511.
51. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 2008, 9:75. 10.1186/1471-2164-9-75, 2265698, 18261238.
52. Bose M, Barber R. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol 2006, 6:0020.
53. Song J, Xu Y, White S, Miller KWP, Wolinsky M. SNPsFinder - a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes. Bioinformatics 2005, 21:2083-2084. 10.1093/bioinformatics/bti176, 15691853.
54. Jukes T, Cantor C. Evolution of protein molecules. Mammalian Protein Metabolism 1969, 21-132. New York: Academic Press, Munro HN.