A comparative analysis of the Lyve-SET phylogenomics pipeline for genomic epidemiology of foodborne pathogens

Frontiers in Microbiology

Volumn 8, Issue MAR, 2017, Pages

  Katz, Lee S ^a,b   Griswold, Taylor ^a,c   Williams Newkirk, Amanda J ^a,d   Wagner, Darlene ^a,d   Petkau, Aaron ^e   Sieffert, Cameron ^e   Domselaar, Gary Van ^e   Deng, Xiangyu ^b   Carleton, Heather A ^a  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c OAK RIDGE INSTITUTE FOR SCIENCE AND EDUCATION   (United States)

^d Ihrc Inc   (United States)

^e PUBLIC HEALTH AGENCY OF CANADA   (Canada)

Author keywords

Bacterial pathogen; Foodborne; Genomic epidemiology; Outbreak; SNP pipeline; WgMLST

Indexed keywords

CAMPYLOBACTER JEJUNI; CLADISTICS; COMPUTER INTERFACE; DATA BASE; ESCHERICHIA COLI; GENE MUTATION; HUMAN; INTERMETHOD COMPARISON; LISTERIA; NONHUMAN; PHYLOGENOMICS; PHYLOGENY; PIPELINE; SALMONELLA ENTERICA; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES; WHOLE GENOME SEQUENCING;

EID: 85016616312     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2017.00375     Document Type: Article

References (52)

1. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. doi: 10.1089/cmb.2012.0021
2. Bekal, S., Berry, C., Reimer, A. R., Van Domselaar, G., Beaudry, G., Fournier, E., et al. (2016). 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. 54, 289-295. doi: 10.1128/JCM.02200-15
3. Bergholz, T. M., den Bakker, H. C., Katz, L. S., Silk, B. J., Jackson, K. A., Kucerova, Z., et al. (2015). Determination of evolutionary relationships of outbreak-associated Listeria monocytogenes strains of serotypes 1/2a and 1/2b by whole-genome sequencing. Appl. Environ. Microbiol. 82, 928-938. doi: 10.1128/AEM.02440-15
4. Bertels, F., Silander, O. K., Pachkov, M., Rainey, P. B., and van Nimwegen, E. (2014). Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol. Biol. Evol. 31, 1077-1088. doi: 10.1093/molbev/msu088
5. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics 10:421. doi: 10.1186/1471-2105-10-421
6. Carleton, H., and Gerner-Smidt, P. (2016). Whole-genome sequencing is taking over foodborne disease surveillance. Microbe. 11, 311-317
7. CDC (2014). Multistate Outbreak of Shiga toxin-producing Escherichia coli O121 Infections Linked to Raw Clover Sprouts (Final Update) [cited 2016]. Available online at: http://www.cdc.gov/ecoli/2014/o121-05-14/index.html
8. CDC (2015). Multistate Outbreak of Listeriosis Linked to Commercially Produced, Prepackaged Caramel Apples Made from Bidart Bros. Apples [Updated September 11, 2015]. Available online at: http://www.cdc.gov/listeria/outbreaks/caramel-apples-12-14
9. Chen, Y., and Knabel, S. J. (2008). Prophages in Listeria monocytogenes contain single-nucleotide polymorphisms that differentiate outbreak clones within epidemic clones. J. Clin. Microbiol. 46, 1478-1484. doi: 10.1128/JCM.01873-07
10. Cingolani, P., Platts, A., Wang le, L., Coon, M., Nguyen, T., Wang, L., et al. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80-92. doi: 10.4161/fly.19695
11. Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., et al. (2011). The variant call format and VCFtools. Bioinformatics 27, 2156-2158. doi: 10.1093/bioinformatics/btr330
12. Davis, S., Pettengill, J. B., Luo, Y., Payne, J., Shpuntoff, A., Rand, H., et al. (2015). CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data. PeerJ Comp. Sci. 1:e20. doi: 10.7717/peerj-cs.20
13. Felsenstein, J. (1989). PHYLIP (Version 3.6) Phylogeny Inference Package. Cladistics 5, 164-166
14. Gardner, S. N., Slezak, T., and Hall, B. G. (2015). kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics 31, 2877-2878. doi: 10.1093/bioinformatics/btv271
15. Garrison, E., and Marth, G. (2012). Haplotype-Based Variant Detection from Short-Read Sequencing. arXiv preprint arXiv:12073907
16. Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321. doi: 10.1093/sysbio/syq010
17. Health MDo (2014). Minnesota health officials investigating 13 cases of E. coli O111 infection [cited 2016]. Available online at: http://www.health.state.mn.us/news/pressrel/2014/ecoli071414.html
18. Hoffmann, M., Luo, Y., Monday, S. R., Gonzalez-Escalona, N., Ottesen, A. R., Muruvanda, T., et al. (2016). Tracing origins of the Salmonella bareilly strain causing a foodborne outbreak in the United States. J. Infect. Dis. 213, 502-508. doi: 10.1093/infdis/jiv297
19. Jackson, B. R., Salter, M., Tarr, C., Conrad, A., Harvey, E., Steinbock, L., et al. (2015). Notes from the Field: Listeriosis Associated with Stone Fruit-United States, 2014. Morbidity and mortality weekly report, Public Health Agency of Canada, 282-283
20. Jackson, B. R., Tarr, C., Strain, E., Jackson, K. A., Conrad, A., Carleton, H., et al. (2016). Implementation of nationwide real-time whole-genome sequencing to enhance listeriosis outbreak detection and investigation. Clin. Infect. Dis. 63, 380-386. doi: 10.1093/cid/ciw242
21. Katz, L. S., Petkau, A., Beaulaurier, J., Tyler, S., Antonova, E. S., Turnsek, M. A., et al. (2013). Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. MBio 4:e00398-13. doi: 10.1128/mBio.00398-13
22. Kendall, M., and Colijn, C. (2015). A tree metric using structure and length to capture distinct phylogenetic signals. arXiv preprint arXiv:150705211
23. Kislyuk, A. O., Katz, L. S., Agrawal, S., Hagen, M. S., Conley, A. B., Jayaraman, P., et al. (2010). A computational genomics pipeline for prokaryotic sequencing projects. Bioinformatics 26, 1819-1826. doi: 10.1093/bioinformatics/btq284
24. Koboldt, D. C., Zhang, Q., Larson, D. E., Shen, D., McLellan, M. D., Lin, L., et al. (2012). VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568-576. doi: 10.1101/gr.129684.111
25. Kuhner, M. K., and Felsenstein, J. (1994). A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11, 459-468
26. Lefort, V., Desper, R., and Gascuel, O. (2015). FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol. Biol. Evol. 32, 2798-2800. doi: 10.1093/molbev/msv150
27. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079. doi: 10.1093/bioinformatics/btp352
28. MacCannell, D. (2013). Bacterial strain typing. Clin. Lab. Med. 33, 629-650. doi: 10.1016/j.cll.2013.03.005
29. Maiden, M. C., Bygraves, J. A., Feil, E., Morelli, G., Russell, J. E., Urwin, R., et al. (1998). Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. U.S.A. 95, 3140-3145. doi: 10.1073/pnas.95.6.3140
30. Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Res. 27, 209-220
31. Marler-Clark (2008). Hendricks' Farm and Dairy Raw Milk 2008 [cited 2016]. Available online at: http://www.outbreakdatabase.com/details/hendricks-farm-and-dairy-raw-milk-2008/
32. Mercante, J. W., Morrison, S. S., Desai, H. P., Raphael, B. H., and Winchell, J. M. (2016). Genomic analysis reveals novel diversity among the 1976 Philadelphia Legionnaires' Disease outbreak isolates and additional ST36 strains. PLoS ONE 11:e0164074. doi: 10.1371/journal.pone.0164074
33. Milne, I., Stephen, G., Bayer, M., Cock, P. J., Pritchard, L., Cardle, L., et al. (2013). Using Tablet for visual exploration of second-generation sequencing data. Brief. Bioinform. 14, 193-202. doi: 10.1093/bib/bbs012
34. Morganti, M., Scaltriti, E., Cozzolino, P., Bolzoni, L., Casadei, G., Pierantoni, M., et al. (2015). Processing-dependent and clonal contamination patterns of Listeria monocytogenes in the cured ham food chain revealed by genetic analysis. Appl. Environ. Microbiol. 82, 822-831. doi: 10.1128/AEM.03103-15
35. Moura, A., Criscuolo, A., Pouseele, H., Maury, M. M., Leclercq, A., Tarr, C., et al. (2016). Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat. Microbiol. 2:16185. doi: 10.1038/nmicrobiol.2016.185
36. Oksanen, J., Kindt, R., Legendre, P., O'Hara, B., Stevens, M. H. H., Oksanen, M. J., et al. (2007). The Vegan Package. Community ecology package
37. Paradis, E., Claude, J., and Strimmer, K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289-290. doi: 10.1093/bioinformatics/btg412
38. Petkau, A., Mabon, P., Sieffert, C., Knox, N., Cabral, J., Iskander, M., et al. (2016). SNVPhyl: A Single Nucleotide Variant phylogenomics pipeline for whole-genome based microbial genomic epidemiology. Biorxiv. doi: 10.1101/092940
39. Pettengill, J. B., Luo, Y., Davis, S., Chen, Y., Gonzalez-Escalona, N., Ottesen, A., et al. (2014). An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella. PeerJ 2:e620. doi: 10.7717/peerj.620
40. Ponstingl, H., and Ning, Z. (2010). SMALT-a new mapper for DNA sequencing reads. F1000Research Posters 1:313
41. Robinson, D. F., and Foulds, L. R. (1981). Comparison of phylogenetic trees. Math. Biosci. 53, 131-147. doi: 10.1016/0025-5564(81)90043-2
42. Rödelsperger, C., Guo, G., Kolanczyk, M., Pletschacher, A., Kohler, S., Bauer, S., et al. (2011). Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions. Nucleic Acids Res. 39, 2492-2502. doi: 10.1093/nar/gkq1081
43. Shirey, B., Johnson, S., Maliha, I., Luquez, C., Hill, K., and Maslanka, S. (2016). "Distinguishing outbreaks of botulism using a reference-based SNP analysis and high quality reference genome sequences of Clostridium botulinum," in 11th Annual Sequencing, Finishing, and Analysis in the Future Meeting. Santa Fe, NM: Los Alamos National Laboratory
44. Smouse, P. E., Long, J. C., and Sokal, R. R. (1986). Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Syst. Zool. 35, 627-632. doi: 10.2307/2413122
45. Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., et al. (2002). The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12, 1611-1618. doi: 10.1101/gr.361602
46. Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313. doi: 10.1093/bioinformatics/btu033
47. Swaminathan, B., Gerner-Smidt, P., Ng, L. K., Lukinmaa, S., Kam, K. M., Rolando, S., et al. (2006). Building PulseNet International: an interconnected system of laboratory networks to facilitate timely public health recognition and response to foodborne disease outbreaks and emerging foodborne diseases. Foodborne Pathog. Dis. 3, 36-50. doi: 10.1089/fpd.2006.3.36
48. Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725-2729. doi: 10.1093/molbev/mst197
49. Tataryn, J., Morton, V., Cutler, J., McDonald, L., Whitfield, Y., Billard, B., et al. (2014). Outbreak of E. coli O157: H7 Associated with Lettuce Served at Fast Food Chains in the Maritimes and Ontario, Canada, Dec 2012. Canada Communicable Disease Report, Public Health Agency of Canada, 40(S1):2
50. Vos, M., and Didelot, X. (2009). A comparison of homologous recombination rates in bacteria and archaea. ISME J. 3, 199-208. doi: 10.1038/ismej.2008.93
51. Vos, R. A., Caravas, J., Hartmann, K., Jensen, M. A., and Miller, C. (2011). BIO::Phylo-phyloinformatic analysis using perl. BMC Bioinformatics 12:63. doi: 10.1186/1471-2105-12-63
52. Zhou, Y., Liang, Y., Lynch, K. H., Dennis, J. J., and Wishart, D. S. (2011). PHAST: a fast phage search tool. Nucleic Acids Res. 39, W347-W352. doi: 10.1093/nar/gkr485