Comparative genomics of enterohemorrhagic Escherichia coli O145: H28 demonstrates a common evolutionary lineage with Escherichia coli O157: H7

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Cooper, Kerry K ^a   Mandrell, Robert E ^a   Louie, Jacqueline W ^a   Korlach, Jonas ^b   Clark, Tyson A ^b   Parker, Craig T ^a   Huynh, Steven ^a   Chain, Patrick S ^c   Ahmed, Sanaa ^c   Carter, Michelle Q ^a  

^a WESTERN REGIONAL RESEARCH CENTER   (United States)

^b PACIFIC BIOSCIENCES   (United States)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Comparative genomics; DNA methylation; Enterohemorrhagic Escherichia coli; O145; Shiga toxin producing Escherichia coli

Indexed keywords

METHYLTRANSFERASE; SHIGA TOXIN; VIRULENCE FACTOR;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BELGIUM; CONTROLLED STUDY; ENTEROHEMORRHAGIC ESCHERICHIA COLI; ENTEROHEMORRHAGIC ESCHERICHIA COLI O145 H28; EPIDEMIC; EPIGENETICS; ESCHERICHIA COLI O157; EVOLUTION; GENE CASSETTE; GENOME SIZE; GENOMICS; HORIZONTAL GENE TRANSFER; ICE CREAM; LETTUCE; METHYLATION; METHYLOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMID; PROPHAGE; SEROTYPE; SHIGA TOXIN PRODUCING ESCHERICHIA COLI; SHIGELLA; UNITED STATES;

ESCHERICHIA COLI; LACTUCA; SHIGELLA;

BIOLOGICAL EVOLUTION; ENTEROHEMORRHAGIC ESCHERICHIA COLI; ESCHERICHIA COLI; ESCHERICHIA COLI O157; ESCHERICHIA COLI PROTEINS; GENOME, BACTERIAL; GENOMICS; METHYLTRANSFERASES; PHYLOGENY; PROPHAGES; SEROTYPING; SHIGA TOXIN; SHIGELLA; VIRULENCE FACTORS;

EID: 84892410834     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-17     Document Type: Article

References (75)

1. Levine MM. Escherichia coli that cause diarrhea: enterotoxigenic, enteropathogenic, enteroinvasive, enterohemorrhagic, and enteroadherent. J Infect Dis 1987, 155(3):377-389. 10.1093/infdis/155.3.377, 3543152.
2. Manning SD, Motiwala AS, Springman AC, Qi W, Lacher DW, Ouellette LM, Mladonicky JM, Somsel P, Rudrik JT, Dietrich SE, et al. Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc Natl Acad Sci U S A 2008, 105(12):4868-4873. 10.1073/pnas.0710834105, 2290780, 18332430.
3. Shen S, Mascarenhas M, Morgan R, Rahn K, Karmali MA. Identification of four fimbria-encoding genomic islands that are highly specific for verocytotoxin-producing Escherichia coli serotype O157 strains. J Clin Microbiol 2005, 43(8):3840-3850. 10.1128/JCM.43.8.3840-3850.2005, 1233952, 16081921.
4. Nataro JP, Kaper JB. Diarrheagenic Escherichia coli. Clin Microbiol Rev 1998, 11(1):142-201. 121379, 9457432.
5. Karmali MA, Mascarenhas M, Shen S, Ziebell K, Johnson S, Reid-Smith R, Isaac-Renton J, Clark C, Rahn K, Kaper JB. Association of genomic O island 122 of Escherichia coli EDL 933 with verocytotoxin-producing Escherichia coli seropathotypes that are linked to epidemic and/or serious disease. J Clin Microbiol 2003, 41(11):4930-4940. 10.1128/JCM.41.11.4930-4940.2003, 262514, 14605120.
6. Ju W, Cao G, Rump L, Strain E, Luo Y, Timme R, Allard M, Zhao S, Brown E, Meng J. Phylogenetic analysis of non-O157 Shiga toxin-producing Escherichia coli strains by whole-genome sequencing. J Clin Microbiol 2012, 50(12):4123-4127. 10.1128/JCM.02262-12, 3502965, 23052305.
7. Johnson KE, Thorpe CM, Sears CL. The emerging clinical importance of non-O157 Shiga toxin-producing Escherichia coli. Clin Infect Dis 2006, 43(12):1587-1595. 10.1086/509573, 17109294.
8. Mead PS, Slutsker L, Dietz V, McCaig LF, Bresee JS, Shapiro C, Griffin PM, Tauxe RV. Food-related illness and death in the United States. Emerg Infect Dis 1999, 5(5):607-625. 10.3201/eid0505.990502, 2627714, 10511517.
9. Mathusa EC, Chen Y, Enache E, Hontz L. Non-O157 Shiga toxin-producing Escherichia coli in foods. J Food Prot 2010, 73(9):1721-1736.
10. Hoffmann S, Batz MB, Morris JG. Annual cost of illness and quality-adjusted life year losses in the United States due to 14 foodborne pathogens. J Food Prot 2012, 75(7):1292-1302. 10.4315/0362-028X.JFP-11-417, 22980013.
11. Scallan E, Mahon BE. Foodborne diseases active surveillance network (FoodNet) in 2012: a foundation for food safety in the United States. Clin Infec Dis 2012, 54(Suppl 5):S381-S384.
12. Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011, 365(8):709-717. 10.1056/NEJMoa1106920, 3168948, 21793740.
13. Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, et al. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 2011, 365(8):718-724. 10.1056/NEJMoa1107643, 21793736.
14. Rosales A, Hofer J, Zimmerhackl LB, Jungraithmayr TC, Riedl M, Giner T, Strasak A, Orth-Holler D, Wurzner R, Karch H. Need for long-term follow-up in enterohemorrhagic Escherichia coli-associated hemolytic uremic syndrome due to late-emerging sequelae. Clin Infect Dis 2012, 54(10):1413-1421. 10.1093/cid/cis196, 22412065.
15. Coombes BK, Gilmour MW, Goodman CD. The evolution of virulence in non-o157 shiga toxin-producing Escherichia coli. Front Microbiol 2011, 2:90. 3153049, 21833329.
16. Norman KN, Strockbine NA, Bono JL. Association of nucleotide polymorphisms within the O-antigen gene cluster of Escherichia coli O26, O45, O103, O111, O121, and O145 with serogroups and genetic subtypes. Appl Environ Microbiol 2012, 78(18):6689-6703. 10.1128/AEM.01259-12, 3426686, 22798363.
17. Hegde NV, Cote R, Jayarao BM, Muldoon M, Lindpaintner K, Kapur V, Debroy C. Detection of the top six non-O157 Shiga toxin-producing Escherichia coli O groups by ELISA. Foodborne Pathog Dis 2012, 9(11):1044-1048. 10.1089/fpd.2012.1231, 23134286.
18. Brooks JT, Sowers EG, Wells JG, Greene KD, Griffin PM, Hoekstra RM, Strockbine NA. Non-O157 Shiga toxin-producing Escherichia coli infections in the United States, 1983-2002. J Infect Dis 2005, 192(8):1422-1429. 10.1086/466536, 16170761.
19. Schmidt MA. LEEways: tales of EPEC, ATEC and EHEC. Cellular Microbiol 2010, 12(11):1544-1552.
20. Croxen MA, Finlay BB. Molecular mechanisms of Escherichia coli pathogenicity. Nat Rev Microbiol 2010, 8(1):26-38.
21. Perna NT, Plunkett G, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 2001, 409(6819):529-533. 10.1038/35054089, 11206551.
22. Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M, Oshima K, Kodama T, Abe H, Nakayama K, Kurokawa K, et al. Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci U S A 2009, 106(42):17939-17944. 10.1073/pnas.0903585106, 2764950, 19815525.
23. Johnson TJ, Nolan LK. Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol Mol Biol Rev 2009, 73(4):750-774. 10.1128/MMBR.00015-09, 2786578, 19946140.
24. Lim JY, Yoon J, Hovde CJ. A brief overview of Escherichia coli O157:H7 and its plasmid O157. J Microbiol Biotechnol 2010, 20(1):5-14. 3645889, 20134227.
25. Eppinger M, Mammel MK, Leclerc JE, Ravel J, Cebula TA. Genomic anatomy of Escherichia coli O157:H7 outbreaks. Proc Natl Acad Sci U S A 2011, 108(50):20142-20147. 10.1073/pnas.1107176108, 3250189, 22135463.
26. Kulasekara BR, Jacobs M, Zhou Y, Wu Z, Sims E, Saenphimmachak C, Rohmer L, Ritchie JM, Radey M, McKevitt M, et al. Analysis of the genome of the Escherichia coli O157:H7 2006 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence. Infection Immunity 2009, 77(9):3713-3721. 10.1128/IAI.00198-09, 2738036, 19564389.
27. Feng PC, Monday SR, Lacher DW, Allison L, Siitonen A, Keys C, Eklund M, Nagano H, Karch H, Keen J, et al. Genetic diversity among clonal lineages within Escherichia coli O157:H7 stepwise evolutionary model. Emerg Infect Dis 2007, 13(11):1701-1706. 10.3201/eid1311.070381, 3375798, 18217554.
28. Wick LM, Qi W, Lacher DW, Whittam TS. Evolution of genomic content in the stepwise emergence of Escherichia coli O157:H7. J Bacteriol 2005, 187(5):1783-1791. 10.1128/JB.187.5.1783-1791.2005, 1064018, 15716450.
29. Kyle JL, Cummings CA, Parker CT, Quinones B, Vatta P, Newton E, Huynh S, Swimley M, Degoricija L, Barker M, et al. Escherichia coli serotype O55:H7 diversity supports parallel acquisition of bacteriophage at Shiga toxin phage insertion sites during evolution of the O157:H7 lineage. J Bacteriol 2012, 194(8):1885-1896. 10.1128/JB.00120-12, 3318487, 22328665.
30. Jarvis KG, Giron JA, Jerse AE, McDaniel TK, Donnenberg MS, Kaper JB. Enteropathogenic Escherichia coli contains a putative type III secretion system necessary for the export of proteins involved in attaching and effacing lesion formation. Proc Natl Acad Sci U S A 1995, 92(17):7996-8000. 10.1073/pnas.92.17.7996, 41273, 7644527.
31. Reid SD, Herbelin CJ, Bumbaugh AC, Selander RK, Whittam TS. Parallel evolution of virulence in pathogenic Escherichia coli. Nature 2000, 406(6791):64-67. 10.1038/35017546, 10894541.
32. Abu-Ali GS, Lacher DW, Wick LM, Qi W, Whittam TS. Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex. BMC Genomics 2009, 10:296. 10.1186/1471-2164-10-296, 2713265, 19575794.
33. Yang Z, Kim J, Zhang C, Zhang M, Nietfeldt J, Southward CM, Surette MG, Kachman SD, Benson AK. Genomic instability in regions adjacent to a highly conserved pch prophage in Escherichia coli O157:H7 generates diversity in expression patterns of the LEE pathogenicity island. J Bacteriol 2009, 191(11):3553-3568. 10.1128/JB.01738-08, 2681921, 19329643.
34. Xiong Y, Wang P, Lan R, Ye C, Wang H, Ren J, Jing H, Wang Y, Zhou Z, Bai X, et al. A novel Escherichia coli O157:H7 clone causing a major hemolytic uremic syndrome outbreak in China. PloS one 2012, 7(4):e36144. 10.1371/journal.pone.0036144, 3338595, 22558360.
35. Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, et al. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 2001, 8(1):11-22. 10.1093/dnares/8.1.11, 11258796.
36. Folster JP, Pecic G, Taylor E, Whichard J. Characterization of isolates from an outbreak of multidrug-resistant, Shiga toxin-producing Escherichia coli O145 in the United States. Antimicrob Agents Chemother 2011, 55(12):5955-5956. 10.1128/AAC.05545-11, 3232767, 21930875.
37. Taylor EV, Nguyen TA, Machesky KD, Koch E, Sotir MJ, Bohm SR, Folster JP, Bokanyi R, Kupper A, Bidol SA, et al. Multistate outbreak of Escherichia coli O145 infections associated with romaine lettuce consumption, 2010. J Food Prot 2013, 76(6):939-944. 10.4315/0362-028X.JFP-12-503, 23726187.
38. De Schrijver K, Buvens G, Posse B, Van den Branden D, Oosterlynck O, De Zutter L, Eilers K, Pierard D, Dierick K, Van Damme-Lombaerts R, et al. Outbreak of verocytotoxin-producing E. coli O145 and O26 infections associated with the consumption of ice cream produced at a farm, Belgium, 2007. Euro Surveill 2008, 13(7):61-64.
39. Buvens G, Posse B, De Schrijver K, De Zutter L, Lauwers S, Pierard D. Virulence profiling and quantification of verocytotoxin-producing Escherichia coli O145:H28 and O26:H11 isolated during an ice cream-related hemolytic uremic syndrome outbreak. Foodborne Pathog Dis 2011, 8(3):421-426. 10.1089/fpd.2010.0693, 21166561.
40. Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 2012, 30(7):693-700. 10.1038/nbt.2280, 3707490, 22750884.
41. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC genomics 2011, 12:402. 10.1186/1471-2164-12-402, 3163573, 21824423.
42. Murray IA, Clark TA, Morgan RD, Boitano M, Anton BP, Luong K, Fomenkov A, Turner SW, Korlach J, Roberts RJ. The methylomes of six bacteria. Nucleic Acids Res 2012, 40(22):11450-11462. 10.1093/nar/gks891, 3526280, 23034806.
43. Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng Z, Losic B, Mahajan MC, Jabado OJ, et al. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol 2012, 30(12):1232-1239. 10.1038/nbt.2432, 3879109, 23138224.
44. Pupo GM, Lan R, Reeves PR. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc Natl Acad Sci U S A 2000, 97(19):10567-10572. 10.1073/pnas.180094797, 27065, 10954745.
45. Pupo GM, Karaolis DK, Lan R, Reeves PR. Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies. Infect Immunity 1997, 65(7):2685-2692.
46. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. Alignment of whole genomes. Nucleic Acids Res 1999, 27(11):2369-2376. 10.1093/nar/27.11.2369, 148804, 10325427.
47. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52(5):696-704. 10.1080/10635150390235520, 14530136.
48. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688-2690. 10.1093/bioinformatics/btl446, 16928733.
49. Steyert SR, Kaper JB. Contribution of urease to colonization by Shiga toxin-producing Escherichia coli. Infect Immunity 2012, 80(8):2589-2600.
50. Rump LV, Fischer M, Gonzalez-Escalona N. Prevalence, distribution and evolutionary significance of the IS629 insertion element in the stepwise emergence of Escherichia coli O157:H7. BMC Microbiol 2011, 11:133. 10.1186/1471-2180-11-133, 3271280, 21672218.
51. Rump LV, Fischer M, Gonzalez-Escalona N. Different IS629 transposition frequencies exhibited by Escherichia coli O157:H7 strains in the stepwise evolutionary model. Appl Environ Microbiol 2011, 77(14):5030-5033. 10.1128/AEM.00249-11, 3147399, 21622790.
52. Yokoyama E, Hashimoto R, Etoh Y, Ichihara S, Horikawa K, Uchimura M. Biased distribution of IS629 among strains in different lineages of enterohemorrhagic Escherichia coli serovar O157. Infect Genet Evol 2011, 11(1):78-82. 10.1016/j.meegid.2010.10.007, 21035566.
53. Wong AR, Pearson JS, Bright MD, Munera D, Robinson KS, Lee SF, Frankel G, Hartland EL. Enteropathogenic and enterohaemorrhagic Escherichia coli: even more subversive elements. Mol Microbiol 2011, 80(6):1420-1438. 10.1111/j.1365-2958.2011.07661.x, 21488979.
54. Carter MQ, Louie JW, Fagerquist CK, Sultan O, Miller WG, Mandrell RE. Evolutionary silence of the acid chaperone protein HdeB in enterohemorrhagic Escherichia coli O157:H7. Appl Environ Microbiol 2012, 78(4):1004-1014. 10.1128/AEM.07033-11, 3273018, 22179243.
55. Gould LH, Mody RK, Ong KL, Clogher P, Cronquist AB, Garman KN, Lathrop S, Medus C, Spina NL, Webb TH, et al. Increased recognition of non-O157 Shiga toxin-producing Escherichia coli infections in the United States during 2000-2010: epidemiologic features and comparison with E. coli O157 Infections. Foodborne Pathog Dis 2013, 10(5):453-460. 10.1089/fpd.2012.1401, 23560425.
56. Murphy KC, Ritchie JM, Waldor MK, Lobner-Olesen A, Marinus MG. Dam methyltransferase is required for stable lysogeny of the Shiga toxin (Stx2)-encoding bacteriophage 933 W of enterohemorrhagic Escherichia coli O157:H7. J Bacteriol 2008, 190(1):438-441. 10.1128/JB.01373-07, 2223730, 17981979.
57. Casadesus J, Low D. Epigenetic gene regulation in the bacterial world. Microbiol Mol Biol Rev 2006, 70(3):830-856. 10.1128/MMBR.00016-06, 1594586, 16959970.
58. Wallecha A, Munster V, Correnti J, Chan T, van der Woude M. Dam-and OxyR-dependent phase variation of agn43: essential elements and evidence for a new role of DNA methylation. J Bacteriol 2002, 184(12):3338-3347. 10.1128/JB.184.12.3338-3347.2002, 135096, 12029051.
59. Braaten BA, Nou X, Kaltenbach LS, low DA. Methylation patterns in pap regulatory DNA control pyelonephritis-associated pili phase variation in E. coli. Cell 1994, 76(3):577-588. 10.1016/0092-8674(94)90120-1, 7906204.
60. Sarnacki SH, Marolda CL, Noto Llana M, Giacomodonato MN, Valvano MA, Cerquetti MC. Dam methylation controls O-antigen chain length in Salmonella enterica serovar enteritidis by regulating the expression of Wzz protein. J Bacteriol 2009, 191(21):6694-6700. 10.1128/JB.00839-09, 2795312, 19717610.
61. Miller WG, Pearson BM, Wells JM, Parker CT, Kapitonov VV, Mandrell RE. Diversity within the Campylobacter jejuni type I restriction-modification loci. Microbiology 2005, 151(Pt 2):337-351.
62. Ahmed SA, Awosika J, Baldwin C, Bishop-Lilly KA, Biswas B, Broomall S, Chain PS, Chertkov O, Chokoshvili O, Coyne S, et al. Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2. PloS one 2012, 7(11):e48228. 10.1371/journal.pone.0048228, 3486847, 23133618.
63. Han C, Chain P. Finishing repetitive regions automatically with dupfinisher. Proceedings of 2006 International Conference on Bioinformatics & Computational Biology: 2006 2006, Las Vegas, Nevada, USA: CSREA Press.
64. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012, 28(12):1647-1649. 10.1093/bioinformatics/bts199, 3371832, 22543367.
65. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:75. 10.1186/1471-2164-9-75, 2265698, 18261238.
66. Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, Korlach J, Turner SW. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 2010, 7(6):461-465. 10.1038/nmeth.1459, 2879396, 20453866.
67. Clark TA, Murray IA, Morgan RD, Kislyuk AO, Spittle KE, Boitano M, Fomenkov A, Roberts RJ, Korlach J. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res 2012, 40(4):e29. 10.1093/nar/gkr1146, 3287169, 22156058.
68. Bose M, Barber RD. Prophage finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol 2006, 6(3):223-227.
69. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011, 39(Suppl 2):W347-W352. 3125810, 21672955.
70. Ou HY, He X, Harrison EM, Kulasekara BR, Thani AB, Kadioglu A, Lory S, Hinton JC, Barer MR, Deng Z, et al. MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res 2007, 35(Web Server issue):W97-W104. 1933208, 17537813.
71. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30(14):3059-3066. 10.1093/nar/gkf436, 135756, 12136088.
72. Abascal F, Zardoya R, Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 2005, 21(9):2104-2105. 10.1093/bioinformatics/bti263, 15647292.
73. Abbott JC, Aanensen DM, Bentley SD. WebACT: an online genome comparison suite. Methods Mol Biol 2007, 395:57-74. 10.1007/978-1-59745-514-5_4, 17993667.
74. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. ACT: the artemis comparison tool. Bioinformatics 2005, 21(16):3422-3423. 10.1093/bioinformatics/bti553, 15976072.
75. Darling AE, Mau B, Perna NT. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PloS one 2010, 5(6):e11147. 10.1371/journal.pone.0011147, 2892488, 20593022.