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Phylogenetic background and habitat drive the genetic diversification of Escherichia coli


Autoři: Marie Touchon aff001;  Amandine Perrin aff001;  Jorge André Moura de Sousa aff001;  Belinda Vangchhia aff003;  Samantha Burn aff003;  Claire L. O’Brien aff005;  Erick Denamur aff006;  David Gordon aff003;  Eduardo PC Rocha aff001
Působiště autorů: Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France aff001;  Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, rue Dr Roux, Paris, France aff001;  Sorbonne Université, Collège doctoral, F-75005 Paris, France aff002;  Sorbonne Université, Collège doctoral, Paris, France aff002;  Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia aff003;  Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram, India aff004;  School of Medicine, University of Wollongong, Northfields Ave Wollongong, Australia aff005;  Université de Paris, IAME, UMR 1137, INSERM, Paris, 75018, France aff006;  Université de Paris, IAME, UMR, INSERM, Paris, France aff006;  AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, 75018, Paris, France aff007;  AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France aff007
Vyšlo v časopise: Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. PLoS Genet 16(6): e32767. doi:10.1371/journal.pgen.1008866
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008866

Souhrn

Escherichia coli is mostly a commensal of birds and mammals, including humans, where it can act as an opportunistic pathogen. It is also found in water and sediments. We investigated the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000 isolates from the Australian continent. Since many previous studies focused on clinical isolates, we investigated mostly other isolates originating from humans, poultry, wild animals and water. These strains represent the species genetic diversity and reveal widespread associations between phylogroups and isolation sources. The analysis of strains from the same sequence types revealed very rapid change of gene repertoires in the very early stages of divergence, driven by the acquisition of many different types of mobile genetic elements. These elements also lead to rapid variations in genome size, even if few of their genes rise to high frequency in the species. Variations in genome size are associated with phylogroup and isolation sources, but the latter determine the number of MGEs, a marker of recent transfer, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. After a while, the divergence of gene repertoires becomes linear with phylogenetic distance, presumably reflecting the continuous turnover of mobile element and the occasional acquisition of adaptive genes. Surprisingly, the phylogroups with smallest genomes have the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements. This suggests that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these genomes are from freshwater isolates and have peculiar traits, including a specific capsule, suggesting adaptation to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species.

Klíčová slova:

Animal phylogenetics – Bacterial genomics – Bird genomics – Comparative genomics – Phylogenetic analysis – Population genetics – Virulence factors – Color codes


Zdroje

1. Berg RD. The indigenous gastrointestinal microflora. Trends Microbiol. 1996;4(11):430–5. doi: 10.1016/0966-842x(96)10057-3 8950812.

2. Gordon DM, Cowling A. The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects. Microbiology. 2003;149(Pt 12):3575–86. doi: 10.1099/mic.0.26486-0 14663089.

3. Tenaillon O, Skurnik D, Picard B, Denamur E. The population genetics of commensal Escherichia coli. Nat Rev Microbiol. 2010;8(3):207–17. doi: 10.1038/nrmicro2298 20157339.

4. Ishii S, Ksoll WB, Hicks RE, Sadowsky MJ. Presence and growth of naturalized Escherichia coli in temperate soils from Lake Superior watersheds. Appl Environ Microbiol. 2006;72(1):612–21. doi: 10.1128/AEM.72.1.612-621.2006 16391098; PubMed Central PMCID: PMC1352292.

5. Ishii S, Sadowsky MJ. Escherichia coli in the Environment: Implications for Water Quality and Human Health. Microbes Environ. 2008;23(2):101–8. doi: 10.1264/jsme2.23.101 21558695.

6. van Elsas JD, Semenov AV, Costa R, Trevors JT. Survival of Escherichia coli in the environment: fundamental and public health aspects. ISME J. 2011;5(2):173–83. doi: 10.1038/ismej.2010.80 20574458; PubMed Central PMCID: PMC3105702.

7. Berthe T, Ratajczak M, Clermont O, Denamur E, Petit F. Evidence for coexistence of distinct Escherichia coli populations in various aquatic environments and their survival in estuary water. Appl Environ Microbiol. 2013;79(15):4684–93. doi: 10.1128/AEM.00698-13 23728810; PubMed Central PMCID: PMC3719502.

8. Donnenberg MS. Escherichia coli: virulence mechanisms of a versatile pathogen. New York: Academic Press, New York; 2002.

9. Kaper JB, Nataro JP, Mobley HL. Pathogenic Escherichia coli. Nat Rev Microbiol. 2004;2(2):123–40. doi: 10.1038/nrmicro818 15040260.

10. Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, et al. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol. 2006;60(5):1136–51. doi: 10.1111/j.1365-2958.2006.05172.x 16689791; PubMed Central PMCID: PMC1557465.

11. Croxen MA, Finlay BB. Molecular mechanisms of Escherichia coli pathogenicity. Nat Rev Microbiol. 2010;8(1):26–38. doi: 10.1038/nrmicro2265 19966814.

12. Leimbach A, Hacker J, Dobrindt U. E. coli as an all-rounder: the thin line between commensalism and pathogenicity. Curr Top Microbiol Immunol. 2013;358:3–32. doi: 10.1007/82_2012_303 23340801.

13. Gomes TA, Elias WP, Scaletsky IC, Guth BE, Rodrigues JF, Piazza RM, et al. Diarrheagenic Escherichia coli. Braz J Microbiol. 2016;47 Suppl 1:3–30. doi: 10.1016/j.bjm.2016.10.015 27866935; PubMed Central PMCID: PMC5156508.

14. Vila J, Saez-Lopez E, Johnson JR, Romling U, Dobrindt U, Canton R, et al. Escherichia coli: an old friend with new tidings. FEMS Microbiol Rev. 2016;40(4):437–63. doi: 10.1093/femsre/fuw005 28201713.

15. Cassini A, Hogberg LD, Plachouras D, Quattrocchi A, Hoxha A, Simonsen GS, et al. Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis. Lancet Infect Dis. 2019;19(1):56–66. doi: 10.1016/S1473-3099(18)30605-4 30409683; PubMed Central PMCID: PMC6300481.

16. Chaudhuri RR, Henderson IR. The evolution of the Escherichia coli phylogeny. Infect Genet Evol. 2012;12(2):214–26. doi: 10.1016/j.meegid.2012.01.005 22266241.

17. Ochman H, Selander RK. Standard reference strains of Escherichia coli from natural populations. J Bacteriol. 1984;157(2):690–3. 6363394; PubMed Central PMCID: PMC215307.

18. Didelot X, Meric G, Falush D, Darling AE. Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. BMC Genomics. 2012;13:256. doi: 10.1186/1471-2164-13-256 22712577; PubMed Central PMCID: PMC3505186.

19. Dixit PD, Pang TY, Studier FW, Maslov S. Recombinant transfer in the basic genome of Escherichia coli. Proc Natl Acad Sci U S A. 2015;112(29):9070–5. doi: 10.1073/pnas.1510839112 26153419; PubMed Central PMCID: PMC4517234.

20. Beghain J, Bridier-Nahmias A, Le Nagard H, Denamur E, Clermont O. ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microb Genom. 2018;4(7). doi: 10.1099/mgen.0.000192 29916797; PubMed Central PMCID: PMC6113867.

21. Lu S, Jin D, Wu S, Yang J, Lan R, Bai X, et al. Insights into the evolution of pathogenicity of Escherichia coli from genomic analysis of intestinal E. coli of Marmota himalayana in Qinghai-Tibet plateau of China. Emerg Microbes Infect. 2016;5(12):e122. doi: 10.1038/emi.2016.122 27924811; PubMed Central PMCID: PMC5180367.

22. Clermont O, Dixit OVA, Vangchhia B, Condamine B, Bridier-Nahmias A, Denamur E, et al. Characterisation and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential. Environ Microbiol. 2019. doi: 10.1111/1462-2920.14713 31188527.

23. Bergthorsson U, Ochman H. Distribution of chromosome length variation in natural isolates of Escherichia coli. Mol Biol Evol. 1998;15(1):6–16. doi: 10.1093/oxfordjournals.molbev.a025847 9491600.

24. Escobar-Paramo P, Le Menac'h A, Le Gall T, Amorin C, Gouriou S, Picard B, et al. Identification of forces shaping the commensal Escherichia coli genetic structure by comparing animal and human isolates. Environ Microbiol. 2006;8(11):1975–84. doi: 10.1111/j.1462-2920.2006.01077.x 17014496.

25. Vollmerhausen TL, Ramos NL, Gundogdu A, Robinson W, Brauner A, Katouli M. Population structure and uropathogenic virulence-associated genes of faecal Escherichia coli from healthy young and elderly adults. J Med Microbiol. 2011;60(Pt 5):574–81. doi: 10.1099/jmm.0.027037-0 21292854.

26. Smati M, Clermont O, Bleibtreu A, Fourreau F, David A, Daubie AS, et al. Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level. Microbiologyopen. 2015;4(4):604–15. doi: 10.1002/mbo3.266 26033772; PubMed Central PMCID: PMC4554456.

27. Bok E, Mazurek J, Myc A, Stosik M, Wojciech M, Baldy-Chudzik K. Comparison of Commensal Escherichia coli Isolates from Adults and Young Children in Lubuskie Province, Poland: Virulence Potential, Phylogeny and Antimicrobial Resistance. Int J Environ Res Public Health. 2018;15(4). doi: 10.3390/ijerph15040617 29597292; PubMed Central PMCID: PMC5923659.

28. Gordon DM, Stern SE, Collignon PJ. Influence of the age and sex of human hosts on the distribution of Escherichia coli ECOR groups and virulence traits. Microbiology. 2005;151(Pt 1):15–23. doi: 10.1099/mic.0.27425-0 15632421.

29. Escobar-Paramo P, Grenet K, Le Menac'h A, Rode L, Salgado E, Amorin C, et al. Large-scale population structure of human commensal Escherichia coli isolates. Appl Environ Microbiol. 2004;70(9):5698–700. doi: 10.1128/AEM.70.9.5698-5700.2004 15345464; PubMed Central PMCID: PMC520916.

30. Skurnik D, Bonnet D, Bernede-Bauduin C, Michel R, Guette C, Becker JM, et al. Characteristics of human intestinal Escherichia coli with changing environments. Environ Microbiol. 2008;10(8):2132–7. doi: 10.1111/j.1462-2920.2008.01636.x 18459976.

31. Duriez P, Clermont O, Bonacorsi S, Bingen E, Chaventre A, Elion J, et al. Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations. Microbiology. 2001;147(Pt 6):1671–6. doi: 10.1099/00221287-147-6-1671 11390698.

32. Power ML, Littlefield-Wyer J, Gordon DM, Veal DA, Slade MB. Phenotypic and genotypic characterization of encapsulated Escherichia coli isolated from blooms in two Australian lakes. Environ Microbiol. 2005;7(5):631–40. doi: 10.1111/j.1462-2920.2005.00729.x 15819845.

33. Walk ST, Alm EW, Calhoun LM, Mladonicky JM, Whittam TS. Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches. Environ Microbiol. 2007;9(9):2274–88. doi: 10.1111/j.1462-2920.2007.01341.x 17686024.

34. Ratajczak M, Laroche E, Berthe T, Clermont O, Pawlak B, Denamur E, et al. Influence of hydrological conditions on the Escherichia coli population structure in the water of a creek on a rural watershed. BMC Microbiol. 2010;10:222. doi: 10.1186/1471-2180-10-222 20723241; PubMed Central PMCID: PMC2933670.

35. Anastasi EM, Matthews B, Stratton HM, Katouli M. Pathogenic Escherichia coli found in sewage treatment plants and environmental waters. Appl Environ Microbiol. 2012;78(16):5536–41. doi: 10.1128/AEM.00657-12 22660714; PubMed Central PMCID: PMC3406122.

36. Picard B, Garcia JS, Gouriou S, Duriez P, Brahimi N, Bingen E, et al. The link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect Immun. 1999;67(2):546–53. 9916057; PubMed Central PMCID: PMC96353.

37. Johnson JR, Delavari P, Kuskowski M, Stell AL. Phylogenetic distribution of extraintestinal virulence-associated traits in Escherichia coli. J Infect Dis. 2001;183(1):78–88. doi: 10.1086/317656 11106538.

38. Moulin-Schouleur M, Reperant M, Laurent S, Bree A, Mignon-Grasteau S, Germon P, et al. Extraintestinal pathogenic Escherichia coli strains of avian and human origin: link between phylogenetic relationships and common virulence patterns. J Clin Microbiol. 2007;45(10):3366–76. doi: 10.1128/JCM.00037-07 17652485; PubMed Central PMCID: PMC2045314.

39. Riley LW. Pandemic lineages of extraintestinal pathogenic Escherichia coli. Clin Microbiol Infect. 2014;20(5):380–90. doi: 10.1111/1469-0691.12646 24766445.

40. Stoppe NC, Silva JS, Carlos C, Sato MIZ, Saraiva AM, Ottoboni LMM, et al. Worldwide Phylogenetic Group Patterns of Escherichia coli from Commensal Human and Wastewater Treatment Plant Isolates. Front Microbiol. 2017;8:2512. doi: 10.3389/fmicb.2017.02512 29312213; PubMed Central PMCID: PMC5742620.

41. Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol. 2008;190(20):6881–93. doi: 10.1128/JB.00619-08 18676672; PubMed Central PMCID: PMC2566221.

42. Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 2009;5(1):e1000344. doi: 10.1371/journal.pgen.1000344 19165319; PubMed Central PMCID: PMC2617782.

43. Lukjancenko O, Wassenaar TM, Ussery DW. Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol. 2010;60(4):708–20. doi: 10.1007/s00248-010-9717-3 20623278; PubMed Central PMCID: PMC2974192.

44. Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, et al. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics. 2015;15(2):141–61. doi: 10.1007/s10142-015-0433-4 25722247; PubMed Central PMCID: PMC4361730.

45. Petty NK, Ben Zakour NL, Stanton-Cook M, Skippington E, Totsika M, Forde BM, et al. Global dissemination of a multidrug resistant Escherichia coli clone. Proc Natl Acad Sci U S A. 2014;111(15):5694–9. doi: 10.1073/pnas.1322678111 24706808; PubMed Central PMCID: PMC3992628.

46. Tettelin H, Riley D, Cattuto C, Medini D. Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol. 2008;11(5):472–7. doi: 10.1016/j.mib.2008.09.006 19086349.

47. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2016;44(D1):D286–93. doi: 10.1093/nar/gkv1248 26582926; PubMed Central PMCID: PMC4702882.

48. Patel IR, Gangiredla J, Mammel MK, Lampel KA, Elkins CA, Lacher DW. Draft Genome Sequences of the Escherichia coli Reference (ECOR) Collection. Microbiol Resour Announc. 2018;7(14). doi: 10.1128/MRA.01133-18 30533715; PubMed Central PMCID: PMC6256646.

49. Gonzalez-Alba JM, Baquero F, Canton R, Galan JC. Stratified reconstruction of ancestral Escherichia coli diversification. BMC Genomics. 2019;20(1):936. doi: 10.1186/s12864-019-6346-1 31805853; PubMed Central PMCID: PMC6896753.

50. Wagner A, Lewis C, Bichsel M. A survey of bacterial insertion sequences using IScan. Nucleic Acids Res. 2007;35(16):5284–93. doi: 10.1093/nar/gkm597 17686783; PubMed Central PMCID: PMC2018620.

51. Touchon M, Rocha EP. Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol. 2007;24(4):969–81. doi: 10.1093/molbev/msm014 17251179.

52. Bobay LM, Touchon M, Rocha EP. Pervasive domestication of defective prophages by bacteria. Proc Natl Acad Sci U S A. 2014;111(33):12127–32. doi: 10.1073/pnas.1405336111 25092302; PubMed Central PMCID: PMC4143005.

53. Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ. 2015;3:e985. doi: 10.7717/peerj.985 26038737; PubMed Central PMCID: PMC4451026.

54. Royer G, Decousser JW, Branger C, Dubois M, Medigue C, Denamur E, et al. PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level. Microb Genom. 2018;4(9). doi: 10.1099/mgen.0.000211 30265232.

55. Guglielmini J, Neron B, Abby SS, Garcillan-Barcia MP, de la Cruz F, Rocha EP. Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion. Nucleic Acids Res. 2014;42(9):5715–27. doi: 10.1093/nar/gku194 24623814; PubMed Central PMCID: PMC4027160.

56. Cury J, Oliveira PH, de la Cruz F, Rocha EPC. Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements. Mol Biol Evol. 2018;35(11):2850. doi: 10.1093/molbev/msy182 30418640; PubMed Central PMCID: PMC6231490.

57. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006;34(Database issue):D32–6. doi: 10.1093/nar/gkj014 16381877; PubMed Central PMCID: PMC1347377.

58. Cury J, Jove T, Touchon M, Neron B, Rocha EP. Identification and analysis of integrons and cassette arrays in bacterial genomes. Nucleic Acids Res. 2016;44(10):4539–50. doi: 10.1093/nar/gkw319 27130947; PubMed Central PMCID: PMC4889954.

59. Domingues S, da Silva GJ, Nielsen KM. Integrons: Vehicles and pathways for horizontal dissemination in bacteria. Mob Genet Elements. 2012;2(5):211–23. doi: 10.4161/mge.22967 23550063; PubMed Central PMCID: PMC3575428.

60. Vieira G, Sabarly V, Bourguignon PY, Durot M, Le Fevre F, Mornico D, et al. Core and panmetabolism in Escherichia coli. J Bacteriol. 2011;193(6):1461–72. doi: 10.1128/JB.01192-10 21239590; PubMed Central PMCID: PMC3067614.

61. Sabarly V, Aubron C, Glodt J, Balliau T, Langella O, Chevret D, et al. Interactions between genotype and environment drive the metabolic phenotype within Escherichia coli isolates. Environ Microbiol. 2016;18(1):100–17. doi: 10.1111/1462-2920.12855 25808978.

62. Diaz E, Ferrandez A, Prieto MA, Garcia JL. Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev. 2001;65(4):523–69, table of contents. doi: 10.1128/MMBR.65.4.523-569.2001 11729263; PubMed Central PMCID: PMC99040.

63. Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, et al. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci U S A. 2013;110(50):20338–43. doi: 10.1073/pnas.1307797110 24277855; PubMed Central PMCID: PMC3864276.

64. Meric G, Kemsley EK, Falush D, Saggers EJ, Lucchini S. Phylogenetic distribution of traits associated with plant colonization in Escherichia coli. Environ Microbiol. 2013;15(2):487–501. doi: 10.1111/j.1462-2920.2012.02852.x 22934605.

65. Chen L, Zheng D, Liu B, Yang J, Jin Q. VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on. Nucleic Acids Res. 2016;44(D1):D694–7. doi: 10.1093/nar/gkv1239 26578559; PubMed Central PMCID: PMC4702877.

66. Cascales E, Buchanan SK, Duche D, Kleanthous C, Lloubes R, Postle K, et al. Colicin biology. Microbiol Mol Biol Rev. 2007;71(1):158–229. doi: 10.1128/MMBR.00036-06 17347522; PubMed Central PMCID: PMC1847374.

67. van Heel AJ, de Jong A, Montalban-Lopez M, Kok J, Kuipers OP. BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res. 2013;41(Web Server issue):W448–53. doi: 10.1093/nar/gkt391 23677608; PubMed Central PMCID: PMC3692055.

68. Jang J, Hur HG, Sadowsky MJ, Byappanahalli MN, Yan T, Ishii S. Environmental Escherichia coli: ecology and public health implications-a review. J Appl Microbiol. 2017;123(3):570–81. doi: 10.1111/jam.13468 28383815.

69. Hazen TH, Leonard SR, Lampel KA, Lacher DW, Maurelli AT, Rasko DA. Investigating the Relatedness of Enteroinvasive Escherichia coli to Other E. coli and Shigella Isolates by Using Comparative Genomics. Infect Immun. 2016;84(8):2362–71. doi: 10.1128/IAI.00350-16 27271741; PubMed Central PMCID: PMC4962626.

70. Stoesser N, Sheppard AE, Pankhurst L, De Maio N, Moore CE, Sebra R, et al. Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131. MBio. 2016;7(2):e02162. doi: 10.1128/mBio.02162-15 27006459; PubMed Central PMCID: PMC4807372.

71. Shaik S, Ranjan A, Tiwari SK, Hussain A, Nandanwar N, Kumar N, et al. Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages. MBio. 2017;8(5). doi: 10.1128/mBio.01596-17 29066550; PubMed Central PMCID: PMC5654935.

72. Gordon DM, Geyik S, Clermont O, O'Brien CL, Huang S, Abayasekara C, et al. Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection. mSphere. 2017;2(3). doi: 10.1128/mSphere.00168-17 28593194; PubMed Central PMCID: PMC5451516.

73. Johnson TJ, Elnekave E, Miller EA, Munoz-Aguayo J, Flores Figueroa C, Johnston B, et al. Phylogenomic Analysis of Extraintestinal Pathogenic Escherichia coli Sequence Type 1193, an Emerging Multidrug-Resistant Clonal Group. Antimicrob Agents Chemother. 2019;63(1). doi: 10.1128/AAC.01913-18 30348668; PubMed Central PMCID: PMC6325179.

74. Jorgensen SL, Stegger M, Kudirkiene E, Lilje B, Poulsen LL, Ronco T, et al. Diversity and Population Overlap between Avian and Human Escherichia coli Belonging to Sequence Type 95. mSphere. 2019;4(1). doi: 10.1128/mSphere.00333-18 30651401; PubMed Central PMCID: PMC6336079.

75. Dobrindt U, Chowdary MG, Krumbholz G, Hacker J. Genome dynamics and its impact on evolution of Escherichia coli. Med Microbiol Immunol. 2010;199(3):145–54. doi: 10.1007/s00430-010-0161-2 20445988.

76. Juhas M. Horizontal gene transfer in human pathogens. Crit Rev Microbiol. 2015;41(1):101–8. doi: 10.3109/1040841X.2013.804031 23862575.

77. Stokes HW, Gillings MR. Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS Microbiol Rev. 2011;35(5):790–819. doi: 10.1111/j.1574-6976.2011.00273.x 21517914.

78. von Wintersdorff CJ, Penders J, van Niekerk JM, Mills ND, Majumder S, van Alphen LB, et al. Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer. Front Microbiol. 2016;7:173. doi: 10.3389/fmicb.2016.00173 26925045; PubMed Central PMCID: PMC4759269.

79. Goldstone RJ, Smith DGE. A population genomics approach to exploiting the accessory 'resistome' of Escherichia coli. Microb Genom. 2017;3(4):e000108. doi: 10.1099/mgen.0.000108 28785420; PubMed Central PMCID: PMC5506381.

80. Frazao N, Sousa A, Lassig M, Gordo I. Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut. Proc Natl Acad Sci U S A. 2019;116(36):17906–15. doi: 10.1073/pnas.1906958116 31431529; PubMed Central PMCID: PMC6731689.

81. Kaas RS, Friis C, Ussery DW, Aarestrup FM. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC Genomics. 2012;13:577. doi: 10.1186/1471-2164-13-577 23114024; PubMed Central PMCID: PMC3575317.

82. Manges AR, Geum HM, Guo A, Edens TJ, Fibke CD, Pitout JDD. Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages. Clin Microbiol Rev. 2019;32(3). doi: 10.1128/CMR.00135-18 31189557; PubMed Central PMCID: PMC6589867.

83. Collins RE, Higgs PG. Testing the infinitely many genes model for the evolution of the bacterial core genome and pangenome. Mol Biol Evol. 2012;29(11):3413–25. doi: 10.1093/molbev/mss163 22752048.

84. Wolf YI, Makarova KS, Lobkovsky AE, Koonin EV. Two fundamentally different classes of microbial genes. Nat Microbiol. 2016;2:16208. doi: 10.1038/nmicrobiol.2016.208 27819663.

85. Paul JH. Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J. 2008;2(6):579–89. doi: 10.1038/ismej.2008.35 18521076.

86. Bichsel M, Barbour AD, Wagner A. Estimating the fitness effect of an insertion sequence. J Math Biol. 2013;66(1–2):95–114. doi: 10.1007/s00285-012-0504-2 22252506.

87. San Millan A, MacLean RC. Fitness Costs of Plasmids: a Limit to Plasmid Transmission. Microbiol Spectr. 2017;5(5). doi: 10.1128/microbiolspec.MTBP-0016-2017 28944751.

88. Mira A, Ochman H, Moran NA. Deletional bias and the evolution of bacterial genomes. Trends Genet. 2001;17(10):589–96. doi: 10.1016/s0168-9525(01)02447-7 11585665.

89. Lawrence JG, Hendrix RW, Casjens S. Where are the pseudogenes in bacterial genomes? Trends Microbiol. 2001;9(11):535–40. doi: 10.1016/s0966-842x(01)02198-9 11825713.

90. van Houte S, Buckling A, Westra ER. Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev. 2016;80(3):745–63. doi: 10.1128/MMBR.00011-16 27412881; PubMed Central PMCID: PMC4981670.

91. Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, et al. Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination. Mol Biol Evol. 2017;34(10):2537–54. doi: 10.1093/molbev/msx173 28595308; PubMed Central PMCID: PMC5850285.

92. Touchon M, Bernheim A, Rocha EP. Genetic and life-history traits associated with the distribution of prophages in bacteria. ISME J. 2016;10(11):2744–54. doi: 10.1038/ismej.2016.47 27015004; PubMed Central PMCID: PMC5113838.

93. Hacker J, Blum-Oehler G, Muhldorfer I, Tschape H. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol. 1997;23(6):1089–97. doi: 10.1046/j.1365-2958.1997.3101672.x 9106201.

94. Penades JR, Chen J, Quiles-Puchalt N, Carpena N, Novick RP. Bacteriophage-mediated spread of bacterial virulence genes. Curr Opin Microbiol. 2015;23:171–8. doi: 10.1016/j.mib.2014.11.019 25528295.

95. Touchon M, Bobay LM, Rocha EP. The chromosomal accommodation and domestication of mobile genetic elements. Curr Opin Microbiol. 2014;22:22–9. doi: 10.1016/j.mib.2014.09.010 25305534.

96. Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. Ecology drives a global network of gene exchange connecting the human microbiome. Nature. 2011;480(7376):241–4. doi: 10.1038/nature10571 22037308.

97. Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature. 2016;535(7612):435–9. doi: 10.1038/nature18927 27409808; PubMed Central PMCID: PMC4983458.

98. Batut B, Knibbe C, Marais G, Daubin V. Reductive genome evolution at both ends of the bacterial population size spectrum. Nat Rev Microbiol. 2014;12(12):841–50. doi: 10.1038/nrmicro3331 25220308.

99. Brewer TE, Handley KM, Carini P, Gilbert JA, Fierer N. Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'. Nat Microbiol. 2016;2:16198. doi: 10.1038/nmicrobiol.2016.198 27798560.

100. O'Brien CL, Bringer MA, Holt KE, Gordon DM, Dubois AL, Barnich N, et al. Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli. Gut. 2017;66(8):1382–9. doi: 10.1136/gutjnl-2015-311059 27196580.

101. Blyton MD, Gordon DM. Genetic Attributes of E. coli Isolates from Chlorinated Drinking Water. PLoS One. 2017;12(1):e0169445. doi: 10.1371/journal.pone.0169445 28107364.

102. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–9. doi: 10.1093/bioinformatics/btu153 24642063.

103. Ingle DJ, Valcanis M, Kuzevski A, Tauschek M, Inouye M, Stinear T, et al. In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages. Microb Genom. 2016;2(7):e000064. doi: 10.1099/mgen.0.000064 28348859; PubMed Central PMCID: PMC5343136.

104. Pfeifer B, Wittelsburger U, Ramos-Onsins SE, Lercher MJ. PopGenome: an efficient Swiss army knife for population genomic analyses in R. Mol Biol Evol. 2014;31(7):1929–36. doi: 10.1093/molbev/msu136 24739305; PubMed Central PMCID: PMC4069620.

105. Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A. 2009;106(45):19126–31. doi: 10.1073/pnas.0906412106 19855009; PubMed Central PMCID: PMC2776425.

106. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016;17(1):132. doi: 10.1186/s13059-016-0997-x 27323842; PubMed Central PMCID: PMC4915045.

107. Steinegger M, Soding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35(11):1026–8. doi: 10.1038/nbt.3988 29035372.

108. Steinegger M, Soding J. Clustering huge protein sequence sets in linear time. Nat Commun. 2018;9(1):2542. doi: 10.1038/s41467-018-04964-5 29959318; PubMed Central PMCID: PMC6026198.

109. Snipen L, Liland KH. micropan: an R-package for microbial pan-genomics. BMC Bioinformatics. 2015;16:79. doi: 10.1186/s12859-015-0517-0 25888166; PubMed Central PMCID: PMC4375852.

110. Nakamura T, Yamada KD, Tomii K, Katoh K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics. 2018;34(14):2490–2. doi: 10.1093/bioinformatics/bty121 29506019; PubMed Central PMCID: PMC6041967.

111. Eddy SR. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol. 2008;4(5):e1000069. doi: 10.1371/journal.pcbi.1000069 18516236; PubMed Central PMCID: PMC2396288.

112. Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7(10):e1002195. doi: 10.1371/journal.pcbi.1002195 22039361; PubMed Central PMCID: PMC3197634.

113. Filipski A, Murillo O, Freydenzon A, Tamura K, Kumar S. Prospects for building large timetrees using molecular data with incomplete gene coverage among species. Mol Biol Evol. 2014;31(9):2542–50. doi: 10.1093/molbev/msu200 24974376; PubMed Central PMCID: PMC4137717.

114. Hedge J, Wilson DJ. Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not. mBio. 2014;5(6):e02158. doi: 10.1128/mBio.02158-14 25425237; PubMed Central PMCID: PMC4251999.

115. Lapierre M, Blin C, Lambert A, Achaz G, Rocha EP. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography. Mol Biol Evol. 2016;33(7):1711–25. doi: 10.1093/molbev/msw048 26931140; PubMed Central PMCID: PMC4915353.

116. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–74. doi: 10.1093/molbev/msu300 25371430; PubMed Central PMCID: PMC4271533.

117. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol. 2018;35(2):518–22. doi: 10.1093/molbev/msx281 29077904; PubMed Central PMCID: PMC5850222.

118. Luo C, Walk ST, Gordon DM, Feldgarden M, Tiedje JM, Konstantinidis KT. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci U S A. 2011;108(17):7200–5. doi: 10.1073/pnas.1015622108 21482770; PubMed Central PMCID: PMC3084108.

119. Paradis E, Schliep K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics. 2018. doi: 10.1093/bioinformatics/bty633 30016406.

120. Snel B, Bork P, Huynen MA. Genome phylogeny based on gene content. Nat Genet. 1999;21(1):108–10. doi: 10.1038/5052 9916801.

121. Csuros M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics. 2010;26(15):1910–2. doi: 10.1093/bioinformatics/btq315 20551134.

122. Oliveira PH, Touchon M, Rocha EP. Regulation of genetic flux between bacteria by restriction-modification systems. Proc Natl Acad Sci U S A. 2016;113(20):5658–63. doi: 10.1073/pnas.1603257113 27140615; PubMed Central PMCID: PMC4878467.

123. Brynildsrud O, Bohlin J, Scheffer L, Eldholm V. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol. 2016;17(1):238. doi: 10.1186/s13059-016-1108-8 27887642; PubMed Central PMCID: PMC5124306.

124. Draper NR SH. Applied Regression Analysis. York JWSN, editor1998.

125. Abby SS, Neron B, Menager H, Touchon M, Rocha EP. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS One. 2014;9(10):e110726. doi: 10.1371/journal.pone.0110726 25330359; PubMed Central PMCID: PMC4201578.

126. Guglielmini J, Quintais L, Garcillan-Barcia MP, de la Cruz F, Rocha EP. The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet. 2011;7(8):e1002222. doi: 10.1371/journal.pgen.1002222 21876676; PubMed Central PMCID: PMC3158045.

127. Rendueles O, Garcia-Garcera M, Neron B, Touchon M, Rocha EPC. Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens. PLoS Pathog. 2017;13(7):e1006525. doi: 10.1371/journal.ppat.1006525 28742161; PubMed Central PMCID: PMC5542703.

128. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–4. doi: 10.1093/jac/dks261 22782487; PubMed Central PMCID: PMC3468078.

129. Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M, Landraud L, et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother. 2014;58(1):212–20. doi: 10.1128/AAC.01310-13 24145532; PubMed Central PMCID: PMC3910750.


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