High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4

Nucleic Acids Research

Volumn 43, Issue 1, 2015, Pages 348-360

  Yamaichi, Yoshiharu ^a,b,c   Chao, Michael C ^a,b   Sasabe, Jumpei ^a,b,d   Clark, Lars ^a,b   Davis, Brigid M ^a,b   Yamamoto, Nozomi ^e   Mori, Hiroshi ^e   Kurokawa, Ken ^e   Waldor, Matthew K ^a,b,f  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c INSTITUTE FOR INTEGRATIVE BIOLOGY OF THE CELL I2BC   (France)

^d KEIO UNIVERSITY   (Japan)

^e TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^f HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXTENDED SPECTRUM BETA LACTAMASE; METHYLTRANSFERASE; PROTEIN M ECOGIX; UNCLASSIFIED DRUG; TRANSPOSON;

ARTICLE; ENZYME ACTIVITY; ESCHERICHIA COLI; ESCHERICHIA COLI O104:H4; GENE INSERTION; GENE SEQUENCE; GENETIC ANALYSIS; HIGH THROUGHPUT SEQUENCING; HORIZONTAL GENE TRANSFER; NONHUMAN; PLASMID; TRANSPOSON; BACTERIAL GENE; DNA SEQUENCE; GENE LIBRARY; GENETICS;

ESCHERICHIA COLI;

DNA TRANSPOSABLE ELEMENTS; ESCHERICHIA COLI; GENE LIBRARY; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PLASMIDS; SEQUENCE ANALYSIS, DNA;

EID: 84941088781     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1262     Document Type: Article

References (49)

1. Carattoli, A. (2013) Plasmids and the spread of resistance. Int. J. Med. Microbiol., 303, 298-304.
2. Juhas, M. (2013) Horizontal gene transfer in human pathogens. Crit. Rev. Microbiol. , doi:10.3109/1040841X.2013.804031.
3. Scheutz, F., Nielsen, E.M., Frimodt-Møller, J., Boisen, N., Morabito, S., Tozzoli, R., Nataro, J.P. and Caprioli, A. (2011) Characteristics of the enteroaggregative Shiga toxin/verotoxin-producing Escherichia coli O104:H4 strain causing the outbreak of haemolytic uraemic syndrome in Germany, May to June 2011. Euro. Surveill., 16, pii19889.
4. Frank, C., Werber, D., Cramer, J.P., Askar, M., Faber, M., an der Heiden, M., Bernard, H., Fruth, A., Prager, R., Spode, A. et al. (2011) Epidemic profile of Shiga-Toxin-producing Escherichia coli O104:H4 outbreak in Germany.N. Engl. J. Med., 365, 1771-1780.
5. Bielaszewska, M., Mellmann, A., Zhang, W., Köck, R., Fruth, A., Bauwens, A., Peters, G. and Karch, H. (2011) Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study. Lancet Infect. Dis., 11, 671-676.
6. Munera, D., Ritchie, J.M., Hatzios, S.K., Bronson, R., Fang, G., Schadt, E.E., Davis, B.M. and Waldor, M.K. (2014) Autotransporters but not pAA are critical for rabbit colonization by Shiga toxin-producing Escherichia coli O104:H4. Nat. Commun., 5, 3080.
7. Grad, Y.H., Lipsitch, M., Feldgarden, M., Arachchi, H.M., Cerqueira, G.C., Fitzgerald, M., Godfrey, P., Haas, B.J., Murphy, C.I., Russ, C. et al. (2012) Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc. Natl Acad. Sci. U.S.A., 109, 3065-3070.
8. Rasko, D.A., Webster, D.R., Sahl, J.W., Bashir, A., Boisen, N., Scheutz, F., Paxinos, E.E., Sebra, R., Chin, C.S., Iliopoulos, D. et al. (2011) Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.N. Engl. J. Med., 365, 709-717.
9. Rohde, H., Qin, J., Cui, Y., Li, D., Loman, N.J., Hentschke, M., Chen, W., Pu, F., Peng, Y., Li, J. et al. (2011) Open-source genomic analysis of Shiga-Toxin-producing E. coli O104:H4. N. Engl. J. Med., 365, 718-724.
10. Mayer, C.L., Leibowitz, C.S., Kurosawa, S. and Stearns-Kurosawa, D.J. (2012) Shiga toxins and the pathophysiology of hemolytic uremic syndrome in humans and animals. Toxins, 4, 1261-1287.
11. Ghafourian, S., Sadeghifard, N., Soheili, S. and Sekawi, Z. (2014) Extended spectrum beta-lactamases: definition, classification and epidemiology. Curr. Issues Mol. Biol., 17, 11-22.
12. Ahmed, S.A., Awosika, J., Baldwin, C., Bishop-Lilly, K.A., Biswas, B., Broomall, S., Chain, P.S., Chertkov, O., Chokoshvili, O., Coyne, S. et al. (2012) 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, 7, e48228.
13. Brzuszkiewicz, E., Thürmer, A., Schuldes, J., Leimbach, A., Liesegang, H., Meyer, F.D., Boelter, J., Petersen, H., Gottschalk, G. and Daniel, R. (2011) Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC). Arch. Microbiol., 193, 883-891.
14. Grad, Y.H., Godfrey, P., Cerquiera, G.C., Mariani-Kurkdjian, P., Gouali, M., Bingen, E., Shea, T.P., Haas, B.J., Griggs, A., Young, S. et al. (2013) Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-Term evolution of an emerging pathogen. MBio, 4, e00452-e00412.
15. Christie, P.J., Whitaker, N. and Gonźalez-Rivera, C. (2014) Mechanism and structure of the bacterial type IV secretion systems. Biochim. Biophys. Acta, 1843, 1578-1591.
16. Singh, P.K. and Meijer, W.J. (2014) Diverse regulatory circuits for transfer of conjugative elements. FEMS Microbiol. Lett. , 358, 119-128.
17. Smet, A., Van Nieuwerburgh, F., Vandekerckhove, T.T., Martel, A., Deforce, D., Butaye, P. and Haesebrouck, F. (2010) Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences. PLoS One, 5, e11202.
18. Fischer, J., Rodriguez, I., Baumann, B., Guiral, E., Beutin, L., Schroeter, A., Kaesbohrer, A., Pfeifer, Y., Helmuth, R. and Guerra, B. (2014) blaCTX-M-15-carrying Escherichia coli and Salmonella isolates from livestock and food in Germany. J. Antimicrob. Chemother. , 69, 2951-2958.
19. Garcia-Ferńandez, A., Chiaretto, G., Bertini, A., Villa, L., Fortini, D., Ricci, A. and Carattoli, A. (2008) Multilocus sequence typing of IncI1 plasmids carrying extended-spectrum beta-lactamases in Escherichia coli and Salmonella of human and animal origin. J. Antimicrob. Chemother., 61, 1229-1233.
20. Sampei, G., Furuya, N., Tachibana, K., Saitou, Y., Suzuki, T., Mizobuchi, K. and Komano, T. (2010) Complete genome sequence of the incompatibility group I1 plasmid R64. Plasmid, 64, 92-103.
21. Asano, K. and Mizobuchi, K. (1998) Copy number control of IncIalpha plasmid ColIb-P9 by competition between pseudoknot formation and antisense RNA binding at a specific RNA site. EMBO J., 17, 5201-5213.
22. Nekrasov, S.V., Agafonova, O.V., Belogurova, N.G., Delver, E.P. and Belogurov, A.A. (2007) Plasmid-encoded antirestriction protein ArdA can discriminate between type I methyltransferase and complete restriction-modification system. J. Mol. Biol., 365, 284-297.
23. Fang, G., Munera, D., Friedman, D.I., Mandlik, A., Chao, M.C., Banerjee, O., Feng, Z., Losic, B., Mahajan, M.C., Jabado, O.J. et al. (2012) Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-Time sequencing. Nat. Biotechnol., 30, 1232-1239.
24. Komano, T., Yoshida, T., Narahara, K. and Furuya, N. (2000) The transfer region of IncI1 plasmid R64: similarities between R64 tra and legionella icm/dot genes. Mol. Microbiol., 35, 1348-1359.
25. Rees, C.E., Bradley, D.E. and Wilkins, B.M. (1987) Organization and regulation of the conjugation genes of IncI1 plasmid colIb-P9. Plasmid, 18, 223-236.
26. van Opijnen, T. and Camilli, A. (2013) Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nat. Rev. Microbiol., 11, 435-442.
27. Barquist, L., Boinett, C.J. and Cain, A.K. (2013) Approaches to querying bacterial genomes with transposon-insertion sequencing. RNA Biol., 10, 1161-1169.
28. Singer, M., Baker, T.A., Schnitzler, G., Deischel, S.M., Goel, M., Dove, W., Jaacks, K.J., Grossman, A.D., Erickson, J.W. and Gross, C.A. (1989) A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev., 53, 1-24.
29. Domenico, P., Salo, R.J., Cross, A.S. and Cunha, B.A. (1994) Polysaccharide capsule-mediated resistance to opsonophagocytosis in Klebsiella pneumoniae. Infect. Immun., 62, 4495-4499.
30. Chiang, S.L. and Rubin, E.J. (2002) Construction of a mariner-based transposon for epitope-Tagging and genomic targeting. Gene, 296, 179-185.
31. Datsenko, K.A. and Wanner, B.L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. U.S.A., 97, 6640-6645.
32. Gibson, D.G., Young, L., Chuang, R.Y., Venter, J.C., Hutchison, C.A. and Smith, H.O. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods, 6, 343-345.
33. Milton, D.L., O'Toole, R., Horstedt, P. and Wolf-Watz, H. (1996) Flagellin A is essential for the virulence of Vibrio anguillarum. J. Bacteriol., 178, 1310-1319.
34. Guzman, L.M., Belin, D., Carson, M.J. and Beckwith, J. (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J. Bacteriol., 177, 4121-4130.
35. Kusano, K., Naito, T., Handa, N. and Kobayashi, I. (1995) Restriction-modification systems as genomic parasites in competition for specific sequences. Proc. Natl Acad. Sci. U.S.A., 92, 11095-11099.
36. Chao, M.C., Pritchard, J.R., Zhang, Y.J., Rubin, E.J., Livny, J., Davis, B.M. and Waldor, M.K. (2013) High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data. Nucleic Acids Res., 41, 9033-9048.
37. Pritchard, J.R., Chao, M.C., Abel, S., Davis, B.M., Zhang, Y.J., Baronowski, K., Rubin, E.J. and Waldor, M.K. (2014) ARTIST: high-resolution genome-wide assessment of fitness using transposon-insertion sequencing. PLoS Genet., 10, e1004782.
38. Martin, M. (2011) Cutadapt removes adapter sequences from high-Throughput sequencing reads. EMBnet. J., 17, 10-12.
39. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
40. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
41. Livak, K.J. and Schmittgen, T.D. (2001) Analysis of relative gene expression data using real-Time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods, 25, 402-408.
42. Johnson, T.J., Shepard, S.M., Rivet, B., Danzeisen, J.L. and Carattoli, A. (2011) Comparative genomics and phylogeny of the IncI1 plasmids: a common plasmid type among porcine enterotoxigenic Escherichia coli. Plasmid, 66, 144-151.
43. Asano, K. and Mizobuchi, K. (1998) An RNA pseudoknot as the molecular switch for translation of the repZ gene encoding the replication initiator of IncIalpha plasmid ColIb-P9. J. Biol. Chem., 273, 11815-11825.
44. Yoshida, T., Kim, S.R. and Komano, T. (1999) Twelve pil genes are required for biogenesis of the R64 thin pilus. J. Bacteriol., 181, 2038-2043.
45. Kim, S.R. and Komano, T. (1997) The plasmid R64 thin pilus identified as a type IV pilus. J. Bacteriol., 179, 3594-3603.
46. Furuya, N. and Komano, T. (1996) Nucleotide sequence and characterization of the trbABC region of the IncI1 Plasmid R64: existence of the pnd gene for plasmid maintenance within the transfer region. J. Bacteriol., 178, 1491-1497.
47. Kim, S.R., Funayama, N. and Komano, T. (1993) Nucleotide sequence and characterization of the traABCD region of IncI1 plasmid R64. J. Bacteriol., 175, 5035-5042.
48. Komano, T., Funayama, N., Kim, S.R. and Nisioka, T. (1990) Transfer region of IncI1 plasmid R64 and role of shufflon in R64 transfer. J. Bacteriol., 172, 2230-2235.
49. Komano, T. (1999) Shufflons: multiple inversion systems and integrons. Annu. Rev. Genet., 33, 171-191.