Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Brolund, Alma ^a,b   Franzén, Oscar ^b,d   Melefors, Öjar ^a,b   Tegmark Wisell, Karin ^a,b   Sandegren, Linus ^c  

^a SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

^b KAROLINSKA INSTITUTE   (Sweden)

^c UPPSALA UNIVERSITY   (Sweden)

^d MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIKACIN; AMINOGLYCOSIDE ANTIBIOTIC AGENT; BETA LACTAM ANTIBIOTIC; BETA LACTAMASE CTX M; CEFADROXIL; CEFOTAXIME; CHLORAMPHENICOL; EXTENDED SPECTRUM BETA LACTAMASE; MACROLIDE; MECILLINAM; NITROFURANTOIN; QUINOLINE DERIVED ANTIINFECTIVE AGENT; SULFONAMIDE; TETRACYCLINE; TRIMETHOPRIM;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; ESCHERICHIA COLI; GENE DOSAGE; GENETIC VARIABILITY; GEOGRAPHY; HIDDEN MARKOV MODEL; HIGH THROUGHPUT SEQUENCING; MULTIDRUG RESISTANCE; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMID; PROPHAGE; PULSED FIELD GEL ELECTROPHORESIS; SEQUENCE HOMOLOGY;

BETA-LACTAMASES; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DNA REPLICATION; DRUG RESISTANCE, BACTERIAL; ESCHERICHIA COLI; ESCHERICHIA COLI INFECTIONS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR SEQUENCE DATA; MOLECULAR TYPING; PHYLOGENY; PLASMIDS; PROPHAGES; URINARY TRACT INFECTIONS;

ESCHERICHIA COLI;

EID: 84878981289     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0065793     Document Type: Article

References (37)

1. Pitout JDD, Laupland KB, (2008) Extended-spectrum beta-lactamase-producing Enterobacteriaceae: an emerging public-health concern. The Lancet infectious diseases 8: 159-166.
2. Pitout JD, (2010) Infections with extended-spectrum beta-lactamase-producing Enterobacteriaceae: changing epidemiology and drug treatment choices. Drugs 70: 313-333.
3. Bush K, Jacoby GA, Medeiros AA, (1995) A functional classification scheme for beta-lactamases and its correlation with molecular structure. Antimicrob Agents Chemother 39: 1211-1233.
4. Ambler RP, (1980) The structure of beta-lactamases. Philos Trans R Soc Lond B Biol Sci 289: 321-331.
5. Giske CG, Sundsfjord AS, Kahlmeter G, Woodford N, Nordmann P, et al. (2009) Redefining extended-spectrum beta-lactamases: balancing science and clinical need. J Antimicrob Chemother 63: 1-4.
6. Cantón R, González-Alba JM, Galán JC, (2012) CTX-M Enzymes: Origin and Diffusion. Frontiers in microbiology 3: 110.
7. Ripoll A, Baquero F, Novais A, Rodríguez-Domínguez MJ, Turrientes M-C, et al. (2011) In vitro selection of variants resistant to beta-lactams plus beta-lactamase inhibitors in CTX-M beta-lactamases: predicting the in vivo scenario? Antimicrobial agents and chemotherapy 55: 4530-4536.
8. Smet A, Van Nieuwerburgh F, Vandekerckhove TT, Martel A, Deforce D, et al. (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.
9. Wilkins BM, (2002) Plasmid promiscuity: meeting the challenge of DNA immigration control. Environ Microbiol 4: 495-500.
10. Carattoli A, (2011) Plasmids in Gram negatives: Molecular typing of resistance plasmids. Int J Med Microbiol 301: 654-658.
11. Brolund A, Haeggman S, Edquist PJ, Gezelius L, Olsson-Liljequist B, et al. (2010) The DiversiLab system versus pulsed-field gel electrophoresis: characterisation of extended spectrum beta-lactamase producing Escherichia coli and Klebsiella pneumoniae. J Microbiol Methods 83: 224-230.
12. Barton BM, Harding GP, Zuccarelli AJ, (1995) A general method for detecting and sizing large plasmids. Anal Biochem 226: 235-240.
13. Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL, et al. (2005) Identification of plasmids by PCR-based replicon typing. J Microbiol Methods 63: 219-228.
14. Tofteland S, Haldorsen B, Dahl KH, Simonsen GS, Steinbakk M, et al. (2007) Effects of phenotype and genotype on methods for detection of extended-spectrum-beta-lactamase-producing clinical isolates of Escherichia coli and Klebsiella pneumoniae in Norway. J Clin Microbiol 45: 199-205.
15. Garcia-Fernandez A, Carattoli A, (2010) Plasmid double locus sequence typing for IncHI2 plasmids, a subtyping scheme for the characterization of IncHI2 plasmids carrying extended-spectrum beta-lactamase and quinolone resistance genes. J Antimicrob Chemother 65: 1155-1161.
16. Garcia-Fernandez A, Chiaretto G, Bertini A, Villa L, Fortini D, et al. (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.
17. Jolley KA, Maiden MCJ, (2010) BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC bioinformatics 11: 595.
18. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
19. Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic acids research 38: D211-22.
20. Eddy SR, (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform 23: 205-211.
21. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
22. Johnson JR, Johnston B, Clabots C, Kuskowski MA, Castanheira M, (2010) Escherichia coli sequence type ST131 as the major cause of serious multidrug-resistant E. coli infections in the United States. Clinical infectious diseases? 51: 286-294.
23. Sherley M, Gordon DM, Collignon PJ, (2003) Species differences in plasmid carriage in the Enterobacteriaceae. Plasmid 49: 79-85.
24. Brolund A, Wisell KT, Edquist PJ, Elfstrom L, Walder M, et al. (2010) Development of a real-time SYBRGreen PCR assay for rapid detection of acquired AmpC in Enterobacteriaceae. J Microbiol Methods 82: 229-233.
25. Brolund A, Sundqvist M, Kahlmeter G, Grape M, (2010) Molecular characterisation of trimethoprim resistance in Escherichia coli and Klebsiella pneumoniae during a two year intervention on trimethoprim use. PLoS One 5: e9233.
26. Łobocka MB, Rose DJ, Plunkett G, Rusin M, Samojedny A, et al. (2004) Genome of bacteriophage P1. Journal of bacteriology 186: 7032-7068.
27. Miquel S, Peyretaillade E, Claret L, De Vallee A, Dossat C, et al. (2010) Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82. PLoS One 5.
28. Burian J, Guller L, Macor M, Kay WW, (1997) Small cryptic plasmids of multiplasmid, clinical Escherichia coli. Plasmid 37: 2-14.
29. Woodford N, Carattoli A, Karisik E, Underwood A, Ellington MJ, et al. (2009) Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom, all belonging to the international O25:H4-ST131 clone. Antimicrob Agents Chemother 53: 4472-4482.
30. Chen SL, Hung C-S, Xu J, Reigstad CS, Magrini V, et al. (2006) Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proceedings of the National Academy of Sciences of the United States of America 103: 5977-5982.
31. Yi H, Xi Y, Liu J, Wang J, Wu J, et al. (2010) Sequence analysis of pKF3-70 in Klebsiella pneumoniae: probable origin from R100-like plasmid of Escherichia coli. PLoS One 5: e8601.
32. Coque TM, Novais A, Carattoli A, Poirel L, Pitout J, et al. (2008) Dissemination of clonally related Escherichia coli strains expressing extended-spectrum beta-lactamase CTX-M-15. Emerg Infect Dis 14: 195-200.
33. Sandegren L, Linkevicius M, Lytsy B, Melhus A, Andersson DI (2011) Transfer of an Escherichia coli ST131 multiresistance cassette has created a Klebsiella pneumoniae-specific plasmid associated with a major nosocomial outbreak. J Antimicrob Chemother.
34. Bengtsson S, Naseer U, Sundsfjord A, Kahlmeter G, Sundqvist M, (2012) Sequence types and plasmid carriage of uropathogenic Escherichia coli devoid of phenotypically detectable resistance. The Journal of antimicrobial chemotherapy 67: 69-73.
35. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution 28: 2731-2739.
36. Darling AE, Mau B, Perna NT, (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PloS one 5: e11147.
37. Guy L, Kultima JR, Andersson SGE, (2010) genoPlotR: comparative gene and genome visualization in R. Bioinformatics. 26: 2334-2335.