Pathogen microevolution in high resolution

Science Translational Medicine

Volumn 2, Issue 16, 2010, Pages

  Aziz, Ramy K ^a   Nizet, Victor ^b  

^a CAIRO UNIVERSITY   (Egypt)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA LACTAM ANTIBIOTIC; FUSIDIC ACID; PANTON VALENTINE LEUKOCIDIN; PENICILLIN BINDING PROTEIN 2A; PSEUDOMONIC ACID; QUINOLINE DERIVED ANTIINFECTIVE AGENT; RIFAMPICIN; TRIMETHOPRIM;

ANTIBIOTIC RESISTANCE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL SURVIVAL; BACTERIAL TRANSMISSION; BACTERIAL VIRULENCE; BACTERIUM ISOLATE; CLINICAL PRACTICE; DEVICE INFECTION; DISEASE SURVEILLANCE; DNA FINGERPRINTING; GENE FUNCTION; GENE SEQUENCE; GENE SWITCHING; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; GEOGRAPHIC ORIGIN; HOSPITAL INFECTION; HOSPITALIZATION; HUMAN; INFECTION CONTROL; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; MOLECULAR CLONING; MOLECULAR EPIDEMIOLOGY; MOLECULAR EVOLUTION; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROCESS MODEL; PUBLIC HEALTH PROBLEM; SHORT SURVEY; SINGLE NUCLEOTIDE POLYMORPHISM; STAPHYLOCOCCAL BACTEREMIA; STRUCTURAL GENOMICS;

EVOLUTION, MOLECULAR; GENOMICS; GENOTYPE; GEOGRAPHY; HUMANS; METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 77953004087     PISSN: 19466234     EISSN: 19466242     Source Type: Journal    
DOI: 10.1126/scitranslmed.3000713     Document Type: Short Survey

References (34)

1. R. D. Fleischmann, M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J. F. Tomb, B. A. Dougherty, J. M. Merrick, K. McKenney, G. Sutton, W. FitzHugh, C. Fields, J. D. Gocayne, J. Scott, R. Shirley, L. Liu, A. Glodek, J. M. Kelley, J. F. Weidman, C. A. Phillipps, T. Spriggs, E. Hedblom, M. D. Cotton, T. R. Utterback, M. C. Hanna, D. T. Nguyen, D. M. Saudek, R. C. Brandon, L. D. Fine, J. L. Fritchman, J. L. Fuhrmann, N. S. Geoghagen, C. L. Gnehm, L. A. McDonald, K. V. Small, C. M. Fraser, H. O. Smith, J. C. Venter, Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512 (1995).
2. S. C. Schuster, Next-generation sequencing transforms today's biology. Nat. Methods 5, 16-18 (2008).
3. D. Wu, P. Hugenholtz, K. Mavromatis, R. Pukall, E. Dalin, N. N. Ivanova, V. Kunin, L. Goodwin, M. Wu, B. J. Tindall, S. D. Hooper, A. Pati, A. Lykidis, S. Spring, I. J. Anderson, P. D'haeseleer, A. Zemla, M. Singer, A. Lapidus, M. Nolan, A. Copeland, C. Han, F. Chen, J. F. Cheng, S. Lucas, C. Kerfeld, E. Lang, S. Gronow, P. Chain, D. Bruce, E. M. Rubin, N. C. Kyrpides, H. P. Klenk, J. A. Eisen, A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462, 1056-1060 (2009).
4. J. Kaiser, DNA sequencing. A plan to capture human diversity in 1000 genomes. Science 319, 395 (2008). (Pubitemid 351160548)
5. P. J. Turnbaugh, R. E. Ley, M. Hamady, C. M. Fraser-Liggett, R. Knight, J. I. Gordon, The human microbiome project. Nature 449, 804-810 (2007).
6. S. Harris, E. J. Feil, M. T. Holden, M. A. Quail, E. K. Nickerson, N. Chantratita, S. Gardete, A. Tavares, N. Day, J. A. Lindsay, J. D. Edgeworth, H. de Lencastre, J. Parkhill, S. J. Peacock, S. Bentley, Evolution of MRSA during hospital transmission and intercontinental spread. Science 327, 469-474 (2010).
7. L. K. McNeil, R. K. Aziz, In silico reconstruction of the metabolic and pathogenic potential of bacterial genomes using subsystems. Genome Dyn. 6, 21-34 (2009).
8. L. L. Poon, Y. Guan, J. M. Nicholls, K. Y. Yuen, J. S. Peiris, The aetiology, origins, and diagnosis of severe acute respiratory syndrome. Lancet Infect. Dis. 4, 663-671 (2004). (Pubitemid 39452519)
9. G. Neumann, T. Noda, Y. Kawaoka, Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 459, 931-939 (2009).
10. C. M. Fraser, A genomics-based approach to biodefence preparedness. Nat. Rev. Genet. 5, 23-33 (2004).
11. A. Dance, Anthrax case ignites new forensics field. Nature 454, 813 (2008).
12. R. Rappuoli, A. Covacci, Reverse vaccinology and genomics. Science 302, 602 (2003).
13. M. C. Maiden, J. A. Bygraves, E. Feil, G. Morelli, J. E. Russell, R. Urwin, Q. Zhang, J. Zhou, K. Zurth, D. A. Caugant, I. M. Feavers, M. Achtman, B. G. Spratt, 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 (1998).
14. N. Woodford, D. M. Livermore, Infections caused by Gram-positive bacteria: A review of the global challenge. J. Infect. 59 (suppl. 1), S4-S16 (2009).
15. European Antimicrobial Resistance Surveillance System (EARSS), MRSA Prevalence Figures (2008) (http://www.rivm.nl/earss/database).
16. D. J. Farrell, R. E. Mendes, J. E. Ross, R. N. Jones, Linezolid surveillance program results for 2008 (LEADER Program for 2008). Diagn. Microbiol. Infect. Dis. 65, 392-403 (2009).
17. H. Goto, K. Shimada, H. Ikemoto, T. Oguri, Study Group on Antimicrobial Susceptibility of Pathogens Isolated from Respiratory Infections, Antimicrobial susceptibility of pathogens isolated from more than 10, 000 patients with infectious respiratory diseases: A 25-year longitudinal study. J. Infect. Chemother. 15, 347-360 (2009).
18. R. M. Klevens, M. A. Morrison, J. Nadle, S. Petit, K. Gershman, S. Ray, L. H. Harrison, R. Lynfield, G. Dumyati, J. M. Townes, A. S. Craig, E. R. Zell, G. E. Fosheim, L. K. McDougal, R. B. Carey, S. K. Fridkin, Active Bacterial Core surveillance (ABCs) MRSA Investigators, Invasive methicillinresistant Staphylococcus aureus infections in the United States. JAMA 298, 1763-1771 (2007).
19. H. F. Chambers, F. R. Deleo, Waves of resistance: Staphylococcus aureus in the antibiotic era. Nat. Rev. Microbiol. 7, 629-641 (2009).
20. Next-generation sequencing technologies are becoming more widely available and cost-efficient. Platforms by other vendors, including FLX(454) (454 Life Sciences, a Roche Company), ABI SOLID (Life Technologies), and Helicos HeliScope (Helico Bioscience Corporation), could provide similar functionalities as Agilent/Illumina for genome-wide microbial strain characterization.
21. M. Aires-de-Sousa, B. Correia, H. de Lencastre, Multilaboratory Project Collaborators, Changing patterns in frequency of recovery of five methicillin-resistant Staphylococcus aureus clones in Portuguese hospitals: Surveillance over a 16-year period. J. Clin. Microbiol. 46, 2912-2917 (2008).
22. J. D. Edgeworth, G. Yadegarfar, S. Pathak, R. Batra, J. D. Cockfield, D. Wyncoll, R. Beale, J. A. Lindsay, An outbreak in an intensive care unit of a strain of methicillin-resistant Staphylococcus aureus sequence type 239 associated with an increased rate of vascular access device-related bacteremia. Clin. Infect. Dis. 44, 493-501 (2007).
23. D. S. Smyth, L. K. McDougal, F. W. Gran, A. Manoharan, M. C. Enright, J. H. Song, H. de Lencastre, D. A. Robinson, F. R. DeLeo, Population structure of a hybrid clonal group of methicillin-resistant Staphylococcus aureus, ST239- MRSA-III. PLoS ONE 5, e8582 (2010).
24. M. A. Aldeyab, D. L. Monnet, J. M. López-Lozano, C. M. Hughes, M. G. Scott, M. P. Kearney, F. A. Magee, J. C. McElnay, Modelling the impact of antibiotic use and infection control practices on the incidence of hospital-acquired methicillin-resistant Staphylococcus aureus: A time-series analysis. J. Antimicrob. Chemother. 62, 593-600 (2008).
25. J. A. Lindsay, M. T. Holden, Staphylococcus aureus: Superbug, super genome? Trends Microbiol. 12, 378-385 (2004).
26. J. A. Lindsay, M. T. Holden, Understanding the rise of the superbug: Investigation of the evolution and genomic variation of Staphylococcus aureus. Funct. Integr. Genomics 6, 186-201 (2006).
27. F. C. Tenover, R. V. Goering, Methicillin-resistant Staphylococcus aureus strain USA300: Origin and epidemiology. J. Antimicrob. Chemother. 64, 441-446 (2009).
28. I. G. Bae, G. T. Tonthat, M. E. Stryjewski, T. H. Rude, L. F. Reilly, S. L. Barriere, F. C. Genter, G. R. Corey, V. G. Fowler Jr., Presence of genes encoding the Panton-Valentine leukocidin exotoxin is not the primary determinant of outcome in patients with complicated skin and skin structure infections due to methicillin-resistant Staphylococcus aureus: Results of a multinational trial. J. Clin. Microbiol. 47, 3952-3957 (2009).
29. M. Labandeira-Rey, F. Couzon, S. Boisset, E. L. Brown, M. Bes, Y. Benito, E. M. Barbu, V. Vazquez, M. Höök, J. Etienne, F. Vandenesch, M. G. Bowden, Staphylococcus aureus Panton-Valentine leukocidin causes necrotizing pneumonia. Science 315, 1130-1133 (2007). (Pubitemid 46328024)
30. J. Bubeck Wardenburg, A. M. Palazzolo-Ballance, M. Otto, O. Schneewind, F. R. DeLeo, Panton-Valentine leukocidin is not a virulence determinant in murine models of community- associated methicillin-resistant Staphylococcus aureus disease. J. Infect. Dis. 198, 1166-1170 (2008).
31. N. Ahmed, J. E. Stajich, A flood of microbial genomes- Do we need more? PLoS ONE 4, e5831 (2009).
32. P. Sumby, A. R. Whitney, E. A. Graviss, F. R. DeLeo, J. M. Musser, Genome-wide analysis of group A streptococci reveals a mutation that modulates global phenotype and disease specificity. PLoS Pathog. 2, e5 (2006).
33. M. J. Walker, A. Hollands, M. L. Sanderson-Smith, J. N. Cole, J. K. Kirk, A. Henningham, J. D. McArthur, K. Dinkla, R. K. Aziz, R. G. Kansal, A. J. Simpson, J. T. Buchanan, G. S. Chhatwal, M. Kotb, V. Nizet, DNase Sda1 provides selection pressure for a switch to invasive group A streptococcal infection. Nat. Med. 13, 981-985 (2007).
34. R. K. Aziz, M. Kotb, Rise and persistence of global M1T1 clone of Streptococcus pyogenes. Emerg. Infect. Dis. 14, 1511-1517 (2008).