Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 18, 2014, Pages 6738-6743

  Uhlemann, Anne Catrin ^a   Dordel, Janina ^b   Knox, Justin R ^a   Raven, Kathy E ^c   Parkhill, Julian ^b   Holden, Matthew T G ^b,d   Peacock, Sharon J ^b,c   Lowy, Franklin D ^a  

^a NewYork Presbyterian Hospital   (United States)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d UNIVERSITY OF ST ANDREWS   (United Kingdom)

Author keywords

CC8; Drug resistance; Genomics; Phylogeny

Indexed keywords

CIPROFLOXACIN; NUCLEOTIDE; QUINOLONE DERIVATIVE;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL COLONIZATION; BACTERIAL TRANSMISSION; BACTERIUM ISOLATE; CLADISTICS; CLONE; COMMUNITY ASSOCIATED METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS INFECTION; CONTROLLED STUDY; DRUG EXPOSURE; GENE SEQUENCE; HOUSEHOLD; HUMAN; MAJOR CLINICAL STUDY; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS INFECTION; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MUTATION RATE; NONSENSE MUTATION; PATHOGENESIS; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; RESERVOIR; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES; URBAN POPULATION;

CC8; DRUG RESISTANCE; GENOMICS; PHYLOGENY;

CASE-CONTROL STUDIES; COMMUNITY-ACQUIRED INFECTIONS; DRUG RESISTANCE, MULTIPLE, BACTERIAL; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; HUMANS; METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS; MOLECULAR EPIDEMIOLOGY; NEW YORK CITY; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; STAPHYLOCOCCAL INFECTIONS; UNITED STATES; URBAN POPULATION;

EID: 84899807742     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1401006111     Document Type: Article

References (48)

1. David MZ, Daum RS (2010) Community-associated methicillin-resistant Staphylococcus aureus: Epidemiology and clinical consequences of an emerging epidemic. Clin Microbiol Rev 23(3):616-687.
2. Fridkin SK, et al.; Active Bacterial Core Surveillance Program of the Emerging Infections Program Network (2005) Methicillin-resistant Staphylococcus aureus disease in three communities. N Engl J Med 352(14):1436-1444.
3. McDougal LK, et al. (2003) Pulsed-field gel electrophoresis typing of oxacillin-resistant Staphylococcus aureus isolates from the United States: Estab lishing a national database. J Clin Microbiol 41(11):5113-5120.
4. Moran GJ, et al.; EMERGEncy ID Net Study Group (2006) Methicillin-resistant S. aureus infections among patients in the emergency department. N Engl J Med 355(7): 666-674.
5. Talan DA, et al.; EMERGEncy ID Net Study Group (2011) Comparison of Staphylococcus aureus from skin and soft-tissue infections in US emergency department pat ients, 2004 and 2008. Clin Infect Dis 53(2):144-149.
6. Li M et al 2010 Comparative analysis of virulence and toxin expression of global community-associated methicillin-resistant Staphylococcus aureus strains J Infect Dis 202 12 1866 -1876
7. Li M, et al. (2009) Evolution of virulence in epidemic community-associated methicillinresistant Staphylococcus aureus. Proc Natl Acad Sci USA 106(14):5883-5888.
8. Diep BA, et al. (2006) Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet 367(9512): 731-739.
9. Joshi GS, Spontak JS, Klapper DG, Richardson AR (2011) Arginine catabolic mobile element encoded speG abrogates the unique hypersensitivity of Staphylococcus aureus to exogenous polyamines. Mol Microbi ol 82(1):9-20.
10. Kennedy AD, et al. (2008) Epidemic community-associated methicillin-resistant Staphylococcus aureus: Recent clonal expansion and diversification. Proc Natl Acad Sci USA 105(4):1327-1332.
11. Tewhey R, et al. (2012) Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300. BMC Genomics 13(1):508.
12. Uhlema nn AC, et al. (2012) Toward an understanding of the evolution of Staphylococcus aureus strain USA300 during colonization in community households. Genome Biol Evol 4(12):1275-1285.
13. Prosperi M, et al. (2013) Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the genomic era: A cross-sectional study. Sci Rep 3:1902.
14. Uhlemann AC, et al. (2011) The environment as an unrecognized reservoir for community-associated methicillin resistant Staphylococcus aureus USA300: A case-control study. PLoS ONE 6(7):e22407.
15. Knox J, et al. (2012) Environmental contamination as a risk factor for intra-household Staphylococcus aureus transmission. PLoS ONE 7(11):e49900.
16. Harris SR, et al. (2010) Evolution of MRSA during hospital transmission and intercontinental spread. Science 327(5964):469-474.
17. Holden MT, et al. (2013) A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res 23(4): 653-664.
18. DeLeo FR, et al. (2011) Molecular differentiation of historic phage-type 80/81 and contemporary epidemic Staphylococcus aureus. Proc Natl Acad Sci USA 108(44):18091-18096.
19. McAdam PR, et al. (2012) Molecular tracing of the emergence, adaptation, and transmission of hospital-associ ated methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci USA 109(23):9107-9112.
20. Harris SR, et al. (2013) Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: A descriptive study. Lancet Infect Dis 13(2): 130-136.
21. Török ME, et al. (2013) Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak. J Clin Microbiol 51(2):611-614.
22. Gardy JL, et al. (2011) Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 364(8):730-739.
23. Highlander SK, et al. (2007) Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. BMC Microbiol 7:99.
24. Golubchik T, et al. (2013) Within-host evolution of Staphylococcus aureus during asymptomatic carriage. PLoS ONE 8(5):e61319.
25. Yang W, Ni L, Somerville RL (1993) A stationary-phase protein of Escherichia coli that affects the mo de of association between the trp repressor protein and operatorbearing DNA. Proc Natl Acad Sci USA 90(12):5796-5800.
26. Carey J, et al. (2007) WrbA bridges bacterial flavodoxins and eukaryotic NAD(P)H: Quinone oxidoreductases. Protein Sci 16(10):2301-2305.
27. Kishko I, et al. (2012) Biphasic kinetic behavior of E. coli WrbA, an FMN-dependent NAD(P)H:quinone oxidoreductase. PLoS ONE 7(8):e43902.
28. Thurlow LR, et al. (2013) Functional modularity of the arginine catabolic mobile element contributes to the success of USA300 methicillin-resistant Staphylococcus aureus. Cell Host Microbe 13(1):100-107.
29. McDougal LK, et al. (2010) Emergence of resistance among USA300 methicillinresistant Staphylococcus aureus isolates causing invasive disease in the United States. Antimicrob Agents Chemother 54(9):3804-3811.
30. Kennedy AD, et al. (2010) Complete nucleotide sequence analysis of plasmids in strains of Staphylococcus aureus clone USA300 reveal s a high level of identity among isolates with closely related core genome sequences. J Clin Microbiol 48(12):4504-4511.
31. Diep BA, et al. (2008) Emergence of multidrug-resistant, community-associated, methicillinresistant Staphylococcus aureus clone USA300 in men who have sex with men. Ann Intern Med 148(4):249-257.
32. Knight GM, et al. (2012) Shift in dominant hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) clones over time. J Antimicrob Chemother 67(10): 2514-2522.
33. Landrum ML, et al. (2012) Epidemiology of Staphylococcus aureus blood and skin and soft tissue infections in the US military health system, 2005-2010. JAMA 308(1):50-59.
34. Seybold U, et al. (2006) Emergence of community-associated methici llin-resistant Staphylococcus aureus USA300 genotype as a major cause of health care-associated blood stream infections. Clin Infect Dis 42(5):647-656.
35. Böcher S, et al. (2010) The search and destroy strategy prevents spread and long-term carriage of methicillin-resistant Staphylococcus aureus: Results from the follow-up screening of a large ST22 (E-MRSA 15) outbreak in Denmark. Clin Microbiol Infect 16(9):1427-1434.
36. Croucher NJ, et al. (2011) Rapid pneumococcal evolution in response to clinical interventions. Science 331(6016):430-434.
37. Albers CA, et al. (2011) Dindel: Accurate indel calls from short-read data. Genome Res 21(6):961-973.
38. Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21(Suppl 1):i351-i358.
39. Reuter S, et al. (2013) Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. JAMA Intern Med 173(15):1397-1404.
40. Stamatakis A, Ludwig T, Meier H (2005) RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21(4):456-463.
41. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29(8):1969-1973.
42. Baele G, et al. (2012) Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol Biol Evol 29(9):2157-2167.
43. Baele G, Li WL, Drummond AJ, Suchard MA, Lemey P (2013) Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. Mol Biol Evol 30(2):239-243.
44. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821-829.
45. Milheiriço C, Oliveira DC, de Lencastre H (2007) Multiplex PCR strategy for subtyping the staphylococcal cassette chromosome mec type IV in methicillin-resistant Staphylococcus aureus: ' SCCmec IV multiplex'. J Antimicrob Chemother 60(1):42-48.
46. Damborg P, Bartels MD, Boye K, Guardabassi L, Westh H (2011) Structural variations of staphylococcal cassette chromosome mec type IVa in Staphylococcus aureus clonal complex 8 and unrelated lineages. Antimicrob Agents Chemother 55(8):3932-3935.
47. Goerke C, et al. (2009) Diversity of prophages in dominant Staphylococcus aureus clonal lineages. J Bacteriol 191(11):3462-3468.
48. Carver TJ, et al. (2005) ACT: The Artemis Comparison Tool. Bioinformatics 21(16): 3422-3423.