Assessment of molecular typing methods to determine invasiveness and to differentiate clones of Streptococcus pneumoniae

Infection, Genetics and Evolution

Volumn 7, Issue 6, 2007, Pages 708-716

  Obert, Caroline A ^a   Gao, Geli ^a   Sublett, Jack ^a   Tuomanen, Elaine I ^a   Orihuela, Carlos J ^b  

^a ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^b University of Texas Health Science Center   (United States)

Author keywords

CGH; Comparison; MILST; MLST; PFGE; Phylogenetics; Pneumococcus

Indexed keywords

ANTIBIOTIC AGENT; GENOMIC DNA; OXACILLIN; PENICILLIN G;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL STRAIN; BACTERIUM CARRIER; CHILD; COMMUNITY ACQUIRED PNEUMONIA; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; HUMAN; HUMAN CELL; INFANT; MINIMUM INHIBITORY CONCENTRATION; MOLECULAR CLONING; MOLECULAR TYPING; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; SPECIES INVASION; STRAIN DIFFERENCE; STRAIN IDENTIFICATION; STREPTOCOCCUS PNEUMONIAE; UNITED STATES;

CARRIER STATE; COHORT STUDIES; ELECTROPHORESIS, GEL, PULSED-FIELD; EPIDEMIOLOGY, MOLECULAR; GENES, BACTERIAL; HUMANS; MICROBIAL SENSITIVITY TESTS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; STREPTOCOCCAL INFECTIONS; STREPTOCOCCUS PNEUMONIAE;

BACTERIA (MICROORGANISMS); STREPTOCOCCUS PNEUMONIAE;

EID: 35448986475     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2007.07.011     Document Type: Article

References (61)

1. Anonymous. Recommendations of the immunization practices advisory committee pneumococcal polysaccharide vaccine. MMWR 38 5 (1989) 64-68, 73-76
2. Arguedas A., Dagan R., et al. Microbiology of otitis media in Costa Rican children. 1999 through 2001. Pediatr. Infect. Dis. J. 22 12 (2003) 1063-1068
3. Carlisle J.B., Gratten M., et al. Molecular epidemiology of multiple drug resistant type 6B Streptococcus pneumoniae in the Northern Territory and Queensland, Australia. Epidemiol. Infect. 126 1 (2001) 25-29
4. Clarke S.C., Lawrie D., et al. Genetic relatedness of antibiotic-resistant pneumococci isolated during case clusters. J. Med. Microbiol. 53 Pt 11 (2004) 1097-1099
5. Clarke S.C., Scott K.J., et al. Erythromycin resistance in invasive serotype 14 pneumococci is highly related to clonal type. J. Med. Microbiol. 53 Pt 11 (2004) 1101-1103
6. CLSI. Performance Standards for Antimicrobial Susceptibility Testing Approved Standard M100-S16 (2006), Clinical Laboratory Standards Institute, Wayne, PA
7. Coffey T.J., Dowson C.G., et al. Horizontal transfer of multiple penicillin-binding protein genes, and capsular biosynthetic genes, in natural populations of Streptococcus pneumoniae. Mol. Microbiol. 5 9 (1991) 2255-2260
8. Cooper J.E., and Feil E.J. Multilocus sequence typing: what is resolved?. Trends Microbiol. 12 8 (2004) 373-377
9. Dagan R., Givon-Lavi N., et al. Reduction of nasopharyngeal carriage of Streptococcus pneumoniae after administration of a 9-valent pneumococcal conjugate vaccine to toddlers attending day care centers. J. Infect. Dis. 185 7 (2002) 927-936
10. Diggle M.A., and Clarke S.C. Truncated xpt gene present in invasive Streptococcus pneumoniae may have implications for MLST schemes. J. Med. Microbiol. 54 10 (2005) 909-912
11. Dopazo J., Mendoza A., et al. Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate. Microb. Drug Resist. 7 2 (2001) 99-125
12. Enright M.C., and Spratt B.G. A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 144 Pt 11 (1998) 3049-3060
13. Feil E.J., Smith J.M., et al. Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154 4 (2000) 1439-1450
14. Foxman B., and Riley L. Molecular epidemiology: focus on infection. Am. J. Epidemiol. 153 12 (2001) 1135-1141
15. Gamboa L., Camou T., et al. Dissemination of Streptococcus pneumoniae clone Colombia5-19 in Latin America. J. Clin. Microbiol. 40 11 (2002) 3942-3950
16. Gertz Jr. R.E., McEllistrem M.C., et al. Clonal distribution of invasive pneumococcal isolates from children and selected adults in the united states prior to 7-valent conjugate vaccine introduction. J. Clin. Microbiol. 41 9 (2003) 4194-4216
17. Gherardi G., Whitney C.G., et al. Major related sets of antibiotic-resistant pneumococci in the United States as determined by pulsed-field gel electrophoresis and pbp1a-pbp2b-pbp2x-dhf restriction profiles. J. Infect. Dis. 181 1 (2000) 216-229
18. Givon-Lavi N., Dagan R., et al. Marked differences in pneumococcal carriage and resistance patterns between day care centers located within a small area. Clin. Infect. Dis. 29 5 (1999) 1274-1280
19. Hall T. BioEdit: a user-friendly biological seqeunce alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symposium Series 41 (1999) 95-98
20. Harper M.B. Nasopharyngeal colonization with pathogens causing otitis media: how does this information help us?. Pediatr. Infect. Dis. J. 18 12 (1999) 1120-1124
21. Hausdorff W.P., Bryant J., et al. Which pneumococcal serogroups cause the most invasive disease: implications for conjugate vaccine formulation and use, part I. Clin. Infect. Dis. 30 1 (2000) 100-121
22. Hermans P.W., Sluijter M., et al. Comparative study of five different DNA fingerprint techniques for molecular typing of Streptococcus pneumoniae strains. J. Clin. Microbiol. 33 6 (1995) 1606-1612
23. Hoskins J., Alborn Jr. W.E., et al. Genome of the bacterium Streptococcus pneumoniae strain R6. J. Bacteriol. 183 19 (2001) 5709-5717
24. Hunter P.R., and Gaston M.A. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J. Clin. Microbiol. 26 11 (1988) 2465-2466
25. Kellner J.D., and Ford-Jones E.L. Streptococcus pneumoniae carriage in children attending 59 Canadian child care centers. Toronto Child Care Centre Study Group. Arch. Pediatr. Adolesc. Med. 153 5 (1999) 495-502
26. Kellner J.D., McGeer A., et al. The use of Streptococcus pneumoniae nasopharyngeal isolates from healthy children to predict features of invasive disease. Pediatr. Infect. Dis. J. 17 4 (1998) 279-286
27. Ko A.I., Reis J.N., et al. Clonally related penicillin-nonsusceptible Streptococcus pneumoniae serotype 14 from cases of meningitis in Salvador, Brazil. Clin. Infect. Dis. 30 1 (2000) 78-86
28. Kornelisse R.F., Sluijter M., et al. Molecular epidemiological characteristics of pneumococcal meningitis in children. Eur. J. Clin. Microbiol. Infect. Dis. 15 8 (1996) 635-638
29. Lacks S., and Hotchkiss R.D. A study of the genetic material determining an enzyme in Pneumococcus. Biochim. Biophys. Acta 39 (1960) 508-518
30. Llull D., Lopez R., et al. Clonal origin of the type 37 Streptococcus pneumoniae. Microb. Drug Resist. 6 4 (2000) 269-275
31. Lopez B., Cima M.D., et al. Epidemiological study of Streptococcus pneumoniae carriers in healthy primary-school children. Eur. J. Clin. Microbiol. Infect. Dis. 18 11 (1999) 771-776
32. Macias E.A., Mason Jr. E.O., et al. Comparison of E test with standard broth microdilution for determining antibiotic susceptibilities of penicillin-resistant strains of Streptococcus pneumoniae. J. Clin. Microbiol. 32 2 (1994) 430-432
33. Maiden M.C., Bygraves J.A., et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95 6 (1998) 3140-3145
34. Marchese A., Ramirez M., et al. Molecular epidemiology of penicillin-resistant Streptococcus pneumoniae isolates recovered in Italy from 1993 to 1996. J. Clin. Microbiol. 36 10 (1998) 2944-2949
35. McDougal L.K., Facklam R., et al. Analysis of multiply antimicrobial-resistant isolates of Streptococcus pneumoniae from the United States. Antimicrob. Agents Chemother. 36 10 (1992) 2176-2184
36. Medina M.J., Greene C.M., et al. Novel antibiotic-resistant pneumococcal strains recovered from the upper respiratory tracts of HIV-infected adults and their children in Kisumu, Kenya. Microb. Drug Resist. 11 1 (2005) 9-17
37. Miller M.L., Obert C.A., et al. Cephalosporin-resistant pneumococci and sickle cell disease. Emerg. Infect. Dis. 11 8 (2005) 1192-1196
38. Muller-Graf C.D., Whatmore A.M., et al. Population biology of Streptococcus pneumoniae isolated from oropharyngeal carriage and invasive disease. Microbiology 145 Pt 11 (1999) 3283-3293
39. Musher D.M. Infections caused by Streptococcus pneumoniae: clinical spectrum, pathogenesis, immunity, and treatment. Clin. Infect. Dis. 14 4 (1992) 801-807
40. Nylander J. MrModeltest: Program Distributed by the Author (2004), Evolutionary Biology Centre, Uppsala University
41. Obert C., Sublett J., et al. Identification of a candidate Streptococcus pneumoniae core genome and regions of diversity correlated with invasive pneumococcal disease. Infect. Immun. 74 8 (2006) 4766-4777
42. Pletz M.W., McGee L., et al. Levofloxacin-resistant invasive Streptococcus pneumoniae in the United States: evidence for clonal spread and the impact of conjugate pneumococcal vaccine. Antimicrob. Agents Chemother. 48 9 (2004) 3491-3497
43. Richter S.S., Heilmann K.P., et al. The molecular epidemiology of Streptococcus pneumoniae with quinolone resistance mutations. Clin. Infect. Dis. 40 2 (2005) 225-235
44. Robinson D.A., Edwards K.M., et al. Clones of Streptococcus pneumoniae isolated from nasopharyngeal carriage and invasive disease in young children in central Tennessee. J. Infect. Dis. 183 10 (2001) 1501-1507
45. Sandgren A., Sjostrom K., et al. Effect of clonal and serotype-specific properties on the invasive capacity of Streptococcus pneumoniae. J. Infect. Dis. 189 5 (2004) 785-796
46. Savor C., Pfaller M.A., et al. Comparison of genomic methods for differentiating strains of Enterococcus faecium: assessment using clinical epidemiologic data. J. Clin. Microbiol. 36 11 (1998) 3327-3331
47. Serrano I., Melo-Cristino J., et al. Characterization of the genetic lineages responsible for pneumococcal invasive disease in Portugal. J. Clin. Microbiol. 43 4 (2005) 1706-1715
48. Silva N.A., McCluskey J., et al. Genomic diversity between strains of the same serotype and multilocus sequence type among pneumococcal clinical isolates. Infect. Immun. 74 6 (2006) 3513-3518
49. Skoczynska A., and Hryniewicz W. Genetic relatedness, antibiotic susceptibility, and serotype distribution of Streptococcus pneumoniae responsible for meningitis in Poland 1997-2001. Microb. Drug Resist. 9 2 (2003) 175-182
50. Song J.H., Lee N.Y., et al. Spread of drug-resistant Streptococcus pneumoniae in Asian countries: Asian Network for Surveillance of Resistant Pathogens (ANSORP) Study. Clin. Infect. Dis. 28 6 (1999) 1206-1211
51. Song J.H., Yang J.W., et al. Molecular characterization of multidrug-resistant Streptococcus pneumoniae isolates in Korea. The Asian Network for Surveillance of Resistant Pathogens (ANSORP) Study Group. J. Clin. Microbiol. 38 4 (2000) 1641-1644
52. Swiatlo E., Crain M.J., et al. DNA polymorphisms and variant penicillin-binding proteins as evidence that relatively penicillin-resistant pneumococci in western Canada are clonally related. J. Infect. Dis. 174 4 (1996) 884-888
53. * and other methods) (1997), Sinauer Associates, Sunderland, MA
54. Tenover F.C., Arbeit R.D., et al. How to select and interpret molecular strain typing methods for epidemiological studies of bacterial infections: a review for healthcare epidemiologists. Molecular Typing Working Group of the Society for Healthcare Epidemiology of America. Infect. Control Hosp. Epidemiol. 18 6 (1997) 426-439
55. Tettelin H., Nelson K.E., et al. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293 5529 (2001) 498-506
56. Tonnaer E.L., Rijkers G.T., et al. Genetic relatedness between pneumococcal populations originating from the nasopharynx, adenoid, and tympanic cavity of children with otitis media. J. Clin. Microbiol. 43 7 (2005) 3140-3144
57. Veenhoven R., Bogaert D., et al. Effect of conjugate pneumococcal vaccine followed by polysaccharide pneumococcal vaccine on recurrent acute otitis media: a randomised study. Lancet 361 9376 (2003) 2189-2195
58. Wertz J.E., Valletta-Goldstone C.M., et al. A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J. Evol. Biol. 16 6 (2003) 1236-1248
59. Yoshida R., Hirakata Y., et al. Genetic analysis of serotype 23F Streptococcus pneumoniae isolates from several countries by penicillin-binding protein gene fingerprinting and pulsed-field gel electrophoresis. Chemotherapy 45 3 (1999) 158-165
60. Zhang W., Jayarao B.M., et al. Multi-virulence-locus sequence typing of Listeria monocytogenes. Appl. Environ. Microbiol. 70 2 (2004) 913-920
61. Zhou J., Enright M.C., et al. Identification of the major Spanish clones of penicillin-resistant pneumococci via the Internet using multilocus sequence typing. J. Clin. Microbiol. 38 3 (2000) 977-986