Chapter 8 : Distinguishing Pathovars from Nonpathovars:

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One defining feature of a pathovar is that, in a human host, it colonizes the same nonsterile ecologic niche in which nonpathovars establish themselves as commensals. This chapter talks about a bacterial organism, , that colonizes the oro- and naso-pharynx of the human host in similar proportions worldwide. The major current epidemiologic concerns regarding pneumococcal infections include the determinants of the emergence and spread in the community of drug-resistant strains of the pneumococcus and the relationship between asymptomatic carriage and disease. The latter addresses the issue of whether or not any strain that asymptomatically colonizes a host is also capable of causing invasive disease. Molecular epidemiologic approaches to these issues are discussed.

Citation: Riley L. 2004. Distinguishing Pathovars from Nonpathovars: , p 209-227. In Molecular Epidemiology of Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/9781555817688.ch8

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1. Berchieri, A.,, and P. A. Barrow. 1990. Further studies on the inhibition of colonization of the chicken alimentary tract with Salmonella typhimurium by precolonization with an avirulent mutant. Epidemiol. Infect. 194:427441.
2. Bogaert, D.,, N. T. Ha,, M. Sluijter,, N. Lemmens,, R. De Groot,, and P. W. Hermans. 2003. Molecular epidemiology of pneumococcal carriage among children with upper respiratory tract infections in Hanoi, Vietnam. J. Clin. Microbiol. 40: 39033908.
3. Bogaerts, J.,, P. Lepage,, H. Taelman,, D. Rouvroy,, J. Batungwanayo,, P. Kestelyn,, D. G. Hitimana,, P. Van de Perre,, J. Vandepitte,, L. Verbist,, and J. Verhaegen.1993. Antimicrobial susceptibility and serotype distribution of Streptococcus pneumoniae from Rwanda, 1984-1990. J. Infect. 27:157168.
4. Breiman, R. F.,, J. C. Butler,, F. C. Tenover,, J. A. Elliott,, and R. R. Facklam. 1994. Emergence of drug-resistant pneumococcal infections in the United States. JAMA 271:18311835.
5. Brueggemann, A. B.,, D. T. Griffiths,, E. Meats,, T. Peto,, D. W. Crook,, and B. G. Spratt. 2003. Clonal relationships between invasive and carriage Streptococcus pneumoniae and serotype- and clone-specific differences in invasive disease potential. J. Infect. Dis. 187:14241432.
6. Bruyn, G. A. W.,, B. J. M. Zegers,, and R. von Furth. 1992. Mechanism of host defense against infection with Streptococcus pneumoniae. Clin. Infect. Dis. 14: 251262.
7. Chen, H. C.,, and N. J. Stern. 2001. Competitive exclusion of heterologous Campylobacter spp. in chicks. Appl. Environ. Microbiol. 67:848851.
8. Coffey, T. J.,, C. G. Dowson,, M. Daniels,, and B. G. Spratt. 1995. Genetics and molecular biology of β-lactam-resistant pneumococci. Microb. Drug Resist. 1: 2934.
9. Coffey, T. J.,, C. G. Dowson,, M. Daniels,, J. Zhou,, C. Martin,, B. G. Spratt,, and J. M. Musser. 1991. Horizontal transfer of multiple penicillin-binding protein genes, and capsular biosynthetic genes, in natural populations of Streptococcus pneumoniae. Mol. Microbiol. 5:22552260.
10. Coffey, T. J.,, S. Berron,, M. Daniels,, E. Garcia-Leoni,, E. Cercenado,, E. Bouza,, A. Fenoll,, and B. G. Spratt. 1996. Multiply antibiotic-resistant Streptococcus pneumoniae recovered from Spanish hospitals (1988-1994): novel major clones of serotypes 14, 19F, and 15F. Microbiology 142:27472757.
11. Davies, T.,, R. V. Goering,, M. Lovgren,, J. A. Talbot,, M. R. Jacobs,, and P. C. Applebaum. 1999. Molecular epidemiological survey of penicillin-resistant Streptococcus pneumoniae from Asia, Europe, and North America. Diagn. Microbiol. Infect. Dis. 34:712.
12. de Andrade, A. L.,, F. C. Pimenta,, M. C. Brandileone,, C. A. Laval,, M. L. Guerra,, J. G. de Andrade,, and J. L. Di Fabio. 2003. Genetic relationship between Streptococcus pneumoniae isolates from nasopharyngeal and cerebrospinal fluid of two infants with pneumococcal meningitis. J. Clin. Microbiol. 4:39703972.
13. Dillard, J. P.,, M. W. Vandersea,, and J. Yother. 1995. Characterization of the cassette containing genes for type 3 capsular polysaccharide biosynthesis in Streptococcus pneumoniae. J. Exp. Med. 181:973983.
14. Doyle, M. G.,, A. L. Morrow,, R. Van,, and L. K. Pickering. 1992. Intermediate resistance of Streptococcus pneumoniae to penicillin in children in day-care centers. Pediatr. Infect. Dis. J. 11:831835.
15. Dunne, W. M., Jr.,, K. S. Kehl,, C. A. Holland-Staley,, A. B. Brueggemann,, M. A. Pfaller,, and G. V. Doern. 2001 Comparison of results generated by serotyping, pulsed-field restriction analysis, ribotyping, and repetitive-sequence PCR used to characterize penicillin-resistant pneumococci from the United States. J. Clin. Microbiol. 39:17911795.
16. Duval-Iflah, Y.,, J. P. Chappuis,, R. Ducluzeau,, and P. Raibaud. 1983. Intraspecific interactions between Escherichia coli strains in human newborns and gnotobiotic mice and piglets. Prog. Food Nutr. Sci. 7:107116.
17. Enright, M. C.,, and B. G. Spratt. 1998. A multilocus sequence typing for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 144:30493060.
18. Fenoll, A.,, I. Jado,, D. Vicioso,, A. Pérez,, and J. Casal. 1998. Evolution of Streptococcus pneumoniae serotypes and antibiotic resistance in Spain: update (1990 to 1996). J. Clin. Microbiol. 36:34473454.
19. Fenoll, A.,, M. Bourgon,, R. Munoz,, D. Vicioso,, and J. Casal. 1991. Serotype distribution and antimicrobial resistance of Streptococcus pneumoniae isolates causing systemic infections in Spain, 1979-1989. Rev. Infect. Dis. 13:5660.
20. Figueiredo, A. M.,, R. Austrain,, P. Urgaskova,, L. A. Teixeira,, and A. Tomasz. 1995. Novel penicillin-resistant clones of Streptococcus pneumoniae in the Czech Republic and Slovakia. Microb. Drug Resist. 1:7178.
21. Gray, B. M.,, G. M. Converse III,, and H. C. Dillon. 1980. Epidemiologic studies of Streptococcus pneumoniae in infants: acquisition, carriage, and infection during the first 24 months of life. J. Infect. Dis. 142:923933.
22. Hall, L. M.,, R. A. Whiley,, B. Duke,, R. C. George,, and E. Efstratiou. 1996. Genetic relatedness within and between serotypes of Streptococcus pneumoniae from the United Kingdom: analysis of multilocus enzyme electrophoresis, pulsed-field gel electrophoresis, and antimicrobial resistance patterns. J. Clin. Microbiol. 34:853859.
23. Hansman, D.,, and M. M. Bullen. 1967. A resistant pneumococcus. Lancet ii:264265.
24. Hermans, P. W. M.,, M. Sluijter,, T. Hoogenboezem,, H. Heersma,, A. van Belkum,, and R. de Groot. 1995. Comparative study of five different DNA fingerprint techniques for molecular typing of Streptococcus pneumoniae strains. J. Clin. Microbiol. 33:16061612.
25. Janoff, E. N.,, R. F. Breiman,, C. L. Daley,, and P. C. Hopewell. 1992. Pneumococcal disease during HIV infection: epidemiologic, clinical, and immunologic perspectives. Ann. Intern. Med. 117:314324.
26. John, T. J.,, R. Pai,, M. K. Lalitha,, M. V. Jesudason,, K. N. Brahmandathan,, G. Sridharan,, and M. C. Steinhoff. 1996. Prevalence of pneumococcal serotypes in invasive diseases in southern India. Indian J. Med. Res. 104:205207.
27. Kalin, M. 1998. Pneumococcal serotypes and their clinical relevance. Thorax 53:159162.
28. Kam, K. M.,, K. Y. Luey,, S. M. Fung,, P. P. Yiu,, T. J. Harden,, and M. M. Cheung. 1995. Emergence of multiple-antibiotic-resistant Streptococcus pneumoniae in Hong Kong. Antimicrob. Agents Chemother. 39:26672670.
29. Kellner, J. D.,, A. McGeer,, M. S. Cetron,, D. E. Low,, J. C. Butler,, A. Matlo,, J. Talbot,, and E. L. Ford-Jones. 1998. The use of Streptococcus pneumoniae nasopharyngeal isolates from healthy children to predict features of invasive disease. Pediatr. Infect. Dis. J. 17:279286.
30. Klein, J. O. 1981. The epidemiology of pneumococcal disease in infants and children. Rev. Infect. Dis. 3:246253.
31. Klugman, K. P. 1990. Pneumococcal resistance to antibiotics. Clin. Microbiol. Rev. 3:171196.
32. Leach, A. J.,, J. B. Boswell,, V. Asche,, T. G. Nienhuys,, and J. D. Mathews. 1994. Bacterial colonization of the nasopharynx predicts very early onset and persistence of otitis media in Australian Aboriginal infants. Pediatr. Infect. Dis. J. 13:983989.
33. Lefevre, J. C.,, M. A. Bertrand,, and G. Faucon. 1995. Molecular analysis by pulsed field gel electrophoresis of penicillin-resistant Streptococcus pneumoniae from Toulouse, France. Eur. J. Clin. Microbiol. Infect. Dis. 14:491497.
34. Levin, B. R.,, and R. Antia. 2001. Why we don’t get sick: the within-host population dynamics of bacterial infections. Science 292:11121115.
35. Liu, P. Y.-F.,, B.-S. Hu,, C.-P. Fung,, Y.-J. Lau,, Z.-Y. Shi,, and Y.-H. Lin. 1998. Molecular epidemiology of penicillin-resistant Streptococcus pneumoniae isolated in Central Taiwan. Diagn. Microbiol. Infect. Dis. 31:511515.
36. Lloyd-Evans, N.,, T. J. D. O’Dempsey,, I. Baldeh,, O. Secka,, E. Dernda,, J. E. Todd,, T. F. McArdle,, W. S. Banya,, and B. M. Greenwood. 1996. Nasopharyngeal carriage of pneumococci in Gambian children and in their families. Pediatr. Infect. Dis. J. 15:866871.
37. Loda, F. A.,, A. M. Collier,, W. P. Glezen,, K. Strangert,, W. A. Clyde,, and F. W. Denny. 1975. Occurrence of Diplococcus pneumoniae in the upper respiratory tract of children. J. Pediatr. 87:10871093.
38. Maiden, M. C. J.,, J. A. Bygraves,, E. Feil,, J. E. Russell,, R. Urwin,, Q. Zhang,, J. Zhou,, K. Zurth,, D. A. Caugant,, I. M. Feavers,, M. Achtman,, and B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95: 31403145.
39. Manges, A. R.,, J. R. Johnson,, B. Foxman,, T. T. O’Bryan,, K. R. Fullerton,, and L. W. Riley. 2001. Widespread distribution of urinary tract infections caused by a multidrug resistant Escherichia coli clonal group. N. Engl. J. Med. 345:10071013.
40. Marton, A.,, M. Gulyas,, R. Munoz,, and A. Tomasz. 1991. Extremely high incidence of antibiotic resistance in clinical isolates of Streptococcus pneumoniae in Hungary. J. Infect. Dis. 163:542548.
41. Mastro, T. D.,, N. K. Nomani,, Z. Ishaq,, A. Ghafoor,, N. F. Shaukat,, E. Esko,, M. Leinonen,, J. Henrichsen,, R. F. Breiman,, B. Schwartz et al. 1993. Use of nasopharyngeal isolates of Streptococcus pneumoniae and Haemophilus influenzae from children in Pakistan for surveillance for antimicrobial resistance. Pediatr. Infect. Dis. J. 12:824830.
42. McDougal, L. K.,, J. K. Rasheed,, J. W. Biddle,, and F. C. Tenover. 1995. Identification of multiple clones of extended-spectrum cephalosporin-resistant Streptococcus pneumoniae from the United States. Antimicrob. Agents Chemother. 39:22822288.
43. McDougal, L. K.,, R. Facklam,, M. Reeves,, S. Hunter,, J. M. Swenson,, B. C. Hill,, and F. C. Tenover. 1992. Analysis of multiply antimicrobial-resistant isolates of Streptococcus pneumoniae from the United States. Antimicrob. Agents Chemother. 36:21762184.
44. McGee, L.,, L. McDougal,, J. Zhou,, B. G. Spratt,, F. C. Tenover,, R. George,, R. Hakenbeck,, W. Hryniewicz,, J. C. Lefévre,, A. Tomasz,, and K. P. Klugman. 2001. Nomenclature of major antimicrobial-resistant clones of Streptococcus pneumoniae defined by the Pneumococcal Molecular Epidemiology Network. J. Clin. Microbiol. 39:25652571.
45. Montgomery, J. M.,, D. Lehmann,, T. Smith,, A. Michael,, B. Joseph,, T. Lupiwa,, C. Coakley,, V. Spooner,, B. Best,, and I. D. Riley. 1990 Bacterial colonization of the upper respiratory tract and its association with acute lower respiratory infections in highland children of Papua New Guinea. Rev. Infect. Dis. 12(Suppl. 8):S1006S1016.
46. Monto, A. S. 1989. Acute respiratory infection in children of developing countries: challenge of the 1990s. Rev. Infect. Dis. 11:498505.
47. Müller-Graf, C. D. M.,, A. M. Whatmore,, S. J. King,, K. Trzcinski,, A. P. Pickerill,, N. Doherty,, J. Paul,, D. Griffiths,, D. Crook,, and C. G. Dowson. 1999. Population biology of Streptococcus pneumoniae isolated from oropharyngeal carriage and invasive disease. Microbiology 145:32833293.
48. Munoz, R.,, T. J. Coffey,, M. Daniels,, C. G. Dowson,, G. Laible,, J. Casal,, R. Hakenbeck,, M. Jacobs,, J. M. Musser,, B. G. Spratt,, and A. Tomasz. 1991. Intercontinental spread of a multiresitant clone of serotype 23F Streptococcus pneumoniae. J. Infect. Dis. 164:302306.
49.National Committee for Clinical Laboratory Standards. 1994. Performance Standards for Antimicrobial Susceptibility Testing. National Committee for Clinical Laboratory Standards, Villanova, Pa.
50. Nisbet, D. 2002. Defined competitive exclusion cultures in the prevention of enteropathogen colonisation in poultry and swine. Antonie Leeuwenhoek 81:481486.
51. Onderdonk, A.,, B. Marshall,, R. Cisneros,, and S. B. Levy. 1981. Competition between congenic Escherichia coli K-12 strains in vivo. Infect. Immun. 32:7479.
52. Overweg, K.,, P. W. M. Hermans,, K. Trzcinski,, M. Sluijter,, R. de Groot,, and W. Hryniewicz. 1999. Multidrug-resistant Streptococcus pneumoniae in Poland: identification of emerging clones. J. Clin. Microbiol. 37:17391745.
53. Perez-Trallero, E.,, J. M. Marimon,, A. Gonzalez,, and L. Iglesias. 2003. Spain (14)-5 international multiresistant Streptococcus pneumoniae clone resistant to fluoroquinolones and other families of antibiotics. J. Antimicrob. Chemother. 51: 715719.
54. Porat, N.,, R. Trefler,, and R. Dagan. 2001. Persistence of two invasive Streptococcus pneumoniae clones of serotype 1 and 5 in comparison to that of multiple clones of serotypes 6B and 23F among children in southern Israel. J. Clin. Microbiol. 39:18271832.
55. Read, A. F.,, and L. H. Taylor,. 2000. Within-host ecology of infectious diseases: patterns and consequences, p. 5975. In R. C. A. Thompson (ed.), Molecular Epidemiology of Infectious Diseases. Oxford University Press, New York, N.Y.
56. Read, A. F.,, and L. H. Taylor. 2001. The ecology of genetically diverse infections. Science 292:10991102.
57. Reichler, M. R.,, A. A. Allphin,, R. F. Breiman,, J. R. Schreiber,, J. E. Arnold,, L. K. McDougal,, R. R. Facklam,, B. Boxerbaum,, D. May,, R. O. Walton, et al. 1992. The spread of multiply-resistant Streptococcus pneumoniae at a day care center in Ohio. J. Infect. Dis. 166:13461353.
58. Richter, S. S.,, K. P. Heilmann,, S. L. Coffman,, H. K. Huynh,, A. B. Brueggemann,, M. A. Pfaller,, and G. V. Doern. 2002. The molecular epidemiology of penicillin-resistant Streptococcus pneumoniae in the United States, 1994-2000. Clin. Infect. Dis. 34:330339.
59. Robinson, D. A.,, D. E. Briles,, M. J. Crain,, and S. K. Hollingshead. 2002. Evolution and virulence of serogroup 6 pneumococci on a global scale. J. Bacteriol. 184:63676375.
60. Robinson, D. A.,, J. S. Turner,, R. R. Facklam,, A. J. Parkinson,, R. F. Breiman,, M. Gratten,, M. C. Steinhoff,, S. K. Hollingshead,, D. E. Briles,, and M. J. Crain. 1999. Molecular characterization of a globally distributed lineage of serotype 12F Streptococcus pneumoniae causing invasive disease. J. Infect. Dis. 179:414422.
61. Robinson, D. A.,, K. M. Edwards,, K. B. Waites,, D. E. Briles,, M. J. Crain,, and S. K. Hollingshead. 2001. Clones of Streptococcus pneumoniae isolated from nasopharyngeal carriage and invasive disease in young children in Central Tennessee. J. Infect. Dis. 183:15011507.
62. Robinson, D. A.,, S. K. Hollingshead,, J. M. Musser,, A. J. Parkinson,, D. E. Briles,, and M. J. Crain. 1998. The IS1167 insertion sequence is a phylogenetically informative marker among isolates of serotype 6B Streptococcus pneumoniae. J. Mol. Evol. 47:222229.
63. Robinson, K. A.,, W. Baughman,, G. Rothrock,, N. L. Barrett,, M. Pass,, C. Lexau,, B. Damaske,, K. Stefonek,, B. Barnes,, J. Patterson,, E. R. Zell,, A. Schuchat,, C. G. Whitney, and Active Bacterial Core Surveillance (ABCs)/Emerging Infections Program Network. 2001. Epidemiology of invasive Streptococcus pneumoniae infections in the United States, 1995-1998: opportunities for prevention in the conjugate vaccine era. JAMA 285:17291735.
64. Scott, J. A. G.,, A. J. Hall,, R. Dagan,, J. M. S. Dixon,, S. J. Eykyn,, A. Fenoll,, M. Hortal,, L. P. Jette,, J. H. Jorgensen,, F. Lamothe,, C. Latorre,, J. T. Macfarlane,, D. M. Shlaes,, L. E. Smart,, and A. Taunay. 1996. Serotype specific epidemiology of Streptococcus pneumoniae: association with age, sex, and geography in 7,000 episodes of invasive disease. Clin. Infect. Dis. 22:973981.
65. Shi, Z.-Y.,, M. C. Enright,, P. Wilkinson,, D. Griffiths,, and B. G. Spratt. 1998. Identification of the three major clones of multiply antibiotic-resistant Streptococcus pneumoniae in Taiwanese hospitals by multilocus sequence typing. J. Clin. Microbiol. 36:35143519.
66. Sibold, C.,, J. Wang,, J. Henrichsen,, and R. Hakenbeck. 1992. Genetic relationships of penicillin-susceptible and -resistant Streptococcus pneumoniae strains isolated on different continents. Infect. Immun. 60:41194126.
67. Smith, A. M.,, and K. P. Klugman. 1995. Alterations in penicillin-binding protein 2B from penicillin-resistant wild-type strains of Streptococcus pneumoniae. Antimicrob. Agents Chemother. 39:859867.
68. Smith, A. M.,, and K. P. Klugman. 1997. Three predominant clones identified within penicillin-resistant South African isolates of Streptococcus pneumoniae. Microb. Drug Resist. 3:385389.
69. Soares, S.,, K. G. Kristinsson,, J. M. Musser,, and A. Tomasz. 1993. Evidence for the introduction of a multiresistant clone of serotype 6B Streptococcus pneumoniae from Spain to Iceland in the late 1980s. J. Infect. Dis. 168:158163.
70. Song, J.-H.,, N. Y. Lee,, S. Ichiyama,, R. Yoshida,, Y. Hirakata,, W. Fu,, A. Chongthaleong,, N. Aswapokee,, C.-H. Chium,, M. K. Lalitha,, K. Thomas,, J. Perera,, T. T. Yee,, F. Jamal,, U. C. Warsa,, B. X. Vinh,, M. R. Jacobs,, P. C. Applebaum,, C. H. Pai, and the ANSORP Study Group. 1999. Spread of drug-resistant Streptococcus pneumoniae in Asian countries: Asian Network for Surveillance of Resistant Pathogens (ANSORP) study. Clin. Infect. Dis. 28:12061211.
71. Stern, N. J.,, N. A. Cox,, J. S. Bailey,, M. E. Berrang,, and M. T. Musgrove. 2001. Comparison of mucosal competitive exclusion and competitive exclusion treatment to reduce Salmonella and Campylobacter spp. colonization in broiler chickens. Poult. Sci. 80:156160.
72. Swiatlo, E.,, M. J. Crain,, L. S. McDaniel,, A. Brooks-Walter,, T. J. Coffey,, B. G. Spratt,, D. A. Morrison,, and D. E. Briles. 1996. DNA polymorphisms and variant penicillin-binding proteins as evidence that relatively penicillin-resistant pneumococci in western Canada are clonally related. J. Infect. Dis. 174:884888.
73. Takala, A. K.,, J. Vuopio-Varkila,, E. Tarkka,, M. Leinonen,, and J. M. Musser. 1996. Subtyping of common pediatric pneumococcal serotypes from invasive disease and pharyngeal carriage in Finland. J. Infect. Dis. 173:128135.
74. Tamayo, M.,, R. Sá-Leão,, I. Santos Sanches,, E. Castañeda,, and H. De Lencastre. 1999. Dissemination of a chloramphenicol- and tetracycline-resistant but penicillin-susceptible invasive clone of serotype 5 Streptococcus pneumoniae in Colombia. J. Clin. Microbiol. 37:23372342.
75. Zangwill, K. M.,, C. M. Vadheim,, A. M. Vannier,, L. S. Hemenway,, D. P. Greenberg,, and J. I. Ward. 1996. Epidemiology of invasive pneumococcal disease in Southern California: implications for the design and conduct of pneumococcal conjugate vaccine efficacy trial. J. Infect. Dis. 174:752759.


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Table 8.1

International pneumococcal clones recognized to have contributed to the increase in antimicrobial resistance worldwide

Adapted from reference .

ATCC, American Type Culture Collection.

Citation: Riley L. 2004. Distinguishing Pathovars from Nonpathovars: , p 209-227. In Molecular Epidemiology of Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/9781555817688.ch8

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