Microbial communities of the upper respiratory tract and otitis media in children

mBio

Volumn 2, Issue 1, 2011, Pages

  Laufer, Alison S ^a   Metlay, Joshua P ^b   Gent, Janneane F ^a   Fennie, Kristopher P ^c   Kong, Yong ^d   Pettigrewa, Melinda M ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c YALE UNIVERSITY SCHOOL OF NURSING   (United States)

^d YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA 16S;

ACTINOMYCES; ARTICLE; BACTERIAL COLONIZATION; BACTERIUM; CHILD; CONTROLLED STUDY; CORYNEBACTERIUM; CROSS-SECTIONAL STUDY; DNA EXTRACTION; DOLOSIGRANULUM; FEMALE; HAEMOPHILUS; HUMAN; INFANT; LACTOCOCCUS; MALE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROFLORA; NEISSERIA; NONHUMAN; NOSE SMEAR; OTITIS MEDIA; POLYMERASE CHAIN REACTION; PRESCHOOL CHILD; PRIORITY JOURNAL; PROPIONIBACTERIUM; PYROSEQUENCING; ROTHIA; STAPHYLOCOCCUS; STREPTOCOCCUS PNEUMONIAE; UNITED STATES; UPPER RESPIRATORY TRACT; VEILLONELLA; CLASSIFICATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NEWBORN; NOSE; PHYLOGENY;

ACTINOMYCES; CORYNEBACTERIUM; DOLOSIGRANULUM; HAEMOPHILUS; LACTOCOCCUS; NEISSERIA; PROPIONIBACTERIUM; ROTHIA; STAPHYLOCOCCUS; STREPTOCOCCUS PNEUMONIAE; VEILLONELLA;

BACTERIA; CHILD; CHILD, PRESCHOOL; CROSS-SECTIONAL STUDIES; FEMALE; HUMANS; INFANT; INFANT, NEWBORN; MALE; MOLECULAR SEQUENCE DATA; NOSE; OTITIS MEDIA; PHYLOGENY; STREPTOCOCCUS PNEUMONIAE;

EID: 79955092594     PISSN: None     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00245-10     Document Type: Article

References (54)

1. Revai, K., D. Mamidi, and T. Chonmaitree. 2008. Association of nasopharyngeal bacterial colonization during upper respiratory tract infection and the development of acute otitis media. Clin. Infect. Dis. 46:e34-e37.
2. Watson, K., K. Carville, J. Bowman, P. Jacoby, T. V. Riley, A. J. Leach, and D. Lehmann, and the Kalgoorlie Otitis Media Research Project Team. 2006. Upper respiratory tract bacterial carriage in Aboriginal and non-Aboriginal children in a semi-arid area of Western Australia. Pediatr. Infect. Dis. J. 25:782-790.
3. Dagan, R., N. Givon-Lavi, O. Zamir, and D. Fraser. 2003. Effect of a nonavalent conjugate vaccine on carriage of antibiotic-resistant Streptococcus pneumoniae in day-care centers. Pediatr. Infect. Dis. J. 22:532-540.
4. Syrjanen, R. K., T. M. Kilpi, T. H. Kaijalainen, E. E. Herva, and A. K. Takala. 2001. Nasopharyngeal carriage of Streptococcus pneumoniae in Finnish children younger than 2 years old. J. Infect. Dis. 184:451-459.
5. Bogaert, D., R. De Groot, and P. W. Hermans. 2004. Streptococcus pneumoniae colonisation: the key to pneumococcal disease. Lancet Infect. Dis. 4:144-154.
6. Gray, B. M., G. M. Converse III, and H. C. Dillon, Jr. 1980. Epidemiologic studies of Streptococcus pneumoniae in infants: acquisition, carriage, and infection during the first 24 months of life. J. Infect. Dis. 142:923-933.
7. Faden, H., L. Duffy, R. Wasielewski, J. Wolf, D. Krystofik, and Y. Tung. 1997. Relationship between nasopharyngeal colonization and the development of otitis media in children. Tonawanda/Williamsville Pediatrics. J. Infect. Dis. 175:1440-1445.
8. Chonmaitree, T., K. Revai, J. J. Grady, A. Clos, J. A. Patel, S. Nair, J. Fan, and K. J. Henrickson. 2008. Viral upper respiratory tract infection and otitis media complication in young children. Clin. Infect. Dis. 46:815-823.
9. Chung, M. H., S. R. Griffith, K. H. Park, D. J. Lim, and T. F. DeMaria. 1993. Cytological and histological changes in the middle ear after inoculation of influenza A virus. Acta Otolaryngol. 113:81-87.
10. Regev-Yochay, G., R. Dagan, M. Raz, Y. Carmeli, B. Shainberg, E. Derazne, G. Rahav, and E. Rubinstein. 2004. Association between carriage of Streptococcus pneumoniae and Staphylococcus aureus in children. JAMA 292: 716-720.
11. Madhi, S. A., P. Adrian, L. Kuwanda, C. Cutland, W. C. Albrich, and K. P. Klugman. 2007. Long-term effect of pneumococcal conjugate vaccine on nasopharyngeal colonization by Streptococcus pneumoniae-and associated interactions with Staphylococcus aureus and Haemophilus influenzae colonization-in HIV-infected and HIV-uninfected children. J. Infect. Dis. 196:1662-1666.
12. Klepac-Ceraj, V., K. P. Lemon, T. R. Martin, M. Allgaier, S. W. Kembel, A. A. Knapp, S. Lory, E. L. Brodie, S. V. Lynch, B. J. Bohannan, J. L. Green, B. A. Maurer, and R. Kolter. 2010. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environ. Microbiol. 12:1293-1303.
13. Armbruster, C. E., W. Hong, B. Pang, K. E. Weimer, R. A. Juneau, J. Turner, and W. E. Swords. 2010. Indirect pathogenicity of Haemophilus influenzae and Moraxella catarrhalis in polymicrobial otitis media occurs via interspecies quorum signaling. mBio 1:-e00102-10.
14. Lysenko, E. S., A. J. Ratner, A. L. Nelson, and J. N. Weiser. 2005. The role of innate immune responses in the outcome of interspecies competition for colonization of mucosal surfaces. PLoS Pathog. 1:e1.
15. Kuramitsu, H. K., X. He, R. Lux, M. H. Anderson, and W. Shi. 2007. Interspecies interactions within oral microbial communities. Microbiol. Mol. Biol. Rev. 71: 653-670.
16. Brogden, K. A., and J. M. Guthmiller. 2002. Polymicrobial diseases. ASM Press, Washington, DC.
17. Jacoby, P., K. Watson, J. Bowman, A. Taylor, T. V. Riley, D. W. Smith, and D. Lehmann, and the Kalgoorlie Otitis Media Research Project Team. 2007. Modelling the co-occurrence of Streptococcus pneumoniae with other bacterial and viral pathogens in the upper respiratory tract. Vaccine 25:2458-2464.
18. Harrison, L. M., J. A. Morris, D. R. Telford, S. M. Brown, and K. Jones. 1999. The nasopharyngeal bacterial flora in infancy: effects of age, gender, season, viral upper respiratory tract infection and sleeping position. FEMS Immunol. Med. Microbiol. 25: 19-28.
19. Pitkaranta, A., M. Roivainen, K. Blomgren, J. Peltola, T. Kaijalainen, R. Raty, T. Ziegler, E. Ronkko, K. Hatakka, R. Korpela, T. Poussa, M. Leinonen, and T. Hovi. 2006. Presence of viral and bacterial pathogens in the nasopharynx of otitis-prone children. A prospective study. Int. J. Pediatr. Otorhinolaryngol. 70: 647-654.
20. Savage, D. C. 1977. Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 31:107-133.
21. Costello, E. K., C. L. Lauber, M. Hamady, N. Fierer, J. I. Gordon, and R. Knight. 2009. Bacterial community variation in human body habitats across space and time. Science 326: 1694-1697.
22. Langendijk, P. S., F. Schut, G. J. Jansen, G. C. Raangs, G. R. Kamphuis, M. H. Wilkinson, and G. W. Welling. 1995. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNAtargeted probes and its application in fecal samples. Appl. Environ. Microbiol. 61: 3069-3075.
23. Hamady, M., J. J. Walker, J. K. Harris, N. J. Gold, and R. Knight. 2008. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 5:235-237.
24. Andersson, A. F., M. Lindberg, H. Jakobsson, F. Backhed, P. Nyren, and L. Engstrand. 2008. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 3:e2836.
25. Sogin, M. L., H. G. Morrison, J. A. Huber, D. M. Welch, S. M. Huse, P. R. Neal, J. M. Arrieta, and G. J. Herndl. 2006. Microbial diversity in the deep sea and the underexplored ''rare biosphere.'' Proc. Natl. Acad. Sci. U. S. A. 103:12115-12120.
26. Dethlefsen, L., S. Huse, M. L. Sogin, and D. A. Relman. 2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6:e280.
27. Parameswaran, P., R. Jalili, L. Tao, S. Shokralla, B. Gharizadeh, M. Ronaghi, and A. Z. Fire. 2007. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res. 35:e130.
28. Worthen, P. L., C. J. Gode, and J. Graf. 2006. Culture-independent characterization of the digestive-tract microbiota of the medicinal leech reveals a tripartite symbiosis. Appl. Environ. Microbiol. 72: 4775-4781.
29. Ley, R. E., P. J. Turnbaugh, S. Klein, and J. I. Gordon. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022-1023.
30. Van de Peer, Y., S. Chapelle, and R. De Wachter. 1996. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res. 24:3381-3391.
31. Chakravorty, S., D. Helb, M. Burday, N. Connell, and D. Alland. 2007. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J. Microbiol. Methods 69: 330-339.
32. Huse, S. M., D. M. Welch, H. G. Morrison, and M. L. Sogin. 2010. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12: 1889-1898.
33. Quince, C., A. Lanzen, T. P. Curtis, R. J. Davenport, N. Hall, I. M. Head, L. F. Read, and W. T. Sloan. 2009. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 6:639-641.
34. Faden, H., J. Stanievich, L. Brodsky, J. Bernstein, and P. L. Ogra. 1990. Changes in nasopharyngeal flora during otitis media of childhood. Pediatr. Infect. Dis. J. 9: 623-626.
35. Lemon, K. P., V. Klepac-Ceraj, H. K. Schiffer, E. L. Brodie, S. V. Lynch, and R. Kolter. 2010. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. mBio 1(3):e00129-10.
36. Pettigrew, M. M., J. F. Gent, K. Revai, J. A. Patel, and T. Chonmaitree. 2008. Microbial interactions during upper respiratory tract infections. Emerg. Infect. Dis. 14:1584-1591.
37. Kononen, E., R. Syrjanen, A. Takala, and H. Jousimies-Somer. 2003. Nasopharyngeal carriage of anaerobes during health and acute otitis media by two years of age. Diagn. Microbiol. Infect. Dis. 46:167-172.
38. Jokipii, A. M., P. Karma, K. Ojala, and L. Jokipii. 1977. Anaerobic bacteria in chronic otitis media. Arch. Otolaryngol. 103: 278-280.
39. Dowd, S. E., R. D. Wolcott, Y. Sun, T. McKeehan, E. Smith, and D. Rhoads. 2008. Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP). PLoS One 3:e3326.
40. Peleg, A. Y., E. Tampakakis, B. B. Fuchs, G. M. Eliopoulos, R. C. Moellering, Jr., and E. Mylonakis. 2008. Prokaryote-eukaryote interactions identified by using Caenorhabditis elegans. Proc. Natl. Acad. Sci. U. S. A. 105:14585-14590.
41. Sibley, C. D., K. Duan, C. Fischer, M. D. Parkins, D. G. Storey, H. R. Rabin, and M. G. Surette. 2008. Discerning the complexity of community interactions using a Drosophila model of polymicrobial infections. PLoS Pathog. 4:e1000184.
42. Lancaster, H., D. Ready, P. Mullany, D. Spratt, R. Bedi, and M. Wilson. 2003. Prevalence and identification of tetracycline-resistant oral bacteria in children not receiving antibiotic therapy. FEMS Microbiol. Lett. 228: 99-104.
43. Seville, L. A., A. J. Patterson, K. P. Scott, P. Mullany, M. A. Quail, J. Parkhill, D. Ready, M. Wilson, D. Spratt, and A. P. Roberts. 2009. Distribution of tetracycline and erythromycin resistance genes among human oral and fecal metagenomic DNA. Microb. Drug Resist. 15: 159-166.
44. Wu, H. M., B. H. Harcourt, C. P. Hatcher, S. C. Wei, R. T. Novak, X. Wang, B. A. Juni, A. Glennen, D. J. Boxrud, J. Rainbow, S. Schmink, R. D. Mair, M. J. Theodore, M. A. Sander, T. K. Miller, K. Kruger, A. C. Cohn, T. A. Clark, N. E. Messonnier, L. W. Mayer, and R. Lynfield. 2009. Emergence of ciprofloxacin-resistant Neisseria meningitidis in North America. N. Engl. J. Med. 360:886-892.
45. Luppens, S. B., D. Kara, L. Bandounas, M. J. Jonker, F. R. Wittink, O. Bruning, T. M. Breit, J. M. Ten Cate, and W. Crielaard. 2008. Effect of Veillonella parvula on the antimicrobial resistance and gene expression of Streptococcus mutans grown in a dual-species biofilm. Oral Microbiol. Immunol. 23:183-189.
46. Heikkinen, T., J. Marttila, A. A. Salmi, and O. Ruuskanen. 2002. Nasal swab versus nasopharyngeal aspirate for isolation of respiratory viruses. J. Clin. Microbiol. 40:4337-4339.
47. Greiner, O., P. Day, P. Bosshard, F. Imeri, M. Altwegg, and D. Nadal. 2001. Quantitative detection of Streptococcus pneumoniae in nasopharyngeal secretions by real-time PCR. J. Clin. Microbiol. 39: 3129-3134.
48. Rapola, S., E. Salo, P. Kiiski, M. Leinonen, and A. K. Takala. 1997. Comparison of four different sampling methods for detecting pharyngeal carriage of Streptococcus pneumoniae and Haemophilus influenzae in children. J. Clin. Microbiol. 35:1077-1079.
49. Capeding, M. R., H. Nohynek, L. T. Sombrero, L. G. Pascual, E. S. Sunico, G. A. Esparar, E. Esko, M. Leinonen, and P. Ruutu. 1995. Evaluation of sampling sites for detection of upper respiratory tract carriage of Streptococcus pneumoniae and Haemophilus influenzae among healthy Filipino infants. J. Clin. Microbiol. 33:3077-3079.
50. Huber, J. A., H. G. Morrison, S. M. Huse, P. R. Neal, M. L. Sogin, and D. B. Mark Welch. 2009. Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environ. Microbiol. 11:1292-1302.
51. DeSantis, T. Z., P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Andersen. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72: 5069-5072.
52. Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
53. Cole, J. R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, T. Marsh, G. M. Garrity, and J. M. Tiedje. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145.
54. Claesson, M. J., O. O'Sullivan, Q. Wang, J. Nikkila, J. R. Marchesi, H. Smidt, W. M. de Vos, R. P. Ross, and P. W. O'Toole. 2009. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 4:e6669.