A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children

PLoS Neglected Tropical Diseases

Volumn 11, Issue 10, 2017, Pages

  Salter, Susannah J ^a   Turner, Claudia ^b,c,e   Watthanaworawit, Wanitda ^b   de Goffau, Marcus C ^a   Wagner, Josef ^a   Parkhill, Julian ^a   Bentley, Stephen D ^a   Goldblatt, David ^d   Nosten, Francois ^b,c   Turner, Paul ^b,c,e  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b SHOKLO MALARIA RESEARCH UNIT   (Thailand)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

^e Angkor Hospital for Children   (Cambodia)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; DIPHTHERIA PERTUSSIS TETANUS VACCINE; HAEMOPHILUS INFLUENZAE VACCINE; PNEUMOCOCCUS VACCINE; RNA 16S; ANTIINFECTIVE AGENT;

ACINETOBACTER; ACTINOBACILLUS; AGE; ARTICLE; BACTERIAL FLORA; CHILD; COHORT ANALYSIS; CORYNEBACTERIUM; EAST ASIAN; FLAVOBACTERIACEAE; HAEMOPHILUS; HUMAN; HUMAN CELL; HUMAN RESPIRATORY SYNCYTIAL VIRUS; INFANT; LONGITUDINAL STUDY; METAPNEUMOVIRUS; MORAXELLA; NASOPHARYNX; NEISSERIA; ORNITHOBACTERIUM; PNEUMONIA; POLYMERASE CHAIN REACTION; PRESCHOOL CHILD; REFUGEE CAMP; RESPIRATORY TRACT INFECTION; SEROTYPE; STAPHYLOCOCCUS; STREPTOCOCCUS PNEUMONIAE; VACCINATION; BACTERIUM; CLASSIFICATION; FEMALE; GENETICS; HETEROZYGOTE; ISOLATION AND PURIFICATION; MALE; MICROBIOLOGY; MICROFLORA; MORAXELLACEAE; NEWBORN; REFUGEE; RESPIRATORY TRACT INFECTIONS;

AGE FACTORS; ANTI-BACTERIAL AGENTS; BACTERIA; CARRIER STATE; COHORT STUDIES; FEMALE; HUMANS; INFANT; INFANT, NEWBORN; LONGITUDINAL STUDIES; MALE; MICROBIOTA; MORAXELLACEAE; NASOPHARYNX; PNEUMONIA; REFUGEES; RESPIRATORY TRACT INFECTIONS; RNA, RIBOSOMAL, 16S; STREPTOCOCCUS PNEUMONIAE;

EID: 85032151246     PISSN: 19352727     EISSN: 19352735     Source Type: Journal    
DOI: 10.1371/journal.pntd.0005975     Document Type: Article

References (32)

1. Kinabo GD, van der Ven A, Msuya LJ, Shayo AM, Schimana W, Ndaro A, et al. Dynamics of nasopharyngeal bacterial colonisation in HIV-exposed young infants in Tanzania. Tropical Medicine and International Health. 2013;18(3):286–95. doi: 10.1111/tmi.12057 23320622
2. Stearns JC, Davidson CJ, McKeon S, Whelan FJ, Fontes ME, Schryvers AB, et al. Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. ISME Journal. 2015;9(5):1246–59. doi: 10.1038/ismej.2014.250 25575312
3. Garenne M, Ronsmans C, Campbell H, The magnitude of mortality from acute respiratory infections in children under 5 years in developing countries. World Health Statistic Quarterly. 1992;45:180–91.
4. Langdon A, Crook N, Dantas G, The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Medicine. 2016;8:39. doi: 10.1186/s13073-016-0294-z 27074706
5. Suárez-Arrabal MC, Mella C, Lopez SM, Brown NV, Hall MW, Hammond S, et al. Nasopharyngeal bacterial burden and antibiotics: Influence on inflammatory markers and disease severity in infants with respiratory syncytial virus bronchiolitis. The Journal of Infection. 2015;71(4):458–69. doi: 10.1016/j.jinf.2015.06.010 26149186
6. Hilty M, Qi W, Brugger SD, Frei L, Agyeman P, Frey PM, et al. Nasopharyngeal microbiota in infants with acute otitis media. The Journal of Infectious Diseases. 2012;205(7):1048–55. doi: 10.1093/infdis/jis024 22351941
7. Turner C, Turner P, Carrara V, Burgoine K, Tha Ler Htoo S, Watthanaworawit W, et al. High rates of pneumonia in children under two years of age in a South East Asian refugee population. PLoS One. 2013;8(1):e54026. doi: 10.1371/journal.pone.0054026 23320118
8. Vissing NH, Chawes BL, Bisgaard H, Increased risk of pneumonia and bronchiolitis after bacterial colonization of the airways as neonates. American Journal of Respiratory and Critical Care Medicine. 2013;188(10):1246–52. doi: 10.1164/rccm.201302-0215OC 24090102
9. de Steenhuijsen Piters WA, Bogaert D, Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure. MBio. 2016;7(1):e00009–16. doi: 10.1128/mBio.00009-16 26838716
10. Bomar L, Brugger SD, Yost BH, Davies SS, Lemon KP, Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols. MBio. 2016;7(1):e01725–15. doi: 10.1128/mBio.01725-15 26733066
11. Pettigrew MM, Gent JF, Revai K, Patel JA, Chonmaitree T, Microbial interactions during upper respiratory tract infections. Emerging Infectious Diseases. 2008;14(10):1584–91. doi: 10.3201/eid1410.080119 18826823
12. Biesbroek G, Tsivtsivadze E, Sanders EA, Montijn R, Veenhoven RH, Keijser BJ, et al. Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. American Journal of Respiratory and Critical Care Medicine. 2014;190(11):1283–92. doi: 10.1164/rccm.201407-1240OC 25329446
13. Bosch AA, Biesbroek G, Trzcinski K, Sanders EA, Bogaert D, Viral and bacterial interactions in the upper respiratory tract. PLoS Pathogens. 2013;9(1):e1003057. doi: 10.1371/journal.ppat.1003057 23326226
14. Zehr ES, Bayles DO, Boatwright WD, Tabatabai LB, Register KB, Complete genome sequence of Ornithobacterium rhinotracheale strain ORT-UMN 88. Standards in Genomic Sciences. 2014;9:16. doi: 10.1186/1944-3277-9-16 25780507
15. Kwambana BA, Mohammed NI, Jeffries D, Barrer M, Adegbola RA, Antonio M, Differential effects of frozen storage on the molecular detection of bacterial taxa that inhabit the nasopharynx. BMC Clinical Pathology. 2011;11:2. doi: 10.1186/1472-6890-11-2 21261963
16. Feazel LM, Santorico SA, Robertson CE, Bashraheil M, Scott JA, Frank DN, et al. Effects of Vaccination with 10-Valent Pneumococcal Non-Typeable Haemophilus influenza Protein D Conjugate Vaccine (PHiD-CV) on the Nasopharyngeal Microbiome of Kenyan Toddlers. PLoS One. 2015;10(6):e0128064. doi: 10.1371/journal.pone.0128064 26083474
17. Bogaert D, Keijser B, Huse S, Rossen J, Veenhoven R, van Gils E, et al. Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PLoS One. 2011;6(2):e17035. doi: 10.1371/journal.pone.0017035 21386965
18. Mika M, Mack I, Korten I, Qi W, Aebi S, Frey U, et al. Dynamics of the nasal microbiota in infancy: a prospective cohort study. The Journal of Allergy and Clinical Immunology. 2015;135(4):905–12. doi: 10.1016/j.jaci.2014.12.1909 25636948
19. Numminen E, Chewapreecha C, Turner C, Goldblatt D, Nosten F, Bentley SD, et al. Climate induces seasonality in pneumococcal transmission. Scientific Reports. 2015;5:11344. doi: 10.1038/srep11344 26067932
20. Marsh RL, Kaestli M, Chang AB, Binks MJ, Pope CE, Hoffman LR, et al. The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx. Microbiome. 2016;4:37. doi: 10.1186/s40168-016-0182-1 27388563
21. Turner P, Turner C, Jankhot A, Helen N, Lee SJ, Day NP, et al. A longitudinal study of Streptococcus pneumoniae carriage in a cohort of infants and their mothers on the Thailand-Myanmar border. PLoS ONE. 2012;7(5):e38271. Epub 2012/06/14. doi: 10.1371/journal.pone.0038271 22693610.
22. Turner C, Turner P, Carrara V, Burgoine K, Tha Ler Htoo S, Watthanaworawit W, et al. High Rates of Pneumonia in Children under Two Years of Age in a South East Asian Refugee Population. PLoS ONE. 2013;8(1):e54026. Epub 2013/01/16. doi: 10.1371/journal.pone.0054026 23320118.
23. O'Brien KL, Nohynek H, Report from a WHO Working Group: standard method for detecting upper respiratory carriage of Streptococcus pneumoniae. Pediatr Infect Dis J. 2003;22(2):e1–11. Epub 2003/02/15. doi: 10.1097/01.inf.0000049347.42983.77 12586987.
24. Turner P, Turner C, Watthanaworawit W, Cararra V, Cicelia N, Deglise C, et al. Respiratory virus surveillance in hospitalised pneumonia patients on the Thailand-Myanmar border. BMC Infect Dis. 2013;13:434. doi: 10.1186/1471-2334-13-434 24498873
25. WHOCough or difficulty breathing. Pocket book of hospital care for children: guidelines for the management of common illnesses with limited resources. 2nd Edition ed: World Health Organisation; 2013. p. 75–124.
26. Turner P, Hinds J, Turner C, Jankhot A, Gould K, Bentley SD, et al. Improved detection of nasopharyngeal cocolonization by multiple pneumococcal serotypes by use of latex agglutination or molecular serotyping by microarray. J Clin Microbiol. 2011;49(5):1784–9. Epub 2011/03/18. doi: 10.1128/JCM.00157-11 21411589.
27. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology. 2009;75(23):7537–41. doi: 10.1128/AEM.01541-09 19801464
28. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Research. 2014;42:D633–42. doi: 10.1093/nar/gkt1244 24288368
29. Hammer Ø, Harper DAT, Ryan PD, PAST: Paleontological statistics software package for education and data analysis. Palaeontologica Electronica. 2001;4(1):9.
30. Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML, Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. The ISME Journal. 2015;9:968–79. doi: 10.1038/ismej.2014.195 25325381
31. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar et al. ARB: a software environment for sequence data. Nucleic Acids Research. 2004;32(4):1363–71. doi: 10.1093/nar/gkh293 14985472
32. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biology. 2014;12:87. doi: 10.1186/s12915-014-0087-z 25387460