1887

Abstract

Acute respiratory infections (ARIs) constitute one of the leading causes of antibiotic administration, hospitalization and death among children <5 years old. The upper respiratory tract microbiota has been suggested to explain differential susceptibility to ARIs and modulate ARI severity. The aim of the present study was to investigate the relation of nasopharyngeal microbiota and other microbiological parameters with respiratory health and disease, and to assess nasopharyngeal microbiota diagnostic utility for discriminating between different respiratory health statuses. We conducted a prospective case–control study at Hospital Sant Joan de Deu (, ) from 2014 to 2018. This study included three groups of children <18 years with gradual decrease of ARI severity: cases with invasive pneumococcal disease (IPD) (representative of lower respiratory tract infections and systemic infections), symptomatic controls with mild viral upper respiratory tract infections (URTI), and healthy/asymptomatic controls according to an approximate case–control ratio 1:2. Nasopharyngeal samples were collected from participants for detection, quantification and serotyping of pneumococcal DNA, viral DNA/RNA detection and 16S rRNA gene sequencing. Microbiological parameters were included on case–control classification models. A total of 140 subjects were recruited (IPD=27, URTI=48, healthy/asymptomatic control=65). Children’s nasopharyngeal microbiota composition varied according to respiratory health status and infection severity. The IPD group was characterized by overrepresentation of , higher frequency of invasive pneumococcal serotypes, increased rate of viral infection and underrepresentation of potential protective bacterial species such as and . Microbiota-based classification models differentiated cases from controls with moderately high accuracy. These results demonstrate the close relationship existing between a child’s nasopharyngeal microbiota and respiratory health, and provide initial evidence of the potential of microbiota-based diagnostics for differential diagnosis of severe ARIs using non-invasive samples.

Funding
This study was supported by the:
  • Sant Joan de Deu Foundation (Award AFR2015)
    • Principle Award Recipient: Muñoz-AlmagroCarmen
  • Instituto de Salud Carlos III (Award FI17/00248)
    • Principle Award Recipient: Henares BonillaDesiree
  • Instituto de Salud Carlos III (Award PI16/00174)
    • Principle Award Recipient: Muñoz-AlmagroCarmen
  • Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (Award Ayuda SEIMC)
    • Principle Award Recipient: Henares BonillaDesiree
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2021-10-26
2024-12-08
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References

  1. Henares D, Brotons P, de Sevilla MF, Fernandez-Lopez A, Hernandez-Bou S et al. Supplementary material. Figshare; 2021 https://doi.org/10.6084/m9.figshare.13280435.v3
  2. World Health Organization Global Health Observatory | by category | number of deaths by region - acute lower respiratory infections. http://apps.who.int/gho/data/view.main.CM1002015REG6-CH9?lang=en accessed 22 Nov 2020
  3. WHO Global Health Observatory | by category | number of deaths (thousands) - data by WHO region. https://apps.who.int/gho/data/view.main.CM1300N?lang=en accessed 22 Nov 2020
  4. Rogawski ET, Platts-Mills JA, Seidman JC, John S, Mahfuz M et al. Use of antibiotics in children younger than two years in eight countries: a prospective cohort study. Bull World Health Organ 2017; 95:49–61 [View Article] [PubMed]
    [Google Scholar]
  5. De Steenhuijsen Piters WAA, Sanders EAM, Bogaert D. The role of the local microbial ecosystem in respiratory health and disease. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140294 [View Article] [PubMed]
    [Google Scholar]
  6. Obaro S, Adegbola R. The pneumococcus: carriage, disease and conjugate vaccines. J Med Microbiol 2002; 51:98–104 [View Article] [PubMed]
    [Google Scholar]
  7. Balsells E, Dagan R, Yildirim I, Gounder PP, Steens A et al. The relative invasive disease potential of Streptococcus pneumoniae among children after PCV introduction: a systematic review and meta-analysis. J Infect 2018; 77:368–378 [View Article] [PubMed]
    [Google Scholar]
  8. Bosch A, De Steenhuijsen Piters WAA, Van Houten MA, Chu M, Biesbroek G et al. Maturation of the infant respiratory microbiota, environmental drivers, and health consequences. Am J Respir Crit Care Med 2017; 196:1582–1590 [View Article] [PubMed]
    [Google Scholar]
  9. Relman DA. The human microbiome: ecosystem resilience and health. Nutr Rev 2012; 70:S2–S9 [View Article]
    [Google Scholar]
  10. Biesbroek G, Tsivtsivadze E, Sanders EAM, Montijn R, Veenhoven RH et al. Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Am J Respir Crit Care Med 2014; 190:1283–1292 [View Article] [PubMed]
    [Google Scholar]
  11. Bosch A, Levin E, van Houten MA, Hasrat R, Kalkman G et al. Development of upper respiratory tract microbiota in infancy is affected by mode of delivery. EBioMedicine 2016; 9:336–345 [View Article] [PubMed]
    [Google Scholar]
  12. Biesbroek G, Bosch A, Wang X, Keijser BJF, Veenhoven RH et al. The impact of breastfeeding on nasopharyngeal microbial communities in infants. Am J Respir Crit Care Med 2014; 190:298–308 [View Article] [PubMed]
    [Google Scholar]
  13. Mika M, Maurer J, Korten I, Allemann A, Aebi S et al. Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case–control study. Microbiome 2017; 5:85 [View Article] [PubMed]
    [Google Scholar]
  14. Chonmaitree T, Jennings K, Golovko G, Khanipov K, Pimenova M et al. Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media. PLoS One 2017; 12:e0180630 [View Article] [PubMed]
    [Google Scholar]
  15. Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD et al. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat Med 2017; 23:314–326 [View Article] [PubMed]
    [Google Scholar]
  16. Salter SJ, Turner C, Watthanaworawit W, de Goffau MC, Wagner J et al. 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 Negl Trop Dis 2017; 11:e0005975 [View Article] [PubMed]
    [Google Scholar]
  17. Lappan R, Imbrogno K, Sikazwe C, Anderson D, Mok D et al. A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera. BMC Microbiol 2018; 18:13 [View Article] [PubMed]
    [Google Scholar]
  18. Pettigrew MM, Laufer AS, Gent JF, Kong Y, Fennie KP et al. Upper respiratory tract microbial communities, acute otitis media pathogens, and antibiotic use in healthy and sick children. Appl Environ Microbiol 2012; 78:6262–6270 [View Article] [PubMed]
    [Google Scholar]
  19. Hanada S, Pirzadeh M, Carver KY, Deng JC. Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. Front Immunol 2018; 9:2640 [View Article] [PubMed]
    [Google Scholar]
  20. Kaul D, Rathnasinghe R, Ferres M, Tan GS, Barrera A et al. Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection. Nat Commun 2020; 11:2537 [View Article] [PubMed]
    [Google Scholar]
  21. van Houten CB, Cohen A, Engelhard D, Hays JP, Karlsson R et al. Antibiotic misuse in respiratory tract infections in children and adults – a prospective, multicentre study (TAILORED Treatment). Eur J Clin Microbiol Infect Dis 2019; 38:505–514 [View Article] [PubMed]
    [Google Scholar]
  22. Man WH, van Houten MA, Mérelle ME, Vlieger AM, Chu M et al. Bacterial and viral respiratory tract microbiota and host characteristics in children with lower respiratory tract infections: a matched case-control study. Lancet Respir Med 2019; 7:417–426 [View Article] [PubMed]
    [Google Scholar]
  23. Teo SM, Mok D, Pham K, Kusel M, Serralha M et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe 2015; 17:704–715 [View Article] [PubMed]
    [Google Scholar]
  24. Vissing NH, Chawes BLK, Bisgaard H. Increased risk of pneumonia and bronchiolitis after bacterial colonization of the airways as neonates. Am J Respir Crit Care Med 2013; 188:1246–1252 [View Article] [PubMed]
    [Google Scholar]
  25. Camelo-Castillo A, Henares D, Brotons P, Galiana A, Rodríguez JC et al. Nasopharyngeal microbiota in children with invasive pneumococcal disease: identification of bacteria with potential disease-promoting and protective effects. Front Microbiol 2019; 10:11 [View Article] [PubMed]
    [Google Scholar]
  26. Panda S, Khader E, Casellas F, López Vivancos J, García Cors M et al. Short-term effect of antibiotics on human gut microbiota. PLoS One 2014; 9:e95476 [View Article] [PubMed]
    [Google Scholar]
  27. Ramsay M. Chapter 25 Pneumococcal. In The Green Book of Immunisation London: Public Health England; 2020
    [Google Scholar]
  28. Brueggemann AB, Griffiths DT, Meats E, Peto T, Crook DW et al. Clonal relationships between invasive and carriage Streptococcus pneumoniae and serotype- and clone-specific differences in invasive disease potential. J Infect Dis 2003; 187:1424–1432 [View Article] [PubMed]
    [Google Scholar]
  29. Sleeman KL, Griffiths D, Shackley F, Diggle L, Gupta S et al. Capsular serotype-specific attack rates and duration of carriage of Streptococcus pneumoniae in a population of children. J Infect Dis 2006; 194:682–688 [View Article] [PubMed]
    [Google Scholar]
  30. del Amo E, Selva L, de Sevilla MF, Ciruela P, Brotons P et al. Estimation of the invasive disease potential of Streptococcus pneumoniae in children by the use of direct capsular typing in clinical specimens. Eur J Clin Microbiol Infect Dis 2015; 34:705–711 [View Article] [PubMed]
    [Google Scholar]
  31. CDCNCIRD Chapter 8 Identification and characterization of Streptococcus pneumoniae. In Laboratory Methods for the Diagnosis of Meningitis Atlanta, GA: Centers for Disease Control and Prevention; 2020 https://www.cdc.gov/meningitis/lab-manual/chpt08-id-characterization-streppneumo.html
    [Google Scholar]
  32. Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011; 27:863–864 [View Article] [PubMed]
    [Google Scholar]
  33. Magoc T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 2011; 27:2957–2963 [View Article] [PubMed]
    [Google Scholar]
  34. Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013; 10:996–998 [View Article] [PubMed]
    [Google Scholar]
  35. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73:5261–5267 [View Article] [PubMed]
    [Google Scholar]
  36. Allard G, Ryan FJ, Jeffery IB, Claesson MJ. SPINGO: a rapid species-classifier for microbial amplicon sequences. BMC Bioinformatics 2015; 16:324 [View Article] [PubMed]
    [Google Scholar]
  37. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010; 26:266–267 [View Article] [PubMed]
    [Google Scholar]
  38. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010; 7:335–336 [View Article] [PubMed]
    [Google Scholar]
  39. Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 2018; 6:226 [View Article] [PubMed]
    [Google Scholar]
  40. Vatanen T, Kostic AD, D’Hennezel E, Siljander H, Franzosa EA et al. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 2016; 165:842–853 [View Article] [PubMed]
    [Google Scholar]
  41. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014; 12:87 [View Article] [PubMed]
    [Google Scholar]
  42. Cao Q, Sun X, Rajesh K, Chalasani N, Gelow K et al. Effects of rare microbiome taxa filtering on statistical analysis. Front Microbiol 2021; 11:607325 [View Article] [PubMed]
    [Google Scholar]
  43. R Core Team R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2018 https://www.gbif.org/tool/81287/r-a-language-and-environment-for-statistical-computing
  44. Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P et al. Package ‘vegan’; Community ecology package; 2020 https://cran.r-project.org/web/packages/vegan/vegan.pdf
  45. Ho Man W, De Steenhuijsen Piters WA, Bogaert D. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat Rev Microbiol 2017; 15:259–270 [View Article] [PubMed]
    [Google Scholar]
  46. Biesbroek G, Wang X, Keijser BJF, Eijkemans RMJ, Trzciński K et al. Seven-valent pneumococcal conjugate vaccine and nasopharyngeal microbiota in healthy children. Emerg Infect Dis 2014; 20:201–210 [View Article] [PubMed]
    [Google Scholar]
  47. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L et al. Metagenomic biomarker discovery and explanation. Genome Biol 2011; 12:R60 [View Article] [PubMed]
    [Google Scholar]
  48. Smith DJ, Badrick AC, Zakrzewski M, Krause L, Bell SC et al. Pyrosequencing reveals transient cystic fibrosis lung microbiome changes with intravenous antibiotics. Eur Respir J 2014; 44:922–930 [View Article] [PubMed]
    [Google Scholar]
  49. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner ACR et al. The human oral microbiome. J Bacteriol 2010; 192:5002–5017 [View Article] [PubMed]
    [Google Scholar]
  50. Mokoena MP. Lactic acid bacteria and their bacteriocins: classification, biosynthesis and applications against uropathogens: a mini-review. Molecules 2017; 22:E1255 [View Article] [PubMed]
    [Google Scholar]
  51. Gareau MG, Sherman PM, Walker WA. Probiotics and the gut microbiota in intestinal health and disease. Nat Rev Gastroenterol Hepatol 2010; 7:503–514 [View Article] [PubMed]
    [Google Scholar]
  52. Brugger SD, Eslami SM, Pettigrew MM, Escapa IF, Henke MM et al. Dolosigranulum pigrum cooperation and competition in human nasal microbiota. bioRxiv 2019678698
    [Google Scholar]
  53. Kelly MS, Surette MG, Smieja M, Pernica JM, Rossi L et al. The nasopharyngeal microbiota of children with respiratory infections in Botswana. Pediatr Infect Dis J 2017; 36:e211–e218 [View Article]
    [Google Scholar]
  54. Mays TD, Holdeman LV, Moore WEC, Rogosa M, Johnson JL. Taxonomy of the genus Veillonella Prévot. Int J Syst Bacteriol 1982; 32:28–36
    [Google Scholar]
  55. Sakwinska O, Schmid VB, Berger B, Bruttin A, Keitel K et al. Nasopharyngeal microbiota in healthy children and pneumonia patients. J Clin Microbiol 2014; 52:1590–1594 [View Article] [PubMed]
    [Google Scholar]
  56. Hasegawa K, Linnemann RW, Mansbach JM, Ajami NJ, Espinola JA et al. Nasal airway microbiota profile and severe bronchiolitis in infants: a case-control study. Pediatr Infect Dis J 2017; 36:1044–1051 [View Article] [PubMed]
    [Google Scholar]
  57. Drago L, Toscano M, De Grandi R, Grossi E, Padovani EM et al. Microbiota network and mathematic microbe mutualism in colostrum and mature milk collected in two different geographic areas: Italy versus Burundi. ISME J 2017; 11:875–884 [View Article] [PubMed]
    [Google Scholar]
  58. Holgerson PL, Vestman NR, Claesson R, Öhman C, Domellöf M et al. Oral microbial profile discriminates breast-fed from formula-fed infants. J Pediatr Gastroenterol Nutr 2013; 56:127–136 [View Article] [PubMed]
    [Google Scholar]
  59. Yamasaki K, Kawanami T, Yatera K, Fukuda K, Noguchi S et al. Significance of anaerobes and oral bacteria in community-acquired pneumonia. PLoS One 2013; 8:e63103 [View Article] [PubMed]
    [Google Scholar]
  60. Llena C, Almarche A, Mira A, López MA. Antimicrobial efficacy of the supernatant of Streptococcus dentisani against microorganisms implicated in root canal infections. J Oral Sci 2019; 61:184–194 [View Article] [PubMed]
    [Google Scholar]
  61. Marsh PD, Zaura E. Dental biofilm: ecological interactions in health and disease. J Clin Periodontol 2017; 44:S12–S22 [View Article] [PubMed]
    [Google Scholar]
  62. De Steenhuijsen Piters WAA, Heinonen S, Hasrat R, Bunsow E, Smith B et al. Nasopharyngeal microbiota, host transcriptome, and disease severity in children with respiratory syncytial virus infection. Am J Respir Crit Care Med 2016; 194:1104–1115 [View Article] [PubMed]
    [Google Scholar]
  63. Edouard S, Million M, Bachar D, Dubourg G, Michelle C et al. The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens. Eur J Clin Microbiol Infect Dis 2018; 37:1725–1733 [View Article] [PubMed]
    [Google Scholar]
  64. Lanaspa M, Bassat Q, Medeiros MM, Muñoz-Almagro C. Respiratory microbiota and lower respiratory tract disease. Expert Rev Anti Infect Ther 2017; 15:703–711 [View Article] [PubMed]
    [Google Scholar]
  65. Huang YJ, Lynch SV. The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications. Expert Rev Respir Med 2011; 5:809–821 [View Article]
    [Google Scholar]
  66. Man WH, Clerc M, De Steenhuijsen Piters WAA, van Houten MA, Chu M et al. Loss of microbial topography between oral and nasopharyngeal microbiota and development of respiratory infections early in life. Am J Respir Crit Care Med 2019; 200:760–770 [View Article] [PubMed]
    [Google Scholar]
  67. Dubourg G, Edouard S, Raoult D. Relationship between nasopharyngeal microbiota and patient’s susceptibility to viral infection. Expert Rev Anti Infect Ther 2019; 17:437–447 [View Article] [PubMed]
    [Google Scholar]
  68. Harris M, Clark J, Coote N, Fletcher P, Harnden A et al. British Thoracic Society guidelines for the management of community acquired pneumonia in children: update 2011. Thorax 2011; 66:ii1–ii23 [View Article]
    [Google Scholar]
  69. Wubbel L, Muniz L, Ahmed A, Trujillo M, Carubelli C et al. Etiology and treatment of community-acquired pneumonia in ambulatory children. Pediatr Infect Dis J 1999; 18:98–104 [View Article] [PubMed]
    [Google Scholar]
  70. Rodrigues CMC, Groves H. Community-acquired pneumonia in children: the challenges of microbiological diagnosis. J Clin Microbiol 2018; 56:e01318-17 [View Article] [PubMed]
    [Google Scholar]
  71. Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA et al. Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol 2014; 52:139–146 [View Article] [PubMed]
    [Google Scholar]
  72. Graspeuntner S, Bohlmann MK, Gillmann K, Speer R, Kuenzel S et al. Microbiota-based analysis reveals specific bacterial traits and a novel strategy for the diagnosis of infectious infertility. PLoS One 2018; 13:e0191047 [View Article] [PubMed]
    [Google Scholar]
  73. Kai S, Matsuo Y, Nakagawa S, Kryukov K, Matsukawa S et al. Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION nanopore sequencer. FEBS Open Bio 2019; 9:548–557 [View Article] [PubMed]
    [Google Scholar]
  74. Houck PM, Bratzler DW, Nsa W, Ma A, Bartlett JG. Timing of antibiotic administration and outcomes for medicare patients hospitalized with community-acquired pneumonia. Arch Intern Med 2004; 164:637–644 [View Article] [PubMed]
    [Google Scholar]
  75. Llor C, Bjerrum L. Antimicrobial resistance: risk associated with antibiotic overuse and initiatives to reduce the problem. Ther Adv Drug Saf 2014; 5:229–241 [View Article] [PubMed]
    [Google Scholar]
  76. Edgar RC, Valencia A. Updating the 97% identity threshold for 16S ribosomal RNA OTUs. Bioinformatics 2018; 34:2371–2375 [View Article]
    [Google Scholar]
  77. Escobar-Zepeda A, Godoy-Lozano EE, Raggi L, Segovia L, Merino E et al. Analysis of sequencing strategies and tools for taxonomic annotation: defining standards for progressive metagenomics. Sci Rep 2018; 8:12034 [View Article]
    [Google Scholar]
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