Evidence of persistence of spp. in the cystic fibrosis lung Free

Abstract

spp. represent a diverse genus of bacteria, frequently identified by both culture and molecular methods in the lungs of patients with chronic respiratory infection. However, their role in the pathogenesis of chronic lung infection is unclear; therefore, a more complete understanding of their molecular epidemiology is required.

Pulsed Field Gel Electrophoresis (PFGE) and Random Amplified Polymorphic DNA (RAPD) assays were developed and used to determine the degree of similarity between sequential isolates (=42) from cystic fibrosis (CF) patients during periods of clinical stability and exacerbation.

A wide diversity of PFGE and RAPD banding patterns were observed, demonstrating considerable within-genus heterogeneity. In 8/12 (66.7 %) cases, where the same species was identified at sequential time points, pre- and post-antibiotic treatment of an exacerbation, PFGE/RAPD profiles were highly similar or identical. Congruence was observed between PFGE and RAPD (adjusted Rand coefficient, 0.200; adjusted Wallace 0.459, 0.128). Furthermore, some isolates could not be adequately assigned a species name on the basis of 16S rRNA analysis: these isolates had identical PFGE/RAPD profiles to .

The similarity in PFGE and RAPD banding patterns observed in sequential CF isolates may be indicative of the persistence of this genus in the CF lung. Further work is required to determine the clinical significance of this finding, and to more accurately distinguish differences in pathogenicity between species.

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2017-06-01
2024-03-29
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References

  1. Shah HN, Collins DM. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. Int J Syst Bacteriol 1990; 40:205–208 [View Article][PubMed]
    [Google Scholar]
  2. Ueki A, Akasaka H, Satoh A, Suzuki D, Ueki K. Prevotella paludivivens sp. nov., a novel strictly anaerobic, Gram-negative, hemicellulose-decomposing bacterium isolated from plant residue and rice roots in irrigated rice-field soil. Int J Syst Evol Microbiol 2007; 57:1803–1809 [View Article][PubMed]
    [Google Scholar]
  3. Shah HN, Olsen I, Bernard K, Finegold SM, Gharbia S et al. Approaches to the study of the systematics of anaerobic, Gram-negative, non-sporeforming rods: current status and perspectives. Anaerobe 2009; 15:179–194 [View Article][PubMed]
    [Google Scholar]
  4. Brook I. Microbiology and management of joint and bone infections due to anaerobic bacteria. J Orthop Sci 2008; 13:160–169 [View Article][PubMed]
    [Google Scholar]
  5. Brook I. The role of anaerobic bacteria in sinusitis. Anaerobe 2006; 12:5–12 [View Article][PubMed]
    [Google Scholar]
  6. Worlitzsch D, Tarran R, Ulrich M, Schwab U, Cekici A et al. Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients. J Clin Invest 2002; 109:317–325 [View Article][PubMed]
    [Google Scholar]
  7. Tunney MM, Field TR, Moriarty TF, Patrick S, Doering G et al. Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. Am J Respir Crit Care Med 2008; 177:995–1001 [View Article][PubMed]
    [Google Scholar]
  8. Fodor AA, Klem ER, Gilpin DF, Elborn JS, Boucher RC et al. The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations. PLoS One 2012; 7:e45001 [View Article][PubMed]
    [Google Scholar]
  9. Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L et al. Analysis of the lung microbiome in the "healthy" smoker and in COPD. PLoS One 2011; 6:e16384 [View Article][PubMed]
    [Google Scholar]
  10. Cabrera-Rubio R, Garcia-Núñez M, Setó L, Antó JM, Moya A et al. Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease. J Clin Microbiol 2012; 50:3562–3568 [View Article][PubMed]
    [Google Scholar]
  11. Einarsson GG, Comer DM, McIlreavey L, Parkhill J, Ennis M et al. Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers. Thorax 2016; 71:795–803 [View Article][PubMed]
    [Google Scholar]
  12. Park H, Shin JW, Park SG, Kim W. Microbial communities in the upper respiratory tract of patients with asthma and chronic obstructive pulmonary disease. PLoS One 2014; 9:e109710 [View Article][PubMed]
    [Google Scholar]
  13. Hilty M, Burke C, Pedro H, Cardenas P, Bush A et al. Disordered microbial communities in asthmatic airways. PLoS One 2010; 5:e8578 [View Article][PubMed]
    [Google Scholar]
  14. Tunney MM, Einarsson GG, Wei L, Drain M, Klem ER et al. Lung microbiota and bacterial abundance in patients with bronchiectasis when clinically stable and during exacerbation. Am J Respir Crit Care Med 2013; 187:1118–1126 [View Article][PubMed]
    [Google Scholar]
  15. Tunney MM, Klem ER, Fodor AA, Gilpin DF, Moriarty TF et al. Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis. Thorax 2011; 66:579–584 [View Article][PubMed]
    [Google Scholar]
  16. Lane DJ. 16S/23S rRNA sequencing. In Stackerbrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, UK: John Wiley & Sons; 1991 pp. 115–175
    [Google Scholar]
  17. Muyzer G, de Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 1993; 59:695–700[PubMed]
    [Google Scholar]
  18. Watanabe-Kato T, Hayashi JI, Terazawa Y, Hoover CI, Nakayama K et al. Isolation and characterization of transposon-induced mutants of Porphyromonas gingivalis deficient in fimbriation. Microb Pathog 1998; 24:25–35 [View Article][PubMed]
    [Google Scholar]
  19. Takanashi K, Kishi M, Okuda K, Ishihara K. Colonization by Porphyromonas gingivalis and Prevotella intermedia from teeth to osseointegrated implant regions. Bull Tokyo Dent Coll 2004; 45:77–85[PubMed] [CrossRef]
    [Google Scholar]
  20. Mahenthiralingam E, Campbell ME, Foster J, Lam JS, Speert DP. Random amplified polymorphic DNA typing of Pseudomonas aeruginosa isolates recovered from patients with cystic fibrosis. J Clin Microbiol 1996; 34:1129–1135[PubMed]
    [Google Scholar]
  21. Mahenthiralingam E, Campbell ME, Henry DA, Speert DP. Epidemiology of Burkholderia cepacia infection in patients with cystic fibrosis: analysis by randomly amplified polymorphic DNA fingerprinting. J Clin Microbiol 1996; 34:2914–2920[PubMed]
    [Google Scholar]
  22. Fothergill JL, White J, Foweraker JE, Walshaw MJ, Ledson MJ et al. Impact of Pseudomonas aeruginosa genomic instability on the application of typing methods for chronic cystic fibrosis infections. J Clin Microbiol 2010; 48:2053–2059 [View Article][PubMed]
    [Google Scholar]
  23. Carriço JA, Silva-Costa C, Melo-Cristino J, Pinto FR, de Lencastre H et al. Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes. J Clin Microbiol 2006; 44:2524–2532 [View Article][PubMed]
    [Google Scholar]
  24. Severiano A, Pinto FR, Ramirez M, Carriço JA. Adjusted Wallace coefficient as a measure of congruence between typing methods. J Clin Microbiol 2011; 49:3997–4000 [View Article][PubMed]
    [Google Scholar]
  25. Dickson RP, Erb-Downward JR, Prescott HC, Martinez FJ, Curtis JL et al. Cell-associated bacteria in the human lung microbiome. Microbiome 2014; 2:28 [View Article][PubMed]
    [Google Scholar]
  26. Brook I. Anaerobic pulmonary infections in children. Pediatr Emerg Care 2004; 20:636–640 [View Article][PubMed]
    [Google Scholar]
  27. Brook I, Frazier EH. Immune response to Fusobacterium nucleatum and Prevotella intermedia in the sputum of patients with acute exacerbation of chronic bronchitis. Chest 2003; 124:832–833 [View Article][PubMed]
    [Google Scholar]
  28. Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B et al. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome 2013; 1:19 [View Article][PubMed]
    [Google Scholar]
  29. Ulrich M, Beer I, Braitmaier P, Dierkes M, Kummer F et al. Relative contribution of Prevotella intermedia and Pseudomonas aeruginosa to lung pathology in airways of patients with cystic fibrosis. Thorax 2010; 65:978–984 [View Article][PubMed]
    [Google Scholar]
  30. Zemanick ET, Harris JK, Wagner BD, Robertson CE, Sagel SD et al. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS One 2013; 8:e62917 [View Article][PubMed]
    [Google Scholar]
  31. Larsen JM, Musavian HS, Butt TM, Ingvorsen C, Thysen AH et al. Chronic obstructive pulmonary disease and asthma-associated Proteobacteria, but not commensal Prevotella spp., promote Toll-like receptor 2-independent lung inflammation and pathology. Immunology 2015; 144:333–342 [View Article][PubMed]
    [Google Scholar]
  32. Larsen JM, Steen-Jensen DB, Laursen JM, Søndergaard JN, Musavian HS et al. Divergent pro-inflammatory profile of human dendritic cells in response to commensal and pathogenic bacteria associated with the airway microbiota. PLoS One 2012; 7:e31976 [View Article][PubMed]
    [Google Scholar]
  33. Dupin C, Tamanai-Shacoori Z, Ehrmann E, Dupont A, Barloy-Hubler F et al. Oral Gram-negative anaerobic bacilli as a reservoir of β-lactam resistance genes facilitating infections with multiresistant bacteria. Int J Antimicrob Agents 2015; 45:99–105 [View Article][PubMed]
    [Google Scholar]
  34. Sherrard LJ, Graham KA, McGrath SJ, McIlreavey L, Hatch J et al. Antibiotic resistance in Prevotella species isolated from patients with cystic fibrosis. J Antimicrob Chemother 2013; 68:2369–2374 [View Article][PubMed]
    [Google Scholar]
  35. Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE et al. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol 1995; 33:2233–2239[PubMed]
    [Google Scholar]
  36. Fey PD, Rupp ME. Molecular epidemiology in the public health and hospital environments. Clin Lab Med 2003; 23:885–901 [View Article][PubMed]
    [Google Scholar]
  37. Goering RV. Pulsed field gel electrophoresis: a review of application and interpretation in the molecular epidemiology of infectious disease. Infect Genet Evol 2010; 10:866–875 [View Article][PubMed]
    [Google Scholar]
  38. Nemoy LL, Kotetishvili M, Tigno J, Keefer-Norris A, Harris AD et al. Multilocus sequence typing versus pulsed-field gel electrophoresis for characterization of extended-spectrum beta-lactamase-producing Escherichia coli isolates. J Clin Microbiol 2005; 43:1776–1781 [View Article][PubMed]
    [Google Scholar]
  39. Malachowa N, Sabat A, Gniadkowski M, Krzyszton-Russjan J, Empel J et al. Comparison of multiple-locus variable-number tandem-repeat analysis with pulsed-field gel electrophoresis, spa typing, and multilocus sequence typing for clonal characterization of Staphylococcus aureus isolates. J Clin Microbiol 2005; 43:3095–3100 [View Article][PubMed]
    [Google Scholar]
  40. Coenye T, Spilker T, Martin A, Lipuma JJ. Comparative assessment of genotyping methods for epidemiologic study of Burkholderia cepacia genomovar III. J Clin Microbiol 2002; 40:3300–3307 [View Article][PubMed]
    [Google Scholar]
  41. de Lencastre H, Couto I, Santos I, Melo-Cristino J, Torres-Pereira A et al. Methicillin-resistant Staphylococcus aureus disease in a Portuguese hospital: characterization of clonal types by a combination of DNA typing methods. Eur J Clin Microbiol Infect Dis 1994; 13:64–73 [View Article][PubMed]
    [Google Scholar]
  42. Moore G, Cookson B, Gordon NC, Jackson R, Kearns A et al. Whole-genome sequencing in hierarchy with pulsed-field gel electrophoresis: the utility of this approach to establish possible sources of MRSA cross-transmission. J Hosp Infect 2015; 90:38–45 [View Article][PubMed]
    [Google Scholar]
  43. Salipante SJ, Sengupta DJ, Cummings LA, Land TA, Hoogestraat DR et al. Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology. J Clin Microbiol 2015; 53:1072–1079 [View Article][PubMed]
    [Google Scholar]
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