Molecular identification of Staphylococcus aureus in airway samples from children with cystic fibrosis

PLoS ONE

Volumn 11, Issue 1, 2016, Pages

  Johnson, Emily J ^a   Zemanick, Edith T ^b   Accurso, Frank J ^b   Wagner, Brandie D ^b,c   Robertson, Charles E ^a   Harris, J Kirk ^b  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b University of Colorado Denver and Children s Hospital Colorado   (United States)

^c Food Science and Human Nutrition   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; BACTERIAL PROTEIN;

AIR SAMPLING; ARTICLE; BACTERIUM IDENTIFICATION; CHILD; CONTROLLED STUDY; CYSTIC FIBROSIS; DISEASE ASSOCIATION; DNA EXTRACTION; FEMALE; GENE FUNCTION; GENE IDENTIFICATION; HUMAN; MAJOR CLINICAL STUDY; MALE; MOLECULAR DYNAMICS; NONHUMAN; POLYMERASE CHAIN REACTION; POPULATION ABUNDANCE; PRESCHOOL CHILD; QUANTITATIVE ANALYSIS; RESPIRATORY TRACT INFECTION; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; STAPHYLOCOCCUS AUREUS; ADOLESCENT; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; RESPIRATORY SYSTEM;

ADOLESCENT; BACTERIAL PROTEINS; CHILD; CYSTIC FIBROSIS; FEMALE; HUMANS; MALE; RESPIRATORY SYSTEM; RNA, RIBOSOMAL, 16S; STAPHYLOCOCCUS AUREUS;

EID: 84958231298     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0147643     Document Type: Article

References (30)

1. Gibson RL, Burns JL, Ramsey BW Pathophysiology and management of pulmonary infections in cystic fibrosis. Am J Respir Crit Care Med. 2003; 168(8):918-51. Epub 2003/10/14. doi:10.1164/rccm.200304-505SO 168/8/918 [pii]. PMID: 14555458.
2. Sibley CD, Rabin H, Surette MG Cystic fibrosis: a polymicrobial infectious disease. Future Microbiol. 2006; 1:53-61. Epub 2007/07/31. doi:10.2217/17460913.1.1.53 PMID: 17661685.
3. Cox MJ, Allgaier M, Taylor B., Baek MS, Huang YJ, Daly RA, et al. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS ONE. 2010; 5(6):e11044. Epub 2010/06/30. doi:10.1371/journal.pone.0011044 PMID: 20585638; PubMed Central PMCID: PMC2890402.
4. Deschaght P, De Baere T, Van Simaey L, Van Daele S, De Baets F, De Vos D, et al. Comparison of the sensitivity of culture, PCR and quantitative real-time PCR for the detection of Pseudomonas aeruginosa in sputum of cystic fibrosis patients. BMC microbiology. 2009; 9:244. doi:10.1186/1471-2180-9-244 PMID: 19943966; PubMed Central PMCID: PMC2789735.
5. Filkins LM, Hampton TH, Gifford A.H., Gross MJ, Hogan DA, Sogin ML, et al Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. J Bacteriol. 2012; 194(17):4709-17. Epub 2012/07/04. doi:10.1128/JB.00566-12 PMID: 22753064; PubMed Central PMCID: PMC3415522.
6. Zemanick ET, Wagner BD, Sagel S.D., Stevens MJ, Accurso FJ, Harris JK. Reliability of quantitative real-time PCR for bacterial detection in cystic fibrosis airway specimens. PLoSONE. 2010; 5(11): e15101. Epub 2010/12/15. doi:10.1371/journal.pone.0015101 PMID: 21152087; PubMed Central PMCID: PMC2994853.
7. Zhao J, Carmody LA, Kalikin L.M., Li J., Petrosino JF, Schloss PD, et al. Impact of enhanced Staphylococcus DNA extraction on microbial community measures in cystic fibrosis sputum. PLoS ONE. 2012; 7 (3):e33127. Epub 2012/03/14. doi:10.1371/journal.pone.0033127 PMID: 22412992; PubMed Central PMCID: PMC3297625.
8. Maidhof H, Reinicke B, Blümel P, Berger-Bächi B, Labischinski H. femA, which encodes a factor essential for expression of methicillin resistance, affects glycine content of peptidoglycan in methicillin-resis-tantandmethicillin-susceptible Staphylococcus aureus strains. J Bacteriol. 1991; 173(11):3507-13. PMID: 2045371; PubMed Central PMCID: PMCPMC207965.
9. Matsuda K, Tsuji H, Asahara T, Kado Y, Nomoto K. Sensitive quantitative detection of commensal bacteria by rRNA-targeted reverse transcription-PCR. Appl Environ Microbiol. 2007; 73(1):32-9. Epub 2006/10/31. doi:AEM.01224-06 [pii] doi: 10.1128/AEM.01224-06 PMID: 17071791; PubMed Central PMCID: PMC1797142.
10. Johnson S, Kruger D, Labischinski H. FemA of Staphylococcus aureus: isolation and immunodetection. FEMS Microbiol Lett. 1995; 132(3):221-8. PMID: 7590176.
11. Francois P, Pittet D, Bento M, Pepey B, Vaudaux P, Lew D, et al. Rapid detection of methicillin-resistant Staphylococcus aureus directly from sterile or nonsterile clinical samples by a new molecular assay. J Clin Microbiol. 2003; 41(1):254-60. PMID: 12517857; PubMed Central PMCID: PMC149566.
12. Lynch SV, Bruce KD The cystic fibrosis airway microbiome. Cold Spring Harbor perspectives in medicine. 2013; 3(3):a009738. Epub 2013/03/05. doi:10.1101/cshperspect.a009738 PMID: 23457293.
13. Caverly LJ, Zhao J, LiPuma JJ Cystic fibrosis lung microbiome: Opportunities to reconsider management of airway infection. Pediatr Pulmonol. 2015; 50 Suppl 40:S31-8. doi:10.1002/ppul.23243 PMID: 26335953.
14. Burns JL, Emerson J, Stapp J.R., Yim DL, Krzewinski J, Louden L, et al Microbiology of sputum from patients at cystic fibrosis centers in the United States. Clin Infect Dis. 1998; 27(1):158-63. Epub 1998/ 07/24. PMID: 9675470.
15. Hara N, Alkanani AK, Ir D, Robertson CE, Wagner BD, Frank DN, et al. Prevention of virus-induced type 1 diabetes with antibiotic therapy. J Immunol. 2012; 189(8):3805-14. Epub 2012/09/19. doi:10.4049/jimmunol.1201257 PMID: 22988033.
16. Markle JG, Frank DN, Mortin-Toth S, Robertson C.E., Feazel LM, Rolle-Kampczyk U, et al. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science. 2013; 339 (6123):1084-8. Epub 2013/01/19. doi:10.1126/science.1233521 PMID: 23328391.
17. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998; 8(3):186-94. Epub 1998/05/16. PMID: 9521922.
18. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998; 8(3):175-85. PMID: 9521921.
19. Edgar RC, Haas BJ, Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011; 27(16):2194-200. Epub 2011/06/28. doi:10.1093/bioinformatics/btr381 PMID: 21700674; PubMed Central PMCID: PMC3150044.
20. Schloss PD, Westcott SL Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. 2011; 77(10):3219-26. doi:10.1128/AEM.02810-10 PMID: 21421784; PubMed Central PMCID: PMC3126452.
21. Pruesse E, Peplies J, Glockner FO SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012; 28(14):1823-9. Epub 2012/05/05. doi:10.1093/bioinformatics/bts252 PMID: 22556368; PubMed Central PMCID: PMC3389763.
22. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013; 41(Database issue):D590-6. Epub 2012/11/30. doi:10.1093/nar/gks1219 PMID: 23193283; PubMed Central PMCID: PMC3531112.
23. Robertson CE, Harris JK, Wagner B.D., Granger D., Browne K, Tatem B, et al Explicet: Graphical user interface software for the management, analysis and visualization of microbial ecology data and metadata. Bioinformatics. 2013.
24. Altschul SF, Gish W, Miller W., Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. Epub 1990/10/05. doi: 10.1006/jmbi.1990.9999 S0022283680799990 [pii]. 2231712. PMID: 2231712
25. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007; 35(21):7188-96. Epub 2007/10/20. doi:gkm864 [pii] doi: 10.1093/nar/gkm864 PMID: 17947321; PubMed Central PMCID: PMC2175337.
26. Zemanick ET, Harris JK, Wagner B.D., Robertson CE, Sagel SD, Stevens MJ, et al Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS ONE. 2013; 8(4):e62917. Epub 2013/05/07. doi:10.1371/journal.pone.0062917 PMID: 23646159; PubMed Central PMCID: PMC3639911.
27. Janda JM, Abbott SL 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol. 2007; 45(9):2761-4. doi:10.1128/JCM.01228-07 PMID: 17626177; PubMed Central PMCID: PMC2045242.
28. Mahboubi MA, Carmody LA, Foster B.K., Kalikin LM, VanDevanter DR, LiPuma JJ. Culture-based and culture-independent bacteriologic analysis of cystic fibrosis respiratory specimens. J Clin Microbiol. 2015. doi:10.1128/JCM.02299-15 PMID: 26699705.
29. Kobayashi N, Wu H, Kojima K., Taniguchi K, Urasawa S, Uehara N., et al. Detection of mecA, femA, and femB genes in clinical strains of staphylococci using polymerase chain reaction. Epidemiol Infect. 1994; 113(2):259-66. PMID: 7925664; PubMed Central PMCID: PMCPMC2271538.
30. van Griethuysen A., van Loo I, van Belkum A, Vandenbroucke-Grauls C, Wannet W, van Keulen P, et al. Loss of the mecA gene during storage of methicillin-resistant Staphylococcus aureus strains. J Clin Microbiol. 2005; 43(3):1361-5. doi:10.1128/JCM.43.3.1361-1365.2005 PMID: 15750108; PubMed Central PMCID: PMC1081222.