Culture-independent identification of nontuberculous mycobacteria in cystic fibrosis respiratory samples

PLoS ONE

Volumn 11, Issue 4, 2016, Pages

  Caverly, Lindsay J ^a   Carmody, Lisa A ^a   Haig, Sarah Jane ^b   Kotlarz, Nadine ^b   Kalikin, Linda M ^a   Raskin, Lutgarde ^b   LiPuma, John J ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ATPE GENE; ATYPICAL MYCOBACTERIUM; BACTERIAL GENE; BACTERIOLYSIS; BACTERIUM CULTURE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; CLINICAL ARTICLE; CONTROLLED STUDY; CYSTIC FIBROSIS; DNA EXTRACTION; GENE SEQUENCE; HUMAN; LUNG INFECTION; LUNG LAVAGE; MICROBIAL COMMUNITY; MYCOBACTERIUM ABSCESSUS; MYCOBACTERIUM AVIUM; NONHUMAN; POLYMERASE CHAIN REACTION; PREVALENCE; QUANTITATIVE ANALYSIS; RESPIRATORY TRACT INFECTION; SEQUENCE ANALYSIS; SPUTUM ANALYSIS; ATYPICAL MYCOBACTERIOSIS; GENETICS; MICROBIOLOGY; SPUTUM;

BACTERIAL DNA; RNA 16S;

CYSTIC FIBROSIS; DNA, BACTERIAL; HUMANS; MYCOBACTERIUM INFECTIONS, NONTUBERCULOUS; NONTUBERCULOUS MYCOBACTERIA; PREVALENCE; RESPIRATORY TRACT INFECTIONS; RNA, RIBOSOMAL, 16S; SPUTUM;

EID: 84971601529     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0153876     Document Type: Article

References (39)

1. Olivier KN, Weber DJ, Wallace RJ Jr, Faiz AR, Lee JH, et al. (2003) Nontuberculous mycobacteria. I: multicenter prevalence study in cystic fibrosis. Am J RespirCrit Care Med 167:828-834. PMID: 12433668
2. Salsgiver EL, Fink AK, Knapp EA, LiPuma JJ, Olivier KN, et al. (2015) Changing Epidemiology of the Respiratory Bacteriology of Patients with Cystic Fibrosis. Chest 149: 390-400.
3. Esther CR Jr, Esserman DA, Gilligan P, Kerr A, Noone PG (2010) Chronic Mycobacterium abscessus infection and lung function decline in cystic fibrosis. J Cyst Fibros 9:117-123. doi: 10.1016/j.jcf.2009. 12.001 PMID: 20071249
4. Martiniano SL, Sontag MK, Daley CL, Nick JA, Sagel SD (2014) Clinical significance of a first positive nontuberculous mycobacteria culture in cystic fibrosis. Ann AmThoracSoc 11: 36-44. doi: 10.1513/AnnalsATS.201309-310OC PMID: 24251858
5. Esther CR Jr, Henry MM, Molina PL, Leigh MW (2005) Nontuberculous mycobacterial infection in young children with cystic fibrosis. Pediatr Pulmonol 40:39-44. PMID: 15858802
6. Levy I, Grisaru-Soen G, Lerner-Geva L, Kerem E, Blau H, et al. (2008) Multicentercross-sectional study of nontuberculous mycobacterial infections among cystic fibrosis patients, Israel. Emerg Infect Dis 14: 378-384. doi: 10.3201/eid1403.061405 PMID: 18325250
7. Mahboubi MA, Carmody LA, Foster BK, Kalikin LM, VanDevanter DR, et al. (2015) Culture-based and culture-independent bacteriologic analysis of cystic fibrosis respiratory specimens. J Clin Microbiol 54: 613-619. doi: 10.1128/JCM.02299-15 PMID: 26699705
8. Cheung MK, Lam WY, Fung WY, Law PT, Au CH, et al. (2013) Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing. PLoS One 8: e54574. doi: 10.1371/journal.pone. 0054574 PMID: 23365674
9. Cui Z, Zhou Y, Li H, Zhang Y, Zhang S, et al. (2012) Complex sputum microbial composition in patients with pulmonary tuberculosis. BMC Microbiol 12: 276. doi: 10.1186/1471-2180-12-276 PMID: 23176186
10. Wu J, Liu W, He L, Huang F, Chen J, et al. (2013) Sputum microbiota associated with new, recurrent and treatment failure tuberculosis. PLoSOne 8: e83445. doi: 10.1371/journal.pone.0083445 PMID: 24349510
11. Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, et al. (2012) Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A 109: 5809-5814. doi: 10.1073/pnas. 1120577109 PMID: 22451929
12. Carmody LA, Zhao J, Schloss PD, Petrosino JF, Murray S, et al. (2013) Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Ann AmThoracSoc 10:179-187. doi: 10.1513/AnnalsATS.201211-107OC PMID: 23802813
13. Carmody LA, Zhao J, Kalikin LM, LeBar W, Simon RH, et al. (2015) The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation. Microbiome 3:12. doi: 10.1186/s40168-015-0074-9 PMID: 25834733
14. Zhao J, Evans CR, Carmody LA, LiPuma JJ (2015) Impact of storage conditions on metabolite profiles of sputum samples from persons with cystic fibrosis. J Cyst Fibros 14: 468-473. doi: 10.1016/j.jcf.2015.02.004 PMID: 25725986
15. Plain KM, Waldron AM, Begg DJ, de Silva K, Purdie AC, et al. (2015) Efficient, validated method for detection of mycobacterial growth in liquid culture media by use of bead beating, magnetic-particle-based nucleic acid isolation, and quantitative PCR. J Clin Microbiol 53:1121-1128. doi: 10.1128/JCM. 03521-14 PMID: 25609725
16. Amaro A, Duarte E, Amado A, Ferronha H, Botelho A (2008) Comparison of three DNA extraction methods for Mycobacterium bovis, Mycobacterium tuberculosis and Mycobacterium avium subsp. avium. LettAppl Microbiol 47: 8-11. doi: 10.1111/j.1472-765X.2008.02372.x PMID: 18498320
17. Kaser M, Ruf MT, Hauser J, Marsollier L, Pluschke G (2009) Optimized method for preparation of DNA from pathogenic and environmental mycobacteria. Appl Environ Microbiol 75: 414-418. doi: 10.1128/AEM.01358-08 PMID: 19047396
18. Tell LA, Foley J, Needham ML, Walker RL (2003) Comparison of four rapid DNA extraction techniques for conventional polymerase chain reaction testing of three Mycobacterium spp. that affect birds. Avian Dis 47:1486-1490. PMID: 14709001
19. Radomski N, Kreitmann L, McIntosh F, Behr MA (2013) The critical role of DNA extraction for detection of mycobacteria in tissues. PLoS One 8: e78749. doi: 10.1371/journal.pone.0078749 PMID: 24194951
20. Odumeru J, Gao A, Chen S, Raymond M, Mutharia L (2001) Use of the bead beaterfor preparation of Mycobacteriumparatuberculosis template DNA in milk. Can J Vet Res 65: 201-205. PMID: 11768125
21. Madiraju MV, Qin MH, Rajagopalan M (2000) Development of simple and efficient protocol for isolation of plasmids from mycobacteria using zirconia beads. Lett Appl Microbiol 30:38-41. PMID: 10728558
22. Hanauer DA, Mei Q, Law J, Khanna R, Zheng K (2015) Supporting information retrieval from electronic health records: A report of University of Michigan's nine-year experience in developing and using the Electronic Medical Record Search Engine (EMERSE). J Biomed Inform 55: 290-300. doi: 10.1016/j. jbi.2015.05.003 PMID: 25979153
23. Zhao J, Carmody LA, Kalikin LM, Li J, Petrosino JF, et al. (2012) Impact of enhanced Staphylococcus DNA extraction on microbial community measures in cystic fibrosis sputum. PLoSOne 7: e33127. doi: 10.1371/journal.pone.0033127 PMID: 22412992
24. Radomski N, Roguet A, Lucas FS, Veyrier FJ, Cambau E, et al. (2013) atpE gene as a new useful specific molecular target to quantify Mycobacterium in environmental samples. BMC Microbiol 13: 277. doi: 10.1186/1471-2180-13-277 PMID: 24299240
25. Nadkarni MA, Martin FE, Jacques NA, Hunter N (2002) Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148: 257-266. PMID: 11782518
26. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79: 5112-5120. doi: 10.1128/AEM.01043-13 PMID: 23793624
27. White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoSComputBiol 5: e1000352. doi: 10.1371/journal.pcbi.1000352 PMID: 19360128
28. R: A Language and EnvironmentforStatistical Computing. (2015) Vienna, Austria: R Foundation for Statistical Computing.
29. Johnson EJ, Zemanick ET, Accurso FJ, Wagner BD, Robertson CE, et al. (2016) Molecular Identification of Staphylococcus aureus in Airway Samples from Children with Cystic Fibrosis. PLoS One 11: e0147643. doi: 10.1371/journal.pone.0147643 PMID: 26808658
30. McNeil MR, Brennan PJ (1991) Structure, function and biogenesis of the cell envelope of mycobacteria in relation to bacterial physiology, pathogenesis and drug resistance; some thoughts and possibilities arising from recent structural information. Res Microbiol 142: 451-463. PMID: 1871433
31. Chakravorty S, Tyagi JS (2001) Novel use of guanidinium isothiocyanate in the isolation of Mycobacteriumtuberculosis DNA from clinical material. FEMS Microbiol Lett 205:113-117. PMID: 11728724
32. Rubin BK (2009) Mucus, phlegm, and sputum in cystic fibrosis. Respir Care 54: 726-732; discussion 732. PMID: 19467160
33. Bercovier H, Kafri O, Sela S (1986) Mycobacteria possess a surprisingly small number of ribosomal RNA genes in relation to the size of their genome. Biochem Biophys Res Commun 136:1136-1141. PMID: 3013168
34. Nessar R, Cambau E, Reyrat JM, Murray A, Gicquel B (2012) Mycobacterium abscessus: a new antibiotic nightmare. J Antimicrob Chemother 67: 810-818. doi: 10.1093/jac/dkr578 PMID: 22290346
35. Coenye T, Vandamme P (2003) Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol Lett 228: 45-49. PMID: 14612235
36. Pollock HM, Wieman EJ (1977) Smear results in the diagnosis of mycobacterioses using blue light fluorescence microscopy. J Clin Microbiol 5: 329-331. PMID: 404313
37. Griffith DE, Aksamit T, Brown-Elliott BA, Catanzaro A, Daley C, et al. (2007) An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med 175:367-416. PMID: 17277290
38. Stressmann FA, Rogers GB, Marsh P, Lilley AK, Daniels TW, et al. (2011) Does bacterial density in cystic fibrosis sputum increase prior to pulmonary exacerbation? J Cyst Fibros 10: 357-365. doi: 10.1016/j.jcf.2011.05.002 PMID: 21664196
39. Clooney AG, Fouhy F, Sleator RD, A OD, Stanton C, et al. (2016) Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis. PLoS One 11: e0148028. doi: 10.1371/journal.pone.0148028 PMID: 26849217