Molecular diagnostics: The changing culture of medical microbiology

Bioengineered Bugs

Volumn 3, Issue 1, 2012, Pages 1-7

  Bullman, Susan ^a   Lucey, Brigid ^a   Sleator, Roy D ^a  

^a Munster Technological University   (Ireland)

Author keywords

Automated; Bacteriology; Clinical; Molecular diagnostics; Omics

Indexed keywords

ARTICLE; BACTERIOLOGY; BIOMEDICINE; CLINICAL LABORATORY; INFECTION; MOLECULAR DIAGNOSIS; PATIENT CARE;

MICROBIOLOGY; MODELS, THEORETICAL; PATHOLOGY, MOLECULAR;

EID: 84858115677     PISSN: 19491018     EISSN: 19491026     Source Type: Journal    
DOI: 10.4161/bbug.3.1.19011     Document Type: Article

References (57)

1. Schachter J. DFA, EIA, PCR, LCR and other technologies: what tests should be used for diagnosis of chlamydia infections? Immunol Invest 1997; 26: 157-161; PMID:9037620; http://dx.doi.org/10.3109/08820139709048923
2. Antibiotic resistance: government accepts the recommendations from the ACMSF. Advisory Committee onthe Microbiological Safety of Food. Vet Rec 2000; 146:478-479; PMID:10887992
3. Weile J, Knabbe C. Current applications and future trends of molecular diagnostics in clinical bacteriology. Anal Bioanal Chem 2009; 394:731-742; PMID:19377839; http://dx.doi.org/10.1007/s00216-009-2779-8
4. Vossen RH, Aten E, Roos A, den Dunnen JT. High resolution melting analysis (HRMA): more than justsequence variant screening. Hum Mutat 2009; 30:860-866; PMID:19418555; http://dx.doi.org/10.1002/humu.21019
5. Hidalgo-Grass C, Strahilevitz J. High-resolution melt curve analysis for identification of single nucleotide mutations in the quinolone resistance gene aac(6')-Ibcr. Antimicrob Agents Chemother 2010; 54:3509-511; PMID:20498320; http://dx.doi.org/10.1128/AAC.00485-10
6. Woodford N, Sundsfjord A. Molecular detection of antibiotic resistance: when and where? J Antimicrob Chemother 2005; 56:259-261; PMID:15967769;http://dx.doi.org/10.1093/jac/dki195
7. Van Eldere J. Changing needs, opportunities and constraints for the 21st century microbiology laboratory. Clin Microbiol Infect 2005; 11(Suppl 1):15-18;PMID:15816102; http://dx.doi.org/10.1111/j.1469-0691.2005.01084.x
8. Procop GW. Molecular diagnostics for the detection and characterization of microbial pathogens. Clin Infect Dis 2007; 45(Suppl 2):S99-S111; PMID:17683022;http://dx.doi.org/10.1086/519259
9. Speers DJ. Clinical applications of molecular biologyfor infectious diseases. Clin Biochem Rev 2006; 27:39-51; PMID:16886046
10. Tenover FC. Potential impact of rapid diagnostic tests on improving antimicrobial use. Ann N Y Acad Sci 2010; 1213:70-80; PMID:21054433; http://dx.doi.org/10.1111/j.1749-6632.2010.05827.x
11. Murphy J, Bustin SA. Reliability of real-time reversetranscription PCR in clinical diagnostics: gold standard or substandard? Expert Rev Mol Diagn 2009; 9:187-197; PMID:19298142; http://dx.doi.org/10.1586/14737159.9.2.187
12. Okeke IN, Peeling RW, Goossens H, Auckenthaler R, Olmsted SS, de Lavison JF, et al. Diagnostics as essential tools for containing antibacterial resistance. Drug Resist Updat 2011; 14:95-106; PMID:21398170; http://dx.doi.org/10.1016/j.drup.2011.02.002
13. Simor AE. Diagnosis, management, and prevention of Clostridium diffi cile infection in long-term care facilities: a review. J Am Geriatr Soc 2010; 58:1556-1564; PMID:20646106; http://dx.doi.org/10.1111/j.1532-5415.2010.02958.x
14. Olano JP, Walker DH. Diagnosing emerging and reemerging infectious diseases: the pivotal role of the pathologist. Arch Pathol Lab Med 2011; 135:83-91;PMID:21204714
15. Derion T. Considerations for the planning and conduct of reproducibility studies of in vitro diagnostic tests for infectious agents. Biotechnol Annu Rev 2003; 9:249-258; PMID:14650929; http://dx.doi.org/10.1016/S1387-2656(03)09004-5
16. Szczepura A, Westmoreland D, Vinogradova Y, Fox J, Clark M. Evaluation of molecular techniques in prediction and diagnosis of cytomegalovirus disease in immunocompromised patients. Health Technol Assess 2006; 10:1-176; PMID:16595079
17. Bullman S, Corcoran D, O'Leary J, Lucey B, Byrne D, Sleator RD. Campylobacter ureolyticus: an emerging gastrointestinal pathogen? FEMS Immunol Med Microbiol 2011; 61:228-230; PMID:21320172; http://dx.doi.org/10.1111/j.1574-695X.2010.00760.x
18. O'Leary J, Corcoran D, Lucey B. Comparison of the Enteric Bio multiplex PCR system with routine culture for detection of bacterial enteric pathogens. J Clin Microbiol 2009; 47:3449-3453; PMID:19726596;http://dx.doi.org/10.1128/JCM.01026-09
19. Bullman S, Corcoran D, O'Leary J, O'Hare D, Lucey B, Sleator RD. Emerging dynamics of human campylobacteriosis in Southern Ireland. FEMS Immunol Med Microbiol 2011; 63:248-253; PMID:22077228; http://dx.doi.org/10.1111/j.1574-695X.2011.00847.x
20. Pallen MJ, Wren BW. Bacterial pathogenomics. Nature 2007; 449:835-842; PMID:17943120; http://dx.doi.org/10.1038/nature06248
21. Dorrell N, Hinchliffe SJ, Wren BW. Comparative phylogenomics of pathogenic bacteria by microarray analysis. Curr Opin Microbiol 2005; 8:620-626; PMID:16125441; http://dx.doi.org/10.1016/j.mib.2005.08.012
22. Delsuc F, Brinkmann H, Philippe H. Phylogenomicsand the reconstruction of the tree of life. Nat Rev Genet 2005; 6:361-375; PMID:15861208; http://dx.doi.org/10.1038/nrg1603
23. Sleator RD. Phylogenetics. Arch Microbiol 2011; 193:235-239; PMID:21249334; http://dx.doi.org/10.1007/s00203-011-0677-x
24. Stabler RA, Gerding DN, Songer JG, Drudy D, Brazier JS, Trinh HT, et al. Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains. J Bacteriol 2006; 188:7297-7305; PMID:17015669; http://dx.doi.org/10.1128/JB.00664-06
25. Sokurenko EV, Hasty DL, Dykhuizen DE. Pathoadaptive mutations: gene loss and variation in bacterial pathogens. Trends Microbiol 1999; 7:191-5; PMID:10354593; http://dx.doi.org/10.1016/S0966-842X(99)01493-6
26. Clokie M. PCR and partial sequencing of bacteriophage genomes. Methods Mol Biol 2009; 502:47-55;PMID:19082551; http://dx.doi.org/10.1007/978-1-60327-565-1_5
27. Rappuoli R. From Pasteur to genomics: progress and challenges in infectious diseases. Nat Med 2004; 10:1177-1185; PMID:15516917; http://dx.doi.org/10.1038/nm1129
28. Fredericks DN, Relman DA. Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates. Clin Microbiol Rev 1996; 9:18-33;PMID:8665474
29. Falkow S. Molecular Koch's Postulates Applied to Microbial Patho genicity. Rev Infect Dis 1988; 10: S274-S276; PMID:3055197
30. Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW. Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol 2007; 8:R267; PMID:18088402; http://dx.doi.org/10.1186/gb-2007-8-12-r267
31. Curran T, Coulter WA, Fairley DJ, McManus T, Kidney J, Larkin M, et al. Development of a novel DNA microarray to detect bacterial pathogens in patients with chronic obstructive pulmonary disease (COPD). J Microbiol Methods 2010; 80:257-261;PMID:20074591; http://dx.doi.org/10.1016/j.mimet.2010.01.004
32. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, et al. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci USA 2002; 99:15687-1592; PMID:12429852; http://dx.doi.org/10.1073/pnas.242579699
33. Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, et al. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 1996; 93:6025-6030; PMID:8650213; http://dx.doi.org/10.1073/pnas.93.12.6025
34. Bae JW, Rhee SK, Nam YD, Park YH. Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes. Nucleic Acids Res 2005; 33:e113; PMID:16030349; http://dx.doi.org/10.1093/nar/gni112
35. Gardner SN, Jaing CJ, McLoughlin KS, Slezak TR. Amicrobial detection array (MDA) for viral and bacterial detection. BMC Genomics 2010; 11:668; PMID: 21108826; http://dx.doi.org/10.1186/1471-2164-11-668
36. Jaing C, Gardner S, McLoughlin K, Mulakken N, Alegria-Hartman M, Banda P, et al. A functional gene array for detection of bacterial virulence elements. PLoS ONE 2008; 3:e2163; PMID:18478124; http://dx.doi.org/10.1371/journal.pone.0002163
37. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The sequence of the human genome. Science 2001; 291:1304-1351; PMID:11181995; http://dx.doi.org/10.1126/science.1058040
38. Cravchik A, Subramanian G, Broder S, Venter JC. Sequence analysis of the human genome: implications for the understanding of nervous system function and disease. Arch Neurol 2001; 58:1772-1778; PMID:11708983; http://dx.doi.org/10.1001/archneur.58.11.1772
39. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature 2001; 409: 860-921; PMID:11237011; http://dx.doi.org/10.1038/35057062
40. Kumar D. From evidence-based medicine to genomic medicine. Genomic Med 2007; 1:95-104; PMID:18923934; http://dx.doi.org/10.1007/s11568-007-9013-6
41. Bischoff SC. 'Gut health': a new objective in medicine? BMC Med 2011; 9:24; PMID:21401922; http://dx.doi.org/10.1186/1741-7015-9-24
42. Hattori M, Taylor TD. The human intestinal micro biome:a new frontier of human biology. DNA Res2009; 16:1-12; PMID:19147530; http://dx.doi.org/10.1093/dnares/dsn03343
43. Blaser MJ. Harnessing the power of the human microbiome. Proc Natl Acad Sci USA 2010; 107:6125-12 PMID:20360554; http://dx.doi.org/10.1073/pnas.1002112107
44. Fujimura KE, Slusher NA, Cabana MD, Lynch SV. Role of the gut microbiota in defining human health. Expert Rev Anti Infect Ther 2010; 8:435-44;PMID:20377338; http://dx.doi.org/10.1586/eri.10.14
45. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J. Metagenomic pyrosequencing and microbial identification. Clin Chem 2009; 55:856-86;PMID:19264858; http://dx.doi.org/10.1373/clinchem.2008.107565
46. Sleator RD. The human superorganism- of microbes and men. Med Hypotheses 2010; 74:214-21 PMID:19836146; http://dx.doi.org/10.1016/j.mehy.2009.08.047
47. Preza D, Olsen T, Willumsen T, Boches SK, Cotton SL, Grinde BL, et al. Microarray analysis of the microflora of root caries in elderly. Eur J Clin Microbiol Infect Dis 2009; 28:509-517; PMID:19039610;http://dx.doi.org/10.1007/s10096-008-0662-8
48. Colombo AP, Boches SK, Cotton SL, Goodson JM, Kent R, Haffajee AD, et al. Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. J Periodontol 2009; 80:1421-1432; PMID:19722792; http://dx.doi.org/10.1902/jop.2009.090185
49. Farrell JJ, Zhang L, Zhou H, Chia D, Elashoff D, Akin D, et al. Variations of oral micro biota are associated with pancreatic diseases including pancreatic cancer. Gut 2011; PMID:21994333; http://dx.doi.org/10.1136/gutjnl-2011-300784
50. Docktor MJ, Paster BJ, Abramowicz S, Ingram J, Wang YE, Correll M, et al. Alterations in diversity of the oral microbiome in pediatric inflammatory bowel disease. Inflamm Bowel Dis 2011; PMID:21987382;http://dx.doi.org/10.1002/ibd.21874
51. Dandekar T, Dandekar G. Pharmacogenomic strategies against microbial resistance: from bright to bleak to innovative. Pharmacogenomics 2010; 11:1193-1196; PMID:20860457; http://dx.doi.org/10.2217/pgs.10.18
52. Laing RE, Hess P, Shen Y, Wang J, Hu SX. The role and impact of SNPs in pharmacogenomics and personalized medicine. Curr Drug Metab 2011; 12: 460-486; PMID:21453271; http://dx.doi.org/10.2174/138920011795495268
53. Eichelbaum M, Ingelman-Sundberg M, Evans WE. Pharmacogenomics and Individualised Drug Therapy. Annu Rev Med 2006; 57:119-137; PMID:16409140;http://dx.doi.org/10.1146/annurev.med.56.082103.104724
54. Ouahchi K, Lindeman N, Lee C. Copy number varients and pharmacogenomics. Future Medicine 2006; 7:25-29.
55. Fellay J, Marzolini C, Meaden ER, Back DJ, Buclin T, Chave JP, et al. Response to antiretroviral treatment in HIV-1-infected individuals with allelic variants of the multidrug resistance transporter 1: a pharmacogenetics study. Lancet 2002; 359:30-36; PMID:11809184; http://dx.doi.org/10.1016/S0140-6736(02)07276-8
56. Quirk E, McLeod H, Powderly W. The pharmacogenetics of antiretroviral therapy: a review of studies to date. Clin Infect Dis 2004; 39:98-106; PMID:15206060; http://dx.doi.org/10.1086/421557
57. Abrahams E, Silver M. The case for personalized medicine. J Diabetes Sci Technol 2009; 3:680-684;PMID:20144313