Bacterial population genomics and infectious disease diagnostics

Trends in Biotechnology

Volumn 28, Issue 12, 2010, Pages 611-618

  Joseph, Sandeep J ^a   Read, Timothy D ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOMES; BACTERIAL PATHOGENS; BACTERIAL POPULATION; BIOINFORMATIC TOOLS; CLINICAL INVESTIGATION; COMMONLY USED; DIAGNOSTIC ASSAYS; FURTHER DEVELOPMENT; GENOME SEQUENCING; GENOMIC DATABASE; GENOMICS; INFECTIOUS DISEASE;

BIOINFORMATICS; GENES;

BACTERIOLOGY;

ANTIBIOTIC AGENT; ANTIINFECTIVE AGENT; BOTULINUM TOXIN E; NUCLEIC ACID;

ANTIBIOTIC RESISTANCE; BACILLUS ANTHRACIS; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BIOINFORMATICS; DIAGNOSTIC PROCEDURE; DNA SEQUENCE; DRUG SENSITIVITY; EPIDEMIOLOGICAL DATA; FORENSIC GENETICS; GENE LIBRARY; GENE SEQUENCE; GENETIC ANALYSIS; GENOMICS; INFECTION; METAGENOMICS; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; MICROARRAY ANALYSIS; MULTILOCUS SEQUENCE TYPING; MULTIPLE LOCUS VARIABLE NUMBER TANDEM REPEAT ANALYSIS; NONHUMAN; NUCLEIC ACID AMPLIFICATION; PATHOGENESIS; POPULATION GENETICS; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; VARIABLE NUMBER OF TANDEM REPEAT;

BACTERIA; BACTERIAL INFECTIONS; BACTERIOLOGICAL TECHNIQUES; BIODIVERSITY; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOME; MOLECULAR DIAGNOSTIC TECHNIQUES;

BACTERIA (MICROORGANISMS);

EID: 78149464701     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2010.09.001     Document Type: Review

References (83)

1. Morse S.A., Budowle B. Microbial forensics: application to bioterrorism preparedness and response. Infect. Dis. Clin. North Am. 2006, 20:455-473. xi.
2. Read T.D., et al. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 2002, 296:2028-2033.
3. Van Ert M.N., et al. Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain. J. Clin. Microbiol. 2007, 45:47-53.
4. Fricke W.F., et al. The role of genomics in the identification, prediction, and prevention of biological threats. PLoS Biol. 2009, 7:e1000217.
5. Shendure J., Ji H. Next-generation DNA sequencing. Nat. Biotechnol. 2008, 26:1135-1145.
6. Chen P.E., et al. Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing. PLoS ONE 2010, 5:e12397.
7. Chain P.S., et al. Genomics. Genome project standards in a new era of sequencing. Science 2009, 326:236-237.
8. Beres S.B., et al. Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:4371-4376.
9. Harris S.R., et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327:469-474.
10. Bentley S. Sequencing the species pan-genome. Nat. Rev. Microbiol. 2009, 7:258-259.
11. Tettelin H., et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial " pan-genome" Proc. Natl. Acad. Sci. U. S. A. 2005, 102:13950-13955.
12. Thomas C.M., Nielsen K.M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 2005, 3:711-721.
13. Brussow H., et al. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 2004, 68:560-602.
14. Burrus V., Waldor M.K. Shaping bacterial genomes with integrative and conjugative elements. Res. Microbiol. 2004, 155:376-386.
15. Mira A., et al. Deletional bias and the evolution of bacterial genomes. Trends Genet. 2001, 17:589-596.
16. Touzain F., et al. Small variable segments constitute a major type of diversity of bacterial genomes at the species level. Genome Biol. 2010, 11:R45.
17. Moser M.J., et al. Multiplexed detection of anthrax-related toxin genes. J. Mol. Diagn. 2006, 8:89-96.
18. Bentley S.D., Parkhill J. Comparative genomic structure of prokaryotes. Annu. Rev. Genet. 2004, 38:771-792.
19. Didelot X., Maiden M.C. Impact of recombination on bacterial evolution. Trends Microbiol. 2010, 18:315-322.
20. Ambur O.H., et al. Genome dynamics in major bacterial pathogens. FEMS Microbiol. Rev. 2009, 33:453-470.
21. Oyarzabal O.A., et al. Conjugative transfer of chromosomally encoded antibiotic resistance from Helicobacter pylori to Campylobacter jejuni. J. Clin. Microbiol. 2007, 45:402-408.
22. Soyer Y., et al. Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes. BMC Evol. Biol. 2009, 9:264.
23. Ince J., McNally A. Development of rapid, automated diagnostics for infectious disease: advances and challenges. Expert Rev. Med. Devices 2009, 6:641-651.
24. Nakamura A., et al. Diagnostic value of PCR analysis of bacteria and fungi from blood in empiric-therapy-resistant febrile neutropenia. J. Clin. Microbiol. 2010, 48:2030-2036.
25. Al Amri A., et al. Multiplex PCR for direct identification of Campylobacter spp. in human and chicken stools. J. Med. Microbiol. 2007, 56:1350-1355.
26. Perez-Roth E., et al. Multiplex PCR for simultaneous identification of Staphylococcus aureus and detection of methicillin and mupirocin resistance. J. Clin. Microbiol. 2001, 39:4037-4041.
27. Kimura B., et al. Rapid, quantitative PCR monitoring of growth of Clostridium botulinum type E in modified-atmosphere-packaged fish. Appl. Environ. Microbiol. 2001, 67:206-216.
28. Phillippy A.M., et al. Comprehensive DNA signature discovery and validation. PLoS Comput. Biol. 2007, 3:e98.
29. Slezak T., et al. Comparative genomics tools applied to bioterrorism defence. Brief Bioinform. 2003, 4:133-149.
30. Probert W.S., et al. Identification and evaluation of new target sequences for specific detection of Bordetella pertussis by real-time PCR. J. Clin. Microbiol. 2008, 46:3228-3231.
31. Xiao L., et al. Detection and characterization of human Ureaplasma species and serovars by real-time PCR. J. Clin. Microbiol. 2010, 48:2715-2723.
32. O'Sullivan M.V., et al. Rapid identification of methicillin-resistant Staphylococcus aureus transmission in hospitals by use of phage-derived open reading frame typing enhanced by multiplex PCR and reverse line blot assay. J. Clin. Microbiol. 2010, 48:2741-2748.
33. Maiden M.C. Multilocus sequence typing of bacteria. Annu Rev. Microbiol. 2006, 60:561-588.
34. Dean D., et al. Predicting phenotype and emerging strains among Chlamydia trachomatis infections. Emerg. Infect. Dis. 2009, 15:1385-1394.
35. Read T.D., et al. Rapid multi-locus sequence typing using microfluidic biochips. PLoS ONE 2010, 5:e10595.
36. Yazdankhah S.P., Lindstedt B.A. Variable number tandem repeat typing of bacteria. Methods Mol. Biol. 2007, 396:395-405.
37. Rivero-Perez B., et al. Evaluation of multiple-locus variable-number tandem-repeat analysis for typing a polyclonal hospital-acquired methicillin-resistant Staphylococcus aureus population in an area where such infections are endemic. J. Clin. Microbiol. 2010, 48:2991-2994.
38. Comas I., et al. Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS One 2009, 4:e7815.
39. Johansson A., et al. Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis. J. Bacteriol. 2004, 186:5808-5818.
40. Schouls L.M., et al. Multiple-locus variable number tandem repeat analysis of Staphylococcus aureus: comparison with pulsed-field gel electrophoresis and spa-typing. PLoS One 2009, 4:e5082.
41. Pourcel C., et al. Improved multiple-locus variable-number tandem-repeat assay for Staphylococcus aureus genotyping, providing a highly informative technique together with strong phylogenetic value. J. Clin. Microbiol. 2009, 47:3121-3128.
42. Radtke A., et al. Rapid multiple-locus variant-repeat assay (MLVA) for genotyping of Streptococcus agalactiae. J. Clin. Microbiol. 2010, 48:2502-2508.
43. Schwarz R., et al. Evaluation of one- and two-color gene expression arrays for microbial comparative genome hybridization analyses in routine applications. J. Clin. Microbiol. 2010, 48:3105-3110.
44. Kostrzynska M., Bachand A. Application of DNA microarray technology for detection, identification, and characterization of food-borne pathogens. Can J. Microbiol. 2006, 52:1-8.
45. Wang Q., et al. Development of a DNA microarray for detection and serotyping of enterotoxigenic Escherichia coli. J. Clin. Microbiol. 2010, 48:2066-2074.
46. Zwick M.E., et al. Genotyping of Bacillus cereus strains by microarray-based resequencing. PLoS ONE 2008, 3:e2513.
47. McNamara S.E., et al. Comparison of probe hybridization array typing to multilocus sequence typing for pathogenic Escherichia coli. J. Clin. Microbiol. 2009, 47:596-602.
48. Stabler R.A., et al. Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains. J. Bacteriol. 2006, 188:7297-7305.
49. Gryadunov D., et al. Evaluation of hybridisation on oligonucleotide microarrays for analysis of drug-resistant Mycobacterium tuberculosis. Clin. Microbiol. Infect. 2005, 11:531-539.
50. Leinberger D.M., et al. Integrated detection of extended-spectrum-beta-lactam resistance by DNA microarray-based genotyping of TEM, SHV, and CTX-M genes. J. Clin. Microbiol. 2010, 48:460-471.
51. You Y., et al. A novel DNA microarray for rapid diagnosis of enteropathogenic bacteria in stool specimens of patients with diarrhea. J. Microbiol. Methods 2008, 75:566-571.
52. Yoo S.M., et al. DNA microarray-based identification of bacterial and fungal pathogens in bloodstream infections. Mol. Cell Probe. 2010, 24:44-52.
53. Shi L., et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol. 2006, 24:1151-1161.
54. Nordberg E.K. YODA: selecting signature oligonucleotides. Bioinformatics 2005, 21:1365-1370.
55. Apte A., Singh S. AlleleID: a pathogen detection and identification system. Methods Mol. Biol. 2007, 402:329-346.
56. Phillippy A.M., et al. Efficient oligonucleotide probe selection for pan-genomic tiling arrays. BMC Bioinformatics 2009, 10:293.
57. Achtman M. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu. Rev. Microbiol. 2008, 62:53-70.
58. Kuroda M., et al. Genome-wide single nucleotide polymorphism typing method for identification of Bacillus anthracis species and strains among B. cereus group species. J. Clin. Microbiol. 2010, 48:2821-2829.
59. Best E.L., et al. Real-time single-nucleotide polymorphism profiling using Taqman technology for rapid recognition of Campylobacter jejuni clonal complexes. J. Med. Microbiol. 2005, 54:919-925.
60. Ben-Darif E., et al. Development of a multiplex primer extension assay for rapid detection of Salmonella isolates of diverse serotypes. J. Clin. Microbiol. 2010, 48:1055-1060.
61. Ben Shabat M., et al. Development and evaluation of a novel single-nucleotide-polymorphism real-time PCR assay for rapid detection of fluoroquinolone-resistant Mycoplasma bovis. J. Clin. Microbiol. 2010, 48:2909-2915.
62. Holt K.E., et al. High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children. BMC Infect. Dis. 2010, 10:144.
63. Bouakaze C., et al. Identification and genotyping of Mycobacterium tuberculosis complex species by use of a SNaPshot Minisequencing-Based Assay. J. Clin. Microbiol. 2010, 48:1758-1766.
64. Holt K.E., et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat. Genet. 2008, 40:987-993.
65. Pearson T., et al. Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:13536-13541.
66. Lewis T., et al. High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. J. Hosp. Infect. 2010, 75:37-41.
67. Baldry S. Attack of the clones. Nat. Rev. Microbiol. 2010, 8:390.
68. Aziz R.K., Nizet V. Pathogen microevolution in high resolution. Sci. Transl. Med. 2010, 2. 16ps14.
69. Keim P., et al. Multiple-locus variable-number tandem repeat analysis reveals genetic relationships with Bacillus anthracis. J. Bacteriol. 2000, 182:2928-2936.
70. Gilmour M.W., et al. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics 2010, 11:120.
71. Ioerger T.R., et al. Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa. PLoS ONE 2009, 4:e7778.
72. Wooley J.C., et al. A primer on metagenomics. PLoS Comput. Biol. 2010, 6:e1000667.
73. Grice E.A., et al. Topographical and temporal diversity of the human skin microbiome. Science 2009, 324:1190-1192.
74. Palacios G., et al. A new arenavirus in a cluster of fatal transplant-associated diseases. N. Engl. J. Med. 2008, 358:991-998.
75. Briese T., et al. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog. 2009, 5:e1000455.
76. Peterson J., et al. The NIH Human Microbiome Project. Genome Res. 2009, 19:2317-2323.
77. Berglund E.C., et al. Computational resources in infectious disease: limitations and challenges. PLoS Comput. Biol. 2009, 5:e1000481.
78. Parkhill J., et al. Genomic information infrastructure after the deluge. Genome Biol. 2010, 11:402.
79. Orvis J., et al. Ergatis: a web interface and scalable software system for bioinformatics workflows. Bioinformatics 2010, 26:1488-1492.
80. Stewart A.C., et al. DIYA: a bacterial annotation pipeline for any genomics lab. Bioinformatics 2009, 25:962-963.
81. Goecks J., et al. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010, 11:R86.
82. Lefebure T., Stanhope M.J. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol. 2007, 8:R71.
83. Schuch R., Fischetti V.A. The secret life of the anthrax agent Bacillus anthracis: bacteriophage-mediated ecological adaptations. PLoS One 2009, 4:e6532.