Abstract
The comparative genomics of multiple bacterial strains has become one of the most powerful tools in microbial classification, systematics and evolution. It is also key to the study of the evolutionary dynamics of genomes, gene families, and new functional elements, as well as to the identification of genes that are subject to positive selection and to the identification of lineage-specific genes that are species- and strain-specific. The latter are of special interest as they may play a role in the exclusive ecological adaptations to particular niches on genus-, species-, and strain-specific levels. The focus of this chapter is on new comparative genomics approaches and metagenomics. These can be employed in the molecular identification of bacterial pathogens, in genotyping, and in the detection of virulence genes and other markers.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ahmadian A, Ehn M, Hober S (2006) Pyrosequencing: history, biochemistry and future. Clinica Chimica Acta 363:83–94
Akopyanz N, Bukanov NO, Westblom TU et al (1992a) DNA diversity among clinical isolates of Helicobacter pylori detected by PCRbased RAPD fingerprinting. Nucleic Acids Res 20:5137–5142
Akopyanz N, Bukanov NO, Westblom TU et al (1992b) PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori. Nucleic Acids Res 20:6221–6225
Amann R, Fuchs BM, Behrens S (2001) The identification of microorganisms by fluorescence in situ hybridisation. Curr Opin Biotechnol 12:231–236
Amann RI, Krumholz L, Stahl DA (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172:762–770
Amor KB, Vaughan EE, De Vos WM, Amor (2007) Advanced molecular tools for the identification of lactic acid bacteria. J Nutr 137:741S–747S
Barken KB, Haagensen JAJ, Tolker-Nielsen T (2007) Advances in nucleic acid-based diagnostics of bacterial infections. Clin Chim Acta 384:1–11
Blattner FR, Plunkett III G, Bloch CA et al (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453–1474
Blome B, Braun A, Sobarzo V et al (2008) Molecular identification and quantification of bacteria from endodontic infections using realtime polymerase chain reaction. Oral Microbiol Immunol 23:384–390
Brehony C, Jolley KA, Maiden MCJ (2007) Multilocus sequence typing for global surveillance of meningococcal disease. FEMS Microbiol Rev 31:15–26
Bryant PA, Venter D, Robins-Browne R et al (2004) Chips with everything: DNA microarrays in infectious diseases. Lancet Infect Dis 4:100–111
Cassone M, Giordano A, Pozzi G (2007) Bacterial DNA microarrays for clinical microbiology: the early logarithmic phase. Front Biosci 12:2658–2669
Chang H-W, Sung Y, Kim K-H et al (2008) Development of microbial genome-probing microarrays using digital multiple displacement amplification of uncultivated microbial single cells. Environ Sci Technol Environ 42:6058–6064
Cole ST, Brosch R, Parkhill J et al (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537–544
Daims H, Ramsing NB, Schleifer KH et al (2001) Cultivationindependent, semiautomatic determination of absolute bacterial cell numbers in environmental samples by fluorescence in situ hybridization. Appl Environ Microbiol 67:5810–5818
Deepak SA, Kottapalli KR, Rakwal R et al (2007) Real-Time PCR: Revolutionizing detection and expression analysis of genes. Current Genom 8:234–251
Devulder G, de Montclos MP, Flandrois JP (2005) A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model. Intern J Syst Evol Microbiol 55:293–302
Deyde VM, Okomo-Adhiambo M, Sheu TG et al (2009) Pyrosequencing as a tool to detect molecular markers of resistance to neuraminidase inhibitors in seasonal influenza A viruses. Antiviral Res 81:16–24
Dutka-Malen S, Evers S, Courvalin P (1995) Detection of glycopeptide resistance genotypes and identification to the species level of clinically relevant enterococci by PCR. J Clin Microbiol 33(1):24–27
Eckburg PB, Bik EM, Bernstein C et al (2005) Microbiology: diversity of the human intestinal microbial flora. Science 308(5728):1635–1638
Espy MJ, Uhl JR, Sloan LM et al (2006) Real-Time PCR in clinical microbiology: applications for routine laboratory testing. Clin Microbiol Rev 19(1):165–256
Fleischmann RD, Adams MD, White O et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512
Fournier P-E, Drancourt M, Raoult D (2007) Bacterial genome sequencing and its use in infectious diseases. Lancet Infect Dis 7:711–723
Fredricks DN, Schubert MM, Myerson D (2005) Molecular identification of an invasive gingival bacterial community. Clin Infect Dis 41:e1–e4
Garcia CA, Ahmadian A, Gharizadeh B et al (2000) Mutation detection by pyrosequencing: sequencing of exons 5 - 8 of the p53 tumor suppressor gene. Gene 253:249–257
Gharizadeh B, Ohlin A, Molling P et al (2003) Multiple group-specific sequencing primers for reliable and rapid DNA sequencing. Mol Cell Probes 17:203–210
Gupta PK. (2008) Single-molecule DNA sequencing technologies for future genomics research. Trends Biotech 26(11):602–611
Hall N (2007) Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol 210:1518–1525
Handelsman J, Rondon MR, Brady SF et al (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249
Harris JK, De Groote MA, Sagel SD et al (2007) Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Microbiol 104(51):20529–20533
Heid CA, Stevens J, Livak KJ et al (1996) Real time quantitative PCR. Genome Res 6:986–994
Hillemann D, Weizenegger M, Kubica T et al (2005) Use of the genotype MTBDR assay for rapid detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis complex isolates. J Clin Microbiol 43:3699–3703
Hogardt M, Trebesius K, Geiger AM et al (2000) Specific and rapid detection by fluorescent in situ hybridization of bacteria in clinical samples obtained from cystic fibrosis patients. J Clin Microbiol 38:818–825
Hudson ME (2007) Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Res 8(1):3–17
Huson DH, Auch AF, Qi J et al (2007) MEGAN analysis of metagenomic data. Genome Res 17:377–386
Jelsbak L, Johansen HK, Frost AL et al (2007) Molecular epidemiology and dynamics of Pseudomonas aeruginosa population in cystic fibrosis lungs. Infect Immun 75:2214–2224
Kaushik DK, Sehgal D (2008) Developing antibacterial vaccines in genomics and proteomics era. Scand J Immunol 67(3):245–252
Kempf VA, Trebesius K, Autenrieth IB (2000) Fluorescent in situ hybridization allows rapid identification of microorganisms in blood cultures. J Clin Microbiol. 38:830–838
Klenk HP, Clayton RA, Tomb JF et al (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364–370
Korczak B, Frey J, Schrenzel J et al (2005) Use of diagnostic microarrays for determination of virulence gene patterns of Escherichia coli K1, a major cause of neonatal meningitis. J Clin Microbiol 43:1024–1031
Koreen L, Ramaswamy SV, Graviss EA et al (2004) Spa typing method for discriminating among Staphylococcus aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation. J Clin Microbiol 42:792–799
Krogfelt KA, Lehours P, Megraud F (2005) Diagnosis of Helicobacter pylori infection. Helicobacter 10(Suppl1):5–13
Lane DJ, Pace B, Olsen GJ et al (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955–6959
Lasken RS (2007) Single-cell genomic sequencing using multiple displacement amplification. Curr Opin Microbiol 10(5):510–516
Manichanh C, Chapple CE, Frangeul L et al (2008) A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res 36(16):5180–5188
Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380
Mignard S, Flandrois J-P (2008) A seven-gene, multilocus, genus-wide approach to the phylogeny of mycobacteria using supertrees. Intern J System Evol Microbiol 58:1432–1441
Monstein HJ, Ellnebo-Svedlund K (2002) Molecular typing of Helicobacter pylori by virulence-gene based multiplex PCR and RT-PCR analysis. Helicobacter 7:287–296
Morales G, Wiehlmann L, Gudowius P et al (2004) Structure of Pseudomonas aeruginosa populations analyzed by single nucleotide polymorphism and pulsed-field gel electrophoresis genotyping. J Bacteriol 186:4228–4237
Moter A, Gobel UB (2000) Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods 41:85–112
Neonakis IK, Gitti Z, Krambovitis E et al (2008) Molecular diagnostic tools in mycobacteriology. J Microbiol Methods 75(1):1–11
O’Sullivan DJ (2000) Methods for analysis of the intestinal microflora. Curr Iss Intest Microbiol 1:39–50
Ota N, Hirano K, Warashina M et al (1998) Determination of interactions between structured nucleic acids by fluorescence resonance energy transfer (FRET): selection of target sites for functional nucleic acids. Nucleic Acids Res 26:735–743
Palladino S, Kay ID, Costa AM et al (2003) Real-time PCR for the rapid detection of vanA and vanB genes. Diagn Microbiol Infect Dis 45:81–84
Palomino JC (2005) Nonconventional and new methods in the diagnosis of tuberculosis: feasibility and applicability in the field. Eur Respir J 26:339–350
Peters RP, Savelkoul PH, Simoons-Smit AM et al (2006) Faster identification of pathogens in positive blood cultures by fluorescence in situ hybridization in routine practice. J Clin Microbiol 44:119–123
Poppert S, Essig A, Marre R et al (2002) Detection and differentiation of chlamydiae by fluorescence in situ hybridization. Appl Environ Microbiol 68:4081–4089
Poppert S, Essig A, Stoehr B et al (2005) Rapid diagnosis of bacterial meningitis by real-time PCR and fluorescence in situ hybridization. J Clin Microbiol 43:3390–3397
Poulsen LK, Ballard G, Stahl DA (1993) Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl Environ Microbiol 59:1354–1360
Rappuoli R (2004) From Pasteur to genomics: progress and challenges in infectious diseases. Nat Med 10(11):1177–1185
Rhee M, Burns MA (2006) Nanopore sequencing technology: research trends and applications. Trends Biotechnol 24:580–586
Riesenfeld CS, Schloss PD, Handelsman J (2004) METAGENOMICS: genomic analysis of microbial communities. Annu Rev Genet 38:525–552
Riggio MP, Lennon A, Rolph HJ et al (2008) Molecular identification of bacteria on the tongue dorsum of subjects with and without halitosis. Oral Dis 14(3):251–258
Ronaghi M, Elahi E (2002) Pyrosequencing for microbial typing. J Chromatog B 782(1–2):67–72
Ryan D, Rahimi M, Lund J et al (2007) Towards nanoscale genome sequencing. Trends Biotechnol 25:385–389
Sachse K, Hotzel H, Slickers P et al (2005) DNA microarraybased detection and identification of Chlamydia and Chlamyophila spp. Mol Cell Probes 19:41–50
Sanger F, Air GM, Barrell BG et al (1977) Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265:687–695
Sharma P, Kumari H, Kumar M et al (2008) From bacterial genomics to metagenomics: concept, tools and recent advances. Indian J Microbiol 48(2):173–194
Shendure J, Porreca GJ, Reppas NB et al (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728–1732
Shopsin B, Gomez M, Montgomery SO et al (1999) Evaluation of protein A gene polymorphic region DNA sequencing for typing of Staphylococcus aureus strains. J Clin Microbiol 37:3556–3563
Sidarenka AV, Novik GI, Akimov VN (2008) Application of molecular methods to classification and identification of bacteria of the genus Bifidobacterium. Microbiol 77(3):251–260
Singh A, Goering RV, Simjee S et al (2006) Application of molecular techniques to the study of hospital infection. Clin Microbiol Rev 19(3):512–530
Sogaard M, Stender H, Schonheyder HC (2005) Direct identification of major blood culture pathogens, including Pseudomonas aeruginosa and Escherichia coli, by a panel of fluorescence in situ hybridization assays using peptide nucleic acid probes. J Clin Microbiol 43:1947–1949
Stabler RA, Marsden GL, Witney AA et al (2005) Identification of pathogenspecific genes through microarray analysis of pathogenic and commensal Neisseria species. Microbiol 151:2907–2922
Stampone L, Del Grosso M, Boccia D et al (2005) Clonal spread of a vancomycin-resistant Enterococcus faecium strain among bloodstream-infecting isolates in Italy. J Clin Microbiol 43:1575–1580
Stavrum R, Valvatne H, Bø TH et al (2008) Genomic diversity among Beijing and non-Beijing Mycobacterium tuberculosis isolates from Myanmar. PLoS One 3(4):e1973
Sunde PT, Olsen I, Gobel UB et al (2003) Fluorescence in situ hybridization (FISH) for direct visualization of bacteria in periapical lesions of asymptomatic root-filled teeth. Microbiol 149:1095–1102
Thurnheer T, Gmur R, Guggenheim B. (2004) Multiplex FISH analysis of a sixspecies bacterial biofilm. J Microbiol Methods 56:37–47
Tortoli E (2003) Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin Microbiol Rev 16(2):319–354
Tyagi S, Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14:303–308
Uhl JR, Adamson SC, Vetter EA et al (2003) Comparison of LightCycler PCR, rapid antigen immunoassay, and culture for detection of group A streptococci from throat swabs. J Clin Microbiol 41:242–249
Urwin R, Maiden MC (2003) Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol 11:479–487
Valasek MA, Repa JJ. (2005) The power of real-time PCR. Adv Physiol Educ 29:151–159
Wagner M, Horn M, Daims H (2003) Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr Opin Microbiol 6:302–309
Warren DK, Liao RS, Merz LR et al (2004) Detection of methicillin-resistant Staphylococcus aureus directly from nasal swab specimens by a real-time PCR assay. J Clin Microbiol 42:5578–5581
Wecke J, Kersten T, Madela K et al (2000) A novel technique for monitoring the development of bacterial biofilms in human periodontal pockets. FEMS Microbiol Lett 191:95–101
Wellinghausen N, Wirths B, Poppert S (2006) Fluorescence in situ hybridization for rapid identification of Achromobacter xylosoxidans and Alcaligenes faecalis recovered from cystic fibrosis patients. J Clin Microbiol 44:3415–3417
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
Wommack KE, Bhavsar J, Ravel J (2008) Metagenomics: read length matters. Appl Environ Microbiol 74(5):1453–1463
Woodford N, Johnson AP (2004) Genomics, proteomics, and clinical bacteriology. Humana Press, Totowa, NJ
Yang J-R, Wu F-T, Tsai J-L et al (2007) Comparison between O serotyping method and multiplex real-time PCR to identify diarrheagenic Escherichia coli in Taiwan. J Clin Microbiol 45(11):3620–3625
Yang S, Rothman RE (2004) PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings. Lancet Infect Dis 4:337–348
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Ivanova, E.P., Kurilenko, A., Wang, F., Crawford, R.J. (2010). Comparative Genomics of Pathogens. In: Sintchenko, V. (eds) Infectious Disease Informatics. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-1327-2_4
Download citation
DOI: https://doi.org/10.1007/978-1-4419-1327-2_4
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4419-1326-5
Online ISBN: 978-1-4419-1327-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)