Chapter 12 : Repetitive Sequence-Based PCR Typing of Bacteria and Fungi

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Repetitive Sequence-Based PCR Typing of Bacteria and Fungi, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816834/9781555814977_Chap12-1.gif /docserver/preview/fulltext/10.1128/9781555816834/9781555814977_Chap12-2.gif


Of the number of molecular typing methods that have been described including multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), DNA sequencing of variable genes, ribotyping, PCR ribotyping, restriction fragment length polymorphism analysis, randomly amplified polymorphic DNA (RAPD) analysis, amplified fragment length polymorphism (AFLP) analysis, and repetitive sequence-based PCR (rep-PCR), this chapter focuses on typing of bacteria and fungi specifically using rep-PCR. The theory of rep-PCR is discussed with a comparison of the workflow for traditional gel-based rep-PCR and an automated commercially available system. It is important that the culture be pure, as rep-PCR primer binding sites are widely distributed among bacterial genera. The repetitive extragenic palindrome (REP) was the first repetitive element described in bacteria. The chromosomal locations of the enterobacterial repetitive intergenic consensus (ERIC) elements differ among species but are conserved throughout the kingdom . In addition to bacteria, various fungi have been associated with nosocomial infections. Filamentous fungi, such as species and the Zygomycetes, also contribute to the growing list of health care-associated (HA) infections. While the debate continues over the most cost-effective approach for reducing HA infections, it is clear that some form of an active surveillance program is a key component of effective infection control strategies. Future applications for automated rep-PCR include extension of the menu of both bacterial and fungal pathogens and expansion of the online databases.

Citation: Frye S, Healy M. 2011. Repetitive Sequence-Based PCR Typing of Bacteria and Fungi, p 199-212. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch12

Key Concept Ranking

Restriction Fragment Length Polymorphism
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

Diagram comparing the workflow of manual or gel-based rep-PCR to the workflow of automated rep-PCR. Specific changes are noted for each step in the workflow.

Citation: Frye S, Healy M. 2011. Repetitive Sequence-Based PCR Typing of Bacteria and Fungi, p 199-212. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch12
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

Graphic illustrating fragment separation. (a) Manual rep-PCR using agarose gel electrophoresis and detection and analysis with camera or scanned imaging and dendrogram created with separate gel compare software. (b) Automated rep-PCR using microfluidics chip and analysis with the accompanying DiversiLab software.

Citation: Frye S, Healy M. 2011. Repetitive Sequence-Based PCR Typing of Bacteria and Fungi, p 199-212. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch12
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3

Graphic of the interpretation tool provided in the DiversiLab software to aid with analysis and interpretation. (A) Steps of analysis indicated by tabs; (B) patterns can be assigned “rep” types to organize samples and libraries; (C) users can easily toggle between virtual gel images and sample graphs; (D and E) pop-up overlays can be visualized to better compare two samples.

Citation: Frye S, Healy M. 2011. Repetitive Sequence-Based PCR Typing of Bacteria and Fungi, p 199-212. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch12
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Aanensen, D. M.,, and B. G. Spratt. 2005. The multilocus sequence typing network: mlst.net. Nucleic Acids Res. 33:W728W733.
2. Anderson, B.,, S. Nicholas,, B. Sprague,, J. Campos,, B. Short, and, N. Singh. 2008. Molecular and descriptive epidemiology of multidrug-resistant Enterobacteriaceae in hospitalized infants. Infect. Control Hosp. Epidemiol. 29:250255.
3. Arbeit, R. D.,, A. Slutsky,, T. W. Barber,, J. N. Maslow,, S. Niemczyk,, J. O. Falkinham III,, G. T. O’Connor, and, C. F. von Reyn. 1993. Genetic diversity among strains of Mycobacterium avium causing monoclonal and polyclonal bacteremia in patients with AIDS. J. Infect. Dis. 167:13841390.
4. Arpin, C.,, V. Dubois,, J. Maugein,, J. Jullin,, B. Dutilh,, J. P. Brochet,, G. Larribet,, I. Fischer, and, C. Quentin. 2005. Clinical and molecular analysis of extended-spectrum β-lactamase-producing enterobacteria in the community setting. J. Clin. Microbiol. 43:50485054.
5. Atkinson, R. M.,, J. J. Lipuma,, D. B. Rosenbluth, and, W. M. Dunne, Jr. 2006. Chronic colonization with Pandoraea apista in cystic fibrosis patients determined by repetitive-element-sequence PCR. J. Clin. Microbiol. 44:833836.
6. Bagley, M. J.,, S. L. Anderson, and, B. May. 2001. Choice of methodology for assessing genetic impacts of environmental stressors: polymorphism and reproducibility of RAPD and AFLP fingerprints. Ecotoxicology 10:239244.
7. Balajee, S. A.,, L. Sigler, and, M. E. Brandt. 2007. DNA and the classical way: identification of medically important molds in the 21st century. Med. Mycol. 45:475490.
8. Bart-Delabesse, E.,, C. Cordonnier, and, S. Bretagne. 1999. Usefulness of genotyping with microsatellite markers to investigate hospital-acquired invasive aspergillosis. J. Hosp. Infect. 42:321327.
9. Bart-Delabesse, E.,, J. Sarfati,, J. P. Debeaupuis,, W. van Leeuwen,, A. van Belkum,, S. Bretagne, and, J. P. Latge. 2001. Comparison of restriction fragment length polymorphism, microsatellite length polymorphism, and random amplification of polymorphic DNA analyses for fingerprinting Aspergillus fumigatus isolates. J. Clin. Microbiol. 39:26832686.
10. Bennasar, A.,, G. de Luna,, B. Cabrer, and, J. Lalucat. 2000. Rapid identification of Salmonella typhimurium, S. enteritidis and S. virchow isolates by polymerase chain reaction based fingerprinting methods. Int. Microbiol. 3:3138.
11. Bertin, M. L.,, J. Vinski,, S. Schmitt,, C. Sabella,, L. Danziger-Isakov,, M. McHugh,, G. W. Procop,, G. Hall,, S. M. Gordon, and, J. Goldfarb. 2006. Outbreak of methicillin-resistant Staphylococcus aureus colonization and infection in a neonatal intensive care unit epidemiologically linked to a healthcare worker with chronic otitis. Infect. Control Hosp. Epidemiol. 27:581585.
12. Bertout, S.,, F. Renaud,, T. De Meeus,, M. A. Piens,, B. Lebeau,, M. A. Viviani,, M. Mallie,, J. M. Bastide, et al. 2000. Multilocus enzyme electrophoresis analysis of Aspergillus fumigatus strains isolated from the first clinical sample from patients with invasive aspergillosis. J. Med. Microbiol. 49:375381.
13. Bostock, A.,, M. N. Khattak,, R. Matthews, and, J. Burnie. 1993. Comparison of PCR fingerprinting, by random amplification of polymorphic DNA, with other molecular typing methods for Candida albicans. J. Gen. Microbiol. 139:21792184.
14. Brisse, S.,, V. Fussing,, B. Ridwan,, J. Verhoef, and, R. J. Willems. 2002. Automated ribotyping of vancomycin-resistant Enterococcus faecium isolates. J. Clin. Microbiol. 40:19771984.
15. Budowle, B.,, J. A. Beaudry,, N. G. Barnaby,, A. M. Giusti,, J. D. Bannan, and, P. Keim. 2207. Role of law enforcement response and microbial forensics in investigation of bioterrorism. Croat. Med. J. 48:437449.
16. Buffington, J.,, R. Reporter,, B. A. Lasker,, M. M. McNeil,, J. M. Lanson,, L. A. Ross,, L. Mascola, and, W. R. Jarvis. 1994. Investigation of an epidemic of invasive aspergillosis: utility of molecular typing with the use of random amplified polymorphic DNA probes. Pediatr. Infect. Dis. J. 13:386393.
17. Calbo, E.,, V. Romani,, M. Xercavins,, L. Gomez,, C. G. Vidal,, S. Quintana,, J. Vila, and, J. Garau. 2006. Risk factors for community-onset urinary tract infections due to Escherichia coli harbouring extended-spectrum beta-lactamases. J. Antimicrob. Chemother. 57:780783.
18. Cangelosi, G. A.,, R. J. Freeman,, K. N. Lewis,, D. Livingston-Rosanoff,, K. S. Shah,, S. J. Milan, and, S. V. Goldberg. 2004. Evaluation of a high-throughput repetitive-sequence-based PCR system for DNA fingerprinting of Mycobacterium tuberculosis and Mycobacterium avium complex strains. J. Clin. Microbiol. 42:26852693.
19. Carretto, E.,, D. Barbarini,, C. Farina,, A. Grosini,, P. Nicoletti, and, E. Manso. 2008. Use of the DiversiLab semiautomated repetitive-sequence-based polymerase chain reaction for epidemiologic analysis on Acinetobacter baumannii isolates in different Italian hospitals. Diagn. Microbiol. Infect. Dis. 60:17.
20. Castro, V. A.,, A. N. Thrasher,, M. Healy,, C. M. Ott, and, D. L. Pierson. 2004. Microbial characterization during the early habitation of the International Space Station. Microb. Ecol. 47:119126.
21. Centers for Disease Control and Prevention. 1995. Recommendations for preventing the spread of vancomycin resistance. Recommendations of the Hospital Infection Control Practices Advisory Committee (HICPAC). MMWR Recommend. Rep. 44:113.
22. Centers for Disease Control and Prevention. 2004. National nosocomial infections surveillance (NNIS) system report, data summary from January 1992 through June 2004, issued October 2004. Am. J. Infect. Control 32:470485.
23. Chatzidaki-Livanis, M.,, M. A. Hubbard,, K. Gordon,, V. J. Harwood, and, A. C. Wright. 2006. Genetic distinctions among clinical and environmental strains of Vibrio vulnificus. Appl. Environ. Microbiol. 72:61366141.
24. Chau, A. S.,, C. A. Mendrick,, F. J. Sabatelli,, D. Loebenberg, and, P. M. McNicholas. 2004. Application of real-time quantitative PCR to molecular analysis of Candida albicans strains exhibiting reduced susceptibility to azoles. Antimicrob. Agents Chemother. 48:21242131.
25. Chazalet, V.,, J. P. Debeaupuis,, J. Sarfati,, J. Lortholary,, P. Ribaud,, P. Shah,, M. Cornet,, H. Vu Thien,, E. Gluckman,, G. Brucker, and, J. P. Latge. 1998. Molecular typing of environmental and patient isolates of Aspergillus fumigatus from various hospital settings. J. Clin. Microbiol. 36:14941500.
26. Chen, K. W.,, H. J. Lo,, Y. H. Lin, and, S. Y. Li. 2005. Comparison of four molecular typing methods to assess genetic relatedness of Candida albicans clinical isolates in Taiwan. J. Med. Microbiol. 54:249258.
27. Cleland, D.,, P. Krader, and, D. Emerson. 2008. Use of the DiversiLab repetitive sequence-based PCR system for genotyping and identification of Archaea. J. Microbiol. Methods 73:172178.
28. Cohen, A. L.,, D. Calfee,, S. K. Fridkin,, S. S. Huang,, J. A. Jernigan,, E. Lautenbach,, S. Oriola,, K. M. Ramsey,, C. D. Salgado, and, R. A. Weinstein. 2008. Recommendations for metrics for multidrug-resistant organisms in healthcare settings: SHEA/HICPAC position paper. Infect. Control Hosp. Epidemiol. 29:901913.
29. Cookson, B. D.,, D. A. Robinson,, A. B. Monk,, S. Murchan,, A. Deplano,, R. de Ryck,, M. J. Struelens,, C. Scheel,, V. Fussing,, S. Salmenlinna,, J. Vuopio-Varkila,, C. Cuny,, W. Witte,, P. T. Tassios,, N. J. Legakis,, W. van Leeuwen,, A. van Belkum,, A. Vindel,, J. Garaizar,, S. Haeggman,, B. Olsson-Liljequist,, U. Ransjo,, M. Muller-Premru,, W. Hryniewicz,, A. Rossney,, B. O’Connell,, B. D. Short,, J. Thomas,, S. O’Hanlon, and, M. C. Enright. 2007. Evaluation of molecular typing methods in characterizing a European collection of epidemic methicillin-resistant Staphylococcus aureus strains: the HARMONY collection. J. Clin. Microbiol. 45:18301837.
30. Curtis, L.,, S. Cali,, L. Conroy,, K. Baker,, C. H. Ou,, R. Hershow,, F. Norlock-Cruz, and, P. Scheff. 2005. Aspergillus surveillance project at a large tertiary-care hospital. J. Hosp. Infect. 59:188196.
31. Dahl, K. H.,, G. S. Simonsen,, O. Olsvik, and, A. Sundsfjord. 1999. Heterogeneity in the vanB gene cluster of genomically diverse clinical strains of vancomycin-resistant enterococci. Antimicrob. Agents Chemother. 43:11051110.
32. Davis, K. A.,, J. J. Stewart,, H. K. Crouch,, C. E. Florez, and, D. R. Hospenthal. 2004. Methicillin-resistant Staphylococcus aureus (MRSA) nares colonization at hospital admission and its effect on subsequent MRSA infection. Clin. Infect. Dis. 39:776782.
33. Denning, D. W. 1998. Invasive aspergillosis. Clin. Infect. Dis. 26:781803.
34. De Vegas, E. Z.,, B. Nieves,, M. Araque,, E. Velasco,, J. Ruiz, and, J. Vila. 2006. Outbreak of infection with Acinetobacter strain RUH 1139 in an intensive care unit. Infect. Control Hosp. Epidemiol. 27:397403.
35. Diaz-Guerra, T. M.,, J. V. Martinez-Suarez,, F. Laguna, and, J. L. Rodriguez-Tudela. 1997. Comparison of four molecular typing methods for evaluating genetic diversity among Candida albicans isolates from human immunodeficiency virus-positive patients with oral candidiasis. J. Clin. Microbiol. 35:856861.
36. Diep, B. A.,, F. Perdreau-Remington, and, G. F. Sensabaugh. 2003. Clonal characterization of Staphylococcus aureus by multilocus restriction fragment typing, a rapid screening approach for molecular epidemiology. J. Clin. Microbiol. 41:45594564.
37. Edelstein, M.,, M. Pimkin,, I. Palagin,, I. Edelstein, and, L. Stratchounski. 2003. Prevalence and molecular epidemiology of CTX-M extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Russian hospitals. Antimicrob. Agents Chemother. 47:37243732.
38. Espinel-Ingroff, A.,, J. A. Vazquez,, D. Boikov, and, M. A. Pfaller. 1999. Evaluation of DNA-based typing procedures for strain categorization of Candida spp. Diagn. Microbiol. Infect. Dis. 33:231239.
39. Falkinham, J. O., III. 1996. Epidemiology of infection by nontuberculous mycobacteria. Clin. Microbiol. Rev. 9:177215.
40. Faria, N. A.,, D. C. Oliveira,, H. Westh,, D. L. Monnet,, A. R. Larsen,, R. Skov, and, H. de Lencastre. 2005. Epidemiology of emerging methicillin-resistant Staphylococcus aureus (MRSA) in Denmark: a nationwide study in a country with low prevalence of MRSA infection. J. Clin. Microbiol. 43:18361842.
41. Fontana, C.,, M. Favaro,, S. Minelli,, M. C. Bossa,, G. P. Testore,, F. Leonardis,, S. Natoli, and, C. Favalli. 2008. Acinetobacter baumannii in intensive care unit: a novel system to study clonal relationship among the isolates. BMC Infect. Dis. 8:79.
42. Gascoyne-Binzi, D. M.,, R. E. Barlow,, R. Frothingham,, G. Robinson,, T. A. Collyns,, R. Gelletlie, and, P. M. Hawkey. 2001. Rapid identification of laboratory contamination with Mycobacterium tuberculosis using variable number tandem repeat analysis. J. Clin. Microbiol. 39:6974.
43. Georghiou, P. R.,, A. M. Doggett,, M. A. Kielhofner,, J. E. Stout,, D. A. Watson,, J. R. Lupski, and, R. J. Hamill. 1994. Molecular fingerprinting of Legionella species by repetitive element PCR. J. Clin. Microbiol. 32:29892994.
44. Gilson, E.,, J. M. Clement,, D. Brutlag, and, M. Hofnung. 1984. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 3:14171421.
45. Gira, A. K.,, A. H. Reisenauer,, L. Hammock,, U. Nadiminti,, J. T. Macy,, A. Reeves,, C. Burnett,, M. A. Yakrus,, S. Toney,, B. J. Jensen,, H. M. Blumberg,, S. W. Caughman, and, F. S. Nolte. 2004. Furunculosis due to Mycobacterium mageritense associated with footbaths at a nail salon. J. Clin. Microbiol. 42:18131817.
46. Godoy, P.,, J. Cano,, J. Gene,, J. Guarro,, A. L. Hofling-Lima, and, A. Lopes Colombo. 2004. Genotyping of 44 isolates of Fusarium solani, the main agent of fungal keratitis in Brazil. J. Clin. Microbiol. 42:44944497.
47. Goldberg, T. L.,, T. R. Gillespie, and, R. S. Singer. 2006. Optimization of analytical parameters for inferring relationships among Escherichia coli isolates from repetitive-element PCR by maximizing correspondence with multi-locus sequence typing data. Appl. Environ. Microbiol. 72:60496052.
48. Goulding, J. N.,, J. V. Hookey,, J. Stanley,, W. Olver,, K. R. Neal,, D. A. Ala’Aldeen, and, C. Arnold. 2000. Fluorescent amplified-fragment length polymorphism genotyping of Neisseria meningitidis identifies clones associated with invasive disease. J. Clin. Microbiol. 38:45804585.
49. Harrington, S. M.,, F. Stock,, A. L. Kominski,, J. D. Campbell,, J. C. Hormazabal,, S. Livio,, L. Rao,, K. L. Kotloff,, S. O. Sow, and, P. R. Murray. 2007. Genotypic analysis of invasive Streptococcus pneumoniae from Mali, Africa, by semiautomated repetitive-element PCR and pulsed-field gel electrophoresis. J. Clin. Microbiol. 45:707714.
50. Healy, M.,, K. Reece,, D. Walton,, J. Huong,, K. Shah, and, D. P. Kontoyiannis. 2004. Identification to the species level and differentiation between strains of Aspergillus clinical isolates by automated repetitive-sequence-based PCR. J. Clin. Microbiol. 42:40164024.
51. Healy, M.,, J. Huong,, T. Bittner,, M. Lising,, S. Frye,, S. Raza,, R. Schrock,, J. Manry,, A. Renwick,, R. Nieto,, C. Woods,, J. Versalovic, and, J. R. Lupski. 2005. Microbial DNA typing by automated repetitive-sequence-based PCR. J. Clin. Microbiol. 43:199207.
52. Healy, M.,, K. Reece,, D. Walton,, J. Huong,, S. Frye,, I. I. Raad, and, D. P. Kontoyiannis. 2005. Use of the Diversi Lab System for species and strain differentiation of Fusarium species isolates. J. Clin. Microbiol. 43:52785280.
53. Heinemann, S.,, F. Symoens,, B. Gordts,, H. Jannes, and, N. Nolard. 2004. Environmental investigations and molecular typing of Aspergillus flavus during an outbreak of postoperative infections. J. Hosp. Infect. 57:149155.
54. Hiett, K. L.,, G. R. Siragusa,, N. A. Cox,, R. J. Buhr,, M. T. Musgrove,, N. J. Stern, and, J. L. Wilson. 2003. Genotype analyses of Campylobacter isolated from the gastrointestinal tracts and the reproductive tracts of broiler breeder roosters. Avian Dis. 47:406414.
55. Higgins, C. F.,, G. F. Ames,, W. M. Barnes,, J. M. Clement, and, M. Hofnung. 1982. A novel intercistronic regulatory element of prokaryotic operons. Nature 298:760762.
56. Hirschwerk, D.,, C. C. Ginocchio,, M. Bythrow, and, S. Condon. 2006. Diminished susceptibility to daptomycin accompanied by clinical failure in a patient with methicillin-resistant Staphylococcus aureus bacteremia. Infect. Control Hosp. Epidemiol. 27:315317.
57. Huang, S. S.,, D. S. Yokoe,, V. L. Hinrichsen,, L. S. Spurchise,, R. Datta,, I. Miroshnik, and, R. Platt. 2006. Impact of routine intensive care unit surveillance cultures and resultant barrier precautions on hospital-wide methicillin-resistant Staphylococcus aureus bacteremia. Clin. Infect. Dis. 43:971978.
58. Hulton, C. S.,, C. F. Higgins, and, P. M. Sharp. 1991. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol. Microbiol. 5:825834.
59. Inglis, T. J.,, L. O’Reilly,, N. Foster,, A. Clair, and, J. Sampson. 2002. Comparison of rapid, automated ribotyping and DNA macrorestriction analysis of Burkholderia pseudomallei. J. Clin. Microbiol. 40:31983203.
60. Jersek, B.,, E. Tcherneva,, N. Rijpens, and, L. Herman. 1996. Repetitive element sequence-based PCR for species and strain discrimination in the genus Listeria. Lett. Appl. Microbiol. 23:5560.
61. Johnson, J. R.,, and C. Clabots. 2000. Improved repetitive-element PCR fingerprinting of Salmonella enterica with the use of extremely elevated annealing temperatures. Clin. Diagn. Lab. Immunol. 7:258264.
62. Jones, S. W.,, M. E. Dobson,, S. C. Francesconi,, R. Schoske, and, R. Crawford. 2005. DNA assays for detection, identification, and individualization of select agent microorganisms. Croat. Med. J. 46:522529.
63. Kang, H. P.,, and W. M. Dunne. 2003. Stability of repetitive-sequence PCR patterns with respect to culture age and subculture frequency. J. Clin. Microbiol. 41:26942696.
64. Khoury, J.,, M. Jones,, A. Grim,, W. M. Dunne, Jr., and, V. Fraser. 2005. Eradication of methicillin-resistant Staphylococcus aureus from a neonatal intensive care unit by active surveillance and aggressive infection control measures. Infect. Control Hosp. Epidemiol. 26:616621.
65. Kingsley, M. T.,, T. M. Straub,, D. R. Call,, D. S. Daly,, S. C. Wunschel, and, D. P. Chandler. 2002. Fingerprinting closely related xanthomonas pathovars with random nonamer oligonucleotide microarrays. Appl. Environ. Microbiol. 68:63616370.
66. Koeuth, T.,, J. Versalovic, and, J. R. Lupski. 1995. Differential subsequence conservation of interspersed repetitive Streptococcus pneumoniae BOX elements in diverse bacteria. Genome Res. 5:408418.
67. Kontoyiannis, D. P.,, and G. P. Bodey. 2002. Invasive aspergillosis in 2002: an update. Eur. J. Clin. Microbiol. Infect. Dis. 21:161172.
68. Kontoyiannis, D. P.,, M. S. Lionakis,, R. E. Lewis,, G. Chamilos,, M. Healy,, C. Perego,, A. Safdar,, H. Kantarjian,, R. Champlin,, T. J. Walsh, and, I. I. Raad. 2005. Zygomycosis in a tertiary-care cancer center in the era of Aspergillus-active antifungal therapy: a case-control observational study of 27 recent cases. J. Infect. Dis. 191:13501360.
69. Kostman, J. R.,, M. B. Alden,, M. Mair,, T. D. Edlind,, J. J. LiPuma, and, T. L. Stull. 1995. A universal approach to bacterial molecular epidemiology by polymerase chain reaction ribotyping. J. Infect. Dis. 171:204208.
70. Land, M. H.,, K. Rouster-Stevens,, C. R. Woods,, M. L. Cannon,, J. Cnota, and, A. K. Shetty. 2005. Lactobacillus sepsis associated with probiotic therapy. Pediatrics 115:178181.
71. Lasker, B. A. 2002. Evaluation of performance of four genotypic methods for studying the genetic epidemiology of Aspergillus fumigatus isolates. J. Clin. Microbiol. 40:28862892.
72. Latge, J. P. 1999. Aspergillus fumigatus and aspergillosis. Clin. Microbiol. Rev. 12:310350.
73. Leenders, A.,, A. van Belkum,, S. Janssen,, S. de Marie,, J. Kluytmans,, J. Wielenga,, B. Lowenberg, and, H. Verbrugh. 1996. Molecular epidemiology of apparent outbreak of invasive aspergillosis in a hematology ward. J. Clin. Microbiol. 34:345351.
74. Lessing, M. P.,, J. Z. Jordens, and, I. C. Bowler. 1995. Molecular epidemiology of a multiple strain outbreak of methicillin-resistant Staphylococcus aureus amongst patients and staff. J. Hosp. Infect. 31:253260.
75. Li, X.,, N. Brown,, A. S. Chau,, J. L. Lopez-Ribot,, M. T. Ruesga,, G. Quindos,, C. A. Mendrick,, R. S. Hare,, D. Loebenberg,, B. DiDomenico, and, P. M. McNicholas. 2004. Changes in susceptibility to posaconazole in clinical isolates of Candida albicans. J. Antimicrob. Chemother. 53:7480.
76. Liao, R. S.,, G. A. Storch,, R. S. Buller,, R. C. Orscheln,, E. R. Mardis,, J. R. Armstrong, and, W. M. Dunne, Jr. 2006. Blinded comparison of repetitive-sequence PCR and multilocus sequence typing for genotyping methicillin-resistant Staphylococcus aureus isolates from a children’s hospital in St. Louis, Missouri. J. Clin. Microbiol. 44:22542257.
77. Lindstedt, B. A. 2005. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 26:25672582.
78. Lobato, M. J.,, E. Landeras,, M. A. Gonzalez-Hevia, and, M. C. Mendoza. 1998. Genetic heterogeneity of clinical strains of Yersinia enterocolitica traced by ribotyping and relationships between ribotypes, serotypes, and biotypes. J. Clin. Microbiol. 36:32973302.
79. Lopez-Ribot, J. L.,, R. K. McAtee,, W. R. Kirkpatrick,, S. Perea, and, T. F. Patterson. 2000. Comparison of DNA-based typing methods to assess genetic diversity and relatedness among Candida albicans clinical isolates. Rev. Iberoam. Micol. 17:4954.
80. MacCannell, D. R.,, T. J. Louie,, D. B. Gregson,, M. Laverdiere,, A. C. Labbe,, F. Laing, and, S. Henwick. 2006. Molecular analysis of Clostridium difficile PCR ribotype 027 isolates from Eastern and Western Canada. J. Clin. Microbiol. 44:21472152.
81. Martin, B.,, O. Humbert,, M. Camara,, E. Guenzi,, J. Walker,, T. Mitchell,, P. Andrew,, M. Prudhomme,, G. Alloing,, R. Hakenbeck, et al. 1992. A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae. Nucleic Acids Res. 20:34793483.
82. Martin-Lozano, D.,, J. M. Cisneros,, B. Becerril,, L. Cuberos,, T. Prados,, C. Ortiz-Leyba,, E. Canas, and, J. Pachon. 2002. Comparison of a repetitive extragenic palindromic sequence-based PCR method and clinical and microbiological methods for determining strain sources in cases of nosocomial Acinetobacter baumannii bacteremia. J. Clin. Microbiol. 40:45714575.
83. McDougal, L. K.,, C. D. Steward,, G. E. Killgore,, J. M. Chaitram,, S. K. McAllister, and, F. C. Tenover. 2003. Pulsed-field gel electrophoresis typing of oxacillin-resistant Staphylococcus aureus isolates from the United States: establishing a national database. J. Clin. Microbiol. 41:51135120.
84. Merz, W. G. 1990. Candida albicans strain delineation. Clin. Microbiol. Rev. 3:321334.
85. Mishaan, A. M.,, E. O. Mason, Jr.,, G. Martinez-Aguilar,, W. Hammerman,, J. J. Propst,, J. R. Lupski,, P. Stankiewicz,, S. L. Kaplan, and, K. Hulten. 2005. Emergence of a predominant clone of community-acquired Staphylococcus aureus among children in Houston, Texas. Pediatr. Infect. Dis. J. 24:201206.
86. Mohapatra, B. R.,, K. Broersma, and, A. Mazumder. 2007. Comparison of five rep-PCR genomic fingerprinting methods for differentiation of fecal Escherichia coli from humans, poultry and wild birds. FEMS Microbiol. Lett. 277:98106.
87. Moroney, S. M.,, L. C. Heller,, J. Arbuckle,, M. Talavera, and, R. H. Widen. 2007. Staphylococcal cassette chromosome mec and Panton-Valentine leukocidin characterization of methicillin-resistant Staphylococcus aureus clones. J. Clin. Microbiol. 45:10191021.
88. Munoz, P.,, J. Guinea,, T. Pelaez,, C. Duran,, J. L. Blanco, and, E. Bouza. 2004. Nosocomial invasive aspergillosis in a heart transplant patient acquired during a break in the HEPA air filtration system. Transpl. Infect. Dis. 6:5054.
89. Noordhoek, G. T.,, S. A. Scheltinga,, P. Caesar,, L. M. Schouls, and, J. E. Degener. 1997. PCR-based DNA fingerprinting of Staphylococcus haemolyticus to investigate nosocomial infections. Clin. Microbiol. Infect. 3:356364.
90. Northey, G.,, M. Gal,, A. Rahmati, and, J. S. Brazier. 2005. Subtyping of Clostridium difficile PCR ribotype 001 by REP-PCR and PFGE. J. Med. Microbiol. 54:543547.
91. Odds, F. C.,, D. L. Brawner,, J. Staudinger,, P. T. Magee, and, D. R. Soll. 1992. Typing of Candida albicans strains. J. Med. Vet. Mycol. 30(Suppl. 1):8794.
92. O’Donnell, K.,, D. A. Sutton,, M. G. Rinaldi,, K. C. Magnon,, P. A. Cox,, S. G. Revankar,, S. Sanche,, D. M. Geiser,, J. H. Juba,, J. A. van Burik,, A. Padhye,, E. J. Anaissie,, A. Francesconi,, T. J. Walsh, and, J. S. Robinson. 2004. Genetic diversity of human pathogenic members of the Fusarium oxysporum complex inferred from multilocus DNA sequence data and amplified fragment length polymorphism analyses: evidence for the recent dispersion of a geographically widespread clonal lineage and nosocomial origin. J. Clin. Microbiol. 42:51095120.
93. Olive, D. M.,, and P. Bean. 1999. Principles and applications of methods for DNA-based typing of microbial organisms. J. Clin. Microbiol. 37:16611669.
94. Olson, A. B.,, A. K. Andrysiak,, D. M. Tracz,, J. Guard-Bouldin,, W. Demczuk,, L. K. Ng,, A. Maki,, F. Jamieson, and, M. W. Gilmour. 2007. Limited genetic diversity in Salmonella enterica serovar Enteritidis PT13. BMC Microbiol. 7:87.
95. Papadomichelakis, E.,, F. Kontopidou,, A. Antoniadou,, G. Poulakou,, E. Koratzanis,, P. Kopterides,, I. Mavrou,, A. Armaganidis, and, H. Giamarellou. 2008. Screening for resistant gram-negative microorganisms to guide empiric therapy of subsequent infection. Intensive Care Med. 34:21692175.
96. Patel, S. J.,, and P. L. Graham III. 2007. Use of molecular typing in infection control. Pediatr. Infect. Dis. J. 26:527529.
97. Pounder, J. I.,, S. Williams,, D. Hansen,, M. Healy,, K. Reece, and, G. L. Woods. 2005. Repetitive-sequence-PCR-based DNA fingerprinting using the Diversilab system for identification of commonly encountered dermatophytes. J. Clin. Microbiol. 43:21412147.
98. Pounder, J. I.,, D. Hansen, and, G. L. Woods. 2006. Identification of Histoplasma capsulatum, Blastomyces dermatitidis, and Coccidioides species by repetitive-sequence-based PCR. J. Clin. Microbiol. 44:29772982.
99. Price, D. L.,, R. B. Simmons,, S. A. Crow, Jr., and, D. G. Ahearn. 2005. Mold colonization during use of preservative-treated and untreated air filters, including HEPA filters from hospitals and commercial locations over an 8-year period (1996-2003). J. Ind. Microbiol. Biotechnol. 32:319321.
100. Proudy, I.,, D. Bougle,, E. Coton,, M. Coton,, R. Leclercq, and, M. Vergnaud. 2008. Genotypic characterization of Enterobacter sakazakii isolates by PFGE, BOX-PCR and sequencing of the fliC gene. J. Appl. Microbiol. 104:2634.
101. Pujol, C.,, S. Joly,, S. R. Lockhart,, S. Noel,, M. Tibayrenc, and, D. R. Soll. 1997. Parity among the randomly amplified polymorphic DNA method, multilocus enzyme electrophoresis, and Southern blot hybridization with the moderately repetitive DNA probe Ca3 for fingerprinting Candida albicans. J. Clin. Microbiol. 35:23482358.
102. Raad, I.,, J. Tarrand,, H. Hanna,, M. Albitar,, E. Janssen,, M. Boktour,, G. Bodey,, M. Mardani,, R. Hachem,, D. Kontoyiannis,, E. Whimbey, and, K. Rolston. 2002. Epidemiology, molecular mycology, and environmental sources of Fusarium infection in patients with cancer. Infect. Control Hosp. Epidemiol. 23:532537.
103. Radford, S. A.,, E. M. Johnson,, J. P. Leeming,, M. R. Millar,, J. M. Cornish,, A. B. Foot, and, D. W. Warnock. 1998. Molecular epidemiological study of Aspergillus fumigatus in a bone marrow transplantation unit by PCR amplification of ribosomal intergenic spacer sequences. J. Clin. Microbiol. 36:12941299.
104. Rahmati, A.,, M. Gal,, G. Northey, and, J. S. Brazier. 2005. Subtyping of Clostridium difficile polymerase chain reaction (PCR) ribotype 001 by repetitive extragenic palindromic PCR genomic fingerprinting. J. Hosp. Infect. 60:5660.
105. Rangel-Frausto, M. S.,, P. Rhomberg,, R. J. Hollis,, M. A. Pfaller,, R. P. Wenzel,, C. M. Helms, and, L. A. Herwaldt. 1999. Persistence of Legionella pneumophila in a hospital’s water system: a 13-year survey. Infect. Control Hosp. Epidemiol. 20:793797.
106. Roberts, K.,, C. F. Smith,, A. M. Snelling,, K. G. Kerr,, K. R. Banfield,, P. A. Sleigh, and, C. B. Beggs. 2008. Aerial dissemination of Clostridium difficile spores. BMC Infect. Dis. 8:7.
107. Rodriguez-Bano, J.,, M. D. Navarro,, L. Romero,, M. A. Muniain,, E. J. Perea,, R. Perez-Cano,, J. R. Hernandez, and, A. Pascual. 2006. Clinical and molecular epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli as a cause of nosocomial infection or colonization: implications for control. Clin. Infect. Dis. 42:3745.
108. Rodriguez-Barradas, M. C.,, R. J. Hamill,, E. D. Houston,, P. R. Georghiou,, J. E. Clarridge,, R. L. Regnery, and, J. E. Koehler. 1995. Genomic fingerprinting of Bartonella species by repetitive element PCR for distinguishing species and isolates. J. Clin. Microbiol. 33:10891093.
109. Ross, T. L.,, W. G. Merz,, M. Farkosh, and, K. C. Carroll. 2005. Comparison of an automated repetitive sequence-based PCR microbial typing system to pulsed-field gel electrophoresis for analysis of outbreaks of methicillin-resistant Staphylococcus aureus. J. Clin. Microbiol. 43:56425647.
110. Rwego, I. B.,, T. R. Gillespie,, G. Isabirye-Basuta, and, T. L. Goldberg. 2008. High rates of Escherichia coli transmission between livestock and humans in rural Uganda. J. Clin. Microbiol. 46:31873191.
111. Saeed, S.,, M. G. Fakih,, K. Riederer,, A. R. Shah, and, R. Khatib. 2006. Interinstitutional and intrainstitutional transmission of a strain of Acinetobacter baumannii detected by molecular analysis: comparison of pulsed-field gel electrophoresis and repetitive sequence-based polymerase chain reaction. Infect. Control Hosp. Epidemiol. 27:981983.
112. Shopsin, B.,, and B. N. Kreiswirth. 2001. Molecular epidemiology of methicillin-resistant Staphylococcus aureus. Emerg. Infect. Dis. 7:323326.
113. Shutt, C. K.,, J. I. Pounder,, S. R. Page,, B. J. Schaecher, and, G. L. Woods. 2005. Clinical evaluation of the DiversiLab microbial typing system using repetitive-sequence-based PCR for characterization of Staphylococcus aureus strains. J. Clin. Microbiol. 43:11871192.
114. Silbert, S.,, M. A. Pfaller,, R. J. Hollis,, A. L. Barth, and, H. S. Sader. 2004. Evaluation of three molecular typing techniques for nonfermentative Gram-negative bacilli. Infect. Control Hosp. Epidemiol. 25:847851.
115. Singh, N.,, M. M. Leger,, J. Campbell,, B. Short, and, J. M. Campos. 2005. Control of vancomycin-resistant enterococci in the neonatal intensive care unit. Infect. Control Hosp. Epidemiol. 26:646649.
116. Siragusa, G. R.,, M. D. Danyluk,, K. L. Hiett,, M. G. Wise, and, S. E. Craven. 2006. Molecular subtyping of poultry-associated type A Clostridium perfringens isolates by repetitive-element PCR. J. Clin. Microbiol. 44:10651073.
117. Smith, S. P.,, A. R. Manges, and, L. W. Riley. 2008. Temporal changes in the prevalence of community-acquired antimicrobial-resistant urinary tract infection affected by Escherichia coli clonal group composition. Clin. Infect. Dis. 46:689695.
118. Snelling, A. M.,, P. Gerner-Smidt,, P. M. Hawkey,, J. Heritage,, P. Parnell,, C. Porter,, A. R. Bodenham, and, T. Inglis. 1996. Validation of use of whole-cell repetitive extragenic palindromic sequence-based PCR (REP-PCR) for typing strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii complex and application of the method to the investigation of a hospital outbreak. J. Clin. Microbiol. 34:11931202.
119. Soll, D. R. 2000. The ins and outs of DNA fingerprinting the infectious fungi. Clin. Microbiol. Rev. 13:332370.
120. Spigaglia, P.,, and P. Mastrantonio. 2003. Evaluation of repetitive element sequence-based PCR as a molecular typing method for Clostridium difficile. J. Clin. Microbiol. 41:24542457.
121. Stern, M. J.,, G. F. Ames,, N. H. Smith,, E. C. Robinson, and, C. F. Higgins. 1984. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37:10151026.
122. Stoeckel, D. M.,, M. V. Mathes,, K. E. Hyer,, C. Hagedorn,, H. Kator,, J. Lukasik,, T. L. O’Brien,, T. W. Fenger,, M. Samadpour,, K. M. Strickler, and, B. A. Wiggins. 2004. Comparison of seven protocols to identify fecal contamination sources using Escherichia coli. Environ. Sci. Technol. 38:61096117.
123. Storms, V.,, M. Baele,, R. Coopman,, A. Willems,, T. de Baere,, F. Haesebrouck,, G. Verschraegen,, M. Gillis, and, M. Vaneechoutte. 2002. Study of the intra- and inter-laboratory reproducibility of partial single base C-sequencing of the 16S rRNA gene and its applicability for the identification of members of the genus Streptococcus. Syst. Appl. Microbiol. 25:5259.
124. Stumpf, A. N.,, A. Roggenkamp, and, H. Hoffmann. 2005. Specificity of enterobacterial repetitive intergenic consensus and repetitive extragenic palindromic polymerase chain reaction for the detection of clonality within the Enterobacter cloacae complex. Diagn. Microbiol. Infect. Dis. 53:916.
125. Suppola, J. P.,, E. Kolho,, S. Salmenlinna,, E. Tarkka,, J. Vuopio-Varkila, and, M. Vaara. 1999. vanA and vanB incorporate into an endemic ampicillin-resistant vancomycin-sensitive Enterococcus faecium strain: effect on interpretation of clonality. J. Clin. Microbiol. 37:39343939.
126. Taha, M. K. 2002. Molecular detection and characterization of Neisseria meningitidis. Expert Rev. Mol. Diagn. 2:143150.
127. Tavanti, A.,, N. A. Gow,, S. Senesi,, M. C. Maiden, and, F. C. Odds. 2003. Optimization and validation of multilocus sequence typing for Candida albicans. J. Clin. Microbiol. 41:37653776.
128. Tenover, F. C.,, R. D. Arbeit,, R. V. Goering,, P. A. Mickelsen,, B. E. Murray,, D. H. Persing, and, B. Swaminathan. 1995. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 33:22332239.
129. van Belkum, A. 2003. High-throughput epidemiologic typing in clinical microbiology. Clin. Microbiol. Infect. 9:86100.
130. van Belkum, A.,, P. T. Tassios,, L. Dijkshoorn,, S. Haeggman,, B. Cookson,, N. K. Fry,, V. Fussing,, J. Green,, E. Feil,, P. Gerner-Smidt,, S. Brisse, and, M. Struelens. 2007. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin. Microbiol. Infect. 13(Suppl. 3):146.
131. Vanlaere, E.,, J. J. Lipuma,, A. Baldwin,, D. Henry,, E. De Brandt,, E. Mahenthiralingam,, D. Speert,, C. Dowson, and, P. Vandamme. 2008. Burkholderia latens sp. nov., Burkholderia diffusa sp. nov., Burkholderia arboris sp. nov., Burkholderia seminalis sp. nov. and Burkholderia metallica sp. nov., novel species within the Burkholderia cepacia complex. Int. J. Syst. Evol. Microbiol. 58:15801590.
132. Vazquez, J. A.,, A. Beckley,, J. D. Sobel, and, M. J. Zervos. 1991. Comparison of restriction enzyme analysis and pulsed-field gradient gel electrophoresis as typing systems for Candida albicans. J. Clin. Microbiol. 29:962967.
133. Vazquez, J. A.,, D. Boikov,, S. G. Boikov, and, A. S. Dajani. 1997. Use of electrophoretic karyotyping in the evaluation of Candida infections in a neonatal intensive-care unit. Infect. Control Hosp. Epidemiol. 18:3237.
134. Versalovic, J.,, T. Koeuth, and, J. R. Lupski. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19:68236831.
135. Versalovic, J.,, V. Kapur,, E. O. Mason, Jr.,, U. Shah,, T. Koeuth,, J. R. Lupski, and, J. M. Musser. 1993. Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones. J. Infect. Dis. 167:850856.
136. Versalovic, J.,, V. Kapur,, T. Koeuth,, G. H. Mazurek,, T. S. Whittam,, J. M. Musser, and, J. R. Lupski. 1995. DNA fingerprinting of pathogenic bacteria by fluorophore-enhanced repetitive sequence-based polymerase chain reaction. Arch. Pathol. Lab. Med. 119:2329.
137. Versalovic, J.,, and J. R. Lupski. 2002. Molecular detection and genotyping of pathogens: more accurate and rapid answers. Trends Microbiol. 10:S15S21.
138. von Reyn, C. F.,, J. N. Maslow,, T. W. Barber,, J. O. Falkinham III, and, R. D. Arbeit. 1994. Persistent colonisation of potable water as a source of Mycobacterium avium infection in AIDS. Lancet 343:11371141.
139. Vos, P.,, R. Hogers,, M. Bleeker,, M. Reijans,, T. van de Lee,, M. Hornes,, A. Frijters,, J. Pot,, J. Peleman,, M. Kuiper, et al. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23:44074414.
140. Walsh, T. J.,, and A. H. Groll. 1999. Emerging fungal pathogens: evolving challenges to immunocompromised patients for the twenty-first century. Transpl. Infect. Dis. 1:247261.
141. Wang, S. H.,, J. E. Mangino,, K. Stevenson,, M. A. Yakrus,, R. Cooksey,, W. R. Butler,, M. Healy,, M. G. Wise,, L. S. Schlesinger, and, P. Pancholi. 2008. Characterization of “Mycobacterium paraffinicum” associated with a pseudo-outbreak. J. Clin. Microbiol. 46:18501853.
142. Wiedmann, M. 2002. Subtyping of bacterial foodborne pathogens. Nutr. Rev. 60:201208.
143. Wise, M. G.,, M. Healy,, K. Reece,, R. Smith,, D. Walton,, W. Dutch,, A. Renwick,, J. Huong,, S. Young,, J. Tarrand, and, D. P. Kontoyiannis. 2007. Species identification and strain differentiation of clinical Candida isolates using the DiversiLab system of automated repetitive sequence-based PCR. J. Med. Microbiol. 56:778787.
144. Wise, M. G.,, G. R. Siragusa,, J. Plumblee,, M. Healy,, P. J. Cray, and, B. S. Seal. 2008. Predicting Salmonella enterica serotypes by repetitive sequence-based PCR. J. Microbiol. Methods 76:1824.
145. Woods, C. R.,, T. Koeuth,, M. M. Estabrook, and, J. R. Lupski. 1996. Rapid determination of outbreak-related strains of Neisseria meningitidis by repetitive elementbased polymerase chain reaction genotyping. J. Infect. Dis. 174:760767.
146. Wu, F.,, and P. Della-Latta. 2002. Molecular typing strategies. Semin. Perinatol. 26:357366.
147. Zaidi, N.,, K. Konstantinou, and, M. Zervos. 2003. The role of molecular biology and nucleic acid technology in the study of human infection and epidemiology. Arch. Pathol. Lab. Med. 127:10981105.
148. Zhang, Q.,, R. Kennon,, M. A. Koza,, K. Hulten, and, J. E. Clarridge III. 2002. Pseudoepidemic due to a unique strain of Mycobacterium szulgai: genotypic, phenotypic, and epidemiological analysis. J. Clin. Microbiol. 40:11341139.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error