Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system

BMC Microbiology

Volumn 8, Issue , 2008, Pages

  Ma, Liang ^a   Taylor, Stephanie ^a   Jensen, Jørgen S ^b   Myers, Leann ^c   Lillis, Rebecca ^a   Martin, David H ^a  

^a LOUISIANA STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STATENS SERUM INSTITUT   (Denmark)

^c TULANE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BACTERIAL INFECTION; BACTERIAL STRAIN; CONTROLLED STUDY; FEMALE; GENETIC ANALYSIS; GENETIC MARKER; GENOME; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MALE; MOLECULAR TYPING; MYCOPLASMA GENITALIUM; NUCLEOTIDE SEQUENCE; SEXUAL TRANSMISSION; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; CLASSIFICATION; DISEASE TRANSMISSION; DNA SEQUENCE; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; POLYMERASE CHAIN REACTION; SEXUALLY TRANSMITTED DISEASE; TANDEM REPEAT;

MYCOPLASMA GENITALIUM; MYCOPLASMATALES;

BACTERIAL DNA; RIBOSOME RNA;

BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; DNA, BACTERIAL; FEMALE; GENETIC MARKERS; GENOME, BACTERIAL; GENOTYPE; HUMANS; MALE; MOLECULAR SEQUENCE DATA; MYCOPLASMA GENITALIUM; MYCOPLASMA INFECTIONS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, RIBOSOMAL; SEQUENCE ANALYSIS, DNA; SEXUALLY TRANSMITTED DISEASES, BACTERIAL; TANDEM REPEAT SEQUENCES;

EID: 49549102681     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-8-130     Document Type: Article

References (35)

1. Signs and symptoms of urethritis and cervicitis among women with or without Mycoplasma genitalium or Chlamydia trachomatis infection. L Falk H Fredlund JS Jensen, Sex Transm Infect 2005 81 1 73 78 15681728 10.1136/sti.2004.010439
2. Mucopurulent cervicitis and Mycoplasma genitalium. LE Manhart CW Critchlow KK Holmes SM Dutro DA Eschenbach CE Stevens PA Totten, J Infect Dis 2003 187 4 650 657 10.1086/367992 12599082
3. Association between Mycoplasma genitalium and acute endometritis. CR Cohen LE Manhart EA Bukusi S Astete RC Brunham KK Holmes SK Sinei JJ Bwayo PA Totten, Lancet 2002 359 9308 765 766 10.1016/S0140-6736(02)07848-0 11888591
4. Associations between Mycoplasma genitalium, Chlamydia trachomatis, and pelvic inflammatory disease. I Simms K Eastick H Mallinson K Thomas R Gokhale P Hay A Herring PA Rogers, Sex Transm Infect 2003 79 2 154 156 12690141 10.1136/sti.79.2.154
5. Serological investigation of Mycoplasma genitalium in infertile women. HF Clausen J Fedder M Drasbek PK Nielsen B Toft HJ Ingerslev S Birkelund G Christiansen, Hum Reprod 2001 16 9 1866 1874 10.1093/humrep/16.9.1866 11527890
6. Mycoplasma genitalium: prevalence, clinical significance, and transmission. C Anagrius B Lore JS Jensen, Sex Transm Infect 2005 81 6 458 462 10.1136/sti.2004.012062 16326846
7. Symptomatic urethritis is more prevalent in men infected with Mycoplasma genitalium than with Chlamydia trachomatis. L Falk H Fredlund JS Jensen, Sex Transm Infect 2004 80 4 289 293 15295128 10.1136/sti.2003.006817
8. The association of Chlamydia trachomatis and Mycoplasma genitalium with non-gonococcal urethritis: observations on heterosexual men and their female partners. FE Keane BJ Thomas CB Gilroy A Renton D Taylor-Robinson, Int J STD AIDS 2000 11 7 435 439 10.1258/0956462001916209 10919484
9. Mycoplasma genitalium infection and host antibody immune response in patients infected by HIV, patients attending STD clinics and in healthy blood donors. RY Wang T Grandinetti JW Shih SH Weiss CL Haley MM Hayes SC Lo, FEMS Immunol Med Microbiol 1997 19 3 237 245 10.1111/j.1574-695X.1997.tb01093.x 9453394
10. Sequence-based typing of Mycoplasma genitalium reveals sexual transmission. SV Hjorth E Bjornelius P Lidbrink L Falk B Dohn L Berthelsen L Ma DH Martin JS Jensen, J Clin Microbiol 2006 44 6 2078 2083 16757601 10.1128/JCM.00003-06
11. High prevalence of Mycoplasma genitalium in the lower genitourinary tract of women attending a sexually transmitted disease clinic in Paris, France. I Casin D Vexiau-Robert P De La Salmoniere A Eche B Grandry M Janier, Sex Transm Dis 2002 29 6 353 359 10.1097/00007435-200206000-00008 12035026
12. Use of TaqMan 5' nuclease real-time PCR for quantitative detection of Mycoplasma genitalium DNA in males with and without urethritis who were attendees at a sexually transmitted disease clinic. JS Jensen E Bjornelius B Dohn P Lidbrink, J Clin Microbiol 2004 42 2 683 692 14766837 10.1128/JCM.42.2.683-692.2004
13. Single-nucleotide polymorphisms in the rRNA operon and variable numbers of tandem repeats in the lipoprotein gene among Mycoplasma genitalium strains from clinical specimens. L Ma DH Martin, J Clin Microbiol 2004 42 10 4876 4878 15472369 10.1128/JCM.42.10.4876-4878.2004
14. Proximal region of the gene encoding cytadherence-related protein permits molecular typing of Mycoplasma genitalium clinical strains by PCR-restriction fragment length polymorphism. O Musatovova C Herrera JB Baseman, J Clin Microbiol 2006 44 2 598 603 16455921 10.1128/JCM.44.2.598-603.2006
15. Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution. EP Rocha A Blanchard, Nucleic Acids Res 2002 30 9 2031 2042 11972343 10.1093/nar/30.9.2031
16. Short-sequence DNA repeats in prokaryotic genomes. A van Belkum S Scherer L van Alphen H Verbrugh, Microbiol Mol Biol Rev 1998 62 2 275 293 9618442
17. The minimal gene complement of Mycoplasma genitalium. CM Fraser JD Gocayne O White MD Adams RA Clayton RD Fleischmann CJ Bult AR Kerlavage G Sutton JM Kelley, Science 1995 270 5235 397 403 10.1126/science.270.5235.397 7569993
18. Characterization of repetitive DNA in the Mycoplasma genitalium genome: possible role in the generation of antigenic variation. SN Peterson CC Bailey JS Jensen MB Borre ES King KF Bott CA Hutchison 3rd, Proc Natl Acad Sci U S A 1995 92 25 11829 11833 8524858 10.1073/pnas.92.25.11829
19. Intrastrain heterogeneity of the mgpB gene in Mycoplasma genitalium is extensive in vitro and in vivo and suggests that variation is generated via recombination with repetitive chromosomal sequences. SL Iverson-Cabral SG Astete CR Cohen EP Rocha PA Totten, Infect Immun 2006 74 7 3715 3726 16790744 10.1128/IAI.00239-06
20. Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome. L Ma JS Jensen L Myers J Burnett M Welch Q Jia DH Martin, Mol Microbiol 2007 66 1 220 236 17784912 10.1111/j.1365-2958.2007. 05911.x
21. mgpB and mgpC sequence diversity in Mycoplasma genitalium is generated by segmental reciprocal recombination with repetitive chromosomal sequences. SL Iverson-Cabral SG Astete CR Cohen PA Totten, Mol Microbiol 2007 66 1 55 73 10.1111/j.1365-2958.2007.05898.x 17880423
22. Amplified-fragment length polymorphism fingerprinting of Mycoplasma species. B Kokotovic NF Friis JS Jensen P Ahrens, J Clin Microbiol 1999 37 10 3300 3307 10488196
23. Analysis of variation in tandem repeats in the intron of the major surface glycoprotein expression site of the human form of Pneumocystis carinii. L Ma G Kutty Q Jia H Imamichi L Huang C Atzori P Beckers G Groner CB Beard JA Kovacs, J Infect Dis 2002 186 11 1647 1654 10.1086/345721 12447742
24. Application of automated DNA sizing technology for genotyping microsatellite loci. JS Ziegle Y Su KP Corcoran L Nie PE Mayrand LB Hoff LJ McBride MN Kronick SR Diehl, Genomics 1992 14 4 1026 1031 10.1016/S0888-7543(05) 80126-0 1478644
25. Integrating patterns of polymorphism at SNPs and STRs. BA Payseur AD Cutter, Trends Genet 2006 22 8 424 429 10.1016/j.tig.2006.06.009 16806567
26. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. G Levinson GA Gutman, Molecular biology and evolution 1987 4 3 203 221 3328815
27. Effect of repeat copy number on variable-number tandem repeat mutations in Escherichia coli O157:H7. AJ Vogler C Keys Y Nemoto RE Colman Z Jay P Keim, Journal of bacteriology 2006 188 12 4253 4263 16740932 10.1128/JB.00001-06
28. Mutations, mutation rates, and evolution at the hypervariable VNTR loci of Yersinia pestis. AJ Vogler CE Keys C Allender I Bailey J Girard T Pearson KL Smith DM Wagner P Keim, Mutation research 2007 616 1-2 145 158 17161849
29. The association of Mycoplasma hominis, Ureaplasma urealyticum and Mycoplasma genitalium with bacterial vaginosis: observations on heterosexual women and their male partners. FE Keane BJ Thomas CB Gilroy A Renton D Taylor-Robinson, Int J STD AIDS 2000 11 6 356 360 10.1258/0956462001916056 10872907
30. Role of Mycoplasma genitalium and Ureaplasma urealyticum in acute and chronic nongonococcal urethritis. P Horner B Thomas CB Gilroy M Egger D Taylor-Robinson, Clin Infect Dis 2001 32 7 995 1003 10.1086/319594 11264026
31. Mycoplasma genitalium infections in asymptomatic men and men with urethritis attending a sexually transmitted diseases clinic in New Orleans. L Mena X Wang TF Mroczkowski DH Martin, Clin Infect Dis 2002 35 10 1167 1173 10.1086/343829 12410476
32. Concordance between Neisseria gonorrhoeae genotypes recovered from known sexual contacts. N Bilek IM Martin G Bell GR Kinghorn CA Ison BG Spratt, J Clin Microbiol 2007 45 11 3564 3567 17855579 10.1128/JCM.01453-07
33. Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains: a web-based resource. F Denoeud G Vergnaud, BMC Bioinformatics 2004 5 4 14715089 10.1186/1471-2105-5-4
34. Primer3 on the WWW for general users and for biologist programmers. S Rozen H Skaletsky, Methods Mol Biol 2000 132 365 386 10547847
35. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. PR Hunter MA Gaston, J Clin Microbiol 1988 26 11 2465 2466 3069867