Detection of Rifampin-resistant M. tuberculosis in a Multiplex PCR Assay

Finicky M l l BMolecular Beacons

Sloppy M l l BMolecular Beacons

Effect of Number of Mismatched Basepairs on Probe-Target Stabilityp g y

Comparison of Probe Sequence to Target Sequence Species Tm

5Õ -AA C GGA T AGG A CCA C GGG ATG C ATG T CCTG TGG T GGA A AGC A A-3 Õ asiaticum 755Õ -AA C GGA T AGG A CCA C ATGCTG CAT G GT GT GTG G TGG A AAG C AA- 3 Õ branderi 735Õ -AA C GGA T AGG A CCA TG GG ATG C ATG T CTTG TGG T GGA A AGC A A-3 Õ celatum 725Õ -AA C GGA T AGG A CCA C GGG ATG C ATG T CTTG TGG T GGA A AGC A A-3 Õ tuberculosis 715Õ -AA C GGA T AGG A CCA C GGCAT GCA T GT GCTG TGG T GGA A AGC A A-3 Õ chubuense 715Õ -AA C GGA T AGG A CCA C GGG AT TCA TGT C CTG TGG T GGA A AGC A A-3 Õ marinum 715Õ AA C GGA T AGG A CCA C GGG AT TCA TGT C CTG TGG T GGA A AGC A A 3 Õ marinum 715Õ -AA C GGA T AGG A CCA C ATGTC GC ATG GT GT GTG G TGG A AAG C AA- 3 Õ shimoidei 715Õ -AA C GGA T AGG A CCA TG GG ATG C ATG T TC TG TGG T GGA A AGC A A-3 Õ terrae 705Õ -AA C GGA T AGG A CCA C TT GGC GC ATG CCTTG TGG T GGA A AGC A A-3 Õ gastri 695Õ -AA C GGA T AGG A CC TCA AGA CGC ATG T CTTCTG GTG G AAA G CAA - 3Õ avium 685Õ AA C GGA T AGG A CCA C GC GCTTCA TG GT GT GTG G TGG A AAG C AA 3 Õ senegalense 665Õ -AA C GGA T AGG A CCA C GC GCTTCA TG GT GT GTG G TGG A AAG C AA- 3 Õ senegalense 665Õ -AA C GGA T AGG A CC TT TA GGC GC ATG T CTTTA GG TGG A AAG C AA- 3 Õ intracellulare 645Õ -AA C GAAT AGG A CCA C GGCAT TCA TGT GC TG TGG T GGA A AGC A A-3 Õ tokaiense 635Õ -AA C GGA T AGG A CC GCGC GCTTCA TG GT GT GTG G TGG A AAG C AA- 3 Õ engbaekii 635Õ -AA C GGA T AGG A CC TCA AGGC GC ATG CCTT TG TGG G GAA A GCA A -3Õ haemophilum 63

Õ Õ l i 635Õ -AA C GGA T AGG A CC CCGA GGC GC ATG CCTTG GGG TGG A AAG C AA- 3 Õ szulgai 635Õ -AA C GGA T AGG A CCA TT CTG C GC ATG T GGGGT GGT G GAA A GCA A -3Õ xenopi 635Õ -AA C GGA T AGG A CC GCGC ATC GAAT GGT GT GTG G TGG A AAG C AA- 3 Õ triviale 635Õ -AA C GGA T AGG A CC TT TT GGC GC ATG CCTTTTG GTG G AAA G CAA - 3Õ lentiflavum 625Õ -AA C GAAT ATGA CCA C GC GCTTCA TG GT GT GTG G TGG A AAG C AA- 3 Õ fortuitum 595Õ -AA C GAAT AGG A CC CCGA GGC GC ATG CCTTG GGG TGG A AAG C AA- 3 Õ malmoense 585Õ -AA C GGA T AGG A CCA C ACA CTTCA TG GT GAGT GGT G CAA A GCA A -3Õ chelonae 565Õ -AA C GAAT AGG A TCA TG GCC TG CAT G GG TTG TGG T GGA A AGC A A-3 Õ rhodesiae 525Õ -AA C GAAT ATGA CC GCGC TC TTCA TG GG GT GTG G TGG A AAG C AA- 3 Õ diernhoferi 495Õ -AA C GAAT AGG A TCA TG GCC TTCA TG GG TTG TGG T GGA A AGC A A-3 Õ aichiense 44

Melting Temperature of Hybrids Formed by Six Different Sloppy Molecular Beacon Probes with 16s rRNA Amplicons from 61 Different Bacterial Genera

75

80

60

65

70

m

Probe 1Probe 2Probe 3

50

55

60T m

Probe 3Probe 4Probe 5Probe 6

40

45

50

40

Each vertical line on the X axis shows the Tm profile of a different bacterial species. The profiles are plotted in alphabetical order:

Acinetobacter calcoaceticus; Actinomyces meyeri; Aerococcus viridans; Aeromonas hydrophila; Arcanobacterium pyogenes; Bacillus anthracis;Bartonella henselae; Bifidobacterium breve; Bordetella pertussis; Borrelia burgdorferi; Brucella melitensis; Burkholderia mallei; Campylobacter jejuni;Chlamydia psittaci; Citrobacter freundii; Clostridium botulinum; Corynebacterium diptheriae; Coxiella burnetti; Ehrlichia chaffeensis; Eikenella corrodens;Enterobacter aerogenes; Enterococcus faecium; Escherichia coli O157H7; Fransicella tularensis; Fusobacteriam necrophorum; Haemophilus influenzae;Hafnia alvei; Helicobacter pylori; Kingella kingae; Klebsiella pneumoniae; Lactobacillus fermenticum; Legionella pneumophilla; Leptospira biflexa;Leuconostoc mesenteroides; Listeria grayi; Moraxella catarrhalis; Morganella morganii; Mycoplasma pneumoniae; Neisseria gonorrhoeae; NocadiaFarcinica; Oligella urethralis; Pasteurella multocda; Porphyromonas gingivalis; Prevotella melaninogenica; Propionibacterium acnes; Proteus vulgaris;Providencia alcalifaciens; Pseudomonas aeruginosa; Rhodococcus equi; Rickettsia prowazekii; Salmonella typhi; Serratia marcescens; Shigella flexneri;Staphylococcus aureus; Stenotrophomonas maltophilia; Streptobacillus moniliformis; Streptococcus agalactiae; Treponema palidum; UreaplasmaUrealyticum; Vibrio cholerae; Yersinia pestis

People Who Did the WorkPeople Who Did the Work

Sanjay Tyagi Fred Russell Kramerj y y gPublic Health Research Institute Public Health Research Institute

Salvatore Marras Hiyam El-HajjPublic Health Research Institute Public Health Research Institute

Jacqueline Vet Diana BratuP bli H lth R h I tit t Cit U i it f N Y kPublic Health Research Institute City University of New York

Dan-Oscar Antson Moon-Yeun KimLudwig Institute for Cancer Research Dongguk University College of MedicineLudwig Institute for Cancer Research Dongguk University College of Medicine

David Alland Soumitesh ChakravortyNew Jersey Medical School New Jersey Medical School

Amy PiatekWorld Health Organization

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