Lan NTN, Jones-Lo ´pez EC, Lev M, Burday M,
Ayakaka I, Mugerwa RD, McMillan B, WinnDeen E, Christel L, Dailey P, Perkins MD,
Persing DH, Alland D (2010) Rapid detection
of Mycobacterium tuberculosis and rifampin
resistance by use of on-demand, near-patient
technology. J Clin Microbiol 48(1):229–237.
https://doi.org/10.1128/JCM.01463-09
6. Zaczek A, Brzostek A, Augustynowicz-Kopec
E et al (2009) Genetic evaluation of relationship between mutations in rpoB and resistance
of Mycobacterium tuberculosis to rifampin.
BMC Microbiol 9:10. https://doi.org/10.
1186/1471-2180-9-10
7. Fitzwater SP, Sechler GA, Jave O, Coronel J,
Mendoza M, Gilman RH, Friedland JS, DAJ M
(2013) Second-line anti-tuberculosis drug
concentrations for susceptibility testing in the
MODS assay. Eur Respir J 41(5):1163–1171.
https://doi.org/10.1183/09031936.
00059812
8. Kiet VS, Lan NT, An DD, Dung NH, Hoa DV,
van Vinh Chau N, Chinh NT, Farrar J, Caws M
(2010) Evaluation of the MTBDRsl test for
detection of second-line-drug resistance in
Mycobacterium tuberculosis. J Clin Microbiol
48(8):2934–2939. https://doi.org/10.1128/
JCM.00201-10
9. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ,
Shah L, Brodkin E, Rempel S, Moore R,
Zhao Y, Holt R, Varhol R, Birol I et al (2011)
Whole-genome sequencing and social-network
analysis of a tuberculosis outbreak. N Engl J
Med
364:730–739.
https://doi.org/10.
1056/NEJMoa1003176
10. Walker TM, Ip CLC, Harrell RH, Evans JT,
Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ,
Hawkey PM, Crook DW, Parkhill J, Harris D,
Walker S, Bowden R, Monk P, Smith G, Peto
TEA (2013) Whole-genome sequencing to
delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study.
Lancet Infect Dis 13(2):137–146. https://
doi.org/10.1016/S1473-3099(12)70277-3
11. Depledge DP, Palser AL, Watson SJ, Lai IY-C,
Gray ER et al (2011) Specific capture and
whole-genome sequencing of viruses from clinical samples. PLoS One 6(11):e27805.
https://doi.org/10.1371/journal.pone.
0027805
12. Brown AC, Bryant JM, Einer-Jensen K et al
(2015) Rapid whole genome sequencing of
M. tuberculosis directly from clinical samples. J
Clin Microbiol 53(7):2230–2237
13. McEvoy CRE, Cloete R, Mu ¨ller B, Schu ¨rch
AC, van Helden PD, Gagneux S, Warren RM,
Gey van Pittius NC (2012) Comparative analysis of Mycobacterium tuberculosis pe and ppe
genes reveals high sequence variation and an
apparent absence of selective constraints.
PLoS One 7(4):e30593. https://doi.org/10.
1371/journal.pone.0030593
14. Christiansen MT, Brown AC, Kundu S et al
(2014) Whole-genome enrichment and
sequencing of Chlamydia trachomatis directly
from clinical samples. BMC Infect Dis 14:591
15. Depledge DP, Kundu S, Jensen NJ et al (2014)
Deep sequencing of viral genomes provides
insight into the evolution and pathogenesis of
varicella zoster virus and its vaccine in humans.
Mol Biol Evol 31:397–409
16. Lassalle F, Depledge D, Reeves M, Brown AC,
Christiansen MT, Tutill H, Williams R, EinerJensen K, Holdstock J, Atkinson C, Brown JR,
van Loenen F, Clark D, Griffiths P, Verjans G,
Schutten M, Milne R, Balloux F, Breuer J
(2016) Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution
of human cytomegalovirus genomes. Virus
Evol 2(1):vew017. https://doi.org/10.1093/
ve/vew017
17. Brown JR, Roy S, Ruis C, Romero EY, Shah D,
Williams R, Breuer J (2016) Norovirus wholegenome sequencing by SureSelect target
enrichment: a robust and sensitive method. J
Clin Microbiol 54:2530–2537. https://doi.
org/10.1128/JCM.01052-16.
480
Amanda Claire Brown
Ayakaka I, Mugerwa RD, McMillan B, WinnDeen E, Christel L, Dailey P, Perkins MD,
Persing DH, Alland D (2010) Rapid detection
of Mycobacterium tuberculosis and rifampin
resistance by use of on-demand, near-patient
technology. J Clin Microbiol 48(1):229–237.
https://doi.org/10.1128/JCM.01463-09
6. Zaczek A, Brzostek A, Augustynowicz-Kopec
E et al (2009) Genetic evaluation of relationship between mutations in rpoB and resistance
of Mycobacterium tuberculosis to rifampin.
BMC Microbiol 9:10. https://doi.org/10.
1186/1471-2180-9-10
7. Fitzwater SP, Sechler GA, Jave O, Coronel J,
Mendoza M, Gilman RH, Friedland JS, DAJ M
(2013) Second-line anti-tuberculosis drug
concentrations for susceptibility testing in the
MODS assay. Eur Respir J 41(5):1163–1171.
https://doi.org/10.1183/09031936.
00059812
8. Kiet VS, Lan NT, An DD, Dung NH, Hoa DV,
van Vinh Chau N, Chinh NT, Farrar J, Caws M
(2010) Evaluation of the MTBDRsl test for
detection of second-line-drug resistance in
Mycobacterium tuberculosis. J Clin Microbiol
48(8):2934–2939. https://doi.org/10.1128/
JCM.00201-10
9. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ,
Shah L, Brodkin E, Rempel S, Moore R,
Zhao Y, Holt R, Varhol R, Birol I et al (2011)
Whole-genome sequencing and social-network
analysis of a tuberculosis outbreak. N Engl J
Med
364:730–739.
https://doi.org/10.
1056/NEJMoa1003176
10. Walker TM, Ip CLC, Harrell RH, Evans JT,
Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ,
Hawkey PM, Crook DW, Parkhill J, Harris D,
Walker S, Bowden R, Monk P, Smith G, Peto
TEA (2013) Whole-genome sequencing to
delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study.
Lancet Infect Dis 13(2):137–146. https://
doi.org/10.1016/S1473-3099(12)70277-3
11. Depledge DP, Palser AL, Watson SJ, Lai IY-C,
Gray ER et al (2011) Specific capture and
whole-genome sequencing of viruses from clinical samples. PLoS One 6(11):e27805.
https://doi.org/10.1371/journal.pone.
0027805
12. Brown AC, Bryant JM, Einer-Jensen K et al
(2015) Rapid whole genome sequencing of
M. tuberculosis directly from clinical samples. J
Clin Microbiol 53(7):2230–2237
13. McEvoy CRE, Cloete R, Mu ¨ller B, Schu ¨rch
AC, van Helden PD, Gagneux S, Warren RM,
Gey van Pittius NC (2012) Comparative analysis of Mycobacterium tuberculosis pe and ppe
genes reveals high sequence variation and an
apparent absence of selective constraints.
PLoS One 7(4):e30593. https://doi.org/10.
1371/journal.pone.0030593
14. Christiansen MT, Brown AC, Kundu S et al
(2014) Whole-genome enrichment and
sequencing of Chlamydia trachomatis directly
from clinical samples. BMC Infect Dis 14:591
15. Depledge DP, Kundu S, Jensen NJ et al (2014)
Deep sequencing of viral genomes provides
insight into the evolution and pathogenesis of
varicella zoster virus and its vaccine in humans.
Mol Biol Evol 31:397–409
16. Lassalle F, Depledge D, Reeves M, Brown AC,
Christiansen MT, Tutill H, Williams R, EinerJensen K, Holdstock J, Atkinson C, Brown JR,
van Loenen F, Clark D, Griffiths P, Verjans G,
Schutten M, Milne R, Balloux F, Breuer J
(2016) Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution
of human cytomegalovirus genomes. Virus
Evol 2(1):vew017. https://doi.org/10.1093/
ve/vew017
17. Brown JR, Roy S, Ruis C, Romero EY, Shah D,
Williams R, Breuer J (2016) Norovirus wholegenome sequencing by SureSelect target
enrichment: a robust and sensitive method. J
Clin Microbiol 54:2530–2537. https://doi.
org/10.1128/JCM.01052-16.
480
Amanda Claire Brown