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Items: 18

1.

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.

Meehan CJ, Goig GA, Kohl TA, Verboven L, Dippenaar A, Ezewudo M, Farhat MR, Guthrie JL, Laukens K, Miotto P, Ofori-Anyinam B, Dreyer V, Supply P, Suresh A, Utpatel C, van Soolingen D, Zhou Y, Ashton PM, Brites D, Cabibbe AM, de Jong BC, de Vos M, Menardo F, Gagneux S, Gao Q, Heupink TH, Liu Q, Loiseau C, Rigouts L, Rodwell TC, Tagliani E, Walker TM, Warren RM, Zhao Y, Zignol M, Schito M, Gardy J, Cirillo DM, Niemann S, Comas I, Van Rie A.

Nat Rev Microbiol. 2019 Sep;17(9):533-545. doi: 10.1038/s41579-019-0214-5. Review.

PMID:
31209399
2.

GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions.

Farhat MR, Freschi L, Calderon R, Ioerger T, Snyder M, Meehan CJ, de Jong B, Rigouts L, Sloutsky A, Kaur D, Sunyaev S, van Soolingen D, Shendure J, Sacchettini J, Murray M.

Nat Commun. 2019 May 13;10(1):2128. doi: 10.1038/s41467-019-10110-6.

3.

Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting.

Dixit A, Freschi L, Vargas R, Calderon R, Sacchettini J, Drobniewski F, Galea JT, Contreras C, Yataco R, Zhang Z, Lecca L, Kolokotronis SO, Mathema B, Farhat MR.

Sci Rep. 2019 Apr 3;9(1):5602. doi: 10.1038/s41598-019-41967-8.

4.

Rifampicin and rifabutin resistance in 1003 Mycobacterium tuberculosis clinical isolates.

Farhat MR, Sixsmith J, Calderon R, Hicks ND, Fortune SM, Murray M.

J Antimicrob Chemother. 2019 Jun 1;74(6):1477-1483. doi: 10.1093/jac/dkz048.

PMID:
30793747
5.

Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings.

Schubert B, Maddamsetti R, Nyman J, Farhat MR, Marks DS.

Nat Microbiol. 2019 Feb;4(2):328-338. doi: 10.1038/s41564-018-0309-1. Epub 2018 Dec 3.

6.

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B.

N Engl J Med. 2018 Oct 11;379(15):1403-1415. doi: 10.1056/NEJMoa1800474. Epub 2018 Sep 26.

7.
8.

Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes.

Nebenzahl-Guimaraes H, van Laarhoven A, Farhat MR, Koeken VACM, Mandemakers JJ, Zomer A, van Hijum SAFT, Netea MG, Murray M, van Crevel R, van Soolingen D.

Am J Respir Crit Care Med. 2017 Jun 1;195(11):1519-1527. doi: 10.1164/rccm.201605-1042OC.

9.

Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value.

Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, Stolte C, Nebenzahl-Guimaraes H, Jacobson K, Sloutsky A, Kaur D, Posey J, Kreiswirth BN, Kurepina N, Rigouts L, Streicher EM, Victor TC, Warren RM, van Soolingen D, Murray M.

Am J Respir Crit Care Med. 2016 Sep 1;194(5):621-30. doi: 10.1164/rccm.201510-2091OC.

10.

Gyrase Mutations Are Associated with Variable Levels of Fluoroquinolone Resistance in Mycobacterium tuberculosis.

Farhat MR, Jacobson KR, Franke MF, Kaur D, Sloutsky A, Mitnick CD, Murray M.

J Clin Microbiol. 2016 Mar;54(3):727-33. doi: 10.1128/JCM.02775-15. Epub 2016 Jan 13.

11.

The nature, patterns, clinical outcomes, and financial impact of intraoperative adverse events in emergency surgery.

Ramly EP, Bohnen JD, Farhat MR, Razmdjou S, Mavros MN, Yeh DD, Lee J, Butler K, De Moya M, Velmahos GC, Kaafarani HM.

Am J Surg. 2016 Jul;212(1):16-23. doi: 10.1016/j.amjsurg.2015.07.023. Epub 2015 Oct 24.

PMID:
26601649
12.

Concordance of Mycobacterium tuberculosis fluoroquinolone resistance testing: implications for treatment.

Farhat MR, Mitnick CD, Franke MF, Kaur D, Sloutsky A, Murray M, Jacobson KR.

Int J Tuberc Lung Dis. 2015 Mar;19(3):339-41. doi: 10.5588/ijtld.14.0814.

13.

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens.

Farhat MR, Shapiro BJ, Sheppard SK, Colijn C, Murray M.

Genome Med. 2014 Nov 15;6(11):101. doi: 10.1186/s13073-014-0101-7. eCollection 2014.

14.

Systematic review of allelic exchange experiments aimed at identifying mutations that confer drug resistance in Mycobacterium tuberculosis.

Nebenzahl-Guimaraes H, Jacobson KR, Farhat MR, Murray MB.

J Antimicrob Chemother. 2014 Feb;69(2):331-42. doi: 10.1093/jac/dkt358. Epub 2013 Sep 20. Review.

15.

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis.

Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PK, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina N, Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M.

Nat Genet. 2013 Oct;45(10):1183-9. doi: 10.1038/ng.2747. Epub 2013 Sep 1.

16.

Disturbance of respiratory muscle control in a patient with early-stage multiple sclerosis.

Farhat MR, Loring SH, Riskind P, Weinhouse G.

Eur Respir J. 2013 Jun;41(6):1454-6. doi: 10.1183/09031936.00172312. No abstract available.

17.

A comparison of early versus late initiation of renal replacement therapy in critically ill patients with acute kidney injury: a systematic review and meta-analysis.

Karvellas CJ, Farhat MR, Sajjad I, Mogensen SS, Leung AA, Wald R, Bagshaw SM.

Crit Care. 2011;15(1):R72. doi: 10.1186/cc10061. Epub 2011 Feb 25. Review.

18.

Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production.

Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, Cheng TY, Moody DB, Murray M, Galagan JE.

PLoS Comput Biol. 2009 Aug;5(8):e1000489. doi: 10.1371/journal.pcbi.1000489. Epub 2009 Aug 28.

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