Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics

Clinical Infectious Diseases - Tập 64 Số 11 - Trang 1494-1501 - 2017
Abigail L. Manson1, Thomas Abeel1,2, James E. Galagan3,4, Jagadish Chandrabose Sundaramurthi5, Alex Salazar1,2, Thies Gehrmann2, Siva Kumar Shanmugam5, Kannan Palaniyandi5, Sujatha Narayanan5, Soumya Swaminathan5, Ashlee M. Earl1
1Broad Institute of MIT and Harvard, Cambridge, Massachusetts
2Delft Bioinformatics Lab, Delft University of Technology, The Netherlands
3Department of Biomedical Engineering, and
4National Emerging Infectious Diseases Laboratory, Boston University , Massachusetts;
5National Institute for Research in Tuberculosis, New Delhi, India

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WHO, 2016, Global Tuberculosis Report 2016

Gutierrez, 2006, Predominance of ancestral lineages of Mycobacterium tuberculosis in India, Emerg Infect Dis, 12, 1367, 10.3201/eid1209.050017

Narayanan, 2008, Genomic interrogation of ancestral Mycobacterium tuberculosis from south India, Infect Genet Evol, 8, 474, 10.1016/j.meegid.2007.09.007

Comas, 2013, Out-of-Africa migration and neolithic coexpansion of Mycobacterium tuberculosis with modern humans, Nat Genet, 45, 1176, 10.1038/ng.2744

Merker, 2015, Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage, Nat Genet, 47, 242, 10.1038/ng.3195

Reed, 2009, Major Mycobacterium tuberculosis lineages associate with patient country of origin, J Clin Microbiol, 47, 1119, 10.1128/JCM.02142-08

Singh, 2015, Genetic diversity and drug susceptibility profile of Mycobacterium tuberculosis isolated from different regions of India, J Infect, 71, 207, 10.1016/j.jinf.2015.04.028

Shanmugam, 2011, Drug resistance among different genotypes of Mycobacterium tuberculosis isolated from patients from Tiruvallur, South India, Infect Genet Evol, 11, 980, 10.1016/j.meegid.2011.03.011

Kandhakumari, 2015, Spoligotype patterns of Mycobacterium tuberculosis isolated from extra pulmonary tuberculosis patients in Puducherry, India, Indian J Med Microbiol, 33, 267, 10.4103/0255-0857.154871

2012, Facing the Reality of Drug-Resistant Tuberculosis in India: Challenges and Potential Solutions: Summary of a Joint Workshop by the Institute of Medicine, the Indian National Science Academy, and the Indian Council of Medical Research

Selvakumar, 2015, High rates of ofloxacin resistance in Mycobacterium tuberculosis among both new and previously treated patients in Tamil Nadu, South India, PLoS One, 10, e0117421, 10.1371/journal.pone.0117421

Jacobson, 2010, Treatment outcomes among patients with extensively drug-resistant tuberculosis: systematic review and meta-analysis, Clin Infect Dis, 51, 6, 10.1086/653115

Ali, 2015, Whole genome sequencing based characterization of extensively drug-resistant mycobacterium tuberculosis isolates from Pakistan, PLoS ONE, 10, 1

Anderson, 2014, Transmission of multidrug-resistant tuberculosis in the UK: a cross-sectional molecular and epidemiological study of clustering and contact tracing, Lancet Infect Dis, 14, 406, 10.1016/S1473-3099(14)70022-2

Casali, 2014, Evolution and transmission of drug-resistant tuberculosis in a Russian population, Nat Genet, 46, 279, 10.1038/ng.2878

Farhat, 2013, Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis, Nat Genet, 1

Walker, 2015, Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study, Lancet Infect Dis, 3099, 1

Zhang, 2013, Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance, Nat Genet, 45, 1255, 10.1038/ng.2735

Desjardins, 2016, Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance, Nat Genet, 48, 544, 10.1038/ng.3548

Verma, 2014, Evaluation of gidB alterations responsible for streptomycin resistance in Mycobacterium tuberculosis, J Antimicrob Chemother, 69, 2935, 10.1093/jac/dku273

Mani, 2001, Mutations in the rpoB gene of multidrug-resistant Mycobacterium tuberculosis clinical isolates from India, J Clin Microbiol, 39, 2987, 10.1128/JCM.39.8.2987-2990.2001

Chatterjee, 2010, Strains of Mycobacterium tuberculosis from western Maharashtra, India, exhibit a high degree of diversity and strain-specific associations with drug resistance, cavitary disease, and treatment failure, J Clin Microbiol, 48, 3593, 10.1128/JCM.00430-10

Gupta, 2014, A study of Mycobacterium tuberculosis genotypic diversity and drug resistance mutations in Varanasi, north India, Indian J Med Res, 139, 892

Purwar, 2011, Determination of drug susceptibility patterns and genotypes of Mycobacterium tuberculosis isolates from Kanpur district, North India, Infect Genet Evol, 11, 469, 10.1016/j.meegid.2010.12.010

Sankar, 2013, Molecular characterization of Mycobacterium tuberculosis isolates from North Indian patients with extrapulmonary tuberculosis, Tuberculosis (Edinb), 93, 75, 10.1016/j.tube.2012.10.005

Arora, 2009, Characterization of predominant Mycobacterium tuberculosis strains from different subpopulations of India, Infect Genet Evol, 9, 832, 10.1016/j.meegid.2009.05.008

Cohen, 2015, Evolution of extensively drug-resistant tuberculosis over four decades: whole genome sequencing and dating analysis of Mycobacterium tuberculosis isolates from KwaZulu-Natal, PLoS Med, 12, e1001880, 10.1371/journal.pmed.1001880

Williams, 2015, Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing, Emerg Infect Dis, 21, 1082, 10.3201/eid2106.141903

Jenkins, 2011, Quantifying the burden and trends of isoniazid resistant tuberculosis, 1994–2009, PLoS One, 6, e22927, 10.1371/journal.pone.0022927

WHO, 2012, WHO monitoring of Xpert MTB/RIF roll-out

Eldholm, 2015, Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain, Nat Commun, 6, 7119, 10.1038/ncomms8119

Coll, 2015, Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences, Genome Med, 7, 51, 10.1186/s13073-015-0164-0

Unissa, 2015, Investigation of Ser315 substitutions within katG gene in isoniazid-resistant clinical isolates of Mycobacterium tuberculosis from south India, Biomed Res Int, 2015, 257983, 10.1155/2015/257983

Boehme, 2010, Rapid molecular detection of tuberculosis and rifampin resistance, N Engl J Med, 363, 1005, 10.1056/NEJMoa0907847

Telenti, 1993, Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis, Lancet, 341, 647, 10.1016/0140-6736(93)90417-F

Cade, 2010, Isoniazid-resistance conferring mutations in Mycobacterium tuberculosis KatG: catalase, peroxidase, and INH-NADH adduct formation activities, Protein Sci, 19, 458, 10.1002/pro.324

van Rie, 2005, Reinfection and mixed infection cause changing Mycobacterium tuberculosis drug-resistance patterns, Am J Respir Crit Care Med, 172, 636, 10.1164/rccm.200503-449OC

Warren, 2004, Patients with active tuberculosis often have different strains in the same sputum specimen, Am J Respir Crit Care Med, 169, 610, 10.1164/rccm.200305-714OC

Baldeviano-Vidalón, 2005, Multiple infection with resistant and sensitive M. tuberculosis strains during treatment of pulmonary tuberculosis patients, Int J Tuberc Lung Dis, 9, 1155

Fang, 2008, Mixed infections of Mycobacterium tuberculosis in tuberculosis patients in Shanghai, China, Tuberculosis (Edinb), 88, 469, 10.1016/j.tube.2008.02.002

Wollenberg, 2017, Whole genome sequencing of Mycobacterium tuberculosis provides insight into the evolution and genetic composition of drug-resistant tuberculosis in Belarus, J Clin Microbiol, 55, 457, 10.1128/JCM.02116-16

Eldholm, 2014, Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient, Genome Biol, 15, 490, 10.1186/s13059-014-0490-3

Gutacker, 2006, Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites, J Infect Dis, 193, 121, 10.1086/498574

Gutacker, 2002, Genome-wide analysis of synodnymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains, Genetics, 162, 1533, 10.1093/genetics/162.4.1533

, 2012, Morphological Characterization of Mycobacterium tuberculosis

Das, 2013, Genetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients, BMC Genomics, 14, 404, 10.1186/1471-2164-14-404

Periwal, 2015, Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome, PLoS One, 10, e0122979, 10.1371/journal.pone.0122979

Pai, 2006, Nosocomial tuberculosis in India, Emerg Infect Dis, 12, 1311, 10.3201/eid1209.051663

Chatterjee, 2013, Global transcriptional profiling of longitudinal clinical isolates of Mycobacterium tuberculosis exhibiting rapid accumulation of drug resistance, PLoS One, 8, e54717, 10.1371/journal.pone.0054717

Sreevatsan, 1996, Characterization of rpsL and rrs mutations in streptomycin- resistant Mycobacterium tuberculosis isolates from diverse geographic localities, Antimicrob Agents Chemother, 40, 1024, 10.1128/AAC.40.4.1024