Publications:

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MycoVarP: Mycobacterium Variant and Drug Resistance Prediction Pipeline for Whole-Genome Sequence Data Analysis.

Frontiers In Bioinformatics

Swargam, Sandeep S; Kumari, Indu I; Kumar, Amit A; Pradhan, Dibyabhaba D; Alam, Anwar A; Singh, Harpreet H; Jain, Anuja A; Devi, Kangjam Rekha KR; Trivedi, Vishal V; Sarma, Jogesh J; Hanif, Mahmud M; Narain, Kanwar K; Ehtesham, Nasreen Zafar NZ; Hasnain, Seyed Ehtesham SE; Ahmad, Shandar S

Publication Date: 2021

Variant appearance in text: GC: S450L

PubMed Link: 36303799

Variant Present in the following documents:

• Main text
• fbinf-01-805338.pdf

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Whole-Genome Sequencing to Identify Missed Rifampicin and Isoniazid Resistance Among Tuberculosis Isolates-Chennai, India, 2013-2016.

Frontiers In Microbiology

Tamilzhalagan, Sembulingam S; Shanmugam, Sivakumar S; Selvaraj, Ashok A; Suba, Sakthi S; Suganthi, Chittibabu C; Moonan, Patrick K PK; Surie, Diya D; Sathyanarayanan, Mukesh Kumar MK; Gomathi, Narayanan Shivaram NS; Jayabal, Lavanya L; Sachdeva, Kuldeep Singh KS; Selvaraju, Sriram S; Swaminathan, Soumya S; Tripathy, Srikanth Prasad SP; Hall, Patricia J PJ; Ranganathan, Uma Devi UD

Publication Date: 2021

Variant appearance in text: GC: S450L

PubMed Link: 34880835

Variant Present in the following documents:

• Main text

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Genomic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Strains From Patients in Kazakhstan.

Frontiers In Genetics

Daniyarov, Asset A; Molkenov, Askhat A; Rakhimova, Saule S; Akhmetova, Ainur A; Yerezhepov, Dauren D; Chingissova, Lyailya L; Bismilda, Venera V; Toksanbayeva, Bekzat B; Rakisheva, Anar A; Akilzhanova, Ainur A; Kozhamkulov, Ulan U; Kairov, Ulykbek U

Publication Date: 2021

Variant appearance in text: GC: S450L

PubMed Link: 34858467

Variant Present in the following documents:

• Main text

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The whole-genome sequencing in predicting Mycobacterium tuberculosis drug susceptibility and resistance in Papua, Indonesia.

Bmc Genomics

Maladan, Yustinus Y; Krismawati, Hana H; Wahyuni, Tri T; Tanjung, Ratna R; Awaludin, Kamla K; Audah, Kholis Abdurachim KA; Parikesit, Arli Aditya AA

Publication Date: 2021-11-22

Variant appearance in text: GC: S450L

PubMed Link: 34802420

Variant Present in the following documents:

• Main text

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Thin-Layer-Agar-Based Direct Phenotypic Drug Susceptibility Testing on Sputum in Eswatini Rapidly Detects Mycobacterium tuberculosis Growth and Rifampicin Resistance Otherwise Missed by WHO-Endorsed Diagnostic Tests.

Antimicrobial Agents And Chemotherapy

Ardizzoni, E E; Ariza, E E; Mulengwa, D D; Mpala, Q Q; de La Tour, R R; Maphalala, G G; Varaine, F F; Kerschberger, B B; Graulus, P P; Page, A L AL; Niemann, S S; Dreyer, V V; Van Deun, A A; Decroo, T T; Rigouts, L L; de Jong, B C BC

Publication Date: 2021-05-18

Variant appearance in text: GC: S450L

PubMed Link: 33722892

Variant Present in the following documents:

• Main text
• aac.02263-20.pdf

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Magnitude of Phenotypic and MTBDRplus Line Probe Assay First-Line Anti-Tuberculosis Drug Resistance Among Tuberculosis Patients; Northwest Ethiopia.

Infection And Drug Resistance

Yigzaw, Wubet Birhan WB; Torrelles, Jordi B JB; Wang, Shu-Hua SH; Tessema, Belay B

Publication Date: 2021

Variant appearance in text: GC: S450L

PubMed Link: 33603414

Variant Present in the following documents:

• Main text
• idr-14-497.pdf

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Genomic analysis of Latin American-Mediterranean family of Mycobacterium tuberculosis clinical strains from Kazakhstan.

Memorias Do Instituto Oswaldo Cruz

Tarlykov, Pavel P; Atavliyeva, Sabina S; Alenova, Arike A; Ramankulov, Yerlan Y

Publication Date: 2020

Variant appearance in text: GC: Ser450Leu

PubMed Link: 32965331

Variant Present in the following documents:

• Main text

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Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil.

Scientific Reports

Verza, Mirela M; Scheffer, Mara Cristina MC; Salvato, Richard Steiner RS; Schorner, Marcos André MA; Barazzetti, Fernando Hartmann FH; Machado, Hanalydia de Melo HM; Medeiros, Taiane Freitas TF; Rovaris, Darcita Buerger DB; Portugal, Isabel I; Viveiros, Miguel M; Perdigão, João J; Kritski, Afrânio A; Bazzo, Maria Luiza ML

Publication Date: 2020-07-30

Variant appearance in text: GC: Ser450Leu

PubMed Link: 32732910

Variant Present in the following documents:

• Main text
• 41598_2020_Article_69755.pdf

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Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing.

Emerging Microbes & Infections

Perdigão, João J; Silva, Carla C; Maltez, Fernando F; Machado, Diana D; Miranda, Anabela A; Couto, Isabel I; Rabna, Paulo P; Florez de Sessions, Paola P; Phelan, Jody J; Pain, Arnab A; McNerney, Ruth R; Hibberd, Martin L ML; Mokrousov, Igor I; Clark, Taane G TG; Viveiros, Miguel M; Portugal, Isabel I

Publication Date: 2020-12

Variant appearance in text: GC: S450L

PubMed Link: 32538300

Variant Present in the following documents:

• Main text
• TEMI_9_1774425.pdf

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Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate, 3485_MTB, from Nur-Sultan, Kazakhstan.

Microbiology Resource Announcements

Tarlykov, Pavel P; Atavliyeva, Sabina S; Alenova, Arike A; Ramankulov, Yerlan Y

Publication Date: 2020-03-05

Variant appearance in text: GC: Ser450Leu

PubMed Link: 32139580

Variant Present in the following documents:

• Main text
• MRA.00025-20.pdf

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Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan.

Scientific Reports

Jabbar, Abdul A; Phelan, Jody E JE; de Sessions, Paola Florez PF; Khan, Taj Ali TA; Rahman, Hazir H; Khan, Sadiq Noor SN; Cantillon, Daire M DM; Wildner, Leticia Muraro LM; Ali, Sajid S; Campino, Susana S; Waddell, Simon J SJ; Clark, Taane G TG

Publication Date: 2019-10-18

Variant appearance in text: GC: S450L

PubMed Link: 31628383

Variant Present in the following documents:

• 41598_2019_Article_51562.pdf

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Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis.

Plos Biology

Payne, Joshua L JL; Menardo, Fabrizio F; Trauner, Andrej A; Borrell, Sonia S; Gygli, Sebastian M SM; Loiseau, Chloe C; Gagneux, Sebastien S; Hall, Alex R AR

Publication Date: 2019-05

Variant appearance in text: GC: S450L

PubMed Link: 31083647

Variant Present in the following documents:

• Main text

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

Scientific Reports

Dixit, Avika A; Freschi, Luca L; Vargas, Roger R; Calderon, Roger R; Sacchettini, James J; Drobniewski, Francis F; Galea, Jerome T JT; Contreras, Carmen C; Yataco, Rosa R; Zhang, Zibiao Z; Lecca, Leonid L; Kolokotronis, Sergios-Orestis SO; Mathema, Barun B; Farhat, Maha R MR

Publication Date: 2019-04-03

Variant appearance in text: GC: S450L

PubMed Link: 30944370

Variant Present in the following documents:

• Main text
• 41598_2019_Article_41967.pdf

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Genome Sequencing of Polydrug-, Multidrug-, and Extensively Drug-Resistant Mycobacterium tuberculosis Strains from South India.

Microbiology Resource Announcements

Shanmugam, Sivakumar S; Kumar, Narender N; Nair, Dina D; Natrajan, Mohan M; Tripathy, Srikanth Prasad SP; Peacock, Sharon J SJ; Swaminathan, Soumya S; Ranganathan, Uma Devi UD

Publication Date: 2019-03-21

Variant appearance in text: GC: S450L

PubMed Link: 30938706

Variant Present in the following documents:

• Main text

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Genome Sequences and Comparative Analysis of Two Extended-Spectrum Extensively-Drug Resistant Mycobacterium tuberculosis Strains.

Frontiers In Pharmacology

Kayani, Masood R MR; Zheng, Yong-Chang YC; Xie, Fu-Cun FC; Kang, Kai K; Li, Han-Yu HY; Zhao, Hai-Tao HT

Publication Date: 2018

Variant appearance in text: GC: S450L

PubMed Link: 30618776

Variant Present in the following documents:

• Main text
• fphar-09-01492.pdf

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Mycobacterium tuberculosis carrying a rifampicin drug resistance mutation reprograms macrophage metabolism through cell wall lipid changes.

Nature Microbiology

Howard, Nicole C NC; Marin, Nancy D ND; Ahmed, Mushtaq M; Rosa, Bruce A BA; Martin, John J; Bambouskova, Monika M; Sergushichev, Alexey A; Loginicheva, Ekaterina E; Kurepina, Natalia N; Rangel-Moreno, Javier J; Chen, Liang L; Kreiswirth, Barry N BN; Klein, Robyn S RS; Balada-Llasat, Joan-Miquel JM; Torrelles, Jordi B JB; Amarasinghe, Gaya K GK; Mitreva, Makedonka M; Artyomov, Maxim N MN; Hsu, Fong-Fu FF; Mathema, Barun B; Khader, Shabaana A SA

Publication Date: 2018-10

Variant appearance in text: GC: S450L

PubMed Link: 30224802

Variant Present in the following documents:

• Main text

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A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions.

Microbial Genomics

Bainomugisa, Arnold A; Duarte, Tania T; Lavu, Evelyn E; Pandey, Sushil S; Coulter, Chris C; Marais, Ben J BJ; Coin, Lachlan M LM

Publication Date: 2018-07

Variant appearance in text: GC: Ser450Leu

PubMed Link: 29906261

Variant Present in the following documents:

• Main text
• mgen-4-188.pdf

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Variant discovery in the sheep milk transcriptome using RNA sequencing.

Bmc Genomics

Suárez-Vega, Aroa A; Gutiérrez-Gil, Beatriz B; Klopp, Christophe C; Tosser-Klopp, Gwenola G; Arranz, Juan José JJ

Publication Date: 2017-02-15

Variant appearance in text: GC: Ser450Leu

PubMed Link: 28202015

Variant Present in the following documents:

• 12864_2017_3581_MOESM1_ESM.xlsx, sheet 1

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Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study.

Plos Medicine

Casali, Nicola N; Broda, Agnieszka A; Harris, Simon R SR; Parkhill, Julian J; Brown, Timothy T; Drobniewski, Francis F

Publication Date: 2016-10

Variant appearance in text: GC: S450L

PubMed Link: 27701423

Variant Present in the following documents:

• Main text
• pmed.1002137.pdf

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Whole-Genome Sequencing of Two Latin American-Mediterranean Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolates from Medellín, Colombia.

Genome Announcements

Alvarez, N N; Haft, D D; Hurtado, U A UA; Robledo, J J; Rouzaud, F F

Publication Date: 2016-03-31

Variant appearance in text: GC: S450L

PubMed Link: 27034498

Variant Present in the following documents:

• Main text

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Whole-Genome Sequence of a Beijing Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate from Buenaventura, Colombia.

Genome Announcements

Alvarez, N N; Haft, D D; Hurtado, U A UA; Robledo, J J; Rouzaud, F F

Publication Date: 2016-01-14

Variant appearance in text: GC: S450L

PubMed Link: 26769935

Variant Present in the following documents:

• Main text
• e01549-15.pdf

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Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal.

Plos Medicine

Cohen, Keira A KA; Abeel, Thomas T; Manson McGuire, Abigail A; Desjardins, Christopher A CA; Munsamy, Vanisha V; Shea, Terrance P TP; Walker, Bruce J BJ; Bantubani, Nonkqubela N; Almeida, Deepak V DV; Alvarado, Lucia L; Chapman, Sinéad B SB; Mvelase, Nomonde R NR; Duffy, Eamon Y EY; Fitzgerald, Michael G MG; Govender, Pamla P; Gujja, Sharvari S; Hamilton, Susanna S; Howarth, Clinton C; Larimer, Jeffrey D JD; Maharaj, Kashmeel K; Pearson, Matthew D MD; Priest, Margaret E ME; Zeng, Qiandong Q; Padayatchi, Nesri N; Grosset, Jacques J; Young, Sarah K SK; Wortman, Jennifer J; Mlisana, Koleka P KP; O'Donnell, Max R MR; Birren, Bruce W BW; Bishai, William R WR; Pym, Alexander S AS; Earl, Ashlee M AM

Publication Date: 2015-09

Variant appearance in text: GC: S450L

PubMed Link: 26418737

Variant Present in the following documents:

• Main text
• pmed.1001880.pdf

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Whole-Genome Sequence of a Multidrug-Resistant Mycobacterium tuberculosis Beijing Sequence Type 10 Isolate from an Outbreak in Thailand.

Genome Announcements

Coker, Olabisi O OO; Regmi, Sanjib M SM; Suriyaphol, Prapat P; Chininmanu, Kwanrutai K; Prammananan, Therdsak T; Chaiprasert, Angkana A

Publication Date: 2014-08-14

Variant appearance in text: GC: S450L

PubMed Link: 25125647

Variant Present in the following documents:

• Main text
• e00803-14.pdf

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Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients.

Plos One

Merker, Matthias M; Kohl, Thomas A TA; Roetzer, Andreas A; Truebe, Leona L; Richter, Elvira E; Rüsch-Gerdes, Sabine S; Fattorini, Lanfranco L; Oggioni, Marco R MR; Cox, Helen H; Varaine, Francis F; Niemann, Stefan S

Publication Date: 2013

Variant appearance in text: GC: S450L

PubMed Link: 24324807

Variant Present in the following documents:

• Main text
• pone.0082551.pdf

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High-resolution melting curve analysis for rapid detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis clinical isolates.

Journal Of Clinical Microbiology

Choi, Go Eun GE; Lee, Sun Min SM; Yi, Jongyoun J; Hwang, Sang Hyun SH; Kim, Hyung Hoi HH; Lee, Eun Yup EY; Cho, Eun Hae EH; Kim, Jee Hee JH; Kim, Hwa-Jung HJ; Chang, Chulhun L CL

Publication Date: 2010-11

Variant appearance in text: GC: S450L

PubMed Link: 20844231

Variant Present in the following documents:

• Main text

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