Article
Microbiology
Francy J. Perez-Llanos, Viola Dreyer, Ivan Barilar, Christian Utpatel, Thomas A. Kohl, Martha Isabel Murcia, Susanne Homolka, Matthias Merker, Stefan Niemann
Summary: An outbreak of Mycobacterium tuberculosis complex (MTBC) bacteria was identified among the indigenous populations in the Colombian Amazon region. Whole genome sequencing (WGS) was used to analyze the transmission of MTBC strains and it was found that the use of an alternative reference genome and repetitive regions improved the phylogenetic resolution. The study also revealed the presence of multiple clones in some patients, indicating within-host MTBC diversity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Genetics & Heredity
Glennah Kerubo, Perpetua Ndungu, Yassir Adam Shuaib, Evans Amukoye, Gunturu Revathi, Susanne Homolka, Samuel Kariuki, Matthias Merker, Stefan Niemann
Summary: Using whole-genome sequencing, this study found that L4 strains are the main causative agent of TB in Nairobi, with emerging concerns of MDR strain transmission in urban settings. Enhanced infection control measures and contact tracing for MDR TB patients are crucial to break the transmission chains.
Article
Microbiology
Simon Robinne, Jamal Saad, Madjid Morsli, Zelika Harouna Hamidou, Fatah Tazerart, Michel Drancourt, Sophie Alexandra Baron
Summary: This study reports a method using MALDI-TOF-MS technology to discriminate Mycobacterium tuberculosis complex mycobacteria, which can be easily implemented in clinical microbiology laboratories.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Immunology
Andre C. Pereira, Ana C. Reis, Monica V. Cunha
Summary: Genomic epidemiology was used to study the spread and spatiotemporal patterns of Mycobacterium bovis in animal tuberculosis in Portugal. The study found that M. bovis continues to circulate among cattle, wild boar, and red deer, with red deer playing a significant role in transmission among wildlife hosts and wild boar connecting the wildlife community and livestock. The study highlights the importance of combining genomic epidemiology with phylodynamic inference.
EMERGING MICROBES & INFECTIONS
(2023)
Article
Microbiology
Typhaine Billard-Pomares, Julie Marin, Pauline Quagliaro, Frederic Mechai, Violaine Walewski, Samira Dziri, Etienne Carbonnelle
Summary: This study conducted whole-genome sequencing on Mycobacterium tuberculosis complex strains isolated from patients in a high-incidence tuberculosis department in France and explored their epidemiological and phylogenetic characteristics. The patients had an average age of 36 years old and were from Africa, Asia, Europe, and America. Strains isolated from extrapulmonary samples were associated with Asian patients, while strains isolated from pulmonary samples were associated with European patients. There was a high level of lineage diversity, with lineage 3 associated with lymph node tuberculosis. Whole-genome sequencing showed high sensitivity in predicting drug resistance. It is an essential tool for better understanding local tuberculosis epidemiology and drug susceptibilities.
Article
Microbiology
Jessica Comin, Isabel Otal, Sofia Samper
Summary: The aim of this study was to investigate the genetic variability of the insertion sequence (IS) 6110 in the Mycobacterium tuberculosis complex (MTBC). The results showed a high mutation rate in IS6110, with low-copy-number strains having higher mutation rates than high-copy-number strains. Additionally, specific IS6110 variants were found in certain strains, and Haarlem and X family strains shared a common IS6110 copy in a specific location.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Charlotte Genestet, Elisabeth Hodille, Albin Bernard, Maxime Vallee, Gerard Lina, Adrien Le Meur, Guislaine Refregier, Oana Dumitrescua
Summary: This study compared membrane-based spoligotyping with whole-genome sequencing (WGS)-based spoligotyping and found good overall agreement between the two methods. In silico spoligotyping could be used as a smooth transition for tuberculosis (TB) diagnosis and epidemiological survey.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biotechnology & Applied Microbiology
Gabriel Morey-Leon, Derly Andrade-Molina, Juan Carlos Fernandez-Cadena, Luisa Berna
Summary: This study reveals for the first time the variability of circulating resistant strains between men and women in Ecuador. The use of whole genome sequencing allows for the identification of emerging resistance and an increase in fluoroquinolone resistance is detected. Further sampling efforts are needed to determine the overall variability and to generate better health policies.
Article
Multidisciplinary Sciences
Roger Vargas Jr, Michael J. Luna, Luca Freschi, Maximillian Marin, Ruby Froom, Kenan C. Murphy, Elizabeth A. Campbell, Thomas R. Ioerger, Christopher M. Sassetti, Maha Reda Farhat
Summary: This study investigates the role of insertions and deletions (INDELs) in genomic homopolymeric tracts (HT) in regulating gene expression in pathogenic bacteria, specifically within the Mycobacterium tuberculosis complex (MTBC). Through analysis of 31,428 clinical isolates, the researchers identified phase-variants of INDEL events that are under positive selection. Further experiments confirmed that a putatively adaptive phase-variant in the ESX-1 system alters the expression of the critical virulence mediator, espA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Caitlin Uren, Eileen G. Hoal, Marlo Moller
Summary: Research on the relationship between MTBC and human host is limited, with focus on genetic association studies that have shown inconsistent results. There is a need to reconsider research methods and understand the coupled evolution of the pathogen and host as a possible key to resolving the issue.
HUMAN MOLECULAR GENETICS
(2021)
Article
Genetics & Heredity
Mireia Coscolla, Sebastien Gagneux, Fabrizio Menardo, Chloe Loiseau, Paula Ruiz-Rodriguez, Sonia Borrell, Isaac Darko Otchere, Adwoa Asante-Poku, Prince Asare, Leonor Sanchez-Buso, Florian Gehre, C. N'Dira Sanoussi, Martin Antonio, Dissou Affolabi, Janet Fyfe, Patrick Beckert, Stefan Niemann, Abraham S. Alabi, Martin P. Grobusch, Robin Kobbe, Julian Parkhill, Christian Beisel, Lukas Fenner, Erik C. Bottger, Conor J. Meehan, Simon R. Harris, Bouke C. de Jong, Dorothy Yeboah-Manu, Daniela Brites
Summary: This study sheds new light on the genomic diversity and evolutionary history of M. africanum, revealing that the most likely ancestral distribution of L9 is East Africa, while L5 and L6 are most likely from the Eastern part of West Africa, with important differences in their phylogeographical substructure and genetic diversity. The study also indicates that previous associations of drug resistance with lineage are likely influenced by sample bias or geography.
MICROBIAL GENOMICS
(2021)
Review
Multidisciplinary Sciences
Moein Zangiabadian, Donya Malekshahian, Erfan Arabpour, Sahel Shafiee Dolat Abadi, Fartous Yazarlou, Narjess Bostanghadiri, Rosella Centis, AmirHossein Akbari Aghababa, Mohammad Farahbakhsh, Mohammad Javad Nasiri, Giovanni Sotgiu, Giovanni Battista Migliori
Summary: This systematic review evaluated the outcomes and adverse events of liposomal amikacin for inhalation (LAI) in Mycobacterium avium complex (MAC) pulmonary disease. The results showed that adding LAI to guideline-based therapies can increase the sputum culture conversion rate and achieve early sustained and durable negative sputum culture. However, further large-scale research is needed to confirm these findings.
Article
Immunology
Tyler S. Brown, Linrui Tang, Shaheed Vally Omar, Lavania Joseph, Graeme Meintjes, Gary Maartens, Sean Wasserman, N. Sarita Shah, Maha R. Farhat, Neel R. Gandhi, Nazir Ismail, James C. M. Brust, Barun Mathema
Summary: Characterizing serial Mycobacterium tuberculosis (Mtb) isolates collected during bedaquiline (BDQ)-based treatment provides insights into the etiologies of BDQ resistance. The study found that BDQ-resistant TB can arise through multiple processes, including transmission of strains with pre-existing resistance. Capturing the within-host diversity of these infections could potentially improve clinical diagnosis, population-level surveillance, and molecular diagnostic test development.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Infectious Diseases
Ekaterina Chernyaeva, Mikhail Rotkevich, Ksenia Krasheninnikova, Alla Lapidus, Dmitrii E. Polev, Natalia Solovieva, Viacheslav Zhuravlev, Piotr Yablonsky, Stephen J. O'Brien
Summary: This study analyzed whole-genome sequences of Mycobacterium tuberculosis strains from pulmonary and extrapulmonary tuberculosis cases, finding genetic sub-strains associated with differences in disease localization and drug resistance patterns. HIV was significantly associated with the development of extrapulmonary tuberculosis in certain genetic subgroups.
Article
Biotechnology & Applied Microbiology
Yustinus Maladan, Hana Krismawati, Tri Wahyuni, Ratna Tanjung, Kamla Awaludin, Kholis Abdurachim Audah, Arli Aditya Parikesit
Summary: The study utilized whole-genome sequencing of TB clinical samples from Papua, Indonesia to detect mutations associated with TB-drug resistance, revealing multiple mutations in genes linked to resistance against various TB drugs. The results contribute to the surveillance of TB-drug resistance, identifying MDR samples but no XDR samples, with resistance mainly observed against the second-line drug Amikacin.
Article
Multidisciplinary Sciences
Tanmoy Roychowdhury, Saurav Mandal, Alok Bhattacharya
SCIENTIFIC REPORTS
(2015)
Article
Multidisciplinary Sciences
Taejeong Bae, Livia Tomasini, Jessica Mariani, Bo Zhou, Tanmoy Roychowdhury, Daniel Franjic, Mihovil Pletikos, Reenal Pattni, Bo-Juen Chen, Elisa Venturini, Bridget Riley-Gillis, Nenad Sestan, Alexander E. Urban, Alexej Abyzov, Flora M. Vaccarino
Article
Biotechnology & Applied Microbiology
Tanmoy Roychowdhury, Vinod Kumar Singh, Alok Bhattacharya
Article
Biotechnology & Applied Microbiology
Sarbashis Das, Tanmoy Roychowdhury, Parameet Kumar, Anil Kumar, Priya Kalra, Jitendra Singh, Sarman Singh, H. K. Prasad, Alok Bhattacharya
Article
Multidisciplinary Sciences
Mukesh Kumar, Nagavara Prasad Gantasala, Tanmoy Roychowdhury, Prasoon Kumar Thakur, Prakash Banakar, Rohit N. Shukla, Michael G. K. Jones, Uma Rao
Article
Multidisciplinary Sciences
Devendra Kumar Biswal, Tanmoy Roychowdhury, Priyatama Pandey, Veena Tandon
Editorial Material
Multidisciplinary Sciences
Nenad Sestan
Article
Multidisciplinary Sciences
Anahita Amiri, Gianfilippo Coppola, Soraya Scuderi, Feinan Wu, Tanmoy Roychowdhury, Fuchen Liu, Sirisha Pochareddy, Yurae Shin, Alexias Safi, Lingyun Song, Ying Zhu, Andre M. M. Sousa, Mark Gerstein, Gregory E. Crawford, Nenad Sestan, Alexej Abyzov, Flora M. Vaccarino
Article
Biochemistry & Molecular Biology
Tanmoy Roychowdhury, Alexej Abyzov
NUCLEIC ACIDS RESEARCH
(2019)
Article
Multidisciplinary Sciences
Wei Zhou, Ben Brumpton, Omer Kabil, Julius Gudmundsson, Gudmar Thorleifsson, Josh Weinstock, Matthew Zawistowski, Jonas B. Nielsen, Layal Chaker, Marco Medici, Alexander Teumer, Silvia Naitza, Serena Sanna, Ulla T. Schultheiss, Anne Cappola, Juha Karjalainen, Mitja Kurki, Morgan Oneka, Peter Taylor, Lars G. Fritsche, Sarah E. Graham, Brooke N. Wolford, William Overton, Humaira Rasheed, Eirin B. Haug, Maiken E. Gabrielsen, Anne Heidi Skogholt, Ida Surakka, George Davey Smith, Anita Pandit, Tanmoy Roychowdhury, Whitney E. Hornsby, Jon G. Jonasson, Leigha Senter, Sandya Liyanarachchi, Matthew D. Ringel, Li Xu, Lambertus A. Kiemeney, Huiling He, Romana T. Netea-Maier, Jose Mayordomo, Theo S. Plantinga, Jon Hrafnkelsson, Hannes Hjartarson, Erich M. Sturgis, Aarno Palotie, Mark Daly, Cintia E. Citterio, Peter Arvan, Chad M. Brummett, Michael Boehnke, Albert de la Chapelle, Kari Stefansson, Kristian Hveem, Cristen J. Willer, Bjorn Olav Asvold
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Jonas B. Nielsen, Oren Rom, Ida Surakka, Sarah E. Graham, Wei Zhou, Tanmoy Roychowdhury, Lars G. Fritsche, Sarah A. Gagliano Taliun, Carlo Sidore, Yuhao Liu, Maiken E. Gabrielsen, Anne Heidi Skogholt, Brooke Wolford, William Overton, Ying Zhao, Jin Chen, He Zhang, Whitney E. Hornsby, Akua Acheampong, Austen Grooms, Amanda Schaefer, Gregory J. M. Zajac, Luis Villacorta, Jifeng Zhang, Ben Brumpton, Mari Loset, Vivek Rai, Pia R. Lundegaard, Morten S. Olesen, Kent D. Taylor, Nicholette D. Palmer, Yii-Der Chen, Seung H. Choi, Steven A. Lubitz, Patrick T. Ellinor, Kathleen C. Barnes, Michelle Daya, Nicholas Rafaels, Scott T. Weiss, Jessica Lasky-Su, Russell P. Tracy, Ramachandran S. Vasan, L. Adrienne Cupples, Rasika A. Mathias, Lisa R. Yanek, Lewis C. Becker, Patricia A. Peyser, Lawrence F. Bielak, Jennifer A. Smith, Stella Aslibekyan, Bertha A. Hidalgo, Donna K. Arnett, Marguerite R. Irvin, James G. Wilson, Solomon K. Musani, Adolfo Correa, Stephen S. Rich, Xiuqing Guo, Jerome I. Rotter, Barbara A. Konkle, Jill M. Johnsen, Allison E. Ashley-Koch, Marilyn J. Telen, Vivien A. Sheehan, John Blangero, Joanne E. Curran, Juan M. Peralta, Courtney Montgomery, Wayne H-H Sheu, Ren-Hua Chung, Karen Schwander, Seyed M. Nouraie, Victor R. Gordeuk, Yingze Zhang, Charles Kooperberg, Alexander P. Reiner, Rebecca D. Jackson, Eugene R. Bleecker, Deborah A. Meyers, Xingnan Li, Sayantan Das, Ketian Yu, Jonathon LeFaive, Albert Smith, Tom Blackwell, Daniel Taliun, Sebastian Zollner, Lukas Forer, Sebastian Schoenherr, Christian Fuchsberger, Anita Pandit, Matthew Zawistowski, Sachin Kheterpal, Chad M. Brummett, Pradeep Natarajan, David Schlessinger, Seunggeun Lee, Hyun Min Kang, Francesco Cucca, Oddgeir L. Holmen, Bjorn O. Asvold, Michael Boehnke, Sekar Kathiresan, Goncalo R. Abecasis, Y. Eugene Chen, Cristen J. Willer, Kristian Hveem
NATURE COMMUNICATIONS
(2020)
Article
Biology
Saurav Mandal, Tanmoy Roychowdhury, Alok Bhattacharya
Summary: The study analyzed the hypervariable and hypovariable regions of the SARS-CoV-2 genome, comparing it with other Coronaviruses and found some changes in the virus genome. It also suggests that over time, the virus may undergo mutations and the possibility of emergence of modified viruses.
JOURNAL OF BIOSCIENCES
(2021)
Article
Genetics & Heredity
Tanmoy Roychowdhury, Haocheng Lu, Whitney E. Hornsby, Bradley Crone, Gao T. Wang, Dong-chuan Guo, Anoop K. Sendamarai, Poornima Devineni, Maoxuan Lin, Wei Zhou, Sarah E. Graham, Brooke N. Wolford, Ida Surakka, Zhenguo Wang, Lin Chang, Jifeng Zhang, Michael Mathis, Chad M. Brummett, Tori L. Melendez, Michael J. Shea, Karen Meekyong Kim, G. Michael Deeb, Himanshu J. Patel, Jonathan Eliason, Kim A. Eagle, Bo Yang, Santhi K. Ganesh, Ben Brumpton, Bjorn Olav Asvold, Anne Heidi Skogholt, Kristian Hveem, Saiju Pyarajan, Derek Klarin, Philip S. Tsao, Scott M. Damrauer, Suzanne M. Leal, Dianna M. Milewicz, Y. Eugene Chen, Minerva T. Garcia-Barrio, Cristen J. Willer
Summary: A genome-wide scan identified a significant association of TCF7L2 variants with thoracic aortic aneurysm (TAA), which is the strongest known genetic risk factor for TAA. Although different causal variants may exist for TAA and type 2 diabetes at this locus, an opposite direction of effect was observed. Additionally, increased expression of TCF7L2 was found to be associated with TAA disease risk through promoting vascular smooth muscle cell apoptosis.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Genetics & Heredity
Derek Klarin, Poornima Devineni, Anoop K. Sendamarai, Anthony R. Angueira, Sarah E. Graham, Ying H. Shen, Michael G. Levin, James P. Pirruccello, Ida Surakka, Purushotham R. Karnam, Tanmoy Roychowdhury, Yanming Li, Minxian Wang, Krishna G. Aragam, Kaavya Paruchuri, Verena Zuber, Gabrielle E. Shakt, Noah L. Tsao, Renae L. Judy, Ha My T. Vy, Shefali S. Verma, Daniel J. Rader, Ron Do, Joseph E. Bavaria, Girish N. Nadkarni, Marylyn D. Ritchie, Stephen Burgess, Dong-chuan Guo, Patrick T. Ellinor, Scott A. LeMaire, Dianna M. Milewicz, Cristen J. Willer, Pradeep Natarajan, Philip S. Tsao, Saiju Pyarajan, Scott M. Damrauer
Summary: We conducted a GWAS of TAAD and identified 21 risk loci, providing evidence that TAAD is different from other vascular diseases. Our findings suggest that TAAD is not solely inherited through large effect size protein-altering variants and has a genetic architecture similar to other complex traits.