All publications

2023

C. Bei, J. Zhu, P. H. Culviner, E. J. Rubin, S. M. Fortune, Q. Gao* & Q. Liu*. Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis. bioRxiv (2023). DOI: 10.1101/2023.08.20.553992

M.-Z. Deng†, Q. Liu†, S.-J. Cui, H. Fu, M. Gan, Y.-Y. Xu, X. Cai, W. Sha, G.-P. Zhao, S. M. Fortune & L.-D. Lyu. Mycobacterial DnaQ is an Alternative Proofreader Ensuring DNA Replication Fidelity. bioRxiv, 2023.2010.2024.563508 (2023). DOI: 10.1101/2023.10.24.563508

S. Stanley, X. Wang, Q. Liu, Y. Y. Kwon, A. M. Frey, N. D. Hicks, A. J. Vickers, S. Hui & S. M. Fortune*. Ongoing evolution of the Mycobacterium tuberculosis lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressure. bioRxiv (2023). DOI: 10.1101/2023.10.09.561592 S.

Stanley, C. N. Spaulding, Q. Liu, M. R. Chase, D. T. M. Ha, P. V. K. Thai, N. H. Lan, D. D. A. Thu, N. L. Quang, J. Brown, N. D. Hicks, X. Wang, M. Marin, N. C. Howard, A. J. Vickers, W. M. Karpinski, M. C. Chao, M. R. Farhat, M. Caws, S. J. Dunstan, N. T. T. Thuong & S. M. Fortune*. High-throughput phenogenotyping of Mycobacteria tuberculosis clinical strains reveals bacterial determinants of treatment outcomes. bioRxiv (2023). DOI: 10.1101/2023.04.09.536166

C. Zhu, T. Yang, J. Yin, H. Jiang, H. E. Takiff, Q. Gao, Q. Liu* & W. Li*. The Global Success of Mycobacterium tuberculosis Modern Beijing Family Is Driven by a Few Recently Emerged Strains. Microbiol Spectr 11, e0333922 (2023).

Y. Chen, Q. Jiang, Q. Liu, M. Gan, H. E. Takiff & Q. Gao*. Whole-Genome Sequencing Exhibits Better Diagnostic Performance than Variable-Number Tandem Repeats for Identifying Mixed Infections of Mycobacterium tuberculosis. Microbiol Spectr 11, e0357022 (2023).

Q. Jiang, H. C. Liu, Q. Liu, J. E. Phelan, F. X. Tao, X. Q. Zhao, J. Wang, J. R. Glynn, H. E. Takiff, T. G. Clark, K. L. Wan & Q. Gao. The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China. Microbiol Spectr 11, e0399122 (2023).

2022

Q. Liu†, J. Zhu†, C. L. Dulberger, S. Stanley, S. Wilson, E. S. Chung, X. Wang, P. Culviner, Y. J. Liu, N. D. Hicks, G. H. Babunovic, S. R. Giffen, B. B. Aldridge, E. C. Garner, E. J. Rubin, M. C. Chao & S. M. Fortune. Tuberculosis treatment failure associated with evolution of antibiotic resilience. Science, 378, 1111-1118 (2022).

Y. Luo†, C. Huang†, Q. Liu†, N. Howard, X. Li, J. Zhu, T. Amariuta, S. Asgari, K. Ishigaki, R. Calderon, D. B. Moody, L. Lecca, S. M. Fortune, M. B. Murray & S. Raychaudhuri. A FLOT1 host regulatory allele is associated with a recently expanded Mtb clade in patients with tuberculosis. medRxiv, 2022.2002.2007.22270622 (2022).

T. Yang, M. Gan, Q. Liu, W. Liang, Q. Tang, G. Luo, T. Zuo, Y. Guo, C. Hong, Q. Li, W. Tan & Q. Gao. SAM-TB: a whole genome sequencing data analysis website for detection of Mycobacterium tuberculosis drug resistance and transmission. Brief Bioinform 23 (2022).

H. Wang, X. Rong, G. Zhao, Y. Zhou, Y. Xiao, D. Ma, X. Jin, Y. Wu, Y. Yan, H. Yang, Y. Zhou, M. Qian, C. Niu, X. Hu, D. Q. Li, Q. Liu, Y. Wen, Y. Z. Jiang, C. Zhao & Z. M. Shao. The microbial metabolite trimethylamine N-oxide promotes antitumor immunity in triple-negative breast cancer. Cell Metabolism 34, 581-594 e588 (2022).

J. Tong, L. Meng, C. Bei, Q. Liu, M. Wang, T. Yang, H. E. Takiff, S. Zhang, Q. Gao, C. Wang & B. Yan. Modern Beijing sublineage of Mycobacterium tuberculosis shift macrophage into a hyperinflammatory status. Emerg Microbes Infect 11, 715-724 (2022).

F. G. Tomasi, A. M. J. Hall, J. T. P. Schweber, C. L. Dulberger, K. McGowen, Q. Liu, S. M. Fortune, S. Helaine & E. J. Rubin. A tRNA-Acetylating Toxin and Detoxifying Enzyme in Mycobacterium tuberculosis. Microbiol Spectr 10, e0058022 (2022).

R. Pi, X. Chen, J. Meng, Q. Liu, Y. Chen, C. Bei, C. Wang & Q. Gao. Drug Degradation Caused by mce3R Mutations Confers Contezolid (MRX-I) Resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother, e0103422 (2022).

Y. Chen, Q. Liu, H. E. Takiff & Q. Gao. Comprehensive genomic analysis of Mycobacterium tuberculosis reveals limited impact of high-fitness genotypes on MDR-TB transmission. J Infect 85, 49-56 (2022).

A. F. Carey, X. Wang, N. Cicchetti, C. N. Spaulding, Q. Liu, F. Hopkins, J. Brown, J. Sixsmith, R. Sutiwisesak, S. M. Behar, T. R. Ioerger & S. M. Fortune. Multiplexed Strain Phenotyping Defines Consequences of Genetic Diversity in Mycobacterium tuberculosis for Infection and Vaccination Outcomes. mSystems 7, e0011022 (2022).

2021

Q. Liu†*, H. Liu†, L. Shi, M. Gan, X. Zhao, L. D. Lyu, H. E. Takiff, K. Wan & Q. Gao. Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau. Proc Natl Acad Sci U S A 118 (2021).

Y. Chen†, L. Ji†, Q. Liu†, J. Li, C. Hong, Q. Jiang, M. Gan, H. E. Takiff, W. Yu, W. Tan & Q. Gao. Lesion Heterogeneity and Long-Term Heteroresistance in Multidrug-Resistant Tuberculosis. J Infect Dis 224, 889-893 (2021).

W. Dong, X. Nie, H. Zhu, Q. Liu, K. Shi, L. You, Y. Zhang, H. Fan, B. Yan, C. Niu, L. D. Lyu, G. P. Zhao & C. Yang. Mycobacterial fatty acid catabolism is repressed by FdmR to sustain lipogenesis and virulence. Proc Natl Acad Sci U S A 118 (2021).

T. Yang, Y. Wang, Q. Liu, Q. Jiang, C. Hong, L. Wu, S. Li, C. Zhu, H. Takiff, W. Yu, W. Tan & Q. Gao. A population-based genomic epidemiological study of the source of tuberculosis infections in an emerging city: Shenzhen, China. Lancet Reg Health West Pac 8, 100106 (2021).

F. Menardo, L. K. Rutaihwa, M. Zwyer, S. Borrell, I. Comas, E. C. Conceição, M. Coscolla, H. Cox, M. Joloba, H. Y. Dou, J. Feldmann, L. Fenner, J. Fyfe, Q. Gao, D. García de Viedma, A. L. Garcia-Basteiro, S. M. Gygli, J. Hella, H. Hiza, L. Jugheli, L. Kamwela, M. Kato-Maeda, Q. Liu, S. D. Ley, C. Loiseau, S. Mahasirimongkol, B. Malla, P. Palittapongarnpim, N. Rakotosamimanana, V. Rasolofo, M. Reinhard, K. Reither, M. Sasamalo, R. Silva Duarte, C. Sola, P. Suffys, K. V. Batista Lima, D. Yeboah-Manu, C. Beisel, D. Brites & S. Gagneux. Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim. F1000Res 10, 60 (2021).

T. Luo, P. Xu, Y. Zhang, J. L. Porter, M. Ghanem, Q. Liu, Y. Jiang, J. Li, Q. Miao, B. Hu, B. P. Howden, J. A. M. Fyfe, M. Globan, W. He, P. He, Y. Wang, H. Liu, H. E. Takiff, Y. Zhao, X. Chen, Q. Pan, M. A. Behr, T. P. Stinear & Q. Gao. Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii. Nat Commun 12, 2491 (2021).

Y. Chen, Q. Jiang, J. Zou, T. Yang, Q. Liu, G. Luo, M. Gan, Y. Jiang, H. E. Takiff, L. Lu & Q. Gao. Deep whole-genome sequencing reveals no evidence for heteroresistance influencing treatment outcomes among drug-susceptible tuberculosis patients. Tuberculosis (Edinb) 130, 102120 (2021).

2020

Q. Liu†, J. Wei†, Y. Li†, M. Wang, J. Su, Y. Lu, M. G. López, X. Qian, Z. Zhu, H. Wang, M. Gan, Q. Jiang, Y. X. Fu, H. E. Takiff, I. Comas, F. Li, X. Lu, S. M. Fortune & Q. Gao. Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments. Science Advances 6, eaba4901 (2020).

Q. Liu†, Q. Liu†, H. Meng, H. Lv, Y. Liu, J. Liu, H. Wang, L. He, J. Qin, Y. Wang, Y. Dai, M. Otto & M. Li. Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production. Cell Host Microbe 27, 68-78 e65 (2020).

J. Tong†, Q. Liu†, J. Wu, Y. Jiang, H. E. Takiff & Q. Gao. Mycobacterium tuberculosis strains of the modern Beijing sublineage excessively accumulate triacylglycerols in vitro. Tuberculosis (Edinb) 120, 101892 (2020).

K. S. Walter, C. Colijn, T. Cohen, B. Mathema, Q. Liu, J. Bowers, D. M. Engelthaler, A. Narechania, D. Lemmer, J. Croda & J. R. Andrews. Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences. Microb Genom 6 (2020).

R. Pi, Q. Liu, H. E. Takiff & Q. Gao. Fitness Cost and Compensatory Evolution in Levofloxacin-Resistant Mycobacterium aurum. Antimicrob Agents Chemother 64 (2020).

Q. Jiang, Q. Liu, L. Ji, J. Li, Y. Zeng, L. Meng, G. Luo, C. Yang, H. E. Takiff, Z. Yang, W. Tan, W. Yu & Q. Gao. Citywide Transmission of Multidrug-resistant Tuberculosis Under China's Rapid Urbanization: A Retrospective Population-based Genomic Spatial Epidemiological Study. Clin Infect Dis 71, 142-151 (2020).

N. D. Hicks, S. R. Giffen, P. H. Culviner, M. C. Chao, C. L. Dulberger, Q. Liu, S. Stanley, J. Brown, J. Sixsmith, I. D. Wolf & S. M. Fortune. Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis. PLoS Pathog 16, e1009063 (2020).

2019

R. Pi†, Q. Liu†, Q. Jiang & Q. Gao. Characterization of linezolid-resistance-associated mutations in Mycobacterium tuberculosis through WGS. J Antimicrob Chemother 74, 1795-1798 (2019).

C. J. Meehan, G. A. Goig, T. A. Kohl, L. Verboven, A. Dippenaar, M. Ezewudo, M. R. Farhat, J. L. Guthrie, K. Laukens, P. Miotto, B. Ofori-Anyinam, V. Dreyer, P. Supply, A. Suresh, C. Utpatel, D. van Soolingen, Y. Zhou, P. M. Ashton, D. Brites, A. M. Cabibbe, B. C. de Jong, M. de Vos, F. Menardo, S. Gagneux, Q. Gao, T. H. Heupink, Q. Liu, C. Loiseau, L. Rigouts, T. C. Rodwell, E. Tagliani, T. M. Walker, R. M. Warren, Y. Zhao, M. Zignol, M. Schito, J. Gardy, D. M. Cirillo, S. Niemann, I. Comas & A. Van Rie. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol 17, 533-545 (2019).

2018

Q. Liu, A. Ma, L. Wei, Y. Pang, B. Wu, T. Luo, Y. Zhou, H. X. Zheng, Q. Jiang, M. Gan, T. Zuo, M. Liu, C. Yang, L. Jin, I. Comas, S. Gagneux, Y. Zhao, C. S. Pepperell & Q. Gao. China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis. Nature Ecology Evolution 2, 1982-1992 (2018). Comments in “K. I. Bos. TB's Chinese travels. Nature Ecology Evolution 2, 1842-1843 (2018).”

Q. Liu†, T. Zuo†, P. Xu, Q. Jiang, J. Wu, M. Gan, C. Yang, R. Prakash, G. Zhu, H. E. Takiff & Q. Gao. Have compensatory mutations facilitated the current epidemic of multidrug-resistant tuberculosis? Emerg Microbes Infect 7, 98 (2018).

Y. Wang†, Q. Liu†, Q. Liu†, Q. Gao, H. Lu, H. Meng, Y. Xie, Q. Huang, X. Ma, H. Wang, J. Qin, Q. Li, T. Li, Q. Xia & M. Li. Phylogenetic analysis and virulence determinant of the host-adapted Staphylococcus aureus lineage ST188 in China. Emerg Microbes Infect 7, 45 (2018).

C. Yang, L. Lu, J. L. Warren, J. Wu, Q. Jiang, T. Zuo, M. Gan, M. Liu, Q. Liu, K. DeRiemer, J. Hong, X. Shen, C. Colijn, X. Guo, Q. Gao & T. Cohen. Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis. Lancet Infect Dis 18, 788-795 (2018).

Q. Jiang, L. Lu, J. Wu, C. Yang, R. Prakash, T. Zuo, Q. Liu, J. Hong, X. Guo & Q. Gao. Assessment of tuberculosis contact investigation in Shanghai, China: An 8-year cohort study. Tuberculosis (Edinb) 108, 10-15 (2018). C. R. Consortium. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. N Engl J Med 379, 1403-1415 (2018). 

2017

A. Trauner†, Q. Liu†, L. E. Via, X. Liu, X. Ruan, L. Liang, H. Shi, Y. Chen, Z. Wang, R. Liang, W. Zhang, W. Wei, J. Gao, G. Sun, D. Brites, K. England, G. Zhang, S. Gagneux, C. E. Barry, 3rd & Q. Gao. The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy. Genome Biology 18, 71 (2017). Comments in “S. A. Christenson. The path of least antibiotic resistance. Science Translational Medicine 9 (2017).”

C. Yang, T. Luo, X. Shen, J. Wu, M. Gan, P. Xu, Z. Wu, S. Lin, J. Tian, Q. Liu, Z. Yuan, J. Mei, K. DeRiemer & Q. Gao. Transmission of multidrug-resistant Mycobacterium tuberculosis in Shanghai, China: a retrospective observational study using whole-genome sequencing and epidemiological investigation. Lancet Infect Dis 17, 275-284 (2017).

C. A. Nsofor, Q. Jiang, J. Wu, M. Gan, Q. Liu, T. Zuo, G. Zhu & Q. Gao. Transmission is a Noticeable Cause of Resistance Among Treated Tuberculosis Patients in Shanghai, China. Sci Rep 7, 7691 (2017).

2016

Q. Liu, T. Luo, X. Dong, G. Sun, Z. Liu, M. Gan, J. Wu, X. Shen & Q. Gao. Genetic features of Mycobacterium tuberculosis modern Beijing sublineage. Emerg Microbes Infect 5, e14 (2016).

D. Stucki, D. Brites, L. Jeljeli, M. Coscolla, Q. Liu, A. Trauner, L. Fenner, L. Rutaihwa, S. Borrell, T. Luo, Q. Gao, M. Kato-Maeda, M. Ballif, M. Egger, R. Macedo, H. Mardassi, M. Moreno, G. Tudo Vilanova, J. Fyfe, M. Globan, J. Thomas, F. Jamieson, J. L. Guthrie, A. Asante-Poku, D. Yeboah-Manu, E. Wampande, W. Ssengooba, M. Joloba, W. Henry Boom, I. Basu, J. Bower, M. Saraiva, S. E. G. Vaconcellos, P. Suffys, A. Koch, R. Wilkinson, L. Gail-Bekker, B. Malla, S. D. Ley, H. P. Beck, B. C. de Jong, K. Toit, E. Sanchez-Padilla, M. Bonnet, A. Gil-Brusola, M. Frank, V. N. Penlap Beng, K. Eisenach, I. Alani, P. Wangui Ndung'u, G. Revathi, F. Gehre, S. Akter, F. Ntoumi, L. Stewart-Isherwood, N. E. Ntinginya, A. Rachow, M. Hoelscher, D. M. Cirillo, G. Skenders, S. Hoffner, D. Bakonyte, P. Stakenas, R. Diel, V. Crudu, O. Moldovan, S. Al-Hajoj, L. Otero, F. Barletta, E. Jane Carter, L. Diero, P. Supply, I. Comas, S. Niemann & S. Gagneux. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nature Genetics 48, 1535-1543 (2016).

M. Gan, Q. Liu, C. Yang, Q. Gao & T. Luo. Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis. PLoS One 11, e0159029 (2016).

2015

Q. Liu, L. E. Via, T. Luo, L. Liang, X. Liu, S. Wu, Q. Shen, W. Wei, X. Ruan, X. Yuan, G. Zhang, C. E. Barry, 3rd & Q. Gao. Within patient microevolution of Mycobacterium tuberculosis correlates with heterogeneous responses to treatment. Sci Rep 5, 17507 (2015). F1000 Recommended.

T. Luo, I. Comas, D. Luo, B. Lu, J. Wu, L. Wei, C. Yang, Q. Liu, M. Gan, G. Sun, X. Shen, F. Liu, S. Gagneux, J. Mei, R. Lan, K. Wan & Q. Gao. Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. Proc Natl Acad Sci U S A 112, 8136-8141 (2015).

2014

J. Li, X. Gao, T. Luo, J. Wu, G. Sun, Q. Liu, Y. Jiang, Y. Zhang, J. Mei & Q. Gao. Association of gyrA/B mutations and resistance levels to fluoroquinolones in clinical isolates of Mycobacterium tuberculosis. Emerg Microbes Infect 3, e19 (2014).

2013

Q. Liu, T. Luo, J. Li, J. Mei & Q. Gao. Triplex real-time PCR melting curve analysis for detecting Mycobacterium tuberculosis mutations associated with resistance to second-line drugs in a single reaction. J Antimicrob Chemother 68, 1097-1103 (2013).

† Equal contributions
*Corresponding authors