Qingyun Liu, PhD

Research Interests

Keywords:

Bacterial evolution; population genomics; infectious diseases; Mycobacterium tuberculosis; Mycobacterium abscessus; nontuberculous mycobacteria; antibiotic resistance; treatment outcomes; transmissibility; bacterial physiology

Lab Website

I am a microbiologist and geneticist leading a research program that integrates population genomics, clinical cohorts, and experimental microbiology to understand how bacterial pathogens evolve in real-world human infections. We focus on the genetic and physiological mechanisms that drive drug resistance, treatment failure, transmissibility, and persistence in Mycobacterium tuberculosis, Mycobacterium abscessus, and other emerging bacterial pathogens.

Our work begins with large-scale genomic analyses of clinical isolates to identify bacterial variants and pathways associated with important disease phenotypes, including antibiotic resistance, transmission success, and poor treatment outcomes. We then use high-throughput phenotyping, microbial genetics, and infection models to define the functional consequences of these evolved changes and to establish causal mechanisms.

A major goal of the lab is to uncover bacterial vulnerabilities that can be translated into improved diagnostics, therapeutics, vaccines, and public health interventions. More broadly, we aim to understand how pathogen evolution shapes infectious disease emergence and clinical outcomes.

Current Research Areas

1. Bacterial determinants of Mtb transmissibility
2. Evolution and mechanisms of drug resistance in Mtb and M. abscessus
3. Bacterial predictors of treatment outcomes in M. abscessus infection
4. High-throughput phenotyping of clinically evolved bacterial traits
5. Translation of pathogen genomics into diagnostics and intervention strategies

Training Program Affiliations:

• Bioinformatics and Computational Biology
• Genetics and Molecular Biology

Publications (Selected)

• Yang T, Beach KE, Zhu C, Gan M, Wang W, Zhou H, Peng L, Wang S, Cai L, Li W, Davis JB, Cicchetti N, Slechta ES, Barker A, Shakir SM, Carey AF, Liu Q. Genomic analysis of global Mycobacterium abscessus isolates reveals ongoing evolution of drug-resistance-associated genes. J Infect Dis. 2025;231(5):1150–1154.
• Bei C, Zhu J, Culviner PH, Gan M, Rubin EJ, Fortune SM, Gao Q, Liu Q. Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis. Nat Commun. 2024;15(1):3088. PMID: 38600064; PMCID: PMC11006872.
• Liu Q, Zhu J, Dulberger CL, Stanley S, Wilson S, Chung ES, Wang X, Culviner P, Liu YJ, Hicks ND, Babunovic GH, Giffen SR, Aldridge BB, Garner EC, Rubin EJ, Chao MC, Fortune SM. Tuberculosis treatment failure associated with evolution of antibiotic resilience. Science. 2022;378:1111–1118.
• Liu Q, Liu H, Shi L, Gan M, Zhao X, Lyu LD, Takiff HE, Wan K, Gao Q. Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau. Proc Natl Acad Sci U S A. 2021;118.
• Liu Q, Wei J†, Li Y†, Wang M, Su J, Lu Y, López MG, Qian X, Zhu Z, Wang H, Gan M, Jiang Q, Fu YX, Takiff HE, Comas I, Li F, Lu X, Fortune SM, Gao Q. Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments. Sci Adv. 2020;6:eaba4901.
• Liu Q, Liu Q, Meng H, Lv H, Liu Y, Liu J, Wang H, He L, Qin J, Wang Y, Dai Y, Otto M, Li M. Staphylococcus epidermidis contributes to healthy maturation of the nasal microbiome by stimulating antimicrobial peptide production. Cell Host Microbe. 2020;27:68–78.e5.
• Liu Q, Ma A, Wei L, Pang Y, Wu B, Luo T, Zhou Y, Zheng HX, Jiang Q, Gan M, Zuo T, Liu M, Yang C, Jin L, Comas I, Gagneux S, Zhao Y, Pepperell CS, Gao Q. China’s tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis. Nat Ecol Evol. 2018;2:1982–1992.
• Trauner A, Liu Q, Via LE, Liu X, Ruan X, Liang L, Shi H, Chen Y, Wang Z, Liang R, Zhang W, Wei W, Gao J, Sun G, Brites D, England K, Zhang G, Gagneux S, Barry CE III, Gao Q. The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy. Genome Biol. 2017;18:71.

Qingyun Liu in UNC Genetics News