Jason Limberis, PhD
Assistant Researcher
Medicine
School of Medicine

My research focusses on the causative agent of tuberculosis, Mycobacterium tuberculosis: I apply a combination of wet work and bioinformatics to investigate genomic and transcriptional associates of drug resistance, clinical outcomes, and patient infectiousness. See www.SemiQuant.com for more information.

Education & Training

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• BSc Hons Molecular Biology Stellenbosch University
• BSc Molecular Biology with Biotechnology Stellenbosch University
• Internship Bioinformatics The Centre for Genomic Regulation
• PhD Medicine University of Cape Town

Interests

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• bioinformatics
• tuberculosis
• infectious diseases
• biosignatures
• epidemiology
• infectivity
• infectiousness
• machine learning

Websites

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• SemiQuant (SemiQuant.com)

Publications (24)

Top publication keywords:
Multiplex Polymerase Chain ReactionDiarylquinolinesMacrophages, AlveolarTuberculosis, Lymph NodeHigh-Throughput Nucleotide SequencingTuberculosis, Multidrug-ResistantLinezolidTuberculosis, PulmonaryMycobacterium tuberculosisRNA, Long NoncodingExtensively Drug-Resistant TuberculosisSequence AnalysisTuberculosisBiological AssayAntitubercular Agents

• Turbolysis: A low-cost, small footprint alternative to commercial bead beaters for cell lysis.
  HardwareX 2024 Limberis JD, Metcalfe JZ
• Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection.
  PLoS pathogens 2024 Zheng W, Chang IC, Limberis J, Budzik JM, Zha BS, Howard Z, Chen L, Ernst JD
• primerJinn: a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and performing in silico PCR.
  BMC bioinformatics 2023 Limberis JD, Metcalfe JZ
• selSeq: A method for the enrichment of non-polyadenylated RNAs including enhancer and long non-coding RNAs for sequencing.
  PloS one 2023 Limberis JD, Nalyvayko A, Ernst JD, Metcalfe JZ
• Bedaquiline resistance in patients with drug-resistant tuberculosis in Cape Town, South Africa: a retrospective longitudinal cohort study.
  The Lancet. Microbe 2023 Derendinger B, Dippenaar A, de Vos M, Huo S, Alberts R, Tadokera R, Limberis J, Sirgel F, Dolby T, Spies C, Reuter A, Folkerts M, Allender C, Lemmer D, Van Rie A, Gagneux S, Rigouts L, Te Riele J, …

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• A simple, single-tube overlapping amplicon-targeted Illumina sequencing assay.
  PloS one 2023 Limberis JD, Nalyvayko A, Ernst JD, Metcalfe JZ
• primerJinn - a tool for rationally designing multiplex PCR primer sets and in silico PCR.
  Research square 2023 Limberis JD, Metcalfe JZ
• Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection.
  Research square 2023 Zheng W, Chang IC, Limberis J, Budzik J, Zha BS, Howard Z, Chen L, Ernst J
• Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection.
  bioRxiv : the preprint server for biology 2023 Zheng W, Chang IC, Limberis J, Budzik JM, Zha BS, Howard Z, Chen L, Ernst JD
• Circularization of rv0678 for Genotypic Bedaquiline Resistance Testing of Mycobacterium tuberculosis.
  Microbiology spectrum 2023 Limberis JD, Nalyvayko A, Ernst JD, Metcalfe JZ
• Comparative Performance of Genomic Methods for the Detection of Pyrazinamide Resistance and Heteroresistance in Mycobacterium tuberculosis.
  Journal of clinical microbiology 2021 Whitfield MG, Engelthaler DM, Allender C, Folkerts M, Heupink TH, Limberis J, Warren RM, Van Rie A, Metcalfe JZ
• Genetic variants and their association with phenotypic resistance to bedaquiline in Mycobacterium tuberculosis: a systematic review and individual isolate data analysis.
  The Lancet. Microbe 2021 Ismail N, Rivière E, Limberis J, Huo S, Metcalfe JZ, Warren RM, Van Rie A
• Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis.
  EBioMedicine 2021 Naidoo CC, Nyawo GR, Sulaiman I, Wu BG, Turner CT, Bu K, Palmer Z, Li Y, Reeve BWP, Moodley S, Jackson JG, Limberis J, Diacon AH, van Helden PD, Clemente JC, Warren RM, Noursadeghi M, Segal LN, Theron…
• Bacterial and host determinants of cough aerosol culture positivity in patients with drug-resistant versus drug-susceptible tuberculosis.
  Nature medicine 2020 Theron G, Limberis J, Venter R, Smith L, Pietersen E, Esmail A, Calligaro G, Te Riele J, de Kock M, van Helden P, Gumbo T, Clark TG, Fennelly K, Warren R, Dheda K
• A Human Lung Challenge Model to Evaluate the Safety and Immunogenicity of PPD and Live Bacillus Calmette-Guérin.
  American journal of respiratory and critical care medicine 2020 Davids M, Pooran A, Hermann C, Mottay L, Thompson F, Cardenas J, Gu J, Koeuth T, Meldau R, Limberis J, Gina P, Srivastava S, Calder B, Esmail A, Tomasicchio M, Blackburn J, Gumbo T, Dheda K
• Differential RD-1-specific IFN-γ host responses to diverse Mycobacterium tuberculosis strains in HIV-uninfected persons may be explained by genotypic variation in the ESX-1 region.
  International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2020 Tomasicchio M, Limberis J, van der Merwe R, Jacobson R, Meldau R, Theron G, Nicol M, Warren R, Dheda K
• A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic.
  BMC medicine 2020 Klopper M, Heupink TH, Hill-Cawthorne G, Streicher EM, Dippenaar A, de Vos M, Abdallah AM, Limberis J, Merker M, Burns S, Niemann S, Dheda K, Posey J, Pain A, Warren RM
• A regimen containing bedaquiline and delamanid compared to bedaquiline in patients with drug-resistant tuberculosis.
  The European respiratory journal 2020 Olayanju O, Esmail A, Limberis J, Dheda K
• Same-Day Tools, Including Xpert Ultra and IRISA-TB, for Rapid Diagnosis of Pleural Tuberculosis: a Prospective Observational Study.
  Journal of clinical microbiology 2019 Meldau R, Randall P, Pooran A, Limberis J, Makambwa E, Dhansay M, Esmail A, Dheda K
• Linezolid interruption in patients with fluoroquinolone-resistant tuberculosis receiving a bedaquiline-based treatment regimen.
  International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2019 Olayanju O, Esmail A, Limberis J, Gina P, Dheda K
• Long-term bedaquiline-related treatment outcomes in patients with extensively drug-resistant tuberculosis from South Africa.
  The European respiratory journal 2018 Olayanju O, Limberis J, Esmail A, Oelofse S, Gina P, Pietersen E, Fadul M, Warren R, Dheda K
• Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study.
  The Lancet. Respiratory medicine 2017 Dheda K, Limberis JD, Pietersen E, Phelan J, Esmail A, Lesosky M, Fennelly KP, Te Riele J, Mastrapa B, Streicher EM, Dolby T, Abdallah AM, Ben-Rached F, Simpson J, Smith L, Gumbo T, van Helden P, …
• Selected questions and controversies about bedaquiline: a view from the field.
  The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 2016 Dheda K, Esmail A, Limberis J, Maartens G
• Xpert MTB/RIF Results in Patients With Previous Tuberculosis: Can We Distinguish True From False Positive Results?
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Theron G, Venter R, Calligaro G, Smith L, Limberis J, Meldau R, Chanda D, Esmail A, Peter J, Dheda K