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Microbiology Logo Microbiology & Immunology
Te Tari Moromoroiti me te Ārai Mate

Dr Htin Lin Aung

Research interests:

Antimicrobial resistance, health inequalities, genome sequencing, clinical microbiology, molecular microbiology, molecular diagnostics, molecular epidemiology, host-pathogen interaction, global public health

Current research:

Antimicrobial Resistance (AMR) is a global public health emergency. Drug-resistant tuberculosis (TB) including multidrug-resistant (MDR-TB) and extensively drug-resistant (XDR-TB) is the main cause of deaths related to AMR. In addition, TB disproportionally affects socio-economically disadvantaged individuals and communities across the world. 

Using TB as an examplar, our research goal is to tackle health inequalities and AMR with a transdisciplinary, integrative approach employing cutting-edge technologies such as next- and third generation whole-genome sequencing (Illumina and Oxford Nanopore).

Research in my group is focused on:

1. Characterisation of genetic diversity and population structure of Mycobacterium tuberculosis (Mtb) in low- and high TB burden settings  

2. Decoding the genetic basis of NZ unique Mycobacterium tuberculosis (Mtb) strains for their virulence and host specificity in Māori and Pasifika 

3. Identification of the genetic basis for resistance in Mtb and the consequent development of diagnostics and anti-TB drugs

4. Investigating the genomic landscape of Mycobacterium bovis, a causative agent of bovine TB, at the wildlife-livestock-human interface using a One Health approach

5. Understanding the molecular epidemiology of TB transmission in the populations/communities for effective policy interventions

6. Engagement with affected communities to understand perceptions of TB and barriers to care


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Aung Lab 

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Lab Lunchtime Run

Tackling tuberculosis in the lab and on the frontline

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Tuberculosis Clinic, Yangon, Myanmar

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 Myanmar Team at the National Tuberculosis Reference Laboratory

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Next-generation illumina iSeq sequencing at the National Tuberculosis Reference Laboratory, Myanmar

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Third-generation long-read Nanopore sequencing

LD Export

Community Engagement

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 With Māori and Pasifika students from the Department of Microbiology and Immunology

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 With Māori students at Wairoa College, Hawkes Bay 


Pacific Intermediate Sciences Holiday Programme at the Department of Microbiology and Immunology


Christensen P, Cinzah R, Suwanarusk R, Chua A, Kaneko O, Kyle D, Aung HL, Matheson J, Bifani P, Renia L, Cook GM, Snounou G, and Russell B. Extended blood stage sensitivity profiles of Plasmodium vivax to doxycycline and tafenoquine using Plasmodium cynomolgi as a model. Antimicrobial Agents and Chemotherapy (In Press).

Tun T, Baleivanualala SC, Erdmann MB, Gimenez G, Aung HL. (2023) An extensively drug-resistant Pseudomonas aeruginosa isolate from Myanmar. Journal of Global Antimicrobial Resistance 2023 Nov 20;36:1-3. doi: 10.1016/j.jgar.2023.11.004.

Phyu AN, Aung ST, Palittapongarnpim P, Htet KKK, Mahasirimongkol S, Ruangchai W, Jaemsai B, Aung HL, Maung HMW, Chaiprasert A, Pungrassami P, Chongsuvivatwong V.  (2023) Genomic Sequencing Profiles of Mycobacterium tuberculosis in Mandalay Region, Myanmar. Trop Med Infect Dis. 8(4):239. doi: 10.3390/tropicalmed8040239.

Aung ST, Nyunt WW, Moe MM, Aung HL, Lwin TD (2022) The fourth national tuberculosis prevalence survey in Myanmar. PLOS Global Public Health doi:10.1371/journal.pgph.0000588

Mulholland CV, Gimenez G, Williamson A, Mackenzie S, Thorpe D, Karalus N, Cursons RT, Playlet VM, Roberts SA, Cook GM, Arcus VL, Aung HL (2022) Complete genome sequence of a New Zealand Mycobacterium tuberculosis strain responsible for ongoing transmission over the last 30 years. Microbiology Resource Announcement  doi: 10.1128/mra.00781-22

Phyu AN, Aung ST, Palittapongarnpim P, Htet KKK, Mahasirimongkol S, Aung HL, Chaiprasert A, Chongsuvivatwong V. (2022) Distribution of Mycobacterium tuberculosisLineages and Drug Resistance in Upper Myanmar. Trop Med Infect Dis. 7(12):448. doi: 10.3390/tropicalmed7120448

Christensen P, Racklyeft A, Ward KE, Matheson J, Suwanarusk R, Chua ACY, Kaneko O, Aung HL, Rénia L, Amanzougaghene N, Magneron V, Lemaitre J, Le Grand R, Kyle D, Bifani P, Cook GM, Snounou G, Russell B (2022) Improving in vitro continuous cultivation of Plasmodium cynomolgi, a model for P. vivax. Parasitology International 89:102589. doi: 10.1016/j.parint.2022.102589.

Aung HL, Nyunt WW, Fong Y, Biggs PJ, Winkworth RC, Lockhart PJ, Yeo TW, Hill PC, Cook GM and Aung ST (2021) Genomic profiling of Mycobacterium tuberculosis strains in Myanmar: urgent need for expanded resistance testing and new oral regimens. Emerging Infectious Diseases 27 (11) 2848

Aung ST, Thu A, Aung HL, Thu M (2021) Measuring catastrophic costs due to tuberculosis in Myanmar. Tropical Medicine and Infectious Disease 6,130. tropicalmed6030130

Humblestone L, Arnold B, Aung HL (2021) Translating whole-genome-sequence data for drug-resistant Mycobacterium tuberculosis diagnostics in clinics. The New Zealand Medical Journal 134(1533):99-101

Parker HA, Dickerhof N, Forrester L, Ryburn H, Smyth L, Messens J, Aung HL, Cook GM, Kettle AJ, and Hampton MB (2021) Mycobacterium smegmatis resists the bactericidal activity of hypochlorous acid produced in neutrophil phagosomes. Journal of Immunology

McDonald SK, Matisoo-Smith EA, Buckley HR, Walter RK, Aung HL, Collins CJ, Cook GM, Kardailsky O, Krause J and Knapp M (2020) TB or not TB – the conundrum of Pre-European tuberculosis in the Pacific. Philosophical Transactions of the Royal Society B

Maung HMW, Palittapongarnpim P, Aung HL, Surachat K, Nyunt WW, Chongsuvivatwong V (2020) Geno-spatial distribution of Mycobacterium tuberculosis and drug resistance profiles in Myanmar-Thai border area. Tropical Medicine and Infectious Disease

Aung HL, Devine TJ, Mulholland CV, Arcus VL, Cook GM (2019) Tackling tuberculosis in the Indigenous People of New Zealand. The Lancet Public Health

Nyunt WW, Cook GM, Aung HL, Aung ST (2019) Identification of the prevalence of isoniazid resistance without concurrent rifampicin resistance in Myanmar using whole-genome sequencing (WGS) The International Journal of Tuberculosis and Lung Disease 23(10):S502

Aung HL and Devine TJ (2019) Reducing the burden of tuberculosis in Māori, the Indigenous people of New Zealand. The Lancet Global Health

Lee BM, Harold LK, Almeida DV, Afriat-Jurnou L, Aung HL, Forde BM, Hards K, Pidot SJ, Ahmed FH, Mohamed AE, Taylor MC, West NP; Stinear TP, Greening C, Beatson SA, Nuermberger EL, Cook GM, Jackson CJ. (2019) Predicting nitroimidazole antibiotic resistance mutations in Mycobacterium tuberculosis with protein engineering PLoS Pathogens

Mulholland CV, Shockey A, Aung HL, Cursons R, O'Toole R, Gautam S, Brites D, Gagneux S, Roberts SA, Karalus N, Cook GM, Pepperell C, Arcus VL. (2019) Dispersal of Mycobacterium tuberculosis driven by historical European trade in the South Pacific. Frontiers in Microbiology

Aung HL, Nyunt WW, Fong Y, Russell B, Cook GM, Aung ST. (2018) Whole-genome sequencing reveals the evidence of acquired resistance to antituberculosis drugs in Myanmar. Emerging Infectious Diseases doi:10.3201/eid2411.180465  

Htun KS, Fong Y, Kyaw AA, Aung ST, Oo KZ, Zaw T, Lockhart PJ, Russell B, Cook GM, Aung HL, Hlaing TM (2018) Upper Respiratory Tract Microbiota of Patients Living with HIV, HIV/TB and TB from Myanmar. Data in Brief 4;21:354-357

Basu I, Bower JE, Roberts SA, Henderson G, Aung HL, Cook G, Lowe O, Newton S. (2018) Utility of whole-genome sequencing for multidrug-resistant Mycobacterium tuberculosis isolates in a reference TB laboratory in New Zealand. The New Zealand Medical Journal 14;131(1487):15-22

Lu X, Williams Z, Hards K, Tang J, Cheung CY, Aung HL, Wang B, Liu Z, Hu X, Lenaerts A, Woolhiser L, Hastings C, Zhang X, Wang Z, Rhee K, Ding K, Zhang T, Cook GM. (2018) A pyrazolo[1,5-a]pyridine inhibitor of the respiratory cytochrome bcc complex for the treatment of drug-resistant tuberculosis. ACS Infectious Diseases 8;5(2):239-249

Mulholland CV, Thorpe D, Cursons RT, Karalus N, Fong Y, Arcus VL, Cook GM, Aung HL (2018) Evaluation of the Rapid Molecular Diagnostic Test for the New Zealand Mycobacterium tuberculosis Rangipo Strain in a Clinical Setting. The New Zealand Medical Journal 131(1478):70-72

Aung HL, Nyunt WW, Fong Y, Cook GM, Aung ST., (2017) First two extensively drug-resistant tuberculosis cases from Myanmar treated with bedaquiline. Clinical Infectious Diseases 65(3):531-532

Aung HL, Tun T, Nyunt WW, Fong Y, Crump JA, Thinn KK, Aung ST, Cook GM. (2017) Association between mutations in anti-tuberculosis drug resistance-conferring genes and treatment outcomes in Myanmar. Infectious Diseases doi: 10.1080/23744235.2017.1404632

Mortuza R, Aung HL, Taiaroa G, Opel-Reading HK, Kleffmann T, Cook GM, Krause KL(2017) Overexpression of a newly identified D-amino acid transaminase in Mycobacterium smegmatis complements glutamate racemase deletion. Molecular Microbiology 107(2):198-213

Nakatani Y, Opel-Reading HK, Merker M, Machado D, Andres S, Kumar SS, Moradigaravand D, Coll F, Perdigão J, Portugal I, Schön T, Nair D, Devi KRU, Kohl TA, Beckert P, Clark TG, Maphalala G, Khumalo D, Diel R, Klaos K, Aung HL, Cook GM, Parkhill J, Peacock SJ, Swaminathan S, Viveiros M, Niemann S, Krause KL, Köser CU. (2017) Role of alanine racemase mutations in Mycobacterium tuberculosis D-cycloserine resistance. Antimicrobial Agents and Chemotherapy 61(12):e01575-17

Nyunt WW, Aung ST, Cook GM, Aung HL (2017) Evaluation of the MTBDRsltest for detection of second-line resistance in drug-resistant Mycobacterium tuberculosisstrains in Myanmar. Infectious Disease 49:(11-12) 865-866.

Mulholland CV, Ruthe A, Cursons RT, Durrant R, Karalus N, Coley K, Bower J, Permina E, Coleman MJ, Roberts SA, Arcus VL, Cook GM, Aung HL (2017) Rapid Diagnosis of the Mycobacterium tuberculosis Rangipo strain responsible for the largest recurring TB cluster in New Zealand. Diagnostic Microbiology and Infectious Disease 88:138-140

Nyunt WW, Aung ST, Lwin T, Cook GM, Aung HL (2017) First- and second-line anti-tuberculosis drug resistance patterns among previous treatment failure patients in Myanmar. Journal of Global Antimicrobial Resistance 9:34-35.

Aung HL, Tun T, Permina E, Nyunt WW, Aung ST, Thinn KK, Crump JA, Cook GM (2016) Draft genome sequences of the drug-resistant Mycobacterium tuberculosis isolates from Myanmar. Genome Announcements 4: (5).

Petridis M, Vickers C, Robson J, McKenzie JL, Bereza M, Sharrock A, Aung HL, Arcus VL, Cook GM (2016) Structure and function of AmtR in Mycobacterium smegmatis: Implications for post-transcriptional regulation of urea metabolism through a small antisense RNA. Journal of Molecular Biology 428(21):4315-4329.

Tun T, Aye KS, Nyunt WW, Crump JA, Nakajima C, Suzuki Y, Thinn KK, Cook GM, Aung HL (2016) Genotypic diversity of Mycobacterium tuberculosis strains in Myanmar. Infectious Diseases 49(3):237-239.

Tun T, Nyunt WW, Latt KZ, Samaranayaka A, Crump JA, Thinn KK, Cook GM, Aung HL (2016) Drug-resistant tuberculosis among previously treated patients in Yangon, Myanmar. International Journal of Mycobacteriology 5: 366-367.

Aung HL, Tun T, Moradigaravand D, Köser CU, Nyunt WW, Aung ST, Lwin T, Thinn KK, Crump JA, Parkhill J, Peacock SJ, Cook GM, Hill PC (2016) Whole-genome sequencing of multidrug-resistant Mycobacterium tuberculosis isolates from Myanmar. Journal of Global Antimicrobial Resistance 6: 113-117.

Aung HL, Dixon LL, Smith LJ, Sweeney NP, Robson JR, Berney M, Buxton RS, Green J, Cook GM(2015) Novel regulatory roles of cAMP receptor proteins (CRPs) in fast-growing environmental mycobacteria Microbiology161: 648-661.

Aung HL, Samaranayaka CU, Enright R, Beggs KT, Monk BC (2015) Characterisation of the DNA gyrase from the thermophilic eubacterium Thermus thermophiles Protein Expression and Purification 107: 62-67.

Aung HL, Dey D, Janssen PH, Ronimus RS, Cook GM (2015) A high-throughput screening assay for identification of inhibitors of the A1AO-ATP synthase of the rumen methanogen Methanobrevibacter ruminantiumM1 Journal of Microbiological Methods110: 15-1.

Aung HL, Berney M, Cook GM (2014) Hypoxia-activated cytochrome bdexpression in Mycobacterium smegmatisis cAMP receptor protein (CRP)-dependent. Journal of Bacteriology196: 3091-3097.

McMillan DG, Ferguson SA, Dey D, Schröder K, Aung HL, Carbone V, Attwood GT, Ronimus RS, Meier T, Janssen PH, Cook GM (2011) A1Ao-ATP synthase of Methanobrevibacter ruminantium couples sodium ions for ATP synthesis under physiological conditions. The Journal of biological chemistry286: 39882-39892.