GEMS 2027 Thematic Cluster: A Multi-Scale Investigation of Climate-Associated Antimicrobial Resistance Dynamics across Molecular, Community and Clinical Dimensions.

Antimicrobial resistance (AMR) and climate change represent two converging global health emergencies, yet the biological and epidemiological pathways connecting them remain poorly characterised. This cluster addresses that gap through three independently executable projects that together build a coherent, multi-scale program of evidence linking climate exposures to AMR dynamics across molecular, community and clinical settings.

Impact: These projects generate the foundational scientific evidence needed to embed climate adaptation into AMR surveillance frameworks, stewardship programmes, and public health policy.

Note: The projects listed below represent three indicative topics within this thematic cluster. If you wish to propose an alternative research topic aligned with this cluster, please consult the designated main supervisor to secure their agreement prior to submitting your application.

The candidate selection criteria for Projects 1 and 3 prioritize local candidates best equipped to manage on-the-ground community engagement, local hospital operations, and multi-scale data collection.

Project 1 (Jeffrey Cheah School of Medicine and Health Sciences )

Shotgun Metagenomic Profiling of Seasonal and Climatic Effects on Gut Microbiome and Resistome Dynamics in a Community Cohort

Climate change and extreme weather events are increasingly recognised as drivers of antimicrobial resistance (AMR), yet their influence on the human gut microbiome and resistome remains poorly understood.

This project will engage a community-based cohort to investigate climate-associated changes in gut microbial composition and AMR gene dynamics longitudinally. Serial stool samples will be collected from community participants and matched for sociodemographic and clinical factors.

Shotgun metagenomic sequencing will be used to characterise gut microbiome and resistome. Metagenomic data will be integrated with open-source meteorological data. The outcome from this study will generate foundational evidence to inform AMR surveillance strategies and the design of climate-responsive public health interventions.

Selection Criteria

Essential Criteria

  • Academic Qualifications: Bachelor’s degree requiring at least four years of full-time study with First Class Honours (H1) or a Master’s degree by research (H2A equivalent or CGPA ≥ 3.50) in Bioinformatics, Computational Biology, Genomics, Microbiology, or a closely related discipline from a recognized university.
  • English Language Proficiency: Meets Monash Graduate Education English Language Proficiency requirements (e.g., IELTS minimum overall score of 6.5 with no individual band below 6.0, or TOEFL/PTE equivalent).
  • Core Technical Competencies: Demonstrated experience with high-throughput sequencing data analysis and proficiency in Unix/Linux command-line environments and statistical programming (R or Python).
  • Residency & Field Access: Malaysian Citizenship or Permanent Residency (strongly desired due to the operational demands of longitudinal community cohort recruitment, local fieldwork coordination, and participant retention).

Preferred Criteria

  • Language Proficiency: Fluency in Malay language (spoken and written) to facilitate direct engagement and matched sociodemographic data collection with local community participants.
  • Sample Handling & Data Management: Hands-on experience in managing human biological specimens (stool) and handling multivariate epidemiological datasets.

For enquiries, please contact Dr Polly Yap 

For more information about this project, please visit our GEMS website.

How to Apply

When you apply for admission into your preferred degree program you will be able to select your scholarship type. No separate application is required.

By clicking on a course, you will be directed to further information, including details on ‘How to Apply’.

However, before applying for a GEMS, it is recommended that you first contact the main supervisor for this GEMS research topic. Please provide details of your academic background and achievements to the supervisor so that they can assess your suitability for the GEMS research topic you are interested in.

Main Supervisor (Malaysia): Dr Polly Yap

Associate Supervisor (Malaysia): Dr Vengadesh Letchumanan, Assoc. Prof. Chong Chun Wie

Associate Supervisor (Australia): Prof. Anton Peleg, Dr Andre Mu

Project 2 (School of Science)

Decoding the climate–resistance link: spectral and transcriptomic responses of resistant and sensitive E. coli to environmental stress

Climate change is intensifying the environmental stresses bacteria face, and rising temperatures are increasingly linked to antimicrobial resistance (AMR).

This project examines how climate-relevant stressors reshape resistant versus sensitive Escherichia coli. In the first phase, E. coli will be isolated and characterised from stool samples collected from consenting volunteers, yielding matched resistant and sensitive strains. These will be exposed to controlled climate-relevant stressors, elevated temperature, with vibrational spectroscopy (ATR-FTIR and Raman) tracking the evolving biochemical fingerprint and matched RNA sequencing (RNA-seq) resolving the underlying transcriptomics. To capture in vivo-like infection conditions, the Galleria mellonella larval model, well established in Dr Tan's lab, will be used at elevated temperatures to examine how climate stressors alter bacterial responses and virulence, again profiled by spectroscopy and RNA-seq. Integrating these layers will reveal whether resistance alters stress adaptation and whether warming modulates virulence, thereby informing AMR mechanisms, host–pathogen dynamics, and potentially rapid diagnostics.

Selection Criteria

Essential Criteria

  • Academic Qualifications: Bachelor’s degree requiring at least four years of full-time study with First Class Honours (H1) or a Master’s degree by research (H2A equivalent or CGPA ≥ 3.50) in Microbiology, Genomics, Biochemistry, or a closely related discipline from a recognized university.
  • English Language Proficiency: Meets Monash Graduate Education English Language Proficiency requirements (e.g., IELTS minimum overall score of 6.5 with no individual band below 6.0, or TOEFL/PTE equivalent).

Preferred Criteria

  • Genomics & Bioinformatics: Demonstrated experience with processing/ analyzing microbial genomic data.
  • Spectral Chemistry (Advantage): Prior experience with analytical spectroscopy, with specific advantages in ATR-FTIR (Attenuated Total Reflection Fourier-Transform Infrared) or Raman spectroscopy.

For enquiries, please contact Dr Patrick Tan Hock Siew

For more information about this project, please visit our GEMS website.

How to Apply

When you apply for admission into your preferred degree program you will be able to select your scholarship type. No separate application is required.

By clicking on a course, you will be directed to further information, including details on ‘How to Apply’.

However, before applying for a GEMS, it is recommended that you first contact the main supervisor for this GEMS research topic. Please provide details of your academic background and achievements to the supervisor so that they can assess your suitability for the GEMS research topic you are interested in.

Main Supervisor (Malaysia):  Dr Patrick Tan Hock Siew

Associate Supervisor (Malaysia): Dr Foo Su Chern

Associate Supervisor (Australia): Prof. Anton Peleg, Dr Kamila Kochan

Project 3 (Jeffrey Cheah School of Medicine and Health Sciences)

Climate Change and ESKAPEE pathogen Resistance: A Localised Mixed-Methods Study

Growing evidence shows that climate-induced temperature rises directly accelerate bacterial growth and resistance mutations, while extreme weather events indirectly affect healthcare disruptions and antibiotic misuse. This mixed-methods project will investigate how localised climate extremes - specifically heatwaves and flooding - influence the prevalence and resistance profiles of ESKAPEE pathogens within a Malaysian hospital’s catchment area.

The study begins with a scoping review to map the current scientific understanding of climate-driven resistance and identify empirical gaps. To examine this locally, the quantitative phase utilises retrospective datasets of clinical isolates and localised meteorological data, employing time-series modeling to identify correlations and lag-effects between weather anomalies and resistance trends. Complementing this, the qualitative phase uses semi-structured interviews with healthcare providers to explore operational vulnerabilities and behavioral drivers within the hospital's existing antimicrobial stewardship (AMS) programme during weather crises.

Ultimately, this study bridges planetary health and epidemiology to fortify the current AMS programme against climate-driven resistance patterns.

Selection Criteria

Essential Criteria

  • Academic Qualifications: Bachelor’s degree requiring at least four years of full-time study with First Class Honours (H1) or a Master’s degree by research (H2A equivalent or CGPA ≥ 3.50) in Public Health, Epidemiology, Medical Sociology, Biostatistics, or Health Sciences from a recognized university.
  • English Language Proficiency: Meets Monash Graduate Education English Language Proficiency requirements (e.g., IELTS minimum overall score of 6.5 with no individual band below 6.0, or TOEFL/PTE equivalent).
  • Research Competencies: Demonstrated foundational knowledge in quantitative statistical analyses alongside experience in qualitative research methodologies.
  • Residency & Institutional Access: Malaysian Citizenship or Permanent Residency (strongly desired to facilitate security clearance, institutional access to public hospital settings, and navigation of local administrative workflows).

Preferred Criteria

  • Mixed-Methods Execution: Practical experience in designing semi-structured interviews, performing thematic analysis using qualitative software (e.g., NVivo, ATLAS.ti), and running quantitative time-series modeling (e.g., STATA, R, or SPSS).
  • Language & Communication Skills: Excellent spoken and written Malay language to conduct qualitative interviews with healthcare personnel and translate complex findings into local policy contexts.
  • Clinical & Domain Knowledge: Working understanding of hospital Antimicrobial Stewardship (AMS) protocols, clinical ESKAPEE pathogen trends, or planetary health concepts.
  • Research Output: Proven track record in academic writing, including published journal articles, policy briefs, or research grant contributions.

Optional Criteria

  • Stakeholder Engagement: Prior involvement in interacting with healthcare authorities (such as the Ministry of Health Malaysia) or community healthcare advocates.
  • Sociological Frameworks: Familiarity with risk analysis mapping, sociology of medicine, or frameworks examining public trust in scientific policy during health crises.

For enquiries, please contact Dr Nur Alia Johari

For more information about this project, please visit our GEMS website.

How to Apply

When you apply for admission into your preferred degree program you will be able to select your scholarship type. No separate application is required.

By clicking on a course, you will be directed to further information, including details on ‘How to Apply’.

However, before applying for a GEMS, it is recommended that you first contact the main supervisor for this GEMS research topic. Please provide details of your academic background and achievements to the supervisor so that they can assess your suitability for the GEMS research topic you are interested in.

Main Supervisor (Malaysia): Dr Nur Alia Johari

Associate Supervisor (Malaysia): Dr Hamimatunnisa Joha,  Dr Geetha Maniam

Associate Supervisor (Australia): Prof. Mark Davis