AGTC Genomics Presents Latest Clinical Metagenomics Findings at Malaysia Microbiome Meeting 2026

Oct 6

6 min read

NGS-based approach demonstrates high concordance with conventional microbiology while enabling broad, unbiased detection of bacterial, viral, fungal and parasitic pathogens in under 24 hours

KUALA LUMPUR, 3 October 2026 — AGTC Genomics presented its latest findings on Clinical Metagenomics for infectious disease diagnosis at the Malaysia Microbiome Meeting 2026, held from 3–4 October at Sunway University.

Prof. Chee Onn Leong of AGTC Genomics was invited to speak in the AI, Multi-Omics and the Future scientific programme on “From Microbiome Sequencing to Clinical Insights – Towards Culture-Free Clinical Metagenomics and AMR Detection.”

The presentation highlighted emerging evidence from AGTC Genomics' clinical metagenomics work showing high concordance in pathogen detection with conventional diagnostic methods, including bacterial culture and targeted PCR, while demonstrating an important additional advantage: the ability to search broadly for potential infectious organisms without requiring clinicians to specify the pathogen in advance.

Changing the clinical question

Traditional infectious disease diagnostics are generally hypothesis-driven. Based on a patient's symptoms, clinical history and examination, clinicians must decide which organism they suspect and then request the corresponding culture, antigen test, serology or PCR assay.

This approach works well when the suspected pathogen is known. The challenge arises when it is not.

Patients with severe infections may have negative bacterial cultures or PCR results because the causative organism is not included in the test panel, is difficult to culture, is present at low abundance, or is a virus, fungus or parasite that was not initially suspected. Previous antimicrobial treatment may further reduce the yield of conventional culture.

AGTC Genomics' Clinical Metagenomics approach is designed to change the question from: “What pathogen should I test for?” to “What is causing the infection?”

Using shotgun metagenomic next-generation sequencing, genetic material present within a clinical sample can be analysed broadly rather than testing sequentially for individual organisms.

The current AGTC Clinical Metagenomics reference catalogue contains 693 pathogenic species across bacteria, viruses, fungi and parasites, comprising 242 bacterial species, 226 fungal/parasitic species and 225 viral species. The analytical approach can also report organisms outside the predefined catalogue when detected.

This provides clinicians with a much wider diagnostic window — approaching 700 or more clinically relevant organisms in a single investigation — without having to correctly predict the causative pathogen before testing begins.

One sample. Broad detection. Rapid clinical insight.

A key focus of the work presented at the meeting was translating metagenomics from a research technology into a clinically practical diagnostic tool.

The AGTC Genomics Clinical Metagenomics workflow is designed with a turnaround time of less than 24 hours, enabling broad pathogen investigation while the information may still influence acute clinical management.

Unlike targeted PCR, which searches only for predetermined genetic targets, shotgun metagenomic sequencing analyses microbial genetic material within the specimen without target-specific amplification. The method can simultaneously investigate bacteria, viruses, fungi and parasites, while also providing taxonomic and functional information.

The approach may be particularly valuable when:

routine culture is negative or inconclusive;
targeted PCR panels fail to identify a pathogen;
a patient is critically ill and a broad differential diagnosis is required;
an immunocompromised patient may have an atypical or opportunistic infection;
polymicrobial infection is suspected;
fastidious or non-cultivable organisms may be involved; or
prior antimicrobial treatment has reduced culture yield.

These are among the clinical situations specifically identified for consideration of Clinical Metagenomics testing.

Detection alone is not enough

AGTC Genomics also emphasised that broad sequencing should not be interpreted simply as a list of every microorganism detected.

The central challenge in clinical metagenomics is determining whether a detected organism represents the true pathogen, colonisation, contamination or an incidental finding.

For this reason, sequencing findings must be interpreted together with microbial abundance, specimen type, host factors, symptoms, imaging, laboratory findings and the overall clinical presentation.

This distinction is particularly important because the objective of Clinical Metagenomics is not simply to detect more microorganisms, but to identify the most clinically plausible cause of infection and provide information that can support treatment decisions.

AGTC's test therefore reports detected organisms together with relative abundance and clinical context, supported by taxonomic annotation, functional profiling and gene prediction.

From Research Validation to Multi-Hospital Implementation

The clinical metagenomics programme is now progressing beyond analytical validation towards broader clinical implementation.

AGTC Genomics, IMU University and Universiti Malaya Medical Centre (UMMC) have recently secured a joint research fund from Malaysia’s Ministry of Science, Technology and Innovation (MOSTI) to further evaluate and implement Clinical Metagenomics across participating hospitals.

The collaborative programme will focus on generating real-world clinical evidence for the use of metagenomic sequencing in patients with suspected infectious diseases, particularly those with negative or inconclusive conventional microbiology results, severe infections, atypical presentations or suspected antimicrobial-resistant infections.

A major component of the project will also be the development of a Malaysia-focused infectious disease genomic database and antimicrobial resistance reference database.

This is important because the distribution of infectious organisms and antimicrobial resistance mechanisms can differ substantially between countries, hospitals and patient populations. Building a locally derived dataset will allow microbial genomic findings to be interpreted against pathogens and resistance patterns that are more representative of Malaysian clinical practice.

The programme is expected to support the development of:

a local infectious disease pathogen genomic reference database;
an antimicrobial resistance gene and mutation reference database;
hospital-derived data on pathogen prevalence and microbial genomic profiles;
clinical correlation between metagenomic findings and conventional culture or PCR results;
improved bioinformatics algorithms for distinguishing clinically relevant pathogens from colonisers or contaminants; and
an evidence base for incorporating metagenomic sequencing into future infectious disease diagnostic pathways.

Prof. Chee Onn Leong said the collaboration represents an important next step in translating sequencing technology into routine clinical care.

“The value of clinical metagenomics will ultimately depend not simply on how many organisms we can sequence, but on how accurately we can interpret what those signals mean for an individual patient. Through this collaboration with IMU and UMMC, supported by MOSTI, we hope to generate Malaysian clinical evidence and build a local infectious disease and antimicrobial resistance genomic reference resource. This will help us move from detecting microorganisms towards identifying the organism most likely to be driving the patient’s disease and, ultimately, supporting more appropriate treatment.

The initiative also addresses the growing challenge of antimicrobial resistance (AMR). By integrating pathogen identification with genomic information associated with antimicrobial resistance, the research aims to explore how sequencing could eventually support faster recognition of resistant infections and complement conventional phenotypic susceptibility testing.

This complements the broader direction presented by AGTC Genomics at the Malaysia Microbiome Meeting: moving infectious disease diagnostics from a series of targeted tests towards a more comprehensive model of broad detection, rapid interpretation and clinically actionable insight.

Supporting evidence-based infectious disease diagnostics

According to AGTC Genomics, the high concordance observed between its NGS-based approach and established culture and PCR methods provides important supporting evidence that metagenomic sequencing can reproduce clinically recognised pathogen findings while considerably expanding the range of organisms investigated simultaneously.

More importantly, its potential value may lie in the cases where conventional testing does not provide an answer.

Rather than ordering multiple sequential tests — potentially involving bacterial culture followed by different viral, fungal or parasitic assays — Clinical Metagenomics provides a broad investigation from a single clinical specimen.

“The objective is not to replace every culture or PCR test. These remain extremely important clinical tools. What metagenomics gives us is another option when we do not know what we are looking for, when routine investigations are negative, or when time is critical. We want to move infectious disease diagnostics from asking, ‘Which pathogen should I test for?’ towards asking a much more clinically meaningful question: ‘What is actually causing the infection?’ If we can answer that question rapidly and reliably, we can potentially help clinicians move from empirical treatment towards more informed and precise antimicrobial therapy.” said Prof. Chee Onn Leong.

Towards culture-free clinical metagenomics

AGTC Genomics believes Clinical Metagenomics could become an increasingly important complement to established microbiology, particularly for diagnostically challenging infections.

The technology does not eliminate the role of conventional microbiology. Culture remains important for phenotypic antimicrobial susceptibility testing and targeted molecular assays remain highly effective when a particular pathogen is strongly suspected.

Instead, Clinical Metagenomics addresses a different diagnostic gap: the patient in whom the causative pathogen remains unknown.

AGTC Genomics' current workflow performs shotgun metagenomic sequencing with taxonomic and functional bioinformatics analysis, with sequencing and reporting undertaken within its CAP-accredited laboratory. The company also provides clinician support for test selection and interpretation.

The broader research programme is continuing to explore rapid sequencing, antimicrobial resistance detection and AI-enabled pathogen–phenotype interpretation, with the aim of connecting microbial genomic signals more directly with clinical presentation.

From broad sequencing to actionable medicine

The work presented at the Malaysia Microbiome Meeting reflects a broader transition in infectious disease genomics:

One sample. Broad detection. Rapid interpretation. Actionable treatment.

Rather than simply creating another sequencing assay, the goal is to help close the diagnostic uncertainty between a critically ill patient and the correct treatment — while building the clinical evidence required for responsible adoption of metagenomic sequencing in routine healthcare.

About AGTC Genomics

AGTC Genomics is a Malaysian genomics and precision diagnostics company focused on translating advanced genomic technologies into clinically applicable solutions. Its capabilities span precision oncology, inherited disease, infectious disease genomics, pharmacogenomics, microbiome and other genomic applications, supported by next-generation sequencing, molecular diagnostics and bioinformatics infrastructure.