i3S Diagnostics is a clinical infectious diseases diagnostics laboratory providing high-priority long-read sequencing services for pathogenic microorganisms. Our focus is unbiased metagenomic microbe detection across sample types, paired with genomic antimicrobial resistance (AMR) characterization at the whole-genome sequencing level, delivered on a daily clinical schedule to support time-sensitive decisions.

Our mission is to translate advanced genomics into routine clinical microbiology in a way that is usable at the bedside and reliable for infection control and public health. AMR results are reported to guide and complement phenotypic antimicrobial susceptibility testing (AST), adding context on resistance determinants and relevant mutations to support stewardship and multidisciplinary case review.

We serve hospitals (including emergency and ICU), public health units, private clinics, reference laboratories, patient associations, and other non-governmental organizations. Our team combines clinical microbiology, genomics and bioinformatics to ensure scientific rigor and clinically interpretable reporting.

Our facility supports highthroughput workflows with automated nucleic acid extraction and scalable sample processing infrastructure. Instrumentation and automation are selected to enable reproducibility, throughput, and timely reporting for both clinical and translational needs.

When to use NGS

Next-Generation Sequencing (NGS) is useful when conventional microbiology is negative, delayed or limited by prior antibiotic treatments, fastidious organisms, or suspected co-infection. It is a complement to culture and targeted PCR, helping broaden detection and refine management when clinical suspicion remains high.

Genomic AMR findings are reported to complement phenotypic AST by identifying resistance determinants and relevant mutations that may inform therapy and infection control. This supports antimicrobial stewardship by improving early alignment between likely resistance mechanisms and treatment choices while awaiting or interpreting AST.

What you receive

You receive a clinical report with detected organisms and clinically relevant AMR findings, plus access to discussion with a molecular microbiology scientist. Delivery of results can be via e-mail or Laboratory Information System (LIS) integration depending on partner setup.

Innovation of our tests

Our testing supports agnostic, culture-free, pathogen search and co-infection detection, including detection of fastidious organisms. We prioritize reduced turnaround times and a decision-oriented report structure for clinical usability.

Daily clinical long-read sequencing services for rapid unbiased metagenomic pathogen detection across sample types, and antimicrobial resistance characterization to support targeted therapy, AST, and stewardship. 

1) Metagenomic Pathogen Identification (mNGS)

What we report: Bacteria, viruses, fungi, parasites, co-infections.

Sample type: Body fluids and tissues.

Turnaround options: Rapid ~6h; Standard 48h.

Request mNGS or pre-test sample advice

2) Antimicrobial Resistance Profiling (whole-genome sequencing level)

What we report: Species-level ID, resistance determinant genes, clinically relevant mutations, sequence typing.

Sample type: Cultured bacterial or fungal isolates.

Turnaround options: Rapid ~6h; Standard 48h.

Submit isolate and discuss interpretation

3) Combined Metagenomic Pathogen Identification & Antimicrobial Resistance Profiling

What we report: Broad pathogen detection plus partial AMR profile (genes or mutations) when supported by sample context.

Sample type: Body fluids and tissues.

Turnaround options: Standard 48h.

Request combined test or case discussion

4) Outbreak Support

What we report: Species ID, co-infections, resistance determinants, clinically relevant mutations, sequence typing, and epidemiological context (scope depending on study type).

Sample type: Cultured bacterial or fungal isolates.

Turnaround options: Rapid ~6h; Standard 48h; Extended (epidemiology study) ~5 days.

Contact us and start outbreak support 

5) Custom Assays (R&D → Clinical test development)

Scope: New method development, validation and clinical deployment, aligned with operational and reporting requirements.

Propose a project or Translational consultation

Ordering

How to order

1. Portal request or download requisition form.

2. Confirm assay type (Rapid vs Standard) and sample type (isolate vs body fluid/tissue).

3. Follow the sample collection guide (including contamination notes and low-biomass warnings) and check rejection criteria.

4. Ship to the delivery address listed in the Contacts section and include clinical context for interpretation.

Cut-off times    

Rapid assays: 12h00     

Standard assays: 15h00

Pre-test consultation (recommended)

Use case discussion to select the most appropriate service and avoid preventable pre-analytical errors (sample type, volume, contamination risk, low biomass).

Past services

Public health and research initiatives related to COVID-19 diagnostics

Since the beginning of the SARS-CoV-2 pandemic, the laboratory has maintained collaboration with ARS-Norte public health services and corporate partners, supporting clinical and public health by providing molecular diagnostic services for 1) SARS-CoV-2 detection by RT-qPCR in nasopharyngeal swab or saliva specimens, 2) serological and rapid antigen testing for COVID-19, 3) highthroughput RT-qPCR SARS-CoV-2 detection for large groups populations daily screenings for corporate partners.

The team contributed to the characterization of circulating SARS-CoV-2 variants through short-read sequencing, in partnership with the National Institute of Health Doutor Ricardo Jorge (INSA).

Services included the evaluation of the antimicrobial performance of innovative materials, including textile surfaces, providing experimental evidence to support product development and validation.

More information here

Automated nucleic acid extraction

Automated nucleic acid extraction workflows are available to support reproducibility, scalability, and compatibility with downstream molecular and genomic methods.

Highthroughput sample analysis infrastructure

Highthroughput workflows are supported by programmable liquid handling infrastructure for efficient and reproducible sample processing.

Diagnostic and advisory services

Consultancy and diagnostic support are available for healthcare institutions and other sectors (including food, textile, and corporate environments) for microbiological and biosafety strategies.

R&D

Ongoing Projects

MetAGNOSTICS- Metagenomics for personalized infectious diseases diagnostics. In collaboration with Centro Materno-Infantil do Norte, Unidade Local de Saúde de Santo António.

DiSTIG.MA: Diagnosis of Sexually Transmitted Infections by gonorrhoea - a Metagenomics Approach. In collaboration with Hospital de Santo António, Unidade Local de Saúde de Santo António

FLATFARE- Inovação para melhoria do bem-estar animal em contexto intensivo de produção de pregado e linguado. In collaboration with FLATLANTIC Actividades Piscícolas, S.A.

Completed Projects

DeepFastCoV. SARS-CoV-2 infectivity and co-infections.

InfSeq. NGS sequencing of cell-free DNA for pathogen identification.

Awards

Recognised in 2025 by Comissão de Coordenação e Desenvolvimento Regional do Norte (CCDR NORTE) with the “Mais a Norte” - Innovation award. More information here https://www.youtube.com/watch?v=oFbvzEKNCq8.

Clinical liaison

Discuss clinical case, pre-test guidance, or post-report interpretation

rute.oliveira@i3s.up.pt

Operational

Ordering, logistics

Phone nr. +00351 226 074 990

i3sdiagnostics@i3s.up.pt

Delivery address

A/C i3S Diagnostics

IPATIMUP

Rua Júlio Amaral de Carvalho, nº 45

4200-135 Porto, Portugal