The Pathogen Diagnostics and Genomic Epidemiology Research Group (DxEpiPath), formerly known as Clinical Virology and New Diagnostic Tools Group, was created in 2010 and promotes multidisciplinary translational research to improve the prevention, diagnostics, and management of infections caused by viruses and other pathogens that have an impact on clinical applications and public health. Through new diagnostic tools and models of care, the group is contributing to the elimination of viral hepatitis in vulnerable populations. The team is also applying different genomic sequencing strategies to characterize the epidemiology and contribute to the control of highly transmissible pathogens, often involved in outbreaks; the group specialises in genomic epidemiology and surveillance of SARS-CoV-2, tuberculosis, Monkeypox virus and drug resistant bacteria. Regarding tuberculosis, Elisa Martró led a multicenter, population-based genomic epidemiology study of Mycobacterium tuberculosis complex strains in Catalonia (TB-SEQ) that resulted in the implementation of this new strategy into formal tuberculosis prevention and control activities, in which the full group is involved.

The group is located at the Microbiology Service, Clinical Laboratory North Metropolitan Area (LCMN) of Germans Trias i Pujol University Hospital and is part of the Clinical Microbiology and Experimental Infectious Pathology Group, a consolidated research group funded by the Catalan Government (2021 SGR 00931). Three group members belong to the Epidemiology and Public Health Networking Biomedical Research Centre (CIBERESP Group 27, together with CEEISCAT).

Keywords: Molecular diagnostics, genomic epidemiology, outbreaks, viral hepatitis, SARS-CoV-2 and other respiratory viruses, tuberculosis, antimicrobial resistance (AMR).

Pathogen Diagnostics and Genomic Epidemiology

Group leader

  • Elisa Martró, PhD
    Elisa Martró, PhD

    Elisa Martró, PhD

    Elisa Martró (BSc, PhD) did her Master's in Clinical Microbiology at the Microbiology Department of Germans Trias i Pujol University Hospital (HUGTiP), within Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain. Then, she was guest researcher at the Centers for Disease Control and Prevention (CDC) in Atlanta, USA, where she undertook the experimental part of her PhD from 2001 to 2003. Afterwards, she completed her predoctoral training at the Center of Epidemiological Studies on HIV/STIs in Catalonia (CEEISCAT), and defended her doctoral thesis in 2005, for which she received two awards. Back at HUGTiP’s Microbiology Department, Dr Martró started a research line on hepatitis C virus in 2006 as a postdoc, and since 2010 as a principal investigator, when she entered the Miguel Servet program for researchers in the Spanish Health System.

    Currently, Elisa Martró is senior group leader (R4) of the Pathogen Diagnostics and Genomic Epidemiology Group at IGTP. Her research is focused on improving the diagnosis and treatment of hepatitis B and C in vulnerable populations through novel assays and integrated models of care, and in genomic epidemiology of pathogens with public health impact, including tuberculosis. She actively collaborates in two public health programs in Catalonia (viral hepatitis and tuberculosis). She belongs to the Epidemiology and Public Health Networking Biomedical Research Centre (CIBERESP; Group 27) of Instituto de Salud Carlos III, and to the Clinical and Experimental Microbiology Group (2021SGR00931; consolidated research group in Catalonia by AGAUR).

    Over the last five years, E. Martró has directed 11 research projects as principal investigator, including six competitive and five non-competitive projects (two of them internationally funded). Additionally, she has signed five agreements with public and private entities. She has also collaborated in 12 projects (including three European calls and two international calls). In this period, she has been involved in 28 scientific articles published in peer reviewed journals.

    Contact: emartro(ELIMINAR)@igtp.cat
    ORCID: 0000-0002-2867-6649

Research lines

Viral hepatitis

Viral hepatitis is a global public health challenge, comparable to other major communicable diseases, including HIV, tuberculosis and malaria. In 2016, the WHO launched the first Global Health Sector Strategy on Viral Hepatitis with the aim of eliminating viral hepatitis as a major public health threat by 2030. In order to achieve this ambitious goal, a rapid and massive scale-up of diagnosis and treatment is required.

Hepatitis C

Hepatitis C virus (HCV) chronic infection is characterised by a slow and silent progression, and it is the leading cause of liver-related morbidity and mortality worldwide due to HCV-related complications, which include: cirrhosis, hepatocellular carcinoma and liver failure. With the advent of highly-effective new antiviral drugs, HCV infection can be currently cured by antiviral treatment in most patients. However, many infected people are unaware of their infection and, therefore, are not eligible for treatment. This is especially relevant among vulnerable populations, such as people who inject drugs or migrants from endemic countries.

The main research activity of this group focuses on the molecular study of HCV and involves aspects of basic oriented, clinical and public health research, which have been developed through overlapping competitive research projects and collaboration agreements with the industry. The group is working towards the elimination of HCV infection in collaboration with the Public Health Agency of Catalonia (within the Plan for the Prevention and Control of Hepatitis C in Catalonia), CEEISCAT and other groups through two main strategies:

  • Improvement of the diagnosis of active HCV infection and linkage to care.
    • Design and implementation of new diagnostic assays and screening strategies in community and healthcare settings.
    • Promoting the micro-elimination of HCV in vulnerable populations through new models of care including education, prevention, screening, and linkage to care and treatment, and combating reinfection.
  • Characterisation of the molecular epidemiology of HCV: assessment of epidemiological markers (prevalence, incidence, acute infection) and transmission dynamics in key populations by next generation sequencing and phylogenetic analysis to understand how the virus spreads and contribute to its control.

Hepatitis B

Regarding hepatitis B virus (HBV), the group has been working on two main activities in vulnerable populations:

  • Design and implementation of new strategies for education, screening, and linkage to care and treatment.
  • Assessment of HBV vaccination needs and targeted vaccination strategies.

The team is also working to expand screening of vulnerable populations not only for viral hepatitis, but also for other infectious diseases such as sexually transmitted infections (STI) and tuberculosis, in an integrated and people-centered way.

Molecular diagnostics and genomic epidemiology of other infectious diseases

Over the last five years, this research group has been applying its knowledge in next-generation sequencing and phylogenetic analysis - previously acquired in the field of HCV - to other pathogens with clinical and public health interest. By sequencing the genome of pathogen samples from patients, we can study the origin of outbreaks, how they spread and evolve, and which strategies may contain them. In this way, genomics can guide decisions of infection control teams and public health authorities about how to target their efforts to control transmission. Additionally, whole genome sequencing has become the reference method for typing and studying antimicrobial resistance for a growing number of pathogens. Pathogen genomics is increasingly being used for a new generation of diagnostics and therapeutics.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Following the first pandemic wave of coronavirus disease 2019 (COVID-19), the emergence of SARS-CoV-2 variants has led to waves of infections across the globe. With the COVID-19 pandemic, genomic surveillance has been implemented at scale worldwide for the first time, with an unprecedented rate of genome data generation, greater than for any other pathogen.

  • Genomic surveillance of circulating variants, for the early detection of mutations, monitoring of virus evolution and evaluating how variants might hamper detection by diagnostic tests, as well as influence effectiveness of vaccines and antivirals, to ultimately inform public health interventions.
  • Genomic epidemiology studies of outbreaks in hospitals, long-term care facilities and other closed settings, in order to characterize virus spread and translate genomic information into meaningful clinical reports for infection control teams in order to improve outbreak control.

The group is also working to expand this line of research to other respiratory viruses, such as influenza virus and respiratory syncytial virus (RSV).

Tuberculosis (TB)

Worldwide, TB is the second leading infectious killer after COVID-19 (above HIV/AIDS). Multidrug-resistant TB (MDR-TB) remains a public health concern and a health security threat. Ending the TB epidemic by 2030 is among the health targets of the United Nations Sustainable Development Goals. Despite significant progress in the control of Mycobacterium tuberculosis complex (MTBC) transmission, traditional contact-tracing strategies have limitations that can be overcome using whole genome sequencing (WGS) data as a high-resolution epidemiological marker.

The group led a pioneering prospective, population-based, multicentre study of genomic epidemiology of the MTBC strains circulating in Catalonia, in collaboration with Iñaki Comas (IBV-CSIC), Pere-Joan Cardona (CIBERES), CEEISCAT and other research groups within CIBERESP, and a network of public and private laboratories, that was subsequently implemented whithin the Tuberculosis Prevention and Control Program (Dept. de Salut, Generalitat de Catalunya), with the following objectives:

  • To characterise by WGS how TB is being transmitted in Catalonia and its determinants, in order to improve the control and prevention of this infection to ultimately implement and integrate MTBC genomics into formal epidemiological surveillance activities in Catalonia.
  • To evaluate the use of WGS as the new reference methodology for the detection of resistance markers in the clinical microbiology laboratory.

In 2024, a new project has been granted for the design and piloting of a new decentralized screening strategy of tuberculosis, integrated into viral hepatitis and HIV/STI screening programs in vulnerable populations.

Antimicrobial resistant bacteria

  • Genomic epidemiology of outbreaks and circulating strains of multidrug-resistant bacteria, including carbapenemase or extended-spectrum beta-lactamase (ESBL) producing Klebsiella pneumoniae and/or, vancomycin-resistant Enteroccocus faecium, or methicillin-resistant Staphylococcus aureus.
  • Validation of molecular assays for the diagnosis of bacterial infections and resistance genes in collaboration with industry. The group has especially worked in the molecular diagnostics of sepsis, a time-dependent syndrome that represents the main cause of death by infection worldwide, therefore shortening the time to microbiological diagnosis saves lives. More recently, a real-time 16S rRNA sequencing assay from direct clinical samples is being validated for the microbiological diagnosis of infections that need an urgent diagnosis and conventional diagnostics methods show limitations.

Sexually Transmitted Infections (STI)

The prevalence of STIs is currently increasing worldwide. This research group has optimised various diagnostic techniques adapted for minimally-invasive sampling (especially urine, saliva, and fingerpick blood) for the screening of STI in vulnerable populations attending alternative testing centers, contributing to their epidemiological characterization with public health applications. It has also performed molecular diagnostics and epidemiology studies of human Papillomavirus (HPV), Treponema pallidum, and Monkeypox virus.


Active projects

Pilot hepatitis C simplified screening and linkage to treatment strategy in community pharmacies (HepTestFarma)

PI: Elisa Martró
Funding agency: Becas Gilead a Proyectos de Microeliminación en Hepatitis C (5ª Convocatoria, 2022)
Agency code: GIL181
Duration: 01/01/2023 - 31/12/2024

Cost-effectiveness of a community intervention versus a healthcare-based strategy for promoting the prevention, diagnosis and treatment of hepatitis B and C in immigrants in Catalonia (HepBClink)

PI: Elisa Martró
Funding agency: Instituto de Salud Carlos III (ISCIII)
Agency code: PI19/0568
Duration: 01/01/2020 - 31/12/2024

New decentralized screening strategy of tuberculosis, integrated into viral hepatitis and HIV/STI screening programs in vulnerable populations (IntegraTB)

PI: Elisa Martró
Funding agency: Instituto de Salud Carlos III (ISCIII)
Agency code: PI23/00528
Duration: 01/01/2024 – 31/12/2026

Brand-specific COVID-19 vaccine effectiveness against severe COVID-19 disease in Europe (COVIDRIVE)

PI: International consortium coordinated by FISABIO; PI at IGTP: Irma Casas
Funding agency: P-95 CVBA Development Aid
Agency code: COVIDRIVE
Duration: 24/05/2021 - 31/05/2024
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Defining the best strategy for global HCV screening, linkage-to-care, education and prevention in PWID population

PI: Sabela Lens
Funding agency: Gilead Sciences, Inc (Foster City CA, EEUU) (HCV CHIME program: Conquering Hepatitis vIa Micro-Elimination)
Duration: 01/10/2018 – 30/09/2024

Epidemiological modelling of SARS-CoV2 in a post-pandemic surveillance context: an open platform for mid-term scenarios and short-term predictions

PI: Clara Prats Soler
Funding agency: Fundación BBVA
Duration: 01/07/2022 - 30/06/2024

Grup de Microbiologia Clínica i Patologia Infecciosa Experimental. Ajuts de suport als grups de recerca consolidats de Catalunya

PI: Pere-Joan Cardona
Funding agency: Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR)
Agency code: 2021 SGR 00931
Duration: 2022 - 2024

Consolidation of WGS and RT-PCR activities for SARS-CoV-2 in Spain towards sustainable use and integration of enhanced infrastructure and processes in the RELECOV network (RELECOV 2.0)

PI: Inmaculada Casas (ISCIII); PI at IGTP: Pere-Joan Cardona
Degree of contribution: Steering Committee
Funding agency: Horizon Europe: EU4H Project Grants
Agency code: EU4H-2022-DGA-MS-IBA-01-02
Duration: 01/07/2023 – 30/06/2025
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Screening of bloodborne viruses in the emergency department of Hospital Germans Trias i Pujol

PI: Rosa Mª Morillas, Elisa Martró, Anna Carreres, Eugènia Negredo
Funding agency: Gilead Sciences, S.L.U.
Agency code: FOCUS Program
Duration: 27/06/2022 – 26/09/2024

Centre de suport del Programa de Vigilància de la Tuberculosi a Catalunya

PI: Pere-Joan Cardona
Funding agency: Departament de Salut, Generalitat de Catalunya
Agency code: GC106/2022
Duration: 2022 -2024

Past projects

Population-based genomic epidemiology study for tailored strategies for surveillance and control of tuberculosis (TB-SEQ)

PI: Elisa Martró. Co-PI: Iñaki Comas
Funding agency: CIBER en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCII)
Agency code: ESP22PI06
Duration: 01/01/2022 - 31/12/2023

Genomic epidemiology of SARS-CoV-2 in Catalonia: virologic surveillance and outbreak control

PI: Marc Noguera (IrsiCaixa). Co-PI: Elisa Martró (IGTP, CIBERESP)
Funding agency: Fundació Marató de TV3
Agency code: 342/C/2021
Duration: 23/09/2021 - 22/09/2023

Enhancing Whole Genome Sequencing (WGS) and/or Reverse Transcription Polymerase Chain Reaction (RT-PCR) national infrastructures and capacities to respond to the COVID-19 pandemic in the EU and EEA

PI: Cristobal Belda Iniesta (ISCIII) ; PI at IGTP: Ignacio Blanco, Pere-Joan Cardona
Funding agency: European Centre for Disease Prevention and Control (ECDC)
Agency code: ECDC.HERA.2021.024
Duration: 03/09/2021 - 30/09/2022

Development of Robust and Innovative Vaccine Effectiveness (IMI-DRIVE_3)

PI: International consortium coordinated by FISABIO. PI at IGTP: Guillermo Mena, Irma Casas
Funding agency: Innovative Medicines Initiative
Duration: 15/09/2021 - 30/06/2022

Scientific publications

Highlighted publications

Bordoy AE, Vallès X, Fernández-Náger J, Sánchez-Roig M, Fernández-Recio J, Saludes V, Noguera-Julian M, Blanco I, Martró E; Quatre Camins COVID-19 Study Group. Analysis of a large SARS-CoV-2 (Alpha) outbreak in a Catalan prison using conventional and genomic epidemiology. J Infect Dis. 2024 Apr 4:jiae161. DOI: 1093/infdis/jiae161.

Wang-Wang JH, Bordoy AE, Martró E, Quesada MD, Pérez-Vázquez M, Guerrero-Murillo M, Tiburcio A, Navarro M, Castellà L, Sopena N, Casas I, Saludes V, Giménez M, Cardona PJ. Evaluation of Fourier Transform Infrared Spectroscopy as a First-Line Typing Tool for the Identification of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Outbreaks in the Hospital Setting. Front Microbiol. 2022 Jun 9;13:897161. DOI: 3389/fmicb.2022.897161.

Martró E, Ouaarab H, Saludes V, Buti M, Treviño B, Roade L, Egea-Cortés L, Reyes-Ureña J, Not A, Majó X, Colom J, Gómez I Prat J; HepClink Study Group. Pilot hepatitis C micro-elimination strategy in Pakistani migrants in Catalonia through a community intervention. Liver Int. 2022 Aug;42(8):1751-1761. DOI: 1111/liv.15327.

Antuori A, Montoya V, Piñeyro D, Sumoy L, Joy J, Krajden M, González-Gómez S, Folch C, Casabona J, Matas L, Colom J, Saludes V, Martró E; HepCdetect II Study Group. Characterization of Acute HCV Infection and Transmission Networks in People Who Currently Inject Drugs in Catalonia: Usefulness of Dried Blood Spots. Hepatology. 2021 Aug;74(2):591-606. DOI: 1002/hep.31757.

Saludes V, Antuori A, Folch C, González N, Ibáñez N, Majó X, Colom J, Matas L, Casabona J, Martró E; HepCdetect II Study Group. Utility of a one-step screening and diagnosis strategy for viremic HCV infection among people who inject drugs in Catalonia. Int J Drug Policy. 2019 Dec;74:236-245. DOI: 1016/j.drugpo.2019.10.012.


Additional information

Collaborative networks

Epidemiology and Public Health Networking Biomedical Research Centre (CIBERESP)

The CIBER in its thematic area of Epidemiology and Public Health focuses its activities on two key aspects: knowing the magnitude and distribution of public health problems and identifying their determining factors to evaluate the effectiveness and efficiency of interventions, whether these are from the field of public policies or practical implementations of prevention and resolution. It is made up of 48 multidisciplinary and multicenter research groups and its current scientific organization model consists of the establishment of a training plan and six research programs:

P1. Epidemiology and control of chronic diseases
P2. Prevention, Surveillance and Control of Communicable Diseases (PREVICET)
P3. Biological and behavioral determinants in the acquisition and spread of communicable diseases in vulnerable populations (DAPET Program)
Q4. Social Determinants of Health
Q5. Epidemiology and prevention of environmental and occupational health
Q6. Research in health services and clinical practice

E. Martró, A. Not and V. Saludes belong to Group 27.

National Laboratory Network for SARS-CoV-2 Genomic Sequencing (RELECOV)

The objectives of this network are to improve the preparedness measures for future health emergencies on the basis of strengthening the response of regional health systems in Spain and coordination among them and with the national level. The establisment of a consolidation of RELECOV network aims the provision of a flexible surveillance network of laboratories (adaptable to the epidemiological situation), to perform genomic studies of SARS CoV-2, rapid RT-PCR assys for variant detection and participate in public health interventions (e.g. antivirals) in order to contribute to the knowledge base, guide patient management, and inform the public health response. This netwok has also expanded to influenza and respiratory syncytial virus.

More information


A public-private-partnership to monitor COVID-19 vaccination programs for public health institutes and brand-specific vaccine effectiveness for pharma companies. This network stems from the DRIVE network on influenza virus, and will expand to include respiratory syncytial virus and other pathogens (ID.DRIVE).

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Doctoral theses

Title: Micro-elimination of hepatitis B and C in vulnerable populations through new strategies for the promotion of education, screening and treatment
Author: Anna Not
Director: Elisa Martró
University: Universitat Autònoma de Barcelona (UAB)
Date of defense: expected in 2024

Title: Feasibility and acceptability of new models of hepatitis B care among African populations: implications for achieving the WHO viral hepatitis elimination targets.
Author: Camila Picchio (ISGlobal)
Directors: Jeffrey V. Lazarus, Elisa Martró
University: Universitat de Barcelona (UB)
Date of defense: 11/2023

Title: Improving the diagnosis and molecular characterization of viremic infection by the Hepatitis C virus in people who inject drugs
Author: Adrián Antuori (HUGTiP)
Directors: Elisa Martró, Verónica Saludes
University: Universitat Autònoma de Barcelona (UAB)
Date of defense: 03/2022


Elisa Martró took part in the thrid episode of IGTP’s podcast Un bri de ciència on viral hepatitis, which was launched on World Hepatitis Day 2023.

The course “Actualización en viruela del mono. La perspectiva del laboratorio de Microbiología” is available at: https://campus.seimc.org/cursos/detalle/actualizacion-en-viruela-del-mono-la-perspectiva-del-laboratorio-de-microbiologia/185

Other publications that the group wants to highlight are:


- Campus Can Ruti, , Divulgació

Es tanca un nou cicle de visites de La Marató als laboratoris de l'IGTP

Un cop més, el programa "Visita la recerca" de la Fundació La Marató de TV3 ha conclòs amb èxit a l'Institut de Recerca Germans Trias i Pujol (IGTP), on una vintena de col·laboradors han tingut l'oportunitat de descobrir de primera mà els projectes de recerca que reben suport a través d'aquesta iniciativa solidària. 

- Recerca, Projectes,

El CEEISCAT comparteix els resultats del projecte TÉSTATE en VIH i hepatitis C

Dos estudis del CEEISCAT-IGTP han avaluat una estratègia online d'autopresa de mostres de VIH i VHC, demostrant que és eficaç i segura.

+ Notícies