The Pathogen Diagnostics and Genomic Epidemiology research group, 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 the most 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. Some members belong to the Epidemiology and Public Health Networking Biomedical Research Centre (CIBERESP Group 27, together with CEEISCAT).
This group is located in the Microbiology Service, Clinical Laboratory North Metropolitan Area (LCMN) of the 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 Generalitat de Catalonia (2021 SGR 00931).
Keywords: Molecular diagnostics, genomic epidemiology, outbreaks, viral hepatitis, SARS-CoV-2 and other respiratory viruses, tuberculosis, antimicrobial resistance (AMR).
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 virus (HCV) chronic infection is characterized 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.
In 2018 the group expanded its activity on HCV to also include hepatitis B virus (HBV), with 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 5 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).
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.
Since December 2021 the group is leading an ongoing prospective, population-based, multicentre study of genomic epidemiology of the MTBC strains circulating in Catalonia, co-led with Iñaki Comas (IBV-CSIC), and in direct collaboration with Pere-Joan Cardona (CIBERES), CEEISCAT and other research groups within CIBERESP, and a network of public and private laboratories 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.
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 optimized 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.
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)
Start date: 01/01/2023
End date: 31/12/2024
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
Start date: 01/01/2022
End date: 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
Start date: 23/09/2021
End date: 22/09/2023
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
Start date: 01/01/2020
End date: 31/12/2024
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)
Start date: 01/10/2018
End date: 30/09/2022
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, Departament de Física de la Universitat Politècnica de Catalunya
Funding agency: Fundación BBVA
Start date: 01/07/2022
End date: 30/06/2024
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
Start date: 24/05/2021
End date: 24/05/2023
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
Start date: 03/09/2021
End date: 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
Start date: 15/09/2021
End date: 30/06/2022
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
Start date: 2022
End date: 2024
Forns X, Colom J, García-Retortillo M, Quer JC, Lens S, Martró E, Domínguez-Hernández R, Casado MÁ, Buti M. Point-of-care hepatitis C testing and treatment strategy for people attending harm reduction and addiction centres for hepatitis C elimination. J Viral Hepat. 2022 Mar;29(3):227-230. DOI: 10.1111/jvh.13634. PMID: 34806812; PMCID: PMC9299793.
Raïch-Regué D, Muñoz-Basagoiti J, Perez-Zsolt D, Noguera-Julian M, Pradenas E, Riveira-Muñoz E, Giménez N, Carabaza A, Giménez F, Saludes V, Martró E, Robert N, Blanco I, Paredes R, Ruiz L, Ballana E, Clotet B, Blanco J, Izquierdo-Useros N. Performance of SARS-CoV-2 Antigen-Detecting Rapid Diagnostic Tests for Omicron and Other Variants of Concern. Front Microbiol. 2022 May 10;13:810576. DOI: 10.3389/fmicb.2022.810576. PMID: 35620108; PMCID: PMC9127986.
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: 10.3389/fmicb.2022.897161. PMID: 35756036; PMCID: PMC9218594.
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: 10.1111/liv.15327. PMID: 35635535.
Sirera G, Videla S, Saludes V, Castellà E, Sanz C, Ariza A, Clotet B, Martró E. Prevalence of HPV-DNA and E6 mRNA in lung cancer of HIV-infected patients. Sci Rep. 2022 Aug 1;12(1):13196. DOI: 10.1038/s41598-022-17237-5. PMID: 35915124; PMCID: PMC9343353.
Catlett B, Hajarizadeh B, Cunningham E, Wolfson-Stofko B, Wheeler A, Khandaker-Hussain B, Feld JJ, Martró E, Chevaliez S, Pawlotsky JM, Bharat C, Cunningham PH, Dore GJ, Applegate T, Grebely J. Diagnostic Accuracy of Assays Using Point-of-Care Testing or Dried Blood Spot Samples for the Determination of Hepatitis C Virus RNA: A Systematic Review. J Infect Dis. 2022 Sep 21;226(6):1005-1021. DOI: 10.1093/infdis/jiac049. PMID: 35150578.
Ferrer L, González V, Martró E, Folch C, Saludes V, Muñoz R, Rodríguez V, Morales A, Meroño M, Morey F, Sanjosé S, Casabona J. High HIV/STI prevalence among cisgender men and transgender women sex workers attending community-based centres in Barcelona, Spain: The Sweetie Project. Int J STD AIDS. 2022 Oct;33(12):1045-1053. DOI: 10.1177/09564624221116536. PMID: 36113447.
López-Muñoz I, Torrella A, Pérez-Quílez O, Castillo-Zuza A, Martró E, Bordoy AE, Saludes V, Blanco I, Soldevila L, Estrada O, Valerio L, Roure S, Vallès X. SARS-CoV-2 Secondary Attack Rates in Vaccinated and Unvaccinated Household Contacts during Replacement of Delta with Omicron Variant, Spain. Emerg Infect Dis. 2022 Oct;28(10):1999-2008. DOI: 10.3201/eid2810.220494. PMID: 36037811; PMCID: PMC9514368.
Català M, Coma E, Alonso S, Andrés C, Blanco I, Antón A, Bordoy AE, Cardona PJ, Fina F, Martró E, Medina M, Mora N, Saludes V, Prats C, Prieto-Alhambra D, Alvarez-Lacalle E. Transmissibility, hospitalization, and intensive care admissions due to omicron compared to delta variants of SARS-CoV-2 in Catalonia: A cohort study and ecological analysis. Front Public Health. 2022 Aug 12;10:961030. DOI: 10.3389/fpubh.2022.961030. Erratum in: Front Public Health. 2022 Nov 03;10:1060328. PMID: 36033822; PMCID: PMC9412031.
Lens S, Miralpeix A, Gálvez M, Martró E, González N, Rodríguez-Tajes S, Mariño Z, Saludes V, Reyes-Urueña J, Majó X, Colom J, Forns X. HCV microelimination in harm reduction centres has benefits beyond HCV cure but is hampered by high reinfection rates. JHEP Rep. 2022 Sep 13;4(12):100580. DOI: 10.1016/j.jhepr.2022.100580. PMID: 36316992; PMCID: PMC9617206.
Bordoy AE, Saludes V, Panisello Yagüe D, Clarà G, Soler L, Paris de León A, Casañ C, Blanco-Suárez A, Guerrero-Murillo M, Rodríguez-Ponga B, Noguera-Julian M, Català-Moll F, Pey I, Armengol MP, Casadellà M, Parera M, Pluvinet R, Sumoy L, Clotet B, Giménez M, Martró E, Cardona PJ, Blanco I. Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes. Sci Rep. 2022 Dec 17;12(1):21818. DOI: 10.1038/s41598-022-25719-9. PMID: 36528712; PMCID: PMC9758454.
Bordoy AE, Vallès X, Not A, Chiner-Oms Á, Saludes V, Torres Cervós J, Roset Roig A, Juan-Andres C, Sureda H, Pardo-Amil V, García I, Guitart Rossell G, Cambra Cibeira L, Casañ C, Giménez M, Blanco I, Torres-Puente M, Cancino-Muñoz I, González-Candelas F, Comas I, Martró E. Epidemiological and Genomic Analysis of a Large SARS-CoV-2 Outbreak in a Long-Term Care Facility in Catalonia, Spain. mSphere. 2022 Dec 21;7(6):e0034622. DOI: 10.1128/msphere.00346-22. PMID: 36448779; PMCID: PMC9769531.
Not A, Saludes V, Gálvez M, Miralpeix A, Bordoy AE, González N, González-Gómez S, Muntané L, Reyes-Urueña J, Majó X, Colom J, Forns X, Lens S, Martró E. Usefulness of dried blood spot samples for monitoring hepatitis C treatment outcome and reinfection among people who inject drugs in a test-and-treat program. J Med Virol. 2023 Feb;95(2):e28544. DOI: 10.1002/jmv.28544. PMID: 36727653.
To mark World Hepatitis Day, the podcast 'Un Bri de Ciència' dedicates an episode to viral hepatitis, specifically focusing on Hepatitis B and C, which are considered to be the most severe types. Researcher Elisa Martró unravels what we know about these diseases and discusses her projects, both in the hospital setting and in communities, working with vulnerable populations. The podcast enhances the mission of awareness and dissemination of IGTP.
A study with people who inject drugs evaluated a minimally invasive test based on dried blood spots (DBS) for the monitoring of hepatitis C virus (HCV) infection. The use of DBS samples for HCV RNA detection and genotyping was shown to effectively assess cure after treatment and to differentiate between reinfection and treatment failure. The results support the viability of decentralizing treatment and post-treatment monitoring for people who inject drugs, who frequently face challenges accessing the healthcare system. The study has been published in the Journal of Medical Virology.