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Integrating genomic surveillance for tuberculosis control in Catalonia

A E Bordoy(1) V Saludes(1,2) E Sicart-Torres(3) S Pequeño(3) M G López(4) L Gavaldà(3) P Ciruela(2,3) L Soler(1) M Alseda(3) A Antuori(1) M Bosch(3) S González-Gómez(1) S Esteban-Cucó(5) P Cano(3) E Vicente(5) L Clotet(3) G Tudó(6,7) L Curto(3) J González(6,7,8) N Follia(3) M T Tórtola(8,9) J P Millet(2,10,11) R Prieto(10) T Soler(12) A Tarrès(3) M D Guerrero(12) G Ferrús(3) I Prats(13) J Mendioroz(3) F Alcaide(6,14) L Fernández(14) E Cuchí(15) M Garrigó(16) P Costa(17) A Casabella(18) A Pulido(19) E Picó-Plana(21) J López(20) G Trujillo(20) N Torrellas(22) X Casas(11) D Panisello-Yagüe(1) G Clarà(1) A C Pelegrin(1) A Domínguez(2,6) M Torres-Puente(4) P Godoy(2,23) C Rius(2,10) E Muntada(2,24) E López-Corbeto(2,24) J Casabona(2,24) P J Cardona(1,25,26) I Comas(2,4) E Martró(1,2)

1:1Microbiology Department, Laboratori Clínic Metropolitana Nord. Institut de Recerca i Hospital Germans Trias i Pujol (IGTP) – Badalona, Catalonia (Spain); 2:CIBER in Epidemiology and Public Health (CIBERESP) – Madrid (Spain); 3:Agència de Salut Pública de Catalunya, Departament de Salut, Generalitat de Catalunya - Barcelona (Spain); 4:Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV)-CSIC – Valencia (Spain); 5:Laboratori de Referència de Catalunya – El Prat de Llobregat, Catalonia (Spain); 6:Universitat de Barcelona – Barcelona, Catalonia (Spain); 7:7Hospital Clínic de Barcelona-ISGlobal - Barcelona, Catalonia (Spain); 8:CIBER in Infectious Diseases (CIBERINFEC) – Madrid (Spain); 9:Hospital Universitari Vall d'Hebron – Barcelona, Catalonia (Spain); 10:Programa de Prevenció i Control de la Tuberculosi de Barcelona (PPCTB). Servei d’Epidemiologia (SEPID). Agència de Salut Pública de Barcelona (ASPB) – Barcelona, Catalonia (Spain); 11:Serveis Clínics – Barcelona, Catalonia (Spain); 12:Consorci del Laboratori Intercomarcal (CLILAB) de l'Alt Penedès, l'Anoia i el Garraf – Vilafranca del Penedès, Catalonia (Spain); 13:Hospital Universitari Arnau de Vilanova – Lleida, Catalonia (Spain); 14:Hospital Universitari de Bellvitge-IDIBELL –L'Hospitalet de Llobregat, Catalonia (Spain); 15:CATLAB-Centre Analítiques Terrassa AIE – Terrassa, Catalonia (Spain); 16:Hospital de la Santa Creu i Sant Pau – Barcelona, Catalonia (Spain); 17:Laboratori Clínic Territorial de Girona. Hospital Universitari de Girona Dr. Josep Trueta – Girona, Catalonia (Spain); 18:Àrea de Microbiologia, Servei de Laboratoris Clínics, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona – Sabadell, Catalonia (Spain); 19:Hospital General de Granollers - Granollers (Spain), 20Hospital Universitari Joan XXIII – Tarragona, Catalonia (Spain); 20:Fundació Althaia. Hospital Sant Joan de Déu – Manresa, Catalonia (Spain); 21:Hospital Universitari Joan XXIII – Tarragona, Catalonia (Spain); 22:Laboratori Fundació Hospital de Palamós – Palamós, Catalonia (Spain); 23:Institut de Recerca Biomédica de Lleida (IRBLleida)-Universitat de Lleida – Lleida, Catalonia (Spain); 24:Centre d’Estudis Epidemiològics sobre les ITS i Sida de Catalunya (CEEISCAT) – Badalona, Catalonia (Spain); 25:CIBER in Respiratory Diseases (CIBERES) – Madrid (Spain); 26:Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Catalonia (Spain)


The rise in tuberculosis (TB) incidence and drug resistance due to the COVID-19 pandemic makes TB control a major Public Health issue. The integration of genomic surveillance of Mycobacterium tuberculosis complex (MTBC) strains into formal epidemiological surveillance activities allows the characterization of transmission clusters and the monitoring of genotypic resistances. We describe the first 1.5 years of genomic surveillance of TB in Catalonia.


Genomic surveillance was implemented within the TB Control Program in Catalonia in 2022. All cultured strains from a network of 43 laboratories were obtained for centralized WGS. Recent transmission clusters (≤5 SNPs) were identified by phylogenetic analysis, reported to the Public Health Authorities and compared to conventional contact tracing data.


Sequencing and epidemiological data was combined for 816 of 1081 (75.5%) culture-positive notified cases (Jan. 2022-June 2023). Forty-four different lineages were detected, being L4.10 (20.3%) and L4.1.2 (16.3%) the most abundant. 61.4% of sequenced strains corresponded to cases in migrants. 33 (4.0%) cases were monoresistant (8 to INH, 1 to RIF, 4 to FQ, 20 to other). MDR cases accounted for 1.2% and pre-XDR for 0.1%. 76 transmission clusters were identified (clustering ratio 29.5%, 241/816), 9 (11.2%) of which were formed by resistant strains. Conventional contact tracing had identified at least one epidemiological link for 27.8% of clustered cases.


The implementation of genomic surveillance of MTBC strains has evidenced substantial local transmission and can help to detect and stop transmission chains and epidemic outbreaks previously unnoticed by traditional contact tracing strategies.

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