Using genomics to understand the origin and dispersion of multidrug and extensively drug resistant tuberculosis in Portugal

Portugal is a low incidence country for tuberculosis (TB) disease. Now figuring among TB low incidence countries, it has since the 1990s reported multidrug resistant and extensively drug resistant (XDR) TB cases, driven predominantly by two strain-types: Lisboa3 and Q1. This study describes the largest characterization of the evolutionary trajectory of M/XDR-TB strains in Portugal, spanning a time-period of two decades. By combining whole-genome sequencing and phenotypic susceptibility data for 207 isolates, we report the geospatial patterns of drug resistant TB, particularly the dispersion of Lisboa3 and Q1 clades, which underly 64.2% and 94.0% of all MDR-TB and XDR-TB isolates, respectively. Genomic-based similarity and a phylogenetic analysis revealed multiple clusters (n = 16) reflecting ongoing and uncontrolled recent transmission of M/XDR-TB, predominantly associated with the Lisboa3 and Q1 clades. These clades are now thought to be evolving in a polycentric mode across multiple geographical districts. The inferred evolutionary history is compatible with MDR- and XDR-TB originating in Portugal in the 70's and 80's, respectively, but with subsequent multiple emergence events of MDR and XDR-TB particularly involving the Lisboa3 clade. A SNP barcode was defined for Lisboa3 and Q1 and comparison with a phylogeny of global strain-types (n = 28 385) revealed the presence of Lisboa3 and Q1 strains in Europe, South America and Africa. In summary, Portugal displays an unusual and unique epidemiological setting shaped by >40 years of uncontrolled circulation of two main phylogenetic clades, leading to a sympatric evolutionary trajectory towards XDR-TB with the potential for global reach.Financial support was provided by the European Society of Clinical Microbiology and Infectious Diseases, for which we would like to would like to acknowledge the Study Group for Mycobacterial Infections. Supported in part by UID/DTP/04138/2019 from Fundação para a Ciência e Tecnologia (FCT), Portugal. JP [CEECIND/00394/2017] and DM are supported by FCT through Estímulo Individual ao Emprego Científico. DM, IC and MV are funded by project PTDC/BIA-MIC/30692/2017 and the Global Health and Tropical Medicine (GHTM) Research Center (Grant UID/Multi/04413/2013) from FCT. TGC received funding from the MRC UK (Grant no. MR/K000551/1, MR/M01360X/1, MR/N010469/1, MR/R020973/1) and BBSRC UK (BB/R013063/1). SC received funding from the Medical Research Council UK grants (MR/R020973/1) and the BBSRC UK (BB/R013063/1). JPhe is funded by the Medical Research Council UK grants (MR/S03563X/1).