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

João Perdigão,Anabela Miranda,Carla Silva,Pedro Gomes,Diana Machado,Laura Brum,Susana Campino,Miguel Viveiros,Jody E Phelan,Isabel Couto,Isabel Portugal,Fernando Maltez,Taane G Clark

doi:10.1038/s41598-020-59558-3

Abstract

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.

Highlights

Multidrug-resistant (MDR) tuberculosis (TB) poses a serious threat to the WHO goal of eliminating TB by 20351
Tuberculosis clinical isolates: 191 were prospectively collected from 2008 to 2016 and 16 isolates selected retrospectively as to form a sample enriched with drug resistant isolates
XDR-TB isolates originated from multiple districts nationwide but, when considering MDR-TB isolates with SLD drug www.nature.com/scientificreports susceptibility testing (DST) available, were prevalent in Lisbon (41.2%, n = 35/85), Ponta Delgada (100%, n = 5/5) and Setubal (37.5%, n = 3/8) districts, both part of the Lisbon Health Region

Summary

Introduction

Multidrug-resistant (MDR) tuberculosis (TB) poses a serious threat to the WHO goal of eliminating TB by 20351. Portugal recently became a low TB incidence country by reporting a notification rate below 20 cases per 100 000 habitants (17.5/100 000 in 2017)[2]. During the 1990’s, a group of genetically similar MDR and XDR-TB strains circulating in Lisbon were reported, and were characterised using molecular methods into Lisboa[3] (SIT20/LAM1) and Q1 clades (SIT1106/Q1)[3,4]. Both clades bear the RDRIO deletion while comprising distinctive monophyletic clades[5,6]. By investigating the genomic similarity within a phylogenetic framework, we attempt to understand strain diversity, its origin and evolution and, the potential for the established Lisboa[3] and Q1 strains to spread outside of the country

Methods

Results

Discussion

Conclusion