Tuberculosis resistance acquisition in space and time: an analysis of globally diverse M. tuberculosis whole genome sequences

Abstract

Background

Mycobacterium tuberculosis (MTB) whole genome sequencing data can provide insights into temporal and geographic trends in resistance acquisition and inform public health interventions.

Methods

We curated a set of clinical MTB isolates with high quality sequencing and culture-based drug susceptibility data spanning four lineages and more than 20 countries. We constructed geographic and lineage specific MTB phylogenies and used Bayesian molecular dating to infer the most-recent-common-susceptible-ancestor age for 4,869 instances of resistance to 10 drugs.

Findings

Of 8,550 isolates curated, 6,099 from 15 countries met criteria for molecular dating. The number of independent resistance acquisition events was lower than the number of resistant isolates across all countries, suggesting ongoing transmission of drug resistance. Ancestral age distributions supported the presence of old resistance, ≥20 years prior, in the majority of countries. A consistent order of resistance acquisition was observed globally starting with resistance to isoniazid, but resistance ancestral age varied by country. We found a direct correlation between country wealth and resistance age ( R ² = 0.47, P-value= 0.014). Amplification of fluoroquinolone and second-line injectable resistance among multidrug-resistant isolates is estimated to have occurred very recently (median ancestral age 4.7 years IQR 1.9-9.8 prior to sample collection). We found the sensitivity of commercial molecular diagnostics for second-line resistance to vary significantly by country (P-value <0.0003)

Interpretation

Our results highlight that both resistance transmission and amplification are contributing to disease burden globally but are variable by country. The observation that wealthier nations are more likely to have old resistance suggests that programmatic improvements can reduce resistance amplification, but that fit resistant strains can circulate for decades subsequently.

Funding

This work was supported by the NIH BD2K grant K01 ES026835, a Harvard Institute of Global Health Burke Fellowship (MF), Boston Children’s Hospital OFD/BTREC/CTREC Faculty Career Development Fellowship and Bushrod H. Campbell and Adah F. Hall Charity Fund/Charles A. King Trust Postdoctoral Fellowship (AD).

Research in context

Evidence before this study

Acquisition and spread of drug-resistance by Mycobacterium tuberculosis (MTB) varies across countries. Local factors driving evolution of drug resistance in MTB are not well studied.

Added value of this study

We applied molecular dating to 6,099 global MTB patient isolates and found the order of resistance acquisition to be consistent across the countries examined, i.e. acquisition of isoniazid resistance first followed by rifampicin and streptomycin followed by resistance to other drugs. In all countries with data available there was evidence for transmission of resistant strains from patient-to-patient and in the majority for extended periods of time (>20 years).

Countries with lower gross wealth indices were found to have more recent resistance acquisition to the drug rifampicin. Based on the resistance patterns identified in our study we estimate that commercial diagnostic tests vary considerably in sensitivity for second-line resistance diagnosis by country.

Implications of all available evidence

The longevity of resistant MTB in many parts of the world emphasizes its fitness for transmission and its continued threat to public health. The association between country wealth and recent resistance acquisition emphasizes the need for continued investment in TB care delivery and surveillance programs. Geographically relevant diagnostics that take into account a country’s unique distribution of resistance are necessary.