Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis

Abstract

The "Beijing" Mycobacterium tuberculosis (Mtb) lineage 2 (L2) is spreading globally and has been associated with accelerated disease progression and increased antibiotic resistance. Here we performed a phylodynamic reconstruction of one of the L2 sublineages, the central Asian clade (CAC), which has recently spread to western Europe. We find that recent historical events have contributed to the evolution and dispersal of the CAC. Our timing estimates indicate that the clade was likely introduced to Afghanistan during the 1979-1989 Soviet-Afghan war and spread further after population displacement in the wake of the American invasion in 2001. We also find that drug resistance mutations accumulated on a massive scale in Mtb isolates from former Soviet republics after the fall of the Soviet Union, a pattern that was not observed in CAC isolates from Afghanistan. Our results underscore the detrimental effects of political instability and population displacement on tuberculosis control and demonstrate the power of phylodynamic methods in exploring bacterial evolution in space and time.

Keywords: Mycobacterium tuberculosis; antimicrobial resistance; evolution; phylodynamic analysis; tip-dating.

Fig. 1.

Phylogenetic placement and antibiotic resistance of Mtb isolates in the study. (A) Bayesian dated phylogeny of the CAC. The ASF and the CAC to which it belongs are highlighted in orange and blue, respectively. Filled dots indicate the presence of mutations colored by the compound to which they are known or predicted to confer resistance (magenta, isoniazid; purple, rifampicin; blue, kanamycin; green, fluoroquinolones; yellow, pyrazinamide; orange, streptomycin; red, ethionamide; gray, ethambutol). The TMRCA of the CAC lineage is indicated in red. Two clade B isolates (23) served as outgroups. (B) Relative prevalence of multidrug-resistant TB (MDR-TB) stratified by a history of Soviet Union allegiance (blue, ex-Soviet states; yellow, rest of the world).

Fig. S1.

Timed phylogeny with resistance mutations mapped to nodes. Only mutations present in at least two isolates were mapped. The colored dots at the bottom correspond the timing of individual events of resistance emergence in the phylogeny.

Fig. S2.

Placement of CC1 and clade A isolates within the CAC phylogeny.

Fig. 2.

MIRU repeat changes mapped on whole-genome tip-dated phylogeny. Changes in repeat number relative to MtbC15-9 94–32 of nine variable MIRUs loci annotated on the right. Individual state change events are indicated by arrows in the phylogeny. The arrows are colored to match the color of individual MIRU loci, and the direction of the arrows indicates repeat expansion (up) or contraction (down). To the right, the lengths of the horizontal bars indicate repeat numbers for individual loci.

Fig. 3.

Bayesian evolutionary phylogeny of the ASF. Colored bars indicate country of origin of the patient: orange, Afghanistan; gray, other countries. The country of isolation is annotated on the right.

Fig. 4.

A scenario for the spread of the CAC and ASF in time and space. Color shading and arrows indicate the emergence and spread of the CAC (blue) and ASF (orange). Dots represent cases or clusters of cases belonging to either the CAC or the ASF based on genome sequences, except the cases in Turkey, China, and Tajikistan, for which only MIRU data were available. Red shading of countries is used to indicate membership in the Soviet Union. Red triangles symbolize armed invasion. Afg, Afghanistan; Den, Denmark; Ger, Germany; Nor, Norway; Tur, Turkmenistan; Uzb, Uzbekistan.

Fig. 5.

Estimated Mtb substitution rates in the present study and previously published studies. Colors indicates the lineage to which the samples under study belong: blue, lineage 2; red, lineage 4; black, all). Studies using aDNA (11, 12) and human-Mtb codivergence (9) for calibration are annotated separately. The other studies used tip dating (6, 13, 14) or historical information (16), or counted mutations in paired isolates (15) or serial isolates (17).

Fig. S3.

Calculated TMRCA of the ASF (Upper) and tree height including all isolates (Lower) after tip randomization. Error bars cover the 95% HPD.

Fig. S4.

Root-to-tip regression analyses on various sample sets.

Fig. S5.

Root-to-tip randomization test results. The x-axis denotes t values of the randomized tip distances. The red dotted lines indicate the original nonrandomized estimates.

Fig. S6.

Assessing MCMC chain convergence. Panels show trace output for key parameters, posterior probabilities, substitution rates, and TMRCAs, for key nodes for the CAC and ASF datasets. Three independent chains were run for each dataset.

Fig. S7.

Tip date-calibrated Beast phylogeny including all isolates showing posterior probabilities of individual nodes.

Fig. S8.

Tip date-calibrated Beast phylogeny including all 85 isolates showing individual node ages.