GENETIC DIVERSITY AND POPULATION STRUCTURE OF M.

TUBERCULOSIS STRAINS CIRCULATING IN CENTRAL RUSSIA

Shemyakin I.G., State Research Centre for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russia

Research on Tuberculosis

Study settings
Study population
Pop. 6 618 538 I.R. 59/100 000

Moscow

Epidemiologically unlinked M. tuberculosis strains from the Tula, Kaluga, and Moscow regions

Obolensk

Study methods
Kaluga
Pop. 1 041 641 I.R. 72,4 /100 000

Tula
Pop. 1 675 758 I.R. 106.8/100 000

Epidemiological markers (IS6110-RFLP, spoligotyping, MIRU-VNTR typing) Phylogenetic markers (SCG, PGG)

Identification of SNP Clustered Group (SCG)

Position in H37Rv Genome 3352929 92197 473678 1920118 2460626 3111473

SCG1 SCG2 SCG3 SCG4 SCG5 SCG6 SCG7 C G A G C T G T G T A C C G A G C T G T G T A C C G A G C T G T G T A C C G A G C T G T G T A C C G A G C T G T G T A C C G A G C T G T G T A C C G A G C T G T G T A C

SCG2

SCG3

SCG5

SCG6

SCG7

M
1000bp 500bp 200bp

Genetic diversity of M. tuberculosis strains based on their IS6110-RFLP patterns

0.8

0.6

0.4

0.2

Beijing SCG3/PGG2 SCG6/PGG3 SCG2/PGG1

LAM-RUS SCG5/PGG2

Phylogenetic tree
MIRU-VNTR typing

LAM-RUS

SCG 2; PGG 1 SCG 3; PGG 2 SCG 5; PGG 2* SCG 6; PGG 3 SCG 5; PGG 2

Beijing

Prevalence of plcABC::IS6110 genotype in different phylogenetic groups

Ins1 Ins2 Ins3

2632075

plcA
IS6110 insertion

plcB

plcC
phospholipase C genes

2627172

Phylogenetic groups PGG1/SCG2 PGG2/SCG3 PGG2/SCG5 PGG3/SCG6

Total isolate no. 10 30 47 20

Isolates with plcABC::IS6110 genotype 45 (Ins2, plcA) 1 (Ins1, plcA) 1 (Ins3, plcC)

Identification of LAM-RUS strains

plcA U 286bp B plcA IS6110 U H 163bp 410bp C plcA IS6110 U Variable length I R I R R

C M
1000bp 500bp 100bp

Study settings
Study population sets of M. tuberculosis strains recovered in Tula dispensary and Ozerki prison hospital (Tula region) during one-year study Ozerki Study methods Epidemiological markers
IS6110-RFLP, spoligotyping, MIRU-VNTR typing

Tula

Phylogenetic markers
Population: TB incidence rate: Incarceration rate: 1 041 641 106.8/100 000 10.44/1 000

SCG, PGG

Profiling of drug resistance

Patients characteristics

Prison hospital Patient no. Clusters no. Average cluster size % Clustered cases No. of shared clusters 81 11 4.5 72% 7

City dispensary 167 20 3.2 36%

Prevalence of drug resistant TB among new and previously treated patients

Prison hospital n.c. Patient no. Susceptible MDR MDR+KAN 24 25% 50% 29% p.t. 57 5% 86% 82%

City dispensary n.c. 58 31% 20% 12% p.t. 109 19% 59% 46%

Prevalence of strains of different phylogenetic groups in prison and civilian population

Prison hospital
SCG6 6%

City dispensary
SCG6 10%

SCG2 40% SCG5 48%

SCG5 43%

SCG2 29%

SCG3 6%

SCG3 18%

Drug resistance profiles of major M.tuberculosis strains

250 200 150 100 50 0

Susc. Beijing LAM-RUS

KAN STR EMB INH
14(17%) 10(9%) 24(39%)

MDR
44(54%) 81(74%) 8(13%)

MDR+K
25(31%) 73(67%) 4(6%)

Others
Total

Beijing

LAM -RUS

RIF

Others

Major clusters identified by IS6110-RFLP

Beijing
0.8

LAM-RUS

0.6

0.4

0.2

ST252 City dispensary Prison hospital SCG2 SCG6 SCG3 SCG5

Neglected epidemics
Spoligotype ST252: 777477607760771. Belongs to SCG5/PGG2, LAM-RUS strains. Comprises 29% of the study sample (71 of 248 isolates). Prevalent in both prison and civilian population (27 and 44 cases, respectively). Includes 11 newly diagnosed cases. Drug resistance profile STR, KAN, RIF, INH, (EMB) Comprises 53% of all MDR TB in the study population. Genetic markers for drug resistance: S315T katG, D516V rpoB, M306I embB.

Conclusions
Members of tree modern SCG 3, 5 and 6, together with ancestral SCG2 are major contributors to the genetic diversity of the M. tuberculosis strains circulating in central Russia; LAM-RUS family of strains contained an insertion in a unique position in the plcA gene, which can serve as specific genetic marker for this group; Prisons have a significant impact on the TB incidence in the civilian population. Major clusters comprised from isolates recovered in both prison and civilian hospitals, emphasizing the interdependence of two populations; Majority of MDR TB cases in the region are due to Beijing or LAMRUS; Abundance of MDR strains resistant to KAN implies that we may face the XDR epidemics in the region before long.