Distribution of Spoligotyping Defined Genotypic Lineages among Drug-Resistant Mycobacterium tuberculosis Complex Clinical Isolates in Ankara, Turkey

Abstract

BackgroundInvestigation of genetic heterogeneity and spoligotype-defined lineages of drug-resistant Mycobacterium tuberculosis clinical isolates collected during a three-year period in two university hospitals and National Tuberculosis Reference and Research Laboratory in Ankara, Turkey.Methods and FindingsA total of 95 drug-resistant M. tuberculosis isolates collected from three different centers were included in this study. Susceptibility testing of the isolates to four major antituberculous drugs was performed using proportion method on Löwenstein–Jensen medium and BACTEC 460-TB system. All clinical isolates were typed by using spoligotyping and IS6110-restriction fragment length polymorphism (RFLP) methods. Seventy-three of the 95 (76.8%) drug resistant M. tuberculosis isolates were isoniazid-resistant, 45 (47.4%) were rifampicin-resistant, 32 (33.7%) were streptomycin-resistant and 31 (32.6%) were ethambutol-resistant. The proportion of multidrug-resistant isolates (MDR) was 42.1%. By using spoligotyping, 35 distinct patterns were observed; 75 clinical isolates were grouped in 15 clusters (clustering rate of 79%) and 20 isolates displayed unique patterns. Five of these 20 unique patterns corresponded to orphan patterns in the SITVIT2 database, while 4 shared types containing 8 isolates were newly created. The most prevalent M. tuberculosis lineages were: Haarlem (23/95, 24.2%), ill-defined T superfamily (22/95, 23.2%), the Turkey family (19/95, 20%; previously designated as LAM7-TUR), Beijing (6/95, 6.3%), and Latin-America & Mediterranean (LAM, 5/95 or 5.3%), followed by Manu (3/95, 3.2%) and S (1/95, 1%) lineages. Four of the six Beijing family isolates (66.7%) were MDR. A combination of IS6110-RFLP and spoligotyping reduced the clustering rate from 79% to 11.5% among the drug resistant isolates.ConclusionsThe results obtained showed that ill-defined T, Haarlem, the Turkey family (previously designated as LAM7-TUR family with high phylogeographical specifity for Turkey), Beijing and LAM were predominant lineages observed in almost 80% of the drug-Resistant M. tuberculosis complex clinical isolates in Ankara, Turkey.

Genotype distribution of Mycobacterium tuberculosis in theAegean Region and associated demographic factors

“…In a study on 4069 M. tuberculosis strains isolated in İstanbul in 2002-2005, the prevalence of the Beijing genotype was 1.1% (46/4069), the MDR rate was 12.5% (510/4069), the Beijing genotype's prevalence among multidrug-resistant TB isolates was 3.7% (19/510), MDR was found in 41.3% (19/49) of the Beijing strains, and 10 out of the 19 Beijing strains were isolated from patients who were citizens of former Soviet Union countries (17). In three different studies conducted on drug-resistant and multidrug-resistant TB isolates in Turkey, the most common type was ST41 with rates of 26%, 22.5%, and 16.8%, and ST53 was the second most common with rates of 14%, 19.5%, and 15.8% (15,16,18). In our study, the rate of MDR was 3%, six of the 12 multidrug-resistant Figure. The distribution of spoligotypes in different studies on M. tuberculosis strains in Turkey: locations and years of the studies (%).…”

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

“…This includes patterns belonging to the H4 sublineage, relabeled "Ural-2," and some patterns previously classified as belonging to the H3 sublineage but with an additional specific signature (presence of spacer 2 and absence of spacers 29 to 31 and 33 to 36), relabeled "Ural-1." Additionally, two LAM sublineages were recently raised to the independent-lineage level: LAM10-CAM was designated the Cameroon lineage (588), and LAM7-TUR was designated the Turkey lineage (589,590). A major contribution of publicly available global TB genotyping databases is the ease with which one can map genotyping data to describe the TB genetic landscape.…”

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

“…The Turkish (Tur) sublineage was first described in Turkey where it represents 10 to 30% of all clinical isolates depending on regions, and named as " LAM7-Tur" in 2005(Durmaz et al, 2007Kisa et al, 2012;Oral Zeytinli and Koksal, 2012;Otlu et al, 2009;Zozio et al, 2005). The absence of phylogenetic relationship with other LAM sublineages such as the absence of ligB synonymous mutation C1212G led to its progressive renaming as Tur Dos Vultos et al, 2008).…”

“…We did not further exclude SNPs in PE-PPE genes remaining sequences but they represented a minority of the SNPs (n=669; 4.8%). The phylogenetic tree based on WGS data was built using MEGA v.6 based on a string of concatenated SNPs deprived of information concerning position in codon (n=14,013) and was midpoint rooted (Kumar et al, 2004).…”