Analysis of Mycobacterium tuberculosis genetic lineages circulating in Riga and Riga region, Latvia, isolated between 2008 and 2012

Abstract

Although the number of new tuberculosis (TB) cases registered per year has decreased by 3-fold between 2001 and 2017 in Latvia, the TB incidence and rates of multidrug resistant TB in this Baltic country remain substantially higher than in most other European countries. Molecular typing methods of Mycobacterium tuberculosis (MTB) play an important role both in clinical studies of the disease and the epidemiological investigations, allowing to describe and characterize the pathogen's population structure and spread of particular genotypes. Aim of this study was to examine the prevalence of MTB lineages in Riga and Riga region of Latvia within a five-year period (2008 -2012), and to evaluate the discriminatory power (DP) of spoligotyping, standard 24locus MIRU-VNTR and IS6110-RFLP methods in this setting. The results showed that the main MTB spoligotype families were Beijing (25.3%) and LAM (24.3%), followed by T (22.1%), Ural (11.2%), Haarlem (6.6%) and X superfamily (3.4%). This distribution remained stable over the five consecutive years. 67.6% of MTB isolates were pan-susceptible, and 32.4% were resistant to any drug; multi-drug resistance was found in 5.8% of MTB strains, and 7.6% of MTB isolates were extensively drugresistant. Drug resistance was associated with SIT1, SIT283 and SIT42 genotypes, while SIT1 and SIT42 were overrepresented among multi drugresistant MTB strains. Overall, DP of spoligotyping method alone was 0.8953, while DP of both 24-locus MIRU-VNTR analysis and IS6110 RFLP was higher (DP=0.9846 and 0.9927, respectively), mainly due to the improvement of the resolution for the Beijing strains. In conclusion, this work represents the first comprehensive molecular epidemiological description of TB in Latvia, highlighting the high genetic diversity of MTB strains circulating in Riga and Riga region. In combination with detailed epidemiological data this approach was helpful for the in-depth understanding of epidemiological processes in settings where the Next-Gen sequencing is not available as a routine method.

Beijing genotype of Mycobacterium tuberculosis is associated with extensively drug-resistant tuberculosis: A global analysis

“…After evaluating the potential documents, 41 eligible studies were identified [ [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] , [22] , [23] , [24] , [25] , [26] , [27] , [28] , [29] , [30] , [31] , [32] , [33] , [34] , [35] , [36] , [37] , [38] , [39] , [40] , [41] , [42] , [43] , [44] , [45] , [46] , [47] , [48] , [49] , [50] , [51] , [52] , [53] ]. These studies were conducted between 2006–2020 in Europe, Latin America, Asia, and Africa.…”

Spatiotemporal dynamics of drug‐resistant Mycobacterium tuberculosis : Contrasting trends and implications for tuberculosis control in EU high‐priority country

“…Prevalence of the main M. tuberculosis genotypes in Estonia (this study), Poland (SITVIT2), Latvia (Pole et al., 2020), Murmansk, Russia (Mäkinen et al, 2011), Belarus, reanalysed (Zalutskaya et al, 2013), Sweden (Jonsson et al, 2014), Pskov (Mokrousov, Vyazovaya, et al, 2012), Kaliningrad (Vyazovaya et al, 2017), Finland (Smit et al., 2013) and Karelia (Mokrousov et al, 2015). Free map: http://www.amaps.com/mapstoprint/OUTLINE%20MAPS/free_map_of_world.htm…”

“…For example, LAM-RUS is mainly drug-susceptible in Albania, similar to other M. tuberculosis genotypes in that country (Tafaj et al, 2020). In Latvia, not only Beijing SIT1 but also LAM SIT42 were overrepresented among MDR strains (Pole et al, 2020).…”

“…Also, emerging resistant LAM SIT252 and SIT266 were found in Latvia but not in Estonia. In contrast, the prevalence of the most hazardous Russian subtype Beijing B0/W148‐cluster was similar in Estonia (13.7% in 1999, 21.2% in 2015) and neighbouring Russian Pskov region (16.7% in 2009) and was much higher than in Latvia (5.2%; 11/213 clustered isolates [Pole et al., 2020]).…”

“…Given the absence of the Beijing isolates from Estonia-born before 1941, it seems reasonable to conclude that its high prevalence in this country is a result of the Soviet period of its history . The prevalence of the Beijing genotype in Estonia (37%) is similar to the neighbouring Russian Pskov region, 44% but is higher than in Latvia, 25% (Pole et al, 2020 (Mäkinen et al, 2011), Belarus, reanalysed (Zalutskaya et al, 2013), Sweden (Jonsson et al, 2014), Pskov , Kaliningrad (Vyazovaya et al, 2017), Finland (Smit et al, 2013) and Karelia (Mokrousov et al, 2015). Free map: http://www.amaps.com/mapst oprin t/OUTLI NE%20MAP S/free_map_of_world.htm in Estonia than in Latvia (49% versus 11%).…”