Mycobacterium tuberculosis genotipu izplatība un transmisija Vidzemes un Latgales reģionā.
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Date
2023
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Rīgas Stradiņa universitāte
Rīga Stradiņš University
Rīga Stradiņš University
Abstract
Tuberkuloze (TB) ir viena no izplatītākajām infekcijas slimībām pasaulē. 2016. – 2017. gadā Latgales reģionā novēroja visaugstāko saslimstību ar TB salīdzinājumā ar citiem Latvijas reģioniem. Lai pētītu Mycobacterium tuberculosis (Mtb) genotipu dažādību un noteiktu TB transmisijas virzienu, mūsdienās plaši izmanto pilna genoma sekvencēšanas (whole genome sequencing, WGS) pieeju.
Pētnieciskā darba mērķis ir izpētīt Mtb genotipu izplatību noteiktos Vidzemes un Latgales reģiona novados un pilsētās, kā arī izsekot transmisijas virzienu, izmantojot izolātu DNS WGS pieeju.
2016. un 2017. gadā diagnosticēto TB pacientu Mtb izolātu DNS paraugu kopai tika veikta WGS ar Illumina HiSeq tehnoloģiju, iegūto sekvencēšanas datu analīze – Galaxy platformā un transmisijas koku veidošana – PopART 1.7. programmā.
Atbilstoši WGS Mtb celmu klasifikācijai tika noteikti Beijing (2.2.1), CAS (3.), Haarlem (4.1.2.1), EUA (4.1 un 4.1.2), Ural (4.2.1 un 4.2.1.1), LAM (4.3.3), T (4.7 un 4.8) genotipi. Visizplatītākie no tiem bija T (4.8) un LAM (4.3.3). Tika identificēti 11 saistīto TB inficēšanās gadījumu klasteri ar ģenētisko distanci mazāk kā 20 viena nukleotīda variantu (single nucleotide variant, SNV). Izolāti tikai no sešiem klasteriem ir konstatēti ģeogrāfiski tuvu esošos novados vai vienas pilsētas robežās. Transmisijas virzienu bija iespējams noteikt tikai sešos no vienpadsmit identificētiem klasteriem. Antimikrobiālā rezistence pret etionamīdu tika noteikta visiem EUA (4.1.2) klastera izolātiem. Izolāti ar multirezistentu TB (multidrug-resistant TB, MDR-TB) un pre-ekstensīvi rezistentu TB (pre-extensively drug-resistant TB, pre-XDR-TB) nav iekļauti nevienā no identificētiem klasteriem. Tikai 37 no 91 izolātiem tika identificēti klasteros, kas ļauj secināt, ka Mtb genotipi tiek izplatīti un pārnesti ārpus pētītajiem Vidzemes un Latgales reģiona novadiem un pilsētām.
Tuberculosis (TB) is one of the most common infectious diseases worldwide. In 2016-2017, the highest incidence of TB was observed in the Latgale region compared to other regions of Latvia. The whole genome sequencing (WGS) approach is widely used to study the diversity of Mycobacterium tuberculosis (Mtb) genotypes and determine the direction of TB transmission. The aim of this research was to investigate the distribution of Mtb genotypes in certain districts and cities of the Vidzeme and Latgale region, as well as to follow the direction of transmission using the WGS approach. A set of Mtb isolate DNA samples obtained from TB patients in 2016-2017 was sequenced using Illumina HiSeq technology. The analysis of sequencing files was performed on the Galaxy platform. Median joining networks were created in PopART 1.7 software. Beijing (2.2.1), CAS (3), Haarlem (4.1.2.1), EUA (4.1 and 4.1.2), Ural (4.2.1 and 4.2.1.1), LAM (4.3. 3), T (4.7 and 4.8) genotypes were identified. The most common of them were T (4.8) and LAM (4.3.3). 11 clusters of related TB cases with a genetic distance of less than 20 SNV were identified. Isolates from only six clusters have been found in geographically close districts or within the same city. The direction of transmission could only be determined in six of the 11 identified clusters. Antimicrobial resistance to ethionamide was determined for all isolates of the EUA (4.1.2) cluster. Isolates with multidrug-resistant TB (MDR-TB) and pre-extensively drug-resistant TB (pre-XDR-TB) are not included in any of the identified clusters. Mtb genotypes are distributed and transmitted outside the studied districts and cities of the Vidzeme and Latgale regions, as there are only 37 of 91 isolates identified in clusters.
Tuberculosis (TB) is one of the most common infectious diseases worldwide. In 2016-2017, the highest incidence of TB was observed in the Latgale region compared to other regions of Latvia. The whole genome sequencing (WGS) approach is widely used to study the diversity of Mycobacterium tuberculosis (Mtb) genotypes and determine the direction of TB transmission. The aim of this research was to investigate the distribution of Mtb genotypes in certain districts and cities of the Vidzeme and Latgale region, as well as to follow the direction of transmission using the WGS approach. A set of Mtb isolate DNA samples obtained from TB patients in 2016-2017 was sequenced using Illumina HiSeq technology. The analysis of sequencing files was performed on the Galaxy platform. Median joining networks were created in PopART 1.7 software. Beijing (2.2.1), CAS (3), Haarlem (4.1.2.1), EUA (4.1 and 4.1.2), Ural (4.2.1 and 4.2.1.1), LAM (4.3. 3), T (4.7 and 4.8) genotypes were identified. The most common of them were T (4.8) and LAM (4.3.3). 11 clusters of related TB cases with a genetic distance of less than 20 SNV were identified. Isolates from only six clusters have been found in geographically close districts or within the same city. The direction of transmission could only be determined in six of the 11 identified clusters. Antimicrobial resistance to ethionamide was determined for all isolates of the EUA (4.1.2) cluster. Isolates with multidrug-resistant TB (MDR-TB) and pre-extensively drug-resistant TB (pre-XDR-TB) are not included in any of the identified clusters. Mtb genotypes are distributed and transmitted outside the studied districts and cities of the Vidzeme and Latgale regions, as there are only 37 of 91 isolates identified in clusters.
Description
Farmācija
Pharmacy
Veselības aprūpe
Health Care
Pharmacy
Veselības aprūpe
Health Care
Keywords
Tuberkuloze, transmisija, genotipēšana, spoligotipēšana, pilna genoma sekvencēšana, rezistence, Illumina, klasteru identificēšana., Tuberculosis, transmission, resistance, genotyping, spoligotyping, whole genome sequencing, Illumina, cluster detection.