Characteristics Analysis Of TB Transmission And Drug Resistance Based On Whole Genome Sequencing

PART ?Characteristics analysis of tuberculosis transmission in Tibet based on whole-genome sequencingObjective To provide a reference for local administration to formulate the measures of prevention and treatment by analyzingthe recent transmission of TB in Tibetand its risk factors based on the whole-genome sequencing.Methods A total of 576 strains of Mycobacterium tuberculosis from 2006,2009 and 2010 in Tibet were collected.The social,demographic and clinical characteristics of each strain were obtained through epidemiological investigation.The questionnaire data was entered through Epi Data 3.1 software,and then univariate and multivariate analysis were performed to analyze the relevant factors affecting the recent and across region transmission of TB in Tibet.Results(1)With 5 and 12 SNPs as the boundary,196(36.3%)and 308(57.0%)cluster strains were identified among 540 M.tuberculosis strains,respectively.(2)The univariate analysis showed that in 2010,the sputum smear(+),Beijing genotype,and RR / MDR were clustered influencing factors(all P values < 0.05),and the multivariate analysis results suggested that when clusters are defined with SNP? 5 or SNP? 12,in 2010(OR SNP? 5 = 2.72,95% CI: 1.70-4.48;OR SNP?12 = 1.88,95% CI: 1.22-2.97),Beijing genotype(OR SNP?5 = 3.77,95% CI: 1.72-9.49;OR SNP?12 = 4.91,95% CI: 2.48-10.47),and RR /MDR(OR SNP?5 = 2.02,95% CI: 1.39-2.49;OR SNP?12 = 1.69,95% CI: 1.17-2.94)were factors influencing clustering(all P values <0.05).(3)There are slightly more extra-regional links(52.1%)than the intra-regional links(47.8%)in Tibet.Except for Lhasa,which is dominated by intra-regional links(66.1%),the other six districts are dominated by intra-regional links.(4)The distributions of primary and retreated cases in the clusters of different sizes were statistically different(?2=10.766,P=0.005).Conclusion The recent spread of TB in Tibet is relatively obvious,which is closely related to Beijing genotype and RR /MDR,and the size of the transmission clusters is related to case types.Lhasa is dominated by intra-regional transmission,and other regions are dominated by extra-regional transmission.PART ?Analysis of drug resistance-associated mutations among multi-drug resistant Mycobacterium tuberculosis in China based on whole-genome sequencingObjective To analyze the resistance mutational profiles of multi-drug resistant Mycobacterium tuberculosis in China and the correlation between major mutation types and genotypes based on the whole-genome sequencing data.Methods Search and download the genome-wide sequencing data of M.tuberculosis from China published by August 2019 according to the NCBI database.Mutation frequency of drug resistancerelated gene loci based on whole-genome sequencing was used to predict the molecular susceptibility results of strains,and the correlation between mutation types and genotypes was analyzed.Results(1)According to the results of molecular resistance and susceptibility profiles,1122 rifampicinresistant strains were identified from 2019 strains,of which 1024(91.3%)were multidrug-resistant strains.(2)The major mutation types of resistance-related genes of 1024 multidrug-resistant strains to commonly used anti-tuberculosis drugs were kat G S315T(73.2%,isoniazid),rpo B S450L(63.1%,rifampicin),rps L K43R(70.0%,streptomycin),emb B M306V(37.4%,ethambutol),pnc A_promoter T(-11)C(7.9%,pyrazinamide),gyr A A90V(32.3%,fluoroquinolones),rrs A1401G(67.7%,second-line injection drugs),fab G1_promoter C(-15)T(87.0%,Ethionamide),fol C I43T(30.4%,P-aminosalicylic acid).(3)The detection rates of Geno Type MTBDRplus for INH and RFP were 99.1% and 90.0%,and the detection rates of MTBDRs I for FQs and SLID were 95.5% and 88.2%,respectively.(4)The frequency of kat G S315 T,emb B M306 V,rps L K43 R,gyr A A90 V in lineage 2 was significantly higher than that in lineage 4,and fol C I43 Twas only found in lineage 2.The prevalence of kat G S315 Twas significantly higher in the ancient Beijing genotype compared to the modern genotype,in contrast,the prevalence of rps L K43 R was significantly higher in modern Beijing genotype(all P values< 0.05).Conclusion The results showed that the main mutation types of resistancerelated genes of many commonly used anti-tuberculosis drugs in China's MDR strains based on whole-genome sequencing,providing a basis for the development of sensitive and specific rapid molecular detection methods.At the same time,it was also found that the major mutation types of multiple resistance-related genes were related to the genotype of strains.