Effects of Mycobacterium tuberculosis lineages and regions of difference (RD) virulence gene variation on tuberculosis recurrence

Background: China ranks second in the incidence of tuberculosis (TB), and the virulence and infectivity of Mycobacterium tuberculosis (M.tb) in different lineages are different. The variation of virulence genes in the M.tb regions of difference (RD) may be the reason for differences in pathogenicity. Studying the relationship between virulence gene mutations in the RD region of clinical strains of M.tb and TB relapse can provide basic data for the study of TB prevention and control. Methods: A total of 155 M.tb clinical strains were collected in Kashgar Prefecture. Whole-genome sequencing (WGS) was conducted, and mutations in virulence genes in the M.tb RD region were analyzed. The maximum likelihood method was implemented using IQ-TREE software. Logistic regression was used to analyze the relationship between lineage, RD region virulence gene variation, and patient relapse. Results: The 155 strains of M.tb in Kashgar Prefecture belong to 3 M.tb lineages: L2 (45.80%), L3 (32.90%), and L4 (21.30%). In relapsed patients, L2 (70.83%, 17/ 24) was significantly higher than the other lineages (29.17%, 7/24; P<0.05). Relapse was significantly correlated with L2 [odds ratio (OR) =3.505; 95% confidence interval (CI): 1.341-9.158; P=0.011]. In the virulence genes of the RD region, g.4357804 (T.G, OR =4.278; 95% CI: 1.594-11.481; P=0.004), g.4359653 (C.T, OR =3.356; 95% CI: 1.303-8.644; P=0.012), and g.2627618 (C.A, OR =2.676; 95% CI: 1.101-6.502; P=0.030) mutations were significantly associated with patient relapse. The mutation frequencies of g.4357804, g.4359653, and g.2627618 in L2 were significantly higher than those in the non-L2 group (P<0.05). Conclusions: Patients infected with L2 are more prone to relapse, and RD region virulence gene variation is an important factor for the strong pathogenicity and easy relapse after infection associated with L2.