Whole-genome sequencing to characterize the genetic structure and transmission risk of Mycobacterium tuberculosis in Yichang city of China

Abstract

ObjectiveThe burden of both general and drug-resistant tuberculosis in rural areas is higher than that in urban areas in China. To characterize the genetic structure and transmission risk of Mycobacterium tuberculosis in rural China, we used whole genome sequencing to analyze clinical strains collected from patients in two counties of Yichang for three consecutive years.MethodsFrom 2018 to 2020, sputum samples were collected for cultures from patients with suspected tuberculosis in Yidu and Zigui county, and DNA was extracted from the positive strains for genome sequencing. The online SAM-TB platform was used to identify the genotypes and drug resistance-related mutations of each strain, establish a phylogenetic tree, and calculated the genetic distances between pairwise strains. Twelve single nucleotide polymorphisms (SNPs) were used as thresholds to identify transmission clusters. The risk of related factors was estimated by univariable and multivariable logistic regression.ResultsA total of 161 out of the collected 231 positive strains were enrolled for analysis, excluding non-tuberculous mycobacterium and duplicate strains from the same patient. These strains belonged to Lineage 2 (92, 57.1%) and Lineage 4 (69, 42.9%), respectively. A total of 49 (30.4%) strains were detected with known drug resistance-related mutations, including 6 (3.7%) multidrug-resistant-TB (MDR-TB) strains and 11 (6.8%) RIF-resistant INH-susceptible TB (Rr-TB) strains. Six of the MDR/Rr-TB (35.3%) were also resistant to fluoroquinolones, which made them pre-extensively drug-resistant TB (pre-XDR-TB). There were another seven strains with mono-resistance to fluoroquinolones and one strain with resistance to both INH and fluoroquinolones, making the overall rate of fluoroquinolones resistance 8.7% (14/161). A total of 50 strains (31.1%) were identified as transmission clusters. Patients under 45 years old (adjusted odds ratio 3.46 [95% confidential intervals 1.28–9.35]), treatment-naive patients (6.14 [1.39–27.07]) and patients infected by lineage 4 strains (2.22 [1.00–4.91]) had a higher risk of transmission.ConclusionThe drug resistance of tuberculosis in rural China, especially to the second-line drug fluoroquinolones, is relatively serious. The standardized treatment for patients and the clinical use of fluoroquinolones warrant attention. At the same time, the recent transmission risk of tuberculosis is high, and rapid diagnosis and treatment management at the primary care needs to be strengthened.

The Recent Transmission and Associated Risk Factor of Mycobacterium tuberculosis in Golmud City, China

“…The results showed that more than 10% of the strains belong to MDR/RR-TB, which is higher than the national level in China (7.42%), 7 but similar to the level of Yichang city (11.3%). 27 In addition, low fluoroquinolone resistance rate was detected in this study, which is inconsistent with reports from other provinces in China. 17 , 22 , 27 The conflicting result might be due to the frequency and dosage of fluoroquinolone antibiotics used in different regions or the strains selected for the research.…”

“… 27 In addition, low fluoroquinolone resistance rate was detected in this study, which is inconsistent with reports from other provinces in China. 17 , 22 , 27 The conflicting result might be due to the frequency and dosage of fluoroquinolone antibiotics used in different regions or the strains selected for the research. However, this finding favors future applications of fluoroquinolones in TB treatment regimens of shorter duration.…”

“… 5 , 32 In this study, we provided a snapshot of tuberculosis transmission based on cg-MLST analysis and SNP calling methods, both of them get the same results. Our data show that nearly half (46.97%, 62/132) of MTB strains in possible transmission clusters, higher than in rural counties in China (31.4%) 11 and Yichang city (30.1%), 27 indicating recent transmission is a noticeable cause of TB patients in Golmud. The role of recent transmission was even more pronounced for genotype MDR/RR-TB, among which 65.2% (15/23) were found within putative transmission clusters.…”

Evaluation of Xpert®MTB/XDR test for susceptibility testing ofMycobacterium tuberculosisto first and second-line drugs in Uganda

“…5 [15]. In some areas over 30% of the RR-TB patients are already resistant to FQ, pre-XDR, at the start of the treatment [16]. Therefore, implementing the Xpert MTB/XDR test means that more patients will be initiated to DST guided TB treatment.…”

Evaluation of Xpert MTB/XDR test for susceptibility testing of Mycobacterium tuberculosis to first and second-line drugs in Uganda

“…In some settings over 30% of the RR-TB patients are already resistant to FQ, i.e. pre-XDR, at the start of the treatment [ 14 ]. Therefore, implementing the Xpert MTB/XDR test means that more patients will be initiated to DST-guided TB treatment regimen.…”