Comparing Two Mycobacterium tuberculosis Genomes from Chinese Immigrants with Native Genomes Using Mauve Alignments

A comparison of phenotypic and WGS drug susceptibility testing in Mycobacterium tuberculosis isolates from the Republic of Korea

Background

WGS has significant potential to help tackle the major public health problem of TB. The Republic of Korea has the third highest rates of TB of all Organisation for Economic Cooperation and Development countries but there has been very limited use of WGS in TB to date.

Objectives

A retrospective comparison of Mycobacterium tuberculosis (MTB) clinical isolates from 2015 to 2017 from two centres in the Republic of Korea using WGS to compare phenotypic drug susceptibility testing (pDST) and WGS drug susceptibility predictions (WGS-DSP).

Methods

Fifty-seven MTB isolates had DNA extracted and were sequenced using the Illumina HiSeq platform. The WGS analysis was performed using bwa mem, bcftools and IQ-Tree; resistance markers were identified using TB profiler. Phenotypic susceptibilities were carried out at the Supranational TB reference laboratory (Korean Institute of Tuberculosis).

Results

For first-line antituberculous drugs concordance for rifampicin, isoniazid, pyrazinamide and ethambutol was 98.25%, 92.98%, 87.72% and 85.96%, respectively. The sensitivity of WGS-DSP compared with pDST for rifampicin, isoniazid, pyrazinamide and ethambutol was 97.30%, 92.11%, 78.95% and 95.65%, respectively. The specificity for these first-line antituberculous drugs was 100%, 94.74%, 92.11% and 79.41%, respectively. The sensitivity and specificity for second-line drugs ranged from 66.67% to 100%, and from 82.98% to 100%, respectively.

Conclusions

This study confirms the potential role for WGS in drug susceptibility prediction, which would reduce turnaround times. However, further larger studies are needed to ensure current databases of drug resistance mutations are reflective of the TB present in the Republic of Korea.

Current situation of tuberculosis and National Strategic Plan for Tuberculosis Control in Korea

Tuberculosis (TB) remains a serious public health problem in Korea. Korea has the highest incidence rate (59 per 100,000 population) and the second-highest TB mortality rate (four per 100,000 population) among Organisation for Economic Cooperation and Development member countries. However, some progress has been made in TB control over the past decade. The notification rate of new TB cases has been gradually decreasing since reaching its highest rate in 2011 (78.9 per 100,000 population). In 2019, the notification rate of new TB cases was 46.4 per 100,000 population, with a reduction of 9.9% from the 2018 rate. Additionally, the number of multidrug-resistant TB cases decreased from 618 in 2018 to 580 in 2019. This progress is thought the result of various TB control programs including a TB public–private mix model, insurance coverage for TB management, and a contact investigation program. Despite the progress made, new challenges have also emerged. The predominant challenges lie in the relatively increasing burden of TB in the vulnerable population (aging, socio-economically vulnerable, and foreign-born population), the implementation of latent TB infection management, and the high rate of multidrug-resistant TB. Since 2019, the Korean government has been implementing the “Midterm strategies to strengthen TB prevention and management” based on the 2nd National Strategic Plan for Tuberculosis Control (2018-2022). This program will be a turning point of TB control in Korea. The results produced in 2023 is expected to be favorable.

Cross-Contamination versus Outbreak: Pre-XDR Mycobacterial Strains Confirmed by Whole-Genome Sequencing

Whole-genome sequencing (WGS) is promising for the quality control of laboratory facilities for Mycobacterium tuberculosis (MTB) strains. We describe the clinical and laboratory characteristics of false positive versus true positive MTB cultures based on WGS, which were experienced in a real clinical setting. Strain harvest and DNA extraction from seven isolates from pre-extensive drug-resistant (pre-XDR) TB patients transferred to the Korea University Ansan Hospital were performed, and epidemiologic links and clinical information, including the phenotypic drug susceptibility test (pDST), were investigated. WGS was performed using Ion GeneStudio with an ION530tm chip (average sequencing depth, ~100-fold). In the phylogenetic tree, identical and different strains were distributed separately. Five of the seven isolates were identical; the remaining two isolates differed from the others. The images of the referred pre-XDR-TB patients with false positive MTB that were analyzed were of regions close to old TB scars. Further, the results of WGS gene mutation analysis for ethambutol, streptomycin, and fluoroquinolone resistance in all six patients were not concordant with the pDST results. WGS and clinical information were useful in differentiating laboratory cross-contamination from true positive TB, thereby avoiding the unnecessary treatment of false positive patients and delay in treating true positive TB patients, with reliable genotypic drug resistance results.