Inferring Mycobacterium Tuberculosis Drug Resistance and Transmission using Whole-genome Sequencing in a High TB-burden Setting in China

Objective China is among the 30 countries with a high burden of tuberculosis(TB)worldwide,and TB remains a public health concern.Kashgar Prefecture in the southern Xinjiang Autonomous Region is considered as one of the highest TB burden regions in China.However,molecular epidemiological studies of Kashgar are lacking.Methods A population-based retrospective study was conducted using whole-genome sequencing(WGS)to determine the characteristics of drug resistance and the transmission patterns.Results A total of 1,668 isolates collected in 2020 were classified into lineages 2(46.0%),3(27.5%),and 4(26.5%).The drug resistance rates revealed by WGS showed that the top three drugs in terms of the resistance rate were isoniazid(7.4%,124/1,668),streptomycin(6.0%,100/1,668),and rifampicin(3.3%,55/1,668).The rate of rifampicin resistance was 1.8%(23/1,290)in the new cases and 9.4%(32/340)in the previously treated cases.Known resistance mutations were detected more frequently in lineage 2 strains than in lineage 3 or 4 strains,respectively:18.6%vs.8.7 or 9%,P<0.001.The estimated proportion of recent transmissions was 25.9%(432/1,668).Multivariate logistic analyses indicated that sex,age,occupation,lineage,and drug resistance were the risk factors for recent transmission.Despite the low rate of drug resistance,drug-resistant strains had a higher risk of recent transmission than the susceptible strains(adjusted odds ratio,1.414;95%CI,1.023–1.954;P=0.036).Among all patients with drug-resistant tuberculosis(DR-TB),78.4%(171/218)were attributed to the transmission of DR-TB strains.Conclusion Our results suggest that drug-resistant strains are more transmissible than susceptible strains and that transmission is the major driving force of the current DR-TB epidemic in Kashgar.

Comparison of Xpert MTB/RIF, Real Amp, and CPA Tests in Detecting Mycobacterium tuberculosis

Today, tuberculosis (TB) remains a global public health threat associated with significantly high rates of morbidity and mortality. The World Health Organization's (WHO) Global Tuberculosis Report 2018[1] has reported that in 2017, 10.0 million people across the world had developed TB diseases that resulted in an estimated 1.6 million deaths, and 889, 000 people developed TB in China that led to 39, 000 TB-related deaths. Therefore, rapid and accurate detection of Mycobacterium tuberculosis (MTB) is important for initiating early treatment and reducing mortality. Traditional diagnostic methods for pulmonary TB incorporate chest radiography and sputum smear microscopy;however, several cases of tuberculosis go undiagnosed because of the low sensitivity of smear microscopy[2].

Comparison of Two Molecular Assays For Detecting Smear Negative Pulmonary Tuberculosis

Objective To compare the performance of MTBDRplus V2 and Xpert MTB/RIF for detecting smear negative pulmonary tuberculosis （PTB）. Methods Clinical PTB suspects were enrolled consecutively in Anhui Chest Hospital and Xi＇an Chest Hospital from January to December in 2014. The sputum samples of smear negative PTB suspects were collected and decontaminated. The sediment was used to conduct MTBDRplus V2, Xpert MTB/RIF and drug susceptibility test （DST）. All the samples with discrepant drug susceptibility result between molecular methods and phenotypic method were confirmed by DNA sequencing. Results A total of 1973 cases were enrolled in this study. The detection rates of Mycobacterium tuberculosis complex （MTBC） by MTBDRplus V2 and Xpert MTB/RIF were 27.67% and 27.98%, respectively. When setting MGIT culture result as a gold standard, the sensitivity and specificity of MTBDRplus V2 were 86.74% and 93.84%, and the sensitivity and specificity of Xpert MTB/RIF were 86.55% and 93.43%, respectively. For the detection of the resistance to rifampin, the sensitivity and specificity of MTBDRplus V2 were 94.34% and 96.62%, and the sensitivity and specificity of Xpert MTB/RIF were 88.68% and 95.96%, respectively. For the detection of the resistance to isoniazid, the sensitivity and specificity of MTBDRplus V2 were 77.38% and 98.02%, respectively. Conclusion MTBDRplus V2 and Xpert MTB/RIF can be used to detect MTBC in smear negative samples with satisfactory performance.

Multicenter Evaluation of the Molecular Line Probe Assay for Multidrug Resistant Mycobacterium Tuberculosis Detection in China

In order to evaluate the performance of a molecular Hain line probe assay （Hain LPA） for rapid detection of rifampicin and isoniazid resistance of Mycobocterium tuberculosis in China, 1612 smear positive patients were consecutively enrolled in this study. Smear positive sputum specimens were collected for Hain LPA and conventional drug susceptibility testing （DST）. The sensitivity and specificity of Hain LPA were analyzed by using conventional DST as golden reference. The sensitivity, specificity, positive predictive value {PPV） and negative predictive value （NPV） for rifampicin resistance detection were 88.33%, 97.66%, 81.54%, and 98.62%, respectively. The sensitivity, specificity, PPV and NPV for isoniazid resistance detection were 80.25%, 98.07%, 87.25%, and 96.78%, respectively. These findings suggested that Hain LPA can be an effective method worthy of broader use in China.

The Feasibility of Sputum Transportation System in China: Effect of Sputum Storage on the Mycobacterial Detection

Sputum transportation from county-level to prefecture-level is an ideal strategy to cover the shortage of the laboratory capability in the resource-poor setting. Here, we firstly evaluated the feasibility of sputum transportation system in China by analyzing the culture and molecular diagnosis results from 1982 smear-positive patients with different delay in processing for culture.

Evaluation of the New Automatic Mycob.T Stainer andScanner for Detecting Acid-fast Bacilli in China

Objective To validate the performance of Mycob. T Stainer and Scanner(MTSS) for detecting acid-fast bacilli(AFB). Methods A total of 3,816 sputum samples from 1,515 tuberculosis(TB) suspects were tested at the Anhui Provincial Chest Hospital and the Linyi People’s Hospital from April-August, 2016. Each specimen was placed on two smear slides. One slide was stained by the ziehl-neelsen(ZN) method to be read by conventional microscopy(CM). The other slide was stained and scanned by MTSS. All specimens were decontaminated with 4% NaO H, and then inoculated into solid culture. The performance of MTSS was assessed. Results MTSS produced higher average positivity rate(27.96%) as compared with the CM(26.83%). The overall sensitivity and specificity of MTSS were 78.9% and 93.9%, respectively. The sensitivity and specificity of CM was 77.4% and 95.0%, respectively. Conclusion MTSS exhibited a favorable performance in the detection of AFB. It may be an alternative to CM for screening TB.

Evaluation of Microsphere-based xMAP Test for gyrA Mutation Identification in Mycobacterium Tuberculosis

Drug-resistant(DR) tuberculosis(TB) is a growing threat to public health[1]. Fluoroquinolone(FQ) antibiotics have long been used as anti-tuberculosis drugs, and their widespread application has led to the development of resistance in clinical isolates of Mycobacterium tuberculosis complex(MTBC).