Prediction of drug resistance profile of multidrug-resistant Mycobacterium tuberculosis (MDR-MTB) isolates from newly diagnosed case by whole genome sequencing (WGS): a study from a high tuberculosis burden country.

OBJECTIVES: Our aim was to assess the ability of the Whole-genome sequencing (WGS) in predicting drug resistance profile of multidrug-resistant mycobacterium tuberculosis (MDR-MTB) from newly diagnosed cases in China. METHODS: We validated the Phenotypic drug Sensitivity Test (pDST) for 12 anti-tuberculosis drugs using the Bactec MGIT 960 system. We described the characteristics of the isolates enrolled and compared the pDST results with resistance profiles predicted by WGS. RESULTS: The pDST showed that of the 43 isolates enrolled, 25.6% were sensitive to rifabutin (RFB); 97.7%、97.7%、93.0% and 93.0% were sensitive to cycloserine (Cs), amikacin/kanamycin (Ak/Km), para-aminosalicylic acid (Pas) and ethionamide Eto), respectively; 18.6% were resistant to fluoroquinolones (FQs) or second-line injections. Genotype DST determined by WGS of Ak/Km、Eto and RFP reached high consistency to 97.7% compared with pDST, followed by moxifloxacin (Mfx) 95.3%, levofloxaci (Lfx) and Pas 93%, streptomycin (Sm) 90.3%. The genotype DST of RFB and EMB showed low consistency with the pDST of 67.2 and 79.1%. WGS also detected 27.9% isolates of pyrazinamide(PZA)-related drug-resistant mutation. No mutations associated with linezolid (Lzd), bedaquiline (Bdq) and clofazimine (Cfz) were detectd. CONCLUSIONS: WGS has the potential to infer resistance profiles without time-consuming phenotypic methods, which could be provide a basis to formulate reasonable treatment in high TB burden areas.

A highly effective and inexpensive standardized treatment of multidrug-resistant tuberculosis: a multicenter prospective study in China.

BACKGROUND: To verify the efficacy and safety of an inexpensive standardized regimen for multidrug-resistant tuberculosis (MDR-TB) with low resistance to isoniazid (INH), a multicenter prospective study was conducted in eastern China. METHODS: Patients diagnosed as MDR-TB with low concentration INH resistance and rifampicin resistance, second-line/injectable agents sensitive were prospectively enrolled, given the regimen of Amikacin (Ak)-Fluoroquinolones (FQs)-Cycloserine (Cs)-Protionamide (Pto)-PasiniaZid (Pa)-Pyrazinamide (Z) for 6 months followed by 12 months of FQs-Cs-Pto-Pa-Z, and then followed up for treatment outcomes and adverse events (AEs). RESULTS: A total of 114 patients were enrolled into the study. The overall favorable treatment rate was 79.8% (91/114). Among 91 cases with favorable treatment, 75.4% (86/114) were cured and 4.4% (5/114) were completed treatment. Regarding to unfavorable outcomes, among 23 cases, 8.8% (10/114) had failures, 8.8% (10/114) losing follow up, 0.9% (1/114) had treatment terminated due to intolerance to drugs and 1.8% (2/114) died. Treatment favorable rate was significantly higher in newly treated MDR-TB (91.7%, 33/36) than that in retreated MDR-TB (74.4%, 58/78, p 0.03). The investigators recorded 42 AEs occurrences in 30 of 114 patients (26.3%). Clinicians rated most AEs as mild or moderate (95.24%, 40/42). CONCLUSIONS: The regimen was proved to be effective, safe and inexpensive. It is suitable for specific drug resistant population, especially for newly-treated patients, which could be expected to be developed into a short-course regimen. Clinical trials registration China Clinical Trial Registry ChiCTR-OPC-16009380.

Effect of the Xpert MTB/RIF on the detection of pulmonary tuberculosis cases and rifampicin resistance in Shanghai, China.

BACKGROUND: Xpert MTB/RIF (Xpert) is an automated molecular test recommended by World Health Organization (WHO) for diagnosis of tuberculosis (TB). This study evaluated the effect of Xpert implementation on the detection of pulmonary TB (PTB) and rifampicin-resistant TB (RR-TB) cases in Shanghai, China. METHODS: Xpert was routinely implemented in 2018 for all presumptive PTB patients. All PTB patients above 15 years-old identified within the Provincial TB Control Program during the first half of each of 2017 and 2018, were enrolled to compare the difference in proportions of bacteriological confirmation, patients with drug susceptibility test (DST) results for rifampicin (ie, DST coverage) and RR-TB detection before and after Xpert's implementation. RESULTS: A total of 6047 PTB patients were included in the analysis with 1691 tested by Xpert in 2018. Percentages of bacteriological confirmation, DST coverage and RR-TB detection in 2017 and 2018 were 50% vs. 59%, 36% vs. 49% and 2% vs. 3%, respectively (all p-values < 0.05). Among 1103 PTB patients who completed sputum smear, culture and Xpert testing in 2018, Xpert detected an additional 121 (11%) PTB patients who were negative by smear and culture, but missed 248 (23%) smear and/or culture positive patients. Besides, it accounted for an increase of 9% in DST coverage and 1% in RR-TB detection. The median time from first visit to a TB hospital to RR-TB detection was 62 days (interquartile range -IQR 48-84.2) in 2017 vs. 9 days (IQR 2-45.7) in 2018 (p-value < 0.001). In the multivariate model, using Xpert was associated with decreased time to RR-TB detection (adjusted hazard ratio = 4.62, 95% confidence interval: 3.18-6.71). CONCLUSIONS: Integrating Xpert with smear, culture and culture-based DST in a routine setting significantly increased bacteriological confirmation, DST coverage and RR-TB detection with a dramatic reduction in the time to RR-TB diagnosis in Shanghai, China. Our findings can be useful for other regions that attempt to integrate Xpert into routine PTB and RR-TB case-finding cascade. Further study should focus on the identification and elimination of operational level challenges to fully utilize the benefit of rapid diagnosis by Xpert.

High incidence and low case detection rate among contacts of tuberculosis cases in Shanghai, China.

BACKGROUND: To assess the effect of a contact investigation strategy by assessing the incidence of tuberculosis and the case detection rate among contacts of tuberculosis patients. METHODS: The pulmonary tuberculosis incidence among contacts was determined retrospectively from a tuberculosis information management system. For each detection method (symptom examination only, symptom examination plus chest radiography or other alternatives), the detection rate of pulmonary tuberculosis patients among contacts was derived from contact investigation form records. RESULTS: Sixty-nine cases of pulmonary tuberculosis were identified among a total of 8137 contacts after an average follow-up of 2.6 years (range: 0.25-5.25) during the period from 2010 to 2014. The incidence density was 329/100,000 person-years (PYs), and the 95% confidence interval (CI) was 256-419/100,000 PYs, which was significantly higher than the notification rate during the same period in the general population (29-30/100,000 PYs). The incidence density was higher (p < 0.0001) among male contacts (462/100,000 PYs) than among female contacts (236/100,000 PYs). The incidence density did not differ (p > 0.05) between contacts whose index case was sputum smear positive and those whose index case was sputum smear negative. Contacts who were biologically related family of the index cases exhibited a higher (p < 0.05) incidence density (475/100,000 PYs) than other contacts (281/100,000 PYs). Fifteen of the 69 incident cases were found through contact investigation, corresponding to a case detection rate via contact investigation of 22% (95% CI: 13-33%). The relevance ratio was 288/100,000 (12/4163) by both chest radiography and symptom survey, which was significantly higher than the rate detected by symptom survey alone, of 57/100,000 (2/3486), p = 0.028. The cumulative incidence in the contacts was 761/100,000 (62/8137) within 3 years from the time that the index cases were diagnosed with pulmonary tuberculosis, which was higher than the incidence rate of 210/100,000 (7/3328) recorded after 3 years (p < 0.001). CONCLUSIONS: The contacts were at higher risk of pulmonary tuberculosis than the general population; however, only approximately 22% of the incident cases could be detected through contact investigation. Therefore, the contact investigation strategy must be improved for better detection of potential pulmonary tuberculosis cases.

Time to Multidrug-Resistant Tuberculosis Treatment Initiation in Association with Treatment Outcomes in Shanghai, China.

In high tuberculosis (TB)-burden countries such as China, the diagnosis of multidrug-resistant tuberculosis (MDR-TB) using conventional drug susceptibility testing (DST) takes months, making treatment delay inevitable. Poor outcomes of MDR-TB might be associated with delayed, even inappropriate, treatment. The purposes of this study were to investigate the time to MDR-TB treatment initiation and to assess the association between early treatment and treatment outcomes. Between April 2011 and December 2014, this population-based retrospective cohort study collected the demographic and clinical characteristics and the drug susceptibility profiles of all registered MDR-TB patients in Shanghai, China. The dates of TB and MDR-TB diagnoses, DST performance, and treatment initiation were extracted to calculate the times to treatment. In total, 284 of 346 MDR-TB patients were eligible for analysis, and 68.3% (194/284) had favored outcomes. The median time to treatment initiation from TB diagnosis was 172 days among those with favored outcomes and 190 days among those with poor outcomes. Treatments initiated within 60 days after performing DST (odds ratio [OR], 2.56; 95% confidence interval [CI], 1.22 to 5.36) and empirical treatments (OR, 2.09; 95% CI, 1.01 to 4.32) were positively associated with favored outcomes. Substantial delays to MDR-TB treatment were observed when conventional DST was used. Early treatment predicted favored outcomes. Rapid diagnostic methods should be scaled up and improvements should be made in patient management and information linkage to reduce treatment delay.

Corrigendum: Assessing heterogeneity of patient and health system delay among TB in a population with internal migrants in China.

[This corrects the article DOI: 10.3389/fpubh.2024.1354515.].

Transmission of fluoroquinolones resistance among multidrug-resistant tuberculosis in Shanghai, China: a retrospective population-based genomic epidemiology study.

Fluoroquinolones (FQ) are essential for the treatment of multidrug-resistant tuberculosis (MDR-TB). The FQ resistance (FQ-R) rate in MDR-TB in China and its risk factors remain poorly understood. We conducted a retrospective, population-based genomic epidemiology study of MDR-TB patients in Shanghai, China, from 2009 to 2018. A genomic cluster was defined as strains with genetic distances ≤ 12 single nucleotide polymorphisms. The transmitted FQ-R was defined as the same FQ resistance-conferring mutations shared by ≥ 2 strains in a genomic cluster. We used multivariable logistic regression analysis to identify the risk factors for drug resistance. Among the total 850 MDR-TB patients included in the study, 72.8% (619/850) were male, the median age was 39 (interquartile range 28, 55) years, 52.7% (448/850) were migrants, and 34.5% (293/850) were previously treated patients. Most of the MDR-TB strains belong to the Beijing lineage (91.7%, 779/850). Overall, the genotypic resistance rate of FQ was 34.7% (295/850), and 47.1% (139/295) FQ-R patients were in genomic clusters, of which 98 (33.2%, 98/295) were presumed as transmitted FQ-R. Patients with treatment-naïve (aOR = 1.84; 95% CI: 1.09, 3.16), diagnosed in a district-level hospital (aOR = 2.69; 95% CI: 1.56, 4.75), and streptomycin resistance (aOR = 3.69; 95% CI: 1.65, 9.42) were significantly associated with the transmission of FQ-R. In summary, the prevalence of FQ-R among MDR-TB patients was high in Shanghai, and at least one-third were transmitted. Enforced interventions including surveillance of FQ drug susceptibility testing and screening among MDR-TB before initiation of treatment were urgently needed.

Assessing heterogeneity of patient and health system delay among TB in a population with internal migrants in China.

Backgrounds: The diagnostic delay of tuberculosis (TB) contributes to further transmission and impedes the implementation of the End TB Strategy. Therefore, we aimed to describe the characteristics of patient delay, health system delay, and total delay among TB patients in Shanghai, identify areas at high risk for delay, and explore the potential factors of long delay at individual and spatial levels. Method: The study included TB patients among migrants and residents in Shanghai between January 2010 and December 2018. Patient and health system delays exceeding 14 days and total delays exceeding 28 days were defined as long delays. Time trends of long delays were evaluated by Joinpoint regression. Multivariable logistic regression analysis was employed to analyze influencing factors of long delays. Spatial analysis of delays was conducted using ArcGIS, and the hierarchical Bayesian spatial model was utilized to explore associated spatial factors. Results: Overall, 61,050 TB patients were notified during the study period. Median patient, health system, and total delays were 12 days (IQR: 3-26), 9 days (IQR: 4-18), and 27 days (IQR: 15-43), respectively. Migrants, females, older adults, symptomatic visits to TB-designated facilities, and pathogen-positive were associated with longer patient delays, while pathogen-negative, active case findings and symptomatic visits to non-TB-designated facilities were associated with long health system delays (LHD). Spatial analysis revealed Chongming Island was a hotspot for patient delay, while western areas of Shanghai, with a high proportion of internal migrants and industrial parks, were at high risk for LHD. The application of rapid molecular diagnostic methods was associated with reduced health system delays. Conclusion: Despite a relatively shorter diagnostic delay of TB than in the other regions in China, there was vital social-demographic and spatial heterogeneity in the occurrence of long delays in Shanghai. While the active case finding and rapid molecular diagnosis reduced the delay, novel targeted interventions are still required to address the challenges of TB diagnosis among both migrants and residents in this urban setting.

Spatial pattern of isoniazid-resistant tuberculosis and its associated factors among a population with migrants in China: a retrospective population-based study.

Background: Isoniazid-resistant, rifampicin-susceptible tuberculosis (Hr-TB) globally exhibits a high prevalence and serves as a potential precursor to multidrug-resistant tuberculosis (MDR-TB). Recognizing the spatial distribution of Hr-TB and identifying associated factors can provide strategic entry points for interventions aimed at early detection of Hr-TB and prevention of its progression to MDR-TB. This study aims to analyze spatial patterns and identify socioeconomic, demographic, and healthcare factors associated with Hr-TB in Shanghai at the county level. Method: We conducted a retrospective study utilizing data from TB patients with available Drug Susceptible Test (DST) results in Shanghai from 2010 to 2016. Spatial autocorrelation was explored using Global Moran's I and Getis-Ord Gi∗ statistics. A Bayesian hierarchical model with spatial effects was developed using the INLA package in R software to identify potential factors associated with Hr-TB at the county level. Results: A total of 8,865 TB patients with DST were included in this analysis. Among 758 Hr-TB patients, 622 (82.06%) were new cases without any previous treatment history. The drug-resistant rate of Hr-TB among new TB cases in Shanghai stood at 7.20% (622/8014), while for previously treated cases, the rate was 15.98% (136/851). Hotspot areas of Hr-TB were predominantly situated in southwestern Shanghai. Factors positively associated with Hr-TB included the percentage of older adult individuals (RR = 3.93, 95% Crl:1.93-8.03), the percentage of internal migrants (RR = 1.35, 95% Crl:1.15-1.35), and the number of healthcare institutions per 100 population (RR = 1.17, 95% Crl:1.02-1.34). Conclusion: We observed a spatial heterogeneity of Hr-TB in Shanghai, with hotspots in the Songjiang and Minhang districts. Based on the results of the models, the internal migrant population and older adult individuals in Shanghai may be contributing factors to the emergence of areas with high Hr-TB notification rates. Given these insights, we advocate for targeted interventions, especially in identified high-risk hotspots and high-risk areas.

Dynamic Prediction Model for Initial Apple Damage.

Prediction models of damage severity are crucial for the damage expression of fruit. In light of issues such as the mismatch of existing models in actual damage scenarios and the failure of static models to meet research needs, this article proposes a dynamic prediction model for damage severity throughout the entire process of apple damage and studies the relationship between the initial bruise form and impact energy distribution of apple damage. From the experiments, it was found that after impact a "cell death zone" appeared in the internal pulp of the damaged part of Red Delicious apples. The reason for the appearance of the cell death zone was that the impact force propagated in the direction of the fruit kernel in the form of stress waves; the continuous action of which continuously compressed the pulp's cell tissue. When the energy absorbed via elastic deformation reached the limit value, intercellular disadhesion of parenchyma cells at the location of the stress wave peak occurred to form cell rupture. The increase in intercellular space for the parenchyma cells near the rupture site caused a large amount of necrocytosis and, ultimately, formed the cell death zone. The depth of the cell death zone was closely related to the impact energy. The correlation coefficient r between the depth of the cell death zone and the distribution of impact energy was slightly lower at the impact height of 50 mm. As the impact height increased, the correlation coefficient r increased, approaching of value of 1. When the impact height was lower (50 mm), the correlation coefficient r had a large distribution range (from 0.421 to 0.983). As the impact height increased, the distribution range significantly decreased. The width of the cell death zone had a poor correlation with the pressure distribution on the impact surface of the apples that was not related to the impact height. In this article, the corresponding relationship between the form and impact energy distribution of the internal damaged tissues in the initial damage of Red Delicious apples was analyzed. This analysis aimed to provide a research concept and theoretical basis for more reliable research on the morphological changes in the damaged tissues of apples in the future, further improving the prediction accuracy of damage severity.

Assessing the spatial heterogeneity of tuberculosis in a population with internal migration in China: a retrospective population-based study.

Background: Internal migrants pose a critical threat to eliminating Tuberculosis (TB) in many high-burden countries. Understanding the influential pattern of the internal migrant population in the incidence of tuberculosis is crucial for controlling and preventing the disease. We used epidemiological and spatial data to analyze the spatial distribution of tuberculosis and identify potential risk factors for spatial heterogeneity. Methods: We conducted a population-based, retrospective study and identified all incident bacterially-positive TB cases between January 1st, 2009, and December 31st, 2016, in Shanghai, China. We used Getis-Ord Gi* statistics and spatial relative risk methods to explore spatial heterogeneity and identify regions with spatial clusters of TB cases, and then used logistic regression method to estimate individual-level risk factors for notified migrant TB and spatial clusters. A hierarchical Bayesian spatial model was used to identify the attributable location-specific factors. Results: Overall, 27,383 bacterially-positive tuberculosis patients were notified for analysis, with 42.54% (11,649) of them being migrants. The age-adjusted notification rate of TB among migrants was much higher than among residents. Migrants (aOR, 1.85; 95%CI, 1.65-2.08) and active screening (aOR, 3.13; 95%CI, 2.60-3.77) contributed significantly to the formation of TB high-spatial clusters. With the hierarchical Bayesian modeling, the presence of industrial parks (RR, 1.420; 95%CI, 1.023-1.974) and migrants (RR, 1.121; 95%CI, 1.007-1.247) were the risk factors for increased TB disease at the county level. Conclusion: We identified a significant spatial heterogeneity of tuberculosis in Shanghai, one of the typical megacities with massive migration. Internal migrants play an essential role in the disease burden and the spatial heterogeneity of TB in urban settings. Optimized disease control and prevention strategies, including targeted interventions based on the current epidemiological heterogeneity, warrant further evaluation to fuel the TB eradication process in urban China.

Effect of mobile health reminders on tuberculosis treatment outcomes in Shanghai, China: A prospective cohort study.

Background: Poor adherence increases the risk of unfavorable outcomes for tuberculosis (TB) patients. Mobile health (mHealth) reminders become promising approaches to support TB patients' treatment. But their effects on TB treatment outcomes remain controversial. In this prospective cohort study, we evaluated the effect of the reminder application (app) and the smart pillbox on TB treatment outcomes compared with the standard care in Shanghai, China. Methods: We recruited new pulmonary TB (PTB) patients diagnosed between April and November 2019 who were aged 18 or above, treated with the first-line regimen (2HREZ/4HR), and registered at Songjiang CDC (Shanghai). All eligible patients were invited to choose the standard care, the reminder app, or the smart pillbox to support their treatment. Cox proportional hazard model was fitted to assess the effect of mHealth reminders on treatment success. Results: 260 of 324 eligible patients enrolled with 88 using standard care, 82 the reminder app, and 90 the smart pillbox, followed for a total of 77,430 days. 175 (67.3%) participants were male. The median age was 32 (interquartile range [IQR] 25 to 50) years. A total of 44,785 doses were scheduled for 172 patients in the mHealth reminder groups during the study period. 44,604 (99.6%) doses were taken with 39,280 (87.7%) monitored by the mHealth reminders. A significant time-dependent downward linear trend was observed in the monthly proportion of dose intake (p < 0.001). 247 (95%) patients were successfully treated. The median treatment duration of successfully treated patients in the standard care group was 360 (IQR 283-369) days, significantly longer than those in the reminder app group (296, IQR 204-365, days) and the smart pillbox group (280, IQR 198-365, days) (both p < 0.01). Using the reminder app and the smart pillbox was associated with 1.58 times and 1.63 times increase in the possibility of treatment success compared with the standard care, respectively (both p < 0.01). Conclusion: The reminder app and the smart pillbox interventions were acceptable and improved the treatment outcomes compared with the standard care under the programmatic setting in Shanghai, China. More high-level evidence is expected to confirm the effect of mHealth reminders on TB treatment outcomes.

Use of Whole-Genome Sequencing to Predict Mycobacterium tuberculosis Complex Drug Resistance from Early Positive Liquid Cultures.

Our objective was to evaluate the performance of whole-genome sequencing (WGS) from early positive liquid cultures for predicting Mycobacterium tuberculosis complex (MTBC) drug resistance. Clinical isolates were obtained from tuberculosis patients at Shanghai Pulmonary Hospital (SPH). Antimicrobial susceptibility testing (AST) was performed, and WGS from early Bactec mycobacterial growth indicator tube (MGIT) 960-positive liquid cultures was performed to predict the drug resistance using the TB-Profiler informatics platform. A total of 182 clinical isolates were enrolled in this study. Using phenotypic AST as the gold standard, the overall sensitivity and specificity for WGS were, respectively, 97.1% (89.8 to 99.6%) and 90.4% (83.4 to 95.1%) for rifampin, 91.0% (82.4 to 96.3%) and 95.2% (89.1 to 98.4%) for isoniazid, 100.0% (89.4 to 100.0%) and 87.3% (80.8 to 92.1%) for ethambutol, 96.6% (88.3 to 99.6%) and 61.8% (52.6 to 70.4%) for streptomycin, 86.8% (71.9 to 95.6%) and 95.8% (91.2 to 98.5%) for moxifloxacin, 86.5% (71.2 to 91.5%) and 95.2% (90.3 to 98.0%) for ofloxacin, 100.0% (54.1 to 100.0%) and 67.6% (60.2 to 74.5%) for amikacin, 100.0% (63.1 to 100.0%) and 67.2% (59.7 to 74.2%) for kanamycin, 62.5% (24.5 to 91.5%) and 88.5% (82.8 to 92.8%) for ethionamide, 33.3% (4.3 to 77.7%) and 98.3% (95.1 to 99.7%) for para-aminosalicylic acid, and 0.0% (0.0 to 12.3%) and 100.0% (97.6 to 100.0%) for cycloserine. The concordances of WGS-based AST and phenotypic AST were as follows: rifampin (92.9%), isoniazid (93.4%), ethambutol (89.6%), streptomycin (73.1%), moxifloxacin (94.0%), ofloxacin (93.4%), amikacin (68.7%), kanamycin (68.7%), ethionamide (87.4%), para-aminosalicylic acid (96.2%) and cycloserine (84.6%). We conclude that WGS could be a promising approach to predict MTBC resistance from early positive liquid cultures. IMPORTANCE In this study, we used whole-genome sequencing (WGS) from early positive liquid (MGIT) cultures instead of solid cultures to predict drug resistance of 182 Mycobacterium tuberculosis complex (MTBC) clinical isolates to predict drug resistance using the TB-Profiler informatics platform. Our study indicates that WGS may be a promising method for predicting MTBC resistance using early positive liquid cultures.

Prevalence of latent tuberculosis infection and incidence of active tuberculosis in school close contacts in Shanghai, China: Baseline and follow-up results of a prospective cohort study.

Background: The management of latent tuberculosis infection (LTBI) is a key action for the realization of the "End tuberculosis (TB) Strategy" worldwide, and it is important to identify priority populations. In this prospective cohort study, we evaluated the prevalence of LTBI and incidence of active TB among close contacts and explored the suitable TB control strategy in schools. Methods: We designed a cohort with 2 years of follow-up, recruiting freshman/sophomore TB patients' close contacts from three administrative districts in Shanghai. These were chosen based on different levels of TB incidence reported in 2019. Questionnaires were included and all participants received both tuberculin skin test (TST) and QuantiFERON-TB Gold (QFT) at baseline, then tracked the outcomes of them during the follow-up period. Results: The prevalence of LTBI was 4.8% by QFT. Univariate analysis showed that the risk of LTBI was higher in those contacting bacteriologically confirmed patients or did not have BCG scars, including smokers. The risk increased with poor lighting and ventilation conditions at contact sites. Multivariate analysis showed that those contacting with bacteriologically confirmed patients (OR=4.180; 95%CI, 1.164-15.011) or who did not have BCG scars (OR=5.054; 95%CI, 2.278-11.214) had a higher risk of being LTBI, as did the current smokers (OR=3.916; 95%CI, 1.508-10.168) and those who had stopped smoking (OR=7.491; 95%CI, 2.222-25.249). During the 2-year follow-up period, three clinically diagnosed cases of TB were recorded, the 2-year cumulative incidence was 0.4% (95%CI 0.1-1.2), the median duration for TB occurrence was 1 year, the incidence rate of active TB was 2.0 per 1000 person-years with a total of 1497.3 observation person-years. For those LTBI, no one initiated preventive treatment, in the QFT (+) cohort, 1 TB case was observed, 71 person-years with an incidence rate of 14.1 14.1 (95%CI 2.5-75.6) per 1000 person-years, in the TST (+++) cohort, 2 TB cases were observed 91.5 person-years with an incidence rate of 21.9 (95%CI 6.0-76.3) per 1000 person-years. Conclusions: The results suggest that school close contacts are one of the key populations for LTBI management. Measures should be taken to further reduce the prevalence of LTBI and the incidence of active TB among them.

Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Shanghai, China.

OBJECTIVE: To evaluate the performance of whole-genome sequencing (WGS) for predicting Mycobacterium tuberculosis (MTB) drug resistance. METHODS: 276 rifampin-resistance tuberculosis (RR-TB) and 30 rifampicin-sensitive clinical isolates were randomly selected from patients with tuberculosis in Shanghai Pulmonary Hospital (SPH). Phenotypic drug susceptibility testing (DST) against six anti-TB drugs was performed, and WGS was used to predict the drug resistance using an online 'TB-Profiler' tool. RESULTS: Using phenotypic susceptibility as the gold standard, the overall sensitivities and specificities for WGS were 94.53% and 92.00% for isoniazid, 97.10% and 100.00% for rifampicin, 97.46% and 64.36% for ethambutol, 97.14% and 95.83% or streptomycin, 93.02% and 98.87% for ofloxacin, and 75.00% and 100.00% for amikacin, respectively. The concordances of WGS-based DST and phenotypic DST were: isoniazid (94.12%), rifampicin (97.39%), ethambutol (77.12%), streptomycin (96.73%), ofloxacin (96.41%) and amikacin (97.06%). CONCLUSIONS: WGS could be a promising approach to predict resistance to isoniazid, rifampicin, ethambutol, streptomycin, ofloxacin, and amikacin.

Incidence of pulmonary tuberculosis in Chinese adults with type 2 diabetes: a retrospective cohort study in Shanghai.

To estimate the incidence of pulmonary tuberculosis (PTB) in Chinese diabetes patients and to evaluate the effect of blood glucose on PTB risk, a retrospective cohort study was built based on the diabetes management system in Shanghai and included 240,692 adults aged 35 or above. Incidences of PTB in all diabetes patients and by subgroups were calculated and compared. Multivariable Cox regression models with restricted cubic splines were used to evaluate the association of fasting plasma glucose (FPG) with the risk of PTB. A total of 439 incident PTB cases were identified in the cohort after an average of 3.83 years of follow-up. The overall PTB incidence rate was 51.3/100,000 in diabetes patients, and annual incidence remained higher than that in general population. The PTB incidence rate of diabetes patients was higher in men than in women (86.2 vs. 22.1 per 100,000) and was highest in patients with body mass index (BMI) < 18.5 kg/m2 (215.2/100,000) or FPG ≥ 10 mmol/L (143.2/100,000). Our results suggest that the risk of tuberculosis may be greater at higher levels of FPG in diabetes patients of normal weight. Specific tuberculosis screening strategies for different characteristic diabetes population should be provided to prevent and control tuberculosis in China.

Transmission of multidrug-resistant Mycobacterium tuberculosis in Shanghai, China: a retrospective observational study using whole-genome sequencing and epidemiological investigation.

BACKGROUND: Multidrug-resistance is a substantial threat to global elimination of tuberculosis. Understanding transmission patterns is crucial for control of the disease. We used a genomic and epidemiological approach to assess recent transmission of multidrug-resistant (MDR) tuberculosis and identify potential risk factors for transmission. METHODS: We did a population-based, retrospective study of patients who tested positive for tuberculosis between Jan 1, 2009, and Dec 31, 2012, in Shanghai, China. We did variable-number-of-tandem-repeat genotyping and whole-genome sequencing of isolates. We measured strain diversity within and between genomically clustered isolates. Genomic and epidemiological data were combined to construct transmission networks. FINDINGS: 367 (5%) of 7982 patients with tuberculosis had MDR tuberculosis and 324 (88%) of these had isolates available for genomic analysis. 103 (32%) of the 324 MDR strains were in 38 genomic clusters that differed by 12 or fewer single nucleotide polymorphisms (SNPs), indicating recent transmission of MDR strains. Patients who had delayed diagnosis or were older than 45 years had high risk of recent transmission. 235 (73%) patients with MDR tuberculosis probably had transmission of MDR strains. Transmission network analysis showed that 33 (87%) of the 38 clusters accumulated additional drug-resistance mutations through emergence or fixation of mutations during transmission. 68 (66%) of 103 clustered MDR strains had compensatory mutations of rifampicin resistance. INTERPRETATION: Recent transmission of MDR tuberculosis strains, with increasing drug-resistance, drives the MDR tuberculosis epidemic in Shanghai, China. Whole-genome sequencing can measure of the heterogeneity of drug-resistant mutations within and between hosts and help to determine the transmission patterns of MDR tuberculosis. FUNDING: National Science and Technology Major Project, National Natural Science Foundation of China, and US National Insitutes of Health.

Recurrent tuberculosis in an urban area in China: Relapse or exogenous reinfection?

Recurrent tuberculosis is an important indicator of the effectiveness of tuberculosis control and can occur by relapse or exogenous reinfection. We conducted a retrospective cohort study on all bacteriologically confirmed tuberculosis cases that were successfully treated between 2000 and 2012 in Shanghai, an urban area with a high number but a low prevalence rate of tuberculosis cases and a low prevalence of HIV infection. Genotyping the Mycobacterium tuberculosis from clinical isolates was used to distinguish between relapse and reinfection. In total, 5.3% (710/13,417) of successfully treated cases had a recurrence, a rate of 7.55 (95% CI 7.01-8.13) episodes per 1000 person-years, more than 18 times the rate of tuberculosis in the general population. Patients who were male, age 30-59, retreatment cases, had cavitation, diabetes, drug-resistant or multidrug-resistant tuberculosis in their initial episode of tuberculosis, were at high risk for a recurrence. Among 141 recurrent cases that had paired isolates, 59 (41.8%) had different genotypes, indicating reinfection with a different strain. Patients who completed treatment were still at high risk of another episode of tuberculosis and exogenous reinfection contributed a significant proportion of the recurrent tuberculosis cases. Targeted control strategies are needed to prevent new tuberculosis infections in this setting.

Efficacy and effect of free treatment on multidrug-resistant tuberculosis.

Multidrug-resistant tuberculosis (MDR-TB) is a serious public health and social issue. It pertains to the type of tuberculosis that is resistant simultaneously to isoniazid and rifampicin. MDR-TB has a high mortality and is expensive to treat. The aim of the present study was to examine the therapeutic effects of individualized free treatment and the relevant influencing factors on the treatment outcome for MDR-TB. A prospective study module was used to analyze the therapeutic outcome of MDR-TB with individualized free treatment for 160 patients between 2011 and 2014. Statistical analysis was performed using the Chi-square or Fisher's exact test, and the odds ratio was calculated using a logistic regression analysis model. In total, 160 patients were enrolled in the study for treatment of MDR-TB. From these, 88 cases completed the course of treatment, and 70 cases were successfully treated. Of the remaining 72 cases, 37 cases exhibited treatment failure, 18 cases were suspended during treatment and 17 patients succumbed to the disease. The results showed that the confounding factors were: i) retreatment (p<0.05); ii) occurrence of diabetes (p<0.001); iii) lesion without improvement in radiography during treatment (p=0.001); iv) positive sputum culture for Mycobacterium tuberculosis after 3-month treatment (p<0.05); and v) termination of treatment due to adverse reaction (p<0.05). These factors were associated with poor treatment outcomes by logistic regression analysis. Adverse drug reaction was observed in 33 cases and treatment was terminated or changed permanently in 29 of these cases. The most common adverse reaction was liver function damage caused by pyrazinamide and leucopenia caused by rifabutin. One patient suffered from serious liver failure. In conclusion, the success rate of long treatment course for MDR-TB is not high due to many adverse reactions. Occurrence of diabetes is the main factor that caused poor efficacy.

Resistance to Second-Line Antituberculosis Drugs and Delay in Drug Susceptibility Testing among Multidrug-Resistant Tuberculosis Patients in Shanghai.

Introduction. Second-line antituberculosis drugs (SLDs) are used for treating multidrug-resistant tuberculosis (MDR-TB). Prolonged delays before confirming MDR-TB with drug susceptibility testing (DST) could result in transmission of drug-resistant strains and inappropriate use of SLDs, thereby increasing the risk of resistance to SLDs. This study investigated the diagnostic delay in DST and prevalence of baseline SLD resistance in Shanghai and described the distribution of SLD resistance with varied delays to DST. Methods. All registered patients from 2011 to 2013 in Shanghai were enrolled. Susceptibility to ofloxacin, amikacin, kanamycin, and capreomycin was tested. Total delay in DST completion was measured from the onset of symptoms to reporting DST results. Results. Resistance to SLDs was tested in 217 of the 276 MDR-TB strains, with 118 (54.4%) being resistant to at least one of the four SLDs. The median total delay in DST was 136 days. Patients with delay longer than median days were roughly twice more likely to have resistance to at least one SLD (OR 2.22, 95% CI 1.19-4.11). Conclusions. During prolonged delay in DST, primary and acquired resistance to SLDs might occur more frequently. Rapid diagnosis of MDR-TB, improved nosocomial infection controls, and regulated treatment are imperative to prevent SLD resistance.