Summary Background Multidrug-resistant tuberculosis (MDR-TB) is a significant threat to tuberculosis elimination worldwide. Understanding the transmission pattern is crucial for its control. We used a genomic epidemiological approach to assess the recent transmission of MDR-TB and potential risk factors for transmission. Methods In a population-based retrospective study, we performed variable-number-of-tandem-repeat (VNTR) genotyping, followed by whole-genome sequencing (WGS) of isolates from all MDR-TB patients in Shanghai, China, 2009-2012. We measured strain diversity within and between genomically clustered patients. Genomic and epidemiologic 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 strains, with increasing drug-resistance, helps drive the MDR-TB epidemic in Shanghai, China. WGS provides a measure of the heterogeneity of drug-resistant mutations within and between hosts and enhances our ability to determine the transmission patterns of MDR-TB. Funding National Science and Technology Major Project, National Natural Science Foundation of China, and US National Insitutes of Health.

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.

Black locust (Robinia pseudoacacia L.) has been widely planted throughout the semiarid Loess Plateau in China. However, black locust plantations likely induce stand degradation and soil desiccation because of high water consumption, high stand density, and insufficient stand management. In this study, five kinds of density types in 19-year-old black locust plantations, including three intact non-thinned control plantation types with different stand densities (1800, 2700, and 3600 trees ha −1 ) and two thinned-treatment plantation types with the same stand densities (1800 trees ha −1 ) were selected to calculate the responses to thinning intensity in the Maliantan catchment within the central Loess Plateau. Gas exchange, leaf area index, associated changes in the photosynthetic carbon fixation capacity (PCFC), and environmental variables (light radiation, air temperature, and soil moisture) were determined throughout the growing season in 2009. The growth, daily leaf-level net CO2 assimilation rate (An), and tree-level PCFC were significantly different among the three intact black locust plantations in their annual growth period. An and PCFC increased as the stand density decreased because of enhanced environmental resource availabilities per individual tree, including the increased exposure to light radiation, canopy air temperature, and soil moisture level. Comparing thinned and non-thinned black locust plantations, we provided ecophysiological evidence that black locust trees could actively adjust their photosynthetic functions from the beginning of the first growing season after thinning to enhance their height, diameter, and canopy diameter during growth and development. This mechanism indicated that the rapid adaptability of black locust in response to plantation thinning on the semiarid Loess Plateau. Based on the same stand density (1800 trees ha −1 ), the low thinning intensity of 33% was more suitable for the sustainable management and increased of photosynthetic carbon fixation capacities of black locust trees on the Loess Plateau in China. These findings can enrich our knowledge of forest plantation dynamics and provide valuable information regarding sustainable plantation management in this ecological fragile region.

Figure 1. Total and TB specific deaths among TB patients during different follow-up years.

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