Ancient Beijing Research Articles

Spatial landscape transformation of Beijing compounds under residents' willingness

Compounds, the evolution of siheyuan, are residence-oriented courtyards in historic blocks, and are more often than not where the low-income people settle. Under the influence of different historical stages and major events, the continuous evolution of compound spatial landscape structures is the witness and representation of ancient time-honored Beijing culture. The authors take nine compounds in Dongsisantiao Hutong as the object of study, and divide spatial landscape transformation process into four stages after detailed surveys. Then, based on the study of Michel de Certeau on the practice of daily life and in connection with the special social structures in compounds, theauthors summarize the modalities of spontaneous spatial landscape transformation practice in compounds. The study aims to provide reference for small-scale spatial landscape transformation in residence-oriented historic blocks and to probe into the relations between man and space landscape in similar historical space.

Old walls, modern city: research on urban memory of disappearing ancient Beijing city walls

Purpose – Ancient city walls are typical linear space elements of Beijing that represent the transformation of urban form over the past 800 years and have greatly influenced the memory of the entire city. However, recently, most of the walls have been torn down in the process of fast urbanization and old city renewal. The purpose of this paper is to focus on people’s cognition and evaluation of urban memory during this pull-down-and-preserve process. Design/methodology/approach – A sample of 380 participants was investigated on a number of issues using questionnaires, including memory case reminders (stability, variability, temporality), emotional bonding with memory case (identity, dependence, authenticity), and socio-demographic variables (age, education, life experience, length of residence). The urban memory cognition model and attitude evaluation value model which were based on Likert scale were used to process the collected data. Findings – In the three aspects of memory case reminders, stability and temporary elements can be most cognized, whereas variability elements are more difficult due to their change over time. As for emotional bonding with memory case, people show a high level of identification with the walls; the walls’ memory being passed down could enhance people’s memory when mentioning Beijing. Further, higher education groups consider the walls’ authenticity to be most important and are unwilling to accept the outcome of walls-ruins parks; older adults have tolerant attitudes to the ruins parks. Originality/value – This study could not only contribute to the excavation of urban memory, but also strengthen citizens’ sense of identity and cohesiveness, thus shaping the spirit and culture of the city. Some findings could provide applicable guidelines for urban heritage protection and contribute a new perspective on the interrelationship between people and their physical surroundings.

Genetic features of Mycobacterium tuberculosis modern Beijing sublineage

Mycobacterium tuberculosis (MTB) Beijing strains have caused a great concern because of their rapid emergence and increasing prevalence in worldwide regions. Great efforts have been made to investigate the pathogenic characteristics of Beijing strains such as hypervirulence, drug resistance and favoring transmission. Phylogenetically, MTB Beijing family was divided into modern and ancient sublineages. Modern Beijing strains displayed enhanced virulence and higher prevalence when compared with ancient Beijing strains, but the genetic basis for this difference remains unclear. In this study, by analyzing previously published sequencing data of 1082 MTB Beijing isolates, we determined the genetic changes that were commonly present in modern Beijing strains but absent in ancient Beijing strains. These changes include 44 single-nucleotide polymorphisms (SNPs) and two short genomic deletions. Through bioinformatics analysis, we demonstrated that these genetic changes had high probability of functional effects. For example, 4 genes were frameshifted due to premature stop mutation or genomic deletions, 19 nonsynonymous SNPs located in conservative codons, and there is a significant enrichment in regulatory network for all nonsynonymous mutations. Besides, three SNPs located in promoter regions were verified to alter downstream gene expressions. Our study precisely defined the genetic features of modern Beijing strains and provided interesting clues for future researches to elucidate the mechanisms that underlie this sublineage’s successful expansion. These findings from the analysis of the modern Beijing sublineage could provide us a model to understand the dynamics of pathogenicity of MTB.

Risk factors for pulmonary cavitation in tuberculosis patients from China

Pulmonary cavitation is one of the most frequently observed clinical characteristics in tuberculosis (TB). The objective of this study was to investigate the potential risk factors associated with cavitary TB in China. A total of 385 smear-positive patients were enrolled in the study, including 192 (49.9%) patients with cavitation as determined by radiographic findings. Statistical analysis revealed that the distribution of patients with diabetes in the cavitary group was significantly higher than that in the non-cavitary group (adjusted odds ratio (OR) (95% confidence interval (CI)):12.08 (5.75–25.35), P<0.001). Similarly, we also found that the proportion of individuals with multidrug-resistant TB in the cavitary group was also higher than that in the non-cavitary group (adjusted OR (95% CI): 2.48 (1.52–4.07), P<0.001). Of the 385 Mycobacterium tuberculosis strains, 330 strains (85.7%) were classified as the Beijing genotype, which included 260 strains that belonged to the modern Beijing sublineage and 70 to the ancient Beijing sublineage. In addition, there were 80 and 31 strains belonging to large and small clusters, respectively. Statistical analysis revealed that cavitary disease was observed more frequently among the large clusters than the small clusters (P=0.037). In conclusion, our findings demonstrate that diabetes and multidrug resistance are risk factors associated with cavitary TB. In addition, there was no significant difference in the cavitary presentation between patients infected with the Beijing genotype strains and those infected with the non-Beijing genotype strains.Emerging Microbes & Infections (2016) 5, e0 doi:10.1038/emi.2016.111; published online 12 October 2016

Phylogenetic assignment of Mycobacterium tuberculosis Beijing clinical isolates in Japan by maximum a posteriori estimation

Intra-species phylogeny of Mycobacterium tuberculosis has been regarded as a clue to estimate its potential risk to develop drug-resistance and various epidemiological tendencies. Genotypic characterization of variable number of tandem repeats (VNTR), a standard tool to ascertain transmission routes, has been improving as a public health effort, but determining phylogenetic information from those efforts alone is difficult. We present a platform based on maximum a posteriori (MAP) estimation to estimate phylogenetic information for M. tuberculosis clinical isolates from individual profiles of VNTR types. This study used 1245 M. tuberculosis clinical isolates obtained throughout Japan for construction of an MAP estimation formula. Two MAP estimation formulae, classification of Beijing family and other lineages, and classification of five Beijing sublineages (ST11/26, STK, ST3, and ST25/19 belonging to the ancient Beijing subfamily and modern Beijing subfamily), were created based on 24 loci VNTR (24Beijing-VNTR) profiles and phylogenetic information of the isolates. Recursive estimation based on the formulae showed high concordance with their authentic phylogeny by multi-locus sequence typing (MLST) of the isolates. The formulae might further support phylogenetic estimation of the Beijing lineage M. tuberculosis from the VNTR genotype with various geographic backgrounds. These results suggest that MAP estimation can function as a reliable probabilistic process to append phylogenetic information to VNTR genotypes of M. tuberculosis independently, which might improve the usage of genotyping data for control, understanding, prevention, and treatment of TB.

Genotyping and molecular characteristics of multidrug-resistant Mycobacterium tuberculosis isolates from China

The aim of this study was to explore the population structure of multidrug-resistant (MDR) tuberculosis strains and distribution of resistance-associated nucleotide alteration among the different genotype MDR strains in China. The genotypes of 376 MDR strain were analyzed by 15-loci MIRU-VNTR and RD105 deletion-targeted multiplex PCR (DTM-PCR) method. In addition, all the MDR isolates were sequenced for genetic mutations conferring rifampicin (rpoB) and isonizid resistance (katG, inhA and oxyR-ahpC). Among the 376 MDR isolates, 261 (69.4%) belonged to Beijing genotype, including 177 modern Beijing strains (67.8%) and 84 ancient Beijing (32.2%) strains. The percentages of streptomycin-resistant, kanamycin-resistant, pre-XDR and XDR TB in modern Beijing genotype were significantly lower than ancient genotype (P < 0.05). The Beijing MDR strains had significantly higher proportions of ofloxacin-resistant and pre-XDR isolates than non-Beijing strains (P < 0.01). In addition, the clustering rate of modern Beijing strains was significantly higher than that of ancient Beijing strains (46.3% vs. 11.9%, P < 0.01). 94.7% and 79.3% of MDR isolates harbored genetic mutations conferring rifampicin and isonizid resistance, respectively, and the most prevalent mutation was located in codon rpoB531 and katG315. In addition, the rpoB531 and katG mutation were more frequently observed among Beijing genotype strains than non-Beijing strains, while non-Beijing genotype showed stronger association with isolates lacking mutation in rifampicin resistance determination region (P < 0.05). Our findings demonstrated that ancient Beijing MDR strains were associated with drug resistance, while modern Beijing MDR strains were more likely to be clustered.

Molecular characterisation of extensively drug-resistant Mycobacterium tuberculosis isolates in China

The emergence of extensively drug-resistant tuberculosis (XDR-TB) in China is a great threat to TB control. To determine the molecular characterisation of XDR-TB isolates from China and the correlations between specific drug resistance-associated mutations and different genotype strains, 58 XDR-TB isolates were sequenced in eight drug loci, including katG, inhA, oxyR–ahpC intergenic region, rpoB, eis, rrs, gyrA and gyrB, and were genotyped using spoligotyping and analysis of the noise transfer function region. Compared with the phenotypic data, the sensitivities and specificities for DNA sequencing were 87.9% and 100.0% for isoniazid (INH), 91.4% and 98.3% for rifampicin (RIF), 60.4% and 100.0% for kanamycin (KAN) and 81.0% and 100.0% for ofloxacin (OFX), respectively. A combination of eight drug loci predicted XDR-TB phenotypes with 53.4% sensitivity (31/58 isolates) and 100.0% specificity. The most frequent mutations among these XDR-TB isolates were katG315 and inhA-15 (for INH), 531, 526 and 516 in rpoB (for RIF), rrs1401 and eis–10 (for KAN) and 94, 90 and 91 in gyrA (for OFX). Also, among these XDR-TB isolates, 44 (75.9%) were identified as Beijing genotype strain, of which 31 (70.5%) belonged to the modern Beijing sublineage. inhA-8, rpoB526 and rpoB531 mutations demonstrated significant statistical associations with ancient and modern Beijing family sublineage (P<0.05). However, Beijing and non-Beijing genotypes showed no association with specific resistance-conferring mutations. These results will be helpful in designing new molecular biology-based techniques to diagnose XDR-TB in China.

Mycobacterium tuberculosis strains spreading in Hanoi, Vietnam: Beijing sublineages, genotypes, drug susceptibility patterns, and host factors

Beijing genotype strains are divided into two major sublineages, ancient (atypical) and modern (typical) types, but their phenotypic variations remain largely unknown. Mycobacterium tuberculosis (MTB) isolates from Hanoi, Vietnam, were analyzed by single-nucleotide polymorphisms and spoligotyping. Patient information and drug susceptibility patterns were obtained. Genetic clustering was assessed by variable number of tandem repeat (VNTR) locus sets. Multivariate analysis was also performed to investigate factors possibly associated with these sublineages. Of the 465 strains tested, 175 (37.6%) belonged to the ancient Beijing sublineage and 97 (20.9%) were of the modern Beijing sublineage. Patients with the Beijing genotype were significantly younger and more undernourished than those with non-Beijing genotype. The proportion of clustered strains calculated from 15 locus-optimized mycobacterial interspersed repetitive units [optimized-(MIRU)15]-, optimized-MIRU24-, optimized-MIRU28-, Japan Anti-Tuberculosis Association (JATA)15-, and JATA18-VNTRs were 55.7%, 49.2%, 33.8%, 44.5%, and 32.0%, respectively. Ancient and modern Beijing genotype strains were more frequently clustered than non-Beijing genotype strains, even when using VNTR sets with high discriminatory power. Isoniazid and streptomycin resistance tended to be more frequently observed in ancient Beijing strains than in modern Beijing strains and others. Our findings may provide insight into area-dependent differences in Beijing family strain characteristics.

Disclosure of Selective Advantages in the “modern” Sublineage of the Mycobacterium tuberculosis Beijing Genotype Family by Quantitative Proteomics

The Mycobacterium tuberculosis Beijing genotype, consisting of the more ancient (atypical) and modern (typical) emerging sublineage, is one of the most prevalent and genetically conserved genotype families and has often been associated with multidrug resistance. In this study, we employed a 2D-LC-FTICR MS approach, combined with dimethylation of tryptic peptides, to systematically compare protein abundance levels of ancient and modern Beijing strains and identify differences that could be associated with successful spread of the modern sublineage. The data is available via ProteomeXchange using the identifier PXD000931. Despite the highly uniform protein abundance ratios in both sublineages, we identified four proteins as differentially regulated between both sublineages, which could explain the apparent increased adaptation of the modern Beijing strains. These proteins are; Rv0450c/MmpL4, Rv1269c, Rv3137, and Rv3283/sseA. Transcriptional and functional analysis of these proteins in a large cohort of 29 Beijing strains showed that the mRNA levels of Rv0450c/MmpL4 are significantly higher in modern Beijing strains, whereas we also provide evidence that Rv3283/sseA is less abundant in the modern Beijing sublineage. Our findings provide a possible explanation for the increased virulence and success of the modern Beijing sublineage. In addition, in the established dataset of 1817 proteins, we demonstrate the pre-existence of several, possibly unique, antibiotic efflux pumps in the proteome of the Beijing strains. This may reflect an increased ability of Beijing strains to escape exposure to antituberculosis drugs.

The pattern of cytokine production in vitro induced by ancient and modern Beijing Mycobacterium tuberculosis strains.

It is unclear to what extent the host-responses elicited by Beijing versus non-Beijing strains of Mycobacterium tuberculosis (MTB) contribute to the predominance of modern Beijing strains in Taiwan and some other Asian countries. The purpose of this study was to compare the expression profiles of virulence-related genes in human monocyte-derived macrophages infected in vitro with Beijing (ancient and modern strains) and non-Beijing strains (EAI strains) of MTB that are epidemic in Taiwan. We found that modern Beijing strains induced lower levels of pro-inflammatory cytokines, whereas EAI strains induced higher levels. Notably, the most prevalent modern Beijing sub-lineage, possessing intact RD150 and RD142 chromosomal regions, induced very low levels of pro-inflammatory cytokines, especially interleukin-1β. Moreover, in an intracellular growth assay, the survival of the same modern Beijing strain in human monocyte-derived macrophages was significantly higher than that of an ancient Beijing strain and an EAI strain. Taken together, these results may explain why modern Beijing strains of MTB predominate in Taiwan.

Molecular Genotyping of Mycobacterium tuberculosis in Mie Prefecture, Japan, Using Variable Numbers of Tandem Repeats Analysis

The variable numbers of tandem repeats (VNTR) analysis is a method frequently employed as a molecular epidemiological tool for Mycobacterium tuberculosis genetic fingerprinting. In this study, we characterized the population of M. tuberculosis circulating in Mie Prefecture, Japan, and assessed the utility of the proposed JATA12- and 15-VNTR analyses of 158 M. tuberculosis clinical isolates using 25 VNTR loci. The results revealed that the ancient Beijing sublineage is the most prevalent M. tuberculosis strain in Mie Prefecture, accounting for 85.0% of 113 Beijing lineage isolates. Our results also showed that JATA-VNTR using well-selected loci is as reliable as standardized 15-locus MIRU-VNTR. Furthermore, JATA15-VNTR analysis reliably improved the discriminatory power compared with basic JATA12-VNTR analysis. In summary, our data suggest that JATA-VNTR is a useful tool for discrimination of M. tuberculosis in areas where ancient Beijing strains are frequently isolated.

Investigation on Mycobacterium tuberculosis Diversity in China and the Origin of the Beijing Clade

BackgroundInvestigation of the genetic diversity of Mycobacterium tuberculosis in China has shown that Beijing genotype strains play a dominant role in the tuberculosis (TB) epidemic. In order to examine the strain diversity in the whole country, and to study the evolutionary development of Beijing strains, we sought to genotype a large collection of isolates using different methods.Methodology/Principal FindingsWe applied a 15-loci VNTR typing analysis on 1,586 isolates from the Beijing municipality and 12 Chinese provinces or autonomous regions. The data was compared to that of 900 isolates from various other worldwide geographic regions outside of China. A total of 1,162/1,586 (73.2%) of the isolates, distributed into 472 VNTR types, were found to belong to the Beijing genotype family and this represented 56 to 94% of the isolates in each of the localizations. VNTR typing revealed that the majority of the non-Beijing isolates fall into two genotype families, which represented 17% of the total number of isolates, and seem largely restricted to China. A small number of East African Indian genotype strains was also observed in this collection. Ancient Beijing strains with an intact region of difference (RD) 181, as well as strains presumably resembling ancestors of the whole Beijing genotype family, were mainly found in the Guangxi autonomous region.Conclusions/SignificanceThis is the largest M. tuberculosis VNTR-based genotyping study performed in China to date. The high percentage of Beijing isolates in the whole country and the presence in the South of strains representing early branching points may be an indication that the Beijing lineage originated from China, probably in the Guangxi region. Two modern lineages are shown here to represent the majority of non-Beijing Chinese isolates. The observed geographic distribution of the different lineages within China suggests that natural frontiers are major factors in their diffusion.

High transmissibility of the modern Beijing Mycobacterium tuberculosis in homeless patients of Japan

A population-based study of Mycobacterium tuberculosis isolated from homeless tuberculosis patients was performed during 2002-2004 in Osaka City, Japan. The data show that the ancient Beijing subfamily was predominant, whereas clustered isolates based on refined variable number of tandem repeats genotyping (19 loci) mainly belonged to the modern Beijing subfamily, suggesting its increased transmissibility.

Genetic diversity of theMycobacterium tuberculosisBeijing family in East Asia revealed through refined population structure analysis

The Beijing/W family is the endemic lineage of Mycobacterium tuberculosis in East Asia: it has disseminated worldwide. To elucidate its genetic diversity in Japan, phylogenetic reconstruction was performed using 403 M. tuberculosis Beijing family clinical isolates. Variable number of tandem repeats analysis revealed the strains from Japan to be dispersed mainly among five subgroups in a phylogenetic tree. Interestingly, the genotypes of the strains from China and Mongolia were restricted mainly to a single branch; they exhibited high clonality. IS6110 insertion in the NTF region was also analyzed. The majority (78.6%) of Japanese isolates belonged to the ancient sublineage. The modern Beijing strains were observed to correspond to the branch containing the foreign strains, although the ancient Beijing strains were dispersed among the tree's other branches. Our results reflect the singular genetic diversity and the epidemiological pattern of Beijing M. tuberculosis in Japan.