Direct Signal Detection Without Data‐Aided: A MIMO Functional Network Approach

Functional network (FN) has been successfully applied in many fields, but so far no methods of direct signal detection (DSD) using FN have been published. In this chapter, a novel DSD approach using FN, which can be applied to cases with a plural source signal sequence, with short sequence, and even with the absence of a training sequence, is presented. Firstly, a multiple‐input multiple‐output FN (MIMOFN), in which the initial input vector is devised via QR decomposition of the receiving signal matrix, is constructed to solve the special issues of DSD. In the meantime, the design method for the neural function of this special MIMOFN is proposed. Then the learning rule for the parameters of neural functions is trained and updated by back‐propagation (BP) algorithm. The correctness and effectiveness of the new approach are verified by simulation results, together with some special simulation phenomena of the algorithm. The proposed method can detect the source sequence directly from the observed output data by utilizing MIMOFN without a training sequence and estimating the channel impulse response

The Performance of Pleural Fluid T-SPOT.TB Assay for Diagnosing Tuberculous Pleurisy in China: A Two-Center Prospective Cohort Study

The performance of T-SPOT.TB (T-SPOT) assay in diagnosing pleural tuberculosis (plTB) is inconsistent. In this study, we compared the performance of peripheral blood (PB) and pleural fluid (PF) T-SPOT assay in diagnosing plTB. Between July 2017 and March 2018, 218 and 210 suspected plTB patients were prospectively enrolled from Wuhan (training) and Guangzhou (validation) cohort, respectively. PB T-SPOT, PF T-SPOT, and other conventional tests were simultaneously performed. Our data showed the performance of PB T-SPOT in diagnosing plTB was limited, especially with low sensitivity. However, the results of early secreted antigenic target 6 (ESAT-6) and culture filtrate protein 10 (CFP-10) in PF T-SPOT were significantly increased compared with those in PB T-SPOT in plTB patients. If using 76 as the cutoff value of MAX (the larger of ESAT-6 and CFP-10) in Wuhan cohort, the sensitivity and specificity of PF T-SPOT to diagnose plTB were 89.76 and 96.70%, respectively. The diagnostic accuracy of PF T-SPOT was better than other routine tests such as pathogen detection methods and biochemical markers. The diagnostic accuracy of PF T-SPOT in Guangzhou cohort was similar to that in Wuhan cohort, with a sensitivity and specificity of 91.07 and 94.90%, respectively. Furthermore, CD4+ T cells were more activated in PF compared with PB, and the frequency of mycobacterium tuberculosis-specific CD4+ T cells in PF was significantly higher than that in PB in plTB patients. In conclusion, the performance of PF T-SPOT is obviously better than PB T-SPOT or other laboratory tests, which suggests that PF T-SPOT assay has been of great value in the diagnosis of pleural tuberculosis

Molecular Characterization of Prothionamide-Resistant Mycobacterium tuberculosis Isolates in Southern China

Prothionamide (PTH) has been widely used in the treatment of tuberculosis (TB), especially multidrug resistant tuberculosis (MDR-TB), while data regarding prevalence of resistance-causing mutation is limited. In this study, we aimed to investigate the molecular characteristics of PTH-resistant MTB isolates, and also analyzed the risk factors for PTH resistance among Mycobacterium tuberculosis (MTB) isolates in southern China. A total of 282 MTB isolates were enrolled in from Guangzhou Chest Hospital. Among these isolates, 46 (16.3%) were resistant to PTH. Statistical analysis revealed that PTH resistance was more likely to be associated with resistance to levofloxacin (LFX; OR: 2.18, 95% CI: 1.02–4.63; P = 0.04). Of the 46 PTH-resistant MTB isolates, 37 (80.4%) isolates harbored 19 different mutation types, including 10 (21.7%) isolates with double nucleotide substitutions and 27 (58.7%) with single nucleotide substitution. The mutations in ethA (51.4%, 19/37) were most frequently observed among PTH-resistant isolates, followed by 16 (43.2%) in the promoter of inhA and 6 (16.2%) in inhA. In addition, no significant difference was found in the distribution of isolates with different mutation types between Beijing and non-Beijing genotypes (P > 0.05). In conclusion, our data demonstrate that high diversity of genetic mutations conferring PTH resistance is identified among MTB isolates from southern China. Mutations in inhA, ethA, mshA, and ndh genes confer increased resistance of MTB to PTH. Ancient Beijing genotype strains have higher proportion of drug resistance compared with modern Beijing strains. In addition, PTH resistance is more likely to be observed in the LFX-resistant MTB isolates

Mutation EthA(W21R) confers co-resistance to prothionamide and ethionamide in both Mycobacterium bovis BCG and Mycobacterium tuberculosis H37Rv

Ethionamide (ETA) and prothionamide (PRO) are interchangeably used in tuberculosis (TB) chemotherapy regimens. Subtle discrepancies between biochemical and genetic information on the modes of sensitivity and resistance of isoniazid (INH) and ETA warrants further studies. We report a new mutation - EthA(W21R) - in Mycobacterium bovis Bacillus Calmette-Guerin that corresponds with co-resistance to both PRO and ETA, which to the best of our knowledge has not been reported before. Our findings suggest that mutation EthA(W21R) could be used as a marker site for testing PRO and ETA cross-resistance

Epidemiology of pulmonary disease due to nontuberculous mycobacteria in Southern China, 2013–2016

Abstract Background Pulmonary nontuberculous mycobacteria (NTM) disease is of increasing public health concern in China. Information is limited regarding risk factors associated with this disease in China. The objective of this study was to describe the epidemiology of pulmonary disease due to NTM in Southern China. Methods We retrospectively reviewed the medical records of pulmonary NTM patients registered in the Guangzhou Chest Hospital with positive mycobacterial cultures during 2013–2016. We described sex, age, residence, treatment history, laboratory examination results and comorbidities of pulmonary NTM patients. Results Among the 607 NTM cases, the most prevalent species were Mycobacterium avium complex (44.5%), Mycobacterium abscessus complex (40.5%), Mycobacterium kansasii (10.0%) and Mycobacterium fortuitum (2.8%). The male:female ratio was significantly lower among patients infected with rapidly growing mycobacteria (RGM) than among those with slowly growing mycobacteria (SGM). The risk of developing SGM disease significantly increased with advancing age. In addition, pulmonary RGM diseases were more common in migrant population than resident population. Notably, patients with pulmonary RGM diseases were significantly more likely to have bronchiectasis underlying noted than those with SGM diseases. No significant difference was observed in in vitro drug susceptibility among NTM species. Conclusion Our data illustrate that the M. avium complex is the most predominant causative agent of pulmonary NTM disease in Southern China. Female, migrant population, the presence of bronchiectasis are independent risk factors for pulmonary diseases due to RGM. In addition, the prevalence of SGM increases significantly with advancing age

Comparative Analysis of Whole-Genome and Methylome Profiles of a Smooth and a Rough Mycobacterium abscessus Clinical Strain

Mycobacterium abscessus is a fast growing Mycobacterium species mainly causing skin and respiratory infections in human. M. abscessus is resistant to numerous drugs, which is a major challenge for the treatment. In this study, we have sequenced the genomes of two clinical M. abscessus strains having rough and smooth morphology, using the single molecule real-time and Illumina HiSeq sequencing technology. In addition, we reported the first comparative methylome profiles of a rough and a smooth M. abscessus clinical strains. The number of N4-methylcytosine (4mC) and N6-methyladenine (6mA) modified bases obtained from smooth phenotype were two-fold and 1.6 fold respectively higher than that of rough phenotype. We have also identified 4 distinct novel motifs in two clinical strains and genes encoding antibiotic-modifying/targeting enzymes and genes associated with intracellular survivability having different methylation patterns. To our knowledge, this is the first report about genome-wide methylation profiles of M. abscessus strains and identification of a natural linear plasmid (15 kb) in this critical pathogen harboring methylated bases. The pan-genome analysis of 25 M. abscessus strains including two clinical strains revealed an open pan genome comprises of 7596 gene clusters. Likewise, structural variation analysis revealed that the genome of rough phenotype strain contains more insertions and deletions than the smooth phenotype and that of the reference strain. A total of 391 single nucleotide variations responsible for the non-synonymous mutations were detected in clinical strains compared to the reference genome. The comparative genomic analysis elucidates the genome plasticity in this emerging pathogen. Furthermore, the detection of genome-wide methylation profiles of M. abscessus clinical strains may provide insight into the significant role of DNA methylation in pathogenicity and drug resistance in this opportunistic pathogen

Molecular Targets Related Drug Resistance Mechanisms in MDR-, XDR-, and TDR-Mycobacterium tuberculosis Strains

Tuberculosis (TB) is a formidable infectious disease that remains a major cause of death worldwide today. Escalating application of genomic techniques has expedited the identification of increasing number of mutations associated with drug resistance in Mycobacterium tuberculosis. Unfortunately the prevalence of bacillary resistance becomes alarming in many parts of the world, with the daunting scenarios of multidrug-resistant tuberculosis (MDR-TB), extensively drug-resistant tuberculosis (XDR-TB) and total drug-resistant tuberculosis (TDR-TB), due to number of resistance pathways, alongside some apparently obscure ones. Recent advances in the understanding of the molecular/ genetic basis of drug targets and drug resistance mechanisms have been steadily made. Intriguing findings through whole genome sequencing and other molecular approaches facilitate the further understanding of biology and pathology of M. tuberculosis for the development of new therapeutics to meet the immense challenge of global health

Engineering More Stable, Selectable Marker-Free Autoluminescent Mycobacteria by One Step

<div><p>In our previous study, we demonstrated that the use of the autoluminescent <i>Mycobacterium tuberculosis</i> as a reporter strain had the potential to drastically reduce the time, effort, animals and costs consumed in evaluation of the activities of drugs and vaccines in live mice. However, the strains were relatively unstable and lost reporter with time without selection. The kanamycin selection marker used wasn’t the best choice as it provides resistance to amino glycosides which are an important class of second line drugs used in tuberculosis treatment. In addition, the marker could limit utility of the strains for screening of new potential drugs or evaluating drug combinations for tuberculosis treatment. Limited selection marker genes for mycobacterial genetic manipulation is a major drawback for such a marker-containing strain in many research fields. Therefore, selectable marker-free, more stable autoluminescent mycobacteria are highly needed. After trying several strategies, we created such mycobacterial strains successfully by using an integrative vector and removing both the resistance maker and integrase genes by Xer site-specific recombination in one step. The corresponding plasmid vectors developed in this study could be very convenient in constructing other selectable marker-free, more stable reporter mycobacteria with diverse applications.</p></div