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Article ; Online: Advances in understanding immune homeostasis in latent tuberculosis infection.

Niu, Liangfei / Wang, Hao / Luo, Geyang / Zhou, Jing / Hu, Zhidong / Yan, Bo

WIREs mechanisms of disease

2024 , Page(s) e1643

Abstract: Nearly one-fourth of the global population is infected by Mycobacterium tuberculosis (Mtb), and approximately 90%-95% remain asymptomatic as latent tuberculosis infection (LTBI), an estimated 5%-10% of those with latent infections will eventually ... ...

Abstract	Nearly one-fourth of the global population is infected by Mycobacterium tuberculosis (Mtb), and approximately 90%-95% remain asymptomatic as latent tuberculosis infection (LTBI), an estimated 5%-10% of those with latent infections will eventually progress to active tuberculosis (ATB). Although it is widely accepted that LTBI transitioning to ATB results from a disruption of host immune balance and a weakening of protective immune responses, the exact underlying immunological mechanisms that promote this conversion are not well characterized. Thus, it is difficult to accurately predict tuberculosis (TB) progression in advance, leaving the LTBI population as a significant threat to TB prevention and control. This article systematically explores three aspects related to the immunoregulatory mechanisms and translational research about LTBI: (1) the distinct immunocytological characteristics of LTBI and ATB, (2) LTBI diagnostic markers discovery related to host anti-TB immunity and metabolic pathways, and (3) vaccine development focus on LTBI. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology Infectious Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Genetics/Genomics/Epigenetics.
Language	English
Publishing date	2024-02-13
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2692-9368
ISSN (online)	2692-9368
DOI	10.1002/wsbm.1643
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Article: Probing infectious disease by single-cell RNA sequencing: Progresses and perspectives.

Luo, Geyang / Gao, Qian / Zhang, Shuye / Yan, Bo

Computational and structural biotechnology journal

2020 Volume 18, Page(s) 2962–2971

Abstract: The increasing application of single-cell RNA sequencing (scRNA-seq) technology in life science and biomedical research has significantly increased our understanding of the cellular heterogeneities in immunology, oncology and developmental biology. This ... ...

Abstract	The increasing application of single-cell RNA sequencing (scRNA-seq) technology in life science and biomedical research has significantly increased our understanding of the cellular heterogeneities in immunology, oncology and developmental biology. This review will summarize the development of various scRNA-seq technologies; primarily discussing the application of scRNA-seq on infectious diseases, and exploring the current development, challenges, and potential applications of scRNA-seq technology in the future.
Keywords	covid19
Language	English
Publishing date	2020-10-21
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2020.10.016
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Article ; Online: Temporal and cellular analysis of granuloma development in mycobacterial infected adult zebrafish.

Luo, Geyang / Zeng, Dong / Liu, Jianxin / Li, Duoduo / Takiff, Howard E / Song, Shu / Gao, Qian / Yan, Bo

Journal of leukocyte biology

2023 Volume 115, Issue 3, Page(s) 525–535

Abstract: Because granulomas are a hallmark of tuberculosis pathogenesis, the study of the dynamic changes in their cellular composition and morphological character can facilitate our understanding of tuberculosis pathogenicity. Adult zebrafish infected with ... ...

Abstract	Because granulomas are a hallmark of tuberculosis pathogenesis, the study of the dynamic changes in their cellular composition and morphological character can facilitate our understanding of tuberculosis pathogenicity. Adult zebrafish infected with Mycobacterium marinum form granulomas that are similar to the granulomas in human patients with tuberculosis and therefore have been used to study host-mycobacterium interactions. Most studies of zebrafish granulomas, however, have focused on necrotic granulomas, while a systematic description of the different stages of granuloma formation in the zebrafish model is lacking. Here, we characterized the stages of granulomas in M. marinum-infected zebrafish, including early immune cell infiltration, nonnecrotizing granulomas, and necrotizing granulomas, using corresponding samples from patients with pulmonary tuberculosis as references. We combined hematoxylin and eosin staining and in situ hybridization to identify the different immune cell types and follow their spatial distribution in the different stages of granuloma development. The macrophages in zebrafish granulomas were shown to belong to distinct subtypes: epithelioid macrophages, foamy macrophages, and multinucleated giant cells. By defining the developmental stages of zebrafish granulomas and the spatial distribution of the different immune cells they contain, this work provides a reference for future studies of mycobacterial granulomas and their immune microenvironments.
MeSH term(s)	Animals ; Humans ; Zebrafish/microbiology ; Mycobacterium ; Tuberculosis ; Mycobacterium Infections, Nontuberculous ; Granuloma/microbiology ; Granuloma/pathology ; Mycobacterium tuberculosis
Language	English
Publishing date	2023-11-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605722-6
ISSN	1938-3673 ; 0741-5400
ISSN (online)	1938-3673
ISSN	0741-5400
DOI	10.1093/jleuko/qiad145
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Article ; Online: Negative Regulator Nlrc3-like Maintain the Balanced Innate Immune Response During Mycobacterial Infection in Zebrafish.

Niu, Liangfei / Luo, Geyang / Liang, Rui / Qiu, Chenli / Yang, Jianwei / Xie, Lingling / Zhang, Kaile / Tian, Yu / Wang, Decheng / Song, Shu / Takiff, Howard E / Wong, Ka-Wing / Fan, Xiaoyong / Gao, Qian / Yan, Bo

Frontiers in immunology

2022 Volume 13, Page(s) 893611

Abstract: The NOD-like receptors (NLRs) have been shown to be involved in infection and autoinflammatory disease. Previously, we identified a zebrafish NLR, ...

Abstract	The NOD-like receptors (NLRs) have been shown to be involved in infection and autoinflammatory disease. Previously, we identified a zebrafish NLR,
MeSH term(s)	Animals ; Humans ; Immunity, Innate ; Inflammasomes/metabolism ; Intercellular Signaling Peptides and Proteins/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; Mycobacterium Infections, Nontuberculous ; NLR Proteins/metabolism ; Zebrafish/metabolism ; Zebrafish Proteins/metabolism
Chemical Substances	Inflammasomes ; Intercellular Signaling Peptides and Proteins ; Intracellular Signaling Peptides and Proteins ; NLR Proteins ; Zebrafish Proteins ; nlrc3l protein, zebrafish
Language	English
Publishing date	2022-05-25
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.893611
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Article ; Online: Discrete-Time Nonzero-Sum Games for Multiplayer Using Policy-Iteration-Based Adaptive Dynamic Programming Algorithms.

Zhang, Huaguang / Jiang, He / Luo, Chaomin / Xiao, Geyang

IEEE transactions on cybernetics

2017 Volume 47, Issue 10, Page(s) 3331–3340

Abstract: In this paper, we investigate the nonzero-sum games for a class of discrete-time (DT) nonlinear systems by using a novel policy iteration (PI) adaptive dynamic programming (ADP) method. The main idea of our proposed PI scheme is to utilize the iterative ... ...

Abstract	In this paper, we investigate the nonzero-sum games for a class of discrete-time (DT) nonlinear systems by using a novel policy iteration (PI) adaptive dynamic programming (ADP) method. The main idea of our proposed PI scheme is to utilize the iterative ADP algorithm to obtain the iterative control policies, which not only ensure the system to achieve stability but also minimize the performance index function for each player. This paper integrates game theory, optimal control theory, and reinforcement learning technique to formulate and handle the DT nonzero-sum games for multiplayer. First, we design three actor-critic algorithms, an offline one and two online ones, for the PI scheme. Subsequently, neural networks are employed to implement these algorithms and the corresponding stability analysis is also provided via the Lyapunov theory. Finally, a numerical simulation example is presented to demonstrate the effectiveness of our proposed approach.
Language	English
Publishing date	2017-10
Publishing country	United States
Document type	Journal Article
ISSN	2168-2275
ISSN (online)	2168-2275
DOI	10.1109/TCYB.2016.2611613
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Article ; Online: SAM-TB: a whole genome sequencing data analysis website for detection of Mycobacterium tuberculosis drug resistance and transmission.

Yang, Tingting / Gan, Mingyu / Liu, Qingyun / Liang, Wenying / Tang, Qiqin / Luo, Geyang / Zuo, Tianyu / Guo, Yongchao / Hong, Chuangyue / Li, Qibing / Tan, Weiguo / Gao, Qian

Briefings in bioinformatics

2022 Volume 23, Issue 2

Abstract: Whole genome sequencing (WGS) can provide insight into drug-resistance, transmission chains and the identification of outbreaks, but data analysis remains an obstacle to its routine clinical use. Although several drug-resistance prediction tools have ... ...

Abstract	Whole genome sequencing (WGS) can provide insight into drug-resistance, transmission chains and the identification of outbreaks, but data analysis remains an obstacle to its routine clinical use. Although several drug-resistance prediction tools have appeared, until now no website integrates drug-resistance prediction with strain genetic relationships and species identification of nontuberculous mycobacteria (NTM). We have established a free, function-rich, user-friendly online platform for MTB WGS data analysis (SAM-TB, http://samtb.szmbzx.com) that integrates drug-resistance prediction for 17 antituberculosis drugs, detection of variants, analysis of genetic relationships and NTM species identification. The accuracy of SAM-TB in predicting drug-resistance was assessed using 3177 sequenced clinical isolates with results of phenotypic drug-susceptibility tests (pDST). Compared to pDST, the sensitivity of SAM-TB for detecting multidrug-resistant tuberculosis was 93.9% [95% confidence interval (CI) 92.6-95.1%] with specificity of 96.2% (95% CI 95.2-97.1%). SAM-TB also analyzes the genetic relationships between multiple strains by reconstructing phylogenetic trees and calculating pairwise single nucleotide polymorphism (SNP) distances to identify genomic clusters. The incorporated mlstverse software identifies NTM species with an accuracy of 98.2% and Kraken2 software can detect mixed MTB and NTM samples. SAM-TB also has the capacity to share both sequence data and analysis between users. SAM-TB is a multifunctional integrated website that uses WGS raw data to accurately predict antituberculosis drug-resistance profiles, analyze genetic relationships between multiple strains and identify NTM species and mixed samples containing both NTM and MTB. SAM-TB is a useful tool for guiding both treatment and epidemiological investigation.
MeSH term(s)	Antitubercular Agents/pharmacology ; Antitubercular Agents/therapeutic use ; Data Analysis ; Drug Resistance ; Mycobacterium tuberculosis ; Phylogeny ; Whole Genome Sequencing/methods
Chemical Substances	Antitubercular Agents
Language	English
Publishing date	2022-02-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbac030
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Zs.A 6262: Show issues

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Article ; Online: Deep whole-genome sequencing reveals no evidence for heteroresistance influencing treatment outcomes among drug-susceptible tuberculosis patients.

Chen, Yiwang / Jiang, Qi / Zou, Jingyan / Yang, Tingting / Liu, Qingyun / Luo, Geyang / Gan, Mingyu / Jiang, Yuan / Takiff, Howard E / Lu, Liping / Gao, Qian

Tuberculosis (Edinburgh, Scotland)

2021 Volume 130, Page(s) 102120

Abstract: The purpose of this study was to investigate the minimum level of heteroresistance that predicts poor tuberculosis treatment outcomes. This retrospective study enrolled 45 new tuberculosis patients with varied treatment outcomes and 16 drug-susceptible ... ...

Abstract	The purpose of this study was to investigate the minimum level of heteroresistance that predicts poor tuberculosis treatment outcomes. This retrospective study enrolled 45 new tuberculosis patients with varied treatment outcomes and 16 drug-susceptible retreatment cases. Pretreatment isolates from these 61 patients were whole genome sequenced to detect heteroresistance. Heteroresistance was not found in isolates from any of the new patients, but was detected in isolates from retreatment patients who were nevertheless cured. The results of our small series of patients suggest that heteroresistance <1%, the threshold used to define resistance with the phenotypic proportion method, is not associated with poor treatment outcomes.
MeSH term(s)	Adult ; Aged ; Drug Resistance, Bacterial ; Female ; Genome, Bacterial ; Humans ; Male ; Middle Aged ; Mycobacterium tuberculosis/drug effects ; Mycobacterium tuberculosis/genetics ; Retrospective Studies ; Treatment Outcome ; Tuberculosis/drug therapy ; Tuberculosis/microbiology ; Whole Genome Sequencing
Language	English
Publishing date	2021-08-14
Publishing country	Scotland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2046804-0
ISSN	1873-281X ; 1472-9792
ISSN (online)	1873-281X
ISSN	1472-9792
DOI	10.1016/j.tube.2021.102120
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Article ; Online: Citywide Transmission of Multidrug-resistant Tuberculosis Under China's Rapid Urbanization: A Retrospective Population-based Genomic Spatial Epidemiological Study.

Jiang, Qi / Liu, Qingyun / Ji, Lecai / Li, Jinli / Zeng, Yaling / Meng, Liangguang / Luo, Geyang / Yang, Chongguang / Takiff, Howard E / Yang, Zheng / Tan, Weiguo / Yu, Weiye / Gao, Qian

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2019 Volume 71, Issue 1, Page(s) 142–151

Abstract: Background: Population movement could extend multidrug-resistant tuberculosis (MDR-TB) transmission and complicate its global prevalence. We sought to identify the high-risk populations and geographic sites of MDR-TB transmission in Shenzhen, the most ... ...

Abstract	Background: Population movement could extend multidrug-resistant tuberculosis (MDR-TB) transmission and complicate its global prevalence. We sought to identify the high-risk populations and geographic sites of MDR-TB transmission in Shenzhen, the most common destination for internal migrants in China. Methods: We performed a population-based, retrospective study in patients diagnosed with MDR-TB in Shenzhen during 2013-2017. By defining genomic clusters with a threshold of 12-single-nucleotide polymorphism distance based on whole-genome sequencing of their clinical strains, the clustering rate was calculated to evaluate the level of recent transmission. Risk factors were identified by multivariable logistic regression. To further delineate the epidemiological links, we invited the genomic-clustered patients to an in-depth social network investigation. Results: In total, 105 (25.2%) of the 417 enrolled patients with MDR-TB were grouped into 40 genome clusters, suggesting recent transmission of MDR strains. The adjusted risk for student to have a clustered strain was 4.05 (95% confidence interval, 1.06-17.0) times greater than other patients. The majority (70%, 28/40) of the genomic clusters involved patients who lived in different districts, with residences separated by an average of 8.76 kilometers. Other than household members, confirmed epidemiological links were also identified among classmates and workplace colleagues. Conclusions: These findings demonstrate that local transmission of MDR-TB is a serious problem in Shenzhen. While most transmission occurred between people who lived distant from each other, there was clear evidence that transmission occurred in schools and workplaces, which should be included as targeted sites for active case finding.The average residential distance between genomic-clustered cases was more than 8 kilometers, while schools and workplaces, identified as sites of transmission in this study, deserve increased vigilance for targeted case finding of multidrug-resistant tuberculosis.
MeSH term(s)	Antitubercular Agents/pharmacology ; Antitubercular Agents/therapeutic use ; China/epidemiology ; Genomics ; Humans ; Mycobacterium tuberculosis/genetics ; Retrospective Studies ; Tuberculosis, Multidrug-Resistant/drug therapy ; Tuberculosis, Multidrug-Resistant/epidemiology ; Urbanization
Chemical Substances	Antitubercular Agents
Language	English
Publishing date	2019-09-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciz790
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Article ; Online: Human Chrysomya bezziana myiasis

PLoS Neglected Tropical Diseases, Vol 13, Iss 10, p e

A systematic review.

2019 Volume 0007391

Abstract: BACKGROUND:Myiasis due to Old World screw-worm fly, Chrysomya bezziana, is an important obligate zoonotic disease in the OIE-list of diseases and is found throughout much of Africa, the Indian subcontinent, southeast and east Asia. C. bezziana myiasis ... ...

Abstract	BACKGROUND:Myiasis due to Old World screw-worm fly, Chrysomya bezziana, is an important obligate zoonotic disease in the OIE-list of diseases and is found throughout much of Africa, the Indian subcontinent, southeast and east Asia. C. bezziana myiasis causes not only morbidity and death to animals and humans, but also economic losses in the livestock industries. Because of the aggressive and destructive nature of this disease in hosts, we initiated this study to provide a comprehensive understanding of human myiasis caused by C. bezziana. METHODS:We searched the databases in English (PubMed, Embase and African Index Medicus) and Chinese (CNKI, Wanfang, and Duxiu), and international government online reports to 6th February, 2019, to identify studies concerning C. bezziana. Another ten human cases in China and Papua New Guinea that our team had recorded were also included. RESULTS:We retrieved 1,048 reports from which 202 studies were ultimately eligible for inclusion in the present descriptive analyses. Since the first human case due to C. bezziana was reported in 1909, we have summarized 291 cases and found that these cases often occurred in patients with poor hygiene, low socio-economic conditions, old age, and underlying diseases including infections, age-related diseases, and noninfectious chronic diseases. But C. bezziana myiasis appears largely neglected as a serious medical or veterinary condition, with human and animal cases only reported in 16 and 24 countries respectively, despite this fly species being recorded in 44 countries worldwide. CONCLUSION:Our findings indicate that cryptic myiasis cases due to the obligate parasite, C. bezziana, are under-recognized. Through this study on C. bezziana etiology, clinical features, diagnosis, treatment, epidemiology, prevention and control, we call for more vigilance and awareness of the disease from governments, health authorities, clinicians, veterinary workers, nursing homes, and also the general public.
Keywords	Arctic medicine. Tropical medicine ; RC955-962 ; Public aspects of medicine ; RA1-1270
Subject code	610
Language	English
Publishing date	2019-10-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Human Chrysomya bezziana myiasis: A systematic review.

Zhou, Xianyi / Kambalame, Dzinkambani Moffat / Zhou, Sitong / Guo, Xiang / Xia, Dan / Yang, Yemei / Wu, Rangke / Luo, Juan / Jia, Fenglong / Yuen, Mingchi / Xu, Yuehua / Dai, Geyang / Li, Li / Xie, Tian / Puthiyakunnon, Santhosh / Wei, Wenxia / Xie, Lixian / Liang, Siting / Feng, Yuqin /

Huang, Songgen / Hu, Yongxuan / Mo, Qianzhen / Mai, Rongjia / Zhang, Xiaoqing / Spradbery, Philip / Zhou, Xiaohong

PLoS neglected tropical diseases

2019 Volume 13, Issue 10, Page(s) e0007391

Abstract: Background: Myiasis due to Old World screw-worm fly, Chrysomya bezziana, is an important obligate zoonotic disease in the OIE-list of diseases and is found throughout much of Africa, the Indian subcontinent, southeast and east Asia. C. bezziana myiasis ... ...

Abstract	Background: Myiasis due to Old World screw-worm fly, Chrysomya bezziana, is an important obligate zoonotic disease in the OIE-list of diseases and is found throughout much of Africa, the Indian subcontinent, southeast and east Asia. C. bezziana myiasis causes not only morbidity and death to animals and humans, but also economic losses in the livestock industries. Because of the aggressive and destructive nature of this disease in hosts, we initiated this study to provide a comprehensive understanding of human myiasis caused by C. bezziana. Methods: We searched the databases in English (PubMed, Embase and African Index Medicus) and Chinese (CNKI, Wanfang, and Duxiu), and international government online reports to 6th February, 2019, to identify studies concerning C. bezziana. Another ten human cases in China and Papua New Guinea that our team had recorded were also included. Results: We retrieved 1,048 reports from which 202 studies were ultimately eligible for inclusion in the present descriptive analyses. Since the first human case due to C. bezziana was reported in 1909, we have summarized 291 cases and found that these cases often occurred in patients with poor hygiene, low socio-economic conditions, old age, and underlying diseases including infections, age-related diseases, and noninfectious chronic diseases. But C. bezziana myiasis appears largely neglected as a serious medical or veterinary condition, with human and animal cases only reported in 16 and 24 countries respectively, despite this fly species being recorded in 44 countries worldwide. Conclusion: Our findings indicate that cryptic myiasis cases due to the obligate parasite, C. bezziana, are under-recognized. Through this study on C. bezziana etiology, clinical features, diagnosis, treatment, epidemiology, prevention and control, we call for more vigilance and awareness of the disease from governments, health authorities, clinicians, veterinary workers, nursing homes, and also the general public.
MeSH term(s)	Animals ; Databases, Factual ; Diptera/cytology ; Diptera/pathogenicity ; Diptera/physiology ; Humans ; Hygiene ; Life Cycle Stages ; Screw Worm Infection/diagnosis ; Screw Worm Infection/epidemiology ; Screw Worm Infection/prevention & control ; Screw Worm Infection/therapy ; Socioeconomic Factors ; Treatment Outcome ; Zoonoses/epidemiology ; Zoonoses/parasitology
Language	English
Publishing date	2019-10-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Systematic Review
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2727
ISSN (online)	1935-2735
ISSN	1935-2727
DOI	10.1371/journal.pntd.0007391
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