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Advances in genotypic antimicrobialresistance testing: a comprehensive review

Science China Life Sciences 2025年第1期68卷 130-143页

作者： Boheng Duan Xianjun Zeng Junping Peng Huan Kui College of Nanchang University Department of Imaging The Second Affiliated Hospital of Nanchang University NHC Key Laboratory of Systems Biology of pathogens National Institute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical College Key Laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical Sciences & Peking Union Medical College Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education) State Key Laboratory of Respiratory Health and MultimorbidityNational Institute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical College

Antimicrobial resistance(AMR) represents a substantial threat to global public health, complicating the treatment of common infections and leading to prolonged illness and escalated healthcare expenses. To effectively combat AMR, timely and accurate detection is crucial for AMR surveillance and individual-based therapy. Phenotypic antibiotic resistance testing(AST) has long been considered the gold standard in clinical applications, serving as the foundation for clinical AMR diagnosis and optimized therapy. It has significantly contributed to ensuring patients′ health and the development of novel antimicrobials. Despite advancements in automated culture-based AST technologies,inherent limitations impede the widespread use of phenotypic AST in AMR surveillance. Genotypic AST technologies offer a promising alternative option, exhibiting advantages of rapidity, high sensitivity, and specificity. With the continuous advancement and expanding applications of genotypic AST technologies, such as microfluidics, mass spectrometry, and high-resolution melting curve analysis, new vigor has been injected into the development and clinical implementation of genotypic AST technologies. In this narrative review, we discuss the principles, applications, and advancements of emerging genotypic AST methods in clinical settings. The comprehensive review aims to highlight the significant scientific potential of emerging genotypic AST technologies in clinical AMR diagnosis, providing insights to enhance existing methods and explore novel approaches.

关键词： antimicrobial resistance (AMR) genotypic antibiotic resistance testing (AST) AST technologies review

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Molecular dissection of phage lysin PlySs2: integrity of the catalytic and cell wall binding domains is essential for its broad lytic activity

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Virologica Sinica 2015年第1期30卷 45-51页

作者： Yanling Huang Hang Yang Junping Yu Hongping Wei Key Laboratory of Special pathogens and Biosafety Center for Emerging Infectious Diseases Wuhan Institute of Virology Chinese Academy of Sciences

The novel phage lysin PlySs2, is reported to be highly active against various bacteria, including staphylococci, streptococci and Listeria. However, the molecular mechanisms underlying its broad lytic spectrum remain to be established. In the present study, the lytic activity of the catalytic domain(CD, PlySc) and binding specificity of the cell wall binding domain(CBD, PlySb) of PlySs2 were examined. Our results showed that PlySc alone maintains very limited lytic activity. Enhanced green fluorescent protein(EGFP)-fused PlySb displayed high binding affinity to the streptococcal strains tested, including ***, ***, and ***, but not staphylococci, supporting its utility as a good CBD donor for streptococcal-targeted lysin engineering. EGFP-fused intact PlySs2 similarly displayed high affinity for streptococci, but not staphylococci. Notably, four truncated PlySb fragments showed no binding capacity. These findings collectively indicate that integrity of the PlySc and PlySb domains is an essential determinant of the broad lytic activity of PlySs2.

关键词： streptococci lysin cell wall binding domain catalytic domain bacterial resistance

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Zika virus: a flavivirus caused pandemics in Latin America

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Virologica Sinica 2016年第2期31卷 101-102页

作者： Si-Qing Liu Bo Zhang Key Laboratory of Special pathogens and Biosafety Center for Emerging Infectious Diseases Wuhan Institute of Virology Chinese Academy of Sciences

Since early 2015,an unprecedented outbreak of Zika virus(ZIKV)infection that recognized in northeast Brazil has spread to Latin America(Schuler-Faccini,2016).As of January 2016,there has been confirmed autochthonous t... 详细信息

关键词： unprecedented Brazil Zika virus Latin northeast outbreak spread Aedes outside imported

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ON COUNTING THE FREQUENCY DISTRIBUTION OF STRING MOTIFS IN MOLECULAR SEQUENCES

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International Journal of Biomathematics 2012年第6期5卷 121-139页

作者： MATTIA C. F. PROSPERI LUCIANO PROSPERI REBECCA R. GRAY MARCO SALEMI Department of Pathology Immunology and Laboratory MedicineCollege of Medicine Emerging Pathogens Institute University of Florida Department of ZoologyUniversity of Oxford Oxford UK Department of PathologyImmunology and Laboratory Medicine College of Medicine emerging pathogens institute University of FloridaP. O. Box 103633 2055 Mowry Road GainesviUe FL 32610-3633 USA

This work investigates frequency distributions of strings within a text. The mathematical derivation accounts for variable alphabet size, character probabilities, and string/text lengths, under both the Bernoullian and the Markovian model for string generation. The analysis is limited to the set of nonclumpable strings, that cannot overlap with them selves. Two formulae （exact and approximated） are derived, calculating the frequency distribution of a string of length m found inside a text of length n （with m 〈： n）. The approximated formula has a constant complexity （in contrast to an exponential com plexity of the exact） and makes it applicable to very long texts. The proposed formulae were applied to analyze string frequencies in a portion of the human genome, and to recalculate frequencies of known repeated motif within genes, associated to genetic dis eases. A comparison with stateoftheart methods was provided. The formulae presentedhere can be of use in the statistical evaluation of specific motif frequencies within very long texts （e.g. genes or genomes） and help in characterizing motifs in pathologic conditions.

关键词： Combinatorics genetics genomics.

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Identification of a novel strain of influenza A (H9N2) virus in chicken

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Virologica Sinica 2015年第4期30卷 309-312页

作者： Ning Wang Zheng Ruan Yun Wan Bo Wang Si-Hua Zhang Xing-Yi Ge Center for emerging Infectious Diseases CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of VirologyChinese Academy of Sciences Wuhan Center For Severe Animal Disease Control and Prevention

Dear Editor,Avian Influenza virus(AIV)H9N2 subtype viruses circulate widely in domestic fowl,and usually cause mild clinical signs in poultry(Li et al.,2005).Occasionally,avian H9N2 can infect humans and cause mild clinical symptoms(Peiris et al.,1999;Lin et al.,2000).Genetic analysis indicates that the H9N2 genotype viruses exist in major poultry species(such as duck and chicken)and in minor poultry species(such as quail,partridge,chukar,pheasant,and guinea fowl)(Guan et al.,2000;Li et al.,2005).Meanwhile,frequent reassortment events

关键词： chicken poultry guinea avian genotype Influenza su

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Why were so few people infected with H7N9 influenza A viruses in China from late 2017 to 2018?

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Science China(Life Sciences) 2018年第11期61卷 1442-1444页

作者： Xiaoman Wei Jie Cui CAS Key Laboratory of Special pathogens and Biosafety Center for Emerging Infectious DiseasesWuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China University of Chinese Academy of Sciences Beijing 100049China

Since the first human infection case with H7N9 avian influenza virus(AIVs)was identified in March 2013,there has six viral outbreak waves recorded in China as of September *** *** have been 1,567 confirmed cases of human H7N9 infection and 615 *** fatality rate is around 40%(http://***/csr/don/05-september-2018-ah7n9-china/en/).In general,the H7N9 virus has posed a great threat in avian and human health.

关键词： human In China

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An improved method for identifying SUMOylation sites of viral proteins

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Virologica Sinica 2017年第6期32卷 537-540页

作者： Yan Liu Zhongyuan Tan Bo Shu Yuan Zhang Caishang Zheng Xianliang Ke Xi Chen Hanzhong Wang Zhenhua Zheng CAS Key Laboratory of Special pathogens and Biosafety Center for Emerging Infectious DiseasesWuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China Wuhan institutes of Biotechnology Wuhan 430071China

Dear Editor, In recent years, post-translational modifications （PTMs） by small ubiquitin-related modifiers （SUMOs） have emerged as an important regulatory mechanism for both cellular and viral processes （Ribet and Cossart, 2010）. Identifying the SUMOylation sites of the target protein is important to understand the molecular mechanism under- lying SUMO modification and virus-host interactions, as well as provide new insights into antiviral drug develop- ment （Wimmer and Schreiner, 2015）. Traditional site- directed mutagenesis for identifying viral protein SUMO- ylation sites lacks a specific aim and is laborious （McManus et al., 2016）. Recently, mass spectrometry （MS） has been employed as an accurate and sensitive tool to identify PTM sites, thereby greatly expanding the number of known SUMOylated proteins （Pedrioli et al., 2006）. However, during viral infection, SUMOylation is highly dynamic and SUMOylated viral proteins often have low abundance, which makes studying SUMOylation under natural conditions difficult.

关键词： An improved method identifying SUMOylation sites of viral proteins

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Bayesian evolutionary analysis for emerging infectious disease:an exemplified application for H7N9 avian influenza viruses

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Science China(Life Sciences) 2017年第12期60卷 1392-1395页

作者： Xiaoman Wei Mingyue Chen Jie Cui CAS Key Laboratory of Special pathogens and Biosafety Center for Emerging Infectious DiseasesWuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China University of Chinese Academy of Sciences Beijing 100049China

Dear Editor,Ever since the first human infection with H7N9 avian influenza virus（AIV）was reported in China in March 2013,there have been five H7N9 AIV pandemics in ***5 began earlier than the previous four waves,spr... 详细信息

关键词： Bayesian evolutionary infectious disease

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Cloning, expression, and antiviral activity of interferon β from the Chinese microbat, Myotis davidii

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Virologica Sinica 2015年第6期30卷 425-432页

作者： Ying-Zi Liang Li-Jun Wu Qian Zhang Peng Zhou Mei-Niang Wang Xing-Lou Yang Xing-Yi Ge Lin-Fa Wang Zheng-Li Shi Key Laboratory of Special pathogens and Biosafety Wuhan Institute of Virology Chinese Academy of Sciences Department of Plastic Surgery Xijing Hospital Fourth Military Medical University Program in emerging Infectious Diseases Duke-National University of Singapore Graduate Medical School

Bats are natural reservoir hosts for many viruses that produce no clinical symptoms in ***, bats may have evolved effective mechanisms to control viral replication. However, little information is available on bat immune responses to viral infection. Type I interferon(IFN) plays a key role in controlling viral infections. In this study, we report the cloning, expression, and biological activity of interferon β(IFNβ) from the Chinese microbat species, Myotis davidii. We demonstrated the upregulation of IFNB and IFN-stimulated genes in a kidney cell line derived from M. davidii after treatment with poly I:C or infection with Sendai virus. Furthermore, the recombinant IFNβ inhibited vesicular stomatitis virus and bat adenovirus replication in cell lines from two bat species, M. davidii and Rhinolophus sinicus. We provide the first in vitro evidence of IFNβ antiviral activity in microbats, which has important implications for virus interactions with these hosts.

关键词： bat interferon IFN-stimulated genes antiviral activity

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Pulsed dynamic electrolysis enhanced PEMWE hydrogen production:Revealing the effects of pulsed electric fields on protons mass transport and hydrogen bubble escape

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Journal of Energy Chemistry 2025年第1期100卷 201-214页

作者： Xuewei Zhang Wei Zhou Yuming Huang Liang Xie Tonghui Li Huimin Kang Lijie Wang Yang Yu Yani Ding Junfeng Li Jiaxiang Chen Miaoting Sun Shuo Cheng Xiaoxiao Meng Jihui Gao Guangbo Zhao School of Energy Science and Engineering Harbin Institute of Technology China Datang Technology Innovation Co. Ltd

The transition of hydrogen sourcing from carbon-intensive to water-based methodologies is underway,with renewable energy-powered proton exchange membrane water electrolysis （PEMWE） emerging as the preeminent pathway for hydrogen *** remarkable advancements in this field,confronting the sluggish electrochemical kinetics and inherent high-energy consumption arising from deteriorated mass transport within PEMWE systems remains a formidable *** impediment stems primarily from the hindered protons mass transfer and the untimely hydrogen bubbles *** address these challenges,we harness the inherent variability of electrical energy and introduce an innovative pulsed dynamic water electrolysis *** to constant voltage electrolysis (hydrogen production rate:51.6 m L h-1,energy consumption:5.37 kWh Nm-3H2),this strategy (hydrogen production rate:66 m L h-1,energy consumption:3.83 kWh Nm-3H2) increases the hydrogen production rate by approximately 27%and reduces the energy consumption by about 28%.Furthermore,we demonstrate the practicality of this system by integrating it with an off-grid photovoltaic （PV） system designed for outdoor operation,successfully driving a hydrogen production current of up to 500 mA under an average voltage of approximately 2 *** combined results of in-situ characterization and finite element analysis reveal the performance enhancement mechanism:pulsed dynamic electrolysis （PDE） dramatically accelerates the enrichment of protons at the electrode/solution interface and facilitates the release of bubbles on the electrode *** such,PDE-enhanced PEMWE represents a synergistic advancement,concurrently enhancing both the hydrogen generation reaction and associated transport *** promising technology not only redefines the landscape of electrolysis-based hydrogen production but also holds immense potential for broadening its application across a diverse spectrum of electrocatalytic endeavors.

关键词： Electrolysis

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