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Advances in genotypic antimicrobialresistance testing: a comprehensive review

Science China Life Sciences 2025年第01期 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.

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Comparative analysis of whole genome structure of Streptococcus suis using whole genome PCR scanning

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Science China(Life Sciences) 2008年第1期51卷 21-26页

作者： XIONG ZhaoHui WEI CanDong YANG Jian peng junping XU XingYe WANG Yu JIN Qi State Key Lab for Molecular Virology and Genetic Engineering Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 100176China Chinese Center for Disease Control and Prevention Beijing 100050China Institute of Pathogen Biology Chinese Academy of Medical SciencesBeijing 100730China

An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis. WGPScanning analysis showed that all primer pairs yielded PCR products of the expected sizes in all four strains tested. The nucleotide sequences of all the detected virulence factor genes are identical in the four strains and MLST results showed that the four isolates studied and reference strain all belonged to the ST1 com-plex. No new genetic changes were found in the genome structure of the isolates from this Sichuan outbreak.

关键词： Streptococcus suis whole genome PCR scanning multilocus sequence typing(MLST)

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Global transcriptional profiles of Trichophyton rubrum in response to Flucytosine

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Science China(Life Sciences) 2009年第12期52卷 1173-1185页

作者： ZHAO Rong BIN Wen DIAO YouJiang YANG Jian LIU Tao peng junping JIN Qi State Key Laboratory for Molecular Virology and Genetic Engineering National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 100176China Institute of Pathogen Biology Chinese Academy of Medical SciencesBeijing 100730China

Trichophyton rubrum (***) is one of the most common human fungal pathogens that cause chronic infections of the skin and nails. To identify antifungal responsive genes, cDNA microarray analysis was performed for T. rubrum to reveal global transcriptional profiles of drug-specific responses to 5-Flucytosine (5-FC). cDNA microarray was constructed from the T. rubrum expressed sequence tag (ESTs) database, the minimum inhibitory concentration (MIC) of 5-FC was determined, and microarray hybridization and data analysis were applied. The expression pattern of 7 genes observed by microarray was confirmed by the quantitative real-time reverser transcription polymerase chain reaction (RT-PCR). Data analysis indicated that a total of 474 genes were found differentially expressed, 196 showed an increase in expression and 278 showed a decrease in expression. Marked down-regulation of genes involved in nucleotide metabolism (such as CDC21), transcription (such as E2F1), and RNA processing (such as SGN1, RIM4 and NOP1) was observed. Other genes involved in signal transduction, chaperones, inorganic ion transport, secondary metabolite biosynthesis, amino acid transport, lipid transport and potential drug resistance mechanism were also affected by 5-FC. Quantitative real-time RT-PCR of the selected genes confirmed the reliability of the microarray results. This is the first analysis of transcriptional profiles in response to 5-FC for T. rubrum. The findings may be valuable for the identification of genes involved in mechanisms of action and mechanisms of antifungal drug resistance of 5-FC.

关键词： Trichophyton rubrum cDNA microarray 5-Flucytosine gene expression

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Nanoscale superconductivity of ?-Ga islands grown by molecular beam epitaxy

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Science China(Physics,Mechanics & Astronomy) 2015年第10期58卷 89-93页

作者： ZHANG HuiMin peng junping GUAN JiaQi LI Zhi SONG CanLi WANG LiLi HE Ke MA XuCun XUE QiKun Institute of Physics Chinese Academy of Sciences State Key Laboratory of Low-Dimensional Quantum Physics Department of Physics Tsinghua University Collaborative Innovation Center for Quantum Matter

We report on the preparation and superconductivity of metastable γ-Ga islands on Si(111) substrate. The Ga grows in a typical Volmer-Weber mode at a low temperature of 110 K, resulting in formation of Ga nanoislands at various sizes with the identical γ-phase. In-situ low temperature scanning tunneling spectra reveal quantized electronic states in ultrathin Ga islands. It is found that both the lateral size and thickness of the Ga islands strongly suppress the superconductivity. Due to substantial surface energy contribution, the transition temperature Tc scales inversely with the island thickness and the minimum thickness for the occurrence of superconductivity is calculated to be two monolayers.

关键词： γ-Ga superconductivity size effects molecular beam epitaxy

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Determining antimicrobial resistance profiles and identifying novel mutations of Neisseria gonorrhoeae genomes obtained by multiplexed MinION sequencing

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Science China(Life Sciences) 2020年第7期63卷 1063-1070页

作者： Chi Zhang Feng Wang Cansheng Zhu Leshan Xiu Yamei Li Li Li Bo Liu Yizhun Li Yaling Zeng Boyang Guo junping peng NHC Key Laboratory'of Systems Biology of Pathogens Institute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100176China Shenzhen Center for Chronic Disease Control Shenzhen 518020China Department of STD Laboratory Shaanxi Provincial Institute for Skin Disease and STD ControlXi'an 710003China

Gonorrhea is one of the most common sexually transmitted diseases worldwide. To cure infection and prevent transmission,timely and appropriate antimicrobial therapy is necessary. Unfortunately, Neisseria gonorrhoeae, the etiological agent of gonorrhea, has acquired nearly all known mechanisms of antimicrobial resistance(AMR), thereby compromising the efficacy of antimicrobial therapy. Treatment failure resulting from AMR has become a global public health concern. Whole-genome sequencing is an effective method to determine the AMR characteristics of N. gonorrhoeae. Compared with next-generation sequencing, the MinION sequencer(Oxford Nanopore Technologies(ONT)) has the advantages of long read length and portability. Based on a pilot study using MinION to sequence the genome of N. gonorrhoeae, we optimized the workflow of sequencing and data analysis in the current study. Here we sequenced nine isolates within one flow cell using a multiplexed sequencing strategy. After hybrid assembly with Illumina reads, nine integral circular chromosomes were obtained. By using the online tool Pathogenwatch and a BLAST-based workflow, we acquired complete AMR profiles related to seven classes of antibiotics. We also evaluated the performance of ONT-only assemblies. Most AMR determinants identified by ONT-only assemblies were the same as those identified by hybrid assemblies. Moreover, one of the nine assemblies indicated a potentially novel antimicrobial-related mutation located in mtrR which results in a frame-shift, premature stop codon, and truncated *** addition, this is the first study using the MinION sequencer to obtain complete genome sequences of N. gonorrhoeae strains which are epidemic in China. This study shows that complete genome sequences and antimicrobial characteristics of *** can be obtained using the MinION sequencer in a simple and cost-effective manner, with hardly any knowledge of bioinformatics required. More importantly, this strategy provid

关键词： nanopore sequencing MinION sequencer Neisseria gonorrhoeae whole-genome sequencing antimicrobial resistance

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Development and performance evaluation of a culture-independent nanopore amplicon-based sequencing method for accurate typing and antimicrobial resistance profiling in Neisseria gonorrhoeae

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Science China(Life Sciences) 2024年第2期67卷 421-423页

作者： Chi Zhang Lulu Zhang Feng Wang Yaling Zeng Liying Sun Di Wang Yamei Li Liqin Wang junping peng NHC Key Laboratory of Systems Biology of Pathogens Institute of Pathogen BiologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100176China Key Laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical SciencesBeijing 100730China Shenzhen Center for Chronic Disease Control Shenzhen 518020China

Dear Editor,Bacterial antimicrobial resistance(AMR)poses a serious threat to global human health(Antimicrobial Resistance Collaborators,2022).Comprehensive profiling of AMR and accurate molecular typing are important for tracking and controlling the emergence and dissemination of antibiotic-resistant bacteria(Yahara et al.,2021).We previously developed a multiplex amplicon sequencing-based method for directly sequencing AMR-related loci in *** from clinical samples(Zhang et al.,2021).

关键词： gonorrhoeae resistance

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Genomic compositions and phylogenetic analysis of Shigella boydii subgroup

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Science China(Life Sciences) 2006年第1期49卷 46-52页

作者： WANG Jing ZHANG Xiaobing peng junping YANG E BIN Wen YANG Jian DONG Jie SUN Lilian XU Xingye JIN Qi State Key Laboratory for Molecular Virology and Genetic Engineering Beijing 100176China School of Medicine Xi’an Jiaotong UniversityXi’an 710061China School of Pharmaceutical Engineering Shengyang Pharmaceutical UniversityShengyang 110016China

Comparative Genomic Hybridization (CGH) microarray analysis was used tocompare the genomic compositions of all eighteen Shigella boydii serotype representative *** results indicated the genomic ''backbone'' of this subgroup contained 2552 ORFs homologous tononpatho-genic E. coli K12. Compared with the genome of K12199 ORFs were found to be absent in allS. boydii serotype representatives, including mainly outer membrane protein genes and O-antigenbiosynthesis genes. Yet the specific ORFs of S. boydii subgroup contained basically bacteriophagegenes and the function unknown (FUN) genes. Some iron metabolism, transport and type Ⅱ secretionsystem related genes were found in most representative strains. According to the CGH phylogeneticanalysis, the eighteen S. boydii serotype representatives were divided into four groups, in whichserotype C13 strain was remarkably distinguished from the other serotype strains. This groupingresult corresponded to the distribution of some metabolism related genes. Furthermore, the analysisof genome backbone genes, specific genes, and the phylogenetic trees allowed us to discover theevolution laws of S. boydii and to find out important clues to pathogenesis research, vaccinationand the therapeutic medicine development.

关键词： S.boydii comparative genomic hybridization(CGH) strain-specific ORFs evolution

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Comparative genomics and phylogenetic analysis of S. dysenteriae subgroup

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Science China(Life Sciences) 2005年第4期48卷 406-413页

作者： YANG E BIN Wen peng junping ZHANG Xiaobing WANG Jing YANG Jian DONG Jie CHU Yonglie ZHANG Jinghai JIN Qi School of Medicine Xi’an Jiaotong UniversityXi’an 710061China School of Pharmaceutical Engineering Shenyang Pharmaceutical UniversityShenyang 110016China State Key Laboratory for Molecular Virology and Genetic Engineering Beijing 100176China

Genomic compositions of representatives of thirteen S. dysenteriae serotypes were investigated by performing comparative genomic hybridization (CGH) with microarray containing the whole genomic ORFs (open reading frames, ORFs) of E. coli K12 strain MG1655 and spe-cific ORFs of S. dysenteriae A1 strain Sd51197. The CGH results indicated the genomes of the serotypes contain 2654 conserved ORFs originating from E. coli. However, 219 intrinsic genes of E. coli including those prophage genes, molecular chaperones, synthesis of specific O antigen and so on were absent. Moreover, some specific genes such as type II secretion system associ-ated components, iron transport related genes and some others as well were acquired through horizontal transfer. According to phylogenic trees based on genetic composition, it was demon-strated that A1, A2, A8, A10 were distinct from the other S. dysenteriae serotypes. Our results in this report may provide new insights into the physiological process, pathogenicity and evolution of S. dysenteriae.

关键词： S.dysenteriae subgroup DNA microarray comparative genomics.

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A multiplex method for detection of SARS-CoV-2 variants based on MALDI-TOF mass spectrometry

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Biosafety and Health 2023年第2期5卷 101-107页

作者： Ziyuan Zhao Liying Sun Liqin Wang Xiaodong Li junping peng NHC Key Laboratory of Systems Biology of Pathogens Institute of Pathogen BiologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100730China Key Laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China Shimadzu China Innovation Center Shimadzu CorporationBeijing 100020China

The recent outbreak of the coronavirus disease 2019(COVID-19)pandemic and the continuous evolution of the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)have highlighted the significance of new detection methods for global monitoring and *** quantitative reverse transcription PCR(RT-qPCR),the current gold standard for diagnosis,performs excellently in genetic testing,its multiplexing capability is limited because of the signal crosstalk of various ***,we present a highly effi-cient platform which combines 17-plex assays with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry(MALDI-TOF MS),enabling the targeting of 14 different mutation sites of the spike *** using a set of 324 nasopharyngeal swabs or sputum clinical samples with SARS-CoV-2 MS method was identical to that with the *** detection consistency of mutation sites was 97.9%(47/48)com-pared to Sanger sequencing without cross-reaction with other respiratory-related ***,the MS method is highly potent to track and assess SARS-CoV-2 changes in a timely manner,thereby aiding the continuous response to viral variation and prevention of further transmission.

关键词： COVID-19 SARS-CoV-2 Multiplexing capability MALDI-TOF mass spectrometry Viral variation

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Research progress in Shigella in the postgenomic era

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Science China(Life Sciences) 2010年第11期53卷 1284-1290页

作者： peng junping, YANG Jian & JIN Qi State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology,Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100176, China 1. State Key Laboratory for Molecular Virology and Genetic Engineering Institute of Pathogen Biology Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100176 China

Gram-negative,facultative intracellular anaerobes of the genus Shigella,the principal etiologic agents of shigellosis,continue to pose a threat to public health. Shigellosis causes 1.1 million deaths with over 164 million annual cases. The Shigella spp. can be divided into four serogroups:Shigella dysenteriae,Shigella flexneri, Shigella boydii and Shigella sonnei. The completion of seven Shigella genome sequences of representative strains from each of the Shigella species has introduced an era of whole-genome *** paper reviews contemporary understanding of genomics,transcriptomics,proteomics and the structural biology of Shigella.

关键词： Shigella genomics transcriptomics proteomics structural biology

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