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10. Krait2: a versatile software for microsatellite investigation, visualization and marker development.

Author

Du, Lianming, Chen, Jiahao, Sun, Dalin, Zhao, Kelei, Zeng, Qianglin, and Yang, Nan

Subjects
TANDEM repeats, GENETIC regulation, LIFE sciences, SOURCE code, MICROSATELLITE repeats
Abstract

Background: Microsatellites are highly polymorphic repeat sequences ubiquitously interspersed throughout almost all genomes which are widely used as powerful molecular markers in diverse fields. Microsatellite expansions play pivotal roles in gene expression regulation and are implicated in various neurological diseases and cancers. Although much effort has been devoted to developing efficient tools for microsatellite identification, there is still a lack of a powerful tool for large-scale microsatellite analysis. Results: We present Krait2, a user-friendly graphical tool for investigating perfect, imperfect and compound microsatellites from FASTA and FASTQ formatted genomic datasets. Krait2 not only provides features such as primer design, repeat filtering, repeat annotation and statistical analysis, but also offers various output formats to support customized downstream analysis. Moreover, it has capability of analyzing multiple genomes simultaneously and conducting comparative analysis. Conclusions: Krait2 is a versatile and easy-to-use software for both novices and experts to identify and analyze microsatellites. The installer and source code are available at https://github.com/lmdu/krait2. [ABSTRACT FROM AUTHOR]

Published
2025
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11. Rapid Response to Penpulimab Combined With Anlotinib and Chemotherapy in a Thoracic SMARCA4‐UT Without PD‐L1 Expression: A Case Report and Review of Literature.

Author

Wang, Yuanhang, Zhao, Kelei, Zhang, Jingjing, Yuan, Xiaohan, Liu, Yanting, Zhang, Jinghang, Lu, Ping, and Zhang, Min

Subjects
*IMMUNE checkpoint inhibitors, *ANLOTINIB, *THERAPEUTICS, *COMPUTED tomography, *OVERALL survival
Abstract

SMARCA4‐deficient undifferentiated tumor (SMARCA4‐UT) in the chest is a high‐grade malignant tumor that grows rapidly and often carries a poor prognosis. Unfortunately, there are currently no effective treatment available until now. Here, we report a case of SMARCA4‐UT in a patient who showed a swift response to a combination treatment of penpulimab, anlotinib, and chemotherapy. A 55‐year‐old man was diagnosed with thoracic SMARCA4‐UT along with metastases to multiple lymph nodes, the pleura, and bones. Immunohistochemical (IHC) testing indicated the absence of PD‐L1 expression in tumor cells. He was given sintilimab and anlotinib as first line treatment. However, a follow‐up chest CT revealed progressive disease (PD) after the first cycle treatment. Subsequently, the second line regimen was modified to etoposide and cisplatin (EP) combined with anlotinib and penpulimab. The effectiveness evaluation revealed partial remission (PR) following two cycles of the second‐line regimen treatment. Notably, the patient's progress‐free survival (PFS) exceeds 7 months and the overall survival up to 12 months. Our case implies that a combination of chemotherapy, anlotinib, and penpulimab might offer a promising therapeutic approach for PD‐L1‐negative thoracic SMARCA4‐UT. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Feasibility of hydromorphone PCA 10-day simple mode home management of patients in severe pain: A prospective multicenter study.

Author

Zhao, Kelei, primary, Han, Yu, additional, Li, Chunqing, additional, Zhang, Guifang, additional, He, Junling, additional, Chang, Wei, additional, Yin, Haiqing, additional, Cui, Yuelong, additional, Dong, Yanhu, additional, Yao, Yibo, additional, Chen, Guorong, additional, Wang, Pei, additional, Tang, Dongxia, additional, Dong, Hua, additional, Zhang, Qiang, additional, Li, Bo, additional, Zhang, Min, additional, Ji, Yinghua, additional, and Lu, Ping, additional

Published
2024
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24. Modification of social cheating facilitates the stabilization and chronic infection of polymorphicPseudomonas aeruginosapopulation

Author

Zhao, Kelei, primary, Yang, Xiting, additional, Zeng, Qianglin, additional, Zhang, Yige, additional, Li, Heyue, additional, Li, Jing Shirley, additional, Liu, Huan, additional, Du, Liangming, additional, Wu, Yi, additional, Huang, Gui, additional, Huang, Ting, additional, Zhang, Yamei, additional, Zhou, Hui, additional, Wang, Xinrong, additional, Chu, Yiwen, additional, and Zhou, Xikun, additional

Published
2023
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30. Structural basis of sRNA RsmZ regulation ofPseudomonas aeruginosavirulence

Author

Jia, Xinyu, primary, Pan, Zhiling, additional, Yuan, Yang, additional, Luo, Bingnan, additional, Luo, Yongbo, additional, Mukherjee, Sunandan, additional, Jia, Guowen, additional, Liu, Liu, additional, Ling, Xiaobin, additional, Yang, Xiting, additional, Miao, Zhichao, additional, Wei, Xiawei, additional, Bujnicki, Janusz M., additional, Zhao, Kelei, additional, and Su, Zhaoming, additional

Published
2022
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35. Co-Occurrence of the blaKPC-2 and Mcr-3.3 Gene in Aeromonas caviae SCAc2001 Isolated from Patients with Diarrheal Disease

Author

Tang,Lingtong, Huang,Jianglian, She,Junping, Zhao,Kelei, and Zhou,Yingshun

Subjects
bla KPC-2, Infection and Drug Resistance, virulence factors, secondary metabolism products, mcr-3.3, Aeromonas caviae, Original Research
Abstract

Lingtong Tang,1,2,* Jianglian Huang,3,* Junping She,1 Kelei Zhao,4 Yingshun Zhou1 1Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou 646000, Sichuan, People’s Republic of China; 2Department of Clinical Laboratory, People’s Hospital of Gao County, Yibing 644000, Sichuan, People’s Republic of China; 3Department of Clinical Laboratory, The Second Affiliated Hospital of Xiamen Medical College, Xiaman 361600, People’s Republic of China; 4Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, Sichuan, People’s Republic of China*These authors contributed equally to this workCorrespondence: Yingshun ZhouDepartment of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan 646000, People’s Republic of China, No. 319, Zhongshan Road, Tel +86-0830-3160073Email yingshunzhou@swmu.edu.cnKelei ZhaoAntibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, No. 168, Huaguan Road, Chengdu 610052, Sichuan, People’s Republic of ChinaTel +86– 028– 84216035Email zhaokelei@cdu.edu.cnPurpose: To characterize the genetic feature of a multi-drug-resistant Aeromonas caviae strain isolated from the diarrhea sample of a 45-year-old male patient with acute diarrhea.Materials and Methods: Whole-genome of the A. caviae strain SCAc2001 was sequenced via the Illumina system, followed by a series of bioinformatic analyses to describe the genetic feature.Results: The genome sequence of A. caviae SCAc2001 was assembled into 340 scaffolds (305 of them were > 1000 bp in length and 4,487,370 bp in total) with an average G+C content of 61.09%. Phylogenetic analysis showed that the A. caviae SCAc2001 strain was highly similar to the A. caviae strain R25-2 and T25-39. Resistome analysis identified that A. caviae SCAc2001 carried 13 antimicrobial resistance genes, including β-lactams (blaKPC, blaCTX-M-14, blaTEM-1, blaOXA-10, blaOXA-427, blaVEB-3 and blaMOX-6), aminoglycosides (aadA1), fluoroquinolones (aac(6ʹ)-Ib-cr), phenicol resistance (catB3), sulfonamide (sul1), trimethoprim (dfrA5) and colistin resistance (mcr-3.3).And also, A. caviae ScAc2001 carried 54 putative virulence genes including the type IV pilus, fimbria, flagellarthe, and hemolysin A encoding genes, and 12 pathogen–host interactions (PHI) genes. There were also four genomic islands and eight prophages in the genome of A. caviae ScAc2001. In addition, A. caviae SCAc2001 also carried three secondary metabolism products coding clusters including nonribosomal peptide synthetases (nrps), hserlactone and bacteriocin.Conclusion: A. caviae ScAc2001 carries many resistance genes, a variety of virulence factors, PHI genes and four genomic islands and eight prophages, which poses a severe threat to infectious diseases control strategies, diagnosis methods and clinical treatment.Keywords: Aeromonas caviae, blaKPC-2, mcr-3.3, virulence factors, secondary metabolism products &nbsp

Published
2020

36. Identification of a Multidrug Resistant Pseudomonas aeruginosa Isolate Harboring Infrequent Red Fluorescence Plasmid from COPD Patient

Author

Zeng,Qianglin, Yang,Xiting, Li,Heyue, Zhang,Jiajie, Zhang,Yamei, Zhou,Hui, Zhao,Kelei, Zeng,Qianglin, Yang,Xiting, Li,Heyue, Zhang,Jiajie, Zhang,Yamei, Zhou,Hui, and Zhao,Kelei

Abstract

Qianglin Zeng,1 Xiting Yang,1 Heyue Li,2 Jiajie Zhang,1 Yamei Zhang,1 Hui Zhou,1 Kelei Zhao1 1Affiliated Hospital/Clinical College of Chengdu University, Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, 610106, People’s Republic of China; 2Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, People’s Republic of ChinaCorrespondence: Kelei Zhao, Affiliated Hospital/Clinical College of Chengdu University, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025, Chengluo Avenue, Chengdu, Sichuan, 610106, People’s Republic of China, Email zhaokelei@cdu.edu.cnAbstract: Pseudomonas aeruginosa is a notorious Gram-negative opportunistic pathogen that normally causes acute and chronic infections in a wide range of hosts. In this study, a multi-resistant P. aeruginosa isolate L1a harboring an infrequent plasmid with red fluorescence was obtained from the bronchoalveolar lavage fluid of a patient with chronic obstructive pulmonary disease. The results of susceptibility testing and virulence-related phenotypic identification revealed that P. aeruginosa L1a was resistant to levofloxacin, cefepime, aztreonam, and imipenem and showed significantly stronger capacities for swimming and pyocyanin production than the reference strain PAO1. The genome of P. aeruginosa L1a was assembled into one circular chromosome (6,216,913 bp) and one circular plasmid (9111 bp). P. aeruginosa L1a was found to belong to the multilocus sequence type ST549, and serotype O5, and carried 8 drug resistance genes and 18 multidrug efflux pump-related genes in the chromosomal DNA. The plasmid pL1a harbored a tetracycline resistant gene tetA and a functional red fluorescence protein. This study reports a multidrug resistant P. aeruginosa clinical isolate harbori

Published
2022

39. Polyphasic Identification and Genomic Insights of Leptothermofonsia sichuanensis gen. sp. nov., a Novel Thermophilic Cyanobacteria Within Leptolyngbyaceae

Author

Tang, Jie, primary, Shah, Mahfuzur R., additional, Yao, Dan, additional, Jiang, Ying, additional, Du, Lianming, additional, Zhao, Kelei, additional, Li, Liheng, additional, Li, Meijin, additional, Waleron, Michal M., additional, Waleron, Malgorzata, additional, Waleron, Krzysztof, additional, and Daroch, Maurycy, additional

Published
2022
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