Article
Infectious Diseases
Yu Qi, Jun-Ze Xue, Shuang-shuang Li, Emad Mohammed Elken, M. Aman Haqmal, Xue-Song Li, Guan-Yi Xu, Ling-Cong Kong, Hong-Xia Ma
Summary: This study investigated the antibiotic resistance and pathogenicity mechanism of Klebsiella pneumoniae in Jilin Province. The results showed that the JP20 strain exhibited high antibiotic resistance and strong pathogenicity. Whole-genome sequencing revealed that the antibiotic resistance genes were mainly carried by an IncR plasmid, and the loss of outer membrane porin OmpK36 may play a role in carbapenem resistance. These findings provide a basis for monitoring and understanding the antibiotic resistance mechanism of K. pneumoniae.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2023)
Article
Microbiology
Pengcheng Du, Chao Liu, Shuaihua Fan, Stephen Baker, Jun Guo
Summary: Multidrug-resistant hypervirulent Klebsiella pneumoniae of sequence type 23 (MDR-ST23-hvKp) is becoming increasingly important in China. This study analyzed the genomic characteristics of MDR and non-MDR isolates and identified the genetic elements associated with MDR-ST23-hvKp. The findings highlight the need for genomic surveillance and control studies of this pathogen.
MICROBIOLOGY SPECTRUM
(2022)
Article
Food Science & Technology
Yingwei Xu, Ling Ni, Huiqiong Guan, Dailing Chen, Si Qin, Lanming Chen
Summary: This study reported the genetic diversity of Klebsiella pneumoniae strains in edible aquatic animals in Shanghai, China. The strains exhibited virulence-related genes and drug resistance. Additionally, higher abundance of the bacterium was found in bottom-dwelling aquatic animals.
Article
Infectious Diseases
Huixian Liang, Xinhui Li, He Yan
Summary: Multidrug-resistant Klebsiella pneumoniae poses a serious threat to public health. This study analyzed the genetic structure of plasmids and chromosomes in a swine-origin K. pneumoniae strain and found that the plasmids could act as reservoirs for antimicrobial resistance genes and transfer resistance between different strains.
Review
Biochemistry & Molecular Biology
Karolina Stojowska-Swedrzynska, Adrianna Lupkowska, Dorota Kuczynska-Wisnik, Ewa Laskowska
Summary: Klebsiella pneumoniae is a common pathogen responsible for various infections, and its multidrug resistance has been recognized as a significant public health threat. Heteroresistance, a frequent phenotype in pathogens, may be associated with an increased risk of recurrent infections and treatment failure in K. pneumoniae.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Stephen Mark Edward Fordham, Anna Mantzouratou, Elizabeth Sheridan
Summary: Colistin is a last resort antibiotic for treating carbapenemase producing Klebsiella pneumoniae. The insertion of IS elements into the mgrB gene is a mechanism that causes colistin resistance. Plasmids carrying IS elements are common in K. pneumoniae, with ISKpn25 being mostly carried by IncFIB(pQil) plasmids, while ISKpn26 and ISKpn14 are often associated with IncFII(pHN7A8) plasmids. ISKpn25 is identified in 26 out of 34 countries that contain any of the IS elements, while ISKpn26, ISKpn14, and IS903B are most frequently found in China. Plasmids carrying ISKpn25, ISKpn14, and ISKpn26 have a higher count of carbapenemase genes compared to IS903B-carrying plasmids. IS903B-bearing plasmids have a higher count of environmental source isolations compared to ISKpn25, ISKpn14, and ISKpn26 bearing plasmids. The presence of carbapenemase in combination with IS elements could lead to an extensively drug-resistant profile in K. pneumoniae, limiting treatment options.
Article
Genetics & Heredity
Cuidan Li, Xiaoyuan Jiang, Tingting Yang, Yingjiao Ju, Zhe Yin, Liya Yue, Guannan Ma, Xuebing Wang, Ying Jing, Xinhua Luo, Shuangshuang Li, Xue Yang, Fei Chen, Dongsheng Zhou
Summary: The dissemination of carbapenemase-producing Klebsiella pneumoniae (cpKP) is driven by specific combinations of host-blaKPC-carrying plasmids, which are associated with strong population expansion in 2007-2008. This study provides insights into the molecular epidemiology and genetic basis for the spread of ST11/CG258 cpKP in China.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Infectious Diseases
Xuemei Yang, Xiaoxuan Liu, Yating Xu, Edward Wai-Chi Chan, Rong Zhang, Sheng Chen
Summary: This study identified a transferable conjugative plasmid carrying azithromycin resistance genes in Klebsiella pneumoniae, which could be transmitted to Escherichia coli and Salmonella enterica, resulting in azithromycin resistance. In addition, the plasmid could assist in the transfer of a virulence plasmid carried by the K. pneumoniae strain to other bacteria, facilitating the dissemination of these determinants.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2022)
Article
Microbiology
Fredrik Hakonsholm, Marit A. K. Hetland, Iren H. Loehr, Bjorn Tore Lunestad, Nachiket P. Marathe
Summary: This study aimed to determine the genetic background of antibiotic and heavy metal resistance genes in antibiotic-resistant K. pneumoniae isolated from marine bivalves. Complete genome sequencing was conducted on five antibiotic-resistant isolates, and plasmid transfer potential was examined through conjugation experiments. The results revealed the co-occurrence of antibiotic and heavy metal resistance genes on a conjugative IncFIB plasmid, highlighting the potential dissemination route for antimicrobial resistance through the marine environment and seafood.
Article
Biodiversity Conservation
Huiqiong Guan, Lu Xie, Lanming Chen
Summary: Our recent research in Shanghai, China revealed the presence of Klebsiella pneumoniae in aquatic animals. These isolates showed multiple antibiotic and heavy metal resistance profiles, as well as considerable genome variation. This study provides important insights into the genomes of K. pneumoniae derived from aquatic animals.
Article
Microbiology
Xiaoli Wang, Bin Tang, Guitian Liu, Meng Wang, Jingyong Sun, Ruoming Tan, Tingting Pan, Jieming Qu, Jialin Liu, Hong-Yu Ou, Hongping Qu
Summary: Klebsiella pneumoniae poses a critical challenge to clinical and public health due to the global spread of conjugative and nonconjugative plasmids associated with carbapenem-resistant, hypervirulent, and even dual-resistant and hypervirulent strains. This study identified a clinically significant CRKP strain and demonstrated the high conjugation ability of its IncN3 plasmid, which can mobilize nonconjugative virulence or resistance plasmids. The findings suggest a need for further monitoring of the transmission of pathogenicity and genetic evolution of carbapenem-resistant and hypervirulent K. pneumoniae strains.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Vitus Silago, Stephen E. Mshana
Summary: This study analyzed K. pneumoniae isolates from clinical specimens in a tertiary hospital in Mwanza, Tanzania, and found that they carried multiple antibiotic resistance genes and plasmid replicons. The findings highlight the need for genomic-based surveillance in low- and middle-income countries to monitor the spread of high-risk global clones, epidemic plasmids, and antibiotic resistance genes.
Article
Medicine, General & Internal
Ying Zhou, Yang Yang, Xiaobin Li, Dongxing Tian, Wenxiu Ai, Weiwen Wang, Bingjie Wang, Barry N. Kreiswirth, Fangyou Yu, Liang Chen, Xiaofei Jiang
Summary: In this study, the native CRISPR system of K. pneumoniae was used to successfully cure multidrug-resistant IncFII plasmids through conjugation-mediated delivery of the CRISPR-Cas3 system. The work demonstrated that CRISPR-mediated plasmid curing could re-sensitize drug-resistant K. pneumoniae to multiple antibiotics.
Article
Immunology
Susan Realegeno, Kevin Ward, Omai B. Garner, Shangxin Yang
Summary: This study identified an unusual non-carbapenemase-producing CRKP carrying a rare plasmid-borne inducible AmpC gene, with whole genome sequencing revealing multiple resistance genes. Monitoring and identification of CRKP, especially with complex resistance patterns, is crucial for effective management of infections.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Microbiology
Jinzhao Long, Jiangfeng Zhang, Yanyan Xi, Jiaxue Zhao, Yuefei Jin, Haiyan Yang, Shuaiyin Chen, Guangcai Duan
Summary: This study investigates the role of CRISPR-positive plasmids in the spread of antibiotic resistance genes and virulence genes in the Klebsiella genus. It reveals that CRISPR-positive plasmids engage in fierce competition with other plasmid types, impacting the dynamics of plasmid transmission.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Biochemistry & Molecular Biology
Qinglan Sun, Chang Shu, Wenyu Shi, Yingfeng Luo, Guomei Fan, Jingyi Nie, Yuhai Bi, Qihui Wang, Jianxun Qi, Jian Lu, Yuanchun Zhou, Zhihong Shen, Zhen Meng, Xinjiao Zhang, Zhengfei Yu, Shenghan Gao, Linhuan Wu, Juncai Ma, Songnian Hu
Summary: This research established an evaluation and prewarning system to monitor the genomic variation risks of SARS-CoV-2. It analyzed the effects of known and virtual variations on viral properties from the perspectives of genomics and structural biology, and verified the effectiveness of these characteristics for risk prediction using an artificial intelligence algorithm.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Sen Wang, Shenghan Gao, Jingyi Nie, Xinyu Tan, Junhua Xie, Xiaochun Bi, Yan Sun, Sainan Luo, Qianhui Zhu, Jianing Geng, Wanfei Liu, Qiang Lin, Peng Cui, Songnian Hu, Shuangyang Wu
Summary: This study updated the 93-11 genome assembly to a gap-less sequence using various methods and techniques. The comparison with the reference genome confirmed the mapping of sequencing data from indica rice to the 93-11 genome. The study also identified gene expression patterns related to seed development, alternative splicing of starch synthesis-related genes, and genomic variations.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Li Wang, Tao Yu, Yaxin Zhu, Yingfeng Luo, Fan Dong, Xuemei Lin, Wenzhong Zhao, Zilong He, Songnian Hu, Zhiyang Dong
Summary: This study demonstrates that microbial networks on the scalp and hair surface of dandruff patients are less stable compared to their healthy counterparts, with lower node degree and more positive and stronger links. Lactobacillus bacteria have extensive interactions with other bacteria or fungi on the scalp and hair surface.
Article
Microbiology
Na Liu, Xin Zheng, Qianhui Zhu, Zilong He, Songnian Hu
Summary: Acinetobacter baumannii is a common hospital pathogen that has been increasing in strains carrying the NDM-1 gene. Through investigating 186 strains with the NDM-1 gene, this study aims to provide a theoretical basis for preventing the dissemination of NDM-1 in A. baumannii.
CURRENT MICROBIOLOGY
(2022)
Article
Environmental Sciences
Kexin Li, Qianhui Zhu, Fan Jiang, Huixia Li, Jingying Liu, Tao Yu, Yiyang Du, Li Yang, Zilong He, Songnian Hu
Summary: Our study revealed significant changes in microbial composition within months in ICUs, with significant differences in alpha and beta diversities among the 12 sampling months in each ICU. Additionally, several HAI-related bacteria persisted, including Acinetobacter, Pseudomonas, Staphylococcus, Escherichia, and Enterococcus. Source tracking analysis indicated that most bacteria in both ICUs originated from buildings or human skin.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Mianzhi Yao, Qianhui Zhu, Jin Zou, Abebe Mekuria Shenkutie, Songnian Hu, Jiuxin Qu, Zilong He, Polly H. M. Leung
Summary: In this study, the genome assembly and characterization of a uropathogenic E. coli ST405 strain, SZESBLEC201, were reported. The strain carries three plasmids, with two of them harboring antibiotic resistance genes. Only one plasmid can be transferred via conjugation. The unique virulence pattern of SZESBLEC201 compared to genetically similar strains and the global spread of antibiotic resistance genes were highlighted.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Medicine, General & Internal
Yuting Wang, SongNian Hu, XinYu Tan, Qingqing Sang, Peng Shi, Chun Wang, Daoqian Sang
Summary: This study aimed to identify possible pathogenic gene mutations in a family with tuberous sclerosis complexes (TSCs). Through clinical evaluations and genetic sequencing, a splicing site mutation was found in the 9th intron region of TSC1. This suggests that mutations in intron regions may contribute to the development of TSC.
INTERNATIONAL JOURNAL OF GENERAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Jianing Geng, Sainan Luo, Hui-Ru Shieh, Hsing-Yi Wang, Songnian Hu, Yi-Ywan M. Chen
Summary: This study identified CodY orthologues and corresponding regulons in Gram-negative Synergistetes, and confirmed a novel palindromic sequence with AT-rich arms in the promoters of putative codY-containing operons. The function of this consensus sequence was tested using a recombinant CodY protein in Synergistetes, showing similarities to Firmicutes CodY.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Yongqin Liu, Mukan Ji, Tao Yu, Julian Zaugg, Alexandre M. Anesio, Zhihao Zhang, Songnian Hu, Philip Hugenholtz, Keshao Liu, Pengfei Liu, Yuying Chen, Yingfeng Luo, Tandong Yao
Summary: The study presents a comprehensive glacier microbial genome and gene catalog from Tibetan glaciers, which includes genomes and metagenome-assembled genomes representing 968 candidate species from 30 phyla. The catalog also contains over 25 million non-redundant protein-encoding genes and has demonstrated its utility in exploring secondary metabolite biosynthetic potentials, identifying virulence factors, and comparing global glacier metagenomes.
NATURE BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Tao Yang, Rong Liu, Yingfeng Luo, Songnian Hu, Dong Wang, Chenyu Wang, Manish K. Pandey, Song Ge, Quanle Xu, Nana Li, Guan Li, Yuning Huang, Rachit K. Saxena, Yishan Ji, Mengwei Li, Xin Yan, Yuhua He, Yujiao Liu, Xuejun Wang, Chao Xiang, Rajeev K. Varshney, Hanfeng Ding, Shenghan Gao, Xuxiao Zong
Summary: In this study, a de novo assembly and annotation of a pea cultivar ZW6 was reported, which showed significant improvements in contig length and sequence quality compared to existing ones. The genome diversity analysis revealed that Pisum abyssinicum is a distinct species from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses identified Mendel's genes related to stem length and seed shape, as well as candidate genes for pod form. The construction of a pan-genome of 116 pea accessions revealed distinct functional enrichment in preferred genes of P. abyssinicum and P. fulvum. These findings provide insights into pea genome evolution and domestication, and offer valuable genomic resources for pea improvement.
Article
Immunology
Si Yu, Xiaomeng Ge, Hui Xu, Bei Tan, Bowen Tian, Yujie Shi, Yimin Dai, Yue Li, Songnian Hu, Jiaming Qian
Summary: This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI. The results showed that IBD patients with CDI had decreased bacterial alpha diversity and significant differences in bacterial and fungal beta diversity compared to healthy individuals and IBD patients without CDI. Specific bacterial and fungal taxa were overrepresented in IBD patients with CDI. These findings provide insights into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Microbiology
Yahui Guo, Xiaojie Yu, Jixiao Wang, De Hua, Yuanhai You, Qingbo Wu, Qinglong Ji, Jianzhong Zhang, Liefei Li, Yuan Hu, Zhonghui Wu, Xiaoyue Wei, Lianqun Jin, Fanliang Meng, Yuhua Yang, Xiaofeng Hu, Lijin Long, Songnian Hu, Heyuan Qi, Juncai Ma, Wenwen Bei, Xiaomei Yan, Haibin Wang, Zilong He
Summary: ST7 Staphylococcus aureus, which is highly prevalent in humans, pigs, and food in China, has rarely been reported to cause staphylococcal food poisoning (SFP). However, a recent outbreak of SFP caused by ST7 S. aureus strains occurred in two kindergartens in Hainan Province, China. Whole-genome sequencing analysis revealed the genetic characteristics and phylogenetic relationships of these SFP strains and provided insights into the potential risk of this emergent ST7 clone for SFP.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Zhi-Lin Ling, Bin Cao, Song-Nian Hu, Jia-Ning Geng, Fei Liu, Dong-Mei Liu, Rui-Lin Zhao
Summary: Agaricus sinodeliciosus, a rare wild edible mushroom from northwest China, shows unique genome changes and activates specific genes for saline-alkali tolerance. Transcriptomic analyses reveal the importance of carbon and nitrogen utilization, cell stability, and fruit body formation under mildly alkaline conditions. This research enhances our understanding of the genomic evolution and mechanisms of A. sinodeliciosus in tolerance to saline-alkali environments.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Qianhui Zhu, Shenghan Gao, Binghan Xiao, Zilong He, Songnian Hu
Summary: In this study, a novel plasmid prediction tool called Plasmer was proposed, which combines the advantages of shared k-mers and genomic features. Plasmer can predict plasmids in multiple species and has achieved high accuracy on contigs above 500 bp. It outperforms existing methods in terms of performance and has balanced sensitivity and specificity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Chang Shu, Qinglan Sun, Guomei Fan, Kesheng Peng, Zhengfei Yu, Yingfeng Luo, Shenghan Gao, Juncai Ma, Tao Deng, Songnian Hu, Linhuan Wu
Summary: The VarEPS-Influ database is a risk assessment system for influenza virus variations that comprehensively evaluates various aspects of mutations, including physical and chemical properties, structural features, receptor affinity, antibody binding capacity, etc., and considers factors such as time and spatial distribution and host species distribution. It accurately evaluates and predicts the risk of influenza virus variations.
NUCLEIC ACIDS RESEARCH
(2023)
