Article
Microbiology
Suzanne Paley, Ingrid M. Keseler, Markus Krummenacker, Peter D. Karp
Summary: The researchers developed a method to automatically propagate curated gene and protein knowledge from one database to related strains, significantly increasing the value and utility of the target databases. The target databases received updates for a large number of proteins, with additional protein complexes, reaction assignments, and GO annotations.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Cong Liu, Peng Wang, Yu Dai, Yu Liu, Yanying Song, Lanping Yu, Chenglian Feng, Mengda Liu, Zhijing Xie, Yingli Shang, Shuhong Sun, Fangkun Wang
Summary: The extensive use of antibiotics has led to antimicrobial resistance and multi drug resistance in Escherichia coli, posing challenges for bacterial treatment and public health. Monitoring the resistance of E. coli throughout the broiler fattening period is crucial for the poultry industry and public health.
Article
Immunology
Shuaishuai Luo, Cuiyi Liao, Jinju Peng, Songruo Tao, Tengyue Zhang, Yue Dai, Yuexia Ding, Yi Ma
Summary: The widespread use of antibiotics in animal agriculture has led to increased resistance in Escherichia coli, which often carry complex virulence factors. Correlation analysis of resistance, virulence, and serotype data from pathogenic bacteria on farms and in the surrounding environment is valuable in improving public health management.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Cell Biology
Zhenyu Wang, Dan Gu, Yaming Hong, Yachen Hu, Jiaojie Gu, Yuanyue Tang, Xiaohui Zhou, Yunzeng Zhang, Xinan Jiao, Qiuchun Li
Summary: This study elucidates the genetic mechanism underlying the generation of Salmonella 4,[5],12:i:- from S. Typhimurium and demonstrates that Salmonella 4,[5],12:i:- exhibits higher colonization and survival abilities in mice.
Article
Environmental Sciences
Jung-Sheng Chen, Bing-Mu Hsu, Wen-Chien Ko, Jiun-Ling Wang
Summary: This study focused on the distribution of antimicrobial-resistant E. coli in two rivers with different urbanization levels. It found that E. coli from Kaoping River, with drainage mainly from livestock farming, had higher resistance to antibiotics and more positive detection of antibiotic-resistance genes compared to Tamsui River. The study provides insights into the specific management of different waste streams across urban areas and highlights the need for periodic surveillance of the effects of wastewater treatment plants and livestock waste on river contamination.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Microbiology
Esdras Matheus Gomes da Silva, Karina Mastropasqua Rebello, Young-Jun Choi, Vitor Gregorio, Alexandre Rossi Paschoal, Makedonka Mitreva, James H. McKerrow, Ana Gisele da Costa Neves-Ferreira, Fabio Passetti
Summary: This study used RNA-Seq and MS/MS data to improve the annotation of the Angiostrongylus costaricensis genome, providing evidence of novel genes, alternative splicing, and SNVs. The improved genome annotation could contribute to the development of drugs, kits, and vaccines for treating and preventing AA.
Article
Genetics & Heredity
Jia-Qi Cui, Wen-Hua Liu, Can Zhang, Ling Zou, Hui-Ying Ren
Summary: This study investigates the genome sequences of three bacteriophages that infect Escherichia coli, revealing their lytic capability and absence of virulence factors and antibiotic resistance genes. These phages have potential in biocontrol of bacteria.
Article
Biochemistry & Molecular Biology
Aike Jeucken, Miaomiao Zhou, Marc M. S. M. Wosten, Jos F. Brouwers
Summary: n-Butanol is a versatile compound that shows promise as a biofuel, with potential applications in producing complex molecules like bioplastics. This study investigated the impact of n-butanol on E. coli lipid metabolism, identifying key lipids and pathways influencing n-butanol tolerance. The research provides new insights into bacterial lipid metabolism.
Article
Biochemistry & Molecular Biology
Henry Gould, William Cheung, James D. Finnigan, Jose Munoz-Munoz, Simon J. Charnock, Gary W. Black
Summary: Escherichia coli is a valuable research tool for many biology fields, especially for producing recombinant enzymes. By analyzing the metabolomes of these recombinant E. coli clones, unknown enzyme activities can be revealed. This study analyzed various extraction methods against cell free extracts of these clones to achieve high coverage of potential metabolites within E. coli. Two extraction methods were selected for their ability to produce a high number of ions, wide mass coverage, and complementarity to each other.
Article
Infectious Diseases
Guerrino Macori, Scott Nguyen, Ankita Naithani, Daniel Hurley, Li Bai, Farid El Garch, Frederique Woehrle, Christine Miossec, Benjamin Roques, Peadar O'Gaora, James L. Bono, Seamus Fanning
Summary: This study revealed a diverse population structure of Escherichia coli isolated from bovine faeces and milk samples, showing no specific correlation between phylogroups and pathotypes. The antimicrobial resistance of isolates was confirmed phenotypically, with genomic predictions successfully identifying resistance to colistin. Genetic analysis of four isolates found complex plasmids encoding both antibiotic resistant and virulence genes, including the mcr-1 resistance determinant. These findings provide early evidence of mcr-1 presence in Europe and highlight the diversity of resistance elements in E. coli strains associated with bovine diseases.
Article
Chemistry, Analytical
Alexis Delabriere, Philipp Warmer, Vincenth Brennsteiner, Nicola Zamboni
Summary: Metabolomics shows promise in various research areas, but processing large-scale data remains a challenge. The SLAW workflow addresses this by offering advanced algorithms and optimization for non-targeted LC-MS data, achieving efficient and scalable analysis with superior performance compared to existing workflows like openMS and XCMS.
ANALYTICAL CHEMISTRY
(2021)
Article
Food Science & Technology
Tianqi Cui, Yue Wu, Zeyu Peng, Qingfeng Ban, Mingyang Wang, Jianjun Cheng, Yunqing Jiang
Summary: In this study, spermidine capped carbon dots (S-PCDs) were synthesized and shown to have strong antibacterial activity against E. coli and multi-drug resistant E. coli (MREC). The research also revealed the antibacterial mechanism and persistent antibacterial effect of S-PCDs, suggesting their potential application value in the treatment of foodborne diseases.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Veterinary Sciences
Nicolas Galarce, Gabriel Arriagada, Fernando Sanchez, Beatriz Escobar, Mauricio Miranda, Sofia Matus, Rocio Vilches, Camila Varela, Carlos Zelaya, Josefa Peralta, Esteban Paredes-Osses, Gerardo Gonzalez-Rocha, Lisette Lapierre
Summary: This study aimed to characterize the antimicrobial resistance of Escherichia coli strains isolated from healthy household dogs in Chile. The results showed that the isolated E. coli strains exhibited resistance to multiple drugs and carried antimicrobial resistance genes considered critical for human health. These findings can be used as a basis for future surveillance programs and control measures against antimicrobial resistance.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Microbiology
Quang Huy Nguyen, Thi Thu Hang Le, Son Thai Nguyen, Kieu-Oanh Thi Nguyen, Dong Van Quyen, Juliette Hayer, Anne-Laure Banuls, Tam Thi Thanh Tran
Summary: In Vietnamese hospitals, the presence of extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant (CR) Escherichia coli isolates has been observed. The spread of antimicrobial resistance (AMR) genes through plasmid transmission is primarily responsible for the emergence of multidrug-resistant E. coli strains and the dissemination of AMR genes via horizontal gene transfer. Therefore, it is crucial to thoroughly investigate the characteristics of AMR gene-harboring plasmids in clinical multidrug-resistant bacterial isolates.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Jiaqi Cui, Wenshi Zhong, Wenhua Liu, Can Zhang, Ling Zou, Huiying Ren
Summary: A lysogenic phage vB_EcoP_DE5, belonging to the Kuravirus genus, was isolated from donkey-derived Escherichia coli and showed sensitivity to temperature and pH changes. The whole genome sequencing revealed its double-stranded DNA genome with 126 identified functional genes. The sequencing of the lysogenic phage DE5 enhances our understanding of lysogenic phages and their therapeutic applications.
Article
Biochemical Research Methods
Veronika Kucharova Pettersen, Hans Steinsland, Harald G. Wiker
Summary: The study on the proteomes of E. coli and Shigella strains reveals intra-species variation at the protein level, which is not necessarily correlated with genetic relatedness. Proteins associated with stress response and metabolism show substantial variation between strains, while some pathogenic E. coli strains have similar protein profiles despite genetic differences.
Article
Biotechnology & Applied Microbiology
Christine Drengenes, Tomas M. L. Eagan, Ingvild Haaland, Harald G. Wiker, Rune Nielsen
Summary: This study found that the number of PCR steps can affect the final description of bacterial communities, especially for samples with low bacterial load. Although differences in relative abundance of specific bacterial genera were observed across different setups, the removal of contaminants did not resolve differences in results between sequencing setups. Further research is needed to understand how variations in PCR setups and reagents may contribute to observed protocol bias.
Biographical-Item
Immunology
Harald G. Wiker, Tom Eirik Mollnes, Peter Garred, Gunnar Bjune, Bjarne Bjorvatn
SCANDINAVIAN JOURNAL OF IMMUNOLOGY
(2021)
Article
Hematology
Hanne Braathen, Joar Sivertsen, Turid Helen Felli Lunde, Geir Strandenes, Paul Christoffer Lindemann, Jorg Assmus, Tor Audun Hervig, Torunn Oveland Apelseth
Summary: This study showed that reducing leukocytes and storing at 20-24 degrees C and 33-37 degrees C for up to 24 h can reduce the risk of E. coli contamination in CPDA-1 whole blood. Subsequent storage at 2-6 degrees C further decreases E. coli growth.
Article
Microbiology
Marwan Mansoor Ali Mohammed, Veronika Kucharova Pettesen, Audun H. Nerland, Harald G. Wiker, Vidar Bakken
Summary: The study identified significant changes in the proteomes of Fusobacterium nucleatum and Porphyromonas gingivalis during biofilm formation, with many proteins involved in metabolic pathways related to biofilm formation.
Article
Infectious Diseases
Mical Paul, Elena Carrara, Pilar Retamar, Thomas Tangden, Roni Bitterman, Robert A. Bonomo, Jan de Waele, George L. Daikos, Murat Akova, Stephan Harbarth, Celine Pulcini, Jose Garnacho-Montero, Katja Seme, Mario Tumbarello, Paul Christoffer Lindemann, Sumanth Gandra, Yunsong Yu, Matteo Bassetti, Johan W. Mouton, Evelina Tacconelli, Jesus Rodriguez-Bano
Summary: These guidelines address the targeted antibiotic treatment of 3GCephRE and carbapenem-resistant Gram-negative bacteria, focusing on the effectiveness of individual antibiotics and on combination versus monotherapy. Most recommendations are based on low-certainty evidence.
CLINICAL MICROBIOLOGY AND INFECTION
(2022)
Article
Infectious Diseases
Aasmund Fostervold, Marit A. K. Hetland, Ragna Bakksjo, Eva Bernhoff, Kathryn E. Holt, Orjan Samuelsen, Gunnar Skov Simonsen, Arnfinn Sundsfjord, Kelly L. Wyres, Iren Hoyland Lohr
Summary: The study used nationwide surveillance data to examine longitudinal changes in Klebsiella pneumoniae isolates in Norway, focusing on ESBL-producing strains. The results revealed a diverse ESBL population dominated by specific clonal groups carrying bla(CTX-M-15), indicating convergence of virulence and resistance determinants. Klebsiella variicola was found to be a frequent cause of infection but rarely carried ESBLs.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2022)
Article
Respiratory System
Rune Nielsen, Yaxin Xue, Inge Jonassen, Ingvild Haaland, Oyvind Kommedal, Harald G. Wiker, Christine Drengenes, Per S. Bakke, Tomas M. L. Eagan
Summary: The study found that the lower airway microbiome varies between examinations, but there is compositional stability within an individual, supporting the idea of a transient airway microbiota with a potentially more stable individual core microbiome.
BMC PULMONARY MEDICINE
(2021)
Article
Microbiology
Dag Harald Skutlaberg, Harald G. Wiker, Haima Mylvaganam, Anna INFECT Study Grp, Anna Norrby-Teglund, Steinar Skrede
Summary: Biofilm formation has been observed in muscle and soft tissue samples from patients with necrotizing soft tissue infection caused by Streptococcus pyogenes. However, the clinical importance of this observation is unclear. This study characterized the biofilm forming capacity in a collection of S. pyogenes isolates causing Necrotizing Soft Tissue Infection (NSTI) and investigated its association with emm type and clinical characteristics of the patients. The results showed that the biofilm forming capacity of emm1 isolates was different from other emm types, but there was no significant association between biofilm forming capacity and clinical characteristics of the patients. The impact of biofilm formation in NSTI caused by S. pyogenes on clinical outcomes remains uncertain.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Einar M. H. Martinsen, Tomas M. L. Eagan, Harald G. Wiker, Elise O. Leiten, Gunnar R. Husebo, Kristel S. Knudsen, Solveig Tangedal, Walter Sanseverino, Andreu Paytuvi-Gallart, Rune Nielsen
Summary: This study suggests that the stability of the pulmonary mycobiome is lower compared to the oral mycobiome, and neither the diagnosis of COPD nor the use of intercurrent antibiotics seemed to influence the stability.
Article
Neurosciences
Daniel Dahlberg, Jutta Rummel, Sonia Distante, Gustavo Antonio De Souza, Maria Ekman Stensland, Espen Mariussen, Helge Rootwelt, Oyvind Voie, Bjornar Hassel
Summary: The cyst fluid of cystic glioblastomas contains various hormones, which may originate from the circulation, the tumor, or the brain tissue. The wide variation in hormone concentrations in the fluid may have differential effects on tumor growth.
FLUIDS AND BARRIERS OF THE CNS
(2022)
Article
Immunology
Ida Marie Hoel, Iman A. Mohammed Ali, Sheeba Ishtiaq, Lisbet Sviland, Harald Wiker, Tehmina Mustafa
Summary: The study successfully generated polyclonal antibodies to replace the limited supply of anti-MPT64 antibodies, through testing various antigen-adjuvant combinations and immunisation protocols in mice and rabbits. By screening and pooling the best performing polyclonal antibodies, the new antibody achieved a sensitivity similar to the reference antibody but with slightly reduced specificity.
Article
Infectious Diseases
Rebecca A. Gladstone, Alan McNally, Anna K. Pontinen, Gerry Tonkin-Hill, John A. Lees, Kusti Skyten, Francois Cleon, Martin O. K. Christensen, Bjorg C. Haldorsen, Kristina K. Bye, Karianne W. Gammelsrud, Reidar Hjetland, Angela Kummel, Hege E. Larsen, Paul Christoffer Lindemann, Iren H. Lohr, Ashild Marvik, Einar Nilsen, Marie T. Noer, Gunnar S. Simonsen, Martin Steinbakk, Stale Tofteland, Marit Vattoy, Stephen D. Bentley, Nicholas J. Croucher, Julian Parkhill, Pal J. Johnsen, Orjan Samuelsen, Jukka Corander
Summary: This study found that CC131 clade A isolates, predominantly antimicrobial susceptible, were established early and sustained, indicating that resistance is not necessary for clonal success. However, in the low antibiotic use setting of Norway, resistance to important antimicrobial classes has rapidly been selected for in CC131 clade A isolates. This underscores the importance of genomic surveillance in understanding the complex ecology of multidrug resistance dissemination and competition.
Meeting Abstract
Respiratory System
Bahareh Jouleh, Ingvild Haaland, Fahimeh Khorsand, Randi Sandvik, Tharmini Kalananthan, Rune Nielsen, Taeraneh Jouleh, Harald Wiker, Per Bakke, Nathalie Reuter, Tomas Eagan
EUROPEAN RESPIRATORY JOURNAL
(2020)
Article
Respiratory System
Elise Orvedal Leiten, Rune Nielsen, Harald Gotten Wiker, Per Sigvald Bakke, Einar Marius Hjellestad Martinsen, Christine Drengenes, Solveig Tangedal, Gunnar Reksten Husebo, Tomas Mikal Lind Eagan
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)