Article
Veterinary Sciences
Anna Kopcakova, Slavomira Salamunova, Peter Javorsky, Rastislav Sabo, Jaroslav Legath, Silvia Ivorova, Maria Piknova, Peter Pristas
Summary: Understanding the diversity of Paenibacillus larvae, the cause of American foulbrood disease, is crucial for disease investigations. Protein fingerprinting-based MALDI-TOF method provides more insight into P. larvae diversity compared to current DNA fingerprinting methods.
VETERINARY SCIENCES
(2022)
Article
Microbiology
Nadege C. Toney, Wenming Zhu, Bette Jensen, Jarrett Gartin, Karen Anderson, David Lonsway, Maria Karlsson, J. Kamile Rasheed
Summary: This study evaluated the ability of the Bruker Biotyper matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) platform to accurately identify 314 nontuberculous mycobacteria (NTM). The results showed that MALDI-TOF had an accuracy of 94% in identifying NTM, with higher accuracy for rapidly growing mycobacteria (99%) compared to slowly growing mycobacteria (87%). Additional sequencing of the rpoB gene was required for certain species to improve identification accuracy.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Microbiology
Praveen Rahi, Mitesh Khairnar, Ashwini Hagir, Avinash Narayan, Kunal R. Jain, Datta Madamwar, Aabeejjeet Pansare, Yogesh Shouche
Summary: A novel bacterial strain ADMK78(T) was isolated from saline desert soil, identified as a new species named Peteryoungia desertarenae based on phylogenetic analysis, physiological characteristics, and genetic similarities with related species. The study also proposed reclassifications of several Rhizobium species into the genera Peteryoungia and Ciceribacter, based on core gene phylogeny and ANI values.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Infectious Diseases
Ana Candela, Manuel J. Arroyo, Maria Sanchez-Cueto, Mercedes Marin, Emilia Cercenado, Gema Mendez, Patricia Munoz, Luis Mancera, David Rodriguez-Temporal, Belen Rodriguez-Sanchez
Summary: The study evaluated matrix-assisted laser desorption ionization-iime of flight mass spectrometry (MALDI-TOF MS) and Fourier-transform infrared spectroscopy (FTIR-S) as diagnostic alternatives for the detection of Pseudomonas aeruginosa sequence type (ST) 175 isolates involved in a hospital outbreak. The results showed that the combination of these two technologies, along with machine learning tools, can effectively monitor high-risk clones and isolates in nosocomial outbreaks.
TRANSBOUNDARY AND EMERGING DISEASES
(2023)
Article
Microbiology
Lakshmi Narayanan, Ozan Ozdemir, Navatha Alugubelly, Reshma Ramachandran, Michelle Banes, Mark Lawrence, Hossam Abdelhamed
Summary: The study used Tn mutagenesis to identify genes and pathways affecting the growth and fitness of Listeria monocytogenes in minimal medium. The findings revealed that biosynthesis of purines, pyrimidines, ATP, and branched-chain fatty acids plays an important role in the pathogenesis of L. monocytogenes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Ehsan Asghari, Annika Kiel, Bernhard Peter Kaltschmidt, Martin Wortmann, Nadine Schmidt, Bruno Huesgen, Andreas Huetten, Cornelius Knabbe, Christian Kaltschmidt, Barbara Kaltschmidt
Summary: New ecological trends and changes in consumer behavior are leading to increased biofilm formation in household appliances, creating a demand for new antimicrobial materials and surfaces. Laboratory-cultivated biofilms identified bacterial strains using MALDI-TOF-MS and analyzed the main genera found in these habitats, such as Staphylococci and pseudomonads, offering better understanding of biofilm formation mechanisms.
Article
Dermatology
Taketoshi Futatsuya, Tatsuki Mura, Kazushi Anzawa, Takashi Mochizuki, Akira Shimizu, Yoshitsugu Iinuma
Summary: This study simplified the sample preparation method for Exophiala species using MALDI-TOF MS, and identified 31 clinical isolates in Japan by enriching the library with added data. The modified method can be used in clinical practice and facilitates early diagnosis of rare Exophiala fungal infections.
JOURNAL OF DERMATOLOGY
(2023)
Article
Engineering, Environmental
Anna Pinar-Mendez, Sonia Fernandez, David Baquero, Carles Vilaro, Belen Galofre, Susana Gonzalez, Lidia Rodrigo-Torres, David R. Arahal, M. Carmen Macian, Maria A. Ruvira, Rosa Aznar, Laia Caudet-Segarra, Laura Sala-Comorera, Francisco Lucena, Anicet R. Blanch, Cristina Garcia-Aljaro
Summary: According to European Directives, water intended for human consumption in Europe must meet specific sanitary criteria, including the absence of certain bacterial indicators. Heterotrophic bacteria in drinking water are used to assess water quality. The development of a MALDI-TOF MS library for drinking water bacteria has the potential to improve the identification of bacteria present in drinking water.
Article
Infectious Diseases
Margarita Estreya Zvezdanova, Manuel Gonzalez de Aledo, Jose Israel Lopez-Mirones, Jesus Ortega, Andres Canut, Carmen Castro, Carmen Gomez, Silvia Hernaez, Marina Oviano, Maria Ercibengoa, Miriam Alkorta, Patricia Munoz, David Rodriguez-Temporal, Belen Rodriguez-Sanchez
Summary: This study aimed to validate an optimized sample preparation method coupled with the use of an in-house library for the identification of filamentous fungi using MALDI-TOF MS. The results showed high rates of correct identification for most fungal species, although some species, such as Trichophyton spp., were still difficult to identify.
Article
Biochemistry & Molecular Biology
Eliza Matuszewska, Joanna Matysiak, Grzegorz Rosinski, Elzbieta Kedzia, Weronika Zabek, Jaroslaw Zawadzinski, Jan Matysiak
Summary: The research aims to expand the understanding of the proteomic composition of fresh royal jelly (RJ) by using the ProteoMiner(TM) pre-treatment technique, which resulted in the detection of more proteins compared to traditional methods. The study identified hypothetical proteins whose existence has been predicted without experimental evidence, as well as uncharacterized proteins with unknown functions in RJ.
Article
Infectious Diseases
Jothi Ranjani, Ramamoorthy Sivakumar, Paramasamy Gunasekaran, Ganesan Velmurugan, Subbiah Ramasamy, Jeyaprakash Rajendhran
Summary: This study investigated the genetic requirements of Pseudomonas aeruginosa for infection in rat cardiomyocytes and identified essential genes associated with adhesion and invasion. The findings are important for the development of new treatment targets and potential therapeutic strategies.
INFECTION GENETICS AND EVOLUTION
(2022)
Article
Microbiology
Maaike C. de Vries, B. J. A. Hoeve-Bakker, Maaike J. C. van den Beld, Amber C. A. Hendriks, Airien S. D. Harpal, Ramon C. E. A. Noomen, Frans A. G. Reubsaet
Summary: Francisella tularensis, a zoonotic bacterium, is not included in the standard library of the most commonly used mass spectrometry systems. By building an in-house Francisella library and defining specific biomarkers, F. tularensis can be accurately differentiated at subspecies level. These strategies can be used as a fast and specific method to identify F. tularensis in clinical laboratory setting.
Article
Mycology
Elaine Cristina Francisco, Mexx Ebbing, Arnaldo Lopes Colombo, Ferry Hagen
Summary: We evaluated the identification performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for 21 clinical T. asteroides strains. The commercial database failed to distinguish between T. japonicum and T. asteroides, emphasizing the need for improvements and not excluding the possibility of T. asteroides misidentification.
Article
Microbiology
Paul Tetteh Asare, Chi-Hsien Lee, Vera Hurlimann, Youzheng Teo, Aline Cuenod, Nermin Akduman, Cordula Gekeler, Afrizal Afrizal, Myriam Corthesy, Claire Kohout, Vincent Thomas, Tomas de Wouters, Gilbert Greub, Thomas Clavel, Eric G. Pamer, Adrian Egli, Lisa Maier, Pascale Vonaesch
Summary: This study developed a MALDI-TOF MS plugin database called CLOSTRI-TOF for rapid identification of non-pathogenic human commensal gastrointestinal bacteria. The database successfully identified 98% and 93% of the strains, and classified 82% of isolates from healthy volunteers. It expands the number of species that can be identified by MALDI-TOF MS.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
David Sanchez, Ignacio Torres, Estela Gimenez, Eliseo Albert, Rosa Maria Costa, Carmelo Padron, Diego Carretero, Javier Colomina, David Navarro
Summary: We developed and evaluated a simple and low-cost method using MALDI-TOF MS to detect MER resistance in Pseudomonas aeruginosa directly from blood. The method correctly classified 88.9% of isolates when tested with BC samples containing 99 P. aeruginosa isolates. It also achieved 100% correct categorization in prospectively collected BC samples.
JOURNAL OF MICROBIOLOGICAL METHODS
(2023)
Article
Microbiology
Alejandro Arce-Rodriguez, Debbie Pankratz, Matthias Preusse, Pablo I. Nikel, Susanne Haeussler
Summary: In response to the antibiotic crisis, researchers have explored strategies to sensitize bacteria to available antibiotics. By manipulating the redox homeostasis of Pseudomonas aeruginosa, they found that increased NADH levels can lead to both higher antibiotic resistance and enhanced antibiotic killing through the generation of reactive oxygen species (ROS). Their findings also suggest that increased NADH levels can result in low-virulence phenotypes and reduced pathogenicity traits.
Article
Biotechnology & Applied Microbiology
Alexander Jeske, Alejandro Arce-Rodriguez, Janne G. Thoeming, Jurgen Tomasch, Susanne Haeussler
Summary: This study analyzed the transcriptional profiles and genomic sequence variations of clinical Pseudomonas aeruginosa isolates to uncover convergent changes in gene expression patterns. A defective IasR gene was found to be the cause of the majority of observed expression patterns, and lasR-deficient strains exhibited a transcriptional response consistent with biofilm growth without requiring an environmental trigger. These findings provide insights into the long-term evolutionary pathways and success of lasR mutants in clinical P. aeruginosa.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Biotechnology & Applied Microbiology
Lisa Neffe, Lisa Abendroth, Willfried Bautsch, Susanne Haeussler, Juergen Tomasch
Summary: This study investigates the plasmid diversity and distribution patterns in clinical Escherichia coli isolates, highlighting their crucial role in the dissemination of antibiotic resistance genes.
Article
Biochemistry & Molecular Biology
Sarina Bense, Julius Witte, Matthias Preusse, Michal Koska, Lorena Pezoldt, Astrid Droge, Oliver Hartmann, Mathias Musken, Julia Schulze, Timm Fiebig, Heike Baehre, Sebastian Felgner, Andreas Pich, Susanne Haeussler
Summary: C-di-GMP signaling directly affects bacterial behavior by influencing protein functionality, and it can also have a global impact on gene transcription or translation. This study investigated the effects of changes in intracellular c-di-GMP levels on gene expression and protein production in Pseudomonas aeruginosa, and found that an increase in c-di-GMP levels caused a switch in phenotype before any changes in gene transcription or protein abundance were observed.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J. Brito, C. Titus Brown, Jan Buchmann, Aydin Buluc, Bo Chen, Rayan Chikhi, Philip T. L. C. Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E. Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A. Gray, Lars Hestbjerg Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt Jorgensen, Silas D. Kieser, Terje Klemetsen, Axel Kola, Mikhail Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre, Chenhao Li, Antoine Limasset, Fabio Malcher-Miranda, Serghei Mangul, Vanessa R. Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R. Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C. Piro, Jacob S. Porter, Simon Rasmussen, Evan R. Rees, Knut Reinert, Bernhard Renard, Espen Mikal Robertsen, Gail L. Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal, Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa, Soren Johannes Sorensen, Ashleigh Thomas, Chengxuan Tong, Mirko Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu, Ruben Garrido-Oter, Petra Gastmeier, Stephane Hacquard, Susanne Haeussler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges, Alexander Sczyrba, Alice Carolyn McHardy
Summary: This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis. The results show substantial improvements in assembly, but related strains and assembly quality still pose challenges. Taxon profilers and binners excel at higher bacterial ranks but underperform for viruses and Archaea. The need to improve reproducibility is emphasized by the clinical pathogen detection results.
Article
Immunology
Janne G. Thoeming, Susanne Haeussler
Summary: Biofilm-associated bacteria show various levels of drug tolerance, which are greatly influenced by the choice of antibiotics. This study investigated the antimicrobial susceptibility profiles of clinical Pseudomonas aeruginosa isolates under biofilm growth conditions, revealing a broad distribution of biofilm-induced tolerance phenotypes and the presence of conditional tolerance levels far higher than previously believed. Colistin appears to act independently of the tolerance mechanisms of individual strains, which may make it a valuable therapeutic option for chronic biofilm-associated infections.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Michal Koska, Adrian Kordes, Jelena Erdmann, Sven D. Willger, Janne G. Thoeming, Heike Baehre, Susanne Haeussler
Summary: This study reveals that the regulation of c-di-GMP levels and colony morphology in Pseudomonas aeruginosa can follow different evolutionary paths. The delayed switching of c-di-GMP levels in response to fluctuating environmental conditions may provide a unique opportunity to close the gap between short-term phenotypic and long-term genetic adaptation.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Kathrin Alpers, Elisabeth Vatareck, Lothar Groebe, Mathias Muesken, Maren Scharfe, Susanne Haeussler, Jurgen Tomasch
Summary: Pseudomonas aeruginosa undergoes a transition from fast growth with overlapping cell cycles to sustained slow growth with non-overlapping cell cycles when cultivated under standard laboratory conditions. This transition is characterized by sequential changes in transcriptional activity along the chromosome and a shift in quorum sensing activity. RNA sequencing of subpopulations identified distinct gene expression patterns for replicating and nonreplicating cells.
Article
Oncology
Leah S. Stockman, Daniel A. Gundersen, Ajami Gikandi, Ruth N. Akindele, Ludmila Svoboda, Sarah Pohl, Mark R. Drews, Christopher S. Lathan
Summary: Cancer disparities among historically marginalized populations are addressed through a clinical outreach program that integrates cancer diagnostic services and patient navigation within a community-based primary healthcare setting. The program aims to expedite cancer diagnoses and establish collaborative care between oncology specialists and primary care providers. The majority of patients self-identified as Black and Hispanic, with a high prevalence of comorbid health conditions and financial distress.
JCO ONCOLOGY PRACTICE
(2023)
Article
Biochemical Research Methods
Debbie Pankratz, Nicolas Oswaldo Gomez, Agnes Nielsen, Ayten Mustafayeva, Melisa Guer, Fabian Arce-Rodriguez, Pablo Ivan Nikel, Susanne Haeussler, Alejandro Arce-Rodriguez
Summary: Much of our current understanding of microbiology is based on the application of genetic engineering procedures. In this article, a method for precise and efficient engineering of Pseudomonas aeruginosa is presented. This method utilizes targeted double-strand DNA breaks and efficient recombinase to introduce a range of genetic modifications, reducing the time required for these manipulations.
Article
Infectious Diseases
Janne G. Thoming, Susanne Haeussler
Summary: This chapter reviews recent developments in transcriptional profiling of Pseudomonas aeruginosa infections and explains how advanced RNA-seq technology can provide new insights into the establishment and maintenance of these infections. It also discusses the use of large transcriptome datasets from clinical isolates to gain a greater understanding of bacterial adaptation during the infection process. Global genotype phenotype correlation studies have shed light on new evolutionary pathways and strategies used by P. aeruginosa to build a biofilm.
PSEUDOMONAS AERUGINOSA: Biology, Pathogenesis and Control Strategies
(2022)