Article
Multidisciplinary Sciences
Thomas W. Scott, Alan Grafen, Stuart A. West
Summary: Crozier's paradox suggests that genetic kin recognition is not evolutionarily stable. However, this study shows that allowing for multiple social encounters before each interaction can eliminate this paradox and stabilize genetic kin recognition. Rare tags are better indicators of relatedness and help individuals avoid interactions with non-cooperative cheats.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Balint Stewart, Nicole Gruenheit, Amy Baldwin, Rex Chisholm, Daniel Rozen, Adrian Harwood, Jason B. Wolf, Christopher R. L. Thompson
Summary: This study investigates natural variation in predatory performance in the microbial predator Dictyostelium discoideum. The researchers found widespread nontransitive differences among strains in predatory success across different bacterial prey, which can facilitate strain coexistence in multi-prey environments. Furthermore, most mutations had prey-specific effects, highlighting the potential for prey-specific effects to weaken selection and prevent the emergence of an optimal generalist predator.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Julia M. Kreiner, Tom R. Booker
Summary: Quantifying the impact of human activity on the capacity of populations to persist is crucial for conservation biology. Studying the population collapse of sea otters due to fur trade can provide insights into the consequences of population collapse on species persistence.
Article
Biochemistry & Molecular Biology
Supriya Khedkar, Georgy Smyshlyaev, Ivica Letunic, Oleksandr M. Maistrenko, Luis Pedro Coelho, Askarbek Orakov, Sofia K. Forslund, Falk Hildebrand, Mechthild Luetge, Thomas S. B. Schmidt, Orsolya Barabas, Peer Bork
Summary: Prokaryotic Mobile Genetic Elements (MGEs) play important roles in evolution and the spread of antibiotic resistance. However, current understanding of their global dispersal is limited. In this study, a computational framework was developed to capture different MGE types and their cargos, allowing for a better understanding of MGE dispersal. The findings were integrated into a resource, providing a valuable tool for future research on the mobile part of genomes and its horizontal dispersal.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Suzanne Humphrey, Alfred Fillol-Salom, Nuria Quiles-Puchalt, Rodrigo Ibarra-Chavez, Andreas F. Haag, John Chen, Jose R. Penades
Summary: It is commonly thought that horizontal transfer of most bacterial chromosomal genes is limited, in comparison with the frequent transfer of mobile genetic elements. Humphrey et al. show that, actually, phage-mediated lateral transduction of core chromosomal genes can be more efficient than the transfer of mobile genetic elements via conjugation or generalized transduction.
NATURE COMMUNICATIONS
(2021)
Review
Genetics & Heredity
Floriane Laumay, Hugo Benchetrit, Anna-Rita Corvaglia, Nathalie van der Mee-marquet, Patrice Francois
Summary: The CC398 lineage of Staphylococcus aureus, initially described as livestock colonizers, has now been found to cause severe infections in humans, even in patients without contact with animals. Recent studies suggest that CC398 strains are evolving towards increased virulence and antibiotic resistance.
Review
Microbiology
Alexandra J. Weisberg, Jeff H. Chang
Summary: Mobile genetic elements (MGEs) play a key role in the evolution of bacteria and the traits that impact host and ecosystem health. This article synthesizes recent findings on MGEs using a hierarchical and modular system framework, highlighting their emergent properties of flexibility, robustness, and genetic capacity that impact bacterial evolution. Some traits of MGEs can be stored, shared, and diversified across different MGEs, bacterial taxa, and time, contributing to functionality maintenance and trait diversification. The study of MGEs has long been challenging, but the implementation of new technologies and strategies allows for their analysis in new and powerful ways.
ANNUAL REVIEW OF MICROBIOLOGY
(2023)
Review
Genetics & Heredity
Michael L. L. Weltzer, Daniel Wall
Summary: Social diversification in microbes is an evolutionary process driven by horizontal gene transfer, resulting in the acquisition of new genes and changes in social traits. These changes include discriminating behaviors mediated by newly acquired effectors. This process benefits the selfish elements by selectively discriminating against recent ancestors, facilitating their proliferation and benefiting the host. The study of population dynamics and the roles of mobile genetic elements (MGEs) through next-generation sequencing has shed new light on the mechanisms and consequences of diversification.
Article
Biochemistry & Molecular Biology
Georgy Smyshlyaev, Alex Bateman, Orsolya Barabas
Summary: This study identified that MGE-related YR proteins evolved by acquiring a specific domain essential for their mobility function, providing new insights for MGE recognition and annotation, as well as serving as a valuable resource for functional analysis of YRs and aiding computational tool development.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Review
Genetics & Heredity
Manas Joshi, Adamandia Kapopoulou, Stefan Laurent
Summary: The study highlights the significant role of genetic variation within cis-regulatory elements (CREs) in influencing gene expression, phenotypic changes, and potentially speciation. Recent advancements in high-throughput sequencing technologies have furthered the understanding of the impact of such variation on local adaptation and evolution within natural populations.
FRONTIERS IN GENETICS
(2021)
Article
Biology
Joshua M. Jones, Ilana Grinberg, Avigdor Eldar, Alan D. Grossman
Summary: Horizontal gene transfer is a major force in bacterial evolution facilitated by mobile genetic elements like ICEBs1, which provide benefits to host cells by inhibiting development processes such as biofilm formation and sporulation. Activation of ICEBs1 results in a frequency-dependent selective advantage for host cells, allowing them to exploit their neighbors and grow more prior to development, ultimately increasing propagation of the element.
Article
Biochemistry & Molecular Biology
Zoe Weiss, Saurja DasGupta
Summary: REVERSE is a web server that implements an integrated computational pipeline through a graphical user interface, enabling rapid analysis of NGS data obtained from in vitro selection/evolution experiments.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Thomas Lenormand, Denis Roze
Summary: The current theory suggests that degenerated sex chromosomes, such as the mammalian Y chromosome, evolve through three steps: recombination arrest, Y degeneration, and dosage compensation. Our study shows that early emergence of dosage compensation helps maintain Y-linked inversions, while the degeneration of these inversions is caused by regulatory divergence between the X and Y chromosomes. Contrary to current theory, this process occurs without selective pressure related to sexual dimorphism.
Article
Biochemistry & Molecular Biology
Eduardo P. C. Rocha, David Bikard
Summary: Prokaryotes possess mobile genetic elements that enable horizontal gene transfer between cells. These elements contain defense systems to filter, control, or inactivate other elements. The abundance of defense systems in these mobile genetic elements sheds new light on their role as tools of intragenomic conflict.
Article
Computer Science, Artificial Intelligence
K. S. Suresh, R. Venkatesan, S. Venugopal
Summary: Mobile robot path planning is a significant research area in industrial automation, aiming to determine the optimal path for a robot to reach its destination while avoiding obstacles. This paper proposes a mobile robot path search method based on multi-objective genetic algorithm, which considers safety, distance, smoothness, traveling time, and collision-free path as objectives to obtain the optimal path. Experimental results show that the proposed method has lower time complexity and achieves higher safety, reduced energy consumption, and shorter traveling time compared to existing methods.
Review
Biotechnology & Applied Microbiology
Abraham G. Moller, Jodi A. Lindsay, Timothy D. Read
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2019)
Review
Infectious Diseases
K. Becker, F. Schaumburg, A. Kearns, A. R. Larsen, J. A. Lindsay, R. L. Skov, H. Westh
CLINICAL MICROBIOLOGY AND INFECTION
(2019)
Review
Multidisciplinary Sciences
Quentin J. Leclerc, Jodi A. Lindsay, Gwenan M. Knight
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2019)
Article
Microbiology
Sian Marie Frosini, Ross Bond, Alex J. McCarthy, Claudia Feudi, Stefan Schwarz, Jodi A. Lindsay, Anette Loeffler
Article
Infectious Diseases
Valerie O. Baede, Michael Z. David, Arjana Tambic Andrasevic, Dominique S. Blanc, Michael Borg, Grainne Brennan, Boudewijn Catry, Aurelie Chabaud, Joanna Empel, Hege Enger, Marie Hallin, Marina Ivanova, Andreas Kronenberg, Kuntaman Kuntaman, Anders Rhod Larsen, Katrien Latour, Jodi A. Lindsay, Bruno Pichon, Dewi Santosaningsih, Leo M. Schouls, Francois Vandenesch, Guido Werner, Dorota Zabicka, Helena Zemlickova, Harald Seifert, Margreet C. Vos
Summary: This study examined 24 MRSA surveillance programs in 16 countries and found that the current programs rely on heterogeneous data collection systems, which hampers international epidemiological monitoring and research. To harmonize MRSA surveillance, the study suggests improving data integration, establishing central biobanks for MRSA isolates, and expanding surveillance to include skin and soft-tissue infection cases.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2022)
Article
Multidisciplinary Sciences
Jesper Larsen, Claire L. Raisen, Xiaoliang Ba, Nicholas J. Sadgrove, Guillermo F. Padilla-Gonzalez, Monique S. J. Simmonds, Igor Loncaric, Heidrun Kerschner, Petra Apfalter, Rainer Hartl, Ariane Deplano, Stien Vandendriessche, Barbora Cerna Bolfikova, Pavel Hulva, Maiken C. Arendrup, Rasmus K. Hare, Celine Barnadas, Marc Stegger, Raphael N. Sieber, Robert L. Skov, Andreas Petersen, Oystein Angen, Sophie L. Rasmussen, Carmen Espinosa-Gongora, Frank M. Aarestrup, Laura J. Lindholm, Suvi M. Nykasenoja, Frederic Laurent, Karsten Becker, Birgit Walther, Corinna Kehrenberg, Christiane Cuny, Franziska Layer, Guido Werner, Wolfgang Witte, Ivonne Stamm, Paolo Moroni, Hannah J. Jorgensen, Herminia de Lencastre, Emilia Cercenado, Fernando Garcia-Garrote, Stefan Borjesson, Sara Haeggman, Vincent Perreten, Christopher J. Teale, Andrew S. Waller, Bruno Pichon, Martin D. Curran, Matthew J. Ellington, John J. Welch, Sharon J. Peacock, David J. Seilly, Fiona J. E. Morgan, Julian Parkhill, Nazreen F. Hadjirin, Jodi A. Lindsay, Matthew T. G. Holden, Giles F. Edwards, Geoffrey Foster, Gavin K. Paterson, Xavier Didelot, Mark A. Holmes, Ewan M. Harrison, Anders R. Larsen
Summary: This study reveals that methicillin-resistant Staphylococcus aureus (MRSA) strains were present in European hedgehogs before the discovery of antibiotics and have spread among hedgehog populations and between hedgehogs and secondary hosts. The study also shows that the hedgehog dermatophyte Trichophyton erinacei produces two beta-lactam antibiotics that give an advantage to MRSA strains. These findings emphasize the importance of understanding and managing antibiotic resistance in both wild animals and different ecosystems.
Article
Infectious Diseases
Anneke S. de Vos, Sake J. de Vlas, Jodi A. Lindsay, Mirjam E. E. Kretzschmar, Gwenan M. Knight
Summary: The study showed that higher prevalence may advantage a CC by allowing it to acquire antimicrobial resistances more easily. Due to density dependence in competition, dominance in an area can depend on historic contingencies; the MRSA CC that happened to be first could stay dominant because of its high prevalence advantage. This could help explain the stability of geographic differences in MRSA CC.
Article
Microbiology
Quentin J. Leclerc, Jacob Wildfire, Arya Gupta, Jodi A. Lindsay, Gwenan M. Knight
Summary: Research has shown that bacteriophages can lead to the evolution of multidrug-resistant bacteria through transduction in a short period of 8 hours, with the transmission of resistance genes occurring early. Mathematical models demonstrate that the dynamic interactions between phages and bacteria are crucial for the evolution of resistant strains.
Article
Biochemical Research Methods
Quentin J. Leclerc, Jodi A. Lindsay, Gwenan M. Knight
Summary: Depending on timing and concentration, phage and antibiotics can either work together to kill bacteria faster, or phage can generate multidrug-resistant bacteria by transduction which are then selected for by antibiotics.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Correction
Microbiology
Quentin J. Leclerc, Jacob Wildfire, Arya Gupta, Jodi A. Lindsay, Gwenan M. Knight
Article
Infectious Diseases
Valerie O. Baede, Arya Gupta, Gwenan M. Knight, Leo M. Schouls, Ken Laing, Mehri Tavakol, Anais Barray, Sake J. de Vlas, Anneke S. de Vos, Antoni P. A. Hendrickx, Madeeha Khan, Mirjam E. Kretzschmar, Willem J. B. van Wamel, Gerard Lina, Francois Vandenesch, Margreet C. Vos, Adam A. Witney, Jean-Philippe Rasigade, Jodi A. Lindsay
Summary: The MACOTRA consortium aimed to identify bacterial markers of epidemic success of MRSA isolates in Europe using a representative MRSA collection originating from France, the Netherlands and the United Kingdom. The results showed that MRSA antibiotic resistance profiles and antibiotic usage were associated with the incidence of infection and successful clonal spread, but there were variations among countries.
CLINICAL MICROBIOLOGY AND INFECTION
(2023)
Article
Infectious Diseases
J. B. Readman, M. Acman, A. Hamawandi, Cheng-Hsun Chiu, M. Sharland, J. A. Lindsay, J. F. Standing
Summary: In neonatal ICUs, ubiquitous infection with ESBL-producing Enterobacteriaceae is a major concern due to increasing antibiotic resistance. Distinguishing between bacterial and viral sepsis often leads to empirical antibiotics being used, contributing to resistance. Through testing, it was found that combining cefotaxime or ampicillin with sulbactam and gentamicin effectively inhibits the growth of ESBL-producing isolates and clears the infection. This combination showed consistent bactericidal activity at clinically achievable concentrations.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Microbiology
Quentin Leclerc, Alastair Clements, Helen Dunn, James Hatcher, Jodi A. Lindsay, Louis Grandjean, Gwenan M. Knight
Summary: This study examined the antimicrobial resistance dynamics of Staphylococcus aureus in a UK pediatric hospital. It found that the changes in resistance were mainly driven by within-host evolution and between-host transmission. The study also highlighted the value of routine surveillance data in understanding antimicrobial resistance dynamics at both the individual and hospital levels.
JOURNAL OF MEDICAL MICROBIOLOGY
(2023)
Meeting Abstract
Pharmacology & Pharmacy
Madeeha Khan, Jodi Lindsay, Emma Baker
BRITISH JOURNAL OF PHARMACOLOGY
(2021)
Article
Immunology
Aderonke Odutola, Christian Bottomley, Syed A. Zaman, Jodi Lindsay, Muhammed Shah, Ilias Hossein, Malick Ndiaye, Chidebere D. Osuorah, Yekini Olatunji, Henry Badji, Usman N. A. Ikumapayi, Ahmad Manjang, Rasheed Salaudeen, Lamin Ceesay, Momodou Jasseh, Richard A. Adegbola, Tumani Corrah, Philip C. Hill, Brian M. Greenwood, Grant A. Mackenzie
EMERGING INFECTIOUS DISEASES
(2019)