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.
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
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)
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)
Article
Microbiology
Wangxiao Zhou, Ye Jin, Yanzi Zhou, Yuan Wang, Luying Xiong, Qixia Luo, Yonghong Xiao
Summary: The study characterized the genomic features of the ST72 lineage in a global context, revealing potential international and interregional transmission of ST72 isolates. Variations in resistance genes, virulence genes, and mobile genetic elements were observed among different clades, indicating a diverse genetic landscape within the ST72 lineage. ST72 MRSA isolates showed higher antibiotic resistance than ST72 MSSA isolates, highlighting the importance of understanding the transmission dynamics and genotypic characteristics of this lineage.
Article
Biochemistry & Molecular Biology
Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis
Summary: REBASE is a comprehensive database of information about restriction-modification (RM) system components, providing details on recognition and cleavage sites for restriction enzymes and DNA methyltransferases, their commercial availability, sensitivity to methylation, crystal and sequence data. The database is regularly updated and can be accessed through a website and FTP.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Michelle Su, Michelle H. Davis, Jessica Peterson, Claudia Solis-Lemus, Sarah W. Satola, Timothy D. Read
Summary: VISA resistance is typically caused by accumulation of chromosomal mutations in six common genes, but the effect of these mutations on fitness and resistance contribution varies among different strain backgrounds.
Article
Microbiology
Cristian A. Suarez, Soledad T. Carrasco, Facundo N. A. Brandolisio, Virginia Abatangelo, Carina A. Boncompain, Natalia Peresutti-Bacci, Hector R. Morbidoni
Summary: Epidemiology and virulence studies have revealed that temperate bacteriophages play a crucial role in the evolution of Staphylococcus aureus due to their abundance and genomic diversity. This study focuses on the isolation, genome sequencing, and analysis of 14 bacteriophages from lysogenic S. aureus strains of human and veterinary origin. The findings provide insights into the genetic composition and distinctive features of these bacteriophages, revealing their potential impact on host evolution.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biology
Pengju Zhao, Lihong Gu, Yahui Gao, Zhangyuan Pan, Lei Liu, Xingzheng Li, Huaijun Zhou, Dongyou Yu, Xinyan Han, Lichun Qian, George E. Liu, Lingzhao Fang, Zhengguang Wang
Summary: This study found that transposable elements (TEs), particularly young short interspersed nuclear elements (SINEs), play important roles in genetic polymorphisms, chromatin architecture, gene regulatory networks, and genomic evolution in pigs. Silencing of young SINEs was observed through histone modifications, DNA methylation, and decreased accessibility, but some active young SINE transcripts showed tissue-specific expression. The presence of population-specific dimorphic SINEs suggested their involvement in local adaptation, and these SINEs were found to be associated with candidate genes related to complex traits in pigs.
COMMUNICATIONS BIOLOGY
(2023)
Review
Microbiology
Jhih-Hang Jiang, David R. Cameron, Cara Nethercott, Marta Aires-de-Sousa, Anton Y. Peleg
Summary: This review focuses on the mechanisms that trigger the establishment and maintenance of current, dominant MRSA lineages across the globe. Factors that influence MRSA's ability to colonize and cause disease within a host are discussed, with an emphasis on colonization and niche adaptation. Understanding these mechanisms may lead to the development of targeted therapies.
CLINICAL MICROBIOLOGY REVIEWS
(2023)
Article
Infectious Diseases
Vincenzo Pennone, Miguel Prieto, Avelino Alvarez-Ordonez, Jose F. Cobo-Diaz
Summary: This study analyzed publicly available genomes of Staphylococcus aureus and identified different antimicrobial resistance genes (ARGs) in chromosomes and plasmids. Differences in the distribution of ARGs and clonal complexes (CC) were observed among continents. Temporal changes over the past 20 years showed a decrease in MRSA and macrolide resistance occurrence in plasmids, while the occurrence of ARGs associated with aminoglycoside resistance increased.
Article
Genetics & Heredity
Soyoun Park, Dongyun Jung, Bridget O'Brien, Janina Ruffini, Forest Dussault, Alexis Dube-Duquette, Elodie Demontier, Jean-Francois Lucier, Francois Malouin, Simon Dufour, Jennifer Ronholm
Summary: Staphylococcus aureus is a versatile bacterium that causes bovine mastitis. This study investigates the evolutionary relationship between bovine and human-associated S. aureus, focusing on the genetic composition that leads to successful bovine infection. The results reveal distinct genetic differences between bovine and human isolates, as well as the presence of specific genes in bovine isolates. The study also highlights the role of restriction-modification systems in shaping clonal diversification and limiting gene exchange.
MICROBIAL GENOMICS
(2022)
Article
Microbiology
Patricia Reed, Moritz Sorg, Dominik Alwardt, Lucia Serra, Helena Veiga, Simon Schaper, Mariana G. Pinho
Summary: Researchers have optimized a CRISPR interference system for gene knockdown in Staphylococcus aureus, a Gram-positive bacterial pathogen. This system enables efficient knockdown of essential and non-essential genes and has been used to construct a mutant library for studying gene functions in S. aureus.
Article
Biochemistry & Molecular Biology
Acer VanWallendael, Mariano Alvarez
Summary: The study investigated the use of Mash, a k-mer analysis tool, for basic population genetic analyses of polyploid sequences. Results showed that Mash accurately estimated pairwise genetic differences for polyploids and diploids up to 476 times faster than alignment-based methods. However, Mash genetic distance estimates could be biased by per-sample read depth.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Microbiology
Jo-Ann McClure, Sahreena Lakhundi, Amani Niazy, George Dong, Osahon Obasuyi, Paul Gordon, Sidong Chen, John M. Conly, Kunyan Zhang
Summary: Detailed genetic analysis was conducted on the Staphylococcus aureus (SA) sequence type ST59, revealing the concurrent but separate evolution of North American and East Asian lineages, with extensive diversification observed in the East Asian lineage and the presence of mobile element structure (MES) as a major difference between the two continental lineages.
FRONTIERS IN MICROBIOLOGY
(2021)
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)
