Article
Biochemistry & Molecular Biology
Yan-Yan Liu, Wei-Tao Jin, Xiao-Xin Wei, Xiao-Quan Wang
Summary: Subtropical East Asia is a diversification center for white pines, with the formation of monsoon-driven evergreen broadleaved forests playing a significant role in their diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biology
Paul Lambey, Omolade Otun, Xiaojing Cong, Francois Hoh, Luc Brunel, Pascal Verdie, Claire M. Grison, Fanny Peysson, Sylvain Jeannot, Thierry Durroux, Cherine Bechara, Sebastien Granier, Cedric Leyrat
Summary: The study characterized the interaction of LukE with chemokine receptors ACKR1, CCR2, and CCR5, revealing the location of receptor sulfotyrosine binding sites in the toxins. This work provides new insights into chemokine receptor recognition by leukotoxins and suggests that the conserved sulfotyrosine binding pocket could be a target for future drug development.
Article
Food Science & Technology
Cheng Qian, Kristine Castaneda-Gulla, Evelyn Sattlegger, Anthony N. Mutukumira
Summary: Raw and frozen poultry products are often contaminated with Staphylococcus aureus. This study investigated the contamination sources of S. aureus in poultry production in New Zealand. The results showed that all samples from the processing plant and live chickens at the farm were contaminated with S. aureus. The study also identified the sequence types and enterotoxin genes of the S. aureus isolates.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2022)
Article
Ecology
Meng-Yun Chen, Wen-Kai Teng, Liang Zhao, Chun-Xiang Hu, Yang-Kai Zhou, Bo-Ping Han, Li-Rong Song, Wen-Sheng Shu
Summary: Based on phylogenetic and comparative genomic analyses of 650 cyanobacterial genomes, this study revealed that terrestrial cyanobacteria expand gene families to cope with fluctuating environments, while many marine strains undergo gene contraction to adapt to nutrient-poor conditions. Genes strongly associated with specific habitats, such as those involved in light sensing, chemotaxis, and nutrient transporters, are crucial for the survival and adaptation of cyanobacteria. Furthermore, a significant proportion of genes facilitating habitat adaptation are acquired through horizontal gene transfer, with terrestrial cyanobacteria showing higher rates of genetic exchanges.
Article
Multidisciplinary Sciences
Jia-Ju Lu, Er-Qi He, Wen-Qing Bao, Jian-Sheng Chen, Sheng-Ren Sun, San-Ji Gao
Summary: This study identified six near-complete genome sequences of SCYLV, revealing high genetic divergences at nucleotide levels and significant recombinant events occurring between geographical origins and host crops. Phylogenetic analysis clustered the isolates into three phylogroups and showed infrequent gene flow between Africa and Asia/America, while frequent gene flow was observed between Asia and America. These findings contribute to a better understanding of genetic diversity and evolutionary dynamics of SCYLV.
SCIENTIFIC REPORTS
(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
Microbiology
Muhammad Ali Syed, Bushra Jamil, Hazem Ramadan, Maria Rukan, Shahzad Ali, Shahid Ahmad Abbasi, Tiffanie A. Woodley, Charlene R. Jackson
Summary: The study characterized Staphylococcus aureus isolates from a tertiary care hospital in Rawalpindi, Pakistan, and found high levels of resistance, particularly for MRSA strains. The majority of S. aureus isolates belonged to specific spa types, with the most common clone identified as ST772-t657 (Bengal Bay clone).
Article
Microbiology
Viktoria Rungelrath, Adeline R. Porter, Natalia Malachowa, Brett A. Freedman, Jacqueline M. Leung, Jovanka M. Voyich, Michael Otto, Scott D. Kobayashi, Frank R. DeLeo
Summary: Staphylococcus aureus is a significant human pathogen that can cause a variety of diseases, with neutrophils playing a crucial role in host defense against S. aureus infections. The study showed that disruption of phagosome integrity and escape of S. aureus from the phagosome into the cytoplasm are not necessary for neutrophil lysis, indicating independent phenomena.
MICROBIOLOGY SPECTRUM
(2021)
Article
Immunology
Junrong Liang, Zhen Zhu, Ruiting Lan, Jing Meng, Bram Vrancken, Shan Lu, Dong Jin, Jing Yang, Jianping Wang, Tian Qin, Ji Pu, Li Zhang, Kui Dong, Mingchao Xu, Huaiyu Tian, Taijiao Jiang, Jianguo Xu
Summary: This study sequenced Shigella flexneri isolates from animals and humans in China to determine their relationships and evolutionary history. It found that different lineages of S. flexneri exist in animals and humans, suggesting possible transmission between these two reservoirs. The study also highlighted the importance of animals as hosts for S. flexneri and the need for further research on the public health threat they may pose.
EMERGING MICROBES & INFECTIONS
(2022)
Article
Veterinary Sciences
Dae-Sung Ko, Nam-Hyung Kim, Eun-Kyung Kim, Eun-Jin Ha, Young-Hye Ro, Danil Kim, Kang-Seuk Choi, Hyuk-Joon Kwon
Summary: By studying the different genotypes of Staphylococcus aureus in humans and cows, it was determined that some predominant human genotypes have adapted to or caused occasional infections in cows. Comparative genomics revealed differences in the number of pseudogenes between RST4-1 and RST2-1 strains, with most pseudogenes being strain-specific.
RESEARCH IN VETERINARY SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Stefano Ravaioli, Davide Campoccia, Werner Ruppitsch, Franz Allerberger, Alessandro Poggi, Emanuele Chisari, Lucio Montanaro, Carla Renata Arciola
Summary: This study evaluated the usefulness of automated ribotyping as a screening tool for identifying S. aureus genetic lineages. Results showed that automated ribotyping can predict spa and MLST clonal complexes, but its high cost and lower discriminatory power could be obstacles for fine genotyping analysis. However, automated ribotyping has advantages such as automation, ease of execution, stability, typeability, and reproducibility, making it a reliable method to be used alongside gold standard methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Nathita Phumthanakorn, Sybille Schwendener, Valentina Dona, Pattrarat Chanchaithong, Vincent Perreten, Nuvee Prapasarakul
Summary: This study conducted genomic comparative analyses of MRSP isolates from dogs and humans, revealing differences in prophage distribution and identification of a novel composite pathogenicity island in ST181 isolates. Among the different STs, ST45 isolates showed the highest genomic diversity, suggesting potential host adaptation leading to different colonization patterns.
Article
Microbiology
Ryota Miyazawa, So Shimoda, Keiichi Matsuda, Ryuta Tobe, Tasuke Ando, Hiroshi Yoneyama
Summary: Staphylococcus aureus is a major pathogen in humans and livestock, causing serious issues such as bovine mastitis. This study monitored cases of intramammary infection caused by S. aureus in the Miyagi Prefecture, Japan, and analyzed the strains obtained from dairy farms. The study found recurrent cases of infection and identified a Methicillin-Sensitive SA (MSSA) ST398 strain isolated from mastitis-containing cows, which is the first confirmed case in Japan. The results highlight the importance of nationwide surveillance to manage the distribution of ST398 strains in dairy farms for human and animal health.
Review
Multidisciplinary Sciences
M. McCauley, T. L. Goulet, C. R. Jackson, S. Loesgen
Summary: Microorganisms are crucial for the health and resilience of cnidarians. However, comparing cnidarian microbiomes across studies is challenging due to the variety of protocols used. In this study, researchers analyzed 12,010 cnidarian microbiome samples, along with samples from other organisms, to identify the factors influencing cnidarian microbiomes. They found a wide diversity of archaeal and bacterial phyla associated with cnidarians and identified key bacteria influenced by host characteristics, sampling depth, and ocean location. This systematic review provides a framework for understanding cnidarian microbiomes and their response to stress.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Masako Osada, Meiji Soe Aung, Noriko Urushibara, Mitsuyo Kawaguchiya, Nobuhide Ohashi, Mina Hirose, Nobumichi Kobayashi
Summary: This study investigated the prevalence, antimicrobial resistance, and genetic determinants of Staphylococcus/Mammaliicoccus species in retail ground meat in Japan. The findings revealed the presence of resistant and diverse strains, as well as the potential plasmid transmission mechanism.
Article
Biotechnology & Applied Microbiology
James Redfern, Janine Wallace, Alex van Belkum, Magali Jaillard, Elliot Whittard, Roobinidevi Ragupathy, Joanna Verran, Peter Kelly, Mark Charles Enright
Summary: Pseudomonas aeruginosa is a common environmental microorganism that can form biofilms on indwelling device surfaces, promoting adhesion and survival. Research identified accessory genes and core-genome SNPs associated with enhanced biofilm production at 22 degrees C, including a 165 kb genomic island with heavy metal resistance genes.
Article
Multidisciplinary Sciences
Monica Trujillo, Kristen Cheung, Anna Gao, Irene Hoxie, Sherin Kannoly, Nanami Kubota, Kaung Myat San, Davida S. Smyth, John J. Dennehy
Summary: The protocol outlines a safe, cost-effective, and reproducible method for detecting the genetic signal of SARS-CoV-2 in wastewater through steps such as pasteurization. It has been adopted by the New York City Department of Environmental Protection for monitoring the prevalence of SARS-CoV-2 in wastewater across all five boroughs of the city. In the future, it could be utilized for detecting various clinically relevant viruses in wastewater and serving as the foundation for a surveillance strategy for monitoring community spread of both known and emerging viral pathogens.
Article
Immunology
Elliot Whittard, James Redfern, Guoqing Xia, Andrew Millard, Roobinidevi Ragupathy, Sladjana Malic, Mark C. Enright
Summary: This study validates the potential of phage therapy for treating Staphylococcus aureus infections by examining the characteristics and host range of lytic S. aureus phages. Phages with the widest host range and effective killing abilities against various isolates were identified, showing promise as therapeutic candidates for future studies.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Immunology
George Blundell-Hunter, Mark C. Enright, David Negus, Matthew J. Dorman, Gemma E. Beecham, Derek J. Pickard, Phitchayapak Wintachai, Supayang P. Voravuthikunchai, Nicholas R. Thomson, Peter W. Taylor
Summary: Capsular polysaccharides allow clinically important clones of Klebsiella pneumoniae to cause severe systemic infections in susceptible hosts. Phage-encoded capsule depolymerases offer a potential alternative treatment option when conventional antibiotics become less effective due to multiple drug resistance. Isolating lytic phage from hospital sewage, researchers found various K-types among Klebsiella pneumoniae strains in Thailand, with certain types being more prevalent.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Davida S. Smyth, Monica Trujillo, Devon A. Gregory, Kristen Cheung, Anna Gao, Maddie Graham, Yue Guan, Caitlyn Guldenpfennig, Irene Hoxie, Sherin Kannoly, Nanami Kubota, Terri D. Lyddon, Michelle Markman, Clayton Rushford, Kaung Myat San, Geena Sompanya, Fabrizio Spagnolo, Reinier Suarez, Emma Teixeiro, Mark Daniels, Marc C. Johnson, John J. Dennehy
Summary: Tracking the genetic diversity of SARS-CoV-2 is important to monitor the emergence of novel variants resistant to immunity. The researchers detected increasing frequencies of novel cryptic SARS-CoV-2 lineages in the New York City wastewater, containing mutations rarely observed in clinical samples. These lineages share mutations with the Omicron variant and have expanded tropism and resistance to neutralizing antibodies.
NATURE COMMUNICATIONS
(2022)
Correction
Multidisciplinary Sciences
Davida S. Smyth, Monica Trujillo, Devon A. Gregory, Kristen Cheung, Anna Gao, Maddie Graham, Yue Guan, Caitlyn Guldenpfennig, Irene Hoxie, Sherin Kannoly, Nanami Kubota, Terri D. Lyddon, Michelle Markman, Clayton Rushford, Kaung Myat San, Geena Sompanya, Fabrizio Spagnolo, Reinier Suarez, Emma Teixeiro, Mark Daniels, Marc C. Johnson, John J. Dennehy
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Medicinal
Rosesathorn Soontarach, Potjanee Srimanote, Mark C. Enright, George Blundell-Hunter, Matthew J. Dorman, Nicholas R. Thomson, Peter W. Taylor, Supayang P. Voravuthikunchai
Summary: Nineteen bacteriophages against five main capsular types of multidrug-resistant Acinetobacter baumannii were isolated from hospital sewage. These phages demonstrated high burst size, short latent period, and quick adsorption to bacterial host. They also showed host specificity and stability over a wide range of temperatures and pH. Whole-genome analysis revealed high genomic similarity with double-stranded DNA and absence of toxin-coding genes. The study suggests that these phages have potential to be developed as antibacterial agents.
Article
Engineering, Environmental
Antun Skanata, Fabrizio Spagnolo, Molly Metz, Davida S. Smyth, John J. Dennehy
Summary: Airborne transmission is the main route for various respiratory diseases to infect hosts. A new method has been developed to detect long-range transmission of viable virus particles in closed spaces. By using aerosolized virus and host combinations, the method quantifies airborne transmission and determines the impact of humidity on dispersal.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2022)
Article
Education, Scientific Disciplines
Davida S. Smyth, Simon Chen, Geena Sompanya, Molly Metz, Theresa Conefrey
Summary: ePortfolios serve as digital repositories for students to showcase their learning by curating papers, projects, and reflections from various disciplines. They not only facilitate assessment and career development, but also help students connect their learning to real-world contexts, promoting civic and scientific literacy.
JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION
(2022)
Article
Biotechnology & Applied Microbiology
R. Ragupathy, K. A. Jolley, C. Zamuner, J. B. Jones, J. Redfern, F. Behlau, H. Ferreira, M. C. Enright
Summary: Xanthomonas citri subsp. citri is a major plant pathogen that causes bacterial citrus canker, resulting in substantial economic losses to the citrus industry. Genomic sequencing has provided insights into the evolutionary relationships and distinct pathotypes of X. citri subsp. citri. The core-genome multilocus sequence typing (cgMLST) scheme described in this study will be a valuable resource for studying the epidemiology and evolution of this plant-pathogenic bacteria.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Education, Scientific Disciplines
Davida S. Smyth, Trace Jordan, Robert Seiser, Meghan Moran, Ulla Hasager, Sheryl Sorby, Nathan Kahl, Amy Shachter, Karen Oates
Summary: This project was developed to support public education on the science of vaccines during the COVID-19 pandemic. It produced comprehensive educational materials covering the scientific process, SARS-CoV-2 biology, vaccine development, and science communication. The materials, consisting of modules and informational videos, were successfully piloted in educational settings and increased student trust in vaccines and the scientific process.
JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION
(2023)
Article
Multidisciplinary Sciences
Florencia Cancela, Natalia Ramos, Davida S. Smyth, Claudia Etchebehere, Mabel Berois, Jesica Rodriguez, Caterina Rufo, Alicia Aleman, Liliana Borzacconi, Julieta G. Lopez, Elizabeth Gonzalez, German Botto, Starla Thornhill, Santiago Mirazo, Monica Trujillo
Summary: Monitoring SARS-CoV-2 variants in wastewater samples can effectively track epidemics and enhance health preparedness. Next generation sequencing of viral RNA in wastewater provides a convenient and cost-effective method to understand the molecular epidemiology of SARS-CoV-2 and population dynamics of viral variants at the community level. In Uruguay, we found a transition in viral variant predominance through wastewater surveillance, which correlated with clinical surveillance from nasal swabs.
Article
Public, Environmental & Occupational Health
Amy E. Kirby, Rory M. Welsh, Zachary A. Marsh, Alexander T. Yu, Duc J. Vugia, Alexandria B. Boehm, Marlene K. Wolfe, Bradley J. White, Shannon R. Matzinger, Allison Wheeler, Laura Bankers, Kevin Andresen, Cristal Salatas, Devon A. Gregory, Marc C. Johnson, Monica Trujillo, Sherin Kannoly, Davida S. Smyth, John J. Dennehy, Nicolae Sapoval, Katherine Ensor, Todd Treangen, Lauren B. Stadler, Loren Hopkins
MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT
(2022)
Article
Environmental Sciences
Davida S. Smyth
Article
Medicine, Research & Experimental
Silvia Pires, Adeline Peignier, Jeremy Seto, Davida S. Smyth, Dane Parker