Article
Infectious Diseases
Jakob J. Malin, Christian J. H. von Wintersdorff, John Penders, Paul H. M. Savelkoul, Petra F. G. Wolffs
Summary: This study investigated the longitudinal fluctuations in prevalent antimicrobial resistance genes (ARGs) in non-travelling healthy volunteers and found that the abundance changes of prevalent ARGs were independent of travel behavior.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2023)
Article
Microbiology
Karen Leth Nielsen, Markus Harboe Olsen, Albert Palleja, Soren Roddik Ebdrup, Nikolaj Sorensen, Oksana Lukjancenko, Rasmus L. Marvig, Kirsten Moller, Niels Frimodt-Moller, Frederik Boetius Hertz
Summary: This study investigated the effects of antibiotics on the gut microbiome and resistome of antibiotic-naive patients during neurointensive care. It was found that narrow-spectrum antibiotic treatment increased microbial richness, while broad-spectrum treatment had diverse effects on different patients. Additionally, post-treatment broad-spectrum treatment resulted in higher abundance of antibiotic resistance genes.
Article
Food Science & Technology
Adrian Alvarez-Molina, Jose F. Cobo-Diaz, Elena A. Alexa, Fiona Crispie, Miguel Prieto, Mercedes Lopez, Paul D. Cotter, Avelino Alvarez-Ordonez
Summary: In recent years, advances in high throughput sequencing technologies have opened up new possibilities for environmental monitoring in the food processing industry. This study used whole metagenome sequencing to assess the microbiome and resistome of food processing environments from slaughterhouses, dairy processing plants, and meat processing plants. The results showed that slaughterhouses had more diverse microbiomes and resistomes, while dairy processing plants had the highest variability. Different predominant bacterial genera were found in each industry type. The study also identified the most abundant antimicrobial resistance genes, which were associated with resistance to aminoglycosides, tetracyclines, and quaternary ammonium compounds. The findings have important implications for food safety management systems.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Microbiology
Devin B. Holman, Katherine E. Gzyl, Kathy T. Mou, Heather K. Allen
Summary: Research reveals that the gut microbiome of piglets undergoes significant changes postweaning, with the weaning age having only a temporary effect on the microbiome. Within 7 days postweaning, the gut microbiome of pigs tends to stabilize, showcasing a predictable shift in microbial composition.
Article
Infectious Diseases
Tonatiuh Melgarejo, Nathan Sharp, Janina A. Krumbeck, Guangxi Wu, Young J. Kim, Annika Linde
Summary: A study found that antimicrobial resistance (AMR) genes were present in the urine of companion dogs, suggesting that dogs could serve as reservoirs of clinically relevant antibiotic resistances, which may be linked to the excessive use of antimicrobials in industrial food animal production.
Article
Agriculture, Dairy & Animal Science
Amy Vasquez, Daryl Nydam, Carla Foditsch, Lorin Warnick, Cory Wolfe, Enrique Doster, Paul S. Morley
Summary: This study investigated the impact of selective dry cow therapy on the milk microbiome and resistome, finding no significant differences between treated and untreated cows in terms of microbiome and resistome composition. Larger studies are needed to identify more subtle differences between the groups.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Microbiology
Ashley M. Rooney, Amogelang R. Raphenya, Roberto G. Melano, Christine Seah, Noelle R. Yee, Derek R. MacFadden, Andrew G. McArthur, Pierre H. H. Schneeberger, Bryan Coburn
Summary: This study systematically characterized the performance of short-read Illumina sequencing for antimicrobial resistance gene (ARG) detection in metagenomic samples, providing important information for the study design and assessment of human, animal, and environmental metagenomic antimicrobial resistance studies.
Article
Microbiology
Raffaella Sabatino, Tomasa Sbaffi, Periyasamy Sivalingam, Gianluca Corno, Diego Fontaneto, Andrea Di Cesare
Summary: This study characterized the bacteriophage community and associated antimicrobial resistance genes (ARGs) in wastewater treatment plants. The results showed that bacteriophages have limited contribution to the overall antimicrobial resistome, but further investigation is needed to fully understand their role in microbial communities.
MICROBIOLOGY SPECTRUM
(2023)
Article
Immunology
Jens Christian Norgaard, Mette Jorgensen, Kasper Sommerlund Moestrup, Emma Elizabeth Ilett, Adrian Gabriel Zucco, Ramtin Z. Marandi, Marc Noguera Julian, Roger Paredes, Jens D. Lundgren, Henrik Sengelov, Cameron MacPherson
Summary: By utilizing human gut metagenomics and detailed prescription data, this study identifies novel in vivo associations between the gut microbiome and antibiotic treatment, providing valuable information for antibiotic stewardship to combat antibiotic resistance.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Public, Environmental & Occupational Health
Priyanka Kumari, Binu Mani Tripathi, Ke Dong, Kyung Yeon Eo, Woo-Shin Lee, Junpei Kimura, Naomichi Yamamoto
Summary: This study investigates the risks and ecology of antimicrobial resistance genes (ARGs) in the environment by analyzing the feces of wildlife. The study finds significant differences in bacterial taxonomy composition and resistomes between different animal hosts, as well as selective correlations between certain ARGs and bacteria. This research provides important baseline information for conservation efforts and assessing health risks posed by ARGs and bacterial pathogens from wildlife.
Article
Microbiology
Haniyyah J. Majeed, Maria V. Riquelme, Benjamin C. Davis, Suraj Gupta, Luisa Angeles, Diana S. Aga, Emily Garner, Amy Pruden, Peter J. Vikesland
Summary: This study evaluated antibiotic resistance patterns at different stages of a conventional WWTP, finding that total ARG abundance decreased by approximately 50% from influent to effluent. While 90% of ARGs in the effluent were also detected in influent, taxonomic linkage patterns in effluent were more similar to regional clinical data than patterns in influent. Analysis of resistomes across sampling events helped identify candidate ARGs for surveillance and provided metrics for predicting relative ARG mobility and likelihood of being carried by pathogens.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Enrique Doster, Lee J. Pinnell, Noelle R. Noyes, Jennifer K. Parker, Cameron A. Anderson, Calvin W. Booker, Sherry J. Hannon, Tim A. McAllister, Sheryl P. Gow, Keith E. Belk, Paul S. Morley
Summary: This study investigated the effects of antimicrobial drug use on the resistome and microbiome in beef feedlot cattle using metagenomic sequencing and 16S rRNA gene amplicon sequencing. The results showed that the resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin drug classes. The diversity of bacterial phyla decreased over time in the feedlot, and time in the feedlot had a greater impact on the resistome than antimicrobial drug exposures. Overall, antimicrobial drug exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Roberto B. M. Marano, Chhedi Lal Gupta, Tamar Cozer, Edouard Jurkevitch, Eddie Cytryn
Summary: Treated-wastewater irrigation can transfer antibiotic-resistant bacteria to soil, but their persistence is generally low due to the resilience of the soil microbiome. However, these bacteria and associated antibiotic resistance genes may persist below detection levels and potentially proliferate under copiotrophic conditions. The study demonstrates that short-term enrichment strategies can be applied for environmental antimicrobial risk assessment in the future.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Immunology
Adam G. Stewart, Michael J. Satlin, Sanmarie Schlebusch, Burcu Isler, Brian M. Forde, David L. Paterson, Patrick N. A. Harris
Summary: Despite the widespread belief that antibiotic use is the primary cause of antimicrobial resistance and disruption of the human microbiome, our understanding of the specific effects of antibiotics on the microbiome is still limited. Detecting associations between different antibiotics and specific AMR burdens is currently inconsistent. Utilizing various microbiome analysis tools and conducting microbiome analysis in antibiotic clinical trials could significantly enhance antibiotic development and clinical decision-making.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Infectious Diseases
Erica R. Fuhrmeister, Abigail P. Harvey, Maya L. Nadimpalli, Karin Gallandat, Argaw Ambelu, Benjamin F. Arnold, Joe Brown, Oliver Cumming, Ashlee M. Earl, Gagandeep Kang, Samuel Kariuki, Karen Levy, Chris E. Pinto Jimenez, Jenna M. Swarthout, Gabriel Trueba, Pablo Tsukayama, Colin J. Worby, Amy J. Pickering
Summary: This ecological study found a relationship between access to drinking water and sanitation facilities and the abundance of antibiotic resistance genes in human fecal metagenomes. Increased access to improved water and sanitation was associated with lower antibiotic resistance gene abundance, especially in urban areas. Increasing access to water and sanitation could be an effective strategy to curb antibiotic resistance in low- and middle-income countries.
Article
Ecology
Michelle Wille, Marcel Klaassen
Summary: The seasonal migratory behavior of animals may have evolved to reduce the risk of parasite infection and associated fitness costs. Different age groups may exhibit variations in migration strategy, possibly as a response to infection risk and disease. The phenomenon of oversummering, where juveniles refrain from migrating to breeding grounds, is a prevalent but often overlooked strategy to reduce parasite infection rates.
EVOLUTIONARY ECOLOGY
(2023)
Article
Biology
Michelle Wille, Simeon Lisovski, David Roshier, Marta Ferenczi, Bethany J. J. Hoye, Trent Leen, Simone Warner, Ron A. M. Fouchier, Aeron C. C. Hurt, Edward C. C. Holmes, Marcel Klaassen
Summary: Host susceptibility to LPAIV is influenced by factors such as genetics, ecology, age, and season. This study analyzed data from wild birds in Australia over 11 years and found that host phylogeny is a key driver in determining host range. The study provides insights into the evolutionary ecology of LPAIV in its avian reservoir community and expands our global understanding of LPAIV.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Virology
Janelle R. Wierenga, Kerri J. Morgan, Stuart Hunter, Harry S. Taylor, Lisa S. Argilla, Trudi Webster, Jeremy Dubrulle, Fatima Jorge, Mihnea Bostina, Laura Burga, Edward C. Holmes, Kate McInnes, Jemma L. Geoghegan
Summary: Yellow-eyed penguins in New Zealand are at risk of extinction due to infectious diseases, with respiratory distress syndrome (RDS) causing high mortality in young chicks. A novel and highly abundant gyrovirus belonging to the Anelloviridae family has been identified in 80% of tissue samples from dead chicks. This gyrovirus is closely related to a diseased seabird virus and is likely associated with RDS in yellow-eyed penguin chicks.
Article
Virology
Soufien Sghaier, Corinne Sailleau, Maurilia Marcacci, Sarah Thabet, Valentina Curini, Thameur Ben Hassine, Liana Teodori, Ottavio Portanti, Salah Hammami, Lucija Jurisic, Massimo Spedicato, Lydie Postic, Ines Gazani, Raja Ben Osman, Stephan Zientara, Emmanuel Breard, Paolo Calistri, Jurgen A. Richt, Edward C. Holmes, Giovanni Savini, Francesca Di Giallonardo, Alessio Lorusso
Summary: Epizootic haemorrhagic disease (EHD) is a viral disease transmitted by Culicoides and affects domestic and wild ruminants, particularly white-tailed deer and cattle. Recent outbreaks of EHDV-8 have been reported in cattle farms in central/western Tunisia, spreading rapidly throughout the country with more than 200 confirmed cases. This study emphasizes the need for vaccines targeting various serotypes of EHDV.
Editorial Material
Biochemistry & Molecular Biology
Meng Lu, Wan -Ting He, John H. -O. Pettersson, Guy Baele, Mang Shi, Edward C. Holmes, Na He, Shuo Su
Letter
Infectious Diseases
Michelle Wille, Marcel Klaassen
INFLUENZA AND OTHER RESPIRATORY VIRUSES
(2023)
Editorial Material
Medicine, General & Internal
Tania C. Sorrell, Martin Hensher, Lena A. Sanci
MEDICAL JOURNAL OF AUSTRALIA
(2023)
Article
Plant Sciences
Yuanfei Pan, Mu Liu, Alejandro Sosa, Bo Li, Mang Shi, Xiaoyun Pan
Summary: This study investigates the metacommunities of endophytic fungi in the leaves of an invasive plant and finds that the structure of these fungal communities is influenced by multiple spatial scales and different drivers. These findings are important for understanding the global patterns of fungal diversity.
Article
Genetics & Heredity
Emily L. Gulliver, Vicki Adams, Vanessa Rossetto Marcelino, Jodee Gould, Emily L. Rutten, David R. Powell, Remy B. Young, Gemma L. D'Adamo, Jamia Hemphill, Sean M. Solari, Sarah A. Revitt- Mills, Samantha Munn, Thanavit Jirapanjawat, Chris Greening, Jennifer C. Boer, Katie L. Flanagan, Magne Kaldhusdal, Magdalena Plebanski, Katherine B. Gibney, Robert J. Moore, Julian I. Rood, Samuel C. Forster
Summary: This study analyzed 464 Clostridium perfringens genomes and identified the first putative non-conjugative enterotoxin (CPE)-encoding plasmids and a putative novel conjugative locus (Bcp). Additionally, 102 new C. perfringens genomes were sequenced and archived, including rarely sequenced toxinotype B, C, D, and E isolates. The study revealed the essential role of plasmids and plasmid diversity in C. perfringens pathogenicity and broader biology.
MICROBIAL GENOMICS
(2023)
Editorial Material
Biology
Vanessa Rossetto Marcelino
Letter
Ecology
Marcel Klaassen, Michelle Wille
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Virology
Wan-Ting He, Dongyan Li, Guy Baele, Jin Zhao, Zhiwen Jiang, Xiang Ji, Michael Veit, Marc A. Suchard, Edward C. Holmes, Philippe Lemey, Maciej F. Boni, Shuo Su
Summary: Through retrospective epidemiological study, new lineages of porcine hemagglutinating encephalomyelitis virus (PHEV) complex coronaviruses (CoVs) were discovered in swine populations in China. These novel lineages cause respiratory symptoms without neurological symptoms typically associated with classical PHEV infection. The novel lineages have been circulating in at least eight provinces in southeastern China.
Letter
Virology
Lin Xu, Wei Liu, Mengyu Bie, Tao Hu, Dong Yan, Zhishu Xiao, Edward C. Holmes, Weifeng Shi
Article
Health Care Sciences & Services
J. M. Basseal, C. M. Bennett, P. Collignon, B. J. Currie, D. N. Durrheim, J. Leask, E. S. McBryde, P. McIntyre, F. M. Russell, D. W. Smith, T. C. Sorrell, B. J. Marais
Summary: Australia avoided the worst effects of COVID-19 pandemic, but still faced negative impacts. Lessons from Australia's public health response include the effectiveness of movement restrictions with careful consideration of adverse impacts, the value of disease modeling while acknowledging its limitations, the need for timely national data for reassessment of surveillance structures, the utility of advanced pathogen genomics and novel vaccine technology, the importance of evidence-informed and consultative decisionmaking, addressing major weaknesses in the aged-care sector, adequate infection prevention and control frameworks, prioritizing the interests of young people, recognizing epidemics as a standing threat, and fostering regional and global solidarity.
LANCET REGIONAL HEALTH-WESTERN PACIFIC
(2023)
Article
Biochemical Research Methods
Guowei Chen, Xubo Tang, Mang Shi, Yanni Sun
Summary: In this study, we developed VirBot, a simple yet effective RNA virus identification tool based on protein families and adaptive score cutoffs. Compared to seven popular tools for virus identification, VirBot demonstrated high specificity in metagenomic datasets and superior sensitivity in detecting novel RNA viruses on both simulated and real sequencing data.