Article
Chemistry, Medicinal
Kevin Antraygues, Nina Compagne, Francesca Ruggieri, Kamel Djaout, Zainab Edoo, Maxime Eveque, Leo Faion, Bruna Gioia, Salia Tangara, Anais Vieira Da Cruz, Baptiste Villemagne, Marion Flipo, Alain Baulard, Nicolas Willand
Summary: This article summarizes the joint autumn symposium organized by the French Society for Medicinal Chemistry and the French Microbiology Society, which attracted over 200 researchers from France and abroad, generating high-level scientific dialogue on the most recent advances in combating antimicrobial resistance.
Article
Biochemistry & Molecular Biology
Farah Abdul-Rahman, Daniel Tranchina, David Gresham
Summary: The study demonstrates that in static environments, a small number of high-fitness genotypes dominate the population, leading to decreased genetic diversity. In contrast, fluctuating environments are enriched in genotypes with neutral fitness effects, contributing to the maintenance of genetic diversity. Oscillatory behaviors in response to environmental fluctuation play a role in balancing selection and maintaining genetic diversity.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Food Science & Technology
Nesrine Ben Mhenni, Giulia Alberghini, Valerio Giaccone, Alessandro Truant, Paolo Catellani
Summary: Excessive loads of Pseudomonas in fresh fish products can cause rapid spoilage. The presence of Pseudomonas should be considered by Food Business Operators (FBOs) in both whole and prepared fish products. This study quantified Pseudomonas spp. in fresh fillets of Salmo salar, Gadus morhua and Pleuronectes platessa, and found that more than 50% of the samples had loads of presumptive Pseudomonas no lower than 10(4)-10(5) cfu/g. The study also discovered a high prevalence of antimicrobial resistance among Pseudomonas strains isolated from the fish fillets.
Article
Infectious Diseases
Sumanth Gandra, Gerardo Alvarez-Uria, Dustin Stwalley, Katelin B. Nickel, Kimberly A. Reske, Jennie H. Kwon, Erik R. Dubberke, Margaret A. Olsen, Jason P. Burnham
Summary: This study retrospectively compared the microbiology data of blood, respiratory, and urine cultures from a community hospital in India and two community hospitals in the USA during the COVID-19 pandemic. The proportion of contaminated blood cultures and carbapenem-resistant organisms in respiratory and urine cultures increased significantly during the pandemic period. In the US hospitals, there was a significant increase in methicillin-resistant Staphylococcus aureus in blood cultures. Continuity of antimicrobial stewardship activities and better infection prevention measures are crucial to minimize antimicrobial resistance burden among COVID-19 patients.
Article
Multidisciplinary Sciences
Suk-Won Suh, Yoo Shin Choi, Seong-Ho Choi, Jae Hyuk Do, Hyoung-Chul Oh, Hong Jin Kim, Seung Eun Lee
Summary: The study found that the incidence of common bacteria in bile cultures of acute cholecystitis patients and their antibiotic resistance changed over time, suggesting that these factors should be considered when selecting antibiotics for treating acute cholecystitis. Additionally, in patients with grade I and II acute cholecystitis, early antimicrobial therapy does not appear to impact perioperative outcomes.
SCIENTIFIC REPORTS
(2021)
Article
Environmental Sciences
Michelle Baker, Alexander D. Williams, Steven P. T. Hooton, Richard Helliwell, Elizabeth King, Thomas Dodsworth, Rosa Maria Baena-Nogueras, Andrew Warry, Catherine A. Ortori, Henry Todman, Charlotte J. Gray-Hammerton, Alexander C. W. Pritchard, Ethan Iles, Ryan Cook, Richard D. Emes, Michael A. Jones, Theodore Kypraios, Helen West, David A. Barrett, Stephen J. Ramsden, Rachel L. Gomes, Chris Hudson, Andrew D. Millard, Sujatha Raman, Carol Morris, Christine E. R. Dodd, Jan-Ulrich Kreft, Jon L. Hobman, Dov J. Stekel
Summary: Waste from dairy production is a significant source of contamination from antimicrobial resistant bacteria and genes. Storing slurry waste for at least 60 days can significantly reduce the spread of ARB onto land. Furthermore, further reductions in AMR are unlikely on farms with low antibiotic use.
ENVIRONMENT INTERNATIONAL
(2022)
Article
Biotechnology & Applied Microbiology
Liam P. Brown, Roger Murray, Andrew Scott, Yuan-Ching Tien, Calvin Ho-Fung Lau, Vera Tai, Edward Topp
Summary: This study evaluated the effects of long-term and repeated exposure to macrolide antibiotics on the diversity of soil bacterial community, resistome, and mobilome. At unrealistically high concentrations, macrolide antibiotics altered the overall diversity of resistome and mobilome, enriching for antibiotic resistance genes and mobile genetic elements of concern to human health. However, at realistic antibiotic concentrations, no effect on these endpoints was observed, suggesting that current biosolids land management practices are unlikely to pose a risk to human health due to macrolide antibiotic contamination alone.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biology
Yuseob Kim
Summary: When a population has partial protection from fluctuating selection, such as the presence of a seed bank, the variance in fitness decreases and reproductive success is enhanced. This study explores the impact of this "refuge" from fluctuating selection using a mathematical model that combines demographic and evolutionary dynamics. Contrary to classical predictions, alleles that increase population size fluctuation are positively selected if population density is weakly regulated. This study also reveals the emergence of oscillatory polymorphism under strong density regulation with a constant carrying capacity, highlighting the importance of considering joint demographic and population genetic changes in models to discover novel eco-evolutionary dynamics.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Marcelo D. T. Torres, Sahag Voskian, Paul Brown, Andong Liu, Timothy K. Lu, T. Alan Hatton, Cesar de la Fuente-Nunez
Summary: An ionic liquid with potent antimicrobial activity has been developed, showing effectiveness against clinically relevant bacterial pathogens and in a mouse model. The incorporation of the liquid into surface coatings generates antibiofilm material with high antimicrobial and antifouling activity, making it suitable for medical devices and other settings.
Article
Microbiology
Ka Lip Chew, Sophie Octavia, Deborah Lai, Raymond T. P. Lin, Jeanette W. P. Teo
Summary: The study revealed that Klebsiella quasipneumoniae subspecies cause a spectrum of infections similar to those caused by Klebsiella pneumoniae, with higher susceptibility rates to common antibiotics and low prevalence of virulence genes compared to the latter.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Review
Biology
Petros Ioannou, Stella Baliou, Diamantis P. Kofteridis
Summary: The article summarizes recent advancements in medical research and clinical practice, highlighting the significant limitations of antimicrobial resistance (AMR) on therapeutics for infectious diseases. It emphasizes the urgent need for novel treatments, particularly in the era of increasing AMR. Ongoing research is exploring non-classical therapies, such as bacteriophages or antimicrobial peptides (AMPs), that utilize alternative antimicrobial mechanisms to combat pathogens.
Article
Engineering, Environmental
Jason A. Rothman, Andrew Saghir, Seung-Ah Chung, Nicholas Boyajian, Thao Dinh, Jinwoo Kim, Jordan Oval, Vivek Sharavanan, Courtney York, Amity G. Zimmer-Faust, Kylie Langlois, Joshua A. Steele, John F. Griffith, Katrine L. Whiteson
Summary: This study used untargeted metatranscriptomic sequencing to analyze RNA extracted from municipal wastewater samples. The results showed that wastewater samples contain diverse microbes and provide valuable information about human-associated and medically important microbial populations. The study also found geographical variations in antimicrobial resistance diversity and an increasing abundance of specific antimicrobial resistance genes/variants over time.
Article
Genetics & Heredity
Meike J. Wittmann, Sylvain Mousset, Joachim Hermisson
Summary: Natural selection not only affects the actual loci under selection but also leaves footprints in patterns of genetic variation in linked genetic regions. We developed analytical approximations to characterize the genetic footprint of balancing selection with seasonally fluctuating allele frequencies. Fluctuating balancing selection can lead to an increase in genetic diversity near the selected site but reduces diversity further away due to recurrent bottlenecks of allelic backgrounds. Strong fluctuating balancing selection can even result in a loss of genetic variation in unlinked regions, impacting genome-wide diversity.
Article
Evolutionary Biology
John K. Kelly
Summary: This study characterizes the evolution of SNPs in a population of yellow monkeyflower. It finds that most SNPs exhibit minimal change over time, consistent with neutral evolution. However, a subset of SNPs display strong fluctuations in frequency, which are driven by selection and have a ripple effect on genome-wide variation.
Review
Infectious Diseases
Cherry Lim, Elizabeth A. Ashley, Raph L. Hamers, Paul Turner, Thomas Kesteman, Samuel Akech, Alejandra Corso, Mayfong Mayxay, Iruka N. Okeke, Direk Limmathurotsakul, H. Rogier van Doorn
Summary: This article reviews the strategies for AMR surveillance using routine microbiology results in LMICs, emphasizing the need for support in certain areas. Different surveillance strategies need to be thoroughly understood in terms of their limitations and potential biases to ensure maximum utilization and interpretation of local routine microbiology data.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Article
Immunology
Manon Ragonnet-Cronin, Tanya Golubchik, Sikhulile Moyo, Christophe Fraser, Max Essex, Vlad Novitsky, Erik Volz
Summary: This study shows that the recency of HIV-1 infection can be inferred from viral sequence diversity even among patients on suppressive ART.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Infectious Diseases
Katherine A. Twohig, Tommy Nyberg, Asad Zaidi, Simon Thelwall, Mary A. Sinnathamby, Shirin Aliabadi, Shaun R. Seaman, Ross J. Harris, Russell Hope, Jamie Lopez-Bernal, Eileen Gallagher, Andre Charlett, Daniela De Angelis, Anne M. Presanis, Gavin Dabrera
Summary: A study in England found that patients with COVID-19 infected with the delta variant were more likely to be admitted to hospital or attend emergency care compared to those infected with the alpha variant. This suggests that outbreaks of the delta variant in unvaccinated populations may pose a greater burden on healthcare services.
LANCET INFECTIOUS DISEASES
(2022)
Article
Multidisciplinary Sciences
J. Panovska-Griffiths, B. Swallow, R. Hinch, J. Cohen, K. Rosenfeld, R. M. Stuart, L. Ferretti, F. Di Lauro, C. Wymant, A. Izzo, W. Waites, R. Viner, C. Bonell, C. Fraser, D. Klein, C. C. Kerr
Summary: The English SARS-CoV-2 epidemic is influenced by new viral variants and changing restrictions. Estimations from statistical models and the agent-based model Covasim show that the Delta variant is highly transmissible, and delaying relaxation of restrictions and continuing vaccination can greatly reduce the number of infections.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2022)
Article
Multidisciplinary Sciences
Robert Hinch, Jasmina Panovska-Griffiths, William J. M. Probert, Luca Ferretti, Chris Wymant, Francesco Di Lauro, Nikolas Baya, Mahan Ghafari, Lucie Abeler-Dorner, Christophe Fraser
Summary: This study analyzes the spatial spread of SARS-CoV-2 variants in England using an agent-based model and a statistical model. The results show that the B.1.177 and Alpha variants have higher transmissibility compared to earlier variants. The study also highlights the crucial role of the vaccination program in controlling the epidemic.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2022)
Article
Immunology
Jessica M. Fogel, Ethan A. Wilson, Estelle Piwowar-Manning, Autumn Breaud, William Clarke, Christos Petropoulos, Ayana Moore, Christophe Fraser, Barry Kosloff, Kwame Shanaube, Gert van Zyl, Michelle Scheepers, Sian Floyd, Peter Bock, Helen Ayles, Sarah Fidler, Richard Hayes, Deborah Donnell, Susan H. Eshleman
Summary: The study suggests that universal HIV testing and treatment (UTT) did not lead to an increase in drug resistance. The findings showed that non-seroconverters had higher rates of drug resistance and multi-class resistance compared to seroconverters.
JOURNAL OF THE INTERNATIONAL AIDS SOCIETY
(2022)
Article
Biology
Alexandra Blenkinsop, Melodie Monod, Ard van Sighem, Nikos Pantazis, Daniela Bezemer, Eline op de Coul, Thijs van de Laar, Christophe Fraser, Maria Prins, Peter Reiss, Godelieve J. de Bree, Oliver Ratmann
Summary: More than 60% of HIV infections in Amsterdam residents were estimated to be acquired between 2014-2018, with a high rate of new diagnoses remaining higher than national rates, indicating Amsterdam as a HIV hotspot. A considerable proportion of recent HIV infections in Amsterdam, especially among MSM and heterosexuals, remained undiagnosed, suggesting the need for intensified city-level interventions to prevent HIV infections among residents.
Article
Biology
Sonja Lehtinen, Nicholas J. Croucher, Francois Blanquart, Christophe Fraser
Summary: Bacteriocins, toxic peptides involved in the competition between bacterial strains, play an important role in maintaining diversity in bacterial populations. In epidemiological models, the diversity of bacteriocins is more easily maintained compared to within-host models, and can occur through different mechanisms such as competition-colonization trade-off. Furthermore, bacteriocin diversity can also maintain the coexistence of antibiotic-sensitive and -resistant strains.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemical Research Methods
Christopher E. Overton, Lorenzo Pellis, Helena B. Stage, Francesca Scarabel, Joshua Burton, Christophe Fraser, Ian Hall, Thomas A. House, Chris Jewell, Anel Nurtay, Filippo Pagani, Katrina A. Lythgoe
Summary: During the first year of the COVID-19 pandemic, the EpiBeds model was used in England to predict hospital bed demand and estimate the proportion of individuals following different clinical pathways, providing valuable forecasts for healthcare systems.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Immunology
Kidist Zewdie, Michael Pickles, Sian Floyd, Sarah Fidler, Helen Ayles, Peter Bock, Graeme Hoddinott, Nomtha Mandla, Kwame Shanaube, Musonda Simwinga, Christophe Fraser, Janet Seeley, Estelle Piwowar-Manning, Richard Hayes, Deborah Donnell
Summary: Based on data analysis from 21 research communities in Zambia and South Africa, it was found that traditional male circumcision is not significantly more protective against HIV acquisition compared to medical male circumcision. The uptake of voluntary medical male circumcision was not substantial, even with household-based delivery of HIV testing followed by referral for circumcision.
Article
Infectious Diseases
Suraj Balakrishna, Tom Loosli, Maryam Zaheri, Paul Frischknecht, Michael Huber, Katharina Kusejko, Sabine Yerly, Karoline Leuzinger, Matthieu Perreau, Alban Ramette, Chris Wymant, Christophe Fraser, Paul Kellam, Astrid Gall, Hans H. Hirsch, Marcel Stoeckle, Andri Rauch, Matthias Cavassini, Enos Bernasconi, Julia Notter, Alexandra Calmy, Huldrych F. Gunthard, Karin J. Metzner, Roger D. Kouyos
Summary: This study compared the reliability of Sanger sequencing and Next-generation sequencing (NGS) in detecting HIV drug resistance mutations (DRMs). The results showed good agreement between the two methods when detecting mutations at a threshold of 5% or higher. However, at lower thresholds, NGS detected a substantial number of low-frequency mutations, which were likely to be sequencing errors.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Biology
Lele Zhao, Matthew Hall, Mariateresa de Cesare, George MacIntyre-Cockett, Katrina Lythgoe, Christophe Fraser, David Bonsall, Tanya Golubchik, Luca Ferretti
Summary: The raw material for viral evolution comes from intra-host mutations during replication, transcription, or post-transcription. This study explores the mutational spectrum of SARS-CoV-2 and reveals differences in mutation patterns between the negative and positive strands, potentially influenced by host factors.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Michelle Kendall, Daphne Tsallis, Chris Wymant, Andrea Di Francia, Yakubu Balogun, Xavier Didelot, Luca Ferretti, Christophe Fraser
Summary: The NHS COVID-19 app, launched in England and Wales in September 2020, had a Bluetooth-based contact tracing functionality to reduce the transmission of SARS-CoV-2. The study shows that user engagement and the app's impact on the epidemic varied based on social and epidemic characteristics. The authors also discuss the interaction and complementarity of manual and digital contact tracing approaches.
NATURE COMMUNICATIONS
(2023)
Article
Infectious Diseases
Nick Groves-Kirkby, Ewan Wakeman, Seema Patel, Robert Hinch, Tineke Poot, Jonathan Pearson, Lily Tang, Edward Kendall, Ming Tang, Kim Moore, Scott Stevenson, Bryn Mathias, Ilya Feige, Simon Nakach, Laura Stevenson, Paul O'Dwyer, William Probert, Jasmina Panovska-Griffiths, Christophe Fraser
Summary: This study adapted an agent-based model of COVID-19 to inform planning and decision-making within a healthcare setting. By calibrating the model to health data, it simulated the spread of the virus in England and provided useful projections of future clinical demand for the National Health Service (NHS).
Meeting Abstract
Immunology
S. E. Chaudron, L. Zhao, G. Macinthyre-Crockett, L. Thompson, I. Baudi, M. Limbada, S. Floyd, B. Kosloff, K. Shanaube, S. Fidler, R. Hayes, H. Ayles, J. Herbeck, C. Fraser, D. Bonsall
JOURNAL OF THE INTERNATIONAL AIDS SOCIETY
(2022)
Article
Virology
Lele Zhao, Chris Wymant, Francois Blanquart, Tanya Golubchik, Astrid Gall, Margreet Bakker, Daniela Bezemer, Matthew Hall, Swee Hoe Ong, Jan Albert, Norbert Bannert, Jacques Fellay, M. Kate Grabowski, Barbara Gunsenheimer-Bartmeyer, Huldrych F. Gunthard, Pia Kivela, Roger D. Kouyos, Oliver Laeyendecker, Laurence Meyer, Kholoud Porter, Ard van Sighem, Marc van der Valk, Ben Berkhout, Paul Kellam, Marion Cornelissen, Peter Reiss, Christophe Fraser, Luca Ferretti
Summary: This study investigates the relationship between viral load and transmission fitness in HIV-1. The results suggest that higher set-point viral load is associated with increased infectiousness and transmission fitness. This finding has implications for understanding the evolution and spread of HIV-1.
