Review
Chemistry, Medicinal
Max Cruesemann
Summary: Traditional natural product discovery approaches are limited in terms of dereplication, but recent advances in mass spectrometry, sequencing, and bioinformatics have provided important tools for accelerating and rationalizing natural product discovery. By utilizing signature-based or correlation-based mass spectrometry genome mining approaches, metabolomic and genomic information can be rapidly linked.
Review
Public, Environmental & Occupational Health
Wing-Kee Yiek, Olga Coenen, Mayke Nillesen, Jakko van Ingen, Edmee Bowles, Alma Tostmann
Summary: Healthcare-associated infections are a significant cause of morbidity and mortality in hospitalized patients. Water in the environment can be a source of infection linked to outbreaks in hospitals. Proper handling, cleaning, and disinfection of water-containing medical devices are crucial in reducing microbial transmission to patients.
ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL
(2021)
Article
Multidisciplinary Sciences
Jared Lumpe, Lynette Gumbleton, Andrew Gorzalski, Kevin Libuit, Vici Varghese, Tyler Lloyd, Farid Tadros, Tyler Arsimendi, Eileen Wagner, Craig Stephens, Joel Sevinsky, David Hess, Mark Pandori
Summary: Whole genome sequencing has the potential to revolutionize diagnostics and public health. In order to realize this potential, bioinformatic software that meets diagnostic test quality standards needs to be developed. We developed a software called GAMBIT that uses k-mer based strategies for bacterial identification and incorporates a curated database of 48,224 genomes.
Review
Immunology
Won-Keun Kim, Seungchan Cho, Seung-Ho Lee, Jin Sun No, Geum-Young Lee, Kyungmin Park, Daesang Lee, Seong Tae Jeong, Jin-Won Song
Summary: This article introduces the significant burdens posed by emerging and re-emerging RNA viruses and highlights the role of active surveillance and genomic tracking in identifying and characterizing viral outbreaks. The focus is on Hantaviruses, zoonotic pathogens causing hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome. The study emphasizes the importance of high-resolution phylogeographic relationships between patient- and rodent-derived virus genome sequences to track infection sources.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Infectious Diseases
Audrey Duval, Lulla Opatowski, Sylvain Brisse
Summary: This study aimed to develop a hypothesis-based model to estimate genetic distance thresholds and mutation rates for single-strain food or environmental outbreaks. A forward model was developed to simulate bacterial evolution under specific mutation rates and outbreak durations. The model accurately discriminated outbreak and non-outbreak cases and estimated outbreak parameters. The model was validated using 16 published datasets of bacterial outbreaks.
Review
Medicine, General & Internal
Eimear Kelly, Sean Olann Whelan, Eli Harriss, Sarah Murphy, Andrew J. Pollard, Daniel O'Connor
Summary: This study conducted a systematic review to evaluate the performance of host genomic biomarkers in the diagnosis of bacterial infection. The results showed that host genomic biomarkers have high sensitivity and specificity for bacterial infection, indicating their potential clinical utility, but further validation is needed before clinical implementation.
Article
Genetics & Heredity
Claire Bertelli, Kristen L. Gray, Nolan Woods, Adrian C. Lim, Keith E. Tilley, Geoffrey L. Winsor, Gemma R. Hoad, Ata Roudgar, Adam Spencer, James Peltier, Derek Warren, Amogelang R. Raphenya, Andrew G. McArthur, Fiona S. L. Brinkman
Summary: Outbreaks of virulent and/or drug-resistant bacteria have a significant impact on human health and major economic consequences. Genomic islands (GIs) are of high interest due to their encoding of virulence factors, antimicrobial-resistance (AMR) genes, and other adaptations. However, current computational methods for GI analysis are not suitable for rapid and accurate comparative analysis. IslandCompare is an open-source computational pipeline that enables GI prediction and comparison across multiple bacterial genomes. It provides a dynamic visualization of bacterial core-genome phylogeny and overlays GI predictions and AMR determinants. IslandCompare is accessible through a web-based interface, making it user-friendly for bioinformaticians, biologists, and clinicians.
MICROBIAL GENOMICS
(2022)
Article
Agriculture, Dairy & Animal Science
N. Simon Ekesi, Beata Dolka, Adnan A. K. Alrubaye, Douglas D. Rhoads
Summary: The study found significant variations in BCO-lameness pathogens among different farms, with Escherichia coli possibly undergoing frequent host shifts and Staphylococcus aureus being restricted to poultry for over 40 years. Phylogenomic analysis revealed that specific pathogenicity islands may play a crucial role in the pathogenesis of S. aureus in chickens.
Article
Microbiology
Anton Ambroa, Lucia Blasco, Maria Lopez, Olga Pacios, Ines Bleriot, Laura Fernandez-Garcia, Manuel Gonzalez de Aledo, Concha Ortiz-Cartagena, Andrew Millard, Maria Tomas
Summary: This study analyzed the phage resistance in Acinetobacter baumannii clinical strains using genomic sequencing. The presence of genes associated with phage resistance was found to be higher in 2010 strains compared to 2000 strains, especially genes related to the restriction-modification system and CRISPR-Cas system. Furthermore, these genes were more frequently found in genomic islands of the 2010 strains.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Zhao Chen, David L. Erickson, Jianghong Meng
Summary: Oxford Nanopore sequencing is widely used for bacterial pathogen genome assembly, but high error rates in long reads necessitate polishing with Illumina short reads. NextPolish outperformed Pilon in improving genomic analyses of bacterial pathogens, requiring varying numbers of rounds for different strains. Simulated and real reads showed that the accuracy of genomic analyses depended on the optimization tool and the specific bacterial strain.
Article
Medicine, General & Internal
Louisa G. Gordon, Thomas M. Elliott, Brian Forde, Brett Mitchell, Philip L. Russo, David L. Paterson, Patrick N. A. Harris
Summary: This study aimed to predict the cost and health effects of routine use of whole-genome sequencing (WGS) compared with standard care for bacterial pathogens. By analyzing data from 27 hospitals in Queensland, Australia, the study found that WGS surveillance could prevent a substantial number of hospital patients from being infected with multidrug-resistant organisms, leading to cost savings and reduced mortality. Primary prevention through routine use of WGS is recommended as an investment priority for controlling serious hospital-associated infections.
Article
Food Science & Technology
Lili Chen, Jikai Wang, Ronghua Zhang, Hexiang Zhang, Xiaojuan Qi, Yue He, Jiang Chen
Summary: The study analyzed the characteristics of bacterial foodborne disease outbreaks in Zhejiang Province, finding Vibrio parahaemolyticus and Salmonella to be the most common pathogens, with restaurants, staff canteens, and households being the main outbreak settings, and aquatic products and meat being the primary foods. Outbreaks caused by different pathogens varied in settings and food vehicles.
Review
Chemistry, Multidisciplinary
G. Crivello, L. Fracchia, G. Ciardelli, M. Boffito, C. Mattu
Summary: Bacterial infections present a growing threat to healthcare systems. Bacteria often form biofilms, which are dense 3D structures that make eradication difficult and promote antibiotic resistance. Understanding the composition and mechanical properties of biofilms is crucial for developing effective in vitro models. This review provides an overview of biofilm features, explores factors influencing biofilm composition, and presents various in vitro biofilm models, comparing their advantages and disadvantages.
News Item
Multidisciplinary Sciences
Heidi Ledford
Summary: Cases of paralysis in the United States and Israel indicate that vaccine-derived poliovirus has infected numerous individuals.
Article
Biology
Mohamed Abbas, Anne Cori, Samuel Cordey, Florian Laubscher, Tomas Robalo Nunes, Ashleigh Myall, Julien Salamun, Philippe Huber, Dina Zekry, Virginie Prendki, Anne Iten, Laure Vieux, Valerie Sauvan, Christophe E. Graf, Stephan Harbarth
Summary: This study investigated transmission patterns of SARS-CoV-2 in geriatric settings, focusing on the roles of healthcare workers (HCWs) and elderly patients. The findings revealed that transmission between HCWs was less common compared to transmission between patients and HCWs. Most patient-to-patient transmission occurred in shared wards. This highlights the need for improvement in infection control measures to reduce nosocomial transmission.
Article
Biochemical Research Methods
Liang Wang, Xavier Didelot, Yuhai Bi, George F. Gao
Summary: Since the start of the SARS-CoV-2 pandemic, several variants of concern with increased transmissibility have been reported. Current vaccines only provide partial protection against infection and onward transmission. Through phylogenetic analysis and epidemiological modeling, researchers found that lineage B had significantly higher transmissibility than lineage A and played a major role in the global pandemic. The probability of onward transmission from vaccinated individuals infected with SARS-CoV-2 VOCs was slightly lower but not significantly different from unvaccinated individuals. Tailoring prevention strategies should consider both VOCs and exponentially growing lineages in each country. One dose of vaccination alone cannot efficiently prevent the onward transmission of SARS-CoV-2 VOCs, and nonpharmaceutical interventions should still be implemented during the vaccination period.
BRIEFINGS IN BIOINFORMATICS
(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
Multidisciplinary Sciences
Xavier Didelot, Charles Morris Evans
Summary: The burial rates of males and females in early modern central London were compared to investigate a possible bias towards male mortality in plague years. The study found a higher burial rate for males in each plague year, partly due to a higher population of males in central London. Additionally, the migration of women of childbearing age out of the city during the plague years contributed to the enhanced difference in adult male and female burials. Husbands were also more likely to be buried than their wives. However, this bias was less apparent in some plague years and in non-plague years, there were more burials of boys than girls.
Article
Multidisciplinary Sciences
Katriina Willgert, Xavier Didelot, Meera Surendran-Nair, Suresh Kuchipudi, Rachel M. Ruden, Michele Yon, Ruth H. Nissly, Kurt J. Vandegrift, Rahul K. Nelli, Lingling Li, Bhushan M. Jayarao, Nicole Levine, Randall J. Olsen, James J. Davis, James M. Musser, Peter J. Hudson, Vivek Kapur, Andrew J. K. Conlan
Summary: Understanding the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is crucial for disease control. Research has found no evidence of direct or indirect transmission from deer to humans, but spillback to humans cannot be ruled out.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Denis Volk, Fan Yang-Turner, Xavier Didelot, Derrick W. Crook, David Wyllie
Summary: Researchers have developed a software tool called Catwalk that can quickly detect highly similar sequences in large collections of microbial genomes. The tool performs well and can rapidly identify close relatives of SARS-CoV-2 and Mycobacterium tuberculosis genomes among millions of samples.
MICROBIAL GENOMICS
(2022)
Article
Biology
Jake Carson, Alice Ledda, Luca Ferretti, Matt Keeling, Xavier Didelot
Summary: The bounded coalescent model, which represents the origin of individuals from a common ancestor after a certain date, has important applications in various fields. This study introduces a new algorithm for simulating this model directly, demonstrating its computational efficiency compared to rejection sampling. The study also presents a method for calculating the probability of the last common ancestor occurring after a given date, which is crucial for analyzing phylogenetic data under the bounded coalescent model.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Biology
Xavier Didelot, Julian Parkhill
Summary: In recent years, the practicality of sequencing whole genomes from a large number of bacterial isolates has increased significantly, providing new insights into the evolution and epidemiology of bacterial pathogens. This article presents a step-by-step approach for large-scale genomic epidemiology analyses, focusing on the construction and application of dated phylogenies. The key advantage of this approach is its computational scalability, allowing for the analysis of hundreds or thousands of genomes within a short period of time.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Microbiology
Sadaf Rasheed Mughal, Sadia Ambreen Niazi, Thuy Do, Steven C. Gilbert, Xavier Didelot, David R. Radford, David Beighton
Summary: The aim of this study was to use high-throughput sequencing techniques to investigate the taxonomy of Actinomyces naeslundii and its closely related species. The strains were classified as A. naeslundii and A. oris based on MLST data analysis. Whole genome sequencing was performed on selected strains of A. oris and A. naeslundii, and comparative genomic analysis was carried out. The results showed that A. oris forms six distinct groups, while A. naeslundii forms three. The correct designation of isolates will help in the identification of clinical Actinomyces isolates found in dental plaque and accelerate further research on the biochemical characterization and pathogenesis of this group of microorganisms.
Article
Veterinary Sciences
Mostafa Y. Abdel-Glil, Helmut Hotzel, Herbert Tomaso, Xavier Didelot, Christian Brandt, Christian Seyboldt, Joerg Linde, Stefan Schwarz, Heinrich Neubauer, Hosny El-Adawy
Summary: Campylobacter fetus subsp. venerealis (Cfv) is the cause of bovine genital campylobacteriosis (BGC), which is a trade-relevant disease listed by the World Organization for Animal Health (WOAH). This study aimed to investigate the genomic diversity of German Cfv strains isolated from different federal states in Germany. Whole-genome sequencing and phylogenetic analysis were conducted on 63 Cfv strains collected between 1985 and 2015, and compared with international Cfv isolates. The results showed a genetically conserved Cfv population in Germany, with a lineage that emerged in the nineteenth century and diversified over time. The control interventions in Germany have been successful, as no outbreaks have been reported since 2015.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Microbiology
Kate E. Dingle, Jane Freeman, Xavier Didelot, T. Phuong Quan, David W. Eyre, Jeremy Swann, William D. Spittal, Emma V. Clark, Keith A. Jolley, A. Sarah Walker, Mark H. Wilcox, Derrick W. Crook
Summary: Clostridioides difficile is a significant cause of healthcare-associated infections, with multidrug-resistant strains causing high-mortality outbreaks. Cephalosporin treatment is a known risk factor, and antimicrobial stewardship is important for control. This study investigated the correlation between cephalosporin MICs, amino acid substitutions in penicillin binding proteins, and fluoroquinolone resistance in C. difficile.
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
Luis Roger Esquivel Gomez, Cyril Savin, Voahangy Andrianaivoarimanana, Soloandry Rahajandraibe, Lovasoa Nomena Randriantseheno, Zhemin Zhou, Arthur Kocher, Xavier Didelot, Minoarisoa Rajerison, Denise Kuehnert
Summary: Plague reappeared in the city of Mahajanga, Madagascar in 1991 after a plague-free period of over 60 years. This study used a phylogeographic model to analyze the genome sequences of Yersinia pestis and identified two migrations from the Central Highlands that caused the outbreaks in the 1990s. The pathogen likely survived in wild reservoirs before spillover to humans.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Multidisciplinary Sciences
David Helekal, Matt Keeling, Yonatan H. Grad, Xavier Didelot
Summary: Increasing levels of antibiotic resistance pose a major threat to public health. Understanding the costs and benefits of resistance can lead to better use of antibiotics and prevent the spread of resistance.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Virology
Xavier Didelot, Vinicius Franceschi, Simon D. W. Frost, Ann Dennis, Erik M. Volz
Summary: Inference of effective population size from genomic data can provide insights into demographic history and epidemiological dynamics. A nonparametric approach based on latent process models is developed to estimate the population size dynamics, optimizing parameters using out-of-sample prediction accuracy. The methodology is demonstrated using simulation experiments and applied to HIV-1 and SARS-CoV-2 datasets to estimate the impact of interventions on epidemic dynamics.
Article
Biochemical Research Methods
Xavier Didelot, David Helekal, Michelle Kendall, Paolo Ribeca
Summary: The ability to distinguish imported cases from locally acquired cases is important for selecting public health control strategies. This study proposes an alternative approach using genomic data from a specific location to detect imported cases by comparing them with previous cases from the same location.
