Article
Multidisciplinary Sciences
Md Mamun Monir, Mohammad Tarequl Islam, Razib Mazumder, Dinesh Mondal, Kazi Sumaita Nahar, Marzia Sultana, Masatomo Morita, Makoto Ohnishi, Anwar Huq, Haruo Watanabe, Firdausi Qadri, Mustafizur Rahman, Nicholas Thomson, Kimberley Seed, Rita R. Colwell, Tahmeed Ahmed, Munirul Alam
Summary: In 2022, Bangladesh experienced a severe cholera outbreak, with the icddr,b Dhaka hospital treating more than 1300 patients and 42,000 diarrheal cases. The strains responsible for the outbreak belong to the BD-1.2 subclade, which clusters with the 7PET wave-3 global clade strains. These strains have been present in Bangladesh since 2016, but only became dominant in 2018 and are predominantly associated with endemic cholera. The recent shift in lineage and genetic attributes, including a change in serotype from Ogawa to Inaba, may explain the increasing number of cholera cases in Bangladesh.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Adam C. Retchless, Alex Chen, How-Yi Chang, Amy E. Blain, Lucy A. McNamara, Mustapha M. Mustapha, Lee H. Harrison, Xin Wang
Summary: Meningococcal disease is caused by Neisseria meningitidis and outbreaks occur when the same serogroup causes multiple cases over a short period. Genome sequencing can help identify outbreak strains and track the spread of the bacteria. Genetic similarities can distinguish outbreak strains from non-outbreak isolates, with certain clonal complexes showing low genetic diversity over time.
Article
Multidisciplinary Sciences
Altar M. Munis, Monique Andersson, Alexander Mobbs, Stephen C. Hyde, Deborah R. Gill
Summary: Modeling the spread of SARS-CoV-2 is crucial for understanding and containing outbreaks, with mutations in viral genomes impacting virulence. Analyzing 563 clinical samples in Oxford during the first wave of infections in the UK allowed researchers to track short-term viral evolution, detect mutations of concern, and capture viral diversity, demonstrating the utility of genomic pathogen surveillance in controlling local virus spread.
SCIENTIFIC REPORTS
(2021)
Article
Surgery
Elana Kreiger-Benson, Bruce Gelb, Henry J. Neumann, Sarah Hochman, Jennifer Lighter, Sapna A. Mehta
Summary: By implementing a systematic approach during a large measles outbreak, the study successfully identified and protected at-risk SOT patients. Through education in outbreak areas and testing nonimmune patients, the risk of measles infection in transplant patients was effectively reduced.
AMERICAN JOURNAL OF TRANSPLANTATION
(2021)
Article
Computer Science, Information Systems
Muhammad Farman, Aqeel Ahmad, Ali Akgul, Muhammad Umer Saleem, Muhammad Naeem, Dumitru Baleanu
Summary: The coronavirus pandemic presents a global challenge that requires further scientific research for understanding and control. Analyzing data from different countries can provide insights into the incubation period and other time intervals of COVID-19, aiding decision-making and control strategies.
CMC-COMPUTERS MATERIALS & CONTINUA
(2021)
Article
Multidisciplinary Sciences
Xi Guo, Abhineet Gupta, Anand Sampat, Chengwei Zhai
Summary: The COVID-19 pandemic has impacted work arrangements, leading to the need for risk assessment tools for on-site employment. This study introduces a simulation-based stochastic contact network model to evaluate cumulative incidence in workplaces. The model's validity is supported by comparisons with real-world outbreaks, making it a useful tool for short-term forecasts and assessing control measures.
Article
Immunology
Joshua Nealon, Alain Bouckenooghe, Margarita Cortes, Laurent Coudeville, Carina Frago, Denis Macina, Clarence C. Tam
Summary: Dengue endemicity varies across countries, and there is limited comparative data available. This study used serological data from multiple countries to estimate dengue force of infection (POI) and found that children in endemic countries have early and intense exposure to dengue, increasing their risk of secondary infection. The findings highlight the need for serosurveys at fine spatial resolutions to inform vaccination campaigns.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Immunology
Andreas Walker, Torsten Houwaart, Patrick Finzer, Lutz Ehlkes, Alona Tyshaieva, Maximilian Damagnez, Daniel Strelow, Ashley Duplessis, Jessica Nicolai, Tobias Wienemann, Teresa Tamayo, Malte Kohns Vasconcelos, Lisanna Huelse, Katrin Hoffmann, Nadine Luebke, Sandra Hauka, Marcel Andree, Martin P. Daeumer, Alexander Thielen, Susanne Kolbe-Busch, Klaus Goebels, Rainer Zotz, Klaus Pfeffer, Joerg Timm, Alexander T. Dilthey
Summary: Tracing SARS-CoV-2 population transmission chains remains a major challenge, but this study presents an integrated system of genomic surveillance that is capable of detecting infection chains in a large city during ongoing community transmission. The system combines viral surveillance sequencing, genetically based identification of infection clusters, integration of public health authority contact tracing data, and a user-friendly dashboard application. This integrated system can contribute to the monitoring and potentially improve the management of SARS-CoV-2 transmission in the population.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Immunology
Yi-Chia Huang, Hsiao-Chen Tu, Han-Yueh Kuo, Pei-Lan Shao, Yu-Nong Gong, Hui-Ying Weng, Hung -Yu Shu, Chiung-Hui Kuo, Po-Hsien Kuo, Chien -Hui Chien, Chen-Chi Wu, Ding-Cheng (Derrick) Chan, Meng-Kun Tsai, Shih-Feng Tsai, Chong-Jen Yu
Summary: This case study investigated an outbreak in a COVID-19-designated hospital and a hospital-based skilled nursing facility. The analysis of PCR tests and other studies revealed multiple clusters of COVID-19 infections, suggesting the potential for airborne transmission.
JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION
(2023)
Article
Public, Environmental & Occupational Health
James P. Adamson, Christopher Smith, Nicole Pacchiarini, Thomas Richard Connor, Janet Wallsgrove, Ian Coles, Clare Frost, Angharad Edwards, Jaisi Sinha, Catherine Moore, Steph Perrett, Christie Craddock, Clare Sawyer, Alison Waldram, Alicia Barrasa, Daniel Rh Thomas, Philip Daniels, Heather Lewis
Summary: This study presents an outbreak of COVID-19 in a large male prison in the UK and discusses the control measures implemented. The majority of cases were staff members, with a higher attack rate among them compared to the residents. Whole-genome sequencing was used to determine the genetic relationship between cases and differentiate transmission pathways. The study highlights the importance of timely epidemiological investigation and data visualization in implementing effective control measures and minimizing the impact on resident welfare.
EPIDEMIOLOGY AND INFECTION
(2022)
Article
Immunology
Matthew A. Crane, Aleksandra Popovic, Rohan Panaparambil, Andrew Stolbach, John A. Romley, Khalil G. Ghanem
Summary: Reporting of infectious diseases other than COVID-19 has significantly decreased during the COVID-19 pandemic. The decrease varies depending on the routes of transmission, reporting state, and COVID-19 incidence at the time of reporting. These findings emphasize the importance of continued investment in routine surveillance efforts despite pandemic conditions.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Immunology
Jun Yuan, Zongqiu Chen, Chenghua Gong, Hui Liu, Baisheng Li, Kuibiao Li, Xi Chen, Conghui Xu, Qinlong Jing, Guocong Liu, Pengzhe Qin, Yufei Liu, Yi Zhong, Lijuan Huang, Bao-Ping Zhu, Zhicong Yang
Summary: During a COVID-19 outbreak in Guangzhou, China in April 2020, it was found that sewage transmission of SARS-CoV-2 may occur, highlighting the significance of sewage management during outbreaks.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Environmental Sciences
Ying Zhang, Kongquan Zhu, Weiyi Huang, Zhixuan Guo, Senhua Jiang, Chujun Zheng, Yang Yu
Summary: This article discusses the practical feasibility of wastewater-based epidemiology (WBE) as an early warning and disease surveillance system in order to effectively control sporadic COVID-19 outbreaks in China.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Public, Environmental & Occupational Health
Nicki L. Boddington, Sophia Steinberger, Richard G. Pebody
Summary: Between 14 October 2014 and 13 October 2015, a total of 12,648 passengers from affected countries were screened at five major ports of entry in England. The majority of passengers were assessed as having no direct contact with EVD cases or high-risk events (12,069, 95.4%), although 535 (4.2%) passengers were assessed as requiring public health follow-up. Out of 39 passengers referred to secondary care, none were diagnosed with EVD, but one high-risk passenger later diagnosed with EVD.
JOURNAL OF PUBLIC HEALTH
(2022)
Article
Medicine, General & Internal
Rocio Seijo Bestilleiro, Diana Martinez Senaris, Maria Jose Pereira Rodriguez, Rita Galeiras Vazquez, Raquel Garcia Rodriguez, Maria Teresa Garcia Rodriguez, Cristina Gonzalez Martin, Maria Teresa Seoane Pillado, Vanesa Balboa Barreiro, Valentin Valdes Valina, Sonia Pertega Diaz
Summary: This study reported a nosocomial COVID-19 outbreak in a Spanish hospital, involving 22 confirmed cases among workers and inpatients. Key findings include older patients with immunosuppressive treatments, with some cases having severe outcomes, and the importance of close surveillance and infection control measures in preventing nosocomial outbreaks.
INTERNATIONAL JOURNAL OF MEDICAL SCIENCES
(2021)
Article
Immunology
Mohammed Limbada, David Macleod, Vasty Situmbeko, Ellen Muhau, Osborn Shibwela, Bwalya Chiti, Sian Floyd, Albertus J. Schaap, Richard Hayes, Sarah Fidler, Helen Ayles
Summary: This trial compared two community models of ART delivery, home-based delivery and adherence clubs, with standard of care in terms of effectiveness and feasibility for people with stable HIV. The results demonstrated that these alternative community models were as effective as facility-based care in terms of viral suppression.
Review
Public, Environmental & Occupational Health
Matthew Moher, Margaret Erickson, Paleah Black, Morgan Price, Christopher Fraser, Wendy V. Norman, Silvia Guillemi, Neora Pick, Ruth Elwood Martin
Summary: Studies conducted in the United States have shown that providing cell phones and sustainably monitoring viral load suppression can improve ART adherence for PLWH post-release. Additionally, utilizing Peer Navigators and incentivizing undetectable viral load lead to improved HIV viral load suppression.
Article
Biology
Lerato E. Magosi, Yinfeng Zhang, Tanya Golubchik, Victor DeGruttola, Eric Tchetgen Tchetgen, Vladimir Novitsky, Janet Moore, Pam Bachanas, Tebogo Segolodi, Refeletswe Lebelonyane, Molly Pretorius Holme, Sikhulile Moyo, Joseph Makhema, Shahin Lockman, Christophe Fraser, Myron Max Essex, Marc Lipsitch
Summary: This study emphasizes the importance of population mobility patterns in HIV transmission dynamics and control strategies, based on an analysis of a trial community in Botswana.
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
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
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).
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.