Article
Cell Biology
Qiwen Dong, Huaiying Lin, Marie-Maude Allen, Julian R. Garneau, Jonathan K. Sia, Rita C. Smith, Fidel Haro, Tracy McMillen, Rosemary L. Pope, Carolyn Metcalfe, Victoria Burgo, Che Woodson, Nicholas Dylla, Claire Kohout, Anitha Sundararajan, Evan S. Snitkin, Vincent B. Young, Louis-Charles Fortier, Mini Kamboj, Eric G. Pamer
Summary: Clostridioides difficile strains of different virulence levels contribute to varying severity of colitis. This study found that a natural deletion in the cdtR gene attenuates virulence in epidemic ST1 C. difficile isolates without affecting colonization. Distinguishing strains based on the presence of cdtR may improve the specificity of diagnostic tests for C. difficile colitis.
Article
Microbiology
Maria Kulecka, Edyta Waker, Filip Ambrozkiewicz, Agnieszka Paziewska, Karolina Skubisz, Patrycja Cybula, Lukasz Targonski, Michal Mikula, Jan Walewski, Jerzy Ostrowski
Summary: Our study revealed that the presence of specific genes related to carbon metabolism and oxidative phosphorylation increased the risk of infection recurrence. More core genes were found to be under positive selective pressure in recurrent disease isolates, mainly associated with amino acid metabolism. Prophage elements were more prevalent in single infection isolates, while plasmids did not influence the odds of recurrence.
Article
Immunology
Jen-Chieh Lee, Yuan -Pin Hung, Bo -Yang Tsai, Pei -Jane Tsai, Wen -Chien Ko
Summary: Severe CDIs in the ICU were not rare in this study. The ileus group tended to have more severe presentation, with severe and fulminant CDIs accounting for 65.2% and an ICU mortality rate of 39.1%. Clinicians should be aware of abdominal symptoms and signs other than diarrhea, such as ileus, for timely diagnosis and management of CDI.
JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION
(2021)
Review
Medicine, General & Internal
Ibrahim A. Al-Zahrani
Summary: Clostridioides difficile (C. difficile) infection is a global threat to many healthcare settings. Excessive use of antimicrobials, lack of optimal antibiotic policies, and suboptimal infection control practices have fueled the development of this health issue. Prudent use of antimicrobials and simple infection control measures can significantly reduce infection rates.
SAUDI MEDICAL JOURNAL
(2023)
Article
Microbiology
Pilar Marcos, Aoife Doyle, Paul Whyte, Thomas R. Rogers, Maire McElroy, Seamus Fanning, Jesus Frias, Declan Bolton
Summary: The aim of this study was to characterize C. difficile isolates in Ireland in terms of ribotype and antibiotic resistance. The most common ribotype along the food chain was 078, followed by variant RT078/4. Less common and novel ribotypes were also detected. Majority of the isolates showed resistance to at least one antibiotic, with a significant proportion displaying a multi-drug resistant phenotype.
Article
Infectious Diseases
Quinten R. Ducarmon, Tjomme van der Bruggen, Celine Harmanus, Ingrid M. J. G. Sanders, Laura G. M. Daenen, Ad C. Fluit, Rolf H. A. M. Vossen, Susan L. Kloet, Ed J. Kuijper, Wiep Klaas Smits
Summary: This study reports a patient case of pseudomembranous colitis caused by a rare polymerase chain reaction (PCR) ribotype (RT) 151 Clostridioides difficile strain that produces a single toxin. Genomic analysis revealed that the RT151 strain was unable to be identified using routine commercial tests. The study also provides conclusive evidence for the pathogenicity of C-II isolates of the cryptic clade and highlights the need for vigilance towards C. difficile infections caused by cryptic clade isolates.
CLINICAL MICROBIOLOGY AND INFECTION
(2023)
Review
Public, Environmental & Occupational Health
Peng An Khun, Thomas V. Riley
Summary: This review provides an overview of Clostridium difficile infection (CDI) in southeast Asia, including its prevalence, detection methods, antimicrobial susceptibility profiles, and the potential significance of a One Health approach. CDI is a common cause of hospital-acquired gastroenteritis worldwide, with higher rates observed in high-income countries. Lack of knowledge and awareness about CDI, along with antimicrobial abuse and inadequate education on appropriate usage, contribute to its evolution. Underreporting of CDI rates and misuse of antimicrobial agents pose a significant threat in regions like Indochina, while C. difficile RT 017 strain is endemic in southeast Asia.
AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE
(2022)
Article
Biology
Annamaria Toporova, Katarina Curova, Martin Novotny, Viera Lovayova, Maria Nagyova, Leonard Siegfried, Viktoria Takacova, Anna Liskova, Andrea Longauerova, Michaela Vukusiova Uhrinova, Barbora Dzugasova
Summary: In this study, we confirmed the presence of toxigenic and hypervirulent strains of Clostridioides difficile in stool samples of hospitalized patients. Ribotypes 176, 001, and 027 were identified as the most frequent, with ribotype 176 being predominant. The high incidence of rifampicin resistance in ribotypes 176 and 027 suggests the misuse of broad-spectrum antibiotics in our hospitals during the COVID-19 pandemic.
Article
Biotechnology & Applied Microbiology
Jianfeng Wang, Chu Yang, Chao Zhang, Xiaoyan Mao, An Lizhe
Summary: In this study, the genome of Clostridium difficile was studied using metagenomic technology, revealing its gene sequence information and potential toxicological genes. Through gene function analysis and pathogenicity analysis, the metabolism activity, catalytic activity, carbohydrate-active enzyme genes and other aspects of the bacterium were understood, and an assessment was made on its virulence genes.
Article
Immunology
Janice Cho, Scott Cunningham, Meng Pu, Ryan J. Lennon, Jennifer Dens Higano, Patricio Jeraldo, Priya Sampathkumar, Samantha Shannon, Purna C. Kashyap, Robin Patel
Summary: Through WGS analysis of C. difficile isolates from CDI patients, it was found that 40% of community-acquired CDI patients may have transmission within the same zip code. WGS better differentiates between relapse and reinfection than definitions based on the timing of recurrence.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Infectious Diseases
Jieun Kim, Mi-Ran Seo, Bongyoung Kim, Jinyeong Kim, Mi-Hyun Bae, Hyunjoo Pai
Summary: This study aimed to analyze the genetic relatedness of Clostridioides difficile RT017 strains in a hospital with high prevalence. The majority of the strains were genetically related to CC-A, indicating the transmission and evolution of RT017 strains within the hospital. Variations in antibiotic resistance rates were observed among different CCs, suggesting significant differences in resistance profiles.
Article
Immunology
Ren-feng Zhang, Yu-xia Man, Yuan-yuan Bai, Chun-hong Shao, Chun-mei Liu, Cong-hui Wang, Yong-xing Lei, Yong Wang, Yan Jin
Summary: This study identified and characterized five C. difficile 027 isolates in China, showing high resistance to fluoroquinolones. These isolates were confirmed through MLST, PCR ribotyping, and whole genome sequencing. The findings suggest that C. difficile 027 infections may be neglected in China, warranting further epidemiological studies nationwide.
JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION
(2021)
Review
Biochemistry & Molecular Biology
Andrea Piccioni, Federico Rosa, Federica Manca, Giulia Pignataro, Christian Zanza, Gabriele Savioli, Marcello Covino, Veronica Ojetti, Antonio Gasbarrini, Francesco Franceschi, Marcello Candelli
Summary: The composition of the human microbiome plays a crucial role in health, and alterations in the microbiota can lead to Clostridium difficile infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Multidisciplinary Sciences
Tebelay Dilnessa, Alem Getaneh, Workagegnehu Hailu, Feleke Moges, Baye Gelaw
Summary: A high prevalence of C. difficile was observed among hospitalized patients, emphasizing the need for attention and prevention. The resistance of C. difficile to metronidazole and vancomycin was lower compared to other antibiotics.
Editorial Material
Biotechnology & Applied Microbiology
Zhengming Zhu, Liying Zhu, Ling Jiang
Summary: This article discusses the promising future of using genetic systems and biosensors for targeted improvement of short-chain fatty acid biosynthesis.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Immunology
Sheila F. Lumley, Gillian Rodger, Bede Constantinides, Nicholas Sanderson, Kevin K. Chau, Teresa L. Street, Denise O'Donnell, Alison Howarth, Stephanie B. Hatch, Brian D. Marsden, Stuart Cox, Tim James, Fiona Warren, Liam J. Peck, Thomas G. Ritter, Zoe de Toledo, Laura Warren, David Axten, Richard J. Cornall, E. Yvonne Jones, David Stuart, Gavin Screaton, Daniel Ebner, Sarah Hoosdally, Meera Chand, Derrick W. Crook, Anne-Marie O'donnell, Christopher P. Conlon, Koen B. Pouwels, A. Sarah Walker, Tim E. A. Peto, Susan Hopkins, Timothy M. Walker, Nicole E. Stoesser, Philippa C. Matthews, Katie Jeffery, David W. Eyre
Summary: Natural infection with detectable anti-spike antibodies and two doses of vaccine provide robust protection against SARS-CoV-2 infection, including the B.1.1.7 variant in healthcare workers. Single dose vaccination significantly reduces the risk of symptomatic infection.
CLINICAL 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
Immunology
Karina-Doris Vihta, Koen B. Pouwels, Tim E. A. Peto, Emma Pritchard, David W. Eyre, Thomas House, Owen Gethings, Ruth Studley, Emma Rourke, Duncan Cook, Ian Diamond, Derrick Crook, Philippa C. Matthews, Nicole Stoesser, Ann Sarah Walker
Summary: This study compared the ability of different symptoms to identify SARS-CoV-2 infection at specific time points and by vaccination status. The findings suggest that expanding symptom combinations can improve the sensitivity of PCR testing, but it also increases the number of tests per case. Therefore, when implementing large-scale testing strategies, various factors need to be taken into consideration.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
M. T. Tsakok, R. A. Watson, S. F. Lumley, F. Khan, Z. Qamhawi, A. Lodge, C. Xie, B. Shine, R. Matthews, K. Jeffery, D. W. Eyre, R. Benamore, F. Gleeson
Summary: This study aimed to compare the radiological, biochemical, and clinical severity between patients infected with Alpha-variant SARS-CoV-2 and those infected with pre-existing strains, as well as to determine whether the computed tomography (CT) severity score (CTSS) for COVID-19 pneumonitis is correlated with clinical severity and can predict outcomes.
CLINICAL RADIOLOGY
(2022)
Article
Multidisciplinary Sciences
Adriana Tomic, Donal T. Skelly, Ane Ogbe, Daniel O'Connor, Matthew Pace, Emily Adland, Frances Alexander, Mohammad Ali, Kirk Allott, M. Azim Ansari, Sandra Belij-Rammerstorfer, Sagida Bibi, Luke Blackwell, Anthony Brown, Helen Brown, Breeze Cavell, Elizabeth A. Clutterbuck, Thushan de Silva, David Eyre, Sheila Lumley, Amy Flaxman, James Grist, Carl-Philipp Hackstein, Rachel Halkerston, Adam C. Harding, Jennifer Hill, Tim James, Cecilia Jay, Sile A. Johnson, Barbara Kronsteiner, Yolanda Lie, Aline Linder, Stephanie Longet, Spyridoula Marinou, Philippa C. Matthews, Jack Mellors, Christos Petropoulos, Patpong Rongkard, Cynthia Sedik, Laura Silva-Reyes, Holly Smith, Lisa Stockdale, Stephen Taylor, Stephen Thomas, Timothy Tipoe, Lance Turtle, Vinicius Adriano Vieira, Terri Wrin, Andrew J. Pollard, Teresa Lambe, Chris P. Conlon, Katie Jeffery, Simon Travis, Philip Goulder, John Frater, Alex J. Mentzer, Lizzie Stafford, Miles W. Carroll, William S. James, Paul Klenerman, Eleanor Barnes, Christina Dold, Susanna J. Dunachie
Summary: The trajectories of acquired immunity to SARS-CoV-2 infection vary among individuals, with some immune responses waning over time while others remain stable. A subgroup of participants with higher antibody and T cell responses shows a robust trajectory for longer term immunity, particularly against the infecting strain and several variants. These findings have implications for the understanding of immune protection against novel variants.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Kalisvar Marimuthu, Indumathi Venkatachalam, Vanessa Koh, Stephan Harbarth, Eli Perencevich, Benjamin Pei Zhi Cherng, Raymond Kok Choon Fong, Surinder Kaur Pada, Say Tat Ooi, Nares Smitasin, Koh Cheng Thoon, Paul Anantharajah Tambyah, Li Yang Hsu, Tse Hsien Koh, Partha Pratim De, Thean Yen Tan, Douglas Chan, Rama Narayana Deepak, Nancy Wen Sim Tee, Andrea Kwa, Yiying Cai, Yik-Ying Teo, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, Weizhen Xu, Wei Xin Khong, David Henderson, Nicole Stoesser, David W. Eyre, Derrick Crook, Michelle Ang, Raymond Tzer Pin Lin, Angela Chow, Alex R. Cook, Jeanette Teo, Oon Tek Ng
Summary: Carbapenemase-producing Enterobacterales cause healthcare-associated infections, but modes of transmission are not well understood. This study finds evidence of transmission without direct patient contact, suggesting the presence of undetected environmental reservoirs, as well as plasmid-mediated transmission accounting for 50% of dissemination. The traditional infection control practices based on detecting carriers may not effectively address plasmid-mediated transmission at the population level.
NATURE COMMUNICATIONS
(2022)
Article
Medicine, Research & Experimental
Anna L. McNaughton, Robert S. Paton, Matthew Edmans, Jonathan Youngs, Judith Wellens, Prabhjeet Phalora, Alex Fyfe, Sandra Belij-Rammerstorfer, Jai S. Bolton, Jonathan Ball, George W. Carnell, Wanwisa Dejnirattisai, Christina Dold, David W. Eyre, Philip Hopkins, Alison Howarth, Kreepa Kooblall, Hannah Klim, Susannah Leaver, Lian Ni Lee, Cesar Lopez-Camacho, Sheila F. Lumley, Derek C. Macallan, Alexander J. Mentzer, Nicholas M. Provine, Jeremy Ratcliff, Jose Slon-Compos, Donal Skelly, Lucas Stolle, Piyada Supasa, Nigel Temperton, Chris Walker, Beibei Wang, Duncan Wyncoll, Peter Simmonds, Teresa Lambe, John Kenneth Baillie, Malcolm G. Semple, Peter J. M. Openshaw, Uri Obolski, Marc Turner, Miles Carroll, Juthathip Mongkolsapaya, Gavin Screaton, Stephen H. Kennedy, Lisa Jarvis, Eleanor Barnes, Susanna Dunachie, Jose Lourenco, Philippa C. Matthews, Tihana Bicanic, Paul Klenerman, Sunetra Gupta, Craig P. Thompson
Summary: The immune response to the SARS-CoV-2 virus in fatal COVID-19 cases is enriched for antibodies that target epitopes shared with other endemic coronaviruses, rather than the more protective regions of the virus. This response is correlated with the magnitude of antibody responses to the spike protein of both SARS-CoV-2 and other beta-coronaviruses in individuals admitted to the ICU with fatal outcomes. However, there is no significant difference in antibody responses to the less cross-reactive SARS-CoV-2 nucleocapsid between fatal and nonfatal cases.
Article
Immunology
Karina Doris Vihta, Koen B. Pouwels, Tim Ea Peto, Emma Pritchard, Thomas House, Ruth Studley, Emma Rourke, Duncan Cook, Ian Diamond, Derrick Crook, David A. Clifton, Philippa C. Matthews, Nicole Stoesser, David W. Eyre, Ann Sarah Walkerand
Summary: A UK community study found that loss of taste/smell was less common in Omicron BA.1/BA.2 infections compared to Delta severe acute respiratory syndrome coronavirus 2 infections. There were smaller declines in reported shortness of breath, myalgia, and fatigue/weakness, but increases in sore throat, challenging symptom-based testing algorithms.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Maria T. Tsakok, Robert A. Watson, ShyamalJ. Saujani, Mark Kong, Cheng Xie, Heiko Peschl, Louise Wing, Fiona K. MacLeod, Brian Shine, Nicholas P. Talbot, Rachel E. Benamore, David W. Eyre, Fergus Gleeson
Summary: This study compared the chest CT radiologic findings, biochemical parameters, clinical severity, and hospital outcomes between the SARS-CoV-2 Omicron variant and the Delta variant. The results showed that the Omicron variant demonstrated fewer and less severe changes on chest CT images compared to the Delta variant. Patients with Omicron infection had improved hospital outcomes and less severe disease compared to patients with Delta infection.
Article
Computer Science, Information Systems
Anshul Thakur, Jacob Armstrong, Alexey Youssef, David Eyre, David A. Clifton
Summary: Healthcare is a dynamic field, and clinical AI models often become ineffective due to the evolving demographics, diseases, and therapeutics. Incremental learning is an effective method to adapt these models to distribution shifts, but it can be unreliable as any adverse modification can render the model unsuitable. This paper introduces self-aware SGD, an incremental deep learning algorithm that utilizes a contextual bandit-like sanity check to ensure reliable modifications to a model.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(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
Health Care Sciences & Services
Jenny Yang, Andrew A. S. Soltan, David W. Eyre, Yang Yang, David A. Clifton
Summary: Machine learning is being increasingly used in healthcare, but concerns arise over biases and disparities. This study presents an adversarial training framework to mitigate biases in healthcare data. The framework is applied to rapidly predict COVID-19 and reduce site-specific and demographic biases. The results show improved fairness and clinically-effective screening performances.
NPJ DIGITAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Ben S. Cooper, Stephanie Evans, Yalda Jafari, Thi Mui Pham, Yin Mo, Cherry Lim, Mark G. Pritchard, Diane Pople, Victoria Hall, James Stimson, David W. Eyre, Jonathan M. Read, Christl A. Donnelly, Peter Horby, Conall Watson, Sebastian Funk, Julie V. Robotham, Gwenan M. Knight
Summary: This study uses data from acute hospitals in England to quantify hospital-based transmission of SARS-CoV-2, evaluate the pathways of spread and factors associated with increased transmission risk, and explore the wider consequences. The study estimates that between June 2020 and March 2021, 95,000 to 167,000 inpatients acquired SARS-CoV-2 in hospitals, accounting for 1% to 2% of all hospital admissions during this period.
Article
Computer Science, Artificial Intelligence
Jenny Yang, Andrew A. S. Soltan, David W. Eyre, David A. Clifton
Summary: This study proposes a reinforcement learning-based method to mitigate algorithmic bias in healthcare applications, specifically in COVID-19 screening and patient discharge prediction. The model demonstrates clinically effective screening performance while improving outcome fairness compared to current benchmarks and state-of-the-art methods.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Health Care Sciences & Services
Gisela Robles Aguilar, Lucien R. Swetschinski, Nicole Davis Weaver, Kevin S. Ikuta, Tomislav Mestrovic, Authia P. Gray, Erin Chung, Eve E. Wool, Chieh Han, Anna Gershberg Hayoon, Daniel T. Araki, Ashkan Abdollahi, Ahmed Abu-Zaid, Mohammad Adnan, Ramesh Agarwal, Javad Aminian Dehkordi, Aleksandr Y. Aravkin, Demelash Areda, Ahmed Y. Azzam, Eitan N. Berezin, Akshaya Srikanth Bhagavathula, Zulfiqar A. Bhutta, Soumitra S. Bhuyan, Annie J. Browne, Carlos A. Castaneda-Orjuela, Eeshwar K. Chandrasekar, Patrick R. Ching, Xiao-chen Dai, Gary L. Darmstadt, Fernando Pio De la Hoz, Nancy Diao, Daniel Diaz, Wendel Mombaque dos Santos, David Eyre, Coralith Garcia, Georgina Haines-Woodhouse, Mohammed Bheser Hassen, Nathaniel J. Henry, Susan Hopkins, Md Mahbub Hossain, Kenneth Chukwuemeka Iregbu, Chidozie C. D. Iwu, Jan Adriaan Jacobs, Mark M. Janko, Ronald Jones, Ibraheem M. Karaye, Ibrahim A. Khalil, Imteyaz A. Khan, Taimoor Khan, Jagdish Khubchandani, Suwimon Khusuwan, Adnan Kisa, Giscard Wilfried Koyaweda, Fiorella Krapp, Emmanuelle A. P. Kumaran, Hmwe Hmwe Kyu, Stephen S. Lim, Xuefeng Liu, Stephen Luby, Sandeep B. Maharaj, Christopher Maronga, Miquel Martorell, Jurgen May, Barney McManigal, Ali H. Mokdad, Catrin E. Moore, Ebrahim Mostafavi, Efren Murillo-Zamora, Marisa Marcia Mussi-Pinhata, Ruchi Nanavati, Hasan Nassereldine, Zuhair S. Natto, Farah Naz Qamar, Virginia Nunez-Samudio, Theresa J. Ochoa, Tolulope R. Ojo-Akosile, Andrew T. Olagunju, Antonio Olivas-Martinez, Edgar Ortiz-Brizuela, Pradthana Ounchanum, Jose L. Paredes, Venkata Suresh Patthipati, Shrikant Pawar, Marcos Pereira, Andrew Pollard, Alfredo Ponce-De-Leon, Elton Junio Sady Prates, Ibrahim Qattea, Luis Felipe Reyes, Emmanuel Roilides, Victor Daniel Rosenthal, Kristina E. Rudd, Weerawut Sangchan, Samroeng Seekaew, Allen Seylani, Niloufar Shababi, Sunder Sham, Jose Sifuentes-Osornio, Harpreet Singh, Andy Stergachis, Nidanuch Tasak, Nathan Y. Tat, Areerat Thaiprakong, Pascual R. Valdez, Dereje Y. Yada, Ismaeel Yunusa, Mikhail Sergeevich Zastrozhin, Simon I. Hay, Christiane Dolecek, Benn Sartorius, Christopher J. L. Murray, Mohsen Naghavi
Summary: Antimicrobial resistance (AMR) poses a substantial health threat in the Americas, and specific policy interventions tailored to each country's needs are crucial. Multisectoral and joint cooperative efforts among countries will be key to tackling AMR in the region.
LANCET REGIONAL HEALTH-AMERICAS
(2023)