Review
Food Science & Technology
Richard Harding-Crooks, Darren Smith, Seamus Fanning, Edward M. Fox
Summary: Antimicrobial agents are essential for patient care in modern healthcare systems. However, the emergence and spread of antimicrobial resistance mechanisms are undermining their effectiveness. The proliferation of carbapenem resistance (CR) poses a significant threat to public health, especially through the transmission of carbapenemase-producing Enterobacteriaceae (CPE) infections. This review explores the transmission of CPE through food chains and contaminated foods, and discusses the potential for further dissemination of carbapenemase genes in microbial communities.
COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY
(2023)
Article
Infectious Diseases
Chendi Zhu, Carmen Li, Christopher K. C. Lai, Rita Ng, Ka Yee Chau, Kam Tak Wong, Norman W. S. Lo, Nilakshi Barua, Ying Yang, Veranja Liyanapathirana, Mamie Hui, Raymond W. Lai, Kitty S. C. Fung, Dominic N. Tsang, I. P. Margaret
Summary: This study describes the molecular epidemiology of carbapenemase-producing Enterobacteriaceae (CPE) in patients from Hong Kong hospitals, with increasing isolation rates and dominance of bla(NDM) and bla(IMP) genes. Enhanced containment strategies are required to mitigate the rising trend of CPE in healthcare settings.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2021)
Article
Immunology
Samuel Lipworth, Karina-Doris Vihta, Kevin K. Chau, James Kavanagh, Timothy Davies, Sophie George, Leanne Barker, Ali Vaughan, Monique Andersson, Katie Jeffery, Sarah Oakley, Marcus Morgan, Timothy E. A. Peto, Derrick W. Crook, A. Sarah Walker, Nicole Stoesser
Summary: The study conducted population-level genomic surveillance of bloodstream E. coli and Klebsiella pneumoniae isolates in Oxfordshire, UK, from 2008 to 2018. The most common O-antigens for both organisms were found to impact multidrug resistance and extended-spectrum beta-lactamase resistance in bloodstream infections.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Microbiology
Melese Hailu Legese, Daniel Asrat, Adane Mihret, Badrul Hasan, Amaha Mekasha, Abraham Aseffa, Gote Swedberg
Summary: This multicenter study conducted in Ethiopia focused on the global health threat of sepsis caused by carbapenemase-producing and colistin-resistant Enterobacteriaceae. The study used blood culture and genome sequencing to identify and analyze the isolates, detecting multiple resistance genes and variants. The spread of carbapenemase-producing Enterobacteriaceae in all hospitals is a worrying concern.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Infectious Diseases
Cecile Emeraud, Aba Mahamat, Agnes B. Jousset, Sandrine Bernabeu, Tania Goncalves, Camille Pommier, Delphine Girlich, Aurelien Birer, Christophe Rodriguez, Jean-Michel Pawlotsky, Thierry Naas, Remy A. Bonnin, Laurent Dorte
Summary: Since 2021, the rapid spread of highly resistant NDM-14 producing Klebsiella pneumoniae has been identified in hospitals in France. This strain, primarily imported from Morocco, is highly resistant to most antimicrobials and belongs to a single clone. However, it remains susceptible to colistin, cefiderocol, and the combination of aztreonam/avibactam.
Article
Immunology
Sandra Sanchez-Urtaza, Alain Ocampo-Sosa, Ainhoa Molins-Bengoetxea, Mohammed A. A. El-Kholy, Marta Hernandez, David Abad, Sherine M. M. Shawky, Itziar Alkorta, Lucia Gallego
Summary: This study investigated the genetic characteristics and antimicrobial susceptibility profile of multidrug resistant Acinetobacter baumannii clinical isolates obtained from hospitals in Alexandria, Egypt. The results showed resistance to multiple antibiotics and the presence of various antibiotic resistance genes and virulence factors. The study highlights the importance of investigating molecular epidemiology to control the spread of these multidrug resistant isolates.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Immunology
Tom J. B. de Man, Anna Q. Yaffee, Wenming Zhu, Dhwani Batra, Efe Alyanak, Lori A. Rowe, Gillian McAllister, Heather Moulton-Meissner, Sandra Boyd, Andrea Flinchum, Rachel B. Slayton, Steven Hancock, Maroya Spalding Walters, Alison Laufer Halpin, James Kamile Rasheed, Judith Noble-Wang, Alexander J. Kallen, Brandi M. Limbago
Summary: This investigation identified the largest known outbreak of VIM-producing CRE in the United States, showcasing evidence of in-hospital plasmid transmission and environmental contamination.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Microbiology
Javier E. Canada-Garcia, Natalin Grippo, Eva Ramirez de Arellano, Veronica Bautista, Noelia Lara, Ana Maria Navarro, Teresa Cabezas, Nora Mariela Martinez-Ramirez, Silvia Garcia-Cobos, Jorge Calvo, Emilia Cercenado, Belen Aracil, Maria Perez-Vazquez, Jesus Oteo-Iglesias
Summary: This study analyzed the genomic and phenotypic characteristics of IMP-producing Enterobacterales (IMP-Ent) isolates circulating in Spain. The most frequently detected strains were IMP-8-producing Klebsiella pneumoniae (IMP-Kpn) and IMP-22-producing Enterobacter roggenkampii. However, some IMP-producing strains showed false negative results in EDTA or dipicolinic acid inhibition tests.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Viivi Heljanko, Venla Johansson, Kati Raeisaenen, Veli-Jukka Anttila, Outi Lyytikaeinen, Jari Jalava, Irma Weijo, Jaana-Marija Lehtinen, Kirsi-Maarit Lehto, Anssi Lipponen, Sami Oikarinen, Tarja Pitkanen, Annamari Heikinheimo
Summary: Multi-drug resistance is emerging in Citrobacter freundii in Finland, and this study found that wastewater surveillance could detect CP C. freundii strains causing infections in humans. CP C. freundii isolates were detected in the hospital environment and untreated municipal wastewater, but not in hospital wastewater. Genomic comparison revealed three clusters of isolates from different sources, suggesting the hospital environment as a source of transmission. The study emphasized the persistence of CP C. freundii throughout the sewerage system and the potential of WWS for detection.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Immunology
Tatum D. Mortimer, Preeti Pathela, Addie Crawley, Jennifer L. Rakeman, Ying Lin, Simon R. Harris, Susan Blank, Julia A. Schillinger, Yonatan H. Grad
Summary: The study revealed that the phylogeny of Neisseria gonorrhoeae in New York City reflected global diversity, with clustering by patient sexual behavior and race/ethnicity. Differences in minimum inhibitory concentrations of antibiotics were found between different demographic groups, such as men who have sex with men and heterosexuals, as well as between white and black heterosexuals.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Public, Environmental & Occupational Health
Adriana Jimenez, Kristopher Fennie, L. Silvia Munoz-Price, Boubakari Ibrahimou, Vukosava Pekovic, Lilian M. Abbo, Octavio Martinez, Gemma Rosello, Kathleen Sposato, Yohei Doi, Mary Jo Trepka
Summary: The study found that patients with immunocompromised, mechanical ventilation exposure, or exposure to carbapenems have a higher risk of prolonged CPE carriage. Patients with CPE isolated from multiple body sites had a higher probability of clearing their CPE-carrier status. Infection prevention programs should consider these factors to prevent horizontal transmission and outbreaks.
AMERICAN JOURNAL OF INFECTION CONTROL
(2021)
Review
Infectious Diseases
Mihret Tilahun, Yeshimebet Kassa, Alemu Gedefie, Melaku Ashagire
Summary: Infections due to multidrug-resistant Enterobacteriaceae have become a major global public health issue, with transmission facilitated by inappropriate antimicrobial use and increased global connectivity. Carbapenems, the current medications of choice, are facing increasing resistance globally, necessitating the search for alternative treatment options. Ceftazidime-avibactam is currently the most common treatment option, with other novel drugs under trial for different populations. Treatment should be tailored to patient susceptibility, infection type, and personal characteristics.
INFECTION AND DRUG RESISTANCE
(2021)
Article
Chemistry, Analytical
Giulia Santopolo, Estrella Rojo-Molinero, Antonio Clemente, Marcio Borges, Antonio Oliver, Roberto de la Rica
Summary: The diagnostic kit introduced in this context enables rapid bedside detection of carbapenemase-producing pathogens through colored tests generated by gold nanoparticles. It allows for quick and accurate detection of infections in urine and sputum samples within a few hours, facilitating faster customization of antimicrobial treatments.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Microbiology
Kayzad Nilgiriwala, Marie-Sylvianne Rabodoarivelo, Michael B. Hall, Grishma Patel, Ayan Mandal, Shefali Mishra, Fanantenana Randria Andrianomanana, Kate Dingle, Gillian Rodger, Sophie George, Derrick W. Crook, Sarah Hoosdally, Nerges Mistry, Niaina Rakotosamimanana, Zamin Iqbal, Simon Grandjean Lapierre, Timothy M. Walker
Summary: Universal access to drug susceptibility testing is recommended for newly diagnosed tuberculosis patients. Improved protocols for direct-from-sample sequencing of Mycobacterium tuberculosis are needed to accelerate drug susceptibility testing and molecular typing. Analysis of sputum samples using Illumina and MinION technologies showed variability in sequencing performance based on smear positivity level.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Infectious Diseases
Min Zhang, Jia Li, Yuemei Lu, Weiyuan Wu, Jinsong Wu, Yanji Xu, Yuxin Zhong, Shiyi Liu, Chuchu Lin, Shuye Xu, Dandan Chen, Xuefeng Gao, Yutian Luo, Huaisheng Chen, Xueyan Liu, Wei Huang
Summary: This study investigated the characteristics of ST11 subclones of clinical Klebsiella pneumoniae in China and found different patterns of prevalence and genetic relationships among the subclones, highlighting the importance of highly discriminatory genotyping techniques such as cgMLST scheme.
INFECTION AND DRUG RESISTANCE
(2021)
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
Infectious Diseases
Dongxin Liu, Fei Huang, Guoliang Zhang, Wencong He, Xichao Ou, Ping He, Bing Zhao, Baoli Zhu, Fei Liu, Zhiyuan Li, Chunfa Liu, Hui Xia, Shengfen Wang, Yang Zhou, Timothy M. Walker, Lei Liu, Derrick W. Crook, Yanlin Zhao
Summary: The study evaluated the accuracy of whole-genome sequencing (WGS) in predicting drug resistance in tuberculosis (TB) and its potential use in drug-resistance surveillance. The results showed that WGS can accurately predict susceptibility to isoniazid, rifampin, ethambutol, and six second-line drugs. Specific mutations were found to confer high or low-level resistance.
CLINICAL MICROBIOLOGY AND INFECTION
(2022)
Article
Biochemistry & Molecular Biology
Siyuan Feng, Zhuoxing Wu, Wanfei Liang, Xin Zhang, Xiujuan Cai, Jiachen Li, Lujie Liang, Daixi Lin, Nicole Stoesser, Yohei Doi, Lan-Lan Zhong, Yan Liu, Yong Xia, Min Dai, Liyan Zhang, Xiaoshu Chen, Jian-Rong Yang, Guo-Bao Tian
Summary: The study predicts the evolutionary trajectories of antibiotic resistance genes using a combination of laboratory approaches and deep learning models, providing valuable insights for designing sustainable treatment strategies.
MOLECULAR BIOLOGY AND EVOLUTION
(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
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)
Article
Oncology
Eleni Domzaridou, Tjeerd Van Staa, Andrew G. Renehan, Natalie Cook, William Welfare, Darren M. Ashcroft, Victoria Palin
Summary: This study examines the association between antibiotic treatment and long-term mortality in cancer patients, finding that antibiotic use shortly before cancer diagnosis may reduce the effectiveness of chemotherapy and immunotherapy.