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Articles by Stephen Baker
Identification and genetic characterization of megabase-scale plasmids of Enterobacteriaceae
Abstract Humans and animals are ubiquitously colonized by Enterobacteriaceae, including both commensals and clinically significant pathogens. Here, we report 21 complete Enterobacteriaceae megaplasmid genomes of up to 1.58 Mbp in length spanning two major clades that are highly divergent from previously described plasmids. Of these, three were reconstructed from isolates of Escherichia coli and Shigella flexneri; others were potentially hosted by species of Citrobacter and Enterobacter.
Multifunctional antibody responses from a primate Shigella outbreak inform vaccine design
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Abstract Supplementary Materials REFERENCES AND NOTES Information & Authors Metrics & Citations Check Access References Figures Tables Media Share This article has 0 eLetter . Abstract There is currently no approved vaccine for Shigella spp., a leading cause of diarrhea with increasing rates of antimicrobial resistance. Shigella vaccine development is complicated in part by an incomplete understanding of the structural and molecular determinants of immunity.
By Weixin Xie, Jian Li, Yannick Fotio, Robert Gallant, Paul Savarino, Morgan S. A. Gilman, Ti Lu, Jennifer Hayes, Mark A. Ochoa, Zackary K. Dietz, Eric Peterson, Timothy Scott, Faye A. Hartmann, Stephen Baker, Robert Kaminski, Devin Sok, Andrew C. Kruse, Wendy L. Picking, Saverio Capuano, Hayden R. Schmidt, Sophia Pulido, Nicholas L. Xerri, Torrey Williams
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Science Magazine
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Determining intracellular and extracellular activities of azithromycin against azithromycin-resistant Salmonella Typhi and their association with clinical treatment responses
Keywords Typhoid fever Salmonella Typhi Azithromycin resistant THP-1 macrophages Azithromycin Evidence before this study “We searched PubMed and Web of Science using the terms: (“Typhoid fever” OR “enteric fever” OR “Salmonella Typhi” OR ″S.
Worse Function and Symptoms Among the Most Rural Patients With Advanced Cancer: A Cross-Sectional Analysis
1 Introduction Physical function and quality of life assessment in patients with advanced cancer presents unique challenges. Improvements in cancer survival rates have been documented [1]. However, patients with cancer and survivors frequently experience deleterious sequelae resulting from treatment including impairments in sleep, cognition, quality of life, and physical systems (cardiovascular, pulmonary, neurologic, musculoskeletal) [2].
My Own Normal Reviews
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The characterization of Klebsiella pneumoniae associated with neonatal sepsis in low- and middle-income countries to inform vaccine design - Communications Biology
Abstract Klebsiella pneumoniae is the leading cause of neonatal sepsis, strongly associated to antimicrobial resistance, with no vaccine available. K-antigens (KAg) have been identified as potential targets, but their diversity makes vaccine development challenging. Alternatively, the use of subcapsular O-antigens (OAg) raises questions about antibodies accessibility.
Genomic census of invasive nontyphoidal Salmonella infections reveals global and local human-to-human transmission - Nature Medicine
Abstract Extraintestinal infections caused by Enterobacteriaceae represent a global concern, further exacerbated by the growing prevalence of antimicrobial resistance (AMR). Among these, invasive nontyphoidal Salmonella (iNTS) infections have become increasingly challenging to manage, and their global spread remains poorly understood. Here we compiled 1,115 patient records and generated a comprehensive genomic dataset on iNTS.
Exploiting human immune repertoire transgenic mice for protective monoclonal antibodies against antimicrobial resistant Acinetobacter baumannii - Nature Communications
Abstract The use of monoclonal antibodies for the control of drug resistant nosocomial bacteria may alleviate a reliance on broad spectrum antimicrobials for treatment of infection. We identify monoclonal antibodies that may prevent infection caused by carbapenem resistant Acinetobacter baumannii.
Characterization of a Salmonella enterica serovar Typhimurium lineage with rough colony morphology and multidrug resistance - Nature Communications
Abstract Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of salmonellosis, and the emergence of multidrug-resistant pathovariants has become a growing concern. Here, we investigate a distinct rough colony variant exhibiting a strong biofilm-forming ability isolated in China. Whole-genome sequencing on 2,212 Chinese isolates and 1,739 publicly available genomes reveals the population structure and evolutionary history of the rough colony variants.
Genomic insights unveil the plasmid transfer mechanism and epidemiology of hypervirulent Klebsiella pneumoniae in Vietnam - Nature Communications Original
Abstract Hypervirulent Klebsiella pneumoniae (hvKp) is a significant cause of severe invasive infections in Vietnam, yet data on its epidemiology, population structure and dynamics are scarce. We screened hvKp isolates from patients with bloodstream infections (BSIs) at a tertiary infectious diseases hospital in Vietnam and healthy individuals, followed by whole genome sequencing and plasmid analysis.
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Purpose. Antimicrobial-resistant bacterial infections in low- and middle-income countries (LMICs) are a well-established global health issue. We aimed to assess the prevalence of and epidemiological factors associated with the carriage of ciprofloxacin- and ceftriaxone-resistant Escherichia coli and associated resistance genes in a cohort of 498 healthy children residing in urban Vietnam. Methodology.
Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 1,4,[5],12:i:- ST34 in Southeast Asia | Communications Biology
Abstract Salmonella enterica serotype 1,4,[5],12:i:- (Typhimurium monophasic variant) of sequence type (ST) 34 has emerged as the predominant pandemic genotype in recent decades. Despite increasing reports of resistance to antimicrobials in Southeast Asia, Salmonella ST34 population structure and evolution remained understudied in the region.
Plasma from patients with pulmonary embolism show aggregates that reduce after anticoagulation - Communications Medicine
Abstract Background Microclots, a term also used for amyloid fibrin(ogen) particles and henceforth named aggregates, have recently been reported in the plasma of patients with COVID-19 and long COVID. These aggregates have been implicated in the thrombotic complications of these diseases. Methods Plasma samples from 35 patients with acute pulmonary embolism were collected and analysed by laser scanning confocal microscopy and scanning electron microscopy before and after clotting.
FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2 - Nature
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Author notes These authors jointly supervised this work: Ludovic Vallier; Fotios Sampaziotis Authors and Affiliations Wellcome – MRC Cambridge Stem Cell Institute, Cambridge, UK Teresa Brevini, Stephanie Brown, Scott Dillon, Sagar S. Varankar, Mahnaz Darvish-Damavandi, James A. Heslop, Davide Rossetti, Olivia C. Tysoe, Vasileios Galanakis, Marta Vila-Gonzalez, Johannes Bargehr, Sanjay Sinha, Darran Clements, Peter Humphreys, Simon J. A.
By Teresa Brevini, Mailis Maes, Lu Wang, Marnie L. Brown, Jo Tutchener Sharp, Megan Neary, Lee M. Tatham, James Stewart, Mahnaz Darvish-Damavandi, Thomas Williams, Johannes Bargehr, Sanjay Sinha, Kourosh Saeb-Parsy, Axel Wester, Espen Melum, Chloe Bramwell, Eleanor J. Barnes, Andrew Moon, Ravindra K Gupta, Stephen Baker, Anthony Davenport, Vassilis G. Gorgoulis, Joo-Hyeon Lee, Nicholas J Matheson, Michael Trauner, Andrew Fisher, Christopher Watson, Andrew Owen, Ludovic Vallier
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Nature
Verified
Sarasota Opera hosts national finals of vocal competition
SARASOTA — Sarasota Opera will host the finals for Schmidt Vocal Arts (SVA) national Schmidt Vocal Competition at Sarasota Opera House, June 3-5. The top three winners from each of 13 regional competitions will compete for the first national prize in the competition’s 25-year history. Seven Floridians have qualified after competing in four different regional locations.
Single-cell multi-omics analysis of the immune response in COVID-19
Abstract Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19.
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
Abstract Transmission of SARS-CoV-2 is uncontrolled in many parts of the world; control is compounded in some areas by the higher transmission potential of the B.1.1.7 variant1, which has now been reported in 94 countries. It is unclear whether the response of the virus to vaccines against SARS-CoV-2 on the basis of the prototypic strain will be affected by the mutations found in B.1.1.7. Here we assess the immune responses of individuals after vaccination with the mRNA-based vaccine BNT162b22.
The identification of novel immunogenic antigens as potential Shigella vaccine components
Ruklanthi de Alwis1,2, Li Liang3, Omid Taghavian3, Emma Werner4, Hao Chung The5, 5, Vu Thuy Duong5, D. Huw Davies3, Philip L. Felgner3 & Stephen Baker ORCID: orcid.org/0000-0003-1308-57556 Genome Medicine volume 13, Article number: 8 (2021) Cite this article Abstract Background Shigella is a major diarrheal pathogen for which there is presently no vaccine. Whole genome sequencing provides the ability to predict and derive novel antigens for use as vaccines.
A novel method for measuring phenotypic colistin resistance in Escherichia coli populations from chicken flocks
Environmental Microbiology Nhung Thi Nguyen, Nguyen Thi Phuong Yen, Nguyen Van Ky Thien, Nguyen Van Cuong, Bach Tuan Kiet, James Campbell, Guy Thwaites, Stephen Baker, Ronald B. Geskus, Juan Carrique-Mas DOI: 10.1128/AEM.02597-20 ABSTRACT Colistin is extensively used in animal production in many low- and middle-income countries. There is a need to develop methodologies to benchmark and monitor changes in resistance among mixed commensal bacterial populations in farms.
Protecting intubated patients from the threat of antimicrobial resistant infections with monoclonal antibodies
Recognition that immunisation might affect antimicrobial resistance is increasing.
Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission
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Abstract Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3-week period (April 2020), 1,032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab.
By Lucy Rivett, Nick Jones, Sally Forrest, Jamie Young Verified, William Hamilton Verified, Mark E. Ferris, Luke Meredith, Martin D. Curran, Afzal Chaudhry, Ashley Shaw, John Bradley, Gordon Dougan, Paul J. Lehner, Nicholas J Matheson, Ian Goodfellow, Stephen Baker, Michael P. Weekes, Sushmita Sridhar, Dominic Sparkes, Matthew Routledge, Joana Pereira-Dias, M Estee Torok, Stewart Fuller, Richard J Samworth, Giles Wright
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eLife
Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia
Kelly L. Wyres1, To N. T. Nguyen2, Margaret M. C. Lam1, Louise M. Judd1, Nguyen van Vinh Chau3, David A. B. Dance4,5,6, Margaret Ip7, Abhilasha Karkey5,8, Clare L. Ling5,9, Thyl Miliya10, Paul N. Newton4,5,6, Nguyen Phu Huong Lan3, 4, Paul Turner5,10, Balaji Veeraraghavan11, Phat Voong Vinh2, Manivanh Vongsouvath4, Nicholas R. Thomson6,12, Stephen Baker ORCID: orcid.org/0000-0003-1308-575513 & Kathryn E.
Typhoid conjugate vaccines: a new tool in the fight against antimicrobial resistance
Summary Typhoid fever is an acute systemic infectious disease responsible for an estimated 12–20 million illnesses and over 150 000 deaths annually. In March, 2018, a new recommendation was issued by WHO for the programmatic use of typhoid conjugate vaccines in endemic countries. Health economic analyses of typhoid vaccines have informed funding decisions and national policies regarding vaccine rollout.
Aylesbury Vale: How property is giving us financial security
It’s no secret local authority budgets are being squeezed. Councils the length and breadth of Britain have experienced the effects that squeeze can have on service delivery, and housing is by no means immune. In fact, those of us working in this area are faced with a unique set of challenges – how do we balance shrinking books while meeting the ever-growing demand for homes and regenerated public spaces?
Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens
When antimicrobial drugs were introduced into clinical usage in the mid-20th century, they had an astonishing impact on human health. Infectious bacteria that had threatened our survival were now at the mercy of a chemical arsenal. Previously fatal infections, from whooping cough and scarlet fever to tuberculosis and syphilis, were no longer considered a threat. Antimicrobials substantially reduced the risks associated with child birth, injuries, and invasive medical procedures.
Idea Exchange: How we are creating East Suffolk Council
Last month, formal approval was granted for the voluntary merger of Suffolk Coastal and Waveney DCs – setting in motion the creation of the country’s largest district council.
Tips for successful Rotary project
To celebrate its 100th year, The Rotary Foundation is recognizing 20 global grants that are sustainable, align with one of Rotary’s areas of focus and was designed in cooperation with the community to address a real need. The Rotarians who helped bring these projects to life share advice. Carolina Barrios, Rotary Club of Cartagena de Indias, Colombia The involvement of the Rotary Community Corps of Leticia, Colombia, was essential.
Stephen Baker: Terror attacks and Grenfell fire show our response to emergencies must keep evolving
Stephen Baker: Terror attacks and Grenfell fire show our response to emergencies must keep evolving 10 July, 2017 By Stephen Baker The recent terrible events in Manchester and London have prompted me to ask whether we need to refine our responses to such incidents.
Commitment, flexibility and new skills vital to commercialisation success
In fact, 94% of local authorities now share some services with another authority and 58% own a trading company. However, commercialisation isn’t a straightforward process; whether it’s developing the right skills, or simply knowing how to broker successful partnerships that make real financial sense, strategies need to be bespoke to individual organisations’ needs.
The Patient Will See You Now: The Future of Medicine Is in Your Hands
If you could sum up The Patient Will See You Now in three words, what would they be? Extremely insightful book! Dr Topol does a great job of illustrating the potential future of patient/doctor relationships. He uses many concrete example of different projects and products that are already making this change happen. Who was your favorite character and why? Have you listened to any of Eric Michael Summerer’s other performances before? How does this one compare?
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