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Gacheri J, Hamilton KA, Munywoki P, Wakahiu S, Kiambi K, Fèvre EM, Oluka MN, Guantai EM, Moodley A, Muloi DM. Antibiotic prescribing practices in community and clinical settings during the COVID-19 pandemic in Nairobi, Kenya. PLOS Glob Public Health 2024; 4:e0003046. [PMID: 38662675 PMCID: PMC11045065 DOI: 10.1371/journal.pgph.0003046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
The COVID-19 pandemic has significantly impacted healthcare systems, including antibiotic use practices. We present data on patterns of antibiotic dispensing and use in community and hospital settings respectively in Nairobi, Kenya during the pandemic. We conducted interviews with 243 pharmacies in Nairobi using a standardised questionnaire from November to December 2021. The data collected included demographic characteristics, antibiotic customers, types of antibiotics sold, and antibiotic prescribing practices. Additionally, we retrospectively reviewed health records for 992 and 738 patients admitted in COVID-19 and general wards at two large inpatient hospitals between April 2020 and May 2021, and January 2019 to October 2021, respectively. Demographic, utilisation of laboratory services, treatment, clinical, and outcome data were collected using a modified Global WHO Point Prevalence Surveys (Global-PPS) tool. Almost all pharmacies (91.4%) served customers suspected of having COVID-19 with a mean weekly number of 15.6 customers. All pharmacies dispensed antibiotics, mainly azithromycin and beta lactams to suspected COVID-19 infected customers. 83.4% of hospitalised COVID-19 patients received at least one antibiotic at some point during their hospitalisation, which was significantly higher than the 53.8% in general ward patients (p<0.001). Similarly, the average number of antibiotics administered to COVID-19 patients was higher than that of patients in the general ward (1.74 vs 0.9). Azithromycin and ceftriaxone were the most commonly used antibiotics in COVID-19 patients compared to ceftriaxone and metronidazole in the general wards. Only 2% of antibiotic prescriptions for COVID-19 patients were supported by microbiological investigations, which was consistent with the proportion of 6.8% among the general ward population. Antibiotics were commonly prescribed to customers and patients suspected of having COVID-19 either in community pharmacies or in hospital, without a prescription or laboratory diagnosis. These findings emphasize the crucial role of antibiotic stewardship, particularly in community pharmacies, in the context of COVID-19.
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Affiliation(s)
- June Gacheri
- International Livestock Research Institute, Nairobi, Kenya
- Department of Pharmacology, Clinical Pharmacy and Pharmacy Practice, University of Nairobi, Nairobi, Kenya
| | - Katie A. Hamilton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | | | - Karen Kiambi
- International Livestock Research Institute, Nairobi, Kenya
| | - Eric M. Fèvre
- International Livestock Research Institute, Nairobi, Kenya
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Margaret N. Oluka
- Department of Pharmacology, Clinical Pharmacy and Pharmacy Practice, University of Nairobi, Nairobi, Kenya
| | - Eric M. Guantai
- Department of Pharmacology, Clinical Pharmacy and Pharmacy Practice, University of Nairobi, Nairobi, Kenya
| | - Arshnee Moodley
- International Livestock Research Institute, Nairobi, Kenya
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Dishon M. Muloi
- International Livestock Research Institute, Nairobi, Kenya
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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2
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Rofael S, Leboreiro Babe C, Davrandi M, Kondratiuk AL, Cleaver L, Ahmed N, Atkinson C, McHugh T, Lowe DM. Antibiotic resistance, bacterial transmission and improved prediction of bacterial infection in patients with antibody deficiency. JAC Antimicrob Resist 2023; 5:dlad135. [PMID: 38098890 PMCID: PMC10720947 DOI: 10.1093/jacamr/dlad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Background Antibody-deficient patients are at high risk of respiratory tract infections. Many therefore receive antibiotic prophylaxis and have access to antibiotics for self-administration in the event of breakthrough infections, which may increase antimicrobial resistance (AMR). Objectives To understand AMR in the respiratory tract of patients with antibody deficiency. Methods Sputum samples were collected from antibody-deficient patients in a cross-sectional and prospective study; bacteriology culture, 16S rRNA profiling and PCR detecting macrolide resistance genes were performed. Bacterial isolates were identified using MALDI-TOF, antimicrobial susceptibility was determined by disc diffusion and WGS of selected isolates was done using Illumina NextSeq with analysis for resistome and potential cross-transmission. Neutrophil elastase was measured by a ProteaseTag immunoassay. Results Three hundred and forty-three bacterial isolates from sputum of 43 patients were tested. Macrolide and tetracycline resistance were common (82% and 35% of isolates). erm(B) and mef(A) were the most frequent determinants of macrolide resistance. WGS revealed viridans streptococci as the source of AMR genes, of which 23% also carried conjugative plasmids linked with AMR genes and other mobile genetic elements. Phylogenetic analysis of Haemophilus influenzae isolates suggested possible transmission between patients attending clinic.In the prospective study, a negative correlation between sputum neutrophil elastase concentration and Shannon entropy α-diversity (Spearman's ρ = -0.306, P = 0.005) and a positive relationship with Berger-Parker dominance index (ρ = 0.502, P < 0.001) were found. Similar relationships were noted for the change in elastase concentration between consecutive samples, increases in elastase associating with reduced α-diversity. Conclusions Measures to limit antibiotic usage and spread of AMR should be implemented in immunodeficiency clinics. Sputum neutrophil elastase may be a useful marker to guide use of antibiotics for respiratory infection.
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Affiliation(s)
- Sylvia Rofael
- Centre for Clinical Microbiology, University College London, Royal Free Campus, Pond Street, London, UK
- Faculty of Pharmacy, University of Alexandria, Alexandria, Egypt
| | - Clara Leboreiro Babe
- Centre for Clinical Microbiology, University College London, Royal Free Campus, Pond Street, London, UK
| | - Mehmet Davrandi
- Centre for Clinical Microbiology, University College London, Royal Free Campus, Pond Street, London, UK
| | - Alexandra L Kondratiuk
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, Pears Building, Rowland Hill Street, London, UK
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, Guy’s Campus, King’s College London, London, UK
| | - Naseem Ahmed
- Centre for Clinical Microbiology, University College London, Royal Free Campus, Pond Street, London, UK
| | - Claire Atkinson
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, Pears Building, Rowland Hill Street, London, UK
- Cancer Biology and Therapy Research Group, Divisionof Human Sciences, School of Applied Sciences, London South Bank University, London, UK
| | - Timothy McHugh
- Centre for Clinical Microbiology, University College London, Royal Free Campus, Pond Street, London, UK
| | - David M Lowe
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, Pears Building, Rowland Hill Street, London, UK
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, Pond Street, London, UK
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3
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Buzas D, Bunzel AH, Staufer O, Milodowski EJ, Edmunds GL, Bufton JC, Vidana Mateo BV, Yadav SKN, Gupta K, Fletcher C, Williamson MK, Harrison A, Borucu U, Capin J, Francis O, Balchin G, Hall S, Vega MV, Durbesson F, Lingappa S, Vincentelli R, Roe J, Wooldridge L, Burt R, Anderson RJL, Mulholland AJ, Bristol UNCOVER Group, Hare J, Bailey M, Davidson AD, Finn A, Morgan D, Mann J, Spatz J, Garzoni F, Schaffitzel C, Berger I. In vitro generated antibodies guide thermostable ADDomer nanoparticle design for nasal vaccination and passive immunization against SARS-CoV-2. Antib Ther 2023; 6:277-297. [PMID: 38075238 PMCID: PMC10702856 DOI: 10.1093/abt/tbad024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 01/10/2024] Open
Abstract
Background Due to COVID-19, pandemic preparedness emerges as a key imperative, necessitating new approaches to accelerate development of reagents against infectious pathogens. Methods Here, we developed an integrated approach combining synthetic, computational and structural methods with in vitro antibody selection and in vivo immunization to design, produce and validate nature-inspired nanoparticle-based reagents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Results Our approach resulted in two innovations: (i) a thermostable nasal vaccine called ADDoCoV, displaying multiple copies of a SARS-CoV-2 receptor binding motif derived epitope and (ii) a multivalent nanoparticle superbinder, called Gigabody, against SARS-CoV-2 including immune-evasive variants of concern (VOCs). In vitro generated neutralizing nanobodies and electron cryo-microscopy established authenticity and accessibility of epitopes displayed by ADDoCoV. Gigabody comprising multimerized nanobodies prevented SARS-CoV-2 virion attachment with picomolar EC50. Vaccinating mice resulted in antibodies cross-reacting with VOCs including Delta and Omicron. Conclusion Our study elucidates Adenovirus-derived dodecamer (ADDomer)-based nanoparticles for use in active and passive immunization and provides a blueprint for crafting reagents to combat respiratory viral infections.
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Affiliation(s)
- Dora Buzas
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Adrian H Bunzel
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Oskar Staufer
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol BS8 1TS, UK
- Leibniz Institute for New Materials, Helmholtz Institute for Pharmaceutical Research and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | | | - Grace L Edmunds
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Joshua C Bufton
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | | | - Kapil Gupta
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- Imophoron Ltd, Science Creates Old Market, Midland Rd, Bristol BS2 0JZ UK
| | | | - Maia K Williamson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | | | - Ufuk Borucu
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Julien Capin
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ore Francis
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Georgia Balchin
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Sophie Hall
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Mirella V Vega
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Fabien Durbesson
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS, Aix-Marseille Université, Marseille, France
| | | | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS, Aix-Marseille Université, Marseille, France
| | - Joe Roe
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Linda Wooldridge
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Rachel Burt
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | | | | | | | - Jonathan Hare
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Mick Bailey
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Andrew D Davidson
- Imophoron Ltd, Science Creates Old Market, Midland Rd, Bristol BS2 0JZ UK
| | - Adam Finn
- Bristol University COVID-19 Emergency Research Group, Bristol BS8 1TH, UK
- Children's Vaccine Centre, Bristol Medical School, Bristol BS2 8EF UK
| | - David Morgan
- Imophoron Ltd, Science Creates Old Market, Midland Rd, Bristol BS2 0JZ UK
| | - Jamie Mann
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Joachim Spatz
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol BS8 1TS, UK
- Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Frederic Garzoni
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- Bristol University COVID-19 Emergency Research Group, Bristol BS8 1TH, UK
| | - Imre Berger
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
- Bristol University COVID-19 Emergency Research Group, Bristol BS8 1TH, UK
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Sandoe JAT, Ahmed F, Arumugam P, Guleri A, Horner C, Howard P, Perry J, Prendergast BD, Schwiebert R, Steeds RP, Watkin R, Wendler O, Chambers JB. Expert consensus recommendations for the provision of infective endocarditis services: updated guidance from the Joint British Societies. Heart 2023; 109:e2. [PMID: 36898706 PMCID: PMC10423555 DOI: 10.1136/heartjnl-2022-321791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Infective endocarditis (IE) remains a difficult condition to diagnose and treat and is an infection of high consequence for patients, causing long hospital stays, life-changing complications and high mortality. A new multidisciplinary, multiprofessional, British Society for Antimicrobial Chemotherapy (BSAC)-ledWorking Party was convened to undertake a focused systematical review of the literature and to update the previous BSAC guidelines relating delivery of services for patients with IE. A scoping exercise identified new questions concerning optimal delivery of care, and the systematic review identified 16 231 papers of which 20 met the inclusion criteria. Recommendations relating to endocarditis teams, infrastructure and support, endocarditis referral processes, patient follow-up and patient information, and governance are made as well as research recommendations. This is a report of a joint Working Party of the BSAC, British Cardiovascular Society, British Heart Valve Society, British Society of Echocardiography, Society of Cardiothoracic Surgeons of Great Britain and Ireland, British Congenital Cardiac Association and British Infection Association.
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Affiliation(s)
- Jonathan A T Sandoe
- Microbiology department, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Fozia Ahmed
- Manchester Heart Centre, Manchester University NHS Foundation Trust, Manchester, UK
- The University of Manchester, Manchester, UK
| | - Parthiban Arumugam
- Manchester Heart Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Achyut Guleri
- Microbiology department, Mid Yorkshire Hospitals NHS Trust, Wakefield, UK
| | - Carolyne Horner
- Formerly British Society of Antimicrobial Chemotherapy, Birmingham, UK
| | - Philip Howard
- NHS England North East & Yorkshire, Leeds, UK
- University of Leeds, Leeds, UK
| | - John Perry
- Microbiology department, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Bernard D Prendergast
- Cardiology department, Guy's and St Thomas' NHS Foundation Trust, London, UK
- Cleveland Clinic, London, UK
| | - Ralph Schwiebert
- Microbiology department, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- School of Medicine, University of Leeds, Leeds, UK
| | - Richard Paul Steeds
- Cardiology department, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Richard Watkin
- Cardiology department, University Hospitals Birmingham NHS Foundation Trust, Sutton Coldfield, UK
| | - Olaf Wendler
- Cardiothoracic Surgery, King's College Hospital, King's Health Partners, London, UK
| | - John B Chambers
- Cardiology department, Guy's and St Thomas' NHS Foundation Trust, London, UK
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5
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Elton L, Abdel Hamid MM, Tembo J, Elbadawi H, Maluzi K, Abdelraheem MH, Cullip T, Kabanda C, Roulston K, Honeyborne I, Thomason MJ, Elhag K, Mohammed A, Adam A, Mulonga K, Sikakena K, Matibula P, Kabaso M, Nakazwe R, Fwoloshi S, Zumla A, McHugh TD. A pandemic within a pandemic? Admission to COVID-19 wards in hospitals is associated with increased prevalence of antimicrobial resistance in two African settings. Ann Clin Microbiol Antimicrob 2023; 22:25. [PMID: 37055793 PMCID: PMC10101537 DOI: 10.1186/s12941-023-00575-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Patients who develop severe illness due to COVID-19 are more likely to be admitted to hospital and acquire bacterial co-infections, therefore the WHO recommends empiric treatment with antibiotics. Few reports have addressed the impact of COVID-19 management on emergence of nosocomial antimicrobial resistance (AMR) in resource constrained settings. This study aimed to ascertain whether being admitted to a COVID-19 ward (with COVID-19 infection) compared to a non-COVID-19 ward (as a COVID-19 negative patient) was associated with a change in the prevalence of bacterial hospital acquired infection (HAI) species or resistance patterns, and whether there were differences in antimicrobial stewardship (AMS) and infection prevention and control (IPC) guidelines between COVID-19 and non-COVID-19 wards. The study was conducted in Sudan and Zambia, two resource constrained settings with differing country-wide responses to COVID-19. METHODS Patients suspected of having hospital acquired infections were recruited from COVID-19 wards and non-COVID-19 wards. Bacteria were isolated from clinical samples using culture and molecular methods and species identified. Phenotypic and genotypic resistance patterns were determined by antibiotic disc diffusion and whole genome sequencing. Infection prevention and control guidelines were analysed for COVID-19 and non-COVID-19 wards to identify potential differences. RESULTS 109 and 66 isolates were collected from Sudan and Zambia respectively. Phenotypic testing revealed significantly more multi-drug resistant isolates on COVID-19 wards in both countries (Sudan p = 0.0087, Zambia p = 0.0154). The total number of patients with hospital acquired infections (both susceptible and resistant) increased significantly on COVID-19 wards in Sudan, but the opposite was observed in Zambia (both p = ≤ 0.0001). Genotypic analysis showed significantly more β-lactam genes per isolate on COVID-19 wards (Sudan p = 0.0192, Zambia p = ≤ 0.0001). CONCLUSIONS Changes in hospital acquired infections and AMR patterns were seen in COVID-19 patients on COVID-19 wards compared to COVID-19 negative patients on non-COVID-19 wards in Sudan and Zambia. These are likely due to a potentially complex combination of causes, including patient factors, but differing emphases on infection prevention and control, and antimicrobial stewardship policies on COVID-19 wards were highlighted.
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Affiliation(s)
- Linzy Elton
- Centre for Clinical Microbiology, University College London, London, UK.
| | | | - John Tembo
- HerpeZ, University Teaching Hospital, Lusaka, Zambia
| | - Hana Elbadawi
- Institute for Endemic Diseases, University of Khartoum, Khartoum, Sudan
- MRC Clinical Trials Unit, University College London, London, UK
| | | | - Mohammed H Abdelraheem
- Institute for Endemic Diseases, University of Khartoum, Khartoum, Sudan
- Sudan Atomic Energy Commission, Nuclear Application in Biological Sciences, Khartoum, Sudan
| | - Teresa Cullip
- Institute for Global Health, University College London, London, UK
| | - Caren Kabanda
- HerpeZ, University Teaching Hospital, Lusaka, Zambia
| | - Kerry Roulston
- Centre for Clinical Microbiology, University College London, London, UK
| | | | - Margaret J Thomason
- Centre for Clinical Microbiology, University College London, London, UK
- MRC Clinical Trials Unit, University College London, London, UK
| | - Kamal Elhag
- Soba University Hospital, University of Khartoum, Khartoum, Sudan
| | | | - Abdelsalam Adam
- Soba University Hospital, University of Khartoum, Khartoum, Sudan
| | | | - Kapatiso Sikakena
- University Teaching Hospitals, Department of Internal Medicine, Infectious Diseases Unit, Lusaka, Zambia
| | - Peter Matibula
- University Teaching Hospitals, Department of Internal Medicine, Infectious Diseases Unit, Lusaka, Zambia
| | - Mwewa Kabaso
- University Teaching Hospitals, Department of Internal Medicine, Infectious Diseases Unit, Lusaka, Zambia
| | - Ruth Nakazwe
- University Teaching Hospitals, Department of Internal Medicine, Infectious Diseases Unit, Lusaka, Zambia
| | - Sombo Fwoloshi
- University Teaching Hospitals, Department of Internal Medicine, Infectious Diseases Unit, Lusaka, Zambia
| | - Alimuddin Zumla
- Centre for Clinical Microbiology, University College London, London, UK
- National Institute for Health and Care Research Biomedical Research Centre, University College London, London, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, University College London, London, UK
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6
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Tamma PD, Aitken SL, Bonomo RA, Mathers AJ, van Duin D, Clancy CJ. Infectious Diseases Society of America 2022 Guidance on the Treatment of Extended-Spectrum β-lactamase Producing Enterobacterales (ESBL-E), Carbapenem-Resistant Enterobacterales (CRE), and Pseudomonas aeruginosa with Difficult-to-Treat Resistance (DTR-P. aeruginosa). Clin Infect Dis 2022; 75:187-212. [PMID: 35439291 PMCID: PMC9890506 DOI: 10.1093/cid/ciac268] [Citation(s) in RCA: 164] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/04/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The Infectious Diseases Society of America (IDSA) is committed to providing up-to-date guidance on the treatment of antimicrobial-resistant infections. The initial guidance document on infections caused by extended-spectrum β-lactamase producing Enterobacterales (ESBL-E), carbapenem-resistant Enterobacterales (CRE), and Pseudomonas aeruginosa with difficult-to-treat resistance (DTR-P. aeruginosa) was published on 17 September 2020. Over the past year, there have been a number of important publications furthering our understanding of the management of ESBL-E, CRE, and DTR-P. aeruginosa infections, prompting a rereview of the literature and this updated guidance document. METHODS A panel of 6 infectious diseases specialists with expertise in managing antimicrobial-resistant infections reviewed, updated, and expanded previously developed questions and recommendations about the treatment of ESBL-E, CRE, and DTR-P. aeruginosa infections. Because of differences in the epidemiology of resistance and availability of specific anti-infectives internationally, this document focuses on the treatment of infections in the United States. RESULTS Preferred and alternative treatment recommendations are provided with accompanying rationales, assuming the causative organism has been identified and antibiotic susceptibility results are known. Approaches to empiric treatment, duration of therapy, and other management considerations are also discussed briefly. Recommendations apply for both adult and pediatric populations. CONCLUSIONS The field of antimicrobial resistance is highly dynamic. Consultation with an infectious diseases specialist is recommended for the treatment of antimicrobial-resistant infections. This document is current as of 24 October 2021. The most current versions of IDSA documents, including dates of publication, are available at www.idsociety.org/practice-guideline/amr-guidance/.
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Affiliation(s)
- Pranita D Tamma
- Correspondence: P. D. Tamma, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA ()
| | - Samuel L Aitken
- Department of Pharmacy, University of Michigan Health, Ann Arbor, Michigan, USA
| | - Robert A Bonomo
- Medical Service and Center for Antimicrobial Resistance and Epidemiology, Louis Stokes Cleveland Veterans Affairs Medical Center, University Hospitals Cleveland Medical Center and Departments of Medicine, Pharmacology, Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Amy J Mathers
- Departments of Medicine and Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - David van Duin
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Cornelius J Clancy
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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7
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Chan HTH, Moesser MA, Walters RK, Malla TR, Twidale RM, John T, Deeks HM, Johnston-Wood T, Mikhailov V, Sessions RB, Dawson W, Salah E, Lukacik P, Strain-Damerell C, Owen CD, Nakajima T, Świderek K, Lodola A, Moliner V, Glowacki DR, Spencer J, Walsh MA, Schofield CJ, Genovese L, Shoemark DK, Mulholland AJ, Duarte F, Morris GM. Discovery of SARS-CoV-2 M pro peptide inhibitors from modelling substrate and ligand binding. Chem Sci 2021; 12:13686-13703. [PMID: 34760153 PMCID: PMC8549791 DOI: 10.1039/d1sc03628a] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/05/2021] [Indexed: 12/22/2022] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target, but little is known about structural aspects of how it binds to its 11 natural cleavage sites. We used biophysical and crystallographic data and an array of biomolecular simulation techniques, including automated docking, molecular dynamics (MD) and interactive MD in virtual reality, QM/MM, and linear-scaling DFT, to investigate the molecular features underlying recognition of the natural Mpro substrates. We extensively analysed the subsite interactions of modelled 11-residue cleavage site peptides, crystallographic ligands, and docked COVID Moonshot-designed covalent inhibitors. Our modelling studies reveal remarkable consistency in the hydrogen bonding patterns of the natural Mpro substrates, particularly on the N-terminal side of the scissile bond. They highlight the critical role of interactions beyond the immediate active site in recognition and catalysis, in particular plasticity at the S2 site. Building on our initial Mpro-substrate models, we used predictive saturation variation scanning (PreSaVS) to design peptides with improved affinity. Non-denaturing mass spectrometry and other biophysical analyses confirm these new and effective 'peptibitors' inhibit Mpro competitively. Our combined results provide new insights and highlight opportunities for the development of Mpro inhibitors as anti-COVID-19 drugs.
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Affiliation(s)
- H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Marc A Moesser
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
| | - Rebecca K Walters
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tika R Malla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Helen M Deeks
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tristan Johnston-Wood
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Victor Mikhailov
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - William Dawson
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Petra Lukacik
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - C David Owen
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Takahito Nakajima
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Katarzyna Świderek
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - Alessio Lodola
- Food and Drug Department, University of Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Vicent Moliner
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - David R Glowacki
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - James Spencer
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Martin A Walsh
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Luigi Genovese
- Univ. Grenoble Alpes, CEA, IRIG-MEM-L_Sim 38000 Grenoble France
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Garrett M Morris
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
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8
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Hameed H, King EFB, Doleckova K, Bartholomew B, Hollinshead J, Mbye H, Ullah I, Walker K, Van Veelen M, Abou-Akkada SS, Nash RJ, Horrocks PD, Price HP. Temperate Zone Plant Natural Products-A Novel Resource for Activity against Tropical Parasitic Diseases. Pharmaceuticals (Basel) 2021; 14:227. [PMID: 33800005 PMCID: PMC7998250 DOI: 10.3390/ph14030227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022] Open
Abstract
The use of plant-derived natural products for the treatment of tropical parasitic diseases often has ethnopharmacological origins. As such, plants grown in temperate regions remain largely untested for novel anti-parasitic activities. We describe here a screen of the PhytoQuest Phytopure library, a novel source comprising over 600 purified compounds from temperate zone plants, against in vitro culture systems for Plasmodium falciparum, Leishmania mexicana, Trypanosoma evansi and T. brucei. Initial screen revealed 6, 65, 15 and 18 compounds, respectively, that decreased each parasite's growth by at least 50% at 1-2 µM concentration. These initial hits were validated in concentration-response assays against the parasite and the human HepG2 cell line, identifying hits with EC50 < 1 μM and a selectivity index of >10. Two sesquiterpene glycosides were identified against P. falciparum, four sterols against L. mexicana, and five compounds of various scaffolds against T. brucei and T. evansi. An L. mexicana resistant line was generated for the sterol 700022, which was found to have cross-resistance to the anti-leishmanial drug miltefosine as well as to the other leishmanicidal sterols. This study highlights the potential of a temperate plant secondary metabolites as a novel source of natural products against tropical parasitic diseases.
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Affiliation(s)
- Hamza Hameed
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
- Department of Chemistry, College of Education for Pure Science, University of Mosul, Mosul, Iraq
| | - Elizabeth F. B. King
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
| | - Katerina Doleckova
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
- Department of Biology, Faculty of Life Sciences, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic
| | | | | | - Haddijatou Mbye
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
- MRC Unit The Gambia at LSHTM, Atlantic Boulevard, Fajara, Banjul PO Box 273, The Gambia
| | - Imran Ullah
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Karen Walker
- School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK;
| | - Maria Van Veelen
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
| | | | - Robert J. Nash
- PhytoQuest Limited, Aberystwyth SY23 3EB, UK; (B.B.); (J.H.); (R.J.N.)
| | - Paul D. Horrocks
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
| | - Helen P. Price
- Centre for Applied Entomology and Parasitology, Keele University, Staffordshire ST5 5BG, UK; (H.H.); (E.F.B.K.); (K.D.); (H.M.); (I.U.); (M.V.V.)
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9
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Arafet K, Serrano-Aparicio N, Lodola A, Mulholland AJ, González FV, Świderek K, Moliner V. Mechanism of inhibition of SARS-CoV-2 M pro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity. Chem Sci 2020; 12:1433-1444. [PMID: 34163906 PMCID: PMC8179034 DOI: 10.1039/d0sc06195f] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The SARS-CoV-2 main protease (Mpro) is essential for replication of the virus responsible for the COVID-19 pandemic, and one of the main targets for drug design. Here, we simulate the inhibition process of SARS-CoV-2 Mpro with a known Michael acceptor (peptidyl) inhibitor, N3. The free energy landscape for the mechanism of the formation of the covalent enzyme-inhibitor product is computed with QM/MM molecular dynamics methods. The simulations show a two-step mechanism, and give structures and calculated barriers in good agreement with experiment. Using these results and information from our previous investigation on the proteolysis reaction of SARS-CoV-2 Mpro, we design two new, synthetically accessible N3-analogues as potential inhibitors, in which the recognition and warhead motifs are modified. QM/MM modelling of the mechanism of inhibition of Mpro by these novel compounds indicates that both may be promising candidates as drug leads against COVID-19, one as an irreversible inhibitor and one as a potential reversible inhibitor.
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Affiliation(s)
- Kemel Arafet
- Departament de Química Física i Analítica, Universitat Jaume I 12071 Castelló Spain
| | | | - Alessio Lodola
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma Italy
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol UK
| | - Florenci V González
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I 12071 Castelló Spain
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I 12071 Castelló Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I 12071 Castelló Spain
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10
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Hobson JJ, Edwards S, Slater RA, Martin P, Owen A, Rannard SP. Branched copolymer-stabilised nanoemulsions as new candidate oral drug delivery systems. RSC Adv 2018; 8:12984-12991. [PMID: 35541240 PMCID: PMC9079742 DOI: 10.1039/c8ra01944d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/28/2018] [Indexed: 11/23/2022] Open
Abstract
The delivery of drugs to the bloodstream via oral administration may suffer from a number of complications including poor dissolution, first pass metabolism and the active intervention of efflux transporters such as P-glycoproteins; drugs which are efflux substrates may cause considerable problems across many clinical conditions. Here we have employed a branch-polymer stabilised nanoemulsion strategy to create highly robust oil droplets (e.g. peanut oil, castor oil and soybean oil) containing different dissolved antiretroviral drugs used in the daily fight against HIV/AIDS. Although very limited difference in permeation through a Caco-2 gut epithelium model was seen for efavirenz, the permeation of the protease inhibitor lopinavir was considerably higher (approximately 10-fold) when applied to an epithelium monolayer in emulsion form than the control within an aqueous DMSO vehicle. The presented nanoemulsion approach may allow drug-specific permeation improvements for various drug substances.
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Affiliation(s)
- James J Hobson
- Department of Molecular and Clinical Pharmacology, University of Liverpool Block H, 70 Pembroke Place Liverpool L69 3GF UK
- Department of Chemistry, University of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Stephanie Edwards
- Department of Chemistry, University of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Rebecca A Slater
- Department of Chemistry, University of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Philip Martin
- Department of Molecular and Clinical Pharmacology, University of Liverpool Block H, 70 Pembroke Place Liverpool L69 3GF UK
| | - Andrew Owen
- Department of Molecular and Clinical Pharmacology, University of Liverpool Block H, 70 Pembroke Place Liverpool L69 3GF UK
| | - Steve P Rannard
- Department of Chemistry, University of Liverpool Crown Street Liverpool L69 7ZD UK
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