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Kakaraskoska Boceska B, Vilken T, Xavier BB, Kostyanev T, Lin Q, Lammens C, Ellis S, O'Brien S, da Costa RMA, Cook A, Russell N, Bielicki J, Riddell A, Stohr W, Walker AS, Berezin EN, Roilides E, De Luca M, Romani L, Ballot D, Dramowski A, Wadula J, Lochindarat S, Boonkasidecha S, Namiiro F, Ngoc HTB, Tran MD, Cressey TR, Preedisripipat K, Berkley JA, Musyimi R, Zarras C, Nana T, Whitelaw A, da Silva CB, Jaglal P, Ssengooba W, Saha SK, Islam MS, Mussi-Pinhata MM, Carvalheiro CG, Piddock LJV, Heath PT, Malhotra-Kumar S, Sharland M, Glupczynski Y, Goossens H. Assessment of three antibiotic combination regimens against Gram-negative bacteria causing neonatal sepsis in low- and middle-income countries. Nat Commun 2024; 15:3947. [PMID: 38729951 PMCID: PMC11087563 DOI: 10.1038/s41467-024-48296-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Gram-negative bacteria (GNB) are a major cause of neonatal sepsis in low- and middle-income countries (LMICs). Although the World Health Organization (WHO) reports that over 80% of these sepsis deaths could be prevented through improved treatment, the efficacy of the currently recommended first- and second-line treatment regimens for this condition is increasingly affected by high rates of drug resistance. Here we assess three well known antibiotics, fosfomycin, flomoxef and amikacin, in combination as potential antibiotic treatment regimens by investigating the drug resistance and genetic profiles of commonly isolated GNB causing neonatal sepsis in LMICs. The five most prevalent bacterial isolates in the NeoOBS study (NCT03721302) are Klebsiella pneumoniae, Acinetobacter baumannii, E. coli, Serratia marcescens and Enterobacter cloacae complex. Among these isolates, high levels of ESBL and carbapenemase encoding genes are detected along with resistance to ampicillin, gentamicin and cefotaxime, the current WHO recommended empiric regimens. The three new combinations show excellent in vitro activity against ESBL-producing K. pneumoniae and E. coli isolates. Our data should further inform and support the clinical evaluation of these three antibiotic combinations for the treatment of neonatal sepsis in areas with high rates of multidrug-resistant Gram-negative bacteria.
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Affiliation(s)
- Biljana Kakaraskoska Boceska
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | - Tuba Vilken
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tomislav Kostyanev
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Qiang Lin
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Sally Ellis
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Seamus O'Brien
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | | | - Aislinn Cook
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Neal Russell
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Julia Bielicki
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
- Paediatric Research Centre, University of Basel Children's Hospital, Basel, Switzerland
| | - Amy Riddell
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Wolfgang Stohr
- MRC Clinical Trials Unit, University College London, London, UK
| | | | | | - Emmanuel Roilides
- Infectious Diseases Unit, 3rd Dept Paediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University and Hippokration General Hospital, Thessaloniki, Greece
| | - Maia De Luca
- Infectious Disease Unit, Bambino Gesu Children's Hospital, Rome, Italy
| | - Lorenza Romani
- Infectious Disease Unit, Bambino Gesu Children's Hospital, Rome, Italy
| | - Daynia Ballot
- Department of Pediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jeannette Wadula
- Department of Clinical Microbiology & Infectious Diseases, National Health Laboratory Services, CH Baragwanath Academic Hospital, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | | | | | - Flavia Namiiro
- Mulago Specialized Women's and Neonatal Hospital, Kampala, Uganda
| | | | | | - Tim R Cressey
- AMS-PHPT Research Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | | | - James A Berkley
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Robert Musyimi
- Department of Microbiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charalampos Zarras
- Microbiology Department, Hippokration General Hospital, Thessaloniki, Greece
| | - Trusha Nana
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Microbiology Laboratory, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Cely Barreto da Silva
- Infection Control and Prevention Service, Santa Casa de Sao Paulo, Sao Paulo, Brazil
| | - Prenika Jaglal
- Department of Clinical Microbiology & Infectious Diseases, National Health Laboratory Services, CH Baragwanath Academic Hospital, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Willy Ssengooba
- Makerere University, Department of Medical Microbiology, Kampala, Uganda
| | - Samir K Saha
- Child Health Research Foundation (CHRF), Dhaka, Bangladesh
| | | | | | | | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Paul T Heath
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Michael Sharland
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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Rodriguez-Ruiz JP, Xavier BB, Stöhr W, van Heirstraeten L, Lammens C, Finn A, Goossens H, Bielicki JA, Sharland M, Malhotra-Kumar S. High-resolution genomics identifies pneumococcal diversity and persistence of vaccine types in children with community-acquired pneumonia in the UK and Ireland. BMC Microbiol 2024; 24:146. [PMID: 38678217 PMCID: PMC11055344 DOI: 10.1186/s12866-024-03300-w] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Streptococcus pneumoniae is a global cause of community-acquired pneumonia (CAP) and invasive disease in children. The CAP-IT trial (grant No. 13/88/11; https://www.capitstudy.org.uk/ ) collected nasopharyngeal swabs from children discharged from hospitals with clinically diagnosed CAP, and found no differences in pneumococci susceptibility between higher and lower antibiotic doses and shorter and longer durations of oral amoxicillin treatment. Here, we studied in-depth the genomic epidemiology of pneumococcal (vaccine) serotypes and their antibiotic resistance profiles. METHODS Three-hundred and ninety pneumococci cultured from 1132 nasopharyngeal swabs from 718 children were whole-genome sequenced (Illumina) and tested for susceptibility to penicillin and amoxicillin. Genome heterogeneity analysis was performed using long-read sequenced isolates (PacBio, n = 10) and publicly available sequences. RESULTS Among 390 unique pneumococcal isolates, serotypes 15B/C, 11 A, 15 A and 23B1 were most prevalent (n = 145, 37.2%). PCV13 serotypes 3, 19A, and 19F were also identified (n = 25, 6.4%). STs associated with 19A and 19F demonstrated high genome variability, in contrast to serotype 3 (n = 13, 3.3%) that remained highly stable over a 20-year period. Non-susceptibility to penicillin (n = 61, 15.6%) and amoxicillin (n = 10, 2.6%) was low among the pneumococci analysed here and was independent of treatment dosage and duration. However, all 23B1 isolates (n = 27, 6.9%) were penicillin non-susceptible. This serotype was also identified in ST177, which is historically associated with the PCV13 serotype 19F and penicillin susceptibility, indicating a potential capsule-switch event. CONCLUSIONS Our data suggest that amoxicillin use does not drive pneumococcal serotype prevalence among children in the UK, and prompts consideration of PCVs with additional serotype coverage that are likely to further decrease CAP in this target population. Genotype 23B1 represents the convergence of a non-vaccine genotype with penicillin non-susceptibility and might provide a persistence strategy for ST types historically associated with vaccine serotypes. This highlights the need for continued genomic surveillance.
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Affiliation(s)
- Juan Pablo Rodriguez-Ruiz
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Wolfgang Stöhr
- MRC Clinical Trials Unit, University College London, London, UK
| | - Liesbet van Heirstraeten
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | | | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Julia Anna Bielicki
- Paediatric Infectious Diseases Research Group, St George's University of London, London, UK
| | - Michael Sharland
- Paediatric Infectious Diseases Research Group, St George's University of London, London, UK
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
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3
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Oliver A, Rojo-Molinero E, Arca-Suarez J, Beşli Y, Bogaerts P, Cantón R, Cimen C, Croughs PD, Denis O, Giske CG, Graells T, Daniel Huang TD, Iorga BI, Karatuna O, Kocsis B, Kronenberg A, López-Causapé C, Malhotra-Kumar S, Martínez LM, Mazzariol A, Meyer S, Naas T, Notermans DW, Oteo-Iglesias J, Pedersen T, Pirš M, Poeta P, Poirel L, Pournaras S, Sundsfjord A, Szabó D, Tambić-Andrašević A, Vatcheva-Dobrevska R, Vitkauskienė A, Jeannot K. Pseudomonasaeruginosa antimicrobial susceptibility profiles, resistance mechanisms and international clonal lineages: update from ESGARS-ESCMID/ISARPAE Group. Clin Microbiol Infect 2024; 30:469-480. [PMID: 38160753 DOI: 10.1016/j.cmi.2023.12.026] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
SCOPE Pseudomonas aeruginosa, a ubiquitous opportunistic pathogen considered one of the paradigms of antimicrobial resistance, is among the main causes of hospital-acquired and chronic infections associated with significant morbidity and mortality. This growing threat results from the extraordinary capacity of P. aeruginosa to develop antimicrobial resistance through chromosomal mutations, the increasing prevalence of transferable resistance determinants (such as the carbapenemases and the extended-spectrum β-lactamases), and the global expansion of epidemic lineages. The general objective of this initiative is to provide a comprehensive update of P. aeruginosa resistance mechanisms, especially for the extensively drug-resistant (XDR)/difficult-to-treat resistance (DTR) international high-risk epidemic lineages, and how the recently approved β-lactams and β-lactam/β-lactamase inhibitor combinations may affect resistance mechanisms and the definition of susceptibility profiles. METHODS To address this challenge, the European Study Group for Antimicrobial Resistance Surveillance (ESGARS) from the European Society of Clinical Microbiology and Infectious Diseases launched the 'Improving Surveillance of Antibiotic-Resistant Pseudomonas aeruginosa in Europe (ISARPAE)' initiative in 2022, supported by the Joint programming initiative on antimicrobial resistance network call and included a panel of over 40 researchers from 18 European Countries. Thus, a ESGARS-ISARPAE position paper was designed and the final version agreed after four rounds of revision and discussion by all panel members. QUESTIONS ADDRESSED IN THE POSITION PAPER To provide an update on (a) the emerging resistance mechanisms to classical and novel anti-pseudomonal agents, with a particular focus on β-lactams, (b) the susceptibility profiles associated with the most relevant β-lactam resistance mechanisms, (c) the impact of the novel agents and resistance mechanisms on the definitions of resistance profiles, and (d) the globally expanding XDR/DTR high-risk lineages and their association with transferable resistance mechanisms. IMPLICATION The evidence presented herein can be used for coordinated epidemiological surveillance and decision making at the European and global level.
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Affiliation(s)
- Antonio Oliver
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Estrella Rojo-Molinero
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Arca-Suarez
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Yeşim Beşli
- Department of Medical Microbiology, Amerikan Hastanesi, Istanbul, Turkey
| | - Pierre Bogaerts
- National Center for Antimicrobial Resistance in Gram, CHU UCL Namur, Yvoir, Belgium
| | - Rafael Cantón
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Cansu Cimen
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany; Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter D Croughs
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Olivier Denis
- Department of Microbiology, CHU Namur Site-Godinne, Université Catholique de Louvain, Yvoir, Belgium; Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Tíscar Graells
- Department of Neurobiology, Care Sciences and Society (NVS), Division of Family Medicine and Primary Care, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Te-Din Daniel Huang
- National Center for Antimicrobial Resistance in Gram, CHU UCL Namur, Yvoir, Belgium
| | - Bogdan I Iorga
- CNRS, Institut de Chimie des Substances Naturelles, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Onur Karatuna
- EUCAST Development Laboratory, Clinical Microbiology, Central Hospital, Växjö, Sweden
| | - Béla Kocsis
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Andreas Kronenberg
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Luis Martínez Martínez
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Unidad de Microbiología, Hospital Universitario Reina Sofía, Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, e Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Spain
| | - Annarita Mazzariol
- Microbiology and Virology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Sylvain Meyer
- INSERM UMR 1092 and Université of Limoges, Limoges, France
| | - Thierry Naas
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques: Entérobactéries Résistantes aux Carbapénèmes, Le Kremlin-Bicêtre, France; Équipe INSERM ReSIST, Faculté de Médecine, Université Paris-Saclay, Paris, France
| | - Daan W Notermans
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jesús Oteo-Iglesias
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Mateja Pirš
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Patricia Poeta
- MicroART-Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, Portugal; Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; University of Trás-os-Montes and Alto Douro, Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Vila Real, Portugal
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland; University of Fribourg, Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
| | - Spyros Pournaras
- Laboratory of Clinical Microbiology, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Dora Szabó
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary; Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary
| | - Arjana Tambić-Andrašević
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Zagreb, Croatia; School of Dental Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Astra Vitkauskienė
- Department of Laboratory Medicine, Faculty of Medicine, Medical Academy, Lithuanian University of Health Science, Kaunas, Lithuania
| | - Katy Jeannot
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Besançon, Besançon, France; Laboratoire associé du Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France; Chrono-environnement UMR 6249, CNRS, Université Franche-Comté, Besançon, France
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4
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Braspenning AJMM, Rajakani SG, Sey A, El Bounja M, Lammens C, Glupczynski Y, Malhotra-Kumar S. Assessment of Colistin Heteroresistance among Multidrug-Resistant Klebsiella pneumoniae Isolated from Intensive Care Patients in Europe. Antibiotics (Basel) 2024; 13:281. [PMID: 38534716 DOI: 10.3390/antibiotics13030281] [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: 03/05/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Heteroresistance (HR) to colistin is especially concerning in settings where multi-drug-resistant (MDR) K. pneumoniae are prevalent and empiric use of colistin might lead to treatment failures. This study aimed to assess the frequency of occurrence of colistin HR (CHR) among (MDR) K. pneumoniae (n = 676) isolated from patients hospitalized in 13 intensive care units (ICUs) in six European countries in a clinical trial assessing the impact of decolonization strategies. All isolates were whole-genome-sequenced and studied for in vitro colistin susceptibility. The majority were colistin-susceptible (CS) (n = 597, MIC ≤ 2 µg/mL), and 79 were fully colistin-resistant (CR) (MIC > 2 µg/mL). A total of 288 CS isolates were randomly selected for population analysis profiling (PAP) to assess CHR prevalence. CHR was detected in 108/288 CS K. pneumoniae. No significant association was found between the occurrence of CHR and country, MIC-value, K-antigen type, and O-antigen type. Overall, 92% (617/671) of the K. pneumoniae were MDR with high prevalence among CS (91%, 539/592) and CR (98.7%, 78/79) isolates. In contrast, the proportion of carbapenemase-producing K. pneumoniae (CP-Kpn) was higher among CR (72.2%, 57/79) than CS isolates (29.3%, 174/594). The proportions of MDR and CP-Kpn were similar among CHR (MDR: 85%, 91/107; CP-Kpn: 29.9%, 32/107) and selected CS isolates (MDR: 84.7%, 244/288; CP-Kpn: 28.1%, 80/285). WGS analysis of PAP isolates showed diverse insertion elements in mgrB or even among technical replicates underscoring the stochasticity of the CHR phenotype. CHR isolates showed high sequence type (ST) diversity (Simpson's diversity index, SDI: 0.97, in 52 of the 85 STs tested). CR (SDI: 0.85) isolates were highly associated with specific STs (ST101, ST147, ST258/ST512, p ≤ 0.003). The widespread nature of CHR among MDR K. pneumoniae in our study urge the development of rapid HR detection methods to inform on the need for combination regimens.
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Affiliation(s)
- Anouk J M M Braspenning
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, 2610 Antwerp, Belgium
| | - Sahaya Glingston Rajakani
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, 2610 Antwerp, Belgium
| | - Adwoa Sey
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, 2610 Antwerp, Belgium
| | - Mariem El Bounja
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, 2610 Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, 2610 Antwerp, Belgium
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, 2610 Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, 2610 Antwerp, Belgium
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5
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Neuhann JM, Stemler J, Carcas AJ, Frías-Iniesta J, Akova M, Bethe U, Heringer S, Salmanton-García J, Tischmann L, Zarrouk M, Cüppers A, Grothe J, Leon AG, Mallon P, Negi R, Gaillard C, Saini G, Lammens C, Hotterbeekx A, Loens K, Malhotra-Kumar S, Goossens H, Kumar-Singh S, König F, Yeghiazaryan L, Posch M, Koehler P, Cornely OA. Immunogenicity and reactogenicity of a first booster with BNT162b2 or full-dose mRNA-1273: A randomised VACCELERATE trial in adults ≥75 years (EU-COVAT-1). Vaccine 2023; 41:7166-7175. [PMID: 37919141 DOI: 10.1016/j.vaccine.2023.10.029] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/19/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Vaccination remains crucial for protection against severe SARS-CoV-2 infection, especially for people of advanced age, however, optimal dosing regimens are as yet lacking. METHODS EU-COVAT-1-AGED Part A is a randomised controlled, adaptive, multicentre phase II trial evaluating safety and immunogenicity of a 3rd vaccination (1st booster) in individuals ≥75 years. Fifty-three participants were randomised to full-doses of either mRNA-1273 (Spikevax®, 100 µg) or BNT162b2 (Comirnaty®, 30 µg). The primary endpoint was the rate of 2-fold circulating antibody titre increase 14 days post-vaccination measured by quantitative electrochemiluminescence (ECL) immunoassay, targeting RBD region of Wuhan wild-type SARS-CoV-2. Secondary endpoints included the changes in neutralising capacity against wild-type and 25 variants of concern at 14 days and up to 12 months. Safety was assessed by monitoring of solicited adverse events (AEs) for seven days after on-study vaccination. Unsolicited AEs were collected until the end of follow-up at 12 months, SAEs were pursued for a further 30 days. RESULTS Between 08th of November 2021 and 04th of January 2022, 53 participants ≥75 years received a COVID-19 vaccine as 1st booster. Fifty subjects (BNT162b2 n = 25/mRNA-1273 n = 25) were included in the analyses for immunogenicity at day 14. The primary endpoint of a 2-fold anti-RBD IgG titre increase 14 days after vaccination was reached for all subjects. A 3rd vaccination of full-dose mRNA-1273 provided higher anti-RBD IgG titres (Geometric mean titre) D14 mRNA-127310711 IU/mL (95 %-CI: 8003;14336) vs. BNT162b2: 7090 IU/mL (95 %-CI: 5688;8837). We detected a pattern showing higher neutralising capacity of full-dose mRNA-1273 against wild-type as well as for 23 out of 25 tested variants. INTERPRETATION Third doses of either BNT162b2 or mRNA-1273 provide substantial circulating antibody increase 14 days after vaccination. Full-dose mRNA-1273 provides higher antibody levels with an overall similar safety profile for people ≥75 years. FUNDING This trial was funded by the European Commission (Framework Program HORIZON 2020).
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Affiliation(s)
- Julia M Neuhann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52, 50931 Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Kerpener Str. 62, 50937 Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne Department, Herderstr. 52, 50931 Cologne, Germany
| | - Jannik Stemler
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52, 50931 Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Kerpener Str. 62, 50937 Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne Department, Herderstr. 52, 50931 Cologne, Germany
| | - Antonio J Carcas
- Hospital La Paz, Clinical Pharmacology Service, Institute for Health Research (IdiPAZ), Universidad Autónoma de Madrid, Faculty of Medicine, Madrid, Spain
| | - Jesús Frías-Iniesta
- Hospital La Paz, Clinical Pharmacology Service, Institute for Health Research (IdiPAZ), Universidad Autónoma de Madrid, Faculty of Medicine, Madrid, Spain
| | - Murat Akova
- Hacettepe University School of Medicine, Department of Infectious Diseases, Ankara, Turkey
| | - Ullrich Bethe
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52, 50931 Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Kerpener Str. 62, 50937 Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne Department, Herderstr. 52, 50931 Cologne, Germany
| | - Sarah Heringer
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52, 50931 Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Kerpener Str. 62, 50937 Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne Department, Herderstr. 52, 50931 Cologne, Germany
| | - Jon Salmanton-García
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52, 50931 Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Kerpener Str. 62, 50937 Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne Department, Herderstr. 52, 50931 Cologne, Germany
| | - Lea Tischmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52, 50931 Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Kerpener Str. 62, 50937 Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne Department, Herderstr. 52, 50931 Cologne, Germany
| | - Marouan Zarrouk
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52, 50931 Cologne, Germany
| | - Arnd Cüppers
- University of Cologne, Faculty of Medicine, Clinical Trials Centre Cologne (CTCC Cologne), Gleueler Str. 269, 50935 Cologne, Germany
| | - Jan Grothe
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52, 50931 Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Kerpener Str. 62, 50937 Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne Department, Herderstr. 52, 50931 Cologne, Germany
| | - Alejandro Garcia Leon
- Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin (UCD), Ireland
| | - Patrick Mallon
- Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin (UCD), Ireland
| | - Riya Negi
- Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin (UCD), Ireland
| | - Colette Gaillard
- Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin (UCD), Ireland
| | - Gurvin Saini
- Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin (UCD), Ireland
| | - Christine Lammens
- Laboratory of Medical Microbiology (LMM), Vaccine & Infectious Disease Institute and Biobank Antwerp, University of Antwerp, Belgium
| | - An Hotterbeekx
- Molecular Pathology Group, Laboratory of Cell Biology & Histology and Vaccine & Infectious Disease Institute (CBH), Faculty of Medicine, University of Antwerp, Belgium
| | - Katherine Loens
- Laboratory of Medical Microbiology (LMM), Vaccine & Infectious Disease Institute and Biobank Antwerp, University of Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology (LMM), Vaccine & Infectious Disease Institute and Biobank Antwerp, University of Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology (LMM), Vaccine & Infectious Disease Institute and Biobank Antwerp, University of Antwerp, Belgium
| | - Samir Kumar-Singh
- Molecular Pathology Group, Laboratory of Cell Biology & Histology and Vaccine & Infectious Disease Institute (CBH), Faculty of Medicine, University of Antwerp, Belgium
| | - Franz König
- Medical University of Vienna, Center for Medical Data Science, Spitalgasse 23, 1090 Vienna, Austria
| | - Lusine Yeghiazaryan
- Medical University of Vienna, Center for Medical Data Science, Spitalgasse 23, 1090 Vienna, Austria
| | - Martin Posch
- Medical University of Vienna, Center for Medical Data Science, Spitalgasse 23, 1090 Vienna, Austria
| | - Philipp Koehler
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52, 50931 Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Kerpener Str. 62, 50937 Cologne, Germany
| | - Oliver A Cornely
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52, 50931 Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Kerpener Str. 62, 50937 Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne Department, Herderstr. 52, 50931 Cologne, Germany; University of Cologne, Faculty of Medicine, Clinical Trials Centre Cologne (CTCC Cologne), Gleueler Str. 269, 50935 Cologne, Germany.
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Van Dingenen L, Segers C, Wouters S, Mysara M, Leys N, Kumar-Singh S, Malhotra-Kumar S, Van Houdt R. Dissecting the role of the gut microbiome and fecal microbiota transplantation in radio- and immunotherapy treatment of colorectal cancer. Front Cell Infect Microbiol 2023; 13:1298264. [PMID: 38035338 PMCID: PMC10687483 DOI: 10.3389/fcimb.2023.1298264] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers and poses a major burden on the human health worldwide. At the moment, treatment of CRC consists of surgery in combination with (neo)adjuvant chemotherapy and/or radiotherapy. More recently, immune checkpoint blockers (ICBs) have also been approved for CRC treatment. In addition, recent studies have shown that radiotherapy and ICBs act synergistically, with radiotherapy stimulating the immune system that is activated by ICBs. However, both treatments are also associated with severe toxicity and efficacy issues, which can lead to temporary or permanent discontinuation of these treatment programs. There's growing evidence pointing to the gut microbiome playing a role in these issues. Some microorganisms seem to contribute to radiotherapy-associated toxicity and hinder ICB efficacy, while others seem to reduce radiotherapy-associated toxicity or enhance ICB efficacy. Consequently, fecal microbiota transplantation (FMT) has been applied to reduce radio- and immunotherapy-related toxicity and enhance their efficacies. Here, we have reviewed the currently available preclinical and clinical data in CRC treatment, with a focus on how the gut microbiome influences radio- and immunotherapy toxicity and efficacy and if these treatments could benefit from FMT.
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Affiliation(s)
- Lena Van Dingenen
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Charlotte Segers
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Shari Wouters
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Mohamed Mysara
- Bioinformatics Group, Center for Informatics Science, School of Information Technology and Computer Science, Nile University, Giza, Egypt
| | - Natalie Leys
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Samir Kumar-Singh
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Rob Van Houdt
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
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7
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van Engelen TSR, Reijnders TDY, Paling FP, Bonten MJM, Timbermont L, Malhotra-Kumar S, Kluytmans JAJW, Peters-Sengers H, van der Poll T. Correction: Plasma protein biomarkers reflective of the host response in patients developing Intensive Care Unit-acquired pneumonia. Crit Care 2023; 27:420. [PMID: 37915039 PMCID: PMC10621317 DOI: 10.1186/s13054-023-04700-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Affiliation(s)
- Tjitske S R van Engelen
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Room G2-105, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - Tom D Y Reijnders
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Room G2-105, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Fleur P Paling
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Jan A J W Kluytmans
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hessel Peters-Sengers
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Room G2-105, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Room G2-105, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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8
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Troeman DPR, Hazard D, Timbermont L, Malhotra-Kumar S, van Werkhoven CH, Wolkewitz M, Ruzin A, Goossens H, Bonten MJM, Harbarth S, Sifakis F, Kluytmans JAJW. Postoperative Staphylococcus aureus Infections in Patients With and Without Preoperative Colonization. JAMA Netw Open 2023; 6:e2339793. [PMID: 37906196 PMCID: PMC10618839 DOI: 10.1001/jamanetworkopen.2023.39793] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/06/2023] [Indexed: 11/02/2023] Open
Abstract
Importance Staphylococcus aureus surgical site infections (SSIs) and bloodstream infections (BSIs) are important complications of surgical procedures for which prevention remains suboptimal. Contemporary data on the incidence of and etiologic factors for these infections are needed to support the development of improved preventive strategies. Objectives To assess the occurrence of postoperative S aureus SSIs and BSIs and quantify its association with patient-related and contextual factors. Design, Setting, and Participants This multicenter cohort study assessed surgical patients at 33 hospitals in 10 European countries who were recruited between December 16, 2016, and September 30, 2019 (follow-up through December 30, 2019). Enrolled patients were actively followed up for up to 90 days after surgery to assess the occurrence of S aureus SSIs and BSIs. Data analysis was performed between November 20, 2020, and April 21, 2022. All patients were 18 years or older and had undergone 11 different types of surgical procedures. They were screened for S aureus colonization in the nose, throat, and perineum within 30 days before surgery (source population). Both S aureus carriers and noncarriers were subsequently enrolled in a 2:1 ratio. Exposure Preoperative S aureus colonization. Main Outcomes and Measures The main outcome was cumulative incidence of S aureus SSIs and BSIs estimated for the source population, using weighted incidence calculation. The independent association of candidate variables was estimated using multivariable Cox proportional hazards regression models. Results In total, 5004 patients (median [IQR] age, 66 [56-72] years; 2510 [50.2%] female) were enrolled in the study cohort; 3369 (67.3%) were S aureus carriers. One hundred patients developed S aureus SSIs or BSIs within 90 days after surgery. The weighted cumulative incidence of S aureus SSIs or BSIs was 2.55% (95% CI, 2.05%-3.12%) for carriers and 0.52% (95% CI, 0.22%-0.91%) for noncarriers. Preoperative S aureus colonization (adjusted hazard ratio [AHR], 4.38; 95% CI, 2.19-8.76), having nonremovable implants (AHR, 2.00; 95% CI, 1.15-3.49), undergoing mastectomy (AHR, 5.13; 95% CI, 1.87-14.08) or neurosurgery (AHR, 2.47; 95% CI, 1.09-5.61) (compared with orthopedic surgery), and body mass index (AHR, 1.05; 95% CI, 1.01-1.08 per unit increase) were independently associated with S aureus SSIs and BSIs. Conclusions and Relevance In this cohort study of surgical patients, S aureus carriage was associated with an increased risk of developing S aureus SSIs and BSIs. Both modifiable and nonmodifiable etiologic factors were associated with this risk and should be addressed in those at increased S aureus SSI and BSI risk.
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Affiliation(s)
- Darren P. R. Troeman
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Derek Hazard
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Cornelis H. van Werkhoven
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Martin Wolkewitz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Alexey Ruzin
- Microbial Sciences, R&D BioPharmaceuticals, AstraZeneca Plc, Gaithersburg, Maryland
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Marc J. M. Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Stephan Harbarth
- Infection Control Programme and World Health Organization Collaborating Center, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Frangiscos Sifakis
- now with Gilead Sciences Inc, Foster City, California
- AstraZeneca Plc, Gaithersburg, Maryland
| | - Jan A. J. W. Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
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9
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Rodriguez-Ruiz JP, Lin Q, Lammens C, Smeesters PR, van Kleef-van Koeveringe S, Matheeussen V, Malhotra-Kumar S. Increase in bloodstream infections caused by emm1 group A Streptococcus correlates with emergence of toxigenic M1 UK, Belgium, May 2022 to August 2023. Euro Surveill 2023; 28:2300422. [PMID: 37676145 PMCID: PMC10486196 DOI: 10.2807/1560-7917.es.2023.28.36.2300422] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023] Open
Abstract
Many European countries have recently reported upsurges in invasive group A Streptococcus (iGAS) infections, mainly caused by emm1 Streptococcus pyogenes, specifically the toxigenic M1UK lineage. We present the epidemiology of emm1 causing iGAS in Belgium during 2018-August 2023, and describe an emergence of the toxigenic M1UK lineage in Belgium in mid-2022 that was observed as an increase in bloodstream infections caused by emm1 S. pyogenes that continued into 2023.
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Affiliation(s)
- Juan Pablo Rodriguez-Ruiz
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
| | - Qiang Lin
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
| | - Pierre R Smeesters
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
- Department of Paediatrics, Brussels University Hospital, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Stefanie van Kleef-van Koeveringe
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
- Laboratory of Microbiology, University Hospital Antwerp, Edegem, Antwerp, Belgium
| | - Veerle Matheeussen
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
- Laboratory of Microbiology, University Hospital Antwerp, Edegem, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
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Azzini AM, Canziani LM, Davis RJ, Mirandola M, Hoelscher M, Meyer L, Laouénan C, Giannella M, Rodríguez-Baño J, Boffetta P, Mates D, Malhotra-Kumar S, Scipione G, Stellmach C, Rinaldi E, Hasenauer J, Tacconelli E. How European Research Projects Can Support Vaccination Strategies: The Case of the ORCHESTRA Project for SARS-CoV-2. Vaccines (Basel) 2023; 11:1361. [PMID: 37631929 PMCID: PMC10459328 DOI: 10.3390/vaccines11081361] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
ORCHESTRA ("Connecting European Cohorts to Increase Common and Effective Response To SARS-CoV-2 Pandemic") is an EU-funded project which aims to help rapidly advance the knowledge related to the prevention of the SARS-CoV-2 infection and the management of COVID-19 and its long-term sequelae. Here, we describe the early results of this project, focusing on the strengths of multiple, international, historical and prospective cohort studies and highlighting those results which are of potential relevance for vaccination strategies, such as the necessity of a vaccine booster dose after a primary vaccination course in hematologic cancer patients and in solid organ transplant recipients to elicit a higher antibody titer, and the protective effect of vaccination on severe COVID-19 clinical manifestation and on the emergence of post-COVID-19 conditions. Valuable data regarding epidemiological variations, risk factors of SARS-CoV-2 infection and its sequelae, and vaccination efficacy in different subpopulations can support further defining public health vaccination policies.
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Affiliation(s)
- Anna Maria Azzini
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy; (L.M.C.); (M.M.); (E.T.)
| | - Lorenzo Maria Canziani
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy; (L.M.C.); (M.M.); (E.T.)
| | - Ruth Joanna Davis
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy; (L.M.C.); (M.M.); (E.T.)
| | - Massimo Mirandola
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy; (L.M.C.); (M.M.); (E.T.)
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), 80802 Munich, Germany;
- German Center for Infection Research (DZIF), Partner Site Munich, 80802 Munich, Germany
| | - Laurence Meyer
- Centre de Recherche en Epidemiologie et Sante des Population, Institut National de la Sante et de la Recherche Medicale (INSERM), Universite Paris-Saclay, 94270 Le Kremlin-Bicêtre, France;
| | - Cédric Laouénan
- INSERM, IAME UMR 1137, Universite Paris Cite, 75018 Paris, France;
- Departement d’Epidemiologie Biostatistiques e Recherche Clinique, AP-HP, Hospital Bichat, 75018 Paris, France
| | - Maddalena Giannella
- Infectious Diseases Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Jesús Rodríguez-Baño
- Infectious Diseases and Microbiology Unit, Hospital Universitario Virgen Macarena and Department of Medicine, Biomedicines Institute of Sevilla-CSIC, University of Sevilla, 41004 Sevilla, Spain;
- Centro de Investigacion Biomedica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Paolo Boffetta
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 10041, USA
| | - Dana Mates
- National Institute of Public Health, 050463 Bucharest, Romania;
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, 2000 Antwerp, Belgium;
| | - Gabriella Scipione
- Supercomputing Applications and Innovation Department, Cineca Consorzio Interuniversitario, 40033 Bologna, Italy;
| | - Caroline Stellmach
- Berlin Institute of Health at Charite, Universitätsmedizin Berlin, 10117 Berlin, Germany; (C.S.); (E.R.)
| | - Eugenia Rinaldi
- Berlin Institute of Health at Charite, Universitätsmedizin Berlin, 10117 Berlin, Germany; (C.S.); (E.R.)
| | - Jan Hasenauer
- Life and Medical Sciences Institute, University of Bonn, 53113 Bonn, Germany;
- Institute of Computational Biology, Helmholtz Center Munich—German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Evelina Tacconelli
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy; (L.M.C.); (M.M.); (E.T.)
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Diaz Caballero J, Wheatley RM, Kapel N, López-Causapé C, Van der Schalk T, Quinn A, Shaw LP, Ogunlana L, Recanatini C, Xavier BB, Timbermont L, Kluytmans J, Ruzin A, Esser M, Malhotra-Kumar S, Oliver A, MacLean RC. Mixed strain pathogen populations accelerate the evolution of antibiotic resistance in patients. Nat Commun 2023; 14:4083. [PMID: 37438338 DOI: 10.1038/s41467-023-39416-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 06/12/2023] [Indexed: 07/14/2023] Open
Abstract
Antibiotic resistance poses a global health threat, but the within-host drivers of resistance remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and resistance is thought to emerge due to selection for de novo variants. Here we show that mixed strain populations are common in the opportunistic pathogen P. aeruginosa. Crucially, resistance evolves rapidly in patients colonized by multiple strains through selection for pre-existing resistant strains. In contrast, resistance evolves sporadically in patients colonized by single strains due to selection for novel resistance mutations. However, strong trade-offs between resistance and growth rate occur in mixed strain populations, suggesting that within-host diversity can also drive the loss of resistance in the absence of antibiotic treatment. In summary, we show that the within-host diversity of pathogen populations plays a key role in shaping the emergence of resistance in response to treatment.
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Affiliation(s)
| | - Rachel M Wheatley
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Natalia Kapel
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Thomas Van der Schalk
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Angus Quinn
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Liam P Shaw
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Lois Ogunlana
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Claudia Recanatini
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Jan Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Alexey Ruzin
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Mark Esser
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - R Craig MacLean
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK.
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12
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Rajakani SG, Xavier BB, Sey A, Mariem EB, Lammens C, Goossens H, Glupczynski Y, Malhotra-Kumar S. Insight into Antibiotic Synergy Combinations for Eliminating Colistin Heteroresistant Klebsiella pneumoniae. Genes (Basel) 2023; 14:1426. [PMID: 37510330 PMCID: PMC10378790 DOI: 10.3390/genes14071426] [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: 05/26/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Colistin heteroresistance has been identified in several bacterial species, including Escherichia coli and Klebsiella pneumoniae, and may underlie antibiotic therapy failures since it most often goes undetected by conventional antimicrobial susceptibility tests. This study utilizes population analysis profiling (PAP) and time-kill assay for the detection of heteroresistance in K. pneumoniae and for evaluating the association between in vitro regrowth and heteroresistance. The mechanisms of colistin resistance and the ability of combination therapies to suppress resistance selection were also analysed. In total, 3 (18%) of the 16 colistin-susceptible strains (MIC ≤ 2 mg/L) were confirmed to be heteroresistant to colistin by PAP assay. In contrast to the colistin-susceptible control strains, all three heteroresistant strains showed regrowth when exposed to colistin after 24 h following a rapid bactericidal action. Colistin resistance in all the resistant subpopulations was due to the disruption of the mgrB gene by various insertion elements such as ISKpn14 of the IS1 family and IS903B of the IS5 family. Colistin combined with carbapenems (imipenem, meropenem), aminoglycosides (amikacin, gentamicin) or tigecycline was found to elicit in vitro synergistic effects against these colistin heteroresistant strains. Our experimental results showcase the potential of combination therapies for treatment of K. pneumoniae infections associated with colistin heteroresistance.
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Affiliation(s)
- Sahaya Glingston Rajakani
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, 2610 Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, 2610 Antwerp, Belgium
| | - Adwoa Sey
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, 2610 Antwerp, Belgium
| | - El Bounja Mariem
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, 2610 Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, 2610 Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, 2610 Antwerp, Belgium
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, 2610 Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, 2610 Antwerp, Belgium
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13
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van Engelen TSR, Reijnders TDY, Paling FP, Bonten MJM, Timbermont L, Malhotra-Kumar S, Kluytmans JAJW, Peters-Sengers H, van der Poll T. Plasma protein biomarkers reflective of the host response in patients developing Intensive Care Unit-acquired pneumonia. Crit Care 2023; 27:269. [PMID: 37415223 PMCID: PMC10327365 DOI: 10.1186/s13054-023-04536-0] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Immune suppression has been implicated in the occurrence of pneumonia in critically ill patients. We tested the hypothesis that Intensive Care Unit (ICU)-acquired pneumonia is associated with broad host immune aberrations in the trajectory to pneumonia, encompassing inflammatory, endothelial and coagulation responses. We compared plasma protein biomarkers reflecting the systemic host response in critically ill patients who acquire a new pneumonia (cases) with those who do not (controls). METHODS We performed a nested case-control study in patients undergoing mechanical ventilation at ICU admission with an expected stay of at least 48 h enrolled in 30 hospitals in 11 European countries. Nineteen host response biomarkers reflective of key pathophysiological domains were measured in plasma obtained on study inclusion and day 7, and-in cases-on the day of pneumonia diagnosis. RESULTS Of 1997 patients, 316 developed pneumonia (15.8%) and 1681 did not (84.2%). Plasma protein biomarker analyses, performed in cases and a randomly selected subgroup of controls (1:2 ratio to cases, n = 632), demonstrated considerable variation across time points and patient groups. Yet, cases showed biomarker concentrations suggestive of enhanced inflammation and a more disturbed endothelial barrier function, both at study enrollment (median 2 days after ICU admission) and in the path to pneumonia diagnosis (median 5 days after ICU admission). Baseline host response biomarker aberrations were most profound in patients who developed pneumonia either shortly (< 5 days, n = 105) or late (> 10 days, n = 68) after ICU admission. CONCLUSIONS Critically ill patients who develop an ICU-acquired pneumonia, compared with those who do not, display alterations in plasma protein biomarker concentrations indicative of stronger proinflammatory, procoagulant and (injurious) endothelial cell responses. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02413242, posted April 9th, 2015.
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Affiliation(s)
- Tjitske S R van Engelen
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Room G2-105, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - Tom D Y Reijnders
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Room G2-105, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Fleur P Paling
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Jan A J W Kluytmans
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hessel Peters-Sengers
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Room G2-105, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Room G2-105, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Division of Infectious Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
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14
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Russell NJ, Stöhr W, Plakkal N, Cook A, Berkley JA, Adhisivam B, Agarwal R, Ahmed NU, Balasegaram M, Ballot D, Bekker A, Berezin EN, Bilardi D, Boonkasidecha S, Carvalheiro CG, Chami N, Chaurasia S, Chiurchiu S, Colas VRF, Cousens S, Cressey TR, de Assis ACD, Dien TM, Ding Y, Dung NT, Dong H, Dramowski A, DS M, Dudeja A, Feng J, Glupczynski Y, Goel S, Goossens H, Hao DTH, Khan MI, Huertas TM, Islam MS, Jarovsky D, Khavessian N, Khorana M, Kontou A, Kostyanev T, Laoyookhon P, Lochindarat S, Larsson M, Luca MD, Malhotra-Kumar S, Mondal N, Mundhra N, Musoke P, Mussi-Pinhata MM, Nanavati R, Nakwa F, Nangia S, Nankunda J, Nardone A, Nyaoke B, Obiero CW, Owor M, Ping W, Preedisripipat K, Qazi S, Qi L, Ramdin T, Riddell A, Romani L, Roysuwan P, Saggers R, Roilides E, Saha SK, Sarafidis K, Tusubira V, Thomas R, Velaphi S, Vilken T, Wang X, Wang Y, Yang Y, Zunjie L, Ellis S, Bielicki JA, Walker AS, Heath PT, Sharland M. Patterns of antibiotic use, pathogens, and prediction of mortality in hospitalized neonates and young infants with sepsis: A global neonatal sepsis observational cohort study (NeoOBS). PLoS Med 2023; 20:e1004179. [PMID: 37289666 PMCID: PMC10249878 DOI: 10.1371/journal.pmed.1004179] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [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] [Received: 06/15/2022] [Accepted: 01/19/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND There is limited data on antibiotic treatment in hospitalized neonates in low- and middle-income countries (LMICs). We aimed to describe patterns of antibiotic use, pathogens, and clinical outcomes, and to develop a severity score predicting mortality in neonatal sepsis to inform future clinical trial design. METHODS AND FINDINGS Hospitalized infants <60 days with clinical sepsis were enrolled during 2018 to 2020 by 19 sites in 11 countries (mainly Asia and Africa). Prospective daily observational data was collected on clinical signs, supportive care, antibiotic treatment, microbiology, and 28-day mortality. Two prediction models were developed for (1) 28-day mortality from baseline variables (baseline NeoSep Severity Score); and (2) daily risk of death on IV antibiotics from daily updated assessments (NeoSep Recovery Score). Multivariable Cox regression models included a randomly selected 85% of infants, with 15% for validation. A total of 3,204 infants were enrolled, with median birth weight of 2,500 g (IQR 1,400 to 3,000) and postnatal age of 5 days (IQR 1 to 15). 206 different empiric antibiotic combinations were started in 3,141 infants, which were structured into 5 groups based on the World Health Organization (WHO) AWaRe classification. Approximately 25.9% (n = 814) of infants started WHO first line regimens (Group 1-Access) and 13.8% (n = 432) started WHO second-line cephalosporins (cefotaxime/ceftriaxone) (Group 2-"Low" Watch). The largest group (34.0%, n = 1,068) started a regimen providing partial extended-spectrum beta-lactamase (ESBL)/pseudomonal coverage (piperacillin-tazobactam, ceftazidime, or fluoroquinolone-based) (Group 3-"Medium" Watch), 18.0% (n = 566) started a carbapenem (Group 4-"High" Watch), and 1.8% (n = 57) a Reserve antibiotic (Group 5, largely colistin-based), and 728/2,880 (25.3%) of initial regimens in Groups 1 to 4 were escalated, mainly to carbapenems, usually for clinical deterioration (n = 480; 65.9%). A total of 564/3,195 infants (17.7%) were blood culture pathogen positive, of whom 62.9% (n = 355) had a gram-negative organism, predominantly Klebsiella pneumoniae (n = 132) or Acinetobacter spp. (n = 72). Both were commonly resistant to WHO-recommended regimens and to carbapenems in 43 (32.6%) and 50 (71.4%) of cases, respectively. MRSA accounted for 33 (61.1%) of 54 Staphylococcus aureus isolates. Overall, 350/3,204 infants died (11.3%; 95% CI 10.2% to 12.5%), 17.7% if blood cultures were positive for pathogens (95% CI 14.7% to 21.1%, n = 99/564). A baseline NeoSep Severity Score had a C-index of 0.76 (0.69 to 0.82) in the validation sample, with mortality of 1.6% (3/189; 95% CI: 0.5% to 4.6%), 11.0% (27/245; 7.7% to 15.6%), and 27.3% (12/44; 16.3% to 41.8%) in low (score 0 to 4), medium (5 to 8), and high (9 to 16) risk groups, respectively, with similar performance across subgroups. A related NeoSep Recovery Score had an area under the receiver operating curve for predicting death the next day between 0.8 and 0.9 over the first week. There was significant variation in outcomes between sites and external validation would strengthen score applicability. CONCLUSION Antibiotic regimens used in neonatal sepsis commonly diverge from WHO guidelines, and trials of novel empiric regimens are urgently needed in the context of increasing antimicrobial resistance (AMR). The baseline NeoSep Severity Score identifies high mortality risk criteria for trial entry, while the NeoSep Recovery Score can help guide decisions on regimen change. NeoOBS data informed the NeoSep1 antibiotic trial (ISRCTN48721236), which aims to identify novel first- and second-line empiric antibiotic regimens for neonatal sepsis. TRIAL REGISTRATION ClinicalTrials.gov, (NCT03721302).
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Affiliation(s)
- Neal J. Russell
- Center for Neonatal and Paediatric Infection (CNPI), Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | - Wolfgang Stöhr
- Medical Research Council Clinical Trials Unit at University College London, London, United Kingdom
| | - Nishad Plakkal
- Department of Neonatology, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Pondicherry, India
| | - Aislinn Cook
- Center for Neonatal and Paediatric Infection (CNPI), Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | - James A. Berkley
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Bethou Adhisivam
- Department of Neonatology, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Pondicherry, India
| | - Ramesh Agarwal
- Newborn Division and WHO-CC, All India Institute of Medical Sciences, New Delhi, India
| | - Nawshad Uddin Ahmed
- Child Health Research Foundation (CHRF), Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Manica Balasegaram
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Daynia Ballot
- Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adrie Bekker
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | | | | | | | - Cristina G. Carvalheiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Neema Chami
- Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Suman Chaurasia
- All India Institute of Medical Sciences, Department of Paediatrics, New Delhi, India
| | - Sara Chiurchiu
- Academic Hospital Paediatric Department, Bambino Gesù Children’s Hospital, Rome, Italy
| | | | - Simon Cousens
- Faculty of Epidemiology and Population Health, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Tim R. Cressey
- PHPT/IRD-MIVEGEC, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | | | - Tran Minh Dien
- Vietnam National Children’s Hospital, Hanoi, Vietnam and Surgical Intensive Care Unit, Vietnam National Children’s Hospital, Hanoi, Vietnam
| | - Yijun Ding
- Vietnam National Children’s Hospital, Hanoi, Vietnam and Surgical Intensive Care Unit, Vietnam National Children’s Hospital, Hanoi, Vietnam
| | - Nguyen Trong Dung
- Vietnam National Children’s Hospital, Hanoi, Vietnam and Surgical Intensive Care Unit, Vietnam National Children’s Hospital, Hanoi, Vietnam
| | - Han Dong
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Madhusudhan DS
- Neonatology Department, Seth GS Medical College and King Edward Memorial Hospital, Mumbai, India
| | - Ajay Dudeja
- Department of Neonatology, Lady Hardinge Medical College and Kalawati Saran Children’s Hospital, New Delhi, India
| | - Jinxing Feng
- Department of Neonatology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, University of Antwerp, Antwerp, Belgium
| | - Srishti Goel
- Department of Neonatology, Lady Hardinge Medical College and Kalawati Saran Children’s Hospital, New Delhi, India
| | - Herman Goossens
- Laboratory of Medical Microbiology, University of Antwerp, Antwerp, Belgium
| | - Doan Thi Huong Hao
- Vietnam National Children’s Hospital, Hanoi, Vietnam and Surgical Intensive Care Unit, Vietnam National Children’s Hospital, Hanoi, Vietnam
| | - Mahmudul Islam Khan
- Child Health Research Foundation (CHRF), Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Tatiana Munera Huertas
- Center for Neonatal and Paediatric Infection (CNPI), Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | | | - Daniel Jarovsky
- Pediatric Infectious Diseases Unit, Santa Casa de São Paulo, São Paulo, Brazil
| | - Nathalie Khavessian
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Meera Khorana
- Neonatal Unit, Department of Pediatrics, Queen Sirikit National Institute of Child Health, College of Medicine, Rangsit University, Bangkok, Thailand
| | - Angeliki Kontou
- Neonatology Dept, School of Medicine, Faculty of Health Sciences, Aristotle University and Hippokration General Hospital, Thessaloniki, Greece
| | - Tomislav Kostyanev
- Laboratory of Medical Microbiology, University of Antwerp, Antwerp, Belgium
| | | | | | - Mattias Larsson
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Maia De Luca
- Academic Hospital Paediatric Department, Bambino Gesù Children’s Hospital, Rome, Italy
| | | | - Nivedita Mondal
- Department of Neonatology, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Pondicherry, India
| | - Nitu Mundhra
- Neonatology Department, Seth GS Medical College and King Edward Memorial Hospital, Mumbai, India
| | - Philippa Musoke
- Department of Paediatrics and Child Health, College of Health Sciences, Makerere University and MUJHU Care, Kampala, Uganda
| | - Marisa M. Mussi-Pinhata
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Ruchi Nanavati
- Neonatology Department, Seth GS Medical College and King Edward Memorial Hospital, Mumbai, India
| | - Firdose Nakwa
- Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sushma Nangia
- Department of Neonatology, Lady Hardinge Medical College and Kalawati Saran Children’s Hospital, New Delhi, India
| | - Jolly Nankunda
- Makerere University - Johns Hopkins University Research Collaboration, Kampala, Uganda
| | | | - Borna Nyaoke
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Christina W. Obiero
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Amsterdam UMC, University of Amsterdam, Emma Children’s Hospital, Department of Global Health, Amsterdam, the Netherlands
| | - Maxensia Owor
- Makerere University - Johns Hopkins University Research Collaboration, Kampala, Uganda
| | - Wang Ping
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | | | - Shamim Qazi
- World Health Organization, Maternal, Newborn, Child and Adolescent Health Department, Geneva, Switzerland
| | - Lifeng Qi
- Department of Infectious Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Tanusha Ramdin
- Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Paediatrics and Child Health, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Amy Riddell
- Center for Neonatal and Paediatric Infection (CNPI), Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | - Lorenza Romani
- Academic Hospital Paediatric Department, Bambino Gesù Children’s Hospital, Rome, Italy
| | - Praewpan Roysuwan
- PHPT/IRD-MIVEGEC, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Robin Saggers
- Department of Paediatrics and Child Health, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Emmanuel Roilides
- Infectious Diseases Unit, 3rd Dept Pediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University and Hippokration General Hospital, Thessaloniki, Greece
| | - Samir K. Saha
- Child Health Research Foundation (CHRF), Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Kosmas Sarafidis
- Neonatology Dept, School of Medicine, Faculty of Health Sciences, Aristotle University and Hippokration General Hospital, Thessaloniki, Greece
| | - Valerie Tusubira
- Department of Paediatrics and Child Health, College of Health Sciences, Makerere University and MUJHU Care, Kampala, Uganda
| | - Reenu Thomas
- Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sithembiso Velaphi
- Department of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tuba Vilken
- Laboratory of Medical Microbiology, University of Antwerp, Antwerp, Belgium
| | - Xiaojiao Wang
- Department of Neonatology, Beijing Children’s Hospital, Capital Medical University, National Centre for Children’s Health, Beijing, China
| | - Yajuan Wang
- Department of Neonatology, Children’s Hospital, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing, China
| | - Yonghong Yang
- Department of Neonatology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Liu Zunjie
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Sally Ellis
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Julia A. Bielicki
- Center for Neonatal and Paediatric Infection (CNPI), Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | - A. Sarah Walker
- Medical Research Council Clinical Trials Unit at University College London, London, United Kingdom
| | - Paul T. Heath
- Center for Neonatal and Paediatric Infection (CNPI), Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | - Mike Sharland
- Center for Neonatal and Paediatric Infection (CNPI), Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
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15
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Gupta A, Konnova A, Smet M, Berkell M, Savoldi A, Morra M, Van Averbeke V, De Winter FH, Peserico D, Danese E, Hotterbeekx A, Righi E, De Nardo P, Tacconelli E, Malhotra-Kumar S, Kumar-Singh S. Host immunological responses facilitate development of SARS-CoV-2 mutations in patients receiving monoclonal antibody treatments. J Clin Invest 2023; 133:166032. [PMID: 36727404 PMCID: PMC10014108 DOI: 10.1172/jci166032] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/05/2023] [Indexed: 02/03/2023] Open
Abstract
BackgroundThe role of host immunity in emergence of evasive SARS-CoV-2 Spike mutations under therapeutic monoclonal antibody (mAb) pressure remains to be explored.MethodsIn a prospective, observational, monocentric ORCHESTRA cohort study, conducted between March 2021 and November 2022, mild-to-moderately ill COVID-19 patients (n = 204) receiving bamlanivimab, bamlanivimab/etesevimab, casirivimab/imdevimab, or sotrovimab were longitudinally studied over 28 days for viral loads, de novo Spike mutations, mAb kinetics, seroneutralization against infecting variants of concern, and T cell immunity. Additionally, a machine learning-based circulating immune-related biomarker (CIB) profile predictive of evasive Spike mutations was constructed and confirmed in an independent data set (n = 19) that included patients receiving sotrovimab or tixagevimab/cilgavimab.ResultsPatients treated with various mAbs developed evasive Spike mutations with remarkable speed and high specificity to the targeted mAb-binding sites. Immunocompromised patients receiving mAb therapy not only continued to display significantly higher viral loads, but also showed higher likelihood of developing de novo Spike mutations. Development of escape mutants also strongly correlated with neutralizing capacity of the therapeutic mAbs and T cell immunity, suggesting immune pressure as an important driver of escape mutations. Lastly, we showed that an antiinflammatory and healing-promoting host milieu facilitates Spike mutations, where 4 CIBs identified patients at high risk of developing escape mutations against therapeutic mAbs with high accuracy.ConclusionsOur data demonstrate that host-driven immune and nonimmune responses are essential for development of mutant SARS-CoV-2. These data also support point-of-care decision making in reducing the risk of mAb treatment failure and improving mitigation strategies for possible dissemination of escape SARS-CoV-2 mutants.FundingThe ORCHESTRA project/European Union's Horizon 2020 research and innovation program.
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Affiliation(s)
- Akshita Gupta
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Angelina Konnova
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Mathias Smet
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Matilda Berkell
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Alessia Savoldi
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Matteo Morra
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Vincent Van Averbeke
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and
| | - Fien Hr De Winter
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and
| | - Denise Peserico
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - Elisa Danese
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - An Hotterbeekx
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and
| | - Elda Righi
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | | | - Pasquale De Nardo
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health and
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Samir Kumar-Singh
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences and.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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16
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Babu Rajendran N, Arieti F, Mena-Benítez CA, Galia L, Tebon M, Alvarez J, Gladstone BP, Collineau L, De Angelis G, Duro R, Gaze W, Göpel S, Kanj SS, Käsbohrer A, Limmathurotsakul D, Lopez de Abechuco E, Mazzolini E, Mutters NT, Pezzani MD, Presterl E, Renk H, Rodríguez-Baño J, Săndulescu O, Scali F, Skov R, Velavan TP, Vuong C, Tacconelli E, Avery L, Bonten M, Cassini A, Chauvin C, Compri M, Damborg P, De Greeff S, Del Toro MD, Filter M, Franklin A, Gonzalez-Zorn B, Grave K, Hocquet D, Hoelzle LE, Kalanxhi E, Laxminarayan R, Leibovici L, Malhotra-Kumar S, Mendelson M, Paul M, Muñoz Madero C, Murri R, Piddock LJ, Ruesen C, Sanguinetti M, Schilling T, Schrijver R, Schwaber MJ, Scudeller L, Torumkuney D, Van Boeckel T, Vanderhaeghen W, Voss A, Wozniak T. EPI-Net One Health reporting guideline for antimicrobial consumption and resistance surveillance data: a Delphi approach. Lancet Reg Health Eur 2023; 26:100563. [PMID: 36895445 PMCID: PMC9989632 DOI: 10.1016/j.lanepe.2022.100563] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Strategic and standardised approaches to analysis and reporting of surveillance data are essential to inform antimicrobial resistance (AMR) mitigation measures, including antibiotic policies. Targeted guidance on linking full-scale AMR and antimicrobial consumption (AMC)/antimicrobial residues (AR) surveillance data from the human, animal, and environmental sectors is currently needed. This paper describes the initiative whereby a multidisciplinary panel of experts (56 from 20 countries-52 high income, 4 upper middle or lower income), representing all three sectors, elaborated proposals for structuring and reporting full-scale AMR and AMC/AR surveillance data across the three sectors. An evidence-supported, modified Delphi approach was adopted to reach consensus among the experts for dissemination frequency, language, and overall structure of reporting; core elements and metrics for AMC/AR data; core elements and metrics for AMR data. The recommendations can support multisectoral national and regional plans on antimicrobials policy to reduce resistance rates applying a One Health approach.
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Affiliation(s)
- Nithya Babu Rajendran
- Infectious Diseases, Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Fabiana Arieti
- Infectious Diseases Section, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | | | - Liliana Galia
- Infectious Diseases Section, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maela Tebon
- Infectious Diseases Section, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Julio Alvarez
- VISAVET Health Surveillance Center and Department of Animal Health, Faculty of Veterinary Medicine, Complutense University, Madrid, Spain
| | - Beryl Primrose Gladstone
- Infectious Diseases, Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany.,German Centre for Infection Research (DZIF) Clinical Research Unit for Healthcare Associated and Antibiotic Resistant Bacterial Infections, Tübingen, Germany
| | - Lucie Collineau
- French Agency for Food, Environmental and Occupational Health and Safety, ANSES, Maisons-Alfort, France
| | - Giulia De Angelis
- Dipartimento di Scienze Biotecnologiche di base, Cliniche Intensivologiche e Perioperatorie, Universita Cattolica del Sacro Cuore, Rome, Italy
| | - Raquel Duro
- Unit for the Prevention and Control of Infection and Antimicrobial Resistance, Centro Hospitalar do Tâmega e Sousa, Penafiel, Porto, Portugal
| | - William Gaze
- The European Centre for Environment and Human Health, University of Exeter Medical School, University of Exeter, Penryn, Cornwall, UK
| | - Siri Göpel
- Infectious Diseases, Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany.,German Centre for Infection Research (DZIF) Clinical Research Unit for Healthcare Associated and Antibiotic Resistant Bacterial Infections, Tübingen, Germany
| | - Souha S Kanj
- Department of Internal Medicine, Division of Infectious Diseases, Infection Control Program, Antimicrobial Stewardship Program, American University of Beirut Medical Center, Beirut, Lebanon
| | - Annemarie Käsbohrer
- German Federal Institute for Risk Assessment (BfR), Department 4 - Biological Safety, Berlin, Germany
| | - Direk Limmathurotsakul
- Mahidol Oxford Tropical Medicine Research Unit and Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK
| | | | - Elena Mazzolini
- Department of Epidemiology, Istituto Zooprofilattico Sperimentale delle Venezie, Udine-Padova, Padua, Italy
| | - Nico T Mutters
- Institute for Hygiene and Public Health, Bonn University Hospital, Bonn, Germany.,European Committee on Infection Control, Basel, Switzerland
| | - Maria Diletta Pezzani
- Infectious Diseases Section, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elisabeth Presterl
- European Committee on Infection Control, Basel, Switzerland.,Department of Infection Control and Hospital Epidemiology, Medical University of Vienna, Vienna, Austria.,ESCMID Study Group for Nosocomial Infections, Basel, Switzerland
| | - Hanna Renk
- Department of Paediatric Cardiology, Pulmology and Intensive Care Medicine, University Children's Hospital Tübingen, Tübingen, Germany
| | - Jesús Rodríguez-Baño
- Infectious Diseases and Microbiology Division, Hospital Universitario Virgen Macarena/Department of Medicine, School of Medicine, University of Seville/Biomedicine Institute of Seville (IBiS)/CSIC, Seville, Spain.,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Oana Săndulescu
- Department of Infectious Diseases I, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,National Institute for Infectious Diseases "Prof. Dr. Matei Balș", Bucharest, Romania
| | - Federico Scali
- Istituto Zooprofilattico Sperimentale della Lombardia e Dell'Emilia Romagna, Brescia, Italy
| | - Robert Skov
- Epidemiological Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany.,Vietnamese - German Center for Medical Research, Hanoi, Vietnam
| | - Cuong Vuong
- AiCuris Anti-infective Cures GmbH, Wuppertal, Germany.,Jansen Pharmaceuticals, Beerse, Belgium
| | - Evelina Tacconelli
- Infectious Diseases Section, Department of Diagnostics and Public Health, University of Verona, Verona, Italy.,European Committee on Infection Control, Basel, Switzerland
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17
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Van Dijck C, Laumen JGE, de Block T, Abdellati S, De Baetselier I, Tsoumanis A, Malhotra-Kumar S, Manoharan-Basil SS, Kenyon C, Xavier BB. The oropharynx of men using HIV pre-exposure prophylaxis is enriched with antibiotic resistance genes: A cross-sectional observational metagenomic study. J Infect 2023; 86:329-337. [PMID: 36764395 DOI: 10.1016/j.jinf.2023.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND Phenotypic studies have found high levels of antimicrobial resistance to cephalosporins, macrolides and fluoroquinolones in commensal Neisseria species in the oropharynx of men who have sex with men (MSM) using HIV pre-exposure prophylaxis (PrEP). These species include Neisseria subflava and Neisseria mucosa. This may represent a risk to pathogens like Neisseria gonorrhoeae which tend to take up antibiotic resistance genes (ARGs) from other bacteria. We aimed to explore to what extent the oropharyngeal resistome of MSM using PrEP differed from the general population. METHODS We collected oropharyngeal swabs from 32 individuals of the general population and from 64 MSM using PrEP. Thirty-two MSM had consumed antibiotics in the previous six months, whereas none of the other participants had. Samples underwent shotgun metagenomic sequencing. Sequencing reads were mapped against MEGARes 2.0 to estimate ARG abundance. ARG abundance was compared between groups by zero-inflated negative binomial regression. FINDINGS ARG abundance was significantly lower in the general population than in MSM (ratio 0.41, 95% CI 0.26-0.65). More specifically, this was the case for fluoroquinolones (0.33, 95% CI 0.15-0.69), macrolides (0.37, 95% CI 0.25-0.56), tetracyclines (0.41, 95% CI 0.25-0.69), and multidrug efflux pumps (0.11, 95% CI 0.03-0.33), but not for beta-lactams (1.38, 95% CI 0.73-2.61). There were no significant differences in ARG abundance between MSM who had used antibiotics and those that had not. INTERPRETATION The resistome of MSM using PrEP is enriched with ARGs, independent of recent antibiotic use. Stewardship campaigns should aim to reduce antibiotic consumption in populations at high risk for STIs.
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Affiliation(s)
- Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium; Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
| | - Jolein Gyonne Elise Laumen
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium; Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
| | - Tessa de Block
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium.
| | - Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium.
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium.
| | - Achilleas Tsoumanis
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium.
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
| | | | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium; University of Cape Town, Rondebosch, Cape Town 7700, South Africa.
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
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18
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Ekinci E, Willen L, Rodriguez Ruiz JP, Maertens K, Van Heirstraeten L, Serrano G, Wautier M, Deplano A, Goossens H, Van Damme P, Beutels P, Malhotra-Kumar S, Martiny D, Theeten H. Haemophilus influenzae carriage and antibiotic resistance profile in Belgian infants over a three-year period (2016-2018). Front Microbiol 2023; 14:1160073. [PMID: 37168112 PMCID: PMC10164969 DOI: 10.3389/fmicb.2023.1160073] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/03/2023] [Indexed: 05/13/2023] Open
Abstract
Background Non-typeable Haemophilus influenzae has become increasingly important as a causative agent of invasive diseases following vaccination against H. influenzae type b. The emergence of antibiotic resistance underscores the necessity to investigate typeable non-b carriage and non-typeable H. influenzae (NTHi) in children. Methods Nasopharyngeal swab samples were taken over a three-year period (2016-2018) from 336 children (6-30 months of age) attending daycare centers (DCCs) in Belgium, and from 218 children with acute otitis media (AOM). Biotype, serotype, and antibiotic resistance of H. influenzae strains were determined phenotypically. Mutations in the ftsI gene were explored in 129 strains that were resistant or had reduced susceptibility to beta-lactam antibiotics. Results were compared with data obtained during overlapping time periods from 94 children experiencing invasive disease. Results Overall, NTHi was most frequently present in both carriage (DCC, AOM) and invasive group. This was followed by serotype "f" (2.2%) and "e" (1.4%) in carriage, and "b" (16.0%), "f" (11.7%), and "a" (4.3%) in invasive strains. Biotype II was most prevalent in all studied groups, followed by biotype III in carriage and I in invasive strains. Strains from both groups showed highest resistance to ampicillin (26.7% in carriage vs. 18.1% in invasive group). A higher frequency of ftsI mutations were found in the AOM group than the DCC group (21.6 vs. 14.9% - p = 0.056). Even more so, the proportion of biotype III strains that carried a ftsI mutation was higher in AOM compared to DCC (50.0 vs. 26.3% - p < 0.01) and invasive group. Conclusion In both groups, NTHi was most frequently circulating, while specific encapsulated serotypes for carriage and invasive group were found. Biotypes I, II and III were more frequently present in the carriage and invasive group. The carriage group had a higher resistance-frequency to the analyzed antibiotics than the invasive group. Interestingly, a higher degree of ftsI mutations was found in children with AOM compared to DCC and invasive group. This data helps understanding the H. influenzae carriage in Belgian children, as such information is scarce.
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Affiliation(s)
- Esra Ekinci
- Centre for the Evaluation of Vaccination, University of Antwerp, Wilrijk, Belgium
- *Correspondence: Esra Ekinci,
| | - Laura Willen
- Centre for the Evaluation of Vaccination, University of Antwerp, Wilrijk, Belgium
| | | | - Kirsten Maertens
- Centre for the Evaluation of Vaccination, University of Antwerp, Wilrijk, Belgium
| | | | - Gabriela Serrano
- National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles – Universitair Laboratorium Brussel (LHUB-ULB), Brussels, Belgium
| | - Magali Wautier
- National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles – Universitair Laboratorium Brussel (LHUB-ULB), Brussels, Belgium
| | - Ariane Deplano
- National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles – Universitair Laboratorium Brussel (LHUB-ULB), Brussels, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, University of Antwerp, Wilrijk, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination, University of Antwerp, Wilrijk, Belgium
| | - Philippe Beutels
- Centre for Health Economics Research and Modelling Infectious Diseases, University of Antwerp, Wilrijk, Belgium
| | | | - Delphine Martiny
- National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles – Universitair Laboratorium Brussel (LHUB-ULB), Brussels, Belgium
| | - Heidi Theeten
- Centre for the Evaluation of Vaccination, University of Antwerp, Wilrijk, Belgium
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19
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Konnova A, De Winter FHR, Gupta A, Verbruggen L, Hotterbeekx A, Berkell M, Teuwen LA, Vanhoutte G, Peeters B, Raats S, der Massen IV, De Keersmaecker S, Debie Y, Huizing M, Pannus P, Neven KY, Ariën KK, Martens GA, Bulcke MVD, Roelant E, Desombere I, Anguille S, Berneman Z, Goossens ME, Goossens H, Malhotra-Kumar S, Tacconelli E, Vandamme T, Peeters M, van Dam P, Kumar-Singh S. Predictive model for BNT162b2 vaccine response in cancer patients based on blood cytokines and growth factors. Front Immunol 2022; 13:1062136. [PMID: 36618384 PMCID: PMC9813584 DOI: 10.3389/fimmu.2022.1062136] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Background Patients with cancer, especially hematological cancer, are at increased risk for breakthrough COVID-19 infection. So far, a predictive biomarker that can assess compromised vaccine-induced anti-SARS-CoV-2 immunity in cancer patients has not been proposed. Methods We employed machine learning approaches to identify a biomarker signature based on blood cytokines, chemokines, and immune- and non-immune-related growth factors linked to vaccine immunogenicity in 199 cancer patients receiving the BNT162b2 vaccine. Results C-reactive protein (general marker of inflammation), interleukin (IL)-15 (a pro-inflammatory cytokine), IL-18 (interferon-gamma inducing factor), and placental growth factor (an angiogenic cytokine) correctly classified patients with a diminished vaccine response assessed at day 49 with >80% accuracy. Amongst these, CRP showed the highest predictive value for poor response to vaccine administration. Importantly, this unique signature of vaccine response was present at different studied timepoints both before and after vaccination and was not majorly affected by different anti-cancer treatments. Conclusion We propose a blood-based signature of cytokines and growth factors that can be employed in identifying cancer patients at persistent high risk of COVID-19 despite vaccination with BNT162b2. Our data also suggest that such a signature may reflect the inherent immunological constitution of some cancer patients who are refractive to immunotherapy.
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Affiliation(s)
- Angelina Konnova
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium,Laboratory of Medical Microbiology, Vaccine and Infectious disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Fien H. R. De Winter
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Akshita Gupta
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium,Laboratory of Medical Microbiology, Vaccine and Infectious disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Lise Verbruggen
- Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium
| | - An Hotterbeekx
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Matilda Berkell
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium,Laboratory of Medical Microbiology, Vaccine and Infectious disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Laure-Anne Teuwen
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Greetje Vanhoutte
- Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium,Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Bart Peeters
- Department of Laboratory Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Silke Raats
- Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium
| | - Isolde Van der Massen
- Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium
| | - Sven De Keersmaecker
- Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium
| | - Yana Debie
- Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium,Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Manon Huizing
- Biobank, Antwerp University Hospital, Edegem, Belgium
| | - Pieter Pannus
- Scientific Directorate Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Kristof Y. Neven
- Scientific Directorate Epidemiology and Public Health, Sciensano, Brussels, Belgium,Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium,Federal Public Service (FPS) Health, Food Chain Safety and Environment, Brussels, Belgium
| | - Kevin K. Ariën
- Virology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium,Department of Biomedical Sciences, University of Antwerp, Edegem, Belgium
| | - Geert A. Martens
- Department of Laboratory Medicine, AZ Delta General Hospital, Roeselare, Belgium
| | - Marc Van Den Bulcke
- Scientific Directorate Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Ella Roelant
- Clinical Trial Center (CTC), Clinical Research Centre (CRC) Antwerp, Antwerp University Hospital, University of Antwerp, Edegem, Belgium,StatUa, Center for Statistics, University of Antwerp, Antwerp, Belgium
| | - Isabelle Desombere
- Service Immune response, Scientific Directorate Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Sébastien Anguille
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Zwi Berneman
- Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium,Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Maria E. Goossens
- Scientific Directorate Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Timon Vandamme
- Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium,Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Marc Peeters
- Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium,Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Peter van Dam
- Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium,Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Samir Kumar-Singh
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium,Laboratory of Medical Microbiology, Vaccine and Infectious disease Institute, University of Antwerp, Wilrijk, Belgium,*Correspondence: Samir Kumar-Singh,
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20
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Ekinci E, Van Heirstraeten L, Willen L, Desmet S, Wouters I, Vermeulen H, Lammens C, Goossens H, Van Damme P, Verhaegen J, Beutels P, Theeten H, Malhotra-Kumar S. Serotype 19A and 6C Account for One-Third of Pneumococcal Carriage Among Belgian Day-Care Children Four Years After a Shift to a Lower-Valent PCV. J Pediatric Infect Dis Soc 2022; 12:36-42. [PMID: 36377804 PMCID: PMC9909365 DOI: 10.1093/jpids/piac117] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Pneumococcal conjugate vaccines (PCVs) effectively reduce infection and asymptomatic carriage of Streptococcus pneumoniae vaccine serotypes. In 2016, Belgium replaced its infant PCV13 program by a 4-year period of PCV10. Concomitantly, S. pneumoniae serotype carriage was monitored together with the carriage of other nasopharyngeal pathogens in children attending day-care centers. METHODS From 2016 to 2019, a total of 3459 nasopharyngeal swabs were obtained from children aged 6-30 months. Culture and qPCR were used for the identification of S. pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus and for serotyping and antimicrobial susceptibility assessment of S. pneumoniae strains. RESULTS S. pneumoniae colonization was frequent and stable over the study years. H. influenzae and M. catarrhalis were more frequently carried (P < .001) than S. pneumoniae, by, respectively, 92.3% and 91.0% of children. Prevalence of all PCV13 serotypes together increased significantly over time from 5.8% to 19.6% (P < .001) and was attributable to the increasing prevalence of serotype 19A. Coincidently, non-vaccine serotype 6C increased (P < .001) and the overall pneumococcal non-susceptibility to tetracycline and erythromycin. Non-susceptibility to cotrimoxazole decreased (P < .001). CONCLUSIONS The switch to a PCV program no longer covering serotypes 19A, 6A, and 3 was associated with a sustained increase of serotypes 19A and 6C in healthy children, similarly as in invasive pneumococcal disease. This resulted in a re-introduction of the 13-valent conjugate vaccine during the summer of 2019.
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Affiliation(s)
- Esra Ekinci
- Corresponding Author: Esra Ekinci, Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium. E-mail:
| | | | - Laura Willen
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Stefanie Desmet
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Ine Wouters
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | | | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Jan Verhaegen
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Beutels
- Centre for Health Economics Research and Modelling Infectious Diseases, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Heidi Theeten
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
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21
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Coppens J, Xavier BB, Vlaeminck J, Larsen J, Lammens C, Van Puyvelde S, Goossens H, Larsen AR, Malhotra-Kumar S. Genomic analysis of methicillin-resistant Staphylococcus aureus clonal complex 239 isolated from Danish patients with and without an international travel history. Front Microbiol 2022; 13:1016829. [PMID: 36504833 PMCID: PMC9730231 DOI: 10.3389/fmicb.2022.1016829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction International travel has been a major determinant for the introduction of pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) into naïve geographic areas. MRSA clonal complex 239 (CC239) is a highly virulent clone that is predominant in Asia. The objective of this study was to determine the geographic origin of MRSA CC239 isolates recovered from Danish cases with or without a history of international travel during 2004-2016. Materials and methods Human MRSA isolates with spa types t030 and t037 (n = 60) were obtained from the National Reference Laboratory for Antimicrobial Resistance. For each case, the following data were collected from notification forms: sex, age, isolation year, specimen source (screening swab or clinical sample), infection type, and international travel history. All isolates were whole-genome sequenced, and a comparative genome and phylogenetic analysis was performed. Results The majority of isolates originated from skin and soft tissue (SST) infections and screening swabs. In 31 out of 60 cases reported international travel to different parts of the world. Fifty-four isolates belonged to CC239, including sequence type 239 (ST239) (n = 43), ST241 (n = 5), ST4377 (n = 2), ST4378 (n = 1), ST1465 (n = 1), ST343 (n = 1), and ST592 (n = 1). The majority of the CC239 MRSA isolates (40/54) belonged to well-known geographic clades, including the Asian (n = 12), Serbian (n = 11), South American (n = 2), and Turkish (n = 15). Most MRSA ST239 isolates belonging to the highly virulent Asian clade carried sasX and were recovered from individuals who had travelled to Asia, Africa and the Middle East. Conclusion Our data reveal multiple introductions of MRSA CC239 into Denmark through international travel, which highlights the importance of continued genomic surveillance of MRSA in persons returning from international travel to areas where MRSA is endemic.
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Affiliation(s)
- Jasmine Coppens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Jelle Vlaeminck
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Sandra Van Puyvelde
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium,Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium,*Correspondence: Surbhi Malhotra-Kumar,
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22
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Lin Q, Xavier BB, Alako BTF, Mitchell AL, Rajakani SG, Glupczynski Y, Finn RD, Cochrane G, Malhotra-Kumar S. Screening of global microbiomes implies ecological boundaries impacting the distribution and dissemination of clinically relevant antimicrobial resistance genes. Commun Biol 2022; 5:1217. [DOI: 10.1038/s42003-022-04187-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/28/2022] [Indexed: 11/19/2022] Open
Abstract
AbstractUnderstanding the myriad pathways by which antimicrobial-resistance genes (ARGs) spread across biomes is necessary to counteract the global menace of antimicrobial resistance. We screened 17939 assembled metagenomic samples covering 21 biomes, differing in sequencing quality and depth, unevenly across 46 countries, 6 continents, and 14 years (2005-2019) for clinically crucial ARGs, mobile colistin resistance (mcr), carbapenem resistance (CR), and (extended-spectrum) beta-lactamase (ESBL and BL) genes. These ARGs were most frequent in human gut, oral and skin biomes, followed by anthropogenic (wastewater, bioreactor, compost, food), and natural biomes (freshwater, marine, sediment). Mcr-9 was the most prevalent mcr gene, spatially and temporally; blaOXA-233 and blaTEM-1 were the most prevalent CR and BL/ESBL genes, but blaGES-2 and blaTEM-116 showed the widest distribution. Redundancy analysis and Bayesian analysis showed ARG distribution was non-random and best-explained by potential host genera and biomes, followed by collection year, anthropogenic factors and collection countries. Preferential ARG occurrence, and potential transmission, between characteristically similar biomes indicate strong ecological boundaries. Our results provide a high-resolution global map of ARG distribution and importantly, identify checkpoint biomes wherein interventions aimed at disrupting ARGs dissemination are likely to be most effective in reducing dissemination and in the long term, the ARG global burden.
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23
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Chastre J, François B, Bourgeois M, Komnos A, Ferrer R, Rahav G, De Schryver N, Lepape A, Koksal I, Luyt CE, Sánchez-García M, Torres A, Eggimann P, Koulenti D, Holland TL, Ali O, Shoemaker K, Ren P, Sauser J, Ruzin A, Tabor DE, Akhgar A, Wu Y, Jiang Y, DiGiandomenico A, Colbert S, Vandamme D, Coenjaerts F, Malhotra-Kumar S, Timbermont L, Oliver A, Barraud O, Bellamy T, Bonten M, Goossens H, Reisner C, Esser MT, Jafri HS. Safety, efficacy, and pharmacokinetics of gremubamab (MEDI3902), an anti-Pseudomonas aeruginosa bispecific human monoclonal antibody, in P. aeruginosa-colonised, mechanically ventilated intensive care unit patients: a randomised controlled trial. Crit Care 2022; 26:355. [PMID: 36380312 PMCID: PMC9666938 DOI: 10.1186/s13054-022-04204-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 09/12/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Ventilator-associated pneumonia caused by Pseudomonas aeruginosa (PA) in hospitalised patients is associated with high mortality. The effectiveness of the bivalent, bispecific mAb MEDI3902 (gremubamab) in preventing PA nosocomial pneumonia was assessed in PA-colonised mechanically ventilated subjects. METHODS EVADE (NCT02696902) was a phase 2, randomised, parallel-group, double-blind, placebo-controlled study in Europe, Turkey, Israel, and the USA. Subjects ≥ 18 years old, mechanically ventilated, tracheally colonised with PA, and without new-onset pneumonia, were randomised (1:1:1) to MEDI3902 500, 1500 mg (single intravenous dose), or placebo. The primary efficacy endpoint was the incidence of nosocomial PA pneumonia through 21 days post-dose in MEDI3902 1500 mg versus placebo, determined by an independent adjudication committee. RESULTS Even if the initial sample size was not reached because of low recruitment, 188 subjects were randomised (MEDI3902 500/1500 mg: n = 16/87; placebo: n = 85) between 13 April 2016 and 17 October 2019. Out of these, 184 were dosed (MEDI3902 500/1500 mg: n = 16/85; placebo: n = 83), comprising the modified intent-to-treat set. Enrolment in the 500 mg arm was discontinued due to pharmacokinetic data demonstrating low MEDI3902 serum concentrations. Subsequently, enrolled subjects were randomised (1:1) to MEDI3902 1500 mg or placebo. PA pneumonia was confirmed in 22.4% (n = 19/85) of MEDI3902 1500 mg recipients and in 18.1% (n = 15/83) of placebo recipients (relative risk reduction [RRR]: - 23.7%; 80% confidence interval [CI] - 83.8%, 16.8%; p = 0.49). At 21 days post-1500 mg dose, the mean (standard deviation) serum MEDI3902 concentration was 9.46 (7.91) μg/mL, with 80.6% (n = 58/72) subjects achieving concentrations > 1.7 μg/mL, a level associated with improved outcome in animal models. Treatment-emergent adverse event incidence was similar between groups. CONCLUSIONS The bivalent, bispecific monoclonal antibody MEDI3902 (gremubamab) did not reduce PA nosocomial pneumonia incidence in PA-colonised mechanically ventilated subjects. Trial registration Registered on Clinicaltrials.gov ( NCT02696902 ) on 11th February 2016 and on EudraCT ( 2015-001706-34 ) on 7th March 2016.
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Affiliation(s)
- Jean Chastre
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Sorbonne University, 47-83 Bd de l'Hôpital, 75651, Paris, France.
| | - Bruno François
- Réanimation Polyvalente and Inserm CIC 1435 & UMR 1092, CHU, Limoges, France
| | | | | | - Ricard Ferrer
- SODIR-VHIR Research Group, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Galia Rahav
- Chaim Sheba Medical Center, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Alain Lepape
- Hospices Civils de Lyon Hôpital Lyon Sud, Lyon, France
| | - Iftihar Koksal
- Faculty of Medicine, Trabzon and Acibadem University Faculty of Medicine, Karadeniz Technical University, Istanbul, Turkey
| | - Charles-Edouard Luyt
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Sorbonne University, 47-83 Bd de l'Hôpital, 75651, Paris, France
| | - Miguel Sánchez-García
- Critical Care Department, Hospital Clínico San Carlos, Universidad Complutense, Madrid, Spain
| | - Antoni Torres
- Servei de Pneumologia, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERES, ICREA, Barcelona, Spain
| | - Philippe Eggimann
- Department of Locomotor Apparatus, Centre Hospitalier Universitaire Vaudois CHUV, Lausanne, Switzerland
| | - Despoina Koulenti
- The University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- 2nd Critical Care Department, Attikon University Hospital, National and Kapodistrian, University of Athens, Athens, Greece
| | | | - Omar Ali
- Clinical Research and Development, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca Biopharmaceuticals, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Kathryn Shoemaker
- Clinical Research and Development, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca Biopharmaceuticals, One MedImmune Way, Gaithersburg, MD, 20878, USA
- Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Pin Ren
- Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Julien Sauser
- Infection Control Program, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Alexey Ruzin
- Clinical Research and Development, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca Biopharmaceuticals, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - David E Tabor
- Clinical Research and Development, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca Biopharmaceuticals, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Ahmad Akhgar
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Yuling Wu
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Yu Jiang
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Antonio DiGiandomenico
- Clinical Research and Development, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca Biopharmaceuticals, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | | | | | - Frank Coenjaerts
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Institut d'Investigació Sanitaria Illes Balears, Palma, Spain
| | - Olivier Barraud
- INSERM U1092, Centre Hospitalier Universitaire de Limoges, Université Limoges, Limoges, France
| | - Terramika Bellamy
- Clinical Research and Development, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca Biopharmaceuticals, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Marc Bonten
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Colin Reisner
- Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
- DevPro Biopharma, Basking Ridge, NJ, USA
| | - Mark T Esser
- Clinical Research and Development, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca Biopharmaceuticals, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Hasan S Jafri
- Clinical Research and Development, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca Biopharmaceuticals, One MedImmune Way, Gaithersburg, MD, 20878, USA.
- Late-Stage Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA.
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Vlaeminck J, Lin Q, Xavier BB, De Backer S, Berkell M, De Greve H, Hernalsteens JP, Kumar-Singh S, Goossens H, Malhotra-Kumar S. The dynamic transcriptome during maturation of biofilms formed by methicillin-resistant Staphylococcus aureus. Front Microbiol 2022; 13:882346. [PMID: 35966712 PMCID: PMC9366926 DOI: 10.3389/fmicb.2022.882346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/23/2022] [Accepted: 07/04/2022] [Indexed: 01/21/2023] Open
Abstract
BackgroundMethicillin-resistant Staphylococcus aureus (MRSA), a leading cause of chronic infections, forms prolific biofilms which afford an escape route from antibiotic treatment and host immunity. However, MRSA clones are genetically diverse, and mechanisms underlying biofilm formation remain under-studied. Such studies form the basis for developing targeted therapeutics. Here, we studied the temporal changes in the biofilm transcriptome of three pandemic MRSA clones: USA300, HEMRSA-15, and ST239.MethodsBiofilm formation was assessed using a static model with one representative strain per clone. Total RNA was extracted from biofilm and planktonic cultures after 24, 48, and 72 h of growth, followed by rRNA depletion and sequencing (Illumina Inc., San Diego, CA, United States, NextSeq500, v2, 1 × 75 bp). Differentially expressed gene (DEG) analysis between phenotypes and among early (24 h), intermediate (48 h), and late (72 h) stages of biofilms was performed together with in silico co-expression network construction and compared between clones. To understand the influence of SCCmec and ACME on biofilm formation, isogenic mutants containing deletions of the entire elements or of single genes therein were constructed in USA300.ResultsGenes involved in primarily core genome-encoded KEGG pathways (transporters and others) were upregulated in 24-h biofilm culture compared to 24-h planktonic culture. However, the number of affected pathways in the ST239 24 h biofilm (n = 11) was remarkably lower than that in USA300/EMRSA-15 biofilms (USA300: n = 27, HEMRSA-15: n = 58). The clfA gene, which encodes clumping factor A, was the single common DEG identified across the three clones in 24-h biofilm culture (2.2- to 2.66-fold). In intermediate (48 h) and late (72 h) stages of biofilms, decreased expression of central metabolic and fermentative pathways (glycolysis/gluconeogenesis, fatty acid biosynthesis), indicating a shift to anaerobic conditions, was already evident in USA300 and HEMRSA-15 in 48-h biofilm cultures; ST239 showed a similar profile at 72 h. Last, SCCmec+ACME deletion and opp3D disruption negatively affected USA300 biofilm formation.ConclusionOur data show striking differences in gene expression during biofilm formation by three of the most important pandemic MRSA clones, USA300, HEMRSA-15, and ST239. The clfA gene was the only significantly upregulated gene across all three strains in 24-h biofilm cultures and exemplifies an important target to disrupt early biofilms. Furthermore, our data indicate a critical role for arginine catabolism pathways in early biofilm formation.
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Affiliation(s)
- Jelle Vlaeminck
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Qiang Lin
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Sarah De Backer
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Matilda Berkell
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, University of Antwerp, Antwerp, Belgium
| | - Henri De Greve
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Samir Kumar-Singh
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, University of Antwerp, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- *Correspondence: Surbhi Malhotra-Kumar,
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25
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Savoldi A, Morra M, De Nardo P, Cattelan AM, Mirandola M, Manfrin V, Scotton P, Giordani MT, Brollo L, Panese S, Lanzafame M, Scroccaro G, Berkell M, Lippi G, Konnova A, Smet M, Malhotra-Kumar S, Kumar-Singh S, Tacconelli E. Clinical efficacy of different monoclonal antibody regimens among non-hospitalised patients with mild to moderate COVID-19 at high risk for disease progression: a prospective cohort study. Eur J Clin Microbiol Infect Dis 2022; 41:1065-1076. [PMID: 35727429 PMCID: PMC9209841 DOI: 10.1007/s10096-022-04464-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/31/2022] [Indexed: 11/25/2022]
Abstract
This study aimed to compare the clinical progression of COVID-19 in high-risk outpatients treated with the monoclonal antibodies (mAb) bamlanivimab, bamlanivimab-etesevimab and casirivimab-imdevimab. This is an observational, multi-centre, prospective study conducted from 18 March to 15 July 2021 in eight Italian tertiary-care hospitals including mild-to-moderate COVID-19 outpatients receiving bamlanivimab (700 mg), bamlanivimab-etesevimab (700–1400 mg) or casirivimab-imdevimab (1200–1200 mg). All patients were at high risk of COVID-19 progression according to Italian Medicines Agency definitions. In a patient subgroup, SARS-CoV-2 variant and anti-SARS-CoV-2 serology were analysed at baseline. Factors associated with 28-day all-cause hospitalisation were identified using multivariable multilevel logistic regression (MMLR) and summarised with adjusted odds ratio (aOR) and 95% confidence interval (CI). A total of 635 outpatients received mAb: 161 (25.4%) bamlanivimab, 396 (62.4%) bamlanivimab-etesevimab and 78 (12.2%) casirivimab-imdevimab. Ninety-five (15%) patients received full or partial SARS-CoV-2 vaccination. The B.1.1.7 (Alpha) variant was detected in 99% of patients. Baseline serology showed no significant differences among the three mAb regimen groups. Twenty-eight-day all-cause hospitalisation was 11.3%, with a significantly higher proportion (p 0.001) in the bamlanivimab group (18.6%), compared to the bamlanivimab-etesevimab (10.1%) and casirivimab-imdevimab (2.6%) groups. On MMLR, aORs for 28-day all-cause hospitalisation were significantly lower in patients receiving bamlanivimab-etesevimab (aOR 0.51, 95% CI 0.30–0.88 p 0.015) and casirivimab-imdevimab (aOR 0.14, 95% CI 0.03–0.61, p 0.009) compared to those receiving bamlanivimab. No patients with a history of vaccination were hospitalised. The study suggests differences in clinical outcomes among the first available mAb regimens for treating high-risk COVID-19 outpatients. Randomised trials are needed to compare efficacy of mAb combination regimens in high-risk populations and according to circulating variants.
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Affiliation(s)
- Alessia Savoldi
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Matteo Morra
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Pasquale De Nardo
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy.
| | - Anna Maria Cattelan
- Infectious Disease Unit, Hospital of Padua, Via Giustiniani 2, 35128, Padua, Italy
| | - Massimo Mirandola
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy.,School of Health Sciences, University of Brighton, Brighton, UK
| | - Vinicio Manfrin
- Division of Infectious and Tropical Diseases, S. Bortolo Hospital, Viale Ferdinando Rodolfi 37, 36100, Vicenza, Italy
| | | | - Maria Teresa Giordani
- Infectious Diseases Unit, Alto Vicentino Santorso Hospital, Azienda ULSS 7via Garziere 42, Santorso, Vicenza, Italy
| | - Lucio Brollo
- Division of Internal Medicine and Cardiology, Infectious Diseases and COVID-19 Section, Jesolo Hospital Via Levantina, 104, 30016, Jesolo, Italy
| | - Sandro Panese
- Infectious Diseases Unit, Azienda ULSS 3 Serenissima, Ss. Giovanni E Paolo Hospital, Castello 6777, 30122, Venice, Italy
| | - Massimiliano Lanzafame
- Division of Infectious Diseases, Ospedale Santa Maria Della Misericordia Hospital, Viale Tre Martiri 140, Rovigo, Rovigo, Italy
| | | | - Matilda Berkell
- Lab of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.,Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Giuseppe Lippi
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - Angelina Konnova
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Mathias Smet
- Lab of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Lab of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Samir Kumar-Singh
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
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26
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Van Heirstraeten L, Ekinci E, Smet M, Berkell M, Willen L, Coppens J, Spiessens A, Xavier BB, Lammens C, Verhaegen J, Van Damme P, Goossens H, Beutels P, Matheeussen V, Desmet S, Theeten H, Malhotra-Kumar S. Detection of SARS-CoV-2 in young children attending day-care centres in Belgium, May 2020 to February 2022. Euro Surveill 2022; 27. [PMID: 35620998 PMCID: PMC9137273 DOI: 10.2807/1560-7917.es.2022.27.21.2200380] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Presence of SARS-CoV-2 was monitored in nasopharyngeal samples from young children aged 6−30 months attending day-care centres (DCCs) in Belgium from May 2020−February 2022. SARS-CoV-2 carriage among DCC children was only detected from November 2021, after emergence of Delta and Omicron variants, in 9 of the 42 DCCs screened. In only one DCC, two children tested positive for SARS-CoV-2 at the same sampling time point, suggesting limited transmission of SARS-CoV-2 in Belgian DCCs among young children during the studied period.
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Affiliation(s)
- Liesbet Van Heirstraeten
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Esra Ekinci
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Mathias Smet
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Matilda Berkell
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Laura Willen
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Jasmine Coppens
- Laboratory of Clinical Microbiology, Antwerp University Hospital, Edegem, Belgium
| | - An Spiessens
- Laboratory of Clinical Microbiology, Antwerp University Hospital, Edegem, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Jan Verhaegen
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium.,Laboratory of Clinical Microbiology, Antwerp University Hospital, Edegem, Belgium
| | - Philippe Beutels
- Centre for Health Economics Research and Modelling Infectious Diseases, University of Antwerp, Wilrijk, Belgium
| | - Veerle Matheeussen
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium.,Laboratory of Clinical Microbiology, Antwerp University Hospital, Edegem, Belgium
| | - Stefanie Desmet
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Heidi Theeten
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
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27
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Jongers B, Hotterbeekx A, Bielen K, Vervliet P, Boddaert J, Lammens C, Fransen E, Baggerman G, Covaci A, Goossens H, Malhotra-Kumar S, Jorens PG, Kumar-Singh S. Identification of Potential Urinary Metabolite Biomarkers of Pseudomonas aeruginosa Ventilator-Associated Pneumonia. Biomark Insights 2022; 17:11772719221099131. [PMID: 35592849 PMCID: PMC9112676 DOI: 10.1177/11772719221099131] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/19/2022] [Indexed: 11/16/2022] Open
Abstract
Introduction: Ventilator-associated pneumonia (VAP) caused by Pseudomonas aeruginosa is a major cause of morbidity and mortality in hospital intensive care units (ICU). Rapid identification of P. aeruginosa-derived markers in easily accessible patients’ samples can enable an early detection of P. aeruginosa VAP (VAP-PA), thereby stewarding antibiotic use and improving clinical outcomes. Methods: Metabolites were analysed using liquid chromatography-mass spectrometry (LC-MS) in prospectively collected urine samples from mechanically ventilated patients admitted to the Antwerp University Hospital ICU. Patients were followed from the start of mechanical ventilation (n = 100 patients) till the time of clinical diagnosis of VAP (n = 13). Patients (n = 8) in whom diagnosis of VAP was further confirmed by culturing respiratory samples and urine samples were studied for semi-quantitative metabolomics. Results: We first show that multivariate analyses highly discriminated VAP-PA from VAP–non-PA as well as from the pre-infection groups (R2 = .97 and .98, respectively). A further univariate analysis identified 58 metabolites that were significantly elevated or uniquely present in VAP-PA compared to the VAP–non-PA and pre-infection groups (P < .05). These comprised both a known metabolite of histidine as well as a novel nicotine metabolite. Most interestingly, we identified 3 metabolites that were not only highly upregulated for, but were also highly specific to, VAP-PA, as these metabolites were completely absent in all pre-infection timepoints and in VAP–non-PA group. Conclusions: Considerable differences exist between urine metabolites in VAP-PA compared to VAP due to other bacterial aetiologies as well to non-VAP (pre-infection) timepoints. The unique urinary metabolic biomarkers we describe here, if further validated, could serve as highly specific diagnostic biomarkers of VAP-PA.
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Affiliation(s)
- Bart's Jongers
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, Faculty of Medicine and Health Sciences, Wilrijk, Belgium
| | - An Hotterbeekx
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, Faculty of Medicine and Health Sciences, Wilrijk, Belgium
| | - Kenny Bielen
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, Faculty of Medicine and Health Sciences, Wilrijk, Belgium.,Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | | | - Jan Boddaert
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, Faculty of Medicine and Health Sciences, Wilrijk, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Erik Fransen
- StatUa Center for Statistics, University of Antwerp, Antwerp, Belgium
| | - Geert Baggerman
- CEPROMA - Centre for proteomics and mass spectrometry, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Adrian Covaci
- Toxicological Centre, University of Antwerp, Wilrijk, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Philippe G Jorens
- Department of Critical Care Medicine, Antwerp University Hospital and University of Antwerp, LEMP, Edegem, Belgium
| | - Samir Kumar-Singh
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, Faculty of Medicine and Health Sciences, Wilrijk, Belgium.,Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
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28
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Van Averbeke V, Berkell M, Mysara M, Rodriguez-Ruiz JP, Xavier BB, De Winter FHR, Jongers B', Jairam RK, Hotterbeekx A, Goossens H, Cohen ES, Malhotra-Kumar S, Kumar-Singh S. Host Immunity Influences the Composition of Murine Gut Microbiota. Front Immunol 2022; 13:828016. [PMID: 35371073 PMCID: PMC8965567 DOI: 10.3389/fimmu.2022.828016] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/21/2022] [Indexed: 12/24/2022] Open
Abstract
The influence of gut microbiota on host immunity is widely studied, and its disturbance has been linked to several immune-mediated disorders. Conversely, whether and how inherently disturbed canonical Th1 (pro-inflammatory) and/or Th2 (anti-inflammatory) immune pathways modify the host microbiome is not sufficiently investigated. Here, we characterized the humoral, cellular, and cytokine immunity, and associated alterations in gut microbiota of naïve wild-type mice (C57BL/6 and BALB/c), and mice with deficiencies in Th2 responses (IL-4Rα and IL-33 knockout mice) or in both Th1 and Th2 responses (NOD scid gamma, NSG mice). A global analysis by de novo clustering of 16S rRNA profiles of the gut microbiota independently grouped wild-type immunocompetent (C57BL/6 and BALB/c), Th2-deficient (IL-4Rα-/- and IL-33-/-), and severely immunodeficient (NSG) mice; where wild-type mice, but not Th2 or severely immunodeficient mice, were enriched in gut bacteria that produce short-chain fatty acids. These include members of phyla Firmicutes, Verrucomicrobia, and Bacteroidetes such as Lactobacillus spp., Akkermansia muciniphila, and Odoribacter spp. Further comparison of the two naïve wild-type mouse strains showed higher microbial diversity (Shannon), primarily linked to higher richness (Chao1), as well as a distinct difference in microbial composition (weighted UniFrac) in BALB/c mice compared to C57BL/6. T-cell and blood cytokine analyses demonstrated a Th1-polarization in naïve adaptive immunity in C57BL/6 animals compared to BALB/c mice, and an expected Th2 deficient cellular response in IL-4Rα-/- and IL-33-/- mice compared to its genetic background BALB/c strain. Together, these data suggest that alterations in the Th1/Th2 balance or a complete ablation of Th1/Th2 responses can lead to major alterations in gut microbiota composition and function. Given the similarities between the human and mouse immune systems and gut microbiota, our finding that immune status is a strong driver of gut microbiota composition has important consequences for human immunodeficiency studies.
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Affiliation(s)
- Vincent Van Averbeke
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Matilda Berkell
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium.,Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK-CEN), Mol, Belgium
| | - Juan Pablo Rodriguez-Ruiz
- Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Fien H R De Winter
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Bart 's Jongers
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Ravi Kumar Jairam
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - An Hotterbeekx
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - E Suzanne Cohen
- Bioscience Asthma, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Samir Kumar-Singh
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium.,Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.,Translational Neurosciences, University of Antwerp, Antwerp, Belgium
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29
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Laumen JGE, Abdellati S, Manoharan-Basil SS, Van Dijck C, Van den Bossche D, De Baetselier I, de Block T, Malhotra-Kumar S, Soentjes P, Pirnay JP, Kenyon C, Merabishvili M. Screening of Anorectal and Oropharyngeal Samples Fails to Detect Bacteriophages Infecting Neisseria gonorrhoeae. Antibiotics (Basel) 2022; 11:antibiotics11020268. [PMID: 35203870 PMCID: PMC8868155 DOI: 10.3390/antibiotics11020268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
There are real concerns that Neisseria gonorrhoeae may become untreatable in the near future due to the rapid emergence of antimicrobial resistance. Alternative therapies are thus urgently required. Bacteriophages active against N. gonorrhoeae could play an important role as an antibiotic-sparing therapy. To the best of our knowledge, no bacteriophages active against N. gonorrhoeae have ever been found. The aim of this study was to screen for bacteriophages able to lyse N. gonorrhoeae in oropharyngeal and anorectal swabs of 74 men who have sex with men attending a sexual health clinic in Antwerp, Belgium. We screened 210 swabs but were unable to identify an anti-gonococcal bacteriophage. This is the first report of a pilot screening that systematically searched for anti-gonococcal phages directly from clinical swabs. Further studies may consider screening for phages at other anatomical sites (e.g., stool samples, urine) or in environmental settings (e.g., toilet sewage water of sex clubs or sexually transmitted infection clinics) where N. gonorrhoeae can be found.
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Affiliation(s)
- Jolein Gyonne Elise Laumen
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium;
- Correspondence: ; Tel.: +32-(0)3-345-5398
| | - Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
| | - Sheeba Santhini Manoharan-Basil
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium;
| | - Dorien Van den Bossche
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
| | - Tessa de Block
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium;
| | - Patrick Soentjes
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
- Center for Infectious Diseases, Queen Astrid Military Hospital, Neder-over-Heembeek, 1120 Brussels, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Neder-over-Heembeek, 1120 Brussels, Belgium; (J.-P.P.); (M.M.)
| | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
- Department of Medicine, University of Cape Town, Cape Town 7701, South Africa
| | - Maia Merabishvili
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Neder-over-Heembeek, 1120 Brussels, Belgium; (J.-P.P.); (M.M.)
- Microbiology and Virology (EIBMV), Eliava Institute of Bacteriophage, Tbilisi 0162, Georgia
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30
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van Hal SJ, Willems RJL, Gouliouris T, Ballard SA, Coque TM, Hammerum AM, Hegstad K, Pinholt M, Howden BP, Malhotra-Kumar S, Werner G, Yanagihara K, Earl AM, Raven KE, Corander J, Bowden R. The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis. Lancet Microbe 2022; 3:e133-e141. [PMID: 35146465 PMCID: PMC8810393 DOI: 10.1016/s2666-5247(21)00236-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND The genomic relationships among Enterococcus faecium isolates are the subject of ongoing research that seeks to clarify the origins of observed lineages and the extent of horizontal gene transfer between them, and to robustly identify links between genotypes and phenotypes. E faecium is considered to form distinct groups-A and B-corresponding to isolates derived from patients who were hospitalised (A) and isolates from humans in the community (B). The additional separation of A into the so-called clades A1 and A2 remains an area of uncertainty. We aimed to investigate the relationships between A1 and non-A1 groups and explore the potential role of non-A1 isolates in shaping the population structure of hospital E faecium. METHODS We collected short-read sequence data from invited groups that had previously published E faecium genome data. This hospital-based isolate collection could be separated into three groups (or clades, A1, A2, and B) by augmenting the study genomes with published sequences derived from human samples representing the previously defined genomic clusters. We performed phylogenetic analyses, by constructing maximum-likelihood phylogenetic trees, and identified historical recombination events. We assessed the pan-genome, did resistome analysis, and examined the genomic data to identify mobile genetic elements. Each genome underwent chromosome painting by use of ChromoPainter within FineSTRUCTURE software to assess ancestry and identify hybrid groups. We further assessed highly admixed regions to infer recombination directionality. FINDINGS We assembled a collection of 1095 hospital E faecium sequences from 34 countries, further augmented by 33 published sequences. 997 (88%) of 1128 genomes clustered as A1, 92 (8%) as A2, and 39 (4%) as B. We showed that A1 probably emerged as a clone from within A2 and that, because of ongoing gene flow, hospital isolates currently identified as A2 represent a genetic continuum between A1 and community E faecium. This interchange of genetic material between isolates from different groups results in the emergence of hybrid genomes between clusters. Of the 1128 genomes, 49 (4%) hybrid genomes were identified: 33 previously labelled as A2 and 16 previously labelled as A1. These interactions were fuelled by a directional pattern of recombination mediated by mobile genetic elements. By contrast, the contribution of B group genetic material to A1 was limited to a few small regions of the genome and appeared to be driven by genomic sweep events. INTERPRETATION A2 and B isolates coming into the hospital form an important reservoir for ongoing A1 adaptation, suggesting that effective long-term control of the effect of E faecium could benefit from strategies to reduce these genomic interactions, such as a focus on reducing the acquisition of hospital A1 strains by patients entering the hospital. FUNDING Wellcome Trust.
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Affiliation(s)
- Sebastiaan J van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia,Central Clinical School, University of Sydney, Sydney, NSW, Australia,Correspondence to: Sebastiaan J van Hal, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute, Madrid, Spain,Network Research Centre for Epidemiology and Public Health, Madrid, Spain
| | | | - Kristin Hegstad
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North-Norway, Department of Microbiology and Infection Control, Tromsø, Norway
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Wilrijk, Belgium
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Ashlee M Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, USA
| | | | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway,Parasites and Microbes, Wellcome Sanger Institute, Saffron Walden, UK
| | - Rory Bowden
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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31
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Laumen JGE, Van Dijck C, Manoharan-Basil SS, Abdellati S, De Baetselier I, Cuylaerts V, De Block T, Van den Bossche D, Xavier BB, Malhotra-Kumar S, Kenyon C. Sub-Inhibitory Concentrations of Chlorhexidine Induce Resistance to Chlorhexidine and Decrease Antibiotic Susceptibility in Neisseria gonorrhoeae. Front Microbiol 2021; 12:776909. [PMID: 34899659 PMCID: PMC8660576 DOI: 10.3389/fmicb.2021.776909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/25/2021] [Indexed: 11/21/2022] Open
Abstract
Objectives: Chlorhexidine digluconate (chlorhexidine) and Listerine® mouthwashes are being promoted as alternative treatment options to prevent the emergence of antimicrobial resistance in Neisseria gonorrhoeae. We performed in vitro challenge experiments to assess induction and evolution of resistance to these two mouthwashes and potential cross-resistance to other antimicrobials. Methods: A customized morbidostat was used to subject N. gonorrhoeae reference strain WHO-F to dynamically sustained Listerine® or chlorhexidine pressure for 18 days and 40 days, respectively. Cultures were sampled twice a week and minimal inhibitory concentrations (MICs) of Listerine®, chlorhexidine, ceftriaxone, ciprofloxacin, cefixime and azithromycin were determined using the agar dilution method. Isolates with an increased MIC for Listerine® or chlorhexidine were subjected to whole genome sequencing to track the evolution of resistance. Results: We were unable to increase MICs for Listerine®. Three out of five cultures developed a 10-fold increase in chlorhexidine MIC within 40 days compared to baseline (from 2 to 20 mg/L). Increases in chlorhexidine MIC were positively associated with increases in the MICs of azithromycin and ciprofloxacin. Low-to-higher-level chlorhexidine resistance (2–20 mg/L) was associated with mutations in NorM. Higher-level resistance (20 mg/L) was temporally associated with mutations upstream of the MtrCDE efflux pump repressor (mtrR) and the mlaA gene, part of the maintenance of lipid asymmetry (Mla) system. Conclusion: Exposure to sub-lethal chlorhexidine concentrations may not only enhance resistance to chlorhexidine itself but also cross-resistance to other antibiotics in N. gonorrhoeae. This raises concern regarding the widespread use of chlorhexidine as an oral antiseptic, for example in the field of dentistry.
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Affiliation(s)
- Jolein G E Laumen
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christophe Van Dijck
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | | | - Saïd Abdellati
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Irith De Baetselier
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Vicky Cuylaerts
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tessa De Block
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dorien Van den Bossche
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Basil B Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Chris Kenyon
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Medicine, University of Cape Town, Cape Town, South Africa
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32
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De Winter FHR, Hotterbeekx A, Huizing MT, Konnova A, Fransen E, Jongers B’, Jairam RK, Van averbeke V, Moons P, Roelant E, Le Blon D, Vanden Berghe W, Janssens A, Lybaert W, Croes L, Vulsteke C, Malhotra-Kumar S, Goossens H, Berneman Z, Peeters M, van Dam PA, Kumar-Singh S. Blood Cytokine Analysis Suggests That SARS-CoV-2 Infection Results in a Sustained Tumour Promoting Environment in Cancer Patients. Cancers (Basel) 2021; 13:5718. [PMID: 34830872 PMCID: PMC8616215 DOI: 10.3390/cancers13225718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 10/25/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/26/2022] Open
Abstract
Cytokines, chemokines, and (angiogenic) growth factors (CCGs) have been shown to play an intricate role in the progression of both solid and haematological malignancies. Recent studies have shown that SARS-CoV-2 infection leads to a worse outcome in cancer patients, especially in haematological malignancy patients. Here, we investigated how SARS-CoV-2 infection impacts the already altered CCG levels in solid or haematological malignancies, specifically, whether there is a protective effect or rather a potentially higher risk for major COVID-19 complications in cancer patients due to elevated CCGs linked to cancer progression. Serially analysing immune responses with 55 CCGs in cancer patients under active treatment with or without SARS-CoV-2 infection, we first showed that cancer patients without SARS-CoV-2 infection (n = 54) demonstrate elevated levels of 35 CCGs compared to the non-cancer, non-infected control group of health care workers (n = 42). Of the 35 CCGs, 19 were common to both the solid and haematological malignancy groups and comprised previously described cytokines such as IL-6, TNF-α, IL-1Ra, IL-17A, and VEGF, but also several less well described cytokines/chemokines such as Fractalkine, Tie-2, and T cell chemokine CTACK. Importantly, we show here that 7 CCGs are significantly altered in SARS-CoV-2 exposed cancer patients (n = 52). Of these, TNF-α, IFN-β, TSLP, and sVCAM-1, identified to be elevated in haematological cancers, are also known tumour-promoting factors. Longitudinal analysis conducted over 3 months showed persistence of several tumour-promoting CCGs in SARS-CoV-2 exposed cancer patients. These data demonstrate a need for increased vigilance for haematological malignancy patients as a part of long COVID follow-up.
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Affiliation(s)
- Fien H. R. De Winter
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (F.H.R.D.W.); (A.H.); (A.K.); (B.J.); (R.K.J.); (V.V.a.)
| | - An Hotterbeekx
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (F.H.R.D.W.); (A.H.); (A.K.); (B.J.); (R.K.J.); (V.V.a.)
| | - Manon T. Huizing
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium; (M.T.H.); (A.J.); (Z.B.); (M.P.); (P.A.v.D.)
- Biobank Antwerp, Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium;
| | - Angelina Konnova
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (F.H.R.D.W.); (A.H.); (A.K.); (B.J.); (R.K.J.); (V.V.a.)
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.M.-K.); (H.G.)
| | - Erik Fransen
- StatUa, Center for Statistics, University of Antwerp, 2000 Antwerp, Belgium; (E.F.); (E.R.)
| | - Bart ’s Jongers
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (F.H.R.D.W.); (A.H.); (A.K.); (B.J.); (R.K.J.); (V.V.a.)
| | - Ravi Kumar Jairam
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (F.H.R.D.W.); (A.H.); (A.K.); (B.J.); (R.K.J.); (V.V.a.)
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.M.-K.); (H.G.)
| | - Vincent Van averbeke
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (F.H.R.D.W.); (A.H.); (A.K.); (B.J.); (R.K.J.); (V.V.a.)
| | - Pieter Moons
- Biobank Antwerp, Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium;
| | - Ella Roelant
- StatUa, Center for Statistics, University of Antwerp, 2000 Antwerp, Belgium; (E.F.); (E.R.)
- Clinical Trial Center (CTC), CRC Antwerp, Antwerp University Hospital, University of Antwerp, Drie Eikenstraat 655, 2650 Edegem, Belgium;
| | - Debbie Le Blon
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (D.L.B.); (L.C.)
| | - Wim Vanden Berghe
- PPES Lab Protein Chemistry, Proteomics & Epigenetic Signaling, IPPON, Department Biomedical Sciences, University Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium;
| | - Annelies Janssens
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium; (M.T.H.); (A.J.); (Z.B.); (M.P.); (P.A.v.D.)
| | - Willem Lybaert
- Department of Medical Oncology, AZ Nikolaas, Moerlandstraat 1, 9100 Sint-Niklaas, Belgium;
| | - Lieselot Croes
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (D.L.B.); (L.C.)
- Integrated Cancer Center Ghent, Department of Medical Oncology, AZ Maria Middelares, Buitenring Sint-Denijs 30, 9000 Ghent, Belgium
| | - Christof Vulsteke
- Clinical Trial Center (CTC), CRC Antwerp, Antwerp University Hospital, University of Antwerp, Drie Eikenstraat 655, 2650 Edegem, Belgium;
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (D.L.B.); (L.C.)
- Integrated Cancer Center Ghent, Department of Medical Oncology, AZ Maria Middelares, Buitenring Sint-Denijs 30, 9000 Ghent, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.M.-K.); (H.G.)
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.M.-K.); (H.G.)
| | - Zwi Berneman
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium; (M.T.H.); (A.J.); (Z.B.); (M.P.); (P.A.v.D.)
| | - Marc Peeters
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium; (M.T.H.); (A.J.); (Z.B.); (M.P.); (P.A.v.D.)
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (D.L.B.); (L.C.)
| | - Peter A. van Dam
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium; (M.T.H.); (A.J.); (Z.B.); (M.P.); (P.A.v.D.)
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (D.L.B.); (L.C.)
| | - Samir Kumar-Singh
- Molecular Pathology Group, Laboratory of Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (F.H.R.D.W.); (A.H.); (A.K.); (B.J.); (R.K.J.); (V.V.a.)
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.M.-K.); (H.G.)
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Bielicki JA, Stöhr W, Barratt S, Dunn D, Naufal N, Roland D, Sturgeon K, Finn A, Rodriguez-Ruiz JP, Malhotra-Kumar S, Powell C, Faust SN, Alcock AE, Hall D, Robinson G, Hawcutt DB, Lyttle MD, Gibb DM, Sharland M. Effect of Amoxicillin Dose and Treatment Duration on the Need for Antibiotic Re-treatment in Children With Community-Acquired Pneumonia: The CAP-IT Randomized Clinical Trial. JAMA 2021; 326:1713-1724. [PMID: 34726708 PMCID: PMC8564579 DOI: 10.1001/jama.2021.17843] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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: 12/11/2022]
Abstract
IMPORTANCE The optimal dose and duration of oral amoxicillin for children with community-acquired pneumonia (CAP) are unclear. OBJECTIVE To determine whether lower-dose amoxicillin is noninferior to higher dose and whether 3-day treatment is noninferior to 7 days. DESIGN, SETTING, AND PARTICIPANTS Multicenter, randomized, 2 × 2 factorial noninferiority trial enrolling 824 children, aged 6 months and older, with clinically diagnosed CAP, treated with amoxicillin on discharge from emergency departments and inpatient wards of 28 hospitals in the UK and 1 in Ireland between February 2017 and April 2019, with last trial visit on May 21, 2019. INTERVENTIONS Children were randomized 1:1 to receive oral amoxicillin at a lower dose (35-50 mg/kg/d; n = 410) or higher dose (70-90 mg/kg/d; n = 404), for a shorter duration (3 days; n = 413) or a longer duration (7 days; n = 401). MAIN OUTCOMES AND MEASURES The primary outcome was clinically indicated antibiotic re-treatment for respiratory infection within 28 days after randomization. The noninferiority margin was 8%. Secondary outcomes included severity/duration of 9 parent-reported CAP symptoms, 3 antibiotic-related adverse events, and phenotypic resistance in colonizing Streptococcus pneumoniae isolates. RESULTS Of 824 participants randomized into 1 of the 4 groups, 814 received at least 1 dose of trial medication (median [IQR] age, 2.5 years [1.6-2.7]; 421 [52%] males and 393 [48%] females), and the primary outcome was available for 789 (97%). For lower vs higher dose, the primary outcome occurred in 12.6% with lower dose vs 12.4% with higher dose (difference, 0.2% [1-sided 95% CI -∞ to 4.0%]), and in 12.5% with 3-day treatment vs 12.5% with 7-day treatment (difference, 0.1% [1-sided 95% CI -∞ to 3.9]). Both groups demonstrated noninferiority with no significant interaction between dose and duration (P = .63). Of the 14 prespecified secondary end points, the only significant differences were 3-day vs 7-day treatment for cough duration (median 12 days vs 10 days; hazard ratio [HR], 1.2 [95% CI, 1.0 to 1.4]; P = .04) and sleep disturbed by cough (median, 4 days vs 4 days; HR, 1.2 [95% CI, 1.0 to 1.4]; P = .03). Among the subgroup of children with severe CAP, the primary end point occurred in 17.3% of lower-dose recipients vs 13.5% of higher-dose recipients (difference, 3.8% [1-sided 95% CI, -∞ to10%]; P value for interaction = .18) and in 16.0% with 3-day treatment vs 14.8% with 7-day treatment (difference, 1.2% [1-sided 95% CI, -∞ to 7.4%]; P value for interaction = .73). CONCLUSIONS AND RELEVANCE Among children with CAP discharged from an emergency department or hospital ward (within 48 hours), lower-dose outpatient oral amoxicillin was noninferior to higher dose, and 3-day duration was noninferior to 7 days, with regard to need for antibiotic re-treatment. However, disease severity, treatment setting, prior antibiotics received, and acceptability of the noninferiority margin require consideration when interpreting the findings. TRIAL REGISTRATION ISRCTN Identifier: ISRCTN76888927.
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Affiliation(s)
- Julia A. Bielicki
- Pediatric Infectious Diseases Research Group, Medical Research Council Clinical Trial Unit at University College London, Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Wolfgang Stöhr
- Medical Research Council Clinical Trials Unit at University College London, London, United Kingdom
| | - Sam Barratt
- Medical Research Council Clinical Trials Unit at University College London, London, United Kingdom
| | - David Dunn
- Medical Research Council Clinical Trials Unit at University College London, London, United Kingdom
| | - Nishdha Naufal
- Medical Research Council Clinical Trials Unit at University College London, London, United Kingdom
| | - Damian Roland
- Pediatric Emergency Medicine Leicester Academic (PEMLA) Group, Emergency Department, Leicester, United Kingdom
- SAPPHIRE Group, University of Leicester, Department of Health Sciences, Leicester, United Kingdom
| | - Kate Sturgeon
- Medical Research Council Clinical Trials Unit at University College London, London, United Kingdom
| | - Adam Finn
- Bristol Children’s Vaccine Centre, Schools of Population Sciences and Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Juan Pablo Rodriguez-Ruiz
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Colin Powell
- Emergency Medicine, Sidra Medical and Research Center, Doha, Qatar
- Division of Population Medicine, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Saul N. Faust
- National Institute for Health Research Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Anastasia E. Alcock
- Pediatric Emergency Medicine, Evelina Children’s Hospital, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Dani Hall
- Pediatric Emergency Medicine, Evelina Children’s Hospital, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
- Pediatric Emergency Medicine, Children’s Health Ireland at Crumlin, Ireland
| | - Gisela Robinson
- Pediatric Emergency Medicine, University Hospitals of Derby and Burton NHS Foundation Trust, Derby, United Kingdom
| | - Daniel B. Hawcutt
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
- Pediatric Medicines Research Unit, Alder Hey Children’s NHS Foundation Trust, Liverpool, United Kingdom
| | - Mark D. Lyttle
- Emergency Department, Bristol Royal Hospital for Children, Bristol, United Kingdom
- Faculty of Health and Applied Science, University of the West of England, Bristol, United Kingdom
| | - Diana M. Gibb
- Medical Research Council Clinical Trials Unit at University College London, London, United Kingdom
| | - Mike Sharland
- Pediatric Infectious Diseases Research Group, Medical Research Council Clinical Trial Unit at University College London, Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
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Smet A, Breugelmans T, Michiels J, Lamote K, Arras W, De Man JG, Heyndrickx L, Hauner A, Huizing M, Malhotra-Kumar S, Lammens M, Hotterbeekx A, Kumar-Singh S, Verstraeten A, Loeys B, Verhoeven V, Jacobs R, Dams K, Coenen S, Ariën KK, Jorens PG, De Winter BY. A dynamic mucin mRNA signature associates with COVID-19 disease presentation and severity. JCI Insight 2021; 6:e151777. [PMID: 34448730 PMCID: PMC8525642 DOI: 10.1172/jci.insight.151777] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/25/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND SARS-CoV-2 infection induces mucin overexpression, further promoting disease. Given that mucins are critical components of innate immunity, unraveling their expression profiles that dictate the course of disease could greatly enhance our understanding and management of COVID-19. METHODS Using validated RT-PCR assays, we assessed mucin mRNA expression in the blood of patients with symptomatic COVID-19 compared with symptomatic patients without COVID-19 and healthy controls and correlated the data with clinical outcome parameters. Additionally, we analyzed mucin expression in mucus and lung tissue from patients with COVID-19 and investigated the effect of drugs for COVID-19 treatment on SARS-CoV-2–induced mucin expression in pulmonary epithelial cells. RESULTS We identified a dynamic blood mucin mRNA signature that clearly distinguished patients with symptomatic COVID-19 from patients without COVID-19 based on expression of MUC1, MUC2, MUC4, MUC6, MUC13, MUC16, and MUC20 (AUCROC of 91.8%; sensitivity and specificity of 90.6% and 93.3%, respectively) and that discriminated between mild and critical COVID-19 based on the expression of MUC16, MUC20, and MUC21 (AUCROC of 89.1%; sensitivity and specificity of 90.0% and 85.7%, respectively). Differences in the transcriptional landscape of mucins in critical cases compared with mild cases identified associations with COVID-19 symptoms, respiratory support, organ failure, secondary infections, and mortality. Furthermore, we identified different mucins in the mucus and lung tissue of critically ill COVID-19 patients and showed the ability of baricitinib, tocilizumab, favipiravir, and remdesivir to suppress expression of SARS-CoV-2–induced mucins. CONCLUSION This multifaceted blood mucin mRNA signature showed the potential role of mucin profiling in diagnosing, estimating severity, and guiding treatment options in patients with COVID-19. FUNDING The Antwerp University Research and the Research Foundation Flanders COVID-19 funds.
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Affiliation(s)
- Annemieke Smet
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Tom Breugelmans
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Johan Michiels
- Virology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Kevin Lamote
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Wout Arras
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Joris G De Man
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Leo Heyndrickx
- Virology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Anne Hauner
- Virology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Manon Huizing
- Biobank Antwerpen, Antwerp University Hospital, Edegem, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Martin Lammens
- Department of Histopathology, Antwerp University Hospital, Edegem, Belgium
| | - An Hotterbeekx
- Laboratory of Cell Biology and Histology, Molecular Pathology Group, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Samir Kumar-Singh
- Laboratory of Cell Biology and Histology, Molecular Pathology Group, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Aline Verstraeten
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Bart Loeys
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Veronique Verhoeven
- Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Rita Jacobs
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Critical Care Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Karolien Dams
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Critical Care Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Samuel Coenen
- Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Kevin K Ariën
- Virology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Philippe G Jorens
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Critical Care Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Benedicte Y De Winter
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Division of Gastroenterology and Hepatology, Antwerp University Hospital, Edegem, Belgium
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35
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Mysara M, Berkell M, Xavier BB, De Backer S, Lammens C, Hautekiet V, Petkov S, Goossens H, Kumar-Singh S, Malhotra-Kumar S. Assessing the Impact of Flavophospholipol and Virginiamycin Supplementation on the Broiler Microbiota: a Prospective Controlled Intervention Study. mSystems 2021; 6:e0038121. [PMID: 34463581 DOI: 10.1128/msystems.00381-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/02/2021] [Indexed: 12/13/2022] Open
Abstract
The antibiotic growth promoters (AGPs) flavophospholipol and virginiamycin have been widely used for decades in food animal production. AGP activity is believed to be partly modulated by gut microbial composition although exact AGP-induced changes remain unclear. In a controlled intervention study, we studied the effect of flavophospholipol and virginiamycin on the broiler chicken ileal microbiota spanning from birth to 39 days. Using 16S rRNA gene profiling and prediction of metabolic activity, we show that both AGPs result in dynamic microbial shifts that potentially increase anti-inflammatory mechanisms and bioavailability of several essential nutrients by decreasing degradation (flavophospholipol) or increasing biosynthesis (virginiamycin). Further, virginiamycin-supplemented broilers showed increased colonization with potentially pathogenic bacteria, Clostridium perfringens, Campylobacter, and Escherichia/Shigella spp. Overall, we show that both AGPs induce microbial changes potentially beneficial for growth. However, the increase in (foodborne) pathogens shown here with virginiamycin use could impact not only broiler mortality but also human health. IMPORTANCE Antibiotic growth promoters (AGPs) are commonly used within poultry farming to increase muscle growth. Microbial composition in the gut is known to be influenced by AGP use although exact AGP-induced changes remain unclear. Utilizing 16S rRNA gene profiling, this study provides a first head-to-head comparison of the effect of the two most commonly used AGPs, flavophospholipol and virginiamycin, on the broiler chicken ileum microbiota over time. We found that supplementation with both AGPs altered ileal microbial composition, thereby increasing potential bioavailability of essential nutrients and weight gain. Flavophospholipol showed a slight benefit over virginiamycin as the latter resulted in more extensive microbial perturbations including increased colonization by enteropathogens, which could impact broiler mortality.
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Affiliation(s)
- Mohamed Mysara
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centregrid.8953.7, SCK•CEN, Mol, Belgium
| | - Matilda Berkell
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
- Molecular Pathology group, Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | - Basil Britto Xavier
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | - Sarah De Backer
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | - Christine Lammens
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | | | | | - Herman Goossens
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | - Samir Kumar-Singh
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
- Molecular Pathology group, Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
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36
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Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2021; 75:3491-3500. [PMID: 32780112 PMCID: PMC7662176 DOI: 10.1093/jac/dkaa345] [Citation(s) in RCA: 1320] [Impact Index Per Article: 440.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/30/2020] [Indexed: 12/16/2022] Open
Abstract
Objectives WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results Genotype–phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype–phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. Conclusions WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
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Affiliation(s)
- Valeria Bortolaia
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Rolf S Kaas
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | | | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Vincent Cattoir
- Rennes University Hospital, Department of Clinical Microbiology, Rennes, France.,National Reference Center for Antimicrobial Resistance (lab Enterococci), Rennes, France.,University of Rennes 1, INSERM U1230, Rennes, France
| | - Alain Philippon
- Faculty of Medicine Paris Descartes, Bacteriology, Paris, France
| | - Rosa L Allesoe
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Ana Rita Rebelo
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Alfred Ferrer Florensa
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Linda Fagelhauer
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.,Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Bernd Neumann
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Guido Werner
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Jennifer K Bender
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Kerstin Stingl
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Minh Nguyen
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Jasmine Coppens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Muna F Anjum
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | - Isabelle Kempf
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | | | | | | | - Ana Amaro
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Lurdes Clemente
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Joël Mossong
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Serge Losch
- Laboratoire de Médecine Vétérinaire de l'Etat, Veterinary Services Administration, Dudelange, Luxembourg
| | - Catherine Ragimbeau
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Ole Lund
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
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37
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Kostyanev T, Timbermont L, Vilken T, Lammens C, Malhotra-Kumar S, Glupczynski Y, Goossens H. COMBACTE LAB-Net: building a European laboratory network for clinical trials on anti-infectives. Future Microbiol 2021; 16:635-647. [PMID: 33998261 DOI: 10.2217/fmb-2021-0096] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
LAB-Net, the laboratory network of COMBACTE, has established itself as an indispensable network for clinical trials in infectious diseases that plays a crucial part across 30 clinical studies not only within, but also outside the COMBACTE consortium. Since its official launch in January 2013, LAB-Net has expanded more than threefold and in Q4 2020 it encompasses 841 labs across 41 countries in Europe. In addition, LAB-Net has crossed the European borders and collaborates with more than 300 laboratories spread across the globe. The tight collaboration with partners within COMBACTE and beyond contributed tremendously to the growth of LAB-Net over the years. A sustainable infrastructure beyond COMBACTE-NET is needed to ensure the smooth handover and continuity of the achievements made by the project.
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Affiliation(s)
- Tomislav Kostyanev
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Tuba Vilken
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.,Laboratory of Clinical Biology, University Hospital Antwerp, Antwerp, Belgium
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38
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Wheatley R, Diaz Caballero J, Kapel N, de Winter FHR, Jangir P, Quinn A, Del Barrio-Tofiño E, López-Causapé C, Hedge J, Torrens G, Van der Schalk T, Xavier BB, Fernández-Cuenca F, Arenzana A, Recanatini C, Timbermont L, Sifakis F, Ruzin A, Ali O, Lammens C, Goossens H, Kluytmans J, Kumar-Singh S, Oliver A, Malhotra-Kumar S, MacLean C. Rapid evolution and host immunity drive the rise and fall of carbapenem resistance during an acute Pseudomonas aeruginosa infection. Nat Commun 2021; 12:2460. [PMID: 33911082 PMCID: PMC8080559 DOI: 10.1038/s41467-021-22814-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/31/2021] [Indexed: 02/08/2023] Open
Abstract
It is well established that antibiotic treatment selects for resistance, but the dynamics of this process during infections are poorly understood. Here we map the responses of Pseudomonas aeruginosa to treatment in high definition during a lung infection of a single ICU patient. Host immunity and antibiotic therapy with meropenem suppressed P. aeruginosa, but a second wave of infection emerged due to the growth of oprD and wbpM meropenem resistant mutants that evolved in situ. Selection then led to a loss of resistance by decreasing the prevalence of low fitness oprD mutants, increasing the frequency of high fitness mutants lacking the MexAB-OprM efflux pump, and decreasing the copy number of a multidrug resistance plasmid. Ultimately, host immunity suppressed wbpM mutants with high meropenem resistance and fitness. Our study highlights how natural selection and host immunity interact to drive both the rapid rise, and fall, of resistance during infection.
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Affiliation(s)
| | | | - Natalia Kapel
- University of Oxford, Department of Zoology, Oxford, UK
| | - Fien H R de Winter
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Pramod Jangir
- University of Oxford, Department of Zoology, Oxford, UK
| | - Angus Quinn
- University of Oxford, Department of Zoology, Oxford, UK
| | | | | | - Jessica Hedge
- University of Oxford, Department of Zoology, Oxford, UK
| | - Gabriel Torrens
- Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Thomas Van der Schalk
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | | | - Angel Arenzana
- Departamento de Medicina, Universidad de Sevilla, Seville, Spain
| | - Claudia Recanatini
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | | | - Alexey Ruzin
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Omar Ali
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
- Viela Bio, Gaithersburg, MD, USA
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Jan Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Microvida Laboratory for Medical Microbiology and Department of Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Samir Kumar-Singh
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
- Molecular Pathology Group, Faculty of Medicine-Laboratory of Cell Biology and Histology, University of Antwerp, Wilrijk, Belgium
| | - Antonio Oliver
- Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Craig MacLean
- University of Oxford, Department of Zoology, Oxford, UK.
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39
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van Werkhoven CH, Ducher A, Berkell M, Mysara M, Lammens C, Torre-Cisneros J, Rodríguez-Baño J, Herghea D, Cornely OA, Biehl LM, Bernard L, Dominguez-Luzon MA, Maraki S, Barraud O, Nica M, Jazmati N, Sablier-Gallis F, de Gunzburg J, Mentré F, Malhotra-Kumar S, Bonten MJM, Vehreschild MJGT. Incidence and predictive biomarkers of Clostridioides difficile infection in hospitalized patients receiving broad-spectrum antibiotics. Nat Commun 2021; 12:2240. [PMID: 33854064 PMCID: PMC8046770 DOI: 10.1038/s41467-021-22269-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
Trial enrichment using gut microbiota derived biomarkers by high-risk individuals can improve the feasibility of randomized controlled trials for prevention of Clostridioides difficile infection (CDI). Here, we report in a prospective observational cohort study the incidence of CDI and assess potential clinical characteristics and biomarkers to predict CDI in 1,007 patients ≥ 50 years receiving newly initiated antibiotic treatment with penicillins plus a beta-lactamase inhibitor, 3rd/4th generation cephalosporins, carbapenems, fluoroquinolones or clindamycin from 34 European hospitals. The estimated 90-day cumulative incidences of a first CDI episode is 1.9% (95% CI 1.1-3.0). Carbapenem treatment (Hazard Ratio (95% CI): 5.3 (1.7-16.6)), toxigenic C. difficile rectal carriage (10.3 (3.2-33.1)), high intestinal abundance of Enterococcus spp. relative to Ruminococcus spp. (5.4 (2.1-18.7)), and low Shannon alpha diversity index as determined by 16 S rRNA gene profiling (9.7 (3.2-29.7)), but not normalized urinary 3-indoxyl sulfate levels, predicts an increased CDI risk.
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Affiliation(s)
- Cornelis H van Werkhoven
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | | | - Matilda Berkell
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Mohamed Mysara
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Microbiology Unit, Environment Health and Safety, Belgian Nuclear Research Centre, SCK.CEN, Mol, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Julian Torre-Cisneros
- Maimonides Institute for Research in Biomedicine of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba (UCO), Cordoba, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain
- Departamento de Medicina, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
| | - Delia Herghea
- Oncology Institute Prof. Dr. I Chiricuta, Cluj Napoca, Romania
| | - Oliver A Cornely
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Chair Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Lena M Biehl
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Louis Bernard
- Centre hospitalo-universitaire de Tours, Tours, France
| | | | - Sofia Maraki
- University Hospital of Heraklion, Heraklion, Greece
| | - Olivier Barraud
- Université Limoges, INSERM U1092, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - Maria Nica
- Infectious and Tropical Diseases Hospital "Dr. Victor Babes", Bucharest, Romania
| | - Nathalie Jazmati
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
- Labor Dr. Wisplinghoff, Cologne, Germany
| | | | | | | | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Maria J G T Vehreschild
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany.
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany.
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40
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Berkell M, Mysara M, Xavier BB, van Werkhoven CH, Monsieurs P, Lammens C, Ducher A, Vehreschild MJGT, Goossens H, de Gunzburg J, Bonten MJM, Malhotra-Kumar S. Microbiota-based markers predictive of development of Clostridioides difficile infection. Nat Commun 2021; 12:2241. [PMID: 33854066 PMCID: PMC8047037 DOI: 10.1038/s41467-021-22302-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Antibiotic-induced modulation of the intestinal microbiota can lead to Clostridioides difficile infection (CDI), which is associated with considerable morbidity, mortality, and healthcare-costs globally. Therefore, identification of markers predictive of CDI could substantially contribute to guiding therapy and decreasing the infection burden. Here, we analyze the intestinal microbiota of hospitalized patients at increased CDI risk in a prospective, 90-day cohort-study before and after antibiotic treatment and at diarrhea onset. We show that patients developing CDI already exhibit significantly lower diversity before antibiotic treatment and a distinct microbiota enriched in Enterococcus and depleted of Ruminococcus, Blautia, Prevotella and Bifidobacterium compared to non-CDI patients. We find that antibiotic treatment-induced dysbiosis is class-specific with beta-lactams further increasing enterococcal abundance. Our findings, validated in an independent prospective patient cohort developing CDI, can be exploited to enrich for high-risk patients in prospective clinical trials, and to develop predictive microbiota-based diagnostics for management of patients at risk for CDI.
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Affiliation(s)
- Matilda Berkell
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Mohamed Mysara
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK-CEN, Mol, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Cornelis H van Werkhoven
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Pieter Monsieurs
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK-CEN, Mol, Belgium
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | | | - Maria J G T Vehreschild
- Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | | | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium.
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41
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van Hal SJ, Willems RJL, Gouliouris T, Ballard SA, Coque TM, Hammerum AM, Hegstad K, Westh HT, Howden BP, Malhotra-Kumar S, Werner G, Yanagihara K, Earl AM, Raven KE, Corander J, Bowden R. The global dissemination of hospital clones of Enterococcus faecium. Genome Med 2021; 13:52. [PMID: 33785076 PMCID: PMC8008517 DOI: 10.1186/s13073-021-00868-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The hospital-adapted A1 group of Enterococcus faecium remains an organism of significant concern in the context of drug-resistant hospital-associated infections. How this pathogen evolves and disseminates remains poorly understood. METHODS A large, globally representative collection of short-read genomic data from the hospital-associated A1 group of Enterococcus faecium was assembled (n = 973). We analysed, using a novel analysis approach, global diversity in terms of both the dynamics of the accessory genome and homologous recombination among conserved genes. RESULTS Two main modes of genomic evolution continue to shape E. faecium: the acquisition and loss of genes, including antimicrobial resistance genes, through mobile genetic elements including plasmids, and homologous recombination of the core genome. These events lead to new clones emerging at the local level, followed by the erosion of signals of clonality through recombination, and in some identifiable cases producing new clonal clusters. These patterns lead to new, emerging lineages which are able to spread globally over relatively short timeframes. CONCLUSIONS The ability of A1 E. faecium to continually present new combinations of genes for potential selection suggests that controlling this pathogen will remain challenging but establishing a framework for understanding genomic evolution is likely to aid in tracking the threats posed by newly emerging lineages.
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Affiliation(s)
- Sebastiaan J. van Hal
- Department of Infectious Disesase and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW Australia
- University of Sydney, Sydney, NSW Australia
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrech, Utrecht, The Netherlands
| | | | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | | | - Kristin Hegstad
- Department of Microbiology and Infection Control, Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North-Norway, Tromsø, Norway
- Research Group for Host-Microbe Interactions, UiT – the Arctic University of Norway, Tromsø, Norway
| | - Hendrik T. Westh
- MRSA Knowledge Center, Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Wilrijk, Belgium
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA USA
| | | | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Rory Bowden
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052 Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Melbourne, Victoria Australia
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN UK
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42
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Laumen JGE, Manoharan-Basil SS, Verhoeven E, Abdellati S, De Baetselier I, Crucitti T, Xavier BB, Chapelle S, Lammens C, Van Dijck C, Malhotra-Kumar S, Kenyon C. Molecular pathways to high-level azithromycin resistance in Neisseria gonorrhoeae. J Antimicrob Chemother 2021; 76:1752-1758. [DOI: 10.1093/jac/dkab084] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/28/2021] [Indexed: 01/02/2023] Open
Abstract
Abstract
Background
The prevalence of azithromycin resistance in Neisseria gonorrhoeae is increasing in numerous populations worldwide.
Objectives
To characterize the genetic pathways leading to high-level azithromycin resistance.
Methods
A customized morbidostat was used to subject two N. gonorrhoeae reference strains (WHO-F and WHO-X) to dynamically sustained azithromycin pressure. We tracked stepwise evolution of resistance by whole genome sequencing.
Results
Within 26 days, all cultures evolved high-level azithromycin resistance. Typically, the first step towards resistance was found in transitory mutations in genes rplD, rplV and rpmH (encoding the ribosomal proteins L4, L22 and L34 respectively), followed by mutations in the MtrCDE-encoded efflux pump and the 23S rRNA gene. Low- to high-level resistance was associated with mutations in the ribosomal proteins and MtrCDE efflux pump. However, high-level resistance was consistently associated with mutations in the 23S ribosomal RNA, mainly the well-known A2059G and C2611T mutations, but also at position A2058G.
Conclusions
This study enabled us to track previously reported mutations and identify novel mutations in ribosomal proteins (L4, L22 and L34) that may play a role in the genesis of azithromycin resistance in N. gonorrhoeae.
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Affiliation(s)
- J G E Laumen
- Institute of Tropical Medicine, Department of Clinical Sciences, STI Unit, Antwerp, Belgium
- University of Antwerp, Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Antwerp, Belgium
| | - S S Manoharan-Basil
- Institute of Tropical Medicine, Department of Clinical Sciences, STI Unit, Antwerp, Belgium
| | - E Verhoeven
- Institute of Tropical Medicine, Department of Clinical Sciences, STI Unit, Antwerp, Belgium
- Pfizer, Puurs, Belgium
| | - S Abdellati
- Institute of Tropical Medicine, Department of Clinical Sciences, Clinical Reference Laboratory, Antwerp, Belgium
| | - I De Baetselier
- Institute of Tropical Medicine, Department of Clinical Sciences, Clinical Reference Laboratory, Antwerp, Belgium
| | - T Crucitti
- Centre Pasteur du Cameroun, Yaounde, Cameroon
| | - B B Xavier
- University of Antwerp, Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Antwerp, Belgium
| | - S Chapelle
- University of Antwerp, Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Antwerp, Belgium
| | - C Lammens
- University of Antwerp, Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Antwerp, Belgium
| | - C Van Dijck
- Institute of Tropical Medicine, Department of Clinical Sciences, STI Unit, Antwerp, Belgium
- University of Antwerp, Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Antwerp, Belgium
| | - S Malhotra-Kumar
- University of Antwerp, Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Antwerp, Belgium
| | - C Kenyon
- Institute of Tropical Medicine, Department of Clinical Sciences, STI Unit, Antwerp, Belgium
- Department of Medicine, University of Cape Town, Cape Town, South Africa
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43
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Kuzmenkov AY, Trushin IV, Vinogradova AG, Avramenko AA, Sukhorukova MV, Malhotra-Kumar S, Dekhnich AV, Edelstein MV, Kozlov RS. AMRmap: An Interactive Web Platform for Analysis of Antimicrobial Resistance Surveillance Data in Russia. Front Microbiol 2021; 12:620002. [PMID: 33776956 PMCID: PMC7994358 DOI: 10.3389/fmicb.2021.620002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/08/2021] [Indexed: 11/30/2022] Open
Abstract
Surveillance of antimicrobial resistance (AMR) is crucial for identifying trends in resistance and developing strategies for prevention and treatment of infections. Globally, AMR surveillance systems differ in terms of organizational principles, comprehensiveness, accessibility, and usability of data presentation. Until recently, the data on AMR in Russia were scarcely available, especially to international community, despite the fact that the large prospective multicenter surveillance in Russia was conducted and data were accumulated for over 20 years. We describe the source of data, structure, and functionality of a new-generation web platform, called AMRmap (https://amrmap.net/), for analysis of AMR surveillance data in Russia. The developed platform currently comprises susceptibility data of >40,000 clinical isolates, and the data on abundance of key resistance determinants, including acquired carbapenemases in gram-negatives, are updated annually with information on >5,000 new isolates. The AMRmap allows smart data filtration by multiple parameters and provides interactive data analysis and visualization tools: MIC and S/I/R distribution plots, time-trends and regression plots, associated resistance plots, prevalence maps, statistical significance graphs, and tables.
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Affiliation(s)
- Alexey Y. Kuzmenkov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University of the Ministry of Health of the Russian Federation, Smolensk, Russia
| | - Ivan V. Trushin
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University of the Ministry of Health of the Russian Federation, Smolensk, Russia
| | - Alina G. Vinogradova
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University of the Ministry of Health of the Russian Federation, Smolensk, Russia
| | - Andrey A. Avramenko
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University of the Ministry of Health of the Russian Federation, Smolensk, Russia
| | - Marina V. Sukhorukova
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University of the Ministry of Health of the Russian Federation, Smolensk, Russia
| | | | - Andrey V. Dekhnich
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University of the Ministry of Health of the Russian Federation, Smolensk, Russia
| | - Mikhail V. Edelstein
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University of the Ministry of Health of the Russian Federation, Smolensk, Russia
| | - Roman S. Kozlov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University of the Ministry of Health of the Russian Federation, Smolensk, Russia
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Nguyen MN, Hoang HTT, Xavier BB, Lammens C, Le HT, Hoang NTB, Nguyen ST, Pham NT, Goossens H, Dang AD, Malhotra-Kumar S. Prospective One Health genetic surveillance in Vietnam identifies distinct bla CTX-M-harbouring Escherichia coli in food-chain and human-derived samples. Clin Microbiol Infect 2021; 27:1515.e1-1515.e8. [PMID: 33476808 DOI: 10.1016/j.cmi.2021.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 01/02/2023]
Abstract
OBJECTIVES We performed a One Health surveillance in Hanoi-a region with a high-density human population and livestock production, and a recognized hotspot of animal-associated antimicrobial resistance (AMR)-to study the contribution of blaCTX-M-carrying Escherichia coli and plasmids from food-animal sources in causing human community-acquired urinary tract infections (CA-UTIs). METHODS During 2014-2015, 9090 samples were collected from CA-UTI patients (urine, n = 8564), pigs/chickens from farms and slaughterhouses (faeces, carcasses, n = 448), and from the slaughterhouse environment (surface swabs, water, n = 78). E. coli was identified in 2084 samples. Extended-spectrum β-lactamase (ESBL) production was confirmed in 235 and blaCTX-M in 198 strains by PCR with short-read plasmid sequencing. Fourteen strains were long-read sequenced to enable plasmid reconstruction. RESULTS The majority of the ESBL-producing E. coli strains harboured blaCTX-M (n = 198/235, 84%). High clonal diversity (48 sequence types, STs) and distinct, dominant STs in human sources (ST1193, n = 38/137; ST131, n = 30/137) and non-human sources (ST155, n = 25/61) indicated lack of clonal transmission between habitats. Eight blaCTX-M variants were identified; five were present in at least two sample sources. Human and food-animal strains did not show similar plasmids carrying shared blaCTX-M genes. However, IS6 elements flanking ISEcp1-blaCTX-M-orf477/IS903B structures were common across habitats. CONCLUSIONS In this study, animal-associated blaCTX-ME. coli strains or blaCTX-M plasmids were not direct sources of CA-UTIs or ESBL resistance in humans, respectively, suggesting evolutionary bottlenecks to their adaptation to a new host species. Presence of common IS6 elements flanking blaCTX-M variants in different plasmid backbones, however, highlighted the potential of these transposable elements for AMR transmission either within or across habitats.
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Affiliation(s)
- Minh Ngoc Nguyen
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | | | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Hai Thanh Le
- Vietnam National Children's Hospital, Hanoi, Viet Nam
| | | | | | - Ngoc Thi Pham
- National Institute of Veterinary Research, Hanoi, Viet Nam
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Anh Duc Dang
- Vietnam National Children's Hospital, Hanoi, Viet Nam
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
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Mack I, Sharland M, Berkley JA, Klein N, Malhotra-Kumar S, Bielicki J. Antimicrobial Resistance Following Azithromycin Mass Drug Administration: Potential Surveillance Strategies to Assess Public Health Impact. Clin Infect Dis 2021; 70:1501-1508. [PMID: 31633161 DOI: 10.1093/cid/ciz893] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/17/2019] [Indexed: 12/26/2022] Open
Abstract
The reduction in childhood mortality noted in trials investigating azithromycin mass drug administration (MDA) for trachoma control has been confirmed by a recent large randomized controlled trial. Population-level implementation of azithromycin MDA may lead to selection of multiresistant pathogens. Evidence suggests that repeated azithromycin MDA may result in a sustained increase in macrolide and other antibiotic resistance in gut and respiratory bacteria. Current evidence comes from standard microbiological techniques in studies focused on a time-limited intervention, while MDA implemented for mortality benefits would likely repeatedly expose the population over a prolonged period and may require a different surveillance approach. Targeted short-term and long-term surveillance of resistance emergence to key antibiotics, especially those from the World Health Organization Access group, is needed throughout any implementation of azithromycin MDA, focusing on a genotypic approach to overcome the limitations of resistance surveillance in indicator bacteria.
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Affiliation(s)
- Ines Mack
- Pediatric Infectious Diseases, University Children's Hospital Basel, Basel, Switzerland
| | - Mike Sharland
- Pediatric Infectious Disease Research Group, Institute for Infection and Immunity, St George's University of London, London, United Kingdom
| | - James A Berkley
- Center for Tropical Medicine and Global Health, University of Oxford, United Kingdom.,KEMRI/Wellcome Trust Research Program, Kilifi, Kenya
| | - Nigel Klein
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Julia Bielicki
- Pediatric Infectious Diseases, University Children's Hospital Basel, Basel, Switzerland.,Pediatric Infectious Disease Research Group, Institute for Infection and Immunity, St George's University of London, London, United Kingdom
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Ekinci E, Desmet S, Van Heirstraeten L, Mertens C, Wouters I, Beutels P, Verhaegen J, Malhotra-Kumar S, Theeten H. Streptococcus pneumoniae Serotypes Carried by Young Children and Their Association With Acute Otitis Media During the Period 2016-2019. Front Pediatr 2021; 9:664083. [PMID: 34291017 PMCID: PMC8286995 DOI: 10.3389/fped.2021.664083] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Streptococcus pneumoniae (Sp) is a major cause of acute otitis media (AOM). Pneumococcal conjugate vaccine (PCV) programs have altered pneumococcal serotype epidemiology in disease and carriage. In this study, we used samples collected during a cross-sectional study to examine if the clinical picture of acute otitis media (AOM) in young children exposed to the PCV program in Belgium was related to the carried pneumococcal strains, and if their carriage profile differed from healthy children attending daycare centers. Material/Methods: In three collection periods from February 2016 to May 2018, nasopharyngeal swabs and background characteristics were collected from children aged 6-30 months either presenting at their physician with AOM (AOM-group) or healthy and attending day care (DCC-group). Clinical signs of AOM episodes and treatment schedule were registered by the physicians. Sp was detected, quantified, and characterized using both conventional culture analysis and real-time PCR analysis. Results: Among 3,264 collected samples, overall pneumococcal carriage and density were found at similar rates in both AOM and DCC. As expected non-vaccine serotypes were most frequent: 23B (AOM: 12.3%; DCC: 17.4%), 11A (AOM: 7.5%; DCC: 7.4%) and 15B (AOM: 7.5%; DCC: 7.1%). Serotypes 3, 6C, 7B, 9N, 12F, 17F, and 29 were more often found in AOM than in DCC (p-value < 0.05), whereas 23A and 23B were less often present in AOM (p-value < 0.05). Antibiotic non-susceptibility of Sp strains was similar in both groups. No predictors of AOM severity were identified. Conclusion: In the present study, overall carriage prevalence and density of S. pneumoniae were found similar in young children with AOM and in healthy children attending day-care centers in Belgium. Certain serotypes not currently included in the PCV vaccines were found to be carried more often in children with AOM than in DCC, a finding that might suggest a relationship between these serotypes and AOM.
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Affiliation(s)
- Esra Ekinci
- Centre for Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Stefanie Desmet
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Liesbet Van Heirstraeten
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Colette Mertens
- Centre for Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Ine Wouters
- Centre for Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Philippe Beutels
- Centre for Health Economics Research and Modelling Infectious Diseases, University of Antwerp, Antwerp, Belgium
| | - Jan Verhaegen
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Heidi Theeten
- Centre for Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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Tabor DE, Tkaczyk C, Tovchigrechko A, Sellman BR, McCarthy M, Ren P, Shoemaker K, Jafri HS, François B, Esser MT, Coppens J, Timbermont L, Xavier B, Lammens C, Goossens H, Malhotra-Kumar S, Ruzin A. 1486. Phylogenetic and alpha toxin variant analyses of Staphylococcus aureus strains isolated from patients during the SAATELLITE study. Open Forum Infect Dis 2020. [PMCID: PMC7777803 DOI: 10.1093/ofid/ofaa439.1667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Suvratoxumab is a human monoclonal antibody that neutralizes S. aureus (SA) alpha toxin (AT). SAATELLITE, a phase 2 study of the safety and efficacy of suvratoxumab for reducing the incidence of SA pneumonia (NCT02296320), was conducted within the consortium for Combatting Bacterial Resistance in Europe.
Methods
A total of 304 SA isolates (baseline, onset and last available isolates from suspected serious bacterial infections, SSBIs) collected from the lower respiratory tract samples from 165 subjects during SAATELLITE were subjected to whole genome sequencing.
AT gene (hla) sequences were translated and amino acid variation was identified in comparison to the reference SA USA300 FPR3757. Phylogenetic analysis, genomic annotation and ST analysis were performed.
AT expression in SA culture supernatants was performed by ELISA. Representative isolates with novel AT subtypes that had not been identified in previous studies were tested for hemolytic activity and suvratoxumab neutralizing activity.
Wilcoxon rank sum test and Fisher’s exact test were performed, respectively: a) to compare difference in baseline AT expression in relation to SA pneumonia incidence; b) to evaluate the association between occurrence of AT stop codons and incidence of SA pneumonia at baseline, as well as the association between occurrence of AT stop codons and treatment arms at post baseline.
Results
We identified a total of 44 sequence types (STs) and 21 unique AT subtypes, 7 of which have not been described previously. No substitutions were located in the suvratoxumab binding region and all novel AT subtypes displaying lytic activity were neutralized by suvratoxumab.
We detected stop codons Q113B and W205B in AT sequences in 53 and 2 SA isolates, respectively. We uncovered no significant associations of: 1) baseline AT expression with SA pneumonia incidence [p=0.967]; 2) occurrence of AT gene stop codon with either SA pneumonia incidence [p >0.999] or suvratoxumab treatment [p=0.103; lower frequency of stop codons in suvratoxumab arm versus placebo].
Conclusion
Our data indicated that: 1) suvratoxumab target region in (AT) remains conserved; 2) suvratoxumab is active against all AT variants identified to date; 3) suvratoxumab did not exert pressure on SA clinical isolates for selection of escape mutants.
Disclosures
David E. Tabor, PhD, AstraZeneca (Employee, Shareholder) Andrey Tovchigrechko, PhD, AstraZeneca (Employee, Shareholder)KitePharma, a Gilead company (Employee, Shareholder) Bret R. Sellman, PhD, AstraZeneca (Employee, Shareholder) Michael McCarthy, n/a, AstraZeneca (Employee) Kathryn Shoemaker, MS, AstraZeneca (Employee) Hasan S. Jafri, MD, FAAP, AstraZeneca (Employee) Mark T. Esser, PhD, AstraZeneca (Employee) Alexey Ruzin, PhD, AstraZeneca (Employee, Shareholder)
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Affiliation(s)
| | | | | | | | | | - Pin Ren
- AstraZeneca, South San Francisco, California
| | | | | | | | | | | | | | - Basil Xavier
- University of Antwerp, Wilrijk, Antwerpen, Belgium
| | - Christine Lammens
- University Antwerp, Department of Medical Microbiology, Antwerp, Antwerpen, Belgium
| | - Herman Goossens
- University of Antwerp, Antwerp, Antwerpen, Belgium, Antwerp, Antwerpen, Belgium
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Desmet S, Ekinci E, Wouters I, Decru B, Beuselinck K, Malhotra-Kumar S, Theeten H. No SARS-CoV-2 carriage observed in children attending daycare centers during the intial weeks of the epidemic in Belgium. J Med Virol 2020; 93:1828-1831. [PMID: 33230857 PMCID: PMC7753838 DOI: 10.1002/jmv.26689] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/10/2020] [Accepted: 11/16/2020] [Indexed: 12/24/2022]
Abstract
To gain knowledge about the role of young children attending daycare in the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) epidemic, a random sample of children (n = 84) aged between 6 and 30 months attending daycare in Belgium was studied shortly after the start of the epidemic (February 29th) and before the lockdown (March 18th) by performing in‐house SARS‐CoV‐2 real‐time polymerase chain reaction. No asymptomatic carriage of SARS‐CoV‐2 was detected, whereas common cold symptoms were common (51.2%). Our study shows that in Belgium, there was no sign of early introduction into daycare centers at the moment children being not yet isolated at home, although the virus was clearly circulating. It is clear that more evidence is needed to understand the actual role of young children in the transmission of SARS‐CoV‐2 and their infection risk when attending daycare.
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Affiliation(s)
- Stefanie Desmet
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, Campus Gasthuisberg, Leuven, Belgium
| | - Esra Ekinci
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
| | - Ine Wouters
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
| | - Bram Decru
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, Campus Gasthuisberg, Leuven, Belgium
| | - Kurt Beuselinck
- Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory for Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
| | - Heidi Theeten
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
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49
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Desmet S, Wouters I, Heirstraeten LV, Beutels P, Van Damme P, Malhotra-Kumar S, Maes P, Verhaegen J, Peetermans WE, Lagrou K, Theeten H. In-depth analysis of pneumococcal serotypes in Belgian children (2015-2018): Diversity, invasive disease potential, and antimicrobial susceptibility in carriage and disease. Vaccine 2020; 39:372-379. [PMID: 33308889 DOI: 10.1016/j.vaccine.2020.11.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND Changes in serotype distribution have been described after the switch from the 13-valent pneumococcal conjugate vaccine (PCV13) to the 10-valent pneumococcal conjugate vaccine (PCV10) in Belgium. AIM To describe serotype's invasive disease potential and the detailed evolution of serotype distribution and antimicrobial susceptibility of pneumococcal isolates (carriage and IPD) in children up to 30 months of age over a period during and after the vaccine switch (2015-2018). METHODS S. pneumoniae strains isolated from the nasopharynx of healthy children attending day-care centres (DCCs) and strains from normally sterile sites of children with IPD were serotyped (Quellung-reaction) and antimicrobial susceptibility testing was performed. Invasive disease potential was defined as the serotype-specific odds ratio (OR). RESULTS The highly invasive (OR > 1) serotypes 12F, 1, 3, 24A/B/F, 33F, 19A, and 9N were not frequently carried (<7.5% of carriage strains). Different serotypes dominated in carriage (23B, 23A, 11A, 15B) versus IPD (12F, 19A, 10A, 33F). PCV13 vaccine serotypes increased in carriage (5.4% (25/463) in period 1 vs 10.3% (69/668) in period 3) and in IPD (7.3% (8/110 in period 1 vs 23.9% (34/142) in period 3) due to an increase (p < 0.01) in serotype 19A. The penicillin non-susceptibility of 19A was lower (p = 0.02) in carriage (6.8%) than in IPD (23.5%). Erythromycin and tetracycline non-susceptibility were more frequent (p < 0.01) in IPD (26.0%; 23.0%) compared to carriage strains (18.2%; 14.5%) and penicillin non-susceptibility increased over the three year study period (carriage: 13.4%, 19.8%, 18.5%, p = 0.05; IPD: 11.8%, 15.0%, 20.4%, p = 0.02). CONCLUSION Only some of the serotypes with high invasive disease potential (serotype 1, 3, 19A) in Belgium are included in PCV10 and/or PCV13. This reinforces the need for continuous monitoring, both in healthy children as in children with IPD, to better understand the dynamics of pneumococcal disease, to optimise the composition and implementation of PCVs.
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Affiliation(s)
- Stefanie Desmet
- Reference Centre for Pneumococci, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Ine Wouters
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Liesbet Van Heirstraeten
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Philippe Beutels
- Centre for Health Economics Research and Modelling Infectious Diseases, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Piet Maes
- Reference Centre for Pneumococci, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Jan Verhaegen
- Reference Centre for Pneumococci, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Willy E Peetermans
- Reference Centre for Pneumococci, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Katrien Lagrou
- Reference Centre for Pneumococci, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Heidi Theeten
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
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Vlaeminck J, Raafat D, Surmann K, Timbermont L, Normann N, Sellman B, van Wamel WJB, Malhotra-Kumar S. Exploring Virulence Factors and Alternative Therapies against Staphylococcus aureus Pneumonia. Toxins (Basel) 2020; 12:toxins12110721. [PMID: 33218049 PMCID: PMC7698915 DOI: 10.3390/toxins12110721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 12/13/2022] Open
Abstract
Pneumonia is an acute pulmonary infection associated with high mortality and an immense financial burden on healthcare systems. Staphylococcus aureus is an opportunistic pathogen capable of inducing S. aureus pneumonia (SAP), with some lineages also showing multidrug resistance. Given the high level of antibiotic resistance, much research has been focused on targeting S. aureus virulence factors, including toxins and biofilm-associated proteins, in an attempt to develop effective SAP therapeutics. Despite several promising leads, many hurdles still remain for S. aureus vaccine research. Here, we review the state-of-the-art SAP therapeutics, highlight their pitfalls, and discuss alternative approaches of potential significance and future perspectives.
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Affiliation(s)
- Jelle Vlaeminck
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, 2610 Antwerp, Belgium; (J.V.); (L.T.)
| | - Dina Raafat
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, 17475 Greifswald, Germany; (D.R.); (N.N.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Kristin Surmann
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, 2610 Antwerp, Belgium; (J.V.); (L.T.)
| | - Nicole Normann
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, 17475 Greifswald, Germany; (D.R.); (N.N.)
| | - Bret Sellman
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA;
| | - Willem J. B. van Wamel
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center Rotterdam, 3015 Rotterdam, The Netherlands;
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, 2610 Antwerp, Belgium; (J.V.); (L.T.)
- Correspondence: ; Tel.: +32-3-265-27-52
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