1
|
Narayanan N, Mathers AJ, Wenzler E, Moore NM, Giske CG, Mendes RE, Edelstein PH. Amoxicillin-clavulanate Breakpoints Against Enterobacterales: Rationale for Revision by the Clinical and Laboratory Standards Institute. Clin Infect Dis 2024:ciae201. [PMID: 38626241 DOI: 10.1093/cid/ciae201] [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] [Received: 01/24/2024] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 04/18/2024] Open
Abstract
Amoxicillin-clavulanate (AMC) is among the most frequently prescribed antibiotics globally. It has broad antibacterial activity against gram-positive, gram-negative, and anaerobic bacteria, and has been utilized to treat infections caused by a broad range of pathogens. AMC breakpoints against Enterobacterales were initially set in the 1980s but since then increases in antibiotic resistance, advances in pharmacokinetic (PK)/pharmacodynamic (PD) analyses, and publication of additional clinical data prompted a reassessment by the Clinical and Laboratory Standards Institute (CLSI) Subcommittee on Antimicrobial Susceptibility Testing. Based on this contemporary reappraisal, the CLSI retained the Enterobacterales breakpoints but revised comments regarding dosing associated with use of the AMC breakpoints in the 2022 supplement of M100. This viewpoint provides insight into the CLSI breakpoint reevaluation process and summarizes the data and rationale used to support these revisions to the AMC Enterobacterales breakpoint.
Collapse
Affiliation(s)
- Navaneeth Narayanan
- Department of Pharmacy Practice and Administration, Rutgers University Ernest Mario School of Pharmacy, Piscataway, New Jersey, USA
| | - Amy J Mathers
- Department of Medicine and Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - Eric Wenzler
- Roche Diagnostics Corporation, Indianapolis, IN, USA
| | - Nicholas M Moore
- Departments of Internal Medicine and Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska University Hospital and Karolinska Institute, Stockholm, Sweden
| | | | - Paul H Edelstein
- Department Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, UK
| |
Collapse
|
2
|
Sewunet T, Razavi M, Rosenborg S, Camporeale A, Nowak M, Melnick D, Gasink LB, Eckburg PB, Critchley IA, Nord CE, Giske CG. Effect of tebipenem pivoxil hydrobromide on the normal gut microbiota of a healthy adult population in Sweden: a randomised controlled trial. Lancet Microbe 2024; 5:e355-e365. [PMID: 38432233 DOI: 10.1016/s2666-5247(23)00360-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 10/13/2023] [Accepted: 10/25/2023] [Indexed: 03/05/2024]
Abstract
BACKGROUND Antimicrobials cause perturbations in the composition and diversity of the host microbiome. We aimed to compare gut microbiome perturbations caused by oral tebipenem pivoxil hydrobromide (a novel carbapenem) and by amoxicillin-clavulanic acid (an orally administered β-lactam-β-lactam inhibitor combination widely used in clinical practice). METHODS We did a phase 1, single-centre, randomised, parallel-group, active-control trial to evaluate the effect of tebipenem pivoxil hydrobromide on the human gut microbiota. Healthy participants aged 18 years or older with no documented illnesses during recruitment were enrolled at Karolinska University Hospital (Stockholm, Sweden). Study participants were stratified by sex and block-randomised in a 1:1 ratio to treatment with either tebipenem pivoxil hydrobromide (600 mg orally every 8 h) or amoxicillin-clavulanic acid (500 mg amoxicillin and 125 mg clavulanic acid orally every 8 h). The study included 10 days of treatment (days 1-10) and four follow-up visits (days 14, 21, 90, and 180). The trial was open-label for clinical investigators and patients, but masked for microbiology investigators. Faecal samples were collected at all visits. Sequencing of 16S rDNA was used to measure the diversity metrics, and quantitative culture to quantify selected taxa. The primary outcomes were changes in the α and β diversity and log count of colony-forming units for selected taxa between samples compared with baseline (day 1), and whether any changes reverted during the follow-up period. The analyses were done in the intention-to-treat population. This study was registered with ClinicalTrials.gov (NCT04376554). FINDINGS The study was conducted between Jan 23, 2020, and April 6, 2021. 49 volunteers were screened for eligibility, among whom 30 evaluable participants (14 men and 16 women) were assigned: 15 (50%) to the tebipenem pivoxil hydrobromide group and 15 (50%) to the amoxicillin-clavulanic acid group. Baseline characteristics were similar between groups. Complete follow-up was available for all participants, and all participants except one completed treatment as assigned. The diversity metrics showed significant changes from baseline during the treatment period. Significant decreases in richness were observed on days 4-10 (p≤0·0011) in the amoxicillin-clavulanic acid group and on days 4-14 (p≤0·0019) in the tebipenem pivoxil hydrobromide group. Similarly, evenness was significantly decreased during treatment in the amoxicillin-clavulanic acid group (day 4, p=0·030) and the tebipenem pivoxil hydrobromide group (days 4-10, p<0·0001) compared with baseline. Quantitative cultures showed significant decreases in Enterobacterales (days 4-7, p≤0·0030), Enterococcus spp (days 4-14, p=0·025 to p<0·0001), Bifidobacterium spp (days 2-4, p≤0·026), and Bacteroides spp (days 4-10, p≤0·030) in the tebipenem pivoxil hydrobromide group. Similarly, in amoxicillin-clavulanic acid recipients, significant changes were observed in Enterobacterales (days 4-10, p≤0·048), Bifidobacterium spp (days 2-4, p≤0·013), and Lactobacillus spp (days 2-4, p≤0·020). Samples from the follow-up period were not significantly different from those at baseline in β diversity analysis (PERMANOVA, p>0·99). By the end of the study, no significant change was observed compared with baseline in either group. There were no deaths or severe adverse events. INTERPRETATION The impact of tebipenem pivoxil hydrobromide on the gut microbiome was similar to that of amoxicillin-clavulanic acid. The safety of antibiotic use with regard to the microbiome should be given attention, as dysbiosis is associated with health and disease. FUNDING Spero Therapeutics.
Collapse
Affiliation(s)
- Tsegaye Sewunet
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - Mohammad Razavi
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - Staffan Rosenborg
- Clinical Pharmacology Trial Unit, Department of Clinical Pharmacology, Karolinska University Hospital, Stockholm, Sweden
| | - Angela Camporeale
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | | | | | - Carl Erik Nord
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - Christian G Giske
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Linde-Ozola Z, Classen AY, Giske CG, Göpel S, Eliakim-Raz N, Semret M, Simonsen GS, Vehreschild JJ, Jørgensen SB, Kessel J, Kleppe LKS, Oma DH, Vehreschild MJGT, Vilde A, Dumpis U. Quality, availability and suitability of antimicrobial stewardship guidance: a multinational qualitative study. JAC Antimicrob Resist 2024; 6:dlae039. [PMID: 38486662 PMCID: PMC10939443 DOI: 10.1093/jacamr/dlae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/19/2024] [Indexed: 03/17/2024] Open
Abstract
Background Antimicrobial stewardship (AMS) programmes are established across the world to treat infections efficiently, prioritize patient safety, and reduce the emergence of antimicrobial resistance. One of the core elements of AMS programmes is guidance to support and direct physicians in making efficient, safe and optimal decisions when prescribing antibiotics. To optimize and tailor AMS, we need a better understanding of prescribing physicians' experience with AMS guidance. Objectives To explore the prescribing physicians' user experience, needs and targeted improvements of AMS guidance in hospital settings. Methods Semi-structured interviews were conducted with 36 prescribing physicians/AMS guidance users from hospital settings in Canada, Germany, Israel, Latvia, Norway and Sweden as a part of the international PILGRIM trial. A socioecological model was applied as an overarching conceptual framework for the study. Results Research participants were seeking more AMS guidance than is currently available to them. The most important aspects and targets for improvement of AMS guidance were: (i) quality of guidelines; (ii) availability of infectious diseases specialists; and (iii) suitability of AMS guidance to department context. Conclusions Achieving prudent antibiotic use not only depends on individual and collective levels of commitment to follow AMS guidance but also on the quality, availability and suitability of the guidance itself. More substantial commitment from stakeholders is needed to allocate the required resources for delivering high-quality, available and relevant AMS guidance to make sure that the prescribers' AMS needs are met.
Collapse
Affiliation(s)
| | - Annika Y Classen
- Faculty of Medicine, University of Cologne, Cologne, Germany
- Department I for Internal Medicine, University Hospital Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Christian G Giske
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Siri Göpel
- Department of Internal Medicine I, Division of infectious diseases, University Hospital Tübingen, Tübingen, Germany
- Clinical Research Unit for Healthcare Associated and Antibiotic Resistant Bacterial Infections, German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Noa Eliakim-Raz
- Internal Medicine E, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Makeda Semret
- Infectious Diseases and Medical Microbiology, McGill University Health Centre, Montreal, Canada
| | - Gunnar Skov Simonsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- UiT-The Arctic University of Norway, Tromsø, Norway
| | - Jörg Janne Vehreschild
- Faculty of Medicine, University of Cologne, Cologne, Germany
- Department I for Internal Medicine, University Hospital Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
- Department II of Internal Medicine, Haematology/Oncology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Silje Bakken Jørgensen
- Department of Medical Microbiology and Infection Control and Department of Emergency Care, Akershus University Hospital, Lørenskog, Norway
| | - Johanna Kessel
- Department of Internal Medicine, Infectious Diseases, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - Lars Kåre Selland Kleppe
- Department of Infection Prevention and Control, Stavanger University Hospital, Stavanger, Norway
| | - Dorthea Hagen Oma
- Section for Patient Safety, Haukeland University Hospital, Bergen, Norway
| | - Maria J G T Vehreschild
- Faculty of Medicine, University of Cologne, Cologne, Germany
- Department I for Internal Medicine, University Hospital Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
- Department of Internal Medicine, Infectious Diseases, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - Aija Vilde
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Uga Dumpis
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| |
Collapse
|
5
|
Oldendorff F, Nordberg V, Giske CG, Navér L. A decade of neonatal sepsis in Stockholm, Sweden: Gram-positive pathogens were four times as common as Gram-negatives. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04809-8. [PMID: 38517573 DOI: 10.1007/s10096-024-04809-8] [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] [Received: 01/09/2024] [Accepted: 03/11/2024] [Indexed: 03/24/2024]
Abstract
PURPOSE To assess Gram-positive bacterial (GPB) bloodstream infection (BSI) in neonates, covering incidence, morbidity, mortality, antimicrobial resistance patterns and biomarkers in Region Stockholm, Sweden between 2006 and 2016. METHODS A population-based retrospective epidemiological study including infants with GPB-BSI, admitted to the neonatal units at Karolinska University Hospital (KUH). Data were collected from patient records, the Swedish Neonatal Quality Register, the microbiological laboratory at KUH and the Swedish Public Health Agency. RESULTS We identified 357 infants with GPB-BSI, representing an incidence of 1.47/1000 live births (LB). Group B streptococcus (GBS) was the most common pathogen causing BSI in full-term infants and early-onset sepsis (EOS) (0.20/1000 LB), while coagulase-negative staphylococci (CoNS) were predominant in infants born very preterm and in late-onset sepsis (LOS) (0.79/1000 LB). There were no fatal GBS BSI cases, but 10.2% developed meningitis. The GPB case fatality rate was 9.5% and the sepsis fatality rate 2.8%. In GPB-BSI, 1/10 did not have an elevated C-reactive protein level. Staphylococcus aureus (S. aureus) BSI increased during the study period, but no methicillin or vancomycin resistant strains were found. The antimicrobial resistance (AMR) rate was highest in CoNS isolates. CONCLUSION GPB-BSI was four times more common than Gram-negative BSI in neonates but resulted in lower mortality rate. GBS was the most common pathogen in full-term infants and in EOS. CoNS was the most common pathogen in LOS and infants born very preterm, and the AMR rate was high in these isolates. The increasing trend of S. aureus BSI indicates a need of further investigation.
Collapse
Affiliation(s)
- Frida Oldendorff
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.
- Department of Clinical Science Intervention and Technology (CLINTEC), Division of Pediatrics, Karolinska Institutet, Stockholm, Sweden.
| | - Viveka Nordberg
- Department of Neonatology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Science Intervention and Technology (CLINTEC), Division of Pediatrics, Karolinska Institutet, Stockholm, Sweden
| | - Christian G Giske
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Lars Navér
- Department of Neonatology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Science Intervention and Technology (CLINTEC), Division of Pediatrics, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
6
|
Montelin H, Camporeale A, Hallgren A, Angelin M, Hogvall J, Östholm Balkhed Å, Vading M, Giske CG, Tängdén T. Treatment, outcomes and characterization of pathogens in urinary tract infections caused by ESBL-producing Enterobacterales: a prospective multicentre study. J Antimicrob Chemother 2024; 79:531-538. [PMID: 38197416 PMCID: PMC10904723 DOI: 10.1093/jac/dkad402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
OBJECTIVES Treatment options for urinary tract infections (UTIs) caused by ESBL-producing Enterobacterales are limited. Moreover, evidence to support therapeutic decisions is lacking. This study assessed current treatment strategies and patient and pathogen characteristics in relation to clinical and microbiological outcomes. METHODS Patients with UTI caused by ESBL-producing Enterobacterales were prospectively recruited by investigators at 15 infectious disease hospital departments. Data were collected on patient characteristics, treatments, clinical and microbiological cure 10-14 days after the end of treatment, and relapse within 3 months. Bacterial isolates were subjected to MIC determination and WGS. RESULTS In total, 235 patients (107 febrile UTI, 128 lower UTI) caused by Escherichia coli (n = 223) and Klebsiella spp. (n = 12) were included. Clinical and microbiological cure rates were 83% and 64% in febrile UTI, and 79% and 65% in lower UTI. Great variability in treatments was observed, especially in oral therapy for febrile UTI. No difference was seen in clinical outcomes with piperacillin/tazobactam (n = 28) compared with carbapenems (n = 41). Pivmecillinam was frequently used in lower UTI (n = 62), and was also associated with high clinical cure rates when used as initial therapy (10/10) or follow-up (7/8) for febrile UTI. Recurrent infection, diabetes mellitus and urogenital disease were associated (P < 0.05) with clinical failure and relapse. In E. coli, ST131 was significantly associated with relapse, and haemolysin with microbiological failure or relapse. CONCLUSIONS Antibiotic treatments were highly variable. Patient and pathogen factors were identified as potential determinants of disease presentation and outcomes and may prove useful to guide individualized treatment and follow-up.
Collapse
Affiliation(s)
- Hanna Montelin
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden
| | - Angela Camporeale
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Hallgren
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden
| | - Martin Angelin
- Department of Clinical Microbiology, Infectious Diseases, Umeå University, Umeå, Sweden
| | - Jonas Hogvall
- Department of Infectious Diseases, Karlstad Central Hospital, Karlstad, Sweden
| | - Åse Östholm Balkhed
- Department of Biomedical and Clinical Sciences, Division of Infectious Diseases, Linköping University, Linköping, Sweden
| | - Malin Vading
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Danderyds Hospital, Stockholm, Sweden
| | - Christian G Giske
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Tängdén
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden
| |
Collapse
|
7
|
Örmälä-Tiznado AM, Allander L, Maatallah M, Kabir MH, Brisse S, Sandegren L, Patpatia S, Coorens M, Giske CG. Molecular characteristics, fitness, and virulence of high-risk and non-high-risk clones of carbapenemase-producing Klebsiella pneumoniae. Microbiol Spectr 2024; 12:e0403622. [PMID: 38205958 PMCID: PMC10845972 DOI: 10.1128/spectrum.04036-22] [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: 10/10/2022] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
Extensively drug-resistant (XDR) Klebsiella pneumoniae inflict a notable burden on healthcare worldwide. Of specific concern are strains producing carbapenem-hydrolyzing enzymes, as the therapeutic options for these strains are still very limited. Specific sequence types of K. pneumoniae have been noted for their epidemic occurrence globally, but the mechanisms behind the success of specific clones remain unclear. Herein, we have characterized 20 high-risk clones (HiRCs) and 10 non-HiRCs of XDR K. pneumoniae, exploring factors connected to the epidemiological success of some clones. Isolates were subjected to core genome multilocus sequence typing analysis to determine the clonal relationships of the isolates and subsequently characterized with regard to features known to be linked to overall bacterial fitness and virulence. The genomes were analyzed in silico for capsule types, O antigens, virulence factors, antimicrobial resistance genes, prophages, and CRISPR-Cas loci. In vitro growth experiments were conducted to retrieve proxies for absolute and relative fitness for 11 HiRC and 9 non-HiRC isolates selected based on the clonal groups they belonged to, and infections in a Galleria mellonella insect model were used to evaluate the virulence of the isolates in vivo. This study did not find evidence that virulence factors, prophages, CRISPR-Cas loci, or fitness measured in vitro alone would contribute to the global epidemiological success of specific clones of carbapenemase-producing XDR K. pneumoniae. However, this study did find the HiRC group to be more virulent than the non-HiRC group when measured in vivo in a model with G. mellonella. This suggests that the virulence and epidemiological success of certain clones of K. pneumoniae cannot be explained by individual traits investigated in this study and thus warrant further experiments in the future.IMPORTANCEHerein, we explored potential explanations for the successfulness of some epidemic or high-risk clones of carbapenemase-producing Klebsiella pneumoniae. We found differences in mortality in a larva model but found no clear genomic differences in known virulence markers. Most of the research on virulence in K. pneumoniae has been focused on hypervirulent strains, but here, we try to understand differences within the group of highly resistant strains. The results from the larva virulence model could be used to design experiments in higher animals. Moreover, the data could provide further support to a differentiated infection control approach against extensively drug-resistant strains, based on their classification as high-risk clones.
Collapse
Affiliation(s)
- Anni-Maria Örmälä-Tiznado
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lisa Allander
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Makaoui Maatallah
- Laboratoire d’Analyse, Traitement et Valorisation des Polluants de l’Environnement et des Produits (LATVPEP: LR01ES16), Faculté de Pharmacie de Monastir, Université de Monastir, Monastir, Tunisia
| | - Muhammad Humaun Kabir
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sheetal Patpatia
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Maarten Coorens
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
8
|
Vestberg N, Razavi M, Giske CG, Fang H. Antimicrobial susceptibilities and genomic characteristics of methicillin-resistant Staphylococcus aureus resistant to mupirocin in Stockholm, Sweden. APMIS 2024; 132:94-99. [PMID: 37965984 DOI: 10.1111/apm.13357] [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: 09/05/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
The aim of this study was to investigate antimicrobial susceptibilities and genomic characteristics of mupirocin-resistant MRSA isolates in Stockholm, Sweden. In total, 44 non-duplicate mupirocin-resistant MRSA isolates detected in Stockholm during 2010-2022 were investigated. Antimicrobial susceptibility testing was performed using broth microdilution method and further tested for high-level mupirocin-resistance (MuH) and rifampicin by Etest®. All isolates were subjected to whole genome sequencing. 41 isolates presented MuH with MICs ≥1024 mg/L whilst three isolates displayed low-level mupirocin resistance (MuL). mupA-gene was detected in all MuH isolates. Point mutations in ileS gene leading to N213D and V588F were identified in the three MuL isolates. Mutation in rpoB (H481N) was detected in a rifampicin-resistant isolate. Among the isolates, 15 multi-locus sequence types (MLST) were identified, with the four most common sequence types (ST22, ST72, ST8, and ST125) accounting for 66% of the isolates. Mupirocin-resistant MRSA in Stockholm was uncommon, with a percentage of <0.5% among MRSA cases during 2010-2022. In the present study, most mupirocin-resistant isolates were MuH and mupA-positive, predominantly linked to ST22 or ST72 isolates. MuL-resistance was associated with a point mutation in the IleS protein. A multidrug-resistant ST1-MRSA-IV strain was resistant to both mupirocin and rifampicin.
Collapse
Affiliation(s)
- Nora Vestberg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mohammad Razavi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Hong Fang
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
9
|
Smekal AK, Furebring M, Lipcsey M, Giske CG. Swedish multicentre study of target attainments with β-lactams in the ICU: which MIC parameter should be used? J Antimicrob Chemother 2023; 78:2895-2901. [PMID: 37897332 PMCID: PMC10689903 DOI: 10.1093/jac/dkad327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Therapeutic drug monitoring (TDM) has been suggested to optimize antimicrobial target attainment, typically using 100%T>MIC, in β-lactam treatment in the ICU. The MIC parameter used in this equation is mostly the worst case scenario MIC (MICWCS)-the highest MIC the empirical treatment should cover. However, the impact of the MIC parameter used in pharmacokinetic/pharmacodynamic calculations has been poorly investigated. OBJECTIVES To assess the influence of target attainment rates for two different MIC parameters using actual MICs of the causative pathogens as the primary reference. METHODS In a Swedish multicentre study of target attainment for 138 ICU patients treated with β-lactams, the causative pathogen was isolated and subjected to reference MIC testing. Whenever the strain belonged to the WT distribution, we assigned it to the category MICECOFF (epidemiological cut-off value). In the calculations we compared the MICECOFF and the MICWCS. RESULTS The proportion of patients with target attainment failure for all antibiotics using 100%T>MIC was 45% (95% CI, 37%-53%) for MICWCS and 23% (95% CI, 16%-31%) for MICECOFF. When the target 50%T>4×MIC was used, corresponding attainment failures were 57% (95% CI, 49%-66%) and 25% (95% CI, 17%-32%) for MICWCS and MICECOFF, respectively. CONCLUSIONS MICWCS can overestimate target attainment failure. The use of MICWCS could be one reason for the difficulties in establishing a relationship between target failure and mortality in other studies. Based on findings herein, the MICECOFF, which is based on the MIC of the causative pathogen, should be considered a more suitable alternative. When no pathogen is detected, the MICECOFF of likely pathogens according to infection type should be used.
Collapse
Affiliation(s)
- Anna-Karin Smekal
- Department of Surgical Sciences, Anaesthesiology and Intensive Care, Uppsala University, Uppsala,Sweden
- Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Mia Furebring
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala,Sweden
| | - Miklos Lipcsey
- Department of Surgical Sciences, Anaesthesiology and Intensive Care, Uppsala University, Uppsala,Sweden
- Department of Surgical Sciences, Hedenstierna Laboratory, Uppsala University, Uppsala,Sweden
| | - Christian G Giske
- Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
10
|
Leegaard TM, Justesen US, Matuschek E, Giske CG. Performance of automated antimicrobial susceptibility testing for the detection of antimicrobial resistance in gram-negative bacteria: a NordicAST study. APMIS 2023; 131:543-551. [PMID: 37590014 DOI: 10.1111/apm.13346] [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: 06/27/2023] [Accepted: 08/07/2023] [Indexed: 08/18/2023]
Abstract
Automated testing of antimicrobial susceptibility is common in clinical microbiology laboratories but their ability to detect low-level resistance has been questioned. This Nordic multicentre study aimed to evaluate the performance of commercially available automated AST systems. A phenotypically well-characterised collection of gram-negative bacilli (Escherichia coli (n = 7), Klebsiella pneumoniae (n = 6) and Pseudomonas aeruginosa (n = 7)) with and without resistance mechanisms was examined by Danish (n = 1), Finnish (n = 6), Norwegian (n = 16) and Swedish (n = 5) laboratories. Minimum inhibitory concentrations (MICs) were determined for 12 antimicrobials with automated systems and compared with MICs obtained with gold standard broth microdilution. The automated systems used were VITEK 2 (n = 23), Phoenix (n = 4), MicroScan (n = 1), and ARIS (n = 1). Very major errors were identified for six antimicrobials; cefotaxime (6.9%), meropenem (0.4%), ciprofloxacin (0.7%), ertapenem (4.3%), amikacin (3.4%) and colistin (6.4%). Categorical agreement of MIC for the automated systems compared to broth microdilution ranged from 83% for imipenem to 100% for ampicillin and trimethoprim-sulfamethoxazole. The analysis revealed several important antimicrobials where resistance was underestimated, potentially with significant consequences in patient treatment. The results cast doubt on the use of automated AST in the management of patients with serious infections and suggests that more work is needed to define their limitations.
Collapse
Affiliation(s)
- Truls M Leegaard
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Division of Medicine and Laboratory Sciences, University of Oslo, Oslo, Norway
| | - Ulrik S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | | | - Christian G Giske
- Department of Clinical Microbiology, MTC - Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
11
|
Borsa BA, Hernandez LI, Jiménez T, Tellapragada C, Giske CG, Hernandez FJ. Therapeutic-oligonucleotides activated by nucleases (TOUCAN): A nanocarrier system for the specific delivery of clinical nucleoside analogues. J Control Release 2023; 361:260-269. [PMID: 37541593 DOI: 10.1016/j.jconrel.2023.07.057] [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: 01/10/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023]
Abstract
Nucleoside analogues have been in clinical use since 1960s and they are still used as the first therapeutic option for several cancers and viral infections, due to their high therapeutic efficacy. However, their wide clinical acceptance has been limited due to their high toxicity and severe side effects to patients. Herein, we report on a nanocarrier system that delivers nucleosides analogues in a target-specific manner, making nucleoside-based therapeutics safer and with the possibility to be used in other human conditions. This system, named, Therapeutic OligonUCleotides Activated by Nucleases" (TOUCAN) combines: i) the recognition power of oligonucleotides as substrates, ii) the use of nucleases as enzymatic biomarkers and iii) the clinical efficacy of nucleoside analogues, in a single approach. As a proof-of-concept, we report on a TOUCAN that is activated by a specific nuclease produced by bacteria and releases a therapeutic nucleoside, floxuridine. We demonstrate, for the first time, that, by incorporating a therapeutic nucleoside analogue into oligonucleotide probes, we can specifically inhibit bacterial growth in cultures. In this study, Staphylococcus aureus was selected as the targeted bacteria and the TOUCAN strategy successfully inhibited its growth with minimal inhibitory concentration (MIC) values ranging from 0.62 to 40 mg/L across all tested strains. Moreover, our results indicate that the intravenous administration of TOUCANs at a dose of 20 mg/kg over a 24-h period is a highly effective method for treating bacterial infections in a mouse model of pyomyositis. Importantly, no signs of toxicity were observed in our in vitro and in vivo studies. This work can significantly impact the current management of bacterial infections, laying the grounds for the development of a different class of antibiotics. Furthermore, it can provide a safer delivery platform for clinical nucleoside therapeutics in any human conditions, such as cancer and viral infection, where specific nuclease activity has been reported.
Collapse
Affiliation(s)
- Baris A Borsa
- Wallenberg Center for Molecular Medicine (WCMM), Linköping, Sweden; Department of Physics, Chemistry and Biology (IFM), Linköping University, Sweden; Nucleic Acid Technologies Laboratory (NAT-Lab), Linköping, Sweden
| | - Luiza I Hernandez
- Department of Clinical and Experimental Medicine (IKE), Linköping University, Sweden; SOMAprobes, Science and Technology Park of Gipuzkoa, Donostia-San Sebastian, Spain
| | - Tania Jiménez
- SOMAprobes, Science and Technology Park of Gipuzkoa, Donostia-San Sebastian, Spain
| | - Chaitanya Tellapragada
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Frank J Hernandez
- Wallenberg Center for Molecular Medicine (WCMM), Linköping, Sweden; Department of Physics, Chemistry and Biology (IFM), Linköping University, Sweden; Nucleic Acid Technologies Laboratory (NAT-Lab), Linköping, Sweden.
| |
Collapse
|
12
|
Stubhaug TT, Giske CG, Justesen US, Kahlmeter G, Matuschek E, Sundsfjord A, Skaare D. Antimicrobial susceptibility testing of Bacteroides species by disk diffusion: The NordicAST Bacteroides study. Anaerobe 2023:102743. [PMID: 37253399 DOI: 10.1016/j.anaerobe.2023.102743] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
OBJECTIVES - Antimicrobial susceptibility testing (AST) of anaerobic bacteria has until recently been done by MIC methods. We have carried out a multi-centre evaluation of the newly validated EUCAST disk diffusion method for AST of Bacteroides spp. METHODS - A panel of 30 Bacteroides strains was assembled based on reference agar dilution MICs, resistance gene detection and quantification of cfiA carbapenemase gene expression. Nordic clinical microbiology laboratories (n = 45) performed disk diffusion on Fastidious Anaerobe Agar with 5% mechanically defibrinated horse blood (FAA-HB) for piperacillin-tazobactam, meropenem and metronidazole. RESULTS - A total of 43/45 (95.6%) laboratories carried out disk diffusion per protocol. Intraclass correlation coefficients were 0.87 (0.80-0.93) for piperacillin-tazobactam, 0.95 (0.91-0.97) for meropenem and 0.89 (0.83-0.94) for metronidazole. For metronidazole, one media lot yielded smaller zones and higher variability than another. Piperacillin-tazobactam and meropenem zone diameters correlated negatively with cfiA expression. A meropenem zone diameter of <28 mm in B. fragilis indicated presence of cfiA. Piperacillin-tazobactam had the most false susceptible results. Categorical errors for this antimicrobial were particularly prevalent in cfiA-positive strains, and piperacillin-tazobactam had the highest number of comments describing zone reading difficulties. CONCLUSIONS - Inter-laboratory agreement by disk diffusion was good or very good. The main challenges were media-related variability for metronidazole and categorical disagreement with the reference method for piperacillin-tazobactam in some cfiA-positive strains. An area of technical uncertainty specific for such strains may be warranted.
Collapse
Affiliation(s)
- Tore Taksdal Stubhaug
- Vestfold Hospital Trust, Department of Microbiology, Tønsberg, Norway; University of Oslo, Institute of Clinical Medicine, Oslo, Norway.
| | - Christian G Giske
- Karolinska University Hospital, Department of Clinical Microbiology, Stockholm, Sweden; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ulrik S Justesen
- Odense University Hospital, Department of Clinical Microbiology, Odense, Denmark
| | | | | | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance (K-res), University Hospital of North Norway, Tromsø, Norway; UiT the Arctic University of Norway, Department of Medical Biology, Tromsø, Norway
| | - Dagfinn Skaare
- Vestfold Hospital Trust, Department of Microbiology, Tønsberg, Norway
| |
Collapse
|
13
|
Rystedt K, Hedin K, Tyrstrup M, Skoog-Ståhlgren G, Edlund C, Giske CG, Gunnarsson R, Sundvall PD. Agreement between rapid antigen detection test and culture for group A streptococcus in patients recently treated for pharyngotonsillitis - a prospective observational study in primary care. Scand J Prim Health Care 2023; 41:91-97. [PMID: 36880344 PMCID: PMC10088972 DOI: 10.1080/02813432.2023.2182631] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
OBJECTIVE The aim was to compare rapid antigen detection test (RADT) and throat culture for group A streptococci (GAS) among patients recently treated with penicillin V for GAS pharyngotonsillitis. DESIGN AND SETTING The study was a secondary analysis within a randomized controlled trial comparing 5 versus 10 days of penicillin V for GAS pharyngotonsillitis. Patients were recruited at 17 primary health care centres in Sweden. SUBJECTS We included 316 patients ≥ 6 years of age, having 3-4 Centor criteria, a positive RADT and a positive throat culture for GAS at inclusion, and also having a RADT and throat culture for GAS taken at a follow-up visit within 21 days. MAIN OUTCOME MEASURES RADT and conventional throat culture for GAS. RESULTS This prospective study showed 91% agreement between RADT and culture at follow-up within 21 days. Only 3/316 participants had negative RADT with a positive throat culture for GAS at follow-up, and 27/316 patients with positive RADT had a negative culture for GAS. Log rank test did not reveal any difference in the decline over time of positive tests between RADT and throat culture (p = 0.24). Agreement between RADT and throat culture for GAS at the follow-up was not associated with treatment duration, number of days from inclusion until follow-up, throat symptoms at follow-up, gender, or age. CONCLUSION RADT and culture for GAS agreed to a high extent also after recent penicillin V treatment. RADT for GAS means a low risk for missing the presence of GAS.KEY POINTSTesting for group A streptococci (GAS) before antibiotic treatment can reduce antibiotic prescription for pharyngotonsillitis. It has been proposed that rapid antigen detection tests (RADT) for group A streptococci after recent penicillin V treatment may be falsely positive due to possible persisting antigens from non-viable bacteria.The decline of the presence of GAS was similar between RADT and conventional throat culture in patients who had recently completed penicillin V treatment for GAS pharyngotonsillitisRADT for GAS is useful in identifying the presence of GAS after recent penicillin V treatment.
Collapse
Affiliation(s)
- Karin Rystedt
- Research, Education, Development & Innovation, Primary Health Care, Region Västra Götaland, Sweden
- General Practice/Family Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Närhälsan Hentorp Health Care Center, Gröna vagen, Skövde, Sweden
| | - Katarina Hedin
- Futurum, Region Jönköping County, and Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
- Department of Clinical Sciences in Malmö, Family Medicine, Lund University, Malmö, Sweden
| | - Mia Tyrstrup
- Department of Clinical Sciences in Malmö, Family Medicine, Lund University, Malmö, Sweden
| | - Gunilla Skoog-Ståhlgren
- Unit for Antibiotics and Infection Control, the Public Health Agency of Sweden, Solna, Sweden
| | - Charlotta Edlund
- Unit for Antibiotics and Infection Control, the Public Health Agency of Sweden, Solna, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Ronny Gunnarsson
- Research, Education, Development & Innovation, Primary Health Care, Region Västra Götaland, Sweden
- General Practice/Family Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Pär-Daniel Sundvall
- Research, Education, Development & Innovation, Primary Health Care, Region Västra Götaland, Sweden
- General Practice/Family Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
14
|
Nyblom M, Johnning A, Frykholm K, Wrande M, Müller V, Goyal G, Robertsson M, Dvirnas A, Sewunet T, KK S, Ambjörnsson T, Giske CG, Sandegren L, Kristiansson E, Westerlund F. Strain-level bacterial typing directly from patient samples using optical DNA mapping. Commun Med (Lond) 2023; 3:31. [PMID: 36823379 PMCID: PMC9950433 DOI: 10.1038/s43856-023-00259-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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Identification of pathogens is crucial to efficiently treat and prevent bacterial infections. However, existing diagnostic techniques are slow or have a too low resolution for well-informed clinical decisions. METHODS In this study, we have developed an optical DNA mapping-based method for strain-level bacterial typing and simultaneous plasmid characterisation. For the typing, different taxonomical resolutions were examined and cultivated pure Escherichia coli and Klebsiella pneumoniae samples were used for parameter optimization. Finally, the method was applied to mixed bacterial samples and uncultured urine samples from patients with urinary tract infections. RESULTS We demonstrate that optical DNA mapping of single DNA molecules can identify Escherichia coli and Klebsiella pneumoniae at the strain level directly from patient samples. At a taxonomic resolution corresponding to E. coli sequence type 131 and K. pneumoniae clonal complex 258 forming distinct groups, the average true positive prediction rates are 94% and 89%, respectively. The single-molecule aspect of the method enables us to identify multiple E. coli strains in polymicrobial samples. Furthermore, by targeting plasmid-borne antibiotic resistance genes with Cas9 restriction, we simultaneously identify the strain or subtype and characterize the corresponding plasmids. CONCLUSION The optical DNA mapping method is accurate and directly applicable to polymicrobial and clinical samples without cultivation. Hence, it has the potential to rapidly provide comprehensive diagnostics information, thereby optimizing early antibiotic treatment and opening up for future precision medicine management.
Collapse
Affiliation(s)
- My Nyblom
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Anna Johnning
- grid.5371.00000 0001 0775 6028Department of Mathematical Sciences, Chalmers University of Technology & University of Gothenburg, Gothenburg, 412 96 Sweden ,grid.452079.dDepartment of Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, 412 88 Sweden ,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30 Sweden
| | - Karolin Frykholm
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Marie Wrande
- grid.8993.b0000 0004 1936 9457Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 751 23 Sweden
| | - Vilhelm Müller
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Gaurav Goyal
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Miriam Robertsson
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Albertas Dvirnas
- grid.4514.40000 0001 0930 2361Department of Astronomy and Theoretical Physics, Lund University, Lund, 223 62 Sweden
| | - Tsegaye Sewunet
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 141 86 Sweden
| | - Sriram KK
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Tobias Ambjörnsson
- grid.4514.40000 0001 0930 2361Department of Astronomy and Theoretical Physics, Lund University, Lund, 223 62 Sweden
| | - Christian G. Giske
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 141 86 Sweden ,grid.24381.3c0000 0000 9241 5705Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, 171 76 Sweden
| | - Linus Sandegren
- grid.8993.b0000 0004 1936 9457Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 751 23 Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology & University of Gothenburg, Gothenburg, 412 96, Sweden. .,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30, Sweden.
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96, Sweden. .,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30, Sweden.
| |
Collapse
|
15
|
Fröberg G, Maurer FP, Chryssanthou E, Fernström L, Benmansour H, Boarbi S, Mengshoel AT, Keller PM, Viveiros M, Machado D, Fitzgibbon MM, Mok S, Werngren J, Cirillo DM, Alcaide F, Hyyryläinen HL, Aubry A, Andres S, Nadarajan D, Svensson E, Turnidge J, Giske CG, Kahlmeter G, Cambau E, van Ingen J, Schön T. Towards clinical breakpoints for non-tuberculous mycobacteria - Determination of epidemiological cut off values for the Mycobacterium avium complex and Mycobacterium abscessus using broth microdilution. Clin Microbiol Infect 2023:S1198-743X(23)00060-5. [PMID: 36813087 DOI: 10.1016/j.cmi.2023.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 12/07/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/22/2023]
Abstract
OBJECTIVE For non-tuberculous mycobacteria (NTM), minimum inhibitory concentration (MIC) distributions of wild-type isolates have not been systematically evaluated despite their importance for establishing antimicrobial susceptibility testing (AST) breakpoints. METHODS We gathered MIC distributions for drugs used against the Mycobacterium avium complex (MAC) and Mycobacterium abscessus (MAB) obtained by commercial broth microdilution (SLOMYCOI and RAPMYCOI) from 12 laboratories. Epidemiological cut-off values (ECOFFs) and tentative ECOFFs (TECOFFs) were determined by EUCAST methodology including quality control (QC) strains. RESULTS The clarithromycin ECOFF was 16 mg/L for M. avium (n = 1271) whereas TECOFFs were 8 mg/L for M. intracellulare (n = 415) and 1 mg/L for MAB (n = 1014) confirmed by analysing MAB subspecies without inducible macrolide resistance (n = 235). For amikacin, the ECOFFs were 64 mg/L for MAC and MAB. For moxifloxacin, the WT spanned >8 mg/L for both MAC and MAB. For linezolid, the ECOFF and TECOFF were 64 mg/L for M. avium and M. intracellulare, respectively. Current CLSI breakpoints for amikacin (16 mg/L), moxifloxacin (1 mg/L) and linezolid (8 mg/L) divided the corresponding WT distributions. For QC M. avium and M. peregrinum, ≥95% of MIC values were well within recommended QC ranges. CONCLUSION As a first step towards clinical breakpoints for NTM, (T)ECOFFs were defined for several antimicrobials against MAC and MAB. Broad wild-type MIC distributions indicate a need for further method refinement which is now under development within the EUCAST subcommittee for anti-mycobacterial drug susceptibility testing. In addition, we showed that several CLSI NTM breakpoints are not consistent in relation to the (T)ECOFFs.
Collapse
Affiliation(s)
- Gabrielle Fröberg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Florian P Maurer
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Erja Chryssanthou
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Louise Fernström
- Department of Internal Medicine, Lycksele Hospital, Lycksele, Sweden
| | - Hanaa Benmansour
- AP-HP, GHU Nord, Service de Mycobactériologie Spécialisée et de référence, laboratoire associé au Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Université Paris Cité, Paris, France
| | - Samira Boarbi
- National Reference Center for Tuberculosis and Mycobacteria, Sciensano, Brussels, Belgium
| | - Anne Torunn Mengshoel
- Department of Bacteriology, Division of Infection Control, Norwegian Institute of Public Health, Oslo, Norway
| | | | - Miguel Viveiros
- Unit of Medical Microbiology, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Diana Machado
- Unit of Medical Microbiology, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Margaret M Fitzgibbon
- Irish Mycobacteria Reference Laboratory, St James's Hospital, Dublin, Ireland; Department of Clinical Microbiology, School of Medicine, Trinity College, Dublin, Ireland
| | - Simone Mok
- Irish Mycobacteria Reference Laboratory, St James's Hospital, Dublin, Ireland; Department of Clinical Microbiology, School of Medicine, Trinity College, Dublin, Ireland
| | - Jim Werngren
- Department of Microbiology, Unit for Laboratory Surveillance of Bacterial Pathogens, Public Health Agency of Sweden, Solna, Sweden
| | | | - Fernando Alcaide
- Department of Clinical Microbiology, Bellvitge University Hospital-IDIBELL, University of Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | | | - Alexandra Aubry
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Paris, France
| | - Sönke Andres
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Darshaalini Nadarajan
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Erik Svensson
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - John Turnidge
- School of Biological Sciences and Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gunnar Kahlmeter
- The EUCAST Development Laboratory, Clinical Microbiology, Central Hospital, Växjö, Sweden
| | - Emmanuelle Cambau
- AP-HP, GHU Nord, Service de Mycobactériologie Spécialisée et de référence, laboratoire associé au Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Université Paris Cité, Paris, France
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Thomas Schön
- Department of Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden; Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Infectious Diseases in Östergötland, Linköping University, Linköping, Sweden.
| | | |
Collapse
|
16
|
Rystedt K, Edquist P, Giske CG, Hedin K, Tyrstrup M, Ståhlgren GS, Sundvall PD, Edlund C. Effects of penicillin V on the faecal microbiota in patients with pharyngotonsillitis-an observational study. JAC Antimicrob Resist 2023; 5:dlad006. [PMID: 36816747 PMCID: PMC9931529 DOI: 10.1093/jacamr/dlad006] [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: 08/08/2022] [Accepted: 01/05/2023] [Indexed: 02/17/2023] Open
Abstract
Background The intestinal microbiota functions as a reservoir of antibiotic resistance. Objectives To evaluate penicillin V (phenoxymethylpenicillin) effects on the faecal microbiota with focus on beta-lactam resistance. Methods We included 31 primary care patients with group A streptococcal pharyngotonsillitis treated with penicillin V for 5 (800 mg × 4) or 10 days (1000 mg × 3). Twenty-nine patients contributed with three faecal swab samples each. The faecal specimens were collected at the start of penicillin V treatment, after the last dose and at follow-up 7-9 days after completed treatment. Samples were inoculated semiquantitatively on selective screening agar plates to study beta-lactam resistance, species shifts among Enterobacterales and enterococci, and colonization with Candida spp. and Clostridioides difficile. Representative colonies were identified using MALDI-TOF. Results were analysed by non-parametric statistical methods. Results An increase in the proportion of patients colonized with ampicillin-resistant Enterobacterales, from 52% to 86% (P = 0.007), and Enterobacterales with decreased susceptibility to third-generation cephalosporins, from 32% to 52% (P = 0.034), was observed between the first and second samples. This increase was no longer significant at follow-up. New colonization with ampicillin-resistant Enterobacterales species and non-Enterobacterales Gram-negative species was observed, and persisted at follow-up. Conclusions Following treatment with penicillin V, we observed decreased susceptibility to ampicillin and third-generation cephalosporins, and prolonged colonization with non-Escherichia coli Gram-negative species. These findings challenge the perception that penicillin V has limited ecological effect on the intestinal microbiota, and emphasizes the importance of avoiding even narrow-spectrum antimicrobials when possible.
Collapse
Affiliation(s)
| | - Petra Edquist
- The Public Health Agency of Sweden (PHAS), Solna 171 82, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden,Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Katarina Hedin
- Futurum, Region Jönköping County, and Department of Health, Medicine and Caring Sciences, Linköping University, Linköping,Sweden,Department of Clinical Sciences in Malmö, Family Medicine, Lund University, Malmö, Sweden
| | - Mia Tyrstrup
- Department of Clinical Sciences in Malmö, Family Medicine, Lund University, Malmö, Sweden
| | | | - Pär-Daniel Sundvall
- General Practice/Family Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Box 454, Gothenburg SE-405 30, Sweden,Research, Education, Development & Innovation, Primary Health Care, Region Västra Götaland, Västra Götaland, Sweden,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | | |
Collapse
|
17
|
Mikaeloff F, Gelpi M, Benfeitas R, Knudsen AD, Vestad B, Høgh J, Hov JR, Benfield T, Murray D, Giske CG, Mardinoglu A, Trøseid M, Nielsen SD, Neogi U. Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection. eLife 2023; 12:82785. [PMID: 36794912 PMCID: PMC10017104 DOI: 10.7554/elife.82785] [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: 08/17/2022] [Accepted: 02/15/2023] [Indexed: 02/17/2023] Open
Abstract
Multiomics technologies improve the biological understanding of health status in people living with HIV on antiretroviral therapy (PWH). Still, a systematic and in-depth characterization of metabolic risk profile during successful long-term treatment is lacking. Here, we used multi-omics (plasma lipidomic, metabolomic, and fecal 16 S microbiome) data-driven stratification and characterization to identify the metabolic at-risk profile within PWH. Through network analysis and similarity network fusion (SNF), we identified three groups of PWH (SNF-1-3): healthy (HC)-like (SNF-1), mild at-risk (SNF-3), and severe at-risk (SNF-2). The PWH in the SNF-2 (45%) had a severe at-risk metabolic profile with increased visceral adipose tissue, BMI, higher incidence of metabolic syndrome (MetS), and increased di- and triglycerides despite having higher CD4+ T-cell counts than the other two clusters. However, the HC-like and the severe at-risk group had a similar metabolic profile differing from HIV-negative controls (HNC), with dysregulation of amino acid metabolism. At the microbiome profile, the HC-like group had a lower α-diversity, a lower proportion of men having sex with men (MSM) and was enriched in Bacteroides. In contrast, in at-risk groups, there was an increase in Prevotella, with a high proportion of MSM, which could potentially lead to higher systemic inflammation and increased cardiometabolic risk profile. The multi-omics integrative analysis also revealed a complex microbial interplay of the microbiome-associated metabolites in PWH. Those severely at-risk clusters may benefit from personalized medicine and lifestyle intervention to improve their dysregulated metabolic traits, aiming to achieve healthier aging.
Collapse
Affiliation(s)
- Flora Mikaeloff
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstituteStockholmSweden
| | - Marco Gelpi
- Copenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | | | - Beate Vestad
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Norwegian PSC Research Center, Oslo University Hospital RikshospitaletOsloNorway
| | - Julie Høgh
- Copenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - Johannes R Hov
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Norwegian PSC Research Center, Oslo University Hospital RikshospitaletOsloNorway
- Institute of Clinical Medicine, University of OsloOsloNorway
| | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital – Amager and HvidovreHvidovreDenmark
| | - Daniel Murray
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of CopenhagenCopenhagenDenmark
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstitutetStockholmSweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of TechnologyStockholmSweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College LondonLondonUnited Kingdom
| | - Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Institute of Clinical MedicineOsloNorway
| | | | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstituteStockholmSweden
| |
Collapse
|
18
|
KK S, Wranne MS, Sewunet T, Ekedahl E, Coorens M, Tangkoskul T, Thamlikitkul V, Giske CG, Westerlund F. Identification and characterization of plasmids carrying the mobile colistin resistance gene mcr-1 using optical DNA mapping. JAC Antimicrob Resist 2023; 5:dlad004. [PMID: 36743530 PMCID: PMC9891347 DOI: 10.1093/jacamr/dlad004] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
Objectives Colistin is a last-resort antibiotic, but there has been a rapid increase in colistin resistance, threatening its use in the treatment of infections with carbapenem-resistant Enterobacterales (CRE). Plasmid-mediated colistin resistance, in particular the mcr-1 gene, has been identified and WGS is the go-to method in identifying plasmids carrying mcr-1 genes. The goal of this study is to demonstrate the use of optical DNA mapping (ODM), a fast, efficient and amplification-free technique, to characterize plasmids carrying mcr-1. Methods ODM is a single-molecule technique, which we have demonstrated can be used for identifying plasmids harbouring antibiotic resistance genes. We here applied the technique to plasmids isolated from 12 clinical Enterobacterales isolates from patients at a major hospital in Thailand and verified our results using Nanopore long-read sequencing. Results We successfully identified plasmids encoding the mcr-1 gene and, for the first time, demonstrated the ability of ODM to identify resistance gene sites in small (∼30 kb) plasmids. We further identified bla CTX-M genes in different plasmids than the ones encoding mcr-1 in three of the isolates studied. Finally, we propose a cut-and-stretch assay, based on similar principles, but performed using surface-functionalized cover slips for DNA immobilization and an inexpensive microscope with basic functionalities, to identify the mcr-1 gene in a plasmid sample. Conclusions Both ODM and the cut-and-stretch assay developed could be very useful in identifying plasmids encoding antibiotic resistance in hospitals and healthcare facilities. The cut-and-stretch assay is particularly useful in low- and middle-income countries, where existing techniques are limited.
Collapse
Affiliation(s)
- Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Moa S Wranne
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Elina Ekedahl
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Maarten Coorens
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden,Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | |
Collapse
|
19
|
Atamna A, Margalit I, Ayada G, Babich T, Naucler P, Valik JK, Giske CG, Benito N, Cardona R, Rivera A, Pulcini C, Fattah MA, Haquin J, Macgowan A, Chazan B, Yanovskay A, Ami RB, Landes M, Nesher L, Zaidman-Shimshovitz A, McCarthy K, Paterson DL, Tacconelli E, Buhl M, Mauer S, Rodríguez-Baño J, de Cueto M, Oliver A, de Gopegui ER, Cano A, Machuca I, Gozalo-Marguello M, Martinez-Martinez L, Gonzalez-Barbera EM, Alfaro IG, Salavert M, Beovic B, Saje A, Mueller-Premru M, Pagani L, Vitrat V, Kofteridis D, Zacharioudaki M, Maraki S, Weissman Y, Paul M, Dickstei Y, Yahav D. Outcomes of octogenarians and nonagenarians with Pseudomonas aeruginosa bacteremia: a multicenter retrospective study. Infection 2022:10.1007/s15010-022-01973-x. [PMID: 36571672 DOI: 10.1007/s15010-022-01973-x] [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] [Received: 10/05/2022] [Accepted: 12/19/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND P. aeruginosa bacteremia is a common and severe infection carrying high mortality in older adults. We aimed to evaluate outcomes of P. aeruginosa bacteremia among old adults (≥ 80 years). METHODS We included the 464/2394 (19%) older adults from a retrospective multinational (9 countries, 25 centers) cohort study of individuals hospitalized with P. aeruginosa bacteremia. Bivariate and multivariable logistic regression models were used to evaluate risk factors for 30-day mortality among older adults. RESULTS Among 464 adults aged ≥ 80 years, the mean age was 84.61 (SD 3.98) years, and 274 (59%) were men. Compared to younger patients, ≥ 80 years adults had lower Charlson score; were less likely to have nosocomial acquisition; and more likely to have urinary source. Thirty-day mortality was 30%, versus 27% among patients 65-79 years (n = 894) and 25% among patients < 65 years (n = 1036). Multivariate analysis for predictors of mortality among patients ≥ 80 years, demonstrated higher SOFA score (odds ratio [OR] 1.36, 95% confidence interval [CI] 1.23-1.51, p < 0.001), corticosteroid therapy (OR 3.15, 95% CI: 1.24-8.01, p = 0.016) and hospital acquired P. aeruginosa bacteremia (OR 2.30, 95% CI: 1.33-3.98, p = 0.003) as predictors. Appropriate empirical therapy within 24 h, type of definitive anti-pseudomonal drug, and type of regimen (monotherapy or combination) were not associated with 30-day mortality. CONCLUSIONS In older adults with P. aeruginosa bacteremia, background conditions, place of acquisition, and disease severity are associated with mortality, rather than the antimicrobial regimen. In this regard, preventive efforts and early diagnosis before organ failure develops might be beneficial for improving outcomes.
Collapse
Affiliation(s)
- Alaa Atamna
- Infectious Diseases Unit, Rain Medical Center, Beilinson Hospital, 39 Jabotinsky Road, Petah Tikva, Israel. .,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Ili Margalit
- Infectious Diseases Unit, Rain Medical Center, Beilinson Hospital, 39 Jabotinsky Road, Petah Tikva, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gida Ayada
- Medicine C, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel
| | - Tanya Babich
- Infectious Diseases Unit, Rain Medical Center, Beilinson Hospital, 39 Jabotinsky Road, Petah Tikva, Israel.,Research Authority, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel
| | - Pontus Naucler
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - John Karlsson Valik
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Christian G Giske
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Natividad Benito
- Infectious Diseases Unit, Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau-Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ruben Cardona
- Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Alba Rivera
- Department of Microbiology, Hospital de la Santa Creu i Sant Pau-Institut d'Investigació Biomèdica Sant Pau, Barcelona, Spain
| | - Celine Pulcini
- Université de Lorraine, APEMAC, 54000, Nancy, France.,Infectious Diseases Department, Université de Lorraine, CHRU-Nancy, 54000, Nancy, France
| | - Manal Abdel Fattah
- Infectious Diseases Department, Université de Lorraine, CHRU-Nancy, 54000, Nancy, France
| | - Justine Haquin
- Infectious Diseases Department, Université de Lorraine, CHRU-Nancy, 54000, Nancy, France
| | - Alasdair Macgowan
- Department of Infection Sciences, Pathology Sciences Building, Southmead Hospital, Bristol, UK
| | - Bibiana Chazan
- Infectious Diseases Unit, Emek Medical Center, Afula, Israel.,Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Anna Yanovskay
- Infectious Diseases Unit, Emek Medical Center, Afula, Israel.,Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Ronen Ben Ami
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Infectious Diseases Unit, Sourasky Medical Center, Tel-Aviv, Israel
| | - Michal Landes
- Infectious Diseases Unit, Sourasky Medical Center, Tel-Aviv, Israel
| | - Lior Nesher
- Infectious Disease Institute, Soroka Medical Center, Ben-Gurion University of the Negev, Beer Sheba, Israel
| | - Adi Zaidman-Shimshovitz
- Infectious Disease Institute, Soroka Medical Center, Ben-Gurion University of the Negev, Beer Sheba, Israel
| | - Kate McCarthy
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - David L Paterson
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - Evelina Tacconelli
- Division of Infectious Diseases, Tuebingen University Hospital, Tuebingen, Germany
| | - Michael Buhl
- Division of Infectious Diseases, Tuebingen University Hospital, Tuebingen, Germany
| | - Susanna Mauer
- Division of Infectious Diseases, Tuebingen University Hospital, Tuebingen, Germany
| | - Jesús Rodríguez-Baño
- Hospital Universitario Virgen Macarena, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBiS)/CSIC and CIBERINFEC, Instituto de Salud Carlos III ES, Sevilla, Spain
| | - Marina de Cueto
- Hospital Universitario Virgen Macarena, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBiS)/CSIC and CIBERINFEC, Instituto de Salud Carlos III ES, Sevilla, Spain
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Illes Balears (IdISBa), Palma, Spain
| | - Enrique Ruiz de Gopegui
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Illes Balears (IdISBa), Palma, Spain
| | - Angela Cano
- Infectious Diseases Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Isabel Machuca
- Infectious Diseases Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | | | - Luis Martinez-Martinez
- Microbiology Service, University Hospital Marqués de Valdecilla-IDIVAL, Santander, Spain
| | | | | | - Miguel Salavert
- Infectious Diseases Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Bojana Beovic
- Department of Infectious Diseases, University Medical Centre, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Andreja Saje
- Department of Infectious Diseases, University Medical Centre, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Manica Mueller-Premru
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Leonardo Pagani
- Infectious Diseases Unit, Bolzano Central Hospital, Bolzano, Italy
| | - Virginie Vitrat
- Infectious Diseases Unit, Annecy-Genevois Hospital Center (CHANGE), Annecy, France
| | - Diamantis Kofteridis
- Infectious Disease Unit, Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
| | - Maria Zacharioudaki
- Infectious Disease Unit, Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
| | - Sofia Maraki
- Infectious Disease Unit, Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
| | - Yulia Weissman
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mical Paul
- Infectious Diseases Unit, Rambam Health Care Campus, Haifa, Israel
| | - Yaakov Dickstei
- Infectious Diseases Unit, Rambam Health Care Campus, Haifa, Israel
| | - Dafna Yahav
- Infectious Diseases Unit, Sheba Medical Center, Ramat-Gan, Israel
| | | |
Collapse
|
20
|
Sewunet T, K. K. S, Nguyen HH, Sithivong N, Hoang NTB, Sychareun V, Nengmongvang K, Larsson M, Olson L, Westerlund F, Giske CG. Fecal carriage and clonal dissemination of blaNDM-1 carrying Klebsiella pneumoniae sequence type 147 at an intensive care unit in Lao PDR. PLoS One 2022; 17:e0274419. [PMID: 36194564 PMCID: PMC9531820 DOI: 10.1371/journal.pone.0274419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/29/2022] [Indexed: 12/04/2022] Open
Abstract
OBJECTIVES Carbapenemase-producing Enterobacterales (CPE) are high priority targets of global antimicrobial surveillance. Herein, we determined the colonization rate of CPE on admission to intensive care units in Vientiane, Lao PDR in August-September 2019. METHODS Data regarding clinical conditions, infection control, and antibiotic usage were collected during admission. Rectal swab samples (n = 137) collected during admission were inoculated to selective chromogenic agars, followed by confirmatory tests for extended-spectrum beta-lactamases and carbapenemases. All CPE isolates were sequenced on Illumina (HiSeq2500), reads assembled using SPAdes 3.13, and the draft genomes used to query a database (https://www.genomicepidemiology.org) for resistome, plasmid replicons, and sequence types (ST). Optical DNA mapping (ODM) was used to characterize plasmids and to determine location of resistance genes. Minimum spanning tree was generated using the Bacterial Isolate Genome Sequence database (BIGSdb) and annotated using iTOL. RESULT From 47 Enterobacterales isolated on selective agars, K. pneumoniae (25/47) and E. coli (12/47) were the most prevalent species, followed by K aerogenes (2/47), K. variicola (1/47), and K. oxytoca (1/47). The overall prevalence of ESBLs was 51.0%; E. coli 83.3% (10/12) and Klebsiella spp. 41.3% (12/29). Twenty percent of the K. pneumoniae (5/25) isolates were carbapenem-resistant, and 4/5 contained the blaNDM-1 gene. All blaNDM-1 isolates belonged to ST147 and were indistinguishable with cgMLST. ODM showed that the blaNDM-1 gene was located on identical plasmids in all isolates. CONCLUSION The prevalence of ESBL-producing Enterobacterales was high, while carbapenemases were less common. However, the detection of clonal dissemination of blaNDM-1-producing K. pneumoniae isolates in one of the intensive care units calls for vigilance. Stringent infection prevention and antimicrobial stewardship strategies are highly important measures.
Collapse
Affiliation(s)
- Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Sriram K. K.
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ha Hoang Nguyen
- Hanoi Medical University, Hanoi, Vietnam
- Training and Research Academic Collaboration (TRAC) Sweden, Vietnam
| | - Noikaseumsy Sithivong
- National Center for Laboratory and Epidemiology, Ministry of Health, Vientiane, Lao PDR
| | - Ngoc Thi Bich Hoang
- Department of Microbiology, Vietnam National Children’s Hospital, Hanoi, Vietnam
| | - Vanphanom Sychareun
- Faculty of Postgraduate Studies, University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
| | - Kokasia Nengmongvang
- Faculty of Postgraduate Studies, University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
| | - Mattias Larsson
- Training and Research Academic Collaboration (TRAC) Sweden, Vietnam
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Linus Olson
- Training and Research Academic Collaboration (TRAC) Sweden, Vietnam
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
- Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
21
|
Horiba K, Torii Y, Aizawa Y, Yamaguchi M, Haruta K, Okumura T, Suzuki T, Kawano Y, Kawada JI, Hara S, Saitoh A, Giske CG, Ogi T, Ito Y. Performance of Nanopore and Illumina metagenomic sequencing for pathogen detection and transcriptome analysis in infantile central nervous system infections. Open Forum Infect Dis 2022; 9:ofac504. [PMID: 36299531 PMCID: PMC9587384 DOI: 10.1093/ofid/ofac504] [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: 05/30/2022] [Accepted: 09/28/2022] [Indexed: 12/04/2022] Open
Abstract
Background Infantile central nervous system infections (CNSIs) can be life-threatening and cause severe sequelae. However, the causative microorganism remains unknown in >40% of patients with aseptic infections. This study aimed to analyze the metagenome for detection of pathogens and the transcriptome for host immune responses during infection in a single cerebrospinal fluid (CSF) sample using 2 different next-generation sequencing (NGS) platforms, Nanopore and Illumina. Methods Twenty-eight CNSIs patients (<12 months) were enrolled, and 49 clinical samples (28 CSF and 21 blood) were collected. The DNA extracted from all 49 samples was sequenced using the Illumina sequencer for the detection of pathogens. Extracted RNA was obtained in sufficient quantities from 23 CSF samples and subjected to sequencing on both Nanopore and Illumina platforms. Human-derived reads subtracted during pathogen detection were used for host transcriptomic analysis from both Nanopore and Illumina sequencing. Results RNA metagenomic sequencing using both sequencing platforms revealed putative viral pathogens in 10 cases. DNA sequencing using the Illumina sequencer detected 2 pathogens. The results of Nanopore and Illumina RNA sequencing were consistent; however, the mapping coverage and depth to the detected pathogen genome of Nanopore RNA sequencing were greater than those of Illumina. Host transcriptomic analysis of Nanopore sequencing revealed highly expressed genes related to the antiviral roles of innate immunity from pathogen-identified cases. Conclusions The use of Nanopore RNA sequencing for metagenomic diagnostics of CSF samples should help to elucidate both pathogens and host immune responses of CNSI and could shed light on the pathogenesis of these infections.
Collapse
Affiliation(s)
- Kazuhiro Horiba
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University , Nagoya , Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine , Nagoya , Japan
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
- Department of Pediatrics, TOYOTA Memorial Hospital , Toyota , Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Yuta Aizawa
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences , Niigata , Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Yoshihiko Kawano
- Department of Pediatrics, TOYOTA Memorial Hospital , Toyota , Japan
| | - Jun ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Shinya Hara
- Department of Pediatrics, TOYOTA Memorial Hospital , Toyota , Japan
| | - Akihiko Saitoh
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences , Niigata , Japan
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital , Stockholm , Sweden
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University , Nagoya , Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine , Nagoya , Japan
- Department of Pediatrics and Child Health, Nihon University School of Medicine , Tokyo , Japan
| |
Collapse
|
22
|
Sewunet T, Asrat D, Woldeamanuel Y, Aseffa A, Giske CG. Molecular epidemiology and antimicrobial susceptibility of Pseudomonas spp. and Acinetobacter spp. from clinical samples at Jimma medical center, Ethiopia. Front Microbiol 2022; 13:951857. [PMID: 36204631 PMCID: PMC9530197 DOI: 10.3389/fmicb.2022.951857] [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: 05/24/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction Pseudomonas aeruginosa (P. aeruginosa) and Acinetobacter baumannii (A. baumannii) can cause difficult-to-treat infections. We characterized molecular epidemiology of ceftazidime-resistant P. aeruginosa and carbapenem-resistant A. baumannii at a tertiary hospital in Ethiopia. Materials and methods Non-fermenting gram-negative bacilli (n = 80) isolated from admitted patients were subjected for species identification by MALDI-TOF. Pseudomonas species resistant to ceftazidime or meropenem, and Acinetobacter species resistant to meropenem, or imipenem were selected for whole genome sequencing. DNA extracted with EZ1 Advanced XL instrument (Qiagen, Hilden, Germany) was sequenced on Illumina (HiSeq2500) using libraries prepared by NEXTRA-kits (Illumina). Raw reads were assembled using SPAdes 3.13.0, and assembled genomes were used to query databases for resistome profile and sequence types. Result Among Pseudomonas species isolated, 31.7% (13/41), and 7.3% (3/41) were non-susceptible to ceftazidime, and meropenem, respectively. Carbapenem-resistance was 56.4% (22/39) among Acinetobacter species. Moreover, 92% (12/13) of Pseudomonas species non-susceptible to ceftazidime and/or meropenem, and 89.4% (17/19) of Acinetobacter species encoded multiple resistance genes for at least three classes of antimicrobials. The prevalent β - lactamase genes were blaOXA–486 (53.8%, 7/13), blaCTX–M–15 (23.0%, 3/13) among Pseudomonas, and blaGES–11 (57.8%, 11/19) among Acinetobacter. The blaOXA–51-like β - lactamase, blaOXA–69 (63.1%, 12/19) was the most prevalent carbapenemase gene among Acinetobacter isolates. Single isolates from both P. aeruginosa, and A. baumannii were detected with the blaNDM–1. Sequence type (ST)1 A. baumannii and ST274 P. aeruginosa were the prevalent sequence types. A cgMLST analysis of the ST1 A. baumannii isolates showed that they were closely related and belonged to the international clonal complex one (ICC1). Similarly, ST274 P. aeruginosa isolates were clonally related. Conclusion The prevalence of MDR isolates of Pseudomonas and Acinetobacter spp. was high. A. baumannii isolates were clonally spreading in the admission wards at the hospital. Emergence of blaNDM–1 in the intensive care, and surgical wards of the hospital is a severe threat that requires urgent intervention.
Collapse
Affiliation(s)
- Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- *Correspondence: Tsegaye Sewunet, ;
| | - Daniel Asrat
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
23
|
Antonelli A, Coppi M, Tellapragada C, Hasan B, Maruri A, Gijón D, Morecchiato F, de Vogel C, Verbon A, van Wamel W, Kragh KN, Frimodt-Møller N, Cantón R, Giske CG, Rossolini GM. Isothermal microcalorimetry versus checkerboard assay to evaluate in vitro synergism of meropenem-amikacin and meropenem-colistin combinations against multidrug-resistant Gram-negative pathogens. Int J Antimicrob Agents 2022; 60:106668. [PMID: 36038097 DOI: 10.1016/j.ijantimicag.2022.106668] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/28/2022] [Accepted: 08/21/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To evaluate the activity of meropenem-amikacin and meropenem-colistin combinations with checkerboard broth microdilution (CKBM) compared to isothermal microcalorimetry (ITMC) assays against a multicentric collection of multidrug-resistant Gram-negative (MDR-GN) clinical isolates, to compare the Fractional inhibitory concentration index (FICI) and time to results of CKBM and ITMC assays. METHODS A collection of 333 MDR-GNs showing reduced susceptibility to meropenem (121 Klebsiella pneumoniae, 14 Escherichia coli, 130 Pseudomonas aeruginosa and 68 Acinetobacter baumannii) isolated from different centres (Florence, Madrid, Rotterdam, and Stockholm) was included in the study. The antimicrobial activity of selected combinations was evaluated with CKBM and ITMC. FICI results were interpreted as synergistic/additive and indifferent for values ≤0.5/0.5<x≤1 and >1, respectively. WGS data in a subset of strains was used to evaluate their clonality. RESULTS A total of 254 and 286 strains were tested with meropenem-colistin and meropenem-amikacin combinations with ITMC and CKBM, respectively. Synergism/additive effects were observed with 46 strains (20 K. pneumoniae, 4 E. coli, 22 P. aeruginosa) and 20 strains (3 K. pneumoniae, 11 P. aeruginosa and 6 A. baumannii) with meropenem-amikacin and meropenem-colistin combination, respectively, with CKBM. ITMC showed a good concordance with CKBM with 89.5% and 92.2% of cases interpreted within the same FICI category for meropenem-amikacin and meropenem-colistin combinations, respectively. Most of the synergism/additivity effects were detected within 6 hours by ITMC. CONCLUSIONS ITMC showed a very good concordance with CKBM against a large collection of MDR-GN and could be implemented for the rapid evaluation of in vitro activity of antimicrobial combinations.
Collapse
Affiliation(s)
- Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence Italy; Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine, University of Florence, Florence Italy; Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Chaitanya Tellapragada
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Badrul Hasan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ainhize Maruri
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Desiree Gijón
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Fabio Morecchiato
- Department of Experimental and Clinical Medicine, University of Florence, Florence Italy
| | - Corné de Vogel
- Department of Medical Microbiology and Infectious Diseases, Erasmus University, Rotterdam, Netherlands
| | - Annelies Verbon
- Department of Medical Microbiology and Infectious Diseases, Erasmus University, Rotterdam, Netherlands
| | - Willem van Wamel
- Department of Medical Microbiology and Infectious Diseases, Erasmus University, Rotterdam, Netherlands
| | - Kasper Nørskov Kragh
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark; Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | | | - Rafael Cantón
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER de Enfermedades Infecciosas. Instituto de Salud Carlos III. Madrid, Spain
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Clinical microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence Italy; Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy.
| |
Collapse
|
24
|
Tellapragada C, Ydsten KA, Ternhag A, Giske CG. Evaluation of a pneumonia multiplex PCR panel for detection of bacterial respiratory tract pathogens from serial specimens collected from hospitalized COVID-19 patients. Eur J Clin Microbiol Infect Dis 2022; 41:1093-1098. [PMID: 35727430 PMCID: PMC9210330 DOI: 10.1007/s10096-022-04466-9] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022]
Abstract
We investigated the concordance between the Unyvero Hospitalized Pneumonia (HPN) application and quantitative culture for detection of bacterial pathogens from serial lower respiratory tract (LRT) specimens collected from the same subject. Comparison of results from HPN application and culture was evaluated using 69 LRT samples from 27 subjects, using two evaluation approaches. False positive detections by the HPN application was 29% (20/69) in Evaluation I vs 10% (7/68) in Evaluation II. Additional pathogens detected by the HPN application could be confirmed in many instances by culture positivity for the same organism from previous or subsequent samples from the same subject.
Collapse
Affiliation(s)
- Chaitanya Tellapragada
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Allé 8, 14183, Stockholm, Sweden.
| | | | - Anders Ternhag
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine, Solna, Karolinska Institute, Stockholm, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Allé 8, 14183, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
25
|
Gatermann S, Das S, Dubreuil L, Giske CG, Kahlmeter G, Lina G, Lindemann C, MacGowan A, Meletiadis J, Rossolini GM, Turnidge J, Cantón R. Expected phenotypes and expert rules are important complements to antimicrobial susceptibility testing. Clin Microbiol Infect 2022; 28:764-767. [PMID: 35306191 DOI: 10.1016/j.cmi.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 11/03/2022]
Affiliation(s)
- Sören Gatermann
- Abteilung für Medizinische Mikrobiologie, Ruhr-Universität Bochum, Bochum, Germany.
| | - Shampa Das
- Centre for Antimicrobial Pharmacodynamics, University of Liverpool, Liverpool, United Kingdom
| | | | - Christian G Giske
- Department of Clinical Microbiology L2:02, Karolinska University Hospital, Solna, and Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Gerard Lina
- Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon and Equipe Pathogénie des Staphylocoques, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR 5308, ENS de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Alasdair MacGowan
- Department of Medical Microbiology, Southmead Hospital, Westbury on Trym, Bristol, United Kingdom
| | - Joseph Meletiadis
- Clinical Microbiology Laboratory, Attikon University General Hospital, Haidari, Athens, Greece
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence and Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - John Turnidge
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investiagación Sanitaria (IRYCIS), Madrid, Spain
| |
Collapse
|
26
|
Babich T, Naucler P, Valik JK, Giske CG, Benito N, Cardona R, Rivera A, Pulcini C, Fattah MA, Haquin J, Macgowan A, Grier S, Chazan B, Yanovskay A, Ami RB, Landes M, Nesher L, Zaidman-Shimshovitz A, McCarthy K, Paterson DL, Tacconelli E, Buhl M, Mauer S, Rodríguez-Baño J, de Cueto M, Oliver A, de Gopegui ER, Cano A, Machuca I, Gozalo-Marguello M, Martinez-Martinez L, Gonzalez-Barbera EM, Alfaro IG, Salavert M, Beovic B, Saje A, Mueller-Premru M, Pagani L, Vitrat V, Kofteridis D, Zacharioudaki M, Maraki S, Weissman Y, Paul M, Dickstein Y, Leibovici L, Yahav D. Duration of Treatment for Pseudomonas aeruginosa Bacteremia: a Retrospective Study. Infect Dis Ther 2022; 11:1505-1519. [PMID: 35612693 PMCID: PMC9334465 DOI: 10.1007/s40121-022-00657-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 03/30/2022] [Accepted: 05/09/2022] [Indexed: 12/01/2022] Open
Abstract
INTRODUCTION There is no consensus regarding optimal duration of antibiotic therapy for Pseudomonas aeruginosa bacteremia. We aimed to evaluate the impact of short antibiotic course. METHODS We present a retrospective multicenter study including patients with P. aeruginosa bacteremia during 2009-2015. We evaluated outcomes of patients treated with short (6-10 days) versus long (11-15 days) antibiotic courses. The primary outcome was a composite of 30-day mortality or bacteremia recurrence and/or persistence. Univariate and inverse probability treatment-weighted (IPTW) adjusted multivariate analysis for the primary outcome was performed. To avoid immortal time bias, the landmark method was used. RESULTS We included 657 patients; 273 received a short antibiotic course and 384 a long course. There was no significant difference in baseline characteristics of patients. The composite primary outcome occurred in 61/384 patients in the long-treatment group (16%) versus 32/273 in the short-treatment group (12%) (p = 0.131). Mortality accounted for 41/384 (11%) versus 25/273 (9%) of cases, respectively. Length of hospital stay was significantly shorter in the short group [median 13 days, interquartile range (IQR) 9-21 days, versus median 15 days, IQR 11-26 days, p = 0.002]. Ten patients in the long group discontinued antibiotic therapy owing to adverse events, compared with none in the short group. On univariate and multivariate analyses, duration of therapy was not associated with the primary outcome. CONCLUSIONS In this retrospective study, 6-10 days of antibiotic course for P. aeruginosa bacteremia were as effective as longer courses in terms of survival and recurrence. Shorter therapy was associated with reduced length of stay and less drug discontinuation.
Collapse
Affiliation(s)
- Tanya Babich
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Rabin Medical Center, Research Authority, Beilinson Hospital, Petah-Tikva, Israel
| | - Pontus Naucler
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - John Karlsson Valik
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Christian G Giske
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Natividad Benito
- Infectious Diseases Unit, Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau - Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ruben Cardona
- Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Alba Rivera
- Department of Microbiology, Hospital de la Santa Creu i Sant Pau - Institut d'Investigació Biomèdica Sant Pau, Barcelona, Spain
| | - Celine Pulcini
- Université de Lorraine, APEMAC, 54000, Nancy, France.,Infectious Diseases Department, Université de Lorraine, CHRU-Nancy, 54000, Nancy, France
| | - Manal Abdel Fattah
- Infectious Diseases Department, Université de Lorraine, CHRU-Nancy, 54000, Nancy, France
| | - Justine Haquin
- Infectious Diseases Department, Université de Lorraine, CHRU-Nancy, 54000, Nancy, France
| | - Alasdair Macgowan
- Department of Infection Sciences, Pathology Sciences Building, Southmead Hospital, Bristol, UK
| | - Sally Grier
- Department of Infection Sciences, Pathology Sciences Building, Southmead Hospital, Bristol, UK
| | - Bibiana Chazan
- Infectious Diseases Unit, Rappaport Faculty of Medicine, Technion, Emek Medical Center, Afula, Haifa, Israel
| | - Anna Yanovskay
- Infectious Diseases Unit, Rappaport Faculty of Medicine, Technion, Emek Medical Center, Afula, Haifa, Israel
| | - Ronen Ben Ami
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Infectious Diseases Unit, Sourasky Medical Center, Tel-Aviv, Israel
| | - Michal Landes
- Infectious Diseases Unit, Sourasky Medical Center, Tel-Aviv, Israel
| | - Lior Nesher
- Infectious Disease Institute, Soroka Medical Center, Ben-Gurion University of the Negev, Beer Sheba, Israel
| | - Adi Zaidman-Shimshovitz
- Infectious Disease Institute, Soroka Medical Center, Ben-Gurion University of the Negev, Beer Sheba, Israel
| | - Kate McCarthy
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - David L Paterson
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - Evelina Tacconelli
- Division of Infectious Diseases, Tuebingen University Hospital, Tuebingen, Germany
| | - Michael Buhl
- Division of Infectious Diseases, Tuebingen University Hospital, Tuebingen, Germany
| | - Susanna Mauer
- Division of Infectious Diseases, Tuebingen University Hospital, Tuebingen, Germany
| | - Jesús Rodríguez-Baño
- Departamentos de Medicina y Microbiología, Unidad Clínica de Enfermedades Infecciosas and Microbiología, Hospital Universitario Virgen Macarena, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Seville, Spain
| | - Marina de Cueto
- Departamentos de Medicina y Microbiología, Unidad Clínica de Enfermedades Infecciosas and Microbiología, Hospital Universitario Virgen Macarena, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Seville, Spain
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Illes Balears (IdISBa), Palma, Spain
| | - Enrique Ruiz de Gopegui
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Illes Balears (IdISBa), Palma, Spain
| | - Angela Cano
- Infectious Diseases Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Isabel Machuca
- Infectious Diseases Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | | | - Luis Martinez-Martinez
- Microbiology Service, University Hospital Marqués de Valdecilla-IDIVAL, Santander, Spain
| | | | | | - Miguel Salavert
- Infectious Diseases Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Bojana Beovic
- Department of Infectious Diseases, University Medical Centre, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Andreja Saje
- Department of Infectious Diseases, University Medical Centre, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Manica Mueller-Premru
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Leonardo Pagani
- Infectious Diseases Unit, Annecy-Genevois Hospital Center (CHANGE), Annecy, France
| | - Virginie Vitrat
- Infectious Diseases Unit, Annecy-Genevois Hospital Center (CHANGE), Annecy, France
| | - Diamantis Kofteridis
- Infectious Disease Unit, Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
| | - Maria Zacharioudaki
- Infectious Disease Unit, Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
| | - Sofia Maraki
- Infectious Disease Unit, Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
| | - Yulia Weissman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mical Paul
- Infectious Diseases Unit, Rambam Health Care Campus, Haifa, Israel
| | - Yaakov Dickstein
- Infectious Diseases Unit, Rambam Health Care Campus, Haifa, Israel
| | - Leonard Leibovici
- Rabin Medical Center, Research Authority, Beilinson Hospital, Petah-Tikva, Israel
| | - Dafna Yahav
- Infectious Diseases Unit, Sheba Medical Center, 2 Sheba Road, 52621, Ramat-Gan, Israel.
| |
Collapse
|
27
|
Bolourchi N, Noori Goodarzi N, Giske CG, Nematzadeh S, Haririzadeh Jouriani F, Solgi H, Badmasti F. Comprehensive pan-genomic, resistome and virulome analysis of clinical OXA-48 producing carbapenem-resistant Serratia marcescens strains. Gene 2022; 822:146355. [PMID: 35189248 DOI: 10.1016/j.gene.2022.146355] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/03/2022] [Accepted: 02/15/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly studied as the pathogens associated with hospital acquired infections. However, data on Serratia marcescens are not enough. S. marcescens is now becoming a propensity for its highly antimicrobial-resistant clinical infections. METHODS Four carbapenem-resistant S. marcescens (CR-SM) isolates were obtained from hospitalized patients through routine microbiological experiments. We assembled the isolates genomes using whole genome sequencing (WGS) and compared their resistome and virulome patterns. RESULTS The average length and CG content of chromosomes was 5.33 Mbp and 59.8%, respectively. The number of coding sequences (CDSs) ranged from 4,959 to 4,989. All strains had one single putative conjugative plasmid with IncL incompatibility (Inc) group. The strains harbored blaCTX-M-15, blaTEM-1 and blaSHV-134. All plamsids were positive for blaOXA-48. No blaNDM-1, blaKPC, blaVIM and blaIMP were identified. The blaSRT-2 and aac(6')-Ic genes were chromosomally-encoded. Class 1 integron was detected in strains P8, P11 and P14. The Escher_RCS47 and Salmon_SJ46 prophages played major role in plasmid-mediated carraige of extended spectrum β-lactamases (ESBLs). The CR-SM strains were equipt with typical virulence factors of oppotunistic pathogens including biofilm formation, adhesins, secretory systems and siderophores. The strains did not have ability to produce prodigiosin but were positive for chitinase and EstA. CONCLUSION The presence of conjugative plasmids harboring major β-lactamases within prophage and class 1 integron structures highlights the role of different mobile genetic elements (MGEs) in distribution of AMR factors and more specifically carbapenemases. More molecular studies are required to determine the status of carbapenem resistance in clinical starins. However, appropriate strategies to control the global dissemination of CR-SM are urgent.
Collapse
Affiliation(s)
- Negin Bolourchi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Narjes Noori Goodarzi
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Shoeib Nematzadeh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | | | - Hamid Solgi
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
28
|
Aguilera-Alonso D, Cantón R, Giske CG, Kahlmeter G, Kohns Vasconcelos M, Papan C, Turnidge J. Searching High and Low: Call for a Joint European Society for Paediatric Infectious Diseases-European Committee on Antimicrobial Susceptibility Testing Survey on Dosage of Antibacterial Agents in Children-Part One. Pediatr Infect Dis J 2022; 41:e182-e185. [PMID: 35153290 DOI: 10.1097/inf.0000000000003457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- David Aguilera-Alonso
- Pediatric Infectious Diseases Unit, Gregorio Marañón Hospital, Instituto de Investigación Gregorio Marañón, Unidad de Investigación Materno-Infantil Fundación Familia Alonso, Madrid, Spain, CIBER en Enfermedades Infecciosas, Madrid, Spain
| | - Rafael Cantón
- CIBER en Enfermedades Infecciosas, Madrid, Spain, Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain, EUCAST Clinical Data Coordinator
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden, Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Gunnar Kahlmeter
- EUCAST Technical Data Coordinator, EUCAST Development Laboratory, Växjö, Sweden
| | - Malte Kohns Vasconcelos
- Department for Infectious Diseases and Vaccinology and Department for Paediatric Pharmacolgy, University of Basel Children's Hospital, Basel, Switzerland, Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St. George's, University of London, London, United Kingdom
| | - Cihan Papan
- Centre for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - John Turnidge
- EUCAST Scientific Secretary, University of Adelaide, ESPID-EUCAST Joint Task Force
| |
Collapse
|
29
|
Wallander K, Vondracek M, Giske CG. Evaluation of multi-sample 16S ribosomal DNA sequencing for the diagnosis of postoperative bone and joint infections during antimicrobial treatment. BMC Res Notes 2022; 15:113. [PMID: 35317829 PMCID: PMC8939158 DOI: 10.1186/s13104-022-05992-7] [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: 11/30/2021] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
Objectives Clinicians worldwide struggle to identify the bacterial aetiology of bone and joint infections. Failure to unequivocally identify the pathogen is linked to poor clinical outcomes. We explored the added value of analysing multiple samples per patient with 16S ribosomal DNA (16S rDNA) sequencing in diagnosing postoperative bone and joint infections. All patients had received antimicrobials prior to sampling, and false-negative cultures could be suspected. Bone biopsies obtained from patients with postoperative bone and joint infections for cultures were also subjected to 16S rDNA sequencing. Results In 5/28 infectious episodes, sequencing identified the causative organism of the infection when cultures failed. In 8/28 episodes, the methods led to different results, potentially leading to different antimicrobial choices. The analysis of multiple samples per patient helped rule out potential contaminating pathogens. We conclude that 16S rDNA sequencing has diagnostic value for patients receiving antibiotic treatment. We regard the method as a complement to culturing when the cultures are negative. Multiple samples per patient should be analysed to determine the clinical significance of positive findings.
Collapse
Affiliation(s)
- Katja Wallander
- Department of Infectious Diseases and Venhälsan, Södersjukhuset, Stockholm, Sweden. .,Division of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
| | - Martin Vondracek
- Department of Clinical Microbiology, Karolinska University Hospital Stockholm, Stockholm, Sweden.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital Stockholm, Stockholm, Sweden.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
30
|
Bolourchi N, Giske CG, Nematzadeh S, Mirzaie A, Abhari SS, Solgi H, Badmasti F. Comparative resistome and virulome analysis of clinical NDM-1 producing carbapenem-resistant Enterobacter cloacae complex. J Glob Antimicrob Resist 2022; 28:254-263. [PMID: 35121164 DOI: 10.1016/j.jgar.2022.01.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/02/2021] [Revised: 01/15/2022] [Accepted: 01/22/2022] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Enterobacter cloacae complex (ECC), are causatives of hospital-acquired infections (HAI). The antimicrobial resistance (AMR) and virulence and profiling of ECC promotes our knowledge to be further implemented for their elimination in clinical settings. METHOD We assembled the whole genome of four clinical Carbapenem-resistant ECC (CR-ECC) and characterized their AMR and virulence profiles using whole genome sequencing (WGS). RESULTS The chromosome length of scaled from minimum 3,949,952 bp (for P2) to maximum 4,976,575 bp (for P3). P1 and P2 belonged to ST182. P3 and P4 belonged to ST477 and ST134, respectively. The blaCTX-M-15 gene was detected in P1 plamsid. P1 and P4 harbored the blaTEM-1 and blaOXA-1 genes. blaNDM-1 was found in P1, P3 and P4. No blaOXA-48, blaKPC, blaVIM and blaIMP were identified. The plasmids were non-transferrable and had IncFIB, IncFII, Col and IncC incompatibility groups (Inc). Class 1 integron was deteceted in all strains. Genes related to biofilms, adhesins, siderophores (aerobactin, enterobactin and salmochelin), intrinsic antimicrobial efflux pumps, secretory systems type I to VI, environmental and antibiotic stress response regulators, outer membrane proteins (OMPs) and heavy metals (copper, tellurite, arsenic and zinc) resistance were found in the strains. The number of positive virulence factors was higher for P1 to that of other strains. CONCLUSION The accumulation of AMR genes in Enterobacter spp. and their high endurance in hostile environments is a serious health problem. More genomic investigations are required in to determine their AMR and virulence genetic reservoirs at the global level.
Collapse
Affiliation(s)
- Negin Bolourchi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Shoeib Nematzadeh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Amir Mirzaie
- Department of Biology, Parand Branch, Islamic Azad University, Parand, Iran
| | | | - Hamid Solgi
- Department of Laboratory Medicine, Amin Hospital, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
31
|
Alonso DA, Cantón R, Giske CG, Kahlmeter G, Vasconcelos MK, Papan C, Turnidge J. Searching high and low: Call for a joint ESPID-EUCAST survey on dosage of antibacterial agents in children - Part One. Clin Microbiol Infect 2022; 28:625-627. [PMID: 34999172 DOI: 10.1016/j.cmi.2021.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/03/2022]
Affiliation(s)
- David Aguilera Alonso
- Pediatric Infectious Diseases Unit, Gregorio Marañón Hospital, Instituto de Investigación Gregorio Marañón (IiSGM), Unidad de Investigación Materno-Infantil Fundación Familia Alonso (UDIMIFFA), Madrid, Spain; CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.
| | - Rafael Cantón
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain; Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; EUCAST Clinical Data Coordinator
| | - Christian G Giske
- Division of Clinical microbiology, Department of Laboratory medicine, Karolinska Institutet, Stockholm, Sweden; Clinical microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Gunnar Kahlmeter
- EUCAST Technical Data Coordinator, EUCAST Development Laboratory, Växjö, Sweden
| | - Malte Kohns Vasconcelos
- Department for Infectious Diseases and Vaccinology and Department for Paediatric Pharmacolgy, University of Basel Children's Hospital (UKBB), Basel, Switzerland; Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St. George's, University of London, London, UK
| | - Cihan Papan
- Centre for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | | | | |
Collapse
|
32
|
Oldendorff F, Linnér A, Finder M, Eisenlauer P, Kjellberg M, Giske CG, Nordberg V. Case Report: Fatal Outcome for a Preterm Newborn With Meningitis Caused by Extended-Spectrum β-Lactamase-Producing Escherichia coli Sequence Type 1193. Front Pediatr 2022; 10:866762. [PMID: 35463903 PMCID: PMC9019577 DOI: 10.3389/fped.2022.866762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/11/2022] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION In this case report, we describe an extended-spectrum beta-lactamase (ESBL) - Escherichia coli (E. coli) strain of sequence type (ST) 1193, a novel, virulent, multidrug-resistant (MDR) clone with a rapid global spread. ST 1193 has been more commonly associated with invasive disease than other ESBL-E. coli STs. To our knowledge, this is the first known case in Sweden where a newborn died of an ESBL-E. coli ST 1193 meningitis. We emphasize that the clinical knowledge about the properties of certain MDR-clones should be increased. CASE REPORT A moderately preterm boy was born after preterm prolonged rupture of membranes. The mother had an ESBL-E. coli urinary tract infection during pregnancy. At 36 h of age he developed signs of infection and was given first-line therapy for early onset sepsis. Thereafter he developed seizures. The treatment was changed to cover suspected meningitis. Culture showed growth of the same ESBL- E. coli ST 1193 strain in the child's blood and cerebrospinal fluid, as well as in the mother's urine. Antibiotics were adapted. His condition deteriorated and he developed fulminant septic shock with treatment-resistant seizures. The boy passed away at 3 days of age. CONCLUSION This case highlights the risk of delay in diagnosis when a marking for carriage of MDR-bacteria is falsely removed from a medical record of a pregnant women. Further, it demonstrates that ESBL-E. coli ST 1193 infection in neonates can be fatal. Thus, studies regarding virulence factors of ESBL-E. coli infections in pregnant women and their children are needed to understand the association between this infection and severe invasive disease in newborn children.
Collapse
Affiliation(s)
- Frida Oldendorff
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Agnes Linnér
- Department of Neonatology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Finder
- Department of Neonatology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Science, Intervention and Technology (CLINTEC), Division of Paediatrics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Eisenlauer
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - Malin Kjellberg
- Department of Neonatology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Christian G Giske
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Laboratory, Stockholm, Sweden
| | - Viveka Nordberg
- Department of Neonatology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Science, Intervention and Technology (CLINTEC), Division of Paediatrics, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
33
|
Sriram KK, Ekedahl E, Hoang NTB, Sewunet T, Berglund B, Lundberg L, Nematzadeh S, Nilsson M, Nilsson LE, Le NK, Tran DM, Hanberger H, Olson L, Larsson M, Giske CG, Westerlund F. High diversity of bla NDM-1-encoding plasmids in Klebsiella pneumoniae isolated from neonates in a Vietnamese hospital. Int J Antimicrob Agents 2021; 59:106496. [PMID: 34921976 DOI: 10.1016/j.ijantimicag.2021.106496] [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] [Received: 04/07/2021] [Revised: 09/08/2021] [Accepted: 12/01/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVES The carbapenemase-encoding gene blaNDM-1 has been reported in Vietnam over the last ten years, and blaNDM-producing Enterobacteriaceae are now silently and rapidly spreading. A key factor behind dissemination of blaNDM-1 are plasmids, mobile genetic elements that commonly carry antibiotic resistance genes and spread via conjugation. Here, we characterized the diversity of blaNDM-1-encoding plasmids from neonates at a large Vietnamese hospital . METHODS 18 fecal Klebsiella pneumoniae and Klebsiella quasipneumoniae isolates collected from 16 neonates at a large pediatric hospital in Vietnam were studied with optical DNA mapping (ODM) and next-generation sequencing (NGS). We identified the plasmid(s) carrying blaNDM-1 by combining ODM with Cas9 restriction. By comparing the plasmids between isolates, we could investigate if the same plasmid was present in different patients. RESULTS Although the same plasmid was found among some isolates, ODM confirmed that there were at least 10 different plasmids encoding blaNDM-1 among the 18 isolates collected from 16 neonates, suggesting a large plasmid diversity. The ODM results were in large agreement with the NGS data. Interestingly, some isolates had two distinct plasmids encoding blaNDM-1, which could be readily detected with ODM. Thus far, the coexistence of different plasmids carrying the same carbapenem resistance gene in an isolate encoding blaNDM-1 has rarely been reported, likely due to limitations in existing plasmid characterization techniques. CONCLUSIONS Our results show that the plasmids encoding blaNDM-1 in this cohort were very diverse, suggesting a similar picture in the Vietnamese society. The study also highlights important aspects of the usefulness of ODM for plasmid analysis.
Collapse
Affiliation(s)
- K K Sriram
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Elina Ekedahl
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ngoc Thi Bich Hoang
- Department of Microbiology, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory medicine, Karolinska Institutet, Stockholm, Sweden
| | - Björn Berglund
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Ludwig Lundberg
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden; Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Shoeib Nematzadeh
- Division of Clinical Microbiology, Department of Laboratory medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maud Nilsson
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Lennart E Nilsson
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Ngai Kien Le
- Department of Surgery, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Dien Minh Tran
- Department of Infection Control, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Håkan Hanberger
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Linus Olson
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden; Department of Women and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Mattias Larsson
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory medicine, Karolinska Institutet, Stockholm, Sweden; Clinical microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
34
|
Bolourchi N, Shahcheraghi F, Giske CG, Nematzadeh S, Solgi H, Badmasti F. Genome analysis of an OXA-48-producing carbapenem- and colistin-resistant Klebsiella pneumoniae sequence type 11 clone isolated from an inpatient. Gene Reports 2021. [DOI: 10.1016/j.genrep.2021.101394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
35
|
Sewunet T, Asrat D, Woldeamanuel Y, Ny S, Westerlund F, Aseffa A, Giske CG. Polyclonal spread of bla CTX-M-15 through high-risk clones of Escherichia coli at a tertiary hospital in Ethiopia. J Glob Antimicrob Resist 2021; 29:405-412. [PMID: 34775133 DOI: 10.1016/j.jgar.2021.09.017] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/18/2021] [Accepted: 09/28/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE The burden of antimicrobial resistance and spread of epidemic clones are rarely reported from low-income countries. We aimed to investigate genome-based epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) at a tertiary hospital in Jimma, Ethiopia. METHODS Bacteria were isolated from clinical specimens obtained from Jimma Medical Center and subjected to species identification (MALDI-TOF), antibiotic susceptibility testing (disk diffusion), and whole genome sequencing (Illumina HiSeq2500). Genomic data analysis was performed using the Enterobase and Center for Genomic Epidemiology bioinformatics pipelines. A maximum likelihood tree was generated using FastTree/2.1.8 based on SNPs in shared genomic regions to identify transmission clusters. RESULT E. coli isolates (n=261) were collected from 1,087 single non-repeat clinical specimens over a period of five months in 2016. The prevalence of ESBL-EC was (54.7%, 143/261), and 96% of these isolates were resistant to multiple classes of antibiotics. ESBL-gene blaCTX-M-15 was present in 88.4.% of the isolates (122/138). Genes conferring resistance to aminoglycosides and ciprofloxacin - aac(6')-Ib-cr (62.3%, 86/138), phenicols - catB3 (56.5%, 78/138), sulfonamides - sul1 (68.1%, 94/138), trimethoprim - dfrA17 (57.9%, 80/138) and macrolides - mph(A) (67.3%, 93/138) were detected. The most prevalent sequence types were ST410 (23%), ST648 (17%), ST131 (10%), and ST167 (7%). Isolates of same sequence type collected from different units of the hospital were highly similar in SNP-analysis. CONCLUSION A high prevalence of ESBL, and dissemination of blaCTX-M-15 through multiple high-risk clones of E. coli, was detected. The nosocomial spread of multidrug-resistant ESBL-EC within the hospital puts vulnerable patients at risk for difficult-to-treat infections.
Collapse
Affiliation(s)
- Tsegaye Sewunet
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia; School of Laboratory Sciences, Jimma University, Jimma, Ethiopia; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Sweden.
| | - Daniel Asrat
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia
| | | | - Sofia Ny
- Public Health Agency of Sweden, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Sweden
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Christian G Giske
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Sweden; Karolinska University Hospital, Clinical Microbiology, Sweden
| |
Collapse
|
36
|
Gagliotti C, Högberg LD, Billström H, Eckmanns T, Giske CG, Heuer OE, Jarlier V, Kahlmeter G, Lo Fo Wong D, Monen J, Murchan S, Simonsen GS, Šubelj M, Andrašević AT, Żabicka D, Žemličková H, Monnet DL. Staphylococcus aureus bloodstream infections: diverging trends of meticillin-resistant and meticillin-susceptible isolates, EU/EEA, 2005 to 2018. Euro Surveill 2021; 26:2002094. [PMID: 34794536 PMCID: PMC8603406 DOI: 10.2807/1560-7917.es.2021.26.46.2002094] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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] [Indexed: 04/07/2023] Open
Abstract
BackgroundInvasive infections caused by Staphylococcus aureus have high clinical and epidemiological relevance. It is therefore important to monitor the S. aureus trends using suitable methods.AimThe study aimed to describe the trends of bloodstream infections (BSI) caused by meticillin-resistant S. aureus (MRSA) and meticillin-susceptible S. aureus (MSSA) in the European Union (EU) and the European Economic Area (EEA).MethodsAnnual data on S. aureus BSI from 2005 to 2018 were obtained from the European Antimicrobial Resistance Surveillance Network (EARS-Net). Trends of BSI were assessed at the EU/EEA level by adjusting for blood culture set rate (number of blood culture sets per 1,000 days of hospitalisation) and stratification by patient characteristics.ResultsConsidering a fixed cohort of laboratories consistently reporting data over the entire study period, MRSA percentages among S. aureus BSI decreased from 30.2% in 2005 to 16.3% in 2018. Concurrently, the total number of BSI caused by S. aureus increased by 57%, MSSA BSI increased by 84% and MRSA BSI decreased by 31%. All these trends were statistically significant (p < 0.001).ConclusionsThe results indicate an increasing health burden of MSSA BSI in the EU/EEA despite a significant decrease in the MRSA percentage. These findings highlight the importance of monitoring antimicrobial resistance trends by assessing not only resistance percentages but also the incidence of infections. Further research is needed on the factors associated with the observed trends and on their attributable risk.
Collapse
Affiliation(s)
- Carlo Gagliotti
- Regional Agency for Health and Social Care of Emilia-Romagna, Bologna, Italy
| | | | | | - Tim Eckmanns
- Healthcare-associated infections, surveillance of antimicrobial resistance and consumption, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Ole E Heuer
- European Centre for Disease Prevention and Control, Solna, Sweden
| | - Vincent Jarlier
- Sorbonne Universités (Paris 06) Inserm Centre d'Immunologie et des Maladies Infectieuses (CIMI), UMR 1135 & APHP, Pitié-Salpêtrière hospital, Laboratoire de Bactériologie-Hygiène, Paris, France
| | | | - Danilo Lo Fo Wong
- World Health Organization, Regional Office for Europe, Copenhagen, Denmark
| | - Jos Monen
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Gunnar Skov Simonsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research Group for Host Microbe Interaction, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Norwegian Institute of Public Health, Oslo, Norway
| | - Maja Šubelj
- National Institute of Public Health, University of Ljubljana, Slovenia
| | | | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Helena Žemličková
- National reference laboratory for antibiotics, National Institute of Public Health, Prague, Czech Republic
- Department of Microbiology, 3rd Faculty of Medicine Charles University, University hospital Kralovske Vinohrady, and National Institute of Public Health, Prague, Czech Republic
| | | |
Collapse
|
37
|
Edlund C, Ternhag A, Skoog Ståhlgren G, Edquist P, Östholm Balkhed Å, Athlin S, Månsson E, Tempé M, Bergström J, Giske CG, Hanberger H. The clinical and microbiological efficacy of temocillin versus cefotaxime in adults with febrile urinary tract infection, and its effects on the intestinal microbiota: a randomised multicentre clinical trial in Sweden. Lancet Infect Dis 2021; 22:390-400. [PMID: 34756180 DOI: 10.1016/s1473-3099(21)00407-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/17/2021] [Accepted: 07/05/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Use of third-generation cephalosporins, such as cefotaxime, is associated with an increased risk of selection for antimicrobial resistance, so alternative antibiotics need to be considered. The aim of the present study was to evaluate intestinal colonisation with third-generation cephalosporin-resistant pathogens following use of temocillin-an alternative antibiotic to cefotaxime that is potentially less prone to disturbing the intestinal microbiota-in empirical treatment of febrile urinary tract infection (UTI). METHODS We did a randomised, multicentre, superiority, open-label phase 4 trial in patients who had been admitted to inpatient care in 12 Swedish hospitals with suspected or diagnosed febrile UTI (complicated or uncomplicated). To meet inclusion criteria, a patient was required to have at least one sign or symptom of pyelonephritis (ie, flank pain; costovertebral angle tenderness; and changes to urinary frequency or urgency or dysuria), a fever of 38·0°C or higher, and a positive urine dipstick (for nitrites, white blood cells, or both). Participants were also required to have an indication for intravenous antibiotic treatment. Participants were randomly assigned (1:1) to receive either 2 g temocillin or 1-2 g cefotaxime, by local investigators opening consecutive sealed randomisation envelopes that were generated centrally in advance. Both drugs were administered intravenously every 8 h. The trial was open label for investigators and patients, but those doing the microbiological analyses were masked to the groups. Participants were treated with antibiotics for 7-10 days (or up to 14 days if they had bacteraemia), at least 3 days of which were on the study drug; at day 4 and later, participants who were showing improvement could be given an oral antibiotic (ciprofloxacin, ceftibuten, cefixime, or co-trimoxazole). Patients not showing improvement were regarded as having treatment failures. Rectal swabs were collected at three timepoints: at baseline (before the first dose), after the last dose of study drug, and 7-10 days after treatment stopped. The composite primary outcome was colonisation with Enterobacterales with reduced susceptibility to third-generation cephalosporins, or colonisation with toxin-producing Clostridioides difficile, or both, to evaluate disturbance of the intestinal microbiota. The study is registered in the EU Clinical Trials Register (EudraCT 2015-003898-15). FINDINGS Between May 20, 2016, and July 31, 2019, 207 patients were screened for eligibility, of whom 55 patients were excluded. 152 participants were randomly assigned to groups: 77 (51%) patients received temocillin, 75 (49%) patients received cefotaxime. The composite primary endpoint was met by 18 (26%) of 68 participants receiving temocillin versus 30 (48%) of 62 patients receiving cefotaxime (risk difference -22% [95% CI -42% to -3%]), showing superiority of temocillin versus cefotaxime (ie, less disturbance of the intestinal microbiota). 43 adverse events were reported in 40 (52%) of 77 patients in the temocillin group, versus 46 adverse events in 34 (45%) of 75 patients in the cefotaxime group. Most events were of mild to moderate severity. 21 (27%) patients in the temocillin and 17 (23%) patients in the cefotaxime group had an adverse event that was considered to be associated with the study drug. INTERPRETATION Temocillin was found to be less selective than cefotaxime of Enterobacterales with reduced susceptibility to third-generation cephalosporins, and it could therefore be a favourable alternative in the empirical treatment of febrile UTI. Use of this antibiotic could reduce hospital transmission and health-care-associated infections by these pathogens. FUNDING Public Health Agency of Sweden.
Collapse
Affiliation(s)
| | - Anders Ternhag
- The Public Health Agency of Sweden, Solna, Sweden; Division of Infectious Diseases, Department of Medicine, Karolinska Institutet, Solna, Sweden
| | | | | | - Åse Östholm Balkhed
- Division of Infectious Diseases, Department of Biomedical and Clinical Sciences, Faculty of Medicine, Linköping University, Linköping, Sweden
| | - Simon Athlin
- Department of Infectious Diseases, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Emeli Månsson
- Department of Infectious Diseases and Centre of Clinical Research, Västmanland Hospital, Västerås, Sweden
| | - Maria Tempé
- Sundsvall Härnösand Regional Hospital, Sundsvall, Sweden
| | | | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden; Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Håkan Hanberger
- Division of Infectious Diseases, Department of Biomedical and Clinical Sciences, Faculty of Medicine, Linköping University, Linköping, Sweden.
| | | |
Collapse
|
38
|
G Giske C, Allander T, Fröding I, Ininbergs K, Mölling P, Engstrand L, Albert J. [Precision diagnostics in clinical microbiology]. Lakartidningen 2021; 118:21113. [PMID: 34693512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Genomic methods have had a major impact in clinical microbiology in the last decades. Microbial genomes are relatively small and therefore easier to characterise than human genomes. In both bacteriology and in virology, genomic methods have largely been used for molecular epidemiology, but also for molecular resistance testing of microorganisms. Targeted sequencing of predefined or isolated microorganisms was initially a dominant method but has gradually been supplemented with metagenomic diagnostics. Metagenomics aims at mapping all microorganisms - pathogenic as well as apathogenic - in a sample without determining in advance which agent(s) the analysis is targeting. Finally, there is also an increasing interest in mapping the significance of the microbiome, i.e. normal flora, both in health and disease.
Collapse
Affiliation(s)
- Christian G Giske
- professor, överläkare, Karolinska institutet; Karolinska universitetssjukhuset, Stockholm
| | - Tobias Allander
- docent, överläkare, Karolinska universitetssjukhuset, Stockholm
| | - Inga Fröding
- med dr, överläkare, Karolinska universitetssjukhuset, Stockholm
| | | | - Paula Mölling
- docent, molekylärbiolog, Universitetssjukhuset Örebro
| | - Lars Engstrand
- professor, överläkare, Karolinska institutet; Karolinska universitetssjukhuset, Stockholm
| | - Jan Albert
- professor, överläkare, Karolinska institutet; Karolinska universitetssjukhuset, Stockholm
| |
Collapse
|
39
|
Bolourchi N, Shahcheraghi F, Giske CG, Nematzadeh S, Noori Goodarzi N, Solgi H, Badmasti F. Comparative genome analysis of colistin-resistant OXA-48-producing Klebsiella pneumoniae clinical strains isolated from two Iranian hospitals. Ann Clin Microbiol Antimicrob 2021; 20:74. [PMID: 34688302 PMCID: PMC8542297 DOI: 10.1186/s12941-021-00479-y] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/07/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Carbapenemase-producing Klebsiella pneumoniae (CP-KP) is becoming extensively disseminated in Iranian medical centers. Colistin is among the few agents that retains its activity against CP-KP. However, the administration of colistin for treatment of carbapenem-resistant infections has increased resistance against this antibiotic. Therefore, the identification of genetic background of co-carbapenem, colistin-resistance K. pneumoniae (Co-CCRKp) is urgent for implementation of serious infection control strategies. METHODS Fourteen Co-CCRKp strains obtained from routine microbiological examinations were subjected to molecular analysis of antimicrobial resistance (AMR) using whole genome sequencing (WGS). RESULTS Nine of 14 K. pneumoniae strains belonged to sequence type (ST)-11 and 50% of the isolates had K-locus type 15. All strains carried blaOXA-48 except for P26. blaNDM-1 was detected in only two plasmids associated with P6 and P26 strains belonging to incompatibility (Inc) groups; IncFIB, IncHI1B and IncFII. No blaKPC, blaVIM and blaIMP were identified. Multi-drug resistant (MDR) conjugative plasmids were identified in strains P6, P31, P35, P38 and P40. MICcolistin of K. pneumoniae strains ranged from 4 to 32 µg/ml. Modification of PmrA, PmrB, PhoQ, RamA and CrrB regulators as well as MgrB was identified as the mechanism of colistin resistance in our isolates. Single amino acid polymorphysims (SAPs) in PhoQ (D150G) and PmrB (R256G) were identified in all strains except for P35 and P38. CrrB was absent in P37 and modified in P7 (A200E). Insertion of ISKpn72 (P32), establishment of stop codon (Q30*) (P35 and P38), nucleotides deletion (P37), and amino acid substitution at position 28 were identified in MgrB (P33 and P42). None of the isolates were positive for plasmid-mediated colistin resistance (mcr) genes. P35 and P38 strains carried iutA, iucD, iucC, iucB and iucA genes and are considered as MDR-hypervirulent strains. P6, P7 and P43 had ICEKp4 variant and ICEKp3 was identified in 78% of the strains with specific carriage in ST11. CONCLUSION In our study, different genetic modifications in chromosomal coding regions of some regulator genes resulted in phenotypic resistance to colistin. However, the extra-chromosomal colistin resistance through mcr genes was not detected. Continuous genomic investigations need to be conducted to accurately depict the status of colistin resistance in clinical settings.
Collapse
Affiliation(s)
- Negin Bolourchi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Shoeib Nematzadeh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Narjes Noori Goodarzi
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Solgi
- Department of Laboratory Medicine, Amin Hospital, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
40
|
KK S, Lin YL, Sewunet T, Wrande M, Sandegren L, Giske CG, Westerlund F. A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids. Micromachines (Basel) 2021; 12:1234. [PMID: 34683285 PMCID: PMC8538381 DOI: 10.3390/mi12101234] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/03/2022]
Abstract
Optical DNA mapping (ODM) has developed into an important technique for DNA analysis, where single DNA molecules are sequence-specifically labeled and stretched, for example, in nanofluidic channels. We have developed an ODM assay to analyze bacterial plasmids-circular extrachromosomal DNA that often carry genes that make bacteria resistant to antibiotics. As for most techniques, the next important step is to increase throughput and automation. In this work, we designed and fabricated a nanofluidic device that, together with a simple automation routine, allows parallel analysis of up to 10 samples at the same time. Using plasmids encoding extended-spectrum beta-lactamases (ESBL), isolated from Escherichiacoli and Klebsiellapneumoniae, we demonstrate the multiplexing capabilities of the device when it comes to both many samples in parallel and different resistance genes. As a final example, we combined the device with a novel protocol for rapid cultivation and extraction of plasmids from fecal samples collected from patients. This combined protocol will make it possible to analyze many patient samples in one device already on the day the sample is collected, which is an important step forward for the ODM analysis of plasmids in clinical diagnostics.
Collapse
Affiliation(s)
- Sriram KK
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
| | - Yii-Lih Lin
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
| | - Marie Wrande
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 37 Uppsala, Sweden; (M.W.); (L.S.)
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 37 Uppsala, Sweden; (M.W.); (L.S.)
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
- Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
| |
Collapse
|
41
|
Åkerlund A, Petropoulos A, Malmros K, Tängdén T, Giske CG. Blood culture diagnostics: a Nordic multicentre survey comparison of practices in clinical microbiology laboratories. Clin Microbiol Infect 2021; 28:731.e1-731.e7. [PMID: 34537364 DOI: 10.1016/j.cmi.2021.09.003] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/17/2021] [Accepted: 09/04/2021] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Accurate and rapid microbiological diagnostics are crucial to tailor treatment and improve outcomes in patients with severe infections. This study aimed to assess blood culture diagnostics in the Nordic countries and to compare them with those of a previous survey conducted in Sweden in 2013. METHODS An online questionnaire was designed and distributed to the Nordic clinical microbiology laboratories (CMLs) (n = 76) in January 2018. RESULTS The response rate was 64% (49/76). Around-the-clock incubation of blood cultures (BCs) was supported in 82% of the CMLs (40/49), although in six of these access to the incubators around the clock was not given to all of the cabinets in the catchment area, and 41% of the sites (20/49) did not assist with satellite incubators. Almost half (49%, 24/49) of the CMLs offered opening hours for ≥10 h during weekdays, more commonly in CMLs with an annual output ≥30 000 BCs. Still, positive BCs were left unprocessed for 60-70% of the day due to restrictive opening hours. Treatment advice was given by 23% of CMLs (11/48) in ≥75% of the phone contacts. Rapid analyses (species identification and susceptibility testing with short incubation), performed on aliquots from positive cultures, were implemented in 18% of CMLs (9/49). Compared to 2013, species identification from subcultured colonies (<6 h) had become more common. CONCLUSIONS CMLs have taken action to improve aspects of BC diagnostics, implementing satellite incubators, rapid species identification and susceptibility testing. However, the limited opening hours and availability of clinical microbiologists are confining the advantages of these changes.
Collapse
Affiliation(s)
- Anna Åkerlund
- Division of Clinical Microbiology, Laboratory Medicine, Jönköping, Region Jönköping County, and Department of Clinical and Experimental Medicine, Linköping University, Sweden; Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University Hospital, Linköping, Sweden.
| | - Alexandros Petropoulos
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Malmros
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Thomas Tängdén
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
42
|
KK S, Sewunet T, Wangchinda W, Tangkoskul T, Thamlikitkul V, Giske CG, Westerlund F. Optical DNA Mapping of Plasmids Reveals Clonal Spread of Carbapenem-Resistant Klebsiella pneumoniae in a Large Thai Hospital. Antibiotics (Basel) 2021; 10:antibiotics10091029. [PMID: 34572611 PMCID: PMC8466775 DOI: 10.3390/antibiotics10091029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/26/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CR-KP) in patients admitted to hospitals pose a great challenge to treatment. The genes causing resistance to carbapenems are mostly found in plasmids, mobile genetic elements that can spread easily to other bacterial strains, thus exacerbating the problem. Here, we studied 27 CR-KP isolates collected from different types of samples from 16 patients admitted to the medical ward at Siriraj Hospital in Bangkok, Thailand, using next generation sequencing (NGS) and optical DNA mapping (ODM). The majority of the isolates belonged to sequence type (ST) 16 and are described in detail herein. Using ODM, we identified the plasmid carrying the blaNDM-1 gene in the ST16 isolates and the plasmids were very similar, highlighting the possibility of using ODM of plasmids as a surrogate marker of nosocomial spread of bacteria. We also demonstrated that ODM could identify that the blaCTX-M-15 and blaOXA-232 genes in the ST16 isolates were encoded on separate plasmids from the blaNDM-1 gene and from each other. The other three isolates belonged to ST147 and each of them had distinct plasmids encoding blaNDM-1.
Collapse
Affiliation(s)
- Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
| | - Tsegaye Sewunet
- Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
| | - Walaiporn Wangchinda
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (W.W.); (T.T.); (V.T.)
| | - Teerawit Tangkoskul
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (W.W.); (T.T.); (V.T.)
| | - Visanu Thamlikitkul
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (W.W.); (T.T.); (V.T.)
| | - Christian G. Giske
- Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
- Correspondence: ; Tel.: +46-31-772-3049
| |
Collapse
|
43
|
Zemmour A, Dali-Yahia R, Maatallah M, Saidi-Ouahrani N, Rahmani B, Benhamouche N, Al-Farsi HM, Giske CG. High-risk clones of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolated from the University Hospital Establishment of Oran, Algeria (2011-2012). PLoS One 2021; 16:e0254805. [PMID: 34310625 PMCID: PMC8312963 DOI: 10.1371/journal.pone.0254805] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 07/05/2021] [Indexed: 11/18/2022] Open
Abstract
The purpose of the study was to characterize the resistome, virulome, mobilome and Clustered Regularly Interspaced Short Palindromic Repeats-associated (CRISPR-Cas) system of extended-spectrum β-lactamase producing Klebsiella pneumoniae (ESBL-KP) clinical isolates and to determine their phylogenetic relatedness. The isolates were from Algeria, isolated at the University Hospital Establishment of Oran, between 2011 and 2012. ESBL-KP isolates (n = 193) were screened for several antibiotic resistance genes (ARGs) using qPCR followed by Pulsed-Field Gel Electrophoresis (PFGE). Representative isolates were selected from PFGE clusters and subjected to whole-genome sequencing (WGS). Genomic characterization of the WGS data by studying prophages, CRISPR-Cas systems, Multi-Locus Sequence Typing (MLST), serotype, ARGs, virulence genes, plasmid replicons, and their pMLST. Phylogenetic and comparative genomic were done using core genome MLST and SNP-Based analysis. Generally, the ESBL-KP isolates were polyclonal. The whole genome sequences of nineteen isolates were taken of main PFGE clusters. Sixteen sequence types (ST) were found including high-risk clones ST14, ST23, ST37, and ST147. Serotypes K1 (n = 1), K2 (n = 2), K3 (n = 1), K31 (n = 1), K62 (n = 1), and K151 (n = 1) are associated with hyper-virulence. CRISPR-Cas system was found in 47.4%, typed I-E and I-E*. About ARGs, from 193 ESBL-KP, the majority of strains were multidrug-resistant, the CTX-M-1 enzyme was predominant (99%) and the prevalence of plasmid-mediated quinolone resistance (PMQR) genes was high with aac(6')-lb-cr (72.5%) and qnr's (65.8%). From 19 sequenced isolates we identified ESBL, AmpC, and carbapenemase genes: blaCTX-M-15 (n = 19), blaOXA-48 (n = 1), blaCMY-2 (n = 2), and blaCMY-16 (n = 2), as well as non-ESBL genes: qnrB1 (n = 12), qnrS1 (n = 1) and armA (n = 2). We found IncF, IncN, IncL/M, IncA/C2, and Col replicon types, at least once per isolate. This study is the first to report qnrS in ESBL-KP in Algeria. Our analysis shows the concerning co-existence of virulence and resistance genes and would support that genomic surveillance should be a high priority in the hospital environment.
Collapse
Affiliation(s)
- Assia Zemmour
- Faculté de Sciences de la Nature et la Vie, Département de Génétique Moléculaire Appliquée, Université des Sciences et la Technologie d’Oran Mohamed-Boudiaf USTOMB, Oran, Algérie
- Laboratoire de Génétique Médicale Appliquée à l’Ophtalmologie, Université d’Oran 1, Oran, Algérie
- * E-mail: ,
| | - Radia Dali-Yahia
- Service de bactériologie, Etablissement Hospitalo-Universitaire 1er Novembre 1954, Oran, Algérie
- Faculté de médicine, Université d’Oran 1, Oran, Algérie
| | - Makaoui Maatallah
- Faculté de pharmacie de Monastir, Laboratoire d’Analyse, Traitement et Valorisation des Polluants de l’Environnement et des Produits (LATVPEP: LR01ES16), Université de Monastir, Monastir, Tunisie
| | - Nadjia Saidi-Ouahrani
- Faculté de Sciences de la Nature et la Vie, Département de Génétique Moléculaire Appliquée, Université des Sciences et la Technologie d’Oran Mohamed-Boudiaf USTOMB, Oran, Algérie
| | - Bouabdallah Rahmani
- Faculté de Génie Electrique, Département d’Electronique, Université des Sciences et la Technologie d’Oran Mohamed-Boudiaf USTOMB, Oran, Algérie
| | - Nora Benhamouche
- Faculté de Sciences de la Nature et la Vie, Département de Génétique Moléculaire Appliquée, Université des Sciences et la Technologie d’Oran Mohamed-Boudiaf USTOMB, Oran, Algérie
| | - Hissa M. Al-Farsi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Central Public Health Laboratories, Ministry of Health, Muscat, Sultanate of Oman
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital Solna, Stockholm, Sweden
| |
Collapse
|
44
|
Babich T, Naucler P, Valik JK, Giske CG, Benito N, Cardona R, Rivera A, Pulcini C, Abdel Fattah M, Haquin J, MacGowan A, Grier S, Gibbs J, Chazan B, Yanovskay A, Ami RB, Landes M, Nesher L, Zaidman-Shimshovitz A, McCarthy K, Paterson DL, Tacconelli E, Buhl M, Mauer S, Rodriguez-Bano J, Morales I, Oliver A, Ruiz de Gopegui E, Cano A, Machuca I, Gozalo-Marguello M, Martinez LM, Gonzalez-Barbera EM, Alfaro IG, Salavert M, Beovic B, Saje A, Mueller-Premru M, Pagani L, Vitrat V, Kofteridis D, Zacharioudaki M, Maraki S, Weissman Y, Paul M, Dickstein Y, Leibovici L, Yahav D. Combination versus monotherapy as definitive treatment for Pseudomonas aeruginosa bacteraemia: a multicentre retrospective observational cohort study. J Antimicrob Chemother 2021; 76:2172-2181. [PMID: 33993273 DOI: 10.1093/jac/dkab134] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/31/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa bacteraemia is a common and serious infection. No consensus exists regarding whether definitive combination therapy is superior to monotherapy. We aimed to evaluate the impact of combination therapy on mortality. METHODS This was a multicentre retrospective study (nine countries, 25 centres), including 1277 patients with P. aeruginosa bacteraemia during 2009-15. We evaluated the association between β-lactam plus aminoglycoside or quinolone combination therapy versus β-lactam monotherapy and mortality. The primary outcome was 30 day all-cause mortality. Univariate and multivariate Cox regression analyses were conducted, introducing combination as a time-dependent variable. Propensity score was conducted to adjust for confounding for choosing combination therapy over monotherapy. RESULTS Of 1119 patients included, 843 received definitive monotherapy and 276 received combination therapy (59% aminoglycoside and 41% quinolone). Mortality at 30 days was 16.9% (189/1119) and was similar between combination (45/276; 16.3%) and monotherapy (144/843; 17.1%) groups (P = 0.765). In multivariate Cox regression, combination therapy was not associated with reduced mortality (HR 0.98, 95% CI 0.64-1.53). No advantage in terms of clinical failure, microbiological failure or recurrent/persistent bacteraemia was demonstrated using combination therapy. Likewise, adverse events and resistance development were similar for the two regimens. CONCLUSIONS In this retrospective cohort, no mortality advantage was demonstrated using combination therapy over monotherapy for P. aeruginosa bacteraemia. Combination therapy did not improve clinical or microbiological failure rates, nor affect adverse events or resistance development. Our finding of no benefit with combination therapy needs confirmation in well-designed randomized controlled trials.
Collapse
Affiliation(s)
- Tanya Babich
- Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Pontus Naucler
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet and Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - John Karlsson Valik
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet and Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Christian G Giske
- Department of Laboratory Medicine, Karolinska Institutet and Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Natividad Benito
- Infectious Diseases Unit, Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau-Institut d'Investigació Biomèdica Sant Pau and Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ruben Cardona
- Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Alba Rivera
- Department of Microbiology, Hospital de la Santa Creu i Sant Pau-Institut d'Investigació Biomèdica Sant Pau, Barcelona, Spain
| | - Celine Pulcini
- Université de Lorraine, APEMAC, F-54000, Nancy, France
- Université de Lorraine, CHRU-Nancy, Infectious Diseases Department, F-54000, Nancy, France
| | - Manal Abdel Fattah
- Université de Lorraine, CHRU-Nancy, Infectious Diseases Department, F-54000, Nancy, France
| | - Justine Haquin
- Université de Lorraine, CHRU-Nancy, Infectious Diseases Department, F-54000, Nancy, France
| | - Alasdair MacGowan
- Department of Infection Sciences, Pathology Sciences Building, Southmead Hospital, Bristol, UK
| | - Sally Grier
- Department of Infection Sciences, Pathology Sciences Building, Southmead Hospital, Bristol, UK
| | - Julie Gibbs
- Department of Infection Sciences, Pathology Sciences Building, Southmead Hospital, Bristol, UK
| | - Bibiana Chazan
- Infectious Diseases Unit, Emek Medical Center, Afula, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Anna Yanovskay
- Infectious Diseases Unit, Emek Medical Center, Afula, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Ronen Ben Ami
- Sackler Faculty of Medicine, Tel Aviv University, Israel
- Infectious Diseases Unit, Sourasky Medical Center, Tel-Aviv, Israel
| | - Michal Landes
- Infectious Diseases Unit, Sourasky Medical Center, Tel-Aviv, Israel
| | - Lior Nesher
- Infectious Disease Institute, Soroka Medical Center, Ben-Gurion University of the Negev, Beer Sheba, Israel
| | - Adi Zaidman-Shimshovitz
- Infectious Disease Institute, Soroka Medical Center, Ben-Gurion University of the Negev, Beer Sheba, Israel
| | - Kate McCarthy
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - David L Paterson
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - Evelina Tacconelli
- Division of Infectious Diseases, Tuebingen University Hospital, Tuebingen, Germany
| | - Michael Buhl
- Division of Infectious Diseases, Tuebingen University Hospital, Tuebingen, Germany
| | - Susanna Mauer
- Division of Infectious Diseases, Tuebingen University Hospital, Tuebingen, Germany
| | - Jesus Rodriguez-Bano
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena/Departamento de Medicina, Universidad de Sevilla/Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain
| | - Isabel Morales
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena/Departamento de Medicina, Universidad de Sevilla/Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain
| | - Antonio Oliver
- Servicio de Microbiología & Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Enrique Ruiz de Gopegui
- Servicio de Microbiología & Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Angela Cano
- Infectious Diseases Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Spain
| | - Isabel Machuca
- Infectious Diseases Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Spain
| | | | - Luis Martinez Martinez
- Microbiology Service, University Hospital Marqués de Valdecilla-IDIVAL, Santander, Spain
| | | | | | - Miguel Salavert
- Infectious Diseases Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Bojana Beovic
- Department of Infectious Diseases, University Medical Centre, Ljubljana; Faculty of Medicine, University of Ljubljana, Slovenia
| | - Andreja Saje
- Department of Infectious Diseases, University Medical Centre, Ljubljana; Faculty of Medicine, University of Ljubljana, Slovenia
| | - Manica Mueller-Premru
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Leonardo Pagani
- Infectious Diseases Unit, Bolzano Central Hospital, Bolzano, Italy
| | - Virginie Vitrat
- Infectious Diseases Unit, Annecy-Genevois Hospital Center (CHANGE), Annecy, France
| | - Diamantis Kofteridis
- Infectious Disease Unit, Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
| | - Maria Zacharioudaki
- Infectious Disease Unit, Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
| | - Sofia Maraki
- Infectious Disease Unit, Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
| | - Yulia Weissman
- Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Mical Paul
- Infectious Diseases Unit, Rambam Health Care Campus, Haifa, Israel
| | - Yaakov Dickstein
- Infectious Diseases Unit, Rambam Health Care Campus, Haifa, Israel
| | - Leonard Leibovici
- Medicine E, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel
| | - Dafna Yahav
- Infectious Diseases Unit, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel
| |
Collapse
|
45
|
Kragh KN, Gijón D, Maruri A, Antonelli A, Coppi M, Kolpen M, Crone S, Tellapragada C, Hasan B, Radmer S, de Vogel C, van Wamel W, Verbon A, Giske CG, Rossolini GM, Cantón R, Frimodt-Møller N. Effective antimicrobial combination in vivo treatment predicted with microcalorimetry screening. J Antimicrob Chemother 2021; 76:1001-1009. [PMID: 33442721 PMCID: PMC7953322 DOI: 10.1093/jac/dkaa543] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 06/18/2020] [Accepted: 11/30/2020] [Indexed: 02/01/2023] Open
Abstract
Objectives The worldwide emergence of antibiotic resistance calls for effective exploitation of existing antibiotics. Antibiotic combinations with different modes of action can synergize for successful treatment. In the present study, we used microcalorimetry screening to identify synergistic combination treatments against clinical MDR isolates. The synergistic effects were validated in a murine infection model. Methods The synergy of meropenem combined with colistin, rifampicin or amikacin was tested on 12 isolates (1 Escherichia coli, 5 Klebsiella pneumoniae, 3 Pseudomonas aeruginosa and 3 Acinetobacter baumannii) in an isothermal microcalorimeter measuring metabolic activity. One A. baumannii strain was tested with two individual pairings of antibiotic combinations. The microcalorimetric data were used to predict in vivo efficacy in a murine peritonitis/sepsis model. NMRI mice were inoculated intraperitoneally and after 1 h treated with saline, drug X, drug Y or X+Y. Bacterial load was determined by cfu in peritoneal fluid and blood after 4 h. Results In vitro, of the 13 combinations tested on the 12 strains, 3 of them exhibited a synergistic reduction in MIC (23% n = 3/13), 5 showed an additive effect (38.5% n = 5/13) and 5 had indifferent or antagonistic effects (38.5% n = 5/13). There was a significant correlation (P = 0.024) between microcalorimetry-screening FIC index values and the log reduction in peritoneal fluid from mice that underwent combination treatment compared with the most effective mono treatment. No such correlation could be found between chequerboard and in vivo results (P = 0.16). Conclusions These data support microcalorimetic metabolic readout to predict additive or synergistic effects of combination treatment of MDR infections within hours.
Collapse
Affiliation(s)
- Kasper Nørskov Kragh
- Department of Clinical Microbiology, Rigshospitalet, 2200 Copenhagen N, Denmark.,Costerton Biofilm Center, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Desiree Gijón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Ainhize Maruri
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Firenze, Italy.,Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50121 Firenze, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Firenze, Italy.,Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50121 Firenze, Italy
| | - Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, 2200 Copenhagen N, Denmark
| | - Stephanie Crone
- Department of Clinical Microbiology, Rigshospitalet, 2200 Copenhagen N, Denmark
| | | | - Badrul Hasan
- Department of Laboratory Medicine, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Stine Radmer
- Department of Clinical Microbiology, Rigshospitalet, 2200 Copenhagen N, Denmark
| | - Corné de Vogel
- Department of Medical Microbiology and Infectious Diseases, Erasmus University, Erasmus MC, 3000CA Rotterdam, The Netherlands
| | - Willem van Wamel
- Department of Medical Microbiology and Infectious Diseases, Erasmus University, Erasmus MC, 3000CA Rotterdam, The Netherlands
| | - Annelies Verbon
- Department of Medical Microbiology and Infectious Diseases, Erasmus University, Erasmus MC, 3000CA Rotterdam, The Netherlands
| | - Christian G Giske
- Department of Laboratory Medicine, Karolinska Institutet, 14183 Stockholm, Sweden.,Clinical Microbiology, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Firenze, Italy.,Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50121 Firenze, Italy
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | | |
Collapse
|
46
|
Giske CG, Kahlmeter G, MacGowan A, Turnidge J. Comment on: Efficacy of temocillin against MDR Enterobacterales: a retrospective cohort study. J Antimicrob Chemother 2021; 76:1949-1950. [PMID: 33724352 DOI: 10.1093/jac/dkab081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Gunnar Kahlmeter
- Department of Clinical Microbiology, Central Hospital, Växjö, Sweden
| | - Alasdair MacGowan
- Bristol Centre for Antimicrobial Research and Evaluation (BCARE), Infection Sciences, Severn Pathology, Southmead Hospital, Westbury-on-Trym, Bristol, UK
| | - John Turnidge
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | | |
Collapse
|
47
|
Lin YL, Sewunet T, KK S, Giske CG, Westerlund F. Optical maps of plasmids as a proxy for clonal spread of MDR bacteria: a case study of an outbreak in a rural Ethiopian hospital. J Antimicrob Chemother 2021; 75:2804-2811. [PMID: 32653928 PMCID: PMC7678893 DOI: 10.1093/jac/dkaa258] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 02/03/2020] [Revised: 04/24/2020] [Accepted: 05/14/2020] [Indexed: 01/09/2023] Open
Abstract
Objectives MDR bacteria have become a prevailing health threat worldwide. We here aimed to use optical DNA mapping (ODM) as a rapid method to trace nosocomial spread of bacterial clones and gene elements. We believe that this method has the potential to be a tool of pivotal importance for MDR control. Methods Twenty-four Escherichia coli samples of ST410 from three different wards were collected at an Ethiopian hospital and their plasmids were analysed by ODM. Plasmids were specifically digested with Cas9 targeting the antibiotic resistance genes, stained by competitive binding and confined in nanochannels for imaging. The resulting intensity profiles (barcodes) for each plasmid were compared to identify potential clonal spread of resistant bacteria. Results ODM demonstrated that a large fraction of the patients carried bacteria with a plasmid of the same origin, carrying the ESBL gene blaCTX-M-15, suggesting clonal spread. The results correlate perfectly with core genome (cg)MLST data, where bacteria with the same plasmid also had very similar cgMLST profiles. Conclusions ODM is a rapid discriminatory method for identifying plasmids and antibiotic resistance genes. Long-range deletions/insertions, which are challenging for short-read next-generation sequencing, can be easily identified and used to trace bacterial clonal spread. We propose that plasmid typing can be a useful tool to identify clonal spread of MDR bacteria. Furthermore, the simplicity of the method enables possible future application in low- and middle-income countries.
Collapse
Affiliation(s)
- Yii-Lih Lin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- School of Laboratory Sciences, Department of Microbiology, Jimma University, Jimma, Ethiopia
| | - Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Corresponding author. E-mail:
| |
Collapse
|
48
|
Abstract
![]()
Millions
of individuals currently living with HIV globally are
receiving antiretroviral therapy (ART) that suppresses viral replication
and improves host immune responses. The involvement of gut microbiome
during HIV infection has been studied, exposing correlation with immune
status and inflammation. However, the direct effect of ART on gut
commensals of HIV-infected individuals has been mostly overlooked
in microbiome studies. We used 16S rRNA sequencing (Illumina MiSeq)
for determining the microbiota composition of stool samples from 16
viremic patients before and one year after ART. We also tested the
direct effect of 15 antiretrovirals against four gut microbes, namely, Escherichia coli, Enterococcus faecalis, Bacteroides, and Prevotella to assess their in vitro antibacterial effect. 16S rRNA analysis of fecal samples showed
that effective ART for one year does not restore the microbiome diversity
in HIV-infected patients. A significant reduction in α-diversity
was observed in patients under non-nucleoside reverse transcriptase
inhibitors; (NNRTI; 2 NRTI+NNRTI; NRTIs are nucleoside reverse transcriptase
inhibitors) as compared to ritonavir-boosted protease inhibitors (PI/r;
2 NRTI+PI/r). Prevotella (P = 0.00001) showed a significantly decreased abundance in patients
after ART (n = 16). We also found the direct effect
of antivirals on gut microbes, where zidovudine (ZDV) and efavirenz
(EFV) showed in vitro antimicrobial activity against Bacteroides fragilis and Prevotella. EFV also inhibited the growth of E. faecalis. Therefore, we observed that ART does not reverse the HIV-induced
gut microbiome dysbiosis and might aggravate those microbiota alterations
due to the antibacterial effect of certain antiretrovirals (like EFV,
ZDV). Our results imply that restructuring the microbiota could be
a potential therapeutic target in HIV-1 patients under ART.
Collapse
Affiliation(s)
- Shilpa Ray
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå 901 87, Sweden
| | - Aswathy Narayanan
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
| | - Christian G. Giske
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm 171 76,Sweden
| | - Ujjwal Neogi
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
| | - Anders Sönnerborg
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska University Hospital, Huddinge, Stockholm 141 86, Sweden
| | - Piotr Nowak
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå 901 87, Sweden
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska University Hospital, Huddinge, Stockholm 141 86, Sweden
| |
Collapse
|
49
|
Vehreschild MJGT, Tacconelli E, Giske CG, Peschel A. Beyond COVID-19-a paradigm shift in infection management? Lancet Infect Dis 2021; 21:e117. [PMID: 33045187 PMCID: PMC7546645 DOI: 10.1016/s1473-3099(20)30789-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 01/25/2023]
Affiliation(s)
- Maria J G T Vehreschild
- German Centre for Infection Research, Partner Site Bonn-Cologne, Germany; University of Cologne, Department I of Internal Medicine, Cologne, Germany; Department of Internal Medicine, Infectious Diseases, Goethe University Frankfurt, Frankfurt, Germany
| | - Evelina Tacconelli
- Infectious Diseases Unit, Department of Diagnostics and Public Health, Verona University Hospital, Verona, Italy; Cluster of Excellence EXC2124 "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen 72076, Germany; German Centre for Infection Research, Partner Site Tübingen, Germany
| | - Christian G Giske
- Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen 72076, Germany; Cluster of Excellence EXC2124 "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen 72076, Germany; German Centre for Infection Research, Partner Site Tübingen, Germany.
| |
Collapse
|
50
|
Satlin MJ, Lewis JS, Weinstein MP, Patel J, Humphries RM, Kahlmeter G, Giske CG, Turnidge J. Clinical and Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing Position Statements on Polymyxin B and Colistin Clinical Breakpoints. Clin Infect Dis 2021; 71:e523-e529. [PMID: 32052041 DOI: 10.1093/cid/ciaa121] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [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: 10/10/2019] [Accepted: 02/10/2020] [Indexed: 12/22/2022] Open
Abstract
Recent data on polymyxin pharmacokinetics, pharmacodynamics, toxicity, and clinical outcomes suggest these agents have limited clinical utility. Pharmacokinetics-pharmacodynamics data show a steady-state concentration of 2 μg/mL is required for killing bacteria with colistin minimum inhibitory concentrations of 2 μg/mL. Less than 50% of patients with normal renal function achieve this exposure, and it is associated with high risk of nephrotoxicity. This exposure does not achieve bacterial stasis in pneumonia models. Randomized and observational studies consistently demonstrate increased mortality for polymyxins compared with alternative agents. The Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) are 2 global organizations that establish interpretive criteria for in vitro susceptibility data. CLSI has recently taken the step to eliminate the "susceptible" interpretive category for the polymyxins, whereas EUCAST maintains this interpretive category. This viewpoint describes the opinions of these organizations and the data that were used to inform their perspectives.
Collapse
Affiliation(s)
- Michael J Satlin
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - James S Lewis
- Department of Pharmacy, Oregon Health and Science University, Portland, Oregon, USA
| | - Melvin P Weinstein
- Departments of Medicine and Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Jean Patel
- Beckman Coulter, Sacramento, California, USA
| | - Romney M Humphries
- Accelerate Diagnostics, Tucson, Arizona, USA.,Department of Pathology, University of Arizona, Tucson, Arizona, USA
| | - Gunnar Kahlmeter
- Department of Clinical Microbiology, Växjö Central Hospital, Växjö, Sweden
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - John Turnidge
- Adelaide Medical School, University of Adelaide, South Australia, Australia
| |
Collapse
|