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Fierro CA, Sarnecki M, Spiessens B, Go O, Day TA, Davies TA, van den Dobbelsteen G, Poolman J, Abbanat D, Haazen W. A randomized phase 1/2a trial of ExPEC10V vaccine in adults with a history of UTI. NPJ Vaccines 2024; 9:106. [PMID: 38877036 PMCID: PMC11178786 DOI: 10.1038/s41541-024-00885-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/07/2024] [Indexed: 06/16/2024] Open
Abstract
The safety, reactogenicity, and immunogenicity of 3 doses of ExPEC10V (VAC52416), a vaccine candidate to prevent invasive Escherichia coli disease, were assessed in a phase 1/2a study (NCT03819049). In Cohort 1, ExPEC10V was well tolerated; the high dose was selected as optimal and further characterized in Cohort 2. Cohort 2 comprised a maximum 28-day screening, vaccination (Day 1), double-blind 181-day follow-up, and open-label long-term follow-up until Year 1. Healthy participants (≥60 years) with a history of urinary tract infection (UTI) within 5 years were randomized to receive ExPEC10V or placebo. The primary endpoint evaluated the safety and reactogenicity of ExPEC10V (solicited local and systemic AEs [until Day 15]; unsolicited AEs [until Day 30], SAEs [until Day 181], and immunogenicity [Day 30]) via multiplex electrochemiluminescent (ECL) and multiplex opsonophagocytic assay (MOPA). 416 participants (ExPEC10V, n = 278; placebo, n = 138) were included (mean age [SD], 68.8 [6.52] years; female, 79.6%; White, 96.1%). The incidence of solicited AEs was higher with ExPEC10V (local, 50.0% [n = 139]; systemic, 50.0% [n = 139]) than placebo (15.9% [n = 22]; 38.4% [n = 53]); rates of unsolicited AEs were comparable (ExPEC10V, 28.4% [n = 79]; placebo, 26.1% [n = 36]). No vaccine-related SAEs or deaths were reported. ExPEC10V elicited a robust antibody-mediated immunogenic response across all serotypes with ECL (Day 30 geometric mean fold increase, 2.33-8.18) and demonstrated functional opsonophagocytic killing activity across all measured serotypes (Day 30 geometric mean fold increase, 1.81-9.68). ExPEC10V exhibited an acceptable safety profile and a robust vaccine-induced functional immunogenic response in participants with a history of UTI. Clinical trial registration details: https://clinicaltrials.gov/study/NCT03819049 .
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Affiliation(s)
| | - Michal Sarnecki
- Janssen Research & Development, Infectious Diseases & Vaccines, Janssen Vaccines, Bern, Switzerland
| | - Bart Spiessens
- Janssen Research & Development, Infectious Diseases & Vaccines, Janssen Pharmaceutica, Beerse, Belgium
| | - Oscar Go
- Janssen Research & Development, Raritan, NJ, USA
| | - Tracey A Day
- Bacterial Vaccines Discovery and Early Development, Janssen Vaccines & Prevention B.V., Leiden, Netherlands
| | | | - Germie van den Dobbelsteen
- Bacterial Vaccines Discovery and Early Development, Janssen Vaccines & Prevention B.V., Leiden, Netherlands
| | - Jan Poolman
- Bacterial Vaccines Discovery and Early Development, Janssen Vaccines & Prevention B.V., Leiden, Netherlands.
| | | | - Wouter Haazen
- Janssen Research & Development, Infectious Diseases & Vaccines, Janssen Pharmaceutica, Beerse, Belgium
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Heinz E, Pearse O, Zuza A, Bilima S, Msefula C, Musicha P, Siyabu P, Tewesa E, Graf FE, Lester R, Lissauer S, Cornick J, Lewis JM, Kawaza K, Thomson NR, Feasey NA. Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations. Genome Med 2024; 16:67. [PMID: 38711148 DOI: 10.1186/s13073-024-01342-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Infections caused by multidrug-resistant gram-negative bacteria present a severe threat to global public health. The WHO defines drug-resistant Klebsiella pneumoniae as a priority pathogen for which alternative treatments are needed given the limited treatment options and the rapid acquisition of novel resistance mechanisms by this species. Longitudinal descriptions of genomic epidemiology of Klebsiella pneumoniae can inform management strategies but data from sub-Saharan Africa are lacking. METHODS We present a longitudinal analysis of all invasive K. pneumoniae isolates from a single hospital in Blantyre, Malawi, southern Africa, from 1998 to 2020, combining clinical data with genome sequence analysis of the isolates. RESULTS We show that after a dramatic increase in the number of infections from 2016 K. pneumoniae becomes hyperendemic, driven by an increase in neonatal infections. Genomic data show repeated waves of clonal expansion of different, often ward-restricted, lineages, suggestive of hospital-associated transmission. We describe temporal trends in resistance and surface antigens, of relevance for vaccine development. CONCLUSIONS Our data highlight a clear need for new interventions to prevent rather than treat K. pneumoniae infections in our setting. Whilst one option may be a vaccine, the majority of cases could be avoided by an increased focus on and investment in infection prevention and control measures, which would reduce all healthcare-associated infections and not just one.
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Affiliation(s)
- Eva Heinz
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK.
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK.
| | - Oliver Pearse
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Allan Zuza
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Sithembile Bilima
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - Patrick Musicha
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - Edith Tewesa
- Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Fabrice E Graf
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK
| | - Rebecca Lester
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Division of Infection & Immunity, University College London, London, UK
| | - Samantha Lissauer
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Jennifer Cornick
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Joseph M Lewis
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Kondwani Kawaza
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Nicholas R Thomson
- Parasites and Microbes Program, Wellcome Sanger Institute, Hinxton, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK.
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.
- School of Medicine, St Andrews University, St Andrews, UK.
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Lipworth S, Matlock W, Shaw L, Vihta KD, Rodger G, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto T, Crook D, Walker AS, Stoesser N. The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies. Nat Commun 2024; 15:1612. [PMID: 38383544 PMCID: PMC10881496 DOI: 10.1038/s41467-024-45761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative 'backbone' of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.
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Affiliation(s)
- Samuel Lipworth
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
| | - William Matlock
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Liam Shaw
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
| | | | - Gillian Rodger
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy Davies
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
| | - Alison Vaughan
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Marcus Morgan
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Susan Hopkins
- National Infection Service, United Kingdom Health Security Agency, Colindale, London, UK
| | - Timothy Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
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The Development of Immunological Assays to Evaluate the Level and Function of Antibodies Induced by Klebsiella pneumoniae O-Antigen Vaccines. mSphere 2023; 8:e0068022. [PMID: 36877023 PMCID: PMC10117086 DOI: 10.1128/msphere.00680-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Klebsiella pneumoniae, a Gram-negative bacterium, has been listed as a critical pathogen for urgent intervention by the World Health Organization. With no licensed vaccine and increasing resistance to antibiotics, Klebsiella pneumoniae causes a high incidence of hospital- and community-acquired infections. Recently, there has been progress in anti-Klebsiella pneumoniae vaccine development, which has highlighted the lack of standardized assays to measure vaccine immunogenicity. We have developed and optimized methods to measure antibody level and function after vaccination with an in-development Klebsiella pneumoniae O-antigen vaccine. We describe the qualification of a Luminex-based multiplex antibody binding assay and both an opsonophagocytic killing assay and serum bactericidal assay to measure antibody function. Serum from immunized animals were immunogenic and capable of binding to and killing specific Klebsiella serotypes. Cross-reactivity was observed but limited among serotypes sharing antigenic epitopes. In summary, these results demonstrate the standardization of assays that can be used to test new anti-Klebsiella pneumoniae vaccine candidates, which is important for moving them into clinical trials. IMPORTANCE There is no licensed vaccine for the prevention of Klebsiella pneumoniae infections, and increasing levels of antibiotic resistance make this pathogen a high priority for vaccine and therapeutic development. Standardized assays for testing vaccine immunogenicity are paramount for the development of vaccines, and so in this study, we optimized and standardized both antibody-level and function assays for evaluating in-development K. pneumoniae bioconjugate vaccine response in rabbits.
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Mba IE, Sharndama HC, Anyaegbunam ZKG, Anekpo CC, Amadi BC, Morumda D, Doowuese Y, Ihezuo UJ, Chukwukelu JU, Okeke OP. Vaccine development for bacterial pathogens: Advances, challenges and prospects. Trop Med Int Health 2023; 28:275-299. [PMID: 36861882 DOI: 10.1111/tmi.13865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The advent and use of antimicrobials have played a key role in treating potentially life-threatening infectious diseases, improving health, and saving the lives of millions of people worldwide. However, the emergence of multidrug resistant (MDR) pathogens has been a significant health challenge that has compromised the ability to prevent and treat a wide range of infectious diseases that were once treatable. Vaccines offer potential as a promising alternative to fight against antimicrobial resistance (AMR) infectious diseases. Vaccine technologies include reverse vaccinology, structural biology methods, nucleic acid (DNA and mRNA) vaccines, generalised modules for membrane antigens, bioconjugates/glycoconjugates, nanomaterials and several other emerging technological advances that are offering a potential breakthrough in the development of efficient vaccines against pathogens. This review covers the opportunities and advancements in vaccine discovery and development targeting bacterial pathogens. We reflect on the impact of the already-developed vaccines targeting bacterial pathogens and the potential of those currently under different stages of preclinical and clinical trials. More importantly, we critically and comprehensively analyse the challenges while highlighting the key indices for future vaccine prospects. Finally, the issues and concerns of AMR for low-income countries (sub-Saharan Africa) and the challenges with vaccine integration, discovery and development in this region are critically evaluated.
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Affiliation(s)
- Ifeanyi Elibe Mba
- Department of Microbiology, University of Nigeria, Nsukka, Nigeria
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | | | - Zikora Kizito Glory Anyaegbunam
- Department of Microbiology, University of Nigeria, Nsukka, Nigeria
- Institute for Drug-Herbal Medicine-Excipient Research and Development, University of Nigeria, Nsukka, Nigeria
| | - Chijioke Chinedu Anekpo
- Department of Ear Nose and Throat, College of Medicine, Enugu State University of Science and Technology, Enugu, Nigeria
| | - Ben Chibuzo Amadi
- Pharmaceutical Technology and Industrial Pharmacy, University of Nigeria, Nsukka, Nigeria
| | - Daji Morumda
- Department of Microbiology, Federal University Wukari, Wukari, Taraba, Nigeria
| | - Yandev Doowuese
- Department of Microbiology, Federal University of Health Sciences, Otukpo, Nigeria
| | - Uchechi Justina Ihezuo
- Department of Microbiology, University of Nigeria, Nsukka, Nigeria
- Institute for Drug-Herbal Medicine-Excipient Research and Development, University of Nigeria, Nsukka, Nigeria
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6
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Mills EG, Martin MJ, Luo TL, Ong AC, Maybank R, Corey BW, Harless C, Preston LN, Rosado-Mendez JA, Preston SB, Kwak YI, Backlund MG, Bennett JW, Mc Gann PT, Lebreton F. A one-year genomic investigation of Escherichia coli epidemiology and nosocomial spread at a large US healthcare network. Genome Med 2022; 14:147. [PMID: 36585742 PMCID: PMC9801656 DOI: 10.1186/s13073-022-01150-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Extra-intestinal pathogenic Escherichia coli (ExPEC) are a leading cause of bloodstream and urinary tract infections worldwide. Over the last two decades, increased rates of antibiotic resistance in E. coli have been reported, further complicating treatment. Worryingly, specific lineages expressing extended-spectrum β-lactamases (ESBLs) and fluoroquinolone resistance have proliferated and are now considered a serious threat. Obtaining contemporary information on the epidemiology and prevalence of these circulating lineages is critical for containing their spread globally and within the clinic. METHODS Whole-genome sequencing (WGS), phylogenetic analysis, and antibiotic susceptibility testing were performed for a complete set of 2075 E. coli clinical isolates collected from 1776 patients at a large tertiary healthcare network in the USA between October 2019 and September 2020. RESULTS The isolates represented two main phylogenetic groups, B2 and D, with six lineages accounting for 53% of strains: ST-69, ST-73, ST-95, ST-131, ST-127, and ST-1193. Twenty-seven percent of the primary isolates were multidrug resistant (MDR) and 5% carried an ESBL gene. Importantly, 74% of the ESBL-E.coli were co-resistant to fluoroquinolones and mostly belonged to pandemic ST-131 and emerging ST-1193. SNP-based detection of possible outbreaks identified 95 potential transmission clusters totaling 258 isolates (12% of the whole population) from ≥ 2 patients. While the proportion of MDR isolates was enriched in the set of putative transmission isolates compared to sporadic infections (35 vs 27%, p = 0.007), a large fraction (61%) of the predicted outbreaks (including the largest cluster grouping isolates from 12 patients) were caused by the transmission of non-MDR clones. CONCLUSION By coupling in-depth genomic characterization with a complete sampling of clinical isolates for a full year, this study provides a rare and contemporary survey on the epidemiology and spread of E. coli in a large US healthcare network. While surveillance and infection control efforts often focus on ESBL and MDR lineages, our findings reveal that non-MDR isolates represent a large burden of infections, including those of predicted nosocomial origins. This increased awareness is key for implementing effective WGS-based surveillance as a routine technology for infection control.
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Affiliation(s)
- Emma G. Mills
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Melissa J. Martin
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Ting L. Luo
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Ana C. Ong
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Rosslyn Maybank
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Brendan W. Corey
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Casey Harless
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Lan N. Preston
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Joshua A. Rosado-Mendez
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Scott B. Preston
- grid.414467.40000 0001 0560 6544Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Yoon I. Kwak
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Michael G. Backlund
- grid.414467.40000 0001 0560 6544Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Jason W. Bennett
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Patrick T. Mc Gann
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Francois Lebreton
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
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Mu J, Lei L, Zheng Y, Li D, Li J, Fu Y, Wang G, Liu Y. Comparative study of subcutaneous, intramuscular, and oral administration of bovine pathogenic Escherichia coli bacterial ghost vaccine in mice. Front Immunol 2022; 13:1008131. [DOI: 10.3389/fimmu.2022.1008131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
Escherichia coli is one of the most common bacterial pathogens in cattle. Prophylactic vaccines are considered promising strategies with the potential to reduce the incidence of colibacillosis. Some studies suggested that bacterial ghosts may serve as a novel approach for preventing bacterial infections. However, the roles of administration route on vaccine immunogenicity and efficacy have not been investigated. In this study, the efficacy of vaccination via different immune routes in generating humoral and cellular immune response was compared through subcutaneous (SC), intramuscular (IM), and oral (O) administration in female BALB/c mice with bacterial ghosts prepared using wild type Escherichia coli isolates CE9, while phosphate buffer saline (PBS) and inactivated vaccines containing aluminum adjuvants (Killed) were used as control. Our results showed that the plasmid pBV220-E-aa-SNA containing E. coli was efficiently cleaved at 42°C with 94.8% positive ratio as assessed by colony counts. Transmission electron microscopy (TEM) confirmed bacteria retained intact surface structure while devoid of cytoplasmic component. We found that total IgG titers in killed, IM and SC groups showed significant increase on 7, 14, 21 and 28 days post-immunization. The IgA level of the IM group was higher than that of all other groups on the 28th day. Meanwhile, four experimental groups showed a significant difference in IgA levels compared with PBS control. In the IM group, an increase in the relative percentages of CD3+CD4+ T cells was accompanied by an increase in the relative percentages of splenic CD3+CD8+ T cells. In comparison with the inactivated vaccine, intramuscular CE9 ghosts immunization elicited higher levels of IL-1β, IL-2, IL-6 and IL-12. Subcutaneous and intramuscular immunizations were significantly associated with improved survival in comparison with oral route, traditional vaccine and the control. Pathologic assessment revealed that less severe tissue damage and inflammation were found in lung, kidney, and intestine of IM group compared with other groups. The results above demonstrate that immunization of Escherichia coli CE9 ghosts via intramuscular injection elicits a more robust antigen-specific immune response in mice to prevent the Escherichia coli infection.
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Matsumoto T, Mikamo H, Ohge H, Yanagihara K, Weerdenburg E, Go O, Spiessens B, van Geet G, van den Hoven T, Momose A, Hagiwara Y, Nakayama Y, Poolman J, Geurtsen J, Kaku M. Distribution of extraintestinal pathogenic Escherichia coli O-serotypes and antibiotic resistance in blood isolates collected from patients in a surveillance study in Japan. J Infect Chemother 2022; 28:1445-1451. [PMID: 35843539 DOI: 10.1016/j.jiac.2022.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/23/2022] [Accepted: 07/03/2022] [Indexed: 10/31/2022]
Abstract
INTRODUCTION Invasive extraintestinal pathogenic Escherichia coli (ExPEC) disease (IED), characterised by sepsis and bacteraemia, is a major global healthcare concern worsened by emerging multidrug resistant (MDR) strains. The development of multivalent prophylactic vaccines targeting E. coli strains of IED-associated O-serotypes could address this. A better understanding of O-serotype distribution is required for this purpose. Here, we characterised O-serotype prevalence and drug resistance among ExPEC bacteraemia isolates in Japan. METHODS E. coli blood isolates from patients aged ≥60 years with bacteraemia were obtained from a retrospective surveillance study in Japan (2015-2017). O-serotyping was performed by agglutination; for isolates non-typeable by agglutination, O-genotyping was performed. Antimicrobial susceptibility was evaluated by broth microdilution using a 21-antibiotic panel. The frequency of drug resistant (DR) isolates was evaluated by antimicrobial susceptibility testing. RESULTS Of 401 ExPEC bacteraemia isolates evaluated, the most prevalent O-serotype (≥1%) was O25 (28.7% [n = 115]), followed by O1 (14.2% [n = 57]), O2 (8.5% n = 34]), O6 (5.5% [n = 22]), O75, O18, O13, O16, O15, O4, O46/O134, O86, O8 and O83 (each <5% prevalence). These 14 O-serotypes accounted for 81.5% of isolates collected. In total, 19% (n = 77) of isolates were DR ≥ 3, of which 59.7% were O25. Fluoroquinolone-resistance among all and O25 isolates was most prevalent (35.7% and 84.3%, respectively). Almost all (98%) isolates identified as O25 were of subtype O25B. CONCLUSIONS E. coli serotype O25B showed the highest prevalence and highest multidrug resistance among ExPEC bacteraemia isolates from patients ≥60 years in Japan. Our data may inform development of multivalent glycoconjugate vaccines to prevent IED.
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Affiliation(s)
- Tetsuya Matsumoto
- Department of Infectious Diseases, International University of Health and Welfare, Chiba, Japan; Department of Microbiology, Tokyo Medical University, Tokyo, Japan.
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Aichi, Japan.
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan.
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
| | | | - Oscar Go
- Janssen Research & Development, Raritan, NJ, USA.
| | | | - Gunter van Geet
- Janssen Integrated Data Analytics & Reporting, Beerse, Belgium.
| | | | | | | | | | - Jan Poolman
- Janssen Vaccines & Prevention, Leiden, the Netherlands.
| | | | - Mitsuo Kaku
- Division of Infectious Diseases and Infection Control, Tohoku Medical and Pharmaceutical University, Miyagi, Japan.
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9
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Weerdenburg E, Davies T, Morrow B, Zomer AL, Hermans P, Go O, Spiessens B, van den Hoven T, van Geet G, Aitabi M, DebRoy C, Dudley EG, Bonten M, Poolman J, Geurtsen J. Global Distribution of O Serotypes and Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Collected From the Blood of Patients With Bacteremia Across Multiple Surveillance Studies. Clin Infect Dis 2022; 76:e1236-e1243. [PMID: 35684979 PMCID: PMC9907479 DOI: 10.1093/cid/ciac421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/03/2022] [Accepted: 05/20/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of bacteremia worldwide, with older populations having increased risk of invasive bacterial disease. Increasing resistance to first-line antibiotics and emergence of multidrug-resistant (MDR) strains represent major treatment challenges. ExPEC O serotypes are key targets for potential multivalent conjugate vaccine development. Therefore, we evaluated the O serotype distribution and antibiotic resistance profiles of ExPEC strains causing bloodstream infections across 4 regions. METHODS Blood culture isolates from patients aged ≥60 years collected during 5 retrospective E. coli surveillance studies in Europe, North America, Asia-Pacific, and South America (2011-2017) were analyzed. Isolates were O serotyped by agglutination; O genotyping was performed for nontypeable isolates. Antimicrobial susceptibility testing was also conducted. RESULTS Among 3217 ExPEC blood culture isolates, the most ubiquitous O serotype was O25 (n = 737 [22.9%]), followed by O2, O6, O1, O75, O15, O8, O16, O4, O18, O77 group, O153, O9, O101/O162, O86, and O13 (prevalence of ≥1%). The prevalence of these O serotypes was generally consistent across regions, apart from South America; together, these 16 O serotypes represented 77.6% of all ExPEC bacteremia isolates analyzed. The overall MDR frequency was 10.7%, with limited variation between regions. Within the MDR subset (n = 345), O25 showed a dominant prevalence of 63.2% (n = 218). CONCLUSIONS Predominant O serotypes among ExPEC bacteremia isolates are widespread across different regions. O25 was the most prevalent O serotype overall and particularly dominant among MDR isolates. These findings may inform the design of multivalent conjugate vaccines that can target the predominant O serotypes associated with invasive ExPEC disease in older adults.
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Affiliation(s)
| | - Todd Davies
- Janssen Research & Development, Raritan, New Jersey, USA
| | - Brian Morrow
- Janssen Research & Development, Raritan, New Jersey, USA
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Peter Hermans
- Present affiliation: Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Oscar Go
- Janssen Research & Development, Raritan, New Jersey, USA
| | | | | | - Gunter van Geet
- Janssen Integrated Data Analytics & Reporting, Beerse, Belgium
| | - Moussa Aitabi
- Janssen Integrated Data Analytics & Reporting, Beerse, Belgium
| | - Chitrita DebRoy
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Edward G Dudley
- Department of Food Science, E. coli Reference Center, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Marc Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jan Poolman
- Janssen Vaccines & Prevention, Leiden, the Netherlands
| | - Jeroen Geurtsen
- Correspondence: Jeroen Geurtsen; Janssen Vaccines & Prevention, PO Box 2048, 2301 CA Leiden, the Netherlands ()
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10
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Lewis JM, Mphasa M, Banda R, Beale MA, Mallewa J, Heinz E, Thomson NR, Feasey NA. Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi. Microb Genom 2022; 8:000778. [PMID: 35302438 PMCID: PMC9176273 DOI: 10.1099/mgen.0.000778] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022] Open
Abstract
Members of the Klebsiella pneumoniae species complex, particularly K. pneumoniae subsp. pneumoniae are antimicrobial resistance (AMR) associated pathogens of global importance, and polyvalent vaccines targeting Klebsiella O-antigens are in development. Whole-genome sequencing has provided insight into O-antigen distribution in the K. pneumoniae species complex, as well as population structure and virulence determinants, but genomes from sub-Saharan Africa are underrepresented in global sequencing efforts. We therefore carried out a genomic analysis of extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae species complex isolates colonizing adults in Blantyre, Malawi. We placed these isolates in a global genomic context, and compared colonizing to invasive isolates from the main public hospital in Blantyre. In total, 203 isolates from stool and rectal swabs from adults were whole-genome sequenced and compared to a publicly available multicounty collection and previously sequenced Malawian and Kenyan isolates from blood or sterile sites. We inferred phylogenetic relationships and analysed the diversity of genetic loci linked to AMR, virulence, capsule and LPS O-antigen (O-types). We find that the diversity of Malawian K. pneumoniae subsp. pneumoniae isolates represents the species' population structure, but shows distinct local signatures concerning clonal expansions. Siderophore and hypermucoidy genes were more frequent in invasive versus colonizing isolates (present in 13 % vs 1 %) but still generally lacking in most invasive isolates. O-antigen population structure and distribution was similar in invasive and colonizing isolates, with O4 more common (14%) than in previously published studies (2-5 %). We conclude that host factors, pathogen opportunity or alternate virulence loci not linked to invasive disease elsewhere are likely to be the major determinants of invasive disease in Malawi. Distinct ST and O-type distributions in Malawi highlight the need to sample locations where the burden of invasive Klebsiella disease is greatest to robustly define secular trends in Klebsiella diversity to assist in the development of a useful vaccine. Colonizing and invasive isolates in Blantyre are similar, hence O-typing of colonizing Klebsiella isolates may be a rapid and cost-effective approach to describe global diversity and guide vaccine development.
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Affiliation(s)
- Joseph M. Lewis
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
- University of Liverpool, Liverpool, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Madalitso Mphasa
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Rachel Banda
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - Jane Mallewa
- Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Eva Heinz
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Hinxton, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas A. Feasey
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
- Kamuzu University of Health Sciences, Blantyre, Malawi
- London School of Hygiene and Tropical Medicine, London, UK
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11
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Raffelsberger N, Hetland MAK, Svendsen K, Småbrekke L, Löhr IH, Andreassen LLE, Brisse S, Holt KE, Sundsfjord A, Samuelsen Ø, Gravningen K. Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity. Gut Microbes 2022; 13:1939599. [PMID: 34182896 PMCID: PMC8244762 DOI: 10.1080/19490976.2021.1939599] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Antibiotic resistant Klebsiella pneumoniae is a leading public health threat and gastrointestinal carriage is an established risk factor for subsequent infections during hospitalization. Our study contributes new knowledge of risk factors for gastrointestinal carriage and the genomic population structure of K. pneumoniae colonizing humans in a representative sample of a general population in a community setting. Altogether, 2,975 participants (54% women) >40 y in the population-based Tromsø Study: Tromsø7, Norway (2015-2016) were included. Fecal samples were screened for K. pneumoniae, which were characterized using whole-genome sequencing. Risk factors for carriage were analyzed using multivariable logistic regression on data from questionnaires and the Norwegian Prescription Database. Prevalence of K. pneumoniae gastrointestinal carriage was 16.3% (95% CI 15.0-17.7, no gender difference). Risk factors associated with carriage included age ≥60 y, travel to Greece or Asia past 12 months (adjusted odds ratio 1.49, 95% CI 1.11-2.00), Crohn's disease/ulcerative colitis (2.26, 1.20-4.27), use of proton pump inhibitors (1.62, 1.18-2.22) and non-steroidal anti-inflammatory drugs past 6 months (1.38, 1.04-1.84), and antibiotic use the last month (1.73, 1.05-2.86). Prevalence was higher among those having used combinations of drug classes and decreased over time with respect to preceding antibiotic use. The K. pneumoniae population was diverse with 300 sequence types among 484 isolates distributed across four phylogroups. Only 5.2% of isolates harbored acquired resistance and 11.6% had virulence factors. Identification of risk factors for gastrointestinal carriage allows for identification of individuals that may have higher risk of extraintestinal infection during hospitalization. The findings that specific diseases and drugs used were associated with carriage show an impact of these possibly through modulating the human gut microbiota promoting colonization. The diverse population structure of carriage isolates reflects the ecologically adaptive capacity of the bacterium and challenges for vaccine prospects and the identification of reservoirs as a potential source for human colonization.
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Affiliation(s)
- Niclas Raffelsberger
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway,Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,CONTACT Niclas Raffelsberger Department of Microbiology and Infection Control, University Hospital of North Norway, TromsøN-9038, Norway
| | - Marit Andrea Klokkhammer Hetland
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway,Department of Biological Sciences, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
| | - Kristian Svendsen
- Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Lars Småbrekke
- Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Iren Høyland Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | | | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia,Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Arnfinn Sundsfjord
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Kirsten Gravningen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway,Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
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12
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Lipworth S, Vihta KD, Davies T, Wright S, Tabirao M, Chau K, Vaughan A, Kavanagh J, Barker L, George S, Segal S, Paulus S, Barrett L, Oakley S, Jeffery K, Butcher L, Peto T, Crook D, Walker S, Kadambari S, Stoesser N. Molecular epidemiology and antimicrobial resistance phenotype of paediatric bloodstream infections caused by Gram-negative bacteria. COMMUNICATIONS MEDICINE 2022; 2:101. [PMID: 35968045 PMCID: PMC9372158 DOI: 10.1038/s43856-022-00161-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
Background Gram-negative organisms are common causes of bloodstream infection (BSI) during the neonatal period and early childhood. Whilst several large studies have characterised these isolates in adults, equivalent data (particularly incorporating whole genome sequencing) is lacking in the paediatric population. Methods We perform an epidemiological and sequencing based analysis of Gram-negative bloodstream infections (327 isolates (296 successfully sequenced) from 287 patients) in children <18 years old between 2008 and 2018 in Oxfordshire, UK. Results Here we show that the burden of infection lies predominantly in neonates and that most infections are caused by Escherichia coli, Klebsiella spp. and Enterobacter hormaechei. There is no evidence in our setting that the proportion of antimicrobial resistant isolates is increasing in the paediatric population although we identify some evidence of sub-breakpoint increases in gentamicin resistance. The population structure of E. coli BSI isolates in neonates and children mirrors that in adults with a predominance of STs 131/95/73/69 and the same proportions of O-antigen serotypes. In most cases in our setting there is no evidence of transmission/point-source acquisition and we demonstrate the utility of whole genome sequencing to refute a previously suspected outbreak. Conclusions Our findings support continued use of current empirical treatment guidelines and suggest that O-antigen targeted vaccines may have a role in reducing the incidence of neonatal sepsis.
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Affiliation(s)
- Sam Lipworth
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Karina-Doris Vihta
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.4991.50000 0004 1936 8948Department of Engineering, University of Oxford, Oxford, UK
| | - Tim Davies
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Wright
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Merline Tabirao
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Kevin Chau
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alison Vaughan
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Kavanagh
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leanne Barker
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie George
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Shelley Segal
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephane Paulus
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lucinda Barrett
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Oakley
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Katie Jeffery
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lisa Butcher
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tim Peto
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- grid.4991.50000 0004 1936 8948NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom
- grid.454382.c0000 0004 7871 7212NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Derrick Crook
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- grid.4991.50000 0004 1936 8948NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom
- grid.454382.c0000 0004 7871 7212NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Sarah Walker
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.4991.50000 0004 1936 8948NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom
- grid.454382.c0000 0004 7871 7212NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Seilesh Kadambari
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- grid.4991.50000 0004 1936 8948Department of Paediatrics, University of Oxford, Oxford, UK
| | - Nicole Stoesser
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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13
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Lipworth S, Vihta KD, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto TEA, Crook DW, Walker AS, Stoesser N. Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK. Genome Med 2021; 13:144. [PMID: 34479643 PMCID: PMC8414751 DOI: 10.1186/s13073-021-00947-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022] Open
Abstract
Background The incidence of Gram-negative bloodstream infections (BSIs), predominantly caused by Escherichia coli and Klebsiella species, continues to increase; however, the causes of this are unclear and effective interventions are therefore hard to design. Methods In this study, we sequenced 3468 unselected isolates over a decade in Oxfordshire (UK) and linked this data to routinely collected electronic healthcare records and mandatory surveillance reports. We annotated genomes for clinically relevant genes, contrasting the distribution of these within and between species, and compared incidence trends over time using stacked negative binomial regression. Results We demonstrate that the observed increases in E. coli incidence were not driven by the success of one or more sequence types (STs); instead, four STs continue to dominate a stable population structure, with no evidence of adaptation to hospital/community settings. Conversely in Klebsiella spp., most infections are caused by sporadic STs with the exception of a local drug-resistant outbreak strain (ST490). Virulence elements are highly structured by ST in E. coli but not Klebsiella spp. where they occur in a diverse spectrum of STs and equally across healthcare and community settings. Most clinically hypervirulent (i.e. community-onset) Klebsiella BSIs have no known acquired virulence loci. Finally, we demonstrate a diverse but largely genus-restricted mobilome with close associations between antimicrobial resistance (AMR) genes and insertion sequences but not typically specific plasmid replicon types, consistent with the dissemination of AMR genes being highly contingent on smaller mobile genetic elements (MGEs). Conclusions Our large genomic study highlights distinct differences in the molecular epidemiology of E. coli and Klebsiella BSIs and suggests that no single specific pathogen genetic factors (e.g. AMR/virulence genes/sequence type) are likely contributing to the increasing incidence of BSI overall, that association with AMR genes in E. coli is a contributor to the increasing number of E. coli BSIs, and that more attention should be given to AMR gene associations with non-plasmid MGEs to try and understand horizontal gene transfer networks. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00947-2.
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Affiliation(s)
- Samuel Lipworth
- Nuffield Department of Medicine, University of Oxford, Oxford, UK. .,Oxford University Hospitals NHS Foundation Trust, Oxford, UK. .,John Radcliffe Hospital, Oxford, OX3 9DU, UK.
| | | | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy Davies
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alison Vaughan
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Marcus Morgan
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Susan Hopkins
- National Infection Service, Public Health England, Colindale, London, UK
| | - Timothy E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,John Radcliffe Hospital, Oxford, OX3 9DU, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK.,NIHR Biomedical Research Centre, Oxford, UK
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK.,NIHR Biomedical Research Centre, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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14
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Royer G, Clermont O, Condamine B, Mercier-Darty M, Laouénan C, Lefort A, Denamur E, de Lastours V. O-antigen targeted vaccines against E. coli may be useful in reducing morbidity, mortality and antimicrobial resistance. Clin Infect Dis 2021; 74:364-366. [PMID: 34000003 DOI: 10.1093/cid/ciab458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Guilhem Royer
- Université de Paris, IAME, UMR1137, INSERM, Paris, France.,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France.,Service de Microbiologie, Hôpital Henri Mondor, AP-HP, Créteil, France
| | | | | | - Mélanie Mercier-Darty
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France.,Service de Microbiologie, Hôpital Henri Mondor, AP-HP, Créteil, France
| | - Cédric Laouénan
- Université de Paris, IAME, UMR1137, INSERM, Paris, France.,Department d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, Paris, France
| | - Agnès Lefort
- Université de Paris, IAME, UMR1137, INSERM, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, Clichy, France
| | - Erick Denamur
- Université de Paris, IAME, UMR1137, INSERM, Paris, France.,Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Victoire de Lastours
- Université de Paris, IAME, UMR1137, INSERM, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, Clichy, France
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15
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Royer G, Darty MM, Clermont O, Condamine B, Laouenan C, Decousser JW, Vallenet D, Lefort A, de Lastours V, Denamur E. Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period. Genome Med 2021; 13:77. [PMID: 33952335 PMCID: PMC8097792 DOI: 10.1186/s13073-021-00892-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/22/2021] [Indexed: 11/12/2022] Open
Abstract
Background Escherichia coli is the leading cause of bloodstream infections, associated with a significant mortality. Recent genomic analyses revealed that few clonal lineages are involved in bloodstream infections and captured the emergence of some of them. However, data on within sequence type (ST) population genetic structure evolution are rare. Methods We compared whole genome sequences of 912 E. coli isolates responsible for bloodstream infections from two multicenter clinical trials that were conducted in the Paris area, France, 12 years apart, in teaching hospitals belonging to the same institution (“Assistance Publique-Hôpitaux de Paris”). We analyzed the strains at different levels of granularity, i.e., the phylogroup, the ST complex (STc), and the within STc clone taking into consideration the evolutionary history, the resistance, and virulence gene content as well as the antigenic diversity of the strains. Results We found a mix of stability and changes overtime, depending on the level of comparison. Overall, we observed an increase in antibiotic resistance associated to a restricted number of genetic determinants and in strain plasmidic content, whereas phylogroup distribution and virulence gene content remained constant. Focusing on STcs highlighted the pauci-clonality of the populations, with only 11 STcs responsible for more than 73% of the cases, dominated by five STcs (STc73, STc131, STc95, STc69, STc10). However, some STcs underwent dramatic variations, such as the global pandemic STc131, which replaced the previously predominant STc95. Moreover, within STc131, 95 and 69 genomic diversity analysis revealed a highly dynamic pattern, with reshuffling of the population linked to clonal replacement sometimes coupled with independent acquisitions of virulence factors such as the pap gene cluster bearing a papGII allele located on various pathogenicity islands. Additionally, STc10 exhibited huge antigenic diversity evidenced by numerous O:H serotype/fimH allele combinations, whichever the year of isolation. Conclusions Altogether, these data suggest that the bloodstream niche is occupied by a wide but specific phylogenetic diversity and that highly specialized extra-intestinal clones undergo frequent turnover at the within ST level. Additional worldwide epidemiological studies overtime are needed in different geographical and ecological contexts to assess how generalizable these data are. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00892-0.
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Affiliation(s)
- Guilhem Royer
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France.,Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - Mélanie Mercier Darty
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - Olivier Clermont
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France
| | | | - Cédric Laouenan
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Département d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Jean-Winoc Decousser
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - David Vallenet
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France
| | - Agnès Lefort
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, F-92100, Clichy, France
| | - Victoire de Lastours
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, F-92100, Clichy, France
| | - Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France. .,Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, F-75018, Paris, France.
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