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Oswin HP, Blake E, Haddrell AE, Finn A, Sriskandan S, Reid JP, Halliday A, Goenka A. An assessment of the airborne longevity of group A Streptococcus. Microbiology (Reading) 2024; 170:001421. [PMID: 38180461 PMCID: PMC10866022 DOI: 10.1099/mic.0.001421] [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] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/08/2023] [Indexed: 01/06/2024]
Abstract
Group A streptococcus (GAS) infections result in more than 500 000 deaths annually. Despite mounting evidence for airborne transmission of GAS, little is known about its stability in aerosol. Measurements of GAS airborne stability were carried out using the Controlled Electrodynamic Levitation and Extraction of Bioaerosols onto a Substrate (CELEBS) instrument. CELEBS measurements with two different isolates of GAS suggest that it is aerostable, with approximately 70 % of bacteria remaining viable after 20 min of levitation at 50 % relative humidity (RH), with lower survival as RH was reduced. GAS airborne viability loss was driven primarily by desiccation and efflorescence (i.e. salt crystallization), with high pH also potentially playing a role, given reduced survival in bicarbonate containing droplet compositions. At low enough RH for efflorescence to occur, a greater proportion of organic components in the droplet appeared to protect the bacteria from efflorescence. These first insights into the aerosol stability of GAS indicate that airborne transmission of these respiratory tract bacteria may occur, and that both the composition of the droplet containing the bacteria, and the RH of the air affect the duration of bacterial survival in this environment. Future studies will explore a broader range of droplet and air compositions and include a larger selection of GAS strains.
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Affiliation(s)
- Henry P. Oswin
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, UK
| | - Evie Blake
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Allen E. Haddrell
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, UK
| | - Adam Finn
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Paediatric Immunology and Infectious Diseases, Bristol Royal Hospital for Children, Bristol, UK
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Jonathan P. Reid
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, UK
| | - Alice Halliday
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Anu Goenka
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Paediatric Immunology and Infectious Diseases, Bristol Royal Hospital for Children, Bristol, UK
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2
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Zhi X, Vieira A, Huse KK, Martel PJ, Lobkowicz L, Li HK, Croucher N, Andrew I, Game L, Sriskandan S. Characterization of the RofA regulon in the pandemic M1 global and emergent M1 UK lineages of Streptococcus pyogenes. Microb Genom 2023; 9:001159. [PMID: 38117674 PMCID: PMC10763501 DOI: 10.1099/mgen.0.001159] [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: 08/07/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023] Open
Abstract
The standalone regulator RofA is a positive regulator of the pilus locus in Streptococcus pyogenes. Found in only certain emm genotypes, RofA has been reported to regulate other virulence factors, although its role in the globally dominant emm1 S. pyogenes is unclear. Given the recent emergence of a new emm1 (M1UK) toxigenic lineage that is distinguished by three non-synonymous SNPs in rofA, we characterized the rofA regulon in six emm1 strains that are representative of the two contemporary major emm1 lineages (M1global and M1UK) using RNAseq analysis, and then determined the specific role of the M1UK-specific rofA SNPs. Deletion of rofA in three M1global strains led to altered expression of 14 genes, including six non-pilus locus genes. In M1UK strains, deletion of rofA led to altered expression of 16 genes, including nine genes that were unique to M1UK. Only the pilus locus genes were common to the RofA regulons of both lineages, while transcriptomic changes varied between strains even within the same lineage. Although introduction of the three SNPs into rofA did not impact gene expression in an M1global strain, reversal of three SNPs in an M1UK strain led to an unexpected number of transcriptomic changes that in part recapitulated transcriptomic changes seen when deleting RofA in the same strain. Computational analysis predicted that interactions with a key histidine residue in the PRD domain of RofA would differ between M1UK and M1global. RofA is a positive regulator of the pilus locus in all emm1 strains but effects on other genes are strain- and lineage-specific, with no clear, common DNA binding motif. The SNPs in rofA that characterize M1UK may impact regulation of RofA; whether they alter phosphorylation of the RofA PRD domain requires further investigation.
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Affiliation(s)
- Xiangyun Zhi
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Ana Vieira
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
| | - Kristin K. Huse
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | | | - Ludmila Lobkowicz
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nick Croucher
- MRC Centre for Global Infectious Disease Analysis, Sir Michael Uren Hub, White City Campus, Imperial College London, London,, UK
| | - Ivan Andrew
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Laurence Game
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
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3
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Pearson M, Haslam C, Fosberry A, Jones EJ, Reglinski M, Reeves L, Edwards RJ, Lawrenson RA, Brown JC, Mossakowska D, Pease JE, Sriskandan S. Structure-activity studies of Streptococcus pyogenes enzyme SpyCEP reveal high affinity for CXCL8 in the SpyCEP C-terminal. Sci Rep 2023; 13:19052. [PMID: 37923786 PMCID: PMC10624844 DOI: 10.1038/s41598-023-46036-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
The Streptococcus pyogenes cell envelope protease (SpyCEP) is vital to streptococcal pathogenesis and disease progression. Despite its strong association with invasive disease, little is known about enzymatic function beyond the ELR+ CXC chemokine substrate range. As a serine protease, SpyCEP has a catalytic triad consisting of aspartate (D151), histidine (H279), and serine (S617) residues which are all thought to be mandatory for full activity. We utilised a range of SpyCEP constructs to investigate the protein domains and catalytic residues necessary for enzyme function. We designed a high-throughput mass spectrometry assay to measure CXCL8 cleavage and applied this for the first time to study the enzyme kinetics of SpyCEP. Results revealed a remarkably low Michaelis-Menton constant (KM) of 82 nM and a turnover of 1.65 molecules per second. We found that an N-terminally-truncated SpyCEP C-terminal construct containing just the catalytic dyad of H279 and S617 was capable of cleaving CXCL8 with a similar KM of 55 nM, albeit with a reduced substrate turnover of 2.7 molecules per hour, representing a 2200-fold reduction in activity. We conclude that the SpyCEP C-terminus plays a key role in high affinity substrate recognition and binding, but that the N-terminus is required for full catalytic activity.
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Affiliation(s)
- Max Pearson
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, SW7 2AZ, UK
| | - Carl Haslam
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Andrew Fosberry
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Emma J Jones
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Mark Reglinski
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK
| | - Lucy Reeves
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK
| | - Robert J Edwards
- Department of Medicine, Imperial College London, London, W12 0NN, UK
| | | | - Jonathan C Brown
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK
| | - Danuta Mossakowska
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
| | - James Edward Pease
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK.
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK.
- Centre for Bacterial Resistance Biology, Imperial College London, London, SW7 2AZ, UK.
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4
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McKenna S, Aylward F, Miliara X, Lau RJ, Huemer CB, Giblin SP, Huse KK, Liang M, Reeves L, Pearson M, Xu Y, Rouse SL, Pease JE, Sriskandan S, Kagawa TF, Cooney J, Matthews S. The protease associated (PA) domain in ScpA from Streptococcus pyogenes plays a role in substrate recruitment. Biochim Biophys Acta Proteins Proteom 2023; 1871:140946. [PMID: 37562488 DOI: 10.1016/j.bbapap.2023.140946] [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] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/28/2023] [Accepted: 08/06/2023] [Indexed: 08/12/2023]
Abstract
Annually, over 18 million disease cases and half a million deaths worldwide are estimated to be caused by Group A Streptococcus. ScpA (or C5a peptidase) is a well characterised member of the cell enveleope protease family, which possess a S8 subtilisin-like catalytic domain and a shared multi-domain architecture. ScpA cleaves complement factors C5a and C3a, impairing the function of these critical anaphylatoxins and disrupts complement-mediated innate immunity. Although the high resolution structure of ScpA is known, the details of how it recognises its substrate are only just emerging. Previous studies have identified a distant exosite on the 2nd fibronectin domain that plays an important role in recruitment via an interaction with the substrate core. Here, using a combination of solution NMR spectroscopy, mutagenesis with functional assays and computational approaches we identify a second exosite within the protease-associated (PA) domain. We propose a model in which the PA domain assists optimal delivery of the substrate's C terminus to the active site for cleavage.
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Affiliation(s)
- Sophie McKenna
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Frances Aylward
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Xeni Miliara
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Rikin J Lau
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Camilla Berg Huemer
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Sean P Giblin
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Kristin K Huse
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Mingyang Liang
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Lucy Reeves
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Max Pearson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - James E Pease
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Todd F Kagawa
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Bernal Institute, University of Limerick, Limerick, Ireland
| | - Jakki Cooney
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Bernal Institute, University of Limerick, Limerick, Ireland
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.
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5
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Lamagni T, Guy RL, Sriskandan S, Decraene V, Brown CS. Improving maternal outcomes through early recognition, rapid notification, and investigation of invasive GAS infection. Lancet Microbe 2023; 4:e766. [PMID: 37392752 DOI: 10.1016/s2666-5247(23)00186-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/13/2023] [Indexed: 07/03/2023]
Affiliation(s)
- Theresa Lamagni
- Healthcare-Associated Infection & Antimicrobial Resistance Division, UK Health Security Agency, London, UK.
| | - Rebecca L Guy
- Healthcare-Associated Infection & Antimicrobial Resistance Division, UK Health Security Agency, London, UK
| | - Shiranee Sriskandan
- Faculty of Medicine, Department of Infectious Disease, Imperial College, London, UK; National Institute for Health and Care Research, Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London
| | | | - Colin S Brown
- Healthcare-Associated Infection & Antimicrobial Resistance Division, UK Health Security Agency, London, UK; National Institute for Health and Care Research, Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London
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6
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Durkin SM, da Silva AL, Davies NWS, Sriskandan S. Dengue Encephalopathy or Dengue Encephalitis? You Decide. Open Forum Infect Dis 2023; 10:ofad490. [PMID: 37869404 PMCID: PMC10586725 DOI: 10.1093/ofid/ofad490] [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: 07/03/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
Awareness of neurological sequelae of dengue fever is increasing. However, as this case illustrates, there is a diagnostic conundrum in determining whether certain features are in keeping with dengue encephalopathy or dengue encephalitis. Further consensus is required.
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Affiliation(s)
- Simon M Durkin
- Department of Clinical Infectious Diseases, Hammersmith Hospital, Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Andrea L da Silva
- Department of Radiology, Charing Cross Hospital, Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Nicholas W S Davies
- Department of Neurology, Chelsea and Westminster Hospital, Chelsea and Westminster Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Shiranee Sriskandan
- Department of Clinical Infectious Diseases, Hammersmith Hospital, Imperial College Healthcare National Health Service Trust, London, United Kingdom
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom
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7
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Asturias EJ, Excler JL, Ackland J, Cavaleri M, Fulurija A, Long R, McCulloch M, Sriskandan S, Sun W, Zühlke L, Kim JH, Dale JB, Steer AC. Safety of Streptococcus pyogenes Vaccines: Anticipating and Overcoming Challenges for Clinical Trials and Post-Marketing Monitoring. Clin Infect Dis 2023; 77:917-924. [PMID: 37232372 PMCID: PMC10506775 DOI: 10.1093/cid/ciad311] [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: 02/26/2023] [Revised: 05/09/2023] [Accepted: 05/23/2023] [Indexed: 05/27/2023] Open
Abstract
Streptococcus pyogenes (Strep A) infections result in a vastly underestimated burden of acute and chronic disease globally. The Strep A Vaccine Global Consortium's (SAVAC's) mission is to accelerate the development of safe, effective, and affordable S. pyogenes vaccines. The safety of vaccine recipients is of paramount importance. A single S. pyogenes vaccine clinical trial conducted in the 1960s raised important safety concerns. A SAVAC Safety Working Group was established to review the safety assessment methodology and results of more recent early-phase clinical trials and to consider future challenges for vaccine safety assessments across all phases of vaccine development. No clinical or biological safety signals were detected in any of these early-phase trials in the modern era. Improvements in vaccine safety assessments need further consideration, particularly for pediatric clinical trials, large-scale efficacy trials, and preparation for post-marketing pharmacovigilance.
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Affiliation(s)
- Edwin J Asturias
- Colorado School of Public Health, University of Colorado, Aurora Colorado, USA
- Children’s Hospital, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jean-Louis Excler
- Director General’s Office, International Vaccine Institute, Seoul, Republic of Korea
| | | | - Marco Cavaleri
- Anti-Infectives and Vaccines, European Medicines Agency, Amsterdam, The Netherlands
| | - Alma Fulurija
- Group A Streptococcal and Rheumatic Heart Disease Team, Telethon Kids Institute, Perth, Australia
| | - Raj Long
- Safety and pharmacovigilance, Bill & Melinda Gates Foundation, London, United Kingdom
| | - Mignon McCulloch
- Department of Paediatrics, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | | | | | - Liesl Zühlke
- South African Medical Research Council, Parowvallei, Cape Town, South Africa
- Division of Paediatric Cardiology, Department of Paediatrics, Institute of Child Health, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jerome H Kim
- Director General’s Office, International Vaccine Institute, Seoul, Republic of Korea
- College of Natural Sciences, Seoul National University, Seoul, Republic of Korea
| | - James B Dale
- College of Medicine, University of Tennessee Health Science Center, Memphis Tennessee, USA
| | - Andrew C Steer
- Infection and Immunity Theme, Tropical Diseases Research Group, Murdoch Children's Research Institute, Parkville Victoria, Australia
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8
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Wan Y, Sabnis A, Mumin Z, Potterill I, Jauneikaite E, Brown CS, Ellington MJ, Edwards A, Sriskandan S. IS 1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli. Microb Genom 2023; 9:001102. [PMID: 37672334 PMCID: PMC10569738 DOI: 10.1099/mgen.0.001102] [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: 04/04/2023] [Accepted: 08/16/2023] [Indexed: 09/07/2023] Open
Abstract
Nitrofurantoin is a broad-spectrum first-line antimicrobial used for managing uncomplicated urinary tract infection (UTI). Loss-of-function mutations in chromosomal genes nfsA, nfsB and ribE of Escherichia coli are known to reduce nitrofurantoin susceptibility. Here, we report the discovery of nitrofurantoin heteroresistance in E. coli clinical isolates and a novel genetic mechanism associated with this phenomenon. Subpopulations with lower nitrofurantoin susceptibility than major populations (hereafter, nitrofurantoin-resistant subpopulations) in two E. coli blood isolates (previously whole-genome sequenced) were identified using population analysis profiling. Each isolate was known to have a loss-of-function mutation in nfsA. From each isolate, four nitrofurantoin-resistant isolates were derived at a nitrofurantoin concentration of 32 mg l-1, and a comparator isolate was obtained without any nitrofurantoin exposure. Genomes of derived isolates were sequenced on Illumina and Nanopore MinION systems. Genetic variation between isolates was determined based on genome assemblies and read mapping. Nitrofurantoin minimum inhibitory concentrations (MICs) of both blood isolates were 64 mg l-1, with MICs of major nitrofurantoin-susceptible populations varying from 4 to 8 mg l-1. Two to 99 c.f.u. per million demonstrated growth at the nitrofurantoin concentration of 32 mg l-1, which is distinct from that of a homogeneously susceptible or resistant isolate. Derived nitrofurantoin-resistant isolates had 11-66 kb deletions in chromosomal regions harbouring nfsB, and all deletions were immediately adjacent to IS1-family insertion sequences. Our findings demonstrate that the IS1-associated large-scale genetic deletion is a hitherto unrecognized mechanism of nitrofurantoin heteroresistance and could compromise UTI management. Further, frequencies of resistant subpopulations from nitrofurantoin-heteroresistant isolates may challenge conventional nitrofurantoin susceptibility testing in clinical settings.
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Affiliation(s)
- Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Akshay Sabnis
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Zaynab Mumin
- Reference Services Division, National Infection Service, UK Health Security Agency, London, UK
| | - Isabelle Potterill
- Reference Services Division, National Infection Service, UK Health Security Agency, London, UK
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Colin S. Brown
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Matthew J. Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Andrew Edwards
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
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9
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Zhi X, Li HK, Li H, Loboda Z, Charles S, Vieira A, Huse K, Jauneikaite E, Reeves L, Mok KY, Coelho J, Lamagni T, Sriskandan S. Emerging Invasive Group A Streptococcus M1 UK Lineage Detected by Allele-Specific PCR, England, 2020 1. Emerg Infect Dis 2023; 29:1007-1010. [PMID: 37019153 PMCID: PMC10124639 DOI: 10.3201/eid2905.221887] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Increasing reports of invasive Streptococcus pyogenes infections mandate surveillance for toxigenic lineage M1UK. An allele-specific PCR was developed to distinguish M1UK from other emm1 strains. The M1UK lineage represented 91% of invasive emm1 isolates in England in 2020. Allele-specific PCR will permit surveillance for M1UK without need for genome sequencing.
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10
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McGuire E, Li A, Collin SM, Decraene V, Cook M, Padfield S, Sriskandan S, Van Beneden C, Lamagni T, Brown CS. Time to negative throat culture following initiation of antibiotics for pharyngeal group A Streptococcus: a systematic review and meta-analysis up to October 2021 to inform public health control measures. Euro Surveill 2023; 28. [PMID: 37052678 PMCID: PMC10103550 DOI: 10.2807/1560-7917.es.2023.28.15.2200573] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
BackgroundPublic health guidance recommending isolation of individuals with group A streptococcal (GAS) infection or carriage for 12-24 h from antibiotic initiation to prevent onward transmission requires a strong evidence base.AimTo estimate the pooled proportion of individuals who remain GAS culture-positive at set intervals after initiation of antibiotics through a systematic literature review (PROSPERO CRD42021290364) and meta-analysis.MethodsWe searched Ovid MEDLINE (1946-), EMBASE (1974-) and Cochrane library. We included interventional or observational studies with ≥ 10 participants reporting rates of GAS throat culture positivity during antibiotic treatment for culture-confirmed GAS pharyngitis, scarlet fever and asymptomatic pharyngeal GAS carriage. We did not apply age, language or geographical restrictions.ResultsOf 5,058 unique records, 43 were included (37 randomised controlled studies, three non-randomised controlled trials and three before-and-after studies). The proportion of individuals remaining culture-positive on day 1, day 2 and days 3-9 were 6.9% (95% CI: 2.7-16.8%), 5.4% (95% CI: 2.1-13.3%) and 2.6% (95% CI: 1.6-4.2%). For penicillins and cephalosporins, day 1 positivity was 6.5% (95% CI: 2.5-16.1%) and 1.6% (95% CI: 0.04-42.9%), respectively. Overall, for 9.1% (95% CI: 7.3-11.3), throat swabs collected after completion of therapy were GAS culture-positive. Only six studies had low risk of bias.ConclusionsOur review provides evidence that antibiotics for pharyngeal GAS achieve a high rate of culture conversion within 24 h but highlights the need for further research given methodological limitations of published studies and imprecision of pooled estimates. Further evidence is needed for non-beta-lactam antibiotics and asymptomatic individuals.
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Affiliation(s)
- Emma McGuire
- United Kingdom Health Security Agency (UKHSA), London, United Kingdom
| | - Ang Li
- United Kingdom Health Security Agency (UKHSA), London, United Kingdom
| | - Simon M Collin
- United Kingdom Health Security Agency (UKHSA), London, United Kingdom
| | - Valerie Decraene
- United Kingdom Health Security Agency (UKHSA), London, United Kingdom
| | - Michael Cook
- United Kingdom Health Security Agency (UKHSA), London, United Kingdom
| | - Simon Padfield
- United Kingdom Health Security Agency (UKHSA), London, United Kingdom
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | | | - Theresa Lamagni
- United Kingdom Health Security Agency (UKHSA), London, United Kingdom
| | - Colin S Brown
- NIHR Health Protection Research Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
- United Kingdom Health Security Agency (UKHSA), London, United Kingdom
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Li HK, Zhi X, Vieira A, Whitwell HJ, Schricker A, Jauneikaite E, Li H, Yosef A, Andrew I, Game L, Turner CE, Lamagni T, Coelho J, Sriskandan S. Characterization of emergent toxigenic M1 UK Streptococcus pyogenes and associated sublineages. Microb Genom 2023; 9:mgen000994. [PMID: 37093716 PMCID: PMC10210942 DOI: 10.1099/mgen.0.000994] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/23/2023] [Indexed: 04/25/2023] Open
Abstract
Streptococcus pyogenes genotype emm1 is a successful, globally distributed epidemic clone that is regarded as inherently virulent. An emm1 sublineage, M1UK, that produces increased levels of SpeA toxin was associated with increased scarlet fever and invasive infections in England in 2015/2016. Defined by 27 SNPs in the core genome, M1UK is now dominant in England. To more fully characterize M1UK, we undertook comparative transcriptomic and proteomic analyses of M1UK and contemporary non-M1UK emm1 strains (M1global). Just seven genes were differentially expressed by M1UK compared with contemporary M1global strains. In addition to speA, five genes in the operon that includes glycerol dehydrogenase were upregulated in M1UK (gldA, mipB/talC, pflD, and phosphotransferase system IIC and IIB components), while aquaporin (glpF2) was downregulated. M1UK strains have a stop codon in gldA. Deletion of gldA in M1global abrogated glycerol dehydrogenase activity, and recapitulated upregulation of gene expression within the operon that includes gldA, consistent with a feedback effect. Phylogenetic analysis identified two intermediate emm1 sublineages in England comprising 13/27 (M113SNPs) and 23/27 SNPs (M123SNPs), respectively, that had failed to expand in the population. Proteomic analysis of invasive strains from the four phylogenetic emm1 groups highlighted sublineage-specific changes in carbohydrate metabolism, protein synthesis and protein processing; upregulation of SpeA was not observed in chemically defined medium. In rich broth, however, expression of SpeA was upregulated ~10-fold in both M123SNPs and M1UK sublineages, compared with M113SNPs and M1global. We conclude that stepwise accumulation of SNPs led to the emergence of M1UK. While increased expression of SpeA is a key indicator of M1UK and undoubtedly important, M1UK strains have outcompeted M123SNPs and other emm types that produce similar or more superantigen toxin. We speculate that an accumulation of adaptive SNPs has contributed to a wider fitness advantage in M1UK on an inherently successful emm1 streptococcal background.
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Affiliation(s)
- Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Xiangyun Zhi
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Ana Vieira
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Harry J. Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Amelia Schricker
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, London, UK
| | - Elita Jauneikaite
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- School of Public Health, Imperial College London, London, UK
| | - Hanqi Li
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ahmed Yosef
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ivan Andrew
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Laurence Game
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Claire E. Turner
- The Florey Institute, School of Biosciences, University of Sheffield, South Yorkshire, UK
| | - Theresa Lamagni
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- Centre for Infections, UK Health Security Agency, London, UK
| | - Juliana Coelho
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- Centre for Infections, UK Health Security Agency, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
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Hua C, Urbina T, Bosc R, Parks T, Sriskandan S, de Prost N, Chosidow O. Necrotising soft-tissue infections. Lancet Infect Dis 2023; 23:e81-e94. [PMID: 36252579 DOI: 10.1016/s1473-3099(22)00583-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/05/2022] [Accepted: 08/22/2022] [Indexed: 11/07/2022]
Abstract
The incidence of necrotising soft-tissue infections has increased during recent decades such that most physicians might see at least one case of these potentially life-threatening infections in their career. Despite advances in care, necrotising soft-tissue infections are still associated with high morbidity and mortality, underlining a need for continued education of the medical community. In particular, failure to suspect necrotising soft-tissue infections, fuelled by poor awareness of the disease, promotes delays to first surgical debridement, amplifying disease severity and adverse outcomes. This Review will focus on practical approaches to management of necrotising soft-tissue infections including prompt recognition, initiation of specific management, exploratory surgery, and aftercare. Increased alertness and awareness for these infections should improve time to diagnosis and early referral to specialised centres, with improvement in the prognosis of necrotising soft-tissue infections.
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Affiliation(s)
- Camille Hua
- Service de Dermatologie, Assistance Publique-Hôpitaux de Paris, Créteil, France; Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France; Epidemiology in Dermatology and Evaluation of Therapeutics, Université Paris Est Créteil, Créteil, France; Groupe Infectiologie Dermatologique-Infections Sexuellement Transmissibles, Société Française de Dermatologie, Paris, France
| | - Tomas Urbina
- Service de Médecine Intensive Réanimation, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Romain Bosc
- Service de Chirurgie Plastique, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Tom Parks
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Diseases, Imperial College London, London, UK; MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Nicolas de Prost
- Service de Médecine Intensive Réanimation, Assistance Publique-Hôpitaux de Paris, Créteil, France; CARMAS Research Group, UPEC-Université Paris-Est Créteil Val de Marne, Faculté de médecine de Créteil, Créteil, France
| | - Olivier Chosidow
- Service de Dermatologie, Assistance Publique-Hôpitaux de Paris, Créteil, France; Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France; Groupe Infectiologie Dermatologique-Infections Sexuellement Transmissibles, Société Française de Dermatologie, Paris, France; Research group Dynamyc, Faculté de Santé de Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, Université Paris-Est Créteil, Créteil, France.
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13
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Otter JA, Zhou J, Price JR, Reeves L, Zhu N, Randell P, Sriskandan S, Barclay WS, Holmes AH. SARS-CoV-2 surface and air contamination in an acute healthcare setting during the first and second pandemic waves. J Hosp Infect 2023; 132:36-45. [PMID: 36435307 PMCID: PMC9683853 DOI: 10.1016/j.jhin.2022.11.005] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Surfaces and air in healthcare facilities can be contaminated with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Previously, the authors identified SARS-CoV-2 RNA on surfaces and air in their hospital during the first wave of the coronavirus disease 2019 pandemic (April 2020). AIM To explore whether the profile of SARS-CoV-2 surface and air contamination had changed between April 2020 and January 2021. METHODS This was a prospective, cross-sectional, observational study in a multi-site London hospital. In January 2021, surface and air samples were collected from comparable areas to those sampled in April 2020, comprising six clinical areas and a public area. SARS-CoV-2 was detected using reverse transcription polymerase chain reaction and viral culture. Sampling was also undertaken in two wards with natural ventilation alone. The ability of the prevalent variants at the time of the study to survive on dry surfaces was evaluated. FINDINGS No viable virus was recovered from surfaces or air. Five percent (N=14) of 270 surface samples and 4% (N=1) of 27 air samples were positive for SARS-CoV-2, which was significantly lower than in April 2020 [52% (N=114) of 218 surface samples and 48% (N=13) of 27 air samples (P<0.001, Fisher's exact test)]. There was no clear difference in the proportion of surface and air samples positive for SARS-CoV-2 RNA based on the type of ventilation in the ward. All variants tested survived on dry surfaces for >72 h, with a <3-log10 reduction in viable count. CONCLUSION This study suggests that enhanced infection prevention measures have reduced the burden of SARS-CoV-2 RNA on surfaces and air in healthcare facilities.
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Affiliation(s)
- J A Otter
- National Institute for Healthcare Research Health Protection Research Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London & Public Health England, Hammersmith Hospital, London, UK; Guy's and St. Thomas' NHS Foundation Trust, London, UK.
| | - J Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - J R Price
- National Institute for Healthcare Research Health Protection Research Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London & Public Health England, Hammersmith Hospital, London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, London, UK
| | - L Reeves
- National Institute for Healthcare Research Health Protection Research Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London & Public Health England, Hammersmith Hospital, London, UK
| | - N Zhu
- National Institute for Healthcare Research Health Protection Research Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London & Public Health England, Hammersmith Hospital, London, UK
| | - P Randell
- Imperial College Healthcare NHS Trust, St. Mary's Hospital, London, UK
| | - S Sriskandan
- National Institute for Healthcare Research Health Protection Research Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London & Public Health England, Hammersmith Hospital, London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, London, UK
| | - W S Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - A H Holmes
- National Institute for Healthcare Research Health Protection Research Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London & Public Health England, Hammersmith Hospital, London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, London, UK
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14
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Frost H, Excler JL, Sriskandan S, Fulurija A. Correlates of immunity to Group A Streptococcus: a pathway to vaccine development. NPJ Vaccines 2023; 8:1. [PMID: 36650164 PMCID: PMC9844947 DOI: 10.1038/s41541-022-00593-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/06/2022] [Indexed: 01/19/2023] Open
Abstract
Understanding immunity in humans to Group A Streptococcus (Strep A) is critical for the development of successful vaccines to prevent the morbidity and mortality attributed to Strep A infections. Despite decades of effort, no licensed vaccine against Strep A exists and immune correlates of protection are lacking; a major impediment to vaccine development. In the absence of a vaccine, we can take cues from the development of natural immunity to Strep A in humans to identify immune correlates of protection. The age stratification of incidence of acute Strep A infections, peaking in young children and waning in early adulthood, coincides with the development of specific immune responses. Therefore, understanding the immune mechanisms involved in natural protection from acute Strep A infection is critical to identifying immune correlates to inform vaccine development. This perspective summarises the findings from natural infection studies, existing assays of immunity to Strep A, and highlights the gaps in knowledge to guide the development of Strep A vaccines and associated correlates of protection.
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Affiliation(s)
- Hannah Frost
- grid.1058.c0000 0000 9442 535XMurdoch Children’s Research Institute, Melbourne, VIC Australia
| | - Jean-Louis Excler
- grid.30311.300000 0000 9629 885XInternational Vaccine Institute, Seoul, Republic of Korea
| | - Shiranee Sriskandan
- grid.7445.20000 0001 2113 8111Department of Infectious Disease, Imperial College London, London, UK ,grid.7445.20000 0001 2113 8111MRC Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Alma Fulurija
- grid.414659.b0000 0000 8828 1230Telethon Kid’s Institute, Perth, WA Australia ,grid.1012.20000 0004 1936 7910The University of Western Australia, Perth, WA Australia
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15
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Wan Y, Mills E, Leung RCY, Vieira A, Jauneikaite E, Zhi X, Croucher N, Ellington MJ, Sriskandan S. Nitrofurantoin-resistant Escherichia coli in the UK: genetic determinants, diversity, and undetected occurrences. Access Microbiol 2022. [DOI: 10.1099/acmi.ac2021.po0086] [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] [Indexed: 11/18/2022] Open
Abstract
Background
Antimicrobial resistance in enteric or urinary E. coli might predispose invasive E. coli infection and bacteraemia. Nitrofurantoin resistance occurs in <6% of UK urinary E. coli isolates, however, 2018 national recommendations to prescribe nitrofurantoin for uncomplicated urinary tract infection (UTI) raised concerns for increased prevalence of nitrofurantoin-resistant E. coliin the future. Therefore, we investigated mechanisms of nitrofurantoin resistance in UK E. coli isolates and assessed their occurrences in a large dataset of E. coli genomes.
Methods
To elucidate chromosomal and acquired genetic determinants of nitrofurantoin resistance in E. coli, we analysed whole-genome sequences of nine randomly selected nitrofurantoin-resistant UTI E. coli isolates from West London. We then performed targeted analysis of 12,412 E. coli genomes collected from across the UK and predicted nitrofurantoin susceptibility from identified genotypes.
Results
Using comparative genomics, we found known and novel point mutations or insertion sequences (ISs) in chromosomal genes encoding oxygen-insensitive nitroreductases NfsA and NfsB in the nine isolates. Most of these genetic alterations resulted in gene inactivation. We also identified the same kinds of mutations in NfsA, NfsB, and their associated enzyme RibE in a number of 12,412 E. coli genomes. We also observed homoplasic mutations in all these proteins. By contrast, multidrug efflux pump OqxAB, which confers resistance when horizontally transferred, was only encoded by one genome.
Conclusions
Chromosomal de novo mutations and ISs are main causes of nitrofurantoin resistance in UK E. coli. Prevalence of nitrofurantoin resistance should be monitored among urine, blood, and enteric isolates as nitrofurantoin exposure increases.
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Affiliation(s)
- Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, United Kingdom
| | - Ewurabena Mills
- Imperial College Healthcare NHS Trust, United Kingdom
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, United Kingdom
| | - Rhoda C. Y. Leung
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, United Kingdom
| | - Ana Vieira
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, United Kingdom
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, United Kingdom
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom
| | - Xiangyun Zhi
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, United Kingdom
| | - Nicholas Croucher
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, United Kingdom
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom
| | - Matthew J. Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, United Kingdom
- Antimicrobial Resistance and Healthcare Associated Infections laboratory, National Infections Service, Public Health England, United Kingdom
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, United Kingdom
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Abstract
Introduction. The 16S rRNA methyltransferase (16S RMTase) gene armA is the most common mechanism conferring high-level aminoglycoside resistance in Acinetobacter baumannii, although rmtA, rmtB, rmtC, rmtD and rmtE have also been reported.Hypothesis/Gap statement. The occurrence of 16S RMTase genes in A. baumannii in the UK and Republic of Ireland is currently unknown.Aim. To identify the occurrence of 16S RMTase genes in A. baumannii isolates from the UK and the Republic of Ireland between 2004 and 2015.Methodology. Five hundred and fifty pan-aminoglycoside-resistant A. baumannii isolates isolated from the UK and the Republic of Ireland between 2004 and 2015 were screened by PCR to detect known 16S RMTase genes, and then whole-genome sequencing was conducted to screen for novel 16S RMTase genes.Results. A total of 96.5 % (531/550) of isolates were positive for 16S RMTase genes, with all but 1 harbouring armA (99.8 %, 530/531). The remaining isolates harboured rmtE3, a new rmtE variant. Most (89.2 %, 473/530) armA-positive isolates belonged to international clone II (ST2), and the rmtE3-positive isolate belonged to ST79. rmtE3 shared a similar genetic environment to rmtE2 but lacked an ISCR20 element found upstream of rmtE2.Conclusion. This is the first report of rmtE in A. baumannii in Europe; the potential for transmission of rmtE3 to other bacterial species requires further research.
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Affiliation(s)
- Emma Taylor
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK
- Present address: Department of Bacteriology, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Elita Jauneikaite
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- School of Public Health, Imperial College London, London W2 1PG, UK
| | - Shiranee Sriskandan
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2DD, UK
| | - Neil Woodford
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK
| | - Katie L Hopkins
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London NW9 5EQ, UK
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17
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Cordery R, Purba AK, Begum L, Mills E, Mosavie M, Vieira A, Jauneikaite E, Leung RCY, Siggins MK, Ready D, Hoffman P, Lamagni T, Sriskandan S. Frequency of transmission, asymptomatic shedding, and airborne spread of Streptococcus pyogenes in schoolchildren exposed to scarlet fever: a prospective, longitudinal, multicohort, molecular epidemiological, contact-tracing study in England, UK. Lancet Microbe 2022; 3:e366-e375. [PMID: 35544097 PMCID: PMC9042792 DOI: 10.1016/s2666-5247(21)00332-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Despite recommendations regarding prompt treatment of cases and enhanced hygiene measures, scarlet fever outbreaks increased in England between 2014 and 2018. We aimed to assess the effects of standard interventions on transmission of Streptococcus pyogenes to classroom contacts, households, and classroom environments to inform future guidance. METHODS We did a prospective, longitudinal, multicohort, molecular epidemiological, contact-tracing study in six settings across five schools in Greater London, UK. Schools and nurseries were eligible to participate if they had reported two cases of scarlet fever within 10 days of each other among children aged 2-8 years from the same class, with the most recent case arising in the preceding 48 h. We cultured throat swabs from children with scarlet fever, classroom contacts, and household contacts at four timepoints. We also cultured hand swabs and cough plates from all cases in years 1 and 2 of the study, and from classroom contacts in year 2. Surface swabs from toys and other fomites in classrooms were cultured in year 1, and settle plates from classrooms were collected in year 2. Any sample with S pyogenes detected was recorded as positive and underwent emm genotyping and genome sequencing to compare with the outbreak strain. FINDINGS Six classes, comprising 12 cases of scarlet fever, 17 household contacts, and 278 classroom contacts were recruited between March 1 and May 31, 2018 (year 1), and between March 1 and May 31, 2019 (year 2). Asymptomatic throat carriage of the outbreak strains increased from 11 (10%) of 115 swabbed children in week 1, to 34 (27%) of 126 in week 2, to 26 (24%) of 108 in week 3, and then five (14%) of 35 in week 4. Compared with carriage of outbreak S pyogenes strains, colonisation with non-outbreak and non-genotyped S pyogenes strains occurred in two (2%) of 115 swabbed children in week 1, five (4%) of 126 in week 2, six (6%) of 108 in week 3, and in none of the 35 children in week 4 (median carriage for entire study 2·8% [IQR 0·0-6·6]). Genome sequencing showed clonality of outbreak isolates within each of six classes, confirming that recent transmission accounted for high carriage. When transmissibility was tested, one (9%) of 11 asymptomatic carriers of emm4 and five (36%) of 14 asymptomatic carriers of emm3.93 had a positive cough plate. The outbreak strain was identified in only one (2%) of 60 surface swabs taken from three classrooms; however, in the two classrooms with settle plates placed in elevated locations, two (17%) of 12 and six (50%) of 12 settle plates yielded the outbreak strain. INTERPRETATION Transmission of S pyogenes in schools is intense and might occur before or despite reported treatment of cases, underlining a need for rapid case management. Despite guideline adherence, heavy shedding of S pyogenes by few classroom contacts might perpetuate outbreaks, and airborne transmission has a plausible role in its spread. These findings highlight the need for research to improve understanding and to assess effectiveness of interventions to reduce airborne transmission of S pyogenes. FUNDING Action Medical Research, UK Research Innovation, and National Institute for Health Research.
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Affiliation(s)
- Rebecca Cordery
- London Health Protection Teams, Public Health England, London, UK
| | - Amrit K Purba
- London Health Protection Teams, Public Health England, London, UK
| | - Lipi Begum
- London Health Protection Teams, Public Health England, London, UK
| | - Ewurabena Mills
- Department of Infectious Disease, Imperial College London, London, UK
| | - Mia Mosavie
- Department of Infectious Disease, Imperial College London, London, UK,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Ana Vieira
- Department of Infectious Disease, Imperial College London, London, UK,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK,MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK,MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Rhoda C Y Leung
- Department of Infectious Disease, Imperial College London, London, UK
| | - Matthew K Siggins
- Department of Infectious Disease, Imperial College London, London, UK,MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Derren Ready
- National Infection Service, Public Health England, London, UK,NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK
| | - Peter Hoffman
- National Infection Service, Public Health England, London, UK
| | - Theresa Lamagni
- National Infection Service, Public Health England, London, UK,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK; MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.
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18
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Seethalakshmi PS, Charity OJ, Giakoumis T, Kiran GS, Sriskandan S, Voulvoulis N, Selvin J. Delineating the impact of COVID-19 on antimicrobial resistance: An Indian perspective. Sci Total Environ 2022; 818:151702. [PMID: 34798093 PMCID: PMC8592853 DOI: 10.1016/j.scitotenv.2021.151702] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/24/2021] [Accepted: 11/11/2021] [Indexed: 05/23/2023]
Abstract
The COVID-19 pandemic has shattered millions of lives globally and continues to be a challenge to public health due to the emergence of variants of concern. Fear of secondary infections following COVID-19 has led to an escalation in antimicrobial use during the pandemic, while some antimicrobials have been repurposed as treatments for SARS-CoV-2, further driving antimicrobial resistance. India is one of the largest producers and consumers of antimicrobials globally, hence the task of curbing antimicrobial resistance is a huge challenge. Practices like empirical antimicrobial prescription and repurposing of drugs in clinical settings, self-medication and excessive use of antimicrobial hygiene products may have negatively impacted the prevalence of antimicrobial resistance in India. However, the expanded production of antimicrobials and disinfectants during the pandemic in response to increased demand may have had an even greater impact on the threat of antimicrobial resistance through major impacts on the environment. The review provides an outline of the impact COVID-19 can have on antimicrobial resistance in clinical settings and the possible outcomes on the environment. This review calls for the upgrading of existing antimicrobial policies and emphasizes the need for research studies to understand the impact of the pandemic on antimicrobial resistance in India.
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Affiliation(s)
- P S Seethalakshmi
- Department of Microbiology, Pondicherry University, Puducherry 605014, India.
| | - Oliver J Charity
- NIHR Health Protection Research Unit in Healthcare associated infection and AMR, Department of Infectious Disease, Imperial College London, UK.
| | | | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry 605014, India
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare associated infection and AMR, Department of Infectious Disease, Imperial College London, UK; MRC Centre for Molecular Bacteriology & Infection, Imperial College London, UK.
| | | | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry 605014, India.
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Mehta R, Chekmeneva E, Jackson H, Sands C, Mills E, Arancon D, Li HK, Arkell P, Rawson TM, Hammond R, Amran M, Haber A, Cooke GS, Noursadeghi M, Kaforou M, Lewis MR, Takats Z, Sriskandan S. Antiviral metabolite 3'-deoxy-3',4'-didehydro-cytidine is detectable in serum and identifies acute viral infections including COVID-19. Med 2022; 3:204-215.e6. [PMID: 35128501 PMCID: PMC8801973 DOI: 10.1016/j.medj.2022.01.009] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/14/2021] [Accepted: 01/21/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND There is a critical need for rapid viral infection diagnostics to enable prompt case identification in pandemic settings and support targeted antimicrobial prescribing. METHODS Using untargeted high-resolution liquid chromatography coupled with mass spectrometry, we compared the admission serum metabolome of emergency department patients with viral infections (including COVID-19), bacterial infections, inflammatory conditions, and healthy controls. Sera from an independent cohort of emergency department patients admitted with viral or bacterial infections underwent profiling to validate findings. Associations between whole-blood gene expression and the identified metabolite of interest were examined. FINDINGS 3'-Deoxy-3',4'-didehydro-cytidine (ddhC), a free base of the only known human antiviral small molecule ddhC-triphosphate (ddhCTP), was detected for the first time in serum. When comparing 60 viral with 101 non-viral cases in the discovery cohort, ddhC was the most significantly differentially abundant metabolite, generating an area under the receiver operating characteristic curve (AUC) of 0.954 (95% CI: 0.923-0.986). In the validation cohort, ddhC was again the most significantly differentially abundant metabolite when comparing 40 viral with 40 bacterial cases, generating an AUC of 0.81 (95% CI 0.708-0.915). Transcripts of viperin and CMPK2, enzymes responsible for ddhCTP synthesis, were among the five genes most highly correlated with ddhC abundance. CONCLUSIONS The antiviral precursor molecule ddhC is detectable in serum and an accurate marker for acute viral infection. Interferon-inducible genes viperin and CMPK2 are implicated in ddhC production in vivo. These findings highlight a future diagnostic role for ddhC in viral diagnosis, pandemic preparedness, and acute infection management. FUNDING NIHR Imperial BRC; UKRI.
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Affiliation(s)
- Ravi Mehta
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Elena Chekmeneva
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Heather Jackson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Caroline Sands
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Ewurabena Mills
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | | | - Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- MRC Centre for Molecular Bacteriology & Infection, Imperial College London, London SW7 2AZ, UK
| | - Paul Arkell
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Timothy M. Rawson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
- Division of Infection & Immunity, University College London, London WC1 E6BT, UK
| | - Robert Hammond
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Maisarah Amran
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Anna Haber
- Imperial College Healthcare NHS Trust, London W12 0HS, UK
| | - Graham S. Cooke
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Mahdad Noursadeghi
- Division of Infection & Immunity, University College London, London WC1 E6BT, UK
| | - Myrsini Kaforou
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Matthew R. Lewis
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Zoltan Takats
- National Phenome Centre, Imperial College London, London SW7 2AZ, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- MRC Centre for Molecular Bacteriology & Infection, Imperial College London, London SW7 2AZ, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infection & Antimicrobial Resistance, Imperial College London, London W12 0NN, UK
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20
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Jauneikaite E, Honeyford K, Blandy O, Mosavie M, Pearson M, Ramzan FA, Ellington MJ, Parkhill J, Costelloe CE, Woodford N, Sriskandan S. Bacterial genotypic and patient risk factors for adverse outcomes in Escherichia coli bloodstream infections: a prospective molecular epidemiological study. J Antimicrob Chemother 2022; 77:1753-1761. [PMID: 35265995 PMCID: PMC9155631 DOI: 10.1093/jac/dkac071] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/07/2022] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Escherichia coli bloodstream infections have shown a sustained increase in England, for reasons that are unknown. Furthermore, the contribution of MDR lineages such as ST131 to overall E. coli disease burden and outcome is undetermined. METHODS We genome-sequenced E. coli blood isolates from all patients with E. coli bacteraemia in north-west London from July 2015 to August 2016 and assigned MLST genotypes, virulence factors and AMR genes to all isolates. Isolate STs were then linked to phenotypic antimicrobial susceptibility, patient demographics and clinical outcome data to explore relationships between the E. coli STs, patient factors and outcomes. RESULTS A total of 551 E. coli genomes were analysed. Four STs (ST131, 21.2%; ST73, 14.5%; ST69, 9.3%; and ST95, 8.2%) accounted for over half of cases. E. coli genotype ST131-C2 was associated with phenotypic non-susceptibility to quinolones, third-generation cephalosporins, amoxicillin, amoxicillin/clavulanic acid, gentamicin and trimethoprim. Among 300 patients from whom outcome was known, an association between the ST131-C2 lineage and longer length of stay was detected, although multivariable regression modelling did not demonstrate an association between E. coli ST and mortality. Several unexpected associations were identified between gentamicin non-susceptibility, ethnicity, sex and adverse outcomes, requiring further research. CONCLUSIONS Although E. coli ST was associated with defined antimicrobial non-susceptibility patterns and prolonged length of stay, E. coli ST was not associated with increased mortality. ST131 has outcompeted other lineages in north-west London. Where ST131 is prevalent, caution is required when devising empiric regimens for suspected Gram-negative sepsis, in particular the pairing of β-lactam agents with gentamicin.
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Affiliation(s)
- Elita Jauneikaite
- NIHR Health Protection Research Unit for Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Kate Honeyford
- NIHR Health Protection Research Unit for Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK,Global Digital Health Unit, Department of Primary Care and Public Health, School of Public Health, Imperial College London, London, UK
| | - Oliver Blandy
- NIHR Health Protection Research Unit for Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
| | - Mia Mosavie
- NIHR Health Protection Research Unit for Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
| | - Max Pearson
- NIHR Health Protection Research Unit for Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
| | - Farzan A. Ramzan
- NIHR Health Protection Research Unit for Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
| | - Matthew J. Ellington
- NIHR Health Protection Research Unit for Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK,National Infection Service Laboratories, National Infection Service, UK Health Security Agency (formerly Public Health England), UK
| | - Julian Parkhill
- Wellcome Sanger Institute, Hinxton, Cambridge, UK,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Céire E. Costelloe
- Global Digital Health Unit, Department of Primary Care and Public Health, School of Public Health, Imperial College London, London, UK
| | - Neil Woodford
- NIHR Health Protection Research Unit for Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK,National Infection Service Laboratories, National Infection Service, UK Health Security Agency (formerly Public Health England), UK
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit for Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK,Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK,Corresponding author. E-mail:
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21
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Taylor E, Jauneikaite E, Sriskandan S, Woodford N, Hopkins KL. Detection and characterisation of 16S rRNA methyltransferase-producing Pseudomonas aeruginosa from the UK and Republic of Ireland from 2003-2015. Int J Antimicrob Agents 2022; 59:106550. [PMID: 35176475 DOI: 10.1016/j.ijantimicag.2022.106550] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 11/17/2022]
Abstract
16S rRNA methyltransferase (16S RMTase) genes confer high-level aminoglycoside resistance, reducing treatment options for multidrug-resistant Gram-negative bacteria. Pseudomonas aeruginosa isolates (n = 221) exhibiting high-level pan-aminoglycoside resistance (amikacin, gentamicin and tobramycin MICs ≥64, ≥32 and ≥32 mg/L, respectively) were screened for 16S RMTase genes to determine their occurrence among isolates submitted to a national reference laboratory from December 2003 to December 2015. 16S RMTase genes were identified using two multiplex PCRs, and whole-genome sequencing (WGS) was used to identify other antibiotic resistance genes, sequence types (STs) and the genetic environment of 16S RMTase genes. 16S RMTase genes were found in 8.6% (19/221) of isolates, with rmtB4 (47.4%; 9/19) being most common, followed by rmtD3 (21.1%; 4/19), rmtF2 (15.8%; 3/19) and single isolates harbouring rmtB1, rmtC and rmtD1. Carbapenemase genes were found in 89.5% (17/19) of 16S RMTase-positive isolates, with blaVIM (52.9%; 9/17) being most common. 16S RMTase genes were found in 'high-risk' clones known to harbour carbapenemase genes (ST233, ST277, ST357, ST654 and ST773). Analysis of the genetic environment of 16S RMTase genes identified that IS6100 was genetically linked to rmtB1; IS91 to rmtB4, rmtC or rmtD3; ISCR14 to rmtD1; and rmtF2 was linked to Tn3, IS91 or Tn1721. Although 16S RMTase genes explained only 8.6% of pan-aminoglycoside resistance in the P. aeruginosa isolates studied, the association of 16S RMTase genes with carbapenemase-producers and 'high-risk' clones highlights that continued surveillance is required to monitor spread as well as the importance of suppressing the emergence of dually-resistant clones in hospital settings.
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Affiliation(s)
- Emma Taylor
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK
| | - Elita Jauneikaite
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, UK; School of Public Health, Imperial College London, London W2 1PG, UK
| | - Shiranee Sriskandan
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, UK; MRC Centre for Molecular Bacteriology & Infection, Imperial College London, London SW7 2DD, UK
| | - Neil Woodford
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK
| | - Katie L Hopkins
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK; Antimicrobial Resistance & Mechanisms Service, HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London NW9 5EQ, UK.
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22
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Herdman MT, Cordery R, Karo B, Purba AK, Begum L, Lamagni T, Kee C, Balasegaram S, Sriskandan S. Clinical management and impact of scarlet fever in the modern era: findings from a cross-sectional study of cases in London, 2018-2019. BMJ Open 2021; 11:e057772. [PMID: 34952887 PMCID: PMC9066343 DOI: 10.1136/bmjopen-2021-057772] [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] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/25/2021] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES In response to increasing incidence of scarlet fever and wider outbreaks of group A streptococcal infections in London, we aimed to characterise the epidemiology, symptoms, management and consequences of scarlet fever, and to identify factors associated with delayed diagnosis. DESIGN AND SETTING Cross-sectional community-based study of children with scarlet fever notified to London's three Health Protection Teams, 2018-2019. PARTICIPANTS From 2575 directly invited notified cases plus invitations via parental networks at 410 schools/nurseries with notified outbreaks of confirmed/probable scarlet fever, we received 477 responses (19% of those directly invited), of which 412 met the case definition. Median age was 4 years (range <1 to 16), 48% were female, and 70% were of white ethnicity. OUTCOME MEASURES Preplanned measures included quantitative description of case demographics, symptoms, care-seeking, and clinical, social, and economic impact on cases and households. After survey completion, secondary analyses of factors associated with delayed diagnosis (by logistic regression) and consequences of delayed diagnosis (by Cox's regression), and qualitative analysis of free text comments were added. RESULTS Rash was reported for 89% of cases, but followed onset of other symptoms for 71%, with a median 1-day delay. Pattern of onset varied with age: sore throat was more common at onset among children 5 years and older (OR3.1, 95% CI 1.9 to 5.0). At first consultation, for 28%, scarlet fever was not considered: in these cases, symptoms were frequently attributed to viral infection (60%, 64/106). Delay in diagnosis beyond first consultation occurred more frequently among children aged 5+ who presented with sore throat (OR 2.8 vs 5+without sore throat; 95% CI 1.3 to 5.8). Cases with delayed diagnosis took, on average, 1 day longer to return to baseline activities. CONCLUSIONS Scarlet fever may be initially overlooked, especially among older children presenting with sore throat. Raising awareness among carers and practitioners may aid identification and timely treatment.
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Affiliation(s)
- Michael Trent Herdman
- National Infection Service, Public Health England (now UK Health Security Agency), London, UK
- UK Field Epidemiology Training Programme, Public Health England (now UK Health Security Agency), London, UK
| | - Rebecca Cordery
- South London Health Protection Team, Public Health England (now UK Health Security Agency), London, UK
| | - Basel Karo
- National Infection Service, Public Health England (now UK Health Security Agency), London, UK
| | - Amrit Kaur Purba
- South London Health Protection Team, Public Health England (now UK Health Security Agency), London, UK
| | - Lipi Begum
- South London Health Protection Team, Public Health England (now UK Health Security Agency), London, UK
| | - Theresa Lamagni
- National Infection Service, Public Health England (now UK Health Security Agency), London, UK
| | - Chuin Kee
- Oak Lodge Medical Centre, Barnet, North Central London CCG, London, UK
| | - Sooria Balasegaram
- National Infection Service, Public Health England (now UK Health Security Agency), London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK
- NIHR Health Protection Research Unit in Healthcare-associated infection and AMR, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
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23
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Wan Y, Mills E, Leung RC, Vieira A, Zhi X, Croucher NJ, Woodford N, Jauneikaite E, Ellington MJ, Sriskandan S. Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom. Microb Genom 2021; 7:000702. [PMID: 34860151 PMCID: PMC8767348 DOI: 10.1099/mgen.0.000702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance in enteric or urinary Escherichia coli is a risk factor for invasive E. coli infections. Due to widespread trimethoprim resistance amongst urinary E. coli and increased bacteraemia incidence, a national recommendation to prescribe nitrofurantoin for uncomplicated urinary tract infection was made in 2014. Nitrofurantoin resistance is reported in <6% urinary E. coli isolates in the UK, however, mechanisms underpinning nitrofurantoin resistance in these isolates remain unknown. This study aimed to identify the genetic basis of nitrofurantoin resistance in urinary E. coli isolates collected from north west London and then elucidate resistance-associated genetic alterations in available UK E. coli genomes. As a result, an algorithm was developed to predict nitrofurantoin susceptibility. Deleterious mutations and gene-inactivating insertion sequences in chromosomal nitroreductase genes nfsA and/or nfsB were identified in genomes of nine confirmed nitrofurantoin-resistant urinary E. coli isolates and additional 11 E. coli isolates that were highlighted by the prediction algorithm and subsequently validated to be nitrofurantoin-resistant. Eight categories of allelic changes in nfsA, nfsB, and the associated gene ribE were detected in 12412 E. coli genomes from the UK. Evolutionary analysis of these three genes revealed homoplasic mutations and explained the previously reported order of stepwise mutations. The mobile gene complex oqxAB, which is associated with reduced nitrofurantoin susceptibility, was identified in only one of the 12412 genomes. In conclusion, mutations and insertion sequences in nfsA and nfsB were leading causes of nitrofurantoin resistance in UK E. coli. As nitrofurantoin exposure increases in human populations, the prevalence of nitrofurantoin resistance in carriage E. coli isolates and those from urinary and bloodstream infections should be monitored.
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Affiliation(s)
- Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ewurabena Mills
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Rhoda C.Y. Leung
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Present address: Department of Microbiology, Queen Mary Hospital, Hong Kong S.A.R., PR China
| | - Ana Vieira
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Xiangyun Zhi
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Matthew J. Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
- *Correspondence: Shiranee Sriskandan,
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24
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Abbas A, Abdukahil SA, Abdulkadir NN, Abe R, Abel L, Absil L, Acharya S, Acker A, Adachi S, Adam E, Adrião D, Ageel SA, Ahmed S, Ain Q, Ainscough K, Aisa T, Ait Hssain A, Ait Tamlihat Y, Akimoto T, Akmal E, Al Qasim E, Alalqam R, Alam T, Al-dabbous T, Alegesan S, Alegre C, Alessi M, Alex B, Alexandre K, Al-Fares A, Alfoudri H, Ali I, Ali Shah N, Alidjnou KE, Aliudin J, Alkhafajee Q, Allavena C, Allou N, Altaf A, Alves J, Alves JM, Alves R, Amaral M, Amira N, Ammerlaan H, Ampaw P, Andini R, Andrejak C, Angheben A, Angoulvant F, Ansart S, Anthonidass S, Antonelli M, Antunes de Brito CA, Anwar KR, Apriyana A, Arabi Y, Aragao I, Arali R, Arancibia F, Araujo C, Arcadipane A, Archambault P, Arenz L, Arlet JB, Arnold-Day C, Aroca A, Arora L, Arora R, Artaud-Macari E, Aryal D, Asaki M, Asensio A, Ashley E, Ashraf M, Ashraf S, Asim M, Assie JB, Asyraf A, Atique A, Attanyake AMUL, Auchabie J, Aumaitre H, Auvet A, Azemar L, Azoulay C, Bach B, Bachelet D, Badr C, Baig N, Baillie JK, Baird JK, Bak E, Bakakos A, Bakar NA, Bal A, Balakrishnan M, Balan V, Bani-Sadr F, Barbalho R, Barbosa NY, Barclay WS, Barnett SU, Barnikel M, Barrasa H, Barrelet A, Barrigoto C, Bartoli M, Bartone C, Baruch J, Bashir M, Basmaci R, Basri MFH, Bastos D, Battaglini D, Bauer J, Bautista Rincon DF, Bazan Dow D, Bedossa A, Bee KH, Behilill S, Beishuizen A, Beljantsev A, Bellemare D, Beltrame A, Beltrão BA, Beluze M, Benech N, Benjiman LE, Benkerrou D, Bennett S, Bento L, Berdal JE, Bergeaud D, Bergin H, Bernal Sobrino JL, Bertoli G, Bertolino L, Bessis S, Betz A, Bevilcaqua S, Bezulier K, Bhatt A, Bhavsar K, Bianchi I, Bianco C, Bidin FN, Bikram Singh M, Bin Humaid F, Bin Kamarudin MN, Bissuel F, Biston P, Bitker L, Blanco-Schweizer P, Blier C, Bloos F, Blot M, Blumberg L, Boccia F, Bodenes L, Bogaarts A, Bogaert D, Boivin AH, Bolze PA, Bompart F, Bonfasius A, Borges D, Borie R, Bosse HM, Botelho-Nevers E, Bouadma L, Bouchaud O, Bouchez S, Bouhmani D, Bouhour D, Bouiller K, Bouillet L, Bouisse C, Boureau AS, Bourke J, Bouscambert M, Bousquet A, Bouziotis J, Boxma B, Boyer-Besseyre M, Boylan M, Bozza FA, Brack M, Braconnier A, Braga C, Brandenburger T, Brás Monteiro F, Brazzi L, Breen D, Breen P, Breen P, Brett S, Brickell K, Broadley T, Browne A, Browne S, Brozzi N, Brusse-Keizer M, Buchtele N, Buesaquillo C, Bugaeva P, Buisson M, Burhan E, Burrell A, Bustos IG, Butnaru D, Cabie A, Cabral S, Caceres E, Cadoz C, Callahan M, Calligy K, Calvache JA, Cam J, Campana V, Campbell P, Campisi J, Canepa C, Cantero M, Caraux-Paz P, Cárcel S, Cardellino CS, Cardoso F, Cardoso F, Cardoso N, Cardoso S, Carelli S, Carlier N, Carmoi T, Carney G, Carpenter C, Carqueja I, Carret MC, Carrier FM, Carroll I, Carson G, Carton E, Casanova ML, Cascão M, Casey S, Casimiro J, Cassandra B, Castañeda S, Castanheira N, Castor-Alexandre G, Castrillón H, Castro I, Catarino A, Catherine FX, Cattaneo P, Cavalin R, Cavalli GG, Cavayas A, Ceccato A, Cervantes-Gonzalez M, Chair A, Chakveatze C, Chan A, Chand M, Chantalat Auger C, Chapplain JM, Chas J, Chaudary M, Chávez Iñiguez JS, Chen A, Chen YS, Cheng MP, Cheret A, Chiarabini T, Chica J, Chidambaram SK, Chin-Tho L, Chirouze C, Chiumello D, Cho HJ, Cho SM, Cholley B, Chopin MC, Chow TS, Chow YP, Chua HJ, Chua J, Cidade JP, Cisneros Herreros JM, Citarella BW, Ciullo A, Clarke E, Clarke J, Claure Del Granado R, Clohisey S, Cobb JP, Coca N, Codan C, Cody C, Coelho A, Coles M, Colin G, Collins M, Colombo SM, Combs P, Connolly J, Connor M, Conrad A, Contreras S, Conway E, Cooke GS, Copland M, Cordel H, Corley A, Cormican S, Cornelis S, Cornet AD, Corpuz AJ, Cortegiani A, Corvaisier G, Costigan E, Couffignal C, Couffin-Cadiergues S, Courtois R, Cousse S, Cregan R, Crepy D'Orleans C, Croonen S, Crowl G, Crump J, Cruz C, Cruz Berm JL, Cruz Rojo J, Csete M, Cucino A, Cullen A, Cullen C, Cummings M, Curley G, Curlier E, Curran C, Custodio P, da Silva Filipe A, Da Silveira C, Dabaliz AA, Dagens A, Dahly D, Dalton H, Dalton J, Daly S, D'Amico F, Daneman N, Daniel C, Dankwa EA, Dantas J, D’Aragon F, de Boer M, de Loughry G, de Mendoza D, De Montmollin E, de Oliveira França RF, de Pinho Oliveira AI, De Rosa R, de Silva T, de Vries P, Deacon J, Dean D, Debard A, DeBenedictis B, Debray MP, DeCastro N, Dechert W, Deconninck L, Decours R, Defous E, Delacroix I, Delaveuve E, Delavigne K, Delfos NM, Deligiannis I, Dell'Amore A, Delmas C, Delobel P, Delsing C, Demonchy E, Denis E, Deplanque D, Depuydt P, Desai M, Descamps D, Desvallée M, Dewayanti S, Diallo A, Diamantis S, Dias A, Diaz P, Diaz R, Diaz Diaz JJ, Didier K, Diehl JL, Dieperink W, Dimet J, Dinot V, Diop F, Diouf A, Dishon Y, Dixit D, Djossou F, Docherty AB, Doherty H, Dondorp AM, Dong A, Donnelly CA, Donnelly M, Donohue C, Donohue S, Donohue Y, Doran C, Doran P, Dorival C, D'Ortenzio E, Douglas JJ, Douma R, Dournon N, Downer T, Downey J, Downing M, Drake T, Driscoll A, Dryden M, Duarte Fonseca C, Dubee V, Dubos F, Ducancelle A, Duculan T, Dudman S, Duggal A, Dunand P, Dunning J, Duplaix M, Durante-Mangoni E, Durham III L, Dussol B, Duthoit J, Duval X, Dyrhol-Riise AM, Ean SC, Echeverria-Villalobos M, Egan S, Eira C, El Sanharawi M, Elapavaluru S, Elharrar B, Ellerbroek J, Eloy P, Elshazly T, Elyazar I, Enderle I, Endo T, Eng CC, Engelmann I, Enouf V, Epaulard O, Escher M, Esperatti M, Esperou H, Esposito-Farese M, Estevão J, Etienne M, Ettalhaoui N, Everding AG, Evers M, Fabre I, Fabre M, Faheem A, Fahy A, Fairfield CJ, Fakar Z, Faria P, Farooq A, Farrar JJ, Farshait N, Fateena H, Fatoni AZ, Faure K, Favory R, Fayed M, Feely N, Feeney L, Fernandes J, Fernandes M, Fernandes S, Ferrand FX, Ferrand Devouge E, Ferrão J, Ferraz M, Ferreira B, Ferreira S, Ferrer-Roca R, Ferriere N, Ficko C, Figueiredo-Mello C, Fiorda J, Flament T, Flateau C, Fletcher T, Florio LL, Flynn B, Flynn D, Foley C, Foley J, Fomin V, Fonseca T, Fontela P, Forsyth S, Foster D, Foti G, Fourn E, Fowler RA, Fraher DM, Franch-Llasat D, Fraser C, Fraser JF, Freire MV, Freitas Ribeiro A, Friedrich C, Fritz R, Fry S, Fuentes N, Fukuda M, Gaborieau V, Gaci R, Gagliardi M, Gagnard JC, Gagné N, Gagneux-Brunon A, Gaião S, Gail Skeie L, Gallagher P, Gallego Curto E, Gamble C, Gani Y, Garan A, Garcia R, García Barrio N, Garcia-Diaz J, Garcia-Gallo E, Garimella N, Garot D, Garrait V, Gauli B, Gault N, Gavin A, Gavrylov A, Gaymard A, Gebauer J, Geraud E, Gerbaud Morlaes L, Germano N, ghisulal PK, Ghosn J, Giani M, Giaquinto C, Gibson J, Gigante T, Gilg M, Gilroy E, Giordano G, Girvan M, Gissot V, Gitahi J, Giwangkancana G, Glikman D, Glybochko P, Gnall E, Goco G, Goehringer F, Goepel S, Goffard JC, Goh JY, Golob J, Gomes R, Gomez K, Gómez-Junyent J, Gominet M, Gonzalez A, Gordon P, Gordon A, Gorenne I, Goubert L, Goujard C, Goulenok T, Grable M, Graf J, Grandin EW, Granier P, Grasselli G, Grazioli L, Green CA, Greene C, Greenhalf W, Greffe S, Grieco DL, Griffee M, Griffiths F, Grigoras I, Groenendijk A, Grosse Lordemann A, Gruner H, Gu Y, Guarracino F, Guedj J, Guego M, Guellec D, Guerguerian AM, Guerreiro D, Guery R, Guillaumot A, Guilleminault L, Guimarães de Castro M, Guimard T, Haalboom M, Haber D, Habraken H, Hachemi A, Hadri N, Haidash O, Haider S, Haidri F, Hakak S, Hall A, Hall M, Halpin S, Hamer A, Hamers R, Hamidfar R, Hammond T, Han LY, Haniffa R, Hao KW, Hardwick H, Harrison EM, Harrison J, Harrison SBE, Hartman A, Hashmi J, Hashmi M, Hayat M, Hayes A, Hays L, Heerman J, Heggelund L, Hendry R, Hennessy M, Henriquez A, Hentzien M, Herekar F, Hernandez-Montfort J, Herr D, Hershey A, Hesstvedt L, Hidayah A, Higgins D, Higgins E, HigginsOKeeffe G, Hinchion R, Hinton S, Hiraiwa H, Hitoto H, Ho A, Ho YB, Hoctin A, Hoffmann I, Hoh WH, Hoiting O, Holt R, Holter JC, Horby P, Horcajada JP, Hoshino K, Hoshino K, Houas I, Hough CL, Houltham S, Hsu JMY, Hulot JS, Hussain I, Ijaz S, Illes HG, Imbert P, Imran M, Imran Sikander R, Inácio H, Infante Dominguez C, Ing YS, Iosifidis E, Ippolito M, Isgett S, Ishani PGPI, Isidoro T, Ismail N, Isnard M, Itai J, Ito A, Ivulich D, Jaafar D, Jaafoura S, Jabot J, Jackson C, Jamieson N, Jaquet P, Jassat W, Jaud-Fischer C, Jaureguiberry S, Javidfar J, Jawad I, Jaworsky D, Jayakumar D, Jego F, Jelani AM, Jenum S, Jimbo-Sotomayor R, Job VDP, Joe OY, Jorge García RN, Joseph C, Joseph M, Joshi S, Jourdain M, Jouvet P, June J, Jung A, Jung H, Juzar D, Kafif O, Kaguelidou F, Kaisbain N, Kaleesvran T, Kali S, Kalicinska A, Kalomoiri S, Kamal S, Kamaluddin MAA, Kamaruddin ZAC, Kamarudin N, Kandamby DH, Kandel C, Kang KY, Kant R, Kanwal D, Kanyawati D, Karki B, Karpayah P, Karsies T, Kartsonaki C, Kasugai D, Kataria A, Katz K, Kaur A, Kaur Johal S, Kawasaki T, Kay C, Keane H, Keating S, Kellam P, Kelly A, Kelly A, Kelly C, Kelly N, Kelly S, Kelly Y, Kelsey M, Kennedy R, Kennon K, Kernan M, Kerroumi Y, Keshav S, Kestelyn E, Khalid I, Khalid O, Khalil A, Khan C, Khan I, Khanal S, Kho ME, Khoo D, Khoo R, Khoo S, Khoso N, Kiat KH, Kida Y, Kiiza P, Kildal AB, Kim JB, Kimmoun A, Kindgen-Milles D, King A, Kitamura N, Klenerman P, Klont R, Kloumann Bekken G, Knight S, Kobbe R, Kodippily C, Kohns Vasconcelos M, Koirala S, Komatsu M, Korten V, Kosgei C, Kpangon A, Krawczyk K, Krishnan S, Krishnan V, Kruglova O, Kumar A, Kumar D, Kumar G, Kumar M, Kumar Vecham P, Kuriakose D, Kurtzman E, Kusumastuti NP, Kutsogiannis D, Kutsyna G, Kyriakoulis K, Lachatre M, Lacoste M, Laffey JG, Lagrange M, Laine F, Lairez O, Lakhey S, Lalueza A, Lambert M, Lamontagne F, Langelot-Richard M, Langlois V, Lantang EY, Lanza M, Laouénan C, Laribi S, Lariviere D, Lasry S, Latif N, Launay O, Laureillard D, Lavie-Badie Y, Law A, Lawrence C, Lawrence T, Le M, Le Bihan C, Le Bris C, Le Falher G, Le Fevre L, Le Hingrat Q, Le Maréchal M, Le Mestre S, Le Moal G, Le Moing V, Le Nagard H, Le Turnier P, Leal E, Leal Santos M, Lee BH, Lee HG, Lee J, Lee SH, Lee TC, Lee YL, Leeming G, Lefebvre B, Lefebvre L, Lefevre B, LeGac S, Lelievre JD, Lellouche F, Lemaignen A, Lemee V, Lemeur A, Lemmink G, Lene HS, Lennon J, León R, Leone M, Leone M, Lepiller Q, Lescure FX, Lesens O, Lesouhaitier M, Lester-Grant A, Levy B, Levy Y, Levy-Marchal C, Lewandowska K, L'Her E, Li Bassi G, Liang J, Liaquat A, Liegeon G, Lim KC, Lim WS, Lima C, Lina B, Lina L, Lind A, Lingas G, Lion-Daolio S, Lissauer S, Liu K, Livrozet M, Lizotte P, Loforte A, Lolong N, Loon LC, Lopes D, Lopez-Colon D, Loschner AL, Loubet P, Loufti B, Louis G, Lourenco S, Lovelace-Macon L, Low LL, Lowik M, Loy JS, Lucet JC, Lumbreras Bermejo C, Luna CM, Lungu O, Luong L, Luque N, Luton D, Lwin N, Lyons R, Maasikas O, Mabiala O, MacDonald S, MacDonald S, Machado M, Macheda G, Macias Sanchez J, Madhok J, Maestro de la Calle G, Mahieu R, Mahy S, Maia AR, Maier LS, Maillet M, Maitre T, Malfertheiner M, Malik N, Mallon P, Maltez F, Malvy D, Manda V, Mandei JM, Mandelbrot L, Manetta F, Mangal K, Mankikian J, Manning E, Manuel A, Maria Sant`Ana Malaque C, Marino D, Marino F, Markowicz S, Maroun Eid C, Marques A, Marquis C, Marsh B, Marsh L, Marshal M, Marshall J, Martelli CT, Martin DA, Martin E, Martin-Blondel G, Martinelli A, Martin-Loeches I, Martinot M, Martin-Quiros A, Martins A, Martins J, Martins N, Martins Rego C, Martucci G, Martynenko O, Marwali EM, Marzukie M, Masa Jimenez JF, Maslove D, Maslove D, Mason P, Mason S, Masood S, Masood S, Mat Nor B, Matan M, Mateus Fernandes H, Mathew M, Mathieu D, Mattei M, Matulevics R, Maulin L, Maxwell M, Maynar J, Mazzoni T, Mc Sweeney L, McAndrew L, McArthur C, McCarthy A, McCarthy A, McCloskey C, McConnochie R, McDermott S, McDonald SE, McElroy A, McElwee S, McEneany V, McEvoy N, McGeer A, McKay C, McKeown J, McLean KA, McNally P, McNicholas B, McPartlan E, Meaney E, Mear-Passard C, Mechlin M, Meher M, Mehkri O, Mele F, Melo L, Memon K, Mendes JJ, Menkiti O, Menon K, Mentré F, Mentzer AJ, Mercier E, Mercier N, Merckx A, Mergeay-Fabre M, Mergler B, Merson L, Mesquita A, Metwally O, Meybeck A, Meyer D, Meynert AM, Meysonnier V, Meziane A, Mezidi M, Michelagnoli G, Michelanglei C, Michelet I, Mihelis E, Mihnovit V, Miranda-Maldonado H, Misnan NA, Mohamed NNE, Mohamed TJ, Moin A, Molina D, Molinos E, Molloy B, Mone M, Monteiro A, Montes C, Montrucchio G, Moore S, Moore SC, Morales Cely L, Moro L, Morocho Tutillo DR, Morton B, Motherway C, Motos A, Mouquet H, Mouton Perrot C, Moyet J, Mudara C, Mufti AK, Muh NY, Muhamad D, Mullaert J, Muller F, Müller KE, Munblit D, Muneeb S, Munir N, Munshi L, Murphy A, Murphy A, Murphy L, Murris M, Murthy S, Musaab H, Muyandy G, Myrodia DM, N N, Nagpal D, Nagrebetsky A, Narasimhan M, Narayanan N, Nasim Khan R, Nazerali-Maitland A, Neant N, Neb H, Nekliudov NA, Nelwan E, Neto R, Neumann E, Neves B, Ng PY, Nghi A, Nguyen D, Ni Choileain O, Ni Leathlobhair N, Nichol A, Nitayavardhana P, Nonas S, Noordin NAM, Noret M, Norharizam NFI, Norman L, Notari A, Noursadeghi M, Nowicka K, Nowinski A, Nseir S, Nunez JI, Nurnaningsih N, Nyamankolly E, O Brien F, O'Callaghan A, Occhipinti G, OConnor D, O'Donnell M, Ogston T, Ogura T, Oh TH, O'Halloran S, O'Hearn K, Ohshimo S, Oldakowska A, Oliveira J, Oliveira L, Olliaro PL, O'Neil C, Ong DS, Ong JY, Oosthuyzen W, Opavsky A, Openshaw P, Orakzai S, Orozco-Chamorro CM, Orquera A, Ortoleva J, Osatnik J, O'Shea L, O'Sullivan M, Othman SZ, Ouamara N, Ouissa R, Owyang C, Oziol E, Pabasara HMU, Pagadoy M, Pages J, Palacios A, Palacios M, Palmarini M, Panarello G, Panda PK, Paneru H, Pang LH, Panigada M, Pansu N, Papadopoulos A, Parke R, Parker M, Parra B, Parrini V, Pasha T, Pasquier J, Pastene B, Patauner F, Patel J, Pathmanathan MD, Patrão L, Patricio P, Patrier J, Patterson L, Pattnaik R, Paul C, Paul M, Paulos J, Paxton WA, Payen JF, Peariasamy K, Pedrera Jiménez M, Peek GJ, Peelman F, Peiffer-Smadja N, Peigne V, Pejkovska M, Pelosi P, Peltan ID, Pereira R, Perez D, Periel L, Perpoint T, Pesenti A, Pestre V, Petrou L, Petrov-Sanchez V, Pettersen FO, Peytavin G, Pharand S, Piagnerelli M, Picard W, Picone O, Piero MD, Pierobon C, Piersma D, Pimentel C, Pinto R, Pires C, Pironneau I, Piroth L, Pius R, Piva S, Plantier L, Plotkin D, Png HS, Poissy J, Pokeerbux R, Pokorska-Spiewak M, Poli S, Pollakis G, Ponscarme D, Popielska J, Post AM, Postma DF, Povoa P, Póvoas D, Powis J, Prapa S, Preau S, Prebensen C, Preiser JC, Prinssen A, Pritchard MG, Priyadarshani GDD, Proença L, Pudota S, Puéchal O, Pujo Semedi B, Pulicken M, Puntoni M, Purcell G, Quesada L, Quinones-Cardona V, Quirós González V, Quist-Paulsen E, Quraishi M, Rabaa M, Rabaud C, Rabindrarajan E, Rafael A, Rafiq M, Ragazzo G, Rahman AKHA, Rahman RA, Rahutullah A, Rainieri F, Rajahram GS, Rajapakse N, Ralib A, Ramakrishnan N, Ramanathan K, Ramli AA, Rammaert B, Ramos GV, Rana A, Rangappa R, Ranjan R, Rapp C, Rashan A, Rashan T, Rasheed G, Rasmin M, Rätsep I, Rau C, Ravi T, Raza A, Real A, Rebaudet S, Redl S, Reeve B, Rehan A, Rehman A, Reid L, Reid L, Reikvam DH, Reis R, Rello J, Remppis J, Remy M, Ren H, Renk H, Resende L, Resseguier AS, Revest M, Rewa O, Reyes LF, Reyes T, Ribeiro MI, Richardson D, Richardson D, Richier L, Ridzuan SNAA, Riera J, Rios AL, Rishu A, Rispal P, Risso K, Rivera Nuñez MA, Rizer N, Robb D, Robba C, Roberto A, Roberts S, Robertson DL, Robineau O, Roche-Campo F, Rodari P, Rodeia S, Rodriguez Abreu J, Roessler B, Roger C, Roger PM, Roilides E, Rojek A, Romaru J, Roncon-Albuquerque Jr R, Roriz M, Rosa-Calatrava M, Rose M, Rosenberger D, Rossanese A, Rossetti M, Rossignol B, Rossignol P, Rousset S, Roy C, Roze B, Rusmawatiningtyas D, Russell CD, Ryan M, Ryan M, Ryckaert S, Rygh Holten A, Saba I, Sadaf S, Sadat M, Sahraei V, Saint-Gilles M, Sakiyalak P, Salahuddin N, Salazar L, Saleem J, Saleem J, Sales G, Sallaberry S, Salmon Gandonniere C, Salvator H, Sanchez O, Sánchez Choez X, Sanchez de Oliveira K, Sanchez-Miralles A, Sancho-Shimizu V, Sandhu G, Sandhu Z, Sandrine PF, Sandulescu O, Santos M, Sarfo-Mensah S, Sarmento Banheiro B, Sarmiento ICE, Sarton B, Satyapriya S, Satyawati R, Saviciute E, Savio R, Savvidou P, Saw YT, Schaffer J, Schermer T, Scherpereel A, Schneider M, Schroll S, Schwameis M, Schwartz G, Scott JT, Scott-Brown J, Sedillot N, Seitz T, Selvanayagam J, Selvarajoo M, Semaille C, Semple MG, Senian RB, Senneville E, Sepulveda C, Sequeira F, Sequeira T, Serpa Neto A, Serrano Balazote P, Shadowitz E, Shahidan SA, Shahnaz Hasan M, Shamsah M, Shankar A, Sharjeel S, Sharma P, Shaw CA, Shaw V, Shi H, Shiban N, Shiekh M, Shiga T, Shime N, Shimizu H, Shimizu K, Shimizu N, Shindo N, Shrapnel S, Shum HP, Si Mohammed N, Siang NY, Sibiude J, Siddiqui A, Sigfrid L, Sillaots P, Silva C, Silva MJ, Silva R, Sim Lim Heng B, Sin WC, Singh BC, Singh P, Sitompul PA, Sivam K, Skogen V, Smith S, Smood B, Smyth C, Smyth M, Smyth M, Snacken M, So D, Soh TV, Solis M, Solomon J, Solomon T, Somers E, Sommet A, Song MJ, Song R, Song T, Song Chia J, Sonntagbauer M, Soom AM, Sotto A, Soum E, Sousa AC, Sousa M, Sousa Uva M, Souza-Dantas V, Sperry A, Spinuzza E, Sri Darshana BPSR, Sriskandan S, Stabler S, Staudinger T, Stecher SS, Steinsvik T, Stienstra Y, Stiksrud B, Stolz E, Stone A, Streinu-Cercel A, Streinu-Cercel A, Strudwick S, Stuart A, Stuart D, Subekti D, Suen G, Suen JY, Sukumar P, Sultana A, Summers C, Supic D, Suppiah D, Surovcová M, Suwarti S, Svistunov AA, Syahrin S, Syrigos K, Sztajnbok J, Szuldrzynski K, Tabrizi S, Taccone FS, Tagherset L, Taib SM, Talarek E, Taleb S, Talsma J, Tampubolon ML, Tan KK, Tan LV, Tan YC, Tanaka C, Tanaka H, Tanaka T, Taniguchi H, Tanveer H, Taqdees H, Taqi A, Tardivon C, Tattevin P, Taufik MA, Tawfik H, Tedder RS, Tee TY, Teixeira J, Tejada S, Tellier MC, Teoh SK, Teotonio V, Téoulé F, Terpstra P, Terrier O, Terzi N, Tessier-Grenier H, Tey A, Thabit AAM, Tham ZD, Thangavelu S, Thibault V, Thiberville SD, Thill B, Thirumanickam J, Thompson S, Thomson D, Thomson EC, Thurai SRT, Thuy DB, Thwaites RS, Tierney P, Tieroshyn V, Timashev PS, Timsit JF, Tirupakuzhi Vijayaraghavan BK, Tissot N, Toh JZY, Toki M, Tolppa T, Tonby K, Tonnii SL, Torres A, Torres M, Torres Santos-Olmo RM, Torres-Zevallos H, Towers M, Trapani T, Traynor D, Treoux T, Trieu HT, Tripathy S, Tromeur C, Trontzas I, Trouillon T, Truong J, Tual C, Tubiana S, Tuite H, Turmel JM, Turtle LC, Tveita A, Twardowski P, Uchiyama M, Udayanga PGI, Udy A, Ullrich R, Umer Z, Uribe A, Usman A, Vajdovics C, Val-Flores L, Valle AL, Valran A, Van de Velde S, van den Berge M, van der Feltz M, van der Valk P, Van Der Vekens N, Van der Voort P, Van Der Werf S, van Dyk M, van Gulik L, Van Hattem J, van Lelyveld S, van Netten C, Van Twillert G, van Veen I, Vanel N, Vanoverschelde H, Varghese P, Varrone M, Vasudayan SR, Vauchy C, Vaughan H, Veeran S, Veislinger A, Vencken S, Ventura S, Verbon A, Vidal JE, Vieira C, Vijayan D, Villanueva JA, Villar J, Villeneuve PM, Villoldo A, Vinh Chau NV, Visseaux B, Visser H, Vitiello C, Vonkeman H, Vuotto F, Wahab NH, Wahab SA, Wahid NA, Wainstein M, Wan Muhd Shukeri WF, Wang CH, Webb SA, Wei J, Weil K, Wen TP, Wesselius S, West TE, Wham M, Whelan B, White N, Wicky PH, Wiedemann A, Wijaya SO, Wille K, Willems S, Williams V, Wils EJ, Wing Yiu N, Wong C, Wong TF, Wong XC, Wong YS, Xian GE, Xian LS, Xuan KP, Xynogalas I, Yacoub S, Yakop SRBM, Yamazaki M, Yazdanpanah Y, Yee Liang Hing N, Yelnik C, Yeoh CH, Yerkovich S, Yokoyama T, Yonis H, Yousif O, Yuliarto S, Zaaqoq A, Zabbe M, Zacharowski K, Zahid M, Zahran M, Zaidan NZB, Zambon M, Zambrano M, Zanella A, Zawadka K, Zaynah N, Zayyad H, Zoufaly A, Zucman D. The value of open-source clinical science in pandemic response: lessons from ISARIC. Lancet Infect Dis 2021; 21:1623-1624. [PMID: 34619109 PMCID: PMC8489876 DOI: 10.1016/s1473-3099(21)00565-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/16/2021] [Indexed: 12/31/2022]
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McKenna S, Huse KK, Giblin S, Pearson M, Majid Al Shibar MS, Sriskandan S, Matthews S, Pease JE. The Role of Streptococcal Cell-Envelope Proteases in Bacterial Evasion of the Innate Immune System. J Innate Immun 2021; 14:69-88. [PMID: 34649250 PMCID: PMC9082167 DOI: 10.1159/000516956] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/19/2021] [Indexed: 11/19/2022] Open
Abstract
Bacteria possess the ability to evolve varied and ingenious strategies to outwit the host immune system, instigating an evolutionary arms race. Proteases are amongst the many weapons employed by bacteria, which specifically cleave and neutralize key signalling molecules required for a coordinated immune response. In this article, we focus on a family of S8 subtilisin-like serine proteases expressed as cell-envelope proteases (CEPs) by group A and group B streptococci. Two of these proteases known as Streptococcus pyogenes CEP (SpyCEP) and C5a peptidase cleave the chemokine CXCL8 and the complement fragment C5a, respectively. Both CXCL8 and C5a are potent neutrophil-recruiting chemokines, and by neutralizing their activity, streptococci evade a key defence mechanism of innate immunity. We review the mechanisms by which CXCL8 and C5a recruit neutrophils and the characterization of SpyCEP and C5a peptidase, including both in vitro and in vivo studies. Recently described structural insights into the function of this CEP family are also discussed. We conclude by examining the progress of prototypic vaccines incorporating SpyCEP and C5a peptidase in their preparation. Since streptococci-producing SpyCEP and C5a peptidase are responsible for a considerable global disease burden, targeting these proteases by vaccination strategies or by small-molecule antagonists should provide protection from and promote the resolution of streptococcal infections.
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Affiliation(s)
- Sophie McKenna
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Kristin Krohn Huse
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Sean Giblin
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Max Pearson
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | | | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - James Edward Pease
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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Gibson JF, Pidwill GR, Carnell OT, Surewaard BGJ, Shamarina D, Sutton JAF, Jeffery C, Derré-Bobillot A, Archambaud C, Siggins MK, Pollitt EJG, Johnston SA, Serror P, Sriskandan S, Renshaw SA, Foster SJ. Commensal bacteria augment Staphylococcus aureus infection by inactivation of phagocyte-derived reactive oxygen species. PLoS Pathog 2021; 17:e1009880. [PMID: 34529737 PMCID: PMC8478205 DOI: 10.1371/journal.ppat.1009880] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 06/14/2021] [Revised: 09/28/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022] Open
Abstract
Staphylococcus aureus is a human commensal organism and opportunist pathogen, causing potentially fatal disease. The presence of non-pathogenic microflora or their components, at the point of infection, dramatically increases S. aureus pathogenicity, a process termed augmentation. Augmentation is associated with macrophage interaction but by a hitherto unknown mechanism. Here, we demonstrate a breadth of cross-kingdom microorganisms can augment S. aureus disease and that pathogenesis of Enterococcus faecalis can also be augmented. Co-administration of augmenting material also forms an efficacious vaccine model for S. aureus. In vitro, augmenting material protects S. aureus directly from reactive oxygen species (ROS), which correlates with in vivo studies where augmentation restores full virulence to the ROS-susceptible, attenuated mutant katA ahpC. At the cellular level, augmentation increases bacterial survival within macrophages via amelioration of ROS, leading to proliferation and escape. We have defined the molecular basis for augmentation that represents an important aspect of the initiation of infection. S. aureus is a commensal inhabitant of the human skin and nares. However, it can cause serious diseases if it is able to breach our protective barriers such as the skin, often via wounds or surgery. If infection occurs via a wound, this initial inoculum contains both the pathogen, other members of the microflora and also wider environmental microbes. We have previously described “augmentation”, whereby this other non-pathogenic material can enhance the ability of S. aureus to lead to a serious disease outcome. Here we have determined the breadth of augmenting material and elucidated the cellular and molecular basis for its activity. Augmentation occurs via shielding of S. aureus from the direct bactericidal effects of reactive oxygen species produced by macrophages. This initial protection enables the effective establishment of S. aureus infection. Understanding augmentation not only explains an important facet of the interaction of S. aureus with our innate immune system, but also provides a platform for the development of novel prophylaxis approaches.
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Affiliation(s)
- Josie F. Gibson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
- The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Grace R. Pidwill
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
| | - Oliver T. Carnell
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
| | - Bas G. J. Surewaard
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Daria Shamarina
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
| | - Joshua A. F. Sutton
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
| | - Charlotte Jeffery
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | | | - Cristel Archambaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Matthew K. Siggins
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Eric J. G. Pollitt
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
| | - Simon A. Johnston
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
- The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Pascale Serror
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Stephen A. Renshaw
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
- The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular disease, Medical School, University of Sheffield, Sheffield, United Kingdom
- * E-mail: (SAR); (SJF)
| | - Simon J. Foster
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
- * E-mail: (SAR); (SJF)
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27
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Jauneikaite E, Pichon B, Mosavie M, Fallowfield JL, Davey T, Thorpe N, Nelstrop A, Sriskandan S, Lamb LE. Staphylococcus argenteus transmission among healthy Royal Marines: A molecular epidemiology case-study. J Infect 2021; 83:550-553. [PMID: 34469709 DOI: 10.1016/j.jinf.2021.08.040] [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: 05/27/2021] [Revised: 08/03/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022]
Abstract
Objectives During a prospective study of S. aureus carriage in Royal Marines recruits, six S. argenteus strains were identified in four recruits. As S. argenteus sepsis leads to mortality similar to S. aureus, we determined the potential for within same troop transmission, to evaluate future outbreak risk. Methods We used whole-genome sequencing to characterise S. argenteus and investigate phylogenetic relationships between isolates. Results S. argenteus strains (t5078, ST2250) were detected in 4/40 recruits in the same troop (training cohort) in weeks 1, 6 or 15 of training. No mec, tsst or LukPV genes were detected. We identified differences of 1-17 core SNPs between S. argenteus from different recruits. In two recruits, two S. argenteus strains were isolated; these could be distinguished by 2 and 15 core SNPs. Conclusions The identification of S. argenteus within a single troop from the total recruit population suggests a common source for transmission, though high number of SNPs were identified, both within-host and within-cluster. The high number of SNPs between some isolates may indicate a common source of diverse isolates or a high level of S. argenteus mutation in carriage. S. argenteus is newly recognized species; and understanding of the frequency of genetic changes during transmission and transition from asymptomatic carriage to disease is required.
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Affiliation(s)
- Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W2 1PG, UK.
| | - Bruno Pichon
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W2 1PG, UK; Healthcare Associated Infection and Antimicrobial Resistance, National Infection Service, Public Health England, Colindale, UK
| | - Mia Mosavie
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| | | | | | | | - Andrew Nelstrop
- Commando Training Centre Royal Marines, Lympstone, UK; Defence Primary Healthcare, Plymouth, UK
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| | - Lucy E Lamb
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W2 1PG, UK; Academic Department of Military Medicine, Royal Centre for Defence Medicine (Research and Academia), Birmingham, UK; Royal Free London NHS Foundation Trust, London NW3 2QG, UK.
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28
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Li HK, Kaforou M, Rodriguez-Manzano J, Channon-Wells S, Moniri A, Habgood-Coote D, Gupta RK, Mills EA, Arancon D, Lin J, Chiu YH, Pennisi I, Miglietta L, Mehta R, Obaray N, Herberg JA, Wright VJ, Georgiou P, Shallcross LJ, Mentzer AJ, Levin M, Cooke GS, Noursadeghi M, Sriskandan S. Discovery and validation of a three-gene signature to distinguish COVID-19 and other viral infections in emergency infectious disease presentations: a case-control and observational cohort study. Lancet Microbe 2021; 2:e594-e603. [PMID: 34423323 PMCID: PMC8367196 DOI: 10.1016/s2666-5247(21)00145-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background Emergency admissions for infection often lack initial diagnostic certainty. COVID-19 has highlighted a need for novel diagnostic approaches to indicate likelihood of viral infection in a pandemic setting. We aimed to derive and validate a blood transcriptional signature to detect viral infections, including COVID-19, among adults with suspected infection who presented to the emergency department. Methods Individuals (aged ≥18 years) presenting with suspected infection to an emergency department at a major teaching hospital in the UK were prospectively recruited as part of the Bioresource in Adult Infectious Diseases (BioAID) discovery cohort. Whole-blood RNA sequencing was done on samples from participants with subsequently confirmed viral, bacterial, or no infection diagnoses. Differentially expressed host genes that met additional filtering criteria were subjected to feature selection to derive the most parsimonious discriminating signature. We validated the signature via RT-qPCR in a prospective validation cohort of participants who presented to an emergency department with undifferentiated fever, and a second case-control validation cohort of emergency department participants with PCR-positive COVID-19 or bacterial infection. We assessed signature performance by calculating the area under receiver operating characteristic curves (AUROCs), sensitivities, and specificities. Findings A three-gene transcript signature, comprising HERC6, IGF1R, and NAGK, was derived from the discovery cohort of 56 participants with bacterial infections and 27 with viral infections. In the validation cohort of 200 participants, the signature differentiated bacterial from viral infections with an AUROC of 0·976 (95% CI 0·919−1·000), sensitivity of 97·3% (85·8−99·9), and specificity of 100% (63·1−100). The AUROC for C-reactive protein (CRP) was 0·833 (0·694−0·944) and for leukocyte count was 0·938 (0·840−0·986). The signature achieved higher net benefit in decision curve analysis than either CRP or leukocyte count for discriminating viral infections from all other infections. In the second validation analysis, which included SARS-CoV-2-positive participants, the signature discriminated 35 bacterial infections from 34 SARS-CoV-2-positive COVID-19 infections with AUROC of 0·953 (0·893−0·992), sensitivity 88·6%, and specificity of 94·1%. Interpretation This novel three-gene signature discriminates viral infections, including COVID-19, from other emergency infection presentations in adults, outperforming both leukocyte count and CRP, thus potentially providing substantial clinical utility in managing acute presentations with infection. Funding National Institute for Health Research, Medical Research Council, Wellcome Trust, and EU-FP7.
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Affiliation(s)
- Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London, UK
- Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Myrsini Kaforou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Imperial College London, London, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infection & Antimicrobial Resistance, Imperial College London, London, UK
| | | | - Ahmad Moniri
- Department of Electrical & Electronic Engineering, Imperial College London, London, UK
| | | | - Rishi K Gupta
- Institute of Global Health, University College London, London, UK
| | - Ewurabena A Mills
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Jessica Lin
- Department of Infectious Disease, Imperial College London, London, UK
| | - Yueh-Ho Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ivana Pennisi
- Department of Infectious Disease, Imperial College London, London, UK
| | - Luca Miglietta
- Department of Infectious Disease, Imperial College London, London, UK
- Department of Electrical & Electronic Engineering, Imperial College London, London, UK
| | - Ravi Mehta
- Department of Infectious Disease, Imperial College London, London, UK
| | - Nelofar Obaray
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jethro A Herberg
- Department of Infectious Disease, Imperial College London, London, UK
| | - Victoria J Wright
- Department of Infectious Disease, Imperial College London, London, UK
| | - Pantelis Georgiou
- Department of Electrical & Electronic Engineering, Imperial College London, London, UK
- Centre for Bio-Inspired Technology, Imperial College London, London, UK
| | | | | | - Michael Levin
- Department of Infectious Disease, Imperial College London, London, UK
| | - Graham S Cooke
- Department of Infectious Disease, Imperial College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK
- Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infection & Antimicrobial Resistance, Imperial College London, London, UK
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29
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Taylor E, Bal AM, Balakrishnan I, Brown NM, Burns P, Clark M, Diggle M, Donaldson H, Eltringham I, Folb J, Gadsby N, Macleod M, Ratnaraja NVDV, Williams C, Wootton M, Sriskandan S, Woodford N, Hopkins KL. A prospective surveillance study to determine the prevalence of 16S rRNA methyltransferase-producing Gram-negative bacteria in the UK. J Antimicrob Chemother 2021; 76:2428-2436. [PMID: 34142130 DOI: 10.1093/jac/dkab186] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/06/2021] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES To determine the prevalence of 16S rRNA methyltransferase- (16S RMTase-) producing Gram-negative bacteria in patients in the UK and to identify potential risk factors for their acquisition. METHODS A 6 month prospective surveillance study was conducted from 1 May to 31 October 2016, wherein 14 hospital laboratories submitted Acinetobacter baumannii, Enterobacterales and Pseudomonas aeruginosa isolates that displayed high-level amikacin resistance according to their testing methods, e.g. no zone of inhibition with amikacin discs. Isolates were linked to patient travel history, medical care abroad, and previous antibiotic exposure using a surveillance questionnaire. In the reference laboratory, isolates confirmed to grow on Mueller-Hinton agar supplemented with 256 mg/L amikacin were screened by PCR for 16S RMTase genes armA, rmtA-rmtH and npmA, and carbapenemase genes (blaKPC, blaNDM, blaOXA-48-like and blaVIM). STs and total antibiotic resistance gene complement were determined via WGS. Prevalence was determined using denominators for each bacterial species provided by participating hospital laboratories. RESULTS Eighty-four isolates (44.7%), among 188 submitted isolates, exhibited high-level amikacin resistance (MIC >256 mg/L), and 79 (94.0%) of these harboured 16S RMTase genes. armA (54.4%, 43/79) was the most common, followed by rmtB (17.7%, 14/79), rmtF (13.9%, 11/79), rmtC (12.7%, 10/79) and armA + rmtF (1.3%, 1/79). The overall period prevalence of 16S RMTase-producing Gram-negative bacteria was 0.1% (79/71 063). Potential risk factors identified through multivariate statistical analysis included being male and polymyxin use. CONCLUSIONS The UK prevalence of 16S RMTase-producing Gram-negative bacteria is low, but continued surveillance is needed to monitor their spread and inform intervention strategies.
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Affiliation(s)
- Emma Taylor
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK.,Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Abhijit M Bal
- Microbiology, University Hospital Crosshouse, NHS Ayrshire and Arran, Kilmarnock, KA2 0BE, UK
| | | | - Nicholas M Brown
- Clinical Microbiology and Public Health Laboratory Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QW, UK
| | - Phillipa Burns
- Manchester Medical Microbiology Partnership, Manchester University NHS Foundation Trust, Manchester Royal Infirmary, Oxford Rd, Manchester, M13 9WL, UK
| | - Marilyn Clark
- Department of Medical Microbiology, Ninewells Hospital, Dundee, DD2 1SY, UK
| | - Mathew Diggle
- Nottingham University Hospitals National Health Service Trust, Hucknall Rd, Nottingham, NG5 1PB, UK
| | - Hugo Donaldson
- Imperial College Healthcare NHS Trust, Charing Cross Hospital, Fulham Palace Road, London, W6 8RF, UK
| | - Ian Eltringham
- Microbiology Department, King's College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Jonathan Folb
- Liverpool University Hospitals NHS Foundation Trust, Prescot St, Liverpool, L7 8XP, UK
| | - Naomi Gadsby
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Cres, Edinburgh, EH16 4SA, UK
| | - Mairi Macleod
- Clinical Microbiology, Glasgow Royal Infirmary Hospital, Level 4 New Lister Building, 10-16 Alexandra Parade, Glasgow, G31 2ER, UK
| | - Natasha V D V Ratnaraja
- Department of Microbiology, Sandwell and West Birmingham NHS Trust, Dudley Road, Birmingham, B18 7QH, UK
| | - Cheryl Williams
- Microbiology Laboratory, First Floor, Pathology Laboratory, Royal Oldham Hospital, Rochdale Road, Oldham, OL1 2JH, UK
| | - Mandy Wootton
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Shiranee Sriskandan
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK.,MRC Centre for Molecular Bacteriology & Infection, Imperial College London, London, SW7 2DD, UK
| | - Neil Woodford
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK.,Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Katie L Hopkins
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK.,Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, NW9 5EQ, UK
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30
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Collin SM, Groves N, O'Sullivan C, Jauneikaite E, Patel D, Cunney R, Meehan M, Reynolds A, Smith A, Lindsay D, Doherty L, Davies E, Chalker V, Lamb P, Afshar B, Balasegaram S, Coelho J, Ready D, Brown CS, Efstratiou A, Le Doare K, Sriskandan S, Heath PT, Lamagni T. Uncovering Infant Group B Streptococcal (GBS) Disease Clusters in the United Kingdom and Ireland Through Genomic Analysis: A Population-based Epidemiological Study. Clin Infect Dis 2021; 72:e296-e302. [PMID: 32766850 DOI: 10.1093/cid/ciaa1087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 04/23/2020] [Accepted: 07/28/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The true frequency of hospital outbreaks of invasive group B streptococcal (iGBS; Streptococcus agalactiae) disease in infants is unknown. We used whole genome sequencing (WGS) of iGBS isolates collected during a period of enhanced surveillance of infant iGBS disease in the UK and Ireland to determine the number of clustered cases. METHODS Potentially linked iGBS cases from infants with early (<7 days of life) or late-onset (7-89 days) disease were identified from WGS data (HiSeq 2500 platform, Illumina) from clinical sterile site isolates collected between 04/2014 and 04/2015. We assessed time and place of cases to determine a single-nucleotide polymorphism (SNP) difference threshold for clustered cases. Case details were augmented through linkage to national hospital admission data and hospital record review by local microbiologists. RESULTS Analysis of sequences indicated a cutoff of ≤5 SNP differences to define iGBS clusters. Among 410 infant iGBS isolates, we identified 7 clusters (4 genetically identical pairs with 0 SNP differences, 1 pair with 3 SNP differences, 1 cluster of 4 cases with ≤1 SNP differences) of which 4 clusters were uncovered for the first time. The clusters comprised 16 cases, of which 15 were late-onset (of 192 late-onset cases with sequenced isolates) and 1 an early-onset index case. Serial intervals between cases ranged from 0 to 59 (median 12) days. CONCLUSIONS Approximately 1 in 12 late-onset infant iGBS cases were part of a hospital cluster. Over half of the clusters were previously undetected, emphasizing the importance of routine submission of iGBS isolates to reference laboratories for cluster identification and genomic confirmation.
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Affiliation(s)
- Simon M Collin
- Healthcare-Associated Infection and Antimicrobial Resistance (HCAI & AMR) Division, National Infection Service, Public Health England, London, United Kingdom
| | - Natalie Groves
- Respiratory and Vaccine Preventable Bacteria Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Catherine O'Sullivan
- Paediatric Infectious Diseases Research Group, St George's University of London, London, United Kingdom
| | - Elita Jauneikaite
- NIHR Health Protection Unit in Healthcare-associated Infections and Antimicrobial Resistance, Imperial College, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, United Kingdom
| | - Darshana Patel
- Respiratory and Vaccine Preventable Bacteria Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Robert Cunney
- Health Service Executive Health Protection Surveillance Centre, Dublin, Ireland.,Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland at Temple Street, Dublin, Ireland
| | - Mary Meehan
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland at Temple Street, Dublin, Ireland
| | | | - Andrew Smith
- College of Medical, Veterinary & Life Sciences, Glasgow Dental Hospital & School, University of Glasgow, Glasgow, United Kingdom.,Scottish Microbiology Reference Laboratory, Glasgow, United Kingdom
| | - Diane Lindsay
- Scottish Microbiology Reference Laboratory, Glasgow, United Kingdom
| | | | | | - Victoria Chalker
- Respiratory and Vaccine Preventable Bacteria Reference Unit, National Infection Service, Public Health England, London, United Kingdom.,NIHR Health Protection Unit in Healthcare-associated Infections and Antimicrobial Resistance, Imperial College, London, United Kingdom
| | - Peter Lamb
- Healthcare-Associated Infection and Antimicrobial Resistance (HCAI & AMR) Division, National Infection Service, Public Health England, London, United Kingdom
| | - Baharak Afshar
- Respiratory and Vaccine Preventable Bacteria Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Sooria Balasegaram
- Field Service, National Infection Service, Public Health England, London, United Kingdom
| | - Juliana Coelho
- Respiratory and Vaccine Preventable Bacteria Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Derren Ready
- Respiratory and Vaccine Preventable Bacteria Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Colin S Brown
- Healthcare-Associated Infection and Antimicrobial Resistance (HCAI & AMR) Division, National Infection Service, Public Health England, London, United Kingdom
| | - Androulla Efstratiou
- NIHR Health Protection Unit in Healthcare-associated Infections and Antimicrobial Resistance, Imperial College, London, United Kingdom.,WHO Global Collaborating Centre for Reference and Research on Diphtheria and Streptococcal Infections, National Infection Service, Public Health England, London, United Kingdom
| | - Kirsty Le Doare
- Paediatric Infectious Diseases Research Group, St George's University of London, London, United Kingdom.,Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda.,Pathogen Immunity Group, Public Health England, Porton Down, United Kingdom
| | - Shiranee Sriskandan
- NIHR Health Protection Unit in Healthcare-associated Infections and Antimicrobial Resistance, Imperial College, London, United Kingdom.,MRC Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College, London, United Kingdom
| | - Paul T Heath
- Paediatric Infectious Diseases Research Group, St George's University of London, London, United Kingdom
| | - Theresa Lamagni
- Healthcare-Associated Infection and Antimicrobial Resistance (HCAI & AMR) Division, National Infection Service, Public Health England, London, United Kingdom.,NIHR Health Protection Unit in Healthcare-associated Infections and Antimicrobial Resistance, Imperial College, London, United Kingdom
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31
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Ellington MJ, Davies F, Jauneikaite E, Hopkins KL, Turton JF, Adams G, Pavlu J, Innes AJ, Eades C, Brannigan ET, Findlay J, White L, Bolt F, Kadhani T, Chow Y, Patel B, Mookerjee S, Otter JA, Sriskandan S, Woodford N, Holmes A. A Multispecies Cluster of GES-5 Carbapenemase-Producing Enterobacterales Linked by a Geographically Disseminated Plasmid. Clin Infect Dis 2021; 71:2553-2560. [PMID: 31746994 PMCID: PMC7744980 DOI: 10.1093/cid/ciz1130] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Early and accurate treatment of infections due to carbapenem-resistant organisms is facilitated by rapid diagnostics, but rare resistance mechanisms can compromise detection. One year after a Guiana Extended-Spectrum (GES)-5 carbapenemase-positive Klebsiella oxytoca infection was identified by whole-genome sequencing (WGS; later found to be part of a cluster of 3 cases), a cluster of 11 patients with GES-5-positive K. oxytoca was identified over 18 weeks in the same hospital. METHODS Bacteria were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry, antimicrobial susceptibility testing followed European Committee on Antimicrobial Susceptibility Testing guidelines. Ertapenem-resistant isolates were referred to Public Health England for characterization using polymerase chain reaction (PCR) detection of GES, pulsed-field gel electrophoresis (PFGE), and WGS for the second cluster. RESULTS The identification of the first GES-5 K. oxytoca isolate was delayed, being identified by WGS. Implementation of a GES-gene PCR informed the occurrence of the second cluster in real time. In contrast to PFGE, WGS phylogenetic analysis refuted an epidemiological link between the 2 clusters; it also suggested a cascade of patient-to-patient transmission in the later cluster. A novel GES-5-encoding plasmid was present in K. oxytoca, Escherichia coli, and Enterobacter cloacae isolates from unlinked patients within the same hospital group and in human and wastewater isolates from 3 hospitals elsewhere in the United Kingdom. CONCLUSIONS Genomic sequencing revolutionized the epidemiological understanding of the clusters; it also underlined the risk of covert plasmid propagation in healthcare settings and revealed the national distribution of the resistance-encoding plasmid. Sequencing results also informed and led to the ongoing use of enhanced diagnostic tests for detecting carbapenemases locally and nationally.
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Affiliation(s)
- Matthew J Ellington
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom.,Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infections Service, Public Health England, London, United Kingdom
| | - Frances Davies
- Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Elita Jauneikaite
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Katie L Hopkins
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom.,Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infections Service, Public Health England, London, United Kingdom
| | - Jane F Turton
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infections Service, Public Health England, London, United Kingdom
| | - George Adams
- Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Jiri Pavlu
- Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Andrew J Innes
- Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Christopher Eades
- Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Eimear T Brannigan
- Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Jacqueline Findlay
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infections Service, Public Health England, London, United Kingdom
| | - Leila White
- Microbiology, Royal Preston Hospital, Lancashire Teaching Hospitals National Health Service Foundation Trust, Preston, United Kingdom
| | - Frances Bolt
- Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Tokozani Kadhani
- Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Yimmy Chow
- North West London Health Protection Team, Public Health England, London, United Kingdom
| | - Bharat Patel
- Public Health Laboratory London, National Infections Service, Public Health England, London, United Kingdom
| | - Siddharth Mookerjee
- Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Jonathan A Otter
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom.,Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Shiranee Sriskandan
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Neil Woodford
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom.,Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infections Service, Public Health England, London, United Kingdom
| | - Alison Holmes
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom.,Imperial College Healthcare National Health Service Trust, London, United Kingdom
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Tan LKK, Reglinski M, Teo D, Reza N, Lamb LEM, Nageshwaran V, Turner CE, Wikstrom M, Frick IM, Bjorck L, Sriskandan S. Vaccine-induced, but not natural immunity, against the Streptococcal inhibitor of complement protects against invasive disease. NPJ Vaccines 2021; 6:62. [PMID: 33888727 PMCID: PMC8062509 DOI: 10.1038/s41541-021-00326-3] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/23/2021] [Indexed: 01/25/2023] Open
Abstract
Highly pathogenic emm1 Streptococcus pyogenes strains secrete the multidomain Streptococcal inhibitor of complement (SIC) that binds and inactivates components of the innate immune response. We aimed to determine if naturally occurring or vaccine-induced antibodies to SIC are protective against invasive S. pyogenes infection. Immunisation with full-length SIC protected mice against systemic bacterial dissemination following intranasal or intramuscular infection with emm1 S. pyogenes. Vaccine-induced rabbit anti-SIC antibodies, but not naturally occurring human anti-SIC antibodies, enhanced bacterial clearance in an ex vivo whole-blood assay. SIC vaccination of both mice and rabbits resulted in antibody recognition of all domains of SIC, whereas naturally occurring human anti-SIC antibodies recognised the proline-rich region of SIC only. We, therefore, propose a model whereby natural infection with S. pyogenes generates non-protective antibodies against the proline-rich region of SIC, while vaccination with full-length SIC permits the development of protective antibodies against all SIC domains.
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Affiliation(s)
- Lionel K K Tan
- Section of Adult Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
| | - Mark Reglinski
- Section of Adult Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK.,School of Life Sciences, University of Dundee, Dundee, UK
| | - Daryl Teo
- Section of Adult Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
| | - Nada Reza
- Section of Adult Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
| | - Lucy E M Lamb
- Section of Adult Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK.,Academic Department of Military Medicine, Royal Centre for Defence Medicine, Birmingham, UK
| | - Vaitehi Nageshwaran
- Section of Adult Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
| | - Claire E Turner
- Section of Adult Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK.,The Florey Institute, University of Sheffield, Sheffield, UK
| | - Mats Wikstrom
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.,Amgen Inc, Attribute Sciences, Thousand Oaks, CA, USA
| | - Inga-Maria Frick
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Lars Bjorck
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Shiranee Sriskandan
- Section of Adult Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK.
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33
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Siggins MK, Lynskey NN, Lamb LE, Johnson LA, Huse KK, Pearson M, Banerji S, Turner CE, Woollard K, Jackson DG, Sriskandan S. Extracellular bacterial lymphatic metastasis drives Streptococcus pyogenes systemic infection. Nat Commun 2020; 11:4697. [PMID: 32943639 PMCID: PMC7498588 DOI: 10.1038/s41467-020-18454-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
Unassisted metastasis through the lymphatic system is a mechanism of dissemination thus far ascribed only to cancer cells. Here, we report that Streptococcus pyogenes also hijack lymphatic vessels to escape a local infection site, transiting through sequential lymph nodes and efferent lymphatic vessels to enter the bloodstream. Contrasting with previously reported mechanisms of intracellular pathogen carriage by phagocytes, we show S. pyogenes remain extracellular during transit, first in afferent and then efferent lymphatics that carry the bacteria through successive draining lymph nodes. We identify streptococcal virulence mechanisms important for bacterial lymphatic dissemination and show that metastatic streptococci within infected lymph nodes resist and subvert clearance by phagocytes, enabling replication that can seed intense bloodstream infection. The findings establish the lymphatic system as both a survival niche and conduit to the bloodstream for S. pyogenes, explaining the phenomenon of occult bacteraemia. This work provides new perspectives in streptococcal pathogenesis with implications for immunity. Pathogenic agents can spread from an initial to a secondary site via the lymphatics. Here, using a mouse model of infection, the authors show that S. pyogenes readily transit through sequential lymph nodes within efferent lymphatics to reach the bloodstream and drive systemic infection, while remaining extracellular.
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Affiliation(s)
- Matthew K Siggins
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK. .,MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2DD, UK. .,NLHI, Imperial College London, London, W2 1PG, UK.
| | - Nicola N Lynskey
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK.,MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2DD, UK.,The Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Lucy E Lamb
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK
| | - Louise A Johnson
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Kristin K Huse
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK.,MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2DD, UK
| | - Max Pearson
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK.,MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2DD, UK
| | - Suneale Banerji
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Claire E Turner
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK.,The Florey Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Kevin Woollard
- Centre for Inflammatory Disease, Department of Immunology & Inflammation, Imperial College London, London, W12 0NN, UK
| | - David G Jackson
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, W12 0NN, UK. .,MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2DD, UK.
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Rawson TM, Hernandez B, Moore LSP, Blandy O, Herrero P, Gilchrist M, Gordon A, Toumazou C, Sriskandan S, Georgiou P, Holmes AH. Supervised machine learning for the prediction of infection on admission to hospital: a prospective observational cohort study. J Antimicrob Chemother 2020; 74:1108-1115. [PMID: 30590545 DOI: 10.1093/jac/dky514] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 10/11/2018] [Accepted: 11/14/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Infection diagnosis can be challenging, relying on clinical judgement and non-specific markers of infection. We evaluated a supervised machine learning (SML) algorithm for diagnosing bacterial infection using routinely available blood parameters on presentation to hospital. METHODS An SML algorithm was developed to classify cases into infection versus no infection using microbiology records and six available blood parameters (C-reactive protein, white cell count, bilirubin, creatinine, ALT and alkaline phosphatase) from 160203 individuals. A cohort of patients admitted to hospital over a 6 month period had their admission blood parameters prospectively inputted into the SML algorithm. They were prospectively followed up from admission to classify those who fulfilled clinical case criteria for a community-acquired bacterial infection within 72 h of admission using a pre-determined definition. Predictive ability was assessed using receiver operating characteristics (ROC) with cut-off values for optimal sensitivity and specificity explored. RESULTS One hundred and four individuals were included prospectively. The median (range) cohort age was 65 (21-98) years. The majority were female (56/104; 54%). Thirty-six (35%) were diagnosed with infection in the first 72 h of admission. Overall, 44/104 (42%) individuals had microbiological investigations performed. Treatment was prescribed for 33/36 (92%) of infected individuals and 4/68 (6%) of those with no identifiable bacterial infection. Mean (SD) likelihood estimates for those with and without infection were significantly different. The infection group had a likelihood of 0.80 (0.09) and the non-infection group 0.50 (0.29) (P < 0.01; 95% CI: 0.20-0.40). ROC AUC was 0.84 (95% CI: 0.76-0.91). CONCLUSIONS An SML algorithm was able to diagnose infection in individuals presenting to hospital using routinely available blood parameters.
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Affiliation(s)
- T M Rawson
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, Du Cane Road, London, UK.,Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London, UK
| | - B Hernandez
- Department of Electrical and Electronic Engineering, Imperial College London, South Kensington Campus, London, UK
| | - L S P Moore
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, Du Cane Road, London, UK.,Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London, UK
| | - O Blandy
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, Du Cane Road, London, UK
| | - P Herrero
- Department of Electrical and Electronic Engineering, Imperial College London, South Kensington Campus, London, UK
| | - M Gilchrist
- Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London, UK
| | - A Gordon
- Section of Anaesthetics, Pain Medicine & Intensive Care, Imperial College London, South Kensington Campus, London, UK
| | - C Toumazou
- Department of Electrical and Electronic Engineering, Imperial College London, South Kensington Campus, London, UK
| | - S Sriskandan
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, Du Cane Road, London, UK.,Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London, UK
| | - P Georgiou
- Department of Electrical and Electronic Engineering, Imperial College London, South Kensington Campus, London, UK
| | - A H Holmes
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, Du Cane Road, London, UK.,Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London, UK
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35
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Rawson TM, Hernandez B, Moore LSP, Herrero P, Charani E, Ming D, Wilson RC, Blandy O, Sriskandan S, Gilchrist M, Toumazou C, Georgiou P, Holmes AH. A Real-world Evaluation of a Case-based Reasoning Algorithm to Support Antimicrobial Prescribing Decisions in Acute Care. Clin Infect Dis 2020; 72:2103-2111. [DOI: 10.1093/cid/ciaa383] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/02/2020] [Indexed: 12/16/2022] Open
Abstract
Abstract
Background
A locally developed case-based reasoning (CBR) algorithm, designed to augment antimicrobial prescribing in secondary care was evaluated.
Methods
Prescribing recommendations made by a CBR algorithm were compared to decisions made by physicians in clinical practice. Comparisons were examined in 2 patient populations: first, in patients with confirmed Escherichia coli blood stream infections (“E. coli patients”), and second in ward-based patients presenting with a range of potential infections (“ward patients”). Prescribing recommendations were compared against the Antimicrobial Spectrum Index (ASI) and the World Health Organization Essential Medicine List Access, Watch, Reserve (AWaRe) classification system. Appropriateness of a prescription was defined as the spectrum of the prescription covering the known or most-likely organism antimicrobial sensitivity profile.
Results
In total, 224 patients (145 E. coli patients and 79 ward patients) were included. Mean (standard deviation) age was 66 (18) years with 108/224 (48%) female sex. The CBR recommendations were appropriate in 202/224 (90%) compared to 186/224 (83%) in practice (odds ratio [OR]: 1.24 95% confidence interval [CI]: .392–3.936; P = .71). CBR recommendations had a smaller ASI compared to practice with a median (range) of 6 (0–13) compared to 8 (0–12) (P < .01). CBR recommendations were more likely to be classified as Access class antimicrobials compared to physicians’ prescriptions at 110/224 (49%) vs. 79/224 (35%) (OR: 1.77; 95% CI: 1.212–2.588; P < .01). Results were similar for E. coli and ward patients on subgroup analysis.
Conclusions
A CBR-driven decision support system provided appropriate recommendations within a narrower spectrum compared to current clinical practice. Future work must investigate the impact of this intervention on prescribing behaviors more broadly and patient outcomes.
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Affiliation(s)
- Timothy M Rawson
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London, United Kingdom
- Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom
| | - Bernard Hernandez
- Department of Electrical and Electronic Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Luke S P Moore
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London, United Kingdom
- Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom
- Chelsea & Westminster NHS Foundation Trust, London, United Kingdom
| | - Pau Herrero
- Department of Electrical and Electronic Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Esmita Charani
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Damien Ming
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Richard C Wilson
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London, United Kingdom
- Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom
| | - Oliver Blandy
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Shiranee Sriskandan
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Mark Gilchrist
- Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom
| | - Christofer Toumazou
- Department of Electrical and Electronic Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Alison H Holmes
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London, United Kingdom
- Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom
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McKenna S, Malito E, Rouse SL, Abate F, Bensi G, Chiarot E, Micoli F, Mancini F, Gomes Moriel D, Grandi G, Mossakowska D, Pearson M, Xu Y, Pease J, Sriskandan S, Margarit I, Bottomley MJ, Matthews S. Structure, dynamics and immunogenicity of a catalytically inactive C XC chemokine-degrading protease SpyCEP from Streptococcus pyogenes. Comput Struct Biotechnol J 2020; 18:650-660. [PMID: 32257048 PMCID: PMC7113628 DOI: 10.1016/j.csbj.2020.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 12/21/2022] Open
Abstract
Over 18 million disease cases and half a million deaths worldwide are estimated to be caused annually by Group A Streptococcus. A vaccine to prevent GAS disease is urgently needed. SpyCEP (Streptococcus pyogenes Cell-Envelope Proteinase) is a surface-exposed serine protease that inactivates chemokines, impairing neutrophil recruitment and bacterial clearance, and has shown promising immunogenicity in preclinical models. Although SpyCEP structure has been partially characterized, a more complete and higher resolution understanding of its antigenic features would be desirable prior to large scale manufacturing. To address these gaps and facilitate development of this globally important vaccine, we performed immunogenicity studies with a safety-engineered SpyCEP mutant, and comprehensively characterized its structure by combining X-ray crystallography, NMR spectroscopy and molecular dynamics simulations. We found that the catalytically-inactive SpyCEP antigen conferred protection similar to wild-type SpyCEP in a mouse infection model. Further, a new higher-resolution crystal structure of the inactive SpyCEP mutant provided new insights into this large chemokine protease comprising nine domains derived from two non-covalently linked fragments. NMR spectroscopy and molecular simulation analyses revealed conformational flexibility that is likely important for optimal substrate recognition and overall function. These combined immunogenicity and structural data demonstrate that the full-length SpyCEP inactive mutant is a strong candidate human vaccine antigen. These findings show how a multi-disciplinary study was used to overcome obstacles in the development of a GAS vaccine, an approach applicable to other future vaccine programs. Moreover, the information provided may also facilitate the structure-based discovery of small-molecule therapeutics targeting SpyCEP protease inhibition.
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Affiliation(s)
- Sophie McKenna
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, UK
| | - Enrico Malito
- GlaxoSmithKline, 14200 Shady Grove Road, Rockville, MD 20850, United States
| | - Sarah L. Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, UK
| | | | | | | | - Francesca Micoli
- GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy
| | - Francesca Mancini
- GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy
| | - Danilo Gomes Moriel
- GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy
| | - Guido Grandi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Danuta Mossakowska
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University Krakow, Gronostajowa 7a Str, 30-387 Krakow, Poland
| | - Max Pearson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, UK
| | - James Pease
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | | | | | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, UK
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Turner CE, Holden MTG, Blane B, Horner C, Peacock SJ, Sriskandan S. The Emergence of Successful Streptococcus pyogenes Lineages through Convergent Pathways of Capsule Loss and Recombination Directing High Toxin Expression. mBio 2019; 10:e02521-19. [PMID: 31822586 PMCID: PMC6904876 DOI: 10.1128/mbio.02521-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022] Open
Abstract
Gene transfer and homologous recombination in Streptococcus pyogenes has the potential to trigger the emergence of pandemic lineages, as exemplified by lineages of emm1 and emm89 that emerged in the 1980s and 2000s, respectively. Although near-identical replacement gene transfer events in the nga (NADase) and slo (streptolysin O) loci conferring high expression of these toxins underpinned the success of these lineages, extension to other emm genotype lineages is unreported. The emergent emm89 lineage was characterized by five regions of homologous recombination additional to nga-slo, including complete loss of the hyaluronic acid capsule synthesis locus hasABC, a genetic trait replicated in two other leading emm types and recapitulated by other emm types by inactivating mutations. We hypothesized that other leading genotypes may have undergone similar recombination events. We analyzed a longitudinal data set of genomes from 344 clinical invasive disease isolates representative of locations across England, dating from 2001 to 2011, and an international collection of S. pyogenes genomes representing 54 different genotypes and found frequent evidence of recombination events at the nga-slo locus predicted to confer higher toxin genotype. We identified multiple associations between recombination at this locus and inactivating mutations within hasAB, suggesting convergent evolutionary pathways in successful genotypes. This included common genotypes emm28 and emm87. The combination of no or low capsule and high expression of nga and slo may underpin the success of many emergent S. pyogenes lineages of different genotypes, triggering new pandemics, and could change the way S. pyogenes causes disease.IMPORTANCEStreptococcus pyogenes is a genetically diverse pathogen, with over 200 different genotypes defined by emm typing, but only a minority of these genotypes are responsible for the majority of human infection in high-income countries. Two prevalent genotypes associated with disease rose to international dominance following recombination of a toxin locus that conferred increased expression. Here, we found that recombination of this locus and promoter has occurred in other diverse genotypes, events that may allow these genotypes to expand in the population. We identified an association between the loss of hyaluronic acid capsule synthesis and high toxin expression, which we propose may be associated with an adaptive advantage. As S. pyogenes pathogenesis depends both on capsule and toxin production, new variants with altered expression may result in abrupt changes in the molecular epidemiology of this pathogen in the human population over time.
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Affiliation(s)
- Claire E Turner
- Molecular Biology & Biotechnology, The Florey Institute, University of Sheffield, Sheffield, United Kingdom
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Matthew T G Holden
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Carolyne Horner
- British Society for Antimicrobial Chemotherapy, Birmingham, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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38
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Collin SM, Lamb P, Jauneikaite E, Le Doare K, Creti R, Berardi A, Heath PT, Sriskandan S, Lamagni T. Hospital clusters of invasive Group B Streptococcal disease: A systematic review. J Infect 2019; 79:521-527. [PMID: 31733233 DOI: 10.1016/j.jinf.2019.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 11/04/2019] [Accepted: 11/08/2019] [Indexed: 01/30/2023]
Abstract
OBJECTIVES To characterize outbreaks of invasive Group B Streptococcal (iGBS) disease in hospitals. METHODS Systematic review using electronic databases to identify studies describing iGBS outbreaks/clusters or cross-infection/acquisition in healthcare settings where 'cluster' was defined as ≥2 linked cases. PROSPERO CRD42018096297. RESULTS Twenty-five references were included describing 30 hospital clusters (26 neonatal, 4 adult) in 11 countries from 1966 to 2019. Cross-infection between unrelated neonates was reported in 19 clusters involving an early-onset (<7 days of life; n = 3), late-onset (7-90 days; n = 13) index case or colonized infant (n = 3) followed by one or more late-onset cases (median serial interval 9 days (IQR 3-17, range 0-50 days, n = 45)); linkage was determined by phage typing in 3 clusters, PFGE/MLST/PCR in 8, WGS in 4, non-molecular methods in 4. Postulated routes of transmission in neonatal clusters were via clinical personnel and equipment, particularly during periods of crowding and high patient-to-nurse ratio. Of 4 adult clusters, one was attributed to droplet spread between respiratory cases, one to handling of haemodialysis catheters and two unspecified. CONCLUSIONS Long intervals between cases were identified in most of the clusters, a characteristic which potentially hinders detection of GBS hospital outbreaks without enhanced surveillance supported by genomics.
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Affiliation(s)
- Simon M Collin
- Healthcare-Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK.
| | - Peter Lamb
- Healthcare-Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, UK; NIHR Health Protection Research Unit in Healthcare-Associated Infections and Antimicrobial Resistance, Imperial College, London, UK
| | - Kirsty Le Doare
- Paediatric Infectious Diseases Research Group, St George's University of London, London, UK; MRC/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda; Pathogen Immunity Group, Public Health England, Porton Down, UK
| | - Roberta Creti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Alberto Berardi
- Neonatal Intensive Care Unit, Maternal and Child Department, University Hospital, Modena, Italy
| | - Paul T Heath
- Paediatric Infectious Diseases Research Group, St George's University of London, London, UK
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare-Associated Infections and Antimicrobial Resistance, Imperial College, London, UK; MRC Centre for Molecular Bacteriology & Infection, Imperial College, London, UK
| | - Theresa Lamagni
- Healthcare-Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; NIHR Health Protection Research Unit in Healthcare-Associated Infections and Antimicrobial Resistance, Imperial College, London, UK
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Lynskey NN, Jauneikaite E, Li HK, Zhi X, Turner CE, Mosavie M, Pearson M, Asai M, Lobkowicz L, Chow JY, Parkhill J, Lamagni T, Chalker VJ, Sriskandan S. Emergence of dominant toxigenic M1T1 Streptococcus pyogenes clone during increased scarlet fever activity in England: a population-based molecular epidemiological study. Lancet Infect Dis 2019; 19:1209-1218. [PMID: 31519541 PMCID: PMC6838661 DOI: 10.1016/s1473-3099(19)30446-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/19/2019] [Accepted: 08/12/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Since 2014, England has seen increased scarlet fever activity unprecedented in modern times. In 2016, England's scarlet fever seasonal rise coincided with an unexpected elevation in invasive Streptococcus pyogenes infections. We describe the molecular epidemiological investigation of these events. METHODS We analysed changes in S pyogenes emm genotypes, and notifications of scarlet fever and invasive disease in 2014-16 using regional (northwest London) and national (England and Wales) data. Genomes of 135 non-invasive and 552 invasive emm1 isolates from 2009-16 were analysed and compared with 2800 global emm1 sequences. Transcript and protein expression of streptococcal pyrogenic exotoxin A (SpeA; also known as scarlet fever or erythrogenic toxin A) in sequenced, non-invasive emm1 isolates was quantified by real-time PCR and western blot analyses. FINDINGS Coincident with national increases in scarlet fever and invasive disease notifications, emm1 S pyogenes upper respiratory tract isolates increased significantly in northwest London in the March to May period, from five (5%) of 96 isolates in 2014, to 28 (19%) of 147 isolates in 2015 (p=0·0021 vs 2014 values), to 47 (33%) of 144 in 2016 (p=0·0080 vs 2015 values). Similarly, invasive emm1 isolates collected nationally in the same period increased from 183 (31%) of 587 in 2015 to 267 (42%) of 637 in 2016 (p<0·0001). Sequences of emm1 isolates from 2009-16 showed emergence of a new emm1 lineage (designated M1UK)-with overlap of pharyngitis, scarlet fever, and invasive M1UK strains-which could be genotypically distinguished from pandemic emm1 isolates (M1global) by 27 single-nucleotide polymorphisms. Median SpeA protein concentration in supernatant was nine-times higher among M1UK isolates (190·2 ng/mL [IQR 168·9-200·4]; n=10) than M1global isolates (20·9 ng/mL [0·0-27·3]; n=10; p<0·0001). M1UK expanded nationally to represent 252 (84%) of all 299 emm1 genomes in 2016. Phylogenetic analysis of published datasets identified single M1UK isolates in Denmark and the USA. INTERPRETATION A dominant new emm1 S pyogenes lineage characterised by increased SpeA production has emerged during increased S pyogenes activity in England. The expanded reservoir of M1UK and recognised invasive potential of emm1 S pyogenes provide plausible explanation for the increased incidence of invasive disease, and rationale for global surveillance. FUNDING UK Medical Research Council, UK National Institute for Health Research, Wellcome Trust, Rosetrees Trust, Stoneygate Trust.
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Affiliation(s)
- Nicola N Lynskey
- Department of Infectious Diseases and Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Elita Jauneikaite
- Department of Infectious Diseases and Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK; Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, National Institute for Health Research, Imperial College London, London, UK
| | - Ho Kwong Li
- Department of Infectious Diseases and Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Xiangyun Zhi
- Department of Infectious Diseases and Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Claire E Turner
- Molecular Biology & Biotechnology, University of Sheffield, Sheffield, UK
| | - Mia Mosavie
- Department of Infectious Diseases and Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK; Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, National Institute for Health Research, Imperial College London, London, UK
| | - Max Pearson
- Department of Infectious Diseases and Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK; Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, National Institute for Health Research, Imperial College London, London, UK
| | - Masanori Asai
- Department of Infectious Diseases and Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Ludmila Lobkowicz
- Department of Infectious Diseases and Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - J Yimmy Chow
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, National Institute for Health Research, Imperial College London, London, UK; North-West London Health Protection Team, London Public Health England Centre, Public Health England, London, UK
| | - Julian Parkhill
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, National Institute for Health Research, Imperial College London, London, UK; Wellcome Sanger Institute, Cambridge, UK
| | - Theresa Lamagni
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, National Institute for Health Research, Imperial College London, London, UK; National Infection Service, Public Health England, London, UK
| | - Victoria J Chalker
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, National Institute for Health Research, Imperial College London, London, UK; National Infection Service, Public Health England, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Diseases and Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK; Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, National Institute for Health Research, Imperial College London, London, UK.
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Greer O, Shah NM, Sriskandan S, Johnson MR. Sepsis: Precision-Based Medicine for Pregnancy and the Puerperium. Int J Mol Sci 2019; 20:ijms20215388. [PMID: 31671794 PMCID: PMC6861904 DOI: 10.3390/ijms20215388] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
Sepsis contributes significantly to global morbidity and mortality, particularly in vulnerable populations. Pregnant and recently pregnant women are particularly prone to rapid progression to sepsis and septic shock, with 11% of maternal deaths worldwide being attributed to sepsis. The impact on the neonate is considerable, with 1 million neonatal deaths annually attributed to maternal infection or sepsis. Pregnancy specific physiological and immunological adaptations are likely to contribute to a greater impact of infection, but current approaches to the management of sepsis are based on those developed for the non-pregnant population. Pregnancy-specific strategies are required to optimise recognition and management of these patients. We review current knowledge of the physiology and immunology of pregnancy and propose areas of research, which may advance the development of pregnancy-specific diagnostic and therapeutic approaches to optimise the care of pregnant women and their babies.
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Affiliation(s)
- Orene Greer
- Imperial College London, Academic Department of Obstetrics & Gynaecology, Level 3, Chelsea & Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK.
- Chelsea & Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK.
| | - Nishel Mohan Shah
- Imperial College London, Academic Department of Obstetrics & Gynaecology, Level 3, Chelsea & Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK.
- Chelsea & Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK.
| | - Shiranee Sriskandan
- Imperial College London, NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.
| | - Mark R Johnson
- Imperial College London, Academic Department of Obstetrics & Gynaecology, Level 3, Chelsea & Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK.
- Chelsea & Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK.
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Jauneikaite E, Ferguson T, Mosavie M, Fallowfield JL, Davey T, Thorpe N, Allsopp A, Shaw AM, Fudge D, O'Shea MK, Wilson D, Morgan M, Pichon B, Kearns AM, Sriskandan S, Lamb LE. Staphylococcus aureus colonization and acquisition of skin and soft tissue infection among Royal Marines recruits: a prospective cohort study. Clin Microbiol Infect 2019; 26:381.e1-381.e6. [PMID: 31357012 DOI: 10.1016/j.cmi.2019.07.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 04/28/2019] [Revised: 07/03/2019] [Accepted: 07/13/2019] [Indexed: 10/26/2022]
Abstract
OBJECTIVES Skin and soft tissue infections (SSTIs) are a serious health issue for military personnel. Of particular importance are those caused by methicillin-resistant Staphylococcus aureus and Panton-Valentine leucocidin (PVL)-positive S. aureus (PVL-SA), as they have been associated with outbreaks of SSTIs. A prospective observational study was conducted in Royal Marine (RM) recruits to investigate the prevalence of PVL-SA carriage and any association with SSTIs. METHODS A total of 1012 RM recruits were followed through a 32-week training programme, with nose and throat swabs obtained at weeks 1, 6, 15 and 32. S. aureus isolates were characterized by antibiotic susceptibility testing, spa typing, presence of mecA/C and PVL genes. Retrospective review of the clinical notes for SSTI acquisition was conducted. RESULTS S. aureus colonization decreased from Week 1 to Week 32 (41% to 26%, p < 0.0001). Of 1168 S. aureus isolates, three out of 1168 (0.3%) were MRSA and ten out of 1168 (0.9%) PVL-positive (all MSSA) and 169 out of 1168 (14.5%) were resistant to clindamycin. Isolates showed genetic diversity with 238 different spa types associated with 25 multi-locus sequence type (MLST) clonal complexes. SSTIs were seen in 35% (351/989) of recruits with 3 training days lost per recruit. SSTI acquisition rate was reduced amongst persistent carriers (p < 0.0283). CONCLUSIONS Nose and throat carriage of MRSA and PVL-SA was low among recruits, despite a high incidence of SSTIs being reported, particularly cellulitis. Carriage strains were predominantly MSSA with a marked diversity of genotypes. Persistent nose and/or throat carriage was not associated with SSTI acquisition. Putative person-to-person transmission within troops was identified based on spa typing requiring further research to confirm and explore potential transmission routes.
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Affiliation(s)
- E Jauneikaite
- Department of Medicine, Imperial College London, London, UK; NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare-associated Infections, Imperial College London, London, UK; Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - T Ferguson
- Department of Medicine, Imperial College London, London, UK
| | - M Mosavie
- Department of Medicine, Imperial College London, London, UK; NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare-associated Infections, Imperial College London, London, UK
| | | | - T Davey
- Institute of Naval Medicine, Alverstoke, UK
| | - N Thorpe
- Institute of Naval Medicine, Alverstoke, UK
| | - A Allsopp
- Institute of Naval Medicine, Alverstoke, UK
| | - A M Shaw
- Institute of Naval Medicine, Alverstoke, UK
| | - D Fudge
- Academic Department of Military Medicine, Royal Centre for Defence Medicine (Research and Academia), Birmingham, UK
| | - M K O'Shea
- Academic Department of Military Medicine, Royal Centre for Defence Medicine (Research and Academia), Birmingham, UK; Institute of Microbiology and Infection, The University of Birmingham, Birmingham, UK
| | - D Wilson
- Academic Department of Military Medicine, Royal Centre for Defence Medicine (Research and Academia), Birmingham, UK
| | - M Morgan
- Department of Microbiology, Royal Devon and Exeter Hospital, Exeter, UK
| | - B Pichon
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | - A M Kearns
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | - S Sriskandan
- Department of Medicine, Imperial College London, London, UK; NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare-associated Infections, Imperial College London, London, UK
| | - L E Lamb
- Department of Medicine, Imperial College London, London, UK; Academic Department of Military Medicine, Royal Centre for Defence Medicine (Research and Academia), Birmingham, UK; Royal Free London NHS Foundation Trust, London, UK.
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Herbert R, Hatcher J, Jauneikaite E, Gharbi M, d'Arc S, Obaray N, Rickards T, Rebec M, Blandy O, Hope R, Thomas A, Bamford K, Jepson A, Sriskandan S. Two-year analysis of Clostridium difficile ribotypes associated with increased severity. J Hosp Infect 2019; 103:388-394. [PMID: 31220480 PMCID: PMC6926500 DOI: 10.1016/j.jhin.2019.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 02/28/2019] [Accepted: 06/10/2019] [Indexed: 11/25/2022]
Abstract
Background Certain Clostridium difficile ribotypes have been associated with complex disease phenotypes including recurrence and increased severity, especially the well-described hypervirulent RT027. This study aimed to determine the pattern of ribotypes causing infection and the association, if any, with severity. Methods All faecal samples submitted to a large diagnostic laboratory for C. difficile testing between 2011 and 2013 were subject to routine testing and culture. All C. difficile isolates were ribotyped, and associated clinical and demographic patient data were retrieved and linked to ribotyping data. Results In total, 86 distinct ribotypes were identified from 705 isolates of C. difficile. RT002 and RT015 were the most prevalent (22.5%, N=159). Only five isolates (0.7%) were hypervirulent RT027. Ninety of 450 (20%) patients with clinical information available died within 30 days of C. difficile isolation. RT220, one of the 10 most common ribotypes, was associated with elevated median C-reactive protein and significantly increased 30-day all-cause mortality compared with RT002 and RT015, and with all other ribotypes found in the study. Conclusions A wide range of C. difficile ribotypes were responsible for C. difficile infection presentations. Although C. difficile-associated mortality has reduced in recent years, expansion of lineages associated with increased severity could herald increases in future mortality. Enhanced surveillance for emerging lineages such as RT220 that are associated with more severe disease is required, with genomic approaches to dissect pathogenicity.
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Affiliation(s)
- R Herbert
- Imperial College Healthcare NHS Trust, London, UK
| | - J Hatcher
- Imperial College Healthcare NHS Trust, London, UK
| | - E Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - M Gharbi
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - S d'Arc
- Imperial College Healthcare NHS Trust, London, UK
| | - N Obaray
- Imperial College Healthcare NHS Trust, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - T Rickards
- Imperial College Healthcare NHS Trust, London, UK
| | - M Rebec
- Imperial College Healthcare NHS Trust, London, UK
| | - O Blandy
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - R Hope
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK; National Infection Service, Public Health England, London, UK
| | - A Thomas
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - K Bamford
- Imperial College Healthcare NHS Trust, London, UK
| | - A Jepson
- Imperial College Healthcare NHS Trust, London, UK
| | - S Sriskandan
- Imperial College Healthcare NHS Trust, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK.
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43
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Mosavie M, Blandy O, Jauneikaite E, Caldas I, Ellington MJ, Woodford N, Sriskandan S. Sampling and diversity of Escherichia coli from the enteric microbiota in patients with Escherichia coli bacteraemia. BMC Res Notes 2019; 12:335. [PMID: 31196206 PMCID: PMC6563364 DOI: 10.1186/s13104-019-4369-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/05/2019] [Indexed: 12/03/2022] Open
Abstract
Objective The increase in Escherichia coli bloodstream infections mandates better characterisation of the relationship between commensal and invasive isolates. This study adopted a simple approach to characterize E. coli in the gut reservoir from patients with either E. coli or other Gram-negative bacteraemia, or those without bacteraemia, establishing strain collections suitable for genomic investigation. Enteric samples from patients in the three groups were cultured on selective chromogenic agar. Genetic diversity of prevailing E. coli strains in gut microbiota was estimated by RAPD-PCR. Results Enteric samples from E. coli bacteraemia patients yielded a median of one E. coli RAPD pattern (range 1–4) compared with two (range 1–5) from groups without E. coli bacteraemia. Of relevance to large-scale clinical studies, observed diversity of E. coli among hospitalised patients was not altered by sample type (rectal swab or stool), nor by increasing the colonies tested from 10 to 20. Hospitalised patients demonstrated an apparently limited diversity of E. coli in the enteric microbiota and this was further reduced in those with E. coli bacteraemia. The reduced diversity of E. coli within the gut during E. coli bacteraemia raises the possibility that dominant strains may outcompete other lineages in patients with bloodstream infection. Electronic supplementary material The online version of this article (10.1186/s13104-019-4369-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mia Mosavie
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Oliver Blandy
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Elita Jauneikaite
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Isabel Caldas
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Matthew J Ellington
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.,Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Neil Woodford
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.,Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Shiranee Sriskandan
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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Reglinski M, Sriskandan S, Turner CE. Identification of two new core chromosome-encoded superantigens in Streptococcus pyogenes; speQ and speR. J Infect 2019; 78:358-363. [PMID: 30796950 DOI: 10.1016/j.jinf.2019.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/25/2019] [Accepted: 02/17/2019] [Indexed: 10/27/2022]
Abstract
Superantigens are ubiquitous within the Streptococcus pyogenes genome, which suggests that superantigen-mediated T-cell activation provides a significant selective advantage. S. pyogenes can carry a variable complement of the 11 known superantigens. We have identified two novel S. pyogenes superantigens, denoted speQ and speR, adjacent to each other in the core-chromosome of isolates belonging to eleven different emm-types. Although distinct from other superantigens, speQ and speR were most closely related to speK and speJ, respectively. Recombinant SPEQ and SPER were mitogenic towards human peripheral blood mononuclear cells at ng/ml concentrations, and SPER was found to be more mitogenic than SPEQ.
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Affiliation(s)
- Mark Reglinski
- Department of Infectious Diseases, Imperial College London, London W12 0NN, UK
| | - Shiranee Sriskandan
- Department of Infectious Diseases, Imperial College London, London W12 0NN, UK
| | - Claire E Turner
- Department of Infectious Diseases, Imperial College London, London W12 0NN, UK; Department of Molecular Biology & Biotechnology, The Florey Institute, University of Sheffield, Sheffield S10 2TN, UK.
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45
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Goldblatt J, Lawrenson RA, Muir L, Dattani S, Hoffland A, Tsuchiya T, Kanegasaki S, Sriskandan S, Pease JE. A Requirement for Neutrophil Glycosaminoglycans in Chemokine:Receptor Interactions Is Revealed by the Streptococcal Protease SpyCEP. J Immunol 2019; 202:3246-3255. [PMID: 31010851 PMCID: PMC6526389 DOI: 10.4049/jimmunol.1801688] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/21/2019] [Indexed: 12/17/2022]
Abstract
SpyCEP-cleaved CXCL8 is unable to bind and activate CXCL8 receptors. Neutrophil glycosaminoglycans are required for migration along a CXCL8 gradient.
To evade the immune system, the lethal human pathogen Streptococcus pyogenes produces SpyCEP, an enzyme that cleaves the C-terminal α-helix of CXCL8, resulting in markedly impaired recruitment of neutrophils to sites of invasive infection. The basis for chemokine inactivation by SpyCEP is, however, poorly understood, as the core domain of CXCL8 known to interact with CXCL8 receptors is unaffected by enzymatic cleavage. We examined the in vitro migration of human neutrophils and observed that their ability to efficiently navigate a CXCL8 gradient was compromised following CXCL8 cleavage by SpyCEP. SpyCEP-mediated cleavage of CXCL8 also impaired CXCL8-induced migration of transfectants expressing the human chemokine receptors CXCR1 or CXCR2. Despite possessing an intact N terminus and preserved disulfide bonds, SpyCEP-cleaved CXCL8 had impaired binding to both CXCR1 and CXCR2, pointing to a requirement for the C-terminal α-helix. SpyCEP-cleaved CXCL8 had similarly impaired binding to the glycosaminoglycan heparin. Enzymatic removal of neutrophil glycosaminoglycans was observed to ablate neutrophil navigation of a CXCL8 gradient, whereas navigation of an fMLF gradient remained largely intact. We conclude, therefore, that SpyCEP cleavage of CXCL8 results in chemokine inactivation because of a requirement for glycosaminoglycan binding in productive chemokine:receptor interactions. This may inform strategies to inhibit the activity of SpyCEP, but may also influence future approaches to inhibit unwanted chemokine-induced inflammation.
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Affiliation(s)
- Jennifer Goldblatt
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom.,Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | | | - Luke Muir
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
| | - Saloni Dattani
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ashley Hoffland
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom.,Asthma U.K. Centre in Allergic Mechanisms of Asthma, London, United Kingdom; and
| | - Tomoko Tsuchiya
- Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Shiro Kanegasaki
- Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Shiranee Sriskandan
- Department of Medicine, Imperial College London, London W12 0NN, United Kingdom;
| | - James E Pease
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom; .,Asthma U.K. Centre in Allergic Mechanisms of Asthma, London, United Kingdom; and
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Reglinski M, Sriskandan S. Treatment potential of pathogen-reactive antibodies sequentially purified from pooled human immunoglobulin. BMC Res Notes 2019; 12:228. [PMID: 30992057 PMCID: PMC6466806 DOI: 10.1186/s13104-019-4262-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 03/05/2019] [Accepted: 04/06/2019] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE Intravenous immune globulin (IVIG), pooled from human blood, is a polyspecific antibody preparation that inhibits the super-antigenic proteins associated with streptococcal and staphylococcal toxic shock, and the Shiga toxin. In addition to this toxin-neutralising activity, IVIG contains other pathogen-reactive antibodies that may confer additional therapeutic benefits. We sought to determine if pathogen-reactive antibodies that promote opsonophagocytosis of different organisms can be sequentially affinity-purified from one IVIG preparation. RESULTS Antibodies that recognise cell wall antigens of Streptococcus pyogenes, Staphylococcus aureus, and vancomycin-resistant enterococcus (VRE) were sequentially affinity-purified from a single preparation of commercial IVIG and opsonophagocytic activity was assessed using a flow cytometry assay of neutrophil uptake. Non-specific IgG-binding proteins were removed from the S. aureus preparations using an immobilised Fc fragment column, produced using IVIG cleaved with the Immunoglobulin G-degrading enzyme of S. pyogenes (IdeS). Affinity-purified anti-S. aureus and anti-VRE immunoglobulin promoted significantly higher levels of opsonophagocytic uptake by human neutrophils than IVIG when identical total antibody concentrations were compared, confirming activity previously shown for affinity-purified anti-S. pyogenes immunoglobulin. The opsonophagocytic activities of anti-S. pyogenes, anti-S. aureus, and anti-VRE antibodies that were sequentially purified from a single IVIG preparation were undiminished compared to antibodies purified from previously unused IVIG.
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Affiliation(s)
- Mark Reglinski
- Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Shiranee Sriskandan
- Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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Hutchinson M, Sohal M, Layton M, Sriskandan S, Brett S, Hill P, Youngstein TAB. 139 Steroid-free management of life-threatening haemophagocytic lymphohistiocytosis in the context of suspected lymphoproliferative disease and infection. Rheumatology (Oxford) 2019. [DOI: 10.1093/rheumatology/kez108.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Matthew Hutchinson
- Rheumatology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UNITED KINGDOM
| | - Mamta Sohal
- Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UNITED KINGDOM
| | - Mark Layton
- Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UNITED KINGDOM
| | - Shiranee Sriskandan
- Infectious Diseases, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UNITED KINGDOM
| | - Stephen Brett
- Intensive Care, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UNITED KINGDOM
| | - Peter Hill
- Renal Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UNITED KINGDOM
| | - Taryn A B Youngstein
- Rheumatology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UNITED KINGDOM
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48
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Davies FJ, Olme C, Lynskey NN, Turner CE, Sriskandan S. Streptococcal superantigen-induced expansion of human tonsil T cells leads to altered T follicular helper cell phenotype, B cell death and reduced immunoglobulin release. Clin Exp Immunol 2019; 197:83-94. [PMID: 30815853 PMCID: PMC6591145 DOI: 10.1111/cei.13282] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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] [Accepted: 02/26/2019] [Indexed: 01/18/2023] Open
Abstract
Streptococcal pyrogenic exotoxin (Spe) A expression is epidemiologically linked to streptococcal tonsillo‐pharyngitis and outbreaks of scarlet fever, although the mechanisms by which superantigens confer advantage to Streptococcus pyogenes are unclear. S. pyogenes is an exclusively human pathogen. As the leucocyte profile of tonsil is unique, the impact of SpeA production on human tonsil cell function was investigated. Human tonsil cells from routine tonsillectomy were co‐incubated with purified streptococcal superantigens or culture supernatants from isogenic streptococcal isolates, differing only in superantigen production. Tonsil cell proliferation was quantified by tritiated thymidine incorporation, and cell surface characteristics assessed by flow cytometry. Soluble mediators including immunoglobulin were measured using enzyme‐linked immunosorbent assay. Tonsil T cells proliferated in response to SpeA and demonstrated typical release of proinflammatory cytokines. When cultured in the absence of superantigen, tonsil preparations released large quantities of immunoglobulin over 7 days. In contrast, marked B cell apoptosis and abrogation of total immunoglobulin (Ig)A, IgM, and IgG production occurred in the presence of SpeA and other superantigens. In SpeA‐stimulated cultures, T follicular helper (Tfh) cells showed a reduction in C‐X‐C chemokine receptor (CXCR)5 (CD185) expression, but up‐regulation of OX40 (CD134) and inducible T cell co‐stimulator (ICOS) (CD278) expression. The phenotypical change in the Tfh population was associated with impaired chemotactic response to CXCL13. SpeA and other superantigens cause dysregulated tonsil immune function, driving T cells from Tfh to a proliferating phenotype, with resultant loss of B cells and immunoglobulin production, providing superantigen‐producing bacteria with a probable survival advantage.
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Affiliation(s)
- F J Davies
- Department of Medicine, Imperial College London, London, UK
| | - C Olme
- Department of Medicine, Imperial College London, London, UK
| | - N N Lynskey
- Department of Medicine, Imperial College London, London, UK
| | - C E Turner
- Department of Medicine, Imperial College London, London, UK
| | - S Sriskandan
- Department of Medicine, Imperial College London, London, UK
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Blandy O, Honeyford K, Gharbi M, Thomas A, Ramzan F, Ellington M, Hope R, Holmes A, Johnson A, Aylin P, Woodford N, Sriskandan S. Factors that impact on the burden of Escherichia coli bacteraemia: multivariable regression analysis of 2011–2015 data from West London. J Hosp Infect 2019; 101:120-128. [DOI: 10.1016/j.jhin.2018.10.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/30/2018] [Indexed: 11/24/2022]
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Sharma H, Smith D, Turner CE, Game L, Pichon B, Hope R, Hill R, Kearns A, Sriskandan S. Clinical and Molecular Epidemiology of Staphylococcal Toxic Shock Syndrome in the United Kingdom. Emerg Infect Dis 2019; 24. [PMID: 29350159 PMCID: PMC5782905 DOI: 10.3201/eid2402.170606] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Staphylococcal toxic shock syndrome (TSS) was originally described in menstruating women and linked to TSS toxin 1 (TSST-1)-producing Staphylococcus aureus. Using UK national surveillance data, we ascertained clinical, molecular and superantigenic characteristics of TSS cases. Average annual TSS incidence was 0.07/100,000 population. Patients with nonmenstrual TSS were younger than those with menstrual TSS but had the same mortality rate. Children <16 years of age accounted for 39% of TSS cases, most caused by burns and skin and soft tissue infections. Nonmenstrual TSS is now more common than menstrual TSS in the UK, although both types are strongly associated with the tst+ clonal complex (CC) 30 methicillin-sensitive S. aureus lineage, which accounted for 49.4% of all TSS and produced more TSST-1 and superantigen bioactivity than did tst+ CC30 methicillin-resistant S. aureus strains. Better understanding of this MSSA lineage and infections in children could focus interventions to prevent TSS in the future.
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