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Larsen J, Raisen CL, Ba X, Sadgrove NJ, Padilla-González GF, Simmonds MSJ, Loncaric I, Kerschner H, Apfalter P, Hartl R, Deplano A, Vandendriessche S, Černá Bolfíková B, Hulva P, Arendrup MC, Hare RK, Barnadas C, Stegger M, Sieber RN, Skov RL, Petersen A, Angen Ø, Rasmussen SL, Espinosa-Gongora C, Aarestrup FM, Lindholm LJ, Nykäsenoja SM, Laurent F, Becker K, Walther B, Kehrenberg C, Cuny C, Layer F, Werner G, Witte W, Stamm I, Moroni P, Jørgensen HJ, de Lencastre H, Cercenado E, García-Garrote F, Börjesson S, Hæggman S, Perreten V, Teale CJ, Waller AS, Pichon B, Curran MD, Ellington MJ, Welch JJ, Peacock SJ, Seilly DJ, Morgan FJE, Parkhill J, Hadjirin NF, Lindsay JA, Holden MTG, Edwards GF, Foster G, Paterson GK, Didelot X, Holmes MA, Harrison EM, Larsen AR. Emergence of methicillin resistance predates the clinical use of antibiotics. Nature 2022; 602:135-141. [PMID: 34987223 PMCID: PMC8810379 DOI: 10.1038/s41586-021-04265-w] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022]
Abstract
The discovery of antibiotics more than 80 years ago has led to considerable improvements in human and animal health. Although antibiotic resistance in environmental bacteria is ancient, resistance in human pathogens is thought to be a modern phenomenon that is driven by the clinical use of antibiotics1. Here we show that particular lineages of methicillin-resistant Staphylococcus aureus-a notorious human pathogen-appeared in European hedgehogs in the pre-antibiotic era. Subsequently, these lineages spread within the local hedgehog populations and between hedgehogs and secondary hosts, including livestock and humans. We also demonstrate that the hedgehog dermatophyte Trichophyton erinacei produces two β-lactam antibiotics that provide a natural selective environment in which methicillin-resistant S. aureus isolates have an advantage over susceptible isolates. Together, these results suggest that methicillin resistance emerged in the pre-antibiotic era as a co-evolutionary adaptation of S. aureus to the colonization of dermatophyte-infected hedgehogs. The evolution of clinically relevant antibiotic-resistance genes in wild animals and the connectivity of natural, agricultural and human ecosystems demonstrate that the use of a One Health approach is critical for our understanding and management of antibiotic resistance, which is one of the biggest threats to global health, food security and development.
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Affiliation(s)
- Jesper Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark.
| | - Claire L Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | | | | | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Ariane Deplano
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
| | - Stien Vandendriessche
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
- Laboratory for Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavel Hulva
- Department of Zoology, Charles University, Prague, Czech Republic
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Maiken C Arendrup
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus K Hare
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Céline Barnadas
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Marc Stegger
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N Sieber
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Robert L Skov
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Andreas Petersen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Øystein Angen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sophie L Rasmussen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Wildlife Conservation Research Unit (WildCRU), Department of Zoology, University of Oxford, Tubney, UK
| | - Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Laura J Lindholm
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Frederic Laurent
- Bacteriology Department and French National Reference Center for Staphylococci, Hospices Civils de Lyon, University of Lyon, Lyon, France
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Birgit Walther
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, Berlin, Germany
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus-Liebig University Giessen, Giessen, Germany
| | - Christiane Cuny
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Franziska Layer
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Wolfgang Witte
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | | | - Paolo Moroni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
- Quality Milk Production Services, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA
| | | | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB NOVA, Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Emilia Cercenado
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Fernando García-Garrote
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
- Servicio de Microbiología, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
| | - Stefan Börjesson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Sara Hæggman
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | - Andrew S Waller
- Animal Health Trust, Newmarket, UK
- Intervacc AB, Stockholm, Stockholm, Sweden
- Department of Biomedical Science and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bruno Pichon
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
| | - Matthew J Ellington
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - David J Seilly
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Fiona J E Morgan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Physiology, Development & Neuroscience, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nazreen F Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jodi A Lindsay
- Institute of Infection and Immunity, St George's, University of London, London, UK
| | | | - Giles F Edwards
- Scottish MRSA Reference Laboratory, NHS Greater Glasgow and Clyde, Stobhill Hospital, Glasgow, UK
| | | | - Gavin K Paterson
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Warwick, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Anders R Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
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Gadsby NJ, Helgason KO, Dickson EM, Mills JM, Lindsay DSJ, Edwards GF, Hanson MF, Templeton KE. Molecular diagnosis of Legionella infections--Clinical utility of front-line screening as part of a pneumonia diagnostic algorithm. J Infect 2015; 72:161-70. [PMID: 26632328 DOI: 10.1016/j.jinf.2015.10.011] [Citation(s) in RCA: 16] [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: 06/09/2015] [Revised: 09/29/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
Abstract
OBJECTIVES Urinary antigen testing for Legionella pneumophila serogroup 1 is the leading rapid diagnostic test for Legionnaires' Disease (LD); however other Legionella species and serogroups can also cause LD. The aim was to determine the utility of front-line L. pneumophila and Legionella species PCR in a severe respiratory infection algorithm. METHODS L. pneumophila and Legionella species duplex real-time PCR was carried out on 1944 specimens from hospitalised patients over a 4 year period in Edinburgh, UK. RESULTS L. pneumophila was detected by PCR in 49 (2.7%) specimens from 36 patients. During a LD outbreak, combined L. pneumophila respiratory PCR and urinary antigen testing had optimal sensitivity and specificity (92.6% and 98.3% respectively) for the detection of confirmed cases. Legionella species was detected by PCR in 16 (0.9%) specimens from 10 patients. The 5 confirmed and 1 probable cases of Legionella longbeachae LD were both PCR and antibody positive. CONCLUSIONS Front-line L. pneumophila and Legionella species PCR is a valuable addition to urinary antigen testing as part of a well-defined algorithm. Cases of LD due to L. longbeachae might be considered laboratory-confirmed when there is a positive Legionella species PCR result and detection of L. longbeachae specific antibody response.
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Affiliation(s)
- Naomi J Gadsby
- Medical Microbiology, Dept Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK.
| | - Kristjan O Helgason
- Medical Microbiology, Dept Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Elizabeth M Dickson
- Medical Microbiology, Dept Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Jonathan M Mills
- Medical Microbiology, Dept Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Diane S J Lindsay
- Scottish Haemophilus, Legionella, Meningococcus and Pneumococcus Reference Laboratory, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow, G31 2ER, UK
| | - Giles F Edwards
- Scottish Haemophilus, Legionella, Meningococcus and Pneumococcus Reference Laboratory, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow, G31 2ER, UK
| | - Mary F Hanson
- Medical Microbiology, Dept Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Kate E Templeton
- Medical Microbiology, Dept Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
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McAdam PR, Vander Broek CW, Lindsay DSJ, Ward MJ, Hanson MF, Gillies M, Watson M, Stevens JM, Edwards GF, Fitzgerald JR. Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires' disease outbreak. Genome Biol 2015. [PMID: 25370747 PMCID: PMC4256819 DOI: 10.1186/s13059-014-0504-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Legionnaires’ disease is a severe form of pneumonia caused by the environmental bacterium Legionella pneumophila. Outbreaks commonly affect people with known risk factors, but the genetic and pathogenic complexity of L. pneumophila within an outbreak is not well understood. Here, we investigate the etiology of the major Legionnaires’ disease outbreak that occurred in Edinburgh, UK, in 2012, by examining the evolutionary history, genome content, and virulence of L. pneumophila clinical isolates. Results Our high resolution genomic approach reveals that the outbreak was caused by multiple genetic subtypes of L. pneumophila, the majority of which had diversified from a single progenitor through mutation, recombination, and horizontal gene transfer within an environmental reservoir prior to release. In addition, we discover that some patients were infected with multiple L. pneumophila subtypes, a finding which can affect the certainty of source attribution. Importantly, variation in the complement of type IV secretion systems encoded by different genetic subtypes correlates with virulence in a Galleria mellonella model of infection, revealing variation in pathogenic potential among the outbreak source population of L. pneumophila. Conclusions Taken together, our study indicates previously cryptic levels of pathogen heterogeneity within a Legionnaires’ disease outbreak, a discovery that impacts on source attribution for future outbreak investigations. Furthermore, our data suggest that in addition to host immune status, pathogen diversity may be an important influence on the clinical outcome of individual outbreak infections. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0504-1) contains supplementary material, which is available to authorized users.
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4
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McAdam PR, Vander Broek CW, Lindsay DSJ, Ward MJ, Hanson MF, Gillies M, Watson M, Stevens JM, Edwards GF, Fitzgerald JR. Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires' disease outbreak. Genome Biol 2015; 15:504. [PMID: 25370747 DOI: 10.1186/preaccept-1675723368141690] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Legionnaires' disease is a severe form of pneumonia caused by the environmental bacterium Legionella pneumophila. Outbreaks commonly affect people with known risk factors, but the genetic and pathogenic complexity of L. pneumophila within an outbreak is not well understood. Here, we investigate the etiology of the major Legionnaires' disease outbreak that occurred in Edinburgh, UK, in 2012, by examining the evolutionary history, genome content, and virulence of L. pneumophila clinical isolates. RESULTS Our high resolution genomic approach reveals that the outbreak was caused by multiple genetic subtypes of L. pneumophila, the majority of which had diversified from a single progenitor through mutation, recombination, and horizontal gene transfer within an environmental reservoir prior to release. In addition, we discover that some patients were infected with multiple L. pneumophila subtypes, a finding which can affect the certainty of source attribution. Importantly, variation in the complement of type IV secretion systems encoded by different genetic subtypes correlates with virulence in a Galleria mellonella model of infection, revealing variation in pathogenic potential among the outbreak source population of L. pneumophila. CONCLUSIONS Taken together, our study indicates previously cryptic levels of pathogen heterogeneity within a Legionnaires' disease outbreak, a discovery that impacts on source attribution for future outbreak investigations. Furthermore, our data suggest that in addition to host immune status, pathogen diversity may be an important influence on the clinical outcome of individual outbreak infections.
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5
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Ba X, Harrison EM, Edwards GF, Holden MTG, Larsen AR, Petersen A, Skov RL, Peacock SJ, Parkhill J, Paterson GK, Holmes MA. Novel mutations in penicillin-binding protein genes in clinical Staphylococcus aureus isolates that are methicillin resistant on susceptibility testing, but lack the mec gene. J Antimicrob Chemother 2013; 69:594-7. [PMID: 24216768 PMCID: PMC3922151 DOI: 10.1093/jac/dkt418] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Objectives Methicillin-resistant Staphylococcus aureus (MRSA) is an important global health problem. MRSA resistance to β-lactam antibiotics is mediated by the mecA or mecC genes, which encode an alternative penicillin-binding protein (PBP) 2a that has a low affinity to β-lactam antibiotics. Detection of mec genes or PBP2a is regarded as the gold standard for the diagnosis of MRSA. We identified four MRSA isolates that lacked mecA or mecC genes, but were still phenotypically resistant to pencillinase-resistant β-lactam antibiotics. Methods The four human S. aureus isolates were investigated by whole genome sequencing and a range of phenotypic assays. Results We identified a number of amino acid substitutions present in the endogenous PBPs 1, 2 and 3 that were found in the resistant isolates but were absent in closely related susceptible isolates and which may be the basis of resistance. Of particular interest are three identical amino acid substitutions in PBPs 1, 2 and 3, occurring independently in isolates from at least two separate multilocus sequence types. Two different non-conservative substitutions were also present in the same amino acid of PBP1 in two isolates from two different sequence types. Conclusions This work suggests that phenotypically resistant MRSA could be misdiagnosed using molecular methods alone and provides evidence of alternative mechanisms for β-lactam resistance in MRSA that may need to be considered by diagnostic laboratories.
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Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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6
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Holden MTG, Hsu LY, Kurt K, Weinert LA, Mather AE, Harris SR, Strommenger B, Layer F, Witte W, de Lencastre H, Skov R, Westh H, Zemlicková H, Coombs G, Kearns AM, Hill RLR, Edgeworth J, Gould I, Gant V, Cooke J, Edwards GF, McAdam PR, Templeton KE, McCann A, Zhou Z, Castillo-Ramírez S, Feil EJ, Hudson LO, Enright MC, Balloux F, Aanensen DM, Spratt BG, Fitzgerald JR, Parkhill J, Achtman M, Bentley SD, Nübel U. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res 2013; 23:653-64. [PMID: 23299977 PMCID: PMC3613582 DOI: 10.1101/gr.147710.112] [Citation(s) in RCA: 334] [Impact Index Per Article: 30.4] [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] [Indexed: 11/24/2022]
Abstract
The widespread use of antibiotics in association with high-density clinical care has driven the emergence of drug-resistant bacteria that are adapted to thrive in hospitalized patients. Of particular concern are globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones that cause outbreaks and epidemics associated with health care. The most rapidly spreading and tenacious health-care-associated clone in Europe currently is EMRSA-15, which was first detected in the UK in the early 1990s and subsequently spread throughout Europe and beyond. Using phylogenomic methods to analyze the genome sequences for 193 S. aureus isolates, we were able to show that the current pandemic population of EMRSA-15 descends from a health-care-associated MRSA epidemic that spread throughout England in the 1980s, which had itself previously emerged from a primarily community-associated methicillin-sensitive population. The emergence of fluoroquinolone resistance in this EMRSA-15 subclone in the English Midlands during the mid-1980s appears to have played a key role in triggering pandemic spread, and occurred shortly after the first clinical trials of this drug. Genome-based coalescence analysis estimated that the population of this subclone over the last 20 yr has grown four times faster than its progenitor. Using comparative genomic analysis we identified the molecular genetic basis of 99.8% of the antimicrobial resistance phenotypes of the isolates, highlighting the potential of pathogen genome sequencing as a diagnostic tool. We document the genetic changes associated with adaptation to the hospital environment and with increasing drug resistance over time, and how MRSA evolution likely has been influenced by country-specific drug use regimens.
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Affiliation(s)
- Matthew T G Holden
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB19 1SA, United Kingdom
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Sangal V, Girvan EK, Jadhav S, Lawes T, Robb A, Vali L, Edwards GF, Yu J, Gould IM. Impacts of a long-term programme of active surveillance and chlorhexidine baths on the clinical and molecular epidemiology of meticillin-resistant Staphylococcus aureus (MRSA) in an Intensive Care Unit in Scotland. Int J Antimicrob Agents 2012; 40:323-31. [DOI: 10.1016/j.ijantimicag.2012.06.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/05/2012] [Accepted: 06/07/2012] [Indexed: 11/26/2022]
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García-Álvarez L, Holden MTG, Lindsay H, Webb CR, Brown DFJ, Curran MD, Walpole E, Brooks K, Pickard DJ, Teale C, Parkhill J, Bentley SD, Edwards GF, Girvan EK, Kearns AM, Pichon B, Hill RLR, Larsen AR, Skov RL, Peacock SJ, Maskell DJ, Holmes MA. Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study. Lancet Infect Dis 2011; 11:595-603. [PMID: 21641281 PMCID: PMC3829197 DOI: 10.1016/s1473-3099(11)70126-8] [Citation(s) in RCA: 620] [Impact Index Per Article: 47.7] [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: 12/20/2022]
Abstract
Background Animals can act as a reservoir and source for the emergence of novel meticillin-resistant Staphylococcus aureus (MRSA) clones in human beings. Here, we report the discovery of a strain of S aureus (LGA251) isolated from bulk milk that was phenotypically resistant to meticillin but tested negative for the mecA gene and a preliminary investigation of the extent to which such strains are present in bovine and human populations. Methods Isolates of bovine MRSA were obtained from the Veterinary Laboratories Agency in the UK, and isolates of human MRSA were obtained from diagnostic or reference laboratories (two in the UK and one in Denmark). From these collections, we searched for mecA PCR-negative bovine and human S aureus isolates showing phenotypic meticillin resistance. We used whole-genome sequencing to establish the genetic basis for the observed antibiotic resistance. Findings A divergent mecA homologue (mecALGA251) was discovered in the LGA251 genome located in a novel staphylococcal cassette chromosome mec element, designated type-XI SCCmec. The mecALGA251 was 70% identical to S aureus mecA homologues and was initially detected in 15 S aureus isolates from dairy cattle in England. These isolates were from three different multilocus sequence type lineages (CC130, CC705, and ST425); spa type t843 (associated with CC130) was identified in 60% of bovine isolates. When human mecA-negative MRSA isolates were tested, the mecALGA251 homologue was identified in 12 of 16 isolates from Scotland, 15 of 26 from England, and 24 of 32 from Denmark. As in cows, t843 was the most common spa type detected in human beings. Interpretation Although routine culture and antimicrobial susceptibility testing will identify S aureus isolates with this novel mecA homologue as meticillin resistant, present confirmatory methods will not identify them as MRSA. New diagnostic guidelines for the detection of MRSA should consider the inclusion of tests for mecALGA251. Funding Department for Environment, Food and Rural Affairs, Higher Education Funding Council for England, Isaac Newton Trust (University of Cambridge), and the Wellcome Trust.
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Affiliation(s)
| | - Matthew TG Holden
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Heather Lindsay
- Department of Veterinary Medicine, University of Cambridge, UK
| | - Cerian R Webb
- Department of Veterinary Medicine, University of Cambridge, UK
| | - Derek FJ Brown
- Health Protection Agency, Addenbrooke's Hospital, Cambridge, UK
| | - Martin D Curran
- Health Protection Agency, Addenbrooke's Hospital, Cambridge, UK
| | - Enid Walpole
- Health Protection Agency, Addenbrooke's Hospital, Cambridge, UK
| | - Karen Brooks
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Derek J Pickard
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Stephen D Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Giles F Edwards
- Scottish MRSA Reference Laboratory, NHS Greater Glasgow and Clyde, Stobhill Hospital, Glasgow, UK
| | - E Kirsty Girvan
- Scottish MRSA Reference Laboratory, NHS Greater Glasgow and Clyde, Stobhill Hospital, Glasgow, UK
| | - Angela M Kearns
- Microbiology Services Division, Health Protection Agency, London, UK
| | - Bruno Pichon
- Microbiology Services Division, Health Protection Agency, London, UK
| | - Robert LR Hill
- Microbiology Services Division, Health Protection Agency, London, UK
| | - Anders Rhod Larsen
- Department of Antimicrobial Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Robert L Skov
- Department of Antimicrobial Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | | | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, UK
- Correspondence to: Dr Mark A Holmes, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
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9
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Clarke SC, Diggle MA, Edwards GF. Automated non-culture-based sequence typing of meningococci from body fluids. Br J Biomed Sci 2002; 58:230-4. [PMID: 11787999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
In recent years, the polymerase chain reaction has been used for the non-culture diagnosis of meningococcal disease, and sequence-based typing takes this further by providing the full characterisation normally only available by culture. In this study, porA gene sequencing was used to perform non-culture-based sequence typing of Neisseria meningitidis strains direct from body fluids. Non-culture porA gene sequencing provided the serosubtype of the infecting organism, and proved to be a useful method as N. meningitidis was not isolated from any of the patients in this study. In conclusion, porA gene sequencing is a very useful tool for the non-culture characterisation of meningococci and provides important information for public health management of cases and contacts.
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Affiliation(s)
- S C Clarke
- North Glasgow University Hospital NHS Trust, Department of Microbiology, Stobhill Hospital, UK.
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Diggle MA, Edwards GF, Clarke SC. Automation of fluorescence-based PCR for confirmation of meningococcal disease. J Clin Microbiol 2001; 39:4518-9. [PMID: 11724872 PMCID: PMC88576 DOI: 10.1128/jcm.39.12.4518-4519.2001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2001] [Accepted: 09/13/2001] [Indexed: 11/20/2022] Open
Abstract
A fluorescence-based PCR method was developed, fully automated, and used to confirm infection with Neisseria meningitidis by detection of the meningococcus-specific ctrA gene. The method provided a highly sensitive, high-throughput assay that was reproducible and less labor-intensive than manual methods.
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Affiliation(s)
- M A Diggle
- Scottish Meningococcus and Pneumococcus Reference Laboratory, Glasgow, United Kingdom
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11
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Abstract
The meningococcus is an important cause of morbidity and mortality and a rapid laboratory diagnosis is required through accurate, non-culture-based methods. Body fluids that are easily obtainable are preferred for this route of diagnosis and urine is the specimen of choice as it can be obtained non-invasively. Urine samples were tested from patients with suspected meningococcal disease and tested by latex agglutination and PCR. It was shown that urinary PCR is not useful for the laboratory confirmation of MD but latex agglutination testing may be useful in certain settings prior to confirmatory testing by a reference laboratory.
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Affiliation(s)
- S C Clarke
- Scottish Meningococcus and Pneumococcus Reference Laboratory, House on the Hill, Stobhill Hospital, Glasgow G21 3UW, UK.
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Clarke SC, Diggle MA, Edwards GF. Semiautomation of multilocus sequence typing for the characterization of clinical isolates of Neisseria meningitidis. J Clin Microbiol 2001; 39:3066-71. [PMID: 11526130 PMCID: PMC88298 DOI: 10.1128/jcm.39.9.3066-3071.2001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Scottish Meningococcus and Pneumococcus Reference Laboratory (SMPRL) provides a national service for the laboratory confirmation of meningococcal and pneumococcal disease in Scotland. Part of this service includes the serogrouping of meningococcal isolates followed by typing and subtyping. The procedures for this are labor-intensive but important for the identification of linked cases and the surveillance of disease so that effective public health measures can be taken. However, different strains of meningococci, such as those within the electrophoretic type 37 complex, occurring during case clusters of disease are now indistinguishable by current methods. The SMPRL has started using multilocus sequence typing (MLST) as a routine method for the characterization of isolates of Neisseria meningitidis. MLST produces nucleotide sequence data of seven housekeeping genes providing results that are useful for public health management. However, the method is laborious and time-consuming and therefore lends itself towards automation. The SMPRL therefore developed a semiautomated method for MLST using a 96-well format liquid handler and an automated DNA sequencer. Semiautomated MLST is now provided as a reference service for Scotland. This work describes the methodology required for the characterization of N. meningitidis and highlights its usefulness for public health intervention.
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Affiliation(s)
- S C Clarke
- Scottish Meningococcus and Pneumococcus Reference Laboratory, North Glasgow University Hospital NHS Trust, Stobhill Hospital, Glasgow, United Kingdom.
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Clarke SC, Diggle MA, Reid JA, Thom L, Edwards GF. Introduction of an automated service for the laboratory confirmation of meningococcal disease in Scotland. J Clin Pathol 2001; 54:556-7. [PMID: 11429430 PMCID: PMC1731468 DOI: 10.1136/jcp.54.7.556] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The Scottish Meningococcus and Pneumococcus Reference Laboratory provides a national service for the laboratory confirmation of meningococcal and pneumococcal disease in Scotland. The main tests used for the laboratory confirmation of meningococcal disease are culture, the polymerase chain reaction (PCR), antibody testing, and more recently DNA sequencing. This paper describes the automation of PCR for the laboratory confirmation of meningococcal disease and the typing of meningococcal isolates using DNA sequencing. Both methods have been automated using a robotic liquid handler and automated DNA sequencer. These methods, along with standard culture phenotyping and antibody testing, provide Scotland with an excellent service for the confirmation of meningococcal disease.
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Affiliation(s)
- S C Clarke
- Scottish Meningococcus and Pneumococcus Reference Laboratory, Department of Microbiology, House on the Hill, Stobhill Hospital, Glasgow G21 3UW, UK.
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Clarke SC, Reid J, Thom L, Denham BC, Edwards GF. Meningococcal disease due to serogroup Y in Scotland, 1992-1999. Br J Biomed Sci 2001; 58:17-9. [PMID: 11284218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Meningococcal disease is an important cause of morbidity and mortality. A retrospective analysis was performed of all cases of invasive group-Y disease that were laboratory-confirmed in Scotland between 1992 and 1999. A total of 1881 meningococcal isolates were characterised, 78 of which were serogroup Y. The incidence of non-invasive group-Y disease remained level between 1992 and 1999. Only 12 isolates were from invasive disease, comprising five strain types. Invasive group-Y disease was associated mostly with the young or old. Serogroup-Y meningococcal disease was uncommon and a rare cause of invasive disease in Scotland between 1992 and 1999; however, it is essential that microbiologists are aware of its potential for increasing in incidence due to the recent introduction of the MenC vaccine, and its increased incidence in the USA.
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Affiliation(s)
- S C Clarke
- Scottish Meningococcus and Pneumococcus Reference Laboratory, Department of Microbiology, House on the Hill, Stobhill Hospital, Glasgow, G21 3UW, UK.
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Clarke SC, Christie P, Edwards GF. Pneumococcal disease and asplenia: the importance of vaccination. Health Bull (Edinb) 2001; 59:49-52. [PMID: 12811911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Pneumococcal disease is an important cause of morbidity and mortality, particularly in certain patient groups including those who have been splenectomised or have no functioning spleen. Recent deaths in two asplenic patients from pneumococcal disease should remind doctors of the importance of vaccination in asplenic individuals. The current guidelines for vaccination in such patients are highlighted and discussed. The need for a national asplenic register is also suggested.
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Affiliation(s)
- S C Clarke
- Scottish Meningococcus and Pneumococcus Reference Laboratory, Stobhill Hospital, North Glasgow University Hospitals Trust, Glasgow
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Kyaw MH, Clarke S, Edwards GF, Jones IG, Campbell H. Serotypes/groups distribution and antimicrobial resistance of invasive pneumococcal isolates: implications for vaccine strategies. Epidemiol Infect 2000; 125:561-72. [PMID: 11218207 PMCID: PMC2869640 DOI: 10.1017/s0950268800004787] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Based on the invasive pneumococcal isolates referred to reference laboratories in Scotland in 1988-99, we identified the distribution of serotypes/groups and their antimicrobial resistance patterns in order to evaluate the coverage of polysaccharide and the new pneumococcal conjugate vaccines. A total of 5659 invasive isolates were included. Of these, 5124 (90.5%) were blood isolates, 308 (5.5%) were CSF isolates, 143 (2.5%) were blood and CSF and 84 (1.5%) were other normally sterile isolates. The most prevalent 11 serotypes/groups were 14, 9, 19, 6, 23, 1, 3, 4, 7, 8 and 18, in numerical order. These accounted for 84% of total serotypes/groups. The serotypes/groups included in the 23 and 14-valent polysaccharide vaccines accounted for 96% and 88% of all isolates. Both vaccines accounted for 98% of penicillin non-susceptible and 100% of erythromycin non-susceptible isolates. The 7, 9, and 11-valent conjugate vaccines covered 61, 68 and 80% of invasive isolates respectively. The coverage of these vaccines was substantially higher in youngest age group with 84, 86 and 93% of invasive isolates in children < 2 years included in the 7, 9 and 11-valent conjugate vaccines compared with 58, 64 and 77% in adults > or = 65 years of age. The serotype/group distribution of invasive isolates in Scotland varied from year to year over the period 1993-9. The coverage of the 23-valent vaccine remained above 95% in each year but the coverage of the 7, 9 and 11-valent conjugate vaccines showed more marked fluctuation with coverage as low as 53, 60 and 75% in some years. Continued surveillance of invasive pneumococcal isolates is required to inform the development of appropriate vaccine strategies to prevent pneumococcal disease in Scotland.
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Affiliation(s)
- M H Kyaw
- University of Edinburgh, Health Sciences
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Affiliation(s)
- S C Clarke
- Scottish Meningococcus and Pneumococcus Reference Laboratory, Stobhill Hospital, Glasgow.
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18
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Abstract
We have used molecular techniques to characterize 51 group A streptococci from Scotland and 17 'serious disease' isolates from other countries, in order to establish the clonal structure of invasive Streptococcus pyogenes strains circulating between 1986 and 1993. Strains were grouped by restriction endonuclease analysis, pulsed field gel electrophoresis and ribotyping patterns, and were examined for the presence of alleles of the speA gene by polymerase chain reaction and DNA sequence analysis. Serious and fatal infections in Scotland were caused by several clones. One clone (9 of 51 strains) was M type 1 and possessed the speA gene allele 2. This was the clone previously identified as causing severe infection in the USA. Another clone (5 of 51 strains) was M type 3 and had speA gene allele 3. In view of the clear association of more than one clone with severe, invasive and fatal infections, horizontal gene exchange between genotypes merits further investigation.
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Affiliation(s)
- M Upton
- Department of Medical Microbiology, University of Aberdeen Medical School, Foresterhill, UK
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Edwards GF, Curran ET, McCartney AC, Paterson KR, Girdwood RW, Threlfall EJ, Ward LR. Nosocomial salmonellosis. Commun Dis Rep CDR Rev 1993; 3:R40-1; discussion R42. [PMID: 7693145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- G F Edwards
- Department of Microbiology, Glasgow Royal Infirmary
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Edwards GF, Lindsay G, Taylor EW. A bacteriological assessment of ampicillin with sulbactam as antibiotic prophylaxis in patients undergoing biliary tract operations. The West of Scotland Surgical Infection Study Group. J Hosp Infect 1990; 16:249-55. [PMID: 1979575 DOI: 10.1016/0195-6701(90)90113-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A prospective audit of 644 patients undergoing biliary tract operations has been conducted in ten district general hospitals. All patients received a single dose of ampicillin 2 g and sulbactam 1 g as antibiotic prophylaxis. Bacteria were cultured from the bile of 121 patients. In patients with sterile bile the incidence of postoperative infection was 2.5%, while in those with colonized bile it was 22% (P less than 0.0001). The 35 patients from whose bile bacteria of two or more species were isolated, had a higher incidence of wound infection (34%) than those whose bile yielded only one species of bacterium (17%; P less than 0.05). Seventeen of the 27 patients with colonized bile who developed postoperative infection were shown to be infected by the same organisms that had been isolated from their bile. The patients whose bile yielded organisms resistant to the prophylactic antibiotic combination did not have a significantly higher rate of infection than those from whose bile only sensitive organisms were obtained. A marked difference in sensitivity patterns between the participating hospitals was observed.
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Baldwin GS, Edwards GF, Kiener PA, Tully MJ, Waley SG, Abraham EP. Production of a variant of beta-lactamase II with selectively decreased cephalosporinase activity by a mutant of Bacillus cereus 569/H/9. Biochem J 1980; 191:111-6. [PMID: 6781486 PMCID: PMC1162187 DOI: 10.1042/bj1910111] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
1. Mutants of Bacillus cereus 569/H/9 have been screened in a search for strains that synthesize variants of beta-lactamase II. 2. One of these mutants (strain 569/H/9/1) produces a beta-lactamase II-like enzyme that shows a selective decrease in cephalosporinase activity. 3. beta-Lactamase II from strain 569/H/9/1 has been purified to apparent homogeneity and its kinetic properties have been examined. This enzyme resembles the parent beta-lactamase II in its relative activity with benzylpenicillin as substrate when Zn(II) is replaced by other metal ions, but differs detectably from the parent enzyme in its isoelectric point.
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Edwards GF, Lewis HE, Stafford D. The effect of pholcodine with and without an antihistamine on cough and expectoration. Br J Dis Chest 1977; 71:245-52. [PMID: 22340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Edwards GF, Steel AE, Scott JK, Jordan JW. S-carboxymethylcysteine in the fluidification of sputum and treatment of chronic airway obstruction. Chest 1976; 70:506-13. [PMID: 789027 DOI: 10.1378/chest.70.4.506] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The clinical results and changes in sputum found in both a short-term inpatient trial and a subsequent long-term outpatient investigation (three-month double-blind controlled study) of 82 patients with chronic bronchitis treated with a new mucolytic agent, S-carboxymethylcysteine (Mucodyne), are reported. Fluidification of sputum with reduction in certain measurements of the viscosity of morning sputum aliquots, associated with improvement in the ability to cough up bronchial secretions, significant increase in sputum volume output, and improvement in ventilation (as estimated by the forced expiratory volume in one second), were observed in both trials as dose-related responses, with an increase in the ease of expectoration and a reduction in cough frequency and dyspnea. Therapy with S-carboxymethylcysteine was well tolerated, and there were no serious adverse effects, either immediate or delayed. We suggest that the effect of the drug in fluidifying sputum may be due to a mucoregulatory mechanism which reverses the sputum macromolecular disturbances seen in chronic bronchitis.
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Parsons FM, Edwards GF, Anderson CK, Ahmad S, Clark PB, Hetherington C, Young GA. Regression of malignant tumours in magnesium and potassium depletion induced by diet and haemodialysis. Lancet 1974; 1:243-4. [PMID: 4130249 DOI: 10.1016/s0140-6736(74)92549-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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