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Shaw D, Abad R, Amin-Chowdhury Z, Bautista A, Bennett D, Broughton K, Cao B, Casanova C, Choi EH, Chu YW, Claus H, Coelho J, Corcoran M, Cottrell S, Cunney R, Cuypers L, Dalby T, Davies H, de Gouveia L, Deghmane AE, Demczuk W, Desmet S, Domenech M, Drew R, du Plessis M, Duarte C, Erlendsdóttir H, Fry NK, Fuursted K, Hale T, Henares D, Henriques-Normark B, Hilty M, Hoffmann S, Humphreys H, Ip M, Jacobsson S, Johnson C, Johnston J, Jolley KA, Kawabata A, Kozakova J, Kristinsson KG, Krizova P, Kuch A, Ladhani S, Lâm TT, León ME, Lindholm L, Litt D, Maiden MCJ, Martin I, Martiny D, Mattheus W, McCarthy ND, Meehan M, Meiring S, Mölling P, Morfeldt E, Morgan J, Mulhall R, Muñoz-Almagro C, Murdoch D, Murphy J, Musilek M, Mzabi A, Novakova L, Oftadeh S, Perez-Argüello A, Pérez-Vázquez M, Perrin M, Perry M, Prevost B, Roberts M, Rokney A, Ron M, Sanabria OM, Scott KJ, Sheppard C, Siira L, Sintchenko V, Skoczyńska A, Sloan M, Slotved HC, Smith AJ, Steens A, Taha MK, Toropainen M, Tzanakaki G, Vainio A, van der Linden MPG, van Sorge NM, Varon E, Vohrnova S, von Gottberg A, Yuste J, Zanella R, Zhou F, Brueggemann AB. Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium. Lancet Digit Health 2023; 5:e582-e593. [PMID: 37516557 PMCID: PMC10914672 DOI: 10.1016/s2589-7500(23)00108-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/22/2023] [Accepted: 05/25/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND The Invasive Respiratory Infection Surveillance (IRIS) Consortium was established to assess the impact of the COVID-19 pandemic on invasive diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Streptococcus agalactiae. We aimed to analyse the incidence and distribution of these diseases during the first 2 years of the COVID-19 pandemic compared to the 2 years preceding the pandemic. METHODS For this prospective analysis, laboratories in 30 countries and territories representing five continents submitted surveillance data from Jan 1, 2018, to Jan 2, 2022, to private projects within databases in PubMLST. The impact of COVID-19 containment measures on the overall number of cases was analysed, and changes in disease distributions by patient age and serotype or group were examined. Interrupted time-series analyses were done to quantify the impact of pandemic response measures and their relaxation on disease rates, and autoregressive integrated moving average models were used to estimate effect sizes and forecast counterfactual trends by hemisphere. FINDINGS Overall, 116 841 cases were analysed: 76 481 in 2018-19, before the pandemic, and 40 360 in 2020-21, during the pandemic. During the pandemic there was a significant reduction in the risk of disease caused by S pneumoniae (risk ratio 0·47; 95% CI 0·40-0·55), H influenzae (0·51; 0·40-0·66) and N meningitidis (0·26; 0·21-0·31), while no significant changes were observed for S agalactiae (1·02; 0·75-1·40), which is not transmitted via the respiratory route. No major changes in the distribution of cases were observed when stratified by patient age or serotype or group. An estimated 36 289 (95% prediction interval 17 145-55 434) cases of invasive bacterial disease were averted during the first 2 years of the pandemic among IRIS-participating countries and territories. INTERPRETATION COVID-19 containment measures were associated with a sustained decrease in the incidence of invasive disease caused by S pneumoniae, H influenzae, and N meningitidis during the first 2 years of the pandemic, but cases began to increase in some countries towards the end of 2021 as pandemic restrictions were lifted. These IRIS data provide a better understanding of microbial transmission, will inform vaccine development and implementation, and can contribute to health-care service planning and provision of policies. FUNDING Wellcome Trust, NIHR Oxford Biomedical Research Centre, Spanish Ministry of Science and Innovation, Korea Disease Control and Prevention Agency, Torsten Söderberg Foundation, Stockholm County Council, Swedish Research Council, German Federal Ministry of Health, Robert Koch Institute, Pfizer, Merck, and the Greek National Public Health Organization.
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Affiliation(s)
- David Shaw
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Raquel Abad
- National Reference Laboratory for Meningococci, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Zahin Amin-Chowdhury
- Immunisation and Countermeasures Division, UK Health Security Agency, London, UK
| | | | - Desiree Bennett
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
| | - Karen Broughton
- Staphylococcus and Streptococcus Reference Section, AMRHAI, UK Health Security Agency, London, UK
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Carlo Casanova
- Swiss National Reference Center for Invasive Pneumococci, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Yiu-Wai Chu
- Department of Health, Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Hong Kong Special Administrative Region, China
| | - Heike Claus
- University of Würzburg, Institute for Hygiene and Microbiology, National Reference Centre for Meningococci and Haemophilus influenzae, Würzburg, Germany
| | - Juliana Coelho
- Staphylococcus and Streptococcus Reference Section, AMRHAI, UK Health Security Agency, London, UK
| | - Mary Corcoran
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Robert Cunney
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Lize Cuypers
- National Reference Centre for Streptococcus pneumoniae, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Tine Dalby
- Statens Serum Institut, Department of Infectious Disease Epidemiology & Prevention, Copenhagen, Denmark
| | - Heather Davies
- Meningococcal Reference Laboratory, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ala-Eddine Deghmane
- Institut Pasteur, Univeristé Paris Cité, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Stefanie Desmet
- National Reference Centre for Streptococcus pneumoniae, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Mirian Domenech
- National Center for Microbiology and CIBER of Respiratory Research, Instituto de Salud Carlos III, Madrid, Spain
| | - Richard Drew
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland; Clinical Innovation Unit, Rotunda, Dublin, Ireland
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Helga Erlendsdóttir
- Department of Clinical Microbiology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Norman K Fry
- Immunisation and Vaccine Preventable Diseases Division and Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | - Kurt Fuursted
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Copenhagen, Denmark
| | - Thomas Hale
- Blavatnik School of Government, University of Oxford, Oxford, UK
| | - Desiree Henares
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain
| | - Birgitta Henriques-Normark
- Karolinska Institutet, Karolinska University Hospital, Public Health Agency of Sweden, Stockholm, Sweden
| | - Markus Hilty
- Swiss National Reference Center for Invasive Pneumococci, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Steen Hoffmann
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Copenhagen, Denmark
| | - Hilary Humphreys
- Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland; Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Susanne Jacobsson
- National Reference Laboratory for Neisseria meningitidis, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | | | | | | | - Jana Kozakova
- National Reference Laboratory for Streptococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Karl G Kristinsson
- Department of Clinical Microbiology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Pavla Krizova
- National Reference Laboratory for Meningococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Alicja Kuch
- National Reference Centre for Bacterial Meningitis, Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Shamez Ladhani
- Immunisation and Countermeasures Division, UK Health Security Agency, London, UK
| | - Thiên-Trí Lâm
- University of Würzburg, Institute for Hygiene and Microbiology, National Reference Centre for Meningococci and Haemophilus influenzae, Würzburg, Germany
| | | | - Laura Lindholm
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - David Litt
- Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | | | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Delphine Martiny
- National Belgian Reference Centre for Haemophilus influenzae, Laboratoire des Hôpitaux Universitaires de Bruxelles-Universitair Laboratorium van Brussel, Brussels, Belgium; Faculty of Medicine and Pharmacy, University of Mons, Mons, Belgium
| | | | - Noel D McCarthy
- Population Health Medicine, Public Health and Primary Care, Trinity College Dublin, Dublin, Ireland
| | - Mary Meehan
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
| | - Susan Meiring
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Paula Mölling
- National Reference Laboratory for Neisseria meningitidis, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Julie Morgan
- Streptococcal Reference Laboratory, Institute of Environmental Science and Research Limited, Porirua, New Zealand
| | - Robert Mulhall
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
| | - Carmen Muñoz-Almagro
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain; Medicine Department, Universitat Internacional de Catalunya, Barcelona, Spain
| | | | | | - Martin Musilek
- National Reference Laboratory for Meningococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Alexandre Mzabi
- Ministère de la Santé - Direction de la santé, Luxembourg, Luxembourg
| | - Ludmila Novakova
- National Reference Laboratory for Haemophilus Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Shahin Oftadeh
- NSW Pneumococcal Reference Laboratory, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Sydney, NSW, Australia
| | - Amaresh Perez-Argüello
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Maria Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Benoit Prevost
- National Belgian Reference Centre for Haemophilus influenzae, Laboratoire des Hôpitaux Universitaires de Bruxelles-Universitair Laboratorium van Brussel, Brussels, Belgium
| | | | - Assaf Rokney
- Public Health Laboratories-Jerusalem, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Merav Ron
- Public Health Laboratories-Jerusalem, Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Kevin J Scott
- Bacterial Respiratory Infection Service, Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK
| | - Carmen Sheppard
- Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | - Lotta Siira
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Vitali Sintchenko
- NSW Pneumococcal Reference Laboratory, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Sydney, NSW, Australia; Sydney Institute for Infectious Diseases, University of Sydney, NSW, Australia
| | - Anna Skoczyńska
- National Reference Centre for Bacterial Meningitis, Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | | | | | - Andrew J Smith
- Bacterial Respiratory Infection Service, Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK; College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Anneke Steens
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Muhamed-Kheir Taha
- Institut Pasteur, Univeristé Paris Cité, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
| | | | - Georgina Tzanakaki
- National Meningitis Reference Laboratory, Department of Public Health Policy, School of Public Health, University of West Attica, Athens, Greece
| | - Anni Vainio
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Mark P G van der Linden
- Department of Medical Microbiology, German National Reference Centre for Streptococci, University Hospital RWTH Aachen, Aachen, Germany
| | - Nina M van Sorge
- Department of Medical Microbiology and Infection Prevention, and Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Emmanuelle Varon
- Laboratory of Medical Biology and National Reference Centre for Pneumococci, Intercommunal Hospital of Créteil, Créteil, France
| | - Sandra Vohrnova
- National Reference Laboratory for Streptococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jose Yuste
- National Center for Microbiology and CIBER of Respiratory Research, Instituto de Salud Carlos III, Madrid, Spain
| | - Rosemeire Zanella
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz, São Paulo, Brazil
| | - Fei Zhou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Angela B Brueggemann
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK.
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Adam HJ, Karlowsky JA, Baxter MR, Schellenberg J, Golden AR, Martin I, Demczuk W, Mulvey MR, Zhanel GG. Analysis of MDR in the predominant Streptococcus pneumoniae serotypes in Canada: the SAVE study, 2011-2020. J Antimicrob Chemother 2023; 78:i17-i25. [PMID: 37130586 DOI: 10.1093/jac/dkad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
OBJECTIVES To investigate the levels of MDR in the predominant serotypes of invasive Streptococcus pneumoniae isolated in Canada over a 10 year period. METHODS All isolates were serotyped and had antimicrobial susceptibility testing performed, in accordance with CLSI guidelines (M07-11 Ed., 2018). Complete susceptibility profiles were available for 13 712 isolates. MDR was defined as resistance to three or more classes of antimicrobial agents (penicillin MIC ≥2 mg/L defined as resistant). Serotypes were determined by Quellung reaction. RESULTS In total, 14 138 invasive isolates of S. pneumoniae were tested in the SAVE study (S. pneumoniae Serotyping and Antimicrobial Susceptibility: Assessment for Vaccine Efficacy in Canada), a collaboration between the Canadian Antimicrobial Resistance Alliance and Public Health Agency of Canada-National Microbiology Laboratory. The rate of MDR S. pneumoniae in SAVE was 6.6% (902/13 712). Annual rates of MDR S. pneumoniae decreased between 2011 and 2015 (8.5% to 5.7%) and increased between 2016 and 2020 (3.9% to 9.4%). Serotypes 19A and 15A were the most common serotypes demonstrating MDR (25.4% and 23.5% of the MDR isolates, respectively); however, the serotype diversity index increased from 0.7 in 2011 to 0.9 in 2020 with a statistically significant linear increasing trend (P < 0.001). In 2020, MDR isolates were frequently serotypes 4 and 12F in addition to serotypes 15A and 19A. In 2020, 27.3%, 45.5%, 50.5%, 65.7% and 68.7% of invasive MDR S. pneumoniae were serotypes included in the PCV10, PCV13, PCV15, PCV20 and PPSV23 vaccines, respectively. CONCLUSIONS Although current vaccine coverage of MDR S. pneumoniae in Canada is high, the increasing diversity of serotypes observed among the MDR isolates highlights the ability of S. pneumoniae to rapidly evolve.
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Affiliation(s)
- Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - John Schellenberg
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Alyssa R Golden
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
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Alford MA, Karlowsky JA, Adam HJ, Baxter MR, Schellenberg J, Golden AR, Martin I, Demczuk W, Mulvey MR, Zhanel GG. Antimicrobial susceptibility testing of invasive isolates of Streptococcus pneumoniae from Canadian patients: the SAVE study, 2011-2020. J Antimicrob Chemother 2023; 78:i8-i16. [PMID: 37130584 DOI: 10.1093/jac/dkad065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
OBJECTIVES To assess the antimicrobial susceptibility of 14 138 invasive Streptococcus pneumoniae isolates collected in Canada from 2011 to 2020. METHODS Antimicrobial susceptibility testing was performed using the CLSI M07 broth microdilution reference method. MICs were interpreted using 2022 CLSI M100 breakpoints. RESULTS In 2020, 90.1% and 98.6% of invasive pneumococci were penicillin-susceptible when MICs were interpreted using CLSI meningitis or oral and non-meningitis breakpoints, respectively; 96.9% (meningitis breakpoint) and 99.5% (non-meningitis breakpoint) of isolates were ceftriaxone-susceptible, and 99.9% were levofloxacin-susceptible. Numerically small, non-temporal, but statistically significant differences (P < 0.05) in the annual percentage of isolates susceptible to four of the 13 agents tested was observed across the 10-year study: chloramphenicol (4.4% difference), trimethoprim-sulfamethoxazole (3.9%), penicillin (non-meningitis breakpoint, 2.7%) and ceftriaxone (meningitis breakpoint, 2.7%; non-meningitis breakpoint, 1.2%). During the same period, annual differences in percent susceptible values for penicillin (meningitis and oral breakpoints) and all other agents did not achieve statistical significance. The percentage of isolates with an MDR phenotype (resistance to ≥3 antimicrobial classes) in 2011 and 2020 (8.5% and 9.4%) was not significantly different (P = 0.109), although there was a significant interim decrease observed between 2011 and 2015 (P < 0.001) followed by a significant increase between 2016 and 2020 (P < 0.001). Statistically significant associations were observed between resistance rates to most antimicrobial agents included in the MDR analysis (penicillin, clarithromycin, clindamycin, doxycycline, trimethoprim/sulfamethoxazole and chloramphenicol) and patient age, specimen source, geographic location in Canada or concurrent resistance to penicillin or clarithromycin, but not biological sex of patients. Given the large isolate collection studied, statistical significance did not necessarily imply clinical or public health significance in some analyses. CONCLUSIONS Invasive pneumococcal isolates collected in Canada from 2011 to 2020 generally exhibited consistent in vitro susceptibility to commonly tested antimicrobial agents.
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Affiliation(s)
- Morgan A Alford
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - John Schellenberg
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Alyssa R Golden
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
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Schellenberg JJ, Adam HJ, Baxter MR, Karlowsky JA, Golden AR, Martin I, Demczuk W, Mulvey MR, Zhanel GG. Comparison of PCV10, PCV13, PCV15, PCV20 and PPSV23 vaccine coverage of invasive Streptococcus pneumoniae isolate serotypes in Canada: the SAVE study, 2011-20. J Antimicrob Chemother 2023; 78:i37-i47. [PMID: 37130588 DOI: 10.1093/jac/dkad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND As pneumococci evolve under vaccine, antimicrobial and other selective pressures, it is important to track isolates covered by established (PCV10, PCV13 and PPSV23) and new (PCV15 and PCV20) vaccine formulations. OBJECTIVES To compare invasive pneumococcal disease (IPD) isolates from serotypes covered by PCV10, PCV13, PCV15, PCV20 and PPSV23, collected in Canada from 2011 to 2020, by demographic category and antimicrobial resistance phenotype. METHODS IPD isolates from the SAVE study were initially collected by members of the Canadian Public Health Laboratory Network (CPHLN) as part of a collaboration between the Canadian Antimicrobial Resistance Alliance (CARA) and the Public Health Agency of Canada (PHAC). Serotypes were determined by quellung reaction, and antimicrobial susceptibility testing was performed using the CLSI broth microdilution method. RESULTS A total of 14 138 invasive isolates were collected from 2011 to 2020, with 30.7% of isolates covered by the PCV13 vaccine, 43.6% of isolates covered by the PCV15 vaccine (including 12.9% non-PCV13 serotypes 22F and 33F), and 62.6% of isolates covered by the PCV20 vaccine (including 19.0% non-PCV15 serotypes 8, 10A, 11A, 12F and 15B/C). Non-PCV20 serotypes 2, 9N, 17F and 20, but not 6A (present in PPSV23) represented 8.8% of all IPD isolates. Higher-valency vaccine formulations covered significantly more isolates by age, sex, region and resistance phenotype including MDR isolates. Coverage of XDR isolates did not significantly differ between vaccine formulations. CONCLUSIONS When compared with PCV13 and PCV15, PCV20 covered significantly more IPD isolates stratified by patient age, region, sex, individual antimicrobial resistance phenotypes and MDR phenotype.
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Affiliation(s)
- John J Schellenberg
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Alyssa R Golden
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
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5
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Golden AR, Adam HJ, Karlowsky JA, Baxter M, Schellenberg J, Martin I, Demczuk W, Minion J, Van Caeseele P, Kus JV, McGeer A, Lefebvre B, Smadi H, Haldane D, Yu Y, Mead K, Mulvey MR, Zhanel GG. Genomic investigation of the most common Streptococcus pneumoniae serotypes causing invasive infections in Canada: the SAVE study, 2011-2020. J Antimicrob Chemother 2023; 78:i26-i36. [PMID: 37130587 DOI: 10.1093/jac/dkad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
OBJECTIVES To investigate the lineages and genomic antimicrobial resistance (AMR) determinants of the 10 most common pneumococcal serotypes identified in Canada during the five most recent years of the SAVE study, in the context of the 10-year post-PCV13 period in Canada. METHODS The 10 most common invasive Streptococcus pneumoniae serotypes collected by the SAVE study from 2016 to 2020 were 3, 22F, 9N, 8, 4, 12F, 19A, 33F, 23A and 15A. A random sample comprising ∼5% of each of these serotypes collected during each year of the full SAVE study (2011-2020) were selected for whole-genome sequencing (WGS) using the Illumina NextSeq platform. Phylogenomic analysis was performed using the SNVPhyl pipeline. WGS data were used to identify virulence genes of interest, sequence types, global pneumococcal sequence clusters (GPSC) and AMR determinants. RESULTS Of the 10 serotypes analysed in this study, six increased significantly in prevalence from 2011 to 2020: 3, 4, 8, 9N, 23A and 33F (P ≤ 0.0201). Serotypes 12F and 15A remained stable in prevalence over time, while serotype 19A decreased in prevalence (P < 0.0001). The investigated serotypes represented four of the most prevalent international lineages causing non-vaccine serotype pneumococcal disease in the PCV13 era: GPSC3 (serotypes 8/33F), GPSC19 (22F), GPSC5 (23A) and GPSC26 (12F). Of these lineages, GPSC5 isolates were found to consistently possess the most AMR determinants. Commonly collected vaccine serotypes 3 and 4 were associated with GPSC12 and GPSC27, respectively. However, a more recently collected lineage of serotype 4 (GPSC192) was highly clonal and possessed AMR determinants. CONCLUSIONS Continued genomic surveillance of S. pneumoniae in Canada is essential to monitor for the appearance of new and evolving lineages, including antimicrobial-resistant GPSC5 and GPSC162.
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Affiliation(s)
- Alyssa R Golden
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Heather J Adam
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba, R3A 1R9, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - James A Karlowsky
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba, R3A 1R9, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Melanie Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - John Schellenberg
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Jessica Minion
- Roy Romanow Provincial Laboratory, Saskatchewan Health Authority, 5 Research Drive, Regina, Saskatchewan, S4S 0A4, Canada
| | - Paul Van Caeseele
- Cadham Provincial Laboratory, Shared Health, 750 William Avenue, Winnipeg, Manitoba, R3E 3J7, Canada
| | - Julianne V Kus
- Public Health Ontario Laboratory, 661 University Avenue, Toronto, Ontario, M5G 1M1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle-6th Floor, Toronto, Ontario, M5S 1A8, Canada
| | - Allison McGeer
- Toronto Invasive Bacterial Diseases Network (TIBDN), Department of Microbiology, Mount Sinai Hospital. 600 University Avenue-Suite 171, Toronto, Ontario, M5G 1X5, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, 20045 Ch Ste-Marie, Ste-Anne-de-Bellevue, Québec, H9X 3R5, Canada
| | - Hanan Smadi
- Epidemiology and Surveillance Branch, New Brunswick Department of Health, 520 King Street, Fredericton, New Brunswick, E3B 5G8, Canada
| | - David Haldane
- Department of Pathology and Laboratory Medicine, Queen Elizabeth II Health Science Centre, 1276 South Park Street, Halifax, Nova Scotia, B3H 2Y9, Canada
| | - Yang Yu
- Newfoundland and Labrador Public Health Laboratory, Dr. Leonard A. Miller Centre-Suite 1, 100 Forest Road, St. John's, Newfoundland and Labrador, A1A 1E3, Canada
| | - Kristen Mead
- Provincial Laboratory Services, Queen Elizabeth Hospital, 60 Riverside Drive, Charlottetown, Prince Edward Island, C1A 8T5, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
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Peterson SW, Demczuk W, Martin I, Adam H, Bharat A, Mulvey MR. Identification of bacterial and fungal pathogens directly from clinical blood cultures using whole genome sequencing. Genomics 2023; 115:110580. [PMID: 36792020 DOI: 10.1016/j.ygeno.2023.110580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 01/17/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023]
Abstract
Bloodstream infections are a major cause of morbidity and mortality worldwide. Early administration of appropriate antimicrobial therapy can improve patient survival and prevent antimicrobial resistance (AMR). Whole genome sequencing (WGS) can provide information for pathogen identification, AMR prediction and sequence typing earlier than current phenotypic diagnostic methods. WGS was performed on 97 clinical blood specimens and matched culture isolate pairs. Specimen/isolate pairs were MLST sequence-typed and further characterization was performed on Streptococcus species. WGS correctly identified 91.7% of clinical specimens and 93.2% of matched isolates representing 35 different microbial species. MLST types were assigned for 89.9% of matched cultures and 21.7% of blood specimens, with higher success for blood culture specimens extracted within 3 days (52% characterized) than 7 days (9.3%). This study demonstrates the potential use of WGS for identification and characterization of pathogens directly from blood culture specimens to facilitate timely initiation of appropriate antimicrobial therapies.
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Affiliation(s)
- S W Peterson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - W Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - I Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - H Adam
- Diagnostic Services, Shared Health Manitoba, Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - A Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
| | - M R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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7
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Golden A, Griffith A, Demczuk W, Lefebvre B, McGeer A, Tyrrell G, Zhanel G, Kus J, Hoang L, Minion J, Van Caeseele P, Smadi H, Haldane D, Zahariadis G, Mead K, Steven L, Strudwick L, Li A, Mulvey M, Martin I. Invasive pneumococcal disease surveillance in Canada, 2020. Can Commun Dis Rep 2022; 48:396-406. [PMID: 38124782 PMCID: PMC10732480] [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] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Background Invasive pneumococcal disease (IPD), which is caused by Streptococcus pneumoniae, has been a nationally notifiable disease in Canada since 2000. The use of conjugate vaccines has markedly decreased the incidence of IPD in Canada; however, the distribution of serotypes has shifted in favour of non-vaccine types. This report summarizes the demographics, serotypes and antimicrobial resistance of IPD infections in Canada in 2020. Methods The Public Health Agency of Canada's National Microbiology Laboratory (Winnipeg, Manitoba) collaborates with provincial and territorial public health laboratories to conduct national surveillance of IPD. A total of 2,108 IPD isolates were reported in 2020. Serotyping was performed by Quellung reaction and antimicrobial susceptibilities were determined in collaboration with the University of Manitoba/Canadian Antimicrobial Resistance Alliance. Population-based IPD incidence rates were obtained through the Canadian Notifiable Disease Surveillance System. Results Overall incidence of IPD in Canada decreased significantly from 11.5 (95% confidence interval [CI]: 10.1-13.1) to 6.0 (95% CI: 5.0-7.2), and from 10.0 (95% CI: 9.7-10.3) to 5.9 (95% CI: 5.7-6.2) cases per 100,000 from 2019 to 2020; in those younger than five years and those five years and older, respectively. The most common serotypes overall were 4 (11.2%, n=237), 3 (10.9%, n=229) and 8 (7.2%, n=151). From 2016 to 2020, serotypes with increasing trends (p<0.05) included 4 (6.4%-11.2%), 3 (9.5%-10.9%), 8 (5.2%-7.2%) and 12F (3.6%-5.7%). The overall prevalence of PCV13 serotypes increased over the same period (30.3%-34.9%, p<0.05). Antimicrobial resistance rates in 2020 included 23.0% clarithromycin and 9.9% penicillin (IV meningitis breakpoints). Multidrug-resistant IPD has significantly increased since 2016 (4.2%-9.5%, p<0.05). Conclusion Though the incidence of IPD decreased in 2020 in comparison to previous years across all age groups, disease due to PCV13 serotypes 3 and 4, as well as non-PCV13 serotypes such as 8 and 12F, increased in prevalence. Continued surveillance of IPD is imperative to monitor shifts in serotype distribution and antimicrobial resistance.
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Affiliation(s)
- Alyssa Golden
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Averil Griffith
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC
| | - Allison McGeer
- Toronto Invasive Bacterial Diseases Network (TIBDN), Department of Microbiology, Mount Sinai Hospital, Toronto, ON
| | - Gregory Tyrrell
- Provincial Laboratory for Public Health (Microbiology), Edmonton, AB
| | - George Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB
| | - Julianne Kus
- Public Health Ontario, Toronto, ON
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON
| | - Linda Hoang
- British Columbia Centre for Disease Control, Vancouver, BC
| | | | | | - Hanan Smadi
- New Brunswick Department of Health, Fredericton, NB
| | - David Haldane
- Queen Elizabeth II Health Science Centre, Halifax, NS
| | | | | | - Laura Steven
- Stanton Territorial Hospital Laboratory, Yellowknife, NT
| | | | - Anita Li
- Centre for Immunization & Respiratory Infectious Diseases, Public Health Agency of Canada, Ottawa, ON
| | - Michael Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
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8
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Golden A, Griffith A, Demczuk W, Tyrrell G, Kus J, McGeer A, Domingo MC, Hoang L, Minion J, Van Caeseele P, Smadi H, Haldane D, Zahariadis G, Mead K, Steven L, Strudwick L, Li A, Mulvey M, Martin I. Invasive group A streptococcal disease surveillance in Canada, 2020. Can Commun Dis Rep 2022; 48:407-414. [PMID: 38106647 PMCID: PMC10723789] [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] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Background Invasive group A streptococcal (iGAS) disease (caused by Streptococcus pyogenes) has been a nationally notifiable disease in Canada since 2000. This report summarizes the demographics, emm types and antimicrobial resistance of iGAS infections in Canada in 2020. Methods The Public Health Agency of Canada's National Microbiology Laboratory (Winnipeg, Manitoba) collaborates with provincial and territorial public health laboratories to conduct national surveillance of invasive S. pyogenes. Emm typing was performed on all isolates using the Centers for Disease Control and Prevention emm sequencing protocol. Antimicrobial susceptibilities were determined using Kirby-Bauer disk diffusion according to Clinical and Laboratory Standards Institute guidelines. Population-based iGAS disease incidence rates up to 2019 were obtained through the Canadian Notifiable Disease Surveillance System. Results Overall, the incidence of iGAS disease in Canada has increased from 4.0 to 8.1 cases per 100,000 population from 2009 to 2019. The 2019 incidence represents a slight decrease from the 2018 rate of 8.6 cases per 100,000 population. A total of 2,867 invasive S. pyogenes isolates that were collected during 2020 are included in this report, representing a decrease from 2019 (n=3,194). The most common emm types in 2020 were emm49 (16.8%, n=483) and emm76 (15.0%, n=429), both increasing significantly in prevalence since 2016 (p<0.001). The former most prevalent type, emm1, decreased to 7.6% (n=217) in 2020 from 15.4% (n=325) in 2016. Antimicrobial resistance rates in 2020 included 11.5% resistance to erythromycin, 3.2% resistance to clindamycin and 1.6% nonsusceptibility to chloramphenicol. Conclusion Though the number of collected invasive S. pyogenes isolates decreased slightly in 2020 in comparison to previous years, iGAS disease remains an important public health concern. The emm distribution in Canada has been subtly shifting over the past five years, away from common and well-known emm1 and towards emm49 and emm76. It is important to continue surveillance of S. pyogenes in Canada to monitor expanding replacement emm types, as well as outbreak clones and antimicrobial resistance.
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Affiliation(s)
- Alyssa Golden
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Averil Griffith
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Gregory Tyrrell
- Provincial Laboratory for Public Health (Microbiology), Edmonton, AB
| | - Julianne Kus
- Public Health Ontario, Toronto, ON
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON
| | - Allison McGeer
- Toronto Invasive Bacterial Diseases Network (TIBDN), Department of Microbiology, Mount Sinai Hospital, Toronto, ON
| | - Marc-Christian Domingo
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC
| | - Linda Hoang
- British Columbia Centre for Disease Control, Vancouver, BC
| | | | | | - Hanan Smadi
- New Brunswick Department of Health, Fredericton, NB
| | - David Haldane
- Queen Elizabeth II Health Science Centre, Halifax, NS
| | | | | | - Laura Steven
- Stanton Territorial Hospital Laboratory, Yellowknife, NT
| | | | - Anita Li
- Centre for Immunization & Respiratory Infectious Diseases, Public Health Agency of Canada, Ottawa, ON
| | - Michael Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
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Murad Y, Hung TY, Sadarangani M, Morris SK, Le Saux N, Vanderkooi OG, Kellner JD, Tyrrell GJ, Martin I, Demczuk W, Halperin SA, Bettinger JA. Clinical Presentations and Outcomes of Children in Canada With Recurrent Invasive Pneumococcal Disease From the IMPACT Surveillance Network. Pediatr Infect Dis J 2022; 41:e166-e171. [PMID: 35093996 PMCID: PMC8920017 DOI: 10.1097/inf.0000000000003454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/28/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Invasive pneumococcal disease due to Streptococcus pneumoniae can cause mortality and severe morbidity due to sepsis, meningitis and pneumonia, particularly in young children and the elderly. Recurrent invasive pneumococcal disease is rare yet serious sequelae of invasive pneumococcal disease that is associated with the immunocompromised and leads to a high mortality rate. METHOD This retrospective study reviewed recurrent invasive pneumococcal disease cases from the Canadian Immunization Monitoring Program, ACTive (IMPACT) between 1991 and 2019, an active network for surveillance of vaccine-preventable diseases and adverse events following immunization for children ages 0-16 years. Data were collected from 12 pediatric tertiary care hospitals across all 3 eras of public pneumococcal conjugate vaccine implementation in Canada. RESULTS The survival rate within our cohort of 180 recurrent invasive pneumococcal disease cases was 98.3%. A decrease of 26.4% in recurrent invasive pneumococcal disease due to vaccine serotypes was observed with pneumococcal vaccine introduction. There was also a 69.0% increase in the rate of vaccination in children with preexisting medical conditions compared with their healthy peers. CONCLUSION The decrease in recurrent invasive pneumococcal disease due to vaccine-covered serotypes has been offset by an increase of non-vaccine serotypes in this sample of Canadian children.
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Affiliation(s)
- Yousif Murad
- From the Faculty of Medicine, University of British Columbia, Vancouver, Canada
- Vaccine Evaluation Center, BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Te-Yu Hung
- Vaccine Evaluation Center, BC Children’s Hospital Research Institute, Vancouver, Canada
- Royal Darwin Hospital, Top End Health Service, Northern Territory, Australia
- Royal Melbourne Hospital, Doherty Institute for Infection Immunity, Victoria, Australia
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children’s Hospital Research Institute, Vancouver, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
| | - Shaun K. Morris
- Division of Infectious Diseases, Hospital for Sick Children, Toronto, Canada
- Department of Pediatrics, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Nicole Le Saux
- Children’s Hospital of Eastern Ontario, Paediatric Infectious Disease, Ottawa, ON, Canada
| | - Otto G. Vanderkooi
- Departments of Microbiology, Immunology and Infectious Diseases, Pathology & Laboratory Medicine and Community Health Sciences, Alberta Children’s Hospital, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
| | - James D. Kellner
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
| | - Gregory J. Tyrrell
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
- Alberta Precision Laboratories-Public Health, Edmonton, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Scott A. Halperin
- Canadian Center for Vaccinology, Dalhousie University, IWK Health, and Nova Scotia Health, Halifax, Canada
| | - Julie A. Bettinger
- Vaccine Evaluation Center, BC Children’s Hospital Research Institute, Vancouver, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
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LeBlanc JJ, ElSherif M, Ye L, MacKinnon-Cameron D, Ambrose A, Hatchette TF, Lang ALS, Gillis HD, Martin I, Demczuk W, Andrew MK, Boivin G, Bowie W, Green K, Johnstone J, Loeb M, McCarthy A, McGeer A, Semret M, Trottier S, Valiquette L, Webster D, McNeil S. 1325. Recalibrating Estimates of Pneumococcal Disease in Hospitalized Canadian adults from 2010 to 2017 with Use of an Extended Spectrum Serotype-specific Urine Antigen Detection. Open Forum Infect Dis 2021. [PMCID: PMC8644227 DOI: 10.1093/ofid/ofab466.1517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Pneumococcal vaccine recommendations in Canada include both age- and risk-based guidance. This study aimed to describe the burden of vaccine-preventable pneumococcal community acquired pneumonia (pCAP) and invasive pneumococcal disease (IPD) by age in hospitalized adults. Methods Active surveillance for all-cause CAP and IPD in hospitalized adults was performed from 2010 to 2017, including laboratory results, patient demographics, and outcomes. Streptococcus pneumoniae was detected using blood and sputum culture, or urine antigen detection (UAD). Serotype was assigned using Quellung reaction, PCR, or serotype-specific UADs spanning the 24 serotypes in PCV13 and PPV23 vaccines. Data were categorized by age (16-49, 50-64, 65+, and 50+ years) and over time. Results 11129 ACP cases and 216 cases of IPD (non-CAP) were identified. A laboratory test for S. pneumoniae was performed in 8912 of ACP cases, identifying 1264 (14.2%) as pCAP. Compared to non-pCAP, pCAP cases were more likely to be admitted to intensive care units and require mechanical ventilation. These serious outcomes, as well as mortality, were more prominent in bacteremic pCAP and IPD. Risk factors for death in pCAP included aged 75+ years, immune compromising conditions, and BMI < 18.5. When categorized by age, the proportion of individuals aged 65+ years for pCAP and IPD was 49.8% and 48.6%, and the 50-64 year age cohort represented 31.3% and 29.9%, respectively. The contributions of PCV13 and PPV23 serotypes remained relatively stable over time, and overall represented 57.6% and 90.9% for pCAP, and 35.0% and 72.0% for IPD, respectively. Conclusion Seven years following infant PCV13 immunization programs in Canada, PCV13 and PPV23 serotypes in pCAP and IPD remained predominant causes of pneumococcal disease. Serious outcomes were particularly evident in adults 50+, suggesting pneumococcal vaccines should be encouraged in this age group. Disclosures Jason J. LeBlanc, PhD, FCCM, D[ABMM], GSK (Research Grant or Support)Merck (Grant/Research Support)Pfizer (Grant/Research Support) Todd F Hatchette, MD, GSK (Grant/Research Support)Pfizer (Grant/Research Support) Melissa K. Andrew, MD, PhD, GSK (Grant/Research Support)Pfizer (Grant/Research Support, Advisor or Review Panel member)Sanofi (Consultant, Grant/Research Support, Advisor or Review Panel member)Seqirus (Advisor or Review Panel member) Allison McGeer, MSc,MD,FRCPC,FSHEA, GlaxoSmithKline (Advisor or Review Panel member)Merck (Advisor or Review Panel member, Research Grant or Support)Pfizer (Grant/Research Support, Scientific Research Study Investigator, Advisor or Review Panel member) Louis Valiquette, MD, M.Sc., Cubist (Consultant)GSK (Grant/Research Support)Merck (Consultant)Optimer (Consultant)Pfizer (Grant/Research Support) Shelly McNeil, FRCPC, MD, GSK (Grant/Research Support)Pfizer (Grant/Research Support)Sinofi Pasteur (Grant/Research Support)
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Affiliation(s)
- Jason J LeBlanc
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - May ElSherif
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Lingyun Ye
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Donna MacKinnon-Cameron
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Ardith Ambrose
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Todd F Hatchette
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | | | - Hayley D Gillis
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Walter Demczuk
- National Microbiology Laboratory (NML), Regina, MB, Canada
| | | | - Guy Boivin
- Centre Hospitalier Universitaire de Québec, Québec, Québec, Quebec, QC, Canada
| | - William Bowie
- Vancouver General Hospital, and University of British Columbia, Vancouver, BC, Vancouver, BC, Canada
| | - Karen Green
- Mount Sinai Hospital, Toronto, ON, Toronto, Ontario, Canada
| | - Jennie Johnstone
- Public Health Ontario and University of Toronto, Toronto, ON, Toronto, Ontario, Canada
| | - Mark Loeb
- McMaster University, Hamilton, ON, Hamilton, Ontario, Canada
| | - Anne McCarthy
- Ottawa Hospital General Campus, Ottawa, ON, Ottawa, ON, Canada
| | | | - Makeda Semret
- McGill University Health Centre, Montreal, QC, Montreal, QC, Canada
| | - Sylvie Trottier
- Centre Hospitalier Universitaire de Québec, Québec, Québec (QC), Quebec, QC, Canada
| | - Louis Valiquette
- Université de Sherbrooke, Sherbrooke, Quebec, Canada, Sherbrooke, QC, Canada
| | - Duncan Webster
- Saint John Regional Hospital, St. John, NB., Saint John, NB, Canada
| | - Shelly McNeil
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
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Yang Y, Yang Y, Martin I, Dong Y, Diao N, Wang Y, Demczuk W, Gu W. NG-STAR genotypes are associated with MDR in Neisseria gonorrhoeae isolates collected in 2017 in Shanghai. J Antimicrob Chemother 2021; 75:566-570. [PMID: 31713620 PMCID: PMC7021085 DOI: 10.1093/jac/dkz471] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/08/2019] [Accepted: 10/11/2019] [Indexed: 12/29/2022] Open
Abstract
Objectives To determine the association of Neisseria gonorrhoeae antimicrobial resistance and genotypes using N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR). Methods We characterized 124 N. gonorrhoeae isolates for their antimicrobial susceptibility profiles and NG-STAR ST characteristics using the guidelines of CLSI and EUCAST. The NG-STAR STs of seven loci were analysed. N. gonorrhoeae multiantigen sequence typing (NG-MAST) and MLST analysis was conducted in isolates with specific NG-STAR STs. Results NG-STAR differentiated 124 N. gonorrhoeae isolates into 84 STs, of which 66 STs were novel to the NG-STAR database. NG-STAR ST-199, ST-348, ST-428, ST-497 and ST-1138 were the predominant STs. Three N. gonorrhoeae isolates with ceftriaxone and cefixime MICs ≥1.0 mg/L were grouped as NG-STAR ST-233. NG-STAR ST-202 isolates (n=4) were associated with high azithromycin MICs and had an identical NG-MAST ST. The NG-STAR ST-348 group (n=5) comprised more isolates with reduced susceptibility to cefixime (n=4) than cefixime-susceptible isolates (n=1). Conclusions NG-STAR analysis differentiated N. gonorrhoeae isolates in settings with a high prevalence of antimicrobial resistance. Specific NG-STAR STs are associated with reduced susceptibility to ceftriaxone or cefixime and resistance to azithromycin in N. gonorrhoeae.
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Affiliation(s)
- Yijing Yang
- Shanghai Skin Disease Hospital, Shanghai, China
| | - Yang Yang
- Shanghai Skin Disease Hospital, Shanghai, China
| | - Irene Martin
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Yuan Dong
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
| | - Nannan Diao
- Shanghai Skin Disease Hospital, Shanghai, China
| | - Ying Wang
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
| | - Walter Demczuk
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Weiming Gu
- Shanghai Skin Disease Hospital, Shanghai, China
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Golden AR, Fear T, Baxter M, Adam HJ, Martin I, Demczuk W, Karlowsky JA, Zhanel GG. Invasive pneumococcal disease caused by serotypes 22F and 33F in Canada: the SAVE study 2011-2018. Diagn Microbiol Infect Dis 2021; 101:115447. [PMID: 34192638 DOI: 10.1016/j.diagmicrobio.2021.115447] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/28/2021] [Accepted: 05/30/2021] [Indexed: 11/28/2022]
Abstract
A 15-valent conjugate vaccine that provides protection against Streptococcus pneumoniae serotypes 22F and 33F is in development. Here we report on the prevalence, antimicrobial susceptibility, and clonal structure of these serotypes in Canada. From 2011 to 2018, the SAVE study collected 11,044 invasive S. pneumoniae isolates. Of these, 9.3% (1024/11,044) and 3.8% (416/11,044) were 22F and 33F, respectively. Serotype 22F isolates were susceptible to most antimicrobials tested except clarithromycin, where susceptibility significantly decreased over time (2011: 80.4%, 2018: 52.9%, P < 0.0001). Only 1.6% of serotype 22F isolates were multidrug-resistant (MDR), while 96% of typed strains were clonal cluster (CC) 433. Serotype 33F isolates demonstrated low susceptibility to clarithromycin and trimethoprim/sulfamethoxazole (22.4% and 24.6%, respectively) and 4.8% MDR. Most serotype 33F isolates were CC100, CC673 and CC717. CC100 prevalence increased significantly over time (2011: 50.0%, 2018: 84.8%, P < 0.006). Continued surveillance of these serotypes is crucial to identify further changes in prevalence, antimicrobial susceptibility, and clonal spread.
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Affiliation(s)
- Alyssa R Golden
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.
| | - Thomas Fear
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Melanie Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada; Department of Clinical Microbiology, Health Sciences Centre, Diagnostic Services - Shared Health Manitoba, Winnipeg, MB, Canada
| | - Irene Martin
- National Microbiology Laboratory - Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Walter Demczuk
- National Microbiology Laboratory - Public Health Agency of Canada, Winnipeg, MB, Canada
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada; Department of Clinical Microbiology, Health Sciences Centre, Diagnostic Services - Shared Health Manitoba, Winnipeg, MB, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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13
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Peterson SW, Martin I, Demczuk W, Barairo N, Naidu P, Lefebvre B, Allen V, Hoang L, Hatchette TF, Alexander D, Tomas K, Trubnikov M, Wong T, Mulvey MR. Multiplex real-time PCR assays for the prediction of cephalosporin, ciprofloxacin and azithromycin antimicrobial susceptibility of positive Neisseria gonorrhoeae nucleic acid amplification test samples. J Antimicrob Chemother 2020; 75:3485-3490. [PMID: 32830242 DOI: 10.1093/jac/dkaa360] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 03/06/2020] [Accepted: 07/23/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The incidence of antimicrobial-resistant Neisseria gonorrhoeae (GC) is rising in Canada; however, antimicrobial resistance (AMR) surveillance data are unavailable for infections diagnosed directly from clinical specimens by nucleic acid amplification tests (NAATs), representing over 80% of diagnoses. We developed a set of 10 improved molecular assays for surveillance of GC-AMR and prediction of susceptibilities in NAAT specimens. METHODS Multiplex real-time PCR (RT-PCR) assays were developed to detect SNPs associated with cephalosporin (ponA, porB, mtrR -35delA, penA A311V, penA A501, N513Y, G545S), ciprofloxacin (gyrA S91, parC D86/S87/S88) and azithromycin [23S (A2059G, C2611T), mtrR meningitidis-like promoter] resistance. The assays were validated on 127 gonococcal isolates, 51 non-gonococcal isolates and 50 NAATs with matched culture isolates. SNPs determined from the assay were compared with SNPs determined from in silico analysis of WGS data. MICs were determined for culture isolates using the agar dilution method. RESULTS SNP analysis of the 50 NAAT specimens had 96% agreement with the matched culture RT-PCR analysis. When compared with MICs, presence of penA A311V or penA A501 and two or more other SNPs correlated with decreased susceptibility and presence of three or more other SNPs correlated with intermediate susceptibility to cephalosporins; presence of any associated SNP correlated with ciprofloxacin or azithromycin resistance. NAAT-AMR predictions correlated with matched-culture cephalosporin, ciprofloxacin and azithromycin MICs at 94%, 100% and 98%, respectively. CONCLUSIONS We expanded molecular tests for N. gonorrhoeae AMR prediction by adding new loci and multiplexing reactions to improve surveillance where culture isolates are unavailable.
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Affiliation(s)
- S W Peterson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - I Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - W Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - N Barairo
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - P Naidu
- Provincial Laboratory for Public Health, Edmonton, Alberta, Canada
| | - B Lefebvre
- Laboratoire de santé publique du Québec, Ste-Anne-de-Bellevue, Québec, Canada
| | - V Allen
- Public Health Ontario Laboratories, Toronto, Ontario, Canada
| | - L Hoang
- British Columbia Centres for Disease Control Public Health Microbiology & Reference Laboratory, Vancouver, British Columbia, Canada
| | - T F Hatchette
- Queen Elizabeth II Health Sciences Centre, Halifax, Nova Scotia, Canada
| | - D Alexander
- Cadham Provincial Laboratory, Winnipeg, Manitoba, Canada
| | - K Tomas
- Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - M Trubnikov
- First Nations and Inuit Health Branch, Indigenous Services Canada, Ottawa, Ontario, Canada
| | - T Wong
- First Nations and Inuit Health Branch, Indigenous Services Canada, Ottawa, Ontario, Canada
| | - M R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Hink RK, Adam HJ, Golden AR, Baxter M, Martin I, Nichol KA, Demczuk W, Mulvey MR, Karlowsky JA, Zhanel GG. Comparison of PCV-10 and PCV-13 vaccine coverage for invasive pneumococcal isolates obtained across Canadian geographic regions, SAVE 2011 to 2017. Diagn Microbiol Infect Dis 2020; 99:115282. [PMID: 33341491 DOI: 10.1016/j.diagmicrobio.2020.115282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 01/08/2023]
Abstract
To assess the coverage of invasive Streptococcus pneumoniae by pneumococcal conjugate vaccines (PCV)-10 and PCV-13 across Canada. In total, 9166 invasive S. pneumoniae isolates were collected as part of the SAVE 2011 to 2017 study. Serotyping was performed by the Quellung reaction and antimicrobial susceptibility testing was performed using CLSI methods. The proportion of both PCV-10 and PCV-13 serotypes decreased significantly (P < 0.0001) from 2011 (26.7% and 48.0%, respectively) to 2017 (11.2% and 26.2%). For central, western, and eastern regions of Canada, PCV-13 provided significantly greater (P < 0.0001) coverage at 33.7% (2060/6110), 23.0% (456/1985), and 36.3% (389/1071), respectively, compared to PCV-10 at 15.4% (939/6110), 10.1% (201/1985), and 15.8% (169/1071) coverage. PCV-13 provided significantly greater coverage (53.3%, 282/529) of multidrug-resistant (MDR) isolates (resistant to ≥3 antimicrobial classes) than PCV-10 (14.6%, 77/529, P < 0.0001). PCV-13 provided significantly greater coverage of invasive S. pneumoniae serotypes, as well as coverage of MDR isolates, than PCV-10.
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Affiliation(s)
- Rachel K Hink
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada; Clinical Microbiology, Diagnostic Services, Shared Health, Health Sciences Centre, Winnipeg, Manitoba, R3A 1R9, Canada
| | - Alyssa R Golden
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Melanie Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Kimberly A Nichol
- Clinical Microbiology, Diagnostic Services, Shared Health, Health Sciences Centre, Winnipeg, Manitoba, R3A 1R9, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada; Clinical Microbiology, Diagnostic Services, Shared Health, Health Sciences Centre, Winnipeg, Manitoba, R3A 1R9, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada.
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15
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Dong Y, Yang Y, Wang Y, Martin I, Demczuk W, Gu W. Shanghai Neisseria gonorrhoeae Isolates Exhibit Resistance to Extended-Spectrum Cephalosporins and Clonal Distribution. Front Microbiol 2020; 11:580399. [PMID: 33123111 PMCID: PMC7573285 DOI: 10.3389/fmicb.2020.580399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
The emergence of Neisseria gonorrhoeae strains with resistance (R) to extended-spectrum cephalosporins (ESCsR) represents a public health threat of untreatable gonococcal infections. This study was designed to determine the prevalence and molecular mechanisms of ESCR of Shanghai N. gonorrhoeae isolates. A total of 366 N. gonorrhoeae isolates were collected in 2017 in Shanghai. Susceptibility to ceftriaxone (CRO), cefixime (CFM), azithromycin (AZM), ciprofloxacin (CIP), spectinomycin, penicillin, and tetracycline was determined using the agar dilution method. A subset of 124 isolates was subjected to phylogenetic analysis for nine antimicrobial resistance-associated genes, i.e., penA, porB, ponA, mtrR, 23S rRNA, gyrA, parC, 16S rRNA, and rpsE. Approximately 20.0% of the isolates exhibited CFMR [minimum inhibitory concentration (MIC) >0.125 mg/L], and 5.5% were CROR (MIC > 0.125 mg/L). In total, 72.7% of ESCR isolates were clonal and associated with mosaic penA 10 and 60 alleles. Non-mosaic penA 18 allele and substitutions of PenA A501T, G542S, and PorB1b G213S/Y were observed in non-clonal ESCR. Approximately 6.8% of the isolates showed AZM MIC above the epidemiological cutoff (ECOFF, 1 mg/L), were associated with 23S rRNA A2059G mutation, and did not exhibit clonal distribution. Almost all isolates were CIPR (resistance to ciprofloxacin) and associated with GyrA-91/92 and ParC-85/86/87/88/89/91 alterations. Isolates with ParC S88P substitution were clustered into the ESCR clade. The Shanghai isolates exhibited a high level of ESCR and distinct resistant patterns.
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Affiliation(s)
- Yuan Dong
- Shanghai Skin Disease Hospital, Shanghai, China.,Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yang Yang
- Shanghai Skin Disease Hospital, Shanghai, China
| | - Ying Wang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Irene Martin
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Walter Demczuk
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Weiming Gu
- Shanghai Skin Disease Hospital, Shanghai, China
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16
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Golden AR, Baxter MR, Davidson RJ, Martin I, Demczuk W, Mulvey MR, Karlowsky JA, Hoban DJ, Zhanel GG, Adam HJ. Comparison of antimicrobial resistance patterns in Streptococcus pneumoniae from respiratory and blood cultures in Canadian hospitals from 2007-16. J Antimicrob Chemother 2020; 74:iv39-iv47. [PMID: 31505644 DOI: 10.1093/jac/dkz286] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES To compare the epidemiology and antimicrobial susceptibility patterns of Streptococcus pneumoniae collected from respiratory and blood culture samples in Canada between 2007 and 2016. METHODS S. pneumoniae strains were obtained from Canadian hospitals as part of the ongoing national surveillance study, CANWARD. Isolates were serotyped using the Quellung method. Antimicrobial susceptibility testing was performed using the CLSI broth microdilution method. MDR and XDR were defined as resistance to three or more and five or more classes of antimicrobials, respectively. RESULTS Of the 2581 S. pneumoniae isolates collected, 1685 (65.3%) and 896 (34.7%) were obtained from respiratory and blood samples, respectively. Respiratory isolates demonstrated lower rates of antimicrobial susceptibility than blood isolates to penicillin, ceftriaxone, clarithromycin, clindamycin, doxycycline and trimethoprim/sulfamethoxazole (P ≤ 0.03). From 2007 to 2016, invasive isolates demonstrated trends towards increasing penicillin susceptibility and decreasing clarithromycin susceptibility. MDR was significantly higher in respiratory S. pneumoniae compared with blood (9.1% versus 4.5%, P < 0.0001). Serotypes 11A, 16F, 19F, 23A/B/F, 34, 35B and non-typeable strains were more commonly isolated from respiratory specimens, while 4, 5, 7F, 8, 12F, 14 and 19A were more commonly invasive serotypes. Numerous serotypes, including 3 and 22F, were isolated frequently from both specimen sources. CONCLUSIONS S. pneumoniae from respiratory samples demonstrated lower antimicrobial susceptibilities and higher MDR in a greater diversity of serotypes than isolates obtained from blood. Many serotypes were associated with one specific specimen source, while others were associated with both; genetic characterization is necessary to elucidate the specific factors influencing the ability of these serotypes to commonly cause both invasive and non-invasive disease.
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Affiliation(s)
- Alyssa R Golden
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada
| | - Ross J Davidson
- Queen Elizabeth II Health Sciences Centre, Dalhousie University, 5788 University Avenue, Halifax, Nova Scotia, Canada
| | - Irene Martin
- National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada
| | - Walter Demczuk
- National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,Department of Clinical Microbiology, Health Sciences Centre, Diagnostic Services - Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba, Canada
| | - Daryl J Hoban
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,Department of Clinical Microbiology, Health Sciences Centre, Diagnostic Services - Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,Department of Clinical Microbiology, Health Sciences Centre, Diagnostic Services - Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba, Canada
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17
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Demczuk W, Martin I, Domingo FR, MacDonald D, Mulvey MR. Identification of Streptococcus pyogenes M1 UK clone in Canada. Lancet Infect Dis 2020; 19:1284-1285. [PMID: 31782392 DOI: 10.1016/s1473-3099(19)30622-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/18/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Walter Demczuk
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB R3E 3R2, Canada
| | - Irene Martin
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB R3E 3R2, Canada.
| | | | - Diane MacDonald
- Centre for Immunization and Respiratory Infectious Diseases, Ottawa, ON, Canada
| | - Michael R Mulvey
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB R3E 3R2, Canada
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18
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LeBlanc JJ, ElSherif M, Ye L, MacKinnon-Cameron D, Ambrose A, Hatchette TF, Lang ALS, Gillis HD, Martin I, Demczuk W, Andrew MK, Boivin G, Bowie W, Green K, Johnstone J, Loeb M, McCarthy A, McGeer A, Semret M, Trottier S, Valiquette L, Webster D, McNeil S. 2715. Pneumococcal Community-Acquired Pneumonia Attributed to PCV13 Serotypes in Hospitalized Adults: Comparison of the 50–64 and 65+ Age Groups. Open Forum Infect Dis 2019. [PMCID: PMC6810608 DOI: 10.1093/ofid/ofz360.2392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Methods Results Conclusion Disclosures
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Affiliation(s)
- Jason J LeBlanc
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA) Halifax, NS, Canada,Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - May ElSherif
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA) Halifax, NS, Canada,Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Lingyun Ye
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA) Halifax, NS, Canada,Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Donna MacKinnon-Cameron
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA) Halifax, NS, Canada,Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Ardith Ambrose
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA) Halifax, NS, Canada,Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Todd F Hatchette
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA) Halifax, NS, Canada,Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Amanda L S Lang
- Saskatchewan Health Authority, Roy Romanow Provincial Lab, Regina, SK, Canada
| | - Hayley D Gillis
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA) Halifax, NS, Canada,Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Irene Martin
- National Microbiology Laboratory (NML), Winnipeg, MB, Canada
| | - Walter Demczuk
- National Microbiology Laboratory (NML), Winnipeg, MB, Canada
| | - Melissa K Andrew
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA) Halifax, NS, Canada,Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
| | - Guy Boivin
- Centre Hospitalier Universitaire de Québec, Quebec, QC, Canada
| | - William Bowie
- Vancouver General Hospital, and University of British Columbia, Vancouver, BC, Canada
| | | | | | - Mark Loeb
- McMaster University, Hamilton, ON, Canada
| | | | | | - Makeda Semret
- McGill University Health Centre, Montreal, QC, Canada
| | | | | | | | - Shelly McNeil
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA) Halifax, NS, Canada,Dalhousie University, Halifax, Nova Scotia (NS), Halifax, NS, Canada
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Kandel C, Daneman N, Demczuk W, Gold W, Green K, Martin I, Plevneshi A, Powis J, Rudnick W, Sarabia A, Schwartz B, Simor A, Tyrrell G, Valiquette L, McGeer A. 462. Prospective Surveillance of Invasive Group A Streptococcal Infections in Toronto, Ontario, Canada: 1992–2017. Open Forum Infect Dis 2019. [PMCID: PMC6810799 DOI: 10.1093/ofid/ofz360.535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Background. Background Invasive Group A streptococcal (iGAS) infections remain a substantial source of morbidity and mortality. We explore the clinical and molecular epidemiology of iGAS infections in Toronto, Ontario, Canada over a 26-year period. Methods The Toronto Invasive Bacterial Diseases Network has performed population-based surveillance for iGAS infections in metropolitan Toronto and Peel regions since 1992. Participating microbiology laboratories report and submit sterile site specimens for central processing. M typing was performed on iGAS isolates until September 2006; thereafter emm typing was performed. Clinical information was collected by chart review using standardized collection forms. Results Over the 26-year period there were 2819 iGAS infections, representing an average incidence of 2.85 per 100,000 residents with a nadir of 1.65 in 1993 and a peak of 4.52 in 2014. Nosocomial infections occurred in 8.9% (251/2,819). There was substantial variation in annual incidence rates over the study period with increases from 1992 until 2002 and then 2004 until 2014 (analysis for trend, P < 0.001). Skin and soft-tissue infections were the most common clinical presentation, accounting for 33.2% (936/2,819), followed by bacteremia without a focus in 15.4% (435/2,819). Necrotizing fasciitis was observed in 7.4% (208/2,819) and criteria for toxic shock syndrome were met in 17.6% (497/2,819). Overall case fatality within 30 days of hospitalization was 15.3% (95% confidence interval 14.0 to 16.6) and did not change over time. M serotype distribution varied yearly with the most common type being M1 at 22.2% (626/2,189) followed by M12 at 8.2% (230/2,189), then M89 at 5.8% (163/2,189). Antibiotic susceptibility was available from 1998 onwards with overall clindamycin susceptibility at 92.3% (1,957/2,121) and erythromycin susceptibility at 87.9% (1864/2,121). Conclusion The incidence of iGAS in Toronto, Ontario has varied over time, with no recent increase apparent. Similar to worldwide observations, M1 serotype was the most commonly isolated; most common serotypes demonstrated cyclical variation. Case fatality rates have remained relatively constant making the development of a vaccine imperative. ![]()
Disclosures All authors: No reported disclosures.
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Affiliation(s)
| | | | - Walter Demczuk
- National Microbiology Laboratory (NML), Regina, MB, Canada
| | - Wayne Gold
- University of Toronto, Toronto, ON, Canada
| | | | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Jeff Powis
- University of Toronto, Toronto, ON, Canada
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LeBlanc JJ, ElSherif M, Lang ALS, Gillis HD, Ye L, MacKinnon-Cameron D, Ambrose A, Hatchette TF, Martin I, Demczuk W, Andrew MK, Boivin G, Bowie W, Green K, Johnstone J, Loeb M, McCarthy A, McGeer A, Semret M, Trottier S, Valiquette L, Webster D, McNeil S. 2714. Streptococcus pneumoniae Nasopharyngeal Carriage in Canadian Adults Hospitalized with Community-Acquired Pneumonia from 2010 to 2017. Open Forum Infect Dis 2019. [PMCID: PMC6809650 DOI: 10.1093/ofid/ofz360.2391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background Streptococcus pneumoniae can colonizes the human nasopharynx, and can cause life-threatening infections like community-acquired pneumonia (CAP) and invasive pneumococcal diseases (IPD). In Canada, the 13-valent conjugate vaccine (PCV13) was introduced in childhood immunization since 2010, with hopes that it would not only protect the vaccinated, but also confer indirect protection to adults through herd immunity. Given data on S. pneumoniae nasopharyngeal (NP) carriage in adults is scarce, this study reports on S. pneumoniae-positivity and serotype distribution in adult carriage from years 2010 to 2017. Methods Active surveillance was performed in adults hospitalized with for CAP or IPD from December 2010 to 2017. For assessment of S. pneumoniae carriage, NP swabs were tested using lytA and cpsA real-time PCR. S. pneumoniae-positive NPs were subjected to serotyping using conventional and real-time multiplex PCRs. Results Overall, 6472 NP swabs were tested, and Spn was identified in 366 (5.7%). Of the 366 S. pneumoniae-positive NP swabs, a serotype was assigned in 355 (97.0%). From years 2010 to 2017, the proportion of S. pneumoniae-positive NP swabs declined from 8.9% to 4.3%. This was also reflected in the proportion of serotypeable results attributed to PCV13 serotypes, which also declined from 76.9% to 42.2%. The decline was primarily attributed to PCV13 serotypes 7F and 19A. PCV13 serotype 3 remained predominant throughout the study, as did non-PCV13 serotypes like 22F, 33F, and 11A. On the other hand, a proportional rise over time was noted for non-vaccine serotypes (from 15.4% to 31.1%). This was primarily attributed to serotypes 23A, 15A, and 35B. Conclusion Monitoring serotype trends is important to assess the impact of pneumococcal vaccines. While herd immunity from PCV13 childhood immunization was anticipated, few studies have assessed its impact on adult carriage. This study described Spn serotype distribution in adults over years 2010 to 2017, demonstrating not only a reduction of PCV13 serotypes over time, but a proportional rise in non-vaccine serotypes. These emerging serotypes may represent the emergence of serotype replacement. Ongoing serotype surveillance will be needed to compare S. pneumoniae carriage to serotypes associated with pneumococcal CAP and IPD. Disclosures All authors: No reported disclosures.
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Affiliation(s)
- Jason J LeBlanc
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), Halifax, NS, Canada
- Dalhousie University, Halifax, NS, Canada
| | - May ElSherif
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), Halifax, NS, Canada
- Dalhousie University, Halifax, NS, Canada
| | - Amanda L S Lang
- Saskatchewan Health Authority, Roy Romanow Provincial Lab, Regina, SK, Canada
| | - Hayley D Gillis
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), Halifax, NS, Canada
- Dalhousie University, Halifax, NS, Canada
| | - Lingyun Ye
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), Halifax, NS, Canada
- Dalhousie University, Halifax, NS, Canada
| | - Donna MacKinnon-Cameron
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), Halifax, NS, Canada
- Dalhousie University, Halifax, NS, Canada
| | - Ardith Ambrose
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), Halifax, NS, Canada
- Dalhousie University, Halifax, NS, Canada
| | - Todd F Hatchette
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), Halifax, NS, Canada
- Dalhousie University, Halifax, NS, Canada
| | - Irene Martin
- National Microbiology Laboratory (NML), Winnipeg, MB, Canada
| | - Walter Demczuk
- National Microbiology Laboratory (NML), Winnipeg, MB, Canada
| | - Melissa K Andrew
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), Halifax, NS, Canada
- Dalhousie University, Halifax, NS, Canada
| | - Guy Boivin
- Centre Hospitalier Universitaire de Québec, Québec, QC, Canada
| | - William Bowie
- Vancouver General Hospital, and University of British Columbia, Vancouver, BC, Canada
| | | | | | - Mark Loeb
- McMaster University, Hamilton, ON, Canada
| | | | | | - Makeda Semret
- McGill University Health Centre, Montreal, QC, Canada
| | - Sylvie Trottier
- Centre Hospitalier Universitaire de Québec, Quebec, QC, Canada
| | | | | | - Shelly McNeil
- Canadian Center for Vaccinology (CCfV), IWK Health Centre, Nova Scotia Health Authority (NSHA), Halifax, NS, Canada
- Dalhousie University, Halifax, NS, Canada
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21
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Golden AR, Adam HJ, Karlowsky JA, Baxter M, Nichol KA, Martin I, Demczuk W, Van Caeseele P, Gubbay JB, Lefebvre B, Levett PN, Zahariadis G, Haldane D, Gad R, German G, Gilmour MW, Mulvey MR, Hoban DJ, Zhanel GG. Molecular characterization of predominant Streptococcus pneumoniae serotypes causing invasive infections in Canada: the SAVE study, 2011-15. J Antimicrob Chemother 2019; 73:vii20-vii31. [PMID: 29982573 DOI: 10.1093/jac/dky157] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Objectives This study characterized the 11 most predominant serotypes of invasive Streptococcus pneumoniae infections collected by the annual SAVE study in Canada, between 2011 and 2015. Methods A subset of the 11 most predominant serotypes (7F, 19A, 22F, 3, 12F, 11A, 9N, 8, 33F, 15A and 6C) collected by the SAVE study was analysed using PFGE and MLST, as well as PCR to identify pilus-encoding genes. WGS analyses were performed on a subset of the above isolates plus a random selection of background strains. Results Of the predominant serotypes analysed, 7F, 33F and 19A were obtained more commonly from children <6 years of age, whereas 15A, 6C, 22F and 11A were more common in adults >65 years of age. Pneumococcal pilus PI-1 was identified in antimicrobial-susceptible serotype 15A (61/212) and <10% of 6C isolates (16/188). PI-2 was found in serotype 7F (683/701) and two-thirds of 11A isolates (162/241). Only serotype 19A-ST320 possessed both pili. Molecular and phylogenetic analyses identified serotypes 19A, 15A, 6C, 9N and 33F as highly diverse, whereas 7F, 22F and 11A demonstrated clonality. Antimicrobial resistance determinants were common within diverse serotypes, and usually similar within a clonal complex. Conclusions Despite successful use of conjugate vaccines, S. pneumoniae remains a highly diverse organism in Canada. Several predominant serotypes, both antimicrobial susceptible and MDR, have demonstrated rapid clonal expansion or an increase in diversity. As S. pneumoniae continues to evolve in Canada, WGS will be a necessary component in the ongoing surveillance of antimicrobial-resistant and expanding clones.
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Affiliation(s)
- Alyssa R Golden
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - Heather J Adam
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Clinical Microbiology - Health Sciences Centre, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - James A Karlowsky
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Clinical Microbiology - Health Sciences Centre, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Melanie Baxter
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - Kimberly A Nichol
- Clinical Microbiology - Health Sciences Centre, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Irene Martin
- National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Walter Demczuk
- National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Paul Van Caeseele
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Cadham Provincial Laboratory, 750 William Avenue, Winnipeg, Manitoba R3E 3J7, Canada
| | - Jonathan B Gubbay
- Public Health Ontario, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, 20045 Ch Ste-Marie, Ste-Anne-de-Bellevue, Québec H9X 3R5, Canada
| | - Paul N Levett
- Saskatchewan Disease Control Laboratory, 5 Research Drive, Regina, Saskatchewan S4S 0A4, Canada
| | - George Zahariadis
- Newfoundland and Labrador Public Health Laboratory, Dr. Leonard A. Miller Centre - Suite 1, 100 Forest Road, St John's, Newfoundland and Labrador A1A 1E3, Canada
| | - David Haldane
- Queen Elizabeth II Health Science Centre, 5805 South Street, Halifax, Nova Scotia B3H 1V8, Canada
| | - Rita Gad
- New Brunswick Department of Health, 520 King Street, Fredericton, New Brunswick E3B 5G8, Canada
| | - Gregory German
- Health PEI, 16 Garfield Street, Charlottetown, Prince Edward Island C1A 7N8, Canada
| | - Matthew W Gilmour
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Daryl J Hoban
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Clinical Microbiology - Health Sciences Centre, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - George G Zhanel
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
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22
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Berenger BM, Demczuk W, Gratrix J, Pabbaraju K, Smyczek P, Martin I. Genetic Characterization and Enhanced Surveillance of Ceftriaxone-Resistant Neisseria gonorrhoeae Strain, Alberta, Canada, 2018. Emerg Infect Dis 2019; 25:1660-1667. [PMID: 31407661 PMCID: PMC6711210 DOI: 10.3201/eid2509.190407] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In July 2018, a case of Neisseria gonorrhoeae associated with ceftriaxone treatment failure was identified in Alberta, Canada. We identified the isolate and nucleic acid amplification testing (NAAT) specimen as the ceftriaxone-resistant strain multilocus sequence type 1903/NG-MAST 3435/NG-STAR 233, originally identified in Japan (FC428), with the same penA 60.001 mosaic allele and genetic resistance determinants. Core single-nucleotide variant (SNV) analysis identified 13 SNVs between this isolate and FC428. Culture-independent surveillance by PCR for the A311V mutation in the penA allele and N. gonorrhoeae multiantigen sequence typing directly from NAAT transport media positive for N. gonorrhoeae by NAAT did not detect spread of the strain. We identified multiple sequence types not previously detected in Alberta by routine surveillance. This case demonstrates the benefit of using culture-independent methods to enhance detection, public health investigations, and surveillance to address this global threat.
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Abstract
Campylobacter transducer-like proteins (Tlps), also known as methyl-accepting chemotaxis proteins (MCPs), are associated with virulence as well as niche and host adaptation. While functional attributes of these proteins are being elucidated, little has been published regarding their sequence diversity or chromosomal locations and context, although they appear to define invertible regions within Campylobacter jejuni genomes. Genome assemblies for several species of Campylobacter were obtained from the publicly available NCBI repositories. Genomes from all isolates were obtained from GenBank and assessed for Tlp content, while data from isolates with complete, finished genomes were used to determine the identity of Tlps as well as the gene content of putative invertible elements (IEs) in C. jejuni (Cj) and C. coli (Cc). Tlps from several Campylobacter species were organized into a nomenclature system and novel Tlps were defined and named for Cj and Cc. The content of Tlps appears to be species-specific, though diverse within species. Cj and Cc carried overlapping, related Tlp content, as did the three C. fetus subspecies. Tlp1 was detected in 88% of Cj isolates and approximately 43% of Cc, and was found in a different conserved chromosomal location and genetic context in each species. Tlp1 and Tlp 3 predominated in genomes from Cj whereas other Tlps were detected less frequently. Tlp13 and Tlp20 predominated in genomes from Cc while some Cj/Cc Tlps were not detected at all. Tlps 2–4 and 11–20 were less frequently detected and many showed sequence heterogeneity that could affect substrate binding, signal transduction, or both. Tlps other than Tlp1, 7, and 10 had substantial sequence identity in the C-terminal half of the protein, creating chromosomal repeats potentially capable of mediating the inversion of large chromosomal DNA. Cj and Cc Tlps were both found in association with only 14 different genes, indicating a limited genomic context. In Cj these Tlps defined IEs that were for the most part found at a single chromosomal location and comprised of a conserved set of genes. Cc IEs were situated at very different chromosomal locations, had different structures than Cj IEs, and were occasionally incomplete, therefore not capable of inversion. Tlps may have a role in Campylobacter genome structure and dynamics as well as acting as chemoreceptors mediating chemotactic responses.
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Affiliation(s)
- Clifford Clark
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- * E-mail:
| | - Chrystal Berry
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Walter Demczuk
- Streptococci and STI Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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24
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Lahra MM, Martin I, Demczuk W, Jennison AV, Lee KI, Nakayama SI, Lefebvre B, Longtin J, Ward A, Mulvey MR, Wi T, Ohnishi M, Whiley D. Cooperative Recognition of Internationally Disseminated Ceftriaxone-Resistant Neisseria gonorrhoeae Strain. Emerg Infect Dis 2019; 24. [PMID: 29553335 PMCID: PMC5875269 DOI: 10.3201/eid2404.171873] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Ceftriaxone remains a first-line treatment for patients infected by Neisseria gonorrhoeae in most settings. We investigated the possible spread of a ceftriaxone-resistant FC428 N. gonorrhoeae clone in Japan after recent isolation of similar strains in Denmark (GK124) and Canada (47707). We report 2 instances of the FC428 clone in Australia in heterosexual men traveling from Asia. Our bioinformatic analyses included core single-nucleotide variation phylogeny and in silico molecular typing; phylogenetic analysis showed close genetic relatedness among all 5 isolates. Results showed multilocus sequence type 1903; N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) 233; and harboring of mosaic penA allele encoding alterations A311V and T483S (penA-60.001), associated with ceftriaxone resistance. Our results provide further evidence of international transmission of ceftriaxone-resistant N. gonorrhoeae. We recommend increasing awareness of international spread of this drug-resistant strain, strengthening surveillance to include identifying treatment failures and contacts, and strengthening international sharing of data.
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25
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Schembri J, Gillis HD, Lang ALS, Warhuus M, Martin I, Demczuk W, ElSherif M, McNeil SA, LeBlanc JJ. Multi-target plasmid controls for conventional and real-time PCR-based serotyping of Streptococcus pneumoniae. Plasmid 2018; 98:45-51. [PMID: 30217467 DOI: 10.1016/j.plasmid.2018.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/10/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND Serotyping of Streptococcus pneumoniae is an integral part of disease surveillance, with over 92 serotypes characterized to date using traditional serotyping. To identify the most predominant disease causing serotypes, molecular serotyping methods are now increasingly being used, like conventional and real-time multiplex PCR (cmPCR and rmPCR, respectively). Given that cmPCR consists of eight reactions spanning 41 targets, and rmPCR consists of seven triplex reactions, standardizing positive controls for these assays is challenging. As such, a 43-target plasmid for cmPCR (pSpn-CM1) and a 23 target plasmid for rmPCR (pSpn-RM1) were designed and validated. METHODS Plasmid pSpn-RM1 was designed and synthesized as chimeric DNA sequences to include all PCR target primer binding sites sequences for cmPCR. Plasmid pSpn-RM1 consisted of all primer and probe sequences required for rmPCR. Additional targets (lytA and cpsA) were included in both plasmids for quantification, following their propagation and purification from Escherichia coli. RESULTS When tested using the cmPCR reactions, all targets could be reproducibly be detected using pSpn-CM1 as template, with good amplicon visibility at a concentration of 1.4 (± 0.3) × 105 copies/ml was used. For the rmPCR reactions, all targets were reproducibly amplified with a concentration of 1.1 (± 0.2) × 104 copies/ml of pSpn-RM1, and the PCR efficiency for each target was equivalent to DNA extracted from representative S. pneumoniae serotypes. CONCLUSIONS These quantifiable multi-target plasmids simplify the preparation of controls for PCR-based serotyping of S. pneumoniae, and methods herein could be extended to other highly multiplexed PCR assays.
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Affiliation(s)
- Jack Schembri
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Hayley D Gillis
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Amanda L S Lang
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Michelle Warhuus
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Irene Martin
- Streptococci and STI Unit, National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Walter Demczuk
- Streptococci and STI Unit, National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - May ElSherif
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Shelly A McNeil
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Jason J LeBlanc
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada.
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Hammond-Collins K, Strauss B, Barnes K, Demczuk W, Domingo MC, Lamontagne MC, Lu D, Martin I, Tepper M. Group A Streptococcus Outbreak in a Canadian Armed Forces Training Facility. Mil Med 2018; 184:e197-e204. [DOI: 10.1093/milmed/usy198] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/10/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Karon Hammond-Collins
- Canadian Field Epidemiology Program, Public Health Agency of Canada, 100 Colonnade Drive, Ottawa, ON, Canada
| | - Barbara Strauss
- Directorate of Force Health Protection, Canadian Forces Medical Group Headquarters, Carling Campus, 101 Colonel By Drive, Ottawa, ON, Canada
| | - Kirsten Barnes
- Directorate of Force Health Protection, Canadian Forces Medical Group Headquarters, Carling Campus, 101 Colonel By Drive, Ottawa, ON, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB, Canada
| | - Marc-Christian Domingo
- Laboratoire de santé publique du Québec, 20045 Sainte Marie Rd, Sainte-Anne-de-Bellevue, QC, Canada
| | - Marie-Christine Lamontagne
- Directorate of Force Health Protection, Canadian Forces Medical Group Headquarters, Carling Campus, 101 Colonel By Drive, Ottawa, ON, Canada
| | - Diane Lu
- Directorate of Force Health Protection, Canadian Forces Medical Group Headquarters, Carling Campus, 101 Colonel By Drive, Ottawa, ON, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB, Canada
| | - Martin Tepper
- Directorate of Force Health Protection, Canadian Forces Medical Group Headquarters, Carling Campus, 101 Colonel By Drive, Ottawa, ON, Canada
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27
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Adam HJ, Golden AR, Karlowsky JA, Baxter MR, Nichol KA, Martin I, Demczuk W, Mulvey MR, Gilmour MW, Hoban DJ, Zhanel GG. Analysis of multidrug resistance in the predominant Streptococcus pneumoniae serotypes in Canada: the SAVE study, 2011–15. J Antimicrob Chemother 2018; 73:vii12-vii19. [DOI: 10.1093/jac/dky158] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Heather J Adam
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Alyssa R Golden
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - James A Karlowsky
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Kim A Nichol
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Matthew W Gilmour
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Daryl J Hoban
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - George G Zhanel
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
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28
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Karlowsky JA, Adam HJ, Golden AR, Baxter MR, Nichol KA, Martin I, Demczuk W, Mulvey MR, Gilmour MW, Hoban DJ, Zhanel GG. Antimicrobial susceptibility testing of invasive isolates of Streptococcus pneumoniae from Canadian patients: the SAVE study, 2011–15. J Antimicrob Chemother 2018; 73:vii5-vii11. [DOI: 10.1093/jac/dky156] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- James A Karlowsky
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Heather J Adam
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Alyssa R Golden
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Kim A Nichol
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Matthew W Gilmour
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Daryl J Hoban
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - George G Zhanel
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
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Eyre DW, De Silva D, Cole K, Peters J, Cole MJ, Grad YH, Demczuk W, Martin I, Mulvey MR, Crook DW, Walker AS, Peto TEA, Paul J. WGS to predict antibiotic MICs for Neisseria gonorrhoeae. J Antimicrob Chemother 2018; 72:1937-1947. [PMID: 28333355 PMCID: PMC5890716 DOI: 10.1093/jac/dkx067] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [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: 10/31/2016] [Accepted: 02/08/2017] [Indexed: 11/26/2022] Open
Abstract
Background Tracking the spread of antimicrobial-resistant Neisseria gonorrhoeae is a major priority for national surveillance programmes. Objectives We investigate whether WGS and simultaneous analysis of multiple resistance determinants can be used to predict antimicrobial susceptibilities to the level of MICs in N. gonorrhoeae. Methods WGS was used to identify previously reported potential resistance determinants in 681 N. gonorrhoeae isolates, from England, the USA and Canada, with phenotypes for cefixime, penicillin, azithromycin, ciprofloxacin and tetracycline determined as part of national surveillance programmes. Multivariate linear regression models were used to identify genetic predictors of MIC. Model performance was assessed using leave-one-out cross-validation. Results Overall 1785/3380 (53%) MIC values were predicted to the nearest doubling dilution and 3147 (93%) within ±1 doubling dilution and 3314 (98%) within ±2 doubling dilutions. MIC prediction performance was similar across the five antimicrobials tested. Prediction models included the majority of previously reported resistance determinants. Applying EUCAST breakpoints to MIC predictions, the overall very major error (VME; phenotypically resistant, WGS-prediction susceptible) rate was 21/1577 (1.3%, 95% CI 0.8%–2.0%) and the major error (ME; phenotypically susceptible, WGS-prediction resistant) rate was 20/1186 (1.7%, 1.0%–2.6%). VME rates met regulatory thresholds for all antimicrobials except cefixime and ME rates for all antimicrobials except tetracycline. Country of testing was a strongly significant predictor of MIC for all five antimicrobials. Conclusions We demonstrate a WGS-based MIC prediction approach that allows reliable MIC prediction for five gonorrhoea antimicrobials. Our approach should allow reasonably precise prediction of MICs for a range of bacterial species.
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Affiliation(s)
- David W Eyre
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford National Institute for Health Research Health Protection Research Unit, Oxford, UK
| | - Dilrini De Silva
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford National Institute for Health Research Health Protection Research Unit, Oxford, UK
| | - Kevin Cole
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK.,National Infection Service, Public Health England, UK
| | - Joanna Peters
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK.,National Infection Service, Public Health England, UK
| | - Michelle J Cole
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, London, UK
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford National Institute for Health Research Health Protection Research Unit, Oxford, UK.,National Infection Service, Public Health England, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford National Institute for Health Research Health Protection Research Unit, Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford National Institute for Health Research Health Protection Research Unit, Oxford, UK
| | - John Paul
- National Institute for Health Research Biomedical Research Centre, Oxford, UK.,Brighton and Sussex University Hospitals NHS Trust, Brighton, UK.,National Infection Service, Public Health England, UK
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Teatero S, McGeer A, Tyrrell GJ, Hoang L, Smadi H, Domingo MC, Levett PN, Finkelstein M, Dewar K, Plevneshi A, Athey TBT, Gubbay JB, Mulvey MR, Martin I, Demczuk W, Fittipaldi N. Canada-Wide Epidemic of emm74 Group A Streptococcus Invasive Disease. Open Forum Infect Dis 2018; 5:ofy085. [PMID: 29780850 DOI: 10.1093/ofid/ofy085] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/17/2018] [Indexed: 11/14/2022] Open
Abstract
Background The number of invasive group A Streptococcus (iGAS) infections due to hitherto extremely rare type emm74 strains has increased in several Canadian provinces since late 2015. We hypothesized that the cases recorded in the different provinces are linked and caused by strains of an emm74 clone that recently emerged and expanded explosively. Methods We analyzed both active and passive surveillance data for iGAS infections and used whole-genome sequencing to investigate the phylogenetic relationships of the emm74 strains responsible for these invasive infections country-wide. Results Genome analysis showed that highly clonal emm74 strains, genetically different from emm74 organisms previously circulating in Canada, were responsible for a country-wide epidemic of >160 invasive disease cases. The emerging clone belonged to multilocus sequence typing ST120. The analysis also revealed dissemination patterns of emm74 subclonal lineages across Canadian provinces. Clinical data analysis indicated that the emm74 epidemic disproportionally affected middle-aged or older male individuals. Homelessness, alcohol abuse, and intravenous drug usage were significantly associated with invasive emm74 infections. Conclusions In a period of 20 months, an emm74 GAS clone emerged and rapidly spread across several Canadian provinces located more than 4500 km apart, causing invasive infections primarily among disadvantaged persons.
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Affiliation(s)
- Sarah Teatero
- Public Health Ontario Laboratory, Toronto, ON, Canada
| | - Allison McGeer
- Sinai Health System, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Gregory J Tyrrell
- Alberta Provincial Laboratory for Public Health, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Linda Hoang
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Hanan Smadi
- New Brunswick Department of Health, Communicable Disease and Control, Fredericton, NB, Canada
| | - Marc-Christian Domingo
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Ste-Anne de Bellevue, QC, Canada
| | - Paul N Levett
- Saskatchewan Disease Control Laboratory, Regina, SK, Canada
| | | | - Ken Dewar
- Genome Québec Innovation Centre, and McGill University, Montreal, QC, Canada
| | | | | | - Jonathan B Gubbay
- Public Health Ontario Laboratory, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Nahuel Fittipaldi
- Public Health Ontario Laboratory, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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Lother SA, Demczuk W, Martin I, Mulvey M, Dufault B, Lagacé-Wiens P, Keynan Y. Clonal Clusters and Virulence Factors of Group C and G Streptococcus Causing Severe Infections, Manitoba, Canada, 2012-2014. Emerg Infect Dis 2018. [PMID: 28628457 PMCID: PMC5512470 DOI: 10.3201/eid2307.161259] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
These strains are more likely to cause invasive infection, which is an emerging public health concern as incidence and disease severity are on the rise. The incidence of group C and G Streptococcus (GCGS) bacteremia, which is associated with severe disease and death, is increasing. We characterized clinical features, outcomes, and genetic determinants of GCGS bacteremia for 89 patients in Winnipeg, Manitoba, Canada, who had GCGS bacteremia during 2012–2014. Of the 89 patients, 51% had bacteremia from skin and soft tissue, 70% had severe disease features, and 20% died. Whole-genome sequencing analysis was performed on isolates derived from 89 blood samples and 33 respiratory sample controls: 5 closely related genetic lineages were identified as being more likely to cause invasive disease than non-clade isolates (83% vs. 57%, p = 0.002). Virulence factors cbp, fbp, speG, sicG, gfbA, and bca clustered clonally into these clades. A clonal distribution of virulence factors may account for severe and fatal cases of bacteremia caused by invasive GCGS.
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Abstract
We identified a ceftriaxone-resistant Neisseria gonorrhoeae isolate in a patient in Canada. This isolate carried the penA-60 allele, which differs substantially from its closest relative, mosaic penA XXVII (80% nucleotide identity). Epidemiologic and genomic data suggest spread from Asia. Antimicrobial susceptibility surveillance helps prevent spread of highly resistant N. gonorrhoeae strains.
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Mauffrey F, Fournier É, Demczuk W, Martin I, Mulvey M, Martineau C, Lévesque S, Bekal S, Domingo MC, Doualla-Bell F, Longtin J, Lefebvre B. Comparison of sequential multiplex PCR, sequetyping and whole genome sequencing for serotyping of Streptococcus pneumoniae. PLoS One 2017; 12:e0189163. [PMID: 29236737 PMCID: PMC5728576 DOI: 10.1371/journal.pone.0189163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 08/23/2017] [Accepted: 11/20/2017] [Indexed: 01/22/2023] Open
Abstract
Streptococcus pneumoniae is one of the major causes of pneumonia, meningitis and other pneumococcal infections in young children and elders. Determination of circulating S. pneumoniae serotypes is an essential service by public health laboratories for the monitoring of putative serotype replacement following the introduction of pneumococcal conjugate vaccines (PCVs) and of the efficacy of the immunization program. The Quellung method remains the gold standard for typing S. pneumoniae. Although this method is very effective, it is also costly, time consuming and not totally reliable due to its subjective nature. The objectives of this study were to test and evaluate the efficiency of 3 different molecular methods compared to the Quellung method. Sequential multiplex PCR, sequetyping and whole genome sequencing (WGS) were chosen and tested using a set of diverse S. pneumoniae. One-hundred and eighteen isolates covering 83 serotypes were subjected to multiplex PCR and sequetyping while 88 isolates covering 53 serotypes were subjected to WGS. Sequential multiplex PCR allowed the identification of a significant proportion (49%) of serotypes at the serogroup or subset level but only 27% were identified at the serotype level. Using WGS, 55% to 60% of isolates were identified at the serotype level depending on the analysis strategy used. Finally, sequetyping demonstrated the lowest performance, with 17% of misidentified serotypes. The use of Jin cpsB database instead of the GenBank database slightly improved results but did not significantly impact the efficiency of sequetyping. Although none of these molecular methods may currently replace the Quellung method, WGS remains the most promising molecular pneumococcal serotyping method.
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Affiliation(s)
- Florian Mauffrey
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Éric Fournier
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Christine Martineau
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Simon Lévesque
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Marc-Christian Domingo
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Florence Doualla-Bell
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Jean Longtin
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
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Teatero S, Neemuchwala A, Yang K, Gomes J, Athey TBT, Martin I, Demczuk W, McGeer A, Fittipaldi N. Genetic evidence for a novel variant of the pilus island 1 backbone protein in group B Streptococcus. J Med Microbiol 2017; 66:1409-1415. [PMID: 28923133 DOI: 10.1099/jmm.0.000588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Pili contribute significantly to the pathogenesis of infection of group B Streptococcus (GBS) by facilitating adhesion and invasion of host cells. GBS pilin subunits (the backbone pilin protein, BP, and the ancillary pilin proteins, AP) as well as the specific enzymes required for pilus assembly are encoded by genes located in two separate genomic regions, known as pilus island 1 (PI-1) and PI-2. Our aim was to characterize the pilus profile of a collection of GBS isolates from metropolitan Toronto, Canada. METHODOLOGY The pilus profile of 1332 invasive and colonizing GBS isolates was determined by PCR and, in selected cases, by whole genome sequencing. RESULTS While investigating the pilus profile of a collection of GBS organisms, we discovered that 51 isolates possessed a novel variant of the PI-1 BP, which we named BP-1b. The predicted translated sequences of archetypical GBS BP-1 and novel BP-1b variants shared only 63 % amino acid sequence homology. The novel BP-1b variant was most common among strains of serotype Ib and VI, but was also found among strains of serotypes Ia, II, III and VIII. CONCLUSION We describe a relatively frequent occurrence of a novel PI-1 BP that cannot be detected by a commonly used multiplex PCR scheme, which could lead to strains being mistyped as PI-1 negative. We present PCR primers that can easily be incorporated into the multiplex PCR assay to identify strains with novel BP-1b variant.
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Affiliation(s)
| | | | | | | | | | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Allison McGeer
- Sinai Health System, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Nahuel Fittipaldi
- Public Health Ontario, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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Rudolph K, Martin I, Demczuk W, Kakulphimp J, Bruden D, Zulz T, Bruce M. International circumpolar surveillance interlaboratory quality control program for emm typing of Streptococcus pyogenes, 2011-2015. Diagn Microbiol Infect Dis 2016; 85:398-400. [PMID: 27238635 PMCID: PMC5704931 DOI: 10.1016/j.diagmicrobio.2016.05.005] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/03/2016] [Accepted: 05/08/2016] [Indexed: 11/28/2022]
Abstract
In 2011, an interlaboratory quality control (QC) program for emm typing group A streptococci (GAS) was incorporated into existing international circumpolar surveillance QC programs. From 2011 - 2015, 35 GAS isolates were distributed to three laboratories; emm type-level concordance was 100%, while the overall sub-type level concordance was 83%.
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Affiliation(s)
- Karen Rudolph
- Arctic Investigations Program, Centers for Disease Control and Prevention, Anchorage, Alaska.
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Dana Bruden
- Arctic Investigations Program, Centers for Disease Control and Prevention, Anchorage, Alaska
| | - Tammy Zulz
- Arctic Investigations Program, Centers for Disease Control and Prevention, Anchorage, Alaska
| | - Michael Bruce
- Arctic Investigations Program, Centers for Disease Control and Prevention, Anchorage, Alaska
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Abstract
BACKGROUND Northern populations were at a high risk of developing invasive bacterial diseases (IBDs). Since the last published study that described IBDs in Northern Canada, a number of vaccines against some bacterial pathogens have been introduced into the routine childhood immunization schedule. OBJECTIVE To describe the epidemiology of IBDs in Northern Canada from 2006 to 2013. METHODS Data for 5 IBDs (invasive pneumococcal disease (IPD), invasive Haemophilus influenzae disease (Hi), invasive Group A streptococcal disease (iGAS), invasive meningococcal disease (IMD) and invasive Group B streptococcal disease (GBS)) were extracted from the International Circumpolar Surveillance (ICS) program and the Canadian Notifiable Diseases Surveillance System. Incidence rates were calculated per 100,000 population per year. RESULTS During the study period, the incidence rates of IPD ranged from 16.84-30.97, iGAS 2.70-17.06, Hi serotype b 0-2.78, Hi non-b type 2.73-8.53, and IMD 0-3.47. Except for IMD and GBS, the age-standardized incidence rates of other diseases in Northern Canada were 2.6-10 times higher than in the rest of Canada. Over the study period, rates decreased for IPD (p=0.04), and iGAS (p=0.01), and increased for Hi type a (Hia) (p=0.004). Among IPD cases, the proportion of pneumococcal conjugate vaccine (PCV)7 serotypes decreased (p=0.0004) over the study period. Among Hi cases, 69.8% were Hia and 71.6% of these were in children under than 5 years. Of 13 IMD cases, 8 were serogroup B and 2 of them died. CONCLUSION Northern population in Canada, especially infants and seniors among First Nations and Inuit, are at a high risk of IPD, Hi and iGAS. Hia is the predominant serotype in Northern Canada.
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Affiliation(s)
- YA Li
- Infectious Disease Prevention and Control Branch, Public Health Agency of Canada Ottawa, ON
| | - I Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MN
| | - R Tsang
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MN
| | - SG Squires
- Infectious Disease Prevention and Control Branch, Public Health Agency of Canada Ottawa, ON
| | - W Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MN
| | - S Desai
- Infectious Disease Prevention and Control Branch, Public Health Agency of Canada Ottawa, ON
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Teatero S, McGeer A, Li A, Gomes J, Seah C, Demczuk W, Martin I, Wasserscheid J, Dewar K, Melano RG, Fittipaldi N. Population structure and antimicrobial resistance of invasive serotype IV group B Streptococcus, Toronto, Ontario, Canada. Emerg Infect Dis 2015; 21:585-91. [PMID: 25811284 PMCID: PMC4378482 DOI: 10.3201/eid2014.140759] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [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: 02/02/2023] Open
Abstract
Conjugate vaccines should include polysaccharide or virulence proteins of this serotype to provide complete protection. We recently showed that 37/600 (6.2%) invasive infections with group B Streptococcus (GBS) in Toronto, Ontario, Canada, were caused by serotype IV strains. We report a relatively high level of genetic diversity in 37 invasive strains of this emerging GBS serotype. Multilocus sequence typing identified 6 sequence types (STs) that belonged to 3 clonal complexes. Most isolates were ST-459 (19/37, 51%) and ST-452 (11/37, 30%), but we also identified ST-291, ST-3, ST-196, and a novel ST-682. We detected further diversity by performing whole-genome single-nucleotide polymorphism analysis and found evidence of recombination events contributing to variation in some serotype IV GBS strains. We also evaluated antimicrobial drug resistance and found that ST-459 strains were resistant to clindamycin and erythromycin, whereas strains of other STs were, for the most part, susceptible to these antimicrobial drugs.
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Shigayeva A, Rudnick W, Green K, Chen DK, Demczuk W, Gold WL, Johnstone J, Kitai I, Krajden S, Lovinsky R, Muller M, Powis J, Rau N, Walmsley S, Tyrrell G, Bitnun A, McGeer A. Invasive Pneumococcal Disease Among Immunocompromised Persons: Implications for Vaccination Programs. Clin Infect Dis 2015; 62:139-47. [DOI: 10.1093/cid/civ803] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 07/28/2015] [Indexed: 12/31/2022] Open
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Dutil L, Irwin R, Finley R, Ng LK, Avery B, Boerlin P, Bourgault AM, Cole L, Daignault D, Desruisseau A, Demczuk W, Hoang L, Horsman GB, Ismail J, Jamieson F, Maki A, Pacagnella A, Pillai DR. Ceftiofur resistance in Salmonella enterica serovar Heidelberg from chicken meat and humans, Canada. Emerg Infect Dis 2010; 16:48-54. [PMID: 20031042 PMCID: PMC2874360 DOI: 10.3201/eid1601.090729] [Citation(s) in RCA: 292] [Impact Index Per Article: 20.9] [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: 11/19/2022] Open
Abstract
Use of this drug in chickens may limit effectiveness of cephalosporins in treating human infections. The Canadian Integrated Program for Antimicrobial Resistance Surveillance describes a strong correlation (r = 0.9, p<0.0001) between ceftiofur-resistant Salmonella enterica serovar Heidelberg isolated from retail chicken and incidence of ceftiofur-resistant Salmonella serovar Heidelberg infections in humans across Canada. In Québec, changes of ceftiofur resistance in chicken Salmonella Heidelberg and Escherichia coli isolates appear related to changing levels of ceftiofur use in hatcheries during the study period, from highest to lowest levels before and after a voluntary withdrawal, to increasing levels after reintroduction of use (62% to 7% to 20%, and 34% to 6% to 19%, respectively). These events provide evidence that ceftiofur use in chickens results in extended-spectrum cephalosporin resistance in bacteria from chicken and humans. To ensure the continued effectiveness of extended-spectrum cephalosporins for treating serious infections in humans, multidisciplinary efforts are needed to scrutinize and, where appropriate, limit use of ceftiofur in chicken production in Canada.
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Affiliation(s)
- Lucie Dutil
- Public Health Agency of Canada, Saint-Hyacinthe, Quebec, Canada.
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Olson AB, Andrysiak AK, Tracz DM, Guard-Bouldin J, Demczuk W, Ng LK, Maki A, Jamieson F, Gilmour MW. Limited genetic diversity in Salmonella enterica serovar Enteritidis PT13. BMC Microbiol 2007; 7:87. [PMID: 17908316 PMCID: PMC2137926 DOI: 10.1186/1471-2180-7-87] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 10/01/2007] [Indexed: 11/10/2022] Open
Abstract
Background Salmonella enterica serovar Enteritidis has emerged as a significant foodborne pathogen throughout the world and is commonly characterized by phage typing. In Canada phage types (PT) 4, 8 and 13 predominate and in 2005 a large foodborne PT13 outbreak occurred in the province of Ontario. The ability to link strains during this outbreak was difficult due to the apparent clonality of PT13 isolates in Canada, as there was a single dominant pulsed-field gel electrophoresis (PFGE) profile amongst epidemiologically linked human and food isolates as well as concurrent sporadic strains. The aim of this study was to perform comparative genomic hybridization (CGH), DNA sequence-based typing (SBT) genomic analyses, plasmid analyses, and automated repetitive sequence-based PCR (rep-PCR) to identify epidemiologically significant traits capable of subtyping S. Enteritidis PT13. Results CGH using an oligonucleotide array based upon chromosomal coding sequences of S. enterica serovar Typhimurium strain LT2 and the Salmonella genomic island 1 successfully determined major genetic differences between S. Typhimurium and S. Enteritidis PT13, but no significant strain-to-strain differences were observed between S. Enteritidis PT13 isolates. Individual loci (safA and fliC) that were identified as potentially divergent in the CGH data set were sequenced in a panel of S. Enteritidis strains, and no differences were detected between the PT13 strains. Additional sequence-based typing was performed at the fimA, mdh, manB, cyaA, citT, caiC, dmsA, ratA and STM0660 loci. Similarly, no diversity was observed amongst PT13 strains. Variation in plasmid content between PT13 strains was observed, but macrorestriction with BglII did not identify further differences. Automated rep-PCR patterns were variable between serovars, but S. Enteritidis PT13 strains could not be differentiated. Conclusion None of the methods identified any significant variation between PT13 strains. Greater than 11,300 base pairs of sequence for each of seven S. Enteritidis PT13 strains were analyzed without detecting a single polymorphic site, although diversity between different phage types of S. Enteritidis was observed. These data suggest that Canadian S. Enteritidis PT13 strains are highly related genetically.
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Affiliation(s)
- Adam B Olson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Ashleigh K Andrysiak
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Dobryan M Tracz
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jean Guard-Bouldin
- United States Department of Agricultural, Agricultural Research Service, Athens, GA, USA
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Lai-King Ng
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Anne Maki
- Ontario Central Public Health Laboratory, Ministry of Health and Long-Term Care, Toronto, ON, Canada
| | - Frances Jamieson
- Ontario Central Public Health Laboratory, Ministry of Health and Long-Term Care, Toronto, ON, Canada
| | - Matthew W Gilmour
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
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Currie A, Akwar H, MacDonald W, Saunders A, Baikie M, Sweet L, Landry L, Demczuk W, Panaro L. Home or away? Investigation of Salmonella enteritidis PFGE pattern SENXAI.0003 and SENBNI.0003, phage type 8, the in the Maritimes, 2005. Can Commun Dis Rep 2006; 32:231-9. [PMID: 17076033] [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: 05/12/2023]
Affiliation(s)
- A Currie
- Canadian Field Epidemiology Program, Public Health Agency of Canada, Ontario, Canada
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Abstract
Eleven tailed phages are described. They belong to the Myoviridae, Siphoviridae, or Podoviridae families and represent the ViI, T1, T5, Jersey, N4, and P22 species of enterobacterial phages. Morphology is correlated with host range.Key words: Salmonella, phage morphology.
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Affiliation(s)
- Walter Demczuk
- National Laboratory for Enteric Pathogens, National Microbiology Laboratory, Health Canada, Winnipeg, Manitoba R3E 3R2, Canada
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Demczuk W, Soule G, Clark C, Ackermann HW, Easy R, Khakhria R, Rodgers F, Ahmed R. Phage-based typing scheme for Salmonella enterica serovar Heidelberg, a causative agent of food poisonings in Canada. J Clin Microbiol 2003; 41:4279-84. [PMID: 12958257 PMCID: PMC193816 DOI: 10.1128/jcm.41.9.4279-4284.2003] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [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
Salmonella enterica serovar Heidelberg is perhaps the second most frequent Salmonella serovar isolated from humans and the most common isolated from animals in Canada. This pathogen has shown increasing resistance to antimicrobial agents and mimics the multidrug resistance observed in S. enterica serovar Typhimurium strain DT 104. However, unlike for serovar Typhimurium, a rapid and inexpensive subtyping method has not been available for large-scale surveillance efforts. We developed a phage typing scheme and subtyped 2,523 strains of serovar Heidelberg from outbreaks, sporadic infections, and environmental sources in Canada between January 1991 and December 2000. All strains were sensitive to one or more phages and could be subdivided into 49 phage types. A total of 196 isolates from 13 major outbreaks could be subtyped into six phage types, while 86 strains from family outbreaks were assigned to seven phage types. All strains were typeable, and epidemiologically related strains isolated from patients and implicated foods had identical phage types, antibiograms, and pulsed-field gel electrophoresis (PFGE) patterns. Combining PFGE with phage typing increased the discriminatory power of the analysis beyond that of either method alone. We concluded that this phage typing scheme, in conjunction with PFGE, enhances subtyping of serovar Heidelberg strains. Furthermore, this phage typing scheme is a rapid, economical, stable, and reliable epidemiologic tool for tracing the origin of food-borne disease and for the surveillance of sporadic infections.
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Affiliation(s)
- Walter Demczuk
- National Laboratory for Enteric Pathogens, National Microbiology Laboratory, Health Canada, Winnipeg, Manitoba, Canada
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Mulvey MR, Soule G, Boyd D, Demczuk W, Ahmed R. Characterization of the first extended-spectrum beta-lactamase-producing Salmonella isolate identified in Canada. J Clin Microbiol 2003; 41:460-2. [PMID: 12517894 PMCID: PMC149628 DOI: 10.1128/jcm.41.1.460-462.2003] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [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: 11/20/2022] Open
Abstract
A single Salmonella enterica serovar Typhimurium isolate with an UT2 phage type producing an extended-spectrum beta-lactamase (ESBL) was identified in Canada in 2000. The isolate harbored two plasmids, one containing a bla(TEM-1) gene and the other containing a bla(SHV-2a) gene. The ESBL gene was located on a 70-kb transferable plasmid which also carried tetracycline and trimethoprim resistance elements.
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Affiliation(s)
- Michael R Mulvey
- Nosocomial Infections, National Microbiology Laboratory, Health Canada, Winnipeg, Manitoba, Canada.
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Poppe C, Demczuk W, McFadden K, Johnson RP. Virulence of Salmonella enteritidis phagetypes 4, 8 and 13 and other Salmonella spp. for day-old chicks, hens and mice. Can J Vet Res 1993; 57:281-7. [PMID: 8269367 PMCID: PMC1263641] [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: 01/29/2023]
Abstract
Virulence of three Canadian poultry strains of Salmonella enteritidis, namely phagetypes (PT) 4, 8 and 13, and one Salmonella heidelberg strain was assessed in orally and intraperitoneally inoculated one-day old chickens and compared to the virulence of a human S. enteritidis PT 4 strain from the United Kingdom (UK). The two PT 4 strains were also compared in orally inoculated adult laying hens. In addition, orally inoculated Balb/c mice were used to evaluate virulence of the above strains and two strains of Salmonella typhimurium containing different plasmids. In orally inoculated one-day old chickens, the UK S. enteritidis PT 4 strain was more virulent than the Canadian PT 4 strain. The UK PT 4 strain was also more virulent and invasive in adult laying hens than the Canadian PT 4 strain. The S. enteritidis PT 8 strain and one S. typhimurium strain isolated from a chicken hatchery were the most virulent for orally inoculated Balb/c mice. This strain of S. typhimurium contained the 60 megadalton plasmid associated with virulence for Balb/c mice which was not present in the S. typhimurium strain isolated from a pig with septicemic disease.
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Affiliation(s)
- C Poppe
- Agriculture Canada, Health of Animals Laboratory, Guelph, Ontario
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Poppe C, McFadden KA, Brouwer AM, Demczuk W. Characterization of Salmonella enteritidis strains. Can J Vet Res 1993; 57:176-84. [PMID: 8358678 PMCID: PMC1263620] [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: 01/30/2023]
Abstract
A study was conducted to characterize 318 Salmonella enteritidis strains that were mainly isolated from poultry and their environment in Canada. Biotype, phagetype (PT), plasmid profile (PP), hybridization with a plasmid-derived virulence sequence probe, antibiotic resistance, outer membrane proteins (OMPs), and lipopolysaccharide (LPS) profiles were determined. Relationships of these properties to one another, and their diagnostic and pathogenic significance were assessed. Biotyping indicated that failure to ferment rhamnose was sometimes useful as a marker for epidemiologically related strains. Phagetyping was the most effective method for subdividing S. enteritidis; it distinguished 12 PTs. Phagetype 13 was occasionally associated with septicemia and mortality in chickens. The strains belonged to 15 PPs. A 36 megadalton (MDa) plasmid was found in 97% of the strains. Only the 36 MDa plasmid hybridized with the probe. Seventeen percent of the strains were drug resistant; all strains were sensitive to ciprofloxacin. Thirty-five of 36 strains possessed the same OMP profile, and 36 of 41 strains contained smooth LPS.
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Affiliation(s)
- C Poppe
- Health of Animals Laboratory, Agriculture Canada, Guelph, Ontario
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