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Candeias C, Félix S, Handem S, de Lencastre H, Sá-Leão R. Clonal Changes in the Pneumococcal Population Carried by Portuguese Children during Six Years of Private Use of the 13-Valent Pneumococcal Conjugate Vaccine: the Relative Contribution of Clonal Expansion, Clonal Emergence, and Capsular Switch Events. Microbiol Spectr 2023:e0290922. [PMID: 36946753 PMCID: PMC10100364 DOI: 10.1128/spectrum.02909-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
In Portugal, the 13-valent pneumococcal conjugate vaccine (PCV13) was available for private use from 2010 to 2015 and it was introduced in the National Immunization Program in 2015. We have reported that private use of PCV13 led to extensive serotype replacement and an increase in antimicrobial susceptibility among pneumococci carried by healthy children. We investigated which clonal changes concurred with these observations. A total of 657 pneumococcal strains, representative of a collection of 2,615 isolates, were genotyped by multilocus sequence typing (MLST). The isolates were recovered in 2009 to 2010 (pre-PCV13), 2011 to 2012 (early PCV13), and 2015 to 2016 (late PCV13) from children attending day care centers in two regions of Portugal (one urban, one rural). One-hundred seventy-one sequence types (STs) were identified, corresponding to 18 clonal complexes (CCs) and 58 singletons. Most CCs (n = 17) and several singletons (n = 16) were found in both regions, indicating that they were geographically disseminated. Clonal complexes expressing PCV13 serotypes in circulation in the late PCV13 period were a subset of the ones identified in the pre-PCV13 period and were often associated with antimicrobial resistance. Among those, the most frequent in both regions was CC179, a multidrug-resistant clone of serotype 19F. Serotype replacement, following PCV13 use, was mainly due to expansion of the susceptible lineages expressing non-PCV13 serotypes already in circulation in the pre-PCV13 period. The emergence of ST53, associated with serotype 8, a major cause of disease in several European countries, was observed in the rural region. Potential capsular switching events, unrelated to PCV13 use, were detected. This study improves our understanding of changes triggered by the private use of PCV13 in Portugal. IMPORTANCE Streptococcus pneumoniae (pneumococcus) is a major human respiratory pathogen linked with high morbidity, mortality, and health care-associated costs worldwide. This bacterium often colonizes asymptomatically healthy children. Colonization is a prerequisite for disease and is also essential for transmission between individuals. The 13-valent pneumococcal conjugate vaccine targets 13 of 101 capsular types of pneumococci described to date. This vaccine not only prevents pneumococcal disease but also impacts colonization by decreasing the carriage of vaccine serotypes. Consequently, serotype replacement occurs. The clonal changes occurring during serotype replacement may be due to various mechanisms, such as clonal expansion, emergence, extinction, or capsular switch (vaccine escape). This study shows that in Portugal, the use of PCV13 has led to significant changes in clonal composition and that these were mainly due to the clonal expansion of lineages expressing serotypes not included in the vaccine.
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Affiliation(s)
- Catarina Candeias
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Sofia Félix
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Sara Handem
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB NOVA, Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
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Evidence for the intermediate disturbance hypothesis and exponential decay in replacement in Streptococcus pneumoniae following use of conjugate vaccines. Sci Rep 2022; 12:7510. [PMID: 35525872 PMCID: PMC9079081 DOI: 10.1038/s41598-022-11279-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/06/2022] [Indexed: 11/12/2022] Open
Abstract
Understanding how pneumococci respond to pneumococcal conjugate vaccines (PCVs) is crucial to predict the impact of upcoming higher-valency vaccines. However, stages in pneumococcal community succession following disturbance are poorly understood as long-time series on carriage are scarce and mostly evaluated at end-point measurements. We used a 20-year cross-sectional dataset of pneumococci carried by Portuguese children, and methods from community ecology, to study community assembly and diversity following use of PCV7 and PCV13. Two successional stages were detected upon introduction of each PCV: one in which non-vaccine serotypes increased in abundance, fitted by a broken-stick model, and a second in which the community returned to the original structure, fitted by a geometric series, but with different serotype profile and a drop in richness as great as 24%. A peak in diversity was observed for levels of intermediate vaccine uptake (30–40%) in agreement with the intermediate disturbance hypothesis. Serotype replacement was fitted by an exponential decay model (R2 = 80%, P < 0.001). The half-life for replacement was 8 years for PCV7 and 10 years for PCV13. The structure of the pneumococcal community is resilient to vaccine pressure. The increasing loss of diversity, however, suggests it could eventually reach a threshold beyond which it may no longer recover.
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Chaguza C, Heinsbroek E, Gladstone RA, Tafatatha T, Alaerts M, Peno C, Cornick JE, Musicha P, Bar-Zeev N, Kamng'ona A, Kadioglu A, McGee L, Hanage WP, Breiman RF, Heyderman RS, French N, Everett DB, Bentley SD. Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data. Clin Infect Dis 2021; 70:1294-1303. [PMID: 31094423 PMCID: PMC7768739 DOI: 10.1093/cid/ciz404] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/15/2019] [Indexed: 11/14/2022] Open
Abstract
Background Pneumococcal conjugate vaccines (PCVs) have reduced pneumococcal diseases globally. Pneumococcal genomic surveys elucidate PCV effects on population structure but are rarely conducted in low-income settings despite the high disease burden. Methods We undertook whole-genome sequencing (WGS) of 660 pneumococcal isolates collected through surveys from healthy carriers 2 years from 13-valent PCV (PCV13) introduction and 1 year after rollout in northern Malawi. We investigated changes in population structure, within-lineage serotype dynamics, serotype diversity, and frequency of antibiotic resistance (ABR) and accessory genes. Results In children <5 years of age, frequency and diversity of vaccine serotypes (VTs) decreased significantly post-PCV, but no significant changes occurred in persons ≥5 years of age. Clearance of VT serotypes was consistent across different genetic backgrounds (lineages). There was an increase of nonvaccine serotypes (NVTs)—namely 7C, 15B/C, and 23A—in children <5 years of age, but 28F increased in both age groups. While carriage rates have been recently shown to remain stable post-PCV due to replacement serotypes, there was no change in diversity of NVTs. Additionally, frequency of intermediate-penicillin-resistant lineages decreased post-PCV. Although frequency of ABR genes remained stable, other accessory genes, especially those associated with mobile genetic element and bacteriocins, showed changes in frequency post-PCV. Conclusions We demonstrate evidence of significant population restructuring post-PCV driven by decreasing frequency of vaccine serotypes and increasing frequency of few NVTs mainly in children under 5. Continued surveillance with WGS remains crucial to fully understand dynamics of the residual VTs and replacement NVT serotypes post-PCV.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Darwin College, University of Cambridge, Silver Street, Cambridge
| | - Ellen Heinsbroek
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,HIV and STI Department, National Infection Service, Public Health England, London, United Kingdom
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge
| | - Terence Tafatatha
- Malawi Epidemiology Intervention Research Unit (formerly KPS), Chilumba
| | - Maaike Alaerts
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Center of Medical Genetics, University of Antwerp, Belgium
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, United Kingdom
| | - Jennifer E Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre
| | - Patrick Musicha
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.,Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Naor Bar-Zeev
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Arox Kamng'ona
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Department of Biomedical Sciences, University of Malawi, College of Medicine, Blantyre
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Division of Infection and Immunity, University College London, United Kingdom
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, United Kingdom
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Department of Pathology, University of Cambridge, United Kingdom
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Application of multi-omics technology for the elucidation of anti-pneumococcal activity of 3-acyl-2-phenylamino-1,4-dihydroquinolin-4-one (APDQ) derivative against Streptococcus pneumoniae. Sci Rep 2020; 10:20685. [PMID: 33244098 PMCID: PMC7691496 DOI: 10.1038/s41598-020-77694-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/10/2020] [Indexed: 11/24/2022] Open
Abstract
Streptococcus pneumoniae is one of Gram-positive pathogen that causes invasive pneumococcal disease. Nowadays, many S. pneumoniae strains are resistant to commonly used antibiotics such as β-lactams and macrolides. 3-Acyl-2-phenylamino-1,4-dihydroquinolin-4-one (APDQ) derivatives are known as novel chemicals having anti-pneumococcal activity against S. pneumoniae. The underlying mechanism of the anti-pneumococcal activity of this inhibitor remains unknown. Therefore, we tried to find the anti-pneumococcal mechanism of APDQ230122, one of the APDQ derivatives active against S. pneumoniae. We performed transcriptomic analysis (RNA-Seq) and proteomic analysis (LC–MS/MS analysis) to get differentially expressed genes (DEG) and differentially expressed proteins (DEP) of S. pneumoniae 521 treated with sub-inhibitory concentrations of APDQ230122 and elucidated the comprehensive expression changes of genes and proteins using multi-omics analysis. As a result, genes or proteins of peptidoglycan biosynthesis and DNA replication were significantly down-regulated. Electron microscopy analysis revealed that the structure of peptidoglycan was damaged by APDQ230122 in a chemical concentration-dependent manner. Therefore, we suggest peptidoglycan biosynthesis is a major target of APDQ230122. Multi-omics analysis can provide us useful information to elucidate anti-pneumococcal activity of APDQ230122.
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Huddar S, Park CM, Kim HJ, Jang S, Lee S. Discovery of 4-hydroxy-2-oxo-1,2-dihydroquinolines as potential inhibitors of Streptococcus pneumoniae, including drug-resistant strains. Bioorg Med Chem Lett 2020; 30:127071. [PMID: 32146051 DOI: 10.1016/j.bmcl.2020.127071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 10/24/2022]
Abstract
New therapies for treating drug-resistant pneumococcal infections are urgently needed. The novel scaffold 6-hydroxy-4-oxo-1,2-dihydro-4H-quinoline was shown to have similar efficacies against all three different serotypes of S. pneumoniae, ATCC 49617™ (19F), ATCC BAA-1663™ (15B), and ATCC 700904™ (19A), in a resazurin-based high-throughput screen using the Korea Chemical Bank library. Further studies to identify a new lead with this scaffold, including tricyclic pyrrolo[3,2,1-ij]quinolone and pyrido[3,2,1-ij]quinolone derivatives, led to the identification of 6d, 7d and 12a. Compound 6d (IC50 = 0.92, 0.75, and 0.77 µM), 7d (IC50 = 0.57, 0.66, and 0.38 µM) and 12a (IC50 = 0.27, 1.03, and 0.62 µM) showed submicromolar IC50 values against 19F, 15B, and 19A, respectively, and thus serve as a starting point for further optimization. While some of compounds in this series exhibited acceptable pharmacokinetic profiles in preliminary in vivo rat experiments, the most active compound 12a showed poor solubility and high plasma protein binding. Our current research efforts are focused on optimizing compounds to improve physicochemical properties as well as potency.
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Affiliation(s)
- Srigouri Huddar
- Drug Information Platform Center, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea; Korea University of Science and Technology, Daejeon 34114, Republic of Korea
| | - Chul Min Park
- Center for Convergent Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Hyung Jun Kim
- Discovery Biology Department, Antibacterial Resistance Research Laboratory, Institut Pasteur Korea, Seongnam 13488, Republic of Korea
| | - Soojin Jang
- Discovery Biology Department, Antibacterial Resistance Research Laboratory, Institut Pasteur Korea, Seongnam 13488, Republic of Korea
| | - Sunkyung Lee
- Drug Information Platform Center, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea; Korea University of Science and Technology, Daejeon 34114, Republic of Korea.
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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] [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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Neves FPG, Cardoso NT, Souza ARV, Snyder RE, Marlow MM, Pinto TCA, Teixeira LM, Riley LW. Population structure of Streptococcus pneumoniae colonizing children before and after universal use of pneumococcal conjugate vaccines in Brazil: emergence and expansion of the MDR serotype 6C-CC386 lineage. J Antimicrob Chemother 2019; 73:1206-1212. [PMID: 29401243 DOI: 10.1093/jac/dky001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/28/2017] [Indexed: 01/06/2023] Open
Abstract
Objectives To determine the population structure and change in drug resistance of pneumococci colonizing children before and after the introduction of the 10-valent and 13-valent pneumococcal conjugate vaccines (PCV10/13) in Brazil. Methods We used MLST to analyse 256 pneumococcal isolates obtained from children aged <6 years before (2009-10; n = 125) and after (2014; n = 131) the introduction of the PCV10 and PCV13. Antimicrobial susceptibility and capsular types were previously determined. Results We identified 97 different STs. Ninety (35.2%) isolates were related to international clones. The most frequent lineages were serogroup 6-CC724 (where CC stands for clonal complex) and the MDR serotype 6C-CC386 in the pre- and post-PCV10/13 periods, respectively. Penicillin-non-susceptible pneumococci (PNSP) formed 24% and 38.9% of the pre- and post-PCV10/13 isolates, respectively (P = 0.01). In the pre-PCV10/13 period, serotype 14-ST156 was the predominant penicillin-non-susceptible lineage, but it was not detected in the post-PCV10/13 period. Serotype 14-ST156 and serotype 19A-ST320 complex isolates had the highest penicillin and ceftriaxone MICs in the pre- and post-PCV10/13 periods, respectively. In turn, serotype 6C-CC386 comprised almost 30% of the PNSP and over 40% of the erythromycin-resistant isolates (MIC >256 mg/L) in the post-PCV10/13 period. Conclusions Although PNSP strains were polyclonal, most resistant isolates belonged to a single genotype from each period. Higher erythromycin resistance prevalence (42%) in the post-PCV10/13 period was mainly attributed to MDR serotype 6C-CC386. Ongoing surveillance of pneumococcal clonal composition is important to evaluate PCV use outcomes and to identify factors other than PCVs that drive pneumococcal drug resistance evolution.
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Affiliation(s)
- Felipe P G Neves
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA.,Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, 101 São Domingos, Niterói, RJ 24210-130, Brazil
| | - Nayara T Cardoso
- Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, 101 São Domingos, Niterói, RJ 24210-130, Brazil
| | - Aline R V Souza
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Robert E Snyder
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA
| | - Mariel M Marlow
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA
| | - Tatiana C A Pinto
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lúcia M Teixeira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA
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8
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Mitchell PK, Azarian T, Croucher NJ, Callendrello A, Thompson CM, Pelton SI, Lipsitch M, Hanage WP. Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13. Microb Genom 2019; 5. [PMID: 30777813 PMCID: PMC6421351 DOI: 10.1099/mgen.0.000252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The 13-valent pneumococcal conjugate vaccine (PCV-13) was introduced in the United States in 2010. Using a large paediatric carriage sample collected from shortly after the introduction of PCV-7 to several years after the introduction of PCV-13, we investigate alterations in the composition of the pneumococcal population following the introduction of PCV-13, evaluating the extent to which the post-vaccination non-vaccine type (NVT) population mirrors that from prior to vaccine introduction and the effect of PCV-13 on vaccine type lineages. Draft genome assemblies from 736 newly sequenced and 616 previously published pneumococcal carriage isolates from children in Massachusetts between 2001 and 2014 were analysed. Isolates were classified into one of 22 sequence clusters (SCs) on the basis of their core genome sequence. We calculated the SC diversity for each sampling period as the probability that any two randomly drawn isolates from that period belong to different SCs. The sampling period immediately after the introduction of PCV-13 (2011) was found to have higher diversity than preceding (2007) or subsequent (2014) sampling periods {Simpson’s D 2007: 0.915 [95 % confidence interval (CI) 0.901, 0.929]; 2011: 0.935 [0.927, 0.942]; 2014 : 0.912 [0.901, 0.923]}. Amongst NVT isolates, we found the distribution of SCs in 2011 to be significantly different from that in 2007 or 2014 (Fisher’s exact test P=0.018, 0.0078), but did not find a difference comparing 2007 to 2014 (Fisher’s exact test P=0.24), indicating greater similarity between samples separated by a longer time period than between samples from closer time periods. We also found changes in the accessory gene content of the NVT population between 2007 and 2011 to have been reduced by 2014. Amongst the new serotypes targeted by PCV-13, four were present in our sample. The proportion of our sample composed of PCV-13-only vaccine serotypes 19A, 6C and 7F decreased between 2007 and 2014, but no such reduction was seen for serotype 3. We did, however, observe differences in the genetic composition of the pre- and post-PCV-13 serotype 3 population. Our isolates were collected during discrete sampling periods from a small geographical area, which may limit the generalizability of our findings. Pneumococcal diversity increased immediately following the introduction of PCV-13, but subsequently returned to pre-vaccination levels. This is reflected in the distribution of NVT lineages, and, to a lesser extent, their accessory gene frequencies. As such, there may be a period during which the population is particularly disrupted by vaccination before returning to a more stable distribution. The persistence and shifting genetic composition of serotype 3 is a concern and warrants further investigation.
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Affiliation(s)
- Patrick K Mitchell
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Taj Azarian
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Nicholas J Croucher
- 2MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Alanna Callendrello
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Claudette M Thompson
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen I Pelton
- 3Division of Pediatric Infectious Diseases, Maxwell Finland Laboratory for Infectious Diseases, Boston Medical Center, Boston, MA, USA
| | - Marc Lipsitch
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - William P Hanage
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
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9
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Demczuk WHB, Martin I, Desai S, Griffith A, Caron-Poulin L, Lefebvre B, McGeer A, Tyrrell GJ, Zhanel GG, Gubbay J, Hoang L, Levett PN, Van Caeseele P, Raafat Gad R, Haldane D, Zahariadis G, German G, Daley Bernier J, Strudwick L, Mulvey MR. Serotype distribution of invasive Streptococcus pneumoniae in adults 65 years of age and over after the introduction of childhood 13-valent pneumococcal conjugate vaccination programs in Canada, 2010-2016. Vaccine 2018; 36:4701-4707. [PMID: 29937245 DOI: 10.1016/j.vaccine.2018.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/24/2018] [Accepted: 06/06/2018] [Indexed: 01/22/2023]
Abstract
The 13-valent conjugate vaccine (PCV13) was recommended for childhood immunization programs in 2010 in Canada and has decreased the incidence of invasive pneumococcal disease (IPD) in children and changed the epidemiology of IPD in adults. This study investigated the epidemiology of IPD in adults 65 years of age and older in Canada. A total of 7282 invasive S. pneumoniae isolated from adults ≥65 years old were serotyped from 2010 to 2016 and antimicrobial susceptibility was performed on 2527 isolates. Serotyping was performed by Quellung reaction using commercial antisera and antimicrobial susceptibilities were determined by broth microdilution. PCV7 serotypes decreased non-significantly from 2010 to 2016 from 9.1% (n = 96) to 6.7% (n = 72) while the additional six PCV13 serotypes declined significantly from 39.5% (n = 418) to 18.6% (n = 201) (p < 0.05). The 23-valent pneumococcal polysaccharide vaccine (PPV23) and non-vaccine (NVT) serotypes increased from 26.3% (n = 278) to 36.2% (n = 393) (p < 0.05), and from 25.1% (n = 266) to 38.4% (n = 416) (p < 0.05), respectively. There were no significant changes in antimicrobial resistance rates from 2011 to 2016: 24.1% of the IPD from adults ≥65 years were resistant to clarithromycin (n = 609), 10.0% to doxycycline (n = 254), 11.8% to penicillin (n = 299), 5.2% to cefuroxime (n = 131), 6.6% to clindamycin (n = 168), 6.0% to trimethoprim-sulfamethoxazole (n = 152), and 0.5% (n = 12) to ceftriaxone. Although overall incidence of IPD in adults ≥65 years has remained relatively constant from 2010 to 2016, childhood PCV13 vaccination programs have been successful in indirectly reducing IPD caused by PCV13 serotypes in adults through herd immunity effects.
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Affiliation(s)
- Walter H B 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
| | - Shalini Desai
- Vaccine Preventable Diseases Section, Surveillance and Epidemiology Division, Centre for Immunization and Respiratory Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Averil Griffith
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Laurence Caron-Poulin
- Vaccine Preventable Diseases Section, Surveillance and Epidemiology Division, Centre for Immunization and Respiratory Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Ste-Anne-de-Bellevue, Québec, Canada
| | - Allison McGeer
- Toronto Invasive Bacterial Diseases Network (TIBDN), Department of Microbiology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gregory J Tyrrell
- The Provincial Laboratory for Public Health (Microbiology), Edmonton, Alberta, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Linda Hoang
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Paul N Levett
- Saskatchewan Disease Control Laboratory, Regina, Saskatchewan, Canada
| | | | - Rita Raafat Gad
- New Brunswick, Office of the Chief Medical Officer of Health, New Brunswick Department of Health, Fredericton, New Brunswick, Canada
| | - David Haldane
- Queen Elizabeth II Health Science Centre, Halifax, Nova Scotia, Canada
| | - George Zahariadis
- Newfoundland Public Health Laboratory, St. John's, Newfoundland and Labrador, Canada
| | - Gregory German
- Queen Elizabeth Hospital, Charlottetown, Prince Edward Island, Canada
| | | | - Lori Strudwick
- Yukon Communicable Disease Control, Government of Yukon, Whitehorse, Yukon, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
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10
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Kim HJ, Kim N, Shum D, Huddar S, Park CM, Jang S. Identification of Antipneumococcal Molecules Effective Against Different Streptococcus pneumoniae Serotypes Using a Resazurin-Based High-Throughput Screen. Assay Drug Dev Technol 2018; 15:198-209. [PMID: 28723269 DOI: 10.1089/adt.2017.789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae is a major human pathogen, causing around 1.6 million deaths worldwide each year. By optimizing a resazurin-based assay to detect S. pneumoniae growth in 384-well microplates, we developed a new high-throughput screening (HTS) system for the discovery of antipneumococcal molecules, which was unsuccessful using conventional absorbance measurements. Before applying our protocol to a large-scale screen, we validated the system through a pilot screen targeting about 7,800 bioactive molecules using three different S. pneumoniae serotypes. Primary screenings of a further 27,000 synthetic small molecules facilitated the identification of 3-acyl-2-phenylamino-1,4-dihydropquinolin-4-one (APDQ) derivatives that inhibited growth of S. pneumoniae with MIC90 values <1 μM (0.03-0.81 μM). Five selected APDQ derivatives were also active against Staphylococcus aureus but neither Klebsiella pneumoniae nor Pseudomonas aeruginosa, suggesting that APDQ may act specifically against Gram-positive bacteria. Our results both validated and demonstrated the utility of the resazurin-based HTS system for the identification of new antipneumococcal molecules. Moreover, the identified new antipneumococcal molecules in this study may have potential to be further developed as new antibiotics.
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Affiliation(s)
- Hyung Jun Kim
- 1 Antibacterial Resistance Research Laboratory, Discovery Biology Department, Institut Pasteur Korea , Seongnam-si, Korea
| | - Namyoul Kim
- 2 Assay Development and Screening Group, Screening Sciences and Novel Assay Technologies Department, Institut Pasteur Korea , Seongnam-si, Korea
| | - David Shum
- 2 Assay Development and Screening Group, Screening Sciences and Novel Assay Technologies Department, Institut Pasteur Korea , Seongnam-si, Korea
| | - Srigouri Huddar
- 3 Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology , Daejeon, Korea.,4 Korea University of Science and Technology , Daejeon, Korea
| | - Chul Min Park
- 3 Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology , Daejeon, Korea
| | - Soojin Jang
- 1 Antibacterial Resistance Research Laboratory, Discovery Biology Department, Institut Pasteur Korea , Seongnam-si, Korea
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11
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Lee GM, Kleinman K, Pelton S, Lipsitch M, Huang SS, Lakoma M, Dutta-Linn M, Rett M, Hanage WP, Finkelstein JA. Immunization, Antibiotic Use, and Pneumococcal Colonization Over a 15-Year Period. Pediatrics 2017; 140:peds.2017-0001. [PMID: 28978716 PMCID: PMC5654389 DOI: 10.1542/peds.2017-0001] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/09/2017] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Rates of invasive pneumococcal disease have declined since widespread introduction of pneumococcal conjugate vaccines (PCVs) in the United States. We evaluated the impact of immunization status and recent antibiotic use on an individual child's risk of colonization. METHODS This study extends previously reported data from children <7 years of age seen for well child or acute care visits in Massachusetts communities. Nasopharyngeal swabs were collected during 6 surveillance seasons from 2000 to 2014. Parent surveys and medical record reviews confirmed immunization status and recent antibiotic use. We estimated the proportions of children colonized with PCV7-included, additional PCV13-included, and non-PCV13 serotypes. Risk factors for colonization with additional PCV13-included and non-PCV13 serotypes were assessed by using generalized linear mixed models adjusted for clustering by community. RESULTS Among 6537 children, 19A emerged as the predominant serotype in 2004, with substantial reductions in 2014. Among non-PCV serotypes, 15B/C, 35B, 23B, 11A, and 23A were most common in 2014. We observed greater odds for both additional PCV13 and non-PCV13 colonization in younger children, those with more child care exposure, and those with a concomitant respiratory tract infection. Adjusted odds for additional PCV13 colonization was lower (odds ratio 0.48 [95% confidence interval 0.31-0.75]) among children up-to-date for PCV13 vaccines. Recent antibiotic use was associated with higher odds of additional PCV13 colonization but substantially lower odds of non-PCV13 colonization. CONCLUSIONS Despite the success of pneumococcal vaccines in reducing colonization and disease due to targeted serotypes, ongoing community-based surveillance will be critical to evaluate the impact of interventions on pneumococcal colonization and disease.
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Affiliation(s)
- Grace M. Lee
- Center for Healthcare Research in Pediatrics, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts;,Divisions of Infectious Diseases and
| | - Ken Kleinman
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst School of Public Health and Health Sciences, Amherst, Massachusetts
| | - Stephen Pelton
- Division of Infectious Diseases, Boston Medical Center, Boston, Massachusetts
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts; and
| | - Susan S. Huang
- Division of Infectious Diseases and Health Policy Research Institute, University of California, Irvine School of Medicine, Orange, California
| | - Matt Lakoma
- Center for Healthcare Research in Pediatrics, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Maya Dutta-Linn
- Center for Healthcare Research in Pediatrics, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Melisa Rett
- Center for Healthcare Research in Pediatrics, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts; and
| | - Jonathan A. Finkelstein
- Center for Healthcare Research in Pediatrics, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts;,General Pediatrics, Boston Children’s Hospital, Boston, Massachusetts
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12
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Lourenço J, Watkins ER, Obolski U, Peacock SJ, Morris C, Maiden MCJ, Gupta S. Lineage structure of Streptococcus pneumoniae may be driven by immune selection on the groEL heat-shock protein. Sci Rep 2017; 7:9023. [PMID: 28831154 PMCID: PMC5567354 DOI: 10.1038/s41598-017-08990-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022] Open
Abstract
Populations of Streptococcus pneumoniae (SP) are typically structured into groups of closely related organisms or lineages, but it is not clear whether they are maintained by selection or neutral processes. Here, we attempt to address this question by applying a machine learning technique to SP whole genomes. Our results indicate that lineages evolved through immune selection on the groEL chaperone protein. The groEL protein is part of the groESL operon and enables a large range of proteins to fold correctly within the physical environment of the nasopharynx, thereby explaining why lineage structure is so stable within SP despite high levels of genetic transfer. SP is also antigenically diverse, exhibiting a variety of distinct capsular serotypes. Associations exist between lineage and capsular serotype but these can be easily perturbed, such as by vaccination. Overall, our analyses indicate that the evolution of SP can be conceptualized as the rearrangement of modular functional units occurring on several different timescales under different pressures: some patterns have locked in early (such as the epistatic interactions between groESL and a constellation of other genes) and preserve the differentiation of lineages, while others (such as the associations between capsular serotype and lineage) remain in continuous flux.
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Affiliation(s)
- José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
| | | | - Uri Obolski
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samuel J Peacock
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | | | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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13
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Demczuk WHB, Martin I, Hoang L, Van Caeseele P, Lefebvre B, Horsman G, Haldane D, Gubbay J, Ratnam S, German G, Daley Bernier J, Strudwick L, McGeer A, Zhanel GG, Van Domselaar G, Graham M, Mulvey MR. Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing. PLoS One 2017; 12:e0178040. [PMID: 28531208 PMCID: PMC5439729 DOI: 10.1371/journal.pone.0178040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/08/2017] [Indexed: 12/14/2022] Open
Abstract
Since implementation of the 13-valent polyvalent conjugate vaccine (PCV13) in Canada during 2010, the proportion of PCV13 serotypes causing invasive pneumococcal disease (IPD) has declined from 55% (n = 1492) in 2010 to 31% (n = 764) in 2014. A concurrent increase of non-PCV13 serotypes has occurred and 22F has become the most prevalent serotype in Canada increasing from 7% (n = 183) to 11% (n = 283). Core single nucleotide variant phylogenetic analysis was performed on 137 Streptococcus pneumoniae serotype 22F isolates collected across Canada from 2005-2015. Six phylogenetic lineages (n = 117) were identified among a serotype 22F/ST433 clonal complex (CC), including a recently expanding erythromycin-resistant clone. Erythromycin-resistance was observed in 25 isolates possessing ermB, mef or a 23S rRNA A2061G point mutation; 2 penicillin-resistant isolates had recombinant pbp1a, pbp2a and/or pbp2x; 3 tetracycline-resistant isolates contained tetM; and 1 isolate was multidrug-resistant. Virulence factor analysis indicated a high level of homogeneity among the 22F/ST433 clonal complex strains. A group of 6 phylogenetic outlier strains had differing MLST, antimicrobial resistance and molecular profiles suggestive of capsule switching events. While capsule switch events among S. pneumoniae serotype 22F has been observed, increasing prevalence of S. pneumoniae serotype 22F can be attributed to an evolving homogenous clone expanding nationally through local transmission events.
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Affiliation(s)
- Walter H. B. 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
| | - Linda Hoang
- British Columbia Centre for Disease Control, Vancouver, British, Canada
| | | | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Ste-Anne-de-Bellevue, Québec, Canada
| | - Greg Horsman
- Saskatchewan Disease Control Laboratory, Regina, Saskatchewan, Canada
| | - David Haldane
- Queen Elizabeth II Health Science Centre, Halifax, Nova Scotia, Canada
| | | | - Sam Ratnam
- Newfoundland Public Health Laboratory, St. John’s, Newfoundland and Labrador, Canada
| | - Gregory German
- Queen Elizabeth Hospital, Charlottetown, Prince Edward Island, Canada
| | | | | | - Allison McGeer
- Toronto Invasive Bacterial Diseases Network, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - George G. Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Science Technology Cores and Services Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Morag Graham
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Science Technology Cores and Services Division, 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
- * E-mail:
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14
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Paulo AC, Sá-Leão R. Periodic cycles of pneumococcal serotypes carried by children before and after 7-valent pneumococcal conjugate vaccine. PLoS One 2017; 12:e0176723. [PMID: 28453533 PMCID: PMC5409052 DOI: 10.1371/journal.pone.0176723] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 04/15/2017] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Periodic cycles in the serotype-specific incidence of invasive pneumococcal disease have been described but less is known in carriage. METHODS We analyzed serotype carriage prevalence among children 0-6 years old over a 15-year period that included pre-PCV7 data and a decade of PCV7 use. Mixed generalized additive models were used to study periodic cycles and how PCV7 impacted on them. RESULTS Pneumococcal carriage data of 7,463 children were analyzed. Periodic cycles ranging from 3 to 6 years were observed for PCV7-serotypes (VT) 14, 19F and 23F and for non-PCV7 types (NVT) 3, 6A, 6C, 11A, and NT. An indirect impact of PCV7 on periodic cycles of NVT was observed and could be translated in three ways: (i) a higher amplitude in the PCV7 period (serotypes 3 and 11A), (ii) sustained increase in the prevalence of carriage (serotypes 6C, 19A and NT) and (iii) an increase in the inter-epidemic period (serotypes 3, 6A and NT). An increase in the child's mean age of carriage of VTs 6B, 19F and 23F was observed. Serotypes 3, 6C, 11A and 15A became more frequent in ages previously associated with carriage of VTs. CONCLUSIONS Periodic cycles among serotypes frequently carried exist and can be modeled. These cycles can be perturbed upon introduction of PCVs and can lead to shifts in the mean age of carriage. Cyclic re-emergence of VTs can occur in settings with non-universal vaccine use. These results should be taken into account when interpreting surveillance data on pneumococcal carriage.
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Affiliation(s)
- Ana Cristina Paulo
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Quimíca e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Quimíca e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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15
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Cohen R, Cohen JF, Chalumeau M, Levy C. Impact of pneumococcal conjugate vaccines for children in high- and non–high-income countries. Expert Rev Vaccines 2017; 16:625-640. [DOI: 10.1080/14760584.2017.1320221] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Robert Cohen
- Université Paris Est, IMRB-GRC GEMINI, Créteil, France
- ACTIV, Association Clinique et Thérapeutique Infantile du Val de Marne, Saint-Maur des Fossés, France
- Clinical Research Center (CRC), Centre Hospitalier Intercommunal Créteil, France
- Unité Court Séjour, Petits Nourrissons, Service de Néonatologie, Centre Hospitalier Intercommunal Créteil, France
| | - Jérémie François Cohen
- Obstetrical, Perinatal and Pediatric Epidemiology Research Team (Epopé), Center for Epidemiology and Statistics Sorbonne Paris Cité (CRESS), Paris Descartes University, INSERM U1153, Paris, France
- Service de Pédiatrie Générale, Hôpital Necker-Enfants Malades; AP-HP; Université Paris Descartes, Paris, France
| | - Martin Chalumeau
- Obstetrical, Perinatal and Pediatric Epidemiology Research Team (Epopé), Center for Epidemiology and Statistics Sorbonne Paris Cité (CRESS), Paris Descartes University, INSERM U1153, Paris, France
- Service de Pédiatrie Générale, Hôpital Necker-Enfants Malades; AP-HP; Université Paris Descartes, Paris, France
| | - Corinne Levy
- Université Paris Est, IMRB-GRC GEMINI, Créteil, France
- ACTIV, Association Clinique et Thérapeutique Infantile du Val de Marne, Saint-Maur des Fossés, France
- Clinical Research Center (CRC), Centre Hospitalier Intercommunal Créteil, France
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16
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Neves FPG, Cardoso NT, Snyder RE, Marlow MA, Cardoso CAA, Teixeira LM, Riley LW. Pneumococcal carriage among children after four years of routine 10-valent pneumococcal conjugate vaccine use in Brazil: The emergence of multidrug resistant serotype 6C. Vaccine 2017; 35:2794-2800. [PMID: 28431817 DOI: 10.1016/j.vaccine.2017.04.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/09/2017] [Accepted: 04/10/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND In 2010, the 10-valent pneumococcal conjugate vaccine (PCV10) was introduced free of charge in Brazil as part of the public immunization program. Here we investigated the carriage prevalence, colonization risk factors, capsular types, and antimicrobial resistance among pneumococcal isolates obtained from children in Brazil four years after routine PCV10 use. METHODS Between September and December 2014, we conducted a cross-sectional study among children<6years old who attended one public and two private clinics in Niterói, RJ, Brazil to evaluate pneumococcal nasopharyngeal carriage. Antimicrobial susceptibility and capsular types were determined for all isolates. RESULTS Of 522 children, 118 (22.6%) were pneumococcal carriers. Being≥2years old, attending childcare center, presenting with any symptoms, having acute or chronic respiratory disease, and residing in a slum were associated with pneumococcal carriage. The most prevalent capsular types were 6C (14.5%), 15B/C (11.5%), 11A/D (9.2%), and 6A (7.6%). PCV10 serotypes represented 2.5%. All isolates were susceptible to levofloxacin, rifampicin, and vancomycin. Penicillin non-susceptible pneumococci (PNSP) comprised 39%, with penicillin and ceftriaxone MICs ranging from 0.12-8.0μg/ml and 0.012-1.0μg/ml, respectively. The 33 (28%) erythromycin-resistant isolates (MICs of 1.5 to >256μg/ml) displayed the cMLSB (72.7%) or M (27.3%) phenotypes, harboring the erm(B) and/or mef(A/E) genes. High non-susceptibility rates (>20%) to clindamycin, erythromycin, penicillin, and tetracycline were largely explained by the prevalence of multidrug resistant (MDR) serotype 6C isolates. CONCLUSIONS Effects of universal childhood PCV10 use on carriage were evident, with the near elimination of PCV10 serotypes. The emergence of MDR serotype 6C isolates, however, is a concern. Ongoing surveillance to monitor serotype 6C increase in invasive diseases is warranted.
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Affiliation(s)
- Felipe P G Neves
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA; Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, 101 São Domingos, Niterói, RJ 24210-130, Brazil.
| | - Nayara T Cardoso
- Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, 101 São Domingos, Niterói, RJ 24210-130, Brazil.
| | - Robert E Snyder
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA.
| | - Mariel A Marlow
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA.
| | - Claudete A A Cardoso
- Faculdade de Medicina, Universidade Federal Fluminense, Av. Marquês do Paraná, 303 Centro, Niterói, RJ 24033-900, Brazil.
| | - Lúcia M Teixeira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - bloco I, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA.
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17
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Càmara J, Marimón JM, Cercenado E, Larrosa N, Quesada MD, Fontanals D, Cubero M, Pérez-Trallero E, Fenoll A, Liñares J, Ardanuy C. Decrease of invasive pneumococcal disease (IPD) in adults after introduction of pneumococcal 13-valent conjugate vaccine in Spain. PLoS One 2017; 12:e0175224. [PMID: 28384325 PMCID: PMC5383258 DOI: 10.1371/journal.pone.0175224] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 03/22/2017] [Indexed: 02/01/2023] Open
Abstract
A prospective laboratory-based multicenter study that collected all adult invasive pneumococcal disease (IPD) episodes from 6 Spanish hospitals before (2008-2009) and after (2012-2013). The 13-valent pneumococcal conjugate vaccine (PCV13) licensure was conducted in order to analyze the impact of PCV13 introduction for children on adult IPD. A total of 1558 IPD episodes were detected. The incidence of IPD decreased significantly in the second period by -33.9% (95% CI, -40.3% to -26.8%). IPD due to PCV7 serotypes (-52.7%; 95% CI, -64.2% to -37.5%) and to PCV13 additional serotypes (-55.0% 95% CI, -62.0% to -46.7%) significantly decreased whereas IPD due to non-PCV13 serotypes remained stable (1.0% 95% CI, -12.9% to 17.2%). IPD due to all PCV13 additional serotypes significantly declined with the exception of serotype 3 (-11.3%; 95%CI -35.0% to 21.1%). IPD due to two non-PCV13 serotypes varied: serotype 6C that rose (301.6%; 95%CI, 92.7% to 733.3%, p<0.001), related to the expansion of ST3866C, and serotype 8 that decreased (-34.9%, 95%CI, -57.1 to -1.2, p = 0.049), related to a decline of the ST638. The recombinant clone ST652111A (variant of ST1569V) increased in frequency. The decrease of serotype 19A IPD was linked to a fall in those antibiotic susceptible clones. In the last period, rates of penicillin- and cefotaxime-resistance remained under 10% and 4%, respectively. Adult IPD decreased after the PCV13 introduction in Spain due to herd protection. The spread of multidrug resistant clones (ST3866C, ST652111A) related to non-PCV13 serotypes needs further surveillance.
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Affiliation(s)
- Jordi Càmara
- Hosp. Univ. de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - José María Marimón
- Hosp. Univ. Donostia, Donostia-San Sebastián, Spain
- CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Emilia Cercenado
- CIBER Enfermedades Respiratorias, Madrid, Spain
- Hosp. General Univ. Gregorio Marañón, Madrid, Spain
| | | | - María Dolores Quesada
- CIBER Enfermedades Respiratorias, Madrid, Spain
- H. U. Germans Trias i Pujol, Badalona, Spain
| | | | - Meritxell Cubero
- Hosp. Univ. de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Spain
- CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Emilio Pérez-Trallero
- Hosp. Univ. Donostia, Donostia-San Sebastián, Spain
- CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Asunción Fenoll
- Laboratorio de Referencia de neumococo, ISCIII, Madrid, Spain
| | - Josefina Liñares
- Hosp. Univ. de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Spain
- CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Carmen Ardanuy
- Hosp. Univ. de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Spain
- CIBER Enfermedades Respiratorias, Madrid, Spain
- * E-mail:
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18
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Namkoong H, Ishii M, Funatsu Y, Kimizuka Y, Yagi K, Asami T, Asakura T, Suzuki S, Kamo T, Fujiwara H, Tasaka S, Betsuyaku T, Hasegawa N. Theory and strategy for Pneumococcal vaccines in the elderly. Hum Vaccin Immunother 2016; 12:336-43. [PMID: 26406267 PMCID: PMC5049722 DOI: 10.1080/21645515.2015.1075678] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Pneumonia is the fourth-leading cause of death globally, and Streptococcus pneumoniae is the most important causative pathogen. Because the incidence of pneumococcal diseases is likely to increase with the aging society, we should determine an optimal strategy for pneumococcal vaccination. While consensus indicates that 23-valent pneumococcal polysaccharide vaccine prevents invasive pneumococcal diseases (IPD), its effects on community-acquired pneumonia (CAP) remain controversial. Recently, a 13-valent pneumococcal conjugate vaccine (PCV13) was released. The latest clinical study (CAPiTA study) showed that PCV13 reduced vaccine-type CAP and IPD. Based on these results, the Advisory Committee on Immunization Practices recommended initial vaccination with PCV13 for the elderly. Scientific evidence regarding immunosenescence is needed to determine a more ideal vaccination strategy for the elderly with impaired innate and adaptive immunity. Continuing research on the cost effectiveness of new vaccine strategies considering constantly changing epidemiology is also warranted.
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Affiliation(s)
- Ho Namkoong
- a Division of Pulmonary Medicine Department of Medicine ; Keio University School of Medicine ; Tokyo , Japan
| | - Makoto Ishii
- a Division of Pulmonary Medicine Department of Medicine ; Keio University School of Medicine ; Tokyo , Japan
| | - Yohei Funatsu
- a Division of Pulmonary Medicine Department of Medicine ; Keio University School of Medicine ; Tokyo , Japan
| | - Yoshifumi Kimizuka
- a Division of Pulmonary Medicine Department of Medicine ; Keio University School of Medicine ; Tokyo , Japan
| | - Kazuma Yagi
- a Division of Pulmonary Medicine Department of Medicine ; Keio University School of Medicine ; Tokyo , Japan
| | - Takahiro Asami
- a Division of Pulmonary Medicine Department of Medicine ; Keio University School of Medicine ; Tokyo , Japan
| | - Takanori Asakura
- a Division of Pulmonary Medicine Department of Medicine ; Keio University School of Medicine ; Tokyo , Japan
| | - Shoji Suzuki
- a Division of Pulmonary Medicine Department of Medicine ; Keio University School of Medicine ; Tokyo , Japan
| | - Testuro Kamo
- a Division of Pulmonary Medicine Department of Medicine ; Keio University School of Medicine ; Tokyo , Japan
| | - Hiroshi Fujiwara
- b Center for Infectious Diseases and Infection Control; Keio University School of Medicine ; Tokyo , Japan
| | - Sadatomo Tasaka
- a Division of Pulmonary Medicine Department of Medicine ; Keio University School of Medicine ; Tokyo , Japan
| | - Tomoko Betsuyaku
- a Division of Pulmonary Medicine Department of Medicine ; Keio University School of Medicine ; Tokyo , Japan
| | - Naoki Hasegawa
- b Center for Infectious Diseases and Infection Control; Keio University School of Medicine ; Tokyo , Japan
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19
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Hausdorff WP, Hanage WP. Interim results of an ecological experiment - Conjugate vaccination against the pneumococcus and serotype replacement. Hum Vaccin Immunother 2016; 12:358-74. [PMID: 26905681 PMCID: PMC5049718 DOI: 10.1080/21645515.2015.1118593] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Streptococcus pneumoniae has more than 95 serotypes, each of which presumably can cause sepsis, meningitis, pneumonia, and acute otitis media. Pneumococcal conjugate vaccines (PCV) targeted against a limited number of serotypes have nonetheless revealed an impressive impact on each manifestation of pneumococcal disease. At the same time, growing evidence of significant non-vaccine type (NVT) replacement disease following implementation of infant PCV programs has raised questions about the long-term viability of PCV immunization strategies and how to optimize PCV formulations. We discuss here theoretical and practical considerations regarding serotype replacement, and provide a snapshot of the most important NVT types seen to date after implementation of the 2 higher-valent PCVs.
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Affiliation(s)
| | - William P Hanage
- b Department of Epidemiology ; Center for Communicable Disease Dynamics; Harvard TH Chan School of Public Health ; Boston , MA , USA
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20
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Duvvuri VR, Deng X, Teatero S, Memari N, Athey T, Fittipaldi N, Gubbay JB. Population structure and drug resistance patterns of emerging non-PCV-13 Streptococcus pneumoniae serotypes 22F, 15A, and 8 isolated from adults in Ontario, Canada. INFECTION GENETICS AND EVOLUTION 2016; 42:1-8. [PMID: 27071529 DOI: 10.1016/j.meegid.2016.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/27/2016] [Accepted: 04/07/2016] [Indexed: 10/22/2022]
Abstract
The introduction of pneumococcal conjugate vaccines has led to the emergence of non-vaccine serotypes, which contributed to invasive pneumococcal disease in Canada and worldwide. A significant increase in the prevalence of non-13-valent pneumococcal conjugate vaccine (PCV-13)-included serotypes 22F, 15A, and 8 was observed from 2009 to 2013 in Ontario (all p values<0.01). In this study, whole genome sequencing was conducted on the 25 isolates of serotype 22F, seven of 15A and 10 of 8 to investigate the population structure and antibiotic resistance. All seven serotype 15A isolates were found to be multidrug resistant. From whole genome analysis, we observed recombination events among serotypes 22F, 15A and 8 populations. Serotype 22F (ST433) has emerged into two sub-populations, with 28% (7/25) exhibiting recombination events, and five also acquiring macrolide resistance as a result of recombination. This study enhances the knowledge on the molecular evolution of emerging non-PCV-13 vaccine serotype 22F, including acquisition of resistance genes through recombination events. It underpins the importance of whole genome sequencing in studying Streptococcus pneumoniae population structures and dynamics, and its utility in molecular surveillance.
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Affiliation(s)
| | - Xianding Deng
- Public Health Ontario, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada.
| | | | - Nader Memari
- Public Health Ontario, Toronto, Ontario, Canada.
| | - Taryn Athey
- Public Health Ontario, Toronto, Ontario, Canada.
| | - Nahuel Fittipaldi
- Public Health Ontario, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada.
| | - Jonathan B Gubbay
- Public Health Ontario, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada; The Hospital for Sick Children, Toronto, Ontario, Canada; Mount Sinai Hospital, Toronto, Ontario, Canada.
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21
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The post-vaccine microevolution of invasive Streptococcus pneumoniae. Sci Rep 2015; 5:14952. [PMID: 26492862 PMCID: PMC4615977 DOI: 10.1038/srep14952] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/10/2015] [Indexed: 02/02/2023] Open
Abstract
The 7-valent pneumococcal conjugated vaccine (PCV7) has affected the genetic population of Streptococcus pneumoniae in pediatric carriage. Little is known however about pneumococcal population genomics in adult invasive pneumococcal disease (IPD) under vaccine pressure. We sequenced and serotyped 349 strains of S. pneumoniae isolated from IPD patients in Nijmegen between 2001 and 2011. Introduction of PCV7 in the Dutch National Immunization Program in 2006 preluded substantial alterations in the IPD population structure caused by serotype replacement. No evidence could be found for vaccine induced capsular switches. We observed that after a temporary bottleneck in gene diversity after the introduction of PCV7, the accessory gene pool re-expanded mainly by genes already circulating pre-PCV7. In the post-vaccine genomic population a number of genes changed frequency, certain genes became overrepresented in vaccine serotypes, while others shifted towards non-vaccine serotypes. Whether these dynamics in the invasive pneumococcal population have truly contributed to invasiveness and manifestations of disease remains to be further elucidated. We suggest the use of whole genome sequencing for surveillance of pneumococcal population dynamics that could give a prospect on the course of disease, facilitating effective prevention and management of IPD.
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