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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] [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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Zhu Q, Zhou J, Li F, Shi P, Lu Y, Lin X, Yuan L, Zhuo Z, Shen J. Nasopharyngeal aspirates in children with severe community-acquired pneumonia collected within 3 days before bronchoscopy can partially reflect the pathogens in bronchoalveolar lavage fluids. BMC Infect Dis 2022; 22:814. [PMID: 36319953 PMCID: PMC9623994 DOI: 10.1186/s12879-022-07749-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/17/2022] [Accepted: 09/23/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND There is little evidence about consistency between nasopharyngeal and pulmonary pathogens in children with severe pneumonia. This study aims to compare the difference of pathogens between nasopharyngeal aspirates (NPAs) collected before bronchoscopy and bronchoalveolar lavage fluids (BALFs) in children with severe community-acquired pneumonia (SCAP). METHODS NPAs and BALFs were collected form pediatric SCAP cases hospitalized from January 2018 to March 2019. NPAs were colleced within 3 days before bronchoscopy. Samples were detected by direct immunofluorescence assay (DFA) for seven respiratory viruses and by routine bacterial culture in the clinical microbiology laboratory. Respiratory syncytial virus (RSV), Adenovirus (ADV), Influenza virus types A, B (IV-A and IV-B), Parainfluenza virus 1-3 (PIV1-3) were detected with a commercial assay. The virological and bacteriological detention results of NPAs were compared with the results of BALFs. RESULTS In total 204 cases with mean age of 3.4 ± 2.8 years (IQR, 1 month-14 years) were included in the study. Both NPA and BALF were collected from those cases. The positive rates of pathogen in NPAs and BALFs were 25.0% (51/204) and 36.7% (75/204), respectively (x2 = 6.614, P = 0.010). Respiratory viruses were found in 16.1% (33/204) from NPAs and 32.3% (66/204) from BALFs (x2 = 14.524, P < 0.001). RSV and ADV were the two most frequent detected viruses in NPAs and BALFs. High consistentcy of pathogens between NPAs and BALFs was observed, and 96.9% (32/33) viruses detected in NPAs were also found in BALFs. While bacteria were isolated from 12.7% (26/204) and 10.7% (22/204) of the two kinds of samples, respectively (x2 = 0.378, P = 0.539). In addition, Haemophilus influenzae (HI) was the dominant germ in both samples. CONCLUSION The DFA method used to detect seven respiratory viruses from NPAs collected within 3 days before bronchoscopy can partially reflect the pathogens in the lungs in children with SCAP.
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Affiliation(s)
- Qiguo Zhu
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Junli Zhou
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Fei Li
- Infectious Disease Department, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Peng Shi
- Statistics and data management center, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Yi Lu
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Xiaoliang Lin
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Lin Yuan
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Zhiqiang Zhuo
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Jun Shen
- Infectious Disease Department, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China.
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Stevens EJ, Morse DJ, Bonini D, Duggan S, Brignoli T, Recker M, Lees JA, Croucher NJ, Bentley S, Wilson DJ, Earle SG, Dixon R, Nobbs A, Jenkinson H, van Opijnen T, Thibault D, Wilkinson OJ, Dillingham MS, Carlile S, McLoughlin RM, Massey RC. Targeted control of pneumolysin production by a mobile genetic element in Streptococcus pneumoniae. Microb Genom 2022; 8:000784. [PMID: 35416147 PMCID: PMC9453066 DOI: 10.1099/mgen.0.000784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae is a major human pathogen that can cause severe invasive diseases such as pneumonia, septicaemia and meningitis. Young children are at a particularly high risk, with an estimated 3-4 million cases of severe disease and between 300 000 and 500 000 deaths attributable to pneumococcal disease each year. The haemolytic toxin pneumolysin (Ply) is a primary virulence factor for this bacterium, yet despite its key role in pathogenesis, immune evasion and transmission, the regulation of Ply production is not well defined. Using a genome-wide association approach, we identified a large number of potential affectors of Ply activity, including a gene acquired horizontally on the antibiotic resistance-conferring Integrative and Conjugative Element (ICE) ICESp23FST81. This gene encodes a novel modular protein, ZomB, which has an N-terminal UvrD-like helicase domain followed by two Cas4-like domains with potent ATP-dependent nuclease activity. We found the regulatory effect of ZomB to be specific for the ply operon, potentially mediated by its high affinity for the BOX repeats encoded therein. Using a murine model of pneumococcal colonization, we further demonstrate that a ZomB mutant strain colonizes both the upper respiratory tract and lungs at higher levels when compared to the wild-type strain. While the antibiotic resistance-conferring aspects of ICESp23FST81 are often credited with contributing to the success of the S. pneumoniae lineages that acquire it, its ability to control the expression of a major virulence factor implicated in bacterial transmission is also likely to have played an important role.
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Affiliation(s)
- Emily J Stevens
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Daniel J Morse
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Dora Bonini
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Seána Duggan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Mario Recker
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Exeter, TR10 9FE, UK.,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Stephen Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel J Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Sarah G Earle
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Robert Dixon
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Angela Nobbs
- Bristol Dental School, University of Bristol, Bristol, BS1 2LY, UK
| | - Howard Jenkinson
- Bristol Dental School, University of Bristol, Bristol, BS1 2LY, UK
| | | | - Derek Thibault
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Oliver J Wilkinson
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Mark S Dillingham
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Simon Carlile
- Host Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Rachel M McLoughlin
- Host Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.,Schools of Microbiology and Medicine and APC Microbiome Ireland, University College Cork, Cork, Ireland
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Zintgraff J, Gagetti P, Napoli D, Sanchez Eluchans N, Irazu L, Moscoloni M, Regueira M, Lara CS, Corso A. Invasive Streptococcus pneumoniae isolates from pediatric population in Argentina for the period 2006-2019. Temporal progression of serotypes distribution and antibiotic resistance. Vaccine 2021; 40:459-470. [PMID: 34920903 DOI: 10.1016/j.vaccine.2021.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 11/26/2022]
Abstract
Streptococcus pneumoniae is a major cause of severe invasive disease associated with high mortality and morbidity worldwide. A total of 2908 pneumococcal isolates were analyzed between 2006 and 2019. Gold standard pneumococcal serotyping (the Neufeld-Quellung reaction) was performed to identify the serotypes associated with infection in children < 5 years in Argentina and agar dilution method was carried out to determine their profiles to 14 antimicrobial agents. In 2012, the 13-valent pneumococcal conjugate vaccine (PCV13) was included in the National Immunization Program. In this work we have analyzed the local epidemiology of invasive pneumococcal diseases before and after the introduction of this vaccine in order to understand the epidemiological relevance and impact of PCV13. During the periods compared in the present study there was a significant increase in the proportion of non-PCV13 serotypes, serogroup 24 (246.7%) and 12F (85.7%), and a significant decrease in PCV13 serotypes, including serotypes 14 (91.2%), 5 (95.6%) and 1 (84.6%) among others. Another observation was that serotypes 3 (7.4%) and 19A (4.9%) still remain among the most frequent serotypes despite being part of the PCV13 formulation. Regarding antimicrobial resistance, in the present study we observed an increase in erythromycin resistance during the period of study mainly associated to serotype 14 in the pre-PCV13 period and to serogroup 24 in the post-PCV13 period, which also was the major NVT serotype associated with antimicrobial resistance and MDR. Serotypes 14, 24A/B/F and 19A were in the first three places among isolates resistant to all the antibiotics tested. Our data highlight the importance of continuous surveillance to assess the impact of pneumococcal vaccines and the use of antibiotics in the dynamic of pneumococcal serotypes.
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Affiliation(s)
- Jonathan Zintgraff
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.
| | - Paula Gagetti
- Servicio Antimicrobianos, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Daniela Napoli
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Nahuel Sanchez Eluchans
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Lucia Irazu
- Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Maria Moscoloni
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | | | - Mabel Regueira
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Claudia S Lara
- Servicio de Bacteriología Clínica, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos, Departamento de Bacteriología. Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
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Nakano S, Fujisawa T, Ito Y, Chang B, Matsumura Y, Yamamoto M, Suga S, Ohnishi M, Nagao M. Streptococcus pneumoniae Serotype 12F-CC4846 and Invasive Pneumococcal Disease after Introduction of 13-Valent Pneumococcal Conjugate Vaccine, Japan, 2015-2017. Emerg Infect Dis 2020; 26:2660-2668. [PMID: 33079039 PMCID: PMC7588537 DOI: 10.3201/eid2611.200087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
To prevent invasive pneumococcal disease (IPD), pneumococcal conjugate vaccines (PCVs) have been implemented in many countries; however, many cases of IPD still occur and can be attributable to nonvaccine serotypes of Streptococcus pneumoniae. In Japan, the number of IPD cases attributable to serotype 12F increased from 4.4% in 2015 to 24.6% in 2017 after 13-valent PCV was introduced. To clarify the associated genetic characteristics, we conducted whole-genome sequencing of 75 serotype 12F isolates. We identified 2 sequence types (STs) among the isolates: ST4846, which was the major type, and ST6945. Bayesian analysis suggested that these types diverged in »1942. Among serotype 12F-ST4846, we identified a major cluster, PC-JP12F, whose time of most recent common ancestor was estimated to be »2012. A phylogeographic analysis demonstrated that PC-JP12F isolates spread from the Kanto region, the most populated region in Japan, to other local regions.
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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] [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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Serotype and clonal distribution dynamics of invasive pneumococcal strains after PCV13 introduction (2011-2016): Surveillance data from 23 sites in Catalonia, Spain. PLoS One 2020; 15:e0228612. [PMID: 32027715 PMCID: PMC7004304 DOI: 10.1371/journal.pone.0228612] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 01/21/2020] [Indexed: 01/08/2023] Open
Abstract
Background The objective of this study is to describe incidence and shifts of serotype and clonal distribution of invasive Streptococcus pneumoniae strains in four different age groups (<5 years, 5–17 years, 18–64 years and >65 years) during a period of intermediate PCV13 vaccination coverage (2011–2016) in Catalonia, Spain. Methods We included all pneumococcal strains systematically sent to the Catalan support laboratory for molecular surveillance of invasive pneumococcal disease (IPD) located at Hospital Sant Joan de Deu, Barcelona. Two study periods were considered: 2011–13, early PCV13 vaccination period (EVP) and 2014–2016, late vaccination period (LVP). Results A total of 2142 strains were included in the study. Five years after intermediate introduction of PCV13 in our population, a significant decrease of overall incidence of IPD in children <5 years was observed (incidence rate ratio 0.5, 95% confidence interval 0.4–0.8). However, in seniors older than 65 years, a significant increase of overall incidence of IPD was observed (IRR 1.4, 95% CI 1.1–1.7). The contribution of PCV13 vaccine serotypes to IPD declined significantly in all age groups: from 59% to 38.1% in <5 years; 82.7% to 59% in 5–17 years, 47.8% to 34.1% in 18–64 years and 48.2% to 37% in >65 years. Results found when comparing both periods were consistent with IRRs observed year by year. In children <5 years, the three major serotypes detected were 1, 24F and 19A in EVP vs 24F, 14 and 10A in LVP. Among patients 5–17 years the first three serotypes were 1, 12F and 14 both in EVP and LVP. Among adults 18–64, the three major serotypes detected were 1, 12F and 8 vs 8, 12F and 3, respectively. Finally, in patients >65 years the most frequently isolated serotypes were 3, 19A and 7F vs 3, 14 and 12F, respectively. Regarding clonal complexes (CCs) expressing mainly PCV13 serotypes, significant decreases of the proportions of CC306, CC191 and CC320 were observed, while CC156 showed a significant increase. As for CCs expressing mostly non-PCV13 serotypes, significant increases in ST989, CC53 and CC404 were showed. Conclusions Despite low vaccine coverage in our setting a significant decrease of incidence of IPD was observed in children younger than 5 years. The modest indirect protection against vaccine serotypes causing IPD in elderly indicate the need for the inclusion of more serotypes in future high-valent PCV and vaccinating old adults should be considered.
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8
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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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9
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Status and potential of bacterial genomics for public health practice: a scoping review. Implement Sci 2019; 14:79. [PMID: 31409417 PMCID: PMC6692930 DOI: 10.1186/s13012-019-0930-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
Background Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist’s perspective. Methods In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. Results Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. Conclusions For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist’s perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance. Electronic supplementary material The online version of this article (10.1186/s13012-019-0930-2) contains supplementary material, which is available to authorized users.
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10
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Ohkusu M, Takeuchi N, Ishiwada N, Ohkusu K. Clonal spread of serotype 12F ST4846 Streptococcus pneumoniae. J Med Microbiol 2019; 68:1383-1390. [PMID: 31347997 DOI: 10.1099/jmm.0.001047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Introduction. In 2016-2017, there was an increase in the number of paediatric invasive pneumococcal disease (IPD) cases caused by Streptococcus pneumoniae serotype 12F in Chiba Prefecture, Japan. Serotype 12F is one of the major causative serotypes of IPD following the introduction of pneumococcal conjugate vaccine 13 (PCV13), and outbreaks of IPD caused by serotype 12F have recently been reported in several countries.Aim. Our goal here was to clarify the relationship among local outbreak strains and the outbreak strains in other countries, and for this we analysed clinical isolates of S. pneumoniae serotype 12F using several genetic identification methods.Methodology. All reported IPD cases caused by serotype 12F were reviewed and bacterial strains were collected and analysed. We also analysed S. pneumoniae serotype 12F strains isolated from other time periods, geographical areas, cases of adult IPD and respiratory specimens as control strains. Multi-locus sequence typing, PFGE and multi-locus variable number tandem repeat analysis (MLVA) were conducted on all isolates.Results. All 26 S. pneumoniae serotype 12F isolates, including control strains, belonged to a single sequence type (ST4846) that was the specific ST in Japan. All tested strains demonstrated five MLVA patterns and two PFGE patterns.Conclusion. We determined that the 2016-2017 outbreak of IPD in Chiba Prefecture was caused by clonally related isolates of serotype 12F. The continuous monitoring of IPD caused by serotype 12F is important for evaluating the impact of re-emerging pneumococcal serotypes following the PCV13 introduction era, and MLVA could be a useful tool for identification of outbreak strains.
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Affiliation(s)
- Misako Ohkusu
- Department of Infectious Diseases, Medical Mycology Research Center Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba-shi, Chiba 260-8673, Japan
| | - Noriko Takeuchi
- Department of Infectious Diseases, Medical Mycology Research Center Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba-shi, Chiba 260-8673, Japan
| | - Naruhiko Ishiwada
- Department of Infectious Diseases, Medical Mycology Research Center Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba-shi, Chiba 260-8673, Japan
| | - Kiyofumi Ohkusu
- Department of Microbiology, Tokyo Medical University, 6-1-1, Shinjyuku, Shinjyuku-ku, Tokyo 160-8402, Japan
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11
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Lo SW, Gladstone RA, van Tonder AJ, Lees JA, du Plessis M, Benisty R, Givon-Lavi N, Hawkins PA, Cornick JE, Kwambana-Adams B, Law PY, Ho PL, Antonio M, Everett DB, Dagan R, von Gottberg A, Klugman KP, McGee L, Breiman RF, Bentley SD. Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study. THE LANCET. INFECTIOUS DISEASES 2019; 19:759-769. [PMID: 31196809 PMCID: PMC7641901 DOI: 10.1016/s1473-3099(19)30297-x] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Invasive pneumococcal disease remains an important health priority owing to increasing disease incidence caused by pneumococci expressing non-vaccine serotypes. We previously defined 621 Global Pneumococcal Sequence Clusters (GPSCs) by analysing 20 027 pneumococcal isolates collected worldwide and from previously published genomic data. In this study, we aimed to investigate the pneumococcal lineages behind the predominant serotypes, the mechanism of serotype replacement in disease, as well as the major pneumococcal lineages contributing to invasive pneumococcal disease in the post-vaccine era and their antibiotic resistant traits. METHODS We whole-genome sequenced 3233 invasive pneumococcal disease isolates from laboratory-based surveillance programmes in Hong Kong (n=78), Israel (n=701), Malawi (n=226), South Africa (n=1351), The Gambia (n=203), and the USA (n=674). The genomes represented pneumococci from before and after pneumococcal conjugate vaccine (PCV) introductions and were from children younger than 3 years. We identified predominant serotypes by prevalence and their major contributing lineages in each country, and assessed any serotype replacement by comparing the incidence rate between the pre-PCV and PCV periods for Israel, South Africa, and the USA. We defined the status of a lineage as vaccine-type GPSC (≥50% 13-valent PCV [PCV13] serotypes) or non-vaccine-type GPSC (>50% non-PCV13 serotypes) on the basis of its initial serotype composition detected in the earliest vaccine period to measure their individual contribution toward serotype replacement in each country. Major pneumococcal lineages in the PCV period were identified by pooled incidence rate using a random effects model. FINDINGS The five most prevalent serotypes in the PCV13 period varied between countries, with only serotypes 5, 12F, 15B/C, 19A, 33F, and 35B/D common to two or more countries. The five most prevalent serotypes in the PCV13 period varied between countries, with only serotypes 5, 12F, 15B/C, 19A, 33F, and 35B/D common to two or more countries. These serotypes were associated with more than one lineage, except for serotype 5 (GPSC8). Serotype replacement was mainly mediated by expansion of non-vaccine serotypes within vaccine-type GPSCs and, to a lesser extent, by increases in non-vaccine-type GPSCs. A globally spreading lineage, GPSC3, expressing invasive serotypes 8 in South Africa and 33F in the USA and Israel, was the most common lineage causing non-vaccine serotype invasive pneumococcal disease in the PCV13 period. We observed that same prevalent non-vaccine serotypes could be associated with distinctive lineages in different countries, which exhibited dissimilar antibiotic resistance profiles. In non-vaccine serotype isolates, we detected significant increases in the prevalence of resistance to penicillin (52 [21%] of 249 vs 169 [29%] of 575, p=0·0016) and erythromycin (three [1%] of 249 vs 65 [11%] of 575, p=0·0031) in the PCV13 period compared with the pre-PCV period. INTERPRETATION Globally spreading lineages expressing invasive serotypes have an important role in serotype replacement, and emerging non-vaccine serotypes associated with different pneumococcal lineages in different countries might be explained by local antibiotic-selective pressures. Continued genomic surveillance of the dynamics of the pneumococcal population with increased geographical representation in the post-vaccine period will generate further knowledge for optimising future vaccine design. FUNDING Bill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control.
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Affiliation(s)
- Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
| | | | | | - John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Rachel Benisty
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Noga Givon-Lavi
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | | | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Pierra Y Law
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Pak Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Dean B Everett
- Centre for Inflammation Research, Queens Research Institute, University of Edinburgh, Edinburgh, UK
| | - Ron Dagan
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Keith P Klugman
- Rollins School Public Health, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School Public Health, Emory University, Atlanta, GA, USA; Emory Global Health Institute, Emory University, Atlanta, GA, USA
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12
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Assessment of the local clonal spread of Streptococcus pneumoniae serotype 12F caused invasive pneumococcal diseases among children and adults. J Infect Public Health 2019; 12:867-872. [PMID: 31204116 DOI: 10.1016/j.jiph.2019.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/11/2019] [Accepted: 05/29/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND We conducted active surveillance to elucidate the distribution of Streptococcus pneumoniae serotypes causing invasive pneumococcal disease (IPD) and clarified the genetic relatedness among the isolates in Kobe City, Japan. METHODS Forty-five IPD-causing S. pneumoniae strains were analyzed from March 2016 to May 2018 through active surveillance in Kobe City, Hyogo, Japan. Serotypes were determined by multiplex serotyping PCR and the Quellung reaction with pneumococcal antisera. Fourteen Sp12F strains were subjected to whole-genome sequencing (WGS). RESULTS Among 45 isolates, the most frequent serotypes were 12F (n=14, 31%), 24F (n=5, 11%), and 10A (n=4, 9%). Multilocus sequence typing (MLST) analysis of 14 isolates of Sp12F divided them into ST4846 (n=4) and ST6495 (n=10). WGS showed clonality of the 10 isolates of ST6495, with only 13 single nucleotide polymorphisms in the genomes. Meanwhile, ST4846 strains in Kobe differed from only the outbreak strains of Sp12F ST4846 in Tsuruoka, Japan, reported on 2018. CONCLUSIONS Serotype monitoring showed Sp12F to be the predominant serotype in Kobe, and WGS revealed the clonal spread of Sp12F ST6495 in this city. Thus, the spread of Sp12F could become a serious public health problem in Japan, warranting thorough monitoring in future.
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13
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Epidemiological and clinical features of invasive pneumococcal disease caused by serotype 12F in adults, Japan. PLoS One 2019; 14:e0212418. [PMID: 30789928 PMCID: PMC6383924 DOI: 10.1371/journal.pone.0212418] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/02/2019] [Indexed: 11/19/2022] Open
Abstract
Enhanced surveillance of invasive pneumococcal disease (IPD) in adults was conducted during April 2013–March 2018 in 10 of 47 prefectures in Japan, and a total of 1277 IPD patients were enrolled. An emergence of IPD caused by serotype 12F was identified during May 2015–March 2018 through this surveillance. 12F isolates were composed of four related sequence types. In total, 120 patients with 12F IPD were reported during this period. To characterize the clinical features of 12F IPD, the disease characteristics of these patients were compared with those of 1157 patients with non-12F IPD. Compared with the non-12F IPD patients, a significantly lower proportion of 12F IPD patients was aged 65 years or older (55% vs. 70%), vaccinated with 23-valent pneumococcal polysaccharide (4% vs. 14%), had comorbid illness (65% vs. 77%), or were immunocompromised (19% vs. 30%; all P < 0.05). No significant difference in the proportion of case fatalities was found between the two groups. The proportions of those aged 65 years or older (53% vs. 69%) and with bacteremic pneumonia (35% vs. 69%) were significantly lower in 17 patients who died from 12F IPD than in 205 patients who died from non-12F IPD (all P < 0.05). Differences in clinical features were similarly found between 12F IPD patients and patients in low- or intermediate-level invasive potential serogroups. Our data demonstrated that serotype 12F was associated with IPD in younger adults and a lower proportion of comorbid illness, including immunocompromised conditions, in adult IPD, suggesting the high invasive potential of the serotype 12F. In addition, patients who died from 12F IPD were younger and had proportionately more bacteremia without focus. These findings may provide new insight into the pathogenesis of IPD in adults caused by 12F serotype with a high invasive potential.
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14
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Rokney A, Ben-Shimol S, Korenman Z, Porat N, Gorodnitzky Z, Givon-Lavi N, Ron M, Agmon V, Dagan R, Valinsky L. Emergence of Streptococcus pneumoniae Serotype 12F after Sequential Introduction of 7- and 13-Valent Vaccines, Israel. Emerg Infect Dis 2019; 24:453-461. [PMID: 29460732 PMCID: PMC5823333 DOI: 10.3201/eid2403.170769] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Israel implemented use of 7- and 13-valent pneumococcal vaccine in 2009 and 2010, respectively. We describe results of prospective, population-based, nationwide active surveillance of Streptococcus pneumoniae serotype 12F (Sp12F) invasive pneumococcal disease (IPD) dynamics in the 7 years after vaccine introduction. Of 4,573 IPD episodes during July 2009-June 2016, a total of 434 (9.5%) were caused by Sp12F. Sp12F IPD rates (cases/100,000 population) increased in children <5 years of age, from 1.44 in 2009-2010 to >3.9 since 2011-2012, followed by an increase in all ages. During 2011-2016, Sp12F was the most prevalent IPD serotype. Sp12F isolates were mostly penicillin nonsusceptible (MIC >0.06 µg/mL; MIC50 = 0.12) and predominantly of sequence type 3774), a clone exclusively found in Israel (constituting ≈90% of isolates in 2000-2009). The sharp increase, long duration, and predominance of Sp12F IPD after vaccine implementation reflect a single clone expansion and may represent more than a transient outbreak.
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15
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Beall B, Chochua S, Gertz RE, Li Y, Li Z, McGee L, Metcalf BJ, Ricaldi J, Tran T, Walker H, Pilishvili T. A Population-Based Descriptive Atlas of Invasive Pneumococcal Strains Recovered Within the U.S. During 2015-2016. Front Microbiol 2018; 9:2670. [PMID: 30524382 PMCID: PMC6262371 DOI: 10.3389/fmicb.2018.02670] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/19/2018] [Indexed: 11/17/2022] Open
Abstract
Invasive pneumococcal disease (IPD) has greatly decreased since implementation in the U.S. of the 7 valent conjugate vaccine (PCV7) in 2000 and 13 valent conjugate vaccine (PCV13) in 2010. We used whole genome sequencing (WGS) to predict phenotypic traits (serotypes, antimicrobial phenotypes, and pilus determinants) and determine multilocus genotypes from 5334 isolates (~90% of cases) recovered during 2015–2016 through Active Bacterial Core surveillance. We identified 44 serotypes; 26 accounted for 98% of the isolates. PCV13 serotypes (inclusive of serotype 6C) accounted for 1503 (28.2%) isolates, with serotype 3 most common (657/5334, 12.3%), while serotypes 1 and 5 were undetected. Of 305 isolates from children <5 yrs, 60 (19.7%) were of PCV13 serotypes 19A, 19F, 3, 6B, and 23F (58/60 were 19A, 19F, or 3). We quantitated MLST-based lineages first detected during the post-PCV era (since 2002) that potentially arose through serotype-switching. The 7 predominant emergent post-PCV strain complexes included 23B/CC338, 15BC/CC3280, 19A/CC244, 4/CC439, 15A/CC156, 35B/CC156, and 15BC/CC156. These strains accounted for 332 isolates (6.2% of total) and were more frequently observed in children <5 yrs (17.7%; 54/305). Fifty-seven categories of recently emerged (in the post PCV7 period) putative serotype-switch variants were identified, accounting for 402 isolates. Many of these putative switch variants represented newly emerged resistant strains. Penicillin-nonsusceptibility (MICs > 0.12 μg/ml) was found among 22.4% (1193/5334) isolates, with higher penicillin MICs (2–8 μg/ml) found in 8.0% (425/5334) of isolates that were primarily (372/425, 87.5%) serotypes 35B and 19A. Most (792/1193, 66.4%) penicillin-nonsusceptible isolates were macrolide-resistant, 410 (34.4%) of which were erm gene positive and clindamycin-resistant. The proportion of macrolide-resistant isolates increased with increasing penicillin MICs; even isolates with reduced penicillin susceptibility (MIC = 0.06 μg/ml) were much more likely to be macrolide-resistant than basally penicillin-susceptible isolates (MIC < 0.03 μg/ml). The contribution of recombination to strain diversification was assessed through quantitating 35B/CC558-specific bioinformatic pipeline features among non-CC558 CCs and determining the sizes of gene replacements. Although IPD has decreased greatly and stabilized in the post-PCV13 era, the species continually generates recombinants that adapt to selective pressures exerted by vaccines and antimicrobials. These data serve as a baseline for monitoring future changes within each invasive serotype.
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Affiliation(s)
- Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Sopio Chochua
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Robert E Gertz
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Yuan Li
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Zhongya Li
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Benjamin J Metcalf
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jessica Ricaldi
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Theresa Tran
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Hollis Walker
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Tamara Pilishvili
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
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16
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Local outbreak of Streptococcus pneumoniae serotype 12F caused high morbidity and mortality among children and adults. Epidemiol Infect 2018; 146:1793-1796. [PMID: 30070189 DOI: 10.1017/s0950268818002133] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Pneumococcal serotype replacement is an important issue after the introduction of pneumococcal conjugate vaccine (PCV) in children. After the introduction of 13-valent PCV, the incidence of invasive pneumococcal diseases (IPD) caused by Streptococcus pneumoniae serotype 12F (Sp12F) have increased in some countries; however, an outbreak of Sp12F has not reported in the post-13-valent PCV era. We experienced a local outbreak of Sp12F during March through May 2016 in Tsuruoka city, Japan after the introduction of 13-valent PCV in 2013. The IPD patients were two children and seven adults, three of whom died with a rapid disease progress. Although the clear transmission route was not determined, eight of the nine patients (89%) had close contact with children, which suggests that transmitted colonisation of Sp12F among children and adults might be the source of transmission. Continuous monitoring of IPDs, along with the determination of pneumococcal serotypes, is warranted in the post-13-valent PCV era. New IPD control strategies may be needed if this fatal outbreak continues to occur.
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17
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Lu K, Marino NE, Russell D, Singareddy A, Zhang D, Hardi A, Kaar S, Puri V. Use of Short Message Service and Smartphone Applications in the Management of Surgical Patients: A Systematic Review. Telemed J E Health 2018; 24:406-414. [DOI: 10.1089/tmj.2017.0123] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Keyin Lu
- Saint Louis University School of Medicine, St. Louis, Missouri
- Epharmix Research Center, St. Louis, Missouri
| | - Nikolas E. Marino
- Saint Louis University School of Medicine, St. Louis, Missouri
- Epharmix Research Center, St. Louis, Missouri
| | - David Russell
- Saint Louis University School of Medicine, St. Louis, Missouri
- Epharmix Research Center, St. Louis, Missouri
| | - Aashray Singareddy
- Saint Louis University School of Medicine, St. Louis, Missouri
- Epharmix Research Center, St. Louis, Missouri
| | - Donald Zhang
- Saint Louis University School of Medicine, St. Louis, Missouri
- Epharmix Research Center, St. Louis, Missouri
| | - Angela Hardi
- Becker Medical Library, Washington University in Saint Louis School of Medicine, St. Louis, Missouri
| | - Scott Kaar
- Department of Orthopaedic Surgery, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Varun Puri
- Division of Cardiothoracic Surgery, Washington University in Saint Louis School of Medicine, St. Louis, Missouri
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Kambiré D, Soeters HM, Ouédraogo-Traoré R, Medah I, Sangaré L, Yaméogo I, Sawadogo G, Ouédraogo AS, Ouangraoua S, McGee L, Srinivasan V, Aké F, Congo-Ouédraogo M, Ky Ba A, Whitney CG, Novak RT, Van Beneden C. Early impact of 13-valent pneumococcal conjugate vaccine on pneumococcal meningitis-Burkina Faso, 2014-2015. J Infect 2017; 76:270-279. [PMID: 29253559 PMCID: PMC5821694 DOI: 10.1016/j.jinf.2017.12.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/22/2017] [Accepted: 12/04/2017] [Indexed: 01/01/2023]
Abstract
OBJECTIVES We evaluate early impact of 13-valent pneumococcal conjugate vaccine (PCV13) on pneumococcal meningitis in Burkina Faso. METHODS Nationwide surveillance gathered demographic/clinical information and cerebrospinal fluid (CSF) results for meningitis cases. Pneumococcal cases were confirmed by culture, polymerase chain reaction (PCR), or latex agglutination, and strains serotyped using PCR. We compared incidence (cases per 100,000) in the early post-PCV13 period (2014 and 2015) to average pre-PCV13 incidence (2011-2013). RESULTS In 2015, age-specific pneumococcal meningitis incidences were 8.7 (<1 year), 2.4 (1-4 years), 6.5 (5-14 years), and 2.6 (≥15 years). Compared to 2011-2013, PCV13-serotype incidence among all ages decreased by 32% (95%CI: 23%-39%), with significant decreases among children aged <1 year (76%; 95%CI: 64%-84%) and 1-4 years (58%, 95%CI: 40%-71%). Among all ages, incidence of PCV13 serotypes besides serotype 1 decreased (68%; 95%CI: 59%-75%), but serotype 1 incidence did not. Incidence of non-PCV13 serotypes also decreased (47%; 95%CI: 29%-60%). Among children aged <1 year, serotypes 12F/12A/12B/44/46 (17%), 1 (12%), and 5 (10%) predominated. CONCLUSIONS Following PCV13 introduction, PCV13-serotype meningitis incidence in young children significantly decreased. PCV13 impact on serotype 1 and disease in older children and adults requires continued monitoring.
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Affiliation(s)
- Dinanibè Kambiré
- Centre Hospitalier Universitaire Pédiatrique Charles De Gaulle, Ouagadougou, Burkina Faso.
| | - Heidi M Soeters
- Epidemic Intelligence Service, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA; National Center for Immunization and Respiratory Diseases, CDC, Atlanta, GA, USA.
| | | | - Isaïe Medah
- Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Lassana Sangaré
- Centre Hospitalier Universitaire-Yalgado Ouédraogo, Ouagadougou, Burkina Faso
| | | | | | | | | | - Lesley McGee
- National Center for Immunization and Respiratory Diseases, CDC, Atlanta, GA, USA
| | - Velusamy Srinivasan
- National Center for Immunization and Respiratory Diseases, CDC, Atlanta, GA, USA
| | - Flavien Aké
- Davycas International, Ouagadougou, Burkina Faso
| | | | - Absatou Ky Ba
- Laboratoire National de Santé Publique, Ouagadougou, Burkina Faso
| | - Cynthia G Whitney
- National Center for Immunization and Respiratory Diseases, CDC, Atlanta, GA, USA
| | - Ryan T Novak
- National Center for Immunization and Respiratory Diseases, CDC, Atlanta, GA, USA
| | - Chris Van Beneden
- National Center for Immunization and Respiratory Diseases, CDC, Atlanta, GA, USA
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19
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Eton V, Schroeter A, Kelly L, Kirlew M, Tsang RSW, Ulanova M. Epidemiology of invasive pneumococcal and Haemophilus influenzae diseases in Northwestern Ontario, Canada, 2010-2015. Int J Infect Dis 2017; 65:27-33. [PMID: 28951105 DOI: 10.1016/j.ijid.2017.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/10/2017] [Accepted: 09/15/2017] [Indexed: 10/18/2022] Open
Abstract
INTRODUCTION North American indigenous populations experience a high burden of invasive bacterial infections. Because Streptococcus pneumoniae and Haemophilus influenzae have multiple antigenic variants, the existing vaccines cannot prevent all cases. This study addresses the current epidemiology of invasive H. influenzae and pneumococcal disease (IPD) in a region of Northwestern Ontario, Canada with a relatively high (82%) indigenous population. METHODS Data were retrieved from a retrospective chart review at a hospital servicing a population of 29000 (82% indigenous), during January 2010-July 2015. RESULTS Ten cases of invasive H. influenzae disease and 37 cases of IPD were identified. The incidence of both in the study population (6.3 and 23.1/100000/year, respectively) exceeded national rates (1.6 and 9.0/100000/year). H. influenzae serotype a (Hia) was the most common (50%), followed by non-typeable H. influenzae (20%). In adults, 77% of IPD cases were caused by serotypes included in the 23-valent pneumococcal polysaccharide vaccine. All paediatric IPD cases were caused by serotypes not included in the 13-valent pneumococcal conjugate vaccine. The case-fatality rate was 10% for invasive H. influenzae and 2.7% for IPD. Most cases exhibited substantial co-morbidity. CONCLUSIONS In Northwestern Ontario, the incidence of invasive Hia disease exceeds that of H. influenzae type b (Hib) in the pre-Hib vaccine era. This provides strong support for the development of a new Hia vaccine. Improved pneumococcal vaccination of high-risk adults in the region is warranted.
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Affiliation(s)
- Vic Eton
- Northern Ontario School of Medicine, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada.
| | - Annette Schroeter
- Sioux Lookout Meno Ya Win Health Centre, Sioux Lookout, Ontario, Canada
| | - Len Kelly
- Sioux Lookout Meno Ya Win Health Centre, Sioux Lookout, Ontario, Canada
| | - Michael Kirlew
- Sioux Lookout Meno Ya Win Health Centre, Sioux Lookout, Ontario, Canada; Northern Ontario School of Medicine, Sioux Lookout, Ontario, Canada
| | - Raymond S W Tsang
- Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Marina Ulanova
- Northern Ontario School of Medicine, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada; Lakehead University, Thunder Bay, Ontario, Canada
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20
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Chaguza C, Cornick JE, Andam CP, Gladstone RA, Alaerts M, Musicha P, Peno C, Bar-Zeev N, Kamng'ona AW, Kiran AM, Msefula CL, McGee L, Breiman RF, Kadioglu A, French N, Heyderman RS, Hanage WP, Bentley SD, Everett DB. Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi. Vaccine 2017; 35:4594-4602. [PMID: 28711389 PMCID: PMC5571440 DOI: 10.1016/j.vaccine.2017.07.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 06/23/2017] [Accepted: 07/03/2017] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Pneumococcal infections cause a high death toll in Sub Saharan Africa (SSA) but the recently rolled out pneumococcal conjugate vaccines (PCV) will reduce the disease burden. To better understand the population impact of these vaccines, comprehensive analysis of large collections of pneumococcal isolates sampled prior to vaccination is required. Here we present a population genomic study of the invasive pneumococcal isolates sampled before the implementation of PCV13 in Malawi. MATERIALS AND METHODS We retrospectively sampled and whole genome sequenced 585 invasive isolates from 2004 to 2010. We determine the pneumococcal population genetic structure and assessed serotype prevalence, antibiotic resistance rates, and the occurrence of serotype switching. RESULTS Population structure analysis revealed 22 genetically distinct sequence clusters (SCs), which consisted of closely related isolates. Serotype 1 (ST217), a vaccine-associated serotype in clade SC2, showed highest prevalence (19.3%), and was associated with the highest MDR rate (81.9%) followed by serotype 12F, a non-vaccine serotype in clade SC10 with an MDR rate of 57.9%. Prevalence of serotypes was stable prior to vaccination although there was an increase in the PMEN19 clone, serotype 5 ST289, in clade SC1 in 2010 suggesting a potential undetected local outbreak. Coalescent analysis revealed recent emergence of the SCs and there was evidence of natural capsule switching in the absence of vaccine induced selection pressure. Furthermore, majority of the highly prevalent capsule-switched isolates were associated with acquisition of vaccine-targeted capsules. CONCLUSIONS This study provides descriptions of capsule-switched serotypes and serotypes with potential to cause serotype replacement post-vaccination such as 12F. Continued surveillance is critical to monitor these serotypes and antibiotic resistance in order to design better infection prevention and control measures such as inclusion of emerging replacement serotypes in future conjugate vaccines.
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Affiliation(s)
- Chrispin Chaguza
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Jennifer E Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Cheryl P Andam
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Maaike Alaerts
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Patrick Musicha
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Department of Biomedical Sciences, University of Malawi College of Medicine, Blantyre, Malawi
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Naor Bar-Zeev
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Arox W Kamng'ona
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Department of Biomedical Sciences, University of Malawi College of Medicine, Blantyre, Malawi
| | - Anmol M Kiran
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Department of Biomedical Sciences, University of Malawi College of Medicine, Blantyre, Malawi
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, USA
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, USA
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Division of Infection and Immunity, University College London, London, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephen D Bentley
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Dean B Everett
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.
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21
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Mahmud SM, Sinnock H, Mostaço-Guidolin LC, Pabla G, Wierzbowski AK, Bozat-Emre S. Long-term trends in invasive pneumococcal disease in Manitoba, Canada. Hum Vaccin Immunother 2017; 13:1884-1891. [PMID: 28494193 PMCID: PMC5557215 DOI: 10.1080/21645515.2017.1320006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/02/2017] [Accepted: 04/11/2017] [Indexed: 10/19/2022] Open
Abstract
Invasive pneumococcal disease (IPD) remains a significant public health problem in Manitoba, Canada although publically-funded pneumococcal conjugate (PCV7 and PCV13) and polysaccharide (PPV23) vaccination programs exist. We analyzed routine surveillance and administrative health data to examine trends in IPD rates as these vaccines were introduced. Data on all individuals with a laboratory-confirmed diagnosis of IPD between 2001 and 2014 were obtained from the provincial Communicable Diseases Surveillance database and linked with Manitoba's provincial immunization registry and physician and hospital databases. We calculated IPD incidence rates overall, by serotype and for different population subgroups defined by socio-demographic and clinical (e.g., chronic diseases, immune status) characteristics. Annual IPD incidence (95%CI) was 8.6 (8.2-9.1)/100,000 people during the study period (n = 1092), and rates were higher in recent years and in regions with predominately indigenous populations. Reduction in the incidence of serotypes included in PCV7 have been offset by rising rates of PCV13-only serotypes in children, and more recently by rising rates of PPV-only serotypes and non-vaccine serotypes among young children and older adults (≥ 65 years). Rates were 3 times higher in those with a chronic disease and highest (> 175-fold) among alcoholics, organ-transplant, and chronic kidney failure patients. The case fatality rate was 12.0% within 30 d of diagnosis. Despite the introduction of several vaccination programs, overall rates of IPD have not declined in Manitoba in the last decade, due to increase in incidence of non-PCV7 serotypes. A disproportionately high burden of disease impacts indigenous communities and people with chronic disease.
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Affiliation(s)
- Salaheddin M. Mahmud
- Department of Community Health Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Vaccine and Drug Evaluation Centre, Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Hasantha Sinnock
- Vaccine and Drug Evaluation Centre, Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Luiz C. Mostaço-Guidolin
- Department of Community Health Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Health, Seniors and Active Living, Epidemiology and Surveillance Unit, Government of Manitoba, Winnipeg, Manitoba, Canada
| | - Gurpreet Pabla
- Vaccine and Drug Evaluation Centre, Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Songul Bozat-Emre
- Department of Community Health Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Vaccine and Drug Evaluation Centre, Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Health, Seniors and Active Living, Epidemiology and Surveillance Unit, Government of Manitoba, Winnipeg, Manitoba, Canada
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22
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Impact of pneumococcal conjugate vaccine (PCV7 and PCV13) on pneumococcal invasive diseases in Italian children and insight into evolution of pneumococcal population structure. Vaccine 2017; 35:4587-4593. [PMID: 28716556 DOI: 10.1016/j.vaccine.2017.07.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/29/2017] [Accepted: 07/03/2017] [Indexed: 01/26/2023]
Abstract
BACKGROUND The use of PCV7 for children immunization was gradually implemented in the Italian regions starting from 2006 and was replaced by PCV13 in 2010-2011. In this study we aimed to assess the PCV impact on invasive pneumococcal diseases (IPD) incidence, serotype distribution and antibiotic resistance in Italian children under 5years old. METHODS All IPD cases in children from 5 Italian regions (Emilia-Romagna, Lombardia, A. P. Bolzano, A. P. Trento, and Piemonte) reported through the nationwide surveillance system during 2008-2014 were included in this study. Pneumococcal isolates were subjected to serotyping, antibiotic susceptibility testing, and clonal analysis according to standard methods. RESULTS During the study period overall IPD incidence decreased from 7.8 cases/100,000 inhabitants in 2008 to 3.0 cases/100,000 in 2014 (61% decrease, P<0.001). In particular, from 2008 to 2014, PCV7-type IPD decreased from 2.92 to 0.13 cases/100,000 inhabitants (95% decrease, P<0.001) while PCV13-non-PCV7 type IPD decreased from 3.2 to 0.89 cases/100,000 inhabitants (72% decrease, P=0.008). Conversely, non-vaccine serotype (NVS) IPD increased overtime, becoming more common than PCV13 serotype IPD in 2013-2014. Emergent NVS 24F and 12F were the most prevalent in 2014. Antibiotic resistance testing revealed an overall increasing trend in penicillin resistance, from 14% in 2008 to 23% in 2014. Erythromycin resistance showed a downward trend, from 38% in 2008 to 27% in 2014. While in 2008 PCV13 serotypes were the major responsible for antibiotic resistance, during the following years antimicrobial resistance due to NVS increased, mainly as a result of expansion of pre-existing clones. CONCLUSIONS Both PCVs led to a substantial decrease in vaccine-related IPD incidence in the children population. However NVS-related IPD increased, becoming the most prevalent in the last two-years period. Continuous surveillance is an essential tool to monitor evolution of pneumococcal population causing IPD in children.
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23
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Gladstone RA, Devine V, Jones J, Cleary D, Jefferies JM, Bentley SD, Faust SN, Clarke SC. Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK. Microb Genom 2017; 3:e000119. [PMID: 29026652 PMCID: PMC5628697 DOI: 10.1099/mgen.0.000119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 11/18/2022] Open
Abstract
Serotype replacement has been reported in carriage and disease after pneumococcal conjugate vaccine (PCV) introductions in the UK and globally. We previously described concurrent expansion and decline of sequence types associated with serotype replacement over 5 years following PCV introductions in the UK. Here we use whole-genome sequencing to fully characterise the population structure of pneumococcal isolates collected over seven winters encompassing PCV7 and PCV13 introductions in the UK, investigating the importance of lineages in serotype replacement. We analysed 672 pneumococcal genomes from colonised children of 4 years old or less. The temporal prevalence of 20 lineages, defined by hierarchical Bayesian analysis of population structure (BAPS), was assessed in the context of serotype replacement. Multiple serotypes were detected in the primary winter of sampling within three vaccine-type (VT) lineages BAPS4, BAPS10 and BAPS11, in which serotype replacement were observed. In contrast, serotype replacement was not seen in the remaining three VT lineages (BAPS1, BAPS13 and BAPS14), that expressed a single serotype (6B, 6A and 3, respectively) in the primary winter. One lineage, BAPS1 serotype 6B was undetectable in the population towards the end of the study period. The dynamics of serotype replacement, in this UK population, was preceded by the presence or absence of multiple serotypes within VT lineages, in the pre-PCV population. This observation could help predict which non-vaccine types (NVTs) may be involved in replacement in future PCV introductions here and elsewhere. It could further indicate whether any antibiotic resistance associated with the lineages is likely to be affected by replacement.
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Affiliation(s)
- Rebecca A. Gladstone
- Infection Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Vanessa Devine
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
| | - Jessica Jones
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
| | - David Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
| | - Johanna M. Jefferies
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
- Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | - Stephen D. Bentley
- Infection Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Saul N. Faust
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
- Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, UK
- NIHR Wellcome Trust Clinical Research, Manchester Royal Infirmary, Grafton St, Manchester M13 9WL, UK
| | - Stuart C. Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
- Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, UK
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24
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Kwambana-Adams BA, Asiedu-Bekoe F, Sarkodie B, Afreh OK, Kuma GK, Owusu-Okyere G, Foster-Nyarko E, Ohene SA, Okot C, Worwui AK, Okoi C, Senghore M, Otu JK, Ebruke C, Bannerman R, Amponsa-Achiano K, Opare D, Kay G, Letsa T, Kaluwa O, Appiah-Denkyira E, Bampoe V, Zaman SMA, Pallen MJ, D'Alessandro U, Mwenda JM, Antonio M. An outbreak of pneumococcal meningitis among older children (≥5 years) and adults after the implementation of an infant vaccination programme with the 13-valent pneumococcal conjugate vaccine in Ghana. BMC Infect Dis 2016; 16:575. [PMID: 27756235 PMCID: PMC5070171 DOI: 10.1186/s12879-016-1914-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/11/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND An outbreak of pneumococcal meningitis among non-infant children and adults occurred in the Brong-Ahafo region of Ghana between December 2015 and April 2016 despite the recent nationwide implementation of a vaccination programme for infants with the 13-valent pneumococcal conjugate vaccine (PCV13). METHODS Cerebrospinal fluid (CSF) specimens were collected from patients with suspected meningitis in the Brong-Ahafo region. CSF specimens were subjected to Gram staining, culture and rapid antigen testing. Quantitative PCR was performed to identify pneumococcus, meningococcus and Haemophilus influenzae. Latex agglutination and molecular serotyping were performed on samples. Antibiogram and whole genome sequencing were performed on pneumococcal isolates. RESULTS Eight hundred eighty six patients were reported with suspected meningitis in the Brong-Ahafo region during the period of the outbreak. In the epicenter district, the prevalence was as high as 363 suspected cases per 100,000 people. Over 95 % of suspected cases occurred in non-infant children and adults, with a median age of 20 years. Bacterial meningitis was confirmed in just under a quarter of CSF specimens tested. Pneumococcus, meningococcus and Group B Streptococcus accounted for 77 %, 22 % and 1 % of confirmed cases respectively. The vast majority of serotyped pneumococci (80 %) belonged to serotype 1. Most of the pneumococcal isolates tested were susceptible to a broad range of antibiotics, with the exception of two pneumococcal serotype 1 strains that were resistant to both penicillin and trimethoprim-sulfamethoxazole. All sequenced pneumococcal serotype 1 strains belong to Sequence Type (ST) 303 in the hypervirulent ST217 clonal complex. CONCLUSION The occurrence of a pneumococcal serotype 1 meningitis outbreak three years after the introduction of PCV13 is alarming and calls for strengthening of meningitis surveillance and a re-evaluation of the current vaccination programme in high risk countries.
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Affiliation(s)
- Brenda Anna Kwambana-Adams
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | | | | | | | | | | | - Ebenezer Foster-Nyarko
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | | | | | - Archibald Kwame Worwui
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Catherine Okoi
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Madikay Senghore
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Jacob Kweku Otu
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Chinelo Ebruke
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Richard Bannerman
- Brong Ahafo Regional Health Directorate, Sunyani, Brong Ahafo, Ghana
| | | | - David Opare
- National Public Health Reference Laboratory, Ghana Health Service, Accra, Ghana
| | - Gemma Kay
- Microbiology and Infection Unit, Warwick Medical School, Warwick, UK
| | - Timothy Letsa
- Brong Ahafo Regional Health Directorate, Sunyani, Brong Ahafo, Ghana
| | | | | | | | - Syed M A Zaman
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, Warwick, UK
| | - Umberto D'Alessandro
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia.,London School of Hygiene and Tropical Medicine, London, UK.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Jason M Mwenda
- WHO Regional Office for Africa, Brazzaville, Republic of Congo
| | - Martin Antonio
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia. .,Microbiology and Infection Unit, Warwick Medical School, Warwick, UK. .,London School of Hygiene and Tropical Medicine, London, UK.
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