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Liu J, Garcia Bardales PF, Islam K, Jarju S, Juma J, Mhango C, Naumanga Q, Qureshi S, Sonye C, Ahmed N, Aziz F, Bhuiyan MTR, Charles M, Cunliffe NA, Abdou M, Galagan SR, Gitteh E, Guindo I, Jahangir Hossain M, Jabang AMJ, Jere KC, Kawonga F, Keita M, Keita NY, Kotloff KL, Shapiama Lopez WV, Munga S, Paredes Olortegui M, Omore R, Pavlinac PB, Qadri F, Qamar FN, Azadul Alam Raz SM, Riziki L, Schiaffino F, Stroup S, Traore SN, Pinedo Vasquez T, Yousafzai MT, Antonio M, Cornick JE, Kabir F, Khanam F, Kosek MN, Ochieng JB, Platts-Mills JA, Tennant SM, Houpt ER. Shigella Detection and Molecular Serotyping With a Customized TaqMan Array Card in the Enterics for Global Health (EFGH): Shigella Surveillance Study. Open Forum Infect Dis 2024; 11:S34-S40. [PMID: 38532960 PMCID: PMC10962731 DOI: 10.1093/ofid/ofad574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Background Quantitative polymerase chain reaction (qPCR) targeting ipaH has been proven to be highly efficient in detecting Shigella in clinical samples compared to culture-based methods, which underestimate Shigella burden by 2- to 3-fold. qPCR assays have also been developed for Shigella speciation and serotyping, which is critical for both vaccine development and evaluation. Methods The Enterics for Global Health (EFGH) Shigella surveillance study will utilize a customized real-time PCR-based TaqMan Array Card (TAC) interrogating 82 targets, for the detection and differentiation of Shigella spp, Shigella sonnei, Shigella flexneri serotypes, other diarrhea-associated enteropathogens, and antimicrobial resistance (AMR) genes. Total nucleic acid will be extracted from rectal swabs or stool samples, and assayed on TAC. Quantitative analysis will be performed to determine the likely attribution of Shigella and other particular etiologies of diarrhea using the quantification cycle cutoffs derived from previous studies. The qPCR results will be compared to conventional culture, serotyping, and phenotypic susceptibility approaches in EFGH. Conclusions TAC enables simultaneous detection of diarrheal etiologies, the principal pathogen subtypes, and AMR genes. The high sensitivity of the assay enables more accurate estimation of Shigella-attributed disease burden, which is critical to informing policy and in the design of future clinical trials.
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Affiliation(s)
- Jie Liu
- School of Public Health, Qingdao University, Qingdao, China
| | | | - Kamrul Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Jane Juma
- Centre pour le Développement des Vaccins du Mali (CVD-Mali), Bamako, Mali
| | | | - Queen Naumanga
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Sonia Qureshi
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Catherine Sonye
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Naveed Ahmed
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Fatima Aziz
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Md Taufiqur Rahman Bhuiyan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mary Charles
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | - Nigel A Cunliffe
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
| | - Mahamadou Abdou
- Centre pour le Développement des Vaccins du Mali (CVD-Mali), Bamako, Mali
| | - Sean R Galagan
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Ensa Gitteh
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ibrehima Guindo
- Centre pour le Développement des Vaccins du Mali (CVD-Mali), Bamako, Mali
| | - M Jahangir Hossain
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Abdoulie M J Jabang
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Khuzwayo C Jere
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
- Department of Medical Laboratory Sciences, School of Life Sciences and Health Professions, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Flywell Kawonga
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | - Mariama Keita
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Stephen Munga
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Richard Omore
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Patricia B Pavlinac
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Farah Naz Qamar
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - S M Azadul Alam Raz
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Laura Riziki
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Francesca Schiaffino
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
- Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Suzanne Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | | | | | - Martin Antonio
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jennifer E Cornick
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
| | - Furqan Kabir
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Farhana Khanam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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Lo SW, Mellor K, Cohen R, Alonso AR, Belman S, Kumar N, Hawkins PA, Gladstone RA, von Gottberg A, Veeraraghavan B, Ravikumar KL, Kandasamy R, Pollard SAJ, Saha SK, Bigogo G, Antonio M, Kwambana-Adams B, Mirza S, Shakoor S, Nisar I, Cornick JE, Lehmann D, Ford RL, Sigauque B, Turner P, Moïsi J, Obaro SK, Dagan R, Diawara I, Skoczyńska A, Wang H, Carter PE, Klugman KP, Rodgers G, Breiman RF, McGee L, Bentley SD, Almagro CM, Varon E, Corso A, Davydov A, Maguire A, Kiran A, Moiane B, Beall B, Zhao C, Aanensen D, Everett D, Faccone D, Foster-Nyarko E, Bojang E, Egorova E, Voropaeva E, Sampane-Donkor E, Sadowy E, Nagaraj G, Mucavele H, Belabbès H, Elmdaghri N, Verani J, Keenan J, Lees J, N Nair Thulasee Bhai J, Ndlangisa K, Zerouali K, Bentley L, Titov L, De Gouveia L, Alaerts M, Ip M, de Cunto Brandileone MC, Hasanuzzaman M, Paragi M, Nurse-Lucas M, du Plessis M, Ali M, Croucher N, Wolter N, Givon-Lavi N, Porat N, Köseoglu Eser Ö, Ho PL, Eberechi Akpaka P, Gagetti P, Tientcheu PE, Law P, Benisty R, Mostowy R, Malaker R, Grassi Almeida SC, Doiphode S, Madhi S, Devi Sekaran S, Clarke S, Srifuengfung S, Nzenze S, Kastrin T, Ochoa T, Hryniewicz W, Urban Y. Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study. Lancet Microbe 2022; 3:e735-e743. [PMID: 35985351 PMCID: PMC9519462 DOI: 10.1016/s2666-5247(22)00158-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Serotype 24F is one of the emerging pneumococcal serotypes after the introduction of pneumococcal conjugate vaccine (PCV). We aimed to identify lineages driving the increase of serotype 24F in France and place these findings into a global context. METHODS Whole-genome sequencing was performed on a collection of serotype 24F pneumococci from asymptomatic colonisation (n=229) and invasive disease (n=190) isolates among individuals younger than 18 years in France, from 2003 to 2018. To provide a global context, we included an additional collection of 24F isolates in the Global Pneumococcal Sequencing (GPS) project database for analysis. A Global Pneumococcal Sequence Cluster (GPSC) and a clonal complex (CC) were assigned to each genome. Phylogenetic, evolutionary, and spatiotemporal analysis were conducted using the same 24F collection and supplemented with a global collection of genomes belonging to the lineage of interest from the GPS project database (n=25 590). FINDINGS Serotype 24F was identified in numerous countries mainly due to the clonal spread of three lineages: GPSC10 (CC230), GPSC16 (CC156), and GPSC206 (CC7701). GPSC10 was the only multidrug-resistant lineage. GPSC10 drove the increase in 24F in France and had high invasive disease potential. The international dataset of GPSC10 (n=888) revealed that this lineage expressed 16 other serotypes, with only six included in 13-valent PCV (PCV13). All serotype 24F isolates were clustered in a single clade within the GPSC10 phylogeny and long-range transmissions were detected from Europe to other continents. Spatiotemporal analysis showed GPSC10-24F took 3-5 years to spread across France and a rapid change of serotype composition from PCV13 serotype 19A to 24F during the introduction of PCV13 was observed in neighbouring country Spain. INTERPRETATION Our work reveals that GPSC10 alone is a challenge for serotype-based vaccine strategy. More systematic investigation to identify lineages like GPSC10 will better inform and improve next-generation preventive strategies against pneumococcal diseases. FUNDING Bill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control and Prevention.
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Affiliation(s)
- Stephanie W Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK,Correspondence to: Dr Stephanie W Lo, Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kate Mellor
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Robert Cohen
- ACTIV, Association Clinique et Thérapeutique Infantile du Val-de-Marne, Saint Maur-des-Fossés, France,GPIP, Groupe de Pathologie Infectieuse Pédiatrique, Paris, France,AFPA, Association Française de Pédiatrie Ambulatoire, Saint-Germain-en-Laye, France,Université Paris Est, IMRB-GRC GEMINI, Créteil, France,Clinical Research Center, Centre Hospitalier Intercommunal de Créteil, Créteil, France,Unité Court Séjour, Petits nourrissons, Service de Néonatalogie, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Alba Redin Alonso
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain,Spanish Network of Epidemiology and Public Health, CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Sophie Belman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Narender Kumar
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | | | - Rebecca A Gladstone
- Department of Biostatistics, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Rama Kandasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Churchill Hospital, Oxford, UK,NIHR Oxford Biomedical Research Centre, Oxford, UK,School of Women and Children's Health, University of New South Wales, Sydney, NSW, Australia,Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Sir Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Churchill Hospital, Oxford, UK,NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | - 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
| | - Brenda Kwambana-Adams
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Shaper Mirza
- Microbiology and Immunology Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Sadia Shakoor
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Jennifer E Cornick
- Malawi-Liverpool-Wellcome-Trust, Blantyre, Malawi,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Deborah Lehmann
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Rebecca L Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Betuel Sigauque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Stephen K Obaro
- Division of Pediatric Infectious Disease, University of Nebraska Medical Center Omaha, Omaha, NE, USA,International Foundation against Infectious Diseases in Nigeria, Abuja, Nigeria
| | - Ron Dagan
- Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Idrissa Diawara
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco,National Reference Laboratory, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Anna Skoczyńska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Hui Wang
- Peking University People ‘s Hospital, Beijing, China
| | - Philip E Carter
- Institute of Environmental Science and Research Limited, Kenepuru Science Centre, Porirua, New Zealand
| | - Keith P Klugman
- Rollins School Public Health, Emory University, Atlanta, GA, USA
| | - Gail Rodgers
- Pneumonia Program, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Robert F Breiman
- Rollins School Public Health, Emory University, Atlanta, GA, USA,Emory Global Health Institute, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Carmen Muñoz Almagro
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain,Spanish Network of Epidemiology and Public Health, CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Emmanuelle Varon
- National Reference Center for Pneumococci, Centre Hospitalier Intercommunal de Créteil, Créteil, France
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3
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Chaguza C, Ebruke C, Senghore M, Lo SW, Tientcheu PE, Gladstone RA, Tonkin-Hill G, Cornick JE, Yang M, Worwui A, McGee L, Breiman RF, Klugman KP, Kadioglu A, Everett DB, Mackenzie G, Croucher NJ, Roca A, Kwambana-Adams BA, Antonio M, Bentley SD. Comparative Genomics of Disease and Carriage Serotype 1 Pneumococci. Genome Biol Evol 2022; 14:evac052. [PMID: 35439297 PMCID: PMC9048925 DOI: 10.1093/gbe/evac052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2022] [Indexed: 11/14/2022] Open
Abstract
The isolation of Streptococcus pneumoniae serotypes in systemic tissues of patients with invasive disease versus the nasopharynx of healthy individuals with asymptomatic carriage varies widely. Some serotypes are hyper-invasive, particularly serotype 1, but the underlying genetics remain poorly understood due to the rarity of carriage isolates, reducing the power of comparison with invasive isolates. Here, we use a well-controlled genome-wide association study to search for genetic variation associated with invasiveness of serotype 1 pneumococci from a serotype 1 endemic setting in Africa. We found no consensus evidence that certain genomic variation is overrepresented among isolates from patients with invasive disease than asymptomatic carriage. Overall, the genomic variation explained negligible phenotypic variability, suggesting a minimal effect on the disease status. Furthermore, changes in lineage distribution were seen with lineages replacing each other over time, highlighting the importance of continued pathogen surveillance. Our findings suggest that the hyper-invasiveness is an intrinsic property of the serotype 1 strains, not specific for a "disease-associated" subpopulation disproportionately harboring unique genomic variation.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Darwin College, University of Cambridge, Silver Street, Cambridge, UK
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Chinelo Ebruke
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Madikay Senghore
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephanie W. Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Peggy-Estelle Tientcheu
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Rebecca A. Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Gerry Tonkin-Hill
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jennifer E. Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Archibald Worwui
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F. Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Keith P. Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Dean B. Everett
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Grant Mackenzie
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Murdoch Children’s Research Institute, Parkville, Melbourne, VIC, Australia
- London School of Hygiene & Tropical Medicine, London, UK
| | - Nicholas J. Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Anna Roca
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- London School of Hygiene & Tropical Medicine, London, UK
| | - Brenda A. Kwambana-Adams
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Martin Antonio
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- London School of Hygiene & Tropical Medicine, London, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
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4
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Lo SW, Gladstone RA, van Tonder AJ, Du Plessis M, Cornick JE, Hawkins PA, Madhi SA, Nzenze SA, Kandasamy R, Ravikumar KL, Elmdaghri N, Kwambana-Adams B, Almeida SCG, Skoczynska A, Egorova E, Titov L, Saha SK, Paragi M, Everett DB, Antonio M, Klugman KP, Li Y, Metcalf BJ, Beall B, McGee L, Breiman RF, Bentley SD, von Gottberg A. A mosaic tetracycline resistance gene tet(S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa. J Antimicrob Chemother 2021; 75:512-520. [PMID: 31789384 PMCID: PMC7021099 DOI: 10.1093/jac/dkz477] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/26/2019] [Accepted: 10/16/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We reported tet(S/M) in Streptococcus pneumoniae and investigated its temporal spread in relation to nationwide clinical interventions. METHODS We whole-genome sequenced 12 254 pneumococcal isolates from 29 countries on an Illumina HiSeq sequencer. Serotype, multilocus ST and antibiotic resistance were inferred from genomes. An SNP tree was built using Gubbins. Temporal spread was reconstructed using a birth-death model. RESULTS We identified tet(S/M) in 131 pneumococcal isolates and none carried other known tet genes. Tetracycline susceptibility testing results were available for 121 tet(S/M)-positive isolates and all were resistant. A majority (74%) of tet(S/M)-positive isolates were from South Africa and caused invasive diseases among young children (59% HIV positive, where HIV status was available). All but two tet(S/M)-positive isolates belonged to clonal complex (CC) 230. A global phylogeny of CC230 (n=389) revealed that tet(S/M)-positive isolates formed a sublineage predicted to exhibit resistance to penicillin, co-trimoxazole, erythromycin and tetracycline. The birth-death model detected an unrecognized outbreak of this sublineage in South Africa between 2000 and 2004 with expected secondary infections (effective reproductive number, R) of ∼2.5. R declined to ∼1.0 in 2005 and <1.0 in 2012. The declining epidemic could be related to improved access to ART in 2004 and introduction of pneumococcal conjugate vaccine (PCV) in 2009. Capsular switching from vaccine serotype 14 to non-vaccine serotype 23A was observed within the sublineage. CONCLUSIONS The prevalence of tet(S/M) in pneumococci was low and its dissemination was due to an unrecognized outbreak of CC230 in South Africa. Capsular switching in this MDR sublineage highlighted its potential to continue to cause disease in the post-PCV13 era.
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Affiliation(s)
- Stephanie W Lo
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Andries J van Tonder
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Mignon Du Plessis
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jennifer E Cornick
- Malawi Liverpool Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi.,Institute of Infection & Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Paulina A Hawkins
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan A Nzenze
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Rama Kandasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK
| | - K L Ravikumar
- Department of Microbiology, Kempegowda Institute of Medical Sciences Hospital & Research Centre, Bangalore, India
| | - Naima Elmdaghri
- Department of Microbiology, Faculty of Medicine and Pharmacy, B.P. 9154, Hassan II University of Casablanca, Casablanca, Morocco.,Bacteriology-Virology and Hospital Hygiene Laboratory, University Hospital Centre Ibn Rochd, Casablanca, Morocco
| | - 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 and Tropical Medicine, Fajara, The Gambia
| | - Samanta Cristine Grassi Almeida
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz (IAL), São Paulo, Brazil
| | - Anna Skoczynska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Ekaterina Egorova
- Laboratory of Clinical Microbiology and Biotechnology, Moscow Research Institute for Epidemiology and Microbiology, Moscow, Russian Federation
| | - Leonid Titov
- Laboratory of Clinical and Experimental Microbiology, The Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Samir K Saha
- Department of Microbiology, Dhaka Shishu (Children's) Hospital, Child Health Research Foundation, Dhaka, Bangladesh
| | - Metka Paragi
- Department for Public Health Microbiology, National Laboratory of Health, Environment and Food, Maribor, Slovenia
| | - Dean B Everett
- Malawi Liverpool Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi.,University of Edinburgh, The Queens Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit, The Gambia at The London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Keith P Klugman
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.,Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Yuan Li
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Benjamin J Metcalf
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.,Emory Global Health Institute, Emory University, Atlanta, GA 30322, USA
| | - Stephen D Bentley
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anne von Gottberg
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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5
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Bennett JC, Hetrich MK, Garcia Quesada M, Sinkevitch JN, Deloria Knoll M, Feikin DR, Zeger SL, Kagucia EW, Cohen AL, Ampofo K, Brandileone MCC, Bruden D, Camilli R, Castilla J, Chan G, Cook H, Cornick JE, Dagan R, Dalby T, Danis K, de Miguel S, De Wals P, Desmet S, Georgakopoulou T, Gilkison C, Grgic-Vitek M, Hammitt LL, Hilty M, Ho PL, Jayasinghe S, Kellner JD, Kleynhans J, Knol MJ, Kozakova J, Kristinsson KG, Ladhani SN, MacDonald L, Mackenzie GA, Mad’arová L, McGeer A, Mereckiene J, Morfeldt E, Mungun T, Muñoz-Almagro C, Nuorti JP, Paragi M, Pilishvili T, Puentes R, Saha SK, Sahu Khan A, Savrasova L, Scott JA, Skoczyńska A, Suga S, van der Linden M, Verani JR, von Gottberg A, Winje BA, Yildirim I, Zerouali K, Hayford K. Changes in Invasive Pneumococcal Disease Caused by Streptococcus pneumoniae Serotype 1 Following Introduction of PCV10 and PCV13: Findings from the PSERENADE Project. Microorganisms 2021; 9:microorganisms9040696. [PMID: 33801760 PMCID: PMC8066231 DOI: 10.3390/microorganisms9040696] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 11/17/2022] Open
Abstract
Streptococcus pneumoniae serotype 1 (ST1) was an important cause of invasive pneumococcal disease (IPD) globally before the introduction of pneumococcal conjugate vaccines (PCVs) containing ST1 antigen. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project gathered ST1 IPD surveillance data from sites globally and aimed to estimate PCV10/13 impact on ST1 IPD incidence. We estimated ST1 IPD incidence rate ratios (IRRs) comparing the pre-PCV10/13 period to each post-PCV10/13 year by site using a Bayesian multi-level, mixed-effects Poisson regression and all-site IRRs using a linear mixed-effects regression (N = 45 sites). Following PCV10/13 introduction, the incidence rate (IR) of ST1 IPD declined among all ages. After six years of PCV10/13 use, the all-site IRR was 0.05 (95% credibility interval 0.04–0.06) for all ages, 0.05 (0.04–0.05) for <5 years of age, 0.08 (0.06–0.09) for 5–17 years, 0.06 (0.05–0.08) for 18–49 years, 0.06 (0.05–0.07) for 50–64 years, and 0.05 (0.04–0.06) for ≥65 years. PCV10/13 use in infant immunization programs was followed by a 95% reduction in ST1 IPD in all ages after approximately 6 years. Limited data availability from the highest ST1 disease burden countries using a 3 + 0 schedule constrains generalizability and data from these settings are needed.
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Affiliation(s)
- Julia C. Bennett
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
- Correspondence: (J.C.B.); (M.D.K.)
| | - Marissa K. Hetrich
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
| | - Maria Garcia Quesada
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
| | - Jenna N. Sinkevitch
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
| | - Maria Deloria Knoll
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
- Correspondence: (J.C.B.); (M.D.K.)
| | | | - Scott L. Zeger
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
| | - Eunice W. Kagucia
- KEMRI-Wellcome Trust Research Programme, Epidemiology and Demography Department, Centre for Geographic Medicine-Coast, P.O. Box 230-80108 Kilifi, Kenya; (E.W.K.); (J.A.S.)
| | - Adam L. Cohen
- World Health Organization, 1202 Geneva, Switzerland;
| | - Krow Ampofo
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA;
| | - Maria-Cristina C. Brandileone
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz (IAL), São Paulo 01246-902, Brazil;
| | - Dana Bruden
- Arctic Investigations Program, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Anchorage, AK 99508, USA;
| | - Romina Camilli
- Department of Infectious Diseases, Italian National Institute of Health (Istituto Superiore di Sanità, ISS), 00161 Rome, Italy;
| | - Jesús Castilla
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain; (J.C.); (C.M.-A.)
- Instituto de Salud Pública de Navarra—IdiSNA, 31003 Pamplona, Navarra, Spain
| | - Guanhao Chan
- Singapore Ministry of Health, Communicable Diseases Division, Singapore 308442, Singapore;
| | - Heather Cook
- Centre for Disease Control, Department of Health and Community Services, Darwin, NT 8000, Australia;
| | - Jennifer E. Cornick
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK;
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Chichiri, P.O. Box 30096 Blantyre, Malawi
| | - Ron Dagan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel;
| | - Tine Dalby
- Bacteria, Parasites and Fungi, Statens Serum Institut, DK-2300 Copenhagen, Denmark;
| | - Kostas Danis
- Santé Publique France, the French National Public Health Agency, Saint Maurice CEDEX, 94415 Paris, France;
| | - Sara de Miguel
- Epidemiology Department, Dirección General de Salud Pública, 28009 Madrid, Spain;
| | - Philippe De Wals
- Department of Social and Preventive Medicine, Laval University, Québec, QC G1V 0A6, Canada;
| | - Stefanie Desmet
- Department of Microbiology, Immunology and Transplantation, KU Leuven, BE-3000 Leuven, Belgium;
- National Reference Centre for Streptococcus Pneumoniae, University Hospitals Leuven, 3000 Leuven, Belgium
| | | | - Charlotte Gilkison
- Epidemiology Team, Institute of Environmental Science and Research, Porirua, Wellington 5240, New Zealand;
| | - Marta Grgic-Vitek
- Communicable Diseases Centre, National Institute of Public Health, 1000 Ljubljana, Slovenia;
| | - Laura L. Hammitt
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
- KEMRI-Wellcome Trust Research Programme, Epidemiology and Demography Department, Centre for Geographic Medicine-Coast, P.O. Box 230-80108 Kilifi, Kenya; (E.W.K.); (J.A.S.)
| | - Markus Hilty
- Swiss National Reference Centre for Invasive Pneumococci, Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland;
| | - Pak-Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China;
| | - Sanjay Jayasinghe
- National Centre for Immunisation Research and Surveillance and Discipline of Child and Adolescent Health, Children’s Hospital Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia;
| | - James D. Kellner
- Department of Pediatrics, University of Calgary, and Alberta Health Services, Calgary, AB T3B 6A8, Canada;
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa; (J.K.); (A.v.G.)
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Mirjam J. Knol
- National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands;
| | - Jana Kozakova
- National Institute of Public Health (NIPH), 100 42 Praha, Czech Republic;
| | - Karl G. Kristinsson
- Department of Clinical Microbiology, Landspitali—The National University Hospital, Hringbraut, 101 Reykjavik, Iceland;
| | - Shamez N. Ladhani
- Immunisation and Countermeasures Division, Public Health England, London NW9 5EQ, UK;
| | | | - Grant A. Mackenzie
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London WC1E 7HT, UK;
- Medical Research Council Unit the Gambia at London School of Hygiene & Tropical Medicine, P.O. Box 273 Banjul, The Gambia
- New Vaccines Group, Murdoch Children’s Research Institute, Parkville, Melbourne, VIC 3052, Australia
| | - Lucia Mad’arová
- National Reference Centre for Pneumococcal and Haemophilus Diseases, Regional Authority of Public Health, 975 56 Banská Bystrica, Slovakia;
| | - Allison McGeer
- Toronto Invasive Bacterial Diseases Network, Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Jolita Mereckiene
- HSE Health Protection Surveillance Centre, Mountjoy, Dublin D01 A4A3, Ireland;
| | - Eva Morfeldt
- Department of Microbiology, Public Health Agency of Sweden, 171 82 Solna, Sweden;
| | - Tuya Mungun
- National Center of Communicable Diseases (NCCD), Ministry of Health, Bayanzurkh District, Ulaanbaatar 13336, Mongolia;
| | - Carmen Muñoz-Almagro
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain; (J.C.); (C.M.-A.)
- Medicine Department, Universitat Internacional de Catalunya, 08017 Barcelona, Spain
- Molecular Microbiology Department, Hospital Sant Joan de Déu Research Institute, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - J. Pekka Nuorti
- Department of Health Security, Finnish Institute for Health and Welfare, 00271 Helsinki, Finland;
- Health Sciences Unit, Faculty of Social Sciences, University of Tampere, 33100 Tampere, Finland
| | - Metka Paragi
- Centre for Medical Microbiology, National Laboratory of Health, Environment and Food, 2000 Maribor, Slovenia;
| | - Tamara Pilishvili
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (T.P.); (J.R.V.)
| | - Rodrigo Puentes
- Instituto de Salud Pública de Chile, Santiago 7780050, Santiago Metropolitan, Chile;
| | - Samir K. Saha
- Child Health Research Foundation, Dhaka 1207, Bangladesh;
| | | | - Larisa Savrasova
- Centre for Disease Prevention and Control of Latvia, 1005 Riga, Latvia;
- Doctoral Studies Department, Riga Stradinš University, 1007 Riga, Latvia
| | - J. Anthony Scott
- KEMRI-Wellcome Trust Research Programme, Epidemiology and Demography Department, Centre for Geographic Medicine-Coast, P.O. Box 230-80108 Kilifi, Kenya; (E.W.K.); (J.A.S.)
| | - Anna Skoczyńska
- National Reference Centre for Bacterial Meningitis, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Shigeru Suga
- Infectious Disease Center and Department of Clinical Research, National Hospital Organization Mie Hospital, Tsu, Mie 514-0125, Japan;
| | - Mark van der Linden
- National Reference Center for Streptococci, Department of Medical Microbiology, University Hospital RWTH Aachen, 52074 Aachen, Germany;
| | - Jennifer R. Verani
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (T.P.); (J.R.V.)
- Centers for Disease Control and Prevention (CDC), Center for Global Health (CGH), Division of Global Health Protection (DGHP), P.O. Box 606-00621 Nairobi, Kenya
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa; (J.K.); (A.v.G.)
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Braamfontein, Johannesburg 2000, South Africa
| | - Brita A. Winje
- Department of Infection Control and Vaccine, Norwegian Institute of Public Health, 0456 Oslo, Norway;
| | - Inci Yildirim
- Department of Pediatrics, Yale New Haven Children’s Hospital, New Haven, CT 06504, USA;
| | - Khalid Zerouali
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca 20250, Morocco;
- Department of Microbiology, Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, Casablanca 20000, Morocco
| | - Kyla Hayford
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (M.K.H.); (M.G.Q.); (J.N.S.); (S.L.Z.); (L.L.H.); (K.H.)
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6
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Chaguza C, Heinsbroek E, Gladstone RA, Tafatatha T, Alaerts M, Peno C, Cornick JE, Musicha P, Bar-Zeev N, Kamng'ona A, Kadioglu A, McGee L, Hanage WP, Breiman RF, Heyderman RS, French N, Everett DB, Bentley SD. Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data. Clin Infect Dis 2021; 70:1294-1303. [PMID: 31094423 PMCID: PMC7768739 DOI: 10.1093/cid/ciz404] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/15/2019] [Indexed: 11/14/2022] Open
Abstract
Background Pneumococcal conjugate vaccines (PCVs) have reduced pneumococcal diseases globally. Pneumococcal genomic surveys elucidate PCV effects on population structure but are rarely conducted in low-income settings despite the high disease burden. Methods We undertook whole-genome sequencing (WGS) of 660 pneumococcal isolates collected through surveys from healthy carriers 2 years from 13-valent PCV (PCV13) introduction and 1 year after rollout in northern Malawi. We investigated changes in population structure, within-lineage serotype dynamics, serotype diversity, and frequency of antibiotic resistance (ABR) and accessory genes. Results In children <5 years of age, frequency and diversity of vaccine serotypes (VTs) decreased significantly post-PCV, but no significant changes occurred in persons ≥5 years of age. Clearance of VT serotypes was consistent across different genetic backgrounds (lineages). There was an increase of nonvaccine serotypes (NVTs)—namely 7C, 15B/C, and 23A—in children <5 years of age, but 28F increased in both age groups. While carriage rates have been recently shown to remain stable post-PCV due to replacement serotypes, there was no change in diversity of NVTs. Additionally, frequency of intermediate-penicillin-resistant lineages decreased post-PCV. Although frequency of ABR genes remained stable, other accessory genes, especially those associated with mobile genetic element and bacteriocins, showed changes in frequency post-PCV. Conclusions We demonstrate evidence of significant population restructuring post-PCV driven by decreasing frequency of vaccine serotypes and increasing frequency of few NVTs mainly in children under 5. Continued surveillance with WGS remains crucial to fully understand dynamics of the residual VTs and replacement NVT serotypes post-PCV.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Darwin College, University of Cambridge, Silver Street, Cambridge
| | - Ellen Heinsbroek
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,HIV and STI Department, National Infection Service, Public Health England, London, United Kingdom
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge
| | - Terence Tafatatha
- Malawi Epidemiology Intervention Research Unit (formerly KPS), Chilumba
| | - Maaike Alaerts
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Center of Medical Genetics, University of Antwerp, Belgium
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, United Kingdom
| | - Jennifer E Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre
| | - Patrick Musicha
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.,Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Naor Bar-Zeev
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Arox Kamng'ona
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Department of Biomedical Sciences, University of Malawi, College of Medicine, Blantyre
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Division of Infection and Immunity, University College London, United Kingdom
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre.,Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, United Kingdom
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom.,Department of Pathology, University of Cambridge, United Kingdom
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7
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Chaguza C, Yang M, Cornick JE, du Plessis M, Gladstone RA, Kwambana-Adams BA, Lo SW, Ebruke C, Tonkin-Hill G, Peno C, Senghore M, Obaro SK, Ousmane S, Pluschke G, Collard JM, Sigaùque B, French N, Klugman KP, Heyderman RS, McGee L, Antonio M, Breiman RF, von Gottberg A, Everett DB, Kadioglu A, Bentley SD. Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism. Commun Biol 2020; 3:559. [PMID: 33033372 PMCID: PMC7545184 DOI: 10.1038/s42003-020-01290-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/11/2020] [Indexed: 12/19/2022] Open
Abstract
Hyper-virulent Streptococcus pneumoniae serotype 1 strains are endemic in Sub-Saharan Africa and frequently cause lethal meningitis outbreaks. It remains unknown whether genetic variation in serotype 1 strains modulates tropism into cerebrospinal fluid to cause central nervous system (CNS) infections, particularly meningitis. Here, we address this question through a large-scale linear mixed model genome-wide association study of 909 African pneumococcal serotype 1 isolates collected from CNS and non-CNS human samples. By controlling for host age, geography, and strain population structure, we identify genome-wide statistically significant genotype-phenotype associations in surface-exposed choline-binding (P = 5.00 × 10-08) and helicase proteins (P = 1.32 × 10-06) important for invasion, immune evasion and pneumococcal tropism to CNS. The small effect sizes and negligible heritability indicated that causation of CNS infection requires multiple genetic and other factors reflecting a complex and polygenic aetiology. Our findings suggest that certain pathogen genetic variation modulate pneumococcal survival and tropism to CNS tissue, and therefore, virulence for meningitis.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Darwin College, University of Cambridge, Silver Street, Cambridge, UK.
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jennifer E Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Brenda A Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Stephanie W Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Chinelo Ebruke
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Gerry Tonkin-Hill
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Madikay Senghore
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Stephen K Obaro
- Division of Pediatric Infectious Disease, University of Nebraska Medical Center Omaha, Omaha, NE, USA
- International Foundation against Infectious Diseases in Nigeria, Abuja, Nigeria
| | - Sani Ousmane
- Centre de Recherche Médicale et Sanitaire, Niamey, Niger
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Betuel Sigaùque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Martin Antonio
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Robert F Breiman
- Emory Global Health Institute, Emory University, Atlanta, GA, USA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
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8
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Gladstone RA, Lo SW, Goater R, Yeats C, Taylor B, Hadfield J, Lees JA, Croucher NJ, van Tonder AJ, Bentley LJ, Quah FX, Blaschke AJ, Pershing NL, Byington CL, Balaji V, Hryniewicz W, Sigauque B, Ravikumar K, Almeida SCG, Ochoa TJ, Ho PL, du Plessis M, Ndlangisa KM, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Pollard AJ, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, Metcalf BJ, Li Y, Beall BW, McGee L, Breiman RF, Aanensen DM, Bentley SD. Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates. Microb Genom 2020; 6:e000357. [PMID: 32375991 PMCID: PMC7371119 DOI: 10.1099/mgen.0.000357] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/03/2020] [Indexed: 11/21/2022] Open
Abstract
Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20 kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (tet, erm, cat) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here.
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Affiliation(s)
| | - Stephanie W. Lo
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
| | - Richard Goater
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Corin Yeats
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Ben Taylor
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John A. Lees
- Faculty of Medicine, School of Public Health, Imperial College London, UK
| | | | - Andries J. van Tonder
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Leon J. Bentley
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
| | - Fu Xiang Quah
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
| | - Anne J. Blaschke
- Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA
| | - Nicole L. Pershing
- Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA
| | | | | | - Waleria Hryniewicz
- National Medicines Institute, Division of Clinical Microbiology and Infection Prevention, Warsaw, Poland
| | - Betuel Sigauque
- Fundação Manhiça / Centro de Investigação em Saúde da Manhiça (CISM), Maputo Mozambique, Instituto Nacional de Saúde, inistério de Saúde, Maputo, Mozambique
| | - K.L. Ravikumar
- Central Research Laboratory, Department of Microbiology, Kempegowda Institute of Medical Sciences Hospital & Research Center, Bangalore, India
| | | | - Theresa J. Ochoa
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pak Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, PR China
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Kedibone M. Ndlangisa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - 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
| | - Rachel Benisty
- The Faculty of Health Sciences, Ben-Gurion University of the NegevBeer-Sheva, Israel
| | - Susan A. Nzenze
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A. Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | - 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
| | - Ron Dagan
- The Faculty of Health Sciences, Ben-Gurion University of the NegevBeer-Sheva, Israel
| | | | - Anne von Gottberg
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, PR China
| | | | - Yuan Li
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F. Breiman
- Rollins School Public Health, Emory University, GA, USA
- Emory Global Health Institute, Atlanta, GA, USA
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
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9
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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. Lancet Infect Dis 2019; 19:759-769. [PMID: 31196809 PMCID: PMC7641901 DOI: 10.1016/s1473-3099(19)30297-x] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, Corander J, Page AJ, Marttinen P, Bentley LJ, Ochoa TJ, Ho PL, du Plessis M, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, McGee L, Breiman RF, Bentley SD. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine 2019; 43:338-346. [PMID: 31003929 PMCID: PMC6557916 DOI: 10.1016/j.ebiom.2019.04.021] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Pneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease, caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing to study pneumococcal serotype, antibiotic resistance and invasiveness, in the context of genetic background. METHODS Our dataset of 13,454 genomes, combined with four published genomic datasets, represented Africa (40%), Asia (25%), Europe (19%), North America (12%), and South America (5%). These 20,027 pneumococcal genomes were clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our dataset, we additionally derived serotype and sequence type, and predicted antibiotic sensitivity. We then measured invasiveness using odds ratios that relating prevalence in invasive pneumococcal disease to carriage. FINDINGS The combined collections (n = 20,027) were clustered into 621 GPSCs. Thirty-five GPSCs observed in our dataset were represented by >100 isolates, and subsequently classed as dominant-GPSCs. In 22/35 (63%) of dominant-GPSCs both non-vaccine serotypes and vaccine serotypes were observed in the years up until, and including, the first year of pneumococcal conjugate vaccine introduction. Penicillin and multidrug resistance were higher (p < .05) in a subset dominant-GPSCs (14/35, 9/35 respectively), and resistance to an increasing number of antibiotic classes was associated with increased recombination (R2 = 0.27 p < .0001). In 28/35 dominant-GPSCs, the country of isolation was a significant predictor (p < .05) of its antibiogram (mean misclassification error 0.28, SD ± 0.13). We detected increased invasiveness of six genetic backgrounds, when compared to other genetic backgrounds expressing the same serotype. Up to 1.6-fold changes in invasiveness odds ratio were observed. INTERPRETATION We define GPSCs that can be assigned to any pneumococcal genomic dataset, to aid international comparisons. Existing non-vaccine-serotypes in most GPSCs preclude the removal of these lineages by pneumococcal conjugate vaccines; leaving potential for serotype replacement. A subset of GPSCs have increased resistance, and/or serotype-independent invasiveness.
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Affiliation(s)
| | - Stephanie W Lo
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK
| | - John A Lees
- New York University School of Medicine, New York, NY, USA
| | | | | | - Jukka Corander
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK; Department of Biostatistics, University of Oslo, 0317 Oslo, Norway
| | - Andrew J Page
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Pekka Marttinen
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Espoo, Finland
| | - Leon J Bentley
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Theresa J Ochoa
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pak Leung Ho
- Department of Microbiology, Carol Yu Centre for Infection, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Jennifer E Cornick
- Malawi-Liverpool-Wellcome-Trust Clinical Research Programme, Blantyre, Malawi
| | - 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 London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273 Banjul, the Gambia
| | - Rachel Benisty
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Susan A Nzenze
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, South Africa; Department of Science and Technology, National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, South Africa
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, South Africa; Department of Science and Technology, National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, South Africa
| | | | | | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273 Banjul, the Gambia; Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, 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
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Robert F Breiman
- Rollins School Public Health, Emory University, USA; Emory Global Health Institute, Atlanta, USA
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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12
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Musicha P, Cornick JE, Bar-Zeev N, French N, Masesa C, Denis B, Kennedy N, Mallewa J, Gordon MA, Msefula CL, Heyderman RS, Everett DB, Feasey NA. Trends in antimicrobial resistance in bloodstream infection isolates at a large urban hospital in Malawi (1998-2016): a surveillance study. Lancet Infect Dis 2017; 17:1042-1052. [PMID: 28818544 PMCID: PMC5610140 DOI: 10.1016/s1473-3099(17)30394-8] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 05/31/2017] [Accepted: 06/15/2017] [Indexed: 01/22/2023]
Abstract
Background Bacterial bloodstream infection is a common cause of morbidity and mortality in sub-Saharan Africa, yet few facilities are able to maintain long-term surveillance. The Malawi-Liverpool-Wellcome Trust Clinical Research Programme has done sentinel surveillance of bacteraemia since 1998. We report long-term trends in bloodstream infection and antimicrobial resistance from this surveillance. Methods In this surveillance study, we analysed blood cultures that were routinely taken from adult and paediatric patients with fever or suspicion of sepsis admitted to Queen Elizabeth Central Hospital, Blantyre, Malawi from 1998 to 2016. The hospital served an urban population of 920 000 in 2016, with 1000 beds, although occupancy often exceeds capacity. The hospital admits about 10 000 adults and 30 000 children each year. Antimicrobial susceptibility tests were done by the disc diffusion method according to British Society of Antimicrobial Chemotherapy guidelines. We used the Cochran-Armitage test for trend to examine trends in rates of antimicrobial resistance, and negative binomial regression to examine trends in icidence of bloodstream infection over time. Findings Between Jan 1, 1998, and Dec 31, 2016, we isolated 29 183 pathogens from 194 539 blood cultures. Pathogen detection decreased significantly from 327·1/100 000 in 1998 to 120·2/100 000 in 2016 (p<0·0001). 13 366 (51·1%) of 26 174 bacterial isolates were resistant to the Malawian first-line antibiotics amoxicillin or penicillin, chloramphenicol, and co-trimoxazole; 68·3% of Gram-negative and 6·6% of Gram-positive pathogens. The proportions of non-Salmonella Enterobacteriaceae with extended spectrum beta-lactamase (ESBL) or fluoroquinolone resistance rose significantly after 2003 to 61·9% in 2016 (p<0·0001). Between 2003 and 2016, ESBL resistance rose from 0·7% to 30·3% in Escherichia coli, from 11·8% to 90·5% in Klebsiella spp and from 30·4% to 71·9% in other Enterobacteriaceae. Similarly, resistance to ciprofloxacin rose from 2·5% to 31·1% in E coli, from 1·7% to 70·2% in Klebsiella spp and from 5·9% to 68·8% in other Enterobacteriaceae. By contrast, more than 92·0% of common Gram-positive pathogens remain susceptible to either penicillin or chloramphenicol. Meticillin-resistant Staphylococcus aureus (MRSA) was first reported in 1998 at 7·7% and represented 18·4% of S aureus isolates in 2016. Interpretation The rapid expansion of ESBL and fluoroquinolone resistance among common Gram-negative pathogens, and the emergence of MRSA, highlight the growing challenge of bloodstream infections that are effectively impossible to treat in this resource-limited setting. Funding Wellcome Trust, H3ABionet, Southern Africa Consortium for Research Excellence (SACORE).
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Affiliation(s)
- Patrick Musicha
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; College of Medicine, University of Malawi, Blantyre, Malawi; Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Jennifer E Cornick
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Naor Bar-Zeev
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Neil French
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Clemens Masesa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Neil Kennedy
- College of Medicine, University of Malawi, Blantyre, Malawi; Queen's University, Belfast, UK
| | - Jane Mallewa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; College of Medicine, University of Malawi, Blantyre, Malawi
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; College of Medicine, University of Malawi, Blantyre, Malawi
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Division of Infection and Immunity, University College London, London, UK
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Liverpool School of Tropical Medicine, Liverpool, UK.
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13
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Cornick JE, Tastan Bishop Ö, Yalcin F, Kiran AM, Kumwenda B, Chaguza C, Govindpershad S, Ousmane S, Senghore M, du Plessis M, Pluschke G, Ebruke C, McGee L, Sigaùque B, Collard JM, Bentley SD, Kadioglu A, Antonio M, von Gottberg A, French N, Klugman KP, Heyderman RS, Alderson M, Everett DB. The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1. Vaccine 2017; 35:972-980. [PMID: 28081968 PMCID: PMC5287219 DOI: 10.1016/j.vaccine.2016.12.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 11/29/2016] [Accepted: 12/15/2016] [Indexed: 11/28/2022]
Abstract
Serotype 1 is one of the most common causes of pneumococcal disease worldwide. Pneumococcal protein vaccines are currently being developed as an alternate intervention strategy to pneumococcal conjugate vaccines. Pre-requisites for an efficacious pneumococcal protein vaccine are universal presence and minimal variation of the target antigen in the pneumococcal population, and the capability to induce a robust human immune response. We used in silico analysis to assess the prevalence of seven protein vaccine candidates (CbpA, PcpA, PhtD, PspA, SP0148, SP1912, SP2108) among 445 serotype 1 pneumococci from 26 different countries, across four continents. CbpA (76%), PspA (68%), PhtD (28%), PcpA (11%) were not universally encoded in the study population, and would not provide full coverage against serotype 1. PcpA was widely present in the European (82%), but not in the African (2%) population. A multi-valent vaccine incorporating CbpA, PcpA, PhtD and PspA was predicted to provide coverage against 86% of the global population. SP0148, SP1912 and SP2108 were universally encoded and we further assessed their predicted amino acid, antigenic and structural variation. Multiple allelic variants of these proteins were identified, different allelic variants dominated in different continents; the observed variation was predicted to impact the antigenicity and structure of two SP0148 variants, one SP1912 variant and four SP2108 variants, however these variants were each only present in a small fraction of the global population (<2%). The vast majority of the observed variation was predicted to have no impact on the efficaciousness of a protein vaccine incorporating a single variant of SP0148, SP1912 and/or SP2108 from S. pneumoniae TIGR4. Our findings emphasise the importance of taking geographic differences into account when designing global vaccine interventions and support the continued development of SP0148, SP1912 and SP2108 as protein vaccine candidates against this important pneumococcal serotype.
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Affiliation(s)
- Jennifer E Cornick
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi; Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK.
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Feyruz Yalcin
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anmol M Kiran
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi; Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Benjamin Kumwenda
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Chrispin Chaguza
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi; Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Shanil Govindpershad
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sani Ousmane
- Centre de Recherche Médicale et Sanitaire, Niamey, Niger
| | - Madikay Senghore
- Medical Research Council, Banjul, Gambia; Division of Translational and Systems Medicine, Microbiology and Infection Unit, The University of Warwick, UK
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Beutel Sigaùque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | | | - Stephen D Bentley
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Aras Kadioglu
- Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Martin Antonio
- Medical Research Council, Banjul, Gambia; Division of Translational and Systems Medicine, Microbiology and Infection Unit, The University of Warwick, UK; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil French
- Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, USA
| | - Robert S Heyderman
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | | | - Dean B Everett
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi; Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
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14
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Chaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L, Yang M, Yalcin F, Ousmane S, Govindpersad S, Senghore M, Ebruke C, Du Plessis M, Kiran AM, Pluschke G, Sigauque B, McGee L, Klugman KP, Turner P, Corander J, Parkhill J, Collard JM, Antonio M, von Gottberg A, Heyderman RS, French N, Kadioglu A, Hanage WP, Everett DB, Bentley SD. Understanding pneumococcal serotype 1 biology through population genomic analysis. BMC Infect Dis 2016; 16:649. [PMID: 27821148 PMCID: PMC5100261 DOI: 10.1186/s12879-016-1987-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/30/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. METHODS We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes. RESULTS Population structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat pC194), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1's rarity in carriage and consequently its lower recombination rates. CONCLUSIONS The high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversification and adaptation in different geographical regions. Such geographic adaptation reflects local variations in selection pressures in different locales. Further studies will be required to fully understand the biological mechanisms which makes the ST217 clone highly invasive but unable to successfully colonise the human nasopharynx for long durations which results in lower recombination rates.
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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, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Jennifer E. Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Simon R. Harris
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Cheryl P. Andam
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Massachusetts, MA 02115 USA
| | - Laura Bricio-Moreno
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
| | - Feyruz Yalcin
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Sani Ousmane
- Unité de Biologie, Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Shanil Govindpersad
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Madikay Senghore
- Bacterial Diseases Programme, Medical Research Council (MRC), Banjul, The Gambia
- Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
| | - Chinelo Ebruke
- Bacterial Diseases Programme, Medical Research Council (MRC), Banjul, The Gambia
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
| | - Mignon Du Plessis
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Anmol M. Kiran
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Betuel Sigauque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia GA 30329 USA
| | - Keith P. Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
- Bill and Melinda Gates Foundation, Seattle, WA 98109 USA
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Jean-Marc Collard
- Unité de Biologie, Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Martin Antonio
- Bacterial Diseases Programme, Medical Research Council (MRC), Banjul, The Gambia
- Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Robert S. Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
- Division of Infection and Immunity, University College London, London, WC1E 6BT UK
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
| | - William P. Hanage
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Massachusetts, MA 02115 USA
| | - Dean B. Everett
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Stephen D. Bentley
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
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15
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Cornick JE, Chaguza C, Harris SR, Yalcin F, Senghore M, Kiran AM, Govindpershad S, Ousmane S, Plessis MD, Pluschke G, Ebruke C, McGee L, Sigaùque B, Collard JM, Antonio M, von Gottberg A, French N, Klugman KP, Heyderman RS, Bentley SD, Everett DB, For The PAGe Consortium. Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae. Microb Genom 2015; 1:e000027. [PMID: 28348812 PMCID: PMC5320570 DOI: 10.1099/mgen.0.000027] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/29/2015] [Indexed: 12/20/2022] Open
Abstract
Serotype 1 Streptococcus pneumoniae is a leading cause of invasive pneumococcal disease (IPD) worldwide, with the highest burden in developing countries. We report the whole-genome sequencing analysis of 448 serotype 1 isolates from 27 countries worldwide (including 11 in Africa). The global serotype 1 population shows a strong phylogeographic structure at the continental level, and within Africa there is further region-specific structure. Our results demonstrate that region-specific diversification within Africa has been driven by limited cross-region transfer events, genetic recombination and antimicrobial selective pressure. Clonal replacement of the dominant serotype 1 clones circulating within regions is uncommon; however, here we report on the accessory gene content that has contributed to a rare clonal replacement event of ST3081 with ST618 as the dominant cause of IPD in the Gambia.
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Affiliation(s)
- Jennifer E Cornick
- The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.,University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Chrispin Chaguza
- The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.,University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Simon R Harris
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Feyruz Yalcin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Madikay Senghore
- Medical Research Council, Banjul, The Gambia.,Division of Translational and Systems Medicine, Microbiology and Infection Unit, The University of Warwick, Coventry, UK
| | - Anmol M Kiran
- The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.,University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Shanil Govindpershad
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service; and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sani Ousmane
- Centre de Recherche Médicale et Sanitaire, Niamey, Niger
| | - Mignon Du Plessis
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service; and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Chinelo Ebruke
- Medical Research Council, Banjul, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Beutel Sigaùque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | | | - Martin Antonio
- Medical Research Council, Banjul, The Gambia.,Division of Translational and Systems Medicine, Microbiology and Infection Unit, The University of Warwick, Coventry, UK.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anne von Gottberg
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service; and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil French
- University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Robert S Heyderman
- The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stephen D Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Dean B Everett
- The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.,University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
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16
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Kamng'ona AW, Hinds J, Bar-Zeev N, Gould KA, Chaguza C, Msefula C, Cornick JE, Kulohoma BW, Gray K, Bentley SD, French N, Heyderman RS, Everett DB. High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children. BMC Infect Dis 2015; 15:234. [PMID: 26088623 PMCID: PMC4474563 DOI: 10.1186/s12879-015-0980-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 06/08/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Carriage of either single or multiple pneumococcal serotypes (multiple carriage) is a prerequisite for developing invasive pneumococcal disease. However, despite the reported high rates of pneumococcal carriage in Malawi, no data on carriage of multiple serotypes has been reported previously. Our study provides the first description of the prevalence of multiple pneumococcal carriage in Malawi. METHODS The study was conducted in Blantyre and Karonga districts in Malawi, from 2008 to 2012. We recruited 116 children aged 0-13 years. These children were either HIV-infected (N = 44) or uninfected (N = 72). Nasopharyngeal samples were collected using sterile swabs. Pneumococcal serotypes in the samples were identified by microarray. Strains that could not be typed by microarray were sequenced to characterise possible genetic alterations within the capsular polysaccharide (CPS) locus. RESULTS The microarray identified 179 pneumococcal strains (from 116 subjects), encompassing 43 distinct serotypes and non-typeable (NT) strains. Forty per cent (46/116) of children carried multiple serotypes. Carriage of vaccine type (VT) strains was higher (p = 0.028) in younger (0-2 years) children (71 %, 40/56) compared to older (3-13 years) children (50 %, 30/60). Genetic variations within the CPS locus of known serotypes were observed in 19 % (34/179) of the strains identified. The variants included 13-valent pneumococcal conjugate vaccine (PCV13) serotypes 6B and 19A, and the polysaccharide vaccine serotype 20. Serotype 6B variants were the most frequently isolated (47 %, 16/34). Unlike the wild type, the CPS locus of the 6B variants contained an insertion of the licD-family phosphotransferase gene. The CPS locus of 19A- and 20-variants contained an inversion in the sugar-biosynthesis (rmlD) gene and a 717 bp deletion within the transferase (whaF) gene, respectively. CONCLUSIONS The high multiple carriage in Malawian children provides opportunities for genetic exchange through horizontal gene transfer. This may potentially lead to CPS locus variants and vaccine escape. Variants reported here occurred naturally, however, PCV13 introduction could exacerbate the CPS genetic variations. Further studies are therefore recommended to assess the invasive potential of these variants and establish whether PCV13 would offer cross-protection. We have shown that younger children (0-2 years) are a reservoir of VT serotypes, which makes them an ideal target for vaccination.
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Affiliation(s)
- Arox W Kamng'ona
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Biochemistry Department, University of Malawi, College of Medicine, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Jason Hinds
- Division of Clinical Sciences, St George's, University of London, London, UK.
| | - Naor Bar-Zeev
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Katherine A Gould
- Division of Clinical Sciences, St George's, University of London, London, UK.
| | - Chrispin Chaguza
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Chisomo Msefula
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Microbiology Department, University of Malawi, College of Medicine, Blantyre, Malawi.
| | - Jennifer E Cornick
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Benard W Kulohoma
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. .,International Centre for Insect Physiology and Ecology, Nairobi, Kenya.
| | - Katherine Gray
- Biochemistry Department, University of Malawi, College of Medicine, Blantyre, Malawi.
| | - Stephen D Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, UK. .,Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Neil French
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. .,Malawi Epidemiology and Intervention Research Unit (MEIRU), Karonga, Malawi.
| | - Robert S Heyderman
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Dean B Everett
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
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17
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Chaguza C, Cornick JE, Everett DB. Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae. Comput Struct Biotechnol J 2015; 13:241-7. [PMID: 25904996 PMCID: PMC4404416 DOI: 10.1016/j.csbj.2015.03.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 02/04/2023] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) is a highly recombinogenic bacterium responsible for a high burden of human disease globally. Genetic recombination, a process in which exogenous DNA is acquired and incorporated into its genome, is a key evolutionary mechanism employed by the pneumococcus to rapidly adapt to selective pressures. The rate at which the pneumococcus acquires genetic variation through recombination is much higher than the rate at which the organism acquires variation through spontaneous mutations. This higher rate of variation allows the pneumococcus to circumvent the host innate and adaptive immune responses, escape clinical interventions, including antibiotic therapy and vaccine introduction. The rapid influx of whole genome sequence (WGS) data and the advent of novel analysis methods and powerful computational tools for population genetics and evolution studies has transformed our understanding of how genetic recombination drives pneumococcal adaptation and evolution. Here we discuss how genetic recombination has impacted upon the evolution of the pneumococcus.
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Affiliation(s)
- Chrispin Chaguza
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
| | - Jennifer E Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
| | - Dean B Everett
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
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18
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Cornick JE, Harris SR, Parry CM, Moore MJ, Jassi C, Kamng'ona A, Kulohoma B, Heyderman RS, Bentley SD, Everett DB. Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi. J Antimicrob Chemother 2013; 69:368-74. [PMID: 24080503 PMCID: PMC3886935 DOI: 10.1093/jac/dkt384] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Objectives This study aimed to define the molecular basis of co-trimoxazole resistance in Malawian pneumococci under the dual selective pressure of widespread co-trimoxazole and sulfadoxine/pyrimethamine use. Methods We measured the trimethoprim and sulfamethoxazole MICs and analysed folA and folP nucleotide and translated amino acid sequences for 143 pneumococci isolated from carriage and invasive disease in Malawi (2002–08). Results Pneumococci were highly resistant to both trimethoprim and sulfamethoxazole (96%, 137/143). Sulfamethoxazole-resistant isolates showed a 3 or 6 bp insertion in the sulphonamide-binding site of folP. The trimethoprim-resistant isolates fell into three genotypic groups based on dihydrofolate reductase (encoded by folA) mutations: Ile-100-Leu (10%), the Ile-100-Leu substitution together with a residue 92 substitution (56%) and those with a novel uncharacterized resistance genotype (34%). The nucleotide sequence divergence and dN/dS of folA and folP remained stable from 2004 onwards. Conclusions S. pneumoniae exhibit almost universal co-trimoxazole resistance in vitro and in silico that we believe is driven by extensive co-trimoxazole and sulfadoxine/pyrimethamine use. More than one-third of pneumococci employ a novel mechanism of co-trimoxazole resistance. Resistance has now reached a point of stabilizing evolution. The use of co-trimoxazole to prevent pneumococcal infection in HIV/AIDS patients in sub-Saharan Africa should be re-evaluated.
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Affiliation(s)
- Jennifer E Cornick
- Malawi-Liverpool-Wellcome Clinical Research Programme, University of Malawi, College of Medicine, Blantyre, Malawi
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19
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Cornick JE, Everett DB, Broughton C, Denis BB, Banda DL, Carrol ED, Parry CM. Invasive Streptococcus pneumoniae in children, Malawi, 2004-2006. Emerg Infect Dis 2011; 17:1107-9. [PMID: 21749782 DOI: 10.3201/eid/1706.101404] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Of 176 invasive Streptococcus pneumoniae isolates from children in Malawi, common serotypes were 1 (23%), 6A/B (18%), 14 (6%), and 23F (6%). Coverage with the 7-valent pneumococcal conjugate vaccine (PCV) was 39%; PCV10 and PCV13 increased coverage to 66% and 88%, respectively. We found chloramphenicol resistance in 27% of isolates and penicillin nonsusceptibility in 10% (by using meningitis breakpoints); all were ceftriaxone susceptible.
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Affiliation(s)
- Jennifer E Cornick
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.
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20
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Abstract
Of 176 invasive Streptococcus pneumoniae isolates from children in Malawi, common serotypes were 1 (23%), 6A/B (18%), 14 (6%), and 23F (6%). Coverage with the 7-valent pneumococcal conjugate vaccine (PCV) was 39%; PCV10 and PCV13 increased coverage to 66% and 88%, respectively. We found chloramphenicol resistance in 27% of isolates and penicillin nonsusceptibility in 10% (by using meningitis breakpoints); all were ceftriaxone susceptible.
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Affiliation(s)
- Jennifer E Cornick
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.
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