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Verani JR, Omondi D, Odoyo A, Odiembo H, Ouma A, Ngambi J, Aol G, Audi A, Kiplangat S, Agumba N, Munywoki PK, Onyango C, Hunsperger E, Farrar JL, Kim L, Kobayashi M, Breiman RF, Pimenta FC, da Gloria Carvalho M, Lessa FC, Whitney CG, Bigogo G. Long-term impact of 10-valent pneumococcal conjugate vaccine in Kenya: Nasopharyngeal carriage among children in a rural and an urban site six years after introduction. Vaccine 2024; 42:126120. [PMID: 39004525 DOI: 10.1016/j.vaccine.2024.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/12/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024]
Abstract
BACKGROUND Kenya introduced Synflorix™ (GlaxoSmithKline, PCV10-GSK), a 10-valent pneumococcal conjugate vaccine, in 2011, using three primary doses and, in select areas, catch-up campaigns. Surveys conducted 1-2 years post-introduction showed a stable prevalence of pneumococcal colonization, with declines in vaccine-type carriage. However, little is known about the long-term impact of PCV10-GSK in Kenya. METHODS We conducted a cross-sectional survey of pneumococcal carriage among children aged <5 years in November-December 2017 in Kibera (Nairobi informal settlement, no catch-up) and Asembo (rural western Kenya, 2-dose catch-up for children 1-4 years), using the same methods and settings as prior annual surveys from 2009 to 2013. Participants were randomly selected from an ongoing population-based surveillance platform. Nasopharyngeal swabs were frozen in skim milk-tryptone-glucose-glycerin media within 4 h and underwent culture with broth enrichment for pneumococcus. Isolates were serotyped by polymerase chain reaction and Quellung. RESULTS We enrolled 504 children, including 252 from each site; >90 % of participants had received 3 doses of PCV10-GSK. Pneumococcal colonization was detected in 210 (83.3 %) participants in Kibera and 149 (59.1 %) in Asembo, which was significantly lower than the prevalence observed in 2013 (92.9 % and 85.7 %, respectively). PCV10-GSK serotypes were detected in 35/252 (13.9 %) participants in Kibera and 23/252 (9.1 %) in Asembo, respectively; these prevalences were lower, but not statistically different, from vaccine-type carriage prevalences in 2013 (17.3 % and 13.3 %, respectively). In 2017 in both sites, serotypes 3, 6A, 19A, 19F, and 35B were among the most common serotypes. CONCLUSION Six years post-PCV10-GSK introduction, the prevalence of pneumococcal carriage among children has decreased, and the impact of PCV10-GSK on vaccine-type carriage has plateaued. Kenya recently changed from PCV10-GSK to Pneumosil™ (Serum Institute of India), a 10-valent PCV that includes serotypes 6A and 19A; these data provide historical context for interpreting changes in vaccine-type carriage following the PCV formulation switch.
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Affiliation(s)
- Jennifer R Verani
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States; Division of Global Health Protection, Centers for Disease Control and Prevention, PO Box 606-00621, Village Market, Nairobi, Kenya.
| | - Daniel Omondi
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Arthur Odoyo
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Herine Odiembo
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Alice Ouma
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Juliet Ngambi
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - George Aol
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Allan Audi
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Samwel Kiplangat
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Noel Agumba
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Patrick K Munywoki
- Division of Global Health Protection, Centers for Disease Control and Prevention, PO Box 606-00621, Village Market, Nairobi, Kenya
| | - Clayton Onyango
- Division of Global Health Protection, Centers for Disease Control and Prevention, PO Box 606-00621, Village Market, Nairobi, Kenya
| | - Elizabeth Hunsperger
- Division of Global Health Protection, Centers for Disease Control and Prevention, PO Box 606-00621, Village Market, Nairobi, Kenya
| | - Jennifer L Farrar
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Lindsay Kim
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Miwako Kobayashi
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, 1518 Clifton Rd, Atlanta, GA 30322, United States; Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, 29 Princess of Wales Terrace, Johannesburg 2050, South Africa
| | - Fabiana C Pimenta
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Maria da Gloria Carvalho
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Fernanda C Lessa
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Cynthia G Whitney
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States; Rollins School of Public Health, Emory University, 1518 Clifton Rd, Atlanta, GA 30322, United States
| | - Godfrey Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
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Belman S, Lefrancq N, Nzenze S, Downs S, du Plessis M, Lo SW, McGee L, Madhi SA, von Gottberg A, Bentley SD, Salje H. Geographical migration and fitness dynamics of Streptococcus pneumoniae. Nature 2024; 631:386-392. [PMID: 38961295 PMCID: PMC11236706 DOI: 10.1038/s41586-024-07626-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location1,2. The extent and mechanisms of spread and vaccine-driven changes in fitness and antimicrobial resistance remain largely unquantified. Here using geolocated genome sequences from South Africa (n = 6,910, collected from 2000 to 2014), we developed models to reconstruct spread, pairing detailed human mobility data and genomic data. Separately, we estimated the population-level changes in fitness of strains that are included (vaccine type (VT)) and not included (non-vaccine type (NVT)) in pneumococcal conjugate vaccines, first implemented in South Africa in 2009. Differences in strain fitness between those that are and are not resistant to penicillin were also evaluated. We found that pneumococci only become homogenously mixed across South Africa after 50 years of transmission, with the slow spread driven by the focal nature of human mobility. Furthermore, in the years following vaccine implementation, the relative fitness of NVT compared with VT strains increased (relative risk of 1.68; 95% confidence interval of 1.59-1.77), with an increasing proportion of these NVT strains becoming resistant to penicillin. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in antimicrobial resistance may be transient.
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Affiliation(s)
- Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Global Health Resilience, Earth Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.
| | - Noémie Lefrancq
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Susan Nzenze
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sarah Downs
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Lesley McGee
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, UK
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3
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Mackenzie GA, Hossain I, Salaudeen R, Badji H, Manjang A, Usuf E, Bottomley C, Greenwood B, Hill PC. Impact of pneumococcal conjugate vaccination on pneumococcal nasopharyngeal carriage in the Gambia: Population-based cross-sectional surveys. Vaccine 2024; 42:2680-2686. [PMID: 38490820 PMCID: PMC11004668 DOI: 10.1016/j.vaccine.2024.02.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND The introduction of pneumococcal conjugate vaccines (PCV) has reduced carriage of vaccine-type (VT) pneumococci in many settings. We determined the impact of The Gambia's national PCV programme on carriage of VT pneumococci in the population. METHODS Seven-valent PCV (PCV7) was introduced in August 2009 without catch-up and with doses scheduled at 2, 3, 4 months of age; it was replaced by PCV13 in May 2011. We did cross-sectional carriage surveys in 2009, 2015, and 2017 in age-stratified, population-based samples. Nasopharyngeal specimens were collected and processed according to WHO guidelines. We calculated observed and adjusted prevalence ratios (PR) of VT carriage before and after PCV introduction. FINDINGS We enrolled 2988, 3162, and 2709 participants in 2009, 2015, and 2017 respectively. The baseline (2009) prevalence of VT pneumococcal carriage among children aged 0-4 years was 42.6 %, which declined to 14.9 % and 17.5 % in 2015 and 2017 respectively (adjPR 0.32 [95 % CI 0.27, 0.38] and 0.38 [0.31, 0.46] respectively). VT prevalence among children aged 5-14 years was 16.6 %, 15.1 %, and 15.8 % in the three surveys (2017 vs 2009, adjPR 0.70 [0.58, 0.83]). VT prevalence among 15-44 year-olds was 6.4 %, 5.7 %, and 7.1 % in the three surveys (2017 vs 2009, adjPR 0.59 [0.46, 0.75]), while in those aged ≥ 45 years it was 4.5 %, 6.5 %, and 4.5 % respectively. Non-VT carriage increased in all age-groups. Prevalent residual serotypes were 34 and 15B (age 0-4 years), 3 and 34 (age 5-14 years), and 3 and 16F (age ≥ 15 years). CONCLUSIONS Introduction of PCV was associated with reduced VT pneumococcal carriage in young, and older children, although with substantial residual prevalence. Persisting VT, and non-VT, carriage indicate significant, persistent transmission of pneumococci in the population.
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Affiliation(s)
- Grant A Mackenzie
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia; Murdoch Children's Research Institute, Parkville, 3052 Melbourne, Victoria, Australia; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK; Department of Paediatrics, University of Melbourne, Parkville, 3052 Melbourne, Victoria, Australia.
| | - Ilias Hossain
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia
| | - Rasheed Salaudeen
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia
| | - Henry Badji
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia
| | - Ahmed Manjang
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia
| | - Christian Bottomley
- Tropical Epidemiology Group, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Brian Greenwood
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Philip C Hill
- Centre for International Health, University of Otago, McMillan Street, Dunedin 9010, New Zealand
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von Mollendorf C, Ulziibayar M, Nguyen CD, Batsaikhan P, Suuri B, Luvsantseren D, Narangerel D, de Campo J, de Campo M, Tsolmon B, Demberelsuren S, Dunne EM, Satzke C, Mungun T, Mulholland EK. Effect of Pneumococcal Conjugate Vaccine on Pneumonia Incidence Rates among Children 2-59 Months of Age, Mongolia, 2015-2021. Emerg Infect Dis 2024; 30:490-498. [PMID: 38407131 PMCID: PMC10902538 DOI: 10.3201/eid3003.230864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
Starting in June 2016, the 13-valent pneumococcal conjugate vaccine (PCV13) was introduced into the routine immunization program of Mongolia by using a 2+1 dosing schedule, phased by district. We used prospective hospital surveillance to evaluate the vaccine's effect on pneumonia incidence rates among children 2-59 months of age over a 6-year period. Of 17,607 children with pneumonia, overall adjusted incidence rate ratios showed decreased primary endpoint pneumonia, very severe pneumonia, and probable pneumococcal pneumonia until June 2021. Results excluding and including the COVID-19 pandemic period were similar. Pneumonia declined in 3 districts that introduced PCV13 with catch-up campaigns but not in the 1 district that did not. After PCV13 introduction, vaccine-type pneumococcal carriage prevalence decreased by 44% and nonvaccine-type carriage increased by 49%. After PCV13 introduction in Mongolia, the incidence of more specific pneumonia endpoints declined in children 2-59 months of age; additional benefits were conferred by catch-up campaigns.
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5
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Downs SL, Olwagen CP, Van Der Merwe L, Nzenze SA, Nunes MC, Madhi SA. Streptococcus pneumoniae and other bacterial nasopharyngeal colonization seven years post-introduction of 13-valent pneumococcal conjugate vaccine in South African children. Int J Infect Dis 2023; 134:45-52. [PMID: 37209864 PMCID: PMC10404162 DOI: 10.1016/j.ijid.2023.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/24/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
OBJECTIVES Pneumococcal conjugate vaccines (PCVs) reduce pneumococcal-associated disease by reducing vaccine-serotype (VT) acquisition in vaccinated children, thereby interrupting VT transmission. The 7-valent-PCV was introduced in the South African immunization program in 2009 (13-valent-PCV since 2011) using a 2+1 schedule (at 6, 14, and 40 weeks of age). We aimed to evaluate temporal changes in VT and non-vaccine-serotype (NVT) colonization after 9 years of childhood PCV immunization in South Africa. METHODS Nasopharyngeal swabs were collected from healthy children <60-month-old (n = 571) in 2018 (period-2) and compared with samples (n = 1135) collected during early PCV7-introduction (period-1, 2010-11) in an urban low-income setting (Soweto). Pneumococci were tested for using a multiplex quantitative-polymerase chain reaction serotyping reaction-set. RESULTS Overall pneumococcal colonization in period-2 (49.4%; 282/571) was 27.5% lower than period-1 (68.1%; 773/1135; adjusted odds ratio [aOR]: 0.66; 95% confidence interval [CI]: 0.54-0.88). Colonization by VT was reduced by 54.5% in period-2 (18.6%; 106/571) compared with period-1 (40.9%; 465/1135; aOR: 0.41; 95% CI: 0.3-0.56). Nevertheless, serotype 19F carriage prevalence was higher (8.1%; 46/571) in period-2 compared with period-1 (6.6%; 75/1135; aOR: 2.0; 95% CI: 1.09-3.56). NVT colonization prevalence was similar in period-2 and period-1 (37.8%; 216/571 and 42.4%; 481/1135). CONCLUSION There remains a high residual prevalence of VT, particularly 19F, colonization nine years post-introduction of PCV in the South African childhood immunization program.
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Affiliation(s)
- Sarah L Downs
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science/ National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa.
| | - Courtney P Olwagen
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science/ National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Lara Van Der Merwe
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science/ National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Susan A Nzenze
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Marta C Nunes
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science/ National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Shabir A Madhi
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Department of Science/ National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa; Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
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6
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Olwagen CP, Izu A, Mutsaerts EAML, Jose L, Koen A, Downs SL, Van Der Merwe L, Laubscher M, Nana AJ, Moultrie A, Cutland CL, Dorfman JR, Madhi SA. Single priming and booster dose of ten-valent and 13-valent pneumococcal conjugate vaccines and Streptococcus pneumoniae colonisation in children in South Africa: a single-centre, open-label, randomised trial. THE LANCET. CHILD & ADOLESCENT HEALTH 2023; 7:326-335. [PMID: 36934731 PMCID: PMC10127219 DOI: 10.1016/s2352-4642(23)00025-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 03/17/2023]
Abstract
BACKGROUND Pneumococcal conjugate vaccine (PCV) immunisation has reduced vaccine-serotype colonisation and invasive pneumococcal disease in South Africa, providing the opportunity to consider transitioning from a two-dose (2 + 1) to one-dose (1 + 1) primary series and a booster dose. METHODS In this single-centre, open-label, randomised trial done in South Africa, infants aged 35-49 days without HIV infection, without childhood immunisations except for BCG and polio, and with gestation age at delivery of at least 37 weeks of age, a birthweight of at least 2500 g, and weight of at least 3500 g at the time of enrolment were randomly assigned (1:1:1:1:1:1), through block randomisation (block size of 30), to receive a single priming dose of ten-valent PCV (PCV10) or 13-valent PCV (PCV13) at either 6 weeks (6-week 1 + 1 group) or 14 weeks (14-week 1 + 1 group), compared with two priming doses at 6 weeks and 14 weeks (2 + 1 group), followed by a booster dose at 9 months of age in all groups. The primary objective of the trial has been published previously. We report the secondary objective of the effect of alternative doses of PCV10 and PCV13 on serotype-specific Streptococcus pneumoniae colonisation at 9 months, 15 months, and 18 months of age and a further exploratory analysis in which we assessed non-inferiority of serotype-specific serum IgG geometric mean concentrations 1 month after the booster (10 months of age) and the percentage of participants with serotype-specific IgG titre above the putative thresholds associated with a risk reduction of serotype-specific colonisation between the 1 + 1 and 2 + 1 groups for both vaccines. Non-inferiority was established if the lower limit of the 95% CI for the difference between the proportion of participants (1 + 1 group vs 2 + 1 group) above the putative thresholds was greater than or equal to -10%. All analyses were done in the modified intention-to-treat population, which included all participants who received PCV10 or PCV13 according to assigned randomisation group and for whom laboratory results were available. The trial is registered with ClinicalTrials.gov, NCT02943902. FINDINGS 1564 nasopharyngeal swabs were available for molecular serotyping from 600 infants who were enrolled (100 were randomly assigned to each of the six study groups) between Jan 9 and Sept 20, 2017. There was no significant difference in the prevalence of overall or non-vaccine serotype colonisation between all PCV13 or PCV10 groups. PCV13 serotype colonisation was lower at 15 months of age in the 14-week 1 + 1 group than in the 2 + 1 group (seven [8%] of 85 vs 17 [20%] of 87; odds ratio 0·61 [95% CI 0·38-0·97], p=0·037), but no difference was seen at 9 months (nine [11%] of 86 vs ten [11%] of 89; 0·92 [0·60-1·55], p=0·87) or 18 months (nine [11%] of 85 vs 11 [14%] of 87; 0·78 [0·45-1·22], p=0·61). Compared with the PCV13 2 + 1 group, both PCV13 1 + 1 groups did not meet the non-inferiority criteria for serotype-specific anti-capsular antibody concentrations above the putative thresholds purportedly associated with risk reduction for colonisation; however, the PCV10 14-week 1 + 1 group was non-inferior to the PCV10 2 + 1 group. INTERPRETATION The serotype-specific colonisation data reported in this study together with the primary immunogenicity endpoints of the control trial support transitioning to a reduced 1 + 1 schedule in South Africa. Ongoing monitoring of colonisation should, however, be undertaken immediately before and after transitioning to a PCV 1 + 1 schedule to serve as an early indicator of whether PCV 1 + 1 could lead to an increase in vaccine-serotype disease. FUNDING The Bill & Melinda Gates Foundation.
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Affiliation(s)
- Courtney P Olwagen
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alane Izu
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Eleonora A M L Mutsaerts
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Department of Pediatrics, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Lisa Jose
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Anthonet Koen
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Sarah L Downs
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Lara Van Der Merwe
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Matt Laubscher
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Amit J Nana
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew Moultrie
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Clare L Cutland
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, and African Leadership in Vaccinology Expertise, University of the Witwatersrand, Johannesburg, South Africa
| | - Jeffrey R Dorfman
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Department of Medical Virology, Department of Pathology, Stellenbosch University, Cape Town, South Africa
| | - Shabir A Madhi
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Johannesburg, South Africa; Faculty of Health Science, and African Leadership in Vaccinology Expertise, University of the Witwatersrand, Johannesburg, South Africa.
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7
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Carrim M, Tempia S, Thindwa D, Martinson NA, Kahn K, Flasche S, Hellferscee O, Treurnicht FK, McMorrow ML, Moyes J, Mkhencele T, Mathunjwa A, Kleynhans J, Lebina L, Mothlaoleng K, Wafawanaka F, Gómez-Olivé FX, Cohen C, von Gottberg A, Wolter N. Unmasking Pneumococcal Carriage in a High Human Immunodeficiency Virus (HIV) Prevalence Population in two Community Cohorts in South Africa, 2016-2018: The PHIRST Study. Clin Infect Dis 2023; 76:e710-e717. [PMID: 35717655 PMCID: PMC10169447 DOI: 10.1093/cid/ciac499] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Longitudinal pneumococcus colonization data in high human immunodeficiency virus (HIV) prevalence settings following pneumococcal conjugate vaccine introduction are limited. METHODS In 327 randomly selected households, 1684 individuals were enrolled and followed-up for 6 to 10 months during 2016 through 2018 from 2 communities. Nasopharyngeal swabs were collected twice weekly and tested for pneumococcus using quantitative lytA real-time polymerase chain reaction. A Markov model was fitted to the data to define the start and end of an episode of colonization. We assessed factors associated with colonization using logistic regression. RESULTS During the study period, 98% (1655/1684) of participants were colonized with pneumococcus at least once. Younger age (<5 years: adjusted odds ratio [aOR], 14.1; 95% confidence [CI], 1.8-111.3, and 5-24 years: aOR, 4.8, 95% CI, 1.9-11.9, compared with 25-44 years) and HIV infection (aOR, 10.1; 95% CI, 1.3-77.1) were associated with increased odds of colonization. Children aged <5 years had fewer colonization episodes (median, 9) than individuals ≥5 years (median, 18; P < .001) but had a longer episode duration (<5 years: 35.5 days; interquartile range, 17-88) vs. ≥5 years: 5.5 days (4-12). High pneumococcal loads were associated with age (<1 year: aOR 25.4; 95% CI, 7.4-87.6; 1-4 years: aOR 13.5, 95% CI 8.3-22.9; 5-14 years: aOR 3.1, 95% CI, 2.1-4.4 vs. 45-65 year old patients) and HIV infection (aOR 1.7; 95% CI 1.2-2.4). CONCLUSIONS We observed high levels of pneumococcus colonization across all age groups. Children and people with HIV were more likely to be colonized and had higher pneumococcal loads. Carriage duration decreased with age highlighting that children remain important in pneumococcal transmission.
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Affiliation(s)
- Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
- MassGenics, Duluth, Georgia, USA
| | - Deus Thindwa
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Neil A Martinson
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, Maryland, USA
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefan Flasche
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Orienka Hellferscee
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Florette K Treurnicht
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Azwifarwi Mathunjwa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Katlego Mothlaoleng
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Francesc Xavier Gómez-Olivé
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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8
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Belman S, Lefrancq N, Nzenze S, Downs S, du Plessis M, Lo S, McGee L, Madhi SA, von Gottberg A, Bentley SD, Salje H. Geographic migration and vaccine-induced fitness changes of Streptococcus pneumoniae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524577. [PMID: 36711799 PMCID: PMC9882368 DOI: 10.1101/2023.01.18.524577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location. The extent and mechanisms of spread, and vaccine-driven changes in fitness and antimicrobial resistance (AMR), remain largely unquantified. Using geolocated genome sequences from South Africa (N=6910, 2000-2014) we developed models to reconstruct spread, pairing detailed human mobility data and genomic data. Separately we estimated the population level changes in fitness of strains that are (vaccine type, VT) and are not (non-vaccine type, NVT) included in the vaccine, first implemented in 2009, as well as differences in strain fitness between those that are and are not resistant to penicillin. We estimated that pneumococci only become homogenously mixed across South Africa after about 50 years of transmission, with the slow spread driven by the focal nature of human mobility. Further, in the years following vaccine implementation the relative fitness of NVT compared to VT strains increased (RR: 1.29 [95% CI 1.20-1.37]) - with an increasing proportion of these NVT strains becoming penicillin resistant. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in AMR may be transient.
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Affiliation(s)
- Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute; Hinxton, UK
- Department of Genetics, University of Cambridge; Cambridge, UK
| | - Noémie Lefrancq
- Department of Genetics, University of Cambridge; Cambridge, UK
| | - Susan Nzenze
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service; Johannesburg, South Africa
| | - Sarah Downs
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service; Johannesburg, South Africa
| | - Stephanie Lo
- Parasites and Microbes, Wellcome Sanger Institute; Hinxton, UK
| | | | - Lesley McGee
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shabir A. Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service; Johannesburg, South Africa
| | | | - Henrik Salje
- Department of Genetics, University of Cambridge; Cambridge, UK
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9
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Javaid N, Olwagen C, Nzenze S, Hawkins P, Gladstone R, McGee L, Breiman RF, Bentley SD, Madhi SA, Lo S. Population genomics of pneumococcal carriage in South Africa following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) immunization. Microb Genom 2022; 8. [PMID: 35737523 PMCID: PMC9455715 DOI: 10.1099/mgen.0.000831] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Streptococcus pneumoniae is a major human pathogen responsible for over 317000 deaths in children <5 years of age with the burden of the disease being highest in low- and middle-income countries including South Africa. Following the introduction of the 7-valent and 13-valent pneumococcal conjugate vaccine (PCV) in South Africa in 2009 and 2011, respectively, a decrease in both invasive pneumococcal infections and asymptomatic carriage of vaccine-type pneumococci were reported. In this study, we described the changing epidemiology of the pneumococcal carriage population in South Africa, by sequencing the genomes of 1825 isolates collected between 2009 and 2013. Using these genomic data, we reported the changes in serotypes, Global Pneumococcal Sequence Clusters (GPSCs), and antibiotic resistance before and after the introduction of PCV13. The pneumococcal carriage population in South Africa has a high level of diversity, comprising of 126 GPSCs and 49 serotypes. Of the ten most prevalent GPSCs detected, six were predominantly found in Africa (GPSC22, GPSC21, GPSC17, GPSC33, GPSC34 and GPSC52). We found a significant decrease in PCV7 serotypes (19F, 6B, 23F and 14) and an increase in non-vaccine serotypes (NVT) (16F, 34, 35B and 11A) among children <2 years of age. The increase in NVTs was driven by pneumococcal lineages GPSC33, GPSC34, GPSC5 and GPSC22. Overall, a decrease in antibiotic resistance for 11 antimicrobials was detected in the PCV13 era. Further, we reported a higher resistance prevalence among vaccine types (VTs), as compared to NVTs; however, an increase in penicillin resistance among NVT was observed between the PCV7 and PCV13 eras. The carriage isolates from South Africa predominantly belonged to pneumococcal lineages, which are endemic to Africa. While the introduction of PCV resulted in an overall reduction of resistance in pneumococcal carriage isolates, an increase in penicillin resistance among NVTs was detected in children aged between 3 and 5 years, driven by the expansion of penicillin-resistant clones associated with NVTs in the PCV13 era.
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Affiliation(s)
- Nida Javaid
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- *Correspondence: Nida Javaid, ;
| | - Courtney Olwagen
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Nzenze
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Paulina Hawkins
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Stephen D. Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Shabir A. Madhi
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- *Correspondence: Shabir A. Madhi,
| | - Stephanie Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- *Correspondence: Stephanie Lo,
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10
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Rueda ZV, Bermúdez M, Restrepo A, Garcés C, Morales O, Roya-Pabón C, Carmona LF, Arango C, Albarracín JL, López L, Aguilar Y, Maya MA, Trujillo M, Copete ÁR, Vera C, Herrera M, Giraldo MR, Niño-Cruz GI, Vélez LA. Induced sputum as an adequate clinical specimen for the etiological diagnosis of community-acquired pneumonia (CAP) in children and adolescents. Int J Infect Dis 2022; 116:348-354. [DOI: 10.1016/j.ijid.2022.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 10/19/2022] Open
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11
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Kalizang'oma A, Chaguza C, Gori A, Davison C, Beleza S, Antonio M, Beall B, Goldblatt D, Kwambana-Adams B, Bentley SD, Heyderman RS. Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis. Microb Genom 2021; 7. [PMID: 34550067 PMCID: PMC8715442 DOI: 10.1099/mgen.0.000622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Streptococcus pneumoniae is an important global pathogen that causes bacterial pneumonia, sepsis and meningitis. Beta-lactam antibiotics are the first-line treatment for pneumococcal disease, however, their effectiveness is hampered by beta-lactam resistance facilitated by horizontal genetic transfer (HGT) with closely related species. Although interspecies HGT is known to occur among the species of the genus Streptococcus, the rates and effects of HGT between Streptococcus pneumoniae and its close relatives involving the penicillin binding protein (pbp) genes remain poorly understood. Here we applied the fastGEAR tool to investigate interspecies HGT in pbp genes using a global collection of whole-genome sequences of Streptococcus mitis, Streptococcus oralis and S. pneumoniae. With these data, we established that pneumococcal serotypes 6A, 13, 14, 16F, 19A, 19F, 23F and 35B were the highest-ranking serotypes with acquired pbp fragments. S. mitis was a more frequent pneumococcal donor of pbp fragments and a source of higher pbp nucleotide diversity when compared with S. oralis. Pneumococci that acquired pbp fragments were associated with a higher minimum inhibitory concentration (MIC) for penicillin compared with pneumococci without acquired fragments. Together these data indicate that S. mitis contributes to reduced β-lactam susceptibility among commonly carried pneumococcal serotypes that are associated with long carriage duration and high recombination frequencies. As pneumococcal vaccine programmes mature, placing increasing pressure on the pneumococcal population structure, it will be important to monitor the influence of antimicrobial resistance HGT from commensal streptococci such as S. mitis.
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Affiliation(s)
- Akuzike Kalizang'oma
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | - Chrispin Chaguza
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, 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
| | - Andrea Gori
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | - Charlotte Davison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Martin Antonio
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, World Health Organization, Collaborating Centre for New Vaccines Surveillance, Banjul, Gambia
| | - Bernard Beall
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Atlanta, GA, USA
| | - David Goldblatt
- University College London, Great Ormond Street Institute of Child Health, London, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | | | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
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12
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Bentley SD, Lo SW. Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics. Genome Med 2021; 13:84. [PMID: 34001237 PMCID: PMC8130287 DOI: 10.1186/s13073-021-00901-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/30/2021] [Indexed: 11/10/2022] Open
Abstract
Vaccines are powerful agents in infectious disease prevention but often designed to protect against some strains that are most likely to spread and cause diseases. Most vaccines do not succeed in eradicating the pathogen and thus allow the potential emergence of vaccine evading strains. As with most evolutionary processes, being able to capture all variations across the entire genome gives us the best chance of monitoring and understanding the processes of vaccine evasion. Genomics is being widely adopted as the optimum approach for pathogen surveillance with the potential for early and precise identification of high-risk strains. Given sufficient longitudinal data, genomics also has the potential to forecast the emergence of such strains enabling immediate or pre-emptive intervention. In this review, we consider the strengths and challenges for pathogen genomic surveillance using the experience of the Global Pneumococcal Sequencing (GPS) project as an early example. We highlight the multifaceted nature of genome data and recent advances in genome-based tools to extract useful information relevant to inform vaccine strategies and treatment options. We conclude with future perspectives for genomic pathogen surveillance.
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Affiliation(s)
- Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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13
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Yang Y, Hua CZ, Fang C, Xie YP, Li W, Fu Y, Gao F, Yao KH. Properties of Mucoid Serotype 3 Streptococcus pneumoniae From Children in China. Front Cell Infect Microbiol 2021; 11:648040. [PMID: 33842394 PMCID: PMC8024565 DOI: 10.3389/fcimb.2021.648040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/08/2021] [Indexed: 11/23/2022] Open
Abstract
Objective To investigate the characteristics of hosts, antimicrobial susceptibility, and molecular epidemiology of mucoid serotype 3 Streptococcus pneumoniae (S. pneumoniae) isolated from children in China. Method S. pneumoniae isolates collected between January 2016 and December 2019 were analyzed. S. pneumoniae isolates with mucoid phenotype were selected visually, and serotype 3 isolates were confirmed by Quellung reaction. The antimicrobial susceptibility was measured by E-test. Multilocus sequence typing was used for clonal analysis. Results Twenty (3.04%) isolates of mucoid serotype 3 S. pneumoniae were identified from 657 clinical isolates, and all of them were noninvasive strains. The mean age of the hosts was 5.69 ± 3.28 years. The isolates included: 50.0% from the dissected tonsil or adenoid tissue in children with obstructive sleep apnea-hypopnea syndrome, 45.0% from sputum or bronchial lavages in children with pneumonia, and 5.0% from vaginal secretions of one patient with vulvovaginitis. All isolates were susceptible to penicillin, cefuroxime, ceftriaxone, meropenem, vancomycin, levofloxacin, trimethoprim/sulfamethoxazole, and rifampin but resistant to erythromycin. Sequence type (ST)505 and its clonal complex (CC) were the main genotypes (95%). Antimicrobial susceptibility of ST180 and ST505 were compared, and the minimum inhibitory concentration (MIC) of ST505 isolates was significantly higher than that of ST180 for tetracycline, trimethoprim/sulfamethoxazole, and meropenem. Conclusions Mucoid serotype 3 Streptococcus pneumoniae can be isolated from various body parts, among which the respiratory system is the most common. It can cause noninvasive infection in children, and it has high susceptibility to a variety of antibiotics, especially β-lactams, but is resistant to macrolides. CC505 is the novel clonal complex found in China, which may be related to the worldwide mainstream clonal complex (CC180) but has its own biological characteristics.
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Affiliation(s)
- Ying Yang
- Department of Infectious Diseases, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China.,Department of Neurology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Chun-Zhen Hua
- Department of Infectious Diseases, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Chao Fang
- Clinical Laboratory Center, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Yong-Ping Xie
- Department of Infectious Diseases, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Wei Li
- Clinical Laboratory Center, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Yong Fu
- Department of Otolaryngology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Feng Gao
- Department of Neurology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Kai-Hu Yao
- Department of Microbiology, Beijing Children's Hospital, Capital Medical University, Beijing, China
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14
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Temple B, Nation ML, Dai VTT, Beissbarth J, Bright K, Dunne EM, Hinds J, Hoan PT, Lai J, Nguyen CD, Ortika BD, Phan TV, Thuy HNL, Toan NT, Uyen DY, Satzke C, Smith-Vaughan H, Huu TN, Mulholland K. Effect of a 2+1 schedule of ten-valent versus 13-valent pneumococcal conjugate vaccine on pneumococcal carriage: Results from a randomised controlled trial in Vietnam. Vaccine 2021; 39:2303-2310. [PMID: 33745731 PMCID: PMC8052188 DOI: 10.1016/j.vaccine.2021.02.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Pneumococcal conjugate vaccines (PCVs) generate herd protection by reducing nasopharyngeal (NP) carriage. Two PCVs, PCV10 and PCV13, have been in use for over a decade, yet there are few data comparing their impact on carriage. Here we report their effect on carriage in a 2+1 schedule, compared with each other and with unvaccinated controls. METHODS Data from four groups within a parallel, open-label randomised controlled trial in Ho Chi Minh City contribute to this article. Three groups were randomised to receive a 2+1 schedule of PCV10 (n = 250), a 2+1 schedule of PCV13 (n = 251), or two doses of PCV10 at 18 and 24 months (controls, n = 197). An additional group (n = 199) was recruited at 18 months to serve as controls from 18 to 24 months. NP swabs collected at 2, 6, 9, 12, 18, and 24 months were analysed (blinded) for pneumococcal carriage. This study aimed to determine if PCV10 and PCV13 have a differential effect on pneumococcal carriage, a secondary outcome of the trial. We also describe the serotype distribution among unvaccinated participants. TRIAL REGISTRATION ClinicalTrials.gov NCT01953510. FINDINGS Compared with unvaccinated controls, a 2+1 schedule of PCV10 reduced PCV10-type carriage by 45-62% from pre-booster through to 24 months of age, and a 2+1 schedule of PCV13 reduced PCV13-type carriage by 36-49% at 12 and 18 months of age. Compared directly with each other, there were few differences between the vaccines in their impact on carriage. Vaccine serotypes accounted for the majority of carriage in unvaccinated participants. INTERPRETATION Both PCV10 and PCV13 reduce the carriage of pneumococcal vaccine serotypes. The introduction of either vaccine would have the potential to generate significant herd protection in this population. FUNDING National Health and Medical Research Council of Australia, Bill & Melinda Gates Foundation.
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Affiliation(s)
- Beth Temple
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK; Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Monica Larissa Nation
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Vo Thi Trang Dai
- Department of Microbiology and Immunology, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Kathryn Bright
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Eileen Margaret Dunne
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Jason Hinds
- Institute for Infection and Immunity, St George's, University of London, London, UK; BUGS Bioscience, London Bioscience Innovation Centre, London, UK
| | - Pham Thi Hoan
- Department of Microbiology and Immunology, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Jana Lai
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Cattram Duong Nguyen
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Belinda Daniela Ortika
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Thanh V Phan
- Department of Microbiology and Immunology, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Ho Nguyen Loc Thuy
- Department of Microbiology and Immunology, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Nguyen Trong Toan
- Department of Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Doan Y Uyen
- Department of Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Catherine Satzke
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Heidi Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Tran Ngoc Huu
- Department of Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Kim Mulholland
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK; Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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15
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Ceyhan M, Karadag-Oncel E, Hascelik G, Ustundag G, Gurbuz V, Samlioglu P, Yilmaz N, Ozsurekci Y, Yilmaz E, Aykac K, Oz FN, Uzum O, Orsdemir-Hortu H, Tanir G, Yilmaz-Ciftdogan D, Kurugol Z. Nasopharyngeal carriage of Streptococcus pneumoniae in healthy children aged less than five years. Vaccine 2021; 39:2041-2047. [PMID: 33741188 DOI: 10.1016/j.vaccine.2021.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 01/17/2023]
Abstract
PURPOSE In Turkey, pneumococcal conjugate vaccine (PCV) was introduced to the national immunization program as PCV7 in 2008, and was replaced with PCV13 in 2011. The aim of the study was to demonstrate the pneumococcal carriage rate and the serotype distribution in healthy children under 5 years in Turkey who were vaccinated with PCV13. METHODS We conducted a cross-sectional study including the collection of questionnaire data and nasopharyngeal (NP) specimens among children aged <5 years from five centers from March 2019 to March 2020. Pneumococcal isolates were identified using optochin sensitivity and bile solubility. Serotyping was performed using a latex agglutination kit and Quellung reaction. RESULTS NP swab samples were collected from 580 healthy children. The observed overall carriage rate was 17.8%. None of the hypothesised predictors of S. pneumoniae carriage, except maternal education level was statistically significant (p = 0.017). High maternal education level appeared to decrease the risk (lower vs. higher maternal education OR: 1.992 [95% CI; 1.089-3.643], p = 0.025). The overall NP S. pneumoniae carriage prevalence for the PCV13-vaccinated children was 17.8% (103/580). The most common serotypes detected were serotype 15B (n = 10, 9.7%), serotype 23F (n = 9, 8.7%), serotype 23A (n = 9, 8.7%), serotype 11A (n = 7, 6.7%), serotype 19F (n = 5, 4.8%) and serotype 15F (n = 5, 4.8%). Of the isolates, 28 (27.2%) were in PCV13 vaccine strains (VSs), and 75 (72.8%) strains were non-VS. The serotype coverage rate was 27.2% for PCV13. CONCLUSION The overall S. pneumoniae carriage rate was higher than in earlier studies from Turkey. Post-vaccine era studies from around the world have reported a decrease in VS serotypes and a 'serotype replacement' to non-VS serotypes, as we determined in our study.
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Affiliation(s)
- Mehmet Ceyhan
- Hacettepe University School of Medicine, Department of Pediatric Infectious Diseases, Ankara, Turkey
| | - Eda Karadag-Oncel
- University of Health Sciences, Tepecik Training and Research Hospital, Department of Pediatric Infectious Diseases, İzmir, Turkey
| | - Gulsen Hascelik
- Hacettepe University School of Medicine, Department of Medical Microbiology, Ankara, Turkey
| | - Gulnihan Ustundag
- University of Health Sciences, Tepecik Training and Research Hospital, Department of Pediatric Infectious Diseases, İzmir, Turkey.
| | - Venhar Gurbuz
- Hacettepe University School of Medicine, Department of Pediatric Infectious Diseases, Ankara, Turkey
| | - Pinar Samlioglu
- University of Health Sciences, Tepecik Training and Research Hospital, Department of Medical Microbiology, İzmir, Turkey
| | - Nisel Yilmaz
- University of Health Sciences, Tepecik Training and Research Hospital, Department of Medical Microbiology, İzmir, Turkey
| | - Yasemin Ozsurekci
- Hacettepe University School of Medicine, Department of Pediatric Infectious Diseases, Ankara, Turkey
| | - Elif Yilmaz
- Ege University School of Medicine, Department of Pediatric Infectious Diseases, İzmir, Turkey
| | - Kubra Aykac
- University of Health Sciences, Ankara Training and Research Hospital, Department of Pediatric Infectious Diseases, Ankara, Turkey
| | - Fatma Nur Oz
- University of Health Sciences, Sami Ulus Training and Research Hospital, Department of Pediatric Infectious Diseases, Ankara, Turkey
| | - Ozlem Uzum
- University of Health Sciences, Tepecik Training and Research Hospital, Department of Pediatrics, İzmir, Turkey
| | - Hacer Orsdemir-Hortu
- University of Health Sciences, Tepecik Training and Research Hospital, Department of Pediatrics, İzmir, Turkey
| | - Gonul Tanir
- University of Health Sciences, Sami Ulus Training and Research Hospital, Department of Pediatric Infectious Diseases, Ankara, Turkey
| | - Dilek Yilmaz-Ciftdogan
- University of Health Sciences, Tepecik Training and Research Hospital, Department of Pediatric Infectious Diseases, İzmir, Turkey
| | - Zafer Kurugol
- Ege University School of Medicine, Department of Pediatric Infectious Diseases, İzmir, Turkey
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16
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Assessing reduced-dose pneumococcal vaccine schedules in South Africa. THE LANCET. INFECTIOUS DISEASES 2020; 20:1355-1357. [PMID: 32857991 DOI: 10.1016/s1473-3099(20)30577-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/08/2020] [Indexed: 11/27/2022]
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