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Peno C, Lin TY, Hislop MS, Yolda-Carr D, Farjado K, York A, Pitzer VE, Weinberger DM, Bei AK, Allicock OM, Wyllie AL. A low-cost culture- and DNA extraction-free method for the molecular detection of pneumococcal carriage in saliva. Microbiol Spectr 2024:e0059124. [PMID: 39028185 DOI: 10.1128/spectrum.00591-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/05/2024] [Indexed: 07/20/2024] Open
Abstract
Molecular methods have improved the sensitivity of the detection of pneumococcal carriage in saliva. However, they typically require sample culture enrichment and nucleic acid extraction prior to performing the detection assay and may limit scalability for extensive surveillance of pneumococcus, particularly in low-resource settings. We evaluated the performance of a DNA-extraction-free method for the detection of pneumococcus in saliva. We developed a streamlined qPCR-based protocol for the detection of pneumococcus, omitting culture enrichment and DNA extraction. Using saliva samples collected from children attending childcare centers (New Haven, CT, USA), we evaluated the detection of pneumococcus using saliva lysates as compared to purified DNA extracted from culture-enriched aliquots of the paired samples using qPCR targeting the pneumococcal piaB gene. Of the 759 saliva samples tested from 92 children [median age 3.65 years; IQR (2.46-4.78)], pneumococcus was detected in 358 (47.2%) saliva lysates prepared using the extraction-free protocol and in 369 (48.6%) DNA extracted from culture-enriched samples. We observed near-perfect agreement between the two protocols (Cohen's kappa: 0.92; 95% CI: 0.90-0.95). Despite a high correlation between CT values generated by the two methods (r = 0.93, P < 0.0001), the CT values generated from saliva lysates were higher (lower concentration) than those from culture-enriched samples (ΔCT = 6.69, P < 0.00001). The cost of detecting pneumococcus using saliva lysates was at least fivefold lower (US$2.53) compared to the cost of the culture-enriched method (range: US$13.60-US$19.46). For pneumococcal carriage surveillance in children, our findings suggest that a DNA extraction-free approach may offer a cost-effective alternative to the resource-intensive culture-enrichment method.IMPORTANCESurveillance for carriage of pneumococcus is a key component of evaluating the performance of pneumococcal vaccines and informing new vaccination strategies. To improve the scalability of pneumococcal carriage surveillance, we show that molecular detection of pneumococcus in saliva from children can be performed without culture enrichment and DNA extraction. Our findings show that using the extraction-free method can improve surveillance efforts for pneumococcal carriage in children, overcoming the resource-intensive hurdle that comes with the use of molecular methods, particularly in low-resource settings.
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Affiliation(s)
- Chikondi Peno
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Tzu-Yi Lin
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Maikel S Hislop
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Devyn Yolda-Carr
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Katherine Farjado
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anna York
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Amy K Bei
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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Childs L, Ouedraogo I, Zoma RL, Tarbangdo TF, Sawadogo G, Aké HF, Ouangraoua S, Sanou S, Tran T, Velusamy S, Adebanjo T, Van Beneden CA, McGee L, Kobayashi M. Pneumococcal Carriage in Burkina Faso After 13-Valent Pneumococcal Conjugate Vaccine Introduction and Before a Schedule Change. Open Forum Infect Dis 2024; 11:ofae303. [PMID: 38911949 PMCID: PMC11191361 DOI: 10.1093/ofid/ofae303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/29/2024] [Indexed: 06/25/2024] Open
Abstract
Background In October 2013, Burkina Faso introduced 13-valent pneumococcal conjugate vaccine (PCV13) into the routine childhood immunization program using 3 primary doses with no booster. Previous pneumococcal carriage studies showed reductions in vaccine-type (VT) carriage in children aged <5 years but not in older age groups. Methods We conducted a cross-sectional, age-stratified pneumococcal carriage study among healthy persons aged ≥1 month in Bobo-Dioulasso in March 2020. Pneumococci isolated by culture from nasopharyngeal swabs (all participants) and oropharyngeal swabs (participants aged ≥5 years) were serotyped by polymerase chain reaction; a subset was serotyped by Quellung. Using data from a study with the same design from March 2017, we examined changes in pneumococcal carriage by age group. Results Among 1005 (2017) and 1002 (2020) enrolled participants, VT carriage decreased (21.6% to 15.9%; adjusted prevalence ratio [aPR], 0.76 [95% confidence interval {CI}, .63-.92]). By age group, decline in VT carriage was significant among children aged 5-14 years (28.9% to 16.3%; aPR, 0.57 [95% CI, .39-.84]) but not among children aged <5 years (22.4% to 19.1%; aPR, 0.87 [95% CI, .70-1.09]) or adults aged ≥15 years (12.0% to 5.5%; aPR, 0.52 [95% CI, .26-1.05]). Conclusions Between 3 and 6 years after PCV13 introduction, significant declines in VT carriage were observed in older children, possibly reflecting indirect effects of PCV13 use. VT carriage in children aged <5 years remained stable with almost 1 in 5 carrying VT pneumococci, suggesting limitations to a PCV schedule without a booster dose.
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Affiliation(s)
- Lana Childs
- Infectious Disease Programs, CDC Foundation, Atlanta, Georgia, USA
| | - Issa Ouedraogo
- Direction de la prévention par la vaccination, Ministère de la Santé et de l’Hygiène Publique, Ouagadougou, Burkina Faso
| | | | | | | | | | | | - Soufiane Sanou
- Unité de Bactériologie, Centre Muraz, Bobo-Dioulasso, Burkina Faso
| | - Theresa Tran
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Srinivasan Velusamy
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tolulope Adebanjo
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Chris A Van Beneden
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lesley McGee
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Miwako Kobayashi
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Warda K, Amari S, Boureddane M, Elkamouni Y, Arsalane L, Zouhair S, Bouskraoui M. Changes in pneumococcal serotypes distribution and penicillin resistance in healthy children five years after generalization of PCV10. Heliyon 2024; 10:e25741. [PMID: 38380016 PMCID: PMC10877248 DOI: 10.1016/j.heliyon.2024.e25741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/11/2024] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Objective Streptococcus pneumoniae (S. pneumoniae) nasopharyngeal carriage has significantly decreased after the generalization of pneumococcal vaccination worldwide. This study sought to investigate changes in S. pneumoniae carriage rates, serotype distribution and penicillin non-susceptibility following the generalization of 10-valent pneumococcal conjugate vaccine. Methods A prospective study was conducted in Marrakesh, Morocco, between 2017 and 2018, among healthy children attending vaccination centers. We collected nasopharyngeal swabs and questionnaire data for each child. Using univariate logistic regression, we analyzed the association between S. pneumoniae carriage and various risk factors. Comparisons of serotype diversity and penicillin resistance between 2017 and 2018 and the period before introduction of vaccination (2008-2009, n = 660) were performed using Simpson index and the chi-squared test, respectively. Results During 2017-2018, 515 children aged between 6 and 36 months participated. The S. pneumoniae carriage rate was 43.3%. Looking at the distribution serotypes, the rate of PCV10 serotypes rate was only 9.6%. Among non-vaccine serotypes, an increase in serotypes 6C/6D (22; 14%), 19B/19C (17; 10.8%), and 15B/15C (11; 7%) was observed. A particular increase in serotype diversity was also observed after the generalization of PCV10 (p < 0.001). S. pneumoniae non-susceptible to penicillin decreased, reaching a rate of 26.6% in 2017-2018. Conclusion The significant change in S. pneumoniae carriage, serotype distribution, and penicillin resistance highlights the effectiveness of the pneumococcal conjugate vaccine among children in Marrakesh, Morocco.
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Affiliation(s)
- Karima Warda
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
| | - Sara Amari
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
| | - Majda Boureddane
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
| | - Youssef Elkamouni
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
- Laboratory of Microbiology-Virology and Molecular Biology, Avicenna Military Hospital, Marrakesh, Morocco
| | - Lamiae Arsalane
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
- Laboratory of Microbiology-Virology and Molecular Biology, Avicenna Military Hospital, Marrakesh, Morocco
| | - Said Zouhair
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
- Laboratory of Microbiology-Virology and Molecular Biology, Avicenna Military Hospital, Marrakesh, Morocco
| | - Mohammed Bouskraoui
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
- Department of Pediatrics, Mohamed VI University Hospital Center, Marrakesh, Morocco
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Leong LE, Coldbeck-Shackley RC, McMillan M, Bratcher HB, Turra M, Lawrence A, Kahler C, Maiden MC, Rogers GB, Marshall H. The genomic epidemiology of Neisseria meningitidis carriage from a randomised controlled trial of 4CMenB vaccination in an asymptomatic adolescent population. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024; 43:100966. [PMID: 38169944 PMCID: PMC10758868 DOI: 10.1016/j.lanwpc.2023.100966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/18/2023] [Accepted: 11/01/2023] [Indexed: 01/05/2024]
Abstract
Background Oropharyngeal carriage of Neisseria meningitidis is frequent during adolescence, representing a major source of invasive meningococcal disease. This study examined the impact of a serogroup B vaccination (Bexsero, GSK 4CMenB) programme on adolescent N. meningitidis carriage using genomic data. Methods A total 34,489 oropharyngeal samples were collected as part of a state-wide cluster randomised-controlled trial in South Australia during 2017 and 2018 (NCT03089086). Samples were screened for the presence of N. meningitidis DNA by porA PCR prior to culture. Whole genome sequencing was performed on all 1772 N. meningitidis culture isolates and their genomes were analysed. Findings Unencapsulated meningococci were predominant at baseline (36.3% of isolates), followed by MenB (31.0%), and MenY (20.5%). Most MenB were ST-6058 from hyperinvasive cc41/44, or ST-32 and ST-2870 from cc32. For MenY, ST-23 and ST-1655 from cc23 were prevalent. Meningococcal carriage was mostly unchanged due to the vaccination programme; however, a significant reduction in ST-53 capsule-null meningococci prevalence was observed in 2018 compared to 2017 (OR = 0.52; 95% CI: 0.30-0.87, p = 0.0106). This effect was larger in the vaccinated compared to the control group (OR = 0.37; 95% CI: 0.12-0.98, p = 0.0368). Interpretation While deployment of the 4CMenB vaccination did not alter the carriage of hyperinvasive MenB in the vaccinated population, it altered the carriage of other N. meningitidis sequence types following the vaccination program. Our findings suggest 4CMenB vaccination is unlikely to reduce transmission of hyperinvasive N. meningitidis strains and therefore ongoing targeted vaccination is likely a more effective public health intervention. Funding This work was funded by GlaxoSmithKline Biologicals SA.
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Affiliation(s)
- Lex E.X. Leong
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia
- Microbiome & Host Health, South Australian Health and Medical Research Institute, Bedford Park, 5042, Australia
| | | | - Mark McMillan
- Vaccinology and Immunology Research Trials Unit, Women’s and Children’s Health Network, Adelaide 5000, Australia
- Robinson Research Institute and Adelaide Medical School, The University of Adelaide, Adelaide 5000, Australia
| | - Holly B. Bratcher
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, United Kingdom
| | - Mark Turra
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000, Australia
| | - Andrew Lawrence
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000, Australia
| | | | - Martin C.J. Maiden
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, United Kingdom
| | - Geraint B. Rogers
- Microbiome & Host Health, South Australian Health and Medical Research Institute, Bedford Park, 5042, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, 5042, Australia
| | - Helen Marshall
- Vaccinology and Immunology Research Trials Unit, Women’s and Children’s Health Network, Adelaide 5000, Australia
- Robinson Research Institute and Adelaide Medical School, The University of Adelaide, Adelaide 5000, Australia
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Arya S, Norton N, Kaushik P, Brandtmüller A, Tsoumani E. Recent changes to adult national immunization programs for pneumococcal vaccination in Europe and how they impact coverage: A systematic review of published and grey literature. Hum Vaccin Immunother 2023; 19:2279394. [PMID: 38014651 PMCID: PMC10760380 DOI: 10.1080/21645515.2023.2279394] [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: 08/14/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023] Open
Abstract
Despite widespread use of pneumococcal vaccines throughout Europe, the burden of pneumococcal disease (PD) in adults is considerable. To mitigate this burden, National Immunization Technical Advisory Groups (NITAGs) and Health Technology Assessment (HTA) agencies assess the value of different vaccine schedules for protecting against PD. The aim of this review was to assess the evidence and rationales used by NITAGs/HTA agencies, when considering recent changes to National Immunization Programs (NIPs) for adults, and how identified changes affected vaccine coverage rates (VCRs). A systematic review was conducted of published literature from PubMed® and Embase®, and gray literature from HTA/NITAG websites from the last 5 y, covering 31 European countries. Evidence related to NIP recommendations, epidemiology (invasive PD, pneumonia), health economic assessments and VCRs were collected and synthesized. Eighty-four records providing data for 26 countries were identified. Of these, eight described explicit changes to NIPs for adults in seven countries. Despite data gaps, some trends were observed; first, there appears to be a convergence of NIP recommendations in many countries toward sequential vaccination, with a pneumococcal conjugate vaccine (PCV), followed by pneumococcal polysaccharide vaccine 23. Second, reducing economic or healthcare burden were common rationales for implementing changes. Third, most health economic analyses assessing higher-valency PCVs for adults found its inclusion in NIPs cost-effective. Finally, higher coverage rates were seen in most cases where countries had expanded their NIPs to cover at-risk populations. The findings can encourage agencies to improve surveillance systems and work to reach the NIP's target populations more effectively.
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Affiliation(s)
- Stuti Arya
- Evidence Review and Synthesis, Quantify Research, Mohali, India
| | - Nicholas Norton
- Evidence Review and Synthesis, Quantify Research, Stockholm, Sweden
| | - Puneet Kaushik
- Evidence Review and Synthesis, Quantify Research, Mohali, India
| | - Agnes Brandtmüller
- Center for Observational and Real-World Evidence, MSD, Budapest, Hungary
| | - Eleana Tsoumani
- Center for Observational and Real-World Evidence, MSD, Athens, Greece
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Obolski U, Swarthout TD, Kalizang'oma A, Mwalukomo TS, Chan JM, Weight CM, Brown C, Cave R, Cornick J, Kamng'ona AW, Msefula J, Ercoli G, Brown JS, Lourenço J, Maiden MC, French N, Gupta S, Heyderman RS. The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi. Nat Commun 2023; 14:7477. [PMID: 37978177 PMCID: PMC10656543 DOI: 10.1038/s41467-023-43160-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Streptococcus pneumoniae causes substantial mortality among children under 5-years-old worldwide. Polysaccharide conjugate vaccines (PCVs) are highly effective at reducing vaccine serotype disease, but emergence of non-vaccine serotypes and persistent nasopharyngeal carriage threaten this success. We investigated the hypothesis that following vaccine, adapted pneumococcal genotypes emerge with the potential for vaccine escape. We genome sequenced 2804 penumococcal isolates, collected 4-8 years after introduction of PCV13 in Blantyre, Malawi. We developed a pipeline to cluster the pneumococcal population based on metabolic core genes into "Metabolic genotypes" (MTs). We show that S. pneumoniae population genetics are characterised by emergence of MTs with distinct virulence and antimicrobial resistance (AMR) profiles. Preliminary in vitro and murine experiments revealed that representative isolates from emerging MTs differed in growth, haemolytic, epithelial infection, and murine colonisation characteristics. Our results suggest that in the context of PCV13 introduction, pneumococcal population dynamics had shifted, a phenomenon that could further undermine vaccine control and promote spread of AMR.
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Affiliation(s)
- Uri Obolski
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Todd D Swarthout
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Akuzike Kalizang'oma
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
| | | | - Jia Mun Chan
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
| | - Caroline M Weight
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
- Faculty of Health and Medicine, Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Comfort Brown
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | - Rory Cave
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
| | - Jen Cornick
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Clinical Infection, Microbiology and Immunology, Institute of Infection Veterinary & Ecological Science, University of Liverpool, Liverpool, United Kingdom
| | | | | | - Giuseppe Ercoli
- UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Jeremy S Brown
- UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Universidade Católica Portuguesa, Faculty of Medicine, Biomedical Research Centre, Lisbon, Portugal
| | - Martin C Maiden
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Neil French
- Clinical Infection, Microbiology and Immunology, Institute of Infection Veterinary & Ecological Science, University of Liverpool, Liverpool, United Kingdom
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Robert S Heyderman
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi.
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom.
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7
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Khan D, Thomas SA, Tientcheu PE, Suso SMS, Dupont C, Kwambana-Adams B, Mohammed NI, Nicol MP, Antonio M. Comparison of DNA concentration and bacterial pathogen PCR detection when using two DNA extraction kits for nasopharyngeal/oropharyngeal samples. PLoS One 2023; 18:e0289557. [PMID: 37535692 PMCID: PMC10399880 DOI: 10.1371/journal.pone.0289557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
INTRODUCTION Several important human pathogens that cause life-threatening infections are asymptomatically carried in the Nasopharynx/Oropharynx (NP/OP). DNA extraction is a prerequisite for most culture-independent techniques used to identify pathogens in the NP/OP. However, components of DNA extraction kits differ thereby giving rise to differences in performance. We compared the DNA concentration and the detection of three pathogens in the NP/OP using the discontinued DNeasy PowerSoil Kit (Kit DP) and the DNeasy PowerLyzer PowerSoil Kit (Kit DPP). METHODS DNA was extracted from the same set of 103 NP/OP samples using the two kits. DNA concentration was measured using the Qubit 2.0 Fluorometer. Real-time Polymerase Chain reaction (RT-PCR) was done using the QuantStudio 7-flex system to detect three pathogens: S. pneumoniae, H. influenzae, and N. meningitidis. Bland-Altman statistics and plots were used to determine the threshold cycle (Ct) value agreement for the two kits. RESULTS The average DNA concentration from kit DPP was higher than Kit DP; 1235.6 ng/ml (SD = 1368.3) vs 884.9 ng/ml (SD = 1095.3), p = 0.002. Using a Ct value cutoff of 40 for positivity, the concordance for the presence of S. pneumoniae was 82% (84/102); 94%(96/103) for N. meningitidis and 92%(95/103) for H. influenzae. Kit DP proportionately resulted in higher Ct values than Kit DPP for all pathogens. The Ct value bias of measurement for S. pneumoniae was +2.4 (95% CI, 1.9-3.0), +1.4 (95% CI, 0.9-1.9) for N. meningitidis and +1.4 (95% CI, 0.2-2.5) for H. influenzae. CONCLUSION The higher DNA concentration obtained using kit DPP could increase the chances of recovering low abundant bacteria. The PCR results were reproducible for more than 90% of the samples for the gram-negative H. influenzae and N. meningitidis. Ct value variations of the kits must be taken into consideration when comparing studies that have used the two kits.
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Affiliation(s)
- Dam Khan
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Shola-Able Thomas
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Peggy-Estelle Tientcheu
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sambou M S Suso
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | - Brenda Kwambana-Adams
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Nuredin Ibrahim Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Mark P Nicol
- Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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8
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Claassen-Weitz S, Gardner-Lubbe S, Xia Y, Mwaikono KS, Mounaud SH, Nierman WC, Workman L, Zar HJ, Nicol MP. Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort. MICROBIOME 2023; 11:127. [PMID: 37271810 PMCID: PMC10240772 DOI: 10.1186/s40168-023-01563-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 04/30/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Bacteria colonizing the nasopharynx play a key role as gatekeepers of respiratory health. Yet, dynamics of early life nasopharyngeal (NP) bacterial profiles remain understudied in low- and middle-income countries (LMICs), where children have a high prevalence of risk factors for lower respiratory tract infection. We investigated longitudinal changes in NP bacterial profiles, and associated exposures, among healthy infants from low-income households in South Africa. METHODS We used short fragment (V4 region) 16S rRNA gene amplicon sequencing to characterize NP bacterial profiles from 103 infants in a South African birth cohort, at monthly intervals from birth through the first 12 months of life and six monthly thereafter until 30 months. RESULTS Corynebacterium and Staphylococcus were dominant colonizers at 1 month of life; however, these were rapidly replaced by Moraxella- or Haemophilus-dominated profiles by 4 months. This succession was almost universal and largely independent of a broad range of exposures. Warm weather (summer), lower gestational age, maternal smoking, no day-care attendance, antibiotic exposure, or low height-for-age z score at 12 months were associated with higher alpha and beta diversity. Summer was also associated with higher relative abundances of Staphylococcus, Streptococcus, Neisseria, or anaerobic gram-negative bacteria, whilst spring and winter were associated with higher relative abundances of Haemophilus or Corynebacterium, respectively. Maternal smoking was associated with higher relative abundances of Porphyromonas. Antibiotic therapy (or isoniazid prophylaxis for tuberculosis) was associated with higher relative abundance of anerobic taxa (Porphyromonas, Fusobacterium, and Prevotella) and with lower relative abundances of health associated-taxa Corynebacterium and Dolosigranulum. HIV-exposure was associated with higher relative abundances of Klebsiella or Veillonella and lower relative abundances of an unclassified genus within the family Lachnospiraceae. CONCLUSIONS In this intensively sampled cohort, there was rapid and predictable replacement of early profiles dominated by health-associated Corynebacterium and Dolosigranulum with those dominated by Moraxella and Haemophilus, independent of exposures. Season and antibiotic exposure were key determinants of NP bacterial profiles. Understudied but highly prevalent exposures prevalent in LMICs, including maternal smoking and HIV-exposure, were associated with NP bacterial profiles. Video Abstract.
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Affiliation(s)
- Shantelle Claassen-Weitz
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sugnet Gardner-Lubbe
- Department of Statistics and Actuarial Science, Faculty of Economic and Management Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Yao Xia
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
- Center for Artificial Intelligence and Machine Learning, School of Science, Edith Cowan University, Joondalup, Australia
| | - Kilaza S. Mwaikono
- Computational Biology Group and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Department of Science and Laboratory Technology, Dar Es Salaam Institute of Technology, Dar Es Salaam, Tanzania
| | | | | | - Lesley Workman
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- SAMRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- SAMRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P. Nicol
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
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9
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Downs SL, Madhi SA, van der Merwe L, Nunes MC, Olwagen CP. Optimization of a high-throughput nanofluidic real-time PCR to detect and quantify of 15 bacterial species and 92 Streptococcus pneumoniae serotypes. Sci Rep 2023; 13:4588. [PMID: 36944704 PMCID: PMC10030628 DOI: 10.1038/s41598-023-31820-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
Sensitive tools for detecting concurrent colonizing pneumococcal serotypes are needed for detailed evaluation of the direct and indirect impact of routine pneumococcal conjugate vaccine (PCV) immunization. A high-throughput quantitative nanofluidic real-time PCR (Standard BioTools 'Fluidigm') reaction-set was developed to detect and quantify 92 pneumococcal serotypes in archived clinical samples. Nasopharyngeal swabs collected in 2009-2011 from South African children ≤ 5 years-old, previously serotyped with standard culture-based methods were used for comparison. The reaction-set within the 'Fluidigm' effectively amplified all targets with high efficiency (90-110%), reproducibility (R2 ≥ 0.98), and at low limit-of-detection (< 102 CFU/ml). A blind analysis of 1 973 nasopharyngeal swab samples showed diagnostic sensitivity > 80% and specificity > 95% compared with the referent standard, culture based Quellung method. The qPCR method was able to serotype pneumococcal types with good discrimination compared with Quellung (ROC-AUC: > 0.73). The high-throughput nanofluidic real-time PCR method simultaneously detects 57 individual serotypes, and 35 serotypes within 16 serogroups in 96 samples (including controls), within a single qPCR run. This method can be used to evaluate the impact of current PCV formulations on vaccine-serotype and non-vaccine-serotype colonization, including detection of multiple concurrently colonizing serotypes. Our qPCR method can allow for monitoring of serotype-specific bacterial load, as well as emergence or ongoing transmission of minor or co-colonizing serotypes that may have invasive disease potential.
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Affiliation(s)
- Sarah L 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.
| | - 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
| | - Lara van der Merwe
- 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
| | - Marta C Nunes
- 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
| | - Courtney P Olwagen
- 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.
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10
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Recurrent Acute Otitis Media Environmental Risk Factors: A Literature Review from the Microbiota Point of View. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2030046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Acute otitis media (AOM) constitutes a multifactorial disease, as several host and environmental factors contribute to its occurrence. Prevention of AOM represents one of the most important goals in pediatrics, both in developing countries, in which complications, mortality, and deafness remain possible consequences of the disease, compared to in developed countries, in which this condition has an important burden in terms of medical, social, and economical implications. The strategies for AOM prevention are based on reducing the burden of risk factors, through the application of behavioral, environmental, and therapeutic interventions. The introduction of culture-independent techniques has allowed high-throughput investigation of entire bacterial communities, providing novel insights into the pathogenesis of middle ear diseases through the identification of potential protective bacteria. The upper respiratory tract (URT) is a pivotal region in AOM pathogenesis, as it could act as a source of pathogens than of protective microorganisms for the middle ear (ME). Due to its direct connection with the external ambient, the URT is particularly exposed to the influence of environmental agents. The aim of this review was to evaluate AOM environmental risk factors and their impact on URT microbial communities, and to investigate AOM pathogenesis from the microbiota perspective.
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11
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Senghore M, Chaguza C, Bojang E, Tientcheu PE, Bancroft RE, Lo SW, Gladstone RA, McGee L, Worwui A, Foster-Nyarko E, Ceesay F, Okoi CB, Klugman KP, Breiman RF, Bentley SD, Adegbola R, Antonio M, Hanage WP, Kwambana-Adams BA. Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints. Microb Genom 2022; 8. [PMID: 35119356 PMCID: PMC8942022 DOI: 10.1099/mgen.0.000732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transmission dynamics of Streptococcus pneumoniae in sub-Saharan Africa are poorly understood due to a lack of adequate epidemiological and genomic data. Here we leverage a longitudinal cohort from 21 neighbouring villages in rural Africa to study how closely related strains of S. pneumoniae are shared among infants. We analysed 1074 pneumococcal genomes isolated from 102 infants from 21 villages. Strains were designated for unique serotype and sequence-type combinations, and we arbitrarily defined strain sharing where the pairwise genetic distance between strains could be accounted for by the mean within host intra-strain diversity. We used non-parametric statistical tests to assess the role of spatial distance and prolonged carriage on strain sharing using a logistic regression model. We recorded 458 carriage episodes including 318 (69.4 %) where the carried strain was shared with at least one other infant. The odds of strain sharing varied significantly across villages (χ2=47.5, df=21, P-value <0.001). Infants in close proximity to each other were more likely to be involved in strain sharing, but we also show a considerable amount of strain sharing across longer distances. Close geographic proximity (<5 km) between shared strains was associated with a significantly lower pairwise SNP distance compared to strains shared over longer distances (P-value <0.005). Sustained carriage of a shared strain among the infants was significantly more likely to occur if they resided in villages within a 5 km radius of each other (P-value <0.005, OR 3.7). Conversely, where both infants were transiently colonized by the shared strain, they were more likely to reside in villages separated by over 15 km (P-value <0.05, OR 1.5). PCV7 serotypes were rare (13.5 %) and were significantly less likely to be shared (P-value <0.001, OR −1.07). Strain sharing was more likely to occur over short geographical distances, especially where accompanied by sustained colonization. Our results show that strain sharing is a useful proxy for studying transmission dynamics in an under-sampled population with limited genomic data. This article contains data hosted by Microreact.
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Affiliation(s)
- Madikay Senghore
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia.,Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115, USA
| | - Chrispin Chaguza
- Infection Genomics, Wellcome Sanger Institute, Hinxton, UK.,Darwin College, University of Cambridge, Silver Street, Cambridge, UK.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Ebrima Bojang
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Peggy-Estelle Tientcheu
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Rowan E Bancroft
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Stephanie W Lo
- Infection Genomics, Wellcome Sanger Institute, Hinxton, UK
| | | | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Archibald Worwui
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Ebenezer Foster-Nyarko
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Fatima Ceesay
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Catherine Bi Okoi
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Keith P Klugman
- Rollins School Public Health, Emory University, Atlanta, USA
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | | | - Richard Adegbola
- Immunisation and Global Health Consulting, RAMBICON, Lagos, Nigeria
| | - Martin Antonio
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115, USA
| | - Brenda A Kwambana-Adams
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia.,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
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12
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Peñaloza HF, van der Geest R, Ybe JA, Standiford TJ, Lee JS. Interleukin-36 Cytokines in Infectious and Non-Infectious Lung Diseases. Front Immunol 2021; 12:754702. [PMID: 34887860 PMCID: PMC8651476 DOI: 10.3389/fimmu.2021.754702] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/14/2021] [Indexed: 12/26/2022] Open
Abstract
The IL-36 family of cytokines were identified in the early 2000’s as a new subfamily of the IL-1 cytokine family, and since then, the role of IL-36 cytokines during various inflammatory processes has been characterized. While most of the research has focused on the role of these cytokines in autoimmune skin diseases such as psoriasis and dermatitis, recent studies have also shown the importance of IL-36 cytokines in the lung inflammatory response during infectious and non-infectious diseases. In this review, we discuss the biology of IL-36 cytokines in terms of how they are produced and activated, as well as their effects on myeloid and lymphoid cells during inflammation. We also discuss the role of these cytokines during lung infectious diseases caused by bacteria and influenza virus, as well as other inflammatory conditions in the lungs such as allergic asthma, lung fibrosis, chronic obstructive pulmonary disease, cystic fibrosis and cancer. Finally, we discuss the current therapeutic advances that target the IL-36 pathway and the possibility to extend these tools to treat lung inflammatory diseases.
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Affiliation(s)
- Hernán F Peñaloza
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rick van der Geest
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Joel A Ybe
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, IN, United States
| | - Theodore J Standiford
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Janet S Lee
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, United States
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13
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Peno C, Armitage EP, Clerc M, Balcazar Lopez C, Jagne YJ, Drammeh S, Jarju S, Sallah H, Senghore E, Lindsey BB, Camara J, Bah S, Mohammed NI, Dockrell DH, Kampmann B, Clarke E, Bogaert D, de Silva TI. The effect of live attenuated influenza vaccine on pneumococcal colonisation densities among children aged 24-59 months in The Gambia: a phase 4, open label, randomised, controlled trial. THE LANCET. MICROBE 2021; 2:e656-e665. [PMID: 34881370 PMCID: PMC8632704 DOI: 10.1016/s2666-5247(21)00179-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Influenza and other respiratory viruses promote Streptococcus pneumoniae proliferation in the upper respiratory tract. We sought to investigate for what we believe is the first time, the effect of intranasal live attenuated influenza vaccine (LAIV) on nasopharyngeal S pneumoniae density in a low-income to middle-income country population with high pneumococcal carriage rates. METHODS In an open-label, randomised, controlled trial in The Gambia, 330 healthy children aged 24-59 months were randomly assigned 2:1 to receive one trivalent LAIV dose at enrolment (day 0, intervention) or at the end of active follow-up (day 21, control). The investigator team were initially masked to block size and randomisation sequence to avoid allocation bias. Group allocation was later revealed to the investigator team. The primary outcome was PCR-quantified day 7 and 21 pneumococcal density. Asymptomatic respiratory viral infection at baseline and LAIV strain shedding were included as covariates in generalised mixed-effects models, to assess the effect of LAIV and other variables on pneumococcal densities. The study is registered at ClinicalTrials.gov, NCT02972957, and is closed to recruitment. FINDINGS Between Feb 8 and April 12, 2017, and Jan 15 and March 28, 2018, of 343 children assessed for eligibility, 213 in the intervention group and 108 in the control group completed the study and were included in the final analysis. Although no significant differences were seen in pneumococcal carriage or density at each timepoint when comparing groups, changes from baseline were observed in the LAIV group. The baseline S pneumoniae carriage prevalence was high in both LAIV and control groups (75%) and increased by day 21 in the LAIV group (85%, p=0·0037), but not in the control group (79%, p=0·44). An increase in pneumococcal density from day 0 amounts was seen in the LAIV group at day 7 (+0·207 log10 copies per μL, SE 0·105, p=0·050) and day 21 (+0·280 log10 copies per μL, SE 0·105, p=0·0082), but not in the control group. Older age was associated with lower pneumococcal density (-0·015 log10 copies per μL, SE 0·005, p=0·0030), with the presence of asymptomatic respiratory viruses at baseline (+0·259 log10 copies per μL, SE 0·097, p=0·017), and greater LAIV shedding at day 7 (+0·380 log10 copies per μL, SE 0·167, p=0·024) associated with higher pneumococcal density. A significant increase in rhinorrhoea was reported in the LAIV group compared with the control group children during the first 7 days of the study (103 [48%] of 213, compared with 25 [23%] of 108, p<0·0001), and between day 7 and 21 (108 [51%] of 213, compared with 28 [26%] of 108, p<0·0001). INTERPRETATION LAIV was associated with a modest increase in nasopharyngeal pneumococcal carriage and density in the 21 days following vaccination, with the increase in density lower in magnitude than previously described in the UK. This increase was accelerated when LAIV was administered in the presence of pre-existing asymptomatic respiratory viruses, suggesting that nasopharyngeal S pneumoniae proliferation is driven by cumulative mixed-viral co-infections. The effect of LAIV on pneumococcal density is probably similar to other respiratory viral infections in children. Our findings provide reassurance for the use of LAIV to expand influenza vaccine programmes in low-income to middle-income country populations with high pneumococcal carriage. FUNDING Wellcome Trust.
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Affiliation(s)
- Chikondi Peno
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Edwin P Armitage
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Melanie Clerc
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Carlos Balcazar Lopez
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Ya Jankey Jagne
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sainabou Drammeh
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sheikh Jarju
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Hadijatou Sallah
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Elina Senghore
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Benjamin B Lindsey
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- The Florey Institute & Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, UK
| | - Janko Camara
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sulayman Bah
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Nuredin I Mohammed
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - David H Dockrell
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, The London School of Hygiene & Tropical Medicine, London, UK
| | - Ed Clarke
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Debby Bogaert
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, The Netherlands
| | - Thushan I de Silva
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- The Florey Institute & Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, UK
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14
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Apte A, Dayma G, Naziat H, Williams L, Sanghavi S, Uddin J, Kawade A, Islam M, Kar S, Li Y, Kyaw MH, Juvekar S, Campbell H, Nair H, Saha SK, Bavdekar A. Nasopharyngeal pneumococcal carriage in South Asian infants: Results of observational cohort studies in vaccinated and unvaccinated populations. J Glob Health 2021; 11:04054. [PMID: 34552723 PMCID: PMC8442578 DOI: 10.7189/jogh.11.04054] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Nasopharyngeal pneumococcal carriage (NPC) is a prerequisite for invasive pneumococcal disease and reduced carriage of vaccine serotypes is a marker for the protection offered by the pneumococcal conjugate vaccine (PCV). The present study reports NPC during the first year of life in a vaccinated (with PCV10) cohort in Bangladesh and an unvaccinated cohort in India. Methods A total of 450 and 459 infants were recruited from India and Bangladesh respectively within 0-7 days after birth. Nasopharyngeal swabs were collected at baseline, 18 and 36 weeks after birth. The swabs were processed for pneumococcal culture and identification of serotypes by the Quellung test and polymerase chain reaction (PCR). An identical protocol was applied at both sites. Results Prevalence of NPC was 48% in the Indian and 54.8% in the Bangladeshi cohort at 18 weeks. It increased to 53% and 64.8% respectively at 36 weeks. The average prevalence of vaccine serotypes was higher in the Indian cohort (17.8% vs 9.8% for PCV-10 and 26.1% vs17.6% for PCV-13) with 6A, 6B, 19F, 23F, and 19A as the common serotypes. On the other hand, the prevalence of non-vaccine serotypes was higher (43.6% vs 27.1% for non-PCV13) in the Bangladeshi cohort with 34, 15B, 17F, and 35B as the common serotypes. Overcrowding was associated with increased risk of pneumococcal carriage. The present PCV-13 vaccine would cover 28%-30% and 47%-48% serotypes in the Bangladeshi and Indian cohorts respectively. Conclusions South Asian infants get colonised with pneumococci early in infancy; predominantly vaccine serotypes in PCV naïve population (India) and non-vaccine serotypes in the vaccinated population (Bangladesh). These local findings are important to inform the public health policy and the development of higher valent pneumococcal vaccines.
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Affiliation(s)
- Aditi Apte
- KEM Hospital Research Centre, Pune, Maharashtra, India
| | - Girish Dayma
- KEM Hospital Research Centre, Pune, Maharashtra, India
| | - Hakka Naziat
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Linda Williams
- Centre for Global Health, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | | | - Jamal Uddin
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Anand Kawade
- KEM Hospital Research Centre, Pune, Maharashtra, India
| | - Maksuda Islam
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Sanchita Kar
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - You Li
- Centre for Global Health, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Moe H Kyaw
- Sanofi Pasteur, Swiftwater, Pensylvania, USA
| | - Sanjay Juvekar
- KEM Hospital Research Centre, Pune, Maharashtra, India.,Savitribai Phule University, Pune, Maharashtra, India
| | - Harry Campbell
- Centre for Global Health, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Harish Nair
- Centre for Global Health, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Samir K Saha
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
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15
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Swarthout TD, Ibarz-Pavon A, Kawalazira G, Sinjani G, Chirombo J, Gori A, Chalusa P, Bonomali F, Nyirenda R, Bulla E, Brown C, Msefula J, Banda M, Kachala J, Mwansambo C, Henrion MY, Gordon SB, French N, Heyderman RS. A pragmatic health centre-based evaluation comparing the effectiveness of a PCV13 schedule change from 3+0 to 2+1 in a high pneumococcal carriage and disease burden setting in Malawi: a study protocol. BMJ Open 2021; 11:e050312. [PMID: 34140345 PMCID: PMC8212416 DOI: 10.1136/bmjopen-2021-050312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Streptococcus pneumoniae (the pneumococcus) is commonly carried as a commensal bacterium in the nasopharynx but can cause life-threatening disease. Transmission occurs by human respiratory droplets and interruption of this process provides herd immunity. A 2017 WHO Consultation on Optimisation of pneumococcal conjugate vaccines (PCV) Impact highlighted a substantial research gap in investigating why the impact of PCV vaccines in low-income countries has been lower than expected. Malawi introduced the 13-valent PCV (PCV13) into the national Expanded Programme of Immunisations in 2011, using a 3+0 (3 primary +0 booster doses) schedule. With evidence of greater impact of a 2+1 (2 primary +1 booster dose) schedule in other settings, including South Africa, Malawi's National Immunisations Technical Advisory Group is seeking evidence of adequate superiority of a 2+1 schedule to inform vaccine policy. METHODS A pragmatic health centre-based evaluation comparing impact of a PCV13 schedule change from 3+0 to 2+1 in Blantyre district, Malawi. Twenty government health centres will be randomly selected, with ten implementing a 2+1 and 10 to continue with the 3+0 schedule. Health centres implementing 3+0 will serve as the direct comparator in evaluating 2+1 providing superior direct and indirect protection against pneumococcal carriage. Pneumococcal carriage surveys will evaluate carriage prevalence among children 15-24 months, randomised at household level, and schoolgoers 5-10 years of age, randomly selected from school registers. Carriage surveys will be conducted 18 and 33 months following 2+1 implementation. ANALYSIS The primary endpoint is powered to detect an effect size of 50% reduction in vaccine serotype (VT) carriage among vaccinated children 15-24 months old, expecting a 14% and 7% VT carriage prevalence in the 3+0 and 2+1 arms, respectively. ETHICS AND DISSEMINATION The study has been approved by the Malawi College of Medicine Research Ethics Committee (COMREC; Ref: P05.19.2680), the University College London Research Ethics Committee (Ref: 8603.002) and the University of Liverpool Research Ethics Committee (Ref: 5439). The results from this study will be actively disseminated through manuscript publications and conference presentations. TRIAL REGISTRATION NUMBER NCT04078997.
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Affiliation(s)
- Todd D Swarthout
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Ana Ibarz-Pavon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool Faculty of Health and Life Sciences, Liverpool, UK
| | | | - George Sinjani
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - James Chirombo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Andrea Gori
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Peter Chalusa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Farouck Bonomali
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Roseline Nyirenda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Edwin Bulla
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Comfort Brown
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Jacquline Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | | | | | | | - Marc Yr Henrion
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Stephen B Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Neil French
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool Faculty of Health and Life Sciences, Liverpool, UK
| | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
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16
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Cleary DW, Morris DE, Anderson RA, Jones J, Alattraqchi AG, A Rahman NI, Ismail S, Razali MS, Mohd Amin R, Abd Aziz A, Esa NK, Amiruddin S, Chew CH, Simin H, Abdullah R, Yeo CC, Clarke SC. The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia. NPJ Biofilms Microbiomes 2021; 7:1. [PMID: 33402693 PMCID: PMC7785749 DOI: 10.1038/s41522-020-00173-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022] Open
Abstract
Much microbiome research has focused on populations that are predominantly of European descent, and from narrow demographics that do not capture the socio-economic and lifestyle differences which impact human health. Here we examined the airway microbiomes of the Orang Asli, the indigenous peoples of Malaysia. A total of 130 participants were recruited from two sites in the north-eastern state of Terengganu in Peninsular Malaysia. Using 16S rRNA sequencing, the nasal microbiome was significantly more diverse in those aged 5-17 years compared to 50+ years (p = 0.023) and clustered by age (PERMANOVA analysis of the Bray-Curtis distance, p = 0.001). Hierarchical clustering of Bray-Curtis dissimilarity scores revealed six microbiome clusters. The largest cluster (n = 28; 35.4%) had a marked abundance of Corynebacterium. In the oral microbiomes Streptococcus, Neisseria and Haemophilus were dominant. Using conventional microbiology, high levels of Staphylococcus aureus carriage were observed, particularly in the 18-65 age group (n = 17/36; 47.2% 95% CI: 30.9-63.5). The highest carriage of pneumococci was in the <5 and 5 to 17 year olds, with 57.1% (4/7) and 49.2% (30/61), respectively. Sixteen pneumococcal serotypes were identified, the most common being the nonvaccine-type 23A (14.6%) and the vaccine-type 6B (9.8%). The prevalence of pneumococcal serotypes covered by pneumococcal conjugate vaccines support introduction into a Malaysian national immunisation schedule. In addition, the dominance of Corynebacterium in the airway microbiomes is intriguing given their role as a potentially protective commensal with respect to acute infection and respiratory health.
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Affiliation(s)
- David W Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Trust, Southampton, UK.
| | - Denise E Morris
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Rebecca A Anderson
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Jessica Jones
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Ahmed Ghazi Alattraqchi
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Nor Iza A Rahman
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Salwani Ismail
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Mohd Sayuti Razali
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Rahmah Mohd Amin
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Aniza Abd Aziz
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Nor Kamaruzaman Esa
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Salman Amiruddin
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Ching Hoong Chew
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia
| | - Hafis Simin
- Faculty of Applied Social Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia
- Akademi Seni Budaya dan Warisan Kebangsaan, (ASWARA), Jalan Tun Ismail, Kuala Lumpur, Malaysia
| | - Ramle Abdullah
- Faculty of Applied Social Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia
| | - Chew Chieng Yeo
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Trust, Southampton, UK
- Global Health Research Institute, University of Southampton, Southampton, UK
- School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia
- Centre for Translational Research, IMU Institute for Research, Development and Innovation (IRDI), Kuala Lumpur, Malaysia
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17
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Emergence of Meningitis Caused by Nonvaccine Serotypes of Pneumococcus in Rural United States. Case Rep Pediatr 2020; 2020:2372843. [PMID: 33294245 PMCID: PMC7718068 DOI: 10.1155/2020/2372843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 09/26/2020] [Accepted: 11/21/2020] [Indexed: 11/24/2022] Open
Abstract
Pneumococcal conjugate vaccines have decreased the rates of invasive pneumococcal disease (IPD) in children. Since vaccine introduction, however, rates of infection due to nonvaccine Streptococcus pneumoniae serotypes have increased. We now describe 3 meningitis cases due to the nonvaccine serotypes 35B and 11A from rural United States.
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18
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Application of multi-omics technology for the elucidation of anti-pneumococcal activity of 3-acyl-2-phenylamino-1,4-dihydroquinolin-4-one (APDQ) derivative against Streptococcus pneumoniae. Sci Rep 2020; 10:20685. [PMID: 33244098 PMCID: PMC7691496 DOI: 10.1038/s41598-020-77694-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/10/2020] [Indexed: 11/24/2022] Open
Abstract
Streptococcus pneumoniae is one of Gram-positive pathogen that causes invasive pneumococcal disease. Nowadays, many S. pneumoniae strains are resistant to commonly used antibiotics such as β-lactams and macrolides. 3-Acyl-2-phenylamino-1,4-dihydroquinolin-4-one (APDQ) derivatives are known as novel chemicals having anti-pneumococcal activity against S. pneumoniae. The underlying mechanism of the anti-pneumococcal activity of this inhibitor remains unknown. Therefore, we tried to find the anti-pneumococcal mechanism of APDQ230122, one of the APDQ derivatives active against S. pneumoniae. We performed transcriptomic analysis (RNA-Seq) and proteomic analysis (LC–MS/MS analysis) to get differentially expressed genes (DEG) and differentially expressed proteins (DEP) of S. pneumoniae 521 treated with sub-inhibitory concentrations of APDQ230122 and elucidated the comprehensive expression changes of genes and proteins using multi-omics analysis. As a result, genes or proteins of peptidoglycan biosynthesis and DNA replication were significantly down-regulated. Electron microscopy analysis revealed that the structure of peptidoglycan was damaged by APDQ230122 in a chemical concentration-dependent manner. Therefore, we suggest peptidoglycan biosynthesis is a major target of APDQ230122. Multi-omics analysis can provide us useful information to elucidate anti-pneumococcal activity of APDQ230122.
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19
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Boni-Cisse C, Jarju S, Bancroft RE, Lepri NA, Kone H, Kofi N, Britoh-Mlan A, Zaba FS, Usuf E, Ndow PS, Worwui A, Mwenda JM, Biey JN, Ntsama B, Kwambana-Adams BA, Antonio M. Etiology of Bacterial Meningitis Among Children <5 Years Old in Côte d'Ivoire: Findings of Hospital-based Surveillance Before and After Pneumococcal Conjugate Vaccine Introduction. Clin Infect Dis 2020; 69:S114-S120. [PMID: 31505624 PMCID: PMC6761318 DOI: 10.1093/cid/ciz475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background Bacterial meningitis remains a major disease affecting children in Côte d’Ivoire. Thus, with support from the World Health Organization (WHO), Côte d’Ivoire has implemented pediatric bacterial meningitis (PBM) surveillance at 2 sentinel hospitals in Abidjan, targeting the main causes of PBM: Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Neisseria meningitidis (meningococcus). Herein we describe the epidemiological characteristics of PBM observed in Côte d’Ivoire during 2010–2016. Methods Cerebrospinal fluid (CSF) was collected from children aged <5 years admitted to the Abobo General Hospital or University Hospital Center Yopougon with suspected meningitis. Microbiology and polymerase chain reaction (PCR) techniques were used to detect the presence of pathogens in CSF. Where possible, serotyping/grouping was performed to determine the specific causative agents. Results Overall, 2762 cases of suspected meningitis were reported, with CSF from 39.2% (1083/2762) of patients analyzed at the WHO regional reference laboratory in The Gambia. In total, 82 (3.0% [82/2762]) CSF samples were positive for bacterial meningitis. Pneumococcus was the main pathogen responsible for PBM, accounting for 69.5% (52/82) of positive cases. Pneumococcal conjugate vaccine serotypes 5, 18C, 19F, and 6A/B were identified post–vaccine introduction. Emergence of H. influenzae nontypeable meningitis was observed after H. influenzae type b vaccine introduction. Conclusions Despite widespread use and high coverage of conjugate vaccines, pneumococcal vaccine serotypes and H. influenzae type b remain associated with bacterial meningitis among children aged <5 years in Côte d’Ivoire. This reinforces the need for enhanced surveillance for vaccine-preventable diseases to determine the prevalence of bacterial meningitis and vaccine impact across the country.
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Affiliation(s)
- Catherine Boni-Cisse
- Département de Microbiologie, Université Félix Houphouët Boigny, Abidjan, Côte d'Ivoire;, UFR des Sciences Médicales.,Sentinel Site Surveillance Laboratory of Paediatric Bacterial Meningitis and Rotavirus Diarrhoea, Centre Hospitalier Universitair de Yopougon, Abidjan, Côte d'Ivoire
| | - Sheikh Jarju
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Rowan E Bancroft
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Nicaise A Lepri
- Département de Microbiologie, Université Félix Houphouët Boigny, Abidjan, Côte d'Ivoire;, UFR des Sciences Médicales
| | - Hamidou Kone
- Département de Microbiologie, Université Félix Houphouët Boigny, Abidjan, Côte d'Ivoire;, UFR des Sciences Médicales
| | - N'zue Kofi
- WHO Country Office, Abidjan, Côte d'Ivoire
| | - Alice Britoh-Mlan
- Sentinel Site Surveillance Laboratory of Paediatric Bacterial Meningitis and Rotavirus Diarrhoea, Centre Hospitalier Universitair de Yopougon, Abidjan, Côte d'Ivoire
| | - Flore Sandrine Zaba
- Sentinel Site Surveillance Laboratory of Paediatric Bacterial Meningitis and Rotavirus Diarrhoea, Centre Hospitalier Universitair de Yopougon, Abidjan, Côte d'Ivoire
| | - Effua Usuf
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Peter Sylvanus Ndow
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Archibald Worwui
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Jason M Mwenda
- WHO Regional Office for Africa, Brazzaville, Republic of Congo
| | - Joseph N Biey
- WHO Intercountry Support Team, Ouagadougou, Burkina Faso
| | - Bernard Ntsama
- WHO Intercountry Support Team, Ouagadougou, Burkina Faso
| | - Brenda A Kwambana-Adams
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Martin Antonio
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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20
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Boula A, Senghore M, Ngoh R, Tassadjo F, Fonkoua MC, Nzouankeu A, Njiki MK, Musi J, Bebey S, Ngo Baleba M, Nkembe A, Médjina S, Ndow PS, Worwui A, Kobela M, Nimpa M, Mwenda JM, N'diaye A, Kwambana-Adams BA, Antonio M. Hospital-based Surveillance Provides Insights Into the Etiology of Pediatric Bacterial Meningitis in Yaoundé, Cameroon, in the Post-Vaccine Era. Clin Infect Dis 2020; 69:S148-S155. [PMID: 31505633 PMCID: PMC6761319 DOI: 10.1093/cid/ciz506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Meningitis is endemic to regions of Cameroon outside the meningitis belt including the capital city, Yaoundé. Through surveillance, we studied the etiology and molecular epidemiology of pediatric bacterial meningitis in Yaoundé from 2010 to 2016. Methods Lumbar puncture was performed on 5958 suspected meningitis cases; 765 specimens were further tested by culture, latex agglutination, and/or polymerase chain reaction (PCR). Serotyping/grouping, antimicrobial susceptibility testing, and/or whole genome sequencing were performed where applicable. Results The leading pathogens detected among the 126 confirmed cases were Streptococcus pneumoniae (93 [73.8%]), Haemophilus influenzae (18 [14.3%]), and Neisseria meningitidis (15 [11.9%]). We identified more vaccine serotypes (19 [61%]) than nonvaccine serotypes (12 [39%]); however, in the latter years non–pneumococcal conjugate vaccine serotypes were more common. Whole genome data on 29 S. pneumoniae isolates identified related strains (<30 single-nucleotide polymorphism difference). All but 1 of the genomes harbored a resistance genotype to at least 1 antibiotic, and vaccine serotypes harbored more resistance genes than nonvaccine serotypes (P < .05). Of 9 cases of H. influenzae, 8 were type b (Hib) and 1 was type f. However, the cases of Hib were either in unvaccinated individuals or children who had not yet received all 3 doses. We were unable to serogroup the N. meningitidis cases by PCR. Conclusions Streptococcus pneumoniae remains a leading cause of pediatric bacterial meningitis, and nonvaccine serotypes may play a bigger role in disease etiology in the postvaccine era. There is evidence of Hib disease among children in Cameroon, which warrants further investigation.
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Affiliation(s)
- Angeline Boula
- Centre Mere et Enfant de la Fondation, Yaoundé, Cameroon
| | - Madikay Senghore
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, West Africa Partnerships and Strategy, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Rose Ngoh
- Centre Mere et Enfant de la Fondation, Yaoundé, Cameroon
| | | | | | | | | | | | - Sandrine Bebey
- Centre Mere et Enfant de la Fondation, Yaoundé, Cameroon
| | | | | | | | - Peter S Ndow
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, West Africa Partnerships and Strategy, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Archibald Worwui
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, West Africa Partnerships and Strategy, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | | | - Jason M Mwenda
- WHO Regional Office for Africa, Brazzaville, Republic of Congo
| | | | - Brenda A Kwambana-Adams
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, West Africa Partnerships and Strategy, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Martin Antonio
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, West Africa Partnerships and Strategy, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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21
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Tagbo BN, Bancroft RE, Fajolu I, Abdulkadir MB, Bashir MF, Okunola OP, Isiaka AH, Lawal NM, Edelu BO, Onyejiaka N, Ihuoma CJ, Ndu F, Ozumba UC, Udeinya F, Ogunsola F, Saka AO, Fadeyi A, Aderibigbe SA, Abdulraheem J, Yusuf AG, Sylvanus Ndow P, Ogbogu P, Kanu C, Emina V, Makinwa OJ, Gehre F, Yusuf K, Braka F, Mwenda JM, Ticha JM, Nwodo D, Worwui A, Biey JN, Kwambana-Adams BA, Antonio M. Pediatric Bacterial Meningitis Surveillance in Nigeria From 2010 to 2016, Prior to and During the Phased Introduction of the 10-Valent Pneumococcal Conjugate Vaccine. Clin Infect Dis 2020; 69:S81-S88. [PMID: 31505626 PMCID: PMC6736152 DOI: 10.1093/cid/ciz474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Historically, Nigeria has experienced large bacterial meningitis outbreaks with high mortality in children. Streptococcus pneumoniae (pneumococcus), Neisseria meningitidis (meningococcus), and Haemophilus influenzae are major causes of this invasive disease. In collaboration with the World Health Organization, we conducted longitudinal surveillance in sentinel hospitals within Nigeria to establish the burden of pediatric bacterial meningitis (PBM). Methods From 2010 to 2016, cerebrospinal fluid was collected from children <5 years of age, admitted to 5 sentinel hospitals in 5 Nigerian states. Microbiological and latex agglutination techniques were performed to detect the presence of pneumococcus, meningococcus, and H. influenzae. Species-specific polymerase chain reaction and serotyping/grouping were conducted to determine specific causative agents of PBM. Results A total of 5134 children with suspected meningitis were enrolled at the participating hospitals; of these 153 (2.9%) were confirmed PBM cases. The mortality rate for those infected was 15.0% (23/153). The dominant pathogen was pneumococcus (46.4%: 71/153) followed by meningococcus (34.6%: 53/153) and H. influenzae (19.0%: 29/153). Nearly half the pneumococcal meningitis cases successfully serotyped (46.4%: 13/28) were caused by serotypes that are included in the 10-valent pneumococcal conjugate vaccine. The most prevalent meningococcal and H. influenzae strains were serogroup W and serotype b, respectively. Conclusions Vaccine-type bacterial meningitis continues to be common among children <5 years in Nigeria. Challenges with vaccine introduction and coverage may explain some of these finding. Continued surveillance is needed to determine the distribution of serotypes/groups of meningeal pathogens across Nigeria and help inform and sustain vaccination policies in the country.
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Affiliation(s)
- Beckie N Tagbo
- Institute of Child Health, University of Nigeria Teaching Hospital, Ituku-Ozalla, and.,Department of Paediatrics University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu State
| | - Rowan E Bancroft
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul
| | - Iretiola Fajolu
- Department of Paediatrics, Lagos University Teaching Hospital.,Department of Paediatrics, College of Medicine, University of Lagos
| | | | - Muhammad F Bashir
- Department of Paediatrics, Abubakar Tafawa Balewa University Teaching Hospital, Bauchi
| | | | | | - Namadi M Lawal
- Department of Disease Control and Immunization, National Primary Health Care Development Agency, Abuja
| | - Benedict O Edelu
- Department of Paediatrics University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu State
| | - Ngozi Onyejiaka
- Department of Medical Microbiology and Parasitology, Lagos University Teaching Hospital
| | - Chinonyerem J Ihuoma
- Department of Microbiology, University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu State
| | | | - Uchenna C Ozumba
- Department of Microbiology, University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu State
| | - Frances Udeinya
- Department of Microbiology, University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu State
| | - Folasade Ogunsola
- Department of Medical Microbiology and Parasitology, Lagos University Teaching Hospital
| | - Aishat O Saka
- Department of Paediatrics and Child Health, University of Ilorin Teaching Hospital
| | - Abayomi Fadeyi
- Department of Medical Microbiology and Parasitology, University of Ilorin Teaching Hospital, Kwara
| | - Sunday A Aderibigbe
- Department of Epidemiology and Community Health, University of Ilorin Teaching Hospital, Kwara
| | - Jimoh Abdulraheem
- Department of Medical Microbiology and Parasitology, University of Ilorin Teaching Hospital, Kwara
| | - Adamu G Yusuf
- Medical Microbiology Department, Abubakar Tafawa Balewa University Teaching Hospital, Bauchi
| | - Peter Sylvanus Ndow
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul
| | - Philomena Ogbogu
- Department of Medical Microbiology, University of Benin Teaching Hospital
| | - Chinomnso Kanu
- Department of Community Health, University of Benin Teaching Hospital, and
| | - Velly Emina
- Department of Community Health and Primary Care, Lagos University Teaching Hospital, Nigeria
| | - Olajumoke J Makinwa
- Department of Medical Microbiology and Parasitology, Lagos University Teaching Hospital
| | - Florian Gehre
- Department of Paediatrics University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu State.,Department of Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Kabir Yusuf
- Department of Disease Control and Immunization, National Primary Health Care Development Agency, Abuja
| | | | - Jason M Mwenda
- WHO Regional Office for Africa WHO/AFRO, Republic of Congo, Brazzaville
| | | | | | - Archibald Worwui
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul
| | - Joseph N Biey
- WHO Regional Office for Africa WHO/AFRO, Republic of Congo, Brazzaville
| | - Brenda A Kwambana-Adams
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul
| | - Martin Antonio
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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22
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Folino F, Ruggiero L, Capaccio P, Coro I, Aliberti S, Drago L, Marchisio P, Torretta S. Upper Respiratory Tract Microbiome and Otitis Media Intertalk: Lessons from the Literature. J Clin Med 2020; 9:jcm9092845. [PMID: 32887458 PMCID: PMC7563526 DOI: 10.3390/jcm9092845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Otitis media (OM) is one of the most common diseases occurring during childhood. Microbiological investigations concerning this topic have been primarily focused on the four classical otopathogens (Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pyogenes) mainly because most of the studies have been conducted with culture-dependent methods. In recent years, the introduction of culture-independent techniques has allowed high-throughput investigation of entire bacterial communities, leading to a better comprehension of the role of resident flora in health and disease. The upper respiratory tract (URT) is a region of major interest in otitis media pathogenesis, as it could serve as a source of pathogens for the middle ear (ME). Studies conducted with culture-independent methods in the URT and ME have provided novel insights on the pathogenesis of middle ear diseases through the identification of both possible new causative agents and of potential protective bacteria, showing that imbalances in bacterial communities could influence the natural history of otitis media in children. The aim of this review is to examine available evidence in microbiome research and otitis media in the pediatric age, with a focus on its different phenotypes: acute otitis media, otitis media with effusion and chronic suppurative otitis media.
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Affiliation(s)
- Francesco Folino
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Correspondence:
| | - Luca Ruggiero
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Pasquale Capaccio
- Department of Otolaryngology and Head and Neck Surgery, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (P.C.); (S.T.)
- Department of Biomedical Surgical Dental Science, University of Milan, 20122 Milan, Italy
| | - Ilaria Coro
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Stefano Aliberti
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Lorenzo Drago
- Laboratory of Clinical Microbiology, Department of Biomedical Science for Health, University of Milan, 20122 Milan, Italy;
| | - Paola Marchisio
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Sara Torretta
- Department of Otolaryngology and Head and Neck Surgery, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (P.C.); (S.T.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
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23
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Gladstone RA, Bojang E, Hart J, Harding-Esch EM, Mabey D, Sillah A, Bailey RL, Burr SE, Roca A, Bentley SD, Holland MJ. Mass drug administration with azithromycin for trachoma elimination and the population structure of Streptococcus pneumoniae in the nasopharynx. Clin Microbiol Infect 2020; 27:864-870. [PMID: 32750538 PMCID: PMC8203556 DOI: 10.1016/j.cmi.2020.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 11/18/2022]
Abstract
Objective Mass drug administration (MDA) with azithromycin for trachoma elimination reduces nasopharyngeal carriage of Streptococcus pneumoniae in the short term. We evaluated S. pneumoniae carried in the nasopharynx before and after a round of azithromycin MDA to determine whether MDA was associated with changes in pneumococcal population structure and resistance. Methods We analysed 514 pneumococcal whole genomes randomly selected from nasopharyngeal samples collected in two Gambian villages that received three annual rounds of MDA for trachoma elimination. The 514 samples represented 293 participants, of which 75% were children aged 0–9 years, isolated during three cross-sectional surveys (CSSs) conducted before the third round of MDA (CSS-1) and at 1 (CSS-2) and 6 (CSS-3) months after MDA. Bayesian Analysis of Population Structure (BAPS) was used to cluster related isolates by capturing variation in the core genome. Serotype and multilocus sequence type were inferred from the genotype. Antimicrobial resistance determinants were identified from assemblies, including known macrolide resistance genes. Results Twenty-seven BAPS clusters were assigned. These consisted of 81 sequence types (STs). Two BAPS clusters not observed in CSS-1 (n = 109) or CSS-2 (n = 69), increased in frequency in CSS-3 (n = 126); BAPS20 (8.73%, p 0.016) and BAPS22 (7.14%, p 0.032) but were not associated with antimicrobial resistance. Macrolide resistance within BAPS17 increased after treatment (CSS-1 n = 0/6, CSS-2/3 n = 5/5, p 0.002) and was carried on a mobile transposable element that also conferred resistance to tetracycline. Discussion Limited changes in pneumococcal population structure were observed after the third round of MDA, suggesting treatment had little effect on the circulating lineages. An increase in macrolide resistance within one BAPS highlights the need for antimicrobial resistance surveillance in treated villages.
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Affiliation(s)
| | - Ebrima Bojang
- Medical Research Council Unit The Gambia at LSHTM, Fajara, Banjul, Gambia
| | - John Hart
- London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | | | - David Mabey
- London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Ansumana Sillah
- National Eye Health Programme, Ministry of Health and Social Welfare, Kanifing, Gambia
| | - Robin L Bailey
- London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Sarah E Burr
- London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Anna Roca
- Medical Research Council Unit The Gambia at LSHTM, Fajara, Banjul, Gambia; London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | | | - Martin J Holland
- London School of Hygiene & Tropical Medicine, Keppel Street, London, UK.
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24
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Onwuchekwa C, Edem B, Williams V, Oga E. Estimating the impact of pneumococcal conjugate vaccines on childhood pneumonia in sub-Saharan Africa: A systematic review. F1000Res 2020; 9:765. [PMID: 33335713 PMCID: PMC7713889 DOI: 10.12688/f1000research.25227.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/02/2020] [Indexed: 01/25/2023] Open
Abstract
Background: This study aimed to summarise the evidence on the impact of routine administration of 10-valent and 13-valent pneumococcal conjugate vaccines on pneumonia in children under five years of age in sub-Saharan Africa. Methods: A systematic search of the literature was conducted including primary research reporting on the impact of 10- or 13-valent pneumococcal vaccines on childhood pneumonia in a sub-Saharan African country. Case-control, cohort, pre-post and time-series study designs were eligible for inclusion. Thematic narrative synthesis was carried out to summarise the findings. Results: Eight records were included in the final analysis, 6 records were pre-post or time-series studies, 1 was a case-control study and 1 report combined pre-post and case-control studies. Vaccine impact on clinical pneumonia measured as percentage reduction in risk (%RR) was mostly non-significant. The reduction in risk was more consistent in radiological and pneumococcal pneumonia. Conclusions: Evidence of the positive impact of routine infant pneumococcal vaccination on clinical pneumonia incidence in sub-Saharan Africa is inconclusive. Ongoing surveillance and further research is required to establish the long term trend in pneumonia epidemiology and aetiology after PCV introduction. PROSPERO registration: CRD42019142369 30/09/19.
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Affiliation(s)
| | - Bassey Edem
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Serekunda, The Gambia
| | - Victor Williams
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Emmanuel Oga
- Research Triangle Institue (RTI) International, 6110 Executive Boulevard, Rockville, USA
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25
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Onwuchekwa C, Edem B, Williams V, Oga E. Estimating the impact of pneumococcal conjugate vaccines on childhood pneumonia in sub-Saharan Africa: A systematic review. F1000Res 2020; 9:765. [PMID: 33335713 PMCID: PMC7713889 DOI: 10.12688/f1000research.25227.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 03/31/2024] Open
Abstract
Background: This study aimed to summarise the evidence on the impact of routine administration of 10-valent and 13-valent pneumococcal conjugate vaccines on pneumonia in children under five years of age in sub-Saharan Africa. Methods: A systematic search of the literature was conducted including primary research reporting on the impact of 10- or 13-valent pneumococcal vaccines on childhood pneumonia in a sub-Saharan African country. Case-control, cohort, pre-post and time-series study designs were eligible for inclusion. Thematic narrative synthesis was carried out to summarise the findings. Results: Eight records were included in the final analysis, 6 records were pre-post or time-series studies, 1 was a case-control study and 1 report combined pre-post and case-control studies. Vaccine impact on clinical pneumonia measured as percentage reduction in risk (%RR) was mostly non-significant. The reduction in risk was more consistent in radiological and pneumococcal pneumonia. Conclusions: Evidence of the positive impact of routine infant pneumococcal vaccination on clinical pneumonia incidence in sub-Saharan Africa is inconclusive. Ongoing surveillance and further research is required to establish the long term trend in pneumonia epidemiology and aetiology after PCV introduction. PROSPERO registration: CRD42019142369 30/09/19.
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Affiliation(s)
| | - Bassey Edem
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Serekunda, The Gambia
| | - Victor Williams
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Emmanuel Oga
- Research Triangle Institue (RTI) International, 6110 Executive Boulevard, Rockville, USA
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26
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Chaguza C, Senghore M, Bojang E, Gladstone RA, Lo SW, Tientcheu PE, Bancroft RE, Worwui A, Foster-Nyarko E, Ceesay F, Okoi C, McGee L, Klugman KP, Breiman RF, Barer MR, Adegbola RA, Antonio M, Bentley SD, Kwambana-Adams BA. Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation. Nat Commun 2020; 11:3442. [PMID: 32651390 PMCID: PMC7351774 DOI: 10.1038/s41467-020-17327-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/25/2020] [Indexed: 02/08/2023] Open
Abstract
Genomic evolution, transmission and pathogenesis of Streptococcus pneumoniae, an opportunistic human-adapted pathogen, is driven principally by nasopharyngeal carriage. However, little is known about genomic changes during natural colonisation. Here, we use whole-genome sequencing to investigate within-host microevolution of naturally carried pneumococci in ninety-eight infants intensively sampled sequentially from birth until twelve months in a high-carriage African setting. We show that neutral evolution and nucleotide substitution rates up to forty-fold faster than observed over longer timescales in S. pneumoniae and other bacteria drives high within-host pneumococcal genetic diversity. Highly divergent co-existing strain variants emerge during colonisation episodes through real-time intra-host homologous recombination while the rest are co-transmitted or acquired independently during multiple colonisation episodes. Genic and intergenic parallel evolution occur particularly in antibiotic resistance, immune evasion and epithelial adhesion genes. Our findings suggest that within-host microevolution is rapid and adaptive during natural colonisation.
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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.
| | - Madikay Senghore
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ebrima Bojang
- 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
| | - 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
| | - Rowan E Bancroft
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Archibald Worwui
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ebenezer Foster-Nyarko
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Fatima Ceesay
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Catherine Okoi
- 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, USA
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, USA
| | | | - Michael R Barer
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Richard A Adegbola
- RAMBICON Immunisation & Global Health Consulting, 6A Platinum Close, Lekki, Lagos State, Nigeria
| | - 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
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, 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.
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27
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Usuf E, Christian B, Gladstone R, Bojang E, Jawneh K, Cox I, Jallow E, Bojang A, Greenwood B, Adegbola RA, Bentley SD, Hill PC, Roca A. Persistent and emerging pneumococcal carriage serotypes in a rural Gambian community after ten years of pneumococcal conjugate vaccine pressure. Clin Infect Dis 2020; 73:e3825-e3835. [PMID: 32584973 DOI: 10.1093/cid/ciaa856] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 06/22/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The continuing impact of pneumococcal conjugate vaccines (PCVs) in regions with high pneumococcal transmission is threatened by the persistence of vaccine serotypes (VT) and the emergence of non-vaccine serotypes (NVT). METHODS In 2016, we conducted a cross-sectional carriage survey (CSS5) in a community where PCV7 was first introduced in 2006 during a cluster randomised trial conducted before nationwide introduction of PCV7 (2009) and PCV13 (2011). We estimated the prevalence of PCV13 VT and NVT by age and compared these to earlier surveys before (CSS0), during (CSS1-3), and after the trial but before PCV13 (CSS4). Genomic analysis was conducted for the non-typeable pneumococci. RESULTS The prevalence of PCV13 VT carriage decreased during the 10 years between CSS0 and CSS5 across all age groups (67·6% to 13·5%, p<0.001; 59·8% to 14·4%, p<0.001; 43·1% to 17·9%, p<0.001; and 24·0% to 5·1%, p<0.001 in <2, 2-4, 5-14 and ≥15 years respectively). However, there was no difference between CSS4 and CSS5 in children ≥2 years and adults (children < 2 years, no data). The prevalence of PCV13 NVT increased between CSS0 and CSS5 for children <2 years but decreased in older children and adults.In CSS5, serotypes 3, 6A and 19F were the most common VT and non-typeable isolates, the most common NVT. Among non-typeable isolates, 73·0% lost the ability to express a capsule. Of these, 70·8% were from a VT background. CONCLUSIONS The decrease in PCV13 VT that has occurred since the introduction of PCV13 appears to have plateaued. Significant carriage of these serotypes remains in all age groups.
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Affiliation(s)
- Effua Usuf
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at London School Hygiene and Tropical Medicine, Fajara The Gambia
| | | | | | - Ebrima Bojang
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at London School Hygiene and Tropical Medicine, Fajara The Gambia
| | - Kaddijatou Jawneh
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at London School Hygiene and Tropical Medicine, Fajara The Gambia
| | - Isatou Cox
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at London School Hygiene and Tropical Medicine, Fajara The Gambia
| | - Edrissa Jallow
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at London School Hygiene and Tropical Medicine, Fajara The Gambia
| | - Abdoulie Bojang
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at London School Hygiene and Tropical Medicine, Fajara The Gambia
| | | | - Richard A Adegbola
- RAMBICON, Immunisation & Global Health Consulting, Lekki, Lagos, Nigeria
| | | | - Philip C Hill
- Centre for Global Health, Otago University, Otago New Zealand
| | - Anna Roca
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at London School Hygiene and Tropical Medicine, Fajara The Gambia
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Swarthout TD, Fronterre C, Lourenço J, Obolski U, Gori A, Bar-Zeev N, Everett D, Kamng'ona AW, Mwalukomo TS, Mataya AA, Mwansambo C, Banda M, Gupta S, Diggle P, French N, Heyderman RS. High residual carriage of vaccine-serotype Streptococcus pneumoniae after introduction of pneumococcal conjugate vaccine in Malawi. Nat Commun 2020; 11:2222. [PMID: 32376860 PMCID: PMC7203201 DOI: 10.1038/s41467-020-15786-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 03/28/2020] [Indexed: 12/22/2022] Open
Abstract
There are concerns that pneumococcal conjugate vaccines (PCVs) in sub-Saharan Africa sub-optimally interrupt Streptococcus pneumoniae vaccine-serotype (VT) carriage and transmission. Here we assess PCV carriage using rolling, prospective nasopharyngeal carriage surveys between 2015 and 2018, 3.6–7.1 years after Malawi’s 2011 PCV13 introduction. Carriage decay rate is analysed using non-linear regression. Despite evidence of reduction in VT carriage over the study period, there is high persistent residual carriage. This includes among PCV-vaccinated children 3–5-year-old (16.1% relative reduction from 19.9% to 16.7%); PCV-unvaccinated children 6–8-year-old (40.5% reduction from 26.4% to 15.7%); HIV-infected adults 18-40-years-old on antiretroviral therapy (41.4% reduction from 15.2% to 8.9%). VT carriage prevalence half-life is similar among PCV-vaccinated and PCV-unvaccinated children (3.26 and 3.34 years, respectively). Compared with high-income settings, there is high residual VT carriage 3.6–7.1 years after PCV introduction. Rigorous evaluation of strategies to augment vaccine-induced control of carriage, including alternative schedules and catch-up campaigns, is required. Impact of pneumococcal conjugate vaccines (PCV) in controlling carriage needs to be evaluated to inform vaccine policy. Here, Swarthout et al. show in a prospective rolling cross-sectional study in Malawi a high residual prevalence of vaccine-serotype S. pneumoniae 7 years after PCV introduction.
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Affiliation(s)
- Todd D Swarthout
- 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. .,Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Claudio Fronterre
- CHICAS, Lancaster Medical School, Lancaster University, Lancaster, UK
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
| | - Uri Obolski
- School of Public Health, Tel Aviv University, Tel Aviv, Israel.,Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Andrea Gori
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Naor Bar-Zeev
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,International Vaccine Access Center, Department of International Health, Johns Hopkins University, Baltimore, USA
| | - Dean Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,The Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Arox W Kamng'ona
- Department of Biomedical Sciences, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Thandie S Mwalukomo
- Department of Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Andrew A Mataya
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | | | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, UK
| | - Peter Diggle
- CHICAS, Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Neil French
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - 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
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29
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Tack B, Phoba MF, Barbé B, Kalonji LM, Hardy L, Van Puyvelde S, Ingelbeen B, Falay D, Ngonda D, van der Sande MAB, Deborggraeve S, Jacobs J, Lunguya O. Non-typhoidal Salmonella bloodstream infections in Kisantu, DR Congo: Emergence of O5-negative Salmonella Typhimurium and extensive drug resistance. PLoS Negl Trop Dis 2020; 14:e0008121. [PMID: 32240161 PMCID: PMC7156106 DOI: 10.1371/journal.pntd.0008121] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 04/14/2020] [Accepted: 02/07/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Non-typhoidal Salmonella (NTS) are a major cause of bloodstream infection (BSI) in sub-Saharan Africa. This study aimed to assess its longitudinal evolution as cause of BSI, its serotype distribution and its antibiotic resistance pattern in Kisantu, DR Congo. METHODS As part of a national surveillance network, blood cultures were sampled in patients with suspected BSI admitted to Kisantu referral hospital from 2015-2017. Blood cultures were worked-up according to international standards. Results were compared to similar data from 2007 onwards. RESULTS In 2015-2017, NTS (n = 896) represented the primary cause of BSI. NTS were isolated from 7.6% of 11,764 suspected and 65.4% of 1371 confirmed BSI. In children <5 years, NTS accounted for 9.6% of suspected BSI. These data were in line with data from previous surveillance periods, except for the proportion of confirmed BSI, which was lower in previous surveillance periods. Salmonella Typhimurium accounted for 63.1% of NTS BSI and Salmonella Enteritidis for 36.4%. Of all Salmonella Typhimurium, 36.9% did not express the O5-antigen (i.e. variant Copenhagen). O5-negative Salmonella Typhimurium were rare before 2013, but increased gradually from then onwards. Multidrug resistance was observed in 87.4% of 864 NTS isolates, decreased ciprofloxacin susceptibility in 7.3%, ceftriaxone resistance in 15.7% and azithromycin resistance in 14.9%. A total of 14.2% of NTS isolates, that were all Salmonella Typhimurium, were multidrug resistant and ceftriaxone and azithromycin co-resistant. These Salmonella isolates were called extensively drug resistant. Compared to previous surveillance periods, proportions of NTS isolates with resistance to ceftriaxone and azithromycin and decreased ciprofloxacin susceptibility increased. CONCLUSION As in previous surveillance periods, NTS ranked first as the cause of BSI in children. The emergence of O5-negative Salmonella Typhimurium needs to be considered in the light of vaccine development. The high proportions of antibiotic resistance are worrisome.
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Affiliation(s)
- Bieke Tack
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology and Immunology, KU Leuven, Belgium
- * E-mail:
| | - Marie-France Phoba
- Department of Microbiology, National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
- Department of Microbiology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Barbara Barbé
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Lisette M. Kalonji
- Department of Microbiology, National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
- Department of Microbiology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Liselotte Hardy
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sandra Van Puyvelde
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Brecht Ingelbeen
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dadi Falay
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Dauly Ngonda
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Marianne A. B. van der Sande
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
- Global Health Centre, Julius Center for Health Sciences and Primary Care, University Medical Centrum Utrecht, Utrecht University, Utrecht, Netherlands
| | - Stijn Deborggraeve
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology and Immunology, KU Leuven, Belgium
| | - Octavie Lunguya
- Department of Microbiology, National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
- Department of Microbiology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
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30
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Marsh RL, Aho C, Beissbarth J, Bialasiewicz S, Binks M, Cervin A, Kirkham LAS, Lemon KP, Slack MPE, Smith-Vaughan HC. Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures. Int J Pediatr Otorhinolaryngol 2020; 130 Suppl 1:109836. [PMID: 31879084 PMCID: PMC7085411 DOI: 10.1016/j.ijporl.2019.109836] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To perform a comprehensive review of otitis media microbiome literature published between 1st July 2015 and 30th June 2019. DATA SOURCES PubMed database, National Library of Medicine. REVIEW METHODS Key topics were assigned to each panel member for detailed review. Draft reviews were collated and circulated for discussion when the panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019. The final draft was prepared with input from all panel members. CONCLUSIONS Much has been learned about the different types of bacteria (including commensals) present in the upper respiratory microbiome, but little is known about the virome and mycobiome. A small number of studies have investigated the middle ear microbiome; however, current data are often limited by small sample sizes and methodological heterogeneity between studies. Furthermore, limited reporting of sample collection methods mean that it is often difficult to determine whether bacteria detected in middle ear fluid specimens originated from the middle ear or the external auditory canal. Recent in vitro studies suggest that bacterial interactions in the nasal/nasopharyngeal microbiome may affect otitis media pathogenesis by modifying otopathogen behaviours. Impacts of environmental pressures (e.g. smoke, nutrition) and clinical interventions (e.g. vaccination, antibiotics) on the upper respiratory and middle ear microbiomes remain poorly understood as there are few data. IMPLICATIONS FOR PRACTICE Advances in understanding bacterial dynamics in the upper airway microbiome are driving development of microbiota-modifying therapies to prevent or treat disease (e.g. probiotics). Further advances in otitis media microbiomics will likely require technological improvements that overcome the current limitations of OMICs technologies when applied to low volume and low biomass specimens that potentially contain high numbers of host cells. Improved laboratory models are needed to elucidate mechanistic interactions among the upper respiratory and middle ear microbiomes. Minimum reporting standards are critically needed to improve inter-study comparisons and enable future meta-analyses.
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Affiliation(s)
- Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia.
| | - Celestine Aho
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Jemima Beissbarth
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia
| | - Seweryn Bialasiewicz
- The University of Queensland, Australian Centre for Ecogenomics, Queensland, Australia; Children's Health Queensland, Centre for Children's Health Research, Queensland, Australia
| | - Michael Binks
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia
| | - Anders Cervin
- The University of Queensland Centre for Clinical Research, Royal Brisbane & Women's Hospital, Queensland, Australia
| | - Lea-Ann S Kirkham
- Centre for Child Health Research, University of Western Australia, Western Australia, Australia; Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Western Australia, Australia
| | - Katherine P Lemon
- Forsyth Institute (Microbiology), USA and Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Massachusetts, USA; Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology and Pediatrics, Infectious Diseases Section, Texas Children's Hospital, Baylor College of Medicine, Texas, USA
| | - Mary P E Slack
- School of Medicine, Griffith University, Gold Coast Campus, Queensland, Australia
| | - Heidi C Smith-Vaughan
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia; School of Medicine, Griffith University, Gold Coast Campus, Queensland, Australia
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Lemma M, Bekele Y, Petkov S, Hägglund M, Petros B, Aseffa A, Howe R, Chiodi F. Streptococcus pneumoniae Nasopharyngeal Carriage among PCV-10-Vaccinated HIV-1-Infected Children with Maintained Serological Memory in Ethiopia. Pathogens 2020; 9:pathogens9030159. [PMID: 32106620 PMCID: PMC7157605 DOI: 10.3390/pathogens9030159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/19/2020] [Accepted: 02/23/2020] [Indexed: 11/16/2022] Open
Abstract
Streptococcus pneumoniae (S. pneumoniae) vaccines have substantially reduced the burden of invasive pneumococcal diseases (IPDs) worldwide. Despite high coverage with S. pneumoniae vaccination, upper-respiratory-tract colonization by S. pneumoniae is still common. We assessed maintenance of serological responses to S. pneumoniae serotypes included in PCV-10 by ELISA in HIV-1-infected children (n = 50) and age-matched controls (n = 50) in Ethiopia. We isolated S. pneumoniae in nasopharyngeal swabs and determined S. pneumoniae serotype by whole genome sequencing (WGS). Comparable levels of S. pneumoniae serotype-specific IgG concentrations were detected in plasma of HIV-1-infected children and matched controls, with geometric mean concentrations (GMCs) consistently higher than the protective threshold for PCV-10 serotypes of 0.35 μg/mL. We isolated S. pneumoniae from 38 (out of 97) nasopharyngeal swabs, 25 from HIV-1-infected children and 13 from controls. WGS based serotyping revealed 22 known S. pneumoniae serotypes and 2 nontypeable (NT) isolates. Non-PCV-10 serotypes represented >90% of isolates. We showed that HIV-1-infected children and matched controls in Ethiopia carry a level of maintained serological memory to PCV-10 considered protective for IPDs. We identified a higher proportion of nasopharyngeal carriage with highly pathogenic S. pneumoniae non-PCV strains among HIV-1-infected children compared to controls.
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Affiliation(s)
- Mahlet Lemma
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 9, 17165 Solna, Sweden
- Armauer Hansen Research Institute, Jimma Road, ALERT compound P.O. Box 1005, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Arat Kilo Campus, Addis Ababa, Ethiopia
| | - Yonas Bekele
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 9, 17165 Solna, Sweden
| | - Stefan Petkov
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 9, 17165 Solna, Sweden
| | - Moa Hägglund
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden
| | - Beyene Petros
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Arat Kilo Campus, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Jimma Road, ALERT compound P.O. Box 1005, Addis Ababa, Ethiopia
| | - Rawleigh Howe
- Armauer Hansen Research Institute, Jimma Road, ALERT compound P.O. Box 1005, Addis Ababa, Ethiopia
| | - Francesca Chiodi
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 9, 17165 Solna, Sweden
- Correspondence:
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Habibi Ghahfarokhi S, Mosadegh M, Ahmadi A, Pourmand MR, Azarsa M, Rahbar M, Nikmanesh B. Serotype Distribution and Antibiotic Susceptibility of Streptococcus pneumoniae Isolates in Tehran, Iran: A Surveillance Study. Infect Drug Resist 2020; 13:333-340. [PMID: 32099424 PMCID: PMC7007777 DOI: 10.2147/idr.s234295] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 01/23/2020] [Indexed: 11/23/2022] Open
Abstract
Introduction Encapsulated Streptococcus pneumoniae strains cause high morbidity and mortality, mainly in countries with no pneumococcal conjugate vaccines (PCVs) immunization program. This study investigated the epidemiological changes of S. pneumoniae isolates including serotype distribution and antimicrobial susceptibility in Tehran, Iran. Methods A total of 80 S. pneumoniae samples were collected from patients admitted to Shariati hospital over two periods. Half of the isolates were collected from February to September 2017 and the other half from July 2018 to March 2019. The antimicrobial susceptibility testing and PCV-13 serotype coverage of S. pneumoniae isolates were evaluated among patients with invasive and non-invasive infections. Results The most common serotypes were 23F (17.5%), 14 (16.3%), 3 (16.3%) 19F (12.5%), and 19A (12.5%) in the present study. The vaccine coverage rates of PCV-7, PCV-10 and PCV-13 were 52.6%, 52.6%, and 83.7%, respectively. S. pneumoniae isolates with the serotype of the PCV-13 showed an increasing trend during the study. Nearly half of the S. pneumoniae strains were MDR, while MDR serotype 19A increased (40%) during the study periods. A small minority of isolates (16%) belonged to non-vaccine serotypes, 65% of which were assigned to MDR. In general, the frequency of penicillin resistant and MDR strains were estimated about 27.5% and 51%, respectively. An increase was observed in resistance to erythromycin and co-trimoxazole. Conclusion The results showed that majority of the circulating serotypes in our study are related to PCV-13 serotypes. The use of conjugate vaccine in the immunization program and surveillance of antimicrobial resistance can be effective in reducing the pneumococcal clinical burden.
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Affiliation(s)
- Soheila Habibi Ghahfarokhi
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Mosadegh
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Azarsa
- Department of Microbiology, Khoy University of Medical Sciences, Khoy, Iran
| | - Mohammad Rahbar
- Department of Microbiology, Reference Health Laboratories Research Center, Ministry of Health and Medical Education, Tehran, Iran
| | - Bahram Nikmanesh
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
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Effects of 10-valent pneumococcal conjugate (PCV10) vaccination on the nasopharyngeal microbiome. Vaccine 2020; 38:1436-1443. [DOI: 10.1016/j.vaccine.2019.11.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 11/19/2019] [Accepted: 11/28/2019] [Indexed: 01/02/2023]
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34
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Chaguza C, Senghore M, Bojang E, Lo SW, Ebruke C, Gladstone RA, Tientcheu PE, Bancroft RE, Worwui A, Foster-Nyarko E, Ceesay F, Okoi C, McGee L, Klugman KP, Breiman RF, Barer MR, Adegbola RA, Antonio M, Bentley SD, Kwambana-Adams BA. Carriage Dynamics of Pneumococcal Serotypes in Naturally Colonized Infants in a Rural African Setting During the First Year of Life. Front Pediatr 2020; 8:587730. [PMID: 33489998 PMCID: PMC7820366 DOI: 10.3389/fped.2020.587730] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) carriage precedes invasive disease and influences population-wide strain dynamics, but limited data exist on temporal carriage patterns of serotypes due to the prohibitive costs of longitudinal studies. Here, we report carriage prevalence, clearance and acquisition rates of pneumococcal serotypes sampled from newborn infants bi-weekly from weeks 1 to 27, and then bi-monthly from weeks 35 to 52 in the Gambia. We used sweep latex agglutination and whole genome sequencing to serotype the isolates. We show rapid pneumococcal acquisition with nearly 31% of the infants colonized by the end of first week after birth and quickly exceeding 95% after 2 months. Co-colonization with multiple serotypes was consistently observed in over 40% of the infants at each sampling point during the first year of life. Overall, the mean acquisition time and carriage duration regardless of serotype was 38 and 24 days, respectively, but varied considerably between serotypes comparable to observations from other regions. Our data will inform disease prevention and control measures including providing baseline data for parameterising infectious disease mathematical models including those assessing the impact of clinical interventions such as pneumococcal conjugate vaccines.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom.,Darwin College, University of Cambridge, Cambridge, United Kingdom
| | - Madikay Senghore
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Ebrima Bojang
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Stephanie W Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Chinelo Ebruke
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Peggy-Estelle Tientcheu
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Rowan E Bancroft
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Archibald Worwui
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Ebenezer Foster-Nyarko
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Fatima Ceesay
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Catherine Okoi
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Robert F Breiman
- Emory Global Health Institute, Emory University, Atlanta, GA, United States
| | - Michael R Barer
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Richard A Adegbola
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia.,RAMBICON Immunisation & Global Health Consulting, Lekki, Nigeria
| | - Martin Antonio
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia.,Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom.,Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Brenda A Kwambana-Adams
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia.,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom
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Tin Tin Htar M, Sings HL, Syrochkina M, Taysi B, Hilton B, Schmitt HJ, Gessner BD, Jodar L. The impact of pneumococcal conjugate vaccines on serotype 19A nasopharyngeal carriage. Expert Rev Vaccines 2019; 18:1243-1270. [DOI: 10.1080/14760584.2019.1675521] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Heather L. Sings
- Vaccines Medical Development and Scientific and Clinical Affairs, Pfizer Inc, Collegeville, PA, USA
| | - Maria Syrochkina
- Vaccines Medical Development and Scientific and Clinical Affairs, Pfizer Inc, Moscow, Russia
| | - Bulent Taysi
- Vaccines Medical Development and Scientific and Clinical Affairs, Pfizer Inc, Istanbul, Turkey
| | - Betsy Hilton
- Vaccines Medical Development and Scientific and Clinical Affairs, Pfizer Inc, Collegeville, PA, USA
| | - Heinz-Josef Schmitt
- Vaccines Medical Development and Scientific and Clinical Affairs, Pfizer Inc, Collegeville, PA, USA
| | - Bradford D. Gessner
- Vaccines Medical Development and Scientific and Clinical Affairs, Pfizer Inc, Collegeville, PA, USA
| | - Luis Jodar
- Vaccines Medical Development and Scientific and Clinical Affairs, Pfizer Inc, Collegeville, PA, USA
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Coughtrie AL, Jefferies JM, Cleary DW, Doncaster CP, Faust SN, Kraaijeveld AR, Moore MV, Mullee MA, Roderick PJ, Webb JS, Yuen HM, Clarke SC. Microbial epidemiology and carriage studies for the evaluation of vaccines. J Med Microbiol 2019; 68:1408-1418. [DOI: 10.1099/jmm.0.001046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Abigail L. Coughtrie
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Johanna M. Jefferies
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - David W. Cleary
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | | | - Saul N. Faust
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
- NIHR Southampton Clinical Research Facility, University Hospital Southampton Foundation NHS Trust, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | | | - Michael V. Moore
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Mark A. Mullee
- NIHR Research Design Service South Central, University Hospital Southampton Foundation NHS Trust, Southampton, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Paul J. Roderick
- Global Health Research Institute, University of Southampton, Southampton, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Jeremy S. Webb
- Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Ho Ming Yuen
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Stuart C. Clarke
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
- Global Health Research Institute, University of Southampton, Southampton, UK
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37
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Lo SW, Gladstone RA, van Tonder AJ, Lees JA, du Plessis M, Benisty R, Givon-Lavi N, Hawkins PA, Cornick JE, Kwambana-Adams B, Law PY, Ho PL, Antonio M, Everett DB, Dagan R, von Gottberg A, Klugman KP, McGee L, Breiman RF, Bentley SD. Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study. THE LANCET. INFECTIOUS DISEASES 2019; 19:759-769. [PMID: 31196809 PMCID: PMC7641901 DOI: 10.1016/s1473-3099(19)30297-x] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Invasive pneumococcal disease remains an important health priority owing to increasing disease incidence caused by pneumococci expressing non-vaccine serotypes. We previously defined 621 Global Pneumococcal Sequence Clusters (GPSCs) by analysing 20 027 pneumococcal isolates collected worldwide and from previously published genomic data. In this study, we aimed to investigate the pneumococcal lineages behind the predominant serotypes, the mechanism of serotype replacement in disease, as well as the major pneumococcal lineages contributing to invasive pneumococcal disease in the post-vaccine era and their antibiotic resistant traits. METHODS We whole-genome sequenced 3233 invasive pneumococcal disease isolates from laboratory-based surveillance programmes in Hong Kong (n=78), Israel (n=701), Malawi (n=226), South Africa (n=1351), The Gambia (n=203), and the USA (n=674). The genomes represented pneumococci from before and after pneumococcal conjugate vaccine (PCV) introductions and were from children younger than 3 years. We identified predominant serotypes by prevalence and their major contributing lineages in each country, and assessed any serotype replacement by comparing the incidence rate between the pre-PCV and PCV periods for Israel, South Africa, and the USA. We defined the status of a lineage as vaccine-type GPSC (≥50% 13-valent PCV [PCV13] serotypes) or non-vaccine-type GPSC (>50% non-PCV13 serotypes) on the basis of its initial serotype composition detected in the earliest vaccine period to measure their individual contribution toward serotype replacement in each country. Major pneumococcal lineages in the PCV period were identified by pooled incidence rate using a random effects model. FINDINGS The five most prevalent serotypes in the PCV13 period varied between countries, with only serotypes 5, 12F, 15B/C, 19A, 33F, and 35B/D common to two or more countries. The five most prevalent serotypes in the PCV13 period varied between countries, with only serotypes 5, 12F, 15B/C, 19A, 33F, and 35B/D common to two or more countries. These serotypes were associated with more than one lineage, except for serotype 5 (GPSC8). Serotype replacement was mainly mediated by expansion of non-vaccine serotypes within vaccine-type GPSCs and, to a lesser extent, by increases in non-vaccine-type GPSCs. A globally spreading lineage, GPSC3, expressing invasive serotypes 8 in South Africa and 33F in the USA and Israel, was the most common lineage causing non-vaccine serotype invasive pneumococcal disease in the PCV13 period. We observed that same prevalent non-vaccine serotypes could be associated with distinctive lineages in different countries, which exhibited dissimilar antibiotic resistance profiles. In non-vaccine serotype isolates, we detected significant increases in the prevalence of resistance to penicillin (52 [21%] of 249 vs 169 [29%] of 575, p=0·0016) and erythromycin (three [1%] of 249 vs 65 [11%] of 575, p=0·0031) in the PCV13 period compared with the pre-PCV period. INTERPRETATION Globally spreading lineages expressing invasive serotypes have an important role in serotype replacement, and emerging non-vaccine serotypes associated with different pneumococcal lineages in different countries might be explained by local antibiotic-selective pressures. Continued genomic surveillance of the dynamics of the pneumococcal population with increased geographical representation in the post-vaccine period will generate further knowledge for optimising future vaccine design. FUNDING Bill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control.
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Affiliation(s)
- Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
| | | | | | - John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Rachel Benisty
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Noga Givon-Lavi
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | | | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Pierra Y Law
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Pak Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Dean B Everett
- Centre for Inflammation Research, Queens Research Institute, University of Edinburgh, Edinburgh, UK
| | - Ron Dagan
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Keith P Klugman
- Rollins School Public Health, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School Public Health, Emory University, Atlanta, GA, USA; Emory Global Health Institute, Emory University, Atlanta, GA, USA
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Kombe IK, Munywoki PK, Baguelin M, Nokes DJ, Medley GF. Model-based estimates of transmission of respiratory syncytial virus within households. Epidemics 2019; 27:1-11. [PMID: 30591267 PMCID: PMC6543068 DOI: 10.1016/j.epidem.2018.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) causes a significant respiratory disease burden in the under 5 population. The transmission pathway to young children is not fully quantified in low-income settings, and this information is required to design interventions. METHODS We used an individual level transmission model to infer transmission parameters using data collected from 493 individuals distributed across 47 households over a period of 6 months spanning the 2009/2010 RSV season. A total of 208 episodes of RSV were observed from 179 individuals. We model competing transmission risk from within household exposure and community exposure while making a distinction between RSV groups A and B. RESULTS We find that 32-53% of all RSV transmissions are between members of the same household; the rate of pair-wise transmission is 58% (95% CrI: 30-74%) lower in larger households (≥8 occupants) than smaller households; symptomatic individuals are 2-7 times more infectious than asymptomatic individuals i.e. 2.48 (95% CrI: 1.22-5.57) among symptomatic individuals with low viral load and 6.7(95% CrI: 2.56-16) among symptomatic individuals with high viral load; previous infection reduces susceptibility to re-infection within the same epidemic by 47% (95% CrI: 17%-68%) for homologous RSV group and 39% (95%CrI: -8%-69%) for heterologous group; RSV B is more frequently introduced into the household, and RSV A is more rapidly transmitted once in the household. DISCUSSION Our analysis presents the first transmission modelling of cohort data for RSV and we find that it is important to consider the household social structuring and household size when modelling transmission. The increased infectiousness of symptomatic individuals implies that a vaccine against RSV related disease would also have an impact on infection transmission. Together, the weak cross immunity between RSV groups and the possibility of different transmission niches could form part of the explanation for the group co-existence.
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Affiliation(s)
- Ivy K Kombe
- KEMRI-Wellcome Trust Research Programme, KEMRI Center for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya; Centre for Mathematical Modelling of Infectious Disease and Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK.
| | - Patrick K Munywoki
- KEMRI-Wellcome Trust Research Programme, KEMRI Center for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya
| | - Marc Baguelin
- Centre for Mathematical Modelling of Infectious Disease and Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK
| | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, KEMRI Center for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya; School of Life Sciences and Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, Coventry, CV4 7AL, UK
| | - Graham F Medley
- Centre for Mathematical Modelling of Infectious Disease and Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK
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Picazo JJ, Ruiz-Contreras J, Casado-Flores J, Negreira S, Baquero-Artigao F, Hernández-Sampelayo T, Otheo E, Amo MD, Méndez C. Impact of 13-valent pneumococcal conjugate vaccination on invasive pneumococcal disease in children under 15 years old in Madrid, Spain, 2007 to 2016: The HERACLES clinical surveillance study. Vaccine 2019; 37:2200-2207. [PMID: 30902478 DOI: 10.1016/j.vaccine.2019.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/07/2019] [Accepted: 03/11/2019] [Indexed: 11/28/2022]
Abstract
Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide. Using the data from the HERACLES clinical surveillance study (2007-2016), we describe the population impact of the 13-valent pneumococcal conjugate vaccine (PVC13) on invasive pneumococcal disease (IPD) in children <15 years of age in the Community of Madrid, Spain. After six years of the inclusion of PCV13 in the vaccination calendar (2010-2016), and despite changes in the Regional Immunization Programme that limited its availability, the net benefit incidence rate (IR) of IPD fell by 70.1% (IRR 0.3 [95% CI: 0.22-0.4]; p ≤ 0.001), mainly due to a significant reduction (91%) in the PCV13 serotypes (IRR 0.09 [95% CI: 0.05-0.16], p ≤ 0.001). Furthermore, no significant changes were detected in the IR of IPD caused by non-PCV13 serotypes. The IRs of the aggressive, resistant and most prevalent serotype in the analysed population, the 19A serotype, dramatically decreased from the beginning to the end of the study (98%) [IRR 0.03 (95% CI: 0.00-0.19), p ≤ 0.001], to its almost total disappearance. Remarkably, this reduction led to a pronounced decline in the percentage of cefotaxime-resistant isolates and the incidence of meningitis cases. Assessment of the clinical impact revealed a reduction in the number of all clinical presentations of IPD, confirming the effectiveness of the PCV13. Finally, PCV13 detected by PCR is predicted to have a stronger impact than the one based on culture methods, which can overlook more than 20% of cases of IPD, mainly pleural empyemas.
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Affiliation(s)
- Juan J Picazo
- Medicine Department, School of Medicine, Universidad Complutense, Madrid, Spain.
| | - Jesús Ruiz-Contreras
- PediatricDepartment, Hospital Universitario 12 de Octubre, Madrid, Spain; Pediatric Department, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Juan Casado-Flores
- Pediatric ICU, Hospital Universitario Infantil Niño Jesús, Madrid, Spain; Pediatric Department, School of Medicine, Universidad Autónoma, Madrid, Spain
| | - Sagrario Negreira
- PediatricDepartment, Hospital Universitario 12 de Octubre, Madrid, Spain; Pediatric Department, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Fernando Baquero-Artigao
- Pediatric Department, School of Medicine, Universidad Autónoma, Madrid, Spain; Pediatric Department, Hospital Universitario La Paz, Madrid, Spain
| | - Teresa Hernández-Sampelayo
- Pediatric Department, School of Medicine, Universidad Complutense, Madrid, Spain; Pediatric Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; CIBER of Respiratory Diseases, CIBERES, Madrid, Spain
| | - Enrique Otheo
- Pediatric Department, Hospital Universitario Ramón y Cajal, Madrid, Spain; Faculty of Medicine, Universidad de Alcalá, Madrid, Spain
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Mrkvan T, Pelton SI, Ruiz-Guiñazú J, Palmu AA, Borys D. Effectiveness and impact of the 10-valent pneumococcal conjugate vaccine, PHiD-CV: review of clinical trials and post-marketing experience. Expert Rev Vaccines 2019; 17:797-818. [PMID: 30185083 DOI: 10.1080/14760584.2018.1516551] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
INTRODUCTION Pneumococcal diseases (including septicemia, meningitis, pneumonia, and upper respiratory infections) constitute a major public health problem. The World Health Organization recommends pneumococcal conjugate vaccine immunization of young children worldwide. AREAS COVERED We reviewed evidence on the effects of the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV), which is used in childhood immunization programs in over 45 countries or regions. The effectiveness of PHiD-CV against invasive pneumococcal disease (IPD), pneumonia, and acute otitis media was assessed. We also present its effect on pneumococcal nasopharyngeal carriage (NPC) and indirect effects (herd protection) among unvaccinated individuals. EXPERT COMMENTARY Results from randomized, double-blind trials and post-marketing studies in various countries provide evidence of the protective efficacy, effectiveness, and impact of PHiD-CV against pneumococcal diseases. Data from different geographic locations also show reductions in NPC of vaccine pneumococcal serotypes, laying the foundation for indirect protection against pneumococcal disease. In countries where PHiD-CV is included in childhood immunization programs, there are signs of herd protection for vaccine serotypes among unvaccinated individuals. Although increases in non-vaccine serotype IPD and NPC rates were observed, there was an overall reduction of pneumococcal disease.
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Affiliation(s)
| | - Stephen I Pelton
- b Maxwell Finland Laboratory for Infectious Diseases , Boston University , Boston , MA , USA
| | | | - Arto A Palmu
- c Department of Public Health Solutions , National Institute for Health and Welfare , Tampere , Finland
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Salter SJ, Scott P, Page AJ, Tracey A, de Goffau MC, Cormie C, Ochoa-Montaño B, Ling CL, Tangmanakit J, Turner P, Parkhill J. 'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs. Microb Genom 2019; 5. [PMID: 30720420 PMCID: PMC6421346 DOI: 10.1099/mgen.0.000247] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
'Candidatus Ornithobacterium hominis' represents a new member of the Flavobacteriaceae detected in 16S rRNA gene surveys of people from South-East Asia, Africa and Australia. It frequently colonizes the infant nasopharynx at high proportional abundance, and we demonstrate its presence in 42 % of nasopharyngeal swabs from 12-month-old children in the Maela refugee camp in Thailand. The species, a Gram-negative bacillus, has not yet been cultured, but the cells can be identified in mixed samples by fluorescent hybridization. Here, we report seven genomes assembled from metagenomic data, two to improved draft standard. The genomes are approximately 1.9 Mb, sharing 62 % average amino acid identity with the only other member of the genus, the bird pathogen Ornithobacterium rhinotracheale. The draft genomes encode multiple antibiotic-resistance genes, competition factors, Flavobacterium johnsoniae-like gliding motility genes and a homologue of the Pasteurella multocida mitogenic toxin. Intra- and inter-host genome comparison suggests that colonization with this bacterium is both persistent and strain exclusive.
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Affiliation(s)
| | - Paul Scott
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | - Andrew J Page
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK.,†Present address: Quadram Institute Bioscience, Norwich, UK
| | - Alan Tracey
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | | | - Claire Cormie
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | - Bernardo Ochoa-Montaño
- 2Department of Biochemistry, University of Cambridge, Cambridge, UK.,‡Present address: Illumina Cambridge Ltd, Little Chesterford, UK
| | - Clare L Ling
- 3Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,4Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiraporn Tangmanakit
- 3Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Paul Turner
- 4Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,5Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
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Emgård M, Msuya SE, Nyombi BM, Mosha D, Gonzales-Siles L, Nordén R, Geravandi S, Mosha V, Blomqvist J, Franzén S, Sahlgren F, Andersson R, Skovbjerg S. Carriage of penicillin-non-susceptible pneumococci among children in northern Tanzania in the 13-valent pneumococcal vaccine era. Int J Infect Dis 2019; 81:156-166. [PMID: 30685588 DOI: 10.1016/j.ijid.2019.01.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 01/18/2019] [Accepted: 01/19/2019] [Indexed: 10/27/2022] Open
Abstract
OBJECTIVES To determine the antibiotic susceptibility and serotype distribution of colonizing Streptococcus pneumoniae in Tanzanian children. Serial cross-sectional surveys were performed following the national introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in December 2012. METHODS A total of 775 children less than 2 years of age were recruited at primary health centres in Moshi, Tanzania between 2013 and 2015, and samples were obtained from the nasopharynx. S. pneumoniae were isolated by culture and tested for antibiotic susceptibility by disc diffusion and E-test methods; molecular testing was used to determine serotype/group. RESULTS Penicillin non-susceptibility in the isolated pneumococci increased significantly from 31% (36/116) in 2013, to 47% (30/64) in 2014 and 53% (32/60) in 2015. Non-susceptibility to amoxicillin/ampicillin and ceftriaxone was low (n=8 and n=9, respectively), while 97% (236/244) of the isolates were non-susceptible to trimethoprim-sulfamethoxazole. The majority of the children (54%, n=418) had been treated with antibiotics in the past 3 months, and amoxicillin/ampicillin were overall the most commonly used antibiotics. Carriage of penicillin-non-susceptible pneumococci was more common in children with many siblings. The prevalence of PCV13 serotypes among the detected serotypes/groups decreased from 56% (40/71) in 2013 to 23% (13/56) in 2015. CONCLUSIONS Penicillin non-susceptibility in S. pneumoniae colonizing Tanzanian children increased during an observation period shortly after the introduction of PCV13. Measures to ensure rational use of antibiotics and more effective systems for surveillance of antibiotic resistance and serotype distribution are needed to assure continued effective treatment of pneumococcal disease.
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Affiliation(s)
- Matilda Emgård
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.
| | - Sia E Msuya
- Institute of Public Health, Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania; Department of Community Medicine, Kilimanjaro Christian Medical Centre (KCMC), Moshi, Tanzania
| | - Balthazar M Nyombi
- Institute of Public Health, Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania; Department of Community Medicine, Kilimanjaro Christian Medical Centre (KCMC), Moshi, Tanzania
| | - Dominic Mosha
- Institute of Public Health, Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania
| | - Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Rickard Nordén
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Shadi Geravandi
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Victor Mosha
- Institute of Public Health, Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania
| | - Josefine Blomqvist
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sofie Franzén
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Fredrika Sahlgren
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Rune Andersson
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Susann Skovbjerg
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
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Hsu CF, Hsiao CH, Tseng SF, Chen JR, Liao YJ, Chen SJ, Lin CS, Sytwu HK, Chuang YP. PrtA immunization fails to protect against pulmonary and invasive infection by Streptococcus pneumoniae. Respir Res 2018; 19:187. [PMID: 30253765 PMCID: PMC6157060 DOI: 10.1186/s12931-018-0895-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/17/2018] [Indexed: 12/27/2022] Open
Abstract
Background Streptococcus pneumoniae is a respiratory pathogen causing severe lung infection that may lead to complications such as bacteremia. Current polysaccharide vaccines have limited serotype coverage and therefore cannot provide maximal and long-term protection. Global efforts are being made to develop a conserved protein vaccine candidate. PrtA, a pneumococcal surface protein, was identified by screening a pneumococcal genomic expression library using convalescent patient serum. The prtA gene is prevalent and conserved among S. pneumoniae strains. Its protective efficacy, however, has not been described. Mucosal immunization could sensitize both local and systemic immunity, which would be an ideal scenario for preventing S. pneumoniae infection. Methods We immunized BALB/c mice intranasally with a combination of a PrtA fragment (amino acids 144–1041) and Th17 potentiated adjuvant, curdlan. We then measured the T-cell and antibody responses. The protective efficacy conferred to the immunized mice was further evaluated using a murine model of acute pneumococcal pneumonia and pneumococcal bacteremia. Results There was a profound antigen-specific IL-17A and IFN-γ response in PrtA-immunized mice compared with that of adjuvant control group. Even though PrtA-specific IgG and IgA titer in sera was elevated in immunized mice, only a moderate IgA response was observed in the bronchoalveolar lavage fluid. The PrtA-immunized antisera facilitated the activated murine macrophage, RAW264.7, to opsonophagocytose S. pneumoniae D39 strain; however, PrtA-specific immunoglobulins bound to pneumococcal surfaces with a limited potency. Finally, PrtA-induced immune reactions failed to protect mice against S. pneumoniae-induced acute pneumonia and bacterial propagation through the blood. Conclusions Immunization with recombinant PrtA combined with curdlan produced antigen-specific antibodies and elicited IL-17A response. However, it failed to protect the mice against S. pneumoniae-induced infection. Electronic supplementary material The online version of this article (10.1186/s12931-018-0895-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chen-Fang Hsu
- Department of Pediatrics, Chi Mei Medical Center, Tainan, Taiwan.,Taipei Medical University, Taipei, Taiwan.,Kaohsiung Medical University, Kaohsiung, Taiwan.,Chung Shan Medical University, Taichung, Taiwan
| | - Chen-Hao Hsiao
- Cheng Hsin General Hospital, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Shun-Fu Tseng
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Jian-Ru Chen
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Jou Liao
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Sy-Jou Chen
- Department of Emergency Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.,Graduate Institute of Injury Prevention and Control, College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwan
| | - Chin-Sheng Lin
- Division of Cardiology, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Huey-Kang Sytwu
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan.,National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Yi-Ping Chuang
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan.
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Dube FS, Ramjith J, Gardner-Lubbe S, Nduru P, Robberts FJL, Wolter N, Zar HJ, Nicol MP. Longitudinal characterization of nasopharyngeal colonization with Streptococcus pneumoniae in a South African birth cohort post 13-valent pneumococcal conjugate vaccine implementation. Sci Rep 2018; 8:12497. [PMID: 30131607 PMCID: PMC6104038 DOI: 10.1038/s41598-018-30345-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/23/2018] [Indexed: 12/28/2022] Open
Abstract
Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage and impact on health. We longitudinally investigated pneumococcal carriage dynamics in infants. Pneumococcal isolates were obtained from nasopharyngeal (NP) swabs collected 2-weekly from 137 infants enrolled from birth through their first year of life. Pneumococci were serotyped by sequetyping, confirmed by Quellung. Pneumococci were isolated from 54% (1809/3331) of infants. Median time to first acquisition was 63 days. Serotype-specific acquisition rates ranged from 0.01 to 0.88 events/child-year and did not differ between PCV13 and non-PCV13 serotypes (0.11 events/child-year [95% CI 0.07-0.18] vs. 0.11 events/child-year [95% CI 0.06-0.18]). There was no difference in carriage duration between individual PCV13 and non-PCV13 serotypes (40.6 days [95% CI 31.9-49.4] vs. 38.6 days [95% CI 35.1-42.1]), however cumulatively the duration of carriage of non-PCV13 serotypes was greater than PCV13 serotypes (141.2 days (95% CI 126.6-155.8) vs. 30.7 days (95% CI 22.3-39.0). Frequently carried PCV13 serotypes included 19F, 9V, 19A and 6A, while non-PCV13 serotypes included 15B/15C, 21, 10A, 16F, 35B, 9N and 15A. Despite high immunization coverage in our setting, PCV13 serotypes remain in circulation in this cohort, comprising 22% of isolates. Individual PCV13 serotypes were acquired, on average, at equivalent rate to non-PCV13 serotypes, and carried for a similar duration, although the most common non-PCV13 serotypes were more frequently acquired than PCV13 serotypes.
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Affiliation(s)
- Felix S Dube
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa. .,Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Jordache Ramjith
- Division of Epidemiology & Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Sugnet Gardner-Lubbe
- Department of Statistical Sciences, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Polite Nduru
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - F J Lourens Robberts
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis (CRDM), 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
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa.,SAMRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.,Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Pneumococcal conjugate vaccine 13 delivered as one primary and one booster dose (1 + 1) compared with two primary doses and a booster (2 + 1) in UK infants: a multicentre, parallel group randomised controlled trial. THE LANCET. INFECTIOUS DISEASES 2017; 18:171-179. [PMID: 29174323 PMCID: PMC5805912 DOI: 10.1016/s1473-3099(17)30654-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/29/2022]
Abstract
Background Infants in the UK were first offered a pneumococcal conjugate vaccine (PCV7) in 2006, given at 2 and 4 months of age and a booster dose at 13 months (2 + 1 schedule). A 13-valent vaccine (PCV13) replaced PCV7 in 2010. We aimed to compare the post-booster antibody response in UK infants given a reduced priming schedule of PCV13 (ie, a 1 + 1 schedule) versus the current 2 + 1 schedule and to assess the potential effect on population protection. Methods In this multicentre, parallel group, randomised controlled trial, we recuited infants due to receive their primary immunisations aged up to 13 weeks on first vaccinations by information booklets mailed out via the NHS Child Health Information Service and the UK National Health Application and Infrastructure Services. Eligible infants were randomly assigned (1:1) to receive PCV13 at 2, 4, and 12 months (2 + 1 schedule) or 3 and 12 months of age (1 + 1 schedule) delivered with other routine vaccinations. Randomisation was done by computer-generated permuted block randomisation, with a block size of six. Participants and clinical trial staff were not masked to treatment allocation. The primary endpoint was serotype-specific immunoglobulin G concentrations values (geometric mean concentrations [GMC] in μg/mL) measured in blood samples collected at 13 months of age. Analysis was by modified intention to treat with all individuals included by randomised group if they had a laboratory result. This trial is registered on the EudraCT clinical trial database, number 2015-000817-32, and ClinicalTrials.gov, number NCT02482636. Findings Between September, 2015, and June, 2016, 376 infants were assessed for eligibility. 81 infants were excluded for not meeting the inclusion criteria (n=50) or for other reasons (n=31). 213 eligible infants were enrolled and randomly allocated to group 1 (n=106; 2 + 1 schedule) or to group 2 (n=107; 1 + 1 schedule). In group 1, 91 serum samples were available for analysis 1 month after booster immunisation versus 86 in group 2. At month 13, post-booster, GMCs were equivalent between schedules for serotypes 3 (0·61 μg/mL in group 1 vs 0·62 μg/mL in group 2), 5 (1·74 μg/mL vs 2·11 μg/mL), 7F (3·98 μg/mL vs 3·36 μg/mL), 9V (2·34 μg/mL vs 2·50 μg/mL), and 19A (8·38 μg/mL vs 8·83 μg/mL). Infants given the 1 + 1 schedule had significantly greater immunogenicity post-booster than those given the 2 + 1 schedule for serotypes 1 (8·92 μg/mL vs 3·07 μg/mL), 4 (3·43 μg/mL vs 2·55 μg/mL), 14 (16·9 μg/mL vs 10·49 μg/mL), and 19F (14·76 μg/mL vs 11·12 μg/mL; adjusted p value range <0·001 to 0·047). The 2 + 1 schedule was superior for serotypes 6A, 6B, 18C and 23F (adjusted p value range <0·0001 to 0·017). In a predefined numerical subset of all of the infants recruited to the study (n=40 [20%]), functional serotype-specific antibody was similar between schedules. 26 serious adverse events were recorded in 21 (10%) infants across the study period; 18 (n=13) were in the 2 + 1 group and eight (n=8) in the 1 + 1 group. Only one serious adverse event, a high temperature and refusal to feed after the first vaccination visit in a child on the 2+1 schedule was considered related to vaccine. Interpretation Our findings show that for nine of the 13 serotypes in PCV13, post-booster responses in infants primed with a single dose are equivalent or superior to those seen following the standard UK 2 + 1 schedule. Introducing a 1 + 1 schedule in countries with a mature PCV programme and established herd immunity is likely to maintain population control of vaccine-type pneumococcal disease. Funding NIHR and the Bill & Melinda Gates Foundation.
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