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Kandasamy R, Gurung M, Shrestha S, Gautam MC, Kelly S, Thorson S, Ansari I, Gould K, Hinds J, Kelly DF, Murdoch DR, Pollard AJ, Shrestha S. Decline in pneumococcal vaccine serotype carriage, multiple-serotype carriage, and carriage density in Nepalese children after PCV10 introduction: A pre-post comparison study. Vaccine 2024; 42:4066-4071. [PMID: 38789369 DOI: 10.1016/j.vaccine.2024.05.018] [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: 12/14/2023] [Revised: 04/07/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Carriage studies are an efficient means for assessing pneumococcal conjugate vaccine effect in settings where pneumococcal disease surveillance programmes are not well established. In this study the effect of 10-valent pneumococcal conjugate vaccine (PCV10) introduction on pneumococcal carriage and density among Nepalese children using a bacterial microarray and qPCR was examined. METHODS PCV10 was introduced into the Nepalese infant immunisation schedule in August 2015. Nasopharyngeal swabs were collected from healthy Nepalese children in Kathmandu between April 2014 and December 2021. Samples were plated on blood agar, incubated overnight, and DNA extracted from plate sweeps. Pneumococcal serotyping was done using the Senti-SPv1.5 microarray (BUGS Bioscience, UK). DNA was extracted from swab media and qPCR performed for pneumococcal autolysin (lytA). RESULTS A significant decline in prevalence of PCV10 serotypes was observed when comparing pre-PCV10 with post-PCV10 collection periods (36.5 %, 454/1244 vs 10.3 %, 243/2353, p < 0.0001). Multiple-serotype carriage was also observed to significantly decline when comparing pre-PCV10 with post-PCV10 periods (31.4 %, 390/1244 vs 22.2 %, 522/2353, p < 0.0001). Additionally, a significant decline in median pneumococcal density was observed when comparing pre-PCV10 with post-PCV10 periods (3.3 vs 3.25 log10 GE/ml, p = 0.0196). CONCLUSIONS PCV10 introduction was associated with reduced, prevalence of all PCV10 serotypes, multiple serotype carriage, and pneumococcal carriage density.
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Affiliation(s)
- Rama Kandasamy
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia; National Centre for Immunisation Research and Surveillance, The Children's Hospital at Westmead, Westmead, Australia.
| | - Meeru Gurung
- Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Sonu Shrestha
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Madhav C Gautam
- Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Sarah Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Stephen Thorson
- Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Imran Ansari
- Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Katherine Gould
- Institute for Infection and Immunity, St George's, University of London, United Kingdom; BUGS Bioscience, London Bioscience Innovation Centre, United Kingdom
| | - Jason Hinds
- Institute for Infection and Immunity, St George's, University of London, United Kingdom; BUGS Bioscience, London Bioscience Innovation Centre, United Kingdom
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - David R Murdoch
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Shrijana Shrestha
- Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
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Dekaj E, Gjini E. Pneumococcus and the stress-gradient hypothesis: A trade-off links R 0 and susceptibility to co-colonization across countries. Theor Popul Biol 2024; 156:77-92. [PMID: 38331222 DOI: 10.1016/j.tpb.2024.02.001] [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: 05/30/2022] [Revised: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
Modern molecular technologies have revolutionized our understanding of bacterial epidemiology, but reported data across studies and different geographic endemic settings remain under-integrated in common theoretical frameworks. Pneumococcus serotype co-colonization, caused by the polymorphic bacteria Streptococcus pneumoniae, has been increasingly investigated and reported in recent years. While the global genomic diversity and serotype distribution of S. pneumoniae have been well-characterized, there is limited information on how co-colonization patterns vary globally, critical for understanding the evolution and transmission dynamics of the bacteria. Gathering a rich dataset of cross-sectional pneumococcal colonization studies in the literature, we quantified patterns of transmission intensity and co-colonization prevalence variation in children populations across 17 geographic locations. Linking these data to an SIS model with cocolonization under the assumption of quasi-neutrality among multiple interacting strains, our analysis reveals strong patterns of negative co-variation between transmission intensity (R0) and susceptibility to co-colonization (k). In line with expectations from the stress-gradient-hypothesis in ecology (SGH), pneumococcus serotypes appear to compete more in co-colonization in high-transmission settings and compete less in low-transmission settings, a trade-off which ultimately leads to a conserved ratio of single to co-colonization μ=1/(R0-1)k. From the mathematical model's behavior, such conservation suggests preservation of 'stability-diversity-complexity' regimes in coexistence of similar co-colonizing strains. We find no major differences in serotype compositions across studies, pointing to adaptation of the same set of serotypes across variable environments as an explanation for their differential interaction in different transmission settings. Our work highlights that the understanding of transmission patterns of Streptococcus pneumoniae from global scale epidemiological data can benefit from simple analytical approaches that account for quasi-neutrality among strains, co-colonization, as well as variable environmental adaptation.
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Affiliation(s)
- Ermanda Dekaj
- Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Erida Gjini
- Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.
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Wang J, Qiu L, Bai S, Zhao W, Zhang A, Li J, Zhang JN, Zhou SS, Qiu R, Huang Z, Liu JX, Wang TB, Sun X, Wu J, Zheng Q, He B, Lv M. Prevalence and serotype distribution of nasopharyngeal carriage of Streptococcus pneumoniae among healthy children under 5 years of age in Hainan Province, China. Infect Dis Poverty 2024; 13:7. [PMID: 38238873 PMCID: PMC10797996 DOI: 10.1186/s40249-024-01175-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND The thirteen-valent pneumococcal conjugate vaccine (PCV13) is not included in the national immunization program and is administered voluntarily with informed consent in China. In preparation for assessing the impact of pilot introduction in Hainan Province, we conducted a carriage study among children under 5 years of age from four locations in Hainan Province, China. METHODS From March to June 2022, nasopharyngeal (NP) swabs, collected from healthy children aged younger than 59 months who lived in the 4 different locations (Haikou, Wanning, Baisha and Qiongzhong) in Hainan Province, were tested for pneumococcus using conventional culture. Pneumococcal isolates were serotyped using the Quellung reaction. Risk factors associated with pneumococcal colonization were assessed using univariate analysis and multivariable logistic regression adjusting for age, daycare attendance and other factors. RESULTS Pneumococcus was isolated in 710 (30.4%) of the 2333 children enrolled. Of 737 pneumococci, 29 serotypes were identified; 60.9% were PCV13 serotypes; the most common vaccine serotypes were 6B (20.4%), 19F (13.0%), 6A (11.9%) and 23F (6.1%); and the most common nonvaccine serotypes were 23A (12.9%), 34 (6.1%) and nontypeable (NT) pneumococci (5.6%). Children vaccinated with PCV13 had lower carriage (17.7% vs 32.5%; P = 0.0001) and fewer PCV13 serotypes (41.9% vs 62.7%; P = 0.0017) compared to unimmunized children. After adjustment, NP carriage was higher among children attending daycare (aOR = 2.3, 95% CI: 1.7-3.2), living in rural areas (aOR = 1.4, 95% CI: 1.1-1.8), living with siblings (aOR = 1.3, 95% CI: 1.0-1.6) and whose mothers had completed senior high/technical secondary school (aOR = 1.5, 95% CI: 1.1-2.0). In contrast, completion of 3-4 doses of PCV13 were associated with a lower carriage rate (aOR = 0.6, 95% CI: 0.4-0.9). CONCLUSIONS We established the baseline of pneumococcal carriage, serotype distribution and PCV13 immunization rates among healthy children under 5 years of age in Hainan Province, prior to the introduction of PCV13 into the national immunization program. The high proportion of PCV13 serotypes suggests that PCV13 introduction will likely have a substantial impact on pneumococcal carriage in Hainan Province.
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Affiliation(s)
- Jian Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China
| | - Li Qiu
- Hainan Provincial Center for Disease Control and Prevention, Haikou, China
| | - Shuang Bai
- Beijing Center for Disease Prevention and Control, Beijing, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China
| | - Wei Zhao
- Beijing Center for Disease Prevention and Control, Beijing, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China
| | - Ao Zhang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Jing Li
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Jun-Nan Zhang
- Beijing Center for Disease Prevention and Control, Beijing, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China
| | - Shan-Shan Zhou
- Beijing Center for Disease Prevention and Control, Beijing, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China
| | - Ren Qiu
- Hainan Provincial Center for Disease Control and Prevention, Haikou, China
| | - Zhu Huang
- Haikou Center for Disease Control and Prevention, Haikou, Hainan, China
| | - Jv-Xia Liu
- Wanning Center for Disease Control and Prevention, Wanning, Hainan, China
| | - Ting-Bin Wang
- Baisha County Center for Disease Control and Prevention, Baisha, Hainan, China
| | - Xue Sun
- Qiongzhong County Center for Disease Control and Prevention, Qiongzhong, Hainan, China
| | - Jiang Wu
- Beijing Center for Disease Prevention and Control, Beijing, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China
| | - Qun Zheng
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Bin He
- Hainan Provincial Center for Disease Control and Prevention, Haikou, China.
| | - Min Lv
- Beijing Center for Disease Prevention and Control, Beijing, China.
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China.
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Echlin H, Iverson A, Sardo U, Rosch JW. Airway proteolytic control of pneumococcal competence. PLoS Pathog 2023; 19:e1011421. [PMID: 37256908 PMCID: PMC10259803 DOI: 10.1371/journal.ppat.1011421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 06/12/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023] Open
Abstract
Streptococcus pneumoniae is an opportunistic pathogen that colonizes the upper respiratory tract asymptomatically and, upon invasion, can lead to severe diseases including otitis media, sinusitis, meningitis, bacteremia, and pneumonia. One of the first lines of defense against pneumococcal invasive disease is inflammation, including the recruitment of neutrophils to the site of infection. The invasive pneumococcus can be cleared through the action of serine proteases generated by neutrophils. It is less clear how serine proteases impact non-invasive pneumococcal colonization, which is the key first step to invasion and transmission. One significant aspect of pneumococcal biology and adaptation in the respiratory tract is its natural competence, which is triggered by a small peptide CSP. In this study, we investigate if serine proteases are capable of degrading CSP and the impact this has on pneumococcal competence. We found that CSP has several potential sites for trypsin-like serine protease degradation and that there were preferential cleavage sites recognized by the proteases. Digestion of CSP with two different trypsin-like serine proteases dramatically reduced competence in a dose-dependent manner. Incubation of CSP with mouse lung homogenate also reduced recombination frequency of the pneumococcus. These ex vivo experiments suggested that serine proteases in the lower respiratory tract reduce pneumococcal competence. This was subsequently confirmed measuring in vivo recombination frequencies after induction of protease production via poly (I:C) stimulation and via co-infection with influenza A virus, which dramatically lowered recombination events. These data shed light on a new mechanism by which the host can modulate pneumococcal behavior and genetic exchange via direct degradation of the competence signaling peptide.
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Affiliation(s)
- Haley Echlin
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Amy Iverson
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Ugo Sardo
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Jason W. Rosch
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
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Oyewole ORA, Latzin P, Brugger SD, Hilty M. Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants. MICROBIOME 2022; 10:152. [PMID: 36138483 PMCID: PMC9502908 DOI: 10.1186/s40168-022-01344-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Pneumococcal carriage has often been studied from a serotype perspective; however, little is known about the strain-specific carriage and inter-strain interactions. Here, we examined the strain-level carriage and co-colonization dynamics of Streptococcus pneumoniae in a Swiss birth cohort by PacBio single-molecule real-time (SMRT) sequencing of the plyNCR marker. METHODS A total of 872 nasal swab (NS) samples were included from 47 healthy infants during the first year of life. Pneumococcal carriage was determined based on the quantitative real-time polymerase chain reaction (qPCR) targeting the lytA gene. The plyNCR marker was amplified from 214 samples having lytA-based carriage for pneumococcal strain resolution. Amplicons were sequenced using SMRT technology, and sequences were analyzed with the DADA2 pipeline. In addition, pneumococcal serotypes were determined using conventional, multiplex PCR (cPCR). RESULTS PCR-based plyNCR amplification demonstrated a 94.2% sensitivity and 100% specificity for Streptococcus pneumoniae if compared to lytA qPCR. The overall carriage prevalence was 63.8%, and pneumococcal co-colonization (≥ 2 plyNCR amplicon sequence variants (ASVs)) was detected in 38/213 (17.8%) sequenced samples with the relative proportion of the least abundant strain(s) ranging from 1.1 to 48.8% (median, 17.2%; IQR, 5.8-33.4%). The median age to first acquisition was 147 days, and having ≥ 2 siblings increased the risk of acquisition. CONCLUSION The plyNCR amplicon sequencing is species-specific and enables pneumococcal strain resolution. We therefore recommend its application for longitudinal strain-level carriage studies of Streptococcus pneumoniae. Video Abstract.
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Affiliation(s)
- Oluwaseun Rume-Abiola Oyewole
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland.
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Pneumococcal carriage in unvaccinated children at the time of vaccine implementation into the national immunization program in Poland. Sci Rep 2022; 12:5858. [PMID: 35393439 PMCID: PMC8991213 DOI: 10.1038/s41598-022-09488-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/14/2022] [Indexed: 11/08/2022] Open
Abstract
We investigated pneumococcal carriage among unvaccinated children under five years of age at a time when the conjugate polysaccharide vaccine (PCV) was introduced in Poland into the national immunization program (NIP). Paired nasopharyngeal swab (NPS) and saliva samples collected between 2016 and 2020 from n = 394 children were tested with conventional culture and using qPCR. The carriage rate detected by culture was 25.4% (97 of 394), by qPCR 39.1% (155 of 394), and 40.1% (158 of 394) overall. The risk of carriage was significantly elevated among day care center attendees, and during autumn/winter months. Among isolates cultured, the most common serotypes were: 23A, 6B, 15BC, 10A, 11A. The coverage of PCV10 and PCV13 was 23.2% (23 of 99) and 26.3% (26 of 99), respectively. Application of qPCR lead to detection of 168 serotype carriage events, with serogroups 15, 6, 9 and serotype 23A most commonly detected. Although the highest number of carriers was identified by testing NPS with qPCR, saliva significantly contributed to the overall number of detected carriers. Co-carriage of multiple serotypes was detected in 25.3% (40 of 158) of carriers. The results of this study represent a baseline for the future surveillance of effects of pneumococcal vaccines in NIP in Poland.
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Valente C, Cruz AR, Henriques AO, Sá-Leão R. Intra-Species Interactions in Streptococcus pneumoniae Biofilms. Front Cell Infect Microbiol 2022; 11:803286. [PMID: 35071049 PMCID: PMC8767070 DOI: 10.3389/fcimb.2021.803286] [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] [Received: 10/27/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae is a human pathogen responsible for high morbidity and mortality worldwide. Disease is incidental and is preceded by asymptomatic nasopharyngeal colonization in the form of biofilms. Simultaneous colonization by multiple pneumococcal strains is frequent but remains poorly characterized. Previous studies, using mostly laboratory strains, showed that pneumococcal strains can reciprocally affect each other's colonization ability. Here, we aimed at developing a strategy to investigate pneumococcal intra-species interactions occurring in biofilms. A 72h abiotic biofilm model mimicking long-term colonization was applied to study eight pneumococcal strains encompassing 6 capsular types and 7 multilocus sequence types. Strains were labeled with GFP or RFP, generating two fluorescent variants for each. Intra-species interactions were evaluated in dual-strain biofilms (1:1 ratio) using flow cytometry. Confocal microscopy was used to image representative biofilms. Twenty-eight dual-strain combinations were tested. Interactions of commensalism, competition, amensalism and neutralism were identified. The outcome of an interaction was independent of the capsular and sequence type of the strains involved. Confocal imaging of biofilms confirmed the positive, negative and neutral effects that pneumococci can exert on each other. In conclusion, we developed an experimental approach that successfully discriminates pneumococcal strains growing in mixed biofilms, which enables the identification of intra-species interactions. Several types of interactions occur among pneumococci. These observations are a starting point to study the mechanisms underlying those interactions.
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Affiliation(s)
- Carina Valente
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana R Cruz
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriano O Henriques
- Laboratory of Microbial Development, Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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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: 3] [Impact Index Per Article: 1.0] [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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Bentley SD, Lo SW. Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics. Genome Med 2021; 13:84. [PMID: 34001237 PMCID: PMC8130287 DOI: 10.1186/s13073-021-00901-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/30/2021] [Indexed: 11/10/2022] Open
Abstract
Vaccines are powerful agents in infectious disease prevention but often designed to protect against some strains that are most likely to spread and cause diseases. Most vaccines do not succeed in eradicating the pathogen and thus allow the potential emergence of vaccine evading strains. As with most evolutionary processes, being able to capture all variations across the entire genome gives us the best chance of monitoring and understanding the processes of vaccine evasion. Genomics is being widely adopted as the optimum approach for pathogen surveillance with the potential for early and precise identification of high-risk strains. Given sufficient longitudinal data, genomics also has the potential to forecast the emergence of such strains enabling immediate or pre-emptive intervention. In this review, we consider the strengths and challenges for pathogen genomic surveillance using the experience of the Global Pneumococcal Sequencing (GPS) project as an early example. We highlight the multifaceted nature of genome data and recent advances in genome-based tools to extract useful information relevant to inform vaccine strategies and treatment options. We conclude with future perspectives for genomic pathogen surveillance.
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Affiliation(s)
- Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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Jullien S, Sharma R, Lhamu Mynak M, Henares D, Muñoz-Almagro C, Bassat Q. Pneumococcal nasopharyngeal carriage among Bhutanese children hospitalized with clinical pneumonia: serotypes and viral co-infection. BMC Infect Dis 2020; 20:940. [PMID: 33297987 PMCID: PMC7725031 DOI: 10.1186/s12879-020-05674-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 11/30/2020] [Indexed: 10/26/2022] Open
Abstract
BACKGROUND Pneumococcal nasopharyngeal colonization (PNC) generally precedes pneumococcal disease. The purpose of this study was to determine the prevalence of PNC and to identify the pneumococcal serotypes circulating among Bhutanese children under five years of age admitted with clinical pneumonia, before the introduction of pneumococcal conjugate vaccine (PCV13) in the country. We also aimed to contribute to the understanding of the interplay between PNC and viral co-infection among this population. METHODS This was a prospective study conducted at the Jigme Dorji Wangchuck National Referral Hospital in Bhutan over 12 consecutive months. Children aged 2 to 59 months admitted with WHO-defined clinical pneumonia were eligible for recruitment. We collected blood for bacterial culture and molecular identification of S. pneumoniae, and nasopharyngeal washing for screening of respiratory viruses, and for the detection and capsular typing of S. pneumoniae by real-time polymerase chain reaction (RT-PCR). RESULTS Overall, 189 children were recruited, and PNC was tested in 121 of them (64.0%). PNC was found in 76/121 children (62.8%) and S. pneumoniae was identified in blood (both by culture and RT-PCR) in a single child. Respiratory viruses were detected in a similar proportion among children with (62/70; 88.6%) and without PNC (36/40; 90.0%; p = 1.000), but rhinovirus detection was less common among children with PNC (20/70; 28.6% versus 19/40; 47.5%; p = 0.046). Capsular typing identified 30 different serotypes. Thirty-nine children (51.3%) were colonised with two to five different serotypes. A third of the children presented with serotypes considered highly invasive. Over half of the children (44/76; 57.9%) were carrying at least one serotype included in PCV13. CONCLUSIONS This study provides baseline information on the status of PNC among Bhutanese children admitted with clinical pneumonia prior to the introduction of PCV13, which is valuable to monitor its potential impact. PCV13 could theoretically have averted up to 58% of the pneumococcal infections among the children in this study, suggesting a future role for the vaccine to significantly reduce the burden associated with S. pneumoniae in Bhutan.
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Affiliation(s)
- Sophie Jullien
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic, Universitat de Barcelona, Barcelona, Spain. .,Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan.
| | - Ragunath Sharma
- Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan
| | - Mimi Lhamu Mynak
- Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan
| | - Desiree Henares
- Instituto de Recerca Pediatrica, Hospital Sant Joan de Deu (University of Barcelona), Barcelona, Spain.,CIBER of Epidemiology and Public Health CIBERESP, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Instituto de Recerca Pediatrica, Hospital Sant Joan de Deu (University of Barcelona), Barcelona, Spain.,CIBER of Epidemiology and Public Health CIBERESP, Madrid, Spain.,Department of Medicine, Universitat Internacional of Catalunya, Barcelona, Spain
| | - Quique Bassat
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic, Universitat de Barcelona, Barcelona, Spain.,CIBER of Epidemiology and Public Health CIBERESP, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
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11
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Manenzhe RI, Dube FS, Wright M, Lennard K, Mounaud S, Lo SW, Zar HJ, Nierman WC, Nicol MP, Moodley C. Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants. Front Public Health 2020; 8:543898. [PMID: 33072693 PMCID: PMC7536305 DOI: 10.3389/fpubh.2020.543898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
Background: There remains a significant proportion of deaths due to pneumococcal pneumonia in infants from low- and middle-income countries despite the marginal global declines recorded in the past decade. Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage, patterns of antimicrobial resistance, and impact on health. We longitudinally investigated pneumococcal carriage dynamics in PCV-13 vaccinated infants by collecting nasopharyngeal (NP) samples at 2-weekly intervals from birth through the first year of life from 137 infants. As a proof of concept, 196 NP samples were retrieved from a subset of 23 infants to explore strain-level pneumococcal colonization patterns and associated antimicrobial-resistance determinants. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of pneumococcal and non-pneumococcal bacterial reads. Pneumococcal contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes. In silico pneumococcal capsular and multilocus sequence typing were performed. Results: Of the 196 samples sequenced, 174 had corresponding positive cultures for pneumococci, of which, 152 were assigned an in silico serotype. Metagenomic sequencing detected a single pneumococcal serotype in 85% (129/152), and co-colonization in 15% (23/152) of the samples. Twenty-two different pneumococcal serotypes were identified, with 15B/15C and 16F being the most common non-PCV13 serotypes, while 23F and 19A were the most common PCV13 serotypes. Twenty-six different sequence types (STs), including four novel STs were identified in silico. Mutations in the folA and folP genes, associated with cotrimoxazole resistance, were detected in 89% (87/98) of cotrimoxazole-non-susceptible pneumococci, as well as in the pbp1a and pbp2x genes, in penicillin non-susceptible ST705215B/15C isolates. Conclusions: Metagenomic sequencing of NP samples is a valuable culture-independent technique for a detailed evaluation of the pneumococcal component and resistome of the NP microbiome. This method allowed for the detection of novel STs, as well as co-colonization, with a predominance of non-PCV13 serotypes in this cohort. Forty-eight resistance genes, as well as mutations associated with resistance were detected, but the correlation with phenotypic non-susceptibility was lower than expected.
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Affiliation(s)
- Rendani I Manenzhe
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Felix S Dube
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | | | - Katie Lennard
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Stephanie W Lo
- Parasites and Microbes Program, The Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African - Medical Research Council Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | | | - Mark P Nicol
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Division of Infection and Immunity, University of Western Australia, Perth, WA, Australia
| | - Clinton Moodley
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
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12
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Yasuda I, Suzuki M, Dhoubhadel BG, Terada M, Satoh A, Sando E, Hiraoka T, Kurihara M, Matsusaka N, Kawahara F, Ariyoshi K, Morimoto K. The low carriage prevalence of pneumococcus among community-dwelling older people: A cross-sectional study in Japan. Vaccine 2020; 38:3752-3758. [PMID: 32265047 DOI: 10.1016/j.vaccine.2020.03.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/22/2020] [Accepted: 03/17/2020] [Indexed: 01/28/2023]
Abstract
BACKGROUND The carriage prevalence of pneumococcus among community-dwelling older adults is not fully understood, especially in superaged societies. Our purpose was to elucidate the carriage prevalence of pneumococcus in the upper respiratory tract among Japanese community-dwelling adults aged ≥65 years. METHODS We conducted a cross-sectional study of generally healthy community-dwelling adults aged ≥65 years in Nagasaki city, Japan. Demographic and clinical data and nasopharyngeal, oropharyngeal and saliva samples were collected from February 21st, 2018, to December 17th, 2018. The specimens were tested by culture and molecular methods. RESULTS Among a total of 504 enrolled participants, none were positive for pneumococcus by culture, and 22 were positive by PCR. The overall carriage prevalence was 4.4% (95% CI: 2.8-6.5%). The prevalence was highest in saliva samples, followed by oropharyngeal and nasopharyngeal samples. No demographic characteristics were associated with carriage prevalence, including age (4.7% among participants aged 65-74 years and 4.1% among those 75 years and older). Among the pneumococcal-positive participants, 18.2% were PCV13-covered serotypes. CONCLUSIONS Our data suggest a low carriage prevalence of S. pneumoniae among community-dwelling older people in Japan.
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Affiliation(s)
- Ikkoh Yasuda
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; Department of Clinical Tropical Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Motoi Suzuki
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Mayumi Terada
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; Nijigaoka Hospital, Nagasaki, Japan
| | | | - Eiichiro Sando
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Tomoko Hiraoka
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; Department of Clinical Tropical Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | | | | | | | - Koya Ariyoshi
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; Department of Clinical Tropical Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Konosuke Morimoto
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; Department of Clinical Tropical Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Nijigaoka Hospital, Nagasaki, Japan.
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13
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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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14
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Chan J, Nguyen CD, Dunne EM, Kim Mulholland E, Mungun T, Pomat WS, Rafai E, Satzke C, Weinberger DM, Russell FM. Using pneumococcal carriage studies to monitor vaccine impact in low- and middle-income countries. Vaccine 2019; 37:6299-6309. [PMID: 31500968 DOI: 10.1016/j.vaccine.2019.08.073] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/13/2019] [Accepted: 08/26/2019] [Indexed: 12/15/2022]
Abstract
Pneumococcal disease is a leading cause of childhood mortality, globally. The pneumococcal conjugate vaccine (PCV) has been introduced to many countries worldwide. However there are few studies evaluating PCV impacts in low- and middle-income countries (LMIC) because measuring the impact of PCV on pneumococcal disease in LMICs is challenging. We review the role of pneumococcal carriage studies for the evaluation of PCVs in LMICs and discuss optimal methods for conducting these studies. Fifteen carriage studies from 13 LMICs quantified the effects of PCV on carriage, and identified replacement carriage serotypes in the post-PCV era. Ten studies reported on the indirect effects of PCV on carriage. Results can be used to inform cost-effectiveness evaluations, guide policy decisions on dosing and product, and monitor equity in program implementation. Critically, we highlight gaps in our understanding of serotype replacement disease in LMICs and identify priorities for research to address this gap.
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Affiliation(s)
- Jocelyn Chan
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
| | - Cattram D Nguyen
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Eileen M Dunne
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - E Kim Mulholland
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Tuya Mungun
- National Center of Communicable Diseases (NCCD), Ministry of Health, Ulaanbaatar, Mongolia
| | - William S Pomat
- Papua New Guinea Institute of Medical Research, Infection and Immunity Unit, Goroka, Papua New Guinea; Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Eric Rafai
- Ministry of Health and Medical Services, Suva, Fiji
| | - Catherine Satzke
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States
| | - Fiona M Russell
- New Vaccines Group, Murdoch Children's Research Institute, Melbourne, Australia; Centre for International Child Health, Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
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15
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Comparison of two schedules of two-dose priming with the ten-valent pneumococcal conjugate vaccine in Nepalese children: an open-label, randomised non-inferiority controlled trial. THE LANCET. INFECTIOUS DISEASES 2019; 19:156-164. [DOI: 10.1016/s1473-3099(18)30568-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/24/2018] [Accepted: 09/11/2018] [Indexed: 11/19/2022]
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16
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Satzke C, Dunne EM, Choummanivong M, Ortika BD, Neal EFG, Pell CL, Nation ML, Fox KK, Nguyen CD, Gould KA, Hinds J, Chanthongthip A, Xeuatvongsa A, Mulholland EK, Sychareun V, Russell FM. Pneumococcal carriage in vaccine-eligible children and unvaccinated infants in Lao PDR two years following the introduction of the 13-valent pneumococcal conjugate vaccine. Vaccine 2018; 37:296-305. [PMID: 30502068 DOI: 10.1016/j.vaccine.2018.10.077] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 01/27/2023]
Abstract
Pneumococcal carriage is a prerequisite for disease, and underpins herd protection provided by pneumococcal conjugate vaccines (PCVs). There are few data on the impact of PCVs in lower income settings, particularly in Asia. In 2013, the Lao People's Democratic Republic (Lao PDR) introduced 13-valent PCV (PCV13) as a 3 + 0 schedule (doses at 6, 10 and 14 weeks of age) with limited catch-up vaccination. We conducted two cross-sectional carriage surveys (pre- and two years post-PCV) to assess the impact of PCV13 on nasopharyngeal pneumococcal carriage in 5-8 week old infants (n = 1000) and 12-23 month old children (n = 1010). Pneumococci were detected by quantitative real-time PCR, and molecular serotyping was performed using DNA microarray. Post PCV13, there was a 23% relative reduction in PCV13-type carriage in children aged 12-23 months (adjusted prevalence ratio [aPR] 0.77 [0.61-0.96]), and no significant change in non-PCV13 serotype carriage (aPR 1.11 [0.89-1.38]). In infants too young to be vaccinated, there was no significant change in carriage of PCV13 serotypes (aPR 0.74 [0.43-1.27]) or non-PCV13 serotypes (aPR 1.29 [0.85-1.96]), although trends were suggestive of indirect effects. Over 70% of pneumococcal-positive samples contained at least one antimicrobial resistance gene, which were more common in PCV13 serotypes (p < 0.001). In 12-23 month old children, pneumococcal density of both PCV13 serotypes and non-PCV13 serotypes was higher in PCV13-vaccinated compared with undervaccinated children (p = 0.004 and p < 0.001, respectively). This study provides evidence of PCV13 impact on carriage in a population without prior PCV7 utilisation, and provides important data from a lower-middle income setting in Asia. The reductions in PCV13 serotype carriage in vaccine-eligible children are likely to result in reductions in pneumococcal transmission and disease in Lao PDR.
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Affiliation(s)
- Catherine Satzke
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia.
| | - Eileen M Dunne
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | | | - Belinda D Ortika
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia
| | - Eleanor F G Neal
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Centre for International Child Health, Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Casey L Pell
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia
| | - Monica L Nation
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia
| | - Kimberley K Fox
- Expanded Programme on Immunization, World Health Organization Regional Office for the Western Pacific, Manila, Philippines
| | - Cattram D Nguyen
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Katherine A Gould
- Institute for Infection and Immunity, St. George's, University of London, London, UK; BUGS Bioscience, London Bioscience Innovation Centre, London, UK
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's, University of London, London, UK; BUGS Bioscience, London Bioscience Innovation Centre, London, UK
| | - Anisone Chanthongthip
- Laos-Oxford-Mahosot Hospital Wellcome Trust Research Unit, Vientiane, Lao People's Democratic Republic
| | | | - E Kim Mulholland
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Fiona M Russell
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Centre for International Child Health, Department of Paediatrics, The University of Melbourne, Parkville, Australia
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17
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Birindwa AM, Emgård M, Nordén R, Samuelsson E, Geravandi S, Gonzales-Siles L, Muhigirwa B, Kashosi T, Munguakonkwa E, Manegabe JT, Cibicabene D, Morisho L, Mwambanyi B, Mirindi J, Kabeza N, Lindh M, Andersson R, Skovbjerg S. High rate of antibiotic resistance among pneumococci carried by healthy children in the eastern part of the Democratic Republic of the Congo. BMC Pediatr 2018; 18:361. [PMID: 30453916 PMCID: PMC6241069 DOI: 10.1186/s12887-018-1332-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/31/2018] [Indexed: 12/02/2022] Open
Abstract
Background Pneumococcal conjugate vaccines have been introduced in the infant immunisation programmes in many countries to reduce the rate of fatal pneumococcal infections. In the Democratic Republic of the Congo (DR Congo) a 13-valent vaccine (PCV13) was introduced in 2013. Data on the burden of circulating pneumococci among children after this introduction are lacking. In this study, we aimed to determine the risk factors related to pneumococcal carriage in healthy Congolese children after the vaccine introduction and to assess the antibiotic resistance rates and serotype distribution among the isolated pneumococci. Methods In 2014 and 2015, 794 healthy children aged one to 60 months attending health centres in the eastern part of DR Congo for immunisation or growth monitoring were included in the study. Data on socio-demographic and medical factors were collected by interviews with the children’s caregivers. Nasopharyngeal swabs were obtained from all the children for bacterial culture, and isolated pneumococci were further tested for antimicrobial resistance using disc diffusion tests and, when indicated, minimal inhibitory concentration (MIC) determination, and for serotype/serogroup by molecular testing. Results The pneumococcal detection rate was 21%, being higher among children who had not received PCV13 vaccination, lived in rural areas, had an enclosed kitchen, were malnourished or presented with fever (p value < 0.05). The predominant serotypes were 19F, 11, 6A/B/C/D and 10A. More than 50% of the pneumococcal isolates belonged to a serotype/serogroup not included in PCV13. Eighty per cent of the isolates were not susceptible to benzylpenicillin and non-susceptibility to ampicillin and ceftriaxone was also high (42 and 37% respectively). Almost all the isolates (94%) were resistant to trimethoprim-sulphamethoxazole, while 43% of the strains were resistant to ≥3 antibiotics. Conclusions Our study shows alarmingly high levels of reduced susceptibility to commonly used antibiotics in pneumococci carried by healthy Congolese children. This highlights the importance of local antibiotic resistance surveillance and indicates the needs for the more appropriate use of antibiotics in the area. The results further indicate that improved living conditions are needed to reduce the pneumococcal burden, in addition to PCV13 vaccination. Electronic supplementary material The online version of this article (10.1186/s12887-018-1332-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Archippe M Birindwa
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden. .,Panzi Hospital, Bukavu, Democratic Republic of the Congo. .,Université Evangélique en Afrique, Bukavu, Democratic Republic of the Congo. .,Hôpital Général de Référence de Panzi, BP: 266, Bukavu, DR, Congo.
| | - Matilda Emgård
- 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
| | - Ebba Samuelsson
- 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
| | - Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | | | - Théophile Kashosi
- Université Evangélique en Afrique, Bukavu, Democratic Republic of the Congo
| | | | | | | | | | | | | | - Nadine Kabeza
- Panzi Hospital, Bukavu, Democratic Republic of the Congo
| | - Magnus Lindh
- 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.,CARe - Center for Antibiotic Resistance Research, Gothenburg University, Gothenburg, Sweden
| | - Susann Skovbjerg
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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18
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Voysey M, Pollard AJ, Perera R, Shrestha S, Thorson S, Fanshawe TR. Use of weighted multivariate estimates in trials of multi-serotype vaccines to simplify interpretation of treatment differences. PLoS One 2018; 13:e0196200. [PMID: 29702658 PMCID: PMC5922548 DOI: 10.1371/journal.pone.0196200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 04/07/2018] [Indexed: 11/19/2022] Open
Abstract
Background Many vaccines contain multiple components. Licensed pneumococcal conjugate vaccines (PCV) contain polysaccharides from 7, 10, or 13 different serotypes of Streptococcus pneumoniae. The main outcomes in randomised trials of pneumococcal vaccines are serotype-specific antibody measures. Comparisons are made between groups for each serotype, resulting in multiple separate comparisons of treatment effects which can be complicated to interpret. We investigated methods for computing the overall difference between vaccine groups across all serotypes. Methods Pneumococcal antibody concentrations were obtained from a randomised controlled trial of ten-valent pneumococcal vaccine, conducted in Kathmandu, Nepal. Infants received either 2 priming doses of vaccine at 6 and 14 weeks of age followed by a booster (2+1), or 3 priming doses at 6, 10, and 14 weeks of age with no booster (3+0). The overall difference between vaccine schedules across all serotypes was computed at each visit using a multivariate linear model with equal weights for each serotype. Alternative weights were derived from invasive pneumococcal disease cases in Nepal, Bangladesh and Pakistan, and from estimates of the relative invasiveness of each serotype and used in sensitivity analyses. Results When 10 separate estimates of treatment differences were computed the ratio of antibody responses for each serotype in the 2+1 group compared with the 3+0 group at 10 months of age varied greatly, with serotype-specific GMRs ranging from 2.80 for serotype 14, to 9.14 for serotype 18C. Using equal weights for each serotype, the overall geometric mean ratio (GMR) was 5.02 (95% CI 4.06−6.22) at 10 months of age, and 1.46 (95% CI 1.14−1.88) at 3 years of age. Using weights based on disease incidence gave GMRs ranging from 5.15 to 6.63 at 10 months of age, and 1.47 to 1.78 at 3 years of age. Using weights based on relative invasiveness gave estimates of 6.81 and 1.59, at 10 months and 3 years respectively. Conclusion PCV clinical trial data have a multivariate structure with correlated outcomes for different serotypes. When analysing each serotype separately, the multiple estimates of the treatment effect can complicate the interpretation of trial results. Reporting a single overall estimate which accounts for the correlation between outcomes can simplify such interpretation. Treatment effects can be weighted equally or alternative weights derived from independent data can be used. Many modern vaccines have multiple components, such as quadrivalent meningococcal group ACWY vaccine or four-component group B meningococcal vaccine, thus these methods are widely applicable.
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Affiliation(s)
- Merryn Voysey
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Rafael Perera
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Shrijana Shrestha
- Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Stephen Thorson
- Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Thomas R. Fanshawe
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
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19
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Dunne EM, Murad C, Sudigdoadi S, Fadlyana E, Tarigan R, Indriyani SAK, Pell CL, Watts E, Satzke C, Hinds J, Dewi NE, Yani FF, Rusmil K, Mulholland EK, Kartasasmita C. Carriage of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus in Indonesian children: A cross-sectional study. PLoS One 2018; 13:e0195098. [PMID: 29649269 PMCID: PMC5896896 DOI: 10.1371/journal.pone.0195098] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/18/2018] [Indexed: 11/30/2022] Open
Abstract
Streptococcus pneumoniae is an important cause of infection and commonly colonizes the nasopharynx of young children, along with other potentially pathogenic bacteria. The objectives of this study were to estimate the carriage prevalence of S. pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus in young children in Indonesia, and to examine interactions between these bacterial species. 302 healthy children aged 12–24 months were enrolled in community health centers in the Bandung, Central Lombok, and Padang regions. Nasopharyngeal swabs were collected and stored according to World Health Organization recommendations, and bacterial species detected by qPCR. Pneumococcal serotyping was conducted by microarray and latex agglutination/Quellung. Overall carriage prevalence was 49.5% for S. pneumoniae, 27.5% for H. influenzae, 42.7% for M. catarrhalis, and 7.3% for S. aureus. Prevalence of M. catarrhalis and S. pneumoniae, as well as pneumococcal serotype distribution, varied by region. Positive associations were observed for S. pneumoniae and M. catarrhalis (OR 3.07 [95%CI 1.91–4.94]), and H. influenzae and M. catarrhalis (OR 2.34 [95%CI 1.40–3.91]), and a negative association was found between M. catarrhalis and S. aureus (OR 0.06 [95%CI 0.01–0.43]). Densities of S. pneumoniae, H. influenzae, and M. catarrhalis were positively correlated when two of these species were present. Prior to pneumococcal vaccine introduction, pneumococcal carriage prevalence and serotype distribution varies among children living in different regions of Indonesia. Positive associations in both carriage and density identified among S. pneumoniae, H. influenzae, and M. catarrhalis suggest a synergistic relationship among these species with potential clinical implications.
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Affiliation(s)
- Eileen M. Dunne
- Pneumococcal Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Chrysanti Murad
- Department of Biomedical Sciences, Division of Microbiology, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Sunaryati Sudigdoadi
- Department of Biomedical Sciences, Division of Microbiology, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Eddy Fadlyana
- Department of Child Health, Universitas Padjadjaran/Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | - Rodman Tarigan
- Department of Child Health, Universitas Padjadjaran/Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | | | - Casey L. Pell
- Pneumococcal Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Emma Watts
- Pneumococcal Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Catherine Satzke
- Pneumococcal Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jason Hinds
- Institute for Infection and Immunity, St. George’s University of London, London, United Kingdom
- BUGS Bioscience, London Bioscience Innovation Centre, London, United Kingdom
| | - Nurhandini Eka Dewi
- District Health Office of Central Lombok, Praya, West Nusa Tenggara, Indonesia
| | - Finny Fitry Yani
- Department of Child Health, Universitas Andalas, Padang, West Sumatra, Indonesia
| | - Kusnandi Rusmil
- Department of Child Health, Universitas Padjadjaran/Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | - E. Kim Mulholland
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Cissy Kartasasmita
- Department of Child Health, Universitas Padjadjaran/Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
- * E-mail:
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20
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Invasive Disease Caused Simultaneously by Dual Serotypes of Streptococcus pneumoniae. J Clin Microbiol 2017; 56:JCM.01149-17. [PMID: 29118167 DOI: 10.1128/jcm.01149-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/28/2017] [Indexed: 11/20/2022] Open
Abstract
There are at least 98 known pneumococcal serotypes. Invasive pneumococcal disease (IPD) is usually caused by a single serotype, and dual-serotype IPD is rare. To assess factors associated with dual-serotype IPD, patient information obtained through laboratory-based surveillance for IPD from 2005 through 2014 in South Africa was reviewed. Genomes of isolate pairs from coinfected individuals were sequenced to determine their molecular characteristics. For 30 (91%) of 33 patients with dual serotypes, one or both isolates were a pneumococcal conjugate vaccine (PCV13) serotype. Dual-serotype IPD was associated with children <5 years of age (adjusted odds ratio [aOR], 4.7; 95% confidence interval [95% CI], 1.8 to 11.7), underlying illness (other than HIV) (aOR, 2.8; 95% CI, 1.1 to 6.6) and death (aOR, 2.5; 95% CI, 1.08 to 6.09). For each coinfecting pair, isolates were genotypically unrelated, and their genotypes were common among isolates of the same serotype in South Africa. Of 701 accessory genes identified among dual-serotype IPD isolates, four were common between isolate pairs. Coinfecting isolate pairs had different genotypic backgrounds. The association of dual serotypes with death warrants increased awareness of IPD coinfection caused by two or more serotypes.
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21
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Voysey M, Fanshawe TR, Kelly DF, O’Brien KL, Kandasamy R, Shrestha S, Thorson S, Hinds J, Pollard AJ. Serotype-Specific Correlates of Protection for Pneumococcal Carriage: An Analysis of Immunity in 19 Countries. Clin Infect Dis 2017; 66:913-920. [DOI: 10.1093/cid/cix895] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/19/2017] [Indexed: 01/27/2023] Open
Affiliation(s)
- Merryn Voysey
- Nuffield Department of Primary Care Health Sciences, University of Oxford, United Kingdom
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and National Institute for Health Research Oxford Biomedical Research Centre, United Kingdom
| | - Thomas R Fanshawe
- Nuffield Department of Primary Care Health Sciences, University of Oxford, United Kingdom
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and National Institute for Health Research Oxford Biomedical Research Centre, United Kingdom
| | - Katherine L O’Brien
- International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Rama Kandasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and National Institute for Health Research Oxford Biomedical Research Centre, United Kingdom
| | - Shrijana Shrestha
- Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Stephen Thorson
- Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Jason Hinds
- Institute for Infection and Immunity, St George’s University of London, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and National Institute for Health Research Oxford Biomedical Research Centre, United Kingdom
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22
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Emmadi M, Khan N, Lykke L, Reppe K, G Parameswarappa S, Lisboa MP, Wienhold SM, Witzenrath M, Pereira CL, Seeberger PH. A Streptococcus pneumoniae Type 2 Oligosaccharide Glycoconjugate Elicits Opsonic Antibodies and Is Protective in an Animal Model of Invasive Pneumococcal Disease. J Am Chem Soc 2017; 139:14783-14791. [PMID: 28945368 DOI: 10.1021/jacs.7b07836] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Invasive pneumococcal diseases (IPDs) remain the leading cause of vaccine-preventable childhood death, even though highly effective pneumococcal conjugate vaccines (PCVs) are used in national immunization programs in many developing countries. Licensed PCVs currently cover only 13 of the over 90 serotypes of Streptococcus pneumoniae (Sp), so nonvaccine serotypes are a major obstacle to the effective control of IPD. Sp serotype 2 (ST2) is such a nonvaccine serotype that is the main cause of IPD in many countries, including Nepal, Bangladesh, and Guatemala. Glycoconjugate vaccines based on synthetic oligosaccharides instead of isolated polysaccharides offer an attractive alternative to the traditional process for PCV development. To prevent the IPDs caused by ST2, we identified an effective ST2 neoglycoconjugate vaccine candidate that was identified using a medicinal chemistry approach. Glycan microarrays containing a series of synthetic glycans resembling portions of the ST2 capsular polysaccharide (CPS) repeating unit were used to screen human and rabbit sera and identify epitope hits. Synthetic hexasaccharide 2, resembling one repeating unit (RU) of ST2 CPS, emerged as a hit from the glycan array screens. Vaccination with neoglycoconjugates consisting of hexasaccharide 2 coupled to carrier protein CRM197 stimulates a T-cell-dependent B-cell response that induced CPS-specific opsonic antibodies in mice, resulting in killing of encapsulated bacteria by phagocytic activity. Subcutaneous immunization with neoglycoconjugate protected mice from transnasal challenge with the highly virulent ST2 strain NCTC 7466 by reducing the bacterial load in lung tissue and blood.
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Affiliation(s)
- Madhu Emmadi
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , D-14424 Potsdam, Germany
| | - Naeem Khan
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , D-14424 Potsdam, Germany
| | - Lennart Lykke
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , D-14424 Potsdam, Germany
| | - Katrin Reppe
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin , Charitéplatz 1, 10117 Berlin, Germany
| | - Sharavathi G Parameswarappa
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , D-14424 Potsdam, Germany
| | - Marilda P Lisboa
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , D-14424 Potsdam, Germany
| | - Sandra-Maria Wienhold
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin , Charitéplatz 1, 10117 Berlin, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin , Charitéplatz 1, 10117 Berlin, Germany
| | - Claney L Pereira
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , D-14424 Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , D-14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin , Arnimallee 22, D-14195 Berlin, Germany
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23
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Comparison of traditional culture and molecular qPCR for detection of simultaneous carriage of multiple pneumococcal serotypes in African children. Sci Rep 2017; 7:4628. [PMID: 28680083 PMCID: PMC5498530 DOI: 10.1038/s41598-017-04915-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/22/2017] [Indexed: 11/29/2022] Open
Abstract
S. pneumoniae is a common colonizer of the human nasopharynx in high income and low-middle income countries. Due to limitations of standard culture methods, the prevalence of concurrent colonization with multiple serotypes is unclear. We evaluated the use of multiplex quantitative PCR (qPCR) to detect multiple pneumococcal serotypes/group colonization in archived nasopharyngeal swabs of pneumococcal conjugate vaccine naive children who had previously been investigated by traditional culture methods. Overall the detection of pneumococcal colonization was higher by qPCR (82%) compared to standard culture (71%; p < 0.001), with a high concordance (kappa = 0.73) of serotypes/groups identified by culture also being identified by qPCR. Also, qPCR was more sensitive in detecting multiple serotype/groups among colonized cases (28.7%) compared to culture (4.5%; p < 0.001). Of the additional serotypes detected only by qPCR, the majority were of lower density (<104 CFU/ml) than the dominant colonizing serotype, with serotype/group 6A/B, 19B/F and 23F being the highest density colonizers, followed by serotype 5 and serogroup 9A/L/N/V being the most common second and third colonizers respectively. The ability of qPCR to detect multiple pneumococcal serotypes at a low carriage density might provide better insight into underlying mechanism for changes in serotype colonization in PCV vaccinated children.
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24
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Cui YA, Patel H, O'Neil WM, Li S, Saddier P. Pneumococcal serotype distribution: A snapshot of recent data in pediatric and adult populations around the world. Hum Vaccin Immunother 2017; 13:1-13. [PMID: 28125317 DOI: 10.1080/21645515.2016.1277300] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
S. pneumoniae infection remains a serious public health concern despite the availability of vaccines covering up to 23 of more than 94 known serotypes. The purpose of the present study was to monitor recent serotype distribution data. PubMed, EMBASE, Cochrane Reviews and Ingenta databases were searched. Serotype data covering invasive pneumococcal disease (IPD) and non-IPD were extracted from articles published from March 2014 to March 2015. Fifty-nine studies presented pneumococcal serotype prevalence by specific age categories. Most prevalent serotypes not covered by pneumococcal conjugate vaccines (PCV) were as follows: 15B, 22F, 15A, 23A among children under the age of 7 y with IPD; among adults with IPD: 22F, 11A, 10A, 38 in the 65 y and older age group; 12F, 9N, 8 in the 50-64 year-old age group and 12F, 8, 6C, 16F in the 15-59 age group. Geographic variations in serotype distribution highlight the importance of monitoring evolving pneumococcal serotype prevalence after pneumococcal vaccine implementation.
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Affiliation(s)
| | | | | | - Se Li
- a Merck & Co Inc. , Kenilworth , NJ , USA
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25
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Pneumococcal Colonization in the Familial Context and Implications for Anti-Pneumococcal Immunization in Adults: Results from the BINOCOLO Project in Sicily. Int J Mol Sci 2017; 18:ijms18010105. [PMID: 28067813 PMCID: PMC5297739 DOI: 10.3390/ijms18010105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/29/2016] [Accepted: 12/29/2016] [Indexed: 01/23/2023] Open
Abstract
The spread of Streptococcus pneumoniae within families has been scarcely investigated so far. This feasibility study aimed to estimate the prevalence of pneumococcal carriage in school-aged children and co-habiting relatives and to explore the potential link between the family environment and the sharing of pneumococcal serotypes covered by the vaccine. Oropharyngeal samples of 146 subjects belonging to 36 different family groups were molecularly tested for pneumococcal detection and serotyping. The overall prevalence of pneumococcal carriage was 65.8% (n = 96/146), whereas it was higher among schoolchildren (77.8%, n = 28/36); subjects of seven years of age had the highest odds of being colonized (odds ratio, OR = 5.176; p = 0.145). Pneumococcal serotypes included in the 13-valent conjugate vaccine formulation were largely detected in the study population and multiple serotypes colonization was considerable. Factors relating to a close proximity among people at the family level were statistically associated with pneumococcal carriage (OR = 2.121; p = 0.049), as well as active smoking habit with a clear dose-response effect (ORs = 1.017–3.326). About half of family clusters evidenced similar patterns of carried pneumococcal serotypes and the odds of sustaining a high level of intrafamilial sharing increased with household size (ORs = 1.083–5.000). This study highlighted the potential role played by the family environment in sustaining both the circulation and horizontal transmission of pneumococcus.
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26
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Hausdorff WP, Hanage WP. Interim results of an ecological experiment - Conjugate vaccination against the pneumococcus and serotype replacement. Hum Vaccin Immunother 2016; 12:358-74. [PMID: 26905681 PMCID: PMC5049718 DOI: 10.1080/21645515.2015.1118593] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Streptococcus pneumoniae has more than 95 serotypes, each of which presumably can cause sepsis, meningitis, pneumonia, and acute otitis media. Pneumococcal conjugate vaccines (PCV) targeted against a limited number of serotypes have nonetheless revealed an impressive impact on each manifestation of pneumococcal disease. At the same time, growing evidence of significant non-vaccine type (NVT) replacement disease following implementation of infant PCV programs has raised questions about the long-term viability of PCV immunization strategies and how to optimize PCV formulations. We discuss here theoretical and practical considerations regarding serotype replacement, and provide a snapshot of the most important NVT types seen to date after implementation of the 2 higher-valent PCVs.
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Affiliation(s)
| | - William P Hanage
- b Department of Epidemiology ; Center for Communicable Disease Dynamics; Harvard TH Chan School of Public Health ; Boston , MA , USA
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27
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Valente C, Hinds J, Gould KA, Pinto FR, de Lencastre H, Sá-Leão R. Impact of the 13-valent pneumococcal conjugate vaccine on Streptococcus pneumoniae multiple serotype carriage. Vaccine 2016; 34:4072-8. [PMID: 27325351 DOI: 10.1016/j.vaccine.2016.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 05/22/2016] [Accepted: 06/02/2016] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Pneumococcal multiple serotype carriage is important for evolution of the species and to understand how the pneumococcal population is changing with vaccination. We aimed to determine the impact of the 13-valent pneumococcal conjugate vaccine (PCV13) on multiple serotype carriage. METHODS AND MATERIALS Nasopharyngeal samples from fully vaccinated pneumococcal carriers (4 doses of PCV13, n=141, aged 18-72months) or from non-vaccinated pneumococcal carriers (0 doses of any PCV, n=140, same age group) were analyzed. Multiple serotype carriage was evaluated by DNA hybridization with a molecular serotyping microarray that detects all known serotypes. RESULTS Vaccinated children had a lower prevalence of multiple serotype carriage than the non-vaccinated group (20.6% vs 29.3%, p=0.097), and a significantly lower proportion of PCV13 serotypes (6.4% vs 38.5%, p=0.0001). PCV13 serotypes found among vaccinated children were mostly detected as a minor serotype in co-colonization with a more abundant non-vaccine serotype. Vaccinated children were colonized by a significantly higher proportion of commensal non-pneumococcal Streptococcus spp. (58.2% vs 42.8%, p=0.012). In vaccinated children there were significantly less non-vaccine type (NVT) co-colonization events than expected based on the distribution of these serotypes in non-vaccinated children. CONCLUSIONS The results suggest that vaccinated children have lower pneumococcal multiple serotype carriage prevalence due to higher competitive abilities of non-vaccine serotypes expanding after PCV13 use. This might represent an additional benefit of PCV13, as decreased co-colonization rates translate into decreased opportunities for horizontal gene transfer and might have implications for the evolution and virulence of pneumococci.
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Affiliation(s)
- Carina Valente
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's, University of London, London, UK; BUGS Bioscience, London Bioscience Innovation Centre, London, UK
| | - Katherine A Gould
- Institute for Infection and Immunity, St. George's, University of London, London, UK; BUGS Bioscience, London Bioscience Innovation Centre, London, UK
| | - Francisco R Pinto
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal; Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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28
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Kamng'ona AW, Hinds J, Bar-Zeev N, Gould KA, Chaguza C, Msefula C, Cornick JE, Kulohoma BW, Gray K, Bentley SD, French N, Heyderman RS, Everett DB. High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children. BMC Infect Dis 2015; 15:234. [PMID: 26088623 PMCID: PMC4474563 DOI: 10.1186/s12879-015-0980-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 06/08/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Carriage of either single or multiple pneumococcal serotypes (multiple carriage) is a prerequisite for developing invasive pneumococcal disease. However, despite the reported high rates of pneumococcal carriage in Malawi, no data on carriage of multiple serotypes has been reported previously. Our study provides the first description of the prevalence of multiple pneumococcal carriage in Malawi. METHODS The study was conducted in Blantyre and Karonga districts in Malawi, from 2008 to 2012. We recruited 116 children aged 0-13 years. These children were either HIV-infected (N = 44) or uninfected (N = 72). Nasopharyngeal samples were collected using sterile swabs. Pneumococcal serotypes in the samples were identified by microarray. Strains that could not be typed by microarray were sequenced to characterise possible genetic alterations within the capsular polysaccharide (CPS) locus. RESULTS The microarray identified 179 pneumococcal strains (from 116 subjects), encompassing 43 distinct serotypes and non-typeable (NT) strains. Forty per cent (46/116) of children carried multiple serotypes. Carriage of vaccine type (VT) strains was higher (p = 0.028) in younger (0-2 years) children (71 %, 40/56) compared to older (3-13 years) children (50 %, 30/60). Genetic variations within the CPS locus of known serotypes were observed in 19 % (34/179) of the strains identified. The variants included 13-valent pneumococcal conjugate vaccine (PCV13) serotypes 6B and 19A, and the polysaccharide vaccine serotype 20. Serotype 6B variants were the most frequently isolated (47 %, 16/34). Unlike the wild type, the CPS locus of the 6B variants contained an insertion of the licD-family phosphotransferase gene. The CPS locus of 19A- and 20-variants contained an inversion in the sugar-biosynthesis (rmlD) gene and a 717 bp deletion within the transferase (whaF) gene, respectively. CONCLUSIONS The high multiple carriage in Malawian children provides opportunities for genetic exchange through horizontal gene transfer. This may potentially lead to CPS locus variants and vaccine escape. Variants reported here occurred naturally, however, PCV13 introduction could exacerbate the CPS genetic variations. Further studies are therefore recommended to assess the invasive potential of these variants and establish whether PCV13 would offer cross-protection. We have shown that younger children (0-2 years) are a reservoir of VT serotypes, which makes them an ideal target for vaccination.
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Affiliation(s)
- Arox W Kamng'ona
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Biochemistry Department, University of Malawi, College of Medicine, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Jason Hinds
- Division of Clinical Sciences, St George's, University of London, London, UK.
| | - Naor Bar-Zeev
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Katherine A Gould
- Division of Clinical Sciences, St George's, University of London, London, UK.
| | - Chrispin Chaguza
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Chisomo Msefula
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Microbiology Department, University of Malawi, College of Medicine, Blantyre, Malawi.
| | - Jennifer E Cornick
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Benard W Kulohoma
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. .,International Centre for Insect Physiology and Ecology, Nairobi, Kenya.
| | - Katherine Gray
- Biochemistry Department, University of Malawi, College of Medicine, Blantyre, Malawi.
| | - Stephen D Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, UK. .,Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Neil French
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. .,Malawi Epidemiology and Intervention Research Unit (MEIRU), Karonga, Malawi.
| | - Robert S Heyderman
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Dean B Everett
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
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29
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Hanieh S, Hamaluba M, Kelly DF, Metz JA, Wyres KL, Fisher R, Pradhan R, Shakya D, Shrestha L, Shrestha A, Joshi A, Habens J, Maharjan BD, Thorson S, Bohler E, Yu LM, Kelly S, Plested E, John T, Werno AM, Adhikari N, Murdoch DR, Brueggemann AB, Pollard AJ. Streptococcus pneumoniae carriage prevalence in Nepal: evaluation of a method for delayed transport of samples from remote regions and implications for vaccine implementation. PLoS One 2014; 9:e98739. [PMID: 24905574 PMCID: PMC4048273 DOI: 10.1371/journal.pone.0098739] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 05/07/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Pneumococcal disease is a significant cause of morbidity and mortality in young children in Nepal, and currently available pneumococcal conjugate vaccines offer moderate coverage of invasive disease isolates. METHODS A prevalence study of children aged 1.5 to 24 months in urban and rural Nepal was conducted. In the urban group, nasopharyngeal swabs (NPS) were transported using silica desiccant packages (SDP) with delayed processing (2 weeks), or skim-milk-tryptone-glucose-glycerin (STGG) with immediate processing (within 8 hours). Pneumococcal nasopharyngeal carriage prevalence, serogroup/type distribution and isolate genotypes (as defined by multilocus sequence typing) were determined. RESULTS 1101 children were enrolled into the study: 574 in the urban group and 527 in the rural group. Overall carriage prevalence based on culture from specimens transported and stored in STGG was 58.7% (337/574), compared to 40.9% (235/574) in SDP. There was concordance of detection of pneumococcus in 67% of samples. Using the SDP method, pneumococcal carriage prevalence was higher in the rural population (69.2%; 364/526) compared to the urban population (40.9%; 235/574). Serogroup/type distribution varied with geographical location. Over half of the genotypes identified in both the urban and rural pneumococcal populations were novel. CONCLUSION The combination of delayed culture and transport using SDP underestimates the prevalence of pneumococcal carriage; however, in remote areas, this method could still provide a useful estimate of carriage prevalence and serogroup/type distribution. Vaccine impact is unpredictable in a setting with novel genotypes and limited serotype coverage as described here. Consequently, continued surveillance of pneumococcal isolates from carriage and disease in Nepali children following the planned introduction of pneumococcal conjugate vaccines introduction will be essential.
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Affiliation(s)
- Sarah Hanieh
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Mainga Hamaluba
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Dominic F. Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Jane A. Metz
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Kelly L. Wyres
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Roberta Fisher
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Rahul Pradhan
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Disuja Shakya
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Lochan Shrestha
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Amrita Shrestha
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Anip Joshi
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Jocelyn Habens
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Bishnu D. Maharjan
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Stephen Thorson
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Erik Bohler
- Okhaldhunga Community Hospital, Okhaldhunga, Nepal
| | - Ly-Mee Yu
- Nuffield Department of Primary Care and Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Sarah Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Emma Plested
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Tessa John
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Anja M. Werno
- Department of Pathology, University of Otago, Christchurch, New Zealand
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Neelam Adhikari
- Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - David R. Murdoch
- Department of Pathology, University of Otago, Christchurch, New Zealand
- Canterbury Health Laboratories, Christchurch, New Zealand
| | | | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
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