Rama Kandasamy, Australia
University of New South Wales Women's and Children's HealthPresenter of 3 Presentations
PCV10 IMPACT ON PNEUMOCOCCAL LINEAGES ISOLATED FROM HEALTHY NEPALESE CHILDREN. (ID 736)
- Rama Kandasamy, Australia
- Sonu Shrestha, United Kingdom
- Rebecca Gladstone, Norway
- Stephanie Lo, United Kingdom
- Meeru Gurung, Nepal
- Stephen Thorson, Nepal
- Lesley McGee, United States of America
- Robert F Breiman, United States of America
- Paulina A. Hawkins, Brazil
- Keith P. Klugman, United States of America
- Dominic Kelly, United Kingdom
- David Murdoch, New Zealand
- Andrew J. Pollard, United Kingdom
- Stephen D. Bentley, United Kingdom
- Shrijana Shrestha, Nepal
Abstract
Background
The 10-valent pneumococcal conjugate vaccine (PCV10) was introduced into the Nepalese infant immunisation schedule in August 2015. We aimed to examine how PCV10 introduction in affected pneumococcal lineages.
Methods
DNA from randomly selected nasopharyngeal pneumococcal isolates of healthy community-based Nepalese children in the Kathmandu valley pre- (2009-2014) and post-PCV10 (2017-2018) introduction, underwent whole-genome-sequencing on the Wellcome Sanger Institutes core sequencing pipeline. Isolates were clustered into lineages based on shared sequence and gene content using Population Partitioning Using Nucleotide K-mers (PopPUNK) software.
Results
313 and 284 pre- and post-PCV10 isolates were sequenced. There was a significant reduction in the proportion of PCV10 serotypes when comparing pre 73/313 (23.3%) with post 37/284 (13%) PCV10 samples (p=0.0014). Overall 122 distinct lineages were identified, 98 pre- and 74 post-PCV10. Simpson's index of diversity for the lineages was 0.992 and 0.987 pre- and post-PCV10 respectively. Within the 3 largest PCV10 serotype lineages there were no examples of non-PCV10 serotype isolates pre-vaccination, whereas all 3 lineages contained non-PCV10 serotypes post-vaccination.
Conclusions
PCV10 serotype prevalence significantly declined following PCV10 introduction. However, strain diversity remained high post-PCV10 and there is evidence suggestive of vaccine escape via capsular-switching among lineages possessing predominantly vaccine-covered capsules prior to PCV10 introduction.
GENOME-WIDE ASSOCIATION STUDY OF PNEUMOCOCCAL CARRIAGE AMONG NEPALESE CHILDREN (ID 16)
- Rama Kandasamy, Australia
- Sagida Bibi, United Kingdom
- Sonu Shrestha, United Kingdom
- Daniel O'Connor, United Kingdom
- Clive Hoggart, United Arab Emirates
- Meeru Gurung, Nepal
- Stephen Thorson, Nepal
- Michael J. Carter, United Kingdom
- Dominic Kelly, United Kingdom
- David Murdoch, New Zealand
- Andrew J. Pollard, United Kingdom
- Michael Levin, United Arab Emirates
- Shrijana Shrestha, Nepal
Abstract
Background
Determining the host molecular genetic characteristics of pneumococcal colonisation may inform the development of new clinical interventions which could interrupt pneumococcal transmission and establishment of disease. We performed a genome-wide association study to identify the genes associated with pneumococcal carriage.
Methods
DNA collected from healthy Nepalese children were genotyped using Illumina Global Screening Arrays. Array data underwent QC and filtering before undergoing imputation using the HRC R1.1 2016 reference panel. Nasopharyngeal swabs collected from participants were processed for the presence of pneumococci by conventional microbiological techniques. Association analysis was performed using PLINK 1.9.
Results
Following filtering, 1355 carriers (cases) and 766 non-carriers (controls) were analysed. 10 variants within a single region, were associated with pneumococcal carriage (p<10-8). The variant that had the strongest association with pneumococcal carriage (MAF carriers = 0.07 vs MAF non-carriers = 0.13, OR 0.52, 95% CI 0.42-0.64, p=2.3x10-8), is within an intergenic region between PPFIA2 and CCDC59.
Conclusions
We identified host genetic variants associated with pneumococcal carriage. Further studies confirming this association and its biological role in pneumococcal carriage are needed.
GENOME-WIDE ASSOCIATION STUDY OF COLONISING NASOPHARYNGEAL PNEUMOCOCCI OBTAINED FROM CHILDREN IN NEPAL TO IDENTIFY GENES ASSOCIATED WITH PNEUMONIA. (ID 729)
- Rama Kandasamy, Australia
- Sonu Shrestha, United Kingdom
- John A. Lees, United Kingdom
- Rebecca Gladstone, Norway
- Stephanie Lo, United Kingdom
- Meeru Gurung, Nepal
- Stephen Thorson, Nepal
- Michael J. Carter, United Kingdom
- Lesley McGee, United States of America
- Robert F Breiman, United States of America
- Paulina A. Hawkins, Brazil
- Keith P. Klugman, United States of America
- Dominic Kelly, United Kingdom
- David Murdoch, New Zealand
- Andrew J. Pollard, United Kingdom
- Stephen D. Bentley, United Kingdom
- Shrijana Shrestha, Nepal
Abstract
Background
Identifying the molecular characteristics of pneumococci associated with disease may inform development of new clinical interventions. We aimed to perform a bacterial genome-wide association study to identify pneumococcal genes associated with carriage among children with pneumonia.
Methods
DNA from nasopharyngeal pneumococcal isolates obtained from Nepalese children admitted to hospital with pneumonia (cases) and healthy community-based children (controls), underwent whole-genome-sequencing on the Wellcome Sanger Institutes core sequencing pipeline. The association of variants from sequences mapped against the S. pneumoniae ATCC700669 genome, with cluster of orthologous groups using a fixed effects model, was performed using a python based sequence element enrichment analysis.
Results
245 case and 597 control isolates were sequenced. 405461 variants were identified and 31708 tested after filtering. 20 variants from colonising bacteria had a strong association (p<10-8) with pneumonia. 18/20 of these variants were located within the lacE2 gene. The variant with the strongest association, presence of an A allele at position 1066739, was identified in 240/597 (40%) of controls and 150/245 (61%) of cases (p=10-10).
Conclusions
In this study in Nepal the pneumococcal gene lacE2 was associated with colonisation in children with pneumonia. Studies examining the role of lacE2 in the pathogenesis of pneumococcal pneumonia are needed.
Author Of 6 Presentations
GENOME-WIDE ASSOCIATION STUDY OF COLONISING NASOPHARYNGEAL PNEUMOCOCCI OBTAINED FROM CHILDREN IN NEPAL TO IDENTIFY GENES ASSOCIATED WITH PNEUMONIA. (ID 729)
- Rama Kandasamy, Australia
- Sonu Shrestha, United Kingdom
- John A. Lees, United Kingdom
- Rebecca Gladstone, Norway
- Stephanie Lo, United Kingdom
- Meeru Gurung, Nepal
- Stephen Thorson, Nepal
- Michael J. Carter, United Kingdom
- Lesley McGee, United States of America
- Robert F Breiman, United States of America
- Paulina A. Hawkins, Brazil
- Keith P. Klugman, United States of America
- Dominic Kelly, United Kingdom
- David Murdoch, New Zealand
- Andrew J. Pollard, United Kingdom
- Stephen D. Bentley, United Kingdom
- Shrijana Shrestha, Nepal
Abstract
Background
Identifying the molecular characteristics of pneumococci associated with disease may inform development of new clinical interventions. We aimed to perform a bacterial genome-wide association study to identify pneumococcal genes associated with carriage among children with pneumonia.
Methods
DNA from nasopharyngeal pneumococcal isolates obtained from Nepalese children admitted to hospital with pneumonia (cases) and healthy community-based children (controls), underwent whole-genome-sequencing on the Wellcome Sanger Institutes core sequencing pipeline. The association of variants from sequences mapped against the S. pneumoniae ATCC700669 genome, with cluster of orthologous groups using a fixed effects model, was performed using a python based sequence element enrichment analysis.
Results
245 case and 597 control isolates were sequenced. 405461 variants were identified and 31708 tested after filtering. 20 variants from colonising bacteria had a strong association (p<10-8) with pneumonia. 18/20 of these variants were located within the lacE2 gene. The variant with the strongest association, presence of an A allele at position 1066739, was identified in 240/597 (40%) of controls and 150/245 (61%) of cases (p=10-10).
Conclusions
In this study in Nepal the pneumococcal gene lacE2 was associated with colonisation in children with pneumonia. Studies examining the role of lacE2 in the pathogenesis of pneumococcal pneumonia are needed.
PCV10 IMPACT ON PNEUMOCOCCAL LINEAGES ISOLATED FROM HEALTHY NEPALESE CHILDREN. (ID 736)
- Rama Kandasamy, Australia
- Sonu Shrestha, United Kingdom
- Rebecca Gladstone, Norway
- Stephanie Lo, United Kingdom
- Meeru Gurung, Nepal
- Stephen Thorson, Nepal
- Lesley McGee, United States of America
- Robert F Breiman, United States of America
- Paulina A. Hawkins, Brazil
- Keith P. Klugman, United States of America
- Dominic Kelly, United Kingdom
- David Murdoch, New Zealand
- Andrew J. Pollard, United Kingdom
- Stephen D. Bentley, United Kingdom
- Shrijana Shrestha, Nepal
Abstract
Background
The 10-valent pneumococcal conjugate vaccine (PCV10) was introduced into the Nepalese infant immunisation schedule in August 2015. We aimed to examine how PCV10 introduction in affected pneumococcal lineages.
Methods
DNA from randomly selected nasopharyngeal pneumococcal isolates of healthy community-based Nepalese children in the Kathmandu valley pre- (2009-2014) and post-PCV10 (2017-2018) introduction, underwent whole-genome-sequencing on the Wellcome Sanger Institutes core sequencing pipeline. Isolates were clustered into lineages based on shared sequence and gene content using Population Partitioning Using Nucleotide K-mers (PopPUNK) software.
Results
313 and 284 pre- and post-PCV10 isolates were sequenced. There was a significant reduction in the proportion of PCV10 serotypes when comparing pre 73/313 (23.3%) with post 37/284 (13%) PCV10 samples (p=0.0014). Overall 122 distinct lineages were identified, 98 pre- and 74 post-PCV10. Simpson's index of diversity for the lineages was 0.992 and 0.987 pre- and post-PCV10 respectively. Within the 3 largest PCV10 serotype lineages there were no examples of non-PCV10 serotype isolates pre-vaccination, whereas all 3 lineages contained non-PCV10 serotypes post-vaccination.
Conclusions
PCV10 serotype prevalence significantly declined following PCV10 introduction. However, strain diversity remained high post-PCV10 and there is evidence suggestive of vaccine escape via capsular-switching among lineages possessing predominantly vaccine-covered capsules prior to PCV10 introduction.
MONITORING VACCINE IMPACT ON COMMUNITY CARRIAGE IN NEPAL REVEALS CHANGES IN THE CIRCULATING POPULATION OF PNEUMOCOCCAL SEROTYPES AND ANTIMICROBIAL RESISTANCE GENES (ID 977)
- Sonu Shrestha, United Kingdom
- Rama Kandasamy, Australia
- Susana Camara,
- Merryn Voysey, United Kingdom
- Madhav C. Gautam, Nepal
- Meeru Gurung, Nepal
- Katherine Gould,
- Stephen Thorson, Nepal
- Imran Ansari, Nepal
- Shrijana Shrestha, Nepal
- Maria D. Knoll, United States of America
- David Murdoch, New Zealand
- Dominic Kelly, United Kingdom
- Jason Hinds, United Kingdom
- Andrew J. Pollard, United Kingdom
Abstract
Background
Community carriage of pneumococcal serotypes in children was assessed pre- and post-PCV10 introduction in Nepal to monitor pneumococcal vaccine impact. Molecular serotyping by microarray enabled detection of multiple-serotype carriage plus non-encapsulated pneumococcal lineages, related Streptococcus species and selected antimicrobial resistance genes.
Methods
Nasopharyngeal swabs were collected from healthy Nepalese children in 2014-15 (pre-PCV10) and 2017-18 (post-PCV10). DNA was extracted from plate sweeps of 1,241 and 1,445 swab cultures for pre- and post-vaccine periods respectively and analysed by Senti-SP molecular serotyping microarray.
Results
Comparing carriage among children pre- and post-PCV10, there was a decrease in PCV10 serotype carriage (37% vs 17%) and an increase in non-vaccine serotype carriage (67% vs 73%). There was no change for non-encapsulated pneumococcal lineages (16% vs 16%), an increase in related Streptococcal species (22% vs 25%) and an increase in detection of antimicrobial resistance genes (65% vs 74%). Multiple pneumococcal serotype carriage decreased (24% vs 16%) and multiple carriage including non-encapsulated pneumococci and related Streptococcal species also decreased (45% vs 41%).
Conclusions
Introduction of PCV10 in Nepal has resulted in a decrease in vaccine type carriage within two years. However, increases in carriage of non-vaccine types as well as antimicrobial resistance genes and related Streptococcal species were observed.
GENOME-WIDE ASSOCIATION STUDY OF PNEUMOCOCCAL CARRIAGE AMONG NEPALESE CHILDREN (ID 16)
- Rama Kandasamy, Australia
- Sagida Bibi, United Kingdom
- Sonu Shrestha, United Kingdom
- Daniel O'Connor, United Kingdom
- Clive Hoggart, United Arab Emirates
- Meeru Gurung, Nepal
- Stephen Thorson, Nepal
- Michael J. Carter, United Kingdom
- Dominic Kelly, United Kingdom
- David Murdoch, New Zealand
- Andrew J. Pollard, United Kingdom
- Michael Levin, United Arab Emirates
- Shrijana Shrestha, Nepal
Abstract
Background
Determining the host molecular genetic characteristics of pneumococcal colonisation may inform the development of new clinical interventions which could interrupt pneumococcal transmission and establishment of disease. We performed a genome-wide association study to identify the genes associated with pneumococcal carriage.
Methods
DNA collected from healthy Nepalese children were genotyped using Illumina Global Screening Arrays. Array data underwent QC and filtering before undergoing imputation using the HRC R1.1 2016 reference panel. Nasopharyngeal swabs collected from participants were processed for the presence of pneumococci by conventional microbiological techniques. Association analysis was performed using PLINK 1.9.
Results
Following filtering, 1355 carriers (cases) and 766 non-carriers (controls) were analysed. 10 variants within a single region, were associated with pneumococcal carriage (p<10-8). The variant that had the strongest association with pneumococcal carriage (MAF carriers = 0.07 vs MAF non-carriers = 0.13, OR 0.52, 95% CI 0.42-0.64, p=2.3x10-8), is within an intergenic region between PPFIA2 and CCDC59.
Conclusions
We identified host genetic variants associated with pneumococcal carriage. Further studies confirming this association and its biological role in pneumococcal carriage are needed.
SEROTYPE-SPECIFIC PNEUMOCOCCAL CARRIAGE DENSITY AMONG HEALTHY NEPALESE CHILDREN POST-PCV10 INTRODUCTION (ID 1047)
- Sonu Shrestha, United Kingdom
- Rama Kandasamy, Australia
- Madhav C. Gautam, Nepal
- Meeru Gurung, Nepal
- Stephen Thorson, Nepal
- Imran Ansari, Nepal
- Katherine Gould,
- Michael J. Carter, United Kingdom
- Dominic Kelly, United Kingdom
- David Murdoch, New Zealand
- Andrew J. Pollard, United Kingdom
- Jason Hinds, United Kingdom
- Shrijana Shrestha, Nepal
Abstract
Background
The density of pneumococcal carriage provides an insight into the dynamics of transmission, colonisation and vaccine effect. We aimed to measure serotype-specific carriage density 2-3 years after 10-valent pneumococcal conjugate vaccine (PCV10) introduction, using qPCR and bacterial DNA microarray.
Methods
Nasopharyngeal swabs were collected from healthy Nepalese children from the Kathmandu Valley between April 2017 and August 2018. DNA was extracted from the swab media and qPCR performed for pneumococcal autolysin (lytA). Swab media were also plated on blood agar, incubated overnight, and plate sweeps collected. DNA was extracted from plate sweeps and molecular serotyped using the Senti-SPv1.5 microarray (BUGS Bioscience, UK).
Results
1264 swabs were collected and analysed by both microarray and qPCR. The mean density of PCV10 serotypes was significantly higher than non-PCV10 serotypes (10^3.9 vs 10^3.4 copies/ml, p=0.004). Serotypes 1 (10^4.6 copies/ml, 95% CI 10^3.4-5.9) and 6B (10^4.6 copies/ml, 95% CI 10^3.9-5.3) had the highest mean density. Serotypes 4 (10^2.8 copies/ml, 95% CI 10^1.1-4.5) and 9N (10^2.9copies/ml, 95% CI 10^2.1-3.7) had the lowest mean carriage density.
Conclusions
Serotype 1, which causes the greatest proportion of invasive pneumococcal disease in this setting, was found to have the highest carriage density. Further evaluation of the PCV10 impact on carriage density is needed.
THE IMPACT OF PNEUMOCOCCAL CONJUGATE VACCINE INTRODUCTION IN NEPAL: A SIX-YEAR PAEDIATRIC SURVEILLANCE STUDY (ID 516)
- Shrijana Shrestha, Nepal
- Meeru Gurung, Nepal
- Stephen Thorson, Nepal
- Bhishma Pokhrel, Nepal
- Bibek Khadka, Nepal
- Pratistha Maskey, Nepal
- Puja Amatya, Nepal
- Madhav C. Gautam, Nepal
- Michael J. Carter, United Kingdom
- Rama Kandasamy, Australia
- Brian Wahl, United States of America
- Sarah Kelly, United Kingdom
- Krishna G. Prajapati, Nepal
- Sonu Shrestha, United Kingdom
- Maria Deloria Knoll, United States of America
- Jason Hinds, United Kingdom
- Ganesh Shah, Nepal
- Dominic Kelly, United Kingdom
- David Murdoch, New Zealand
- Merryn Voysey, United Kingdom
- Andrew J. Pollard, United Kingdom
Abstract
Background
S. pneumoniae is a major cause of bacterial pneumonia and an important cause of invasive bacterial disease (IBD) in children under-five years of age in Nepal. Pneumococcal conjugate vaccine, PCV10, was introduced in 2015 with a 2+1 schedule.
Methods
We assessed the programmatic impact of PCV10 introduction using surveillance for nasopharyngeal (NP) colonisation, pneumonia and IBD. NP swabs from pneumonia inpatients and from healthy children, blood cultures from inpatients with suspected IBD, and chest x-rays from inpatient pneumonia cases were obtained over a 6-year period (2014-2019).
Results
The proportion of pneumonia cases with radiographic endpoint-consolidation (likely bacterial) was 34% lower (95%CI 19-46%) in 2018 compared with the pre-vaccine period (2014-2015). Vaccine serotype (VT) carriage in children under 2-years of age with pneumonia in 2019 was 78% lower (95%CI 30-93%) than in the pre-vaccine period.
Among healthy 6-23 month old children (urban and rural cohorts), VT-carriage declined 74% (95%CI 43-82%) by 2019. An increase in PCV13-additional-serotype carriage was seen in 2018 among rural-children (prevalence-ratio 1.65, 95%CI 1.17-2.32), but not urban-children.
Serotype 1 remains the dominant serotype detected in cases of invasive pneumococcal disease.
Conclusions
A decrease in prevalence of endpoint-consolidation-pneumonia and a decrease in vaccine-serotype circulation have been observed post PCV introduction in Nepal.