Effect of introduction of pneumococcal conjugate vaccine immunization on nasopharyngeal colonization of streptococcus pneumoniae in South Africa

A thesis submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Doctor of Philosophy Johannesburg, 19 November 2015Pneumococcal conjugate vaccine (PCV) immunization of children decreases their risk of nasopharyngeal acquisition of vaccine serotypes and concurrently reduces the transmission thereof to PCV-unvaccinated age groups. We studied the impact of routine infant PCV immunization at population level, on the epidemiology of nasopharyngeal pneumococcal colonization in a rural (Agincourt) and an urban (Soweto) South African community with high prevalence of HIV-infection. Furthermore, we delineated the effect of infant PCV immunization on bacterial interactions of Streptococcus pneumoniae with Haemophilus influenzae and Staphylococcus aureus at the population level. Lastly, we assessed the utility of colonization data to predict the impact of childhood PCV immunization on the direct and indirect effect against invasive pneumococcal disease (IPD). Materials and Methods A series of cross sectional colonization surveys were undertaken (in Agincourt and Soweto) between 2009 and 2012. These years were representative of the pre- or early-PCV-era and PCV-era years. The seven valent PCV (PCV7) was introduced into the South African national immunization program in April 2009, using a 6, 14 and 40 weeks of age dosing schedule with no catch up campaign of older children. Subsequently, PCV7 was replaced by 13-valent PCV (PCV13) in May 2011, with a limited catch up campaign. Nasopharyngeal swabs were collected among household members and mother-infant pairs and processed for S. pneumoniae, H. influenzae and S. aureus using standard microbiologic techniques. Additionally, the trends in incidence of IPD for 2005 to 2012 were evaluated. Multivariate logistic regressions were performed to assess the impact of PCV on carriage in different age groups. Adjusted risk ratios (aRR) or adjusted odds ratios (aOR) are reported as measures of impact and association. We compared the predicted changes in IPD among children and their mothers, stratified by HIV, using a theoretical model and compared this to the observed changes in IPD. Results Among rural households, the prevalence of PCV7-serotype colonization among all ages decreased from 18.3% in 2009 to 11.4% in 2011; p<0.0001. This included reductions (adjusted risk ratio; aRR) of 50% (95% Confidence Interval [95%CI]:0.42-0.59), 34% (95%CI: 0.48-0.92) and 64% (95%CI: 0.18- 0.74) in age-groups <2 years, 6-12 years and adults, respectively. The prevalence of PCV7 serotype colonization among primary caregivers decreased from 10.2% in 2009, to 5.4% in 2011, (p<0.001). Non-vaccine serotype colonization prevalence increased by 35% (95%CI: 1.17-1.56) among children <2 year of age in 2011, however, it declined by 45%-54% among adolescents and adults. In urban mother-infant pairs, PCV13serotype colonization decreased from 2010 compared to 2012 among HIV-uninfected (aOR: 0.32; 95%CI: 0.25-0.40) and HIV-infected children (aOR: 0.37; 95%CI: 0.28-0.49), whilst there was an increase in non-vaccine serotype colonization. Decreases in PCV13 serotype colonization were also observed in HIV-uninfected women (aOR: 0.44; 95%CI: 0.23-0.81); with a similar trend in HIV-infected women. Non PCV13 serotype colonization declined in 2012 compared to in 2010 among HIV-infected women (aOR: 0.69, 95%CI: 0.48-0.99). HIV-infected compared to HIV–uninfected women had higher prevalence of overall (20.5% vs. 9.7% in 2010; 13.8% vs. 9.7% in 2012) and PCV13 serotype colonization (8.7% vs. 5.4% in 2010; 4.8% vs. 2.0% in 2012) in both sampling periods; p<0.04 for all observations. For bacterial associations in the rural population, from 2009 to 2011 in children 0-2 years and 3-12 years of age, the prevalence of overall S. pneumoniae colonization decreased from 74.9% to 67.0% (p<0.001). Although there was also a decrease in prevalence of H. influenzae colonization in the 3-12 year age group (55.1% to 45.3%, p<0.001), this was not evident among those <2 years of age. The prevalence of S. aureus colonization remained unchanged in all childhood age groups. In individuals older than 12 years of age, the prevalence of colonization decreased for all studied bacteria including S. pneumoniae (11.2% vs 6.8%), H. influenzae (16.7% vs. 8.8%) and S. aureus (31.2% vs. 23.7%); p<0.001 for all comparisons. Analysing the colonization and IPD findings, between the pre PCV era (2007-2009) and the PCV13 era (2012), we observed reductions in vaccine serotype colonization and IPD due to PCV7 serotypes and the additional six serotypes included in PCV13 among children and women. Using the changes in vaccine serotype colonization over time, the hypothetical model accurately predicted changes in vaccine-serotype IPD incidence compared to the observed changes in PCV-unvaccinated HIV-infected and HIV-uninfected adults; and among children too old to have been immunized. The model, however, underestimated the reduction in vaccine serotype IPD among the child age-group targeted for immunization. The model was, however, not useful in predicting the changes that occurred for non vaccine serotypes either among PCV-vaccinated or PCV-unvaccinated age-groups. Discussion and Conclusion Infant PCV immunization resulted in population wide decreases in vaccine-serotype colonization of S. pneumoniae including among HIV-infected adults in both rural and urban settings. Surveillance of colonization prior and following childhood PCV immunization can be used to infer indirect effects against vaccine-serotype IPD in the community even in high HIV-prevalence settings such ours

Imputing direct and indirect vaccine effectiveness of childhood pneumococcal conjugate vaccine against invasive disease by surveying temporal changes in nasopharyngeal pneumococcal colonization

The limited capabilities in most low-middle income countries to study the benefit of pneumococcal conjugate vaccine (PCV) against invasive pneumococcal disease (IPD), calls for alternate strategies to assess this. We used a mathematical model, to predict the direct and indirect effectiveness of PCV by analyzing serotype specific colonization prevalence and IPD incidence prior to and following childhood PCV immunization in South Africa. We analyzed IPD incidence from 2005-2012 and colonization studies undertaken in HIV-uninfected and HIV-infected child-mother dyads from 2007-2009 (pre-PCV era), in 2010 (7-valent PCV era) and 2012 (13-valent PCV era). We compared the model-predicted to observed changes in IPD incidence, stratified by HIV-status in children >3 months to 5 years and also in women aged >18-45 years. We observed reductions in vaccine-serotype colonization and IPD due to vaccine serotypes among children and women after PCV introduction. Using the changes in vaccine-serotype colonization data, the model-predicted changes in vaccine-serotype IPD incidence rates were similar to the observed changes in PCV-unvaccinated children and adults, but not among children <24 months. Surveillance of colonization prior and following PCV use can be used to impute PCVs' indirect associations in unvaccinated age groups, including in high HIV-prevalence settings

Global distribution of invasive serotype 35D streptococcus pneumoniae isolates following introduction of 13-valent pneumococcal conjugate vaccine

A newly recognized pneumococcal serotype 35D, which differs from the 35B polysaccharide in structure and serology by not binding to factor serum 35a, was recently reported. The genetic basis for this distinctive serology is due to the presence of an inactivating mutation in wciG, which encodes an O-acetyltransferase responsible for O-acetylation of a galactofuranose. Here, we assessed the genomic data of a worldwide pneumococcal collection to identify serotype 35D isolates and understand their geographical distribution, genetic background and invasiveness potential. Of 21,980 pneumococcal isolates, 444 were originally typed as serotype 35B by PneumoCaT. Analysis of wciGrevealed 23 isolates from carriage (n=4) and disease (n=19) with partial or complete loss-of-funtion mutations, including mutations resulting in pre-mature stop codons (n=22) and an in-frame mutation (n=1). These were selected for further analysis. The putative 35D isolates were geographically widespread and 65.2% (15/23) of them was recovered after PCV13 introduction. Compared with serotype 35B, putative serotype 35D isolates have higher invasive disease potentials based on odds ratio (OR) (11.58; 95% CI, 1.42-94.19 vs 0.61; 95% CI, 0.40-0.92) and a higher prevalence of macrolide resistance mediated by mefA (26.1% vs 7.6%, p=0.009). Using Quellung, 50% (10/20) of viable isolates were serotype 35D, 25% (5/20) serotype 35B, and 25% (5/20) a mixture of 35B/35D. The discrepancy between phenotype and genotype requires further investigation. These findings illustrated a global distribution of an invasive serotype 35D among young children post-PCV13 introduction and underlined the invasive potential conferred by the loss of O-acetylation in the pneumococcal capsule

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact

Background: Pneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease, caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing to study pneumococcal serotype, antibiotic resistance and invasiveness, in the context of genetic background. / Methods: Our dataset of 13,454 genomes, combined with four published genomic datasets, represented Africa (40%), Asia (25%), Europe (19%), North America (12%), and South America (5%). These 20,027 pneumococcal genomes were clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our dataset, we additionally derived serotype and sequence type, and predicted antibiotic sensitivity. We then measured invasiveness using odds ratios that relating prevalence in invasive pneumococcal disease to carriage. / Findings: The combined collections (n = 20,027) were clustered into 621 GPSCs. Thirty-five GPSCs observed in our dataset were represented by >100 isolates, and subsequently classed as dominant-GPSCs. In 22/35 (63%) of dominant-GPSCs both non-vaccine serotypes and vaccine serotypes were observed in the years up until, and including, the first year of pneumococcal conjugate vaccine introduction. Penicillin and multidrug resistance were higher (p < .05) in a subset dominant-GPSCs (14/35, 9/35 respectively), and resistance to an increasing number of antibiotic classes was associated with increased recombination (R2 = 0.27 p < .0001). In 28/35 dominant-GPSCs, the country of isolation was a significant predictor (p < .05) of its antibiogram (mean misclassification error 0.28, SD ± 0.13). We detected increased invasiveness of six genetic backgrounds, when compared to other genetic backgrounds expressing the same serotype. Up to 1.6-fold changes in invasiveness odds ratio were observed. / Interpretation: We define GPSCs that can be assigned to any pneumococcal genomic dataset, to aid international comparisons. Existing non-vaccine-serotypes in most GPSCs preclude the removal of these lineages by pneumococcal conjugate vaccines; leaving potential for serotype replacement. A subset of GPSCs have increased resistance, and/or serotype-independent invasiveness

Residual colonization by vaccine serotypes in rural South Africa four years following initiation of pneumococcal conjugate vaccine immunization

Background: We evaluated pneumococcal colonization in children and adults between the time of 7-valent pneumococcal conjugate vaccine (PCV) introduction in the immunization program in April 2009 to two years after transitioning to 13-valent PCV in 2011. Methods: Community-based pneumococcal carriage surveillance was undertaken between May-November 2013 (Period-3; n=1884), with similar surveys in 2009 (Period-1, n=2010) and 2011 (Period-2; n=3659). Households with children below two years had a similar probability of being sampled in all surveys. Nasopharyngeal swabs were processed using standard methods and serotyped by Quellung. Results: In children >9-59 months of age, overall pneumococcal colonization prevalence declined from 81.8% in Period-1 to 65.0% in Period-3 (p<0.001). Reductions of 70% (95%CI: 60%-77%; 41.2% vs. 13.6%) in PCV7-serotypes colonization and 66% (95%CI:48%-78%; 15.3% vs. 4.4%) for the six additional PCV-serotypes in PCV13 (PCV13 add6VT) were observed. There was, however, high residual prevalence of colonization by PCV7-serotypes 19F (14.9% vs. 6.3%) and 23F (8.5% vs. 4.1%), despite reduction of 57% (95%CI:35%-80%) and 52% (95%CI:21%-83%), respectively. Among individuals >12 years of age, there was 61% (95%CI:18%-82%) reduction in PCV7-serotype colonization (3.1% vs. 1.3%; ) and 75% (95%CI: 11%-93%) decrease for PCV13-add6VT (2.1% vs. 0.6%) between Period-1 and Period-3. Conclusions: The residual prevalence of serotypes 19F and 23F in PCV-immunized and unvaccinated age-groups, four years after introducing PCV in the South African public immunization program, suggests ongoing community transmission and transient vaccine effects

A mosaic tetracycline resistance gene tet(S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa

Objectives: We reported tet(S/M) in Streptococcus pneumoniae and investigated its temporal spread in relation to nationwide clinical interventions. Methods: We whole-genome sequenced 12 254 pneumococcal isolates from 29 countries on an Illumina HiSeq sequencer. Serotype, multilocus ST and antibiotic resistance were inferred from genomes. An SNP tree was built using Gubbins. Temporal spread was reconstructed using a birth–death model. Results: We identified tet(S/M) in 131 pneumococcal isolates and none carried other known tet genes. Tetracycline susceptibility testing results were available for 121 tet(S/M)-positive isolates and all were resistant. A majority (74%) of tet(S/M)-positive isolates were from South Africa and caused invasive diseases among young children (59% HIV positive, where HIV status was available). All but two tet(S/M)-positive isolates belonged to clonal complex (CC) 230. A global phylogeny of CC230 (n=389) revealed that tet(S/M)-positive isolates formed a sublineage predicted to exhibit resistance to penicillin, co-trimoxazole, erythromycin and tetracycline. The birth–death model detected an unrecognized outbreak of this sublineage in South Africa between 2000 and 2004 with expected secondary infections (effective reproductive number, R) of ∼2.5. R declined to ∼1.0 in 2005 and <1.0 in 2012. The declining epidemic could be related to improved access to ART in 2004 and introduction of pneumococcal conjugate vaccine (PCV) in 2009. Capsular switching from vaccine serotype 14 to non-vaccine serotype 23A was observed within the sublineage. Conclusions: The prevalence of tet(S/M) in pneumococci was low and its dissemination was due to an unrecognized outbreak of CC230 in South Africa. Capsular switching in this MDR sublineage highlighted its potential to continue to cause disease in the post-PCV13 era

Upper airways colonisation of Streptococcus pneumoniae in adults aged 60 years and older: A systematic review of prevalence and individual participant data meta-analysis of risk factors

Background: Colonisation with Streptococcus pneumoniae can lead to invasive pneumococcal disease and pneumonia. Pneumococcal acquisition and prevalence of colonisation are high in children. In older adults, a population susceptible to pneumococcal disease, colonisation prevalence is reported to be lower, but studies are heterogeneous. Methods: This is a systematic review and meta-analysis of prevalence of, and risk factors for, pneumococcal colonisation in adults ≥ 60 years of age (PROSPERO #42016036891). We identified peer-reviewed studies reporting the prevalence of S. pneumoniae colonisation using MEDLINE and EMBASE (until April 2016), excluding studies of acute disease. Participant-level data on risk factors were sought from each study. Findings: Of 2202 studies screened, 29 were analysable: 18 provided participant-level data (representing 6290 participants). Prevalence of detected pneumococcal colonisation was 0–39% by conventional culture methods and 3–23% by molecular methods. In a multivariate analysis, colonisation was higher in persons from nursing facilities compared with the community (odds ratio (OR) 2•30, 95% CI 1•26–4•21 and OR 7•72, 95% CI 1•15–51•85, respectively), in those who were currently smoking (OR 1•69, 95% CI 1•12–2•53) or those who had regular contact with children (OR 1•93, 95%CI 1•27–2•93). Persons living in urban areas had significantly lower carriage prevalence (OR 0•43, 95%CI 0•27–0•70). Interpretation: Overall prevalence of pneumococcal colonisation in older adults was higher than expected but varied by risk factors. Future studies should further explore risk factors for colonisation, to highlight targets for focussed intervention such as pneumococcal vaccination of high-risk groups. Funding: No funding was required

Visualizing variation within global pneumococcal sequence clusters (GPSCS) and country population snapshots to contextualize pneumococcal isolates

Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemi-nation of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20 kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (tet, erm, cat) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here.Fil: Gladstone, Rebecca A.. Wellcome Sanger Institute; Reino UnidoFil: Lo, Stephanie W.. Wellcome Sanger Institute; Reino UnidoFil: Goater, Richard. Wellcome Sanger Institute; Reino Unido. University of Oxford; Reino UnidoFil: Yeats, Corin. Wellcome Sanger Institute; Reino Unido. University of Oxford; Reino UnidoFil: Taylor, Ben. Wellcome Sanger Institute; Reino Unido. University of Oxford; Reino UnidoFil: Hadfield, James. Fred Hutchinson Cancer Research Center; Estados UnidosFil: Lees, John A.. Imperial College London; Reino UnidoFil: Croucher, Nicholas J.. Imperial College London; Reino UnidoFil: van Tonder, Andries. Wellcome Sanger Institute; Reino Unido. University of Cambridge; Estados UnidosFil: Bentley, Leon J.. Wellcome Sanger Institute; Reino UnidoFil: Quah, Fu Xiang. Wellcome Sanger Institute; Reino UnidoFil: Blaschke, Anne J.. University of Utah; Estados UnidosFil: Pershing, Nicole L.. University of Utah; Estados UnidosFil: Byington, Carrie L.. University of California; Estados UnidosFil: Balaji, Veeraraghavan. Christian Medical College; IndiaFil: Hryniewicz, Waleria. National Medicines Institute; PoloniaFil: Sigauque, Betuel. Instituto Nacional de Saude Maputo; MozambiqueFil: Ravikumar, K. L.. Kempegowda Institute Of Medical Sciences; IndiaFil: Grassi Almeida, Samanta Cristine. Adolfo Lutz Institute; BrasilFil: Ochoa, Theresa J.. Universidad Peruana Cayetano Heredia; PerúFil: Ho, Pak Leung. The University Of Hong Kong; Hong KongFil: du Plessis, Mignon. National Institute for Communicable Diseases; SudáfricaFil: Ndlangisa, Kedibone M.. National Institute for Communicable Diseases; SudáfricaFil: Cornick, Jennifer. Malawi liverpool wellcome Trust Clinical Research Programme; MalauiFil: Kwambana Adams, Brenda. Colegio Universitario de Londres; Reino Unido. Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine; GambiaFil: Benisty, Rachel. Ben Gurion University of the Negev; IsraelFil: Nzenze, Susan A.. University of the Witwatersrand; SudáfricaFil: Madhi, Shabir A.. University of the Witwatersrand; SudáfricaFil: Hawkins, Paulina A.. Emory University; Estados UnidosFil: Faccone, Diego Francisco. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas. Área de Antimicrobianos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Assessing the impact of pneumococcal conjugate vaccines on invasive pneumococcal disease using polymerase chain reaction-based surveillance : an experience from South Africa

BACKGROUND : The use of molecular diagnostic techniques for the evaluation of the impact of pneumococcal conjugate vaccines (PCVs) has not been documented. We aimed to evaluate the impact of PCVs on invasive pneumococcal disease (IPD) using polymerase chain reaction (PCR)-based techniques and compare with results obtained from culture-based methods. METHODS : We implemented two independent surveillance programs for IPD among individuals hospitalized at one large surveillance site in Soweto, South Africa during 2009–2012: (i) PCR-based (targeting the lytA gene) syndromic pneumonia surveillance; and (ii) culture-based laboratory surveillance. Positive samples were serotyped. The molecular serotyping assay included targets for 42 serotypes including all serotypes/serogroups included in the 7-valent (PCV-7) and 13-valent (PCV-13) PCV. The Quellung reaction was used for serotyping of culture-positive cases. We calculated the change in rates of IPD (lytA- or culture-positive) among HIV-uninfected children aged <2 years from the year of PCV-7 introduction (2009) to the post-vaccine years (2011 or 2012). RESULTS : During the study period there were 607 lytA-positive and 1,197 culture-positive cases that were serotyped. Samples with lytA cycle threshold (Ct)-values ≥35 (30.2 %; 123/407) were significantly less likely to have a serotype/ serogroup detected for serotypes included in the molecular serotyping assay than those with Ct-values <35 (78.0 %; 156/200) (p < 0.001). From 2009 to 2012 rates of PCV-7 serotypes/serogroups decreased −63.8 % (95 % CI: −79.3 % to −39.1 %) among lytA-positive cases and −91.7 % (95 % CI: −98.8 % to −73.6 %) among culture-positive cases. Rates of lytA-positive non-vaccine serotypes/serogroups also significantly decreased (−71.7 %; 95 % CI: −81.1 % to −58.5 %) over the same period. Such decline was not observed among the culture-positive non-vaccine serotypes (1.2 %; 95 % CI: −96.7 % to 58.4 %). CONCLUSIONS : Significant downward trends in IPD PCV-7 serotype-associated rates were observed among patients tested by PCR or culture methods; however trends of non-vaccine serotypes/serogroups differed between the two groups. Misclassifications of serotypes/serogroups, affecting the use of non-vaccine serotypes as a control group, may have occurred due to the low performance of the serotyping assay among lytA-positive cases with high Ctvalues. Until PCR methods improve further, culture methods should continue to be used to monitor the effects of PCV vaccination programs on IPD incidence.Additional file 1: Assessing the Impact of Pneumococcal Conjugate Vaccines on Invasive Pneumococcal Disease Using Polymerase Chain Reaction-Based Surveillance: An Experience from South AfricaThis work was supported by Pfizer South Africa (investigator-initiated research agreement number: WS1167521) and the US Centers for Disease Control and Prevention (co-operative agreement number: 5U51IP000155).http://www.biomedcentral.com/bmcinfectdis/am2016Medical Virolog

Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates

Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (tet, erm, cat) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here