Epidemiology of streptococcus pneumoniae post-pneumococcal conjugate vaccine introduction in South Africa

A thesis submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 11 November 2016BACKGROUND Streptococcus pneumoniae is a leading cause of severe invasive bacterial infections globally; estimated to cause over 300,000 deaths in children <5 years in 2015. Pneumococcal conjugate vaccine (PCV) introduction in South Africa has been associated with changes in invasive pneumococcal disease (IPD) risk groups and emerging serotypes. Serotype 1 pneumococcal disease is highly invasive, fluctuates annually but tends to have lower mortality and antibiotic-resistance than other serotypes. Paediatric antiretroviral treatment (ART) and HIV prevention of mother-to-child transmission programme improvements in South Africa have resulted in a growing number of HIV-exposed-uninfected (HEU) children who have higher rates of infectious diseases than unexposed children. It is important to identify risk groups changes with new interventions and define IPD burden pre- and post- PCV introduction in developing countries. OBJECTIVES In South Africa we aimed to estimate severe pneumococcal disease burden in the pre- (2005- 2008) and post-PCV era (2013) amongst HIV-infected (HI) and HIV-uninfected (HU) children <5 years of age; describe the epidemiology of serotype 1 IPD in all age groups from 2003 to 2013; describe the epidemiology of IPD in HEU children <1 year of age from 2009 to 2013 and the risk factors related to IPD in HI and HU children post-PCV introduction (2010 to 2012). All analyses included PCV introduction impact. METHODS A model using national laboratory-based IPD surveillance data as the baseline was used to determine the total burden of severe hospitalised pneumococcal disease and related mortality in South Africa in children aged <5 years. Adjustments were made for specimen-taking practices and care seeking differences. Vaccine probe studies were used to calculate nonbacteraemic pneumococcal pneumonia case numbers. Observed case fatality ratios were applied to estimated case numbers to determine pneumococcal death numbers. All patients with laboratory-confirmed IPD were included in the serotype 1 analysis. We calculated incidence rates, determined factors associated with serotype 1 disease and conducted a space-time analysis using SaTScan with a Bernoulli model for comparison. Maps to visualise serotype 1 clusters were generated using ArcGIS. Surveillance data was used to compare IPD incidence and mortality in HEU, HIVunexposed- uninfected (HUU) and HI infants. Factors associated with HIV status were compared using a multinomial regression model and logistic regression for mortality factors. A matched case-control study nested within the surveillance programme was used to determine risk factors associated with IPD in HU and HI children aged <5 years. Data was analysed using conditional logistic regression. RESULTS In the pre-vaccine era (2005-2008) in South Africa, roughly 196,100 (148,000-251,000) cases of severe pneumococcal disease were estimated annually in children aged <5 years, an incidence of 3799/100,000; the rate was reduced by 67% in 2013, likely due to PCV and other interventions. In addition 8600 (7000-10220) pneumococcal-related annual deaths were estimated pre-vaccine and 3600 in 2013, a rate difference of 99/100,000 child-years. Over an 11-year period two clusters (2003-2004 and 2008-2012) of serotype 1 infection were detected in all age groups with reductions in incidence noted in 2013. Among children aged <5 years, those with serotype 1 IPD had shorter hospital stays, fewer penicillinnonsusceptible cases (adjusted odds ratio (aOR) 0.02, 95% confidence interval (CI) 0.01– 0.05), lower HIV prevalence (aOR 0.19, 95% CI 0.12–0.31) and lower in-hospital death rates (aOR 0.38, 95% CI 0.19–0.76) than children with non-serotype 1 IPD. The incidence of IPD was greatest in HI infants (272-654/100,000), then HEU infants (33- 88/100,000) and HUU infants (18-28/100,000). Young HEU infants (37% [59/175]) were more likely to die than HUU infants (32% [51/228]; adjusted relative risk ratio, 1.76, 95% CI 1.09–2.85]). On case-control analysis a number of factors were shown to be associated with an increased risk of IPD in the post-PCV period. In HU children these factors included underlying medical conditions (aOR = 1.99, 95% CI 1.22–3.22), attending day care (aOR = 1.58, 95% CI 1.01–2.47) or having been exposed to HIV perinatally (aOR = 1.62, 95% CI 1.10–2.37), while PCV vaccination reduced the odds of IPD (aOR = 0.67, 95% CI 0.46– 0.99). Predisposing factors in HI children included malnutrition (aOR = 2.68, 95% CI 1.40– 5.14) and recent tuberculosis (aOR = 5.12, 95% CI 1.69–15.50), while current ART reduced the odds of IPD (aOR = 0.13, 95% CI 0.05–0.38). CONCLUSION Pneumococcal disease represents a major public health burden in young children in South Africa. PCV and other HIV-associated interventions resulted in a significant reduction in both invasive disease and non-bacteraemic pneumonia. Serotype 1 IPD has distinctive clinical features with temporal decreases noted post-PCV13 introduction. With improvements in interventions to prevent and treat HIV, a resultant growing HEU infant population has been observed with an increased risk of IPD compared with HUU children. Risk factors related to socio-economic conditions and intense exposure to infection continues to be important causes of IPD in children. A full understanding of PCV impact on pneumococcal disease burden is needed to support ongoing national policy decisions on PCV use.MT201

Mealiness detection in apples using time resolved reflectance spectroscopy

Mealiness is a textural attribute related to internal fruit disorder that is characterized by the combination of abnormal softness of the fruit and absence of free juiciness in the mouth when eaten by the consumer. Time-resolved laser reflectance spectroscopy was used as a tool to determine mealiness. This new technique in agrofood research may provide physical and chemical information independently and simultaneously, which is relevant to characterize mealiness. Using visible and near infrared lasers as light sources, time-resolved laser reflectance spectroscopy was applied to Golden Delicious and Cox apples (n = 90), to characterize batches of untreated samples and samples that were stored under conditions that promote the development of mealiness (20C & 95% RH). The collected database was clustered into different groups according to their instrumental test values. The optical coefficients were used as explanatory variables to build discriminant functions for mealiness. The performance of the classification models created ranged from 47 to 100% of correctly identified mealy versus nonmealy apples

Factors associated with missed and delayed DTP3 vaccination in children aged 12 - 59 months in two communities in South Africa, 2012 - 2013

Background. Although immunisation services are available to all children in South Africa (SA), many children miss or have delays in receiving vaccines. There are limited data on factors associated with missed or delayed vaccination in children in this setting. Objectives. To assess vaccination coverage and factors associated with missed and delayed diphtheria-tetanus-pertussis vaccine third dose (DTP3) vaccination in children aged 12 - 59 months in two SA communities. Methods. We used data from household-level healthcare utilisation surveys conducted in Soweto in 2012 and in Pietermaritzburg in 2013. Information on vaccination status was recorded from the Road to Health cards or vaccination history from clinics for children aged <5 years. Factors associated with missed or delayed DTP3 vaccination were assessed using unconditional logistic regression. Results. Of a total of 847 eligible children aged 12 - 59 months, 716 had available vaccination information. Overall DTP3 vaccination coverage was high for both sites: 90.6% in Pietermaritzburg and 93.9% in Soweto. However, 32.6% and 25.2% of DTP3 vaccinations were delayed (received after 18 weeks of age) in Pietermaritzburg and Soweto, respectively. The median delay for DTP3 vaccinations was 4.7 weeks (interquartile range 1.7 - 23.0). Factors associated with delayed DTP3 vaccination included being born in 2010 (adjusted odds ratio (aOR) 3.0, 95% confidence interval (CI) 1.4 - 6.3) or 2011 (aOR 2.7, 95% CI 1.3 - 5.7) compared with being born in 2008, probably due to vaccine shortages; a low level of education of the primary caregiver, with children whose caregivers had completed secondary education having lower odds of delayed vaccination (aOR 0.5, 95% CI 0.3 - 0.9) than children whose caregivers only had primary education; and maternal HIV status, with unknown status (aOR 3.5, 95% CI 1.6 - 7.6) associated with higher odds of delay than positive status. Factors associated with missed DTP3 vaccination (not vaccinated by 12 months of age) included two or more children aged <5 years in a household (aOR 2.4, 95% CI 1.2 - 4.9) compared with one child, and household monthly income <ZAR500 (aOR 3.4, 95% CI 1.1 - 11.4) compared with ≥ZAR2 000. Conclusions. Despite high overall DTP3 coverage observed in two communities, many vaccinations were delayed. Vulnerable groups identified in this study should be targeted with improved vaccination services to enhance uptake and timeliness of vaccination

Factors associated with missed and delayed DTP3 vaccination in children aged 12 - 59 months in two communities in South Africa, 2012 - 2013

Background. Although immunisation services are available to all children in South Africa (SA), many children miss or have delays in receiving vaccines. There are limited data on factors associated with missed or delayed vaccination in children in this setting.Objectives. To assess vaccination coverage and factors associated with missed and delayed diphtheria-tetanus-pertussis vaccine third dose (DTP3) vaccination in children aged 12 - 59 months in two SA communities.Methods. We used data from household-level healthcare utilisation surveys conducted in Soweto in 2012 and in Pietermaritzburg in 2013. Information on vaccination status was recorded from the Road to Health cards or vaccination history from clinics for children aged &lt;5 years. Factors associated with missed or delayed DTP3 vaccination were assessed using unconditional logistic regression.Results. Of a total of 847 eligible children aged 12 - 59 months, 716 had available vaccination information. Overall DTP3 vaccination coverage was high for both sites: 90.6% in Pietermaritzburg and 93.9% in Soweto. However, 32.6% and 25.2% of DTP3 vaccinations were delayed (received after 18 weeks of age) in Pietermaritzburg and Soweto, respectively. The median delay for DTP3 vaccinations was 4.7 weeks (interquartile range 1.7 - 23.0). Factors associated with delayed DTP3 vaccination included being born in 2010 (adjusted odds ratio (aOR) 3.0, 95% confidence interval (CI) 1.4 - 6.3) or 2011 (aOR 2.7, 95% CI 1.3 - 5.7) compared with being born in 2008, probably due to vaccine shortages; a low level of education of the primary caregiver, with children whose caregivers had completed secondary education having lower odds of delayed vaccination (aOR 0.5, 95% CI 0.3 - 0.9) than children whose caregivers only had primary education; and maternal HIV status, with unknown status (aOR 3.5, 95% CI 1.6 - 7.6) associated with higher odds of delay than positive status. Factors associated with missed DTP3 vaccination (not vaccinated by 12 months of age) included two or more children aged &lt;5 years in a household (aOR 2.4, 95% CI 1.2 - 4.9) compared with one child, and household monthly income &lt;ZAR500 (aOR 3.4, 95% CI 1.1 - 11.4) compared with ≥ZAR2 000.Conclusions. Despite high overall DTP3 coverage observed in two communities, many vaccinations were delayed. Vulnerable groups identified in this study should be targeted with improved vaccination services to enhance uptake and timeliness of vaccination.

Eff ectiveness of the 13-valent pneumococcal conjugate vaccine against invasive pneumococcal disease in South African children: a case-control study

Background The 13-valent pneumococcal conjugate vaccine (PCV13) was designed to include disease-causing serotypes that are important in low-income and middle-income countries. Vaccine eff ectiveness estimates are scarce in these settings. South Africa replaced PCV7 with PCV13 in 2011 using a 2 + 1 schedule. We aimed to assess the eff ectiveness of two or more doses of PCV13 against invasive pneumococcal disease in children with HIV infection and in those not infected with HIV. Methods Cases of invasive pneumococcal disease in children aged 5 years or younger were identifi ed through national laboratory-based surveillance. Isolates were serotyped with the Quellung reaction or PCR. We sought in-hospital controls for every case, matched for age, HIV status, and study site. We aimed to enrol four controls for every case not infected with HIV and six controls for every case with HIV infection (case-control sets). With conditional logistic regression, we calculated vaccine eff ectiveness as a percentage, with the equation 1 – [adjusted odds ratio for vaccination] × 100. We included data from an earlier investigation of PCV7 to assess vaccine eff ectiveness in children exposed to but not infected with HIV and in malnourished children not infected with HIV. Findings Between January, 2012, and December, 2014, we enrolled children aged 16 weeks or older to our study: 240 were cases not infected with HIV, 75 were cases with HIV infection, 1118 were controls not infected with HIV, and 283 were controls with HIV infection. The eff ectiveness of two or more doses of PCV13 against PCV13-serotype invasive pneumococcal disease was 85% (95% CI 37 to 96) among 11 case-control sets of children not infected with HIV and 91% (–35 to 100) among three case-control sets of children with HIV infection. PCV13 eff ectiveness among 26 case-control sets of children not infected with HIV was 52% (95% CI –12 to 79) against all-serotype invasive pneumococcal disease and 94% (44 to 100) for serotype 19A. Vaccine eff ectiveness against PCV7-serotype invasive pneumococcal disease was 87% (95% CI 38 to 97) in children exposed to HIV but uninfected and 90% (53 to 98) in malnourished children not infected with HIV. Interpretation Our results indicate that PCV13 in a 2 + 1 schedule is eff ective for preventing vaccine-type pneumococcal infections in young children not infected with HIV, including those who are malnourished or who have been exposed to HIV. Although the point estimate for PCV13 vaccine eff ectiveness in children infected with HIV was high, it did not reach signifi cance, possibly because of the small sample size. These fi ndings support recommendations for widespread use of pneumococcal conjugate vaccine in low-income and middle-income countries

Pneumococcal carriage in children in Ulaanbaatar, Mongolia before and one year after the introduction of the 13-valent pneumococcal conjugate vaccine.

BACKGROUND: Nasopharyngeal carriage of Streptococcus pneumoniae precedes disease, is the source of pneumococcal community spread, and the mechanism for herd protection provided by pneumococcal conjugate vaccines (PCVs). There are few PCV impact studies in low- and middle-income countries, particularly in Asia. In 2016, Mongolia introduced the 13-valent PCV (PCV13) in a phased manner using a 2 + 1 schedule, with catch-up. We aimed to assess the impact of PCV13 introduction on nasopharyngeal pneumococcal carriage and density in children in Mongolia. METHODS: We conducted two cross-sectional carriage surveys (pre- and one year post-PCV) at community health clinics in two districts of the capital city, Ulaanbaatar in both May-July 2015 and 2017. The study analysis included 961 children too young to be vaccinated (5-8 weeks old) and 989 children eligible for vaccination (12-23 months old). Pneumococci were detected by quantitative real-time PCR and molecular serotyping performed using DNA microarray. FINDINGS: One year post-PCV introduction, PCV13 serotype carriage reduced by 52% in 12-23 month olds (adjusted prevalence ratio [aPR] 0.48 [95% confidence interval [CI] 0.39-0.59]), with evidence of non-PCV13 serotype replacement (aPR 1.55 [95% CI 1.30-1.85]), compared with the pre-PCV period. In 5-8 week olds, PCV13 serotype carriage reduced by 51% (aPR 0.49 [95% CI 0.33-0.73]) with no significant change in non-PCV13 serotype carriage (aPR 1.10 [95% CI 0.83-1.46]). An increase was observed in both PCV13 and non-PCV13 pneumococcal density post-PCV introduction. Antimicrobial resistance (AMR) genes were common, with 82.3% of samples containing at least one of the 10 AMR genes assessed. CONCLUSION: This study demonstrates substantive PCV13 impact on pneumococcal carriage one year post-vaccine introduction in Mongolia. The reductions in PCV13 serotype carriage are likely to result in reductions in pneumococcal disease including indirect effects. Increases in non-PCV13 serotypes require further monitoring

Aetiology of childhood pneumonia in low- and middle-income countries in the era of vaccination: a systematic review.

BACKGROUND: This systematic review aimed to describe common aetiologies of severe and non-severe community acquired pneumonia among children aged 1 month to 9 years in low- and middle-income countries. METHODS: We searched the MEDLINE, EMBASE, and PubMed online databases for studies published from January 2010 to August 30, 2020. We included studies on acute community-acquired pneumonia or acute lower respiratory tract infection with ≥1 year of continuous data collection; clear consistent case definition for pneumonia; >1 specimen type (except empyema studies where only pleural fluid was required); testing for >1 pathogen including both viruses and bacteria. Two researchers reviewed the studies independently. Results were presented as a narrative summary. Quality of evidence was assessed with the Quality Assessment Tool for Quantitative Studies. The study was registered on PROSPERO [CRD42020206830]. RESULTS: We screened 5184 records; 1305 duplicates were removed. The remaining 3879 titles and abstracts were screened. Of these, 557 articles were identified for full-text review, and 55 met the inclusion criteria - 10 case-control studies, three post-mortem studies, 11 surveillance studies, eight cohort studies, five cross-sectional studies, 12 studies with another design and six studies that included patients with pleural effusions or empyema. Studies which described disease by severity showed higher bacterial detection (Streptococcus pneumoniae, Staphylococcus aureus) in severe vs non-severe cases. The most common virus causing severe disease was respiratory syncytial virus (RSV). Pathogens varied by age, with RSV and adenovirus more common in younger children. Influenza and atypical bacteria were more common in children 5-14 years than younger children. Malnourished and HIV-infected children had higher rates of pneumonia due to bacteria or tuberculosis. CONCLUSIONS: Several viral and bacterial pathogens were identified as important targets for prevention and treatment. Bacterial pathogens remain an important cause of moderate to severe disease, particularly in children with comorbidities despite widespread PCV and Hib vaccination

Estimated severe pneumococcal disease cases and deaths before and after pneumococcal conjugate vaccine introduction in children younger than 5 years of age in South Africa

INTRODUCTION : Streptococcus pneumoniae is a leading cause of severe bacterial infections globally. A full understanding of the impact of pneumococcal conjugate vaccine (PCV) on pneumococcal disease burden, following its introduction in 2009 in South Africa, can support national policy on PCV use and assist with policy decisions elsewhere. METHODS : We developed a model to estimate the national burden of severe pneumococcal disease, i.e. disease requiring hospitalisation, pre- (2005±2008) and post-PCV introduction (2012± 2013) in children aged 0±59 months in South Africa. We estimated case numbers for invasive pneumococcal disease using data from the national laboratory-based surveillance, adjusted for specimen-taking practices. We estimated non-bacteraemic pneumococcal pneumonia case numbers using vaccine probe study data. To estimate pneumococcal deaths, we applied observed case fatality ratios to estimated case numbers. Estimates were stratified by HIV status to account for the impact of PCV and HIV-related interventions. We assessed how different assumptions affected estimates using a sensitivity analysis. Bootstrapping created confidence intervals. RESULTS : In the pre-vaccine era, a total of approximately 107,600 (95% confidence interval [CI] 83,000±140,000) cases of severe hospitalised pneumococcal disease were estimated to have occurred annually. Following PCV introduction and the improvement in HIV interventions, 41,800 (95% CI 28,000±50,000) severe pneumococcal disease cases were estimated in 2012±2013, a rate reduction of 1,277 cases per 100,000 child-years. Approximately 5000 (95% CI 3000±6000) pneumococcal-related annual deaths were estimated in the prevaccine period and 1,900 (95% CI 1000±2500) in 2012±2013, a mortality rate difference of 61 per 100,000 child-years. CONCLUSIONS : While a large number of hospitalisations and deaths due to pneumococcal disease still occur among children 0±59 months in South Africa, we found a large reduction in this estimate that is temporally associated with PCV introduction. In HIV-infected individuals the scale-up of other interventions, such as improvements in HIV care, may have also contributed to the declines in pneumococcal burden.S1 Text. Supplementary material: Estimated severe pneumococcal disease cases and deaths before and after pneumococcal conjugate vaccine introduction in children younger than 5 years of age in South Africa.S1 Table. Population denominators from the Thembisa model for children <5 years of age in South Africa, 2005-2008 and 2012-2013.S2 Table. Sensitivity analysis for case numbers showing key variables altered in analysis, 2005-2008 and 2012-2013.S3 Table. Sensitivity analysis for numbers of deaths showing key variables altered in analysis, 2005-2008 and 2012-2013.S1 Fig. Initial step in estimating the burden of invasive and non-invasive pneumococcal cases in children aged <5 years in South Africa, 2005-2008 and 2012-2013.S2 Fig. Second step in estimating the burden of invasive and non-invasive pneumococcal cases in children <5 years in South Africa, 2005-2008 and 2012-2013.S3 Fig. Tornado sensitivity diagram representing change in pneumococcal case estimates in children <5 years of age in the pre-vaccine era, when values of key variables are modified.S4 Fig. Tornado sensitivity diagram representing change in pneumococcal death estimates in children <5 years of age in the pre-vaccine era, when values of key variables are modified.The National Institute for Communicable Diseases/National Health Laboratory Service (NICD/NHLS), South Africa and the Centers for Disease Control and Prevention (CDC) Global AIDS Program (GAP) Cooperative Agreement (U62/PSO022901).http://www.plosone.orgam2017Paediatrics and Child Healt

Healthcare utilisation patterns for respiratory and gastrointestinal syndromes and meningitis in Msunduzi municipality Pietermaritzburg KwaZuluNatal Province South Africa 2013

Background. Public health facilities are used by the majority of South Africans, and healthcare utilisation surveys have been a useful tool to estimate the burden of disease in a given area.Objectives. To describe care-seeking behaviour in a periurban site with a high prevalence of HIV infection, as well as barriers to seeking appropriate healthcare.Methods. We conducted a cross-sectional household survey in 22 wards of the Msunduzi municipality in KwaZulu-Natal Province, South Africa, from October to December 2013 using a simple random sample of households selected from a 2011 census enumeration. A primary caregiver/adult decision-maker was interviewed regarding demographic data as well as health status and recent self-reported episodes of selected illnesses and healthcare utilisation.Results. Of the 2 238 eligible premises visited, 1 936 households (87%) with a total of 9 733 members were enrolled in the study. Of these, 635 (7%) reported one or more episodes of infectious illness during the study period. Public health clinics were most frequently consulted for all illnesses (361/635, 57%). Private healthcare (general practitioner, private clinic, private hospital) was sought by 90/635 of individuals (14%), only 13/635 (2%) reported seeking care from traditional healers, religious leaders or volunteers, and 71/635 (11%) did not seek any medical care for acute illnesses. Individuals in the lowest income group were more likely to seek care at public health facilities than those in the highest income group (70% v. 32%).Conclusions. Public health facility-based surveillance may be representative of disease patterns in this community, although surveillance at household level shows that high-income individuals may be excluded because they were more likely to use private healthcare, and the proportion of individuals who died at home would have been missed by facility-based surveillance. Data obtained in such surveys may be useful for public health planning.Â

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