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 2017. / Background: Nasopharyngeal colonisation is a pre-requisite for developing bacterial respiratory and invasive disease. Immunisation of children with the pneumococcal conjugate vaccine (PCV) impacts upon colonising pneumococcal serotypes, which in turn could also affect the biome of the nasopharynx in relation to colonisation by other bacteria. Due to limitations in standard culture methods, the association between PCV-immunisation and bacterial carriage density is still unclear, including among HIV-infected children. In this study we aimed to evaluate the effect of infant vaccination with the 7-valent PCV (PCV7) on vaccine-serogroup colonisation in order to determine whether the increase in non-vaccine serotype (NVT) colonisation was due to unmasking of previously low density colonising serotypes or increase in acquisition of NVT. Also, we evaluated the association between PCV7 immunisation and HIV-infection on the prevalence density of nasopharyngeal colonisation by other common potentially pathogenic bacteria. Methods: A multiplex real-time qPCR assay was set up to detect 44 common pneumococcal serotypes and 5 bacterial pathogens including Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus and Streptococcus pyogenes. All assays were optimised according to MIQE guidelines and their ability to detect multiple pneumococcal serotype/group and bacteria in archived nasopharyngeal swabs were evaluated. The multiplex qPCR assays were then used to evaluate vaccine-serotype, non-vaccine serotype and bacterial nasopharyngeal colonisation in achieved swabs of PCV7-vaccinated (at 6, 10 and 14 weeks of age) and PCV-unvaccinated African children at 9 and 15-16 months of age, prior to routine vaccination of children with PCV through the public immunisation program. In order to address the limitations of the qPCR assays, a nanofluidic real-time PCR assay was developed to simultaneously detect 53 pneumococcal serotypes, 6 serotypes of H. influenzae and 11 bacterial pathogens. Further, all assays were optimised and evaluated according to the MIQE guidelines and findings from Fluidigm and traditional qPCR assays were compared. Lastly, Fluidigm was used to evaluate the association of HIV-infection on the prevalence and density of nasopharyngeal colonisation at 9 and 16 months of age by common, potentially pathogenic bacteria including PCV7 pneumococcal serotypes, non-PCV7 serotypes, Haemophilus influenzae, non-typable Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Streptococcus pyogenes, Neisseria meningitidis, Neisseria lactamica, Bordetella pertussis, Bordetella parapertusis, Bordetella bronchiseptica and Bordetella holmesii in achieved nasophartngeal swabs collected from PCV7-vacciniated HIV-infected and HIV-uninfected children. Results: Molecular qPCR was more sensitive than culture in detecting multiple concurrent colonising pneumococcal serotypes as well as other common nasopharyngeal colonisers, with the majority of additional isolates detected by qPCR having a low carriage density (<104 CFU/ml). Further, qPCR identified a lower prevalence of PCV7-serotype colonisation among PCV7-vaccinated compared to PCV-unvaccinated children at 9 and 16 months of age [adjusted Odds Ratio (aOR): 0.37; 95% CI; 0.19-0.7 and 0.41; 95% CI; 0.26-0.63, respectively]; and an increase in NVT-serotype [aOR: 1.88; 95% CI; 1.02-3.48 and 2.2; 95% CI; 1.18-4.1] colonisation respectively. The increase in NVT carriage among PCV7-vaccinees was driven by serotype 19A, which increased by 53.4% (p=0.021) and 70.7% (p<0.001) at 9 and 16 months of age respectively. Further, 19A had a higher density of colonisation in PCV7-vaccinated groups compared to PCV-unvaccinated groups and was more likely to be identified as a primary than non-primary isolate in PCV7-vaccinated children alone. PCV immunisation was also associated with an increased prevalence of H. influenzae at 9 months (55.8% vs. 66.3%, p<0.001) and 16 months (72% vs. 62%, p=0.017) of age, while a temporary increase in the carriage prevalence of S. aureus was found in PCV7-vaccinated (18.9%) compared to PCV-unvaccinated children (11.1%, aOR 2.1; 95% CI 1.0-1.4; p=0.049) at 9 months of age only. The density of pneumococcus (4.68 vs. 4.28 CFU/ml; p=0.007), H. influenzae (3.86 vs. 4.34 CFU/ml; p=0.008), M. catarrhalis (2.98 vs. 3.52 CFU/ml; p<0.001) and S. aureus (3.06 vs. 4.02 CFU/ml; p=0.02) were also higher among PCV7-vaccinated compared to PCV-unvaccinated children at 9 months age, although this difference diminished with increasing age. There was excellent concordance between the qPCR and Fluidigm for carriage prevalence and density of the majority of assays, with Fluidigm identifying an additional 7 pneumococcal serotypes and 11 bacterial species above those detected by qPCR. Further, discordant results between the two PCR methods were strongly associated with a low carriage density (<102 CFU/ml). Using molecular Fluidigm, a lower carriage prevalence of overall pneumococci (58.6% vs. 69.9%; p=0.02), non-vaccine serotypes (27.8% vs. 40%; p=0.047) and H. influenzae (64.2% vs. 42.3%; p=0.01) was identified in HIV-infected children compared to HIV-uninfected children who were immunised with PCV7 at 9 months of age. No difference in the carriage prevalence of overall pneumococci was however found at 16 months of age (p=0.20), although the carriage prevalence of non-vaccine serotypes (50.9% vs. 60.4%; p=0.049) and H. influenzae (56% vs. 73.4%; p=0.02) was lower in HIV-infected children at 16 months of age. In addition, the density of overall pneumococcus was found to be higher in HIV-infected children (4.81 vs. 4.44 CFU/ml; p=0.014), despite the lower carriage prevalence at 9 months of age, which was driven by a higher density of vaccine serotypes/serogroups (4.21 vs. 3.72 CFU/ml; p=0.04). By 16 months of age, there was no difference in density of pneumococcal colonisation between the HIV-infected and HIV-uninfected children (p=0.89). No difference in the density of H. influenzae was found between HIV-infected and HIV-uninfected infants at 9 months of age (p=0.08); however, by 16 months of age, HIV-uninfected children had a higher density of overall H. influenzae colonisation (4.95 vs. 4.32 CFU/ml; p<0.001), which was largely due to the higher carriage density of NThinf in HIV-uninfected children (5.0 vs. 4.23 CFU/ml; p<0.001). Conclusion: Molecular qPCR assays were shown to be a promising alternative to WHO recommended culture in that multiple pneumococcal serotypes and other bacterial pathogens could be simultaneously detected as well as the bacterial load of each colonising bacteria quantified. The mechanism behind the vaccine effect was shown to be a combination of both serotype replacement and unmasking; however, the reduction in PCV7-serotype colonisation impacted on colonisation prevalence and density of other bacterial species of the nasopharynx and the clinical relevance of this needs further exploration in relation to mucosal and invasive disease outcomes, as well as for higher valence vaccines. While the higher carriage density of overall pneumococcus in HIV-infected children, despite the lower carriage prevalence might explain the higher invasive disease burden in HIV-infected compared to HIV-uninfected children even in the era of antiretroviral therapy treatment and PCV immunisation, future studies are required to provide clarity. Nevertheless, the findings from this thesis highlight the importance of continued surveillance of the circulation of pneumococcal serotypes as well as other bacterial pathogens especially in a population with a high burden of HIV-1 infection. / MT2017

Estudos realizados e recomendados pela OMS e UNICEF, indicam alta prevalência de infecções pneumocócicas e meningocócicas, sobretudo em crianças abaixo dos dois anos de idade. O Streptococcus pneumoniae é um dos agentes mais frequentes de pneumonia, otite média aguda (OMA), meningite e sinusite em crianças. O número global de mortes em crianças menores de cinco anos de idade causadas por pneumonia foi de 8,8 milhões, em 2008. O Ministério da Saúde, devido ao alcance de bons resultados com soroconversão por imunização, indicou a implantação das vacinas antipneumocócica 10-valente e meningocócica C conjugadas no calendário vacinal das crianças menores de dois anos de idade. Na presente pesquisa, conduziu-se um estudo transversal com componente retrospectivo desenvolvido nas redes de Atenção Básica e Hospitalar de Guaranésia, cidade de pequeno porte do interior do estado de Minas Gerais. Objetivou-se avaliar o impacto da vacinação na ocorrência de doenças respiratórias em lactentes, considerando o período anterior e posterior à introdução da vacina antipneumocócica 10-valente, no Programa Nacional de Imunização. Na análise estatística definiu-se o período entre 2009 e 2012. O método de estudo adotado foi o um estudo transversal aninhado em uma série temporal, sendo observado que no período pós introdução da vacina antipneumocócica 10 valente conjugada houve uma redução de 40% na prevalência de pneumonia adquirida na comunidade, com diferença estatística entre os dois períodos . Confirmou-se que a oscilação sazonal tem interferência nas doenças estudadas. Em relação ao sexo, constatou-se que o masculino tem predomínio sobre o feminino quanto ao acometimento por pneumonia. Foi observado que o sexo masculino apresentou 28% mais chance de PNM. Em relação à otite média aguda e à rinossinusite, a variável sexo não apresentou predomínio entre elas. Os dados estatísticos, considerando a razão de prevalência (RP = 1,96 (IC95%: 1,52 2,53); p <0,05), sugeriram que não vacinar está associado com a ocorrência de PNM. Constatou-se que a prevalência de PNM foi 70% menor (RP 0,30 (IC95%: 0,24 0,37); p<0,05) nas crianças com vacina em dia comparando-se àquelas com a vacina em atraso, ou seja, manter vacina em dia sugere proteção contra PNM. No entanto, houve 53% menos OMA entre não vacinados do que entre vacinados (RP = 0,47 (IC95%: 0,35 0,64); p<0,05). Diante dos resultados encontrados, pode-se concluir que a vacinação antipneumocócica 10-valente está associada com redução dos casos de pneumonia adquirida na comunidade em lactentes. / Studies and recommended by WHO and UNICEF, indicate a high prevalence of pneumococcal and meningococcal infections, especially in children under two years of age. Streptococcus pneumoniae is one of the most frequent agents of pneumonia, acute otitis media (AOM), meningitis and sinusitis in children. The overall number of deaths in children under five years of age caused by pneumonia was 8.8 million in 2008. The Ministry of Health due to reach good results with seroconversion by immunization, indicated the implementation of pneumococcal vaccines 10- meningococcal C conjugate and brave in the immunization schedule of children under two years of age. In this research, conducted a cross-sectional study with retrospective component developed in primary care networks and Hospital Guaranésia, small town in the state of Minas Gerais. This study aimed to assess the impact of vaccination on the incidence of respiratory diseases in infants, considering the time before and after the introduction of the vaccine pneumococcal 10-valent, the National Immunization Program. Statistical analysis defined the period between 2009 and 2012. The adopted method of study was a cross-sectional study nested in a time series, it was observed that in the post introduction period of pneumococcal vaccine conjugate 10 brave there was a 40% reduction in the prevalence of community-acquired pneumonia, with statistical difference between the two periods. It was confirmed that the seasonal oscillation has interference in the diseases. With regard to gender, it was found that the male is predominant over females in relation to involvement by pneumonia. It was observed that men had 28% more chance of pneumonia. In relation to acute otitis media and sinusitis, sex does not showed a predominance among them. Statistical data, considering the prevalence ratio (PR = 1.96 (95% CI: 1.52 to 2.53), p <0.05), suggested that not vaccinating is associated with the occurrence of pneumonia. It was found that the prevalence of pneumonia was 70% lower (PR 0.30 (95% CI: 0.24 to 0.37), p <0.05) in children with day vaccine is compared to those of the vaccine in delay, ie to keep day suggests vaccine protection against pneumonia. However, there were 53% fewer of AOM than for unvaccinated vaccinated (OR = 0.47 (95% CI: 0.35 to 0.64); p <0.05). Considering the results, it can be concluded that vaccination pneumococcal 10-valent is associated with reduction of cases of community-acquired pneumonia in infants.

Objective To evaluate the cost-effectiveness of introducing the 10-valent pneumococcal conjugate vaccine (PCV10) versus the 13-valent PCV (PCV13) to the National Immunization Schedule in Peru for prevention of pneumococcal disease (PD) in children <5 years of age. Methods The integrated TRIVAC vaccine cost-effectiveness model from the Pan American Health Organization's ProVac Initiative (version 2.0) was applied from the perspective of the Government of Peru. Twenty successive cohorts of children from birth to 5 years were evaluated. Clinical outcomes were pneumococcal pneumonia (PP), pneumococcal meningitis (PM), pneumococcal sepsis (PS) and acute otitis media from any causes (AOM). Measures included prevention of cases, neurological sequelae (NS), auditory sequelae (AS), deaths and disability adjusted life years (DALYs). A sensitivity analyses was also performed. Findings For the 20 cohorts, net costs with PCV10 and PCV13 were US$ 363.26 million and US$ 408.26 million, respectively. PCV10 prevented 570,273 AOM; 79,937 PP; 2217 PM; 3049 PS; 282 NS; 173 AS; and 7512 deaths. PCV13 prevented 419,815 AOM; 112,331 PN; 3116 PM; 4285 PS; 404 NS; 248 AS; and 10,386 deaths. Avoided DALYs were 226,370 with PCV10 and 313,119 with PCV13. Saved treatment costs were US$ 37.39 million with PCV10 and US$ 47.22 million with PCV13. Costs per DALY averted were US$ 1605 for PCV10, and US$ 1304 for PCV13. Sensitivity analyses showed similar results. PCV13 has an extended dominance over PCV10. Conclusion Both pneumococcal vaccines are cost effective in the Peruvian context. Although the net cost of vaccination with PCV10 is lower, PCV13 prevented more deaths, pneumococcal complications and sequelae. Costs per each prevented DALY were lower with PCV13. Thus, PCV13 would be the preferred policy; PCV10 would also be reasonable (and cost-saving relative to the status quo) if for some reason 13-valent were not feasible. / This study was presented at 9th International Symposium of Pneumococci and Pneumococcal Diseases, Hyderabad, India, March 2014, and supported by the National Council of Science, Technology and Technological Innovation of Peru (CONCYTEC) and International Clinical Epidemiology Network (INCLEN Trust) / This study was made possible through the financial support of the Instituto Nacional de Salud (National Institute of Health, Lima, Peru) and the PROVAC Initiative of the Pan American Health Organization (Washington, DC, USA).

Estudos realizados e recomendados pela OMS e UNICEF, indicam alta prevalência de infecções pneumocócicas e meningocócicas, sobretudo em crianças abaixo dos dois anos de idade. O Streptococcus pneumoniae é um dos agentes mais frequentes de pneumonia, otite média aguda (OMA), meningite e sinusite em crianças. O número global de mortes em crianças menores de cinco anos de idade causadas por pneumonia foi de 8,8 milhões, em 2008. O Ministério da Saúde, devido ao alcance de bons resultados com soroconversão por imunização, indicou a implantação das vacinas antipneumocócica 10-valente e meningocócica C conjugadas no calendário vacinal das crianças menores de dois anos de idade. Na presente pesquisa, conduziu-se um estudo transversal com componente retrospectivo desenvolvido nas redes de Atenção Básica e Hospitalar de Guaranésia, cidade de pequeno porte do interior do estado de Minas Gerais. Objetivou-se avaliar o impacto da vacinação na ocorrência de doenças respiratórias em lactentes, considerando o período anterior e posterior à introdução da vacina antipneumocócica 10-valente, no Programa Nacional de Imunização. Na análise estatística definiu-se o período entre 2009 e 2012. O método de estudo adotado foi o um estudo transversal aninhado em uma série temporal, sendo observado que no período pós introdução da vacina antipneumocócica 10 valente conjugada houve uma redução de 40% na prevalência de pneumonia adquirida na comunidade, com diferença estatística entre os dois períodos . Confirmou-se que a oscilação sazonal tem interferência nas doenças estudadas. Em relação ao sexo, constatou-se que o masculino tem predomínio sobre o feminino quanto ao acometimento por pneumonia. Foi observado que o sexo masculino apresentou 28% mais chance de PNM. Em relação à otite média aguda e à rinossinusite, a variável sexo não apresentou predomínio entre elas. Os dados estatísticos, considerando a razão de prevalência (RP = 1,96 (IC95%: 1,52 2,53); p <0,05), sugeriram que não vacinar está associado com a ocorrência de PNM. Constatou-se que a prevalência de PNM foi 70% menor (RP 0,30 (IC95%: 0,24 0,37); p<0,05) nas crianças com vacina em dia comparando-se àquelas com a vacina em atraso, ou seja, manter vacina em dia sugere proteção contra PNM. No entanto, houve 53% menos OMA entre não vacinados do que entre vacinados (RP = 0,47 (IC95%: 0,35 0,64); p<0,05). Diante dos resultados encontrados, pode-se concluir que a vacinação antipneumocócica 10-valente está associada com redução dos casos de pneumonia adquirida na comunidade em lactentes. / Studies and recommended by WHO and UNICEF, indicate a high prevalence of pneumococcal and meningococcal infections, especially in children under two years of age. Streptococcus pneumoniae is one of the most frequent agents of pneumonia, acute otitis media (AOM), meningitis and sinusitis in children. The overall number of deaths in children under five years of age caused by pneumonia was 8.8 million in 2008. The Ministry of Health due to reach good results with seroconversion by immunization, indicated the implementation of pneumococcal vaccines 10- meningococcal C conjugate and brave in the immunization schedule of children under two years of age. In this research, conducted a cross-sectional study with retrospective component developed in primary care networks and Hospital Guaranésia, small town in the state of Minas Gerais. This study aimed to assess the impact of vaccination on the incidence of respiratory diseases in infants, considering the time before and after the introduction of the vaccine pneumococcal 10-valent, the National Immunization Program. Statistical analysis defined the period between 2009 and 2012. The adopted method of study was a cross-sectional study nested in a time series, it was observed that in the post introduction period of pneumococcal vaccine conjugate 10 brave there was a 40% reduction in the prevalence of community-acquired pneumonia, with statistical difference between the two periods. It was confirmed that the seasonal oscillation has interference in the diseases. With regard to gender, it was found that the male is predominant over females in relation to involvement by pneumonia. It was observed that men had 28% more chance of pneumonia. In relation to acute otitis media and sinusitis, sex does not showed a predominance among them. Statistical data, considering the prevalence ratio (PR = 1.96 (95% CI: 1.52 to 2.53), p <0.05), suggested that not vaccinating is associated with the occurrence of pneumonia. It was found that the prevalence of pneumonia was 70% lower (PR 0.30 (95% CI: 0.24 to 0.37), p <0.05) in children with day vaccine is compared to those of the vaccine in delay, ie to keep day suggests vaccine protection against pneumonia. However, there were 53% fewer of AOM than for unvaccinated vaccinated (OR = 0.47 (95% CI: 0.35 to 0.64); p <0.05). Considering the results, it can be concluded that vaccination pneumococcal 10-valent is associated with reduction of cases of community-acquired pneumonia in infants.

Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2014-12-01T16:24:52Z No. of bitstreams: 2 Dissertação- Weslley José Moreira Garcia - 2013.pdf: 1042957 bytes, checksum: a4d228204aeaaf723a235c9bd9929256 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2014-12-04T14:30:35Z (GMT) No. of bitstreams: 2 Dissertação- Weslley José Moreira Garcia - 2013.pdf: 1042957 bytes, checksum: a4d228204aeaaf723a235c9bd9929256 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-12-04T14:30:35Z (GMT). No. of bitstreams: 2 Dissertação- Weslley José Moreira Garcia - 2013.pdf: 1042957 bytes, checksum: a4d228204aeaaf723a235c9bd9929256 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2013-01-23 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Brazil was the first country to introduce the pneumococcal conjugate 10valent vaccine into the National Immunization Program for infants, in 2010. The nasopharyngeal colonization by Streptococcus pneumoniae occurs early in life. It is the first step for the development of invasive diseases. So far no study has evaluated the impact of vaccination on the reduction on pneumococcal carriage. The evaluation of the impact of vaccination should based on technologies with high accuracy. In this investigation we applied molecular technologies, recently developed, to ascertain pneumococcal nasopharyngeal colonization and serotypes. Objectives: (i) to compare the prevalence of S. pneumoniae nasopharyngeal colonization by using real-time PCR (RT-PCR) and multiplex PCR, and culture (“gold standard”) in children residing in Goiania municipality; (ii) to evaluate the simultaneous colonization by different serotypes by using the multiplex PCR technique. Methods: A household populationbased survey was carried out between October/2010 and March/2011 by using a systematic sampling, weighted by census tract. Based on previous studies, the sample size was calculated taking into account an estimated 50% of pneumocococcal carriage. A total of 1,437 nasopharyngeal swabs were collected from children less than 24 months of age. Broth-enriched culture of nasopharynx specimens followed by pneumococcal isolation by both, culture and RT-PCR targeting the lytA gene (S. pneumoniae) were performed. Pneumococcal carriage was defined for RT-PCR Cycle threshold (Ct) < 35.0, and therefore all samples were submitted to multiplex PCR to detect serotypes. ROC curve (Receiver Operating Characteristics) were built up to identify Ct values predicted of S. pneumoniae positive culture. Results: The prevalence of pneumococcal carriage by RT-PCR (56.9%) was statistically higher (p< 0,001), compared to that obtained by culture (39.3%), regardless of the vaccination status. Among the 818 positive children/samples by RT-PCR, in 54.2% of them it was possible to detect the serotype. Simultaneous colonization by different types was found in 6.9% of the children. Ct values Ct33.0 showed the best accuracy (91.4%) to predict positive pneumococcal culture (Sensitivity=88% and Specificity=81.2%). When using Ct values  32.0 we found the best accuracy of multiplex PCR in detecting serotypes (Sensitivity =90% and Specificity =84,7%). Conclusion: Our findings suggest that RT-PCR and multiplex PCR techniques showed great potential to be used in evaluating the vaccination impact. Further studies are needed to evaluate the cost-effectiveness of using these technologies on a large scale. / O Brasil foi o primeiro pais a introduzir a vacina pneumocócica conjugada, 10-valente (PCV10), no Programa de Imunização infantil, em 2010. A colonização nasofaringeana pelo Streptococcus pneumoniae ocorre na infância e é etapa obrigatória para desenvolvimento da doença invasiva. Até o momento nenhum estudo avaliou o impacto da vacinação na redução do estado de portador. Para avaliação do impacto de vacinas deve-se utilizar tecnologias de alta acurácia. Este estudo utiliza técnicas moleculares, recentemente desenvolvidas, para detecção de pneumococo e sorotipos de secreção nasofaringeana.Objetivos: (i) Comparar a prevalência de colonização nasofaringeana por S. pneumoniae pelas técnicas de PCR em tempo real (RT-PCR) e cultura (―padrão-ouro‖) em crianças residentes em Goiânia no primeiro ano de introdução da PCV10; (ii) avaliar a colonização simultânea por pneumococo por diferentes sorotipos por meio da reação de PCR multiplex. Métodos: Um inquérito populacional domiciliar foi conduzido de outubro/2010 a março/2011, com coleta de 1.437 swabs nasofaríngeos de crianças < 24 meses de idade. A amostragem foi sistemática, ponderada por setor censitário, com tamanho da amostra calculado para prevalência esperada de 50% de portador. O isolamento do pneumococo foi realizado a partir do caldo enriquecido (meio STGG). A cultura foi realizada pela semeadura do caldo em placas de Agar sangue de carneiro. A RT-PCR foi direcionada para o gene lytA do pneumococo, utilizando como positividade valores do ciclo da PCR (Ct-Cycle threshold) <35,0. A reação de PCR multiplex para sorotipagem foi realizada para amostras com valores de Ct<35,0. Foram construídas curvas ROC (Receiver Operating Characteristics) para identificação de valores de Ct preditivos de cultura positiva e de tipo capsular. Resultados: A prevalência de pneumococo obtida pela RT-PCR foi de 56,9%, estatisticamente maior do que a prevalência de 39,3% obtida pela cultura (p< 0,001), independente da situação vacinal da criança. Dentre as 818 crianças positivas pela RT-PCR, em 54,2% delas foi possível detectar-se o tipo capsular. Cocolonização por diferentes sorotipos foi encontrada em 6,9% (100/1.437) das crianças. Valores de Ct33,0 apresentaram a melhor acurácia (91,4%) na predição de cultura positiva para pneumococo (sensibilidade/S=88% e especificidade/E=81,2%). Para detecção de sorotipos a melhor acurácia da PCR multiplex foi para valores de Ct32,0 (S=90% e E=84,7%). Conclusão: Os resultados sugerem que as técnicas de PCR em tempo real e multiplex apresentam grande potencial para serem utilizadas em estudos de avaliação de impacto da vacinação, respectivamente no portador e nos sorotipos vacinais. Estudos deverão ser conduzidos para se avaliar o custo-benefício da utilização desta tecnologia em larga escala.

This thesis aimed to elucidate the demographic characteristics associated with elevated or reduced rates of pneumococcal conjugate 13 (PCV13) vaccination. A retrospective cohort study was performed using the Truven Health MarketScan® Database. Three cohorts were created corresponding to populations for which the CDC recommends PCV13 vaccination. Cohort 1: children < 36 months of age. Cohort 2: adults 19-64 years of age with high infection risk. Cohort 3: adults > 65 years of age. Odds of having a PCV13 claim were calculated for each cohort. For Cohort 1, 78% out of a total of 353,214 subjects had a sufficient number of PCV13 doses to meet CDC recommendations. For Cohort 2, 3.7% out of a total of 673,157 subjects had a PCV13 claim. For Cohort 3, 18% of 1,262,531 subjects had a PCV13 claim. Odds of vaccination were generally lower in younger subjects, those with fewer outpatient claims, and those with residence in the Northeast and South regions. In Cohort 2, odds were reduced in subjects with generalized malignancy. Gender and urban residence were poor predictors of vaccination status. By understanding the demographic factors associated with lower rates of vaccination, clinicians may more effectively direct their efforts to increase pneumococcal vaccination coverage.

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Introduction: Despite advances in prevention and treatment of vaccine-preventable diseases, diarrhoeal and pneumococcal diseases remain a major source of morbidity and mortality among children worldwide. The introduction of vaccines has led to dramatic reductions in the burden of infectious diseases and mortality among children. South Africa was the first country in Africa to introduce rotavirus vaccine (RV) and pneumococcal conjugate vaccine (PCV) in 2008 as part of its national immunisation programme. Performance of immunization programmes is commonly measured by the coverage and uptake of vaccines, hence ensuring that every child is immunized at the earliest or appropriate age is an important public health goal. We therefore assessed proportions and factors associated with uptake of RV and PCV among infants who were followed during the routine demographic surveillance system of the Africa Centre Demographic Surveillance Area (DSA) in a rural South Africa setting. Methods: An open cohort of children resident in the DSA aged 12 months or below was prospectively followed between January 2008 and December 2011. Trained interviewers visited households and administered a standardised questionnaire. Mothers and caregivers were asked to show the interviewers the South African Road-To-Health (RTH) card for all children aged 12-23 months at the time of the visit or through maternal recall for children whose RTH card was not available. The RTH card includes dates of all routine vaccinations a child has received. Rotavirus vaccine doses are given at 6 and 14 weeks of age and PCV doses at 6 and 14 weeks and 9 months. Complete uptake was defined as “complete” if a child received all recommended doses of either RV or PCV and incomplete if a child did not receive any dose or received one dose of RV or PCV. Logistic regression models were used to assess factors associated with uptake of RV and PCV separately. Results: A total of 6,263 children were included in the analysis, of which 3,082 (49%) were females. At birth, 3,823 (61%) children were living in rural areas and about one-sixth of the children were living in households located far from a health facility (≥5km). The overall uptake of RV and PCV vaccines among children aged 12 months or below was 50% and 37% respectively. Infants who ever migrated outside the DSA had reduced odds of complete RV and PCV vaccination compared to infants who did not out migrate (adjusted OR=0.49, 95% CI 0.41-0.57) and (adjusted OR=0.52, 95% CI 0.43-0.63) respectively. Complete uptake of RV was associated with the increase in education levels of mothers compared secondary education (adjusted OR=1.70, 95 % CI 1.02-2.34) or tertiary education (adjusted OR=1.80, 95 % CI 0.97-2.44). Infants whose mothers were employed were less likely than infants whose mothers were not employed to have complete vaccination for RV or PCV (adjusted OR=0.71, 95 % CI 0.60-0.84) and (adjusted OR=0.81, 95% CI 0.68-0.96) respectively. Similarly, infants whose mothers were resident in the DSA were more likely than infants whose mothers were not resident to have complete vaccination for RV or PCV (adjusted OR=1.97, 95 % CI 1.49-2.60) and (adjusted OR=1.55, 95% CI 1.16-2.08) respectively. Conclusion and recommendation: The uptake of complete RV and PCV were generally low among children in rural South Africa within our study period. Child outmigration, maternal employment, maternal education and maternal residency in the DSA at child birth were associated with complete uptake of RV and PCV vaccines. Programmes targeting mothers of lower socio-economic status are required. Such programmes may include vaccine awareness and immunization campaigns at the community level to improve vaccine uptake and more targeted interventions in areas with low RV and PCV uptake.

O Streptococcus pneumoniae (pneumococo) constitui um dos mais importantes patógenos bacterianos do trato respiratório, podendo causar infecções invasivas e não invasivas, levando a altas taxas de morbimortalidade, particularmente em crianças menores de cinco anos de idade. A bactéria ganha acesso ao hospedeiro através da colonização da nasofaringe, que representa um importante reservatório para a transmissão deste patógeno na comunidade, contribuindo para a disseminação horizontal de pneumococo entre os indivíduos de uma população. As doenças respiratórias causadas por pneumococo constituem em uma das prioridades atuais em Saúde Pública, recebendo atenção destacada das organizações internacionais da área da saúde, como a Organização Mundial da Saúde. No presente trabalho procura-se conhecer e avaliar a ocorrência da pneumonia adquirida na comunidade (PAC) antes e após a implantação no Calendário Vacinal da Vacina Pneumocócica-10 Valente Conjugada em 2010, na área de abrangência da Superintendência Regional de Saúde (SRS) de Alfenas/MG. Foi realizado um estudo ecológico com componente temporal que incluiu registros de crianças menores que um ano de idade, vacinadas e não vacinadas com a vacina antipneumocócica 10-valente conjugada, no período pré e pós inclusão da vacina no PNI nos municípios da Superintendência Regional de Saúde (SRS) de Alfenas/MG, sendo a vacinação o fator de exposição e a ocorrência de PAC o desfecho, utilizando dados anuais secundários por município para cálculo da cobertura vacinal e das taxas de morbidade por pneumonia em menores de um ano no período de 2007 a 2013. Considerando se os 26 municípios da SRS de Alfenas, houve redução significativa do número de casos de PAC em crianças abaixo de um ano de idade, cuja Razão de Prevalência foi de 0,81 (IC95%: 0,74 0,89; p<0,05). Mesmo com um tempo reduzido de uso, a vacina pneumocócica conjugada 10 valente apresentou um impacto relevante na redução de PAC em crianças, ajustada por cobertura vacinal no período pós vacinação (2011-2013), sendo estatisticamente significativa na maioria dos municípios, o que sugere a efetividade da vacina PCV-10 na prevenção de casos da doença em crianças menores de um ano de idade. / The Streptococcus pneumoniae (pneumococcus) is one of the most important bacterial pathogens of the respiratory tract, may cause invasive and non-invasive infections, leading to high morbidity and mortality rates, particularly in children under five years of age. The bacteria gain access to the host through the nasopharyngeal colonization, which is an important reservoir for the transmission of this pathogen in the community, contributing to the horizontal spread among individuals in a population. Respiratory diseases caused by pneumococcus are in one of the current priorities in Public Health, receiving outstanding attention of international organizations in the health field, such as the World Health Organization. In the present study we aimed to understand and evaluate the occurrence of community acquired pneumonia (CAP) before and after implantation in 10- valent pneumococcal conjugate vaccine in 2010, on the coverage area of the Regional Health Service (SRS) of Alfenas / MG. An ecological study with temporal component was conducted which included records of children under one year old, vaccinated and not vaccinated with 10-valent pneumococcal conjugate vaccine, before and after period inclusion of the vaccine in PNI, in the municipalities of SRS of Alfenas / MG, with vaccination the exposure factor and the occurrence of CAP the outcome, using annual data side by municipality to calculate vaccination coverage and pneumonia morbidity in children under one year old, in the period 2007 to 2013. Considering the 26 municipalities of SRS Alfenas, there was a significant reduction in the number of CAP cases in children under one year old. The prevalence ratio was 0.81 (95%CI: 0.74 - 0.89; p<0.05). Even with a short period of use, the 10-valent pneumococcal conjugate vaccine had a significant impact on the reduction of CAP in children, adjusted for immunization coverage in the post vaccination period (2011-2013) and was statistically significant in most municipalities, which suggests the effectiveness of PCV-10 vaccine in preventing cases of the disease in children under one year of age.

O Streptococcus pneumoniae (pneumococo) constitui um dos mais importantes patógenos bacterianos do trato respiratório, podendo causar infecções invasivas e não invasivas, levando a altas taxas de morbimortalidade, particularmente em crianças menores de cinco anos de idade. A bactéria ganha acesso ao hospedeiro através da colonização da nasofaringe, que representa um importante reservatório para a transmissão deste patógeno na comunidade, contribuindo para a disseminação horizontal de pneumococo entre os indivíduos de uma população. As doenças respiratórias causadas por pneumococo constituem em uma das prioridades atuais em Saúde Pública, recebendo atenção destacada das organizações internacionais da área da saúde, como a Organização Mundial da Saúde. No presente trabalho procura-se conhecer e avaliar a ocorrência da pneumonia adquirida na comunidade (PAC) antes e após a implantação no Calendário Vacinal da Vacina Pneumocócica-10 Valente Conjugada em 2010, na área de abrangência da Superintendência Regional de Saúde (SRS) de Alfenas/MG. Foi realizado um estudo ecológico com componente temporal que incluiu registros de crianças menores que um ano de idade, vacinadas e não vacinadas com a vacina antipneumocócica 10-valente conjugada, no período pré e pós inclusão da vacina no PNI nos municípios da Superintendência Regional de Saúde (SRS) de Alfenas/MG, sendo a vacinação o fator de exposição e a ocorrência de PAC o desfecho, utilizando dados anuais secundários por município para cálculo da cobertura vacinal e das taxas de morbidade por pneumonia em menores de um ano no período de 2007 a 2013. Considerando se os 26 municípios da SRS de Alfenas, houve redução significativa do número de casos de PAC em crianças abaixo de um ano de idade, cuja Razão de Prevalência foi de 0,81 (IC95%: 0,74 0,89; p<0,05). Mesmo com um tempo reduzido de uso, a vacina pneumocócica conjugada 10 valente apresentou um impacto relevante na redução de PAC em crianças, ajustada por cobertura vacinal no período pós vacinação (2011-2013), sendo estatisticamente significativa na maioria dos municípios, o que sugere a efetividade da vacina PCV-10 na prevenção de casos da doença em crianças menores de um ano de idade. / The Streptococcus pneumoniae (pneumococcus) is one of the most important bacterial pathogens of the respiratory tract, may cause invasive and non-invasive infections, leading to high morbidity and mortality rates, particularly in children under five years of age. The bacteria gain access to the host through the nasopharyngeal colonization, which is an important reservoir for the transmission of this pathogen in the community, contributing to the horizontal spread among individuals in a population. Respiratory diseases caused by pneumococcus are in one of the current priorities in Public Health, receiving outstanding attention of international organizations in the health field, such as the World Health Organization. In the present study we aimed to understand and evaluate the occurrence of community acquired pneumonia (CAP) before and after implantation in 10- valent pneumococcal conjugate vaccine in 2010, on the coverage area of the Regional Health Service (SRS) of Alfenas / MG. An ecological study with temporal component was conducted which included records of children under one year old, vaccinated and not vaccinated with 10-valent pneumococcal conjugate vaccine, before and after period inclusion of the vaccine in PNI, in the municipalities of SRS of Alfenas / MG, with vaccination the exposure factor and the occurrence of CAP the outcome, using annual data side by municipality to calculate vaccination coverage and pneumonia morbidity in children under one year old, in the period 2007 to 2013. Considering the 26 municipalities of SRS Alfenas, there was a significant reduction in the number of CAP cases in children under one year old. The prevalence ratio was 0.81 (95%CI: 0.74 - 0.89; p<0.05). Even with a short period of use, the 10-valent pneumococcal conjugate vaccine had a significant impact on the reduction of CAP in children, adjusted for immunization coverage in the post vaccination period (2011-2013) and was statistically significant in most municipalities, which suggests the effectiveness of PCV-10 vaccine in preventing cases of the disease in children under one year of age.