Clonal Analysis ofStreptococcus pneumoniaeNonsusceptible to Penicillin at Day-Care Centers with Index Cases, in a Region with Low Incidence of Resistance: Emergence of an Invasive Type 35B Clone among Carriers

Transmission routes of antibiotic resistant bacteria: a systematic review

Background

Quantification of acquisition routes of antibiotic resistant bacteria (ARB) is pivotal for understanding transmission dynamics and designing cost-effective interventions. Different methods have been used to quantify the importance of transmission routes, such as relative risks, odds ratios (OR), genomic comparisons and basic reproduction numbers. We systematically reviewed reported estimates on acquisition routes’ contributions of ARB in humans, animals, water and the environment and assessed the methods used to quantify the importance of transmission routes.

Methods

PubMed and EMBASE were searched, resulting in 6054 articles published up until January 1st, 2019. Full text screening was performed on 525 articles and 277 are included.

Results

We extracted 718 estimates with S. aureus (n = 273), E. coli (n = 157) and Enterobacteriaceae (n = 99) being studied most frequently. Most estimates were derived from statistical methods (n = 560), mainly expressed as risks (n = 246) and ORs (n = 239), followed by genetic comparisons (n = 85), modelling (n = 62) and dosage of ARB ingested (n = 17). Transmission routes analysed most frequently were occupational exposure (n = 157), travelling (n = 110) and contacts with carriers (n = 83). Studies were mostly performed in the United States (n = 142), the Netherlands (n = 87) and Germany (n = 60). Comparison of methods was not possible as studies using different methods to estimate the same route were lacking. Due to study heterogeneity not all estimates by the same method could be pooled.

Conclusion

Despite an abundance of published data the relative importance of transmission routes of ARB has not been accurately quantified. Links between exposure and acquisition are often present, but the frequency of exposure is missing, which disables estimation of transmission routes’ importance. To create effective policies reducing ARB, estimates of transmission should be weighed by the frequency of exposure occurrence.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07360-z.

Chronic disease and immunosuppression increase the risk for non-vaccine serotype pneumococcal disease - a nationwide population-based study

Background

Demography is changing, with people living longer with comorbidities. In this nationwide population-based study, we investigated the serotype-specific invasive pneumococcal disease (IPD) risk in individuals with comorbidities, and effects of the pneumococcal conjugated vaccine (PCV) child immunization program.

Methods

Cases included 14 096 IPD episodes in Sweden during 2006–2015. Controls (n = 137 289), matched to cases by age, sex, region, and calendar time, were selected from the general population. Comorbidity data was obtained through health registers and grouped as immunocompromising (IC) or chronic medical conditions (CMC).

Results

The prevalence of CMC and IC among elderly cases was 33.9% and 39.4%. New risks identified for IPD were sarcoidosis, inflammatory polyarthropathies, systemic connective tissue, and neurological diseases. The odds ratio (OR) for IPD caused by non-PCV13 compared with PCV13 serotypes was higher in individuals with CMC/IC. Serotypes associated with the highest risk were 16F, 15C, 35F, 19F, and 23A (OR 3–5 for CMC, >10 for IC). Most comorbidities increased post-vaccination, and absolute increases of IPD caused by non-PCV13, PPV23–non-PCV13, and non-PCV13/non-PPV23 serotypes were higher in individuals with IC/CMC compared with healthy persons. Non-PCV13 serotypes 6C, 9N, 11A, 22F, 23A and 35F increased more in those with comorbidities. Mortality due to non-PCV13 serotypes increased in individuals with IC/CMC, while remaining stable in persons without comorbidities.

Conclusions

The PCV child immunization program associates with an increased disease burden of non-vaccine serotypes in individuals with comorbidities. These data are important for vaccine design and optimization of current vaccination strategies.

Serotype and clonal distribution dynamics of invasive pneumococcal strains after PCV13 introduction (2011-2016): Surveillance data from 23 sites in Catalonia, Spain

Background

The objective of this study is to describe incidence and shifts of serotype and clonal distribution of invasive Streptococcus pneumoniae strains in four different age groups (<5 years, 5–17 years, 18–64 years and >65 years) during a period of intermediate PCV13 vaccination coverage (2011–2016) in Catalonia, Spain.

Methods

We included all pneumococcal strains systematically sent to the Catalan support laboratory for molecular surveillance of invasive pneumococcal disease (IPD) located at Hospital Sant Joan de Deu, Barcelona. Two study periods were considered: 2011–13, early PCV13 vaccination period (EVP) and 2014–2016, late vaccination period (LVP).

Results

A total of 2142 strains were included in the study. Five years after intermediate introduction of PCV13 in our population, a significant decrease of overall incidence of IPD in children <5 years was observed (incidence rate ratio 0.5, 95% confidence interval 0.4–0.8). However, in seniors older than 65 years, a significant increase of overall incidence of IPD was observed (IRR 1.4, 95% CI 1.1–1.7). The contribution of PCV13 vaccine serotypes to IPD declined significantly in all age groups: from 59% to 38.1% in <5 years; 82.7% to 59% in 5–17 years, 47.8% to 34.1% in 18–64 years and 48.2% to 37% in >65 years. Results found when comparing both periods were consistent with IRRs observed year by year. In children <5 years, the three major serotypes detected were 1, 24F and 19A in EVP vs 24F, 14 and 10A in LVP. Among patients 5–17 years the first three serotypes were 1, 12F and 14 both in EVP and LVP. Among adults 18–64, the three major serotypes detected were 1, 12F and 8 vs 8, 12F and 3, respectively. Finally, in patients >65 years the most frequently isolated serotypes were 3, 19A and 7F vs 3, 14 and 12F, respectively. Regarding clonal complexes (CCs) expressing mainly PCV13 serotypes, significant decreases of the proportions of CC306, CC191 and CC320 were observed, while CC156 showed a significant increase. As for CCs expressing mostly non-PCV13 serotypes, significant increases in ST989, CC53 and CC404 were showed.

Conclusions

Despite low vaccine coverage in our setting a significant decrease of incidence of IPD was observed in children younger than 5 years. The modest indirect protection against vaccine serotypes causing IPD in elderly indicate the need for the inclusion of more serotypes in future high-valent PCV and vaccinating old adults should be considered.

Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae

S. pseudopneumoniae is an overlooked pathogen emerging as the causative agent of lower-respiratory-tract infections and associated with chronic obstructive pulmonary disease (COPD) and exacerbation of COPD. However, much remains unknown on its clinical importance and epidemiology, mainly due to the lack of specific markers to distinguish it from S. pneumoniae. Here, we provide a new molecular marker entirely specific for S. pseudopneumoniae and offer a comprehensive view of the virulence and colonization genes found in this species. Finally, our results pave the way for further studies aiming at understanding the pathogenesis and epidemiology of S. pseudopneumoniae.

Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. pneumoniae. It is increasingly associated with lower-respiratory-tract infections (LRTI) and a high prevalence of antimicrobial resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional typing methods due to similarities with S. pneumoniae and other members of the mitis group (SMG). Using whole-genome sequencing of LRTI isolates and a comparative genomic approach, we found that a large number of pneumococcal virulence and colonization genes are present in the core S. pseudopneumoniae genome. We also reveal an impressive number of novel surface-exposed proteins encoded by the genome of this species. In addition, we propose a new and entirely specific molecular marker useful for the identification of S. pseudopneumoniae. Phylogenetic analyses of S. pseudopneumoniae show that specific clades are associated with allelic variants of core proteins. Resistance to tetracycline and macrolides, the two most common types of resistance, were found to be encoded by Tn916-like integrating conjugative elements and Mega-2. Overall, we found a tight association of genotypic determinants of AMR and phenotypic AMR with a specific lineage of S. pseudopneumoniae. Taken together, our results shed light on the distribution in S. pseudopneumoniae of genes known to be important during invasive disease and colonization and provide insight into features that could contribute to virulence, colonization, and adaptation.

Serotype and molecular diversity of nasopharyngeal Streptococcus pneumoniae isolates from children before and after vaccination with the ten-valent pneumococcal conjugate vaccine (PCV10) in Ethiopia

Background

Streptococcus pneumoniae is a major human pathogen, and nasopharyngeal colonization is the first step for transmission and pathogenesis of pneumococcal diseases. Ethiopia introduced the 10-valent pneumococcal conjugate vaccine (PCV10) in October 2011. Here we studied nasopharyngeal carriage rates of pneumococci in children and analyzed the serotype and genetic diversity of pneumococcal isolates before first dose and after completion of the vaccine.

Method

A longitudinal study was conducted from February 2013 to November 2016. Totally 789 infants were enrolled at the age of 6 weeks before first dose of PCV10 vaccination, 206 were re-sampled at the age of 9 months, and 201 at 2 years of age after the final dose of PCV10 at the age of 14 weeks. One hundred sixteen children were followed during all the three sampling periods. A total of 422 nasopharyngeal isolates were serotyped using gel diffusion and the Quellung reaction, 325 were typed with pulsed field gel electrophoresis (PFGE), and 12 were selected for multi locus sequence typing (MLST).

Results

Pneumococcal carriage rates at the age of 6 weeks, 9 months and 2 years of age were 26.6% (210/789), 56.8% (117/206) and 48.3% (97/201), respectively. Out of 116 children none of them carried the same strain during the three period and the carriage rate at the age of 6 weeks, 9 months and 2 years were 32.7% (38/116), 59.% (69/116) and 49.1% (57/116) respectively. Totally 59 pneumococcal serotypes were identified among 422 isolates. Serotype 6A (5.0%) dominated followed by 34 (4.5%), 10A (4.0%), 11A (4.0%), 19F (3.8%), 15B (3.8%), 23F (3.6%), and 15A (3.6%). The proportion of non-PCV10 serotypes among the isolates recovered at 6 weeks, 9 months and 2 years was 79.4, 88.9 and 89.7% respectively. Molecular typing of 325 isolates collected at 6 weeks and 9 months of age showed a high genetic diversity.

Conclusion

This study highlights the presence of very diverse serotypes in Ethiopia where non-vaccine serotypes were predominant. Completion of the PCV10 schedule was associated with an approximately 50% reduction of vaccine-type carriage and increase of non-vaccine types. PCV13 would potentially reduce vaccine-type carriage by further 10%.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4024-1) contains supplementary material, which is available to authorized users.

Comparison of the Impact of Pneumococcal Conjugate Vaccine 10 or Pneumococcal Conjugate Vaccine 13 on Invasive Pneumococcal Disease in Equivalent Populations

Background

Pneumococcal conjugate vaccine 10 (PCV10) and pneumococcal conjugate vaccine 13 (PCV13), are used in childhood immunization programs worldwide, but direct comparisons of impacts against invasive pneumococcal disease (IPD) in equivalent populations have not been performed. We compared the vaccines (prevaccination 2007-2009 vs postvaccination 2013-2016) in Sweden, where the 21 counties use either PCV10 or PCV13 (introduced 2009-2010).

Methods

All IPD episodes (n = 16992) were recorded in Sweden during 2005-2016. Of 14 186 isolates from 2007-2016, 13 468 (94.9%) were characterized with serotyping and 12 235 (86.2%) with antibiotic susceptibility. Poisson models assessed changes in incidence over time.

Results

Invasive pneumococcal disease incidences decreased between 2005 and 2016 in vaccinated children (by 68.5%), and in the whole population (by 13.5%), but not among the elderly (increased by 2%) due to a substantial increase in nonvaccine types (NVTs). In 2016, NVTs constituted 72% of IPD cases in the elderly. Serotype 6A declined in PCV10 and PCV13 counties, whereas serotype 19A increased in PCV10 counties. There was no effect against serotype 3. Cross-protection was found between 6B and 6A but not between 19F and 19A. Serotype 6C increased in PCV10 counties, but not in PCV13 counties, suggesting cross-protection with 6A, which is included in PCV13. In the elderly, the increase in NVTs, excluding 6C, was more pronounced in PCV13 counties.

Conclusions

The overall impact of IPD incidences was not statistically different irrespective of vaccine used. The incidence of serotypes, where the effect of the vaccines differed, will influence the cost-effectiveness of which vaccine to use in immunization programs. The dominance of NVTs suggests a limited effect of current pediatric PCVs against IPD in the elderly.

Nasopharyngeal carriage of respiratory pathogens in Warao Amerindians: significant relationship with stunting

OBJECTIVE

To assess risk factors for nasopharyngeal carriage of potential pathogens in geographically isolated Warao Amerindians in Venezuela.

METHODS

In this point prevalence survey, nasopharyngeal swabs were obtained from 1064 Warao Amerindians: 504 children aged 0-4 years, 227 children aged 5-10 years and 333 caregivers. Written questionnaires were completed to obtain information on demographics and environmental risk factors. Anthropometric measurements were performed in children aged 0-4 years.

RESULTS

Carriage rates of Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae and Moraxella catarrhalis were 51%, 7%, 1% and 13%, respectively. Crowding index, method of cooking and tobacco exposure were not associated with increased carriage. In multivariable analysis, an increase in height-for-age Z score (i.e. improved chronic nutritional status) was associated with decreased odds of S. pneumoniae colonisation (OR 0.76, 95% CI 0.70-0.83) in children aged 0-4 years.

CONCLUSIONS

Better knowledge of demographic and environmental risk factors facilitates better understanding of the dynamics of colonisation with respiratory bacteria in an Amerindian population. Poor chronic nutritional status was associated with increased pathogen carriage in children <5 years of age. The high rates of stunting generally observed in indigenous children may fuel the acquisition of respiratory bacteria that can lead to respiratory and invasive disease.

Propensity of pneumococcal carriage serotypes to infect the lower airways of children with chronic endobronchial infections

BACKGROUND

Chronic endobronchial infections in children are responsible for a high disease burden. Streptococcus pneumoniae is frequently isolated; however, few publications have described serotypes associated with non-invasive lower airway infection.

METHODS

Paired nasopharyngeal (NP) swabs and bronchoalveolar lavage (BAL) fluids were collected from children undergoing bronchoscopy for chronic cough. NP swabs were also collected from asymptomatic children in otitis media surveillance studies (controls). Specimens were processed and lower airway infection defined (⩾10⁴ colony forming units/mL BAL) as previously described. Serotype-specific odds ratios (ORs) were calculated (as described for invasive pneumococcal disease) to indicate propensity for infection.

RESULTS

From 2007-2015, paired specimens were processed from 435 children with protracted bacterial bronchitis (PBB), chronic suppurative lung disease (CSLD) or bronchiectasis. S. pneumoniae lower airway infection was detected in 95 children: 27% with PBB and 20% with CSLD/bronchiectasis. Most (91%) children were vaccinated with ⩾2 doses of 7-valent, 10-valent or 13-valent pneumococcal conjugate vaccine. Paired NP and BAL serotype distributions were very similar; prevalent serotypes (>10 isolates) were 19A (9%), 19F, 6C, 35B, 15B, 16F, 15A, 15C, 23A, 23F and 11A. For 21 serotypes found in both NP and BAL specimens, ORs for infection were low; range 0.46 (serotype 23B) to 2.15 (serotype 6A). In the 2008-2013 surveillance studies, NP swabs were collected from 1565 asymptomatic children; 74% were pneumococcal carriers. For 21 of 22 serotypes found in both control NP swabs and BAL specimens, ORs for infection were similarly low; range 0.33 (serotype 23B) to 3.29 (serotype 22F); none was significantly different from 1. The exception was serotype 7B with OR 8.84 (95% CI 1.46, 38.1).

CONCLUSIONS

Most NP carriage serotypes have a similar propensity to cause lower airway infection in children with suppurative lung diseases. Further development of pneumococcal vaccines is needed to prevent non-invasive disease caused by commonly carried serotypes.

Pneumococcal Carriage in Children under Five Years in Uganda-Will Present Pneumococcal Conjugate Vaccines Be Appropriate?

BACKGROUND

Pneumonia is the major cause of death in children globally, with more than 900,000 deaths annually in children under five years of age. Streptococcus pneumoniae causes most deaths, most often in the form of community acquired pneumonia. Pneumococcal conjugate vaccines (PCVs) are currently being implemented in many low-income countries. PCVs decrease vaccine-type pneumococcal carriage, a prerequisite for invasive pneumococcal disease, and thereby affects pneumococcal disease and transmission. In Uganda, PCV was launched in 2014, but baseline data is lacking for pneumococcal serotypes in carriage.

OBJECTIVES

To study pneumococcal nasopharyngeal carriage and serotype distribution in children under 5 years of age prior to PCV introduction in Uganda.

METHODS

Three cross-sectional pneumococcal carriage surveys were conducted in 2008, 2009 and 2011, comprising respectively 150, 587 and 1024 randomly selected children aged less than five years from the Iganga/Mayuge Health and Demographic Surveillance Site. The caretakers were interviewed about illness history of the child and 1723 nasopharyngeal specimens were collected. From these, 927 isolates of S. pneumoniae were serotyped.

RESULTS

Overall, the carriage rate of S. pneumoniae was 56% (957/1723). Pneumococcal carriage was associated with illness on the day of the interview (OR = 1.50, p = 0.04). The most common pneumococcal serotypes were in descending order 19F (16%), 23F (9%), 6A (8%), 29 (7%) and 6B (7%). One percent of the strains were non-typeable. The potential serotype coverage rate for PCV10 was 42% and 54% for PCV13.

CONCLUSION

About half of circulating pneumococcal serotypes in carriage in the Ugandan under-five population studied was covered by available PCVs.

Unaltered pneumococcal carriage prevalence due to expansion of non-vaccine types of low invasive potential 8years after vaccine introduction in Stockholm, Sweden

OBJECTIVE

To evaluate the carriage prevalence, serotype distribution, and antibiotic resistance for pneumococcal carriage isolates collected 4-8years after introduction of pneumococcal conjugate vaccines (PCVs) in Stockholm, Sweden, and to identify risk factors for carriage and calculate the invasive disease potential for emerging serotypes.

METHODS

Nasopharyngeal aspirates were collected from 3024 children aged 0-<5years at regular visits at 23 Child Health Centers in Stockholm County in 2011-2015, and from 787 parents in 2014-2015. The invasive disease potential was calculated for serotypes using invasive disease isolates from 824 patients of all ages identified in the Stockholm County during the same time period as the carriage isolates.

RESULTS

A total carriage prevalence of 30% did not change during the study period. Non-vaccine types (NVT) dominated (94% by 2015) and the most common serotypes in descending order were 11A, 23B, 35F and 21. Risk factors for carriage were: age ⩾3months-<3years, having siblings, attending day-care and having travelled abroad the last 3months. Antibiotic resistance remained low. The invasive disease potential was high for NVT 8, 9N, 12F, and 22F, while low for a majority of emerging NVTs in carriage.

CONCLUSION

The carriage prevalence remained the same 4-8years after vaccine introduction, but serotype replacement became almost complete. A majority of emerging NVTs in carriage showed a low invasive disease potential. Carriage studies are an important complement to invasive disease surveillance to understand the full effect of PCV vaccine programs.

Effects of PCV7 and PCV13 on invasive pneumococcal disease and carriage in Stockholm, Sweden

The effects of pneumococcal conjugated vaccines (PCVs) need to be investigated. In Stockholm County, Sweden, PCV7 was introduced in the childhood immunisation programme in 2007 and changed to PCV13 in 2010.Over 90% of all invasive isolates during 2005-2014 (n=2336) and carriage isolates, 260 before and 647 after vaccine introduction, were characterised by serotyping, molecular typing and antibiotic susceptibility, and serotype diversity was calculated. Clinical information was collected for children and adults with invasive pneumococcal disease (IPD).The IPD incidence decreased post-PCV7, but not post-PCV13, in vaccinated children. Beneficial herd effects were seen in older children and adults, but not in the elderly. The herd protection was more pronounced post-PCV7 than post-PCV13. PCV7 serotypes decreased. IPD caused by PCV13 serotypes 3 and 19A increased post-PCV7. Post-PCV13, serotypes 6A and 19A, but not serotype 3, decreased. The serotype distribution changed in carriage and IPD to nonvaccine types, also in nonvaccinated populations. Expansion of non-PCV13 serotypes was largest following PCV13 introduction. Serotype diversity increased and nonvaccine clones emerged, such as CC433 (serotype 22F) in IPD and CC62 (serotype 11A) in carriage. In young children, meningitis, septicaemia and severe rhinosinusitis, but not bacteraemic pneumonia, decreased.Pneumococcal vaccination leads to expansion of new or minor serotypes/clones, also in nonvaccinated populations.

High prevalence of antibiotic resistance in nasopharyngeal bacterial isolates from healthy children in rural Uganda: A cross-sectional study

BACKGROUND

In Uganda, the main causes of death in children under 5 years of age are malaria and pneumonia--often due to delayed diagnosis and treatment. In preparation for a community case management intervention for pneumonia and malaria, the bacterial composition of the nasopharyngeal flora and its in vitro resistance were determined in children aged five or under to establish baseline resistance to commonly used antibiotics.

METHODS

In a population-based survey in April 2008, nasopharyngeal specimens were collected from 152 randomly selected healthy children under 5 years of age in the Iganga/Mayuge Health and Demographic Surveillance Site (HDSS). Medical history and prior treatment were recorded. Demographic characteristics and risk factors for carriage of resistant strains were obtained from the HDSS census. Bacteria were isolated and analysed for antibiotic susceptibility using disk diffusion and E test.

RESULTS

Streptococcus pneumoniae (S. pneumoniae) carriage was 58.6%, and, while most (80.9%) isolates had intermediate resistance to penicillin, none was highly resistant. Whereas no isolate was resistant to erythromycin, 98.9% were resistant to trimethoprim-sulphamethoxazole (co-trimoxazole).

CONCLUSIONS

In vitro resistance in S. pneumoniae to co-trimoxazole treatment was high, and the majority of isolates had intermediate resistance to penicillin. To inform treatment policies on the clinical efficacy of current treatment protocols for pneumonia in health facilities and at the community level, routine surveillance of resistance in pneumonia pathogens is needed as well as research on treatment efficacy in cases with resistant strains. Improved clinical algorithms and diagnostics for pneumonia should be developed.

Clinical manifestations of invasive pneumococcal disease by vaccine and non-vaccine types

Pneumococcal conjugated vaccines (PCVs) have shown protection against invasive pneumococcal disease by vaccine serotypes, but an increase in non-vaccine serotype disease has been observed. Type-specific effects on clinical manifestation need to be explored. Clinical data from 2096 adults and 192 children with invasive pneumococcal disease were correlated to pneumococcal molecular serotypes. Invasive disease potential for pneumococcal serotypes were calculated using 165 invasive and 550 carriage isolates from children. The invasive disease potential was lower for non-PCV13 compared to vaccine-type strains. Patients infected with non-PCV13 strains had more underlying diseases, were less likely to have pneumonia and, in adults, tended to have a higher mortality. Furthermore, patients infected with pneumococci belonging to clonal serotypes only expressing non-PCV13 capsules had a higher risk for septicaemia and mortality. PCV vaccination will probably lead to a decrease in invasive pneumococcal disease but an alteration in the clinical manifestation of invasive pneumococcal disease. Genetic lineages causing invasive pneumococcal disease in adults often express non-vaccine serotypes, which can expand after vaccination with an increased risk of infection in patients with underlying diseases.

Age-dependent prevalence of nasopharyngeal carriage of streptococcus pneumoniae before conjugate vaccine introduction: a prediction model based on a meta-analysis

Introduction

Data on the prevalence of nasopharyngeal carriage of S.pneumoniae in all age groups are important to help predict the impact of introducing pneumococcal conjugate vaccines (PCV) into routine infant immunization, given the important indirect effect of the vaccine. Yet most carriage studies are limited to children under five years of age. We here explore the association between carriage prevalence and serotype distribution in children aged ≥5 years and in adults compared to children.

Methods

We conducted a systematic review of studies providing carriage estimates across age groups in healthy populations not previously exposed to PCV, using MEDLINE and Embase. We used Bayesian linear meta-regression models to predict the overall carriage prevalence as well as the prevalence and distribution of vaccine and nonvaccine type (VT and NVT) serotypes in older age groups as a function of that in <5 y olds.

Results

Twenty-nine studies compromising of 20,391 individuals were included in the analysis. In all studies nasopharyngeal carriage decreased with increasing age. We found a strong positive linear association between the carriage prevalence in pre-school childen (<5 y) and both that in school aged children (5–17 y olds) and in adults. The proportion of VT serotypes isolated from carriers was consistently lower in older age groups and on average about 73% that of children <5 y among 5–17 y olds and adults respectively. We provide a prediction model to infer the carriage prevalence and serotype distribution in 5–17 y olds and adults as a function of that in children <5 years of age.

Conclusion

Such predictions are helpful for assessing the potential population-wide effects of vaccination programmes, e.g. via transmission models, and thus assist in the design of future pneumococcal conjugate vaccination strategies.

Intraclonal variations among Streptococcus pneumoniae isolates influence the likelihood of invasive disease in children

Background. Pneumococcal serotypes are represented by a varying number of clonal lineages with different genetic contents, potentially affecting invasiveness. However, genetic variation within the same genetic lineage may be larger than anticipated.

Methods. A total of 715 invasive and carriage isolates from children in the same region and during the same period were compared using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Bacterial genome sequencing, functional assays, and in vivo virulence mice studies were performed.

Results. Clonal types of the same serotype but also intraclonal variants within clonal complexes (CCs) showed differences in invasive-disease potential. CC138, a common CC, was divided into several PFGE patterns, partly explained by number, location, and type of temperate bacteriophages. Whole-genome sequencing of 4 CC138 isolates representing PFGE clones with different invasive-disease potentials revealed intraclonal sequence variations of the virulence-associated proteins pneumococcal surface protein A (PspA) and pneumococcal choline-binding protein C (PspC). A carrier isolate lacking PcpA exhibited decreased virulence in mice, and there was a differential binding of human factor H, depending on invasiveness.

Conclusions. Pneumococcal clonal types but also intraclonal variants exhibited different invasive-disease potentials in children. Intraclonal variants, reflecting different prophage contents, showed differences in major surface antigens. This suggests ongoing immune selection, such as that due to PspC-mediated complement resistance through varied human factor H binding, that may affect invasiveness in children.

Pilus adhesin RrgA interacts with complement receptor 3, thereby affecting macrophage function and systemic pneumococcal disease

Pneumococcal pili have been shown to influence pneumococcal colonization, disease development, and the inflammatory response in mice. The role of the pilus-associated RrgA adhesin in pneumococcal interactions with murine and human macrophages was investigated. Expression of pili with RrgA enhanced the uptake of pneumococci by murine and human macrophages that was abolished by antibodies to complement receptor 3 (CR3) and not seen in CR3-deficient macrophages. Recombinant RrgA, but not pilus subunit RrgC, promoted CR3-mediated phagocytosis of coated beads by murine and human macrophages. Flow cytometry showed that purified CR3 binds pneumococcal cells expressing RrgA, and purified RrgA was shown to interact with CR3 and its I domain. In vivo, RrgA facilitated spread of pneumococci from the upper airways and peritoneal cavity to the bloodstream. Earlier onset of septicemia and more rapidly progressing disease was observed in wild-type mice compared to CR3-deficient mice challenged intranasally or intraperitoneally with pneumococci. Motility assays and time-lapse video microscopy showed that pneumococcal stimulation of macrophage motility required RrgA and CR3. These findings, together with the observed RrgA-dependent increase of intracellular survivors up to 10 h following macrophage infection, suggest that RrgA-CR3-mediated phagocytosis promotes systemic pneumococcal spread from local sites.

Streptococcus pneumoniae is a major contributor to morbidity and mortality in infectious diseases globally. Symptomatology is mainly due to pneumococcal interactions with host cells leading to an inflammatory response. However, we still need more knowledge on how pneumococci talk to immune cells and the importance of this interaction. Recently, a novel structure was identified on the pneumococcal surface, an adhesive pilus found in about 30% of clinical pneumococcal isolates. The pilus has been suggested to be important for successful spread of antibiotic-resistant pneumococcal clones globally. Here we sought to identify mechanisms for how the pneumococcal pilin subunit RrgA contributes to disease development by interacting with host immune cells. Our data suggest a new way for how pneumococci may cross talk with phagocytic cells and affect disease progression. An increased understanding of these processes may lead to better strategies for how to treat these common infections.

Human monocytes promote Th1 and Th17 responses to Streptococcus pneumoniae

Streptococcus pneumoniae is a leading cause of bacterial pneumonia, meningitis, and sepsis in children. Human immunity to pneumococcal infections has been assumed to depend on anticapsular antibodies. However, recent findings from murine models suggest that alternative mechanisms, dependent on T helper cells, are also involved. Although the immunological events in which T helper cells contribute to acquired immunity have been studied in mice, little is known about how these responses are generated in humans. Therefore, we examined bacterial and host factors involved in the induction of Th1 and Th17 responses, using a coculture model of human monocytes and CD4(+) T cells. We show that monocytes promote effector cytokine production by memory T helper cells, leading to a mixed Th1/Th17 (gamma interferon [IFN-γ]/interleukin-17 [IL-17]) profile. Both T helper cytokines were triggered by purified pneumococcal peptidoglycan; however, the balance between the two immune effector arms depended on bacterial viability. Accordingly, live pneumococci triggered a Th1-biased response via monocyte production of IL-12p40, whereas heat-killed pneumococci triggered a Th17 response through TLR2 signaling. An increased understanding of human T helper responses is essential for the development of novel pneumococcal vaccines designed to elicit cell-mediated immunity.

Cellular interactions by LPxTG-anchored pneumococcal adhesins and their streptococcal homologues

In this review we focus on three important families of LPxTG-anchored adhesins in the human pathogen Streptococcus pneumoniae, but also their homologues in related streptococci. We discuss the contribution of these streptococcal adhesins to host tropism, pathogenesis and their interactions with different host cell types. The first surface structures discussed are the heteropolymeric pili that have been found in important streptococcal pathogens such as S. pneumoniae, S. pyogenes, S. agalactiae and E. faecalis/faecium. Major and minor pilus subunit proteins are covalently joined and finally attached to the cell wall through the action of specific sortases. The role of pili and individual pilin subunits in adhesion and pathogenesis and their structure and assembly in different streptococcal species are being covered. Furthermore, we address recent findings regarding a family of large glycosylated serine-rich repeat (SRR) proteins that act as fibrillar adhesins for which homologues have been found in several streptococcal species including pneumococci. In the pneumococcal genome both pili and its giant SRR protein are encoded by accessory genes present in particular clonal lineages for which epidemiological information is available. Finally, we briefly discuss the role played by the pneumococcal neuraminidase NanA in adhesion and pathogenesis.

Emergence of a unique penicillin-resistant Streptococcus pneumoniae serogroup 35 strain

We analyzed seven Streptococcus pneumoniae serogroup 35 isolates by pulsed-field gel electrophoresis of the genome and pbp2b gene nucleotide sequences. Three penicillin-susceptible strains and one penicillin-intermediate-resistant strain exhibited 100% identity to prototype R6. Two resistant strains and one other intermediate strain differed from them and contained a unique sequence.

The epidemiology of pneumococcal infections--the Swedish experience

Pneumococcal infections are major contributors to morbidity and mortality world-wide and pose a major public health problem. Despite being a devastating pathogen pneumococci are common colonizers of the upper respiratory tract of healthy children. There is a need for more knowledge on the molecular epidemiology, and pathogenesis of pneumococcal infections to be able to find better strategies for prevention and treatment of these common infections. Here we discuss trends in the vaccine era of the epidemiology of pneumococcal carriage, invasive disease and antibiotic resistance development as well as present national epidemiology data from Sweden of invasive pneumococcal infections during 1987-2006.

Determination of accessory gene patterns predicts the same relatedness among strains of Streptococcus pneumoniae as sequencing of housekeeping genes does and represents a novel approach in molecular epidemiology

Relatedness between isolates of Streptococcus pneumoniae can be determined from sequences of multiple genes belonging to the core genome (multilocus sequence typing [MLST]), but these do not provide information on gene content that may affect the potential of isolates to cause invasive pneumococcal disease. Gene content data, obtained using microarrays, were gathered for 40 clinical isolates of 12 serotypes belonging to 30 multilocus sequence types. We found that sequence variations in housekeeping genes assessed by MLST correlated well with whole-genome microarray analyses identifying the presence/absence of accessory genes/regions. However, isolates belonging to the same clonal complex, as determined by MLST, may not have identical gene contents, potentially affecting virulence. We found fewer intraclonal (same MLST sequence type) differences associated with pneumococcal serotypes of high invasive disease potential, i.e., serotypes rarely found among carriers compared to serotypes frequently found in carriage. Molecular typing of pneumococci based on the presence/absence of 25 genes localized to accessory regions shows the same relatedness among pneumococcal strains as MLST does. We conclude that molecular typing of pneumococci based on variation in the nucleotide sequences of parts of housekeeping genes (MLST) correlates with the presence/absence of genes in the accessory part of the genome. This covariation is likely due to the fact that both sequence variations and gene content variations are created primarily by recombination events in pneumococci.

Clonal success of piliated penicillin nonsusceptible pneumococci

Antibiotic resistance in pneumococci is due to the spread of strains belonging to a limited number of clones. The Spain(9V)-3 clone of sequence type (ST)156 is one of the most successful clones with reduced susceptibility to penicillin [pneumococci nonsusceptible to penicillin (PNSP)]. In Sweden during 2000-2003, a dramatic increase in the number of PNSP isolates was observed. Molecular characterization of these isolates showed that a single clone of sequence type ST156 increased from 40% to 80% of all serotype 14, thus causing the serotype expansion. Additionally, during the same time period, we examined the clonal composition of two serotypes 9V and 19F: all 9V and 20% of 19F isolates belonged to the clonal cluster of ST156, and overall approximately 50% of all PNSP belonged to the ST156 clonal cluster. Moreover, microarray and PCR analysis showed that all ST156 isolates, irrespective of capsular type, carried the rlrA pilus islet. This islet was also found to be present in the penicillin-sensitive ST162 clone, which is believed to be the drug-susceptible ancestor of ST156. Competitive experiments between related ST156 serotype 19F strains confirmed that those containing the rlrA pilus islet were more successful in an animal model of carriage. We conclude that the pilus island is an important biological factor common to ST156 isolates and other successful PNSP clones. In Sweden, a country where the low antibiotic usage does not explain the spread of resistant strains, at least 70% of all PNSP isolates collected during year 2003 carried the pilus islet.

Capsule and D-alanylated lipoteichoic acids protect Streptococcus pneumoniae against neutrophil extracellular traps

Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide. Pneumococci can counteract the action of neutrophils with an antiphagocytic capsule and through electrochemical repulsion of antimicrobial peptides via addition of positive charge to the surface. Pneumococci are captured, but not killed in neutrophil extracellular traps (NETs). Here, we study the role of the polysaccharide capsule and lipoteichoic acid (LTA) modification on pneumococcal interaction with NETs. Expression of capsule (serotypes 1, 2, 4 and 9V) significantly reduced trapping by NETs, but was not required for resistance to NET-mediated killing. Pneumococci contain a dlt operon that mediates the incorporation of d-alanine residues into LTAs, thereby introducing positive charge. Genetic inactivation of dltA in non-encapsulated pneumococci rendered the organism sensitive to killing by antimicrobial components present in NETs. However, the encapsulated dltA mutant remained resistant to NET-mediated killing in vitro. Nevertheless, in a murine model of pneumococcal pneumonia, the encapsulated dltA-mutant strain was outcompeted by the wild-type upon invasion into the lungs and bloodstream. This suggests a non-redundant role for LTA alanylation in pneumococcal virulence at the early stage of invasive disease when capsule expression has been shown to be low.

Modeling pneumococcal resistance to penicillin in southern Sweden using artificial neural networks

In recent decades, penicillin-resistant pneumococci (PRP) have emerged and spread rapidly between and within countries over the world. In this study we developed an iterative artificial neural network (ANN) model to describe and predict the spread of PRP in space and time as a function of antibiotic consumption and a number of different confounders. Retrospective data from 1997 to 2000 on an international epidemic PRP clone (serotype 9V) and antibiotic consumption data from Southern Sweden were used to train the ANN models and data from 2001 to 2003 for evaluation of the model predictions. Five different ANN models were trained, each with independent topology optimization for alternative sets of input variables to find the most descriptive model. The model containing all variables was the only one performing better than the reference linear models, as assessed by the correlation between predictions and observations. The inability to identify a smaller subset of most predictive parameters may reflect either diffuse causal mechanisms or just the absence of critical experimental indicators from the dataset. The iterative ANN model identified is useful to predict future data. The sensitivity analysis of the model suggests that past incidence has a small effect on the number of PRP cases.

Toll-like receptor 9 acts at an early stage in host defence against pneumococcal infection

Toll-like receptor 9 (TLR9) induces an inflammatory response by recognition of unmethylated CpG dinucleotides, mainly present in prokaryotic DNA. So far, TLR9-deficient mice have been shown to be more sensitive than wild-type mice to viral, but not to bacterial infections. Here, we show that mice deficient in TLR9 but not in TLR1, TLR2, TLR4 and TLR6 or IL-1R/IL-18R are more susceptible to a respiratory tract bacterial infection caused by Streptococcus pneumoniae. Intranasal challenge studies revealed that TLR9 plays a protective role in the lungs at an early stage of infection prior to the entry of circulating inflammatory cells. Alveolar as well as bone marrow-derived macrophages deficient in either TLR9 or the myeloid adaptor differentiation protein MyD88 were impaired in pneumococcal uptake and in pneumococcal killing. Our data suggest that in the airways, pneumococcal infection triggers a TLR9 and MyD88-dependent activation of phagocytic activity from resident macrophages leading to an early clearance of bacteria from the lower respiratory tract.

Characteristics of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis and Staphylococcus aureus isolated from the nasopharynx of healthy children attending day-care centres in the Czech Republic

Nasopharyngeal carriage of potential pathogens was studied in 425 healthy 3- to 6-year-old children attending 16 day-care centres (DCCs) in nine Czech cities during the winter 2004-2005. The overall carriage of pathogens was 62.8% (Streptococcus pneumoniae, 38.1%; Haemophilus influenzae, 24.9%; Moraxella catarrhalis, 22.1%; Staphylococcus aureus, 16%). An age-related downward trend was observed for colonization with respiratory pathogens in contrast to Staph. aureus whose carriage was significantly higher among older children. The following serotypes of colonizing S. pneumoniae were the most predominant: 23F (20.6%), 6A (15.1%), 6B (12.7%), 18C (7.8%), 15B and 19F (6% each). The majority (94.3%) of H. influenzae isolates were non-typable; among capsulated isolates, serotype b was not found. Decreased susceptibility to penicillin was determined in 3% of pneumococci; 4.6% of H. influenzae strains and 85.1% of M. catarrhalis strains produced beta-lactamase. As for non-beta-lactam antibiotics, pneumococci resistant to trimethoprim-sulphamethoxazole were the most common (15.7%) among the attendees.

Natural history of drug-resistant clones of Streptococcus pneumoniae colonizing healthy children in Portugal

A total of 3,539 Streptococcus pneumoniae (Pn) were recovered from 4,969 nasopharyngeal samples of children attending 13 day-care centers (DCCs) located in Lisbon, Portugal, during a surveillance study from January, 2001, through March, 2003, integrated in the European intervention project (EURIS, European Resistance Intervention Study). All Pn isolates were tested for anti-biotyping and drug-resistant pneumococci (DRPn) were further tested by serotyping and pulsed-field gel electrophoresis (PFGE). Overall carriage of Pn was very high (71.2%) and 39.9% of the isolates were resistant to antimicrobials (22.5% with decreased susceptibility to penicillin and 17.4% susceptible to penicillin and resistant to other antimicrobials). Serotypes 6B, 14, 23 F, 19F, and 19 A were prevalent among the 1,287 DRPn and 5.8% of the isolates were non-typeable. Eighty PFGE patterns were identified among 1,285 DRPn, and 93.1% of the DRPn belonged to 26 major clonal types that comprised: Pneumococcal Molecular Epidemiology Network (PMEN) clones (76.3%), Portuguese (PT)-DCC clones, previously detected in 1996-1999 (14.3%), and EURIS PT-DCC new clones, identified for the first time in the EURIS study, during 2001-2003 (9.4%). Comparing with previous Portuguese surveillance studies carried out since 1996, we observed that carriage increased from 47% to 71%, but no major changes were detected on the prevalence of pneumococcal serotypes. Moreover, although PMEN clones were predominant in all DCCs, in the present study the majority of them were gradually decreasing in time whereas several PT-DCC and new clones seemed to be increasing.

Clonal and Capsular Types Decide Whether Pneumococci Will Act as a Primary or Opportunistic Pathogen

BACKGROUND

Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide. The role of the different capsular and clonal types in invasive disease severity remains to be defined.

METHODS

Disease severity and disease type were correlated to age, underlying disease, capsular serotype, and clonal type of the causative agent for 494 adult patients with invasive pneumococcal disease.

RESULTS

Pneumococcal isolates of serotypes 1 and 7F were genetically homogenous, had the highest potential to infect previously healthy individuals, and were not causing deaths. Also, type 1 isolates were only found among younger adults, whereas other serotypes were mainly found among elderly persons (e.g., type 23F). Some serotypes and/or clones were more prone to cause more-severe disease, as observed by high APACHE II scores calculated at admission, and were also associated with a high mortality (e.g., clones of type 3 and 11A). We found no evidence of an impact of penicillin resistance on disease severity and disease type.

CONCLUSIONS

We suggest that clones with capsular types 1 and 7F, which are known to have a high invasive disease potential, behave as primary pathogens, whereas clones with other capsular types with a lower relative risk of causing invasive disease are more opportunistic, primarily affecting patients with underlying disease. Disease caused by the latter group, however, was more severe, even in previously healthy individuals.

A pneumococcal pilus influences virulence and host inflammatory responses

Streptococcus pneumoniae (pneumococcus) is a major cause of morbidity and mortality world-wide. The initial event in invasive pneumococcal disease is the attachment of encapsulated pneumococci to epithelial cells in the upper respiratory tract. This work provides evidence that initial bacterial adhesion and subsequent ability to cause invasive disease is enhanced by pili, long organelles able to extend beyond the polysaccharide capsule, previously unknown to exist in pneumococci. These adhesive pili-like appendages are encoded by the pneumococcal rlrA islet, present in some, but not all, clinical isolates. Introduction of the rlrA islet into an encapsulated rlrA-negative isolate allowed pilus expression, enhanced adherence to lung epithelial cells, and provided a competitive advantage upon mixed intranasal challenge of mice. Furthermore, a pilus-expressing rlrA islet-positive clinical isolate was more virulent than a nonpiliated deletion mutant, and it out-competed the mutant in murine models of colonization, pneumonia, and bacteremia. Additionally, piliated pneumococci evoked a higher TNF response during systemic infection, compared with nonpiliated derivatives, suggesting that pneumococcal pili not only contribute to adherence and virulence but also stimulate the host inflammatory response.

Myeloid differentiation factor 88-dependent signalling controls bacterial growth during colonization and systemic pneumococcal disease in mice

The Toll-like receptors (TLRs) and the myeloid differentiation factor 88 (MyD88) are key players in the activation of the innate immune defence during microbial infections. Using different murine infection models, we show that MyD88-dependent signalling is crucial for the activation of the innate immune defence against Streptococcus pneumoniae. Our data demonstrate that both local and systemic inflammatory response to S. pneumoniae depends on the presence of MyD88 to clear bacterial colonization of the upper respiratory tract and to prevent pulmonary and systemic infection in mice. Finally, we described a strong correlation between enhanced bacterial growth in the bloodstream of MyD88-deficient mice and the inability to lower the serum iron concentration in response to infection.

Trends in drug resistance, serotypes, and molecular types of Streptococcus pneumoniae colonizing preschool-age children attending day care centers in Lisbon, Portugal: a summary of 4 years of annual surveillance

Of the nasopharyngeal cultures recovered from 942 day care center (DCC) attendees in Lisbon, Portugal, 591 (62%) yielded Streptococcus pneumoniae during a surveillance performed in February and March of 1999. Forty percent of the isolates were resistant to one or more antimicrobial agents. In particular, 2% were penicillin resistant and 20% had intermediate penicillin resistance. Multidrug resistance to macrolides, lincosamides, and tetracycline was the most frequent antibiotype (17% of all isolates). Serotyping and molecular typing by pulsed-field gel electrophoresis were performed for 202 out of 237 drug-resistant pneumococci (DRPn). The most frequent serotypes were 6B (26%), 14 (22%), 19F (16%), 23F (10%), and nontypeable (12%). The majority (67%) of the DRPn strains were representatives of nine international clones included in the Pneumococcal Molecular Epidemiology Network; eight of them had been detected in previous studies. Fourteen novel clones were identified, corresponding to 26% of the DRPn strains. The remaining 7% of the strains were local clones detected in our previous studies. Comparison with studies conducted since 1996 in Portuguese DCCs identified several trends: (i) the rate of DRPn frequency has fluctuated between 40 and 50%; (ii) the serotypes most frequently recovered have remained the same; (iii) nontypeable strains appear to be increasing in frequency; and (iv) a clone of serotype 33F emerged in 1999. Together, our observations highlight that the nasopharynxes of children in DCCs are a melting pot of successful DRPn clones that are important to study and monitor if we aim to gain a better understanding on the epidemiology of this pathogen.