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1.  Surface Charge of Streptococcus pneumoniae Predicts Serotype Distribution 
Infection and Immunity  2013;81(12):4519-4524.
Streptococcus pneumoniae (pneumococcus) frequently colonizes the human nasopharynx and is an important cause of pneumonia, meningitis, sinusitis, and otitis media. The outer cell surface of pneumococcus may assume various degrees of negative charge depending on the polysaccharide capsule, of which more than 90 serotypes have been identified. The negative charge of capsular polysaccharides has been proposed to electrostatically repel pneumococci from phagocytic cells, and avoidance of phagocytosis correlates with higher carriage prevalence. We hypothesized that the surface charge of pneumococcus contributes to its success in nasopharyngeal carriage by modulating resistance to phagocyte-mediated killing. Here, we measured the surface charge (zeta potential) of laboratory-constructed strains that share a genetic background but differ in serotype and of clinical strains that differ in serotype and genetic background. A more negative surface charge correlated with higher resistance to nonopsonic killing by human neutrophils in vitro. In addition, a more negative zeta potential was associated with higher carriage prevalence in human populations before and after the widespread use of the pneumococcal conjugate vaccine PCV7. We also confirmed that capsule is the major determinant of net surface charge in clinical isolates with diverse backgrounds. We noted that exceptions exist to the idea that a higher magnitude of negative charge predicts higher prevalence. The results indicated that zeta potential is strongly influenced by pneumococcal capsule type but is unlikely to be the only important mechanism by which capsule interacts with host.
doi:10.1128/IAI.00724-13
PMCID: PMC3837974  PMID: 24082068
2.  Influenza Epidemics in Iceland Over 9 Decades: Changes in Timing and Synchrony With the United States and Europe 
American Journal of Epidemiology  2012;176(7):649-655.
Influenza epidemics exhibit a strongly seasonal pattern, with winter peaks that occur with similar timing across temperate areas of the Northern Hemisphere. This synchrony could be influenced by population movements, environmental factors, host immunity, and viral characteristics. The historical isolation of Iceland and subsequent increase in international contacts make it an ideal setting to study epidemic timing. The authors evaluated changes in the timing and regional synchrony of influenza epidemics using mortality and morbidity data from Iceland, North America, and Europe during the period from 1915 to 2007. Cross-correlations and wavelet analyses highlighted 2 major changes in influenza epidemic patterns in Iceland: first was a shift from nonseasonal epidemics prior to the 1930s to a regular winter-seasonal pattern, and second was a change in the early 1990s when a 1-month lag between Iceland and the United States and Europe was no longer detectable with monthly data. There was a moderate association between increased synchrony and the number of foreign visitors to Iceland, providing a plausible explanation for the second shift in epidemic timing. This suggests that transportation might have a minor effect on epidemic timing, but efforts to restrict air travel during influenza epidemics would likely have a limited impact, even for island populations.
doi:10.1093/aje/kws140
PMCID: PMC3530371  PMID: 22962250
airline; Iceland; influenza; synchrony; transportation; wavelets
3.  Influence of Pneumococcal Vaccines and Respiratory Syncytial Virus on Alveolar Pneumonia, Israel 
Emerging Infectious Diseases  2013;19(7):1084-1091.
Postlicensure surveillance of pneumonia incidence can be used to estimate whether pneumococcal conjugate vaccines (PCVs) affect incidence. We used Poisson regression models that control for baseline seasonality to determine the impact of PCVs and the possible effects of variations in virus activity in Israel on these surveillance estimates. PCV was associated with significant declines in radiologically confirmed alveolar pneumonia (RCAP) among patients <6 months, 6–17 months, and 18–35 months of age (–31% [95% CI –51% to –15%], –41% [95% CI –52 to –32%], and –34% [95% CI –42% to –25%], respectively). Respiratory syncytial virus (RSV) activity was associated with strong increases in RCAP incidence, with up to 44% of cases attributable to RSV among infants <6 months of age and lower but significant impacts in older children. Seasonal variations, particularly in RSV activity, masked the impact of 7-valent PCVs, especially for young children in the first 2 years after vaccine introduction.
doi:10.3201/eid1907.121625
PMCID: PMC3713978  PMID: 23763864
pneumococcal conjugate vaccines; pneumonia; RSV; influenza; regression model; surveillance; viruses; Israel; respiratory syncytial virus; alveolar pneumonia
4.  Streptococcus pneumoniae Capsular Serotype Invasiveness Correlates with the Degree of Factor H Binding and Opsonization with C3b/iC3b 
Infection and Immunity  2013;81(1):354-363.
Different capsular serotypes of Streptococcus pneumoniae vary markedly in their ability to cause invasive infection, but the reasons why are not known. As immunity to S. pneumoniae infection is highly complement dependent, variations in sensitivity to complement between S. pneumoniae capsular serotypes could affect invasiveness. We have used 20 capsule-switched variants of strain TIGR4 to investigate whether differences in the binding of the alternative pathway inhibitor factor H (FH) could be one mechanism causing variations in complement resistance and invasive potential between capsular serotypes. Flow cytometry assays were used to assess complement factor binding and complement-dependent neutrophil association for the TIGR4 capsule-switched strains. FH binding varied with the serotype and inversely correlated with the results of factor B binding, C3b/iC3b deposition, and neutrophil association. Differences between strains in FH binding were lost when assays were repeated with pspC mutant strains, and loss of PspC also reduced differences in C3b/iC3b deposition between strains. Median FH binding was high in capsule-switched mutant strains expressing more invasive serotypes, and a principal component analysis demonstrated a strong correlation between serotype invasiveness, high FH binding, and resistance to complement and neutrophil association. Further data obtained with 33 clinical strains also demonstrated that FH binding negatively correlated with C3b/iC3b deposition and that median FH binding was high in strains expressing more invasive serotypes. These data suggest that variations in complement resistance between S. pneumoniae strains and the association of a serotype with invasiveness could be related to capsular serotype effects on FH binding.
doi:10.1128/IAI.00862-12
PMCID: PMC3536142  PMID: 23147038
5.  Broad antibody and T cell reactivity induced by a pneumococcal whole-cell vaccine 
Vaccine  2012;30(29):4316-4322.
Injecting mice with killed cells of non-capsulated strain RM200 adsorbed on Al(OH)3 (pneumococcal whole-cell vaccine; WCV) reduces nasopharyngeal colonization by capsular serotype 6B and prevents fatal aspiration pneumonia by serotype 3 or serotype 5 strains. To further examine the potential for omni-strain immunity, we here examined a panel of clinical isolates and a library of capsule-switch variants in the TIGR4 background. IgG binding to these bacteria in sera of rabbits injected with WCV or Al(OH)3 alone was assayed by ELISA without and with adsorption with cell-wall polysaccharide, a species-common antigen. The examined strains were 23 primary isolates including at least 10 different MLS types and 13 serotypes; 15 of these strains were invasive isolates, subsequently mouse-passed. Additionally, to investigate the effect of capsulation, TIGR4 strain constructs with the capsulation genes of 20 different serotypes was evaluated. In ELISA all strains showed a large difference in IgG binding due to the immunization, of which most of the antibody typically was not adsorbed and presumably directed to exposed protein antigens. Increased binding of IgG in the WCV-immunized serum to the 20 isogenic capsule-switch strains was shown also by flow cytometry. Further, all these 20 strains elicited IL-17A in T cells of WCV-vaccinated mice, a cytokine known to accelerate pneumococcal clearance. Thus WCV induced both humoral and TH17 cell-mediated immunity against all tested strains.
doi:10.1016/j.vaccine.2012.01.034
PMCID: PMC3372861  PMID: 22682288
Streptococcus pneumoniae; vaccine; colonization; sepsis; IL-17; serotype-independence; species-common antigen
6.  Estimating rates of carriage acquisition and clearance and competitive ability for pneumococcal serotypes in Kenya with a Markov transition model 
Epidemiology (Cambridge, Mass.)  2012;23(4):510-519.
BACKGROUND
There are more than 90 serotypes of Streptococcus pneumoniae, with varying biologic and epidemiologic properties. Animal studies suggest that carriage induces an acquired immune response that reduces duration of colonization in a non-serotype-specific fashion.
METHODS
We studied pneumococcal nasopharyngeal carriage longitudinally in Kenyan children aged 3-59 months, following up positive swabs at days 2, 4, 8, 16, and 32, and then monthly thereafter until two swabs were negative for the original serotype. As previously reported, 1868/2840 (66%) of children swabbed at baseline were positive. We estimated acquisition, clearance and competition parameters for 27 serotypes using a Markov transition model .
RESULTS
Point estimates of type-specific acquisition rates ranged from 0.00025/day (type 1) to 0.0031/day (type 19F). Point estimates of time to clearance (inverse of type-specific immune clearance rate) ranged from 28 days (type 20) to 124 days (type 6A). For the serotype most resistant to competition (type 19F), acquisition of other serotypes was 52% less likely (95% confidence interval= 37%-63%) than in an uncolonized host. Fitness components (carriage duration, acquisition rate, lack of susceptibility to competition) were positively correlated with each other and with baseline prevalence, and were associated with biologic properties previously shown to associate with serotype. Duration of carriage declined with age for most serotypes.
CONCLUSIONS
Common S. pneumoniae serotypes appear superior in many dimensions of fitness. Differences in rate of immune clearance are attenuated as children age and become capable of more rapid clearance of the longest-lived serotypes. These findings provide information for comparison after introduction of pneumococcal conjugate vaccine.
doi:10.1097/EDE.0b013e31824f2f32
PMCID: PMC3670084  PMID: 22441543
7.  Impact of the 2009 Influenza Pandemic on Pneumococcal Pneumonia Hospitalizations in the United States 
The Journal of Infectious Diseases  2011;205(3):458-465.
(See the editorial commentary by Grijalva and Griffin on pages 355–7.)
Background. Infection with influenza virus increases the risk for developing pneumococcal disease. The A/H1N1 influenza pandemic in autumn 2009 provided a unique opportunity to evaluate this relationship.
Methods. Using weekly age-, state-, and cause-specific hospitalizations from the US State Inpatient Databases of the Healthcare Cost and Utilization Project 2003–2009, we quantified the increase in pneumococcal pneumonia hospitalization rates above a seasonal baseline during the pandemic period.
Results. We found a significant increase in pneumococcal hospitalizations from late August to mid-December 2009, which corresponded to the timing of highest pandemic influenza activity. Individuals aged 5–19 years, who have a low baseline level of pneumococcal disease, experienced the largest relative increase in pneumococcal hospitalizations (ratio, 1.6 [95% confidence interval {CI}, 1.4–1.7]), whereas the largest absolute increase was observed among individuals aged 40–64 years. In contrast, there was no excess disease in the elderly. Geographical variation in the timing of excess pneumococcal hospitalizations matched geographical patterns for the fall pandemic influenza wave.
Conclusions. The 2009 influenza pandemic had a significant impact on the rate of pneumococcal pneumonia hospitalizations, with the magnitude of this effect varying between age groups and states, mirroring observed variations in influenza activity.
doi:10.1093/infdis/jir749
PMCID: PMC3276240  PMID: 22158564
8.  Serotype replacement in disease following pneumococcal vaccination: A discussion of the evidence 
Lancet  2011;378(9807):1962-1973.
Vaccination with the protein-polysaccharide conjugate vaccine, PCV7, has significantly reduced the burden of pneumococcal disease in populations where it is in widespread use and has had an important public health benefit. This vaccine targets only 7 of the more than 92 pneumococcal serotypes, and there have been concerns that the non-vaccine serotypes (NVTs) could increase in prevalence and reduce the benefits of vaccination. Indeed, among asymptomatic carriers, the prevalence of NVTs has increased substantially, and as a result, there has been little or no net change in the carriage prevalence of the bacteria. In many populations, there has been an increase in pneumococcal disease caused by NVT, but in most cases this increase in NVT disease has been less than the increase in NVT carriage. In this article, we review the evidence for serotype replacement in carriage and disease and address the surveillance biases that might affect these findings. We then discuss possible reasons for the discrepancy between near-complete replacement in carriage and partial replacement for disease, and address the possibility that differences in invasiveness between vaccine serotypes and those causing replacement could contribute to this difference. We contend that the magnitude of serotype replacement in disease can be attributed, in part, to a combination of lower invasiveness of the replacing serotypes, biases in the pre-vaccine carriage data (unmasking), and biases in the disease surveillance systems that could underestimate the true amount of replacement. We conclude by discussing the potential for serotype replacement in disease in the future and the need for ongoing surveillance.
doi:10.1016/S0140-6736(10)62225-8
PMCID: PMC3256741  PMID: 21492929
9.  Prediction of serotypes causing invasive pneumococcal disease in unvaccinated and vaccinated populations 
Epidemiology (Cambridge, Mass.)  2011;22(2):199-207.
Introduction
Before the introduction of the heptavalent pneumococcal conjugate vaccine (Prevnar-7), the relative prevalence of serotypes of Streptococcus pneumoniae was fairly stable worldwide. We sought to develop a statistical tool to predict the relative frequency of different serotypes among disease isolates in the pre- and post-Prevnar-7 eras using the limited amount of data that is widely available.
Methods
We initially used pre-Prevnar-7 carriage prevalence and estimates of invasiveness derived from case-fatality data as predictors for the relative abundance of serotypes causing invasive pneumococcal disease during the pre- and post-Prevnar-7 eras, using negative binomial regression. We fit the model to pre-Prevnar-7 invasive pneumococcal disease data from England and Wales and used these data to (1) evaluate the performance of the model using several datasets and (2) evaluate the utility of the country-specific carriage data. We then fit an alternative model that used polysaccharide structure, a correlate of prevalence that does not require country-specific information and could be useful in determining the post-vaccine population structure, as a predictor.
Results
Predictions from the initial model fit data from several pediatric populations in the pre-Prevnar-7 era. Following the introduction of Prevnar-7, the model still had a good negative predictive value, though substantial unexplained variation remained. The alternative model had a good negative predictive value but poor positive predictive value. Both models demonstrate that the pneumococcal population follows a somewhat predictable pattern even after vaccination.
Conclusions
This approach provides a preliminary framework to evaluate the potential patterns and impact of serotypes causing invasive pneumococcal disease.
doi:10.1097/EDE.0b013e3182087634
PMCID: PMC3142570  PMID: 21646962
10.  Risk of death from pneumococcal pneumonia is a stable serotype-associated property: a meta-analysis 
Background
The 92 capsular serotypes of Streptococcus pneumoniae differ greatly in nasopharyngeal carriage prevalence, invasiveness and disease incidence. There has been some debate, though, as to whether serotype independently affects the outcome of invasive pneumococcal disease (IPD). Published studies have shown variable results with regards to case-fatality ratios for specific serotypes and the role of host factors in affecting these relationships. We evaluated whether risk of death from IPD is a stable serotype-associated property across studies, and then compared the pooled effect estimates with epidemiologic and biological correlates.
Methods
We performed a systematic review and meta-analysis of serotype-specific disease outcome for pneumonia and meningitis cases. Study-specific estimates of risk of death (risk ratio, RR) were pooled from 9 studies that provided serotype-specific data on pneumonia and meningitis using a random-effects method with serotype 14 as the reference. Pooled RRs were compared to RRs from adult cases with low co-morbidity scores to evaluate potential confounding by host factors.
Results
There were significant differences in the RR estimates between serotypes among bacteremic pneumonia cases. Overall, types 1, 7F and 8 were associated with decreased RRs and types 3, 6A, 6B, 9N and 19F were associated with increased RRs. Outcomes among meningitis cases did not differ significantly between types. Serotypes with increased RRs tended to have a high carriage prevalence, low invasiveness, and were more heavily encapsulated in vitro. These results suggest that IPD outcome, like other epidemiologic measures, is a stable serotype-associated property.
doi:10.1086/655828
PMCID: PMC2927802  PMID: 20715907
Serotype; pneumococcus; case-fatality ratio; mortality; capsule; meta-analysis
11.  Expression of the Helicobacter pylori adhesin SabA is controlled via phase variation and the ArsRS signal transduction system 
Microbiology (Reading, England)  2008;154(Pt 8):2231-2240.
Summary
Adaptation to the acidic microenvironment and adherence to mucosal epithelium are essential for persistent colonization of the human stomach by Helicobacter pylori. The expression of SabA, an adhesin implicated in the ability of H. pylori to adhere to the host gastric epithelium, can be modulated by phase variation via slipped-strand mispairing in repetitive nucleotide tracts located in both the promoter and coding regions. This study demonstrates the occurrence of phase variation at the sabA locus within individual strains of H. pylori and among multiple isolates from a single patient. In addition, transcription of SabA is repressed by the acid-responsive ArsRS two-component signal transduction system in vitro. Our results demonstrate that isogenic inactivation of the arsS (jhp0151/HP0165) histidine kinase locus results in a ten-fold, SabA-dependent increase in adherence to gastric epithelial cells in strain J99 (contains in-frame sabA allele) but not in strain 26695 (out-of-frame sabA allele). The combination of transcriptional regulation of the sabA locus by the ArsRS two-component signal transduction system and the generation of subpopulations harboring alternate sabA alleles by slipped-strand mispairing during chromosomal replication could permit H. pylori to rapidly adapt to varying microenvironments or host immune responses. As a pathogen with a paucity of regulatory proteins, this dual regulation indicates that SabA expression is a tightly regulated process in H. pylori infection.
doi:10.1099/mic.0.2007/016055-0
PMCID: PMC2715451  PMID: 18667556
12.  Pneumococcal Capsular Polysaccharide Structure Predicts Serotype Prevalence 
PLoS Pathogens  2009;5(6):e1000476.
There are 91 known capsular serotypes of Streptococcus pneumoniae. The nasopharyngeal carriage prevalence of particular serotypes is relatively stable worldwide, but the host and bacterial factors that maintain these patterns are poorly understood. Given the possibility of serotype replacement following vaccination against seven clinically important serotypes, it is increasingly important to understand these factors. We hypothesized that the biochemical structure of the capsular polysaccharides could influence the degree of encapsulation of different serotypes, their susceptibility to killing by neutrophils, and ultimately their success during nasopharyngeal carriage. We sought to measure biological differences among capsular serotypes that may account for epidemiological patterns. Using an in vitro assay with both isogenic capsule-switch variants and clinical carriage isolates, we found an association between increased carriage prevalence and resistance to non-opsonic neutrophil-mediated killing, and serotypes that were resistant to neutrophil-mediated killing tended to be more heavily encapsulated, as determined by FITC-dextran exclusion. Next, we identified a link between polysaccharide structure and carriage prevalence. Significantly, non-vaccine serotypes that have become common in vaccinated populations tend to be those with fewer carbons per repeat unit and low energy expended per repeat unit, suggesting a novel biological principle to explain patterns of serotype replacement. More prevalent serotypes are more heavily encapsulated and more resistant to neutrophil-mediated killing, and these phenotypes are associated with the structure of the capsular polysaccharide, suggesting a direct relationship between polysaccharide biochemistry and the success of a serotype during nasopharyngeal carriage and potentially providing a method for predicting serotype replacement.
Author Summary
Streptococcus pneumoniae, or pneumococcus, is an important pathogen worldwide and causes a wide range of diseases, mostly in young children and the elderly. There are 91 serotypes of pneumococcus, each of which produces a unique polysaccharide, called the capsule, that attaches to the bacterial surface and prevents it from being cleared by the host. The serotypes differ greatly in their prevalence in the human population. There is currently a vaccine, effective in infancy, which targets seven clinically important serotypes, but several types not covered by the vaccine are beginning to increase in carriage frequency. As a result, it is critical to understand why some serotypes are frequently carried in the human population while others are not. In this study, we find that the high-prevalence serotypes tend to be more heavily encapsulated and more resistant to killing by neutrophils. Significantly, we find that the biochemical properties of the different polysaccharides can be used to predict their carriage frequency both before and after introduction of the vaccine. These results provide a biologically plausible explanation for differences in prevalence between serotypes.
doi:10.1371/journal.ppat.1000476
PMCID: PMC2689349  PMID: 19521509
13.  Expression of the Helicobacter pylori adhesin SabA is controlled via phase variation and the ArsRS signal transduction system 
Microbiology  2008;154(Pt 8):2231-2240.
Adaptation to the acidic microenvironment, and adherence to mucosal epithelium, are essential for persistent colonization of the human stomach by Helicobacter pylori. The expression of SabA, an adhesin implicated in the ability of H. pylori to adhere to the host gastric epithelium, can be modulated by phase variation via slipped-strand mispairing in repetitive nucleotide tracts located in both the promoter region and the coding region. This study demonstrates the occurrence of phase variation at the sabA locus within individual strains of H. pylori, and among multiple isolates from a single patient. In addition, transcription of sabA is repressed by the acid-responsive ArsRS two-component signal transduction system in vitro. Our results demonstrate that isogenic inactivation of the arsS (jhp0151/HP0165) histidine kinase locus results in a 10-fold SabA-dependent increase in adherence to gastric epithelial cells in strain J99 (contains an in-frame sabA allele), but not in strain 26695 (out-of-frame sabA allele). The combination of transcriptional regulation of the sabA locus by the ArsRS two-component signal-transduction system and the generation of subpopulations harbouring alternate sabA alleles by slipped-strand mispairing during chromosomal replication could permit H. pylori to rapidly adapt to varying microenvironments or host immune responses. As a pathogen with a paucity of regulatory proteins, this dual regulation indicates that SabA expression is a tightly regulated process in H. pylori infection.
doi:10.1099/mic.0.2007/016055-0
PMCID: PMC2715451  PMID: 18667556

Results 1-13 (13)