Clones of Streptococcus pneumoniae isolated from nasopharyngeal carriage and invasive disease in young children in central Tennessee

Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis

Recent studies have provided evidence for rapid pathogen genome diversification, some of which could potentially affect the course of disease. We have previously described such variation seen between isolates infecting the blood and cerebrospinal fluid (CSF) of a single patient during a case of bacterial meningitis. Here, we performed whole-genome sequencing of paired isolates from the blood and CSF of 869 meningitis patients to determine whether such variation frequently occurs between these two niches in cases of bacterial meningitis. Using a combination of reference-free variant calling approaches, we show that no genetic adaptation occurs in either invaded niche during bacterial meningitis for two major pathogen species, Streptococcus pneumoniae and Neisseria meningitidis. This study therefore shows that the bacteria capable of causing meningitis are already able to do this upon entering the blood, and no further sequence change is necessary to cross the blood–brain barrier. Our findings place the focus back on bacterial evolution between nasopharyngeal carriage and invasion, or diversity of the host, as likely mechanisms for determining invasiveness.

PCV7-induced changes in pneumococcal carriage and invasive disease burden in Alaskan children

BACKGROUND

Changes in pneumococcal serotype-specific carriage and invasive pneumococcal disease (IPD) after the introduction of pneumococcal conjugate vaccine (PCV7) could inform serotype epidemiology patterns following the introduction of newer conjugate vaccines.

METHODS

We used data from statewide IPD surveillance and annual pneumococcal carriage studies in four regions of Alaska to calculate serotype-specific invasiveness ratios (IR; odds ratio of a carried serotype's likelihood to cause invasive disease compared to other serotypes) in children <5 years of age. We describe changes in carriage, disease burden, and invasiveness between two time periods, the pre-PCV7 period (1996-2000) and the late post-PCV7 period (2006-2009).

RESULTS

Incidence of IPD decreased from the pre- to post-vaccine period (95.7 vs. 57.2 cases per 100,000 children, P<0.001), with a 99% reduction in PCV7 disease. Carriage prevalence did not change between the two periods (49% vs. 50%), although PCV7 serotype carriage declined by 97%, and non-vaccine serotypes increased in prevalence. Alaska pre-vaccine IRs corresponded to pooled results from eight pre-vaccine comparator studies (Spearman's rho=0.44, P=0.002) and to the Alaska post-vaccine period (Spearman's rho=0.28, P=0.029). Relatively invasive serotypes (IR>1) caused 66% of IPD in both periods, although fewer serotypes with IR>1 remained in the post-vaccine (n=9) than the pre-vaccine period (n=13).

CONCLUSIONS

After PCV7 introduction, serotype IRs changed little, and four of the most invasive serotypes were nearly eliminated. If PCV13 use leads to a reduction of carriage and IPD for the 13 vaccine serotypes, the overall IPD rate should further decline.

NOTE

The findings and conclusions in this report are those of the author(s) and do not necessarily represent the official position of the Centers for Disease Control and Prevention.

The capsular serotype of Streptococcus pneumoniae is more important than the genetic background for resistance to complement

The polysaccharide capsule of Streptococcus pneumoniae inhibits phagocytic killing by innate immune mechanisms. Certain serotypes are associated with invasive disease while others with a nasopharyngeal carriage. The invasiveness of serotypes may partly be explained by ability to resist deposition of complement (C3) on the bacterial surface and consequent opsonophagocytic killing. In our previous studies, we observed that clinical isolates of serotypes 1 and 5, which are rarely detected in asymptomatic carriage, were resistant to complement deposition and opsonophagocytosis, whereas serotypes 6B and 23F, both common in carriage, were more sensitive to deposition of C3 and opsonophagocytic killing. However, presence of significant variation in C3 deposition between isolates of the same serotype indicated that factors other than the capsule also affect complement resistance. To distinguish the relative effect of the capsular serotype and other virulence factors on C3 deposition, we compared capsule-switched mutants prepared in genetic backgrounds of pneumococcal strains TIGR4, 603, and 618. Clinical isolates which had the same multilocus sequence type but expressed different serotypes were also compared. We found that the serotype had a significant impact on complement resistance and that the more resistant the strain was to complement, the higher was the concentration of polysaccharide-specific antibodies required for opsonophagocytic killing. Comparison of strains expressing the same capsular polysaccharides in the different genetic backgrounds and various capsular mutants of the same strain suggests that while the genotype affects complement resistance, the serotype is the most important determinant. Differences between serotypes were more significant than the differences between strains.

Serotype-related variation in susceptibility to complement deposition and opsonophagocytosis among clinical isolates of Streptococcus pneumoniae

The polysaccharide capsule is a major virulence factor of Streptococcus pneumoniae; it affects complement resistance and shields the bacterium from phagocytes. Certain capsular serotypes appear to be better able to cause invasive disease than others. Serotypes 1 and 5 are common causes of invasive disease but are rarely isolated from healthy carriers, whereas serotypes 6B and 23F are more frequently isolated from carriage than invasive disease. We have recently shown that serotypes 6B and 19F differ in resistance to complement C3 deposition and opsonophagocytic killing. In this study we assessed the complement resistance and susceptibility to opsonophagocytosis of several other serotypes targeted by the pneumococcal conjugate vaccines. Clinical isolates of serotypes 1, 4, 5, 14, 18C, and 23F were tested along reference strains of corresponding capsular types. The concentration of anticapsular antibodies required for opsonophagocytic killing correlated inversely with C3 deposition on the serotype. Serotype 1 was the most resistant of the clinical isolates to C3 deposition and, along with serotypes 5 and 19F, required the highest concentration of capsule antibodies for opsonophagocytic killing, whereas serotype 23F was the most sensitive to opsonophagocytosis. Sensitivity to C3 deposition and opsonophagocytosis was associated with serotype-specific mortality of invasive pneumococcal disease, suggesting that the primary pathogens, such as serotypes 1 and 5, are more resistant to complement and require a higher concentration of capsule antibodies for opsonophagocytic killing than the opportunistic serotypes such as 6B and 23F, which are associated with a more severe disease outcome.

Non-typeable Streptococcus pneumoniae carriage isolates genetically similar to invasive and carriage isolates expressing capsular type 14 in Brazilian infants

OBJECTIVES

We have recently found a high prevalence of non-typeable pneumococcal isolates (NTPn) circulating in day-care centers in Central Brazil, besides serotype 14 isolates. We therefore examined the genetic relationship among NTPn and serotype 14 from carriage and invasive pneumococcal isolates obtained from children attending emergency rooms enrolled in a population-based surveillance.

METHODS

The isolates were characterized by Quellung reaction serotyping, PCR for the presence of pneumolysin and the loci for a capsule gene (cpsA) and the type 14 gene (cps14H) in all NTPn, and by multilocus sequence typing and pulsed field gel electrophoresis.

RESULTS

87.2% of the isolates were clustered into nine clusters. The major cluster included 41 pneumococcal serotype 14 (28 carriage and 13 invasive isolates) and two NTPn related to the global pneumococcal clone Spain(9V)-3. Overall, 95.4% of the NTPn carriage strains were genetically related to carriage or invasive strains expressing serotype 14. A dominant NTPn lineage was found, that grouped 14 pneumococcal strains. Almost half of the multidrug-resistant isolates grouped into the NTPn cluster.

CONCLUSION

These findings provide baseline data to assess the impact of the pneumococcal vaccination on the molecular epidemiology of Streptococcus pneumoniae. Changes in frequency of NTPn isolates and also genetic changes should be carefully monitored post vaccination, to detect potential vaccine-escape or replacement disease by capsule switched strains, especially in areas where colonization with NTPn has been frequently observed.

Transmission of Streptococcus pneumoniae in an urban slum community

BACKGROUND

Inhabitants of slum settlements represent a significant proportion of the population at risk for pneumococcal disease in developing countries.

METHODS

We conducted a household survey of pneumococcal carriage among residents of a slum community in the city of Salvador, Brazil.

RESULTS

Among 262 subjects, 95 (36%) were colonized with Streptococcus pneumoniae. Children <5 years of age (OR, 8.0; 95% CI, 3.5-18.6) and those who attended schools (OR, 2.7, 95% CI, 1.2-6.0) had significantly higher risk of being colonized. Of 94 isolates obtained from colonized individuals, 51% had serotypes included in the seven-valent pneumococcal conjugate vaccine. Overall, 10% (9 of 94 isolates) were nonsusceptible to penicillin and 28% (27 of 94 isolates) were resistant to cotrimoxazole. BOX-PCR, PFGE and MLST analyses found that 44% of the carriage isolates belonged to 14 distinct clonal groups. Strains of the same clonal group were isolated from multiple members of 9 out of the 39 study households. Nineteen carriage isolates had genotypes that were the same as those identified among 362 strains obtained from active surveillance for meningitis.

CONCLUSIONS

The study's findings indicate that there is significant intra- and inter-household spread of S. pneumoniae in the slum community setting. However, a limited number of clones encountered during carriage among slum residents were found to cause invasive disease.

Streptococcus pneumoniae surface protein PcpA elicits protection against lung infection and fatal sepsis

Previous studies have suggested that pneumococcal choline binding protein A (PcpA) is important for the full virulence of Streptococcus pneumoniae, and its amino acid sequence suggests that it may play a role in cellular adherence. PcpA is under the control of a manganese-dependent regulator and is only expressed at low manganese concentrations, similar to those found in the blood and lungs. PcpA expression is repressed under high manganese concentrations, similar to those found in secretions. In this study, we have demonstrated that PcpA elicits statistically significant protection in murine models of pneumonia and sepsis. In the model of pneumonia with each of four challenge strains, statistically fewer S. pneumoniae cells were recovered from the lungs of mice immunized with PcpA and alum versus mice immunized with alum only. The immunizations reduced the median CFU by 4- to 400-fold (average of 28-fold). In the model of sepsis using strain TIGR4, PcpA expression resulted in shorter times to become moribund and subcutaneous immunization with PcpA increased survival times of mice infected with wild-type PcpA-expressing pneumococci.

Assessment of molecular typing methods to determine invasiveness and to differentiate clones of Streptococcus pneumoniae

In the United States, Streptococcus pneumoniae is the leading cause of community-acquired pneumonia and invasive bacterial disease. As antimicrobial resistance increases, it will become critical to determine if strains circulating in a population are likely to cause invasive pneumococcal disease (IPD). This is possible by comparison of an isolate's genotype to strains known to be invasive. In this work, we compared pulse-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST), comparative genomic hybridization (CGH) and multi-invasive-locus sequence typing (MILST) for their ability to distinguish between known IPD causing and carrier strains using phylogenetic analyses. In addition, we assess the ability of these techniques to determine true clones from highly related strains. The resulting trees suggest that despite similar overall topologies, the clearest picture of invasiveness and genetic relatedness can be viewed when typing methods are used collectively.

Distribution and invasiveness of Streptococcus pneumoniae serotypes in Switzerland, a country with low antibiotic selection pressure, from 2001 to 2004

To describe the serotype-specific epidemiology of colonizing and invasive Streptococcus pneumoniae isolates, which is important for vaccination strategies, we analyzed a total of 2,388 invasive and 1,540 colonizing S. pneumoniae isolates collected between January 2001 and December 2004 within two nationwide surveillance programs. We found that the relative rank orders of the most frequent serotypes (serotypes 1, 3, 4, 6B, 7F, 14, 19F, and 23F) differed among invasive and colonizing isolates. Serotypes 1, 4, 5, 7F, 8, 9V, and 14 had increased invasive potential, and serotypes/serogroups 3, 6A, 7, 10, 11, 19F, and 23F were associated with colonization. The proportion of pediatric serotypes was higher among children < 5 years old (48.5%) and persons > 64 years old (34.1%) than among other age groups (29.1%); it was also higher in West Switzerland (40.2%) than in other geographic regions (34.7%). Likewise, serotype-specific proportions of penicillin-resistant isolates for types 6B, 9V, 14, and 19F were significantly higher in West Switzerland. The relative frequency of pediatric serotypes corresponded with antibiotic consumption patterns. We conclude that the epidemiology of invasive and colonizing S. pneumoniae isolates is influenced by the serotype-specific potential for invasiveness, and therefore, surveillance programs should include colonizing and invasive S. pneumoniae isolates. Antibiotic selection pressure determines the serotype distribution in different age groups and geographic regions and therefore the expected direct and indirect effects of the 7-valent conjugate vaccine.

CCL5 Modulates Pneumococcal Immunity and Carriage

Understanding the requirements for protection against pneumococcal carriage and pneumonia will greatly benefit efforts in controlling these diseases. Recently, it has been shown that genetic polymorphisms can result in diminished expression of CCL5, which results in increased susceptibility to and progression of infectious diseases. We show that CCL5, together with Th cytokine mRNA expression, is temporally up-regulated during pneumococcal carriage. To determine the contribution of CCL5 to pneumococcal surface antigen A-specific humoral and cellular pneumococcal immunity, mice were treated with anti-CCL5 or control Abs before and during Streptococcus pneumoniae strain EF3030-challenge for the initiation of carriage. CCL5 blockade resulted in a decrease of CD4(+) and CD8(+) T cells as well as CD11b(+) cells in the spleen, cervical lymph node, lung, and nasopharyngeal associated lymphoid tissue during the recognition phase of the pneumococcal adaptive immune response. CCL5 blockade significantly reduced the Ag-specific IgG2a and IgG1 Abs in serum and IgA Ab levels in nasal washes. These decreases also corresponded to reductions in Ag-specific T cell (mucosal and systemic) responses. CCL5 inhibition resulted in decreasing the quantity of IL-4- and IFN-gamma-secreting CD4(+) T cells and increasing the number of Ag-specific IL-10-producing CD4(+) T cells; these changes combined also corresponded with the transition from pneumococcal carriage to lethal pneumonia. These data suggest that CCL5 is an essential factor for the induction and maintenance of protective pneumococcal immunity.

Genetic relationship between Streptococcus pneumoniae isolates from nasopharyngeal and cerebrospinal fluid of two infants with Pneumococcal Meningitis

The molecular epidemiology of Streptococcus pneumoniae isolates from carriage and cerebrospinal fluid (CSF) concurrently recovered from the same individual has not yet been reported. By using pulsed-field gel electrophoresis, we demonstrated the genetic linkage among strains from CSF and nasopharynges of two children with pneumococcal meningitis.

How clonal is Staphylococcus aureus?

Staphylococcus aureus is an important human pathogen and represents a growing public health burden owing to the emergence and spread of antibiotic-resistant clones, particularly within the hospital environment. Despite this, basic questions about the evolution and population biology of the species, particularly with regard to the extent and impact of homologous recombination, remain unanswered. We address these issues through an analysis of sequence data obtained from the characterization by multilocus sequence typing (MLST) of 334 isolates of S. aureus, recovered from a well-defined population, over a limited time span. We find no significant differences in the distribution of multilocus genotypes between strains isolated from carriers and those from patients with invasive disease; there is, therefore, no evidence from MLST data, which index variation within the stable "core" genome, for the existence of hypervirulent clones of this pathogen. Examination of the sequence changes at MLST loci during clonal diversification shows that point mutations give rise to new alleles at least 15-fold more frequently than does recombination. This contrasts with the naturally transformable species Neisseria meningitidis and Streptococcus pneumoniae, in which alleles change between 5- and 10-fold more frequently by recombination than by mutation. However, phylogenetic analysis suggests that homologous recombination does contribute toward the evolution of this species over the long term. Finally, we note a striking excess of nonsynonymous substitutions in comparisons between isolates belonging to the same clonal complex compared to isolates belonging to different clonal complexes, suggesting that the removal of deleterious mutations by purifying selection may be relatively slow.

Evolution and virulence of serogroup 6 pneumococci on a global scale

To study the evolution and virulence of pneumococcal populations, we used multilocus sequence typing to identify the major clones among 212 carriage and invasive isolates expressing capsular serogroup 6 from 39 countries. The global population consisted of 8 major complexes and 6 minor complexes of related clones and 32 clones of diverse origin. Surprisingly, serotype 6A clones evolved by mutation nearly as often as by recombination, whereas serotype 6B clones evolved almost exclusively by recombination (P = 0.0029). This is the first report of population genetic differences among serotypes of this species. The largest clonal complex was associated with invasive disease (P = 0.019) and included a common ancestor for five previously identified drug-resistant clones. The putative ancestors of the major clonal complexes were represented by a greater proportion of carriage isolates than were their descendents (P = 0.001), and the ancestors tended to be less virulent than their descendents in a mouse model of infection. These data suggested that virulent serogroup 6 clones have evolved multiple times from less-virulent ancestral clones.

The human polymeric immunoglobulin receptor facilitates invasion of epithelial cells by Streptococcus pneumoniae in a strain-specific and cell type-specific manner

Streptococcus pneumoniae is a gram-positive bacterial pathogen that causes invasive life-threatening disease worldwide. This organism also commonly colonizes the upper respiratory epithelium in an asymptomatic fashion. To invade, this pathogen must traverse the respiratory epithelial barrier, allowing it to cause disease locally or disseminate hematogenously throughout the body. Previous work has demonstrated that S. pneumoniae choline-binding protein A, a pneumococcal surface protein, interacts specifically with the human polymeric immunoglobulin receptor, which is expressed by cells in the respiratory epithelium. Choline-binding protein A is required for efficient colonization of the nasopharynx in vivo. Additionally, a recent study showed that the R6x laboratory strain of S. pneumoniae invades a human pharyngeal cell line in a human polymeric immunoglobulin receptor-dependent manner. These findings raised the possibility that the interaction between choline-binding protein A and human polymeric immunoglobulin receptor may be a key determinant of S. pneumoniae pathogenesis. However, the strain used in prior invasion studies, R6x, is an unencapsulated, nonpathogenic strain. In the present study we determined the relative ability of strain R6x or pathogenic strains to invade a variety of human polymeric immunoglobulin receptor-expressing epithelial cell lines. The results of this work suggest that human polymeric immunoglobulin receptor-dependent enhanced invasion of epithelial cells by S. pneumoniae is a limited phenomenon that occurs in a strain-specific and cell type-specific manner.

The burden of invasive pneumococcal disease and the potential for reduction by immunisation

Streptococcus pneumoniae causes invasive disease world-wide and in all age groups. The reported incidence varies geographically and is increased in certain population groups. The incidence is highest in children less than 2 years and is also increased in the elderly. Mortality remains substantial even in the developed world despite appropriate antimicrobial therapy. The emergence of penicillin-resistant pneumococci highlights the importance of immunisation as a means to prevent disease. This review discusses the burden of invasive pneumococcal disease, identifies high-risk patients and analyses evidence for vaccine efficacy and cost-effectiveness.