Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced.

BACKGROUND: The success of 7-valent pneumococcal conjugate vaccination (PCV-7) introduced to the US childhood immunization schedule in 2000 was partially offset by increases in invasive pneumococcal disease (IPD) and pneumococcal carriage due to non-vaccine serotypes, in particular 19A, in the years that followed. A 13-valent conjugate vaccine (PCV-13) was introduced in 2010. As part of an ongoing study of the response of the Massachusetts pneumococcal population to conjugate vaccination, we report the findings from the samples collected in 2011, as PCV-13 was introduced. METHODS: We used multilocus sequence typing (MLST) to analyze 367 pneumococcal isolates carried by Massachusetts children (aged 3 months-7 years) collected during the winter of 2010-11 and used eBURST software to compare the pneumococcal population structure with that found in previous years. RESULTS: One hundred and four distinct sequence types (STs) were found, including 24 that had not been previously recorded. Comparison with a similar sample collected in 2009 revealed no significant overall difference in the ST composition (p = 0.39, classification index). However, we describe clonal dynamics within the important replacement serotypes 19A, 15B/C, and 6C, and clonal expansion of ST 433 and ST 432, which are respectively serotype 22F and 21 clones. CONCLUSIONS: While little overall change in serotypes or STs was evident, multiple changes in the frequency of individual STs and or serotypes may plausibly be ascribed to the introduction of PCV-13. This 2011 sample documents the initial impact of PCV-13 and will be important for comparison with future studies of the evolution of the pneumococcal population in Massachusetts.

Diversification of bacterial genome content through distinct mechanisms over different timescales.

Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are typically characterized by combinations of infrequently transferred stable genomic islands: those moving primarily through transformation, along with integrative and conjugative elements and phage-related chromosomal islands. The only lineage containing extensive unique sequence corresponds to a set of atypical unencapsulated isolates that may represent a distinct species. However, prophage content is highly variable even within lineages, suggesting frequent horizontal transmission that would necessitate rapidly diversifying anti-phage mechanisms to prevent these viruses sweeping through populations. Correspondingly, two loci encoding Type I restriction-modification systems able to change their specificity over short timescales through intragenomic recombination are ubiquitous across the collection. Hence short-term pneumococcal variation is characterized by movement of phage and intragenomic rearrangements, with the slower transfer of stable loci distinguishing lineages.

Impact of 13-Valent Pneumococcal Conjugate Vaccination on Streptococcus pneumoniae Carriage in Young Children in Massachusetts.

BACKGROUND: In April 2010, a 13-valent pneumococcal conjugate vaccine (PCV13) replaced PCV7 for use in the United States. We evaluated rates of pneumococcal colonization, by serotype and antibiotic resistance, in Massachusetts communities where serial cross-sectional surveillance has been conducted for the past decade. METHODS: Nasopharyngeal swabs were obtained from children 0 to <7 years of age and seen by primary care providers for well child or acute illness visits in 2001, 2004, 2007, 2009, and 2011. Pneumococcal isolates were serotyped by Quellung reaction and classified as PCV7 serotypes (4, 6B, 9V, 14, 18C, 19F, 23F), additional PCV13 serotypes (1, 3, 5, 6A, 7F, 19A), or non-PCV13 serotypes. Changes in colonization and impact of PCV13 were assessed using generalized linear mixed models, adjusting for known risk factors and accounting for clustering by community. RESULTS: Introduction of PCV13 did not affect the rate of overall pneumococcal colonization (31% in 2011). Colonization with non-PCV13 serotypes increased between 2001 and 2011 for all children (odds ratio [OR] per year, 1.12; 95% confidence interval [CI], 1.10, 1.15; P < .0001). 19A remained the second most common serotype in 2011, although a decline from 2009 was observed. Penicillin (7%), erythromycin (28%), ceftriaxone (10%), and clindamycin (10%) nonsusceptibility were commonly identified, concentrated among a small number of serotypes (including 19A, 35B, 15B/C, and 15A). Among healthy children 6-23 months old, colonization with PCV13 serotypes was lower among recipients of PCV13 vaccine (adjusted OR, 0.30; 95% CI, 0.11, 0.78). This effect was not observed in 6- to 23-month-old children with a concomitant respiratory tract infection (adjusted OR 1.36; 95% CI, 0.66, 2.77) or children 2 to <7 years old (adjusted OR, 1.17; 95% CI, 0.58, 2.34). CONCLUSIONS: 13-Valent pneumococcal conjugate vaccine reduced the prevalence of colonization with PCV13 serotypes among children 6-23 months old, but its efficacy was not shown among older children.

Capsular switching as a strategy to increase pneumococcal virulence in experimental otitis media model.

We hypothesized that capsular switch event, in which pneumococcus acquires a new capsule operon by horizontal gene transfer, may result in emergence of strains with increased virulence in acute otitis media. Using serotype 6A strain from a patient with invasive pneumococcal disease and clonally distant serotype 6C strain isolated from asymptomatic carrier we created 6A:6C (6A background with 6C capsule) capsular transformants and applied whole genome macro-restriction analysis to assess conservation of the 6A chassis. Next, we assessed complement (C3) and antibodies deposition on surface of pneumococcal cells and tested capsule recipient, capsule donor and two 6A:6C transformants for virulence in chinchilla experimental otitis media model. Both 6A:6C(1 or 2) transformants bound less C3 compared to 6C capsule-donor strain but more compared to serotype 6A capsule-recipient strain. Pneumococci were present in significantly higher proportion of ears among animals challenged with either of two 6A:6C(1 or 2) transformants compared to chinchillas infected with 6C capsule-donor strain [p < 0.001] whereas a significantly decreased proportion of ears were infected with 6A:6C(1 or 2) transformants as compared to 6A capsule-recipient strain. Our observations though limited to two serotypes demonstrate that capsular switch events can result in Streptococcus pneumoniae strains of enhanced virulence for respiratory tract infection.

Evolving picture of invasive pneumococcal disease in massachusetts children: a comparison of disease in 2007-2009 with earlier periods.

BACKGROUND: As expected, the heptavalent pneumococcal conjugate vaccine (PCV7) had a significant impact on invasive pneumococcal disease (IPD) in children. In addition to the substantial decline in IPD, increased disease due to nonvaccine serotypes and a changing clinical presentation emerged. The objective of this study is to describe these trends in IPD in the late PCV7-era. METHODS: We report on continued, prospective, population-based surveillance of childhood IPD in Massachusetts children during the period 2007 to 2009 and make comparisons with the earlier 2001 to 2006 PCV7-era. Demographic and clinical data were collected for all cases. Streptococcus pneumoniae isolates from normally sterile sites were serotyped and further evaluated using antimicrobial susceptibility testing, multilocus sequence typing and eBURST analysis. IPD incidence rates are calculated by age, year and serotype. RESULTS: There were 326 cases of IPD between 2007 and 2009 in children < 18 years of age. Overall IPD incidence rate was 7.5 cases per 100,000 population and was not statistically different from the observed incidence in 2001 to 2006 (P > 0.05). As compared with the earlier period, the proportion of bacteremic pneumonia among all IPD cases was almost 3-fold greater in 2009 to 2010 (P < 0.01). PCV7 serotypes accounted for 7%, whereas the 13-valent pneumococcal conjugate vaccine serotypes accounted for 77% of all cases between 2007 and 2009. IPD due to serotypes 19A and 7F increased, and 19A and 7F were isolated in 41% and 20% of all IPD cases in the same period, respectively. Serotype 19A also comprised a majority of the penicillin- and ceftriaxone-resistant isolates. Analysis of multilocus sequence typing data showed a significant increase in ST191, ST695 and ST320 and a significant decrease in ST199 and ST180. CONCLUSIONS: The reduction in IPD after introduction of PCV7 persists in Massachusetts children; however, serotypes causing IPD have changed significantly in the last decade. Continued surveillance is necessary to determine the impact of 13-valent pneumococcal conjugate vaccine, as well as track potential changes in disease incidence and character due to non-13-valent pneumococcal conjugate vaccine serotypes.

Pneumococcal carriage and antibiotic resistance in young children before 13-valent conjugate vaccine.

BACKGROUND: We sought to measure trends in Streptococcus pneumoniae carriage and antibiotic resistance in young children in Massachusetts communities after widespread adoption of heptavalent 7-valent pneumococcal conjugate vaccine (PCV7) and before the introduction of the 13-valent PCV (PCV13). METHODS: We conducted a cross-sectional study including collection of questionnaire data and nasopharyngeal specimens among children aged <7 years in primary care practices from 8 Massachusetts communities during the winter season of 2008-2009 and compared with similar studies performed in 2001, 2003-2004, and 2006-2007. Antimicrobial susceptibility testing and serotyping were performed on pneumococcal isolates, and risk factors for colonization in recent seasons (2006-2007 and 2008-2009) were evaluated. RESULTS: We collected nasopharyngeal specimens from 1011 children, 290 (29%) of whom were colonized with pneumococcus. Non-PCV7 serotypes accounted for 98% of pneumococcal isolates, most commonly 19A (14%), 6C (11%), and 15B/C (11%). In 2008-2009, newly targeted PCV13 serotypes accounted for 20% of carriage isolates and 41% of penicillin-nonsusceptible S. pneumoniae. In multivariate models, younger age, child care, young siblings, and upper respiratory illness remained predictors of pneumococcal carriage, despite near-complete serotype replacement. Only young age and child care were significantly associated with penicillin-nonsusceptible S. pneumoniae carriage. CONCLUSIONS: Serotype replacement post-PCV7 is essentially complete and has been sustained in young children, with the relatively virulent 19A being the most common serotype. Predictors of carriage remained similar despite serotype replacement. PCV13 may reduce 19A and decrease antibiotic-resistant strains, but monitoring for new serotype replacement is warranted.

Prevalence and genetic diversity of nontypeable haemophilus influenzae in the respiratory tract of infants and primary caregivers.

BACKGROUND: Nontypeable Haemophilus influenzae (NTHi) causes otitis media, sinusitis, and likely lower respiratory tract infections in children. Colonization, strain diversity, transmission, and antimicrobial susceptibility have implications for both children and their caregivers. METHODS: For 13 months, we conducted a cross-sectional study of NTHi colonization. Upper respiratory tract cultures were performed in 273 infants and children 2 to 26 months of age and their primary caregivers. NTHi isolates were characterized by multilocus sequence typing (MLST), and antibiotic resistance was examined. RESULTS: Of the 273 infants, 44 (16.1%) were colonized with NTHi. Prevalence of NTHi varied from 14% in infants less than 6 months of age to 32% in infants between 19 and 26 months of age (P = 0.003). NTHi-colonized infants were more likely to attend day care (30% vs. 12%), have a recent respiratory infection (68% vs. 38%), have recently taken an antibiotic (27% vs. 9%), and have a primary caregiver who reported asthma (11% vs. 1%), compared with other infants (P < 0.01). In the 44 infants colonized with NTHi, we identified 33 different MLSTs. Of the 44 infant-primary caregiver dyads, 9 (20.5%) were colonized with NTHi, and 7 of these 9 shared identical NTHi strains. We also found beta-lactamase-negative NTHi with minimum inhibitory concentrations >2 µg/mL for amoxicillin and beta-lactamase-positive NTHi with minimum inhibitory concentrations >2 µg/mL for amoxicillin clavulanate. CONCLUSIONS: We found substantial diversity by MLST analysis among NTHi isolates from this community. Infant-primary caregiver dyads usually carried the same strain of NTHi, suggesting that infant-primary caregiver transmission is occurring.

Underlying conditions in children with invasive pneumococcal disease in the conjugate vaccine era.

We analyzed characteristics of invasive pneumococcal disease cases occurring in Massachusetts after the introduction and use of conjugate vaccine by underlying risk. Among 578 cases with sufficient information, 16% had high-risk or presumed high-risk conditions (HR/PHR), 3% had asthma, and 80% had no known risk (NKR). The most common HR/PHR conditions were disorders associated with immunosuppression. HR/PHR cases tended to be older and were more likely to be hospitalized than were children with NKR. Children with asthma presented with pneumonia more often than children with NKR.

Carried pneumococci in Massachusetts children: the contribution of clonal expansion and serotype switching.

BACKGROUND: Vaccination against 7 serotypes of Streptococcus pneumoniae has led to the near extinction of vaccine serotypes in both disease and asymptomatic carriage. In carriage, vaccine serotypes have been replaced by nonvaccine serotypes. METHODS: We used multilocus sequence typing to analyze a sample of 294 isolates of S. pneumoniae carried by Massachusetts children (aged, 3 months-7 years) and examine the results for serotype switching and association with antimicrobial resistance. RESULTS: Eighty-six distinct sequence types (STs) were found, 10 of which exhibited a serotype other than that which would be expected from previous carriage samples. We interpret this as evidence of past or recent serotype switching. Switched variants include ST 320, which is a common and increasing source of multidrug resistance in this community. Switching events within serogroups were more common than expected by chance (P = 0.043 by a Monte Carlo approach). Using multilocus sequence typing data and eBURST analysis, we also describe clonal dynamics within the important replacement serotypes 19A, 15B/C, 35B, and the recently described 6C. CONCLUSIONS: Some strains generated by serotype switching are increasingly important parts of the carriage population. In the case of 19A, it appears that the majority of increase is due to ST 320, a recently reported switched variant. This may have consequences for the STs causing invasive pneumococcal disease.

Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete.

Invasive pneumococcal disease (IPD) has been reduced in the US following conjugate vaccination (PCV7) targeting seven pneumococcal serotypes in 2000. However, increases in IPD due to other serotypes have been observed, in particular 19A. How much this "serotype replacement" will erode the benefits of vaccination and over what timescale is unknown. We used a population genetic approach to test first whether the selective impact of vaccination could be detected in a longitudinal carriage sample, and secondly how long it persisted for following introduction of vaccine in 2000. To detect the selective impact of the vaccine we compared the serotype diversity of samples from pneumococcal carriage in Massachusetts children collected in 2001, 2004 and 2007 with others collected in the pre-vaccine era in Massachusetts, the UK and Finland. The 2004 sample was significantly (p >0.0001) more diverse than pre-vaccine samples, indicating the selective pressure of vaccination. The 2007 sample showed no significant difference in diversity from the pre-vaccine period, and exhibited similar population structure, but with different serotypes. In 2007 the carriage frequency of 19A was similar to that of the most common serotype in pre-vaccine samples. We suggest that serotype replacement involving 19A may be complete in Massachusetts due to similarities in population structure to pre-vaccine samples. These results suggest that the replacement phenomenon occurs rapidly with high vaccine coverage, and may allay concerns about future increases in disease due to 19A. For other serotypes, the future course of replacement disease remains to be determined.

Serotype specific invasive capacity and persistent reduction in invasive pneumococcal disease.

Defining the propensity of Streptococcus pneumoniae (SP) serotypes to invade sterile body sites following nasopharyngeal (NP) acquisition has the potential to inform about how much invasive pneumococcal disease (IPD) may occur in a typical population with a given distribution of carriage serotypes. Data from enhanced surveillance for IPD in Massachusetts children ≤7 years in 2003/04, 2006/07 and 2008/09 seasons and surveillance of SP NP carriage during the corresponding respiratory seasons in 16 Massachusetts communities in 2003/04 and 8 of the 16 communities in both 2006/07 and 2008/09 were used to compute a serotype specific "invasive capacity (IC)" by dividing the incidence of IPD due to serotype x by the carriage prevalence of that same serotype in children of the same age. A total of 206 IPD and 806 NP isolates of SP were collected during the study period. An approximate 50-fold variation in the point estimates between the serotypes having the highest (18C, 33F, 7F, 19A, 3 and 22F) and lowest (6C, 23A, 35F, 11A, 35B, 19F, 15A, and 15BC) IC was observed. Point estimates of IC for most of the common serotypes currently colonizing children in Massachusetts were low and likely explain the continued reduction in IPD from the pre-PCV era in the absence of specific protection against these serotypes. Invasive capacity differs among serotypes and as new pneumococcal conjugate vaccines are introduced, ongoing surveillance will be essential to monitor whether serotypes with high invasive capacity emerge (e.g. 33F, 22F) as successful colonizers resulting in increased IPD incidence due to replacement serotypes.

Changing serotypes causing childhood invasive pneumococcal disease: Massachusetts, 2001-2007.

BACKGROUND: Heptavalent pneumococcal conjugate vaccine (PCV7) was licensed in the United States in February 2000 and distributed in Massachusetts, starting in July 2000 for universal administration to children <2 years of age and selected use in children 2 to 5 years of age. Statewide surveillance was begun in October 2001 to monitor incidence of invasive disease, serotypes causing disease, antimicrobial susceptibility, and risk features associated with ongoing childhood invasive pneumococcal disease (IPD). METHODS: Massachusetts pediatric IPD cases were identified via enhanced passive surveillance of microbiology laboratory reports of pneumococcal isolates from sterile body sites of children <18 years. Serotyping and antimicrobial susceptibility testing were performed on isolates of Streptococcus pneumoniae from normally sterile body fluid. Demographic and clinical data, were collected via follow-up telephone interviews with primary care providers. Incidence rates were derived using Census 2000 denominators. RESULTS: A total of 586 IP cases were reported between October 2001 and September 2007. Among 433 (74%) cases with isolates available for serotyping, 366 (85%) were caused by non-PCV7 serotypes and 67 (15%) were caused by PCV7 serotypes. 19A was the most common cause of any serotype identified episode of IPD (28%). IPD incidence was stable during the 6 study years because, although IPD cases due to PCV7-serotypes decreased, the incidence of non-PCV7 serotype IPD increased from 3.0 cases/100,000 children less than 18 years to a high of 5.3 cases/100,000 during 2005 to 06. Since 2005, ceftriaxone non-susceptible isolates comprised approximately 20% of isolates. There were 8 (1.4%) fatalities from IPD; 5 deaths occurred in children <1 year of age. CONCLUSIONS: Non-PCV7 serotype IPD, especially serotype 19A disease, increased during the 2001 to 2007 surveillance period in Massachusetts. The proportion of ceftriaxone non susceptible isolates also increased, particularly since 2005. Ongoing surveillance will be necessary to detect future increases in IPD incidence or antibiotic resistance in Massachusetts children, changes which have important implications for introduction of second generation pneumococcal conjugate vaccines and presumptive antibiotic choices in critically ill children.

Continued impact of pneumococcal conjugate vaccine on carriage in young children.

OBJECTIVES: The goals were to assess serial changes in Streptococcus pneumoniae serotypes and antibiotic resistance in young children and to evaluate whether risk factors for carriage have been altered by heptavalent pneumococcal conjugate vaccine (PCV7). METHODS: Nasopharyngeal specimens and questionnaire/medical record data were obtained from children 3 months to <7 years of age in primary care practices in 16 Massachusetts communities during the winter seasons of 2000-2001 and 2003-2004 and in 8 communities in 2006-2007. Antimicrobial susceptibility testing and serotyping were performed with S pneumoniae isolates. RESULTS: We collected 678, 988, and 972 specimens during the sampling periods in 2000-2001, 2003-2004, and 2006-2007, respectively. Carriage of non-PCV7 serotypes increased from 15% to 19% and 29% (P < .001), with vaccine serotypes decreasing to 3% of carried serotypes in 2006-2007. The relative contribution of several non-PCV7 serotypes, including 19A, 35B, and 23A, increased across sampling periods. By 2007, commonly carried serotypes included 19A (16%), 6A (12%), 15B/C (11%), 35B (9%), and 11A (8%), and high-prevalence serotypes seemed to have greater proportions of penicillin nonsusceptibility. In multivariate models, common predictors of pneumococcal carriage, such as child care attendance, upper respiratory tract infection, and the presence of young siblings, persisted. CONCLUSIONS: The virtual disappearance of vaccine serotypes in S pneumoniae carriage has occurred in young children, with rapid replacement with penicillin-nonsusceptible nonvaccine serotypes, particularly 19A and 35B. Except for the age group at highest risk, previous predictors of carriage, such as child care attendance and the presence of young siblings, have not been changed by the vaccine.