Type distribution of serogroup 6 Streptococcus pneumoniae and molecular epidemiology of newly identified serotypes 6C and 6D in China

Serotype 6B from a pneumococcal polysaccharide vaccine induces cross-functional antibody responses in adults to serotypes 6A, 6C, and 6D

Cross-reactivity of pneumococcal capsular polysaccharides is a key element for formulating pneumococcal vaccines and evaluating vaccine efficacy. This study examined whether 23-valent pneumococcal polysaccharide vaccine (PPSV23), which only contains 6B, can elicit cross-functional immune responses against recently discovered serotypes (6C and 6D), as well as against 6A, in 2 adult age groups.Young adults (25-51 years; N = 28) and elderly subjects (over 65 years; N = 60) were immunized with PPSV23. Functional antibody responses were determined in pre- and postimmune sera via multiplexed opsonophagocytic killing assay against serotypes 6A/B/C/D.At postimmunization, the geometric mean opsonic indices (OIs) for 6B and nonvaccine serotypes (6A, 6C, and 6D) significantly increased in both age groups. The geometric fold increases of OIs for 6B/A/C/D significantly differed (18.2, 24.8, 3.1, and 7.1, respectively). Proportions of subjects with 4-fold increases in OIs for 6B/A/C/D were 73%, 70%, 31%, and 49%, respectively. Correlations of fold increases in OIs were highest between 6B and 6A, followed by 6B and 6D, then by 6B and 6C. Comparisons of young adults and the elderly revealed that most immunogenicity variables were higher in the former group.Our data demonstrated that 6B in PPSV23 induced cross-functional immune responses against serotypes 6A, 6C, and 6D, according to the degree of similarity in their capsular polysaccharide structures. In addition, we found significant age-related differences in PPSV23-induced cross-reactivity.

Population biology of 225 serogroup 6 Streptococcus pneumoniae isolates collected in China

Background

In this study, we defined the population biology of serogroup 6 Streptococcus pneumoniae collected in China and their antibiotic resistance profiles.

Methods

The serotypes of 225 S. pneumoniae strains isolated between 1997 and 2011 were identified with the Quellung reaction and serotype-specific PCR. All isolated pneumococci were tested for their sensitivity to 11 kinds of antibiotics with the E-test method or disc diffusion. The sequence types (STs) were analyzed with multilocus sequence typing (MLST).

Results

The frequencies of serotypes and subtypes 6A, 6B-I, 6B-II, 6C, and 6D among the 225 isolates were 46.7% (105/225), 19.6% (44/225), 25.8% (58/225), 6.2% (14/225), and 1.8% (4/225), respectively. Serotype 6E was not found in the serotype 6A isolates, and neither serotype 6F nor 6G was identified in any isolate. MLST analysis revealed 58 STs. The most common STs were ST982 (23.1%), ST90 (14.7%), ST4542 (7.6%), and ST2912 (4.9%). The rates of clonal complex 90 (CC90) and CC386 among the oral-penicillin-nonsusceptible isolates decreased over the years, whereas the rates of CC855 and CC3173 increased. The four CCs had similar penicillin MIC distributions, with a maximum MIC of 2 μg/ml.

Conclusions

This study identified the serotypes/subtypes and CCs/STs of group 6 S. pneumoniae present in China. No salient antibiotic-resistant clones were isolated among the serogroup 6 S. pneumoniae.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2334-14-467) contains supplementary material, which is available to authorized users.

Capsular polysaccharide gene diversity of pneumococcal serotypes 6A, 6B, 6C, and 6D

This study was performed to better understand the genetic diversity and evolutionary relatedness of pneumococcal serotypes 6A, 6B, 6C, and 6D. Multi-locus sequence typing (MLST) was performed for 160 serogroup 6 isolates from clinical specimens collected from children between 1991 and 2010. We identified 38 sequence types (STs) comprising five clonal complexes with 12 singletons. Although most STs were confined to a single serotype, some STs were shared by two serotypes, and one ST was shared by three serotypes. Many STs of serotype 6A showed genetic relatedness with those of serotype 6C or 6D in eBURST analysis. Five capsular polysaccharide (cps) genes - wchA, wciO, wciP, wzy, and wzx - were analysed in 74 isolates from our clinical samples and in 36 isolates from GenBank. There were several profiles and clades in each serotype on the analysis of the concatenated sequences of the five cps genes. Small genetic distances between serotypes 6A and 6B and between serotypes 6C and 6D were observed while serotype 6B with an indel sequence formed a distinct clade. When comparing the individual cps genes between the serotypes, there was also a high level of similarity in the wchA and wciO gene sequences between serotype 6C and serotype 6D. On the other hand, serotypes 6A and 6D had the most highly similar wzy and wzx gene sequences. The wzy sequences of serotype 6C were nearly identical (99.6%) to those of serotype 6A clade II strains. In conclusion, we revealed the diversity of the genetic background and cps sequences in each pneumococcal serotype of serogroup 6. Pneumococcal serotype diversity might be attributable to complex serial mutation and recombination events.

Serotype distribution and susceptibility to penicillin and erythromycin among noninvasive or colonization isolates of Streptococcus pneumoniae in northern Japan: a cross-sectional study in the pre-PCV7 routine immunization period

Distribution of serotypes, prevalence of resistance to penicillin and/or erythromycin (EM), and its genetic traits were analyzed for a total of 1,061 noninvasive or colonization isolates of Streptococcus pneumoniae (998 and 61 isolates from children and adults, respectively) in Hokkaido, northern main island of Japan, in the year 2011, the pre-PCV7 routine immunization period. Serotype deduction was performed by sequential multiplex polymerase chain reaction (PCR), employing mutagenic PCR-restriction fragment length polymorphism for discrimination of 6A/C and 6B/D. Unaltered three PBP genes and macrolide resistance genes erm(B) and mef(A/E) were detected by multiplex PCR. Among isolates from children, 25 serotypes, including the prevalent types 6B (17.5%), 19F (15.6%), 23F (12.2%), and 6C (11.6%), were identified, revealing the PCV7 and PCV13 coverage rates as 48.2% and 60.3%, respectively, while serotype 3 was the most frequent (19.0%) among isolates from adults. Most of the pediatric isolates (96.8%) exhibited resistance to EM (minimum inhibitory concentration [MIC], ≥1 μg/ml), with a higher prevalence of erm(B) (67.2%) than mef(A/E) (39.7%). erm(B) was associated with high-level EM resistance (MIC, ≥128 μg/ml) and distributed at high detection rates to major serotypes 23F (85.2%) and 6B (85.1%), as well as minor serotypes 3, 10A, 14, 15B, 15C, 19A, and 23A (>90%). While penicillin-resistant S. pneumoniae (PRSP) (penicillin G-MIC, 2-3 μg/ml) was detected in 7.8% of isolates from children, the most common PBP gene genotype was gPRSP (three altered genes pbp1a, 2x, and 2b; 38.3%), which was detected at higher rates (>60%) in the dominant serotypes 23F, 6B, and 19F, and minor serotypes 6D and 15A. Dominant serotypes in the S. pneumoniae isolates were generally similar to those reported for invasive strains, despite lower coverage rates by PCV7/13. The importance of further surveillance on incidence and drug resistance in the post-PCV7 period was suggested for non-PCV7/13 serotypes 6C, 6D, 10A, 15A, 15B, 15C, 23A, and 35B.

The 7-valent pneumococcal conjugate vaccine elicits cross-functional opsonophagocytic killing responses to Streptococcus pneumoniae serotype 6D in children

Background

We investigated the immune response to serogroup 6 with the opsonophagocytic killing assay (OPKA) in children aged 12–23 months of age after immunization with the 7-valent pneumococcal conjugate vaccine (PCV7) containing serotype 6B.

Methods

Blood samples were obtained from 59 children who had blood sampling for medical examination. Immunization status against PCV7 was confirmed by immunization records and samples were categorized according to immunization status into a booster, primary, or control group. The OPKA was performed for serotypes 6A, 6B, 6C, and 6D.

Results

Subjects with no previous PCV7 immunization history showed opsonic activity for serogroup 6 in 5-30% (according to serotype). In subjects vaccinated with a 3-dose primary series, 81% showed opsonic activity for serotypes 6B and 6D, and 29% showed opsonic activity for serotypes 6A and 6C. Among subjects vaccinated with a booster dose, all subjects had opsonic activity against serotype 6B. Subjects in the booster group with opsonic activity against serotypes 6A, 6C, and 6D were 100%, 78%, and 89%, respectively.

Conclusions

In subjects aged 12–23 months, an immune response is elicited after a primary series of immunizations with PCV7 for serotypes 6B and 6D, and a booster dose enhances a cross reactive immune response against serotypes 6A, 6C and 6D.

Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine

Streptococcus pneumoniae causes invasive infections, primarily at the extremes of life. A seven-valent conjugate vaccine (PCV7) is used to protect against invasive pneumococcal disease in children. Within three years of PCV7 introduction, we observed a fourfold increase in serotype 6C carriage, predominantly due to a single clone. We determined the whole-genome sequences of nineteen S. pneumoniae serotype 6C isolates, from both carriage (n = 15) and disease (n = 4) states, to investigate the emergence of serotype 6C in our population, focusing on a single multi-locus sequence type (MLST) clonal complex 395 (CC395). A phylogenetic network was constructed to identify different lineages, followed by analysis of variability in gene sets and sequences. Serotype 6C isolates from this single geographical site fell into four broad phylogenetically distinct lineages. Variation was seen in the 6C capsular locus and in sequences of genes encoding surface proteins. The largest clonal complex was characterised by the presence of lantibiotic synthesis locus. In our population, the 6C capsular locus has been introduced into multiple lineages by independent capsular switching events. However, rapid clonal expansion has occurred within a single MLST clonal complex. Worryingly, plasticity exists within current and potential vaccine-associated loci, a consideration for future vaccine use, target selection and design.

Spread of multidrug-resistant clonal complex 271 of serotype 19F Streptococcus pneumoniae in Beijing, China: characterization of serotype 19F

We investigated the genetic structure of 120 isolates of serotype 19F Streptococcus pneumoniae from Chinese children with acute respiratory infections collected from 1997 to 2006, and 2010. All strains were susceptible to vancomycin and levofloxacin, and only five strains were not susceptible to penicillin. The non-susceptibility rate to cephalosporins increased from 1997 to 2010. Of 119 erythromycin-resistant strains, 60 carried both ermB and mefA genes. The percentage of clonal complex 271 (CC271) increased from 14.3% in 1997-1998 to 92% in 2010, whereas that of CC983 decreased from 64.3% to 0%. CC271 had a higher non-susceptibility rate to β-lactam antibiotics than CC983 and other CCs. The increased non-susceptibility rate to β-lactam antibiotics in serotype 19F pneumococci was found to be associated with the spread of the international resistant clone CC271 presumably caused by antibiotic pressure. Long-term surveys of serotype 19F S. pneumoniae are required to monitor CC prevalence and trends in antimicrobial resistance.

Clinical implications of pneumococcal serotypes: invasive disease potential, clinical presentations, and antibiotic resistance

Streptococcus pneumoniae can asymptomatically colonize the nasopharynx and cause a diverse range of illnesses. This clinical spectrum from colonization to invasive pneumococcal disease (IPD) appears to depend on the pneumococcal capsular serotype rather than the genetic background. According to a literature review, serotypes 1, 4, 5, 7F, 8, 12F, 14, 18C, and 19A are more likely to cause IPD. Although serotypes 1 and 19A are the predominant causes of invasive pneumococcal pneumonia, serotype 14 remains one of the most common etiologic agents of non-bacteremic pneumonia in adults, even after 7-valent pneumococcal conjugate vaccine (PCV7) introduction. Serotypes 1, 3, and 19A pneumococci are likely to cause empyema and hemolytic uremic syndrome. Serotype 1 pneumococcal meningitis is prevalent in the African meningitis belt, with a high fatality rate. In contrast to the capsule type, genotype is more closely associated with antibiotic resistance. CC320/271 strains expressing serotype 19A are multidrug-resistant (MDR) and prevalent worldwide in the era of PCV7. Several clones of MDR serotype 6C pneumococci emerged, and a MDR 6D clone (ST282) has been identified in Korea. Since the pneumococcal epidemiology of capsule types varies geographically and temporally, a nationwide serosurveillance system is vital to establishing appropriate vaccination strategies for each country.

Genotype replacement within serotype 23FStreptococcus pneumoniaein Beijing, China: characterization of serotype 23F

We investigated the genetic structure of 99 isolates of serotype 23FStreptococcus pneumoniaefrom children with acute respiratory infections collected over two periods from 1997 to 2006, and 2010. All isolates were susceptible to vancomycin and amoxicillin–clavulanic acid; 97 were resistant to erythromycin, 95 of which carried theermBgene and two carried bothmefA/EandermBgenes. Multidrug resistance to three or more classes of antibiotics was exhibited by 90 isolates. Sequence types ST342 and ST81 were the most frequent in 1997–2006 and 2010, respectively. All CC81 isolates were non-susceptible to β-lactam antibiotics and had higher minimum inhibitory concentration values for penicillin than other clone complexes and sequence types. The increased β-lactam antibiotic resistance may have resulted from the replacement of multidrug-resistant clones related to ST81. Long-term studies onS. pneumoniaeserotype 23F, especially the ST81 clone, should be conducted to better understand the epidemiological picture of this pathogen in China.

Exploring bacterial diversity in hospital environments by GS-FLX Titanium pyrosequencing

Understanding microbial populations in hospital environments is crucial for improving human health. Hospital-acquired infections are an increasing problem in intensive care units (ICU). In this work we present an exploration of bacterial diversity at inanimate surfaces of the ICU wards of the University Hospital A Coruña (Spain), as an example of confined hospital environment subjected to selective pressure, taking the entrance hall of the hospital, an open and crowded environment, as reference. Surface swab samples were collected from both locations and recovered DNA used as template to amplify a hypervariable region of the bacterial 16S rRNA gene. Sequencing of the amplicons was performed at the Roche 454 Sequencing Center using GS-FLX Titanium procedures. Reads were pre-processed and clustered into OTUs (operational taxonomic units), which were further classified. A total of 16 canonical bacterial phyla were detected in both locations. Members of the phyla Firmicutes (mainly Staphylococcus and Streptococcus) and Actinobacteria (mainly Micrococcaceae, Corynebacteriaceae and Brevibacteriaceae) were over-represented in the ICU with respect to the Hall. The phyllum Proteobacteria was also well represented in the ICU, mainly by members of the families Enterobacteriaceae, Methylobacteriaceae and Sphingomonadaceae. In the Hall sample, the phyla Proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria were over-represented with respect to the ICU. Over-representation of Proteobacteria was mainly due to the high abundance of Enterobacteriaceae members. The presented results demonstrate that bacterial diversity differs at the ICU and entrance hall locations. Reduced diversity detected at ICU, relative to the entrance hall, can be explained by its confined character and by the existence of antimicrobial selective pressure. This is the first study using deep sequencing techniques made in hospital wards showing substantial hospital microbial diversity.

Novel pneumococcal serotypes 6C and 6D: anomaly or harbinger

Clinical use of the 7-valent pneumococcal protein conjugate (PCV7) vaccine, which includes serotypes 4, 6B, 9V, 14, 18C, 19F, and 23F, dramatically reduced invasive pneumococcal disease (IPD); however, the effectiveness was diminished due to serotype shift. Although shift due to known serotypes was anticipated, shift by misidentified serotypes was unexpected. We describe the experience with newly recognized serotypes 6C and 6D, which were mistyped as serotypes 6A and 6B, respectively. Although serotype 6D caused only occasional infections, IPD due to serotype 6C disease expanded in the PCV7 era. Subsequent studies showed that PCV7 provided cross-protection against serotype 6A but not serotype 6C. The 13-valent pneumococcal protein conjugate (PCV13) vaccine, which includes PCV7 serotypes plus serotypes 1, 3, 5, 6A, 7F, 19A, may provide protection against IPD due to serotypes 6C and 6D. Regardless, this narrative illustrates the potential impact of unrecognized serotypes on the efficacy of a serotype-specific vaccine.

Multidrug-resistant Streptococcus pneumoniae serotype 6D clones in South Korea

To investigate the characteristics of main Streptococcus pneumoniae clones of serotype 6D (ST282 and ST3171) in South Korea, antimicrobial susceptibility testing was performed, and 11 genes around the cps locus were sequenced on ST282(6D), ST3171(6D), and ST81(6A) isolates. The antimicrobial susceptibility patterns were very similar between clones belonging to the same clonal complex, ST81(6A) and ST282(6D); nonsusceptibilities to penicillin and cefuroxime, high MICs of ceftriaxone, and high resistance rates to trimethoprim-sulfamethoxazole. However, ST3171(6D) isolates showed resistance to only macrolides and clindamycin. The sequences of 11 genes around the cps locus indicated the same genetic backgrounds between the ST81(6A) and ST282(6D) isolates. On the other hand, ST3171(6D) isolates showed nucleotide and amino acid differences from ST81(6A) and ST282(6D) isolates in most genes, indicating a different genetic background. The mosaic structure of dexB gene in ST282(6D) isolates indicated that recombination might occur in the dexB gene. Our results suggest that the multidrug-resistant ST282(6D) pneumococcal clone has emerged by serial genetic recombination, including capsular switch.