Characterization of 19A-like 19F pneumococcal isolates from Papua New Guinea and Fiji

Streptococcus pneumoniae serotype 33G: genetic, serological, and structural analysis of a new capsule type

IMPORTANCE

Streptococcus pneumoniae (the pneumococcus) is a bacterial pathogen with the greatest burden of disease in Asia and Africa. The pneumococcal capsular polysaccharide has biological relevance as a major virulence factor as well as public health importance as it is the target for currently licensed vaccines. These vaccines have limited valency, covering up to 23 of the >100 known capsular types (serotypes) with higher valency vaccines in development. Here, we have characterized a new pneumococcal serotype, which we have named 33G. We detected serotype 33G in nasopharyngeal swabs (n = 20) from children and adults hospitalized with pneumonia, as well as healthy children in Mongolia. We show that the genetic, serological, and biochemical properties of 33G differ from existing serotypes, satisfying the criteria to be designated as a new serotype. Future studies should focus on the geographical distribution of 33G and any changes in prevalence following vaccine introduction.

Association between nasopharyngeal colonization with multiple pneumococcal serotypes and total pneumococcal colonization density in young Peruvian children

OBJECTIVES

We examined the association of nasopharyngeal (NP) pneumococcal co-colonization (>1 pneumococcal serotype) and pneumococcal density in young Peruvian children enrolled in a prospective cohort study.

METHODS

NP swabs collected monthly from children aged <3 years during both asymptomatic and acute respiratory illness (ARI) periods underwent culture-enriched microarray for pneumococcal detection and serotyping and lytA polymerase chain reaction for density assessment. We examined the serotypes commonly associated with co-colonization and the distribution of densities by co-colonization, age, current ARI, and other covariates. The association of co-colonization and pneumococcal density was assessed using a multivariable mixed-effects linear regression model, accounting for repeated measures and relevant covariates.

RESULTS

A total of 27 children contributed 575 monthly NP samples. Pneumococcus was detected in 302 of 575 (53%) samples, and co-colonization was detected in 61 of these 302 (20%). The total densities were higher during ARI than non-ARI periods and lowest among the youngest children, increasing with age. In the multivariable analysis, there was no significant association between pneumococcal density and co-colonization (coefficient estimate 0.22, 95% confidence interval 0.11-0.55; reference: single-serotype detections). Serotypes 23B and 19F were detected significantly more frequently as single isolates.

CONCLUSION

Pneumococcal co-colonization was common and not associated with increased pneumococcal density. Differential propensity for co-colonization was observed among individual serotypes.

PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data

Determination of serotypes of Streptococcus pneumoniae is essential for monitoring current vaccine programmes. Since October 2017, pneumococcal serotypes in England have been derived from whole genome sequencing (WGS) data using our bioinformatic tool PneumoCaT. That tool was designed for serotype determination from pure cultures in a reference laboratory. To help determine multiple serotypes in pneumococcal carriage samples, we developed a new software tool named PneumoKITy (Pneumococcal K-mer Integrated Typing) that uses the powerful Mash k-mer screening method for pneumococcal serotyping. Mash k-mer screening is more sequence specific and much faster than the mapping method used in PneumoCaT and can determine 54 (58.1  %) of the 93 serotypes in the SSI Diagnostica phenotypical serotyping scheme to type level with the remainder called to serogroup or subgroup level (e.g., 11A/D). PneumoKITy can be run on both FastQ and assembly input, requiring up to 11× less memory and running up to 29× faster than the current version of PneumoCaT (1.2.1) on FastQ files. PneumoKITy can be used as a rapid, flexible serotype screening method which adds sensitive detection of mixed serotypes, e.g., for nasopharyngeal carriage studies where the presence of multiple serotypes is common. PneumoKITy's ability to function from assembly file, for pure culture serotype detection, increases its speed. This speed potentially enables the software to be run using low infrastructure overhead via web-based platforms. PneumoKITy could be used as a fast initial screening method with other tools used for those serotypes that could not be fully determined to type level if necessary. PneumoKITy was found to be highly accurate and sensitive when run on a panel of FastQ files derived from mixed cultures with all serotypes in 47/51 (92.2  %) of samples being accurately detected. PneumoKITy was also able to accurately estimate the relative abundance of serotypes in the same sample. Estimates being within a mean relative abundance of 1.5 % of the expected abundance in mixtures with known concentrations. PneumoKITy was able to detect minor serotypes with expected abundance of 1 % in the known mixture serotypes. PneumoKITy is a rapid, flexible tool with wide-ranging applications outside of the pure-culture, reference laboratory serotyping remit of PneumoCaT.

Lack of effectiveness of 13-valent pneumococcal conjugate vaccination against pneumococcal carriage density in Papua New Guinean infants

BACKGROUND

Papua New Guinea (PNG) introduced the 13-valent pneumococcal conjugate vaccine (PCV13) in 2014, with administration at 1, 2, and 3 months of age. PCV13 has reduced or eliminated carriage of vaccine types in populations with low pneumococcal carriage prevalence, carriage density and serotype diversity. This study investigated PCV13 impact on serotype-specific pneumococcal carriage prevalence, density, and serotype diversity in PNG infants, who have some of the highest reported rates of pneumococcal carriage and disease in the world.

METHODS

Nasopharyngeal swabs were collected at 1, 4 and 9 months of age from PCV13-vaccinated infants (n = 57) and age-/season-matched, unvaccinated infants (at approximately 1 month, n = 53; 4 months, n = 57; 9 months, n = 52). Serotype-specific pneumococcal carriage density and antimicrobial resistance genes were identified by qPCR and microarray.

RESULTS

Pneumococci were present in 89% of swabs, with 60 different serotypes and four non-encapsulated variants detected. Multiple serotype carriage was common (47% of swabs). Vaccine type carriage prevalence was similar between PCV13-vaccinated and unvaccinated infants at 4 and 9 months of age. The prevalence of non-vaccine type carriage was also similar between cohorts, with non-vaccine types present in three-quarters of samples (from both vaccinated and unvaccinated infants) by 4 months of age. The median pneumococcal carriage density was high and similar at each age group (~7.0 log₁₀genome equivalents/mL). PCV13 had no effect on overall pneumococcal carriage density, vaccine type density, non-vaccine type density, or the prevalence of antimicrobial resistance genes.

CONCLUSION

PNG infants experience dense and diverse pneumococcal colonisation with concurrent serotypes from 1 month of age. PCV13 had no impact on pneumococcal carriage density, even for vaccine serotypes. The low prevalence of vaccine serotypes, high pneumococcal carriage density and abundance of non-vaccine serotypes likely contribute to the lack of PCV13 impact on carriage in PNG infants. Indirect effects of the infant PCV programs are likely to be limited in PNG. Alternative vaccines with broader coverage should be considered.

Characterization of Streptococcus pneumoniae serotype 19F-variants occurring in Brazil uncovers a predominant lineage that can lead to misinterpretation in capsular typing

BACKGROUND

Streptococcus pneumoniae (S. pneumoniae) of serogroup 19 are mainly represented by serotypes 19A and 19F, which are associated with antimicrobial resistance and disease. The wzy gene, a component of the pneumococcal capsular locus, is the target to differentiate serotypes 19A and 19F by PCR-based capsular typing. In the last decade, allelic variants of the wzy^19F gene have been described, leading to misinterpretation of capsular typing results.

METHODS

A collection of 154 serotype 19F S. pneumoniae strains recovered from carriage and disease in Brazil was evaluated to identify and characterize wzy^19F variant isolates.

RESULTS

Eleven (7%) wzy^19F variant isolates were detected and identified as belonging to ST810 (n = 10) or ST13673 (n = 1; single-locus variant of ST810). They were mostly recovered from diseased patients, susceptible to the antimicrobial agents tested (except for one multidrug-resistant strain) and did not harbor pili genes. Sequences of the wzy^19F gene of these variants were identical to each other and to those previously described in Brazil, but slightly different from wzy^19F variants identified in other countries.

CONCLUSION

This study indicated that wzy^19F variants present a geographically driven distribution and was the first to uncover phenotypic and genetic features of a wzy^19F variant lineage occurring in Brazil since 1989.

Impact of Laboratory Methods and Gene Targets on Detection of Streptococcus pneumoniae in Isolates and Clinical Specimens

Background

Timely identification of Streptococcus pneumoniae infections can lead to a decrease in mortality rates. Differentiation of S. pneumoniae from other similar species using traditional culture-based and molecular methods is problematic. In this study, we assessed the efficacy of identifying the blpA and lytA for the detection of S. pneumoniae from isolates and various clinical samples using molecular methods.

Methods

A total of 440 clinical samples were collected from patients with suspected invasive pneumococcal infections during February 2016 to October 2018. Biochemical tests were used to confirm the dubious colonies on 5% sheep blood agar. Fifty-seven confirmed isolates, 57 culture-positive samples, and 57 culture-negative samples were analyzed for the presence of blpA and lytA using both conventional and real-time PCR.

Results

All the isolates and culture-positive samples were positive for blpA and lytA by both PCR methods. Of the 57 culture-negative samples, conventional and real-time PCR amplified blpA from six and two samples, and lytA from seven and two samples, respectively.

Conclusion

The specificity of real-time PCR assay was significantly higher than that of conventional PCR for the identification of S. pneumoniae. In addition, it is suggested that respiratory secretions are not suitable specimen for direct diagnosis of pneumococcal infections.

Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5405 pneumococcal genomes

The pneumococcus is a leading global pathogen and a key virulence factor possessed by the majority of pneumococci is an antigenic polysaccharide capsule ('serotype'), which is encoded by the capsular (cps) locus. Approximately 100 different serotypes are known, but the extent of sequence diversity within the cps loci of individual serotypes is not well understood. Investigating serotype-specific sequence variation is crucial to the design of sequence-based serotyping methodology, understanding pneumococcal conjugate vaccine (PCV) effectiveness and the design of future PCVs. The availability of large genome datasets makes it possible to assess population-level variation among pneumococcal serotypes and in this study 5405 pneumococcal genomes were used to investigate cps locus diversity among 49 different serotypes. Pneumococci had been recovered between 1916 and 2014 from people of all ages living in 51 countries. Serotypes were deduced bioinformatically, cps locus sequences were extracted and variation was assessed within the cps locus, in the context of pneumococcal genetic lineages. Overall, cps locus sequence diversity varied markedly: low to moderate diversity was revealed among serogroups/types 1, 3, 7, 9, 11 and 22; whereas serogroups/types 6, 19, 23, 14, 15, 18, 33 and 35 displayed high diversity. Putative novel and/or hybrid cps loci were identified among all serogroups/types apart from 1, 3 and 9. This study demonstrated that cps locus sequence diversity varied widely between serogroups/types. Investigation of the biochemical structure of the polysaccharide capsule of major variants, particularly PCV-related serotypes and those that appear to be novel or hybrids, is warranted.