Direct Streptococcus pneumoniae real-time PCR serotyping from pediatric parapneumonic effusions

The Molecular Approaches and Challenges of Streptococcus pneumoniae Serotyping for Epidemiological Surveillance in the Vaccine Era

Streptococcus pneumoniae (pneumococcus) belongs to the Gram-positive cocci. This bacterium typically colonizes the nasopharyngeal region of healthy individuals. It has a distinct polysaccharide capsule - a virulence factor allowing the bacteria to elude the immune defense mechanisms. Consequently, it might trigger aggressive conditions like septicemia and meningitis in immunocompromised or older individuals. Moreover, children below five years of age are at risk of morbidity and mortality. Studies have found 101 S. pneumoniae capsular serotypes, of which several correlate with clinical and carriage isolates with distinct disease aggressiveness. Introducing pneumococcal conjugate vaccines (PCV) targets the most common disease-associated serotypes. Nevertheless, vaccine selection pressure leads to replacing the formerly dominant vaccine serotypes (VTs) by non-vaccine types (NVTs). Therefore, serotyping must be conducted for epidemiological surveillance and vaccine assessment. Serotyping can be performed using numerous techniques, either by the conventional antisera-based (Quellung and latex agglutination) or molecular-based approaches (sequetyping, multiplex PCR, real-time PCR, and PCR-RFLP). A cost-effective and practical approach must be used to enhance serotyping accuracy to monitor the prevalence of VTs and NVTs. Therefore, dependable pneumococcal serotyping techniques are essential to precisely monitor virulent lineages, NVT emergence, and genetic associations of isolates. This review discusses the principles, associated benefits, and drawbacks of the respective available conventional and molecular approaches, and potentially the whole genome sequencing (WGS) to be directed for future exploration.

Otopathogens in the middle ear and nasopharynx of children with recurrent acute otitis media

OBJECTIVE

This study aimed to describe the microbiology of the middle ear and nasopharynx, determining the prevalence of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis in a group of children vaccinated with pneumococcal conjugate vaccine (PCV) who underwent ventilation tube insertion for recurrent acute otitis media.

METHODS

We analyzed 278 middle ear effusion and 139 nasopharyngeal samples obtained from 139 children who underwent myringotomy and ventilation tube insertion for recurrent acute otitis media between June 2017 and June 2021. The children's ages ranged from 9 months to 9 years, 10 months, with a median of 21 months. The patients had no signs of acute otitis media or respiratory tract infection and were not on antibiotic therapy at the time of the procedure. The middle ear effusion and nasopharyngeal samples were collected with an Alden-Senturia aspirator and a swab, respectively. Bacteriological studies and multiplex PCR were performed for the detection of the three pathogens. Direct molecular determination of pneumococcal serotypes was performed by real-time PCR. The chi-square test was used to verify associations between categorical variables and measures of strength of association based on prevalence ratios, considering a 95% confidence interval a 5% significance level.

RESULTS

Vaccination coverage was 77.7% with the basic regimen plus booster dose and 22.3% with the basic regimen alone. Middle ear effusion culture identified H. influenzae in 27 children (19.4%), S. pneumoniae in 7 (5.0%), and M. catarrhalis in 7 (5.0%). PCR detected H. influenzae in 95 children (68.3%), S. pneumoniae in 52 (37.4%), and M. catarrhalis in 23 (16.5%), a three-to seven-fold increase compared to culture. In the nasopharynx, culture isolated H. influenzae in 28 children (20.1%), S. pneumoniae in 29 (20.9%), and M. catarrhalis in 12 (8.6%). PCR identified H. influenzae in 84 children (60.4%), S. pneumoniae in 58 (41.7%), and M. catarrhalis in 30 (21.5%), a two-to three-fold increase in detection. The most common pneumococcal serotype was 19A, both in the ears and the nasopharynx. In the ears, of the 52 children who had pneumococcus, 24 (46.2%) had serotype 19A. In the nasopharynx, of the 58 patients who had pneumococcus, 37 (63.8%) had serotype 19A. Of all 139 children, 53 (38.1%) had polymicrobial samples (more than 1 of the 3 otopathogens) in the nasopharynx. Of the 53 children who had polymicrobial samples in the nasopharynx, 47 (88.7%) also had 1 of the 3 otopathogens in the middle ear, mainly H. influenzae (40%-75.5%), especially when it was found in the nasopharynx in conjunction with S. pneumoniae.

CONCLUSION

The prevalence of bacteria in a group of Brazilian children immunized with the PCV who required ventilation tube insertion for recurrent acute otitis media was similar to that reported in other parts of the world after the advent of PCV. H. influenzae was the most frequent bacteria, both in the nasopharynx and the middle ear, while S. pneumoniae serotype 19A was the most common pneumococcus in the nasopharynx and middle ear. Polymicrobial colonization of the nasopharynx was strongly associated with detection of H. influenzae in the middle ear.

Pediatric Complicated Pneumonia Caused by Streptococcus pneumoniae Serotype 3 in 13-Valent Pneumococcal Conjugate Vaccinees, Portugal, 2010-2015

Despite use of 7-valent pneumococcal conjugate vaccine, incidence of pleural effusion and empyema (pediatric complicated pneumococcal pneumonia [PCPP]) is reportedly increasing globally. We cultured and performed PCR on 152 pleural fluid samples recovered from pediatric patients in Portugal during 2010–2015 to identify and serotype Streptococcus pneumoniae. We identified only 17 cases by culture, but molecular methods identified S. pneumoniae in 68% (92/135) of culture-negative samples. The most frequent serotypes were 3, 1, and 19A, together accounting for 62% (68/109) of cases. Nineteen cases attributable to 13-valent pneumococcal conjugate vaccine (PCV13) serotypes (mostly serotype 3) were detected among 22 children age-appropriately vaccinated with PCV13. The dominance of the additional serotypes included in PCV13 among PCPP cases in Portugal continues, even with PCV13 available on the private market (without reimbursement) since 2010 and with average annual coverage of 61% among age-eligible children. Our data suggest reduced effectiveness of PCV13 against serotype 3 PCPP.

Pneumococcal Vaccination and Pneumonia Associated With Pleural Effusion in a Pediatric Population

OBJECTIVE

The aim was to assess the effect of the nonsystematic pneumococcal conjugate vaccine (PCV) on incidence of pneumonia associated with parapneumonic pleural effusion (PPE) in vaccinated and unvaccinated children.

METHODS

Cases were patients <15 years of age who had been diagnosed with pneumonia associated with PPE in a tertiary hospital in Navarra (Spain) between 1995 and 2014. The population <15 years of age and covered by the public health service was used as reference. The vaccination status of the cases and population was obtained from computerized medical records. Logistic regression analyses included vaccination status, age group and time periods: prevaccine (1995-2001) and vaccination with PCV7 (2002-2010) and PCV13 (2011-2014).

RESULTS

A total of 321 cases of PPE were included. The risk of PPE increased between the prevaccine and PCV7 period (adjusted odds ratio [OR], 3.34; 95% confidence interval [CI]: 2.37-4.71), while vaccination with PCV7 was found to be an independent risk factor (OR, 1.44; 95% CI: 1.09-1.89) in the same analysis. In the PCV13 period, the risk of PPE returned to the prevaccination incidence level among children vaccinated with PCV13 (OR, 1.07; 95% CI: 0.56-2.04), while unvaccinated children (OR, 1.69; 95% CI: 0.96-2.98) and overall those vaccinated with PCV7 (OR, 3.64; 95% CI: 2.15-6.17) maintained an increased risk of PPE.

CONCLUSION

The nonsystematic introduction of PCV7 was followed by an increased incidence of PPE. The subsequent introduction of PCV13 was associated with a return to the incidence level in the prevaccine period, mainly in children vaccinated with PCV13.

Trends in Pediatric Complicated Pneumonia in an Ontario Local Health Integration Network

Following the introduction of 7-valent pneumococcal vaccine (PCV7), while overall rates of invasive pneumococcal disease and pneumococcal pneumonia in children declined, rates of empyema increased. We examined changes in the incidence of hospitalization for pediatric complicated pneumonia (PCOMP) in Eastern Ontario, Canada, particularly since the introduction of the 13-valent vaccine (PCV13). A retrospective chart review was carried out evaluating previously healthy children admitted with PCOMP, which included empyema, parapneumonic effusion, necrotizing pneumonia, and lung abscess between 2002 and 2015. Three-hundred seventy-one children were included. Subjects had a median age of four years, and 188/370 (50.8%) required a chest tube. Admission rates changed markedly during this time period. The number of admissions per year rose most sharply between 2009 and 2012, corresponding to the period following introduction of PCV7 and then the occurrence of pandemic influenza A (H1N1). In children who likely received PCV13, the incidence of PCOMP returned to approximately pre-PCV7 levels. In contrast, rates of PCOMP in older children (who would not have received PCV13) remained elevated during the post-PCV13 time period. While rates of PCOMP, particularly in older children, remain elevated following the introduction of PCV13, this might be expected to resolve with more widespread vaccine coverage with PCV13 and herd immunity.

Comparison of sequential multiplex PCR, sequetyping and whole genome sequencing for serotyping of Streptococcus pneumoniae

Streptococcus pneumoniae is one of the major causes of pneumonia, meningitis and other pneumococcal infections in young children and elders. Determination of circulating S. pneumoniae serotypes is an essential service by public health laboratories for the monitoring of putative serotype replacement following the introduction of pneumococcal conjugate vaccines (PCVs) and of the efficacy of the immunization program. The Quellung method remains the gold standard for typing S. pneumoniae. Although this method is very effective, it is also costly, time consuming and not totally reliable due to its subjective nature. The objectives of this study were to test and evaluate the efficiency of 3 different molecular methods compared to the Quellung method. Sequential multiplex PCR, sequetyping and whole genome sequencing (WGS) were chosen and tested using a set of diverse S. pneumoniae. One-hundred and eighteen isolates covering 83 serotypes were subjected to multiplex PCR and sequetyping while 88 isolates covering 53 serotypes were subjected to WGS. Sequential multiplex PCR allowed the identification of a significant proportion (49%) of serotypes at the serogroup or subset level but only 27% were identified at the serotype level. Using WGS, 55% to 60% of isolates were identified at the serotype level depending on the analysis strategy used. Finally, sequetyping demonstrated the lowest performance, with 17% of misidentified serotypes. The use of Jin cpsB database instead of the GenBank database slightly improved results but did not significantly impact the efficiency of sequetyping. Although none of these molecular methods may currently replace the Quellung method, WGS remains the most promising molecular pneumococcal serotyping method.

Development of PCRSeqTyping-a novel molecular assay for typing of Streptococcus pneumoniae

Background

Precise serotyping of pneumococci is essential for vaccine development, to better understand the pathogenicity and trends of drug resistance. Currently used conventional and molecular methods of serotyping are expensive and time-consuming, with limited coverage of serotypes. An accurate and rapid serotyping method with complete coverage of serotypes is an urgent necessity. This study describes the development and application of a novel technology that addresses this need.

Methods

Polymerase chain reaction (PCR) was performed, targeting 1061 bp cpsB region, and the amplicon was subjected to sequencing. The sequence data was analyzed using the National Centre for Biotechnology Information database. For homologous strains, a second round of PCR, sequencing, and data analysis was performed targeting 10 group-specific genes located in the capsular polysaccharide region. Ninety-one pneumococcal reference strains were analyzed with PCRSeqTyping and compared with Quellung reaction using Pneumotest Kit (SSI, Denmark).

Results

A 100% correlation of PCRSeqTyping results was observed with Pneumotest results. Fifty-nine reference strains were uniquely identified in the first step of PCRSeqTyping. The remaining 32 homologous strains out of 91 were also uniquely identified in the second step.

Conclusion

This study describes a PCRSeqTyping assay that is accurate and rapid, with high reproducibility. This assay is amenable for clinical testing and does not require culturing of the samples. It is a significant improvement over other methods because it covers all pneumococcal serotypes, and it has the potential for use in diagnostic laboratories and surveillance studies.

PCR-Based Serotyping of Streptococcus pneumoniae from Culture-Negative Specimens: Novel Primers for Detection of Serotypes within Serogroup 18

Six multiplex-compatible PCR primers were designed to distinguish Streptococcus pneumoniae serotypes within serogroup 18 from culturable/nonculturable pneumococcal specimens, with no cross-reactivity with other serotypes and respiratory organisms. These primers will aid in the generation of better data on vaccine/nonvaccine serotypes in invasive and carriage pneumococcal surveillance and contribute to future vaccine formulation and impact studies.

Direct molecular detection of a broad range of bacterial and viral organisms and Streptococcus pneumoniae vaccine serotypes in children with otitis media with effusion

Background

Otitis media with effusion (OME) causes significant morbidity in children, but the causes of OME and methods for prevention are unclear. To look for potential infectious etiologies, we performed a pilot study using multiple-target real-time polymerase chain reaction (qPCR) for 27 infectious agents, including nine bacterial organisms and 18 respiratory viruses in middle ear fluids (MEFs) from children with OME. QPCR was also performed for the 13 Streptococcus pneumoniae serotypes contained in the current vaccine.

Results

Forty-eight MEF samples were obtained and qPCR detected bacterial nucleic acid (NA) in 39/48 (81 %) and viral NA in 7/48 (15 %). Alloiococcus otitidis and S. pneumoniae were both detected in 15/48 (31 %) MEFs, followed by M. catarrhalis in 14/48 (29 %), H. influenzae in 5/48 (10 %) and M. pneumoniae in 4/48 (8 %). Rhinoviruses were most common virus type detected, found in 4/48 (8 %) MEFs. Serotypes included in the current 13-serotype vaccine were detected in only 3/15 (20 %) S. pneumoniae qPCR-positive MEFs.

Conclusions

Bacteria may play an important role in OME, since over 80 % of MEFs contained bacterial NA. Further research into the role of A. otitidis in OME will be helpful. Serotypes of S. pneumoniae not included in the current 13-serotype vaccine may be involved in OME. Larger studies of OME S. pneumoniae serotypes are needed to help determine which additional serotypes should be included in future vaccine formulations in order to try to prevent OME.

Recent advances in paediatric respiratory medicine

This review highlights important advances in paediatric respiratory medicine since 2014, excluding cystic fibrosis. It focuses mainly on the more common conditions, bronchopulmonary dysplasia, bronchiolitis and preschool wheezing, asthma, pneumonia and sleep, and highlights some of the rarer conditions such as primary ciliary dyskinesia and interstitial lung disease (ILD).