Pleural fluid nucleic acid testing enhances pneumococcal surveillance in children

Assessing the impact of the 13 valent pneumococcal vaccine on childhood empyema in Australia

BACKGROUND

Empyema is a serious complication of pneumonia frequently caused by Streptococcus pneumoniae (SP). We assessed the impact of the 13-valent pneumococcal conjugate vaccine (13vPCV) on childhood pneumonia and empyema after inclusion in the Australian National Immunisation Program.

METHODS

For bacterial pneumonia and empyema hospitalisations, we ascertained incidence rates (IRs) using the National Hospital Morbidity Database International Statistical Classification of Disease discharge codes and relevant population denominators, and calculated incidence rate ratios (IRR) comparing the 13vPCV period (June 2012-May 2017) with the 7vPCV period (June 2007-May 2011). Blood and pleural fluid (PF) cultures and PF PCR of 401 children with empyema from 11 Australian hospitals during the 13vPCV period were compared with our previous study in the 7vPCV period.

FINDINGS

Across 7vPCV and 13vPCV periods, IRs per million children (95% CIs) were 1605 (1588 to 1621) and 1272 (1259 to 1285) for bacterial pneumonia, and 14.23 (12.67 to 15.79) and 17.89 (16.37 to 19.42) for empyema hospitalisations. IRRs were 0.79 (0.78 to 0.80) for bacterial pneumonia and 1.25 (1.09 to 1.44) for empyema. Of 161 empyema cases with SP serotypes, 147 (91.3%) were vaccine types. ST3 accounted for 76.4% of identified serotypes in the 13vPCV period, more than double than the 7vPCV period (p<0.001); ST19A decreased from 36.4% to 12.4%. No cases of ST1 empyema were identified in the 13vPCV period versus 14.5% in the 7vPCV period.

INTERPRETATION

13vPCV resulted in a significant reduction in all-cause hospitalisations for bacterial pneumonia but empyema hospitalisations significantly increased, with emergence of pneumococcal ST3 as the dominant serotype in empyema.

TRIAL REGISTRATION NUMBER

Australian and New Zealand Clinical Trial Registry ACTRN 12614000354684.

Pleural infection: past, present, and future directions

Pleural space infections are increasing in incidence and continue to have high associated morbidity, mortality, and need for invasive treatments such as thoracic surgery. The mechanisms of progression from a non-infected, pneumonia-related effusion to a confirmed pleural infection have been well described in the scientific literature, but the route by which pathogenic organisms access the pleural space is poorly understood. Data suggests that not all pleural infections can be related to lung parenchymal infection. Studies examining the microbiological profile of pleural infection inform antibiotic choice and can help to delineate the source and pathogenesis of infection. The development of radiological methods and use of clinical indices to predict which patients with pleural infection will have a poor outcome, as well as inform patient selection for more invasive treatments, is particularly important. Randomised clinical trial and case series data have shown that the combination of an intrapleural tissue plasminogen activator and deoxyribonuclease therapy can potentially improve outcomes, but the use of this treatment as compared with surgical options has not been precisely defined, particularly in terms of when and in which patients it should be used.

How recent advances in molecular tests could impact the diagnosis of pneumonia

Molecular diagnostic tests have been the single major development in pneumonia diagnostics over recent years. Nucleic acid detection tests (NATs) have greatly improved the ability to detect respiratory viruses and bacterial pathogens that do not normally colonize the respiratory tract. In contrast, NATs do not yet have an established role for diagnosing pneumonia caused by bacteria that commonly colonize the nasopharynx due to difficulties discriminating between pathogens and coincidental carriage strains. New approaches are needed to distinguish infection from colonization, such as through use of quantitative methods and identification of discriminating cut-off levels. The recent realization that the lung microbiome exists has provided new insights into the pathogenesis of pneumonia involving the interaction between multiple microorganisms. New developments in molecular diagnostics must account for this new paradigm.

Pneumococcal Capsules and Their Types: Past, Present, and Future

Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Its virulence is largely due to its polysaccharide capsule, which shields it from the host immune system, and because of this, the capsule has been extensively studied. Studies of the capsule led to the identification of DNA as the genetic material, identification of many different capsular serotypes, and identification of the serotype-specific nature of protection by adaptive immunity. Recent studies have led to the determination of capsular polysaccharide structures for many serotypes using advanced analytical technologies, complete elucidation of genetic basis for the capsular types, and the development of highly effective pneumococcal conjugate vaccines. Conjugate vaccine use has altered the serotype distribution by either serotype replacement or switching, and this has increased the need to serotype pneumococci. Due to great advances in molecular technologies and our understanding of the pneumococcal genome, molecular approaches have become powerful tools to predict pneumococcal serotypes. In addition, more-precise and -efficient serotyping methods that directly detect polysaccharide structures are emerging. These improvements in our capabilities will greatly enhance future investigations of pneumococcal epidemiology and diseases and the biology of colonization and innate immunity to pneumococcal capsules.

Etiology and Incidence of Pleural Empyema in South African Children

BACKGROUND

South Africa introduced the 7-valent pneumococcal conjugate vaccine (PCV7) in 2009 and PCV13 in 2011. The etiology and incidence of childhood empyema in an 8-year period overlapping the introduction of PCV was investigated.

METHODS

Children younger than 12 years admitted with empyema at a tertiary pediatric hospital in Cape Town, South Africa, from December 2006 to December 2011 (cohort A) and January 2012 to December 2014 (cohort B) were investigated. Pathogens were identified by culture of pleural fluid and blood. In addition, polymerase chain reaction targeting bacterial pathogens and Streptococcus pneumoniae serotypes was conducted on pleural fluid in a subset of patients enrolled 2009-2011.

RESULTS

Cohort A: 142 children were prospectively enrolled, with a median age of 17 months (interquartile range 8-43). Most (92%) children were unimmunized with PCV. S. pneumoniae and Staphylococcus aureus were the most common culture-identified pathogens (each 25 of 142; 18%); polymerase chain reaction of pleural fluid increased yield of S. pneumoniae detection by 31% [26 of 54 (48%) vs. 9 of 54 (17%), P < 0.001]. Serotypes were identified for 24 of 26 (92%) patients with S. pneumoniae, of which 22 of 24 (92%) were included in PCV13. Cohort B: 22 patients were retrospectively identified. No pathogen was found in 12 of 22 (54.5%) patients and S. pneumoniae in 1 patient (4.5%). Empyema incidence declined by 50% in cohort B compared with that of cohort A (4.2 vs. 10.4 cases per 1000 pneumonia admissions; risk ratio: 0.5; 95% confidence incidence: 0.3-0.7).

CONCLUSION

S. pneumoniae is the commonest cause of childhood empyema in South Africa. PCV has been highly effective at reducing empyema incidence in South African children.

Clinical outcome of parapneumonic empyema in children treated according to a standardized medical treatment

Treatment of parapneumonic empyema (PE) consists of intravenous antibiotics and, in case of large effusions and persisting fever, pleural chest drain (±intrapleural fibrinolytics) or video-assisted surgical intervention. We standardized the treatment for PE in our tertiary care center choosing a first-step nonsurgical approach. The aim was to evaluate the need for surgery and to collect data on disease course, outcome, and microbiology. For all children treated for PE between 2006 and 2013, data were prospectively collected concerning treatment, length of stay, duration of fever, complications, and causative agent. Of 132 children treated for PE, 20 % needed surgical intervention. Analyzed per year, the need for surgery decreased from almost 40 % in 2007 to 0 % in 2010 again increasing to 40 % although this did not reach statistical significance (p = 0.115). Median duration of "in-hospital fever" was 5 days (IQR, 3-8). The duration of fever correlated with pleural LDH (r = 0.324; p = 0.002) and pleural glucose (r = -0.248; p = 0.021) and was inversely correlated with pleural pH (r = -0.249; p = 0.046). Based on pleural PCR data, 85 % of PE were caused by Streptococcus pneumoniae (40 % serotype 1).

CONCLUSION

After introduction of a standardized primary medical approach (chest drain ± fibrinolysis) for PE in our institution, the need for surgical rescue interventions overall remained at 20 %, which is higher than in some other reports. Difference in microbiology or disease severity could not be proven.

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

Background

To determine the serotypes of Streptococcus pneumoniae responsible for pneumonia complicated by parapneumonic effusion in children, we performed real-time PCR based pneumococcal “serotyping” directly on parapneumonic fluid samples.

Methods

Specimens were collected at two children’s hospitals in Ontario, Canada from 2009 to 2011. Samples in which S. pneumoniae was detected by PCR were tested with serotype-specific 5′exonuclease PCR assays for the 13 serotypes contained in the 13-serotype pneumococcal vaccine.

Results

Thirty-five S. pneumoniae PCR-positive pleural samples were studied. Pneumococcal serotyping PCR assays were positive for 34 of 35 (97%). Serotype 3 was detected most frequently, in 19/35 (54%), followed by serotype 19A in 9/35 (26%), serotype 7 F/A in 4/35 (11%), serotype 1 in 1/35 (3%), and serotype 6A also in 1/35 (3%).

Conclusions

PCR testing demonstrated that the vast majority (97%) of S. pneumoniae parapneumonic effusions were caused by serotypes present in the 13-serotype vaccine that were not present in the original 7 serotype vaccine. This suggests that use of the 13-serotype vaccine could potentially prevent many S. pneumoniae pneumonias complicated by parapneumonic effusion in our region, provided serotype replacement does not occur.

Pneumococcal empyema and complicated pneumonias: global trends in incidence, prevalence, and serotype epidemiology

This review evaluates the serotype epidemiology of complicated pneumococcal pneumonia (CPP) during the period 1990–2012. PubMed and EMBASE were searched using the terms “empyema”, “complicated pneumonia”, “pleural infection”, “necrotizing pneumonia”, “pleural effusion”, “parapneumonic effusion”, “pneumatocele”, or “lung abscess”; “pneumococcal” or “Streptococcus pneumoniae”; and “serotype” for studies on the epidemiology of complicated pneumonias published from January 1, 1990 to October 1, 2013. Studies with data on incidence and serotypes were included; reviews, case reports, and conference abstracts were excluded. Of 152 papers, 84 fitted the inclusion criteria. A few pneumococcal serotypes were predominant causes of CPP, particularly serotypes 1, 19A, 3, 14, and 7F. CPP was a more common manifestation of pneumococcal disease among older (>2 years old) than younger children. The data support increases in both reported incidence rates and proportions of CPP in children and adults during the period 1990–2012; specific increases varied by geographic region. The proportions of serotype 3 and, particularly in Asia, serotype 19A CPP have increased, whereas most studies show declines in serotype 14. Serotype 1 has been a predominant cause of CPP since 1990, while antibiotic resistance was infrequent among serotype 1 isolates. The reported incidence and proportions of CPP among pneumonia cases steadily increased from 1990 to 2012. Several factors might account for these increases, including enhanced disease detection due to a higher index of suspicion, more sophisticated diagnostic assays, and changes in the prevalence of serotypes with capacity to invade the pleural space that were not targeted by the 7-valent pneumococcal conjugate vaccine (PCV7).

Aetiology of paediatric pneumonia after the introduction of pneumococcal conjugate vaccine

We describe the aetiology of community-acquired pneumonia in children before and after the introduction of the pneumococcal conjugate vaccination (PCV) programme in 2006.

Prospective studies were conducted in 2001–2002 (pre-vaccine) and 2009–2011 (post-vaccine) of children aged 0–16 years with radiologically confirmed pneumonia seen in hospital. Investigations included culture, serology, immunofluorescence antibody and urine antigen testing, with an increased use of PCR assays and expanded panels of pathogens in the post-vaccine study.

241 and 160 children were enrolled in the pre- and post-vaccine studies, respectively (73% aged <5 years). Identification of a causative pathogen was higher post-vaccination (61%) than pre-vaccination (48.5%) (p=0.019). Rates of bacterial infections were not different between post- and pre-vaccine studies (17.5% versus 24%, p=0.258). Viral (31%) and mixed (12.5%) infections were found more often post-vaccination (19.5%, p=0.021) than pre-vaccination (5%, p=0.015). Rates of identified pneumococcal infections were comparable between pre- and post-vaccine studies (14.7% versus 17.4%, p=0.557). Diagnosis of pneumococcal infection post-vaccination improved when PCR was used compared to culture (21.6% versus 6%, p=0.0004). Serotypes included in PCV13 but not PCV7 were identified in 75% (18 out of 24) post-vaccination.

Infection with nonvaccine pneumococcal serotypes continues to be a significant cause of pneumonia in children in the UK.

Aetiology of community-acquired pneumonia in children following a pneumococcal conjugate vaccination programmehttp://ow.ly/p9Wub

Pneumococcal diagnosis and serotypes in childhood community-acquired pneumonia

The 7-valent pneumococcal conjugate vaccine (PCV7) was introduced routinely in the UK from September 2006 and replaced by PCV13 in 2010. In a prospective study from 2009 to 2011 of 160 children aged ≤16 years with radiologically confirmed pneumonia, likely pneumococcal infections were identified in 26%. Detection of pneumococci was improved with polymerase chain reaction compared to culture (21.6% versus 6% of children tested, P = 0.0004). Where serotyping was possible, all (n = 23) were non-PCV7 but PCV13 serotypes; 1 (43.5%), 3 (21.7%), 7A/F, and 19A (17.4% each).

Increased paediatric hospitalizations for empyema in Australia after introduction of the 7-valent pneumococcal conjugate vaccine

OBJECTIVE

To examine rates of paediatric hospitalization for empyema and pneumonia in Australia before and after the introduction of the seven-valent pneumococcal conjugate vaccine (PCV7).

METHODS

Rates of paediatric hospitalization for empyema and pneumonia (bacterial, viral and all types) were calculated following the codes of the International Classification of Diseases, tenth revision (ICD-10) as a principal diagnosis. The expected number of hospitalizations after the PCV7 was introduced was estimated on the basis of the observed number of hospitalizations before the introduction of the PCV7. Incidence rate differences (IRDs) and incidence rate ratios (IRRs) were calculated. Hospitalization incidence in each study period was expressed as the number of hospitalizations per million (10(6)) person-years. The population of children aged 0-19 years in Australia from 1998 to 2004 and from 2005 to 2010, as reported by the Australian Bureau of Statistics, was used to calculate the number of person-years in each period.

FINDINGS

In the 5 years following the introduction of the PCV7, hospitalizations for pneumonia were fewer than expected (15 304 fewer; 95% confidence interval, CI: 14 646-15 960; IRD: -552 per 10(6) person-years; 95% CI: -576 to -529 per 10(6) person-years; IRR: 0.78; 95% CI: 0.77-0.78). Hospitalizations for empyema, on the other hand, were more than expected (83 more; 95% CI: 37-128; IRD: 3 per 10(6) person-years; 95% CI: 1-5 per 10(6) person-years; IRR: 1.35; 95% CI: 1.14-1.59). Reductions in hospitalizations were observed for all ICD-10 pneumonia codes across all age groups. The increase in empyema hospitalizations was only significant among children aged 1 to 4 years.

CONCLUSION

The introduction of the PCV7 in Australia was associated with a substantial decrease in hospitalizations for childhood pneumonia and a small increase in hospitalizations for empyema.