This is the first published study to describe the aetiology of CAP in UK children prior to and following the introduction of the PCV7. The timing of this comprehensive study, 3 years after the introduction of PCV7 and during the first year of PCV13, provides a baseline for future comparative studies of the pneumonia aetiology in the same setting. The causative pathogens identified were predominately viruses in both studies, with the detection of pneumococcal infections increasing from pre-to post-vaccine studies, presumably as a consequence of the application of molecular diagnostic methods.
Previous UK studies investigating the aetiology of pneumonia prior to the introduction of the PCV7 were able to identify the causative pathogens in up to 54% of children [17
]. In addition to blood cultures, blood was tested for S. pneumoniae
using PCR and identified 8% of children with pneumococcal pneumonia [18
]. Another study identified 6% pneumococcal infection using pneumolysin ELISA on blood [19
]. The identification rate of 61% for the likely causative pathogens in the post-vaccine study is similar to that reported by Don
], who used serological assays. However, this is lower than the detection rates of ~80% from studies which used serological and/or molecular approaches [21
], but higher than the rates previously found prior to the introduction of the conjugate vaccine [24
]. The improved detection rate between our two studies appears to be related to the different laboratory approaches used.
While molecular diagnostic methods have improved respiratory virus detection and bacterial detection from normally sterile sites, the interpretation of results can be more problematic when it is applied to nasopharyngeal secretions and other respiratory samples [3
]. Additionally, pneumococcal pneumolysin DNA can be detected in the blood of healthy children colonised with pneumococcus [26
]. The pneumolysin gene can also be detected in non-pneumococcal Viridans-group streptococci, particularly S. pseudopneumoniae
and S. mitis
]. Potential confounders resulting from using a pneumolysin PCR in this study therefore include false positives associated with pneumococcal carriage or cross-reactivity with other Viridans-group streptococci. Given the very low pneumococcal carriage rate in this population (7%), the former is unlikely. Although not well explored, viral carriage is also a clinical possibility, leading to positive PCR results that do not necessarily correlate to the observed pneumonia [27
]. Hence the results of PCR-based approaches can be limited in making a definite diagnosis of causative pathogens in pneumonia.
The rates of pneumococcal infection from the two datasets are lower than in studies in other countries [3
], but are higher than those previously described in the UK [18
]. Improvement of pneumococcal identification with the application of PCR when compared to culture alone is consistent with previous studies [9
]. This is similar to the reported increase in a recent Italian study (from 3.8% to 15.4%) [8
]. It is interesting that despite the overall decrease in the incidence and hospitalisation of pneumonia since the introduction of PCV7 [31
], the rates of pneumococcal infection were comparable between the two studies. Replacement with non-PCV7 serotypes causing invasive pneumococcal disease is well recognised [33
], and this may explain our findings in the face of reduction in disease incidence. Where pneumococcal serotyping was possible, with the majority being identified from pleural fluids, all serotypes recovered were non-PCV7 but included in PCV13. This is similar to data from the USA on children with empyema, where 98% were non-PCV7 serotypes and primarily similar to the serotypes in our study [34
]. Despite the lack of comprehensive serotype data, this suggests that PCV13 could substantially reduce invasive pneumococcal disease [35
Serological evidence of Mycoplasma
infection was detected in 12.5% and 9.9% of children in the pre- and post-vaccination studies, respectively, rates that are similar to the published literature [19
]. M. pneumoniae
is traditionally considered a pathogen of older children, and in these studies was identified more frequently in those >5 years of age. No other serological evidence of other “atypical” organisms was identified, although this may have been as a consequence of the lack of convalescent sera. S. aureus
and group A streptococcal infections were often associated with severe pneumonia and empyema [37
]. In keeping with previous findings, group A Streptococcus
can be found in up to 7% of children with pneumonia, compared to 7% and 10.5%, respectively, in the pre- and post-vaccination datasets [19
]. With the introduction of PCV and decrease in pneumococcal pneumonia it is possible that the relative proportion of bacteria such as group A Streptococcus
and S. aureus, as well as M. pneumoniae
causing severe pneumonia will increase.
Viruses, either alone or as co-pathogens, were detected in 25% and 43% of children in the pre- and post-vaccine studies, respectively, with RSV being the most commonly detected pathogen, as previously reported [3
]. This was followed by rhinovirus, influenza and adenovirus at ~7% each, similar to data previously described for the same region [19
]. Diagnosis of viral infection was achieved mainly through the testing of respiratory secretions rather than by serology, which was only positive in seven children with influenza A virus. The improvement in the detection of viruses in the post-vaccine study was mainly achieved by the application of PCR assays for respiratory viral screening. Most of the viruses detected were identified in those aged <5 years, consistent with other studies [2
]. In the post-vaccine study, viral screening was expanded to include eight viruses with their subgroups, including pandemic H1N1, and to delineate their contribution in causing CAP in children in the UK. Considering the timing of the second recruitment period, pandemic influenza A H1N1 as a single pathogen was not implicated in many cases of pneumonia. The low isolation rates of bocavirus, coronavirus and hMPV highlight the minimal contribution of these viruses to the aetiology of pneumonia in children in the UK. The rates of mixed viral–bacterial infection were variable between the two studies and likely to be dependent on the screening methods used to identify the causative pathogens [3
There are several limitations to our data, such as potential seasonal bias to the data of the post-vaccine study in which recruitment was carried out over 18 months which included two winter seasons (48% of enrolled children). Although the post-vaccine study covered two winter seasons, the numbers of children enrolled were fewer than in the pre-vaccine study, which could be a true reflection of decreased disease incidence and hospitalisation. The findings from the post-vaccine study may have been hampered by the lack of convalescent sera, which may have led to the underestimation of the role of atypical bacteria in paediatric pneumonia, but this effect is probably minimal as Mycoplasma infection was only detected in three children by paired serum samples in the pre-vaccine study. Lack of serotype data of the identified pneumococci from the pre-vaccine study limits the true comparison with the serotype profile after the implementation of the conjugate vaccine. Another limitation is the variation between the two studies in the diagnostic methods used and the pathogens investigated, which makes the interpretation of comparative findings guarded. The significant improvement in pathogen identification by the application of more PCR assays adds further evidence to the importance of using these techniques to monitor changes in the epidemiology of paediatric CAP and pneumococcal serotype replacement.
In conclusion, although viruses are the most common cause of pneumonia, around a fifth of children had bacterial infections. The combined use of culture, serology and PCR-based diagnostic tests significantly improved the identification of causative pathogens in paediatric CAP. Replacement of PCV7 with PCV13 was likely to be associated with as significant a reduction in pneumococcal disease as non-PCV7, but PCV13 serotypes predominated. This requires continued surveillance to monitor for the emergence of serotype replacement.