Tag Archives: Bacteria


SIGN/BTS pneumonia guideline revised 2011 – microbiology bit more subtle now: yes, anything between 1/3 and 2/3 are viral, particularly under 2 years, and probably a third are mixed, but you still get pneumococcus and mycoplasma in infants.


Strep pneumoniae (Pneumococcus) is the most common bacterial cause of pneumonia in childhood.

Pneumococcus causes about one-third of radiologically confirmed pneumonia in children aged <2 years.

PCV7 has dramatically decreased IPD due to vaccine serotypes in the UK, but a steady increase in vaccine serotype replacement is evident in the UK.

Group A streptococci and S aureus disease are more likely than pneumococcal to progress to ICU or empyema.

Overall, viruses account for 30-67% of CAP (community acquired pneumonia) cases in childhood and are more frequently identified in children aged <1 year than in those aged >2 years.

1/3 of cases of CAP (8-40%) represent a mixed infection.

Mycoplasma is not unusual in children aged 1-5 years.

Age is a good predictor of the likely pathogens:

  • Viruses alone are found as a cause in younger children in up to 50%.
  • In older children, when a bacterial cause is found, it is most commonly S pneumoniae followed by mycoplasma and chlamydial pneumonia

Wheeze used to be seen as excluding pneumonia, but now only comment is that it can be one of the clinical features of pneumonia, none of which is very specific.  Bacterial pneumonia should be considered in children when there is:

  • persistent or repetitive fever >38.5C, together with chest recession and a raised respiratory rate. [D].

Clinical presentation

Wheeze and chest pain can be symptoms of pneumonia. But none of the symptoms of pneumonia are very specific for pneumonia.

In children over 3yrs, history of difficulty breathing is an additional valuable symptom.

Consider bacterial pneumonia if recurrent/persistent fever >38.5 together with recession and tachypnoea.

  • Re-consultation (in the community) for persistent fever can suggest pneumonia
  • Reassess if pneumonia symptoms do not respond to treatment
  • Refer to hospital if sats <92%
  • Absent breath sounds with dull percussion suggest effusion, refer to hospital
  • Children with pneumonia in hospital should be reassessed if fever persists 48hr after starting treatment, or if there is increased work of breathing or agitation/distress
  • Microbiogical investigations for pneumonia include blood culture, NPA for PCR/IF, serology for resp viruses, Mycoplasma, Chlamydia, pleural fluid C+S/Pneumococcal antigen/PCR.


CXR not useful in mild cases, certainly not necessary if admission not being considered. I would consider if hypoxia was disproportionate to degree of breathlessness (suggests collapse), suspicion of effusion (stony dullness on percussion) or pneumothorax.

CXR is not useful in establishing viral vs bacterial vs atypical aetiology!

Repeat CXR in convalescence is only required for persisting symptoms, lobar collapse or round pneumonia.

CRP etc not useful in establishing viral vs bacterial vs atypical aetiology!

Microbiological investigation not necessary routinely, but important if complications or ICU needed.


Under 2yrs, mild lower resp tract symptoms are not usually due to pneumonia (esp if pneumococcal immunized) so do not need to be given antibiotics – but review if symptoms persist.

No longer age related antibiotic cut offs.

Amoxicillin is first choice, macrolide is an alternative (as is co-amox).  Macrolide should be added if poor response or if severe (D level recommendations though).

In influenza pneumonia (higher rate of staph), co-amoxiclav is recommended [D].  Similarly for measles.

Oral antibiotics equivalent to IV (if tolerated) even in severe disease (PIVOT trial, Nottingham).  But IV for complicated or signs of septicaemia.  Recommended IV antibiotics include amoxicillin, co-amoxiclav, cefuroxime, cefotaxime, ceftriaxone. Rationalize as able, change to oral when clear evidence of improvement.

CAP-IT trial

2021 trial in UK & Ireland – excluded under 6 months and under 6kg or severe underlying chronic condition. Excluded anybody already treated with beta lactam antibiotics for 48+ hrs or any other antibiotic for any duration.

Twice daily amoxicillin 35-50mg/kg/d for 3 days was equivalent to higher doses for 7 days. Longer course had 2 days less cough. [JAMA 2021]

Susan Lipsett et al from Boston suggest that most of these kids would probably have improved without antibiotics anyway – they discharged 80% of kids who fulfilled CAP-IT criteria but who had normal x-rays without antibiotics (!) and only 2% came back! [JAMA Open 2024]


Strongly against NG tubes in severely ill esp infants.  Use smallest nostril if cannot be avoided

Use oxygen if sats <=92%

Monitor bloods daily if on IV fluids

Chest physio is NOT beneficial – at least, not routinely, potentially if focal collapse identified and slow to come out of oxygen.

If going home, advice on managing fever, preventing dehydration, identifying deterioration.

Follow up severe pneumonia, empyema and lung abscess until recovered completely and CXR near normal.


Whooping cough, caused by Bordetella pertussis. B parapertussis can cause similar illness but usually less severe. B. holmesii also seen.

Classically, Catarrhal phase (mild fever, productive cough, no pharyngitis) then Paroxysmal (coughing fits, often associated with vomiting, followed by characteristic inspiratory “whoop”) then Convalescent – persistent cough, traditionally 4-12 weeks (100 days)! Fever is rare, and in fact patients can often look relatively well between paroxysms, with clear chest and no respiratory signs. Young infants may present with apnoea rather than whooping.

Post tussive vomiting is pretty specific in adults, but only 66% in children.

Adult disease presents in its mild form as disturbed sleep, sweating, sinusitis or otitis, protracted cough so not usually diagnosed. Cough associated with choking is characteristic, whereas sweating is not very sensitive or specific. Cough is non-productive (although there may be a sensation of retained secretions – question carefully!).

But probably underdiagnosed, esp where symptoms are chronic but mild, or in the third of cases where symptoms last less than 3 weeks.

In UK children aged 5-15 with persistent cough (ie over 14/7, in many cases severe) identified in primary care, at least 20% had evidence of recent infection with Bordetella pertussis,  (doi:10.1136/bmj.g3668) Hence reported incidence depends on quality of surveillance rather than actual prevalence! Probably the same everywhere, with peaks every 2-5 yrs.

The reason for the chronic, persistent cough is still not clear (many infections cause similar ciliary disruption, and don’t cause such chronic symptoms).

In 2012, national outbreak declared in UK on basis of higher than usual prevalence.  New vaccination in pregnancy campaign, still on going.  Cause uncertain: more sensitive diagnostic methods?  Enhanced awareness and reporting?  Less enduring protection after immunization with acellular vaccines (cf whole cell vaccines)? Mismatch between antigens in acellular vaccines and circulating strains of B pertussis? Although the largest increase in reported incidence seems to be in adolescents, children aged <3 months are at highest risk of serious morbidity and mortality from pertussis.


  • Rarely encephalopathy, including seizures. Probably a direct toxin effect, plus hypoxia during paroxysms.
  • Hernias and rectal prolapse.
  • Secondary pneumonia is not uncommon, so if chest signs are present consider antibiotic treatment to cover other organisms.
  • Pneumothorax, aspiration, rib fractures in elderly
  • Sinusitis, otitis


Although part of universal immunization schedule, immunity (from immunization or exposure) is pretty short lived viz 2-5yrs, so in vaccinated areas severe disease seen either pre-immunization ie young babies, or adolescent/adults after immunity has worn off. Most cases in unvaccinated infants are contracted from a family member, usually the mother. In low coverage areas burden of disease is in 5 yr olds, because of regular exposure through life. Currently programme vaccinating pregnant women – appears to be safe.  Another strategy by which susceptible infants can be protected—cocooning—involves immunizing all close contacts of the infant, not just the mum.  Both approaches have been shown to be cost effective, the US does both.  Other countries boost teenagers.  Better vaccines would be nice! WHO recommends that countries still using whole cell vaccines continue to do so unless they can schedule boosters. See Vaccines.



  • Lymphocytosis can be spectacular but not sensitive. Due to Pertussis toxin, as used in vaccine, which is specific to B pertussis but probably not that important for pathogenesis cf tracheal cytotoxin etc. Hence not seen post immunization (ie adults), in parapertussis, or in neonates (transplacental antibodies).
  • Culture from pernasal swab is not fantastically sensitive but is useful for genetic studies. False negatives mostly due to sampling late in course of disease.
  • PCR more sensitive than culture but false positives common (as usual with PCR).
  • Numerous different ELISA tests � be suspicious of any that are qualitative (pos/neg) rather than quantitative. IgG based are good, whole cell tend to be poor. Mouth swab test available.
  • Serology is of limited use for infants (transfer of maternal IgG), but you can always test the parents (Mum may have stored serum from pregnancy).


Asthma!  Cystic fibrosis.

Mycoplasma and adenovirus can cause chronic cough.


48 hour isolation, 7/7 erythromycin or clarithro, 3/7 azithro. Clarithromycin preferred in neonates, given association with pyloric stenosis (may also be a risk with azithro).  Co-trimoxazole as second line.  Makes little difference to clinical course, but does help reduce transmission. Treat within 3-4 weeks of start of illness. Azithromycin  is as effective as erythromycin, gastrointestinal adverse events are much less, and compliance in general was markedly better [Pediatrics. 2004 Jul;114(1):e96-101 – pmid:15231980].

Still need full immunization course as natural disease does not confer long lasting immunity.


Where vulnerable individuals eg unimmunized infants, asthmatics are exposed to a likely case, there is an argument for giving prophylactic erythromycin to all close contacts. See Health Protection Agency advice. Journal of Public Health Medicine 2002;24(3):200-206.