The value and complications of percutaneous transthoracic lung aspiration for the etiologic diagnosis of community-acquired pneumonia

Aetiology of lobar pneumonia determined by multiplex molecular analyses of lung and pleural aspirate specimens in the Gambia: findings from population-based pneumonia surveillance

OBJECTIVES

To determine the causes of lobar pneumonia in rural Gambia.

DESIGN AND SETTING

Population-based pneumonia surveillance at seven peripheral health facilities and two regional hospitals in rural Gambia. 7-valent pneumococcal conjugate vaccine (PCV7) was introduced routinely in August 2009 and replaced by PCV13 from May 2011.

METHODS

Prospective pneumonia surveillance was undertaken among all ages with referral of suspected pneumonia cases to the regional hospitals. Blood culture and chest radiographs were performed routinely while lung or pleural aspirates were collected from selected, clinically stable patients with pleural effusion on radiograph and/or large, dense, peripheral consolidation. We used conventional microbiology, and from 8 April 2011 to 17 July 2012, used a multiplex PCR assay on lung and pleural aspirates. We calculated proportions with pathogens, associations between coinfecting pathogens and PCV effectiveness.

PARTICIPANTS

2550 patients were admitted with clinical pneumonia; 741 with lobar pneumonia or pleural effusion. We performed 181 lung or pleural aspirates and multiplex PCR on 156 lung and 4 pleural aspirates.

RESULTS

Pathogens were detected in 116/160 specimens, the most common being Streptococcus pneumoniae(n=68), Staphylococcus aureus (n=26) and Haemophilus influenzae type b (n=11). Bacteria (n=97) were more common than viruses (n=49). Common viruses were bocavirus (n=11) and influenza (n=11). Coinfections were frequent (n=55). Moraxella catarrhalis was detected in eight patients and in every case there was coinfection with S. pneumoniae. The odds ratio of vaccine-type pneumococcal pneumonia in patients with two or three compared with zero doses of PCV was 0.17 (95% CI 0.06 to 0.51).

CONCLUSIONS

Lobar pneumonia in rural Gambia was caused primarily by bacteria, particularly S. pneumoniae and S. aureus. Coinfection was common and M. catarrhalis always coinfected with S. pneumoniae. PCV was highly efficacious against vaccine-type pneumococcal pneumonia.

A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease

The demographics and comorbidities of patients with community acquired pneumonia (CAP) vary enormously but stratified treatment is difficult because aetiological studies have failed to comprehensively identify the pathogens. Our aim was to describe the bacterial microbiota of CAP and relate these to clinical characteristics in order to inform future trials of treatment stratified by co-morbidity. CAP patients were prospectively recruited at two UK hospitals. We used 16S rRNA gene sequencing to identify the dominant bacteria in sputum and compositional data analysis to determine associations with patient characteristics. We analysed sputum samples from 77 patients and found a Streptococcus sp. and a Haemophilus sp. were the most relatively abundant pathogens. The Haemophilus sp. was more likely to be dominant in patients with pre-existing lung disease, and its relative abundance was associated with qPCR levels of Haemophilus influenzae. The most abundant Streptococcus sp. was associated with qPCR levels of Streptococcus pneumoniae but dominance could not be predicted from clinical characteristics. These data suggest chronic lung disease influences the microbiota of sputum in patients with CAP. This finding could inform a trial of stratifying empirical CAP antibiotics to target Haemophilus spp. in addition to Streptococcus spp. in those with chronic lung disease.

Triptych of the Hermit Saints: pneumococcal polysaccharide vaccines for the elderly

Pneumococcal pneumonia is a serious disease with considerable morbidity and mortality in the elderly. Despite adequate antibiotic treatment, the long-term mortality of pneumococcal pneumonia remains high. Preventive measures in the form of vaccination, therefore, are warranted. Twenty-three-valent polysaccharide vaccines have a broad coverage but limited efficacy. Pneumococcal conjugate vaccines have been shown in children to be able to prevent invasive and mucosal pneumococcal diseases. It should be realized that the serotype composition of current pneumococcal conjugate vaccines is not tailored for the elderly, and that replacement disease can occur. Yet, the current 13-valent conjugate vaccine has been shown to protect against infections with vaccine serotypes. Long-term mortality of pneumococcal pneumonia should be included in policy making about the introduction of these vaccines for the elderly.

Pneumonia

Pneumonia is an important cause of morbidity and mortality globally. It is the leading cause of death in infants and young children with the majority of these deaths occurring in low income countries. Risk factors affecting incidence and outcome include extremes of age, poor nutrition, immunosuppression, environmental exposures and socioeconomic determinants. Pneumonia can be caused by a wide range of pathogens including bacteria, viruses and fungi, and the etiology varies by epidemiological setting, comorbidities and whether the pneumonia is community-acquired or hospital-acquired. Streptococcus pneumoniae is the major cause of community-acquired bacterial pneumonia while Gram negative bacteria, often resistant to multiple antibiotics, are common causes of hospital-acquired pneumonia and pneumonia in immunosuppressed individuals. Diagnosis is generally clinical and management is based mainly on knowledge of likely causative pathogens as well as clinical severity and presence of known risk factors. Timely and effective antibiotic treatment and oxygen therapy if hypoxemic are critical to patient outcomes. Preventive measures range from improved nutrition and hygiene to specific vaccines that target common causes in children and adults such as the pneumococcal or influenza vaccines.

A review of economic evaluations of 13-valent pneumococcal conjugate vaccine (PCV13) in adults and the elderly

The 13-valent pneumococcal conjugated vaccine (PCV13) is already recommended for some adult groups and is being considered for wider use in many countries. In order to identify the strengths and limitations of the existing economic evaluation studies of PCV13 in adults and the elderly a literature review was conducted. The majority of the studies identified (9 out of 10) found that PCV13 was cost-effective in adults and/or the elderly. However, these results were based on assumptions that could not always be informed by robust evidence. Key uncertainties included the efficacy of PCV13 against non-invasive pneumonia and the herd immunity effect of childhood vaccination programs. Emerging trial evidence on PCV13 in adults from the Netherlands offers the ability to parameterize future economic evaluations with empirical efficacy data. However, it is important that these estimates are used thoughtfully when they are transferred to other settings.

A review of the role of Haemophilus influenzae in community-acquired pneumonia

In an era when Haemophilus influenzae type b (Hib) conjugate vaccine is widely used, the incidence of Hib as a cause of community-acquired pneumonia (CAP) has dramatcally declined. Non-typeable H. influenzae (NTHi) strains and, occasionally, other encapsulated serotypes of H. influenzae are now the cause of the majority of invasive H. influenzae infectons, including bacteraemic CAP. NTHi have long been recognised as an important cause of lower respiratory tract infecton, including pneumonia, in adults, especially those with underlying diseases. The role of NTHi as a cause of non-bacteraemic CAP in children is less clear. In this review the evidence for the role of NTHi and capsulated strains of H. influenzae will be examined.

Epidemiology, etiology, x-ray features, importance of co-infections and clinical features of viral pneumonia in developing countries

Pneumonia is still the number one killer of young children globally, accounting for 18% of mortality in children under 5 years of age. An estimated 120 million new cases of pneumonia occur globally each year. In developing countries, management and prevention efforts against pneumonia have traditionally focused on bacterial pathogens. More recently however, viral pathogens have gained attention as a result of improved diagnostic methods, such as polymerase chain reaction, outbreaks of severe disease caused by emerging pathogens, discovery of new respiratory viruses as well as the decrease in bacterial pneumonia as a consequence of the introduction of highly effective conjugate vaccines. Although the epidemiology, etiology and clinical characterization of viral infections are being studied extensively in the developed world, little data are available from low- and middle-income countries. In this paper, we review the epidemiology, etiology, clinical and radiological features of viral pneumonia in developing countries.

[Which samples to obtain in the emergency department for the microbiological diagnosis of community-acquired pneumonia in the immunocompetent patient?]

Current diagnostic methods allow microbial identification in 50% of patients admitted with severe community-acquired pneumonia (CAP). Guidelines derived from epidemiological data help physicians to start empirical antimicrobial therapy. Definitive microbial diagnosis is useful to guide further pathogen-directed therapy. Blood cultures, cultures of respiratory specimens and urine antigen tests are recommended to determine the causative bacterial pathogen. Positive blood cultures range from 15 to 25% of CAP patients according to severity. Whether sputum specimens represent or not lower respiratory secretions determines its accuracy in CAP microbial diagnosis. In intubated patients, endotracheal aspirates are often of interest. Detection of positive pneumococcal or legionella urinary antigen is often associated with CAP severity. The sensitivity of this test is not decreased in patients who have received antibiotics prior to sampling. Viral pneumonia account for 10 to 40% of severe CAP. Nasal swabs are recommended for influenza identification using polymerase chain reaction (PCR) in order to deliver oseltamivir treatment. In the emergency department, atypical pneumonia serology is less useful than respiratory specimens obtained using fiberoptic bronchoscopy. Serum PCR to diagnose bacterial CAP is not superior to the other usual methods.

Role of interventional pulmonology in the management of complicated parapneumonic pleural effusions and empyema

Pleural infection is a major problem that affects 80,000 cases per year in the UK and USA. It is increasing in incidence, and in an ageing population, it presents a complex challenge that requires a combination of medical therapies and may lead to the need for surgery. This article focuses on the role of the interventional pulmonologist in the diagnosis and management of pleural infection. In particular, we examine the role of pleural ultrasound in diagnostics, thoracocentesis and real-time guided procedures, and the current management strategies, including the controversial role of medical thoracoscopy.

Etiology of severe childhood pneumonia in the Gambia, West Africa, determined by conventional and molecular microbiological analyses of lung and pleural aspirate samples

Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcuspneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. Multiple pathogens were detected frequently, notably Haemophilus influenzae (mostly nontypeable) together with S. pneumoniae.

Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study

BACKGROUND

There is emerging evidence for the presence of an extensive microbiota in human lungs. It is not known whether variations in the prevalence of species of microbiota in the lungs may have aetiological significance in respiratory conditions such as asthma. The aim of the study was to undertake semi-quantitative analysis of the differences in fungal species in pooled sputum samples from asthma patients and controls.

METHODS

Induced sputum samples were collected in a case control study of asthma patients and control subjects drawn from the community in Wandsworth, London. Samples from both groups were pooled and then tested for eukaryotes. DNA was amplified using standard PCR techniques, followed by pyrosequencing and comparison of reads to databases of known sequences to determine in a semi-quantitative way the percentage of DNA from known species in each of the two pooled samples.

RESULTS

A total of 136 fungal species were identified in the induced sputum samples, with 90 species more common in asthma patients and 46 species more common in control subjects. Psathyrella candolleana, Malassezia pachydermatis, Termitomyces clypeatus and Grifola sordulenta showed a higher percentage of reads in the sputum of asthma patients and Eremothecium sinecaudum, Systenostrema alba, Cladosporium cladosporioides and Vanderwaltozyma polyspora showed a higher percentage of reads in the sputum of control subjects. A statistically significant difference in the pattern of fungi that were present in the respective samples was demonstrated using the Phylogenetic (P) test (P < 0.0001).

CONCLUSION

This study is novel in providing evidence for the widespread nature of fungi in the sputum of healthy and asthmatic individuals. Differences in the pattern of fungi present in asthma patients and controls merit further investigation. Of particular interest was the presence of Malassezia pachydermatis, which is known to be associated with atopic dermatitis.

The role of postmortem studies in pneumonia etiology research

The diagnosis of etiology in severe pneumonia remains a challenging area. Postmortem lung tissue potentially increases the sensitivity of investigations for identification of causative pathogens in fatal cases of pneumonia and can confirm antemortem microbiological diagnoses. Tissue sampling allows assessment of histological patterns of disease and ancillary immunohistochemical or molecular diagnostic techniques. It may also enhance the recognition of noninfectious conditions that clinically simulate acute pneumonia. Biobanking of lung tissue or postmortem culture isolates offers opportunities for new pathogen discovery and research into host-pathogen interactions. The Pneumonia Etiology Research for Child Health study proposes a percutaneous needle biopsy approach to obtain postmortem samples, rather than a full open autopsy. This has the advantage of greater acceptability to relatives, but risks greater sampling error. Both approaches may be susceptible to microbiological contamination or pathogen degradation. However, previous autopsy studies have confirmed the value of histological examination in revealing unsuspected pathogens and influencing clinical guidelines for the diagnosis and treatment of future pneumonia cases.

Specimen collection for the diagnosis of pediatric pneumonia

Diagnosing the etiologic agent of pneumonia has an essential role in ensuring the most appropriate and effective therapy for individual patients and is critical to guiding the development of treatment and prevention strategies. However, establishing the etiology of pneumonia remains challenging because of the relative inaccessibility of the infected tissue and the difficulty in obtaining samples without contamination by upper respiratory tract secretions. Here, we review the published and unpublished literature on various specimens available for the diagnosis of pediatric pneumonia. We discuss the advantages and limitations of each specimen, and discuss the rationale for the specimens to be collected for the Pneumonia Etiology Research for Child Health study.

PCR improves diagnostic yield from lung aspiration in Malawian children with radiologically confirmed pneumonia

Background

Accurate data on childhood pneumonia aetiology are essential especially from regions where mortality is high, in order to inform case-management guidelines and the potential of prevention strategies such as bacterial conjugate vaccines. Yield from blood culture is low, but lung aspirate culture provides a higher diagnostic yield. We aimed to determine if diagnostic yield could be increased further by polymerase chain reaction (PCR) detection of bacteria (Streptococcus pneumoniae and Haemophilus influenzae b) and viruses in lung aspirate fluid.

Methods

A total of 95 children with radiological focal, lobar or segmental consolidation had lung aspirate performed and sent for bacterial culture and for PCR for detection of bacteria, viruses and Pneumocystis jirovecii. In children with a pneumococcal aetiology, pneumococcal bacterial loads were calculated in blood and lung aspirate fluid.

Results

Blood culture identified a bacterial pathogen in only 8 patients (8%). With the addition of PCR on lung aspirate samples, causative pathogens (bacterial, viral, pneumocystis) were identified singly or as co-infections in 59 children (62%). The commonest bacterial organism was S.pneumoniae (41%), followed by H. influenzae b (6%), and the commonest virus identified was adenovirus (16%), followed by human bocavirus (HBoV) (4%), either as single or co-infection.

Conclusions

In a select group of African children, lung aspirate PCR significantly improves diagnostic yield. Our study confirms a major role of S.pneumoniae and viruses in the aetiology of childhood pneumonia in Africa.

Impact of human immunodeficiency virus infection on the etiology and outcome of severe pneumonia in Malawian children

BACKGROUND

HIV infection is a major risk factor for death in childhood pneumonia in HIV-endemic regions. Improved case management and preventive strategies require better understanding of the impact of HIV on causes, clinical presentation, and outcome.

METHODS

A prospective, clinical descriptive study of Malawian infants and children with severe pneumonia included blood culture and nasopharyngeal aspiration for diagnosis of pneumocystis pneumonia (PcP). A select group with consolidation on chest radiograph, and without severe hypoxia or hyperinflation, also had lung aspirate taken for culture and identification of bacterial deoxyribonucleic acid by real-time polymerase chain reaction (PCR).

RESULTS

There were 327 study patients with a median age of 11 months (range, 2 months-14 years). HIV prevalence was 51%. There were 58 cases of confirmed bacterial pneumonia, of which the most common bacterial isolates were Streptococcus pneumoniae and Salmonella typhimurium. Of the 54 lung aspirates, only 2 were positive on culture but 27 were positive for bacterial deoxyribonucleic acid by PCR. PcP was confirmed in 16 patients, and was associated with young age, severe hypoxia, HIV infection, and a very poor outcome. The overall case-fatality rate was 10% despite presumptive therapy for PcP and routine broad-spectrum antibiotic treatment appropriate for local antimicrobial susceptibility data. Most of the deaths occurred in infants of 2 to 6 months of age and PcP was associated with 57% of these deaths.

CONCLUSIONS

PcP is a major barrier in reducing the case-fatality rate of severe pneumonia in infants of HIV-endemic communities. The use of PCR on lung aspirate specimens greatly increased the diagnostic yield.

Definite, probable, and possible bacterial aetiologies of community-acquired pneumonia at different CRB-65 scores

According to the recommendations of the Swedish Community-Acquired Pneumonia (CAP) guidelines, the selection of empirical antibiotic therapy should be based on the CRB-65 rule. The guidelines recommend empirical therapy directed predominantly against Streptococcus pneumoniae for patients with low CRB-65 scores and broad-spectrum therapy for patients with high CRB-65 scores. In order to study the utility of the recommendations, we analyzed the data from an aetiological study previously performed on 235 hospitalized adult CAP patients at our medical centre. A definite, probable, or possible bacterial aetiology was noted in 194 cases (83%), including 112 cases (48%) with S. pneumoniae aetiology. The following frequencies of definite-probable aetiologies were noted in the patients with CRB-65 score 0-1 (n=155) and CRB-65 score 2-4 (n=80): S. pneumoniae 30% and 35%, Haemophilus influenzae 6.5% and 14% (p=0.063), Mycoplasma pneumoniae 15% and 5.0% (p=0.019), Chlamydophila species 2.6% and 1.2%, Legionella pneumophila 1.9% and 0%, and Staphylococcus aureus 1.3% and 1.2%, respectively. The high frequency of S. pneumoniae in the study supports the recommendations to predominantly cover this bacterium in the empirical therapy of patients with low CRB-65 scores. In the case of treatment failure in these patients, the study indicates that coverage against M. pneumoniae and H. influenzae should be considered.

Estimating the proportion of pneumonia attributable to pneumococcus in Kenyan adults: latent class analysis

BACKGROUND

Community-acquired pneumonia is a common cause of hospitalization among African adults, and Streptococcus pneumoniae is assumed to be a frequent cause. Pneumococcal conjugate vaccine is currently being introduced into childhood immunization programs in Africa. The case for adult vaccination is dependent on the contribution of the pneumococcus to the hospital pneumonia burden.

METHODS

Pneumococcal diagnosis is complex because there is no gold standard, and culture methods are invalidated by antibiotic use. We used latent class analysis to estimate the proportion of pneumonia episodes caused by pneumococcus. Furthermore, we extended this methodology to evaluate the effect of antimicrobial treatment on test accuracies and the prevalence of the disease. The study combined data from 5 validation studies of pneumococcal diagnostic tests performed on 281 Kenyan adults with pneumonia.

RESULTS

The proportion of pneumonia episodes attributable to pneumococcus was 0.46 (95% confidence interval = 0.36-0.57). Failure to account for the effect of antimicrobial exposure underestimates this proportion as 0.32. A history of antibiotic exposure was a poor predictor of antimicrobial activity in patients' urine. Blood culture sensitivity for pneumococcus was estimated at 0.24 among patients with antibiotic exposure, and 0.75 among those without.

CONCLUSIONS

The large contribution of pneumococcus to adult pneumonia provides a strong case for the investigation of pneumococcal vaccines in African adults.

Pneumonia in severely malnourished children in developing countries - mortality risk, aetiology and validity of WHO clinical signs: a systematic review

OBJECTIVES

To quantify the degree by which moderate and severe degrees of malnutrition increase the mortality risk in pneumonia, to identify potential differences in the aetiology of pneumonia between children with and without severe malnutrition, and to evaluate the validity of WHO-recommended clinical signs (age-specific fast breathing and chest wall indrawing) for the diagnosis of pneumonia in severely malnourished children.

METHODS

Systematic search of the existing literature using a variety of databases (Medline, EMBASE, the Web of Science, Scopus and CINAHL).

RESULTS

Mortality risk: Sixteen relevant studies were identified, which universally showed that children with pneumonia and moderate or severe malnutrition are at higher risk of death. For severe malnutrition, reported relative risks ranged from 2.9 to 121.2; odds ratios ranged from 2.5 to 15.1. For moderate malnutrition, relative risks ranged from 1.2 to 36.5. Aetiology: Eleven studies evaluated the aetiology of pneumonia in severely malnourished children. Commonly isolated bacterial pathogens were Klebsiella pneumoniae, Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, and Haemophilus influenzae. The spectrum and frequency of organisms differed from those reported in children without severe malnutrition. There are very few data on the role of respiratory viruses and tuberculosis. Clinical signs: Four studies investigating the validity of clinical signs showed that WHO-recommended clinical signs were less sensitive as predictors of radiographic pneumonia in severely malnourished children.

CONCLUSIONS

Pneumonia and malnutrition are two of the biggest killers in childhood. Guidelines for the care of children with pneumonia and malnutrition need to take into account this strong and often lethal association if they are to contribute to the UN Millennium Development Goal 4, aiming for substantial reductions in childhood mortality. Additional data regarding the optimal diagnostic approach to and management of pneumonia and malnutrition are required from regions where death from these two diseases is common.

Transthoracic fine-needle aspiration in the aetiological diagnosis of community-acquired pneumonia

Clin Microbiol Infect 2010; 16: 909–911

Abstract

To investigate the safety and practicability of conducting transthoracic fine‐needle aspiration (TFNA) in a general hospital setting, we applied the TFNA procedure to 20 patients hospitalized with community‐acquired pneumonia (CAP) within 36 h of admission. Also, a preliminary assessment was made of the potential value of adding TFNA to conventional methods of diagnostic microbiology. TFNA was easy to perform and caused little discomfort, and no serious adverse events were observed. In spite of ongoing antimicrobial treatment, a likely aetiological diagnosis was established for 14 of 20 (70%) of the patients. TFNA may provide important additional information on the aetiology of CAP.

Is quantitative PCR for the pneumolysin (ply) gene useful for detection of pneumococcal lower respiratory tract infection?

The pneumolysin (ply) gene is widely used as a target in PCR assays for Streptococcus pneumoniae in respiratory secretions. However, false-positive results with conventional ply-based PCR have been reported. The aim here was to study the performance of a quantitative ply-based PCR for the identification of pneumococcal lower respiratory tract infection (LRTI). In a prospective study, fibreoptic bronchoscopy was performed in 156 hospitalized adult patients with LRTI and 31 controls who underwent bronchoscopy because of suspicion of malignancy. Among the LRTI patients and controls, the quantitative ply-based PCR applied to bronchoalveolar lavage (BAL) fluid was positive at >or=10(3) genome copies/mL in 61% and 71% of the subjects, at >or=10(5) genome copies/mL in 40% and 58% of the subjects, and at >or=10(7) genome copies/mL in 15% and 3.2% of the subjects, respectively. Using BAL fluid culture, blood culture, and/or a urinary antigen test, S. pneumoniae was identified in 19 LRTI patients. As compared with these diagnostic methods used in combination, quantitative ply-based PCR showed sensitivities and specificities of 89% and 43% at a cut-off of 10(3) genome copies/mL, of 84% and 66% at a cut-off of 10(5) genome copies/mL, and of 53% and 90% at a cut-off of 10(7) genome copies/mL, respectively. In conclusion, a high cut-off with the quantitative ply-based PCR was required to reach acceptable specificity. However, as a high cut-off resulted in low sensitivity, quantitative ply-based PCR does not appear to be clinically useful. Quantitative PCR methods for S. pneumoniae using alternative gene targets should be evaluated.

Culture versus polymerase chain reaction for the etiologic diagnosis of community-acquired pneumonia in antibiotic-pretreated pediatric patients

Tracheal aspirates were collected from 176 hospitalized antibiotic-pretreated children with community-acquired pneumonia. Haemophilus influenzae and Streptococcus pneumoniae were detected by both culture and target-enriched multiplex (TEM)-PCR whereas Mycoplasma pneumoniae and Chlamydia pneumoniae were detected by TEM-PCR only. TEM-PCR detected more S. pneumoniae (32 vs. 7) and H. influenzae (29 vs. 23) than did culture. TEM-PCR detected an additional 26 M. pneumoniae and 1 C. pneumoniae. TEM-PCR significantly enhances the pathogen-specific diagnosis of CAP in children.

What are the implications for childhood pneumonia of successfully introducing Hib and pneumococcal vaccines in developing countries?

The authors look to the future and imagine the implications of a successful vaccination campaign againstH. influenzae type b and pneumococcus.

Pneumonia research to reduce childhood mortality in the developing world

Pneumonia is an illness, usually caused by infection, in which the lungs become inflamed and congested, reducing oxygen exchange and leading to cough and breathlessness. It affects individuals of all ages but occurs most frequently in children and the elderly. Among children, pneumonia is the most common cause of death worldwide. Historically, in developed countries, deaths from pneumonia have been reduced by improvements in living conditions, air quality, and nutrition. In the developing world today, many deaths from pneumonia are also preventable by immunization or access to simple, effective treatments. However, as we highlight here, there are critical gaps in our understanding of the epidemiology, etiology, and pathophysiology of pneumonia that, if filled, could accelerate the control of pneumonia and reduce early childhood mortality.

A novel Campylobacter jejuni sequence type from a culture-negative patient in the Gambia

The introduction of molecular diagnostic methods is crucial for improved understanding of the aetiology and epidemiology of bacterial infections in communities in resource poor settings. A blood sample from a 7 month old patient diagnosed with malaria in 2001 in a Gambian outpatient clinic was reported as culture negative after it was subjected to traditional bacterial culture protocols. We re-addressed the analysis of the blood sample from this case more recently (after 6.5 years in archival storage) in pilot work establishing 16S rRNA PCR in our molecular laboratory. Initial 16S rRNA PCR results confirmed the presence of bacterial DNA in the sample. 16S rRNA sequence analysis identified the organism as Campylobacter spp. In light of the molecular evidence we successfully grew the organism using appropriate culture conditions and subsequently biochemically confirmed that the isolate was Campylobacter jejuni. PCR and DNA sequencing of a set of seven C. jejuni housekeeping genes and in silico Multilocus Sequence Typing (MLST) analysis revealed that the isolate exhibits a novel sequence type (ST) of C. jejuni (ST 2928) and belongs to ST-443 clonal complex. This study demonstrates the potential for molecular tools to enhance the diagnosis of bacterial infections, which remain a major killer globally, not least in children in the developing world. Improvements in diagnostics are needed, and will be important not only for sick individuals but also for populations, where better measures of disease burden will contribute significantly to the improvement of public health policy.

Bacterial Infections

In Osier’s time, bacterial pneumonia was a dreaded event, so important that he borrowed John Bunyan’s characterization of tuberculosis and anointed the pneumococcus, as the prime pathogen, “Captain of the men of death.”1 One hundred years later much has changed, but much remains the same. Pneumonia is now the sixth most common cause of death and the most common lethal infection in the United States. Hospital-acquired pneumonia is now the second most common nosocomial infection.2 It was documented as a complication in 0.6% of patients in a national surveillance study,3 and has been reported in as many as 20% of patients in critical care units.4 Furthermore, it is the leading cause of death among nosocomial infections.5 Leu and colleagues6 were able to associate one third of the mortality in patients with nosocomial pneumonia to the infection itself. The increase in hospital stay, which averaged 7 days, was statistically significant. It has been estimated that nosocomial pneumonia produces costs in excess of $500 million each year in the United States, largely related to the increased length of hospital stay.

Improving outcomes of elderly patients with community-acquired pneumonia

Community-acquired pneumonia (CAP) is a major cause of morbidity and mortality in elderly patients. Therefore, efforts to optimize the healthcare process for patients with CAP are warranted. An organized approach to management is likely to improve clinical results. Assessing the severity of CAP is crucial to predicting outcome, deciding the site of care, and selecting appropriate empirical therapy. Unfortunately, current prognostic scoring systems for CAP such as CURB-65 (confusion, uraemia, respiratory rate, low blood pressure and 65 years of age) or the Pneumonia Severity Index have not been validated specifically in older adults, in whom assessment of mortality risk alone might not be adequate for predicting outcomes. Obtaining a microbial diagnosis remains problematic and may be particularly challenging in frail elderly persons, who may have greater difficulties producing sputum. Effective empirical treatment involves selection of a regimen with a spectrum of activity that includes the causative pathogen. Although most cases of CAP are probably caused by a single pathogen, dual and multiple infections are increasingly being reported. Streptococcus pneumoniae remains the overriding aetiological agent, particularly in very elderly people. However, respiratory viruses and 'atypical' organisms such as Chlamydia pneumoniae are being described with increasing frequency in old patients, and aspiration pneumonia should also be taken into consideration, particularly in very elderly subjects and those with dementia. Age >65 years is a well established risk factor for infection with drug-resistant S. pneumoniae. Clinicians should be aware of additional risk factors for acquiring less common pathogens or antibacterial-resistant organisms that may suggest that additions or modifications to the basic empirical regimen are warranted. In addition to administration of antibacterials, appropriate supportive therapy, covering management of severe sepsis and septic shock, respiratory failure, as well as management of any decompensated underlying disease, may be critical to improving outcomes in elderly patients with CAP. Immunization with pneumococcal and influenza vaccines has also been demonstrated to be beneficial in numerous large studies. There is good evidence that implementation of guidelines leads to improvement in clinical outcomes in elderly patients with CAP, including a reduction in mortality. Protocols should address a comprehensive set of elements in the process of care and should periodically be evaluated to measure their effects on clinically relevant outcomes. Assessment of functional clinical outcome variables, in addition to survival, is strongly recommended for this population.

[Follow-up criteria for community acquired pneumonias and acute exacerbations of chronic obstructive pulmonary disease]

The follow-up of Community Acquired Pneumonias (CAP) and Acute Exacerbations of Chronic Obstructive Pulmonary Diseases (AECOPD) differs with the setting of care, but overall calls upon the same investigations as the initial evaluations. In the event of initial ambulatory care, the evaluation is carried out primarily on clinical data, at the 2 or 3rd day for the CAP, at the 2nd to 5th day for the AECOPD. In the event of unfavourable evolution, or from the start in the most severe cases, the follow-up is carried out in hospital; clinical evaluation is readily daily, and all the more frequent that the clinical condition is worrying because of the severity or risk factors. The investigations will be limited to those initially abnormal in the event of favourable evolution; on the contrary, unfavourable evolution can justify new investigations which depend on clinical characteristics. Remotely, i.e. 4 to 8 weeks later, must be checked the return at the baseline clinical state, a chest X-ray (CAP), spirometry and arterial blood gas (AECOPD), even bronchoscopy and thoracic CT-scan.

[Contribution of microbiological investigations to the diagnosis of lower respiratory tract infections]

The diagnosis of community-acquired pneumonia is usually based on clinical and radiological criteria. The identification of a causative organism is not required for the diagnosis. Although numerous microbiological techniques are available, their sensitivity and specificity are not high enough to guide first-line antimicrobial therapy. Consequently, this treatment remains most often empiric. If the causative organism is identified, the antimicrobial treatment is adapted. Sputum analysis may be proposed as a diagnostic tool for patients with an acute exacerbation of chronic obstructive pulmonary disease, in specific cases (prior antibiotherapy, hospitalization, failure of the empiric antimicrobial treatment).

Community-acquired pneumonia

This seminar reviews important features and management issues of community-acquired pneumonia (CAP) that are especially relevant to immunocompetent adults in light of new information about cause, clinical course, diagnostic testing, treatment, and prevention. Streptococcus pneumoniae remains the most important pathogen; however, emerging resistance of this organism to antimicrobial agents has affected empirical treatment of CAP. Atypical pathogens have been quite commonly identified in several prospective studies. The clinical significance of these pathogens (with the exception of Legionella spp) is not clear, partly because of the lack of rapid, standardised tests. Diagnostic evaluation of CAP is important for appropriate assessment of severity of illness and for establishment of the causative agent in the disease. Until better rapid diagnostic methods are developed, most patients will be treated empirically. Antimicrobials continue to be the mainstay of treatment, and decisions about specific agents are guided by several considerations that include spectrum of activity, and pharmacokinetic and pharmacodynamic principles. Several factors have been shown to be associated with a beneficial clinical outcome in patients with CAP. These factors include administration of antimicrobials in a timely manner, choice of antibiotic therapy, and the use of a critical pneumonia pathway. The appropriate use of vaccines against pneumococcal disease and influenza should be encouraged. Several guidelines for management of CAP have recently been published, the recommendations of which are reviewed.

Diagnosis of pneumococcal pneumonia by psaA PCR analysis of lung aspirates from adult patients in Kenya

psaA is the gene encoding pneumococcal surface adhesin A (PsaA), a 37-kDa protein expressed on the surface of Streptococcus pneumoniae. PCR primers for psaA have been shown to amplify the target DNA sequence in all 90 serotypes of S. pneumoniae and in none of 67 heterologous pathogens and colonizing bacteria of the upper respiratory tract. Pathogenic bacteria identified in lung aspirate specimens cannot normally be dismissed as contaminants or colonizers, which limit the assay specificity of other respiratory tract specimens. psaA PCR analysis was evaluated in 171 lung aspirates from Kenyan adults with acute pneumonia. The limit of detection was one genome equivalent. Sensitivity, estimated in 35 culture-positive lung aspirates, was 0.83 (95% confidence interval, 0.70 to 0.95). psaA PCR analysis extended the number of identifications of S. pneumoniae in lung aspirates from 35 on culture to 61 by both methods. Of 26 new pneumococcal diagnoses, 19 were corroborated by results of blood culture or urine antigen detection. Sequences of the PCR products from 12 positive samples were identical to the psaA target gene fragment. Using an internal control for the PCR, inhibition of psaA PCR was demonstrated in 17% (8 of 47) of false-negative specimens. The results of a control PCR for the human gene beta-actin suggested that false-negative psaA PCR results are attributable to problems of specimen collection, processing, or DNA extraction in 30% of cases (14 of 47). psaA PCR analysis is a sensitive tool for diagnosis of pneumococcal pneumonia in adults.

Evaluation of the immunochromatographic Binax NOW assay for detection of Streptococcus pneumoniae urinary antigen in a prospective study of community-acquired pneumonia in Spain

We evaluated the Binax NOW rapid immunochromatographic membrane test (ICT) for detection of Streptococcus pneumoniae urinary antigen in a population-based prospective study of adults with community-acquired pneumonia (CAP). ICT was performed with urine samples obtained from 452 (91.7%) of 493 patients enrolled. Pneumococcal antigen was detected in 19 (70.4%) of 27 patients with pneumococcal pneumonia. The test results were more frequently positive for patients who had not received antibiotics before testing (26.6% vs. 12.1%; P=.002). Only 16 (10.3%) of 156 samples obtained from patients with nonpneumococcal pneumonia yielded a positive result. Of the 269 patients who had pneumonia with no pathogen identified, antigen was detected in 69 (25.7%). With conventional microbiological criteria used as the "gold standard," the test had a sensitivity of 70.4% and a specificity of 89.7%. Testing concentrated urine samples with the ICT may be a useful technique for rapid diagnosis of pneumococcal pneumonia in adults with CAP.

Reappraisal of lung tap: review of an old method for better etiologic diagnosis of childhood pneumonia

Identification of the etiology of childhood pneumonia is difficult, even in the cases that most likely have bacterial origins. A positive blood culture result is diagnostic but rare (< 10% of cases), and other noninvasive microbiological methods are nonspecific or are at least shadowed by interpretation problems. However, lung tap (or aspiration), a method developed a century ago, warrants reappraisal, especially since the prevalence of pneumococcal resistance to penicillin is increasing. An analysis of 59 studies that were published in 6 languages led us to conclude that (1) bacterial etiology is disclosed in approximately 50% of cases (virological tests were rarely done); (2) lung tap is safer than is generally considered; (3) potential pneumothorax is mostly symptomless and resolves spontaneously without impairing recovery; and (4) in comparison with routine diagnostic tools, lung tap offers so many advantages that it warrants reconsideration at centers where personnel have experience in handling potential pneumothorax.

Evaluation of Binax NOW, an assay for the detection of pneumococcal antigen in urine samples, performed among pediatric patients

In our evaluation of a new assay for the detection of pneumococcal antigen in urine (Binax NOW; Binax), the test result was no more likely to be positive among 88 children with radiographically confirmed pneumonia than among 198 control subjects; however, it was significantly more likely to be positive among children who were nasopharyngeal carriers of pneumococci. This test is not likely to be useful for distinguishing children with pneumococcal pneumonia from those who are merely colonized.

Aetiology, outcome, and risk factors for mortality among adults with acute pneumonia in Kenya

BACKGROUND

Despite a substantial disease burden, there is little descriptive epidemiology of acute pneumonia in sub-Saharan Africa. We did this study to define the aetiology of acute pneumonia, to estimate mortality at convalescence, and to analyse mortality risk-factors.

METHODS

We studied 281 Kenyan adults who presented to two public hospitals (one urban and one rural) with acute radiologically confirmed pneumonia during 1994-96. We did blood and lung-aspirate cultures, mycobacterial cultures, serotype-specific pneumococcal antigen detection, and serology for viral and atypical agents.

FINDINGS

Aetiology was defined in 182 (65%) patients. Streptococcus pneumoniae was the most common causative agent, being found in 129 (46%) cases; Mycobacterium tuberculosis was found in 26 (9%). Of 255 patients followed up for at least 3 weeks, 25 (10%) died at a median age of 33 years. In multivariate analyses, risk or protective factors for mortality were age (odds ratio 1.51 per decade [95% CI 1.04-2.19]), unemployment (4.42 [1.21-16.1]), visiting a traditional healer (5.26 [1.67-16.5]), visiting a pharmacy (0.30 [0.10-0.91]), heart rate (1.64 per 10 beats [1.24-2.16]), and herpes labialis (15.4 [2.22-107]). HIV-1 seropositivity, found in 52%, was not associated with mortality. Death or failure to recover after 3 weeks was more common in patients with pneumococci of intermediate resistance to benzylpenicillin, which comprised 28% of pneumococcal isolates, than in those infected with susceptible pneumococci (5.60 [1.33-23.6]).

INTERPRETATION

We suggest that tuberculosis is a sufficiently common cause of acute pneumonia in Kenyan adults to justify routine sputum culture, and that treatment with benzylpenicillin remains appropriate for clinical failure due to M. tuberculosis, intermediate-resistant pneumococci, and other bacterial pathogens. However, interventions restricted to hospital management will fail to decrease mortality associated with socioeconomic, educational, and behavioural factors.

Impact of bacterial pneumonias on world child health

Lower respiratory infections (LRIs) are estimated to cause approximately 4 million deaths each year, the majority in previously healthy young children from low-income countries. Bacterial pneumonias are likely to account for the major proportion of deaths but because accurate diagnosis is difficult, their precise contribution is difficult to estimate. Effective protection against two of the most important pathogens (H. influenzae type B and S. pneumoniae) is now available even for young infants. The high cost of these interventions is however likely to prohibit their use in areas likely to benefit most. Case management which can be effective at reducing mortality and which is relatively cheap at present is likely therefore to remain the principal means of tackling bacterial pneumonias globally. Antibiotic resistance to cheap drugs and possibly HIV infection pose a potentially enormous threat to this strategy with the prospect of an increasing global death toll with an even more inequitable distribution of disease as we begin the new century.