Abstract
Introduction
The role of infecting organisms in the pathogenesis of lung disease is well established. Organisms such as Staphylococcus aureus, non-capsulate Haemophilus influenzae, Pseudomonas aeruginosa, Burkholderia cepacia complex (Bcc) and respiratory viruses are well recognized as important pathogens which drive inflammatory responses and lung injury in cystic fibrosis (CF). 1
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JSE
JSE is the sole contributor
Aggressive treatment of airway infection in CF has been one of the key factors in improving long-term survival, and many patients with CF are treated very aggressively with antibiotics to maintain airway sterility. 2 , 3 In the last 10-15 years a number of organisms have been identified that are likely to play a role in airways infection in CF. An increasing number of species have been identified as dominant pathogens in the airway and in addition a wide range of co-infecting organisms have also now been identified.1,4,5
Identification of infecting organisms in CF
It has become increasingly clear that in microbiological culture of airways secretions from people with CF, organisms can be easily missed if not specifically looked for. 6 It is important that media specifically designated for certain pathogens are used. For example, Bcc species will not be identified if the appropriate media is not used.6,7 Following positive culture, identification is usually undertaken using an automated biochemical identification system such as API 20 NE. In this test, organisms are identified by their reaction to specific chemicals, for example oxidase positive or negative. The results from these reactions give them a probability of identification, but this system is far from fool-proof. Common mis-identifications can occur, particularly between organisms such as Bcc and Achromobacter xyloxi- dans. 7 This led to the development of molecular identification, which may be undertaken using specific PCR tests for specific organisms or using a broad-range PCR and sequencing of 16S ribosomal RNA genes.8–12 More recently, metagenomic approaches have been reported which allow for the identification of multiple organisms in a sputum sample. 13 Terminal restriction fragment length polymorphism (T-RFLP) profiling uses a primer set which amplifies the 16S rDNA fragment from all CF pathogens and then uses fluorescently labelled fragments to determine species diversity and relative abundance in any specific samples. 13 A number of groups have identified a wide range of microorganisms in airway secretions for people with CF using this technique. However, for many of these the clinical significance is still unclear.
This method has been used to confirm that P. aeruginosa is the dominant organism in older people with CF, but a wide range of other organisms is also identified.4,5,13 This has recently been confirmed in a study in children using bronchoalveolar lavage. 14 Extensive reviews have recently commented on the identification and treatment of P. aeruginosa and Bcc organisms.1,2,7,14 The rest of this review will focus on the other listed species which are emerging important pathogens (Box 1).
Gram-negative organisms in cystic fibrosis airways
Pseudomonas aeruginosa
Pseudomonas species (others)
Burkholderia cepacia complex
Stenotrophomonas maltophilia
Achromobacter xyloxidans
Pandorea apista
Inquinalus limosus
Ralstonia pikettii
Emerging Gram-negative organisms
An area which often causes challenges in microbiology laboratories is the identification of Gram-negative organisms from CF sputum. The range of organisms found in CF are outlined in Box 1.
Stenotrophomonas maltophilia
S. maltophilia is a relatively common Gram-negative species cultured from sputum in CF. The prevalence ranges from centre to centre, ranging in most series from 3-7%.15–17 A recent study in one centre, however, reported 39% of patients infected with this organism. 16 Molecular typing of this organism within clinics usually shows individual patient strains, suggesting that cross infection is rare. Infection with S. maltophilia is associated with being older, being female, having advanced disease, prior antibiotic therapy and co-infection with aspergillus.16,19 Overall the clinical impact of S. maltophilia infection appears to be modest. In a well-conducted epidemiological study using the Cystic Fibrosis Foundation Registry, Goss et al. demonstrated that there was no significant negative impact of S. maltophilia infection compared to other Gram-negative infections. 15 In contrast, infection with P. aeruginosa or Bcc resulted in a reduction in survival. S. maltophilia is usually constitutively resistant to most antibiotics, particularly β-lactam, aminoglycosides and carbapenems. In contrast, ceftazidime, quinoline, tetracycline and trimethoprin sulphamethoxazole have in vitro activity and may be useful in treating clinical infections or pulmonary exacerbations.20,21
Achromobacter xyloxidans
This organism occurs in less than 10% of people with CF and little is known about its environmental reservoirs or whether patient-to-patient spread occurs. 1 It is usually multi-resistant to anti-pseudomonal antibiotics and is relatively commonly mis-identified as Bcc.22–24 It is frequently resistant to aminoglycosides, colistin and co-trimoxazole, but shows sensitivity to tetracycline, carbapenems and uriedo-penicillin. It is unclear if it has any long-term effect on pulmonary function in CF. 1
Other organisms
There are few studies or case series of other Gram-negative organisms isolated in people with CF. It is prudent to consider all Gram-negative organisms as pathogens. The choice of antibiotics should be guided by the literature as well as specific in vitro antibiotic testing in the laboratory.
Principals of treatment of exacerbations associated with emerging resistant Gram-negative organisms
The treatment of this difficult group of organisms is challenging, as there are a few clinical studies -never mind clinical trials - on which to base treatment decisions. An important study, however, examined the role of synergy testing using combinations of three antibiotics against multi-resistant P. aeruginosa and Bcc. In this landmark study, 251 patients with multi-resistant bacterial infection (P. aeruginosa and Bcc) were enrolled and followed for up to 5 years. 25 During that time, 156 had a pulmonary exacerbation, 64 were randomly assigned to receive therapy directed by a form of synergy testing called MCBT and 68 were treated according to conventional culture-directed therapy. Surprisingly, there was no reduction in the time to next exacerbation in the patients who had antibiotic therapy directed by MCBT testing compared to a control group. The lack of difference between these two approaches probably reflects the practice of empirical prescribing, in that 44% of those randomized using MCBT had meropenem compared to 43% of the control group and 14% of MCBT-treated patients had ceftazidime compared to 20% of the control group. The two groups were treated with essentially the same treatment regime because of previous publication of in vitro sensitivity data for these organisms more generally, based on MCBT testing.26,27 Synergy or combination testing may still be a useful method but on the basis of the current data it suggests that empirical decisions based on knowledge of the background sensitivity of these organisms is an appropriate way to choose antibiotic therapy.
Anaerobe infection
The CF airway is a relatively anaerobic environment and a pivotal study in 2002 demonstrated that the P02 in airway mucus is almost zero. 28 This suggests that the CF airway may be an environment that promotes the growth of anaerobic organisms. A number of studies have recently demonstrated that anaerobes can be identified from the majority of patients with CF while stable and they are almost universally found in high numbers during pulmonary exacerbations associated with P. aeruginosa.29,30 The main organisms identified have been Prevotella and Veilonella. In addition, these anaerobes appear to be multiply resistant to usual anti-anaerobic antibiotics such as clindamycin and metronidazole. The clinical significance of anaerobes is unclear, but as they seem to be so prevalent (in similar numbers to P. aeruginosa), they may well contribute to the pathophysiology of infection in the CF airway.
Non-tuberculous mycobacterial infection in CF
Non-tuberculous mycobacterial (NTM) infection is an increasing problem in people with CF. In the majority of patients this is Mycobacterium avium complex (70% of isolates), with the majority of the rest being Mycobacterium abscesses (16%). 31 A number of important studies have indicated that adults with CF who are infected with non-tuberculous mycobacterium are older and have relative sparing of FEV1, and there may be an association with low body mass index.31–33 Those infected with M. avium complex seem to have a much better outcome that those chronically infected with M. abscesses infection, where a significant decrease in lung function has been demonstrated. The diagnosis of NTM is not easy in CF. The signs and symptoms of NTM infection are very similar to those of CF and in some patients the presence of NTM may be due to non-pathogenic organisms. Clear guidelines have recently been published by the American Thoracic Society (ATS) and the Infectious Disease Society of America (IDSA) to assist in the diagnosis of NTM in adults. These guidelines require the following: 34
‘Pulmonary symptoms, nodular or cavity opacities on chest radiograph or a high resolution CT scan that shows multi-focal bronchiectasis with small nodules and appropriate exclusion of other diagnosis. This must be in addition to a microbiological assessment with positive culture results from at least 2 positive sputum samples or a positive culture from at least one bronchial wash or lavage or a positive culture from a lung biopsy.’
Treatment of NTM is also discussed at length in the ATS/IDSA statement and represents an excellent guide for consideration of this infection. 34 In general, if MAC is thought to be causing symptoms a combination regime should include macrolides, clarithromycin, azithromycin and ethambutol. Antibiotic choice for MAC can be helped by knowing in vitro sensitivities. In contrast, there is no dependable antibiotic regime for M. abscesses and in vitro susceptibilities are of little extra benefit in its treatment. Drugs known to be useful in this condition are amikacin, cefotaxime and imipenem. These may be combined with an oral fluoroquinolone (e.g. moxifloxacin) and macrolide (e.g. azithromycin).
Fungi
Fungal infection in CF again seems to be increasing in prevalence. Data over 10 years suggest an increase in the prevalence of aspergillus from about 6% to around 14%. It is hard to be sure if this is all due to an increased prevalence or simply due to increased reporting. However, it is clear that a wide range of fungi can be associated with airway infection, and with appropriate culture techniques and molecular diagnostic methods a wide range of fungi have been identified; it is possible that some of these may cause infection (Box 2).
Fungi causing infection in cystic fibrosis
Candida albicans
Candida dubliniensis
Aspergillus species
Penicillium species
Saccharomyces
Scedosporium apiospermum
Exophiala dermatitidis
Tricosporon species
Some people with CF develop allergy bronchopulmonary aspergillosis (ABPA) but in some instances fungi may cause bronchitis. Treatment of fungal infection is again challenging as there are a limited number of agents to use. Mostly treatment is based round itraconazole and a voriconazole, though there are no robust clinical trials to inform these decisions.
Conclusions
Infection in the CF airway is poly-microbial and a number of potentially dominant emerging pathogens are present. It is important that appropriate studies are undertaken to identify these organisms and determine the best anti-microbial treatments.
Footnotes
Acknowledgements
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